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Preprint REVIEW | doi:10.20944/preprints202303.0477.v1

Expression of Concern With Regards to the Current Stages of Avian Influenza A (H5N1) Zoonotic Spillover Into Humans

Theodor-Nicolae Carp

Subject: Life Sciences, Immunology Keywords: H5N1; Influenza A; first-line immunity; interferon; mucosal antibodies; immune evasion; sialic acid receptor; natural lymphocytes; adaptive lymphocytes; monocytes; macrophages; cytokines

Online: 28 March 2023 (09:20:04 CEST)

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The Influenza A Virus (IAV) represents a positive-sense, single-stranded RNA-based virus that infects mammals mainly via the respiratory system, although other bodily systems are also infected and undergo various extents of inflammatory pathogenesis. There are two well-known strains of IAV that cause life-threatening disease in mammals; H1N1 and H5N1, and the first strain caused the 1918 IAV H1N1 pandemic that claimed between 30 and 50 million human lives. Due to the significant ability of IAV to evade important immune recognition, the virus was observed to favor the onset of secondary microbial infections (i.e. bacterial or fungal), as the overall performance of the immune system became transiently weakened during the viral infection. During the IAV H1N1 pandemic, many patients died as a result of bacterial pneumonia, as pathogenic bacteria, such as Streptococcus pneumoniae and Haemophilus influenzae, gained a wider opportunity to colonize and infect vital areas of the lower respiratory tract, and such a phenomenon led to the excessive, prophylactic usage of antibiotics due to the increased levels of panic, which in turn favored the natural selection of bacteria with genes that became resistant to such antibiotics. Antibiotics might be required for usage solely when bacteria are known to be colonizing vital areas of the human body, and this aspect is tricky, as colonization is asymptomatic and screening is consequently rare. Recently, new variants of the avian IAV H5N1 strain were transmitted from live, infected birds to mammals, including humans in some isolated cases, and given that there have already been several zoonotic spillover events overall since the beginning of 2023, we are rapidly approaching the time when a zoonotic spillover into humans will mark the first epidemic outbreak of the avian flu in humans. A lethality rate of 60% was projected by the World Health Organization, as the virus was shown to favor the development of life-threatening hyper-inflammatory responses at the levels of alveolar tissues constituted by Type II pneumocytes. There are hints that novel variants of H5N1 are capable of infecting the intestinal layer, as recently, two dolphins died as a result of ingesting infected birds within the area of the British Isles. IAV is known to suppress the production and transmission of Type I Interferons by expressing various non-structural proteins (NSPs), such as NSP1, which was found to be also packaged into exosomes and transmitted to neighboring uninfected cells, thereby preventing them from responding to the virus in the first place. A more pronounced rate of innate immune evasion would probably be observed in H5N1 IAV infection than in the infection caused by recent variants of H1N1 IAV. The H5N1 strain of IAV was also found to secrete a higher concentration of NSP1 than SARS-CoV-2, indicating the existence of an association to the greater mortality rate of H5N1 IAV infection. A direct, prophylactic stimulation of the interferon system using a reduced oral or nasal dosage of recombinant anti-inflammatory and anti-viral interferon glycoproteins may represent the most viable approach to prevent an emergence of a life-threatening H5N1 IAV pandemic. A similar non-invasive approach could be developed for an Marburg Virus (MARV) and a Nipah Virus (NiV) infection of humans, as risks of the emergence of a Marburg epidemic and also of a Nipah epidemic may be substantial at this stage as well. Clinical testing of clinical approaches as such could be of critical importance at the moment. Animals could also benefit from related clinical approaches.

Preprint HYPOTHESIS | doi:10.20944/preprints202303.0476.v1

An Alternative View of Familial Alzheimer’s Disease Genetics

Michael Lardelli

Subject: Life Sciences, Genetics Keywords: Alzheimer's Disease; Familial Alzheimer Disease (FAD); presenilins; Amyloid beta Precursor Pro-tein; mutation

Online: 28 March 2023 (08:24:53 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202303.0461.v1

Phagosomal Escape, Intracellular Survival and Induction of Small Colony Variants of Staphylococcus aureus USA300 in RAW 264.7 Murine Macrophages

Dalida Angela Bivona, Carmelo Bonomo, Paolo Giuseppe Bonacci, Alessia Mirabile, Grete Francesca Privitera, Giuseppe Caruso, Filippo Caraci, Nicolò Musso, Dafne Bongiorno, Stefania Stefani

Subject: Life Sciences, Microbiology Keywords: Staphylococcus aureus; Small Colony Variants; Carnosine; RAW 264.7 murine macrophages; Host-Pathogen Interaction

Online: 27 March 2023 (12:16:26 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202303.0458.v1

Quality and Functional Characterization of Acetic Acid Bacteria Isolated from Farm-Produced Fruit Vinegars

Soo-Hwan Yeo, Sun Hee Kim, Woo Soo Jeong, So-Young Kim

Subject: Life Sciences, Microbiology Keywords: acetic acid bacteria; alcohol tolerance; antioxidant activity; angiotensin-converting enzyme inhibition; α-glucosidase inhibition; Acetobacter cerevisiae; Acetobacter pasteurianus.

Online: 27 March 2023 (10:33:16 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202303.0456.v1

Microbiome and Volatile Metabolic Profile of Acetic Acid Fermentation using Multiple Starters for Traditional Grain Vinegar

Soo-Hwan Yeo, Haram Kong, Sun Hee Kim, Woo Soo Jeong, So-Young Kim

Subject: Life Sciences, Microbiology Keywords: multiple starter; acetic acid fermentation; Acetobacter ascendens; Acetobacter pasteurianus

Online: 27 March 2023 (09:56:02 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202303.0455.v1

Prevalence and Antibiotic Resistance Pattern of Streptococcus, Staphylococcus, Neisseria meningitidis and Enterobacteriaceae in Two Reference Hospitals of Yaoundé: An Overview before and during COVID-19 Pandemic Era

Cecile Ingrid Djuikoue, Willy Yamdeu Djonkouh, Cavin Epie Bekolo, Rodrigue Kamga Wouambo, Raspail Carrel Founou, Paule Dana Djouela Djoulako, Gilder Tonfack Temgoua, Benjamin D. Thumamo Pokam, Nicolas Antoine-Moussiaux, Teke R. Apalata

Subject: Life Sciences, Microbiology Keywords: resistant bacteria; COVID-19 pandemic era; antibiotics

Online: 27 March 2023 (08:59:13 CEST)

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Abstract: The overuse of antibiotic prophylaxis during the COVID-19 pandemic would have led to the devel-opment of antibiotic-resistant bacterial strains, thereby increasing the epidemiological burden of antimicrobi-al resistance. The aim of this study was to determine the prevalence and antibiotic resistance pattern of bacte-ria isolated in 02 referral health facilities in Yaoundé before and during the COVID-19 pandemic era. We conducted a retrospective study over a period of 03 years (from 1 January 2019 to 31 December 2021) in the bacteriology units of the Central and General Hospitals of Yaoundé, Cameroon. The review of the services' registers was done to record bacterial isolates (Streptococcus, Staphylococcus, Neisseria meningitidis and Entero-bacteriaceae) as well as their susceptibility to selected, specific and highly potent antibiotics: Cefixime, Azythromycin and Erythromycin. The relationship between each group of resistant bacteria and the antibiotic of interest was determined by simple linear regression; the comparison of the prevalences of before (2019) and during 2 consecutive years of the COVID-19 pandemic onset (2020 and 2021) was done by the Chi2 test of in-dependence. In all, 426 bacterial strains were included. It appeared that the highest number of bacteria iso-lates and lowest rate of bacterial resistance were recorded during the pre-COVID 2019 period in 2019 (160 isolates vs. 58.8% resistance rate). Conversely, lower bacteria stains but greater resistance burden were rec-orded during the pandemic era (2020 and 2021) with the lowest bacteria amount and peak of bacteria re-sistance registered in 2020, the year of COVID-19 onset (120 isolates vs. 70% resistance in 2020 and 146 iso-lates vs.58.9% resistance in 2021). In contrast to almost all others groups of bacteria where the resistance burden was quite constant over years, the Enterobacteriaceae exhibited greater resistance rate during the pandemic period [60%(48/80) in 2019 to 86.9%(60/69) in 2020 and 64.5%(61/95) in 2021)]. Concerning antibiotics, unlike Erythromycin, Azythromycin related resitance increased during the pandemic period and the resistance to Cefixim tends to decrease the year of the pandemic onset (2020) and re-increase one year therafter. A significant association was found between resistant Enterobacteriaceae strains and Cefixime (R= 0.7; P-value= 0.0001) and also, between resistant Staphylococcus strains and Erythromycin (R= 0.8; P-value= 0.0001). It could be that the more frequent use of these antibiotics has increased resistance rate especially in Enterobacteriaceae. Anticromicrobial resistance should be closely monitor during and after COVID pandemic era.

Preprint HYPOTHESIS | doi:10.20944/preprints202303.0449.v1

Preliminary Examination of the Principle of Self-Organization in Multicellular Organisms: The Difference in Size Between Yao Ming and Myself

Zheming Cao

Subject: Life Sciences, Other Keywords: unstable state cells, growth limit, stem cells, traits

Online: 27 March 2023 (07:50:59 CEST)

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Preprint REVIEW | doi:10.20944/preprints202303.0448.v1

On the Roles of the Nuclear Non-coding RNA-Dependent Membrane-Less Organelles in the Cellular Stress Response

Anastasia A. Gavrilova, Anna S. Fefilova, Irina M. Kuznetsova, Konstantin K. Turoverov, Vladimir N. Uversky, Alexander V. Fonin

Subject: Life Sciences, Biophysics Keywords: LLPS; liquid-liquid phase separation; non-coding RNA; intrinsically disordered proteins; membrane-less organelles; stress-response; biomolecular condensates

Online: 27 March 2023 (05:43:50 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202303.0445.v1

Effects of Silybum marianum L. Seed Extracts on Wound Infection–Causing Bacteria

Shimaa El-Sapagh, Nanis G. Gamal, Mohamed Nour El-Dein El-Sayed, Asmaa Ahmed El-Hefnawy, Mayank Anand Gururani, Awad Yousef Shala

Subject: Life Sciences, Microbiology Keywords: multidrug resistance; wound infection; milk thistle; antibacterial agents; antioxidant activity

Online: 27 March 2023 (04:23:15 CEST)

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Preprint REVIEW | doi:10.20944/preprints202303.0439.v1

Associations between Drugs of Abuse and Toxoplasma gondii Infection

Amani Sastry, Victor M. Jimenez Jr

Subject: Life Sciences, Other Keywords: Drugs of abuse; Toxoplasma gondii; Substance Use Disorder

Online: 27 March 2023 (03:43:57 CEST)

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Toxoplasma gondii (T. gondii) is one of the most common parasites that infect humans. The parasite exists in approximately 40 million people in the United States. Latent infections are frequently associated with tissue cysts of T. gondii in the skeletal muscle and brain tissue that can lead to mental disorders, congenital disorders, and vision dysfunction. Furthermore, self-directed violence, impulsivity, and aggression are associated with T. gondii infection. Dopamine is associated with human behavior including pleasure, aggression, memory, and substance use disorder; however, the result of the studies on the association of T. gondii infection and drugs of abuse are not well understood. The frequency of substance use may be associated with substance-induced modification of dopamine-receptor densities and basal dopaminergic activity. Likewise, T. gondii can directly or indirectly influence dopaminergic activity in infected cells. Based on this hypothesis, the current paper aimed to systematically review all published literature on the association between drugs of abuse and T. gondii infection. Systematic review of controlled studies on T. gondii infection and substance use effects in adults were searched on the electronic databases. Studies have shown that individuals infected with T. gondii display increased risky behavior, such as excessive alcohol consumption. Furthermore, it was observed that T. gondii seropositive subjects had a reduced likelihood of self-reported substance use compared to T. gondii seronegative subjects. This study confirms that SUD is a potential risk factor for behavioral and psychiatric complications associated with T. gondii infection. Ultimately T. gondii infection in the context of drug dependence and the development of SUD remain to be elucidated. Therefore, it is necessary to conduct further research characterizing the mechanisms associated with dopamine metabolism of drug dependence and withdrawal in the context of a T. gondii infection, evaluating the role of inflammation, and identifying potential drug-and-sex specific underpinnings of these associations.

Preprint ARTICLE | doi:10.20944/preprints202303.0437.v1

Differences in Psychological Vulnerability, Mental Health Liter-Acy, Positive Mental Health, and Health Behaviours in Portu-Guese Higher Education Students: A Cross-Sectional Study

Maria José Nogueira, José Carlos Carvalho, Patrício Soares Costa, Carlos Alberto Sequeira

Subject: Life Sciences, Other Keywords: nursing health promotion; literacy; positive mental health; psychological vulnerability; students

Online: 27 March 2023 (03:34:45 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202303.0435.v1

Disease-Specific α-Synuclein Seeding and Structural Properties in Lewy Body Disease and Multiple System Atrophy are Preserved in Formaldehyde-Fixed Paraffin-Embedded Human Brain

Ain Kim, Ivan Martinez-Valbuena, Jun Li, Anthony E. Lang, Gabor Geza Kovacs

Subject: Life Sciences, Molecular Biology Keywords: alpha-synuclein; protein extraction; FFPE; SAA; seeding behavior

Online: 27 March 2023 (03:23:29 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202303.0431.v1

Somatic Evolution of Cancer: A New Synthesis

Ulfat Baing, Rohini Kharate, Milind Watve

Subject: Life Sciences, Other Keywords: Cancer; wound healing; exaptation; somatic evolution

Online: 24 March 2023 (12:35:04 CET)

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Preprint BRIEF REPORT | doi:10.20944/preprints202303.0429.v1

Oral Epithelial Cells Expressing Low or Undetectable Levels of Human Angiotensin-Converting Enzyme 2 are Susceptible SARS-CoV-2Virus Infection in vitro

Laith Ebraham, Chuan Xu, Annie Wang, Divino Rajah, Lewins Walter, Salvatore A.E. Marras, Sanjay Tyagi, Daniel Fine, Carlo Amorin Daep, Theresa Liyun Chang

Subject: Life Sciences, Virology Keywords: SARS-CoV-2; oral epithelial cells; alternative receptors

Online: 24 March 2023 (12:20:07 CET)

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Preprint ARTICLE | doi:10.20944/preprints202303.0426.v1

Phenotypic Characterization and Prevalence of Carbapenemase-Producing Acinetobacter baumanii Isolates in Four Health Facilities in Cameroon

Cécile Ingrid Djuikoue, Benhamed Nadjia, Paule Dana DJOUELA DJOULAKO, Celianthe Guegang, Cedric Seugnou Nana, Rodrigue Kamga Wouambo, Christiane Kiyang Possi, Hélène Valérie Same Njanjo, Yemina Grace Kombeu, Merimé Joel Tchinda Talokou, Benjamin D. Thumamo Pokam, Teke Apalata

Subject: Life Sciences, Microbiology Keywords: Acinetobacter baumannii; Resistance; carbapenemases; Health Facilities

Online: 24 March 2023 (06:49:01 CET)

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Carbapenems have long been considered as treatment of choice for Gram-Negative Bacteria (GNB) infections, and today the clinical utility of this class is threatened by the emergence and spread of resistance favored by its increasing use. According to the WHO, Acinetobacter baumannii, nosocomial infection agent, tops the list of priority antibiotic-resistant pathogens, considered to be the most risky for humans. This study sought to determine the prevalence of Acinetobacter baumannii strains producing carbapenemases in four health facilities in the Center and Littoral regions of Cameroon and the associated risk factors. An analytical cross-sectional study was conducted over a six-month period from January to June 2022. All Acinetobacter baumanii or suspected strains isolated from pathological samples at the bacteriology laboratory of different health facilities were systematically collected and underwent a re-identification. After successfully subculturing and growing on nutrient agar, re-identification and antimicrobial susceptibility Testing (AST) were performed using the VITEK 2 System and the Kirby-Bauer method according to the guidelines of the Clinical and Laboratory Standards Institute (CLSI). Detection and phenotypic characterization of carbapenemases was performed according to adequate standard procedures. A total of 168/226 clinical isolates of Acinetobacter baumannii were confirmed after re-identification of which 52.69% came from male patients, and 55.09% from participants aged between 10-39 years old and 46.71% from pus samples. A very high resistance rates to all families of antibiotics was noted except to colistin (10.2%). About 40.12% of these strains produced carbapenemases with 62.69% of class B and 37.31% of class A. In addition, frequent hospitalisation was significantly associated to the production of carbapenemase among Acinetobacter baumanii (Ajusted-OR=16.53, P-value<0.0001). This study highlighted the emergence of carbapenemase-producing Acinetobacter baumannii which is increasingly growing. Continuous drug-resistant monitoring and preventive measures could help to prevent and curb the dissemination of A.baumanii resistance genes, especially in hospital settings.

Preprint ARTICLE | doi:10.20944/preprints202303.0423.v1

High Dietary Marula (Sclerocarya birrea subsp. caffra) Seed (nut) Cake Induces Detrimental Effects on Performance, Carcass Characteristics and Immuno-Physiology of Broiler Chickens

Makiwa Simeon Mthana, Doctor Mziwenkosi Nhlanhla Mthiyane, Damian Chinedu Onwudiwe, Mulunda Mwanza

Subject: Life Sciences, Other Keywords: broiler; marula seed cake; oleic acid; blood indices; broiler health

Online: 24 March 2023 (02:31:21 CET)

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Preprint ARTICLE | doi:10.20944/preprints202303.0414.v1

Information Entropy of DNA Sequences for Survival Analysis

Alexander Martynenko, Xavier Pastor, Santiago Frid, Jessyca Gil, Xavier Borrat

Subject: Life Sciences, Biophysics Keywords: information entropy; DNA sequences; patients surviving; leukemia

Online: 23 March 2023 (13:23:45 CET)

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Preprint ARTICLE | doi:10.20944/preprints202301.0226.v2

Supporting the Global Biodiversity Framework monitoring with LUI, the Land Use Intensity indicator

Joachim H. Spangenberg

Subject: Life Sciences, Other Keywords: Biodiversity loss; driving forces; Global Biodiversity Framework; hemeroby; Land Use Intensity index LUI

Online: 23 March 2023 (13:05:35 CET)

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Biodiversity loss has been identified as one of the environmental impacts where humankind has been tres-passing planetary boundaries most significantly. Going beyond the pressures causing damages (calling them ‘direct drivers’) and analysing their underlying driving forces, IPBES, the Intergovernmental Sci-ence-Policy Platform for Biodiversity and Ecosystem Services, also identified a series of indirect drivers. The Montreal-Kunming Global Biodiversity Framework GBF including its suggested monitoring approach is intended to and claims to be a policy response to such analyses. However, to assess the human impact on ecosystems as a basis for planning conservation and restoration, as foreseen in the GBF, monitoring ecosystem typologies (in the GBF with reference to the UN statistical standard SEEA ES, which in turn refers to the IUCN ecosystem classification) is not enough. It needs to be complemented with data on the severity of human impacts, and on the history of places, i.e. how and when the current ecosystem status was brought about. In this conceptual paper we suggest LUI, a deliberately simple ordinal scale index for land use intensity changes, to address these two gaps. It is based on the hemeroby concept, measuring the human impact as deviation from naturalness. This makes it an information collection and presentation tool for those working in landscape planning and management. LUI’s simple and intuitively understandable structure makes it suitable for citizens’ science applications, and thus for participative monitoring when extensive statistical data gathering is not feasible, and past data are not available. Of course is can also be used as a simple too for communicating when detailed statistical data series are available. While the aggregate index is expected to communicate well, its components are more relevant to motivate and help policy makers to prioritise their decisions according to the severity of recent anthropogenic ecosystem disturabances.

Preprint ARTICLE | doi:10.20944/preprints202303.0389.v1

Improved Prediction of Antisense Oligonucleotide Efficacy for Exon Skipping Using Ensemble Learning and Feature Selection

Alex Zhu, Shuntaro Chiba, Yuki Shimizu, Katsuhiko Kunitake, Yasushi Okuno, Yoshitsugu Aoki, Toshifumi Yokota

Subject: Life Sciences, Genetics Keywords: antisense oligonucleotides; exon skipping; machine learning; ensemble learning; personalized medicine; n-of-1 therapy, splice switching; genetic disease; splicing; RNA

Online: 22 March 2023 (03:24:48 CET)

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Preprint ARTICLE | doi:10.20944/preprints202303.0378.v1

Comparative Metabolomics Profiling Reveals Key Metabolites and Associated Pathways Regulating Tuber Dormancy in White Yam (Dioscorea rotundata)

Jeremiah S. Nwogha, Abtew G. Wosene, Muthurajan Raveendran, Jude E. Obidiegwu, Cynthia A. Chilaka, Happiness O. Oselebe, Rohit Kambale, Veera Ranjani R.

Subject: Life Sciences, Biotechnology Keywords: Yam tuber; metabolomics; pathways; molecular-mechanism; dormancy; regulation

Online: 21 March 2023 (13:55:59 CET)

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;Yams are economic and medicinal crops with a long growth cycle, spanning between 9-11 months due to the prolonged tuber dormancy. Tuber dormancy has constituted a major constraint in yam production and genetic improvement. In this study, we performed non-targeted comparative metabolomic profiling of tubers of two white yam genotypes, (Obiaoturugo and TDr1100873), to identify metabolites and associated pathways that regulate yam tuber dormancy using gas chromatography-mass spectrometry (GC-MS). Yam tubers were sampled between 42 days after physiological maturity (DAPM) till tuber sprouting. The sampling points include 42-DAPM, 56-DAPM, 87DAPM, 101-DAPM, 115-DAPM, and 143-DAPM. A total of 949 metabolites were annotated, 559 in TDr1100873 and 390 in Obiaoturugo. 39 differentially accumulated metabolites (DAMs) were identified across the studied tuber dormancy stages in the two genotypes. 27 DAMs were conserved between the two genotypes, whereas, 5 DAMs were unique in the tubers of TDr1100873 and 7 DAMs were in the tubers of Obiaoturugo. The differentially accumulated metabolites (DAMs) spread across 14 major functional chemical groups. Amines and biogenic polyamines, amino acids and derivatives, Alcohols, flavonoids, alkaloids, phenols, esters, coumarins and phytohormone positively regulated yam tuber dormancy induction and maintenance, whereas, fatty acids, lipids, nucleotides, carboxylic acids, sugars, terpenoids, benzoquinones, and benzene derivatives positively regulated dormancy breaking and sprouting in tubers of both yam genotypes. Metabolite set enrichment analysis (MSEA) revealed that 12 metabolisms were significantly enriched during yam tuber dormancy stages. Metabolic pathway topology analysis further revealed that six metabolic pathways (linoleic acid metabolic pathway, phenylalanine metabolic pathway, galactose metabolic pathway, starch and sucrose metabolic pathway, alanine-aspartate-glutamine metabolic pathways and purine metabolic pathway) exerted significant impact on yam tuber dormancy regulation. This result provides vital insights into molecular mechanisms regulating yam tuber dormancy.

Preprint ARTICLE | doi:10.20944/preprints202303.0376.v1

Comparison of Injection Saline and External Fixator in Rat Tail’s Disc Degeneration

Md Abdul Khaleque, Eun-Yong Choi, Sang-Eun Park, Hwang-Yong You, Woo-Jin Lee, Do-Kyun Kim, Young-Yul Kim

Subject: Life Sciences, Other Keywords: Intervertebral disc degeneration; nucleus pulposus; autophagy; apoptosis; external fixator; saline injection

Online: 21 March 2023 (11:54:03 CET)

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Purpose: The intervertebral disc is a leading avascular organ in the body that may gather nutrition through diffusion. It maintains homeostasis by the use of autophagy and apoptosis to survive in unfavorable conditions such as stress and mechanical force. Therefore, excessive force and stress beyond normal conditions may cause intervertebral disc degeneration. The purpose of this study was to examine which is the better method, either external fixator (EF) or saline injection (SI), for inducing autophagy and apoptosis-mediated nucleus pulposus (NP) cell death in the discs of rat tail’s. Methods: Sixteen, nine-weeks-old male Sprague–Dawley rat tails were treated with 0.9% saline and EF (two-cross Kirschner wires) for a period ofsix and twelve weeks. Treated discs were dissected to identify the participation of autophagy and apoptosis in intervertebral disc degeneration. For identification purposes, H&E staining, Masson’s trichrome staining, and immunohistochemistry (IHC) for LC3, beclin-1, and P62 in addition to MMP-2, MMP-3, and TIMP-1 were performed. Furthermore, we performed real-time polymerase chain reaction (RT-PCR) to observe autophagy-related gene expression (beclin-1, LC3, and P62) and apoptosis-related gene expression (MMP-2, MMP-3, and TIMP-1). Results: TheEF group showed more insidious NP cell degeneration than the control (Ctrl) group. Degeneration was elevated with increasing compression duration of EF group, whereas the SI group could not distinguish the margin of annulus fibrosus (AF) and NP cells. LC3, beclin-1, and P62 showed the highest and lateral expression whilst MMP-2, MMP-3, and TIMP-1 showed up-regulated and central expression in both groups, although the SI group could not recognize the boundary between NP and AF cells. The EF group showed the highest autophagy-related gene expression whereas the SI group showed lower expression. In addition, the EF group showed more autophagy-accumulating materials than the SI group which elevated with increasing compression duration. Furthermore, the SI group induced the highest apoptotic gene expression, but the EF group showed the lowest expression. Conclusion: The EF method was better for studying autophagy and apoptosis because it enhanced intervertebral disc degeneration after compression, which is actively linked to autophagy and apoptosis. The degeneration process was elevated by increasing the compression duration, but SI could not distinguish AF and NP cell margins.

Preprint ARTICLE | doi:10.20944/preprints202303.0374.v1

A Screening Approach to Assess the Impact of Various Commercial Sources of Crude Marine λ-Carrageenan on the Production of Oligosaccharides with Anti-Heparanase and Anti-Migratory Activities

Chanez Manseur, Hugo Groult, Manon Porta, Pierre-Edouard Bodet, Nicolas Bridiau, Rachida Mersni-Achour, Raphaëlle Petit, Samir Ali-Moussa, Benjamin Musnier, Didier Le Cerf, Tony Varacavoudin, Oualid Haddad, Angela Sutton, Jean-Marie Piot, Thierry Maugard, Ingrid Fruitier-Arnaudin

Subject: Life Sciences, Biochemistry Keywords: marine algae; lambda-carrageenan; oligosaccharides; heparanase; migration; anti-cancer agents

Online: 21 March 2023 (09:16:48 CET)

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Oligosaccharides derived from λ-carrageenan (λ-COs) are gaining interest in the cancer field. They have been recently reported to regulate heparanase (HPSE) activity, a protumor enzyme involved in cancer cell migration and invasion, making them very promising molecules for new therapeutic applications. However, one of the specific features of commercial λ-carrageenan (λ-CARs) is that they are in fact heterogeneous mixtures of different CARs families, and are named according to the thickening purpose of the product which does not reflect the real com-position. Consequently, this can limit their use in a clinical grade. To address this issue, six commercial λ-CARs were compared for which differences in their physiochemical properties were shown. Then, a H2O2-assissed radical depolymerization was applied to each commercial source and the number and weight averaged molar masses (Mn and Mw) and sulfation degree (DS) of the λ-COs produced over time were determined. By adjusting the depolymerization time for each product, almost comparable λ-CO formulations could be obtained in term of molar masses and DS, that ranged within previously reported values suitable for anti-tumor proper-ties. However, when the anti-HPSE activity of these new λ-COs was screened, small changes that could not be attributed only to their small length or DS changes between them were found, suggesting a role of other features such as differences in the initial mixture composition. Further structural MS and NMR analysis revealed indeed qualitative and semi-quantitative differences between the molecular species, especially in the proportion of the anti-HPSE λ-type, other CARs types and adjuvants, but also showed that H2O2-based hydrolysis induced sugar degradation. Finally, when the effects of λ-COs were assessed in an in vitro migration cell-based model, they seemed more related to the proportion of other CAR types in the formulation than to their λ-type-dependent anti-HPSE activity.

Preprint REVIEW | doi:10.20944/preprints202301.0234.v2

Nature of the Interaction of Alpha-D-Mannose and Escherichia coli Bacteria, and Implications for Its Regulatory Classification. A Delphi Panel European Consensus Based on Chemistry and Legal Evidence

Francesco Scaglione, Paola Minghetti, Francesco Ambrosio, Beat Ernst, Vicenzo Ficarra, Marco Gobbi, Kurt Naber, Huub Schellekens

Subject: Life Sciences, Other Keywords: D-mannose; urinary tract infection; FimH adhesin; product classification

Online: 21 March 2023 (03:42:04 CET)

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Preprint ARTICLE | doi:10.20944/preprints202303.0325.v1

Cardiovascular Safety of Hydroxychloroquine-Azithromycin in 424 COVID-19 Patients

Matthieu Million, Jean-Christophe Lagier, Jérôme Hourdain, Frédéric Franceschi, Jean-Claude Deharo, Philippe Parola, Philippe Brouqui

Subject: Life Sciences, Virology Keywords: COVID-19; SARS-CoV-2; hydroxychloroquine; azithromycin; QTc interval; cardiac rhythm; safety; torsades de pointe

Online: 17 March 2023 (11:34:00 CET)

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Preprint ARTICLE | doi:10.20944/preprints202303.0315.v1

The Crystal Structure of Engineered Nitroreductase NTR 2.0 and Impact of F70A and F108Y Mutations on Substrate Specificity

Abigail V Sharrock, Jeff S Mumm, Gintautas Bagdžiūnas, Narimantas Čėnas, Vickery L Arcus, David F. Ackerley

Subject: Life Sciences, Biochemistry Keywords: Type I nitroreductase; NfsB; Crystal structure; Prodrug; Metronidazole; Targeted cellular ablation; Tinidazole; CB1954; Dinitrotoluene

Online: 17 March 2023 (03:22:59 CET)

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Preprint COMMUNICATION | doi:10.20944/preprints202303.0309.v1

Identification of the Binding Epitope of an Anti-Mouse CCR6 Monoclonal Antibody (C6Mab-13) Using 1×Alanine Scanning

Tomohiro Tanaka, Mayuki Tawara, Hiroyuki Suzuki, Mika K. Kaneko, Yukinari Kato

Subject: Life Sciences, Biochemistry Keywords: mouse CCR6; monoclonal antibody; epitope; ELISA; SPR

Online: 16 March 2023 (14:13:28 CET)

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Preprint REVIEW | doi:10.20944/preprints202303.0304.v1

THE REEMERGENCE OF MONKEYPOX IN NIGERIA- A MINI-REVIEW

Nzube Ekpunobi, OLUWAMAYOWA AKINSUYI1, THERESA ARIRI, Temitope Ogunmola

Subject: Life Sciences, Virology Keywords: Monkeypox, , Nigeria, MPXV, Epidemiology, Spillover

Online: 16 March 2023 (10:43:53 CET)

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Preprint REVIEW | doi:10.20944/preprints202303.0301.v1

Autochthonous Cultures to Improve Safety and Stabilize Quality of Traditional Dry Fermented Meats

Franca Rossi, Patrizia Tucci, Ilaria Del Matto, Lucio Marino, Carmela Amadoro, Giampaolo Colavita

Subject: Life Sciences, Microbiology Keywords: traditional dry fermented sausages; protection policy; desired microbiota; lactic acid bacteria; coagulase negative staphylococci; autochthonous cultures; safety; sensory quality

Online: 16 March 2023 (09:02:51 CET)

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Preprint ARTICLE | doi:10.20944/preprints202303.0290.v1

Exploring the Microbiome of Marmara Sea Mucilage: A Shotgun Metagenomics Study

Aycan Gundogdu, Özkan Ufuk Nalbantoğlu, Gizem Karis, Ilknur Sarikaya, Meryem Nisa Erdogan, Mehmet Hora, Herdem Aslan

Subject: Life Sciences, Microbiology Keywords: Mucilage microbiome; Shotgun-metagenome sequencing; Comparative marine microbiome

Online: 15 March 2023 (15:24:58 CET)

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Preprint REVIEW | doi:10.20944/preprints202303.0288.v1

Insights and Interpretation of the Trends for in ovo Sexing Technologies in Papers and Patents

Matthias Corion, Simao Santos, Bart De Ketelaere, Dragana Spasic, Maarten Hertog, Jeroen Lammertyn

Subject: Life Sciences, Biotechnology Keywords: In ovo sexing; male day-old chick culling; animal welfare; optical and non-optical techniques; patents and papers

Online: 15 March 2023 (14:29:43 CET)

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Preprint ARTICLE | doi:10.20944/preprints202303.0276.v1

NGS Data Repurposing Allows Detection of Gastric Cancer Biomarkers in Patient-Derived Extracellular Vesicles

Joaquín J. Maqueda, Mafalda Santos, Marta Ferreira, Sérgio Marinho, Sara Rocha, Mafalda Rocha, Nadine Saraiva, Nuno Bonito, Joana Carvalho, Carla Oliveira

Subject: Life Sciences, Molecular Biology Keywords: tRNA fragments; extracellular vesicles; Gastric Cancer; NGS data repurposing; cancer biomarkers

Online: 15 March 2023 (09:18:23 CET)

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Preprint ARTICLE | doi:10.20944/preprints202303.0266.v1

Integrated Metabolomic and Transcriptomic Study of Klebsiella pneumoniae Strain: Possible Inhibitory Mechanism of Rutin on Strain Growth

Zhibin Wang, Wanxia Shen, Yuejiao Li, Xiaoyun Wang, Fan Jiang, Xiaolin Zhong, Xueping Huang, Jinbo Liu

Subject: Life Sciences, Microbiology Keywords: drug resistance; flavonoids; RNA-seq; Klebsiella pneumoniae; Rutin; antibacterial agents

Online: 15 March 2023 (02:03:17 CET)

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Preprint BRIEF REPORT | doi:10.20944/preprints202303.0207.v2

Sex Age Annotated Omics Data: Enabling Powerful Omics Studies

Pietro Hiram Guzzi, Francesca Cortese, Raffaele Giancotti, Ugo Lomoio, Barbara Puccio, Patrizia Vizza, Giuseppe Tradigo, Pierangelo Veltri

Subject: Life Sciences, Other Keywords: Annotation; Biological Databases; Aging Analysis

Online: 15 March 2023 (02:00:02 CET)

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Preprint ARTICLE | doi:10.20944/preprints202303.0263.v1

Characterisation of Some Rhizobium EPS and Their Biopreservative Potentials on Shelf Life Extension of Musa Species

Stephanie Clara Akpeji, Bukola Christianah AdebayoTayo, Chukwunalu Okolie Ossai

Subject: Life Sciences, Microbiology Keywords: Exopolysaccharides; Rhizobial; Musa paradisiaca; Musa balbisiana Musa acuminata; EPS-producing Rhizobia

Online: 15 March 2023 (01:35:16 CET)

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Exopolysaccharides-EPS are long-chain biopolymer with branched, recurring unit of sugars and non-carbohydrate constituents connected to exterior of cells. Rhizobial, a legume nodulating organism is capable of producing EPS. This study investigated the characteristics’ of some Rhizobium EPS and their effects in shelf life extension of some Musa spp. Rhizobial-EPS was produced using yeast extract mineral medium purified by standard methods. The EPS was characterized to determine functional group, thermal stability, chemical compounds and the monosaccharide component using Fourier Transform Infra-red, Spectroscopy, thermogravimetric Analysis (TGA), Gas Chromatography–Mass Spectrometry and HPLC and their bio-preservative property on post-harvest quality of plantain and different banana was done. The Rhizobial-EPS functional groups were hydroxyl, carboxyl, amine, methyl and ethers associated with polysaccharides. Pentadecanoic acid, octadecanoic acid, oleic acid and heptacosanoic acid, and varied concentration of monosaccharides were detected in the exopolysaccharides. The TGA of the EPS shows a constant loss in weight with two quasi-sharp alterations and almost steady plateau. The EPS coated samples had the lowest weight loss across the samples and as such edible coating was effective in delaying weight loss. The weight loss of Musa paradisiaca (plantain) coated with (EPSA obtained from USDA 110), (EPSB USDA 532C) and (EPSC S2) at the first day were 314 and 314.5g. The initial weight loss of coated and uncoated Musa sp. (Apple Banana), Musa acuminata (Lady Finger), and Musa balbisiana (Cooking Banana), ranged from 72 – 72.7g, 96 – 97g and 95 – 98g respectively. The total sugar of EPS Coated Musa sp. ranges from 0.381 – 0.528mg/L, 0.392 – 0.576 mg/L and 0.41 – 0.598 mg/L at days 1, 2 and 3 respectively. The highest Titratable acidity and pH was observed in EPS coated sample. The results obtained from this study proves that EPS solution is a valuable product for fruit preservation and viable for commercial applications.

Preprint ARTICLE | doi:10.20944/preprints202303.0262.v1

Deciphering the West Eurasian Genetic Footprints in Ancient South India

Bhavna Ahlawat, Lomous Kumar, P J Cherian, Jagmahender S Sehrawat, Niraj Rai, Kumarasamy Thangaraj

Subject: Life Sciences, Molecular Biology Keywords: aDNA; Pattanam; West Eurasia; Haplogroup; South Asia

Online: 14 March 2023 (14:22:19 CET)

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Preprint ARTICLE | doi:10.20944/preprints202303.0253.v1

Capsid Specific Antibody Responses of Domestic Pigs Immunized with Low Virulent African Swine Fever Virus

Priscilla Y.L. Tng, Laila Al-Adwani, Egle Pauletto, Joshua Y.K. Hui, Christopher L. Netherton

Subject: Life Sciences, Immunology Keywords: ASFV; humoral responses; ASFV capsid proteins; ASFV vaccines; ASFV immunity; antigen discovery; luciferase antibody capture assay; luciferase immunoprecipitation assay; viral hemorrhagic fever.

Online: 14 March 2023 (09:43:57 CET)

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Preprint ARTICLE | doi:10.20944/preprints202303.0247.v1

Trees on Farms Provide Both Wood Value and Conservation Value in a Tropical Forest System: A Case Study from Western Kenya

Anton Espira, Christopher Kefa, Mark Lung, Andrew J. Gregory

Subject: Life Sciences, Other Keywords: Kakamega Rain Forest; Conservation; Biodiversity; Complementarity; Agroforestry

Online: 14 March 2023 (06:14:00 CET)

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A primary challenge facing conservationists is reconciling the human needs of forest adjacent communities with the needs of conserving forest biodiversity, especially in tropical regions with growing populations of rural poor. Agroforestry has the potential to simultaneously provide for human needs and enhance forest biodiversity, but the complex interactions and feedbacks between the social and natural dimensions are relatively undescribed and thus systematic implementation is rare. The attributes of trees on farms required for human needs and conservation value may conflict. For example, exotic species in monoculture may provide the most economic value for farmers, while relic or planted indigenous tree mixtures may be more valuable for biological conservation. The objective of this study was to explore whether agroforestry practices in a moist tropical forest ecosystem in Kenya can simultaneously provide timber and fuelwood value to small-holder farmers while extending forest tree biodiversity. We described the agroforestry attributes on farms around a tropical forest, assessed the relationship between number and biomass of timber/fuelwood trees and tree biodiversity, and explored the relationships between forest tree diversity attributes and farm tree diversity attributes on a landscape scale using spatial analysis. We found that the diversity and number of trees on farms in this area are extensive yet variable, but that no significant relationship exists between the number of timber/fuelwood trees and tree diversity. This suggests that the two values of agroforestry may not be in conflict, due mainly to the high diversity of trees used for fuelwood. We also found that trees on farms in the larger landscape add to the conservation value of forest tree biodiversity and could be important components in conservation management. If agroforestry is to play an increasingly active role in conserving biodiversity in human-dominated landscapes, particularly in areas of dense subsistence farmer populations, increase recognition needs to be given to farmer’s perception of the value of trees and their selection of what trees to plant or maintain.

Preprint ARTICLE | doi:10.20944/preprints202303.0098.v2

Antibacterial Potency of Fractions from Psidium guajava Leaves and Bark Crude Extracts against Bacterial Isolates Responsible for Foodborne Infection

JAMES A. NDAKO, , Emmanuel O Oludipe, Surajudeen A. Junaid, Rachael F. Echemita, Victor O. Fajobi, Victor T. Dojumo, Precious J. Ndako, Adedamola O. Omole

Subject: Life Sciences, Microbiology Keywords: Antibacterial activity; Psidium guajava; phytochemical screening; liquid-liquid fractionation

Online: 14 March 2023 (04:07:51 CET)

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Preprint ARTICLE | doi:10.20944/preprints202303.0244.v1

Assessment of Backyard Chicken Farmers' Knowledge, Attitudes, and Practices on Management and Biosecurity in Bangladesh

Ibrahim Khalil, Jobaida Khanom, Mohammad Eliyas, Sudeb Sarker, Md. Harisul Abid, Syed Hossain, Babafela Awosile

Subject: Life Sciences, Other Keywords: backyard chicken; biosecurity; management; knowledge gap; Bangladesh

Online: 14 March 2023 (04:00:24 CET)

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Preprint ARTICLE | doi:10.20944/preprints202303.0241.v1

Analysis of Nipah Virus Replication and Host Proteome Response Patterns in Differentiated Porcine Airway Epithelial Cells Cultured at the Air-Liquid Interface

Martin Müller, Kerstin Fischer, Elisabeth Woehnke, Luca M. Zaeck, Christoph Prönnecke, Michael R. Knittler, Axel Karger, Sandra Diederich, Stefan Finke

Subject: Life Sciences, Virology Keywords: Nipah virus; air-liquid interface culture; respiratory epithelium; mass spectrometry; immune response

Online: 14 March 2023 (02:50:52 CET)

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Preprint ARTICLE | doi:10.20944/preprints202303.0230.v1

Attenuation of Dopaminergic Neurodegeneration in a C. elegans Parkinson’s Model through Regulation of Xanthine Dehydrogenase (XDH-1) Expression by the RNA Editase, ADR-2

Lindsey A. Starr, Luke E. McKay, Kylie N. Peter, Lena M. Seyfarth, Laura A. Berkowitz, Kim A. Caldwell, Guy A. Caldwell

Subject: Life Sciences, Genetics Keywords: alpha-synuclein; ADAR; C. elegans; dopamine; neurodegeneration; Parkinson's disease; RNA editing; xanthine dehydrogenase; ABC transporter

Online: 13 March 2023 (10:34:06 CET)

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Preprint ARTICLE | doi:10.20944/preprints202303.0219.v1

SARS-CoV-2 Positivity and Viral Load during Three Viral Waves in Mumbai, India

Chaitali Nikam, Wilson Suraweera, Sze Hang Fu, Patrick E Brown, Nico Nagelkerke, Prabhat Jha

Subject: Life Sciences, Virology Keywords: SARS-CoV-2 pandemic; PCR positivity; Aleph Delta Omicron waves; Mumbai; India

Online: 13 March 2023 (06:31:08 CET)

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Preprint ARTICLE | doi:10.20944/preprints202303.0218.v1

Bacteriological Analysis of Sachet Water Sold in Obi Local Government Area, Benue State, Nigeria

Monday Oboh, Blessing Olotu

Subject: Life Sciences, Microbiology Keywords: Analysis; bacterial; pathogens,bacteriology; human health

Online: 13 March 2023 (06:23:55 CET)

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Preprint ARTICLE | doi:10.20944/preprints202303.0215.v1

Implementation of the Lean Healthcare System in the Emergency Room of the Hospital de Clinics of the Federal University of Uberlândia: A Case Study

Paulo Sergio de Freitas, Elmiro Santos Resende

Subject: Life Sciences, Other Keywords: Lean in emergencies; Emergency room overcrowding; Lean Healthcare; Health services management; Hospital management

Online: 13 March 2023 (04:33:42 CET)

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Objective: To describe the methodology used and the results found in the implementation of Lean in Emergencies in the Emergency sector of the Hospital de Clínicas of the Federal University of Uberlândia (HC-UFU), verifying the difficulties and particularities that involved the process, as well as the result obtained. Material and methods: For the comparison between the periods before (T1), contemporary (T2) and after (T3) the implementation of Lean, hospital data were used , and the indicators corresponding to 10 variables were analyzed: Male Hospitalization and Female Hospitalization; High Male and High Female; Male Transfer and Female Transfer, Male Death <24h and Female Death <24h; Male Death >24h and Female Death >24h and general occupancy rate. All raw data related to the 36 months of evaluation were provided by the HC-UFU Statistics sector in spreadsheets without identifying patients. The indicators were compared to each other in the three analyzed periods, with the study directed as follows: Previous stage - Pre -intervention (T1): considered between the months of April 2017 to March 2018, completing 12 months before the implementation of Lean; Intra-intervention stage - contemporary (T2): considered between the months of April 2018 to March 2019, in a total of 12 months which was the implementation period; Post-Intervention Stage (T3): later: considered between the months of April 2019 to March 2020, completing 12 months after the implementation of Lean. The Lean in Emergencies scores (NEDOCS and LOS) were only recorded during the period that the implementation team was able to record and were used only to demonstrate trend over time. Comparison of the indicators with those found in other hospital units that also implemented Lean was carried out based on bibliographical research. Results and Discussion: The analysis of the behavior of the indicators did not demonstrate effectiveness related to the implementation of the system in the emergency sector. The failure to obtain better indicators can be attributed to discontinuity in monitoring the project, the lack of involvement of the clinical staff and alignment with the needs of the staff training academy, the difficulty of understanding the project by local and regional public entities. geographical location where the hospital is located, and by users of the health system who were not properly informed about the development of the project. These aspects should be considered in future management projects that may be implemented in the hospital. Despite the result of the implementation of Lean in the emergency sector not having reached the expected goals, the attempt showed windows of opportunity for future action on points that can improve the hospital management process and that should be tested in the next experiences. Conclusion: The methodology followed for the implementation of Lean in Emergencies in the emergency sector of the hospital did not produce improvement in hospital indicators.

Preprint REVIEW | doi:10.20944/preprints202303.0214.v1

Natural Compounds: Co-Delivery Strategies with Chemotherapeutic Agents or Nucleic Acids using Lipid-Based Nanocarriers

Patrícia V. Teixeira, Eduarda Fernandes, Telma B. Soares, Filomena Adega, Carla M. Lopes, Marlene Lúcio

Subject: Life Sciences, Biotechnology Keywords: cancer; conventional therapy; combined therapy; lipid-based nanocarriers; natural compounds

Online: 13 March 2023 (04:32:05 CET)

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Preprint REVIEW | doi:10.20944/preprints202303.0211.v1

Progress on Understanding Metabolic Syndrome, and Knowledge of Its Complex Pathophysiology

Birendra Kumar Jha, Mohammad Imran, Yousuf Mohammed, Laxmi Akhileshwar Jha, Keshav Raj Paudel, Saurav Kumar Jha

Subject: Life Sciences, Endocrinology & Metabolomics Keywords: metabolic syndrome; glucose tolerance; pathophysiology; hyperglycemia; diet

Online: 13 March 2023 (03:58:55 CET)

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Preprint BRIEF REPORT | doi:10.20944/preprints202303.0207.v1

Sex Age Annotated omics Data: Enabling powerful omics studies

Pietro Hiram Guzzi, Francesca Cortese, Raffaele Giancotti, Ugo Lomoio, Barbara Puccio, Patrizia Vizza, Giuseppe Tradigo, Pierangelo Veltri

Subject: Life Sciences, Other Keywords: Annotation Proteome

Online: 13 March 2023 (02:33:36 CET)

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Preprint ARTICLE | doi:10.20944/preprints202303.0185.v1

Allogenic Synovia Derived Mesenchymal Stem Cells for Treat-Ment of Equine Tendinopathies and Desmopathies – The Proof-of-Concept

Inês Leal Reis, Bruna Lopes, Patrícia Sousa, Ana Catarina Sousa, Mariana Branquinho, Ana R. Caseiro, Sílvia Santos Pedrosa, Alexandra Rêma, Cláudia Oliveira, Beatriz Porto, Luís Atayde, Irina Amorim, Rui Alvites, Jorge Miquel Silva Santos, Ana Colette Maurício

Subject: Life Sciences, Biotechnology Keywords: allogenic; cell-based therapies; clinical trials; ligament; mesenchymal stem cells; sport horses; syn-ovial mesenchymal stem cell; tendon

Online: 10 March 2023 (02:53:15 CET)

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Preprint ARTICLE | doi:10.20944/preprints202303.0175.v1

Description of a Novel Fish Pathogen, Plesiomonas shigelloides subsp. Oncorhynchi, Isolated From Rainbow Trout (Oncorhynchus mykiss): First Genome Analysis and Comparative Genomics

Muhammed Duman, Elena Garcia Valdes, Hilal Ay, Soner ALTUN, Izzet Burcin Saticioglu

Subject: Life Sciences, Microbiology Keywords: Whole genome sequence; Plesiomonas genus; Plesiomoniasis; Aquaculture

Online: 9 March 2023 (09:56:40 CET)

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Preprint ARTICLE | doi:10.20944/preprints202303.0173.v1

Predicting the Growth of Vibrio parahaemolyticus in Oysters Under Varying Ambient Temperature

Iker Fernández-Vélez, Gorka Bidegain, Tal Ben-Horin

Subject: Life Sciences, Microbiology Keywords: Vibrio; Oysters; Post-harvest; Modelling; Temperature; Ice-treatment

Online: 9 March 2023 (09:40:44 CET)

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Preprint REVIEW | doi:10.20944/preprints202208.0203.v2

Neural Induction, Embryogenesis, and Tumorigenesis

Ying Cao

Subject: Life Sciences, Cell & Developmental Biology Keywords: neural induction; embryogenesis; tumorigenesis; neural stemness; tumorigenicity; pluripotency; epithelial-mesenchymal transition; tumor microenvironment

Online: 9 March 2023 (06:57:01 CET)

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Characterization of cancer cells and neural stem cells indicates that tumorigenicity and pluripotency are coupled cell properties determined by neural stemness, and tumorigenesis represents a process of progressive loss of original cell identity and gain of neural stemness. This reminds of a most fundamental process required for the development of the nervous system and body axis during embryogenesis, i.e., embryonic neural induction. Neural induction is that, in response to extracellular signals that are secreted by the Spemann-Mangold organizer in amphibians or the node in mammals and inhibit epidermal fate in ectoderm, the ectodermal cells lose their epidermal fate and assume the neural default fate and consequently, turn into neuroectodermal cells. They further differentiate into the nervous system and also some non-neural cells via interaction with adjacent tissues. Failure in neural induction leads to failure of embryogenesis, and ectopic neural induction due to ectopic organizer or node activity or activation of embryonic neural genes causes a formation of secondary body axis or a conjoined twin. During tumorigenesis, cells progressively lose their original cell identity and gain of neural stemness, and consequently, gain of tumorigenicity and pluripotency, due to various intra-/extracellular insults in cells of a postnatal animal. Tumorigenic cells can be induced to differentiation into normal cells and integrate into normal embryonic development within an embryo. However, they form tumors and cannot integrate into animal tissues/organs in a postnatal animal because of lack of embryonic inducing signals. Combination of studies of developmental and cancer biology indicates that neural induction drives embryogenesis in gastrulating embryos but a similar process drives tumorigenesis in a postnatal animal. Tumorigenicity is the manifestation of aberrant occurrence of pluripotent state in a postnatal animal. Pluripotency and tumorigenicity are both but different manifestations of neural stemness in pre- and postnatal stage, respectively, of animal life. The unique property of neural stemness is derived from the evolutionary advantage of neural genes and the neural-biased state of the last common unicellular ancestors of metazoan. Based on these findings, I discuss about some confusion in cancer research, propose to distinguish the causality and associations and discriminate causal and supporting factors involved in tumorigenesis, and suggest revisiting the focus of cancer research.

Preprint ARTICLE | doi:10.20944/preprints202303.0167.v1

Use of 3-Way Voting of Machine Learning Algorithms Improves Prediction Performance of the Efficacy of Antisense-Mediated Exon Skipping and Reduces the Computational Burden

Alex Zhu, Shuntaro Chiba, Yuki Shimizu, Katsuhiko Kunitake, Yasushi Okuno, Yoshitsugu Aoki, Toshifumi Yokota

Subject: Life Sciences, Biotechnology Keywords: antisense oligonucleotides; exon skipping; machine learning; ensemble learning; personalized medicine; n-of-1 therapy; splice switching; genetic disease; splicing; RNA

Online: 9 March 2023 (04:43:55 CET)

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Preprint ARTICLE | doi:10.20944/preprints202303.0160.v1

Hiit Induces Acute Inflammatory Profile in Older Adults In-Volving Il-17 and Il-10 Secretion: A Randomized Controlled Trial Study

Fabiana Rodrigues Scartoni, Diego Augusto Santos Silva, Andrea Carmem Guimarães, Brisa D'Louar Costa Maia, Estevao Scudese, Fabio Nascimento Da Silva, Delson Lustosa Figueiredo, Divaldo Martins de Souza, Carlos Soares Pernambuco, Rayana Nascimento Matos, Elizabeth Carvalho Lugão, Angela Maria Moed Lopes, Larissa Deadame Figueiredo-Nicolete, João Rafael Valentim-Silva

Subject: Life Sciences, Immunology Keywords: Exercise; IL-17; IL-10; Interleukin. Exercise-Induced Inflammatory State

Online: 9 March 2023 (02:11:14 CET)

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Preprint ARTICLE | doi:10.20944/preprints202303.0153.v1

Changes of Raw Texture, Intramuscular Connective Tissue Properties and Collagen Profiles in Broiler Wooden Breasts Pectoralis Muscles During Early Storage

Xueshen Zhu, Eero Puolanne, Per Ertbjerg

Subject: Life Sciences, Other Keywords: wooden breast; collagen profiles; intramuscular connective tissue; thermal properties; postmortem

Online: 8 March 2023 (09:02:27 CET)

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Preprint TECHNICAL NOTE | doi:10.20944/preprints202303.0143.v1

Optimized Protocol for Preservation of Human Platelet Samples for Fluorometric Polyphosphate Quantification

Tomoyuki Kawase, Katsuya Suzuki, Masami Kamimura, Tomoharu Mochizuki, Takashi Ushiki

Subject: Life Sciences, Biochemistry Keywords: platelets; polyphosphate; preservation

Online: 8 March 2023 (03:04:37 CET)

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Preprint REVIEW | doi:10.20944/preprints202303.0140.v1

Autoimmune Inflammatory Reactions Triggered by the COVID-19 Genetic Vaccines in Terminally Differentiated Tissues

Panagis Polykretis, Alberto Donzelli, Janci C. Lindsay, David Wiseman, Anthony M. Kyriakopoulos, Michael Mörz, Paolo Bellavite, Masanori Fukushima, Stephanie Seneff, Peter A. McCullough

Subject: Life Sciences, Immunology Keywords: COVID-19; genetic vaccines; adverse reactions; autoimmunity; immunohistochemistry; spike protein

Online: 8 March 2023 (02:57:33 CET)

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Preprint REVIEW | doi:10.20944/preprints202303.0131.v1

Salinity Stress Mitigation by Polyploidy Induction in Soybean (Glycine max L. Merrill)

Phetole Mangena

Subject: Life Sciences, Cell & Developmental Biology Keywords: Biochemical traits, Colchicine; Glycine max; Morphology; Oryzalin; Polyploidy; Salinity stress; Soybean

Online: 7 March 2023 (09:29:33 CET)

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Preprint ARTICLE | doi:10.20944/preprints202303.0122.v1

Automatic Generation of SBML Kinetic Models from Natural Language Texts using GPT

Kazuhiro Maeda, Hiroyuki Kurata

Subject: Life Sciences, Other Keywords: GPT; language model; kinetic modeling; simulation; systems biology; natural language processing

Online: 7 March 2023 (02:59:59 CET)

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Preprint REVIEW | doi:10.20944/preprints202303.0112.v1

Brief History of Thermodynamic Research on Microorganisms

Marko Popovic

Subject: Life Sciences, Virology Keywords: Viruses; Escherichia coli; Klebsiella aerogenes; Candida utilis; Gibbs energy of biosynthesis; Bi-osynthesis reaction; Enthalpy; Entropy; Pathogen-host interaction

Online: 6 March 2023 (15:47:22 CET)

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Preprint ARTICLE | doi:10.20944/preprints202303.0109.v1

Clinical Diagnosis for Chikungunya Infection: An Essential Aid in a Primary Care Setting Where Serological Confirmation Is Not Available

Juan C. Rueda, Ingris Peláez-Ballestas, Jose-Ignacio Angarita, Ana M. Santos, Carlos Pinzon, Eugenia-Lucia Saldarriaga, Jorge M. Rueda, Elias Forero, Diego L. Saaibi, Paula X. Pavía, Marta Juliana Mantilla, Gustavo Rodríguez-Salas, Juan Camilo Santacruz, Igor Rueda, Mario H. Cardiel, John Londono

Subject: Life Sciences, Virology Keywords: Chikungunya virus; diagnosis; arbovirus infections; clinical decision making; Colombia

Online: 6 March 2023 (15:17:22 CET)

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Preprint REVIEW | doi:10.20944/preprints202301.0456.v2

Quantitative Image Processing for Three-Dimensional Episcopic Images of Biological Structures: Current State and Future Directions

Natalie Aroha Holroyd, Claire Walsh, Lucie Gourmet, Simon Walker-Samuel

Subject: Life Sciences, Microbiology Keywords: episcopic; imaging; microscopy; annotation; quantification

Online: 6 March 2023 (13:52:22 CET)

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Preprint ARTICLE | doi:10.20944/preprints202303.0098.v1

Antibacterial Potency of Fractions from Psidium guajava Leaves and Bark Crude Extracts against Bacterial Isolates Responsible for Foodborne Infection

JAMES A. NDAKO, , Emmanuel O Oludipe, Surajudeen A. Junaid, Rachael F. Echemita, Victor O. Fajobi, Victor T. Dojumo, Precious J. Ndako, Adedamola O. Omole

Subject: Life Sciences, Microbiology Keywords: Antibacterial activity, Psidium guajava; phytochemical screening; liquid-liquid fractionation

Online: 6 March 2023 (07:21:06 CET)

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Preprint ARTICLE | doi:10.20944/preprints202303.0094.v1

Serological Prevalence of Hepatitis C Virus among Febrile Patients Attending a General Hospital in Emohua LGA, Rivers State, Nigeria

Iheanyi Okonko, Happiness Ernest Nwagwu

Subject: Life Sciences, Virology Keywords: Antibodies; HCV; Prevalence; Febrile Patients; Nigeria

Online: 6 March 2023 (06:34:18 CET)

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Preprint ARTICLE | doi:10.20944/preprints202303.0085.v1

Mafosfamide combine with GMI-HBVac against HBV via Treg depletion in HBV-infected mice

Qing Lin, Yiwei Zhong, Bin Wang

Subject: Life Sciences, Immunology Keywords: Chronic hepatitis B infection; Therapeutic vaccines; Regulatory T cells; Functional cure; GMI-HBVac; Mafosfamide

Online: 6 March 2023 (03:37:38 CET)

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Preprint REVIEW | doi:10.20944/preprints202303.0080.v1

Novel Bacteriophage-Based Food Packaging: An Innovative Food Safety Approach

Rajesh V. Wagh, Ruchir Priyadarshi, Jong-Whan Rhim

Subject: Life Sciences, Microbiology Keywords: Virus-fortification; antimicrobial; active packaging films; bacteriophages

Online: 6 March 2023 (02:20:53 CET)

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Preprint ARTICLE | doi:10.20944/preprints202303.0077.v1

Effect of Microencapsulated Basil Extract on Cream Cheese Quality and Stability

Liliana Popescu, Daniela Cojocari, Ildiko Lung, Irina Kacso, Alexandra Ciorîţă, Aliona Ghendov-Mosanu, Greta Balan, Adela Pintea, Rodica Sturza

Subject: Life Sciences, Biochemistry Keywords: microencapsulated basil extract; antimicrobial activity; cream cheese; quality; shelf life.

Online: 6 March 2023 (01:13:55 CET)

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Preprint COMMUNICATION | doi:10.20944/preprints202303.0042.v1

Structured Illumination Microscopy Improves Spot Detection Performance in Spatial Transcriptomics

Alejandro Linares, Carlo Brighi, Sergio Espinola, Francesco Bacchi, Álvaro H. Crevenna

Subject: Life Sciences, Biophysics Keywords: Structured illumination; Spatial transcriptomics; Super-resolution; Gene expression; In situ sequencing; Deconvolution microscopy

Online: 2 March 2023 (10:42:14 CET)

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Preprint ARTICLE | doi:10.20944/preprints202303.0040.v1

The Demographic and Geographic Variations Mediate Fecal and Oral Microbial Dynamics Alteration in Human Population of District Faisalabad

Muhammad Aslam

Subject: Life Sciences, Microbiology Keywords: Gut microbiota; Dysbiosis; Demography; Firmicutes; Proteobacteria; Actinobacteria

Online: 2 March 2023 (10:06:05 CET)

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The gut microbiome offers numerous advantages to the hosts, through a variety of physiological mechanisms like firming up gut integrity or shaping the intestinal epithelium. Studies showed 2172 species are identified and isolated from human beings, ordered into twelve different phyla, of which 93.5% belonged to Bacteroidetes, Firmicutes, Proteobacteria and Actinobacteria. Out of the 12, three phyla are identified. Human microbial communities are affected by the host external factors like dietary patterns, lifestyle factors, antibiotic usage, internal factors gender, host genotype, age and race. To analyze the dysbiosis and bacterial variation in different areas of District Faisalabad 10,000 individuals of age 25–35 years were recruited from the two different rural and urban localities. The oral swab and fecal sample were collected according to prescribed manner. The collected samples from demographically and geographically distinct regions of District Faisalabad were subjected to DNA extraction and quantification. The amplification of 16s rRNA was carried out by PCR and visualized through a transilluminator. The results revealed significant elevated, % abundance of fecal microbial profile Blautia spp, Firmicutes, Ruminococcaceae, in rural population however non-significant difference % abundance of total Bifido, E. coli, Faecali bacteria, total Lactobacillus were identified in both demographically distinct regions. The pathogenic Gamma Protebacteria, Fusobacterium, Campylobacter coli were not detected in both study areas. Out of five orally detected microbial profiles, elevated % abundance of Firmicutes was detected in rural population however non-significant difference was observed in % abundance of total Bifido and E. coli in both populations. Total Lactobacillus and Fusobacterium were not detected in oral sample of both urban and rural population. Conclusively, this research accomplished the potential effects of demographic and geographical induced dysbiosis in the normal microbiome of the oral cavity and intestine that might cause dysbiosis associated disorders.

Preprint ARTICLE | doi:10.20944/preprints202303.0037.v1

PHA4GE Quality Control Contextual Data Tags: Standardized Annotations for Sharing Public Health Sequence Datasets with Known Quality Issues to Facilitate Testing and Training

Emma Griffiths, Catarina Inês Mendes, Finlay Maguire, Jennifer Guthrie, Leonid Chindelevitch, Ilene Karsch-Mizrachi, Zahra Waheed, Rhiannon Cameron, Kathryn Holt, Lee Katz, Robert Petit III, Duncan MacCannell, Mugdha Dave, Paul Oluniyi, Muhammad Ibtisam Nasar, Amogelang Raphenya, William Hsiao, Ruth Timme

Subject: Life Sciences, Other Keywords: quality control; reference datasets; public health; metadata; data sharing

Online: 2 March 2023 (07:50:05 CET)

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As public health laboratories expand their genomic sequencing and bioinformatics capacity for the surveillance of different pathogens, labs must carry out robust validation, training, and optimization of wet- and dry-lab procedures. Achieving these goals for algorithms, pipelines and instruments often requires that lower-quality datasets be made available for analysis and comparison alongside those of higher-quality. This range of data quality in reference sets can complicate the sharing of sub-optimal datasets that are vital for the community and for the reproducibility of assays. Sharing of useful, but sub-optimal datasets requires careful annotation and documentation of known issues to enable appropriate interpretation, avoid being mistaken for better quality information, and for these data (and their derivatives) to be easily identifiable in repositories. Unfortunately, there are currently no standardized attributes or mechanisms for tagging poor-quality datasets, or datasets generated for a specific purpose, to maximize their utility, searchability, accessibility and reuse. The Public Health Alliance for Genomic Epidemiology (PHA4GE) is an international community of scientists from public health, industry and academia focused on improving the reproducibility, interoperability, portability and openness of public health bioinformatic software, skills, tools and data. To address the challenges of sharing lower quality datasets, PHA4GE has developed a set of standardized contextual data tags, namely fields and terms, that can be included in public repository submissions as a means of flagging pathogen sequence data with known quality issues, increasing their discoverability. The contextual data tags were developed through consultations with the community including input from the International Nucleotide Sequence Data Collaboration (INSDC), and have been standardized using ontologies, community-based resources for defining the tag properties and the relationships between them. The standardized tags are agnostic to the organism and the sequencing technique used and thus can be applied to data generated from any pathogen using an array of sequencing techniques. The list of standardized tags is maintained by PHA4GE and can be found at https://github.com/pha4ge/contextual_data_QC_tags. Definitions, ontology IDs, examples of use, as well as a JSON representation, are provided. The PHA4GE QC tags were tested, and are now implemented, by the FDA’s GenomeTrakr laboratory network as part of its routine submission process for SARS-CoV-2 wastewater surveillance. We hope that these simple, standardized tags will help improve communication regarding quality control in public repositories, in addition to making datasets of variable quality more easily identifiable. Suggestions for additional tags can be submitted to PHA4GE via the New Term Request Form in the GitHub repository. By providing a mechanism for feedback and suggestions, we also expect that the tags will evolve with the needs of the community.

Preprint REVIEW | doi:10.20944/preprints202303.0030.v1

Coccidioidomycosis Osteoarticular Dissemination

Benedicte M Moni, Gabriela G Loots, Dina R Weilhammer

Subject: Life Sciences, Microbiology Keywords: Coccidioides; coccidioidomycosis dissemination; skeletal infection; fungal osteomyelitis; fungal synovitis; arthritis; knee joint

Online: 2 March 2023 (04:12:01 CET)

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Preprint ARTICLE | doi:10.20944/preprints202303.0014.v1

Bioinformatics Analyzes of Selectins Polymorphisms Reveal New Potential Cancer Biomarkers

Larissa Teodoro Rabi, Davi Zanoni Valente, Elisangela de Souza Teixeira, Karina Colombera Peres, Natassia Elena Bufalo, Laura Sterian Ward

Subject: Life Sciences, Genetics Keywords: bioinformatics analysis; selectins; cancer

Online: 1 March 2023 (08:48:00 CET)

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Preprint ARTICLE | doi:10.20944/preprints202303.0007.v1

A Virus Genetic System To Analyze the Fusogenicity of Human Cytomegalovirus Glycoprotein B Variants

Xuan Zhou, Giorgia Cimato, Yi-Hua Zhou, Giada Frascaroli, And Wolfram Brune

Subject: Life Sciences, Virology Keywords: Human herpesvirus 5; glycoprotein B; UL55; cell-cell fusion; entry; infectivity

Online: 1 March 2023 (03:05:22 CET)

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Preprint REVIEW | doi:10.20944/preprints202303.0004.v1

Fecal Metagenomics and Metabolomics Identifying Microbial Signatures in Non-Alcoholic Fatty Liver Disease

Satu Pekkala

Subject: Life Sciences, Endocrinology & Metabolomics Keywords: gut microbiota; metabolomics; metagenomics; liver fat; NAFLD; diet; metabolic pathways

Online: 1 March 2023 (02:40:16 CET)

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Preprint BRIEF REPORT | doi:10.20944/preprints202303.0002.v1

NoxO1 Determines Level of ROS Formation by the Nox1 Centered NADPH Oxidase

Dana Maureen Hebchen, Manuela Spaeth, Niklas Müller, Katrin Schröder

Subject: Life Sciences, Molecular Biology Keywords: NoxO1; Nox1; NoxA1; reactive oxygen species

Online: 1 March 2023 (02:27:40 CET)

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Preprint REVIEW | doi:10.20944/preprints202302.0516.v1

The Confound of Hemodynamic Response Function Variability in Resting-State Functional MRI Studies

D Rangaprakash, Robert Barry, Gopikrishna Deshpande

Subject: Life Sciences, Other Keywords: BOLD fMRI; HRF; resting state connectivity; aging; sex differences; confound

Online: 28 February 2023 (09:32:04 CET)

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Preprint ARTICLE | doi:10.20944/preprints202302.0484.v2

Passive Dynamics of the Head, Neck and Forelimb in Equine Foetuses- an Observational Study

Carla M Lusi, Helen M.S. Davies

Subject: Life Sciences, Other Keywords: Passive dynamics; equine; forelimb; head; neck; lameness

Online: 28 February 2023 (06:06:24 CET)

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Preprint ARTICLE | doi:10.20944/preprints202302.0500.v1

Establishment of a Pilot Newborn Screening Program for Spinal Muscular Atrophy in Saint-Petersburg

Anton Kiselev, Marianna Maretina, Sofia Shtykalova, Haya Al-Hilal, Natalia Maslyanyuk, Maria Plokhih, Elena Serebryakova, Marina Frolova, Natalia Shved, Nadezhda Krylova, Arina Il'ina, Svetlana Freund, Natalia Osinovskaya, Iskender Sultanov, Anna Egorova, Anastasia Lobenskaya, Alexander Koroteev, Irina Sosnina, Yulia Gorelik, Olesya Bespalova, Vladislav Baranov, Igor Kogan, Andrey Glotov

Subject: Life Sciences, Genetics Keywords: spinal muscular atrophy; newborn screening; SMN1; SMN2; real-time PCR; dried blood spots; SMA incidence; carrier frequency

Online: 28 February 2023 (03:45:16 CET)

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Preprint ARTICLE | doi:10.20944/preprints202302.0492.v1

Effect of a Blend of Phytogenic Compounds Addition on Rumen Microbiota and Nitrogen Utilization Efficiency during the Supplementation of Grazing Nellore Cattle

Ronyatta Weich Teobaldo, Yury Tatiana Granja-Salcedo, Abmael da Silva Cardoso, Milena Tavares Lima Constancio, Thais Ribeiro Brito, Eliéder Prates Romanzini, Ricardo Andrade Reis

Subject: Life Sciences, Microbiology Keywords: digestibility; essential oils; hydrolyzable tannins; rumen fermentation; ruminal bacteria.

Online: 28 February 2023 (02:41:58 CET)

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Preprint ARTICLE | doi:10.20944/preprints202302.0484.v1

Passive dynamics of the head and forelimb in equine foetuses- an observational study.

Carla M Lusi, Helen M.S. Davies

Subject: Life Sciences, Other Keywords: Passive dynamics, equine, forelimb, head, lameness

Online: 28 February 2023 (02:14:19 CET)

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Preprint REVIEW | doi:10.20944/preprints202302.0482.v1

Reproductive System Abnormalities Accompanied By Environmental Factors Alterations in Rat Model

Muhammad Aslam, Mubashir Abbas

Subject: Life Sciences, Endocrinology & Metabolomics Keywords: Rats; Biological research; Environmental conditions; Stress; Handling

Online: 28 February 2023 (02:04:49 CET)

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Preprint ARTICLE | doi:10.20944/preprints202302.0475.v1

Liver Fibrosis in Individuals With Hepatitis C Virus Genotype 1B From Brazilian Eastern Amazon

Tatiane Lobato Da Silva, Apio Ricardo Nazareth Dias, Juarez Antônio Simões Quaresma, Luiz Fábio Magno Falcão

Subject: Life Sciences, Virology Keywords: Hepatitis C virus; Genetic; Chronic Hepatitis C; Liver, Elastography

Online: 27 February 2023 (13:33:51 CET)

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Preprint REVIEW | doi:10.20944/preprints202302.0473.v1

The Significance and Ethics of Digital Livestock Farming

Suresh Neethirajan

Subject: Life Sciences, Other Keywords: Precision livestock farming; Digital livestock farming; Smart farming; Societal impacts; Data ownership; Open access; Sustainability; Animal ethics; Digital divide; Digital agriculture

Online: 27 February 2023 (10:16:27 CET)

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The emergence of precision and digital livestock farming presents an opportunity for sustainable animal farming practices that enhance animal welfare and health. However, this transformation of modern animal farming through digital technology has several implications for the technological, social, economic, and environmental aspects of farming. It is crucial to analyze the ethical considerations associated with the digitalization of modern animal farming, particularly in the context of human-animal relationships and potential objectification. This analysis can help develop frameworks for improving animal welfare and promoting sustainability in animal farming.One of the primary ethical concerns of digital livestock farming is the potential for a digital divide between farmers who have access to advanced technologies and those who do not. This could lead to a disparity in animal welfare and health outcomes for different groups of animals. Additionally, the use of artificial intelligence in digital livestock farming may lead to a loss of personal connection between farmers and animals, which could impact the animal's well-being. Another ethical concern of digital livestock farming is the potential for objectification of animals as mere data points. The use of sensors and other monitoring technologies can provide valuable data on animal health and behavior, but it is important to remember that animals are sentient beings with complex emotional and social needs. The use of digital technologies should not lead to neglect of animal welfare or a lack of human responsibility towards animals.Furthermore, social context becomes essential while integrating technologies in the livestock farming to overcome ethics. By considering the cultural and societal norms of different communities, we can ensure that the use of digital technologies does not undermine these values. To address these ethical challenges, the development of standards and codes of conduct for the adoption and implementation of digital livestock farming tools and platforms can help ensure that animal welfare and sustainability are prioritized. This can help alleviate the privacy concerns of stakeholders and improve sustainability in animal farming practices. Additionally, the use of virtual and augmented reality technologies can provide a way to enhance human-animal interactions and provide more personalized care to animals, further promoting animal welfare.

Preprint REVIEW | doi:10.20944/preprints202302.0462.v1

Factors Regulating the Differences in Frequency of Infiltration of Th17 and Treg of the Blood-Brain Barrier

Norwin Kubick, Mariusz Sacharczuk, Michel Mickael

Subject: Life Sciences, Immunology Keywords: CD4+ T cells; TCR repertoire; Th17; Treg; paracellular and transcellular

Online: 27 February 2023 (08:45:19 CET)

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Preprint REVIEW | doi:10.20944/preprints202302.0454.v1

Cell-Type Specific Mitochondrial Quality Control in the Brain: A Precise Mechanism of Neurodegeneration

Hariprasath Ragupathy, Manasvi Vukku, Sandeep Kumar Barodia

Subject: Life Sciences, Molecular Biology Keywords: Astrocytes, Microglia, Mitochondria, Neurons, Oligodendrocytes, Oxidative stress

Online: 27 February 2023 (07:34:12 CET)

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Preprint REVIEW | doi:10.20944/preprints202302.0448.v1

Aidan McGinnis, Ru-Rong Ji

Subject: Life Sciences, Cell & Developmental Biology Keywords: dorsal root ganglia; fatty acids; gliopathy; nerve injury; spinal cord

Online: 27 February 2023 (06:35:32 CET)

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Preprint ARTICLE | doi:10.20944/preprints202302.0445.v1

Crystal Structure of Pyrrolysyl-tRNA Synthetase from a Methanogenic Archaeon ISO4-G1 and its Structure-Based Engineering for Highly-Productive Cell-Free Genetic Code Expansion with Non-Canonical Amino Acids

Tatsuo Yanagisawa, Eiko Seki, Hiroaki Tanabe, Yoshifumi Fujii, Kensaku Sakamoto, Shigeyuki Yokoyama

Subject: Life Sciences, Biochemistry Keywords: non-canonical amino acids; genetic code expansion; crystal structure; tRNA; cell-free protein synthesis

Online: 27 February 2023 (06:27:04 CET)

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Preprint REVIEW | doi:10.20944/preprints202302.0444.v1

Understanding the Relationship of the Human Bacteriome with COVID-19 Severity and Recovery

Hassan Zafar, Milton H. Saier, Jr.

Subject: Life Sciences, Microbiology Keywords: SARS-CoV-2; COVID-19; bacteriome; immune system

Online: 27 February 2023 (06:15:38 CET)

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Preprint ARTICLE | doi:10.20944/preprints202302.0443.v1

Molecular Pathways for Muscle and Adipose Tissue are Altered between Animals Classed as Choice or Standard

Sarah A. Haderlie, Jordan K. Hieber, Jane A. Boles, James G. Berardinelli, Jennifer M. Thomson

Subject: Life Sciences, Molecular Biology Keywords: carcass quality; beef cattle; adipose tissue; muscle tissue; transcriptomics

Online: 27 February 2023 (04:56:02 CET)

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Targets for finished livestock are often determined by expected fat, either subcutaneous or intramuscular. These targets are used frequently to improve the chances of acceptable eating quality. Lower intramuscular fat, lack of product uniformity, and reduced or insufficient tenderness can negatively impact beef acceptability. This study aimed to investigate differences in gene expression that potentially alter subsequent metabolism and intercellular signaling in the muscle and proximate intermuscular and subcutaneous adipose tissue in beef carcasses at different fat endpoints. In this study, Longissimus thoracis muscle samples and associated adipose tissue were collected at harvest. RNA was harvested from both tissues, and individual samples were sequenced using RNAseq. Differential expression was determined using edgeR, and p-values were adjusted using the Benjamini-Hochberg method. A corrected p-value of 0.005 and log₂ (fold change) of 1 was set as the threshold to identify differential expression of genes. Comparison between intermuscular fat and subcutaneous fat showed no differences between the genes activated in the two adipose tissue depots, suggesting that subcutaneous fat could be sampled to evaluate changes in adipose tissue. Carcass data allowed the classification of carcasses by projected USDA quality grades (marbling targets). In the comparison between muscle from Standard and Choice carcasses, 15 genes were downregulated, and 20 were upregulated. The insulin receptor substrate 1 (IRS 1) gene was the only known functionally important gene to be differentially expressed. There were 49 downregulated genes and 113 upregulated genes in the comparison between adipose tissue from Standard and Choice carcasses. These genes are mostly related to the metabolism of fat and energy. This potentially indicates that muscle is not changing at the transcript level as much as the adipose tissue at the sampled endpoints. Also, subcutaneous fat can be used to evaluate transcript changes in both subcutaneous and intermuscular fat. However, it is not clear if these fat tissues can be used as surrogates for intramuscular fat or marbling.

Preprint ARTICLE | doi:10.20944/preprints202302.0434.v1

Identification of a NACC1-Regulated Gene Signature Impli-Cated in the Features of Triple-Negative Breast Cancer

Xia Liu, Chrispus Ngule, Hami Hemati, Oluwafunminiyi Obaleye, Amos Oyelami, Felix Oyelami, Xingcong Ren, Jianxun Song, Xiaofang Xiong, Jin-ming Yang

Subject: Life Sciences, Other Keywords: Tumor progression; cancer stem cells; gene signature; NACC1; triple negative breast cancer

Online: 27 February 2023 (03:10:34 CET)

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Preprint ARTICLE | doi:10.20944/preprints202302.0428.v1

Hybrid Spreadable Cheese Analogues with Faba Bean and Tenebrio molitor Flours: Optimisation Using Desirability-Based Mixture Design

Laura Garcia-Fontanals, Raquel Llorente, Juanjo Valderrama, Sergio Bravo, Clara Talens

Subject: Life Sciences, Other Keywords: hybrid cheese; faba bean protein; insect protein; desirability-based mixture design; spreadability texture analysis; sensory analysis

Online: 27 February 2023 (01:44:30 CET)

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Preprint ARTICLE | doi:10.20944/preprints202302.0423.v1

Tyrosine Kinase ALK/LTK Inhibitors Target B Lymphocytes

Valentyn Oksenych

Subject: Life Sciences, Immunology Keywords: B-cell; autoimmune disease; drug repurposing

Online: 24 February 2023 (09:11:37 CET)

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Preprint REVIEW | doi:10.20944/preprints202302.0416.v1

Diphtheria and the AB Toxin Group

Billy Pembroke, Robert C. Will, Archana Madhav, Vignesh Shetty, Ankur Mutreja

Subject: Life Sciences, Microbiology Keywords: AB toxin; diphtheria; botulinum; tetanus; anthrax; cholera; pertussis; shiga toxin; vaccines

Online: 24 February 2023 (03:17:55 CET)

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Preprint REVIEW | doi:10.20944/preprints202302.0405.v1

The Promise of Explainable Deep Learning for Omics Data Analysis: Adding New Discovery Tools to AI

Mariangela Santorsola, Francesco Lescai

Subject: Life Sciences, Genetics Keywords: Explainability; Deep Learning; Artificial Intelligence; Genomics; Transcriptomics

Online: 23 February 2023 (09:32:09 CET)

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Preprint REVIEW | doi:10.20944/preprints202302.0391.v1

Exposing the Small Protein Load of Bacterial Life

Laure Simoens, Igor Fijalkowski, Petra Van Damme

Subject: Life Sciences, Microbiology Keywords: small ORF encoded polypeptides (SEPs); riboproteogenomics; bacterial pathogens; protein tagging; proteomics

Online: 23 February 2023 (01:25:52 CET)

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Preprint ARTICLE | doi:10.20944/preprints202302.0389.v1

Entropic Dynamics in a Theoretical Framework for Biosystems

Richard L Summers

Subject: Life Sciences, Other Keywords: entropic dynamics; biosystems; Kullback Principle of Minimum Information Discrimination; biocontinuum; information geometry

Online: 22 February 2023 (15:32:36 CET)

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Preprint ARTICLE | doi:10.20944/preprints202302.0369.v1

Structure-Function of the Human WAC Protein in GABAergic Neurons: Towards an Understanding of Autosomal Dominant DeSanto-Shinawi Syndrome

Hannah C Rudolph, April M Stafford, Hye-Eun Hwang, Cheol-Hee Kim, Jeremy W Prokop, Daniel Vogt

Subject: Life Sciences, Cell & Developmental Biology Keywords: cell biology; protein sorting; nuclear translocation; protein domain; WAC

Online: 22 February 2023 (02:37:35 CET)

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Preprint REVIEW | doi:10.20944/preprints202302.0361.v1

The Impact of Transjugular Intrahepatic Portosystemic Shunt on Nutrition in Liver Cirrhosis Patients: A Systematic Review

Jakub Gazda, Simone Di Cola, Lucia Lapenna, Saniya Khan, Manuela Merli

Subject: Life Sciences, Other Keywords: Liver cirrhosis; Transjugular intrahepatic portosystemic shunt; Nutritional status; Sar-copenia; Fat tissue

Online: 21 February 2023 (10:36:15 CET)

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Preprint REVIEW | doi:10.20944/preprints202212.0155.v4

Low-Dose Interferon I and III-Based Nasal Sprays: A Good-Looking COVID-19 Vaccine Candidate and a Therapy of the Future?

Theodor-Nicolae Carp, Michael Metoudi, Brent Brown, Vanshika Ojha

Subject: Life Sciences, Virology Keywords: covid-19; pandemic; immune evasion; first-line immunity; viral evolution; interferon; dendritic cells; cytokines; chemokines; innate immunity; adaptive immunity; vaccinology

Online: 21 February 2023 (02:38:38 CET)

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The SARS–CoV-2 infection has caused both acute and chronic COVID–19 disease during the recent pandemic with emerging more transmissible SARS–CoV–2 Omicron variants (BQ1 and XBB1) that have increased demands for more effective immunogens and therapeutic approaches to protect the lives of numerous SARS–CoV-2 affected individuals and reduce overall disease burden that could be affected by concurrent other pathogens causing diseases. Following a worldwide campaign of mass vaccination, there is still a significant demand to quell the harmful effects of novel SARS–CoV–2 infections due to higher mutation rates within specific areas of the SARS–CoV-2 domain, leading to enhanced viral entry, especially within individuals with one or more significant comorbidities, and there is still a dilemma of how prevention of future pandemics will occur as within host animal mutations and cross species transfer naturally occurs. Concerns intersect at a specific point; a gained evolutionary ability of several viruses over the previous centuries to remain undetected during the first stages of infection by means of capping the 5' end of their DNA and RNA genes respectively. This may occur by reducing the rate of host Type I and Type III Interferons (IFN) cellular synthesis, that would usually occur and affect both apoptotic pathways, that facilitate viral replication and clearance, as well as immune cells, that process and present pathogenic antigen epitopes. Furthermore, although methods of vaccination exist, other methods in clinical development remain that could evoke an immune response in different cellular, serum or mucosal compartments being cellular, serum and mucosal that evoke differential antibody responses. Antibodies are classed as natural and synthetic. Natural antibodies are further classified into neutralizing and non-neutralizing, whilst synthetic antibodies are also further classified into monoclonal and polyclonal. As a result of single cell study transcriptome research, viruses do utilize an array of protein receptors for receptor-mediated cellular entry. This, therefore suggests that potential differential production of antibody immunoglobulins (Ig) within serum and mucosal areas remains affected by cytokines, adhesion molecules and chemokines that can be upregulated or downregulated upon host viral infection. Serum plasma antibodies can be multimeric that may not efficiently cross the nasal epithelium cell layer, therefore offering less protection against mucosal inflammation due to mucin proteins. On the other hand, antibodies produced by mucosal plasma cells at epithelial surfaces are known to provide effective immune responses in some viral infections. The existence of developments that stimulate mucosal immune responses has so far only been seen with influenza nasal immunogens. Nevertheless, scientists developed ways of immunization and early treatment worldwide that generally showed good success rates and fewer risks of adverse events, and the still early present stages of COVID-19 research should also be taken into consideration. For example, the administration of human interferons I and III into the nasal mucosa cellular layer, as key mediators of anti–viral activity, can stimulate cellular activity to train the innate and adaptive immune system cells to develop and appropriately stimulate an adequate immune response through B and T cells. Recently, it was discovered that specific plants secrete proteins that also stimulate the production of Type I Interferons. It might be that focusing on directly offering the immune system the information about the genetics and protein structure of the pathogen, rather than training its first-line mechanisms to develop faster, excessively increases its specificity, making it reach a level that brings the virus the opportunity to evolve and escape previously-developed host immune mechanisms. Naturally-selected polymorphic viruses through genetic recombination pose challenges to traditional concepts of cellular and molecular immune system neutralization of these viruses during the first stages of cellular infection. It is until the scientific community realizes this potentially crucial aspect that we will probably continue to face serious epidemics and pandemics of respiratory diseases over the coming several decades, evidenced with dengue fever and more recently monkeypox. Type I IFNs tend to be produced faster than Type III IFNs, and the first induce slightly more abundant pro-inflammatory signals than the latter, meaning that type III IFNs, if produced early, may further decrease the extent of excessive proinflammatory signals. Hence, we believe that nasal sprays containing a low dosage of Type I and Type III IFNs not only represent a relevant COVID-19 therapeutic, but also a potential unknown modulatory therapy of the future. Of note, it has been indicated that IFN I and / or III display significant immunizing and early therapeutic effects for other viral evoked diseases like Influenza (Influenza (A)H1N1), rabies (Rabies lyssavirus), measles (Measles virus), rubella (Rubivirus rubellae), Hepatitis B, HIV-induced AIDS, Ebola, Marburg, as well as bacterial diseases, such as lower respiratory tract infectious diseases induced by Haemophilus influenzae, Streptococcus pneumoniae and Staphylococcus aureus, and a number of oncological diseases, like hepatic melanoma.

Preprint ARTICLE | doi:10.20944/preprints202302.0347.v1

Physico-Chemical Study of Pomegranates of Different Degrees of Maturity

Gharib Hafizov, Samir Hafizov

Subject: Life Sciences, Biochemistry Keywords: Pomegranate; separation of varieties by taste; degree of maturity; fruit weight and ratio of its in-dividual parts; chemical composition; sugar; protein; ascorbic acid; common polyphenols; flavo-noids

Online: 21 February 2023 (02:08:54 CET)

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Preprint REVIEW | doi:10.20944/preprints202302.0333.v1

Antioxidant and Potential Non-antioxidant Roles of Vitamin E in Reproduction of Male Domestic Animals

Yuefeng Gao, Dongmei Qin, Yangyang Shen, Luyang Jian, Peilun Gu

Subject: Life Sciences, Other Keywords: Vitamin E; testis; sperm; antioxidant; reproduction

Online: 20 February 2023 (08:59:03 CET)

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LIFE SCIENCES