Subject: Biology And Life Sciences, Biophysics Keywords: non-ionizing radiation; millimeter waves; novel biomedical applications; yeast; non-invasive devices
Online: 17 September 2020 (07:08:47 CEST)
Nonionizing millimeter-waves (MMW) are reported to interact with cells in a variety of ways. Possible mechanisms of the inhibited cell division effect were investigated using 85-105 GHz MMW irradiation within the ICNIRP (International Commission on Non-Ionizing Radiation Protection) non-thermal 20 mW/cm2 safety standards. ~1.0 mW/cm2 exposure over 5-6 hours treatment on 50 cells/μl samples of Saccharomyces cerevisiae model organism, resulted in 62% growth rate reduction compared to control (sham). The effect was specific for 85-105 GHz range and energy dose and cell density dependent. Irradiation of wild type and Δrad52 (DNA damage repair gene) deletion cells presented no differences of colony growth profiles indicating non-thermal MMW treatment does not cause genetic alterations. Dose versus response relations studied using a standard horn antenna (~1.0 mW/cm2) and compared to that of a compact waveguide (17.17 mW/cm2) for increased power delivery resulted in complete termination of cell division via non-thermal processes supported by temperature rise measurements. Combinations of MMW mediated Structure Resonant Energy Transfer (SRET), membrane modulations eliciting signaling effects, and energetic resonance with biomolecules were indicated to be responsible for the observations reported. Our results provide novel mechanistic insights enabling innovative applications of nonionizing radiation procedures for eliciting targeted biomedical outcomes.
ARTICLE | doi:10.20944/preprints202008.0577.v2
Subject: Physical Sciences, Acoustics Keywords: quantum diode; quantum gate element; novel superconductivity; bias current; memorization property; quantum correlation
Online: 17 November 2020 (12:50:24 CET)
Two opposed p–n diodes are connected with another junction that causes cancellation of the electric field in the depletion layer of each diode by the field of the other diode. This derived quantum diode is called the A system. Another dual diode, constructed by the same process but with the p- and n-types positioned as duality, called the B system. When a bias voltage is applied between the A and B systems, Lorentz conservation imparts a momentum (i.e., a wave number) to the carriers in the absence of any internal voltage. Thus, a superconducting bias current density appears without the need for cooling. The reappearances of electron–hole pairs on the junction surfaces are assumed to be described by entire wavefunctions normalized by the band gap. Based on the bias superconducting current, NOT and NAND gates were constructed from the quantum diode systems. Numerical calculations revealed that the constant phases of the entire wavefunctions of the p-and n-types converged. Accordingly, it was clarified that Bose–Einstein condensation and the Meissner effect (described by the London equation) occurred in the quantum diode systems. Moreover, the systems exhibited rectification characteristics and a switching speed of the order of 10-14 s. Combining this switching property with the large bias superconducting current (of the order of several V), we developed NOT and NAND gates with direct quantum correlations among many qubits, which are unaffected by random and thermal noises. These gates have memorization and initialization properties and are compatible with existing and accumulating programing algorithms. Moreover, when harvesting a divergent current output from these systems, the bias superconducting current and memorization property preserve the formed quantum correlations.
ARTICLE | doi:10.20944/preprints201909.0204.v1
Subject: Public Health And Healthcare, Health Policy And Services Keywords: Office of Innovation; novel drugs; novel therapies; regulatory science; Latin American Regulatory landscape
Online: 18 September 2019 (12:51:16 CEST)
Regulatory agencies across the Latin American Region have strengthened the regulatory science through the development of new tools, standards and various other related parameters to evaluate and assess safety, efficacy, quality and performance. The former have been implemented to promote and incorporate new drugs and technologies, which still, are a challenge to well-established regulatory frameworks. Furthermore, in today’s environment, the existing regulatory framework protecting public’s health creates barriers for market entry of novel drugs and medical devices. This article aims to the pioneering work that Cuban Regulatory Agency (CECMED) has been developing with the aim to build a strong regulatory framework geared to accelerated innovation and the successful transition from research and development to clinical development. The Office of Innovation recently established at the CECMED is the first flagship in Latin America and the Caribbean region. Its aim is to play a leading role as a driving force for the national and regional biopharmaceutical innovation. This article will discuss the Office of Innovation its conceptualisation and management taking into account the Latin American regional and national Cuban context.
REVIEW | doi:10.20944/preprints202307.0143.v1
Subject: Medicine And Pharmacology, Psychiatry And Mental Health Keywords: schizophrenia; schizophrenia theories; novel antipsychotics
Online: 4 July 2023 (07:21:19 CEST)
Schizophrenia is a chronic neuropsychiatric syndrome with a significant impact on daily function and quality of life. All available guidelines suggest a combined treatment approach with pharmacologic agents and psychological interventions. However, one in three patients is a non-responder, the effect on negative and cognitive symptoms is limited, and many drug-related adverse effects complicate clinical management. As a result, discovering novel drugs for schizophrenia presents a significant challenge for psychopharmacology. This narrative review of the literature aims to present recently approved and newly discovered pharmacological substances for the treatment of schizophrenia as well as their suggested mechanism of action. We discuss seven novel drugs, three of which have been approved by the FDA (Olanzapine/Samidorphan, Lumateperone, and Pimavanserin). The rest are under clinical trial investigation (Ulotaront, CVL-231, Xanomeline/Trospium, Brilaroxazine). Additional basic and clinical research is, however, required not only to improve our understanding of the neurobiology and potential novel targets in schizophrenia treatment but also to establish modern and more effective therapeutical interventions with friendlier side-effect profiles.
ARTICLE | doi:10.20944/preprints202208.0091.v1
Subject: Medicine And Pharmacology, Neuroscience And Neurology Keywords: Parkinson’s disease; novel tetracycline; neuroprotection
Online: 3 August 2022 (12:08:08 CEST)
The antibiotic tetracycline demeclocycline (DMC) was recently reported to rescue α-synuclein (α-Syn) fibril-induced pathology. However, the antimicrobial activity of DMC precludes its po-tential use in long-term neuroprotective treatments. Here, we synthesized a DMC derivative with residual antibiotic activity and improved neuroprotective effects. The molecule, called de-rivative demeclocycline (DDMC), was obtained by the removal of both dimethylamino substitu-ents at position 4 and the reduction of the hydroxyl group at position 12a on ring A of DMC. The modifications strongly diminished its antibiotic activity against Gram-positive and Gram-negative bacteria. Moreover, this compound preserved the low toxicity of DMC in dopaminergic cell lines while improving its ability to interfere with α-Syn amyloid-like aggregation, showing the highest effectiveness of all tetracyclines tested. Likewise, DDMC demonstrated the ability to reduce seeding induced by the exogenous addition of α-Syn preformed fibrils (α-SynPFF ) in ex vitro models and in SH-SY5Y-α-Syn-tRFP cells. In addition, in the presence of DDMC, α-SynPFF were less inflammogenic, as they dampened the release of tumor necrosis factor α (TNF-α) and glutamate by microglial cells compared to control fibrils. Our results suggest that DDMC may be a promising drug candidate for hit-to-lead development and preclinical studies in PD and other synucleinopathies.
ARTICLE | doi:10.20944/preprints202203.0367.v1
Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: Salmonella; Novel Antibacterial Agents; Cannabinoids
Online: 28 March 2022 (14:30:09 CEST)
Products derived from Cannabis sativa have gained increased interest and popularity. As these products become common amongst the public, the heath and potential therapeutic values associated with hemp have become a premier focus of research. While the psychoactive and medicinal properties of Cannabis products have been extensively highlighted in literature, the antibacterial properties of CBD have not been explored in depth. This research serves to examine the antibacterial potential of CBD against Salmonella newington and Salmonella typhimurium. In this study we observed bacterial response to CBD exposure through biological assays, bacterial kinetics, and fluorescence microscopy. Additionally, comparative studies between CBD and ampicillin were conducted against Salmonella typhimurium and Salmonella newington to determine comparative efficacy. Furthermore, we observed potential resistance development of our Salmonella spp. against CBD treatment.
ARTICLE | doi:10.20944/preprints202002.0359.v1
Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: novel coronavirus; Wuhan; vaccine; epitopes; peptide
Online: 25 February 2020 (05:18:22 CET)
During December 2019, a novel coronavirus named as 2019-nCoV, has emerged in Wuhan, China. The human to human transmission of this virus has also been established. Untill now the virus has infected more than seven thousand people and has spread to fifteen countries. The World Health Organization (WHO) has declared 2019-nCoV as global health emergency due to its outburst well beyond China. There is need to develop some vaccines or therapeutics to control or prevent 2019-nCoV infections. The bottleneck with current conventional approaches is that these require longer time for vaccine development. However, computer assisted approaches help us to produce effective vaccine in short time compared with conventional methods. In this study, bioinformatics analysis was used to predict B cell and T cell epitopes of surface glycoprotein of 2019-nCoV that could be suitable to trigger significant immune response. The sequence of surface glycoprotein was collected from the database and analyzed to identify the immunogenic epitope. Both B cell and T cell epitopes were analyzed so the predicted epitopes can stimulate both cellular and humoral immune responses. We predicted 13 B cell and 05 T cell epitopes that later on were joined with GPGPG linker to make a single peptide. This computational approach to design a multi epitope peptide vaccine against emerging 2019-nCoV allows us to find novel immunogenic epitopes against the antigen targets of surface 2019-nCoV surface glycoprotein. This multi epitope peptide vaccine may prove effective to combat 2019-nCoV infections.
ARTICLE | doi:10.20944/preprints202002.0179.v1
Subject: Medicine And Pharmacology, Epidemiology And Infectious Diseases Keywords: novel coronavirus; SEIR model; outside China
Online: 14 February 2020 (02:34:55 CET)
Ongoing outbreak of pneumonia caused by novel coronavirus (2019-nCoV) began in December 2019 in Wuhan, China, and the number of new patients continues to increase. On the contrary to ongoing outbreak in China, however, there are limited secondary outbreaks caused by exported case outside the country. We here conducted simulations to estimate the impact of potential secondary outbreaks at a community outside China. Simulations using stochastic SEIR model was conducted, assuming one patient was imported to a community. Among 45 possible scenarios we prepared, the worst scenario resulted in total number of persons recovered or removed to be 997 (95% CrI 990-1,000) at day 100 and maximum number of symptomatic infectious patients per day of 335 (95% CrI 232-478). Calculated mean basic reproductive number (R0) was 6.5 (Interquartile range, IQR 5.6-7.2). However, with good case scenarios with different parameter led to no secondary case. Altering parameters, especially time to hospital visit could change the impact of secondary outbreak. With this multiple scenarios with different parameters, healthcare professionals might be able to prepare for this viral infection better.
ARTICLE | doi:10.20944/preprints202308.1002.v2
Subject: Medicine And Pharmacology, Pediatrics, Perinatology And Child Health Keywords: autism; diagnostic yield; DNA sequencing; novel disorders
Online: 10 October 2023 (05:00:59 CEST)
Autism spectrum disorder (ASD) is a common condition with lifelong implications and a strong hereditary component suggesting genetic underpinnings. The last decade has seen dramatic improvements in DNA sequencing and related bioinformatics and databases. We analyzed the raw DNA sequencing files on the Variantyx® bioinformatics platform for the last 50 ASD patients evaluated with trio whole genome sequencing (trio-WGS). “Qualified” variants were defined as coding, rare, and evolutionarily conserved. Primary Diagnostic Variants (PDV) additionally were in genes directly linked to ASD and matched clinical correlation. A PDV was identified in 34/50 (68%) of cases, including 25 (50%) cases with heterozygous de novo and 10 (20%) with inherited variants. De novo variants in genes directly associated with ASD were far more likely to be Qualifying than non-Qualifying versus a control group of genes not associated with ASD (P = 0.0002, odds ratio 29), validating that most are indeed disease related. Only 14/34 (41%) of PDV cases had the variant listed on the laboratory report, and reanalysis increased diagnostic yield from 28% to 68%. Variants that we assigned as PDVs yet not on the report were predominately de novo in genes not yet reported as ASD associated. Many subjects both with and without a PDV had inherited Qualifying variants in known ASD-associated genes, suggesting polygenic inheritance. Thirty-three subjects (66%) had treatment recommendation(s) based on DNA analyses. Our results demonstrate high yield of trio-WGS for revealing molecular diagnoses in ASD that is greatly enhanced by re-analyzing DNA sequencing files. In contrast to previous reports, de novo variants dominate the findings, mostly representing novel conditions. This has implications to the cause and rising prevalence of autism.
ARTICLE | doi:10.20944/preprints202307.1410.v1
Subject: Biology And Life Sciences, Food Science And Technology Keywords: mantle tissue; novel toxin; scallop; small intestine
Online: 20 July 2023 (10:22:45 CEST)
We previously showed that feeding mice a diet containing 1% mantle tissue decreased food consumption, leading to death. We also isolated and identified toxic substances in the mantle tissue. In the present study, we investigated the characteristics and stability of mantle tissue toxicity. Treatment of mantle tissue with 1 mM HCl, 1 mM NaOH, 1 mM dithiothreitol, and 1 mM H2O2 and heating did not reduce the toxicity of mantle tissue in mice. These results suggest that mantle toxins are stable in tissues, particularly when exposed to acidic and digestive enzymes. We examined whether mantle tissue exhibited acute toxicity. Diets containing 1% and 20% mantle extract showed similar levels of toxicity, demonstrating that feeding of mantle tissue does not lead to acute toxicity. Finally, we examined the toxicity of the mantle tissue against small intestinal tissue. Chronic feeding of mantle tissue to mice changed the color of the small intestine. Real-time PCR analysis showed that mantle tissue feeding caused changes of inflammation and endoplasmic reticulum stress markers in the small intestine. These results suggest that feeding of mantle tissue causes toxicity after causing initial damage to the small intestinal tissue.
ARTICLE | doi:10.20944/preprints202305.0789.v1
Online: 11 May 2023 (04:58:08 CEST)
Teaching and learning a new language is a complex process that requires more than just memorizing vocabulary and grammar rules. Immersing oneself in the target language's culture and history is essential for achieving fluency and accuracy. In recent years, researchers have explored the potential of music as a tool for language learning. This paper discusses the benefits of using music in language learning, including improved listening comprehension, pronunciation and fluency, and cultural understanding. The theoretical framework of sociocultural theory, cognitive load theory, and task-based language learning is presented to support the use of music in language learning. This paper also provides practical recommendations for learners to incorporate music into their language learning routine, as well as resources for finding music in the target language, such as online music platforms and language learning apps. The article concludes by encouraging language learners to incorporate music into their language learning routine and providing resources for finding music in the target language, such as online music platforms and language learning apps. Overall, this paper demonstrates that music can be a powerful and enjoyable tool for enhancing language learning outcomes.
REVIEW | doi:10.20944/preprints202305.0475.v1
Subject: Chemistry And Materials Science, Medicinal Chemistry Keywords: Nutrigenomics; Antimicrobial resistance; Novel Antibiotics; gut microbiome
Online: 8 May 2023 (08:40:22 CEST)
Nutrigenomics is the study of the interaction of nutrition and genes, focusing on the influence of nutrients on the genome, proteome, and metabolome, and how nutrition affects human health. In the context of nutrigenomics, bioactive components are dietary ingredients that may transmit information from the external environment and alter gene expression in the cell, and hence the overall function of the organism. It is critical to consider food not only as a source of energy and essential nutrients necessary for life and growth, but also as a factor impacting health/disease, biochemical processes, biochemical pathway activation and affecting the diversity of the gut microbiome. Antimicrobial resistance in pathogenic and commensal microorganisms has emerged as a major public health concern due to emerging antimicrobial resistance genes in E. coli isolates from pig, cattle, chicken, and turkey meat, against tetracycline, streptomycin, and sulfonamides. Also, Salmonella spp. and Campylobacter spp. have shown antibiotic resistance at farms and slaughterhouses, and in animal-based food products. A correlation has been proven between a critical nutrient-responsive signaling system and catabolite control of gene expression, and a two-component signaling system that drives antibiotic resistance in E. faecalis, revealing a previously unknown integration between the nutritional status of the cell and intrinsic antibiotic resistance. Moreover, different nutrigenomic approaches can be applied to mitigate possible emergence of antimicrobial resistance against novel antibiotics. However, little progress has been achieved in converting nutrigenomics information into clinical advice, so far.
ARTICLE | doi:10.20944/preprints202111.0197.v1
Subject: Biology And Life Sciences, Animal Science, Veterinary Science And Zoology Keywords: dog food; starch; novel ingredient; starch gelatinization
Online: 10 November 2021 (08:53:05 CET)
Gelatinization of starch content in pet foods can be impacted by several factors including moisture, retention time, and ingredients used. Starch gelatinization has been associated with digestibility but isn’t well studied using ingredients common in non-traditional canine diets. The objective of this research was to examine the impacts of dietary ingredient profile (traditional vs non-traditional) and assess impacts to total starch content and starch gelatinization. Traditional diets (n = 10) utilizing meat-based ingredients including chicken, chicken by-product meal, meat and bone meal and plant-based ingredients including rice, barley, oats, and corn were examined in comparison with non-traditional diets (n = 10) utilizing meat-based ingredients including alligator, buffalo, venison, kangaroo, squid, quail, rabbit, rabbit and salmon along with plant-based ingredients including tapioca, peas, chickpeas, lentils, potato, and pumpkin. Representative samples were collected via grab sample technique (5 samples/diet) and were assessed for total starch content as well as percent starch gelatinization. Difference between ingredient type was assessed using a Students t-test in SAS 9.4. Significance was set at P < 0.05. Distribution of total starch content based on ingredient type (traditional vs non-traditional) revealed that mean total starch content was higher in traditional diets as compared to non-traditional diets (P <0.0001). Conversely, starch gelatinization was found to be higher in non-traditional diets (P < 0.0001). Total starch content and total gelatinized starch had a strong negative correlation (P < 0.01) in traditional diets, though no correlation was observed in non-traditional diets. This negative correlation indicates a decrease in total gelatinized starch associated with increased total starch content. These novel data reveal important differences between starch content and gelatinization and could impact manufacturing processes for ingredient types as well as feeding recommendations. Unpredicted variation between ingredient formulations could potentially lead to decreased digestibility and absorption and may result in nutrient deficiencies.
ARTICLE | doi:10.20944/preprints202004.0267.v1
Subject: Medicine And Pharmacology, Epidemiology And Infectious Diseases Keywords: novel coronavirus; COVID-19; epidemic model; epidemiology
Online: 16 April 2020 (08:24:07 CEST)
Italy was the first country in Europe which imposed control measures of travel restrictions, quarantine and contact precautions to tackle the epidemic spread of the novel coronavirus (SARS-CoV-2) in all its regions. While such efforts are still ongoing, uncertainties regarding SARS-CoV-2 transmissibility and ascertainment of cases make it difficult to evaluate the effectiveness of restrictions. Here, we employed a Susceptible-Exposed-Infectious-Recovered-Dead (SEIRD) model to assess SARS-CoV-2 transmission dynamics, working on the number of reported patients in intensive care unit (ICU) and deaths in Sicily (Italy), from 24 February to 13 April. Overall, we obtained a good fit between estimated and reported data, with a small fraction of unreported SARS-CoV-2 cases (19.5%; 95%CI=0%-34.7%) before 10 March lockdown. Interestingly, we estimated that the first set of restrictions reduced transmission rate in the community by 42% (95%CI=38%-46%), and that more stringent measures adopted on 23 March succeeded to drastically curb the transmission rate by 84% (95%CI=80%-88%). Thus, our estimates delineated the characteristics of SARS-CoV2 epidemic before restrictions taking into account unreported data. Further modeling after the adoption of control measures, moreover, indicated that restrictions reduced SARS-CoV2 transmission considerably.
ARTICLE | doi:10.20944/preprints202004.0052.v1
Subject: Medicine And Pharmacology, Epidemiology And Infectious Diseases Keywords: novel coronavirus; epidemiology; COVID-19; epidemic model
Online: 6 April 2020 (12:30:42 CEST)
In the midst of the novel coronavirus (SARS-CoV-2) epidemic, examining reported case data could lead to biased speculations and conclusions. Indeed, estimation of unreported infections is crucial for a better understanding of the current emergency in China and in other countries. In this study, we aimed to estimate the unreported number of infections in China prior to 23 March 2020 restrictions. To do that, we developed a Susceptible-Exposed-Infectious-Recovered-Dead (SEIRD) model which estimated unreported cases and infections from the reported number of deaths. Our approach relied on the fact that observed deaths were less likely to be affected by reporting biases than reported infections. Interestingly, we estimated that R0 was 2.43 (95%CI= 2.42 – 2.44) at the beginning of the epidemic, and that 92.9% (95%CI= 92.5% - 93.1%) of total cases were not reported. Similarly, the proportion of unreported new infections by day ranged from 52.1% to 100%, with a total of 91.8% (95%CI= 91.6% - 92.1%) unreported infections. Agreement between our estimates and those from previous studies proved that our approach was reliable to estimate prevalence and incidence of undocumented SARS-CoV2 infections. Once tested on Chinese data, our model could be applied on other countries with different surveillance and testing policies.
ARTICLE | doi:10.20944/preprints202002.0132.v2
Subject: Biology And Life Sciences, Virology Keywords: 2019-nCoV; SARS-CoV-2; novel corona virus; Wuhan pneumonia
Online: 18 February 2020 (11:52:25 CET)
The rapid development of 2019-2020 Wuhan seafood market pneumonia currently posed a major public health concern in China. Genome sequencing identified a novel beta-coronavirus closely related to SARS-CoV, named 2019-nCoV by WHO, as the cause of this pandemic disease. Viruses with single stranded RNA genome are prone to evolve quickly by accumulation of mutations, such as SNV, INDEL and cross viral recombination, aiding fast transmission among hosts and cross species. Here we collected related genome sequences and investigated variations shared by different strains of 2019-nCoV, identified reoccurrence of SNV mutations in clusters of patients, an indication of rapid evolution of 2019-nCoV at the transmission from animal host to human. The information collected herein would help to understand the dynamics of current pandemic.
ARTICLE | doi:10.20944/preprints202311.0462.v1
Subject: Biology And Life Sciences, Insect Science Keywords: novel food; risk perception; valorization; food safety; insects
Online: 8 November 2023 (03:33:18 CET)
Edible insects can diversify diets, improve livelihoods, contribute to food and nutrition security, and have a smaller ecological impact. European Union has categorized insects as novel food, and recently, in 2021 and 2022, two species: Tenebrio molitor and Acheta domesticus have been authorized for commercialization. Acceptance and perception of food risk derived from insect consumption vary depending on factors impacting insect consumption acceptability, including neophobic tendencies, gender differences, familiarity, and gastronomic perceptions. The aim of this work was to evaluate the perception and acceptance of edible insects by exploring those factors. The study was carried out on higher education students from Universities from Valencia (Spain). Students recognize insects for their high nutritional value, particularly protein content, and have varying knowledge levels about specific nutritional components. In terms of labeling and marketing, removing health and sustainability benefits from packaging can improve consumer responses. Most respondents prefer clear labeling of insect derivatives, quality certification seals, and complete information about insect content. Students consider marketing and knowledge as significant influencers of insect consumption. In summary, the text highlights the multifaceted nature of insect consumption acceptability. These insights offer valuable perspectives on insect consumption dynamics.
ARTICLE | doi:10.20944/preprints202307.2054.v1
Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: Pseudomonas; metallo-beta-lactamase; blaIMP; novel allele; plasmid
Online: 31 July 2023 (04:53:01 CEST)
Multidrug-resistant (MDR) Pseudomonas aeruginosa infections represent major a public health concern and require comprehensive understanding of their genetic make-up. This study investigated the first occurrence of IMP-carrying MDR P. aeruginosa strains from Bulgaria. Whole genome sequencing identified a novel plasmid-mediated blaIMP-100 allele located in a In1300-like integron embedded in a novel putative transposon. Two other closely related chromosomal blaIMP variants IMP-13 and IMP-84 were also detected. The IMP-producers were resistant to last-line drugs including cefiderocol (CFDC) (2 out of 3) and susceptible to colistin. The blaIMP-13/84 cassettes were situated in a In320 integron inserted in a Tn5051-like transposon as previously reported. Lastly, the p47825-IMP plasmid rendered PAO1 transformant resistant to CFDC, suggesting a transferable CFDC resistance. A variety of virulence factors associated with adhesion, antiphagocytosis, iron uptake, quorum-sensing, as well as secretion systems, toxins, and proteases were confirmed, suggesting significant pathogenic potential consistent with the observed strong biofilm formation. Emergence of IMP-producing MDR P. aeruginosa is alarming as they remain unsusceptible even to last geneneration drugs like CFDC. Newly detected IMP-100 was even located in an CFDC-resistant XDR strain.
ARTICLE | doi:10.20944/preprints202305.0866.v1
Subject: Chemistry And Materials Science, Materials Science And Technology Keywords: LC gas sensor; novel structure; ZnO nanowires; NO2
Online: 11 May 2023 (13:52:16 CEST)
This work presents an LC resonant passive wireless gas sensor with a novel structure designed to mitigate the negative impact of substrate. The LC sensor antenna with the new structure and the reader antenna were designed and optimized utilizing HFSS software to improve the transfer efficiency. The superiority of the designed structure compared with the general ones is highlighted and verified. The change in the substrate capacitance has essentially no interference with the parameters to be measured of the LC sensor. The sensor with the new structure was prepared by combining etching and sputtering methods. The structure of the ZnO nanowires (NWs) was characterized to confirm their high purity and wurtzite crystal structure. The LC gas sensors demonstrated excellent wireless sensing performance including a low detection limit of 0.5 ppm NO2, high response of 1.058 and outstanding stability at 180 °C. The developed new sensor structure not only prevented interference from the substrate during gas sensing testing, but also expanded the choice of sensor substrates, playing a critical role in the development of sensors based on LC resonance principle.
ARTICLE | doi:10.20944/preprints202304.0918.v1
Subject: Biology And Life Sciences, Virology Keywords: BCMV; genome; proteome; amino acid substitutions; novel host
Online: 25 April 2023 (10:16:22 CEST)
Bean common mosaic virus from the genus Potyvirus has a wide range of hosts and a very negative impact on cultivated crops from the genus Phaseolus. The risk of viral infection of economically important crops increases even if the carriers of the virus are related plant species growing on agroecological interfaces. Such plant species have emerged as new hosts for BCMV, usually harboring novel genetic variants of the virus. A novel genetic variant of BCMV was isolated from a symptomatic crownvetch plant, where the presence of this virus was confirmed by Western-blotting analysis and by amino acid identities in peptide fragments of CI, HC-pro, and CP proteins using the nanoLC-ESI-Q-TOF. The novel BCMV SVK isolate differed from the most genetically similar one in 0.91% of nucleotides and 1.55% of amino acids. The highest number of amino acid substitutions (8.8% of amino acids) was in the P1 protein, followed by CP (2.44% of amino acids). Minor substitutions were in Hc-pro, CI, and Nib proteins. The symptomatic crownvetch plant was confirmed as a new host and carrier of the novel BCMV isolate.
ARTICLE | doi:10.20944/preprints202207.0157.v1
Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: Methylococcaceae; methanotroph; Indian rice field; Methylmonas; novel species
Online: 11 July 2022 (09:56:06 CEST)
An aerobic methanotroph, strain Kb3T, was isolated from a rhizospheric soil sample collected from a tropical Indian rice field. The cells were motile, Gram-negative bacilli, formed pink colonies and pink turbid/pellicles in the liquid medium. Biochemical characteristics showed that strain Kb3T utilised only methane and methanol as its sole carbon and energy sources. The isolate's 16S rRNA gene sequence expressed 99.52% similarity to the recently described valid species Methylomonas fluvii EbB (Mmf), with 92% query cover. But examining the genome similarity between Kb3 and EbB, a DDH value of 44.20% [41.6 - 46.7%] and an Ortho-ANI value of 91.48 was observed that were below the current cut-off values for species differentiation. Also, the 16S rRNA gene phylogeny and the phylogenomic analysis branched the two species separately. The major fatty acid in Methylomonas sp. Kb3 was C14:0, followed by C16:1 ω5c. The genome sequence revealed the size of strain Kb3 is 5.1 Mb, with the G + C content of 51.8%. Strain Kb3T shared the closest relatedness with Methylomonas sp. LW13 reveals a 99.66% 16S rRNA gene similarity, an Ortho-ANI value of 97.9%, a DDH value of 87.3%, and a close branching in the phylogenomic tree Kb3 and LW13 together form a new species. The genomic and phylogenetic distinction between species Mmf and strain Kb3 supports Kb3T to be described as a novel species within the genus Methylomonas, with the proposed name, Methylomonas aquatica sp. nov. (Mma) and the type strain being Kb3T (=MCC 4012, =JCM 33634, =KCTC 72521).
ARTICLE | doi:10.20944/preprints202009.0446.v1
Subject: Medicine And Pharmacology, Epidemiology And Infectious Diseases Keywords: Novel coronavirus diseases 2019; vaccination; target population; China
Online: 19 September 2020 (05:02:54 CEST)
All countries are facing decisions about which groups to prioritise for COVID-19 vaccination after the first vaccine product has been licensed, at which time supply shortages are inevitable. Here we define the key target populations and their size in China for a phased introduction of COVID-19 vaccination with evolving goals, accounting for the risk of illness and transmission. Essential workers (47.2 million) like healthcare workers could be prioritized for vaccination to maintain essential services. Subsequently, older adults, individuals with underlying health conditions and pregnant women (616.0 million) could be targeted to reduce severe COVID-19 outcomes. Then it could be further extended to target adults without underlying health conditions and children (738.7 million) to reduce symptomatic infections and/or to stop virus transmission. The proposed framework could assist Chinese policy-makers in the design of a vaccination program, and could be generalized to inform other national and regional COVID-19 vaccination strategies.
Subject: Medicine And Pharmacology, Urology And Nephrology Keywords: novel coronavirus infection; renal transplant; acute kidney injury
Online: 12 March 2020 (03:02:03 CET)
Novel coronavirus infection is a recent infective agent that causes severe potentially fatal pneumonia. The clinical presentation includes asymptomatic infection, severe pneumonia, and acute respiratory failure. Data pertaining to the clinical presentation of solid organ transplant recipients are scarce. Two cases of novel coronavirus infection in two recipients of renal transplant with variable clinical presentations and outcomes are reported. The first patient presented with progressive respiratory symptoms, acute renal failure, and passed away, whereas the second one, although presented with respiratory tract symptoms and hypoxemia remained stable and exhibited an excellent clinical recovery despite recent reception of thymoglobulin induction. This paper reports rare cases of novel coronavirus infection in renal transplant recipients. For an enhanced insight of the novel coronavirus infection and acute kidney injury on the clinical presentation, severity, and outcome in solid organ transplant recipients, further investigations are required.
REVIEW | doi:10.20944/preprints201909.0222.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: hearing impairment; novel murine genes; gene enrichment; africa
Online: 19 September 2019 (11:27:27 CEST)
The prevalence of congenital hearing impairment (HI) is highest in Africa. Estimates evaluated genetic causes to account for 31% of HI cases in Africa, but the identification of associated causative genes mutations have been challenging. In this study, we reviewed the potential roles, in humans, of 38 novel genes identified in a murine study. We gathered information from various genomic annotation databases and performed functional enrichment analysis using online resources i.e. genemania and g.proflier. Results revealed that 27/38 genes are express mostly in the brain, suggesting additional cognitive roles. Indeed, HERC1- R3250X had been associated with intellectual disability in a Moroccan family. A homozygous 216-bp deletion in KLC2 was found in two siblings of Egyptian descent with spastic paraplegia. Up to 27/38 murine genes have link to at least a disease, and the commonest mode of inheritance is autosomal recessive (n=8). Network analysis indicates that 20 other genes have intermediate and biological links to the novel genes, suggesting their possible roles in HI. This study will contribute to advance our knowledge in unravelling the biological roles of novel murine HI genes in humans and could enhance the understanding of the genetic causes of HI in Africans.
ARTICLE | doi:10.20944/preprints201807.0372.v1
Subject: Biology And Life Sciences, Plant Sciences Keywords: novel lncRNA; lncRNA conservation; copaifera; epigenetics; adaptive response
Online: 20 July 2018 (04:31:16 CEST)
LncRNA are involved in multiple regulatory pathways, its versatile mode of action has disclosed a new layer in gene regulation. They are reportedly modulated during plant development, with specific tissue functions and in response to stresses. In this study, we analyzed LncRNA from leave samples collected from the legume Copaifera langsdorffii (copaiba) from two divergent ecosystems: Cerrado (CER) and Atlantic Rain Forest (ARF). We identified 8020 novel lncRNAs, from which 2893 transcripts were regulated above 2-fold and 566 above 5-folds in either condition. This putative lncRNA set was compared with seven Fabaceae genomes, of which 1747 and 1879 transcripts (from ARF and CER, respectively) aligned to at least two genomes. Further, 2194 copaiba lncRNAs were successfully mapped to at least one of six Fabaceae transcriptomes. The secondary structures of the lncRNAs that were conserved and differentially expressed between the populations were predicted using in silico methods. Our results indicate the potential involvement of lncRNAs in the adaptation of C. langsdorffii to two different biomes.
ARTICLE | doi:10.20944/preprints202308.0346.v1
Subject: Biology And Life Sciences, Animal Science, Veterinary Science And Zoology Keywords: foals; behavior; handling; haltering; halter training; novel object test
Online: 3 August 2023 (14:32:23 CEST)
It could be helpful if behaviours presented in routine handling could be used as temperament indicators, thus directing tailor-made managements, optimising resources, and animal welfare. We evaluate whether behaviours presented by 25 foals during the first navel treatment and first halter session at weaning. Their behaviour was assessed during a novel object transposition test when they were one year of age. Behavioural parameters presented then were correlated with behaviours presented at navel treatment and haltering. Foals that showed higher exploratory activity during the test correlated to foals that showed less reactivity and less tickling at navel treatment and that were more relaxed and showed less reactivity haltering. Confidence to transpose the novel object was correlated with foals that were more relaxed, showed less reactivity and were less ticklish at navel treatment and were more relaxed during haltering. Transposition style correlated foals less prone to transpose with foals less curious in humans at navel treatment and more vigilant at haltering. Correlations verified between routine management and behaviour test indicate the possibility of early identification of equine temperament, allowing management techniques and specific training for the individual, enhancing training efficiency, animal welfare, and better human-horse interactions.
REVIEW | doi:10.20944/preprints202304.0312.v1
Subject: Biology And Life Sciences, Food Science And Technology Keywords: novel proteins; food safety; allergenicity; mass spectrometry, omic technologies
Online: 13 April 2023 (08:30:53 CEST)
In recent years, novel food is becoming an emerging trend increasingly more demanding in developed countries. Food proteins from vegetables (pulses, legumes, cereals), fungi, bacteria and insects are being researched to introduce them in meat alternatives, beverages, baked products and others. One of the most complex challenges for introducing novel foods on the market is to assure food safety. New alimentary scenarios drive the detection of novel allergens that need to be identified and quantified with the aim of appropriate labelling. Allergenic reactions are mostly caused by proteins of great abundance in foods, most frequently of small molecular mass, glycosylated, water-soluble and with high stability to proteolysis. The most relevant plant and animal food allergens such as lipid transfer proteins, profilins, seed storage proteins, lactoglobulins, caseins, tropomyosins and parvalbumins from fruits, vegetables, nuts, milk, eggs, shellfish, and fish have been investigated. New methods for massive screening in the search of potential allergens must be developed particularly concerning protein databases and other online tools. Moreover, several bioinformatic tools based on sequence alignment, motif identification or 3-D structure predictions should be implemented as well. Finally, targeted proteomics will become a powerful technology for the quantification of these hazardous proteins. The ultimate objective is to build an effective and resilient surveillance network with this cutting-edge technology.
ARTICLE | doi:10.20944/preprints202209.0143.v1
Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: Salmonella; novel antibacterial agents; cannabidiol; co-therapy; bacterial genetics
Online: 12 September 2022 (09:55:22 CEST)
New generation antibiotics are needed to combat the development of resistance to antimicrobials. One of the most promising new classes of antibiotics is cannabidiol (CBD). It is a non-toxic and low-resistance chemical that can be used to treat bacterial infections. The antibacterial activity of Cannabis sativa L. byproducts, specifically CBD, has been of growing interest in the field of novel therapeutics. As research continues to define and characterize the antibacterial activity that CBD possesses against a wide variety of bacterial species it is important to examine potential interaction between CBD and common therapeutics such as broad-spectrum antibiotics. Here, we show that CBD-antibiotic co-therapy can effectively fight S. typhimurium via membrane integrity disruption. This research serves to examine the potential synergy between CBD and three broad-spectrum antibiotics for potential antibiotic-CBD co-therapy. In this study, we reveal that Salmonella typhimurium (S. typhimurium) growth is inhibited at very low dosages of CBD-antibiotic. This interesting finding demonstrates that CBD and CBD-antibiotic co-therapies are viable novel alternatives to combating Salmonella typhimurium.
ARTICLE | doi:10.20944/preprints202205.0407.v1
Subject: Biology And Life Sciences, Plant Sciences Keywords: Fusarium; tomato; novel effector candidates; cell death; Nicotiana benthamiana
Online: 31 May 2022 (03:20:05 CEST)
Fusarium oxysporum f. sp. lycopersici (Fol) causes vascular wilt disease in tomato. Upon colonization of the host, Fol secretes many small effector proteins into the xylem sap to facilitate infection. Besides known SIX (Secreted In Xylem) proteins, the identity of additional effectors that contribute to Fol pathogenicity remains largely unexplored. We have performed a deep RNA-sequencing analysis of Fol race 2-infected tomato, used the sequence data to annotate a published genome assembly generated via PacBio SMRT sequencing of the Fol race 2 reference strain Fol4287, and analysed the resulting transcriptome to identify Fol effector candidates among the newly annotated genes. We examined the Fol-infection expression profiles of all 13 SIX genes present in Fol race 2 and identified 27 new candidate effector genes that were likewise significantly upregulated upon Fol infection. Using Agrobacterium-mediated transformation, we tested the ability of 22 of the new candidate effector genes to suppress or induce cell death in leaves of Nicotiana benthamiana. One effector candidate designated Fol-EC19, encoding a secreted guanyl-specific ribonuclease, was found to trigger cell death and two effector candidates designated Fol-EC14 and Fol-EC20, encoding a glucanase and a secreted trypsin, respectively, were identified that can suppress Bax-mediated cell death. Remarkably, Fol-EC14 and Fol-EC20 were also found to suppress I-2/Avr2- and I/Avr1-mediated cell death. Using the yeast secretion-trap screening system, we showed that these three biologically-active effector candidates each contain a functional signal peptide for protein secretion. Our findings provide a basis for further understanding the virulence functions of Fol effectors.
REVIEW | doi:10.20944/preprints202205.0024.v1
Subject: Medicine And Pharmacology, Gastroenterology And Hepatology Keywords: Outbreak; novel; unknown hepatitis; unknown aetiology; public health promotion
Online: 5 May 2022 (08:02:13 CEST)
Several clusters and individual cases of acute —often severe— hepatitis have been reported in Europe —mainly in the United Kingdom (U.K.)—, the United States (U.S.) and recently in Asia since October 2021. Laboratory investigation of the common viral hepatitis agents (HAV, HBV, HCV, HDV and HEV) yielded negative results prompting the use of the term “acute non hepA–E hepatitis” to describe this condition. The cases were characterized by the manifestations of acute hepatitis (abdominal pain, vomiting, diarrhea, jaundice and very high levels of liver enzymes) affecting children with a median age of 3–4 years. The exact underlying etiology has not been revealed yet; however, a leading hypothesis is that an infectious agent is the culprit underlying cause or at least a risk factor for acute non hepA–E hepatitis occurrence. So far, laboratory testing has shown the presence of adenovirus serotype 41 (Ad–41) which is classified in group F of adenoviruses in about three-fourths of the reported cases. However, the definitive link between adenoviruses and acute non hepA–E hepatitis has not been fully elucidated, which necessitates further investigation of this possible correlation. As of the end of April 2022, more than 200 cases were reported worldwide, the majority of which were in Europe: the U.K. (n=114), Italy (n=17), Spain (n=13), Israel (n=12), the U.S. (n=9), Denmark (n=6), Netherlands and Ireland (n=4), Japan (n=3), Austria, Belgium, France, and Norway (n=2), Germany, Poland, and Romania (n=1). Possible cases are being evaluated in Illinois, Minnesota, North Carolina, Wisconsin states of the U.S., Canada, Singapore and Slovenia. Vigilant surveillance and epidemiologic investigation to identify further cases are warranted at the global level to delineate the features of this emergent public health issue. The possible role of environmental and toxic agents including foodborne toxins should not be overlooked as well. Specific guidelines for identification of further cases is necessary particularly in low-income settings where testing for adenoviruses is not considered routinely. Genetic analysis of Ad–41 isolates is recommended to assess the potential changes in virus genome with subsequent possible altered virus behavior. Immunopathogenesis is another possibility that should be examined as well considering the absence of virus detection in liver biopsies of the affected children in the U.S.
REVIEW | doi:10.20944/preprints202004.0321.v1
Subject: Biology And Life Sciences, Biology And Biotechnology Keywords: 2019 Novel Coronavirus; plants; antiviral compounds; plant recombinant vaccines
Online: 19 April 2020 (04:15:18 CEST)
The proposal of novel drugs and approaches for effective treatment of the novel coronavirus is a necessity after the quick outbreak of the disease. Since the commencement of the coronavirus spread, enormous efforts have been made to protect, alleviate and cure the disease, though no specific treatment has been approved. While there have been convincing results in the use of chemical drugs and interferon therapy, such therapeutic approaches have various drawbacks and lack the required performance for the treatment of the new coronavirus. Medicinal plant species can provide a solution as a source of natural antiviral compounds by the accumulation of secondary metabolites and lectins as well as acting as a platform to express the viral immunogenic proteins. This study reviews the advantages and the results of previous research for the treatment of the novel coronavirus disease and previous generations of similar coronaviruses. Several plant-derived anti coronavirus compounds have been nominated that could be targeted for further research due to the similarity of the coronavirus disease in 2003 and the current coronavirus. This review regards plant species such as Scutellaria baicalensis (Baikal skullcap), and Utrica dioica (Stinging nettle) as suitable candidates for the new coronavirus antiviral research. Furthermore, the use of plants such as Nicotiana tabacum (Tobacco) for the expression of the coronavirus viral antigens can be a target for the future vaccinal research of the new coronavirus due to the efficiency of expression and intrinsic antiviral properties.
ARTICLE | doi:10.20944/preprints202001.0173.v1
Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: wetlands; methanotrophs; India; tropical; novel species; Type Ib; Methylotetracoccus
Online: 16 January 2020 (11:51:52 CET)
We enriched and isolated a novel gammproteobacterial methanotroph; strain FWC3, from tropical freshwater wetland, near Nagaon beach, Alibag, India. FWC3 is a coccoid, flesh pink/peach pigmented, non-motile methanotroph and the cells are present in pairs and as tetracocci. The culture can grow on methane (20%) as well as on a wide range of methanol from concentrations (0.02%-5%). Based on the comparison of genome data, FAME analysis, morphological characters and biochemical characters, FWC3 belongs to the tentatively and newly but not validly described genus ‘Methylotetracoccus’ of which only a single species strain was described, Methylotetracoccus oryzae C50C1. The ANI index between FWC3 and C50C1 strains is 94%, and the DDH value is 55.7%, less than the cut-off values 96% and 70%, respectively. The genome size of FWC3 is smaller (3.4 Mbp) compared to that of C50C1 (4.8 Mbp). Additionally, the FAME profile of FWC3 shows differences in cell wall fatty acid profiles compared to Methylotetracoccus oryzae C50C1. Also, there are other differences on the morphological, physiological and genomic levels. We propose FWC3 to be a member of a novel species of the genus Methylotetracoccus, for which the name Methylotetracoccus aquaticus is proposed. Also, an amended description of the genus Methylotetracoccus gen. nov. is given here. FWC3 is available in two international culture collections with the accession numbers: MCC 4198 (Microbial Culture collection, India) and JCM 33786 (Japan Collection of Microorganisms, Japan).
ARTICLE | doi:10.20944/preprints202307.1271.v1
Subject: Biology And Life Sciences, Ecology, Evolution, Behavior And Systematics Keywords: Acinetobacter thutiue; Acinetobacter kontum; oil-contaminated soil; novel species; Morazellaceae
Online: 19 July 2023 (09:11:19 CEST)
Two isolates of Acinetobacter were isolated from the soil samples of motorbike repairing workshop floors in Vietnam, where motorcycle/scooter repairs generate various types of hazardous waste, including mainly used waste oil and fluids. Two isolates were Gram-stain-negative, coccobacilli-shaped, aerobic, non-motile, non-hemolytic, oxidase-negative, and catalase-positive, designated strains VNH17T and VNK23T. Growth of strains was inhibited by NaCl concentrations above 3% and grew at an optimal temperature of 20-35°C. Phylogenetic analysis based on 16S rRNA gene sequences revealed that two isolated strains formed a lineage within the family Moraxellaceae and clustered as members of the genus Acinetobacter. The predominant respiratory quinones of VNH17T and VNK23T are ubiquinone 9 and ubiquinone 8, and the polar lipids are mainly composed of diphosphatidyl glycerol, phosphatidylglycerol, and phosphatidylethanolamine. The major cellular fatty acids are C18:1ω9c, C16:0 and summed feature 3 (C16:1ω7c and/or C16 : 1ω6c). The DNA G+C content of VNH17T and VNK23T was 42.07% and 41.75%, respectively. In addition, the average nucleotide identity and in silico DNA-DNA hybridization relatedness values between VNH17T and VNK23T as well as between they and phylogenetically related type strains were below the threshold values used for species delineation. Based on genomic, chemotaxonomic, phenotypic and phylogenomic analyses, the isolated strains represent novel species in the genus Acinetobacter, for which the names Acinetobacter thutiue sp. nov. (type strain VNH17T = KACC 23003 = CCTCC AB 2023063), Acinetobacter kontum sp. nov. (type strain VNK23T = KACC 23002 = CCTCC AB 2023064) are proposed.
ARTICLE | doi:10.20944/preprints202209.0004.v2
Subject: Biology And Life Sciences, Virology Keywords: phage Rih21; MRSA; novel bacteriophage; S. aureus; bacteriophage; phage genome analysis
Online: 5 October 2022 (10:13:04 CEST)
From the hospital wastewater, a novel bacteriophage was isolated and characterized. According to characterization properties, this bacteriophage belongs to the Siphoviridae family, the maximum bacteriophage titer was recorded at 37°C and a pH of 7.2, had a 44,789 bp linear double-strand DNA genome, and within the genome sequence, there are 61 genes, all of which are encoded into proteins. Although this bacteriophage does not have any virulence factors or antimicrobial resistance genes and had specific lytic activity against some antimicrobial resistance S. aureus clinical isolates.
ARTICLE | doi:10.20944/preprints202012.0444.v1
Subject: Biology And Life Sciences, Anatomy And Physiology Keywords: novel rumen yeast; screening; isolation; biomass of yeast; cellulase enzyme
Online: 18 December 2020 (07:26:28 CET)
We hypothesized that rumen fluid with yeast producing cellulase enzyme can occur and also produces a high biomass compared to S. cerevisiae. Therefore, the aim of this study was to screen and isolate yeast from rumen fluids with an experimental design method. We optimized a fermentation medium containing sugarcane molasses as a carbon source and urea as a nitrogen source to measure the efficiency of biomass production and cellulase activity. Two fistulated-crossbred Holstein Friesian steers, averaging 350 ± 20 kg body weight, were used to screen and isolate ruminal yeast. The two experiments were designed. A 12 × 3 × 3 factorial was used in a completely randomized design to determine biomass and carboxymethyl cellulase activity. Factor A was isolated yeasts and S. cerevisiae. Factor B was sugarcane molasses (M) concentration. Factor C was urea (U) concentration. Potential yeast was selected for identified and analyzed as a 4 × 3 factorial use in a completely randomized design including. Factor A was incubation times. Factor B was isolated yeast strains including code H-KKU20 (as P. kudriavzevii-KKU20), I-KKU20 (C. tropicalis-KKU20), and C-KKU20 (as Galactomyces sp.-KKU20). Isolation was under aerobic conditions, resulting in a total of 11 different colonies. We noted two appearances of colonies including, asymmetric colonies of isolated yeast (indicated as A, B, C, E, and J) and ovoid colonies (coded as D, F, G, H, I, and K). The highest biomass was observed in three yeasts including codes H, I, and C-KKU20 when inoculated in 25% molasses with 1% urea (M25+U1) (p <0.01). The highest CMCase activity was observed in yeast code H-KKU20 when inoculated in all media solutions (p <0.01). Ruminal yeasts strains H-KKU20, I-KKU20, and C-KKU20 were selected for their ability to produce biomass and their CMCase enzyme synthesis. Identification of isolates H-KKU20 and I-KKU20 revealed that those isolates belonged to Pichia kudriavzevii-KKU20 and Candida tropicalis-KKU20, while C-KKU20 was identified as Galactomyces sp.-KKU20. Two strains provided maximum cell growth: P. kudriavzevii-KKU20 (9.78 and 10.02 Log cell/ml) and C. tropicalis-KKU20 (9.53 and 9.6 Log cells/ml) at 60 and 72 h of incubation time, respectively. The highest ethanol production was observed in S. cerevisiae: 76.4, 77.8, 78.5, and 78.6 g/L at 36, 48, 60, and 72 h of incubation time, respectively (p <0.01). The P. kudriavzevii-KKU20 yielded the least reducing sugar about 30.6 and 29.8 g/L at 60 and 72 h of incubation time, respectively. It could be concluded that screening and isolating yeast from rumen fluids resulted in 11 different characteristics of yeasts. The first novel yeasts discovered in the rumen fluid of cattle were Pichia kudriavzevii-KKU20, Candida tropicalis-KKU20, and Galactomyces sp.- KKU20. P. kudriavzevii-KKU20 had higher results than the other yeasts in terms of biomass production, cellulase enzyme activity, and cell number.
BRIEF REPORT | doi:10.3390/sci2030055
Subject: Public Health And Healthcare, Health Policy And Services Keywords: coronavirus; COVID-19; 2019-nCoV; novel (new) coronavirus; pandemic control
Online: 14 July 2020 (00:00:00 CEST)
The world is currently facing a serious pandemic of coronavirus disease 2019 (COVID-19) which started in Wuhan, China, and was then transmitted rapidly to other countries. Countries applied different methods and procedures in an attempt to prevent or reduce and/or control the incidence of cases and manage existing ones. This paper discusses the methods and procedures applied by Kuwait to control this epidemic, and how effective they have been. The State of Kuwait followed WHO, European CDC, US CDC, and/or other countries’ institutional guidelines, and is still working on containing the disease, given the rising number of cases among Kuwaitis returning from affected areas such as the UK and USA, and migrant workers who bear the highest burden, given their cramped living conditions.
REVIEW | doi:10.20944/preprints202006.0157.v1
Subject: Medicine And Pharmacology, Pathology And Pathobiology Keywords: novel coronavirus; SARS-CoV-2; COVID-19; pneumonia; Betacoronavirus; transmission
Online: 14 June 2020 (03:06:15 CEST)
The emergence of novel coronavirus (SARS-CoV-2) in marked as the highest pathogenic coronavirus that has crossed from the hosts to the human population in the twenty-first century. The spreading of COVID-19 in different chinese cities and around the world is travel-related viral spread with the unprecedented nosocomial outbreaks. It has also shown with high case-fatality rates, indeed to urgent prophylactic and therapeutic settings. Scientific advancements of the SARS-CoV-2 pandemic allowed for rapid progress to understand the epidemiology and pathogenesis of SARS-CoV-2. This review highlights the the genomic structure of SARS-CoV-2 with the proposed roles of genotype and phenotype of SARS-CoV-2 in pathogenesis and discuss recent results supporting treatment strategies of COVID-19 with a special focus on how these new insights may facilitate rational development of SARS-CoV-2 for targeted therapies in the future.
ARTICLE | doi:10.20944/preprints202003.0206.v2
Subject: Medicine And Pharmacology, Epidemiology And Infectious Diseases Keywords: 2019 novel coronavirus infection; corons; SARS-CoV; interferon; systems biology
Online: 23 March 2020 (10:27:57 CET)
As the outbreak of COVID-19 has accelerated, an urgent need for finding strategies to combat the virus is growing. Thus, gaining more knowledge on the pathogenicity mechanisms of SARS-CoV-2, the causing agent of COVID-19, and its interaction with the immune system is of utmost importance. Although this novel virus is not well known yet, its structural and genetic similarity with SARS-CoV as well as the comparable pattern of age-mortality relations suggest that the previous findings on SARS can be applicable for COVID-19. Therefore, a systems biology study was conducted to investigate the most important signaling pathways activated by the virus. The results were then validated through a literature review on COVID-19 and the other closely related viruses, SARS and MERS. Interferons have shown to play a crucial role in the defense against coronavirus diseases. CoV can impede the interferon induction in humans. Moreover, STAT1, a key protein in the interferon-mediated immune response, is antagonized by the virus. This could explain the increased response threshold of immune cells to IFNs during CoV infections. A vivid correlation between the innate immune response threshold and the fatality rates in COVID-19 can be found. Differences in the dynamics of the interferon-related innate immune responses in children, adults, and elderly may explain the reported fatality rates. The increased mortality rates in the elderly can be explained by the higher threshold of interferon-mediated immune responses. Earlier induction of interferons in children and their less developed immune system could contribute to their near to zero fatality rate. Administration of interferon-inducing agents, such as poly (ICLC), could reduce the mortality of SARS at the very early stages of the disease. Interferon-γ combination with an interferon-I might induce synergistic effects and maximize the benefits. However, in-depth research is needed to validate it and determine the optimum dosage and timing to prevent unwanted results. Such interventions can act as a double-edged sword and aid the imbalance of the immune reactions, which may occur at the later stages of the disease. With the advancement of the disease and the virus overload, the responses would shift toward immnopathogenic over-reactions and probably cytokine storm. Moderating the activity of the immune system and supportive care in such conditions might be the optimum approach.
HYPOTHESIS | doi:10.20944/preprints202002.0254.v2
Subject: Medicine And Pharmacology, Pharmacology And Toxicology Keywords: 2019-nCoV; novel coronavirus pneumonia; docking; ACE2; viral main protease
Online: 23 February 2020 (02:09:52 CET)
The 2019 novel coronavirus (2019-nCoV) causes novel coronavirus pneumonia (NCP). Given that approved drug repurposing becomes a common strategy to quickly find antiviral treatments, a collection of FDA-approved drugs can be powerful resources for new anti-NCP indication discoveries. In addition to synthetic compounds, Chinese Patent Drugs (CPD), also play a key role in the treatment of virus related infections diseases in China. Here we compiled major components from 38 CPDs that are commonly used in the respiratory diseases and docked them against two drug targets, ACE2 receptor and viral main protease. According to our docking screening, 10 antiviral components, including hesperidin, saikosaponin A, rutin, corosolic acid, verbascoside, baicalin, glycyrrhizin, mulberroside A, cynaroside, and bilirubin, can directly bind to both host cell target ACE2 receptor and viral target main protease. In combination of the docking results, the natural abundance of the substances, and botanical knowledge, we proposed that artemisinin, rutin, glycyrrhizin, cholic acid, hyodeoxycholic acid, puerarin, oleanic acid, andrographolide, matrine, codeine, morphine, chlorogenic acid, and baicalin (or Yinhuang Injection containing chlorogenic acid and baicalin) might be of value for clinical trials during a 2019-nCov outbreak.
ARTICLE | doi:10.20944/preprints202310.0094.v1
Subject: Biology And Life Sciences, Virology Keywords: Podo virus; temperate phages; Short tail phages, novel phage terminase, Lederbergvirus
Online: 3 October 2023 (08:19:22 CEST)
Salmonella enterica includes enteric pathogens of zoonotic potential, possessing one of the largest pools of temperate phages in their genomes. One such class of phages previously called Podoviridae (Now genera placed directly under class Caudoviricetes temporarily) is the largest group of temperate phages that lysogenize clinically and economically important Salmonella enterica serovars. These phages are capable of generalized transduction and are well known for carrying foreign DNA (mobile genetic elements and resistance genes) to new bacterial species that play a major role in the evolution, pathogenicity, and host adaptability of Salmonella serovars. Here we report a novel species of podo viruses; Salmonella phage BIS08P22 (BIS08) that infects Salmonella enterica serovar Typhimurium strain SE-BS17 (Acc. NO: MZ503545). Phage BIS08 was viable only at biological pH and temperature (pH7 and 37 °C) and features 41,574 -base pair (bp) linear ds DNA genome with 47% GC content. It encodes 73 putative Open Reading Frames (ORFs), has a mosaic arrangement, and shares only 16 core genes with its closest homologs. BIS08 genome possesses only 52 % homology (genome-wide Nucleotide homology by VIRIDIC analysis) with members of the genus Lederbergvirus which is not sufficient to place it in the same genus. This phage has a unique terminase enzyme (DNA packaging motor) with no nucleotide and protein homology with any known member of the Lederbergvirus genus. We carried out a detailed phylogenetic and genome analysis of this novel phage and proposed its placement in a new genus. Our study also suggests a revision in the classification of the genus Lederbergvirus. We also performed in silico structural analysis of the BIS08 unique terminase enzyme comparing it to its close homologs.
REVIEW | doi:10.20944/preprints202304.0180.v1
Subject: Medicine And Pharmacology, Pharmacy Keywords: Methicillin-resistant Staphylococcus aureus; MRSA; antibiotic resistance mechanism; novel therapeutic approaches
Online: 11 April 2023 (03:20:45 CEST)
Staphylococcus aureus (S. aureus), particularly Methicillin-resistant S. aureus (MRSA), is a life-threatening pathogen that causes a variety of infections in hospital and community settings. It poses a significant risk and challenge for global health that hinders our ability to control and treat bacterial infections. Recently, the emergence and spread of variant strains of bacteria, misuse of the limited available options of effective antibiotics, spread of fake drugs, and climate change that increased the contact between humans and animals’ populations carrying different bacterial has significantly increased the incidence of Multi-Drug Resistance strains (MDR). This in turn, has created a severe problem in the infection control treatment of S. aureus infected patients. Treatment options for MRSA infection are increasingly limited and complicated. Unfortunately, different strains of MRSA are showing tolerance and resistance toward vancomycin, which is the standard of care for complicated MRSA. Therefore, it is crucial now to invest developing new effective anti-biotics and synergies, develop and implement national action plans for the management of an-tibiotic resistance, as well as improving our understanding of the antimicrobial resistance mechanisms. Here, in this review we explain the main mechanisms of antibiotic resistance in MRSA and describes different approaches to manipulate it in MRSA, providing a basis for de-signing effective drugs, and shedding some light on the evolution of S. aureus.
ARTICLE | doi:10.20944/preprints202105.0308.v1
Subject: Biology And Life Sciences, Anatomy And Physiology Keywords: Indonesia; biodiversity; novel antibiotics; drug screening; bioactivity; gene cluster networking; GNPS
Online: 13 May 2021 (14:05:00 CEST)
Indonesia is one of the most biodiverse countries in the world and a promising resource for novel natural compound producers. Actinomycetes produce about two-thirds of all clinically used antibiotics. Thus, exploiting Indonesia’s microbial diversity for actinomycetes may lead to the discovery of novel antibiotics. A total of 422 actinomycete strains were isolated from three different unique areas in Indonesia and tested for their antimicrobial activity. Nine potent bioactive strains were prioritized for further drug screening approaches. The nine strains were cultivated in different solid and liquid media and a combination of genome mining analysis and mass spectrometry (MS)-based molecular networking was employed to identify potential novel compounds. By correlating secondary metabolite gene cluster data with MS-based molecular networking results, we identified several gene cluster-encoded biosynthetic products from the nine strains, including naphthyridinomycin, amicetin, echinomycin, tirandamycin, antimycin, and desferrioxamine B. Besides, eight putative ion clusters and numerous gene clusters were detected that could not be associated with any known compound, indicating that the strains can produce novel secondary metabolites. Our results demonstrate that sampling of actinomycetes from unique and biodiversity-rich habitats, such as Indonesia, along with a combination of gene cluster networking and molecular networking approaches, accelerates natural product identification.
ARTICLE | doi:10.20944/preprints202104.0385.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: antibiotic resistance; antimicrobial susceptibility testing; novel diagnostics; polymicrobial; sputum; drug resistant
Online: 14 April 2021 (14:21:15 CEST)
For polymicrobial infections, AtbFinder utilizes a novel paradigm of the population response to antibiotics, enabling bacterial growth in the form of a mixed microbial community and selecting the antibiotics targeting not only the principal pathogen, but also those bacteria that support their growth. TGV medium allowed culturing a more diverse set of bacteria from polymicrobial biospecimens, compared with that achieved with the standard media and enabled, already within 4h, accurate selection of the antibiotics that completely eliminated all cultivatable bacteria from clinical samples. In conclusion, AtbFinder system may be a valuable tool in improving antibiotic selection, enabling targeted empirical therapy and accurate antibiotic replacement, which is especially important in high-risk patients.
ARTICLE | doi:10.20944/preprints202008.0730.v1
Subject: Business, Economics And Management, Business And Management Keywords: risk management and early measures; Novel Corona Virus (COVID-2019); GHS
Online: 31 August 2020 (17:56:33 CEST)
This research paper is mainly aimed to elaborate the initial risk management and measures which government of Pakistan took towards Novel Corona Virus (COVID-2019). This initial response and planning was devised after the early outbreak of COVID-2019 in Wuhan, China in early time of January 2020. Pakistan devised a comprehensive plan that not to evacuate their student from Wuhan, China. The government of Pakistan in compliance with the National Institute of Health (NIH) devised and documented comprehensive plans such as the flight operations postponed related to Umerah pilgrims, which were intended to go to sacred places of KSA (The Kingdom of Saudi Arabia). The process of visa, immigration policy totally changed and the government of Pakistan notified it officially that, no new visas of visit, student, and business would be issued in due course of uncertainty due to COVID-2019. The government of Pakistan also announced medical emergency and notified through the country’s provinces the process of testing and treatment of COVID-2019. The government of Pakistan also allocated funds for medical supplies and named out the particular country’s best laboratories. The government of Pakistan also locked down all the cities with the emergency announcement that people should stay inside the home in quarantine or self-isolation. NIH (The National Institute of Health) played a vital role in executing the planning to cope with COVID – 2019). The National Institute of Health responded as “The Centre for Disease Control”. In aid to the government, the national army of Pakistan responded in a proactive manner towards planed execution. The medical corps of Pakistan army dedicated themselves to treat the suspected patients of COVID – 2019. Due to plans, policies being documented, implemented in such a way productive way that from February 28, 2020 to till date there is not much critical situation and issues are not present. There are much productive results as there is not much boom in a rise of COVID-2019 patients. This lockdown under the authority of the provinces resulted in fruitful outcomes. Background: On January 02, 2020, authorities of the People Republic of China elaborated that they have encountered with a novel type of infectious viral disease 2019. Later on January 12, the authorities from China elaborated the related sequence of Corona Virus diseases 2019 names as COVID – 2019. When COVID-2019 being identified in Wuhan, Hubei China, as an early response the Government of Pakistan in support of the National Institute of Health (Field Epidemiology & Disease Surveillance Division) published a health advisory about novel coronavirus. Methods: According to Global Health Security Index, Pakistan is ranked as 105th country among 195 countries in GHS index. Overall Score of Pakistan is 35.5. The score of Early Detection and Reporting for Epidemics of Potential International Concern is 41.7. A Graphical depiction of the COVID-19 cases placed until April 10, 2020 as well as a graph trend line of recovered as well as death rate is also depicted. According to the graphical facts of Government of Pakistan and World meters, the recovery rate of COVID-19 is about 98 percent and 2.1 percent death rate is reported against the total cases. Trend analysis with line graph was drawn based on available data from official dashboard web portal of the government of Pakistan and worldometers.info. Data figures were incorporated from March to August 18, 2020 in MS Excel and then subsequently deployed to draw trend analysis from managing risk to recovery. Results: The line graph showed a slowdown in the COVID-19 cases and high rate of recoveries from COVID-19 in Pakistan. On March 11, 2020, there were 20 confirmed cases of coronavirus reported in Pakistan. No death was recorded in very first seven days, on March 18, 2020 only two deaths were reported. On August 18, 2020, there were 272128 recoveries, 6201 deaths, total confirmed cases 290445, and total test were 2340072 in Pakistan. As a results, we can report that due to early measures taken by government of Pakistan no mass scale destruction in terms of death and cases been recorded in Pakistan. Conclusions: To till date, the government of Pakistan tried its level best to minimize the coronavirus cases as much as they can. However, the ending of the potential attack of an outbreak would depend upon the well organized and coordinated approach at all levels such as true directed decisions, fully preparedness, as well implementation and evaluation of continuous decisions. As the recovery rate of the cases is 98 percent and merely death rate is 2.1 percent, concluded that in future it would be a good sign to stop the potential outbreak. Also, lock down as well as precautionary measurement taken by the provincial governments resulted a decline number of COVID-19 cases in the country. Another good sign is that merely 4 percent population of Pakistan is of more than 60 years of old it can be concluded that there are less chances of mass death due to outbreak of COVID-19.
REVIEW | doi:10.20944/preprints202006.0350.v1
Subject: Biology And Life Sciences, Biology And Biotechnology Keywords: Antibodies engineering; Computational approach; Novel drugs; Synthetic immunology; Next generation antibodies
Online: 28 June 2020 (20:24:49 CEST)
In the pre era of synthetic antibodies, pharmaceutical companies depend on finding novel drugs from medicinal plants and other traditional resources; while in present, technological advances in biology, computer and robotics give the researchers the ability to rewrite and edit DNA in order to synthesize very large sets of drug candidates; these novel and improved candidates serves the basis for creating another library of drug candidates and so on until we find the right biomolecule for the disease of interest. all these technologies combined together to synthesize therapeutic antibodies for many types of cancer, autoimmune diseases, and infectious diseases, that can address diseases much more readily to very rapidly get therapeutics into patients so that we can potentially have an impact on disease. The antibodies mechanism is recognize and bind to disease cells and pinpoint the immune system to attack those cells effectively. Now a days, they dependent on computational approach to guide and accelerate the process of antibodies engineering by combination of selection system and use of high-throughput data acquisition and analysis to build and construct populations of next generation antibodies that are thermo-stable, non-immunogenic as possible, and to be administered to many humans as possible. In this review, I will discuss the latest in silico methods for antibodies engineering.
REVIEW | doi:10.20944/preprints202004.0511.v1
Subject: Public Health And Healthcare, Public Health And Health Services Keywords: point of care testing; novel coronavirus; COVID-19; rapid testing; LAMP
Online: 29 April 2020 (13:43:54 CEST)
The current coronavirus disease 2019 (COVID-19) pandemic is largely driven by community transmission, after 2019 novel Coronavirus (2019-nCoV or SARS-CoV-2) crosses the borders. To stop the spread, rapid testing is required at community clinics and hospitals. These rapid tests should be comparable with the standard PCR technology. Isothermal amplification technology provides an excellent alternative that is highly amenable to resource limited settings, where expertise and infrastructure to support PCR are not available. In this review, we provide a brief description of isothermal amplification technology, its potential and the gaps that need to be considered for SARS-CoV-2 detection. Among this emerging technology, loop mediated amplification (LAMP) and recombinase polymerase amplification (RPA) technologies have been identified as potential platforms that could be implemented at community level, without samples referral to a centralised laboratory and prolonged turn-around-time associated with the standard COVID-19 RT-PCR test. LAMP, for example, has recently been shown to be comparable with PCR and could be performed in less than 30 min by non-laboratory staff, without RNA extractions commonly associated with PCR. More so, it is cost effective and could easily be scaled up to resource limited settings. Diagnostics developers, scientific community and commercial companies could consider this alternative method to help stop the spread of COVID-19.
REVIEW | doi:10.20944/preprints202004.0189.v1
Subject: Medicine And Pharmacology, Epidemiology And Infectious Diseases Keywords: COVID-19; Coronavirus; SARS CoV; SARS CoV-2; novel CoV; India
Online: 12 April 2020 (09:17:16 CEST)
COVID-19 disease outbreak was started in the December, 2019 in the Wuhan city of China which is also known as the largest transportation hub of China. During the spring festival of China the situation become epidemic. Soon, the virus is imported to many regions including the low income countries. Till now, 234073 infected reported cases of the COVID-19 in the world with the total of 9840 deaths (March 20, 2020). The common symptoms of the COVID-19 are the cough, high fever, sore throat, fatigue and breathlessness. The disease is found to be mild in most of the people, some of cases reported to the pneumonia also with multi organ dysfunction and acute ARDS (acute respiratory distress syndrome). It is found that the incubation period for the infection is 2-14 days which is usually 4 days in maximum of cases. India has reported 283 cases of COVID-19 infections till now with 4 deaths. India is still at stage 2 on local transmission as per WHO report 60. WHO reported 60 clearly stated that there is no community transmission occurred in India yet which can be prevented by the avoiding mass gathering and proper screening of the people. Govt. of India has taken many initiatives to minimize the spread of COVID-19 infection in the country. The infection rate of the COVID-19 in India remains low related to population size of the country. It is because of fast government action to quarantine the suspected people and shut down all its borders. There is a great slowdown in the global economy due to COVID-19 attack which is likely to costs around $1 trillion. The spread of COVID-19 infection can be reduced by minimizing the H-H transmissions. Still there is need of Anti-n-CoV drug development which can replace the supporting therapies for the treatment of infection.
Subject: Medicine And Pharmacology, Pathology And Pathobiology Keywords: Novel coronavirus pneumonia; COVID-19; SARS-CoV-2; Pathology; Critical patient
Online: 9 March 2020 (10:31:10 CET)
Background Critical patients with novel coronavirus pneumonia ( COVID-19) have worse outcome and high mortality. However, the histopathology of critical patient with COVID-19 remains undisclosed. Methods We performed the whole lung biopsy, and described the pathological changes of critical COVID-19 patient done with transplant by HE staining, immunohistochemistry and special staining observed under the microscopy. Findings The whole lungs displayed diffuse congestive appearance and partly haemorrhagic necrosis on gross examination. The haemorrhagic necrosis was prominently present in outer edge of the right lower lung. The cut surfaces of the lung displayed severe congestive and haemorrhagic changes. The main pathological changes showed massive pulmonary interstitial fibrosis, and partly hyaline degeneration, variable degrees of hemorrhagic pulmonary infarction. Small vessels hyperplasia, vessel wall thickening, lumen stenosis, occlusion and microthrombosis formation. Focal monocytes, lymphocytes and plasma cells infiltrating into pulmonary interstitium. Bronchiolitis and alveolitis with proliferation, atrophy, desquamation and squamous metaplasia of epithelial cells. Atrophy, vacuolar degeneration, proliferation, desquamation and squamous metaplasia in alveolar epithelial cells. Alveolar cavity congestion was prominent, and contained mucus, edema fluid, desquamated epithelial cells, and inflammatory cells. We also found several multinucleate giant cells and intracytoplasmic viral inclusion bodies. Special stains including Masson stain, sirius red staining, reticular fibers staining indicated massive pulmonary interstitial fibrosis. Immunohistochemistry showed positive for immunity cells including CD3, CD4, CD8, CD20, CD79a, CD5, CD38 and CD68. Interpretation We demonstrate the pathological findings of critical patient with COVID-19, which might provide a deep insight of the pathogenesis and severity of this disease.
REVIEW | doi:10.20944/preprints202311.0285.v1
Subject: Medicine And Pharmacology, Gastroenterology And Hepatology Keywords: celiac disease (CeD); gluten-free diet (GFD); novel treatment; non-dietary treatment
Online: 6 November 2023 (13:44:55 CET)
.Celiac disease (CeD) is a chronic, autoimmune disorder triggered by the ingestion of gluten, affecting around 1% of the global population. It is a multifactorial disease involving both genetics and environ-mental factors. Nowadays, the only available treatment for CeD is a life-long gluten-free diet (GFD), which can cause a significant burden for patients, since symptoms and mucosal injury can persist de-spite apparent compliance with a GFD. That could also lead to psychological consequences and affect the quality of life of these patients. Thankfully, recent advances in understanding the pathogenesis of CeD and the availability of various targets have made it feasible to explore pharmaceutical treatments specific to CeD. Recently, the FDA has highlighted the unmet needs of adult patients on GFD who expe-rience ongoing symptoms attributed to CeD and also show persistent duodenal villous atrophy. This re-view will outline the limitations of a GFD, describe the targets of potential novel treatment of CeD and provide an overview of the primary clinical trials involving oral and injectable agents for a non-dietary treatment of CeD.
ARTICLE | doi:10.20944/preprints202310.0385.v1
Subject: Biology And Life Sciences, Cell And Developmental Biology Keywords: histone modifications; pediatric leukemia; chromatin acessibility; epigenetics; mass cytometry; JMML; novel targets
Online: 7 October 2023 (09:49:46 CEST)
Juvenile myelomonocytic leukemia (JMML) is a deadly pediatric leukemia driven by RAS pathway mutations, of which >35% are gain-of-function in PTPN11. Although DNA hypermethylation portends severe clinical phenotypes, the landscape of histone modifications and chromatin profiles in JMML patient cells have not been explored. Using global mass cytometry, Epigenetic Time of Flight (EpiTOF), we analyzed hematopoietic stem and progenitor cells (HSPCs) from five JMML patients with PTPN11 mutations. These data revealed statistically significant changes in histone methylation, phosphorylation and acetylation marks that were unique to JMML HSPCs when compared with healthy controls. Consistent with these data, assay for transposase-accessible chromatin with sequencing (ATAC-seq) analysis revealed significant alterations of chromatin profiles at loci encoding post translational modification enzymes, strongly suggesting their mis-regulated expression. Collectively, this study reveals histone modification pathways as an additional epigenetic abnormality in JMML patient HSPCs, thereby uncovering a new family of potential druggable targets for the treatment of JMML.
ARTICLE | doi:10.20944/preprints202307.0856.v1
Subject: Engineering, Industrial And Manufacturing Engineering Keywords: Mitragyna speciosa; mitragynine; novel technology; energy consumption; pulsed electric field; ultrasound extraction
Online: 13 July 2023 (05:06:28 CEST)
The aim of this work was to determine the potential of using a pulsed electric field (PEF) and ultra-sound (US) apparatus to produce mitragynine extracts from Mitragyna speciosa dried leaves. Four modes of the device were tested: PEF, US, US + PEF, and PEF + US. The results were compared with extracts obtained using a conventional technique (maceration, as the control). Changes in the mitragynine content were determined with the liquid chromatography/mass spectrometry (LC-MS/MS) method. The LC-MS/MS analysis showed that the mitragynine contents from kratom extracts using four different modes were different. The highest extraction (106.63 ± 0.85 mg/L) of mitragynine was achieved by the PEF + US procedure, followed by US + PEF (97.27 ± 1.33 mg/L), with increased extraction efficiencies of 45.81 ± 0.59% and 33.00 ± 1.85%, respectively. Moreover, the total energy consumption under the combination technique was 25.0% lower than that with PEF assistance. Furthermore, scanning electron microscopy (SEM) and Fourier Transform Infrared Spectroscopy (FTIR) provided confirmatory evidence for the extraction of M. speciosa by the prototype. This study confirmed that PEF and US devices can be considered a green alternative method and may contribute to the application of agricultural products.
ARTICLE | doi:10.20944/preprints202211.0380.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Heat stress response; novel transcripts; RNA-Sequencing; blood; liver; adrenal glands; rats
Online: 21 November 2022 (07:18:32 CET)
The molecular mechanisms underlying heat stress tolerance in animals to high temperatures remain unclear. This experiment was performed with Sprague-Dawley rats housed at 22 ℃ (control group; CT), and 42 ℃ for 30 min (H30), 60 min (H60), and 120 min (H120). Transcriptomic analysis using RNA-Sequencing (RNA-Seq) from blood (CT and H120), liver (CT, H30, H60, and H120), and adrenal glands (CT, H30, H60, and H120) was performed. The differentially expressed mRNA isoforms (DEIs) were identified and annotated by the CLC Genomics Workbench. Biological process and metabolic pathway analyses were performed using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) database. A total of 225, 5,764, and 4,988 DEIs in the blood, liver, and adrenal glands were observed. Furthermore, the number of novel differentially expressed transcript lengths with annotated genes and the novel differentially expressed transcript with non-annotated genes were 136 and 8 in blood, 3,549 and 120 in the liver, as well as 3,078 and 220 in adrenal glands, respectively. A total of 35 genes were involved in the heat stress response, out of which Dnaja1, LOC680121, Chordc1, AABR07011951.1, Hsp90aa1, Hspa1b, Cdkn1a, Hmox1, Bag3 and Dnaja4 were commonly identified in the liver and adrenal glands, suggesting that these genes may regulate heat stress response through interactions between liver and adrenal glands. The results suggest that the identified mRNA isoforms could be considered as potential candidates for selecting mammals to improve thermotolerance.
REVIEW | doi:10.20944/preprints202202.0052.v1
Subject: Medicine And Pharmacology, Oncology And Oncogenics Keywords: cervical cancer; endometrial cancer; ovarian cancer; 2021 update; novel targeted therapies; immunotherapy
Online: 3 February 2022 (13:02:11 CET)
This review of the meaningful data from 2021 on cervical, endometrial, and ovarian cancers aims to provide an update of the most clinically relevant studies presented at important oncologic congresses during the year [the American Society of Clinical Oncology (ASCO) Annual Meeting, the European Society for Medical Oncology (ESMO) Congress and the Society of Gynecologic Oncology (SGO) Annual Meeting]. Despite the underlying existence of the COVID-19 pandemic, the last year has been notable in terms of research, with significant and promising advances in gynecologic malignancies. Several major studies reporting the effects of innovative therapies for patients with cervical, endometrial, and ovarian cancers might change the medical practice in the future.
ARTICLE | doi:10.20944/preprints202011.0032.v3
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Non-ionizing Radiation; Millimeter waves; Novel biomedical applications; Yeast; Non-invasive devices
Online: 16 April 2021 (14:52:04 CEST)
Nonionizing millimeter-waves (MMW) interact with cells in a variety of ways. Here the inhibited cell division effect was investigated using 85-105 GHz MMW irradiation within the ICNIRP (International Commission on Non-Ionizing Radiation Protection) non-thermal 20 mW/cm2 safety standards. Irradiation using a power density of about 1.0 mW/cm2 , SAR over 5-6 hours on 50 cells/μl samples of Saccharomyces cerevisiae model organism resulted in 62% growth rate reduction compared to the control (sham). The effect was specific for 85-105 GHz range, and was energy and cell density dependent. Irradiation of wild type and Δrad52 (DNA damage repair gene) deleted cells presented no differences of colony growth profiles indicating non-thermal MMW treatment does not cause permanent genetic alterations. Dose versus response relations studied using a standard horn antenna (~1.0 mW/cm2) and compared to that of a compact waveguide (17.17 mW/cm2) for increased power delivery resulted in complete termination of cell division via non-thermal processes supported by temperature rise measurements. We have shown that non-thermal MMW radiation has potential for future use in treatment of yeast related diseases and other targeted biomedical outcomes.
COMMUNICATION | doi:10.20944/preprints202003.0395.v2
Subject: Biology And Life Sciences, Biology And Biotechnology Keywords: Novel coronavirus (SARS-CoV-2); RdRp; HCV; beclabuvir; in silico; molecular docking
Online: 2 April 2020 (11:25:57 CEST)
Recent emergence of novel coronavirus (SARS-CoV-2) all over the world has resulted more than 33,106 global deaths. To date well-established therapeutics modules for infected patients are unknown. In this present initiative, molecular interactions between FDA-approved antiviral drugs against the Hepatitis-C virus (HCV) have been investigated theoretically against the RNA-dependent RNA polymerase (RdRp) of SARS-CoV-2. HCV and SARS-CoV-2 are both +ssRNA viruses. At 25o C beclabuvir, a non-nucleoside inhibitor of the RdRpHCV can efficiently bind to RdRp SARS-CoV-2 (ΔGAutoDock = -9.95 kcal mol-1) with an inhibition constant of 51.03 nM. Both the ΔGLondon and ΔGGBVI / WSA values were - 9.06 and - 6.67 kcal mol-1, respectively for binding of beclabuvir to RdRpSARS-CoV-2. In addition, beclabuvir has also shown better binding free energy with RdRpSARS-CoV-2 (ΔGvina = -8.0 kcal mol-1) than that observed with the Thumb 1 domain of RdRpHCV (ΔGvina = -7.1 kcal mol-1). InterProScan has suggested the RNA-directed 5'-3' polymerase activity exists within 549th to 776th amino acid residues of RdRpSARS-CoV, where the major amino acid residues interacting being I591, Y621, C624, D625, A690, N693, L760, D762, D763, and E813-N817. Molecular interaction suggests occupancy of beclabuvir inside the active site environment of the RdRpSARS-CoV-2, the enzyme essential for viral RNA synthesis. In conclusion, results suggest beclabuvir may serve as an anti-SARS-CoV-2 drug.
REVIEW | doi:10.20944/preprints202003.0197.v3
Subject: Biology And Life Sciences, Virology Keywords: Built Environment (BE); building operations; novel coronavirus; COVID-19; SARS-CoV-2
Online: 2 April 2020 (05:19:41 CEST)
With the rapid spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that results in coronavirus disease 2019 (COVID-19), corporate entities, federal, state, county and city governments, universities, school districts, places of worship, prisons, health care facilities, assisted living organizations, daycares, homeowners, and other building owners and occupants have an opportunity to reduce the potential for transmission through built environment (BE) mediated pathways. Over the last decade, substantial research into the presence, abundance, diversity, function, and transmission of microbes in the BE has taken place and revealed common pathogen exchange pathways and mechanisms. In this paper, we synthesize this microbiology of the BE research and the known information about SARS-CoV-2 to provide actionable and achievable guidance to BE decision makers, building operators, and all indoor occupants attempting to minimize infectious disease transmission through environmentally mediated pathways. We believe this information is useful to corporate and public administrators and individuals responsible for building operations and environmental services in their decision-making process about the degree and duration of social-distancing measures during viral epidemics and pandemics.
COMMUNICATION | doi:10.20944/preprints202003.0350.v1
Subject: Medicine And Pharmacology, Oncology And Oncogenics Keywords: COVID-19; SARS-CoV-2; coronavirus; novel coronavirus; department policy; radiation oncology
Online: 23 March 2020 (09:55:24 CET)
The COVID-19 pandemic is placing unprecedented stress on healthcare systems around the world. Although Radiation Oncology Departments are not at the frontline of fighting this infectious disease, it is important to implement COVID-19 policies to reduce risk of staff and patient exposure, and to limit the risk of department shutdown or downtime. This brief report describes the policy implemented at George Washington University Radiation Oncology to manage the risks of COVID-19. This includes a General Statement related to the priorities of the Radiation Oncology department, a screening procedure for new and follow-up patients, management policies for critical and non-critical patients with COVID-19 or under quarantine, a policy for the management of patients currently under treatment who are diagnosed or placed in quarantine, a clinical escalation action plan, guidelines for staff meetings and travel, and procedure management. This policy was implemented at George Washington University Radiation Oncology after the first case of COVID-19 was reported in Washington DC on March 7, 2020.
ARTICLE | doi:10.20944/preprints202003.0349.v1
Subject: Biology And Life Sciences, Biology And Biotechnology Keywords: novel coronavirus; COVID-19; protease; molecular docking; drug designing; ADME; drug repurposing
Online: 23 March 2020 (09:47:49 CET)
The Novel Coronavirus (COVID-19) is a positive-sense single-stranded RNA ((+)ssRNA) virus. The COVID-19 Main Proteases play very important role in the propagation of the Novel Coronavirus (COVID-19). It has already killed more than 8000 people around the world and thousands of people are getting infected every day. Therefore, it is very important to identify a potential inhibitor against COVID-19 Main Proteases to inhibit the propagation of the Novel Coronavirus (COVID-19). We have applied a drug repurposing approach of computational methodology, depending on the synergy of molecular docking and virtual screening techniques, aimed to identify possible potent inhibitors against Novel Coronavirus (COVID-19) from FDA approved antiviral compounds and from the library of active phytochemicals. On the basis of recently resolved COVID-19 Main Protease crystal structure (PDB:6LU7), the library of 100 FDA approved antiviral compounds and 1000 active components of Indian Medicinal Plants extracted for screening against COVID-19 Main Protease. The compounds were further screened using Pyrex virtual screening tool and then best inhibitors, top 19 compounds optimally docked to the COVID-19 Main Protease structure to understand the participation of specific amino acids with inhibitors at active sites. Total 19 best compounds were identified after screening based on their highest binding affinity with respect to the other screened compounds. Out of 19, 6 best compounds were further screened based on their binding affinity and best ADME properties. Nelfinavir exhibited highest binding energy -8.4 kcal/mol and strong stability with the TRP207, ILE281, LEU282, PHE3, PHE291, GLN127, ARG4, GLY283, GLU288, LYS5, LYS137, TYR126, GLY138, TYR126, SER139 and VAL135 amino acid residues of COVID-19 Main Protease participating in the interaction at the binding pocket. In addition to Nelfinavir (-8.4), Rhein (-8.1), Withanolide D (-7.8), Withaferin A (-7.7), Enoxacin (-7.4), and Aloe-emodin (-7.4) also showed good binding affinity and best ADME properties. Our findings suggest that these compounds can be used as potential inhibitors against COVID-19 Main Protease, which could be helpful in inhibiting the propagation of the Novel Coronavirus (COVID-19). Moreover, further in vitro and in vivo validation of these findings would be very helpful to bring these inhibitors to next level study.
ARTICLE | doi:10.20944/preprints202308.1359.v2
Subject: Medicine And Pharmacology, Cardiac And Cardiovascular Systems Keywords: atrial fibrillation; risk factors; thromboembolic events; novel oral anticoagulants; complications; hospitalization; medication monitoring
Online: 23 August 2023 (07:49:13 CEST)
Atrial fibrillation (AF) is a common arrhythmia associated with various risk factors and significant morbidity and mortality. This article presents findings from a study involving 115 patients with permanent AF. The study examined demographics, risk factors, associated pathologies, complications, and anticoagulant therapy. The results showed a slight predominance of AF in males, with the highest incidence in individuals aged 75 and above. Common risk factors included arterial hypertension, dyslipidaemia, diabetes mellitus type 2, and obesity. Comorbidities such as congestive heart failure, mitral valve regurgitation, and pulmonary disorders were prevalent among the patients. Major complications included congestive heart failure, stroke, and myocardial infarction. Thromboembolic and bleeding risk assessment using CHAD2DS2-VASc and HAS-BLED scores demonstrated a high thromboembolic risk in all patients. The majority of patients were receiving novel oral anticoagulants (NOACs) before admission, while NOACs were also the most prescribed antithrombotic therapy at discharge. The study highlights the importance of risk factor management and appropriate anticoagulant therapy in AF patients to reduce complications and improve outcomes.
HYPOTHESIS | doi:10.20944/preprints202305.0420.v1
Subject: Medicine And Pharmacology, Immunology And Allergy Keywords: macrophage-derived chemokine; MDC/CCL22, chemokines; novel coronavirus infection; COVID-19; post-COVID
Online: 6 May 2023 (10:40:04 CEST)
Macrophage-derived chemokine belongs to the CC subfamily. It is produced by dendritic cells (DCs) and macrophages with or without external stimulation. We have previously shown a statistically significant depletion of MDC/CCL22 concentrations in a number of studies concerning COVID-19. These shifts in concentrations demonstrated stability unrelated to the SARS-CoV-2 genetic variant and remained noticeable even in convalescent patients. In this work, we analyze MDC/CCL22 dynamics in various diseases, including those that manifest with inflammation in lung tissue. In addition, we provide our hypothesis on such a decrease in MDC/CCL22 concentrations in COVID-19. If its secretion by producer cells is unperturbed, then it is possible for viral products to bind to this chemokine and to block its functional activity. There is, however, another possible explanation directly linked to depletion in DC subpopulations and the inhibition of their function. We also discuss MDC/CCL22's role in the immunology of novel coronavirus infection, based on both our own data and other studies.
REVIEW | doi:10.20944/preprints202301.0133.v2
Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: COVID-19 vaccination; mRNA vaccines; Clinical Trials; Safety Assessment; Novel Technologies; Spike protein
Online: 12 January 2023 (03:16:56 CET)
Pharmacovigilance databases are showing evidence of injury in the context of the COVID-19 modified mRNA shots. According to recent publications, adverse event reports linked to the mRNA COVID-19 products largely point to the spike protein as an aetiological agent of adverse events, but we propose that the platform itself may be culpable. To assess the safety of current and future mRNA vaccines, further analysis on the risks due to the platform itself, and not specifically the expressed antigen. If harm can be exclusively and conclusively attributed to the spike protein, then it is possible that future mRNA vaccines expressing other antigens will be safe. If harms are attributable to the platform itself, then regardless of the toxicity, or lack thereof, of the chosen payload therein, the platform may be inherently unsafe, pending modification. In this work, we examine previous studies of RNA-based delivery by a lipid nanoparticle and break down the possible etiological elements of harm.
ARTICLE | doi:10.20944/preprints202206.0321.v1
Subject: Chemistry And Materials Science, Food Chemistry Keywords: coffee leaf tea; novel food; coffee by-products; Coffea arabica; caffeine; epigallocatechin gallate
Online: 23 June 2022 (09:22:46 CEST)
The production of coffee leaf tea (Coffea arabica) in El Salvador and the influences of processing steps on non-volatile compounds and volatile aroma-active compounds were investigated. The tea was produced according to process steps of conventional tea (Camellia sinensis) with available possibilities on the farm. Influencing factors were the leaf type (old, young, yellow, shoots), processing (blending, cutting, rolling, freezing, steaming), drying (sun drying, oven drying, roasting) and fermentation (wild, yeast, Lactobacillus). Subsequently, the samples were analysed for the maximum levels of caffeine, chlorogenic acid, and epigallocatechin gallate permitted by the European Commission. The caffeine content varied between 0.37 g/100 g dry mass (DM) and 1.33 g/100 g DM, the chlorogenic acid between not detectable and 9.35 g /100 g DM and epigallocatechin gallate could not be detected at all. Furthermore, water content, essential oil, ash content, total polyphenols, total catechins, organic acids, and trigonelline were determined. Gas chromatography—mass spectrometry-olfactometry and calculating of the odour activity values (OAVs) were carried out to determine the main aroma-active compounds, which are β-ionone (honey-like, OAV 132-927), decanal (citrus-like, floral, OAV 14-301), α-ionone (floral, OAV 30-100), (E,Z)-2,6-nonadienal (cucumber-like, OAV 18-256), 2,4-nonadienal (melon-like, OAV 2-18), octanal (fruity, OAV 7-23), (E)-2 nonenal (citrus-like, OAV 1-11), hexanal (grassy, OAV 1-10), and 4-heptenal (green, OAV 1-9).
ARTICLE | doi:10.20944/preprints202201.0466.v1
Subject: Medicine And Pharmacology, Ophthalmology Keywords: FOXC1; in vitro studies; novel variant; ophthalmic genetics; intrafamilial variability; anterior segment dysgenesis
Online: 31 January 2022 (13:36:18 CET)
Anterior segment dysgenesis (ASD) encompasses a wide spectrum of developmental abnormalities of the anterior ocular segment, including congenital cataract, iris hypoplasia, aniridia, iridocorneal synechiae, as well as Peters, Axenfeld, and Rieger anomalies. Here, we report a large five-generation Caucasian family exhibiting atypical syndromic ASD segregating with a novel truncating variant of FOXC1. The family history is consistent with highly variable autosomal dominant symptoms including isolated glaucoma, iris hypoplasia, aniridia, cataract, hypothyroidism, congenital heart anomalies, and cystic kidney disease. Whole exome sequencing revealed a novel variant [c.313_314insA; p.(Tyr105*)] in FOXC1 that disrupts the alpha-helical region of the DNA-binding forkhead box domain. In vitro studies using a heterologous cell system revealed aberrant cytoplasmic localization of FOXC1 harboring the Tyr105* variant, likely precluding downstream transcription function. Meta-analysis of the literature highlighted the intrafamilial variability related to FOXC1 truncating alleles. This study highlights the clinical variability in ASD and signifies the importance of combining both clinical and molecular analysis approaches to establish a complete diagnosis.
REVIEW | doi:10.20944/preprints202104.0175.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Gut microbiome; Western and indigenous/traditional cultures; gut health; disease; lifestyle; novel microbials
Online: 6 April 2021 (12:40:04 CEST)
The mammalian gut ecosystem plays critical roles in multiple functions related to health and homeostasis. In many cases, disturbances in the gut ecosystem are associated with a large number of metabolic and chronic diseases and disorders such as diabetes, cancer, and obesity. A diverse community of microorganisms ranging from viruses to bacteria comprise the gut microbiota, which is often considered as an organ in itself. Recent studies have profiled the influence of lifestyles and dietary behavior by comparing the gut microbiome of populations with different cultural underpinnings. In this review, we provide an overview of the studies which report the influence on the gut microbial composition of dietary and lifestyle patterns in different contexts such as western industrialized countries and indigenous cultures (corresponding to different lifestyle gradients such as hunter-gatherers and pastoralists) and how this association may influence health and disease.
REVIEW | doi:10.20944/preprints202104.0008.v1
Subject: Medicine And Pharmacology, Immunology And Allergy Keywords: micronutrients supplementation; micronutrients deficiency; prevention and treatment; novel coronavirus; COVID-19; SARS; MERS
Online: 1 April 2021 (10:21:32 CEST)
Background: Micronutrients has roles in strengthening and maintaining immune function, but its supplementation and/or deficiency effects on respiratory tract infections are inconclusive. This review aims to systematically assess the associations between micronutrient supplementation or deficiency, with novel coronavirus incidence and disease severity. Methods: Systematic literature searches conducted in 5 electronic databases identified 751 unique studies, of which 33 studies (5 supplementation studies, 1 supplementation and deficiency study, and 27 deficiency studies) were eventually included in this review. Proportions of incidence and severity outcomes in each group, and adjusted summary statistics with their relevant 95% confidence intervaIs (CI) were extracted. Data from 19 studies were pooled in meta-analysis using the generic inverse variance method. Findings: A total of 360,346 patients across 16 countries, with a mean age between 32 and 87.7 years, were involved across 33 studies. All studies were on COVID-19 infections. In individuals without micronutrient deficiency, there was a significant reduction on odds of COVID-19 incidence (pooled OR: 0.37, 95% CI: 0.18, 0.78), and ICU admissions or severe/critical disease onset (pooled OR: 0.26, 95% CI: 0.08, 0.89). Insignificant protective effects were observed on other outcome measures – mortality, ICU admission, progression to respiratory-related complications, severe/critical disease onset or requiring respiratory support and hospitalization rate. Conclusion: The absence of micronutrient deficiency significantly reduced COVID-19 incidence and clinical deterioration in hospitalized patients. Usage of micronutrients as prophylaxis and complementary supplement in therapeutic management of COVID-19 patients may be a promising and cost-effective approach warranting in-depth investigation.
REVIEW | doi:10.20944/preprints202009.0552.v1
Subject: Biology And Life Sciences, Insect Science Keywords: Malaria; Amazon; Brazil; Anopheles darlingi; Plasmodium; Control; Challenges; Strategies; Conventional; Novel; Vector; Mosquito
Online: 23 September 2020 (15:26:43 CEST)
In Brazil, malaria transmission is mostly confined to the Amazon, where substantial progress has been achieved towards disease control in the past decade. Vector control has been historically considered a fundamental part of the main malaria control programs implemented in Brazil. However, the conventional vector-control tools have been insufficient to eliminate local vector populations due to the complexity of the Amazonian rainforest environment and ecological features of malaria vector species in the Amazon, especially Anopheles darlingi. Malaria elimination in Brazil and worldwide eradication will require a combination of conventional and new approaches that takes into account the regional specificities of vector populations and malaria transmission dynamics. Here we present an overview on both conventional and novel promising vector-focused tools to curb malaria transmission in the Brazilian Amazon. If well designed and employed, these new vector-based approaches may improve the implementation of malaria-control programs, particularly in remote or difficult-to-access areas and in regions where existing interventions have been unable to eliminate disease transmission. However, much effort still has to be put on research expanding the knowledge of neotropical malaria vectors to set the steppingstones for the development of such innovative tools.
Subject: Computer Science And Mathematics, Mathematics Keywords: Mathematical model; Novel coronavirus -19; Nonstandard finite difference scheme; Emigration rate. 1. Introduction
Online: 9 May 2020 (11:25:34 CEST)
In this research work, we present a mathematical model for novel coronavirus -19 (NCOVID-19) which is consisted on three different compartments susceptible, infected and recovered classes abbreviated as under convex incident rate involving and emigration rate. We first derive the formulation of the model. Also, we give some qualitative aspects for the model including existence of equilibriums and its stability results by using various tools of nonlinear analysis. Then by mean of nonstandard finite difference scheme (NSFD), we simulate the results against the data of Wuhan city for the sixty days. By means of simulation, we show how protection, exposure, emigration, death and cure rates affect the susceptible, infected and recovered population with the passage of time involving emigration. On the basis of simulation, we observe the dynamical behavior due to emigration of susceptible and infected classes or one of these two.
ARTICLE | doi:10.20944/preprints202003.0444.v1
Subject: Engineering, Industrial And Manufacturing Engineering Keywords: COVID-19; SARS-CoV-2; coronavirus; novel coronavirus; 3D printing; N95; respirator; mask
Online: 31 March 2020 (04:44:06 CEST)
The 2019 Novel Coronavirus (COVID-19) has caused an acute reduction in world supplies of personal protective equipment (PPE) due to increased demand. To combat the impending shortage of equipment including N95 masks, the George Washington University Hospital (GWUH) developed a 3D printed reusable N95 comparable respirator that can be used with multiple filtration units. We evaluated several candidate prototype respirator models, 3D printer filaments, and filtration units detailed here. Our most recent working model was based on a respirator found on an open source maker website and was developed with PLA (printer filament), a removable cap, a removable filtration unit consisting of two layers of MERV 16 sandwiched between MERV 13, and removable elastic bands to secure the mask. Our candidate mask passed our own suction test protocol to evaluate leakage and passed a qualitative Bitrix N95 fit test at employee health at GWUH. Further efforts are directed at improving the current model for seal against face, comfort, and sizing. The 3D model is available upon request and in the supplement of this paper. We welcome collaboration with other institutions and suggest other facilities consider mask fit for their own population when exploring this concept.
REVIEW | doi:10.20944/preprints202308.0951.v1
Subject: Medicine And Pharmacology, Medicine And Pharmacology Keywords: pulmonary arterial hypertension associated with connective tissue diseases; drugs; novel drugs; therapy; treatment; prognosis
Online: 11 August 2023 (13:25:08 CEST)
Pulmonary hypertension (PH) is a severe vascular complication of connective tissue diseases (CTD). Patients with CTD may develop PH belonging to different groups: 1) pulmonary arterial hypertension (PAH), 2) PH secondary to lung disease and/or hypoxia, 3) PH due to left heart disease, and 4) chronic thromboembolic pulmonary hypertension (CTEPH). PAH most often develops in systemic scleroderma (SSc), mostly in its limited variant. PAH-CTD is a progressive disease characterized by poor prognosis, therefore the early diagnosis should be established A specific treatment for PAH-CTD is currently available and recommended: prostacyclin derivative (treprostinil, epoprostenol, iloprost, selexipag), nitric oxide and natriuretic pathway: stimulators of soluble guanylate cyclase (sGC: riociguat) and phosphodiesterase 5 inhibitors (PDE5i: sildenafil, tadalafil), endothelin receptor antagonists (ERA: bosentan, macitentan, ambrisentan). Moreover, novel drugs e.g. sotatercept are intensively investigated in the clinical trials. The aim of this paper is to review the literature on the recent advances in treatment strategy and prognosis of patients with PAH-CTD.
ARTICLE | doi:10.20944/preprints202307.0767.v1
Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: novel group of plasmids; plasmid backbone; accessory region; antibiotic resistance; heavy metals resistance; conjugation
Online: 12 July 2023 (09:05:43 CEST)
A novel group of conjugative plasmids of Pseudomonas is characterized. The prototype plasmid pPPUT-Tik1-1 (153663 bp), isolated from a permafrost strain of P. putida Tik1, carries a defective mercury transposon Tn501 and a streptomycin resistance transposon Tn5393. Ten plasmids and 34 contigs with backbone regions closely related to pPPUT-Tik1-1 have been found in Gene Bank. Two of these plasmids isolated from clinical strains of P. putida and P. fulva are almost identical to the ancient plasmid. A characteristic feature of this group of plasmids is the presence of two genes encoding the initiators of replication (repA1 and repA2). None of these genes has high similarity with plasmid replication genes belonging to known incompatibility groups. It has been demonstrated that while pPPUT-Tik1-1-like plasmids have homologous backbone regions they significantly differ by the molecular structure and the functional burden of their accessory regions. Some of the pPPUT-Tik1-1-related plasmids carry determinants of antibiotic resistance and/or heavy metal salts. Some plasmids are characterized by the ability to degrade xenobiotics. Plasmids related to pPPUT-Tik1-1 are characterized by a narrow host range and are found in various species of Pseudomonas genus. A group of shortened plasmids containing the same replication module, but without conjugation genes, were also found. These plasmids also contain other structural changes that strongly distinguish them from plasmids related to pPPUT-Tik1-1. The data obtained indicate the need for a complex approach to the classification of plasmids.
CONCEPT PAPER | doi:10.20944/preprints202305.0554.v1
Subject: Medicine And Pharmacology, Psychiatry And Mental Health Keywords: Parkinson’s Disease; Pre-Clinical Protocol; Novel Combinational Formulation; In Vivo Model; In Vivo Study
Online: 9 May 2023 (03:49:48 CEST)
Parkinson's Disease (PD) is a neurodegenerative disorder that affects the motor system of the human body. Currently, the available treatments are limited and often have undesirable side effects. In this context, the aim of this study was to develop a novel combinational formulation of Apomorphine and Quetiapine and evaluate its efficacy in a rat model of PD. The formulation was prepared using the solvent evaporation technique and characterized for its physicochemical properties. The in-vitro drug release was evaluated using the Franz diffusion cell method, and the pharmacokinetics of the combination was studied in rats. The behavioural and biochemical parameters were evaluated in the rats using the Rotarod, pole test, and biochemical assays. The results showed that the developed formulation had satisfactory physicochemical properties and exhibited sustained drug release. The pharmacokinetic studies showed that the combination exhibited a longer residence time than the individual drugs. The behavioural and biochemical parameters showed that the combination was effective in improving motor function and reducing oxidative stress. In conclusion, the developed Apomorphine and Quetiapine combination formulation showed promising results in improving motor function and reducing oxidative stress in rat model of PD. Further studies are required to evaluate the safety and efficacy of the developed formulation in humans.
ARTICLE | doi:10.20944/preprints202201.0286.v3
Subject: Medicine And Pharmacology, Oncology And Oncogenics Keywords: novel ncRNAs; DE landscape; LSCs and LTCs; LncRNA; MiRNA; CircRNA; ceRNA networks; molecular mechanism
Online: 4 August 2022 (16:29:49 CEST)
ALDH+ H1975 lung adenocarcinoma stem cells (LSCs) are a rare cell population identified in lung adenocarcinoma (LUAD). LSCs can self-renew, drive tumor initiation, growth, metastasis, and recurrence, and are also the predominant cause of poor prognosis due to their intrinsic resistance to drugs and chemotherapy. Consequently, LSCs are a promising target for LUAD therapy. Noncoding RNAs (ncRNAs), including microRNAs (miRNAs), long noncoding RNAs (lncRNAs), and circular RNAs (circRNAs), exert many significant regulatory functions in the pathogenesis of human cancers, showing the necessity for a comprehensive understanding of the mechanisms that underlie lung carcinogenesis. Nonetheless, research on many known transcripts and messenger RNAs (mRNAs) has already generated new information. Unknown biomarkers in ncRNAs and systematic and comprehensive interrelation with unknown ncRNAs and mRNAs may provide further insights into the biology of LUAD. Herein, a set of novel ncRNAs that include miRNAs, lncRNAs, circRNAs, were identified and differentially expressed patterns of ncRNAs and mRNAs in LSCs and ALDH- H1975 LUAD tumor cells (LTCs) were obtained using stringent bioinformatics pipelines. Through a meta-analysis of the identified landscapes, novel competitive endogenous RNA (ceRNA) networks were constructed to reveal the potential molecular mechanisms that regulate the hallmarks of LSCs and LTCs. This study presents a summary of novel ncRNAs and the fundamental roles of differentially expressed ncRNAs implicated in the activity of LSCs and LTCs. In addition, the study also provides a comprehensive resource for the future identification of diagnostic, therapeutic, and prognostic biomarkers in LUAD.
HYPOTHESIS | doi:10.20944/preprints202004.0349.v1
Subject: Medicine And Pharmacology, Pulmonary And Respiratory Medicine Keywords: Novel Coronavirus; respiratory distress; Favipiravir; statistics; correlation; beta thalassemia; immunisation; Italy; Sardinia; regression; heme
Online: 19 April 2020 (13:48:56 CEST)
The novel coronavirus pneumonia (COVID-19) is a contagious acute respiratory infectious disease whose causative agent has been demonstrated to be a novel virus of the coronavirus family, SARSCoV-2. A recent pre-print study has showed a heme attack on the 1-beta chain of hemoglobin by COVID19. Beta-thalassemia results of a default in the hemoglobin beta- chain synthesis. 1,5% global population are heterozygotes for this disease. In this study, by a multiple linear regression, we have analyzed the evolution of COVID-19 infection in three Italian regions (Puglia, Sardinia, Sicilia) with different beta-thalassemic prevalences, in order to search a link. The results have showed that betathalassemic heterozygote population prevalence is correlated to immunity against COVID-19, by a regression. This paper is only for academic discussion, the hypotheses and conclusions needs to be confirmed by further research .
ARTICLE | doi:10.20944/preprints202002.0071.v1
Subject: Biology And Life Sciences, Virology Keywords: 2019-nCoV; novel corona virus; Wuhan virus; drug; vaccine; spike protein; epitope; vaccine design
Online: 5 February 2020 (15:34:15 CET)
The recent outbreak of the new virus in Wuhan city, China from the sea food market has led to the identification of a new strain called the corona virus and named as novel corona virus (2019-nCoV) belonging to Coronaviridae family. This has created major havoc and concern due to the mortality of 250 persons and affecting more than 10,000 people. This virus causes sudden fever, pneumonia and also kidney failure. In this study a computational approach is proposed for drug and vaccine design. The spike protein sequences were collected from a protein database and analysed with various bioinformatics tools to identify suitable natural inhibitors for the N-terminal receptor binding domain of spike protein. Also, it is attempted to identify suitable vaccine candidates by identifying B-Cell and T-cell epitopes. In the drug design, the tanshinone Iia and methyl Tanshinonate were identified as natural inhibitors based on the docking score. In the vaccine design, B-cell epitope VLLPLVSSQCVNLTTRTQLPPAYTN was found to have the highest antigenicity. FVFLVLLPL of MHC class-I allele and FVFLVLLPL of MHC class-II allele were identified as best peptides based on a number of alleles and antigencity scores. The present study identifies natural inhibitors and putative antigenic epitopes which may be useful as effective drug and vaccine candidates for the eradication of novel corona virus.
ARTICLE | doi:10.20944/preprints201808.0056.v1
Subject: Medicine And Pharmacology, Clinical Medicine Keywords: heat-related illness; international classification; heat cramp; syncope; heat exhaustion; heat stroke; novel classification
Online: 3 August 2018 (03:51:27 CEST)
The Japanese Association for Acute Medicine Committee recently proposed a novel classification system for the severity of heat-related illnesses. The illnesses are simply classified into three stages based on symptoms and management or treatment. Stages I, II, and III broadly correspond to heat cramp and syncope, heat exhaustion, and heat stroke, respectively. Our objective was to examine whether this novel severity classification is useful in the diagnosis by healthcare professionals of patients with severe heat-related illness and organ failure. A nationwide surveillance study of heat-related illnesses was conducted between June 1 and September 30, 2012, at emergency departments in Japan. Among the 2130 patients who attended 102 emergency departments, the severity of their heat-related illness was recorded for 1799 patients, who were included in this study. In the patients with heat cramp and syncope or heat exhaustion (but not heat stroke), the blood test data (alanine aminotransferase, creatinine, blood urea nitrogen, and platelet counts) for those classified as stage III were significantly higher than those of patients classified as stage I or II. There were no deaths among the patients classified as stage I. This novel classification may avoid underestimating the severity of heat-related illness.
REVIEW | doi:10.20944/preprints201806.0382.v1
Subject: Engineering, Energy And Fuel Technology Keywords: environmental assessment; novel LCEA model; electricity generating supply systems; lifecycle greenhouse gas grid emission factor
Online: 25 June 2018 (11:03:05 CEST)
Environmental assessment is a concept that has been designed to facilitate the present generation to meet their needs without compromising the ability of future generations to meet their own needs as well. Thus, this concept has drawn significant attention from various scholars, researchers and industrial practitioners around the world over the past three decades. Life Cycle Environmental Assessment (LCEA) is a widely metric used to assess the potential ecological impacts, which can be caused by electricity generating supply systems or by other systems than power production plants. However, the current LCEA model is biased and ineffective. Because, its omits factors that are increasingly contributing to the ecological degradation. This study has identified the omitted factors through a critical analysis of a set of previous journal articles conducted in the energy sector. In light of this, this study has developed a novel LCEA framework addressing those blind spots. The framework developed in this study is holistic in nature including all the life cycle stages of a power supply system such as Extraction of the Raw Material (ERM), Transport of Raw Material (TRM), Conversion of Raw into Electricity (CRE), and Transmission and Distribution of Electricity (TDE) to the end users. The novel developed LCEA model has been tested and applied to nine power generation plants such as coal, gas, nuclear, biomass, geothermal, hydro, solar thermal, wind onshore and wind offshore. The results have demonstrated that of conventional technologies including coal, gas, and nuclear, coal energy generating source has got the highest life cycle greenhouse gas Grid Emission Factor (GEF) of 2866 kg CO2e/MWh, followed by gas with 728 kg CO2e/MWh, and nuclear has got the least GEF of 35 kg CO2e/MWh. Whereas of renewable energy sources biomass has got the highest GEF of 1508 kg CO2e/MWh, followed by solar thermal with 46.6 kg CO2e/MWh, hydro 39 kg CO2e/MWh, wind offshore 25.25 kg CO2e/MWh, wind onshore 10.1 kg CO2e/MWh, and geothermal closes the ranking with 6.23 kg CO2e/MWh.
ARTICLE | doi:10.20944/preprints202005.0279.v1
Subject: Business, Economics And Management, Finance Keywords: novel coronavirus; COVID-19; SARS-CoV-2; pandemic; Chinese stock market; Exponential Generalized Autoregressive Conditional Heteroscedasticity
Online: 17 May 2020 (03:11:38 CEST)
This paper aims to quantify the effect of the deadly novel coronavirus (COVID-19) pandemic outbreak on Chinese stock market performance. Shanghai Stock Exchange Composite Index and its component sector indices are examined in this study. The pandemic is represented by a lockdown dummy, new COVID-19 cases and a dummy for 3 February 2020. First, descriptive analysis is performed on these indices to compare their performances before and during the lockdown period. Next, regression analysis with Exponential Generalized Autoregressive Conditional Heteroscedasticity specification is estimated to quantify the pandemic effect on the Chinese stock market. This paper finds that health care, information technology and telecommunication services sectors were relatively more pandemic-resistant, while other sectors were more severely hurt by the pandemic outbreak. The extent to which each sector was affected by pandemic and sentiments in other financial and commodity markets were reported in details in this paper. The findings of this paper are resourceful for investors to avoid huge loss amid pandemic outburst and the China Securities Regulatory Commission in handling future pandemic occurrence to cool down excessive market sentiments.
REVIEW | doi:10.20944/preprints202306.0932.v1
Subject: Medicine And Pharmacology, Oncology And Oncogenics Keywords: gastric cancer; HER2; immunotherapy; PD-1/PD-L1; antibody-drug conjugate; chemotherapy; trastuzumab; novel therapies; clinical trials
Online: 13 June 2023 (11:15:24 CEST)
Gastric cancer is an aggressive disease with increasing global incidence in recent years. Human epidermal growth receptor 2 (HER2) is overexpressed in approximately 10-20% of gastric cancers. The implementation of targeted therapy against HER2 as part of the standard of care treatment in metastatic disease has improved the prognosis of this subset of patients. However, gastric cancer still has high mortality rates and urgently requires new treatment strategies. The combination of immunotherapy with HER2-targeted therapies has shown synergistic effects in preclinical models, being the rationale behind exploring this combination in clinical trials in locally advanced and metastatic settings. Additionally, the irruption of antibody-drug conjugates and other novel HER2-targeted agents has led to the development of numerous clinical trials showing promising results. This review presents the molecular mechanisms supporting the use of HER2-targeted drugs in combination with immunotherapy and provides an overview of the therapeutic scenario of HER2-positive disease. We focus on the role of immunotherapy but also summarize emerging therapies and combinations under clinical research that may change the standard treatment in HER-2 positive disease in the future.
ARTICLE | doi:10.20944/preprints202304.0057.v1
Subject: Biology And Life Sciences, Ecology, Evolution, Behavior And Systematics Keywords: Asian weaver ants; arboreal dominance; Elaeis guineensis; spatial distribution; ecosystem service; biological control agent; novel nesting behavior
Online: 5 April 2023 (11:14:28 CEST)
The Asian weaver ant (Oecophylla smaragdina) is a natural enemy, generalist predator of diverse major pest species (i.e. the highly destructive oriental fruit fly Bactrocera dorsalis) in economically strategic agricultural landscapes in Australia and Southeast Asia countries. For effective implementation of the weaver ant for biological control of the invasive bagworms Metisa plana, the dominant pest in the oil palm plantation, its distribution was investigated in Malaysia. From 2018-2022, censuses were first carried out to record Oecophylla colonies presence. Oecophylla colonies’ occupation patterns were monitored on 8 selected plantations. To distinguish between brood and barracks nests, 26 captured nests were evaluated to define the main predictor variable for its practical visual identification. More than 11000 palms with 10821 nests for over 500 colonies were sampled in this study. Results showed that O. smaragdina colonies distribution pattern exhibited three-dimensional ubiquitous occupation dominance. We also found that by observing the colony’s dense population spatial arrangements, it demonstrates them as spreading by waves featuring interconnected irregular geometrical patches shaped for each colony. The height to the ground nest location in palm canopies was the significant visual discriminant factor between Brood and barrack nests. Moreover, polydomous arboreal nesting behavior occupation occurred irrespective of palms or associated host plants sizes (≥ 3 m), throughout the year. However, colony nesting behaviors were polydomous and monodomous on shorter plants (≥ 2 m), while being strictly monodomous on small plants (≤ 1.5 m). Colonies occupied an average 3 to 4 palms yearly beginning from the newly founding phase up to the stable mature phase (3 to 4 years). Furthermore, we found that matured stable colonies (3 ≥ age ≥13) occupied 10-12 palms on average, on 800 m2 to 2500 m2 area delimited by a minimum average 20 m2 of “no ants land” zone between each colony. Our results suggest that a sustained agriculture system in this area would be possible with the presence of matured colonies nests exploitation which could provide an efficient biological control ecosystem service.
ARTICLE | doi:10.20944/preprints202105.0546.v1
Subject: Medicine And Pharmacology, Oncology And Oncogenics Keywords: triple negative breast cancer; Pembrolizumab; Atezolizumab; chemotherapy; anti-PD-L1; biomarkers; targeted therapies; development of novel drugs
Online: 24 May 2021 (09:23:50 CEST)
Triple negative breast cancer (TNBC) has a higher mRNA expression of programmed cell death ligand 1 (PD-L1) which is a ligand to programmed cell death protein 1 (PD-1). The binding of the ligand leads to suppressed activity of T-cell-mediated immune response against cancer cells. The approval of anti-PD-L1 drugs including pembrolizumab and atezolizumab in subgroups of TNBC offer potential improvement to the current treatment regimens available for TNBC. We conducted a meta-analysis to review the efficacy of pembrolizumab and atezolizumab for the treatment of TNBC in both adjuvant and neo-adjuvant settings. A systematic strategy was used as per the PRISMA 2020 statement. All statistical analyses were conducted using Review Manager 5.4. Outcome measures included objective response rate, progression free survival, overall survival in adjuvant therapy groups, and pathological complete response rates in neoadjuvant groups. Six clinical trials were included. For adjuvant therapies, the ORR (OR=1.26, P = 0.04) of Atezolizumab/Pembrolizumab plus chemotherapy was higher in intention to treat (ITT) arms than the placebo groups in TNBC. A positive effect size was found for PFS in the ITT arms (Cohen’s d = 1.55, P<0.001). The Atezolizumab plus chemotherapy group had a positive effect size for OS compared to the control groups (Cohen’s d = 0.52, P<0.001). In the neo-adjuvant setting, patients in ITT arms had higher pCR rates as compared to the control groups (OR= 1.61, P = 0.001). Our findings collate evidence of pembrolizumab and atezolizumab as a viable treatment option among patients with TNBC with PDL1+ subgroups deriving benefits.
Subject: Computer Science And Mathematics, Artificial Intelligence And Machine Learning Keywords: COVID-19; 2019 novel coronavirus; SARS-CoV-2; Deep Transfer Learning; Convolutional Neural Network; Machine Learning; CGAN
Online: 5 May 2020 (04:14:58 CEST)
The coronavirus disease 2019 (COVID-19) is the fastest transmittable virus caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The detection of COVID-19 using artificial intelligence techniques and especially deep learning will help to detect this virus in early stages which will reflect in increasing the opportunities of fast recovery of patients worldwide. This will lead to release the pressure off the healthcare system around the world. In this research, classical data augmentation techniques along with CGAN based on a deep transfer learning model for COVID-19 detection in chest CT scan images will be presented. The limited benchmark datasets for covid-19 especially in chest CT images is the main motivation of this research. The main idea is to collect all the possible images for covid-19 that exists until the very writing of this research and use the classical data augmentations along with CGAN to generate more images to help in the detection of the COVID-19. In this study, five different deep convolutional neural network-based models (AlexNet, VGGNet16, VGGNet19, GoogleNet, and ResNet50) have been selected for the investigation to detect the coronavirus infected patient using chest CT radiographs digital images. The classical data augmentations along with CGAN improve the performance of classification in all selected deep transfer models. The Outcomes show that ResNet50 is the most appropriate deep learning model to detect the COVID-19 from limited chest CT dataset using the classical data augmentation with testing accuracy of 82.91%.
Subject: Computer Science And Mathematics, Artificial Intelligence And Machine Learning Keywords: 2019 novel coronavirus; COVID-19; SARS-CoV-2; Deep Transfer Learning; Convolutional Neural Network; Machine Learning; GAN
Online: 7 April 2020 (10:59:04 CEST)
The coronavirus (covid-19) pandemic is putting healthcare systems across the world under unprecedented and increasing pressure according to the World Health Organization (WHO). With the advances in computer algorithms and especially Artificial Intelligence, the detection of this type of virus in the early stages will help in fast recovery and help in releasing the pressure off healthcare systems. In this paper, a GAN with deep transfer learning for coronavirus detection in chest x-ray images is presented. The lack of benchmark datasets for covid-19 especially in chest x-rays images is the main motivation of this research. The main idea is to collect all the possible images for covid-19 that exists until the writing of this research and use the GAN network to generate more images to help in the detection of the virus from the available x-rays images with the highest accuracy possible. The dataset used in this research was collected from different sources and it is available for researchers to download and use it. The number of images in the collected dataset is 307 images for four different types of classes. The classes are the covid-19, normal, pneumonia bacterial, and pneumonia virus. The dataset is divided into 90% for the GAN and the training and the validation phase, while 10% used in the testing phase. The GAN helps in generating more images from the original dataset to be 30 times larger than the originally collected dataset. The GAN also help in overcoming the overfitting problem and made the proposed model more robust. Three deep transfer models are selected in this research for investigation. The models are the Alexnet, Googlenet, and Restnet18. Those models are selected based on their small number of layers on their architectures, which will reflect in reducing the complexity of the models and the consumed memory and time. Using a combination of GAN and deep transfer models prove it is efficiency according to validation, testing accuracy, and performance measurements such as precision, recall, and F1 score. Three case scenarios are tested through the paper, the first scenario which includes 4 classes from the dataset, while the second scenario includes 3 classes and the third scenario includes 2 classes. All the scenarios include the covid-19 class as it is the main target of this research to be detected. In the first scenario, the Googlenet is selected to be the main deep transfer model as it achieves 80.6% in testing accuracy. In the second scenario, the Alexnet is selected to be the main deep transfer model as it achieves 85.2% in testing accuracy, while in the third scenario which includes 2 classes(covid-19, and normal), Googlenet is selected to be the main deep transfer model as it achieves 100% in testing accuracy and 99.9% in the validation accuracy. All the performance measurement strengthen the obtained results through the research. Finally, this research may be considered one of the first trails to use GAN and deep transfer models together to help in detecting coronaviruses (covid-19) within the absence of a benchmark dataset around the world, especially in x-rays chest images.
ARTICLE | doi:10.20944/preprints202003.0440.v1
Subject: Biology And Life Sciences, Virology Keywords: COVID-19; SARS-CoV-2; 2019-nCoV; novel corona virus; drug repurposing; chloroquine; high-risk group; asymptomatic
Online: 30 March 2020 (07:24:16 CEST)
COVID-19 (2019-nCoV) is a pandemic disease with an estimated mortality rate of 3.4% (estimated by the WHO as of March 3, 2020). Until now there is no antiviral drug and vaccine for COVID-19. The current overwhelming situation by COVID-19 patients in hospitals is likely to increase in the next few months. About 15 percent of patients with serious disease in COVID-19 require immediate health services. Rather than waiting for new anti-viral drugs or vaccines that take a few months to years to develop and test, several researchers and public health agencies are attempting to repurpose medicines that are already approved for another similar disease and have proved to be fairly effective. This study aims to identify FDA approved drugs that can be used for drug repurposing and identify biomarkers among high- risk and asymptomatic groups. In this study gene-disease association related to COVID-19 reported mild, severe symptoms and clinical outcomes were determined. The high-risk group was studied related to SARS-CoV-2 viral entry and life cycle by using Disgenet and compared with curated COVID-19 gene data sets from the CTD database. The overlapped gene sets were enriched and the selected genes were constructed for protein-protein interaction networks. Through interactome, key genes were identified for COVID-19 and also for high risk and asymptomatic groups. The key hub genes involved in COVID-19 were VEGFA, TNF, IL-6, CXCL8, IL10, CCL2, IL1B, TLR4, ICAM1, MMP9. The identified key genes were used for drug-gene interaction for drug repurposing. The chloroquine, lenalidomide, pentoxifylline, thalidome, sorafenib, pacitaxel, rapamycin, cortisol, statins were proposed to be probable drug repurposing candidates for the treatment of COVID-19. However, these predicted drug candidates need to be validated through randomized clinical trials. Also, a key gene involved in high risk and the asymptomatic group were identified, which can be used as probable biomarkers for early identification.
Subject: Biology And Life Sciences, Ecology, Evolution, Behavior And Systematics Keywords: non-native populations; geographic expansion; invasiveness; invasibility; dispersal; phenotypic plasticity; evolution; historical ecosystem; hybrid ecosystem; novel ecosystem
Online: 30 October 2019 (07:13:34 CET)
Biological invasions have reached an unprecedented level and the number of introduced species is still increasing worldwide. Despite major advances in invasion science, the determinants of success of introduced species, the magnitude and dimensions of their impact, and the mechanisms sustaining successful invasions are still debated. Empirical studies show divergent impacts of non-native populations on ecosystems and contrasting effects of biotic and abiotic factors on the dynamics of non-native populations; this is hindering the emergence of a unified theory of biological invasions. We propose a synthesis that merges perspectives from population, community, and ecosystem levels. Along a timeline of ecosystem transformation driven by non-native species, from historical to human-modified ecosystems, we order invasion concepts and theories to clarify their chaining and relevance during each step of the invasion process. This temporal sorting of invasion concepts shows that each concept is relevant at a specific stage of the invasion. Concepts and empirical findings on non-native species may appear contradictory. However, we suggest that, when mapped onto an invasion timeline, they may be combined in a complementary way. An overall scheme is proposed to summarise the theoretical dynamics of ecosystems subjected to invasions. For any given case study, this framework provides a guide through the maze of theories and should help choose the appropriate concepts according to the stage of invasion.
ARTICLE | doi:10.20944/preprints201909.0220.v1
Subject: Biology And Life Sciences, Plant Sciences Keywords: novel cytorhabdovirus; high-throughput sequencing; aphid transmission; mechanical inoculation; grafting-mediated virus transmission; fragaria spp.; chaetosiphon fragaefolii
Online: 19 September 2019 (11:17:42 CEST)
Virus diseases of strawberry present several complex problems. More than 25 viruses have been described in the genus Fragaria thus far. Here, we describe a novel rhabdovirus, tentatively named strawberry virus 1 (StrV-1), that infects F. ananassa and F. vesca plants. Genomic sequences of three distinct StrV-1 genotypes co-infecting a single F. ananassa host were obtained using combined Illumina and Ion Proton high-throughput sequencing. StrV-1 was transmitted to herbaceous plants via Aphis fabae and A. ruborum, further mechanically transmitted to Nicotiana occidentalis 37B and sub-transferred to N. benthamiana, N. benthamiana DCL2/4i, N. occidentalis 37B and Physalis floridana plants. Irregular chlorotic sectors on leaf blades and the multiplication of calyx leaves seem to be the diagnostic symptoms for StrV-1 on indexed F. vesca clones. StrV-1 was detected in asymptomatic grafted plants and in 49 out of 159 field strawberry samples via RT-PCR followed by Sanger sequencing. The bacilliform shape of the virions, which have a cytoplasm-limited distribution, their size, and phylogenetic relationships support the assignment of StrV-1 to a distinct species of the genus Cytorhabdovirus. Acyrthosiphon malvae, A. fabae and A. ruborum were shown to transmit StrV-1 under experimental conditions.
ARTICLE | doi:10.20944/preprints202311.0886.v1
Subject: Public Health And Healthcare, Other Keywords: pathological diagnosis; Musashi-1; small cell carcinoma; large cell neuroendocrine carcinoma; lung cancer; surgical specimen; novel marker; immunohistochemistry
Online: 14 November 2023 (10:26:14 CET)
Small cell lung cancer (SCLC) and large cell neuroendocrine carcinoma (LCNEC) have recently been grouped as lung neuroendocrine carcinomas (NECs). Because these lung NECs are clinically malignant and their treatment strategies differ from those of non-SCLC, the quality of diagnosis has a significant prognostic impact. The diagnosis of LCNEC requires positive immunohistochemical staining with chromogranin A, synaptophysin, and CD56, along with morphological diagnosis, and insulinoma-associated protein 1 (INSM1) has been proposed as an additional marker but sometimes experience difficulty in making the diagnosis. We investigated Musashi-1 as a novel immunohistochemical marker in 42 patients with SCLCs and 44 with LCNECs who underwent lung resection between 1998 and 2020 at our institution. We found Musashi-1 expression in 41 (98%) of 42 SCLCs and 40 (90%) of 44 LCNECs. These findings were similar to CD56 expression and superior to synaptophysin, chromogranin A, and INSM1. Musashi-1 also tended to show more diffuse and intense staining, especially in LCNEC, with more cases staining >10% than any other existing markers (Musashi-1, 77%; INSM1, 45%; chromogranin A, 34%; synaptophysin, 41%; and CD56, 66%). In conclusion, we identified Musashi-1 as a novel immunohistochemical staining marker to aid in the diagnosis of lung NEC.
ARTICLE | doi:10.20944/preprints202307.1314.v1
Subject: Physical Sciences, Condensed Matter Physics Keywords: novel (SiC)m/(GeC)n superlattices; interfacial layer thickness; raman intensity profiles; lattice dynamics; localization of atomic displacements
Online: 19 July 2023 (10:07:00 CEST)
Systematic results of lattice dynamical calculation are reported for the novel (SiC)m/(GeC)n superlattices (SLs) by exploiting a modified-linear chain model (M-LCM) and a realistic rigid-ion- model (RIM). By employing the bond polarizability method in the framework of M-LCM, we have simulated Raman intensities for the graded (SiC)10-D/(Si0.5Ge0.5C)D/(GeC)10-D/(Si0.5Ge0.5C)D SLs by carefully integrating interfacial layer thickness D (≡ 0, 1, 2, 3 monolayers (MLs)). The variation of D has initiated considerable up (down) shifts of GeC-, (SiC)-like Raman peaks in the middle of the optical phonon frequency region. With D = 3 MLs, the maximum energy shift (by ~ 47 cm-1) of SiC-like modes has caused substantial changes in the Raman intensity profiles linked to the localization of atomic displacements at the interfacial transition regions. This effect can be considered as a vital tool for authenticating the interfacial structures in technologically important SLs. By using a RIM, we have reported SL phonon dispersions along the growth  as well as in the plane ,  perpendicular to the growth. Our simulations of phonons in the acoustic mode region have not only confirmed the formation of minigaps at the zone center and zone edges but also provided evidence of anti-crossing and phonon confinement. Besides examining angular dependence of zone-center optical modes, we have also discussed phonon folding, confinement and anisotropic behavior in (SiC)m/(GeC)n SLs.
REVIEW | doi:10.20944/preprints202004.0540.v1
Subject: Medicine And Pharmacology, Epidemiology And Infectious Diseases Keywords: cholinergic anti-inflammatory pathway; novel coronavirus; SARS-CoV-2; COVID-19; meta-analysis; Cytokine Release Syndrome; nicotine; smokers
Online: 30 April 2020 (17:01:38 CEST)
SARS-CoV-2 is a new coronavirus that has caused a worldwide pandemic. It produces severe acute respiratory disease (COVID-19), which is fatal in many cases, characterised by cytokine release syndrome (CRS). According to the World Health Organization (WHO), those who smoke are likely to be more vulnerable to infection. Here, in order to clarify the epidemiologic relationship between smoking and COVID-19, we present a systematic literature review until 28 April 2020 and a meta-analysis. It includes 18 recent COVID-19 clinical and epidemiological studies based on smoking patient status from 720 initial studies in China, USA, and Italy. The percentage of hospitalised current smokers was 7.7% (95%CI: 6.9-8.4) in China, 2.3% (95%CI: 1.7-2.9) in the USA and 7.6% (95%CI: 4.2-11.0) in Italy. These percentages were compared to the smoking prevalence of each country and statistically significant differences were found in them all (p <0.0001). By means of the meta-analysis, we offer epidemiological evidence showing that smokers were statistically less likely to be hospitalised (OR=0.18, 95%CI: 0.14-0.23, p<0.01). CRS and exacerbated inflammatory response are associated with aggravation of hospitalise patients. In this scenario, we hypothesise that nicotine, not smoking, could ameliorate the cytokine storm and severe related inflammatory response through the cholinergic-mediated anti-inflammatory pathway.
ARTICLE | doi:10.20944/preprints202310.0754.v1
Subject: Biology And Life Sciences, Food Science And Technology Keywords: Salvia officinalis essential oil; beef tenderloin (musculus psoas major); sous-vide; Salmonella enterica; antimicrobial effect; novel application; active substance
Online: 12 October 2023 (04:59:25 CEST)
Sous-vide is a process in which food is vacuum-sealed and prepared in a water bath, heated to a precise temperature, and circulated in a sous-vide machine. This cooking technique is increasingly common in homes and catering establishments due to its simplicity and affordability. However, manufacturers' and chefs' recommendations for low-temperature and long-term sous-vide cooking in media raise food safety concerns, particularly when preparing beef tenderloin. In this study, Salmonella enterica was found to be inactivated by heat and sage essential oil (EO) in beef tenderloin from musculus psoas major that had undergone sous-vide processing. To determine whether heat treatment was likely to increase the sous-vide efficiency, S. enterica and sage EO were mixed. After being vacuum-packed and injected with S. enterica, the samples were cooked sous-vide for the prescribed time at 50, 55, 60, or 65 °C. On days 1, 3, and 6, the amounts of S. enterica, total bacteria, and coliform bacteria were measured in both groups of sous vide beef tenderloin. Mass spectrometry was used to identify bacterial strains on various days and categories. Each day that was measured, the test group exposed to a temperature of 50 °C for 5 minutes had a higher number of all microbiota. The most isolated microorganisms from the control and treated groups were Pseudomonas fragi, and in the treated group also S. enterica. It has been shown that adding sage essence oil (EO) in combination with the sous-vide gastronomic method leads to the stabilization and safety of beef tenderloin.
ARTICLE | doi:10.20944/preprints202004.0543.v1
Subject: Medicine And Pharmacology, Epidemiology And Infectious Diseases Keywords: Coronavirus; COVID-19; SARS-CoV-2; Pandemic; Paramedic; Infection prevention and control; Aerosols; Aerosol Generating Procedures; Novel virus; Wellbeing
Online: 30 April 2020 (17:20:55 CEST)
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a novel coronavirus that causes the new Coronavirus disease (COVID-19). The symptoms range from mild to severe with a higher incidence of severe cases seen in patients with risk factors such as older age and comorbidities. COVID-19 is mainly spread through the inhalation of respiratory droplets from coughing or sneezing or via contact with droplet-contaminated surfaces. Paramedics should be aware that some aerosol generating procedures (AGPs) may put them at a higher risk of contracting the virus via possible airborne transmission. The use of remote triage clinical assessment is likely to increase as a result of the pandemic. There is no curative drug treatment for the virus and some medications may exacerbate its effects or make patients more susceptible to it. Paramedics should accept that feeling stressed by the pandemic is a natural response. Official guidelines and advice are evolving continually as the evidence on SARS-CoV-2 and COVID-19 grows. Paramedics should keep up to date with the latest clinical guidance from their employers.
Subject: Biology And Life Sciences, Virology Keywords: SARS-CoV-2; COVID-19; novel severe acute respiratory syndrome coronavirus 2; ancestral reconstruction; clonality; source of entry; dispersal routes
Online: 28 June 2020 (09:21:49 CEST)
The coronavirus disease 2019 (COVID-19) was officially declared a pandemic on the 11th March 2020. It is caused by the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), impacting the lower respiratory tract. International travel to Australia during the early stages of the pandemic prior to border closure provided avenues for this virus to spread into Australia. There is little understanding of the clonality of SARS-CoV-2 isolates in Australia, and where they originated. This study aimed to investigate the clonality and ancestral sources of SARS-CoV-2 isolates in Australia using in silico methods. We retrieved 1,346 complete genomes from Australia along with 153 genomes from other countries from the NCBI nucleotide database and Global Initiative On Sharing All Influenza Data (GISAID). We then constructed a representative population of 270 sequences for downstream phylogenetic analysis and ancestral area reconstruction. Overall, two major clusters, one stemming from Europe and another from Asia, especially East Asia, were observed, implying at least two major transmission events with subsequent clades confirming the multiclonality of Australian isolates. We also identified three potential dissemination routes of SARS-CoV-2 into Australia. This study supports the hypothesis of multiple clonality and dispersals of SARS-CoV-2 isolates into Australia.
REVIEW | doi:10.20944/preprints202305.0684.v1
Subject: Physical Sciences, Optics And Photonics Keywords: fiber-optic sensor; tapered optical fiber structure; physical sensors; chemical sensors; gas sensors; novel tapered optical fiber; humanoid tapered fiber structure
Online: 10 May 2023 (04:33:10 CEST)
Optical fiber sensors based on tapered optical fiber (TOF) structure have attracted a considerable amount of attention from researchers due to the advantages of simple fabrication, high stability, diverse structures, and have great potential for applications in many fields such as physics, chemistry and biology. Compared with ordinary optical fibers, TOF with their unique structural characteristics significantly improve the sensitivity and response speed of fiber-optic sensors and broaden the application range. This review presents an overview of the latest research status and characteristics of fiber-optic sensors and TOF sensors. Then the working principle of TOF sensors, fabrication schemes of TOF structures, novel TOF structures in recent years, and the growing emerging application areas are described. Finally, the development trends and challenges of TOF sensors are prospected. The objective of this review is to convey novel perspectives and strategies for the performance optimization and design of TOF sensors based on fiber-optic sensing technologies.
ARTICLE | doi:10.20944/preprints202212.0073.v1
Subject: Medicine And Pharmacology, Pathology And Pathobiology Keywords: SARS-COV-2; respiratory tests; Xpert® Xpress COV-2 plus; Xpert(2) Xpress COV-2/Flu/RSV plus; diagnostic evaluation; novel target
Online: 5 December 2022 (10:17:58 CET)
The Xpert® Xpress SARS-CoV-2 and Xpert® Xpress SARS-CoV-2/Flu/RSV tests were rapidly developed and widely used during the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic. In response to emerging genetic variability, a new SARS-CoV-2 target (RNA-dependent RNA-polymerase) has been added to both tests: Xpert® Xpress CoV-2 plus and Xpert® Xpress CoV-2/Flu/RSV plus test. A rapid evaluation of both tests was performed in South Africa, using residual respiratory specimens. Residual respiratory specimens (n=125) were used to evaluate the Xpert® Xpress CoV-2 plus test and included 50 genotyped specimens. The Xpert® Xpress CoV-2/Flu/RSV plus test was assessed using 45 genotyped SARS-CoV-2 specimens, ten influenza A, ten Influenza B and twenty respiratory syncytial virus specimens. Results were com-pared to in-country standard of care tests. Genotyped specimens tested the performance of the test under pressure from circulating SARS-CoV-2 variants of concern. Reference material was included to assess the test limits and linearity. The Xpert® Xpress CoV-2 plus test performance compared to reference results across residual respiratory specimens was good (positive per-centage agreement (PPA)=95.2%, negative percentage agreement (NPA)=95.0%) The Xpert® Xpress CoV-2/Flu/RSV plus test showed good performance across all residual respiratory specimens (PPA=100%, NPA=98.3%). All genotyped variants of concern were detected by both tests. The Xpert® Xpress CoV-2 plus and Xpert® Xpress CoV-2/Flu/RSV plus tests can be used to diagnose SARS-CoV-2, and to diagnose and differentiate SARS-CoV-2, influenza A, influenza B and respiratory syncytial virus respectively. The NPA was lower than the recommended 99%, but was influenced by the low number of negative specimens tested. The variants of concern assessed did not affect test performance. It is recommended that sites perform their own assessments compared to in-country standard of care tests.
REVIEW | doi:10.20944/preprints202103.0490.v1
Subject: Medicine And Pharmacology, Immunology And Allergy Keywords: Covid-19; Long Covid-19; Long Haulers Covid; Post Covid-19 Syndrome; Post-Acute Covid-19; Corona Virus; SARS-Cov-2; Novel Corona Virus 2019; Post-Acute SARS-CoV-2; PASC, Post-Acute Sequelae of COVID-19; Late Sequelae COVID-19
Online: 18 March 2021 (17:16:52 CET)
Introduction: Despite more than one year passed since the first cases of SARS-CoV-2 were reported, there is still no consensus on the definition and clinical management of post-acute-COVID-19. The condition has heterogeneously been named as Chronic COVID syndrome, Post COVID-19 Syndrome, post-acute sequela of SARS-CoV-2 (PASC), and the more familiar long COVID. Method: In order to capture all relevant published studies, we undertook a multi-step search with no language restriction. The following four-step search strategy was utilized: First, a preliminary (limited) search was conducted on January 20, 2021, in Google Scholar and PubMed to identify the appropriate keywords. Then, on January 30, 2021, we adopted a search strategy of electronic databases from Cochrane Library, PsycINFO, PubMed, Embase, Scopus, and Web of sciences, using those keywords. Then, after duplicate removal, we screened all titles, abstracts, and full texts. This resulted in 66 eligible studies. Subsequently, after a forward and backward search of their references and citations an additional 54 publications were found, resulting in a total of 120 publications that formed the basis of the present analysis. The titles, abstracts, and full-texts of non-English articles were translated using Google Translate for further evaluation. We conducted our scoping review based on the PRISMA-ScR Checklist.Results: We found only one randomized clinical trial in our search. Of the 67 original studies, 22 were cohort and 28 were cross-sectional studies totaling 74.6% of the original studies. Of the total of 120 publications, 59 (49.1%) focused on signs and symptoms, 28 (23.3%) were focused on management, and 13 (10.8%) focused on pathophysiology. Ten (9%) publications focused on imaging studies. Ninety-one percent of the original investigations came from high and upper-middle-income countries, highlighting the scarcity of reports originating from low-income and lower-middle-income countries.Conclusion: The predominant symptoms among those with the so-called “Long COVID” were: fatigue, breathlessness, arthralgia, sleep difficulties, and chest pain. Recent reports also point to the risk of long-term sequela with cutaneous, respiratory, cardiovascular, musculoskeletal, mental health, neurologic, and renal involvement in those who survive the acute phase of the illness. The ambiguity and controversies in its definition have impaired proper recognition and management of those requiring additional support following the resolution of the acute phase of this infection. This has resulted in long-standing distress for the patients and their families. Our findings highlight the need for a multidisciplinary approach, support, and rehabilitation for these patients in terms of long-term mental and physical health.
ARTICLE | doi:10.20944/preprints202006.0165.v2
Subject: Biology And Life Sciences, Virology Keywords: Conserved signature indels (CSIs) specific for SARS and SARS-CoV-2-related viruses. Molecular markers distinguishing different clades of Sarbecovirus, Evolutionary relationships between SARS and SARS-CoV-2-related viruses, Origin of SARS-CoV-2 and Pangolin CoV_MP789 viruses, Novel sequence and structural features of spike and nucleocapsid proteins. Genetic recombination.
Online: 26 August 2020 (10:17:16 CEST)
Both SARS-CoV-2 (COVID-19) and SARS coronaviruses (CoVs) are members of the subgenus Sarbecovirus. To understand the origin of SARS-CoV-2, protein sequences from sarbecoviruses were analyzed to identify highly-specific molecular markers consisting of conserved inserts or deletions (termed CSIs) in the spike (S) and nucleocapsid (N) proteins that are specific for either particular clusters/lineages of these viruses or are commonly shared by specific lineages. Three novel CSIs in the N-terminal domain of the spike protein S1-subunit (S1-NTD) are uniquely shared by the SARS-CoV-2, BatCoV-RaTG13 and most pangolin CoVs, distinguishing this cluster of viruses (SARS-CoV-2r) from all others. In the same positions, where these CSIs are found, related CSIs are also present in two other sarbecoviruses (viz. CoVZXC21 and CoVZC45 forming CoVZC cluster), which form an out group of the SARS-CoV-2r cluster. These three CSIs are not found in the SARS-CoVs. However, both SARS and SARS-CoV-2r CoVs contain two large CSIs in the C-terminal domain of S1 (S1-CTD), which binds the human ACE-2 receptor, that are absent in the CoVZC cluster of CoVs. These results indicate that while the S1-NTD of the SARS-CoV-2r viruses possesses the sequence characteristics of the CoVZC cluster of CoVs, their S1-CTD resembles the SARS viruses. Thus, the spike protein of SARS-CoV-2r viruses has likely originated from a recombination event between the S1-NTD of the CoVZC viruses and the S1-CTD of SARS viruses. This inference is also supported by the amino acid sequence similarity of the S1-NTD and S1-CTD from SARS-CoV-2 compared to the CoVZC and SARS CoVs. We also present evidence that one of the pangolin-CoV_MP789, whose receptor-binding domain is most similar to the SARS-CoV-2, is also derived by a recent recombination between the S1-NTD of the CoVZC CoVs and the S1-CTD of a SARS-CoV-2 related virus. Several other identified CSIs are specific for others clusters of sarbecoviruses including a clade consisting of bat SARS-CoVs (BM48-31/BGR/2008 and SARS_BtKY72). Structural mappings studies show that the identified CSIs are located within surface-exposed loops and form distinct patches on the surface of the spike protein. These surface loops/patches are predicted to interact with other host components and play important role in the biology/pathology of SARS-CoV-2 virus. Lastly, the CSIs specific for the SARS-CoV-2r clade provide novel means for development of new diagnostic and therapeutic targets for these viruses.
ARTICLE | doi:10.20944/preprints201802.0163.v1
Subject: Physical Sciences, Optics And Photonics Keywords: optical metamaterials; fundamental concepts in photonics; light-matter interactions at the subwavelength and nanoscale; fundamental understanding of linear and nonlinear optical processes in novel metamaterials underpinning photonic devices and components; advancing the frontier of nanophotonics with the associated nanoscience and nanotechnology; nanostructures that can serve as building blocks for nano-optical systems; use of nanotechnology in photonics; nonlinear nanophotonics, plasmonics and excitonics; subwavelength components and negative index materials; slowing, store, and processing light pulses; materials with such capabilities that could be used for optical sensing, tunable optical delay lines, optical buffers, high extinction optical switches, novel image processing hardware, and highly-efficient wavelength converters
Online: 26 February 2018 (11:24:39 CET)
Backward electromagnetic waves are extraordinary waves with contra-directed phase velocity and energy flux. Unusual properties of the coherent nonlinear optical coupling of the phase-matched ordinary and backward electromagnetic waves with contra-directed energy fluxes are described which enable greatly-enhanced frequency and propagation direction conversion, parametrical amplification, as well as control of shape of the light pulses. Extraordinary transient processes that emerge in such metamaterials in pulsed regimes are described. The results of the numerical simulation of particular plasmonic metamaterials with hyperbolic dispersion are presented, which prove the possibility to match phases of such coupled guided ordinary and backward electromagnetic waves. Particular properties of the outlined processes in the proposed metamaterial are demonstrated through numerical simulations. Potential applications include ultra-miniature amplifiers, frequency changing reflectors, modulators, pulse shapers, and remotely actuated sensors.