REVIEW | doi:10.20944/preprints202208.0105.v1
Subject: Medicine & Pharmacology, Oncology & Oncogenics Keywords: asian breast cancers; mammography screening; risk-based screening
Online: 4 August 2022 (06:20:25 CEST)
Close to half (45.4%) of 2.3 million breast cancers (BC) diagnosed in 2020 were from Asia. While the burden of breast cancer has been examined on the level of broad geographic regions, literature on more in-depth coverage of the individual countries and subregions of the Asian continent is lacking. This review examines the breast cancer burden in 47 Asian countries. Breast cancer screening guidelines and risk-based screening initiatives are discussed.
REVIEW | doi:10.20944/preprints202109.0103.v1
Subject: Medicine & Pharmacology, Pediatrics Keywords: Neonatal hearing screening; Otoacoustic emissions; Deafness; Newborn screening.
Online: 6 September 2021 (13:57:57 CEST)
Congenital deafness is a major pediatric problem, affecting about 1.5-3 per 1000 newborns. The early treatment through cochlear implantation and auditory rehabilitation has been a historic milestone. Early diagnosis of congenital deafness is an essential requirement to obtain the best results, which is achieved through neonatal screening, a diagnostic practice that we began systematically at the Hospital Clínico in Valencia (Spain) 30 years ago.
ARTICLE | doi:10.20944/preprints201704.0084.v1
Subject: Medicine & Pharmacology, Pediatrics Keywords: extended newborn screening; ethnic screening differences; Roma ethnicity
Online: 14 April 2017 (08:31:47 CEST)
Authors present The First Results of the National Extended Newborn Screening (ENS) in Slovakia in the majority (M) and the Roma (R ) ethnic populations. The follow-up of the ethnicity has been introduced in Newborn Screening for Cystic Fibrosis (NSCF) and after to entire ENS program comprising of 23 Hereditary Metabolic Disorders (HMD). Results: In 2013-2015, a total of 165,648 newborns were investigated in ENS, 23,321 of them (15,3%) were the R ethnic group, a total of 313 positive cases were discovered (total ENS prevalence = 1:529, M=1:758, R=1:198). In the R ethnic group, there was slightly higher prevalence in cong. hypothyreosis (CH), only one case of CF, and no cases of CAH in the R ethnic group. The ENS prevalence of HMD detected by MS/MS was expressively higher in the R ethnic group than in M group (M=1:1670 vs. R=1:234, OR:7,13). Significant differences in the prevalence of individual types of HMD were found. Whereas the PKU and spectrum of aminoaciduria and organic acidurias dominate in the M group, the fatty acids oxidation disorders (MCAD, SCAD) and carnitine defects (CUD) were frequent in the R newborn group. Conclusion: Despite the presented results are preliminary, the ethnic approach to ENS is enabling the recording of the ethnic differences in the screening prevalence of individual disorders, which would be missing during unitary approach.
ARTICLE | doi:10.20944/preprints202203.0176.v2
Subject: Behavioral Sciences, Other Keywords: colorectal cancer screening; breast cancer screening; BC; CRC; cancer prevention; cancer screen-ing; FOBT; mammography; Flanders
Online: 20 May 2022 (12:03:16 CEST)
Despite the recognized benefits of fecal occult blood test (FOBT) and mammography screenings, participation in breast (BC) and colorectal cancer (CRC) screening programs is still suboptimal. This study investigates municipal characteristics associated with their BC/CRC screening uptake profiles among women aged 55–69 years. Using data from 308 municipalities of Flanders from 2014 to 2017, a profile for each municipality based on its BC/CRC screening uptake compared with the median screening uptake was created. Logistic regression with generalized estimating equations was used to assess the associations between municipal characteristics and BC/CRC screening uptake profiles. The overall median uptake of cancer screening was higher for CRC (57.4%) than for BC (54.6%). The following municipal characteristics were associated with worse performance in terms of only CRC, only BC, or both CRC and BC screening uptake, respectively: foreign nationality, self-employment rate, (early) retirement rate, diabetes, disabilities; (early) retirement rate; age group 65–69, foreign nationality, self-employment rate, (early) retirement rate, wage-earners, diabetes. The following municipal characteristics were associated with better performance in terms of only CRC, only BC, or both CRC and BC screening uptake respectively: residential stability, having a partner, having children, jobseeker rate, GP visits, preventive dental visits; having children, GP visits; age group 55–59, residential stability, having a partner, having children, jobseeker rate, higher education, GP visits, preventive dental visits. This study’s results regarding the interrelation between the BC and CRC screening could be used to tailor interventions to improve the participation of the target population in both programs.
REVIEW | doi:10.20944/preprints202109.0287.v1
Subject: Engineering, Biomedical & Chemical Engineering Keywords: drug screening; monodrug or combinatorial drug screening; anti-cancer
Online: 16 September 2021 (13:46:49 CEST)
The up-and-coming microfluidic technology is the most promising platform for designing anti-cancer drugs and new point-of-care diagnostics. Compared to conventional drug screening methods based on Petri dishes and animal studies, drug delivery in microfluidic systems has many advantages. For instance, these platforms offer high throughput drug screening, require a small amount of samples, provide an in vivo-like microenvironment for cells, and eliminate ethical issues associated with animal studies. Multiple cell cultures in microfluidic chips could better mimic the 3D tumor environment using low reagents consumption. The clinical experiments have shown that combinatorial drug treatments have a better therapeutic effect than monodrug therapy. So many attempts were performed in this field in the last decade. This review highlights the applications of microfluidic chips in anti-cancer drug screening and systematically categorizes these systems as a function of sample size and combination of drug screening. Finally, it provides a perspective on the future of the clinical applications of microfluidic systems for anti-cancer drug development.
ARTICLE | doi:10.20944/preprints202012.0346.v1
Online: 14 December 2020 (14:47:20 CET)
The study aimed to estimate the prevalence and associated factors of cervical and breast cancer screening among women in the general population in Jordan. Nationally representative cross-sectional data were analysed from 14,689 women (34 years median age, range 15-49) that took part in the “2017-18 Jordan Population and Family Health Survey”. Information about cancer screening uptake included Pap smear, clinical breast examination, and mammography. Results indicate that the prevalence of ever Pap smear cancer screening was 15.3%, clinical breast examination in the past 12 months 13.9% and ever mammography 8.7%. In adjusted logistic regression analysis, older age, higher wealth, greater media exposure and tobacco use were positively and being Syrian, and living in the southern region were negatively associated with ever Pap smear, clinical breast examination in the past 12 months, and ever mammography. In addition, high decision-making power was associated with the uptake of Pap smear and higher education was associated with ever mammography. The study showed a low cancer screening uptake, and several factors were identified that can assist in promoting cancer screening in Jordan.
REVIEW | doi:10.20944/preprints202210.0148.v1
Subject: Medicine & Pharmacology, Pharmacology & Toxicology Keywords: drug development; high throughput screening; in vivo/in silico screening; zebrafish
Online: 11 October 2022 (10:33:33 CEST)
Introduction: The combination of Virtual Screening (VS) techniques with in vivo screening in the zebrafish model is currently being used in tandem for drug development in a faster and more efficient way. Areas covered: We review the different virtual screening techniques, the use of zebrafish as a vertebrate model for drug discovery and the synergy that exists between them. Expert opinion: We highlight the advantages of combining virtual and zebrafish larvae screening for drug discovery. On the one hand, VS is a faster and cheaper tool for searching active compounds and possible candidates for therapy than in vivo screening when processing large compound libraries. On the other hand, zebrafish larvae form a vertebrate model which allows in vivo screening of large amounts of the compounds. Importantly physiology and chemical response are mostly conserved between zebrafish and mammals. The availability of the transgenic and mutant zebrafish lines allows an analysis of a specific phenotype upon treatment along with toxicity, off-target effect, side effects, and dosage. Advantages of VS, in vivo whole animal approach screening, and the screening combinations are also reviewed.
ARTICLE | doi:10.20944/preprints202111.0263.v2
Subject: Medicine & Pharmacology, Obstetrics & Gynaecology Keywords: Pregnancy; Diabetes; Screening, Lifestyle
Online: 11 January 2022 (12:24:01 CET)
Basildon and Thurrock University Hospital in the East of England region of the United Kingdom (U.K), witnessed rapidly increasing numbers of pregnant women with diabetes, causing overburdened specialist clinics, poorer patient experience and worsening clinical outcomes. This prompted the multidisciplinary team’s remodelling of care pathways, launching the General ownership of Diabetes (GooD) Pregnancy Network in 2014. Contrary to conventional limitation of care to specialist diabetes antenatal clinics, this novel initiative highlights contemporary necessity to equip and empower all maternity stakeholders to deliver basic care of gestational diabetes (GDM). It strategically connects a Midwife Tele-Clinic “hub” to Educating Gestational diabetics Group Sessions (EGGS) and standard antenatal clinics. Patients were key partners, regularly participating in feedback surveys and promoting public awareness by co-producing local newspaper articles that served up their stories as case studies. Furthermore, the EGGS “faculty” includes a former GDM patient whose video testimony has inspired almost 2000 patients and their families; aiming to foster long term healthy lifestyle changes. Final summative evaluation in November 2019 showed the new culture of wider consciousness has shortened ‘diagnosis to first consultation’ intervals and eliminated overbooked specialist clinics (none since January 2016), without further worsening of clinical outcomes. It also boosted research recruitment and avoided additional running costs to the tune of £66,384 a year.
REVIEW | doi:10.20944/preprints202104.0476.v1
Online: 19 April 2021 (12:23:23 CEST)
Background: Nearly two-thirds of acute stroke patients have dysphagia. Dysphagia is difficulty to swallow food or liquids. Early detection of dysphagia is crucial in stroke patients as a result of increased morbidity and mortality due to malnutrition and respiratory tract infections. Aim: Our purpose was to conduct a literature review of dysphagia screening for stroke patient. Methods: We used the bolean operator to search articles of “or” and “and” with the key words were "Dysphagia" or “Screening”, AND "Stroke" or Acute Stroke” AND "Nursing". Data based used were Scopus, Proquest and Science Direct with inclusion criteria using full text in English which published from 2019 to 2021. We obtained 240 articles and then we screened by reading the main focus of articles with paying attention to the topics and the suitability of article content.Result: Twenty five publications relating to dysphagia screening met the inclusion criteria. There are five methods of dysphagia screening performed by nurses or other health workers: 1) a simple Questionnaire Test (4QT) method; 2) Water Swallow Test (WST) method; 3) Bed Side Screening Tool for Dysphagia (BSTD) method; 4) Volume Viscosity Swallow Test (V-VST) method; 5) EAT-10 method.Conclusion: screening is the first step in the identification of swallowing impairment or dysphagia of stroke patient. Dysphagia is an independent predictor of poor patient outcome and prolonged recovery time. Nurse has an important role to conduct a screening and must ensure that the selected tools has high reliability and concurrent validity. Key Words: Dysphagia, Nursing, Screening, Stroke
REVIEW | doi:10.20944/preprints202104.0197.v1
Online: 7 April 2021 (11:45:33 CEST)
ABSTRACT Background: Nearly two-thirds of acute stroke patients have dysphagia. Dysphagia defined as difficulty in swallowing of liquids or food, vary in severity with symptoms ranging from mild throat discomfort to inability to eat. It’s well known that dysphagia is associated with aspiration pneumonia, dehydration, malnutrition, prolonged length of stay, and increased mortality. Early screening reduces pneumonia rates in stroke and it is usually performed by nurses. Dysphagia screening is recommended but no protocol or tool is pointed.Aim: the aim of this study is to conduct a literature review of dysphagia screening for stroke patient Methods: Literature search three databases (Scopus, Proquest, and Science Direct), with the keywords "Dysphagia" AND "Stroke" AND "Nursing", published in English between 2019 and 2021. Result: Twenty five publications relating to dysphagia screening met the inclusion criteria. There are five methods of dysphagia screening performed by nurses or other health workers: 1) a simple Questionnaire Test (4QT) method, which is by asking the following four questions: does the patient cough or choke while eating or drinking; whether the patient takes longer than usual to eat; does the patient change the thickness of the food to be able to swallow, and whether the voice turns hoarse after eating or drinking; 2) Water Swallow Test (WST) method; 3) Bed Side Screening Tool for Dysphagia (BSTD) method; 4) Volume Viscosity Swallow Test (V-VST) method, namely modification of feeding with first pudding, nectar and finally water; 5) Simplified Cough Test Method. The five screening methods for dysphagia above have been tested for sensitivity and specificity, as well as positive and negative predictive valuesConclusion: screening is a first step in the identification of swallowing impairment or dysphagia of stroke patient. Dysphagia is an independent predictor of poor patient outcome and prolonged recovery time. Nurse has an important role to conduct a screening and must ensure that the selected tools has high reliability and concurrent validity. Key Words: Stroke, Dysphagia, Screening, Nursing
ARTICLE | doi:10.20944/preprints201805.0081.v1
Online: 3 May 2018 (13:24:15 CEST)
The incidence of Severe Combined Immunodeficiency (SCID) in Manitoba, (1/15,000), is at least three to four times higher than the national average and that reported from other jurisdictions. It is overrepresented in two population groups: Mennonites (ZAP70 founder mutation) and First Nations of Northern Cree ancestry (IKBKB founder mutation). We have previously demonstrated that in these two populations the most widely utilized T-cell receptor excision circle (TREC) assay is an ineffective newborn screening test to detect SCID as these patients have normal numbers of mature T-cells. We have developed a semi-automated, closed tube, high resolution DNA melting procedure to simultaneously genotype both of these mutations from the same newborn blood spot DNA extract used for the TREC assay. Parallel analysis of all newborn screening specimens utilizing both TREC analysis and the high resolution DNA procedure should provide as complete ascertainment as possible of SCID in the Manitoba population.
ARTICLE | doi:10.20944/preprints202212.0165.v1
Subject: Medicine & Pharmacology, Oncology & Oncogenics Keywords: Colorectal cancer screening; SF-12
Online: 9 December 2022 (01:08:54 CET)
Background: Participation is low (43%) in Australia’s National Bowel Cancer Screening Program which provides a biennial Fecal Immunochemical Test kit mailed to the home of Australians aged 50-74 years. While several factors for non-participation have been identified, the role of mental and physical health on screening behaviour has not been assessed. Methods: Participants of the Australasian Colorectal Cancer Family Registry Cohort were asked to complete a questionnaire on their colorectal cancer screening in the past five years and a validated measure of mental and physical health. The association between mental and physical health and screening was determined for Australian participants aged 45-75 years who had never been diagnosed with colorectal cancer. Multivariable logistic regression was used to adjust for measured potential confounders. Results: Of the 1130 eligible participants, 819 reported colorectal cancer screening in the past five years (72%). After adjusting for potential confounders, there was no evidence that overall mental or physical health was associated with colorectal cancer screening. However, one specific scale, general health, was positively associated with colorectal cancer screening (p=0.014) with those reporting higher levels of general health undergoing screening.Conclusion: We found limited evidence that mental and physical health, as measured by a short questionnaire, are associated with colorectal cancer screening. A potential limitation is reverse causation where previous screening may have impacted mental or physical health. A more detailed study of physical and mental health as barriers or enablers of screening is needed.
ARTICLE | doi:10.20944/preprints201908.0111.v1
Subject: Engineering, Industrial & Manufacturing Engineering Keywords: location; screening; interval estimation model
Online: 8 August 2019 (12:35:55 CEST)
With the focus of great concern of the sustainable development, its evaluation system has become an important operational strategy and practical values. For the purpose of obtaining the stronger indicators and the larger contribution ones, evaluation indicators screening is carried out using interval estimation model, which takes location of production and service facilities of company A as an example. And the weight value of each indicator is further explored, which can provide an direction of decision-making. The result shows that this screening method provides a more scientific evaluation method for enterprise location, decision-making basis for sustainable development of enterprises, and a solid foundation for the construction of the post-evaluation system. The present work implies that this screening method is affected, to different degrees, by the ability, knowledge reserve of the evaluators, which should be more systematic and standardized, and the concept of sustainable development should be strengthened.
ARTICLE | doi:10.20944/preprints201801.0213.v1
Online: 23 January 2018 (09:12:43 CET)
Sirtuins are nicotinamide adenine dinucleotide (NAD+)-dependent class III histone deacetylases and have been linked to the pathogenesis of numerous diseases such as HIV, metabolic disorders, neurodegeneration and cancer. Docking of the virtual pan-African natural products library (p-ANAPL), followed by in vitro testing, resulted in the identification of two inhibitors of sirtuin 1, 2 and 3 (sirt1-3). Two bichalcones; rhuschalcone IV (8) and rhuschalcone I (9), previously isolated from the medicinal plant Rhus pyroides, were shown to be active in the in vitro assay, with rhuschalcone I showing the best activity against sirt1, having an IC50 = 40.8 µM. Based on the docking experiments, suggestions for improving the biological activities of the newly identified hit compounds have been provided.
ARTICLE | doi:10.20944/preprints201806.0284.v1
Subject: Medicine & Pharmacology, Obstetrics & Gynaecology Keywords: cell-free DNA analysis; genetic counseling; noninvasive prenatal screening; prenatal screening; results delivery; telehealth
Online: 19 June 2018 (03:45:49 CEST)
Background: As noninvasive prenatal screening usage grows in the general obstetrics setting, proper patient education on the screen’s benefits and limitations is needed. Objective: Describe the use of a technology platform designed for large-scale dissemination of noninvasive prenatal screening information and results. Study Design: The technology platform functioned as follows: Patients were emailed a link to an noninvasive prenatal screening general-education video upon laboratory receipt of a test requisition. Providers were then notified upon availability of patients’ results. If noninvasive prenatal screening results were negative, the patient was sent an automated email with instructions to access results through a secure portal where she could watch tailored informational videos, request “on-demand” or scheduled genetic counseling, or decline any further services. If genetic counseling was elected, a summary of the session was sent to the ordering provider and patient upon completion. If noninvasive prenatal screening results were positive, either the ordering provider or a board-certified genetic counselor contacted the patient directly to communicate test results and provide counseling. The number and type of results issued through the platform, the number and type of genetic counseling consultations completed, and factors associated with requesting laboratory-delivered genetic counseling were tracked and analyzed for a 39-month period. Results: Over the study period, 67,122 noninvasive prenatal screening results were issued through the platform, and 4,673 patients elected genetic counseling consultations; 95.2% (n=4,450) of consultations were for patients receiving negative results. Over 70% (n= 3,370) of consultations were on-demand rather than scheduled. Median consultation time was 14 minutes for positive results and six minutes for negative results. A positive screen, advanced maternal age, family history, previous history of a pregnancy with a chromosomal abnormality, and other high-risk pregnancy were associated with the greatest odds of electing laboratory-delivered genetic counseling. Conclusions: By combining web education, automated notifications, and genetic counseling, we implemented a service that effectively facilitates results disclosure for ordering providers. These data demonstrate the capability to deliver noninvasive prenatal screening results, education, and counseling—congruent with management guidelines—to a large population, which is imperative to quality care as uptake increases.
REVIEW | doi:10.20944/preprints202205.0071.v1
Subject: Medicine & Pharmacology, Nutrition Keywords: nutrition screening tools; malnutrition; nutritional assessment
Online: 6 May 2022 (10:01:24 CEST)
Malnutrition is a serious problem with negative impact on the quality of life and the evolution of our patients, contributing to an increase in morbidity, hospital stay, mortality and health spending. Early identification is fundamental to implement the necessary therapeutic actions involving adequate nutritional support to prevent or reverse malnutrition. This review presents two complementary methods of fighting malnutrition: nutritional screening and nutritional assessment. Nutritional risk screening is conducted using simple, quick-to-perform tools and is the first line of action in detecting at-risk patients. It should be implemented systematically and periodically on admission to hospital or residential care, as well as on an outpatient basis for patients with chronic conditions. Once patients with a nutritional risk have been detected they should undergo a more detailed nutritional assessment to identify and quantify the type and degree of malnutrition. This should include health history and clinical examination, dietary history, anthropometric measurements, evaluation of the degree of aggression determined by the disease, functional assessment and, whenever possible, some method of measuring body composition.
ARTICLE | doi:10.20944/preprints202107.0379.v1
Subject: Medicine & Pharmacology, Allergology Keywords: Population screening; eye disease; prevalence; awareness
Online: 16 July 2021 (14:36:36 CEST)
Background and Objectives: Vision impairments and related blindness are major public health problems. Prevalence of eye disease and barriers to optimal care markedly vary among different geographic areas. In the Abruzzo region (Central Italy), an epidemiological surveillance on the state of ocular health in the population aged over 50 years was performed in 2019. Materials and Methods: Participants were sampled to be representative of the region inhabitants. Data were collected through a telephone interview and an eye examination. Prevalence of cataract, glaucoma, retinopathy, maculopathy was assessed. The Cohen’s kappa (k) was used to measure the agreement between presence of eye disease and awareness of the disease by the participants. Results: Overall, 983 people with mean age of 66.0±9.5 years were included in the study. The prevalence of cataract, glaucoma, maculopathy, and retinopathy was 52.6%, 5.3%, 5.6%, and 29.1%, respectively. Among the total of affected people, those aware of their condition were 21.8% (k=0.12, slight agreement) for cataract, 65.4% (k=0.78, substantial agreement) for glaucoma, 7.1% (k=0.10, slight agreement) for maculopathy, and 0% for retinopathy (k=-0.004, agreement lower than that expected by chance). Refractive defects were corrected in the vast majority of participants. Conclusion: In the Abruzzo region, about two third of citizens aged 50 years or over suffer from cataract, glaucoma, retinopathy or maculopathy, which are recognized as leading causes of blindness. Many people with eye disease do not know they have it. These data can be used by clinicians and policymakers to undertake clinical, political, and social actions.
ARTICLE | doi:10.20944/preprints202106.0116.v1
Subject: Medicine & Pharmacology, Allergology Keywords: PPTase; NRPS; indigoidine; PptT; antibiotic screening
Online: 3 June 2021 (13:22:33 CEST)
A recently-validated and underexplored drug target in Mycobacterium tuberculosis is PptT, an essential phosphopantetheinyl transferase (PPTase) that plays a critical role in activating enzymes for both primary and secondary metabolism. PptT possesses a deep binding pocket that does not readily accept labelled coenzyme A analogues that have previously been used to screen for PPTase inhibitors. Here we report on the development of a high throughput, colorimetric screen that monitors the PptT-mediated activation of the non-ribosomal peptide synthetase BpsA to a blue pigment (indigoidine) synthesising form in vitro. This screen uses unadulterated coenzyme A, avoiding analogues that may interfere with inhibitor binding, and requires only a single-endpoint measurement. We benchmark the screen using the well-characterised Library of Pharmaceutically Active Compounds (LOPAC1280) collection, and show that it is both sensitive and able to distinguish weak from strong inhibitors. We further show that the BpsA assay can be applied to quantify the level of inhibition and generate consistent EC50 data.
HYPOTHESIS | doi:10.20944/preprints202008.0030.v1
Subject: Medicine & Pharmacology, General Medical Research Keywords: COVID-19; group testing; household; screening
Online: 2 August 2020 (12:48:19 CEST)
In the advent of COVID-19 pandemic, testing is highly essential to be able to isolate, treat infected persons, and finally curb transmission of this infectious respiratory disease. Group testing has been used previously for various infectious diseases and recently reported for large-scale population testing of COVID-19. However, possible sample dilution as a result of large pool sizes has been reported, limiting testing methods’ detection sensitivity. Moreover, the need to sample all individuals prior to pooling overburden the limited resources such as test kits. An alternative proposed strategy where test is performed on pooled samples from individuals representing different households is presented here. This strategy intends to improve group testing method through the reduction in the number of samples collected and pooled during large-scale population testing. Moreover, it introduces database system which enables continuous monitoring of the population’s virus exposure for better decision making.
ARTICLE | doi:10.20944/preprints201709.0102.v1
Subject: Life Sciences, Biotechnology Keywords: drug screening； bone mineralization； osteoclast； zebrafish
Online: 21 September 2017 (06:34:11 CEST)
Currently, drug screening is primarily based on human cell culture for initial high-throughput screening, and subsequently, rodent model to confirm the biological effects. However, the mammalian system is known for time-consuming and highly-cost to be difficult to perform high-throughput drug screening, which exists a critical gap between in vitro cell-based models and the in vivo mammalian models. Therefore, the zebrafish could bridge this gap in preclinical toxicity screening along the drug development pipeline because of its efficiency. We aimed to develop an in vivo zebrafish platform for rapid drug screening. Zebrafish, due to its high genomic conservation with mammals and rapid development and differentiation, it has many advantages, such as short life span, large number of offspring and low cost, easy manipulation for generating transgenic species, to serve as animal model for disease-based research. In 96-well microplates, zebrafish embryos were incubated with small molecular compounds that affected bone mineralization. The level of osteogenic mineralization was evaluated by fluorescent dye staining and quantified by image analysis software. Quantitative real time-PCR (qRT-PCR) was performed to evaluate the biological pathways involved in bone metabolism at the molecular level. The system was validated by demonstrating that response to alendronate and Dorsomorphin in zebrafish. In our study, we screened for 24 compounds within the CYCU-1120~1152 chemical library and identified 3 compounds, pentamidine (CYCU-1140), BML-267 (CYCU-1147), and alendronate (CYCU-1152), increased embryonic mineralization; while 6 compounds, RWJ-60475 (CYCU-1126), levamisole HCL (CYCU-1128), tetramisole HCL (CYCU-1129), fenvalerate (CYCU-1132), NSC-663284 (CYCU-1138), and BML-267ester (CYCU-1148), were inhibitory to bone mineralization. We also found that alendronate enhanced the level of bone mineralization by inhibiting osteoclast-related genes. To sum up, our research showed that zebrafish may have potential to be a drug-screening and mechanism-analysis platform for bone mineralization.
ARTICLE | doi:10.20944/preprints202211.0072.v1
Online: 3 November 2022 (07:47:15 CET)
Artic root is a well-known plant adaptogen with multipotential pharmacological properties. Thin-layer chromatography (TLC) – screening followed by diode-array high-performance liquid chromatography and nuclear magnetic resonance spectroscopy proved to be a reliable and convenient method for simultaneous determination of quality of various herbal raw materials and supplements. This combination allowed for comparing and differentiating arctic root samples as well as defining their authenticity. The study provided information on the chemical and biological properties of the seven chosen samples as well as qualitative and quantitative evaluation of the quality markers: rosavin, salidroside, and p-tyrosol. The absence of rosavin, salidroside, and p-tyrosol in three samples was detected using TLC-screening and confirmed by HPLC-DAD and NMR. The paper highlighted the importance of quality control and strict regulation for herbal medicine supplements and preparations.
COMMUNICATION | doi:10.20944/preprints202203.0118.v1
Subject: Life Sciences, Biochemistry Keywords: myxobacteria; secondary metabolites; multifactorial OSMAC; screening method
Online: 8 March 2022 (08:51:31 CET)
The scarcely investigated myxobacterium Corallococcus coralloides holds a large genome containing many uncharacterized biosynthetic gene clusters (BGCs) that potentially encode the synthesis of entirely new natural products. Despite its promising genomic potential, suitable cultivation conditions have not yet been found to activate the synthesis of new secondary metabolites (SMs). Finding the right cultivation conditions to activate BGCs in the genome remained a major bottleneck and its full biosynthetic potential was so far not retrieved. Here, we therefore applied a bivariate OSMAC approach, using a combination of two elicitor changes at once for activation of BGCs and concomitant SM production by C. coralloides. The bivariate OSMAC screening was carried out in 24-well System Duetz-plates, applying univariate and bivariate OSMAC conditions. We combined biotic additives and organic solvents with minimal media and complex growth medium. The success of the method was evaluated by the number of new mass features detected in the respective extracts. We found synergistic effects in bivariate OSMAC designs. The number of new mass features detected in bivariate OSMAC exceeded the sum of new mass features found in the respective univariate OSMAC with only one elicitor. Overall, the bivariate OSMAC screening led to 26 new mass features, which were not detected in the univariate OSMAC design. Hence, the presence of multiple elicitors in the bivariate OSMAC designs successfully activated the biosynthetic potential in C. coralloides. We propose the bivariate OSMAC designs with a complex combination of elicitors as a straightforward strategy to robustly expand the SM space of microorganisms with large genomes.
Subject: Behavioral Sciences, Applied Psychology Keywords: screening; dementia; intellectual disability; early-onset; neuropsychology
Online: 15 October 2020 (12:01:34 CEST)
Background and Aims: Screening and assessment of cognitive changes in adults with Intellectual Disabilities, mainly Down Syndrome (DS), is crucial to offer appropriate services to their needs. We present a systematic review of the existing instruments assessing dementia, aiming to support researchers and clinicians’ best practice. Methods: Searches were carried out in the databases Web of Science; PubMed; PsycINFO in March 2019 and updated in May 2020. Studies were selected and examined if they: (1) focused on assessing age-related cognitive changes in person with ID; (2) included adults and/or older adults; (3) included scales and batteries for cognitive assessment. Results: Forty-eight cross-sectional studies and twenty-six longitudinal studies were selected representing a total sample of 5,851 participants (4,089 DS and 1,801 with other ID). In those studies, we found 38 scales, questionnaires, and inventories, and 14 batteries for assessing cognitive and behavioural changes in adults with DS and other ID. Conclusion: The most used instrument completed by an informant or carer was the Dementia Questionnaire for Learning Disabilities (DLD), and its previous versions. We discuss the strengths and limitations of the instruments and outline recommendations for future use.
ARTICLE | doi:10.20944/preprints202009.0719.v1
Subject: Medicine & Pharmacology, Allergology Keywords: Diabetes mellitus, screening, HbA1c, fasting plasma glucose
Online: 29 September 2020 (15:12:26 CEST)
Background: Diabetes is a common non-communicable disease that is responsible for about 9% of all deaths and 25% reduction in life expectancy and nearly half of the diabetic patients are not aware of their disease. In this regard, diabetes screening to identify un-known diabetic patients is of great importance. Aims: The aims of this study were first to evaluate the performance of two commonly used diabetes screening tests that are currently recommended by the Iranian national screening program for diabetes (NSPD). Methods: The validities of the two diabetes screening tests were measured among 1057 participants older than 30 years. The studied screening tests included Capillary fasting blood glucose (CBG) and glycated hemoglobin (HbA1c). The golden standard for measuring the validity of the tests was venous fasting plasma glucose (VPG). Results: According to the results, the sensitivity of CBG and HbA1c tests were 69.01% and 84.5% and the specificity of the tests were 95.7% and 79.3% respectively. Positive and negative predictive values were 53.84% and 97.72% for CBG and 22.72% and 98.61% for HbA1c respectively. The recommended cut-points for CBG and HbA1c were 116.5 mg/dl and 7.15% respectively. Using these values as the new cut-points, sensitivity and specificity of CBG and HbA1c changed to 80.30% and 89.10%, and 77.50% and 94.20% respectively. Conclusions: Compared to several other countries, the performance of NSPD is relatively higher in Iran. ROC analysis suggested new cut-points for significantly better performance of NSPD.
COMMUNICATION | doi:10.20944/preprints202003.0184.v2
Subject: Medicine & Pharmacology, Other Keywords: SARS-CoV-2; diagnosis; antibody; serology; screening
Online: 6 April 2020 (14:09:34 CEST)
To date, viral RNA detection is almost the only way to confirm SARS-CoV-2infectionin practice.However, variousreasons can cause low sensitivity for RNA detection, and thisposes aserious challenge to disease control. We tested the performance of detecting total antibody(Ab) and IgM levels in serum by the methods of chemiluminescence, enzyme-linked immunosorbent assay (ELISA), and colloidal golddetection. The datashowed that the sensitivity and specificity for detecting total Ab and IgM levels were high by all three methods, and the sensitivity was higher for detecting total Ab than for detecting IgM. Evidence from studieshas shown thatviral RNA testingcombinedwith serological testing could increase the diagnostic sensitivity while maintaining a high specificity. Specific serology testsfor SARS-CoV-2 havegreat value for clinical practice and public health.
ARTICLE | doi:10.20944/preprints202004.0015.v2
Online: 3 April 2020 (15:08:50 CEST)
Ligand and structure based virtual screening approaches were applied to clinical stage drugs as well as those approved for human use in an attempt to repurpose drugs for potential use against COVID-19. This approach involved ligand-based shape similarity searches, structure-based docking and pharmacophore searches with the help of pharmacophore queries derived from available ligands and receptor structures. Several compounds appeared as hits in pharmacophore and shape similarity searches and those docking to the SARS-CoV-2 viral 3CL protease were then ranked on the basis of docking scores.
ARTICLE | doi:10.20944/preprints201901.0145.v1
Subject: Medicine & Pharmacology, General Medical Research Keywords: obesity; breast screening; mammograms; health service utilization;
Online: 15 January 2019 (09:10:11 CET)
Obesity in Australia is rapidly rising, and is a major public health concern. Obesity increases risk of breast cancer and worse associated outcomes, yet breast screening participation rates in Australia are suboptimal and can be lower in higher risk, obese women. This study qualitatively explored barriers to breast screening participation in obese women in Australia. In-depth interviews (n=29), were conducted with obese women (BMI 30) and key health stakeholders. A disconnect between stakeholders’ and women’s perceptions was found. For women, low knowledge around a heightened need to screen existed, they reported limited desire to prioritize personal health needs, reluctance to screen due to poor body image and prior negative mammographic experiences due to issues with weight. Stakeholders perceived few issues in screening obese women beyond equipment limitations, and health and safety issues. Overall, weight was a taboo topic among our interviewees, indicating that a lack of discourse around this issue may be putting obese women at increased risk of breast cancer morbidity and mortality. Consideration of breast screening policy in obese women is warranted. Targeted health promotion on increased breast cancer risk in obese women is required as is a need to address body image issues and encourage screening participation.
REVIEW | doi:10.20944/preprints201609.0029.v1
Subject: Medicine & Pharmacology, Other Keywords: HLA; type 1 diabetes; ethnicity; screening; haplotype
Online: 7 September 2016 (12:49:02 CEST)
Aims/Hypothesis): Type 1 diabetes is an immune-mediated disease with destruction of the pancreatic β-cells, a process that is conditioned by multiple genes and other factors. HLA counts as the major susceptibility gene. Significant variations in HLA genetic susceptibility to type 1 diabetes between Caucasians, African and Asian and other ethnic groups may have led to the variation in incidence of type 1 diabetes globally. Type 1 diabetes is characterized upon HLA identification. In this chapter we discuss global variations in genetic susceptibility of HLA with regard to type 1 diabetes globally with a particular attention to Arab population. Methods): Haplotype configuration of HLA class I A, B, C and Class II –DR/DQ/DP were studied in Caucasians, African and Asian and in Arab population to see if that is responsible for the exponential rise in the rate of type 1 diabetes. Results): Although Arabs have one of the highest global incidence and prevalence rates of type 1 diabetes, unfortunately, there is a dearth amount of information regarding HLA genetic susceptibility to type 1 diabetes in the Arab world. HLA haplotype configurations contribute to its risk value. However, out of an insufficient present study there are examples of misjudgment of HLA risk according to HLA alleles rather than haplotypes. Conclusion): To date HLA outlooks for the characterization of type 1 diabetes. There is an ethnicity difference in HLA characteristics which is responsible for variation in type 1 diabetes. Although Arab population have contributed heavily in the rise of burden of type 1 diabetes, however, there is significantly a dearth amount of studies on HLA in Arab population. Obviously, any future prediction, prevention or cure of the disease will be based on the HLA genetics. There is a dire need for a systematic screening of HLA for Arab population with type 1 diabetes, identification of Arab HLA-risk values and identify those who are prone to get the disease.
ARTICLE | doi:10.20944/preprints202211.0244.v1
Subject: Life Sciences, Molecular Biology Keywords: aromatic rice; salt screening; RAPD marker; genetic diversity
Online: 14 November 2022 (07:43:36 CET)
Salinity is abiotic stress, which causes adverse environmental conditions for rice cultivation. In particular, local aromatic rice cultivation is heavily influenced by soil salinity stress, which has an impact on global food security. This study aimed to screen local aromatic rice genotypes in a hydroponics experiment using Yoshida solutions to evaluate the effect of increasing NaCl concentrations on the early growth stages of rice seedlings. Genetic diversity along with phylogenetic relationship was assessed using the random amplified polymorphic DNA (RAPD) markers. Out of 20 RAPD markers, 17 markers produced reproducible polymorphic bands. Individuals of all genotypes shared 88 (89.80%) of the 98 total RAPD elements amplified. The genetic distance-focused similarity index ranged from 0.05 to 0.94. The highest genetic distance (0.94) was discovered between genotypes Nayanmoni and Kalijira Barisal, and the lowest was between Badshabhog and Kataribhog (0.05). In addition, the OPS 3(510bp) and OPA 14(1100bp) markers could be used to identify salt-tolerant genotypes. According to genetic distance, the salt stress tolerant check genotype, Pokkali was genetically related to Chinigura as well as Kalijira Barisal. This study established a simple and consistent method for evaluating variability across various aromatic rice genotypes, which will benefit in genotype selection for breeding salinity stress tolerant aromatic rice varieties in Bangladesh.
REVIEW | doi:10.20944/preprints202210.0318.v1
Subject: Medicine & Pharmacology, Other Keywords: HIV; routine screening; financial benefits; Opt-out approach
Online: 21 October 2022 (03:45:01 CEST)
The Centers for Disease Control and Prevention recommends everyone between 13-64 years be tested for HIV at least once as a routine procedure. HIV routine screening is reimbursable by Medicare, Medicaid, expanded Medicaid, and most commercial insurance plans. Yet, scaling-up HIV routine screening remains a challenge. We conducted a scoping review for studies on financial benefits and barriers associated with HIV screening in clinical settings in the U.S. to inform an evidence-based strategy to scale-up HIV routine screening. We searched Ovid MEDLINE®, Cochrane, and Scopus for studies published between 2006 - 2020 in English. The search identified 383 Citations; we screened 220 and excluded 163 (outside the time limit, irrelevant, or outside the U.S.). Of the 220 screened articles, we included 35 and disqualified 155 (did not meet the eligibility criteria). We organized eligible articles under two themes: financial benefits/barriers in healthcare settings (9 articles); and Cost-effectiveness in healthcare settings (26 articles). The review concluded recommendations in three areas: (1) Finance: Incentivize healthcare providers/systems for implementing HIV routine screening and/or separate its reimbursement from bundle payments; (2) Personnel: Encourage nurse-initiated HIV screening programs in primary care settings and educate providers on CDC recommendations; and (3) Approach: Use opt-out approach.
ARTICLE | doi:10.20944/preprints202104.0399.v1
Subject: Medicine & Pharmacology, Allergology Keywords: SFTSV; minigenome assay; antivirals; antiviral screening; favipiravir; ribavirin
Online: 15 April 2021 (07:47:23 CEST)
Severe fever with thrombocytopenia syndrome virus (SFTSV) is an emerging tick-borne bunyavirus that causes severe disease in humans with case fatality rates of approximately 30%. There are few treatment options for SFTSV infection. SFTSV RNA synthesis is conducted using a virus-encoded complex with RNA-dependent RNA polymerase activity that is required for viral propagation. This complex and its activities are, therefore, potential antiviral targets. A library of small molecule compounds was screened using a high-throughput screening (HTS) based on an SFTSV minigenome assay (MGA) in a 96-well microplate format to identify potential lead inhibitors of SFTSV RNA synthesis. The assay confirmed inhibitory activities of previously reported SFTSV inhibitors, favipiravir, and ribavirin. A small-scale screening using MGA identified four candidate inhibitors that inhibited SFTSV minigenome activity by more than 80% while exhibiting less than 20% cell cytotoxicity with selectivity index (SI) values of more than 100. These included mycophenolate mofetil, methotrexate, clofarabine, and bleomycin. Overall, these data demonstrate that the SFTSV MGA is useful for anti-SFTSV drug development research.
Online: 8 March 2020 (17:14:57 CET)
3CLpro is the main protease of the novel coronavirus (SARS-CoV-2) responsible for their intracellular duplication. Based on virtual screening technology, we found 23 approved clinical drugs such as Carfilzomib, Saquinavir, Thymopentin and etc., which showed high affinity with the 3CLpro active sites. These findings suggest that 3CLpro inhibitors might be potential candidates for further activity detection and molecular modification.
ARTICLE | doi:10.20944/preprints202002.0438.v1
Subject: Chemistry, Medicinal Chemistry Keywords: COVID-19; Simeprevir; Protease inhibitor; Virtual screening; Docking
Online: 28 February 2020 (13:14:38 CET)
Coronavirus disease 2019 (COVID-19) has been first appeared in Wuhan, China but its fast transmission, led to its widespread prevalence in various countries and make it a global concern. In addition, lack of a definitive treatment is another concern that needs to be attention. Researchers have come up with several options, which are not certain, but protease inhibitor and some antiviral agent are in the forefront. In this study a virtual screening procedure employing docking of different databases including 1615 FDA approved drugs was used to identify new potential small molecule inhibitors for protease protein of COVID-19. The docking result indicates that among all, simeprevir (Hepatitis C virus (HCV) NS3/4A protease inhibitor) could fit well to the binding pocket of protease and because of some other positive features including ADME profile, might be a helpful treatment option for COVID-19.
Subject: Keywords: c-src-tyrosine kinase; QSAR; molecular descriptors; virtual screening; drug discovery; cancer; molecular docking
Online: 25 October 2019 (11:21:43 CEST)
Prototype of a family of at least nine members, c-src tyrosine kinase is a therapeutically interesting target, because its inhibition might be of interest not only in a number of malignancies, but also in a diverse array of conditions, from neurodegenerative pathologies to certain viral infections. Computational methods in drug discovery are considerably cheaper than conventional methods and offer opportunities of screening very large numbers of compounds in conditions that would be simply impossible within the wet lab experimental settings. We have explored the use of global QSAR models and molecular ligand docking in the discovery of new c-src tyrosine kinase inhibitors. Using a data set of 1038 compounds from ChEMBL and 19 blocks of molecular descriptors, we have developed over 200 QSAR classification models, based on six machine learning algorithms and 17 feature selection methods. We have selected 49 with reasonably good performance (positive predictive value and balanced accuracy higher than 70% in nested cross validation) and the models were assembled by stacking with a simple majority vote and used for the virtual screening of over the “named” ZINC data set (over 100,000 compounds). 744 compounds were predicted by at least 50% of the QSAR models as active, 147 compounds were within the applicability domain and predicted by at least 75% of the models to be active. The latter 147 compounds were submitted to molecular ligand docking using Vina and Ledock, and a number of 90 were predicted to be active based on the binding energy. External data from CHEMBL and PUBCHEM confirmed that at least 7.83% (in the case of QSAR) or 6.67% (in the case of integrated QSAR and molecular docking) of the compounds are active on the c-src target.
ARTICLE | doi:10.20944/preprints201811.0608.v1
Subject: Engineering, Biomedical & Chemical Engineering Keywords: spheroids; concentration gradient generator; drug screening; high-throughput
Online: 28 November 2018 (10:08:05 CET)
Three-dimensional (3D) cell culture is considered more clinically relevant in mimicking the structural and physiological conditions of tumors in vivo compared to two-dimensional cell cultures. In recent years, high-throughput screening (HTS) in 3D cell arrays has been extensively used for drug discovery because of its usability and applicability. Herein, we developed a microfluidic spheroid culture device (μFSCD) with a concentration gradient generator (CGG) that enabled cells to form spheroids and grow in the presence of cancer drug gradients. The device is composed of concave microwells with several serpentine micro-channels which generate a concentration gradient. Once the colon cancer cells (HCT116) formed a single spheroid (approximately 120 μm in diameter) in each microwell, spheroids were perfused in the presence of the cancer drug gradient irinotecan for 3 days. The number of spheroids, roundness, and cell viability, were inversely proportional to the drug concentration. These results suggest that the μFSCD with a CGG has the potential to become an HTS platform for screening the efficacy of cancer drugs.
ARTICLE | doi:10.20944/preprints202301.0200.v1
Subject: Medicine & Pharmacology, Other Keywords: QSPR model; antibacterials; Acinetobacter baumannii; natural products; virtual screening
Online: 11 January 2023 (11:51:38 CET)
As the rate of discovery of new antibacterial compounds towards multidrug resistant bacteria is declining, there is an urge for the search of molecules that could revert this tendency. Acinetobacter baumannii has emerged as a highly virulent Gram-negative bacterium that has acquired multiple mechanisms against antibiotics and is considered of critical priority. In this work we developed a quantitative structure-property relationship (QSPR) model with 592 compounds for the identification of structural parameters related to their property as antibacterial agents against A. baumannii. QSPR mathematical validation (R2 = 70.27, RN = -0.008, aR2 = 0.014 and δK = 0.021) and its prediction ability (Q2LMO= 67.89, Q2EXT = 67.75, a(Q2)= -0.068, δQ = 0.0, rm2 = 0.229, and ∆rm2 = 0.522) were obtained with different statistical parameters; additional validation jobs were done using three sets of external molecules (R2 = 72.89, 71.64 and 71.56). We used the QSPR model to perform a virtual screening on the BIOFACQUIM natural product database. From this screening our model showed that molecules 32 to 35 and 54 to 68, isolated from different extracts of plants of the Ipomoea sp., are potential antibacterial against A. baumannii. Furthermore, biological assays showed that molecules 56 and 60 to 64 have a wide antibacterial activity against clinical isolated strains of A. baumannii, as well as other multidrug resistant bacteria including Staphylococcus aureus, Escherichia coli, Klebsiella pneumonia, and Pseudomonas aeruginosa. Finally, we propose 60 as a potential lead compound due to its broad-spectrum activity and its structural simplicity. Therefore, our QSPR model can be used as a tool for the investigation and search of new antibacterial compounds against A. baumannii.
ARTICLE | doi:10.20944/preprints202211.0250.v1
Subject: Earth Sciences, Environmental Sciences Keywords: snow remote sensing; cloud screening; atmospheric correction; radiative transfer
Online: 14 November 2022 (09:38:42 CET)
We present the update of the Snow and Ice (SICE) property retrieval algorithm proposed initially by Kokhanovsky et al. (2019). The algorithm is based on the spectral measurements of Ocean and Land Color Instrument (OLCI) onboard Sentinel-3 satellites combined with the asymptotic radiative transfer theory valid for weakly absorbing turbid media. The main improvements include the introduction of a new atmospheric correction, retrieval of snow impurity load and properties, retrievals for partially snow-covered ground and also accounting for various thresholds to be used to assess the retrieval quality. The algorithm is available as python and Fortran packages at https://github.com/GEUS-SICE/pySICE. The technique can be applied to various optical sensors (satellite and ground-based) operated in the visible and near infrared regions of electromagnetic spectra.
ARTICLE | doi:10.20944/preprints202111.0455.v1
Subject: Medicine & Pharmacology, Dentistry Keywords: child anxiety disorders; screening; SCARED-C; psychometrics; dental practice
Online: 24 November 2021 (12:48:07 CET)
SCARED-C instrument (the child version, 41 items) is used for screening anxiety in children between 8 to 18 years old and has been first introduced by Birmaher & collab. in 1995, with good psychometric data - internal consistency from α =.74 to .93 - and good discriminative validity indices in the original versions (1997, 1999). Since then, many countries have adopted the scale, for its utility in identifying five subsets of anxiety disorders (subscales): somatic/panic disorder, generalized anxiety, separation anxiety, social phobia, and school avoidance. The present study contains the first Romanian translated and adapted version of the SCARED-C instrument on a community sample of 477 children (8-18 years old) from Mureș county schools. The instrument showed moderate to good internal consistency (α Cronbach from to .63 to .91 for the total scale) and good test-retest reliability (.70) on a subset of 85 children sample. A confirmatory factorial analysis (CFA) was conducted to test the factor structure of the Romanian version of SCARED-C; results showed that SCARED-C has good psychometric properties to be used for screening anxiety in Romanian children and adolescents. The implications for using SCARED-C in dental practice are discussed. Future studies need to be conducted for exploring convergent and discriminative validity of the instrument and the sensitivity to current DSM-V criteria. Application on a dental pediatric sample is also required.
REVIEW | doi:10.20944/preprints202110.0434.v1
Subject: Life Sciences, Other Keywords: Ovarian Cancer; Epidemiology; Risk Factors; Screening; Diagnosis, Mortality; Incidence
Online: 28 October 2021 (11:41:05 CEST)
Abstract – Objective: Ovarian cancer, although not possessing a high incidence, is still the most common cancer-related deaths among women diagnosed with a gynecologic malignancy. The present study aims to highlight the epidemiology, risk factors of this disease and the significance of development of improved early detection strategies. Materials and Methods: This study was conducted using current published English studies by searching PubMed and Google Scholar. The search strategy included the keywords “ovarian cancer”, “diagnosis”, “risk factors”, “screening”, “epidemiology”. Studies on incidence and mortality were also considered. Case reports were excluded.Results: The highest incidence and mortality rates are observed in Central and Eastern Europe, while rates are relatively low in Asia and Africa. These rates are highest among the white population (14.3 per 100,000) and lowest among blacks (10 per 100,000) and Asians (9.7 per 100,000). The risk factors for this disease includes a family history, hormonal factors, nutrition and diet and physical activity, with some of them playing protective roles in reducing risk of ovarian cancers. There are no reliable screening methods for ovarian cancers. The most common diagnosis methods include a transvaginal ultrasound and a blood test to detect CA125 markers.Conclusions: The mortality rate of ovarian cancer is gradually increasing; thus, preventative measures are required to reduce lifetime risk of ovarian cancers and improve mortality rate.
ARTICLE | doi:10.20944/preprints202108.0296.v1
Subject: Medicine & Pharmacology, Pharmacology & Toxicology Keywords: Ephedra alata; antioxidant activity; anti-inflammatory activity; phytochemical screening
Online: 13 August 2021 (09:23:00 CEST)
Ephedra alata Decne. (Ephedraceae) is a medicinal species commonly used to treat cancers, respiratory diseases, fever, and hypertension. The present study aimed to establish a phytochemical profile, evaluate the antioxidant potential and estimate the anti-inflammatory activities of .. Aqueous and methanolic extracts of E. alata aerial parts were phytochemically investigated using standard methods. DPPH, phosphomolybdenum total antioxidant capacity and reducing power assays were used to evaluate the antioxidant activity. Antioxidant activity was determined using total antioxidant capacity, the scavenging activity of the stable DPPH free radical and ferric reducing antioxidant power assays. The anti-inflammatory activity was determined using egg albumin membrane denaturation and human red blood cells membrane stabilizing assays. The anti-inflammatory potential of E. alata extracts was evaluated using human red blood cells membrane stabilization, egg albumin and BSA albumin denaturation assays. Quinones, anthraquinones, steroids, phytosteroids, phenols, terpenoids, flavonoids, saponins, glycosides, Cardiac glycosides, reducing sugars and anthocyanins were present in the E. alata’s aqueous extract, in addition to coumarins and proteins in the methanolic extract. The highest total phenolic and flavonoid content was recorded in the aqueous extract with 8.66 ±0.09 mg GA/g and 248.04 ±1.47 mg Q/g, respectively. On the other hand, E. alata methanolic extract had the highest tannin content of 62.12 ±0.10 mg C/g. The best radical scavenging activity (IC50 = 4.63±0.00 mg/ml) and total antioxidant capacity were exhibited by the E. alata aqueous (7.35±0.12 mg/ml AAE), whereas the methanolic extract possessed the highest reducing power activity (1.81±0.00 mg AAE/ml). Regarding the anti-inflammatory activities, E. alata methanolic extract exerted the highest HRBC stabilization of 34.72 ±0.08% whereas the aqueous extract exhibited the highest bovine serum and Egg albumin denaturation inhibition of 99.22 ±0.02% and 73.31 ±0.90, respectively. Taken together, our results suggest that E. alata aerial parts aqueous and methanolic extracts can be utilized as future antioxidants and anti-inflammatory ethnomedicines owing to their rich bioactive molecules content.
REVIEW | doi:10.20944/preprints202103.0448.v1
Subject: Medicine & Pharmacology, Oncology & Oncogenics Keywords: colorectal cancer screening; test; alternative; non-invasive; CRC; review
Online: 17 March 2021 (16:01:58 CET)
Colorectal cancer (CRC) is one of the leading cancer-related causes of death in the world. Since the 70s, many countries have adopted different CRC screening programs which has resulted in a decrease in mortality. However, current screening test options still present downsides. The commercialized stool-based tests present high false-positive rates and low sensitivity, which negatively affects the detection of early stage carcinogenesis. The gold standard colonoscopy has low uptake due to its invasiveness and the perception of discomfort and embarrassment that the procedure may bring.In this review, we collected and described the latest data about alternative CRC screening techniques that can overcome these disadvantages. Web of Science and PubMed were employed as search engines for studies reporting on CRC screening tests and future perspectives. The searches generated 555 articles, of which 93 titles were selected. Finally, a total of 50 studies, describing 14 different CRC alternative tests, were included. Among the investigated techniques the main feature that could have an impact on CRC screening perception and uptake was the ease of sample collection. Urine, exhaled breath and blood-based tests promise to achieve good diagnostic performance (sensitivity of 63-100%, 90-95%, 47-97%, respectively) while minimizing stress and discomfort for the patient.
ARTICLE | doi:10.20944/preprints202005.0197.v1
Subject: Medicine & Pharmacology, General Medical Research Keywords: COVID-19; SARS-CoV-2; Vietnam; Epidemiology; control; screening
Online: 11 May 2020 (13:02:32 CEST)
IntroductionThe aim of this study is to describe the epidemiology of all COVID-19 patients in Vietnam and to describe the measures of disease control and prevention implemented. MethodsData were recovered from Wikipedia regarding the 2020 coronavirus pandemic in Vietnam. The period covered was from 23 January to 20 April 2020. Descriptive analysis was stratified by gender, age, country of origin, travel history, clinical symptoms and outcome. A survey of disease control and prevention measures was conducted at the Centre for Disease Control in the Thai Binh province, which is responsible for screening and isolating individuals at high risk of COVID-19. ResultsAs of 20 April 2020, Vietnam had recorded 268 confirmed COVID-19 patients. 55.2% were female. 67.9% were aged 20-49 years and 82.5% were Vietnamese. 60.4% of cases were imported from outside Vietnam. Other cases were acquired in Vietnam by individuals in close contact with imported cases. Only one patient who had not travelled had had no known contact with a confirmed case. 63.1% of patients were asymptomatic. 75.7% of patients were discharged. No deaths were recorded. The Thai Binh CDC surveyed a total of 2,203 persons at risk of COVID-19. 336 persons (15.2%) were isolated at hospitals and 1,411 (64.0%) in dedicated isolation facilities. 16.4% reported at least one respiratory symptom. No positive cases confirmed by RT-PCR have been reported in the Thai Binh province to date. ConclusionThe effect of the systematic screening and isolation strategy made it possible to limit local transmission in Vietnam. Vietnam needs to reinforce diagnostic capacities, prevention measures and provide the necessary epidemiological data on which to base interventions. The wider use of rapid serological tests is also advisable in order to be able to conduct extensive screening in the community.
ARTICLE | doi:10.20944/preprints202002.0061.v1
Online: 5 February 2020 (10:59:09 CET)
A novel coronavirus called 2019-nCoV was recently found in Wuhan, Hubei Province of China, and now is spreading across China and other parts of the world. 2019-nCoV spreads more rapidly than SARS-CoV. Unfortunately, there is no drug to combat the virus. It is of high significance to develop a drug that can combat the virus effectively before the situation gets worse. It usually takes a much longer time to develop a drug using traditional methods. For 2019-nCoV, it is now better to rely on some alternative methods to develop drugs that can combat such a disease effectively since 2019-nCoV is highly homologous to SARS-CoV. In this paper, we first collected virus RNA sequences from the GISAID database, translated the RNA sequences into protein sequences, and built a protein 3D model using homology modeling. Coronavirus main protease is considered to be a major therapeutic target, thus this paper focused on drug screening based on the modeled 2019-nCov_main_protease structure. The deep learning based method DFCNN, developed by our group, can identify/rank the protein-ligand interactions with relatively high accuracy. DFCNN is capable of performing virtual screening quickly since no docking or molecular dynamic simulation is needed. DFCNN identifies potential drugs for 2019-nCoV protease by performing drug screening against 4 chemical compound databases. Also, we performed drug screening for all tripeptides against the binding site of 2019-nCov_main_protease since peptides often show better stability, more bio-availability and negligible immune responses. In the end, we provided the list of possible chemical ligands and peptide drugs for experimental validation.
ARTICLE | doi:10.20944/preprints201904.0015.v1
Subject: Medicine & Pharmacology, Clinical Neurology Keywords: dysphagia; FEES; Parkinson’s disease; swallowing speed; screening; water test
Online: 1 April 2019 (13:32:41 CEST)
There is still a lack of a clinical test to reliably identify patients with Parkinson’s disease (PD) being at risk for aspiration. In this prospective, controlled, cross-sectional study we assessed if swallowing speed for water is a useful clinical test to predict aspiration proven by flexible endoscopic evaluation of swallowing (FEES). Due to this we measured the swallowing speed for 90 ml water in 115 consecutive and unselected PD outpatients of all clinical stages and 32 healthy controls. Average swallowing speed was lower in patients compared with controls (6.5 ± 3.9 ml/s vs. 8.5 ± 3.2 ml/s; p < 0.01). The disease-independent widely used threshold of < 10 ml/s showed insufficient sensitivity of 88% and specificity of 19% with unacceptable false-positive rates of 63% for patients and 69% for controls. Receiver operating characteristic (ROC) analysis was carried out to define a suitable cut-off value for detection of aspiration of water (area under the curve 0.72, p < 0.001) in PD patients. The optimized cut-off value was 5.5 ml/s with a sensitivity of 69% and a specificity of 64%. Overall, measuring swallowing speed is prone to methodological errors and not suitable as a screening instrument to predict aspiration in PD patients.
REVIEW | doi:10.20944/preprints201709.0159.v1
Subject: Medicine & Pharmacology, Oncology & Oncogenics Keywords: Key wordsbrest cancer screening, mammography, breast ultrasound, breast MRI
Online: 29 September 2017 (15:00:08 CEST)
Abstract On the background of new research results in screening of breast cancer, together with the expectation of the participants in a screening for breast cancer, the conventional mammography requires supplementation by means of tomosynthesis or additive ultrasound. Alternatively, ultrasound now seems to be an independent method of early detection of breast cancer because of its superior sensitivity, especially in the case of aggressive mammary carcinoma types. The MRI remains at present still a preferred method in high-risk cases and as an additive examination in case of insufficient presentation of the glandular tissue by conventional methods. MRI is also preoperatively valuable for more accurately measuring the extent of multifocal carcinomas.
ARTICLE | doi:10.20944/preprints202301.0107.v1
Subject: Medicine & Pharmacology, Oncology & Oncogenics Keywords: cost analysis; early stage; health economics; lung cancer; screening programme.
Online: 5 January 2023 (11:30:30 CET)
BACKGROUND: The National Lung Screening Trial (ILST) and the NELSON study showed that lung cancer-specific mortality can be reduced by 20-24% using low-dose computed tomography (LDCT) screening in high-risk populations, due to an increase in early-stage diagnoses. RESEARCH QUESTION: How much lung cancer-related direct costs may be reduced using a LDCT screening programme based on the ILST protocol in a public healthcare system?STUDY DESIGN AND METHODS: Cost analysis of lung cancer screening (LCS) vs. usual care in the framework of the retail price of the Catalan public healthcare system. The LCS group included costs of screening (ILST protocol), treatment cost according to weighted average distribution of TNM staging in the NLST and NELSON trials, lung cancer detection rate (CDR) and smoking cessation intervention. The usual care group included treatment costs based on distribution of TNM staging registered in the Spanish index hospital. RESULTS: In the usual care group, treatment costs were €91,959. In the 5-year duration of the LCS programme, the average expected costs per subject were €1,342 (range €1,054-1,832 depending on malignancy in detected nodules) for screening and €32,431 for treatment, with an expected reduction of €952 based on an average CDR of 1.6%. The decrease in cost resulting from stage shift offsets 70.6% of the costs of the screening programme. INTERPRETATION: Baseline 5-year LCS costs are low according to the ILST protocol. In the Catalan public healthcare system, the expense reduction from the stage shift due to the LCS programme compensates a substantial part of its costs.
ARTICLE | doi:10.20944/preprints202212.0140.v1
Subject: Medicine & Pharmacology, Other Keywords: Drug screening; Borrelia afzelii; Borrelia garinii; Persister; Hypocrellin A; biofilm
Online: 8 December 2022 (02:24:04 CET)
Lyme disease (LD) is a tick-transmitted infection caused by Borrelia burgdorferi sensu lato species which includes B. burgdorferi, B. afzelii, and B. garinii. The majority of patients with early LD can be cured by standard treatment, yet some still suffer from post-treatment Lyme disease syndrome (PTLDS). The presence of Borrelia persisters has been proposed as a contributing factor, which cannnot be completely killed by the currently used antibiotics for Lyme disease. Finding new pharmaceuticals targeting Borrelia persisters is crucial in developing more effective treatment. Here, we first confirmed the existence of persisters in cultures of B. garinii and B. afzelii and then conducted high-throughput screening of a custom drug library against persister-rich stationary-phase cultures of B. garinii and B. afzelii. Among 2427 compounds screened, hypocrellin A (HA), anthracycline class of drugs, and topical antibiotics along with some other natural compounds were identified to have strong potential in killing persisters of B. garinii and B. afzelii. HA was the most active anti-Borrelia compound, capable of eradicating stationary-phase Borrelia persisters, in particular when combined with doxycycline and/or ceftriaxone. Liposoluble antioxidant vitamin E was found to antagonize the activity of HA, indicating HA’s target is the cell membrane where HA-triggered reactive oxygen species (ROS) generation took place in the presence of light. HA was found to have distinct bactericidal activity against Borrelia species but had poor or no activity against Gram-positive and Gram-negative bacteria. Identification of the above-mentioned drug candidates may help to develop more effective therapies for LD.
ARTICLE | doi:10.20944/preprints202210.0369.v1
Subject: Medicine & Pharmacology, Oncology & Oncogenics Keywords: Covid-19; health literacy; cancer screening; cancer care; cancer prevention
Online: 25 October 2022 (02:02:04 CEST)
The COVID-19 pandemic has led to numerous delays in cancer-related care and cancer-specific screening, but the extent is not fully understood. For those that experience a delay or disruption in care, health related self-management is required to re-engage in care pathways and the role of health literacy in this pathway has not been explored. The purpose of this analysis is to (1) report the frequency of self-reported delays in cancer treatment and preventative screening services at an academic, NCI-designated center during the COVID-19 pandemic and (2) investigate cancer-related care and screening delays among those with adequate and limited health literacy. A cross-sectional survey was administered from an NCI-designated Cancer Center with a rural catchment area during November 2020 through March 2021. Nearly 19 percent of participants were categorized as having limited health literacy. Twenty percent of those with a cancer diagnosis reported a delay in cancer-related care; and 23-30% of the sample reported a delay in cancer screening. In general, the proportions of delays among those with adequate and limited health literacy were similar with the exception of colorectal cacner screening. There was also a notable difference in the ability to re-engage in cervical cancer screening among those with adequate and limited health literacy. Thus, there is a role for those engaged in cancer-related education and outreach to offer additional navigation resources for those at risk to cancer-related care and screening disruptions. Future study is warranted to investigate the role of health literacy on cancer care engagement.
ARTICLE | doi:10.20944/preprints202209.0334.v1
Subject: Medicine & Pharmacology, Other Keywords: cervical cancer screening; barriers; recommendations; slum; low-resource settings; qualitative
Online: 22 September 2022 (07:31:38 CEST)
Background: Cervical cancer is the fourth most common cancer in women globally despite being a largely treatable and preventable malignancy. Developing countries account for over 80% of all new cases of cervical cancer. Women residing in low-resource settings such as those residing in slums have a higher risk of cervical cancer, and lower uptake of cervical cancer screening. Diverse barriers influence the uptake of cervical cancer screening among women in low-resource settings. Objectives: This qualitative study was carried out prior to a cervical cancer screening program and explored women’s knowledge about cervical cancer, and their perceived barriers and recommendations for the program.Method: Four focus group discussions (FGD) were conducted among 35 women between the ages of 21 – 65 years residing in two urban slums in Lagos, Nigeria. Each FGD was limited to 8-10 participants of women of similar ages. Voice recordings were transcribed verbatim and analysis was done using thematic analysis.Results: Most of the women were not aware of cervical cancer and none knew the symptoms or risk factors of cervical cancer. The participants felt that the cervical cancer screening program would be well accepted in the community, however, they expressed concerns about the cost of the screening test and the sex of the person performing the test. The recommendations proffered for a successful cervical cancer screening program include; reducing the cost of the test or providing the test free of charge, having people that speak the local language as part of the team, using female health care providers, using a private location within the community or nearby PHC, and publicizing the program with the use of SMS, phone calls, town crier, and health talks. It was recommended that organizing health education sessions would help improve women’s poorly perceived susceptibility to cervical cancer.Conclusion: Interventions to increase uptake of cervical cancer screening among women in low resource settings need to improve knowledge and understanding of cervical cancer and address the barriers to cervical cancer screening such as cost, distance, and as much as possible, sex of the healthcare provider should be considered.
ARTICLE | doi:10.20944/preprints202208.0132.v1
Subject: Life Sciences, Microbiology Keywords: civil science; antibiotic producers screening; actinomycetes; reporter systems; chartreusin; pikromycin
Online: 8 August 2022 (05:27:03 CEST)
Since streptomycin discovery, actinomycetes were the main source for new antibiotics, but after the Golden age (1950-1960th) the discovery rate significantly decreased. The high probability to rediscover well-known antibiotics led to a reduction in interest in soil bacteria as a source for new antibiotics. At the same time, actinomycetes remain a very promising reservoir for searching for new active molecules. In this work, we present several reporters containing eye-visible fluorescent protein genes, which can be used to increase the efficiency of determining the mechanism of antibiotics at the very initial stage of screening. Presented reporters and the following pipeline were optimized given the involvement of citizen scientists without specialized skills and equipment in order to utilize the reservoir of soil bacteria in the search for new antibiotic producers. The combination of mechanism-based approaches and civil science has proved its effectiveness in practice revealing a significant increase in the screening rate. Two new strains Streptomyces sp. KB-1 and BV113 were found to produce antibiotics pikromycin and chartreusin, respectively, demonstrating the efficiency of the pipeline.
ARTICLE | doi:10.20944/preprints202207.0133.v1
Subject: Medicine & Pharmacology, Clinical Neurology Keywords: otolith; vestibular; oVEMP; utricular; clinical audiovestibular testing; vestibular screening test
Online: 8 July 2022 (05:55:49 CEST)
We have previously reported that a single test measuring oVEMP n10 to 4000Hz stimuli (either bone-conducted vibration (BCV) or air-conducted sound (ACS)) provides a definitive diagnosis of semicircular canal dehiscence (SCD) in 22 CT-verified patients with a sensitivity of 1.0 and specificity of 1.0. Such a single short screening test has great advantages of speed, minimizing testing time and the exposure of patients to stimulation. However some studies of the 4000Hz test for SCD have reported sensitivity and sensitivity values somewhat less that what we reported.
ARTICLE | doi:10.20944/preprints202206.0186.v1
Subject: Medicine & Pharmacology, Oncology & Oncogenics Keywords: screening model; breast cancer; explainable model; machine learning; Asian women
Online: 13 June 2022 (11:06:10 CEST)
This study aimed to determine the feasibility of the development of an over-the-counter (OTC) screening model using machine learning for breast cancer screening in the Asian women population. Data were retrospectively collected from women who came to the Hospital Universiti Sains Malaysia, Malaysia. Five screening models were developed based on machine learning methods; random forest, artificial neural network (ANN), support vector machine (SVM), elastic-net logistic regression and extreme gradient boosting (XGBoost). Features used for the development of the screening models were limited to information from the patients’ registration form. The model performance was assessed across the dense and non-dense groups. SVM had the best sensitivity while elastic-net logistic regression had the best specificity. In terms of precision, both random forest elastic-net logistic regression had the best performance, while, in terms of PR-AUC, XGBoost had the best performance. Additionally, SVM had a more balanced performance in terms of sensitivity and specificity across the mammographic density groups. The three most important features were age at examination, weight and number of children. In conclusion, OTC models developed from machine learning methods can improve the prognostic process of breast cancer in Asian women.
ARTICLE | doi:10.20944/preprints202202.0107.v1
Subject: Medicine & Pharmacology, Pharmacology & Toxicology Keywords: Malaria; Resistance; Mutation; Virtual screening; Phytochemicals; Dihydrofolate Reductase –Tymidylate Synthase
Online: 8 February 2022 (12:06:36 CET)
Resistance to Pyrimethamine, an antimalarial medicine has been reported to be due to mutations in Dihydrofolate reductase-thymidylate synthase (DHFR-TS). Phytochemicals, particularly from plants that been used in ethnomedicine, have been reported to have privileged structures that might bind strongly to the mutants of DHFR-TS. The aim of this study is to identify phytochemicals of Acalypha wilkesiana, Cymbopogon citratus, Azadirachta indica, and Morinda lucida with high binding affinities for the Plasmodium falciparum DHFR-TS. The three-dimensional structures of the phytochemicals, wide type and mutant forms of DHTR-TS were obtained from PubChem and Protein Databank (PDB) respectively. They were appropriately prepared and molecular docking simulations was implemented to predict binding affinities of the phytochemicals to the wildtype and mutant forms of DHTR-TS. Druglikeness assessment was implemented to triage the top binding phytochemicals and molecular dynamics simulations was done to establish the stability of the interaction of the top-ranked phytochemical with one of the mutants of DHFR-TS. Nineteen phytochemicals showed higher binding affinities to both the wild type and mutant forms DHFR-TS than Pyrimethamine. Molecular dynamics revealed that the receptor-ligand binding of luteolin, the top-ranked, drug like phytochemicals, to the quadruple mutant was stable.
ARTICLE | doi:10.20944/preprints202201.0155.v1
Subject: Life Sciences, Cell & Developmental Biology Keywords: Phenotypic Screening; High Content Imaging; Chemogenomics; Machine Learning; Cell cycle
Online: 11 January 2022 (23:53:13 CET)
Phenotypical screening is a widely used approach in drug discovery for the identification of small molecules with cellular activities. However, functional annotation of identified hits often poses a challenge. The development of small molecules with narrow or exclusive target selectivity such as chemical probes and chemogenomic (CG) libraries, greatly diminishes this challenge, but non-specific effects caused by compound toxicity or interference with basic cellular functions still poses a problem to associate phenotypic readouts with molecular targets. Hence, each compound should ideally be comprehensively characterized regarding its effects on general cell functions. Here, we report an optimized live-cell multiplexed assay that classifies cells based on nuclear morphology, presenting an excellent indicator for cellular responses such as early apoptosis and necrosis. This basic readout in combination with the detection of other general cell damaging activities of small molecules such as changes in cytoskeletal morphology, cell cycle and mitochondrial health provides a comprehensive time-dependent characterization of the effect of small molecules on cellular health in a single experiment. The developed high-content assay offers multi-dimensional comprehensive characterization that can be used to delineate generic effects regarding cell functions and cell viability, allowing an assessment of compound suitability for subsequent detailed phenotypic and mechanistic studies.
ARTICLE | doi:10.20944/preprints202111.0329.v1
Subject: Chemistry, Medicinal Chemistry Keywords: Machine Learning; Deep Learning; Molecular Modeling; Virtual Screening; Drug Discovery
Online: 18 November 2021 (13:59:09 CET)
Virtual screening - predicting which compounds within a specified compound library bind to a target molecule, typically a protein - is a fundamental task in the field of drug discovery. Doing virtual screening well provides tangible practical benefits, including reduced drug development costs, faster time to therapeutic viability, and fewer unforeseen side effects. As with most applied computational tasks, the algorithms currently used to perform virtual screening feature inherent tradeoffs between speed and accuracy. Furthermore, even theoretically rigorous, computationally intensive methods may fail to account for important effects relevant to whether a given compound will ultimately be usable as a drug. Here we investigate the virtual screening performance of the recently released Gnina molecular docking software, which uses deep convolutional networks to score protein-ligand structures. We find, on average, that Gnina outperforms conventional empirical scoring. The default scoring in Gnina outperforms the empirical AutoDock Vina scoring function on 89 of the 117 targets of the DUD-E and LIT-PCBA virtual screening benchmarks with a median 1% early enrichment factor that is more than twice that of Vina. However, we also find that issues of bias linger in these sets, even when not used directly to train models, and this bias obfuscates to what extent machine learning models are achieving their performance through a sophisticated interpretation of molecular interactions versus fitting to non-informative simplistic property distributions.
ARTICLE | doi:10.20944/preprints202111.0249.v1
Subject: Medicine & Pharmacology, Obstetrics & Gynaecology Keywords: cervical cancer screening; HPV self-sampling; sub-Saharan Africa; preference
Online: 15 November 2021 (10:55:02 CET)
Human papillomavirus (HPV) self-sampling (Self-HPV) is a promising strategy to improve cervical cancer screening coverage in low-income countries. However, issues associated with women who prefer conventional HPV clinical-sampling over HPV self-sampling may affect screening participation. To address this issue, our study assessed factors associated with women’s preferences related to Self-HPV. This study was embedded in a large clinical trial recruiting women aged 30–49 years in a primary HPV-based study termed “3T-Approach” (for Test-Triage-Treatment), launched in 2018 at Dschang District Hospital, West Cameroon. Participants were invited to perform a Self-HPV. After the sampling and before receiving the results, participants completed a questionnaire about cervical cancer screening and their preferences and perceptions around Self-HPV. The median age of the 2201 participants was 40.6 (IQR 35–45) years. Most (1693 (76.9%)) preferred HPV self-sampling or had no preference for either method and 508 (23.1%) preferred clinician-sampling. Factors associated with an increased likelihood of reporting a clinician-sampling preference were tertiary educational level (14.4% CI: 12.8–16.1 vs 29.5% CI: 25.6–33.6) and being an employee with higher grade professional or managerial occupations (5.5% CI: 3.8–7.9 vs 2.6% CI: 2.3–2.8). The main reported reason for women preferring clinician-sampling was a lack of “self-expertise”. Most women (>99%) would agree to repeat HPV self-sampling and would recommend it to their relatives. HPV self-sampling in the cultural context of central Africa was well accepted by participants, but some participants would prefer to undergo clinician sampling. Health systems should support well-educated women to increase self-confidence in using HPV self-sampling.
REVIEW | doi:10.20944/preprints202110.0307.v1
Subject: Medicine & Pharmacology, Oncology & Oncogenics Keywords: SARS-Cov-2; COVID-19; oncology; cancer screening; clinical trials
Online: 21 October 2021 (12:45:12 CEST)
The coronavirus disease 2019 (COVID-19) pandemic has caused considerable global disruption to clinical practice. This article will review the impact that the pandemic has had on oncology clinical trials. It will assess the effect of the COVID-19 situation on the initial presentation and investigation of patients with suspected cancer. It will also discuss the impact of the pandemic on the subsequent management of cancer patients and how clinical trial approval, recruitment and conduct were affected during the pandemic. An intriguing aspect of the pandemic is that clinical trials investigating treatments for COVID-19 and vaccinations against the causative virus, SARS-CoV-2, have been approved and conducted at unprecedented speed. In light of this, this re-view will also discuss the potential that this enhanced regulatory environment could have on the running of oncology clinical trials in the future.
ARTICLE | doi:10.20944/preprints202107.0270.v1
Subject: Chemistry, Analytical Chemistry Keywords: drug design; falcipain; malaria; peptidomimetics; Plasmodium falciparum; virtual screening; pharmacophore.
Online: 12 July 2021 (14:48:13 CEST)
In this work antiparasitic peptidomimetics inhibitors (PEP) of falcipain-3 (FP3) of Plasmodium falciparum (Pf) have been proposed using structure-based and computer-aided molecular design. Beginning with the crystal structure of PfFP3-K11017 complex (PDB ID: 3BWK), three-dimensional (3D) models of FP3-PEPx complexes with known activities (IC50exp) were prepared by in situ modification, based on molecular mechanics and implicit solvation to compute Gibbs free energies (GFE) of inhibitor-FP3 complex formation. This resulted in a quantitative structure-activity relationships (QSAR) model based on a linear correlation between computed GFE (ΔΔGcomp) and the experimentally measured IC50exp: (pIC50exp=-(IC50exp/109) =-0.4517×∆∆Gcomp+4.0865 ; R2 = 0.89). Apart from the structure-based relationship, a ligand-based quantitative pharmacophore model (PH4) of novel PEP analogs where substitutions were directed by comparative analysis of the active site interactions was derived using the proposed bound conformations of the PEPx. This provided structural information useful for the design of virtual combinatorial libraries (VL), which was virtually screened based on the 3D-QSAR PH4. The end results were predictory inhibitory activities falling within the low nanomolar concentration range.
REVIEW | doi:10.20944/preprints202106.0285.v1
Subject: Medicine & Pharmacology, Allergology Keywords: QF-PCR; cytogenetics; prenatal diagnosis; aneuploidy; chromosome abnormalities; screening test
Online: 10 June 2021 (09:17:57 CEST)
Early identification of fetal abnormalities is a huge challenge for modern obstetrics. Quantitative fluorescent polymerase chain reaction (QF-PCR) has quickly become an effective means of chromosome anomaly detection due to its advantages in terms of timing, manpower and accuracy. The QF-PCR results also make a significant change in clinicians’ attitude to some extent, assisting them providing parents with professional and valuable advice on pregnancy management. In this review, the advantages and drawbacks of QF-PCR will be explored. By reviewing studies published in Vietnamese Medical Journals, we conclude QF-PCR can become a potential screening test in the field of prenatal diagnosis.
ARTICLE | doi:10.20944/preprints202012.0444.v1
Subject: Biology, Anatomy & Morphology Keywords: novel rumen yeast; screening; isolation; biomass of yeast; cellulase enzyme
Online: 18 December 2020 (07:26:28 CET)
We hypothesized that rumen fluid with yeast producing cellulase enzyme can occur and also produces a high biomass compared to S. cerevisiae. Therefore, the aim of this study was to screen and isolate yeast from rumen fluids with an experimental design method. We optimized a fermentation medium containing sugarcane molasses as a carbon source and urea as a nitrogen source to measure the efficiency of biomass production and cellulase activity. Two fistulated-crossbred Holstein Friesian steers, averaging 350 ± 20 kg body weight, were used to screen and isolate ruminal yeast. The two experiments were designed. A 12 × 3 × 3 factorial was used in a completely randomized design to determine biomass and carboxymethyl cellulase activity. Factor A was isolated yeasts and S. cerevisiae. Factor B was sugarcane molasses (M) concentration. Factor C was urea (U) concentration. Potential yeast was selected for identified and analyzed as a 4 × 3 factorial use in a completely randomized design including. Factor A was incubation times. Factor B was isolated yeast strains including code H-KKU20 (as P. kudriavzevii-KKU20), I-KKU20 (C. tropicalis-KKU20), and C-KKU20 (as Galactomyces sp.-KKU20). Isolation was under aerobic conditions, resulting in a total of 11 different colonies. We noted two appearances of colonies including, asymmetric colonies of isolated yeast (indicated as A, B, C, E, and J) and ovoid colonies (coded as D, F, G, H, I, and K). The highest biomass was observed in three yeasts including codes H, I, and C-KKU20 when inoculated in 25% molasses with 1% urea (M25+U1) (p <0.01). The highest CMCase activity was observed in yeast code H-KKU20 when inoculated in all media solutions (p <0.01). Ruminal yeasts strains H-KKU20, I-KKU20, and C-KKU20 were selected for their ability to produce biomass and their CMCase enzyme synthesis. Identification of isolates H-KKU20 and I-KKU20 revealed that those isolates belonged to Pichia kudriavzevii-KKU20 and Candida tropicalis-KKU20, while C-KKU20 was identified as Galactomyces sp.-KKU20. Two strains provided maximum cell growth: P. kudriavzevii-KKU20 (9.78 and 10.02 Log cell/ml) and C. tropicalis-KKU20 (9.53 and 9.6 Log cells/ml) at 60 and 72 h of incubation time, respectively. The highest ethanol production was observed in S. cerevisiae: 76.4, 77.8, 78.5, and 78.6 g/L at 36, 48, 60, and 72 h of incubation time, respectively (p <0.01). The P. kudriavzevii-KKU20 yielded the least reducing sugar about 30.6 and 29.8 g/L at 60 and 72 h of incubation time, respectively. It could be concluded that screening and isolating yeast from rumen fluids resulted in 11 different characteristics of yeasts. The first novel yeasts discovered in the rumen fluid of cattle were Pichia kudriavzevii-KKU20, Candida tropicalis-KKU20, and Galactomyces sp.- KKU20. P. kudriavzevii-KKU20 had higher results than the other yeasts in terms of biomass production, cellulase enzyme activity, and cell number.
ARTICLE | doi:10.20944/preprints202004.0003.v2
Subject: Biology, Other Keywords: SARS-CoV-2; protease; virtual screening; pharmacophore; inhibitors; natural compounds
Online: 17 April 2020 (11:00:55 CEST)
Background: SARS-CoV-2 that are the causal agent of a current pandemic are enveloped, positive-sense, single-stranded RNA viruses of the Coronaviridae family. Proteases of SARS-CoV-2 are necessary for viral replication, structural assembly and pathogenicity. The ~33.8KDa Mpro protease of SARS-CoV-2 is a non-human homologue and highly conserved among several coronaviruses indicating Mpro could be a potential drug target for Coronaviruses.Methods: Here we performed computational ligand screening of four pharmacophores (OEW, Remdesivir, Hydroxycholoquine and N3) that are presumed to have positive effects against SARS-CoV-2 Mpro protease (6LU7) and also screened 50,000 molecules from the ZINC Database dataset against this protease target.Results: We found 40 pharmacophore-like structures of natural compounds from diverse chemical classes that exhibited better affinity of docking as compared to the known ligands. The 10 best selected ligands namely, ZINC1845382, ZINC1875405, ZINC2092396, ZINC2104424, ZINC44018332, ZINC2101723, ZINC2094526, ZINC2094304, ZINC2104482, ZINC3984030, and ZINC1531664, are mainly classified as β-carboline, Alkaloids and Polyflavonoids, and all of them displayed interactions with dyad CYS145 and HIS41 from the protease pocket in a similar way as with other known ligands.Conclusion: Our results suggest that these 10 molecules could be effective against SARS-CoV-2 protease and may be tested in vitro and in vivo to develop novel drugs against this virus.
ARTICLE | doi:10.20944/preprints201910.0074.v1
Subject: Medicine & Pharmacology, Other Keywords: Pseudomonas aeruginosa; Quorum sensing; Virtual screening; E-pharmacophore; Drug discovery.
Online: 7 October 2019 (12:33:33 CEST)
Pseudomonas aeruginosa is an emerging opportunistic pathogen responsible for cystic fibrosis and nosocomial infections. In addition, empirical treatments are become inefficient due to their multiple-antibiotic resistance and extensive colonizing ability. Quorum sensing (QS) plays a vital role in the regulation of virulence factors in P. aeruginosa. Attenuation of virulence by QS inhibition could be an alternative and effective approach to control infections. Therefore, we sought to discover new QS inhibitors (QSIs) against LasR receptor in P. aeruginosa using chemoinformatics. Initially, a structure-based high-throughput virtual screening was performed using the LasR active site that identified 61404 relevant molecules. E-pharmacophore (ADAHH) screening of these molecules rendered 72 QSI candidates. In standard-precision docking, only 7 compounds were found as potential QSIs due to their higher binding affinity to LasR receptor (-7.53 to -10.32 kcal/mol compared to -7.43 kcal/mol of native ligands). The ADMET properties of these compounds were suitable to be QSIs. Later, extra-precision docking and binding energy calculation suggested ZINC19765885 and ZINC72387263 as the most promising QSIs. The dynamic simulation of the docked complexes showed good binding stability and molecular interactions. The current study suggested that these two compounds could be used in P. aeruginosa QS inhibition to combat bacterial infections.
REVIEW | doi:10.20944/preprints201810.0360.v1
Subject: Chemistry, Medicinal Chemistry Keywords: Molecular Dynamics, CoSolvent Molecular Dynamics, Drug design, Fragment Screening, Docking
Online: 16 October 2018 (12:15:17 CEST)
Molecular dynamics(MD) simulations are playing an increasingly important role in structure-based drug discovery (SBDD). Here we review the use of MD for proteins in aqueous solvation, organic/aqueous mixed solvents (MDmix) and with small ligands, to the classic SBDD problems: binding mode and binding free energy predictions. The simulation of proteins in their condensed state reveals the solvent structure and preferential interaction sites (hot spots) on the protein surface. This information is largely transferable across all classes of protein ligands (from water to drugs) and can be used very effectively to understand ligand recognition and improve the predictive capability of well-established methods such as molecular docking. MD simulations for protein and drug or drug-like compounds are now being used but are still computationally expensive and can only be applied to specific cases. On the other hand, MDmix simulations can now be used in SBDD and we will describe the latest developments and implementations. We expect to see an increase in the application of these techniques to a plethora of protein targets to identify new drug candidates with the advent of new tools and faster computers.
ARTICLE | doi:10.20944/preprints201805.0061.v1
Subject: Medicine & Pharmacology, Sport Sciences & Therapy Keywords: combined elevation test; musculoskeletal screening test; normative data; swimming; adolescent
Online: 3 May 2018 (09:05:21 CEST)
The Combined Elevation Test (CET) is a musculoskeletal screening technique (MST) replicates the streamline position in swimming and is commonly used in various sports. Although the CET is widely used, no normative data exist within an adolescent population. Therefore, the purpose of this study was to develop a normative data set for the CET within an adolescent population and to evaluate the influence various demographic and anthropometric variables. Data was collected for 416 participants aged between 8 and 18 years old. Age and arm span showed a significant correlation with CET scores (arm span rs (105) = .478, p = .000, age rs (416) = .238 p = .000). Regression analysis further quantified the influence of arm span and age on CET scores accounting for 23.1% and 5.3% of variability respectively. These results can be used as a reference point for clinicians and coaches who are using the CET within their assessment.
ARTICLE | doi:10.20944/preprints201702.0025.v1
Subject: Medicine & Pharmacology, Pediatrics Keywords: congenital hypothyroidism; incidence; neonatal screening; thyroid-stimulating hormone; cutoff level
Online: 8 February 2017 (10:54:10 CET)
Lower cutoff levels in screening programs have led to an increase in the proportion of detected cases with transient hypothyroidism, leading to increase of the overall incidence of primary congenital hypothyroidism (CH) in several countries. We have performed retrospective evaluation on the data from 251,008 (96.72%) neonates screened for thyroid-stimulating hormone (TSH) level in dried blood spot specimens taken 48 hours after birth, between 2002 and 2015, using DELFIA method. A TSH value of 15 mIU/L was used as the cutoff point until 2010 and 10 mIU/L thereafter. Primary CH was detected in 127 newborns (1/1976) of which 81.1% had permanent and 18.9% had transient CH. The incidence of primary CH was increased from 1/2489 until to 2010 to 1/1585 thereafter (p=0.131). However, the incidence of permanent CH was slightly increased (p=0.922), while the transient CH incidence had 8-fold increasing after lowering the TSH cutoff level (p<0.001). In cases with permanent CH, we observed lower frequency for thyroid dysgenesis (82.7 vs. 66.7%) and higher frequency for normal in-situ thyroid gland (17.3 vs. 33.3%), for the period with reduced TSH cutoff value. Our findings support the impact of lower TSH cutoff on the increasing incidence of congenital hypothyroidism.
REVIEW | doi:10.20944/preprints202206.0333.v1
Subject: Medicine & Pharmacology, Other Keywords: hPSCs derived-organoids; Culture strategy; Disease modeling; Drug screening; Regenerative therapy
Online: 24 June 2022 (08:11:15 CEST)
Human pluripotent stem cells (hPSCs) have become a powerful tool to generate various kinds of cell types comprising the human body. Recently, organoid technology emerged as a platform to build a physiologically relevant tissue-like structure from the PSCs, which provides a more relevant three-dimensional microenvironment to the actual human body than the conventional monolayer culture system for transplantation, disease modeling, and drug development. Although it holds so many advantages, the organoid culture system still has various problems related to culture methods, which became a challenge to get similar physiological properties to their original tissue counterparts. Here, we discuss the current development of organoid culture methods, including the problem that may arise from the currently available culture systems as well as the possible approach to overcoming the current limitation and improving their optimum utilization for translational application purposes.
ARTICLE | doi:10.20944/preprints202205.0247.v1
Subject: Life Sciences, Virology Keywords: COVID-19; SARS-CoV-2; Variants of Concern; Rapid screening; Mutations
Online: 19 May 2022 (03:31:36 CEST)
Some of the lineages of SARS-CoV-2, the new coronavirus responsible for COVID-19, exhibit higher transmissibility or partial resistance to antibody mediated neutralization and were des-ignated by WHO as Variants of Interests (VOIs) or Concern (VOCs). The aim of this study was to monitor the dissemination of VOIs and VOCs in Venezuela during a year. A 614 nt genomic fragment was sequenced for the detection of some relevant mutations of these variants. Their presence was confirmed by complete genome sequencing, with a correlation higher than 99% between both methodologies. After the previously reported introduction of the Gamma VOC since the beginning of the year 2021, the variants Alpha VOC and Lambda VOI were detected as early as March 2021, at a very low frequency. In contrast, the Mu VOI, detected in May 2021, was able to circulate throughout the country. After the detection of Delta VOC in June 2021, it be-came the predominant circulating variant. With the arrival of the Omicron VOC in December, this variant was able to displace the Delta one in less than one month. This succession of variants was accompanied by a reduction in the Cycle threshold (Ct) values, in agreement with the in-crease in transmissibility described for these variants.
REVIEW | doi:10.20944/preprints202205.0189.v1
Subject: Medicine & Pharmacology, Pathology & Pathobiology Keywords: Raman Spectroscopy; Medical application; Disease screening and diagnosis; Machine learning analyses
Online: 13 May 2022 (10:17:00 CEST)
Raman Spectroscopy has long been anticipated to augment clinical decision making, such as classifying oncological samples. Unfortunately, the complexity of Raman data has thus far inhibited its routine use in clinical settings. Traditional machine learning models have been used to help exploit this information, but recent advances in deep learning have the potential to improve the field. However, there are a number of potential pitfalls with both traditional and deep learning models. We conduct a literature review to ascertain the recent machine learning methods used to classify cancers using Raman spectral data. We find that while deep learning models are popular, and ostensibly outperform traditional learning models, there are many methodological considerations which may be leading to an over-estimation of performance: primarily, small sample sizes which compound upon sub-optimal choices regarding sampling and validation strategies. Amongst several recommendations is a call to collate large benchmark Raman datasets, similar to those that have helped transform digital pathology, which researchers can use to develop and refine deep learning models.
ARTICLE | doi:10.20944/preprints202201.0422.v1
Subject: Behavioral Sciences, General Psychology Keywords: Perinatal Mental Health; Anxiety Disorders; Perinatal Anxiety; Fear of Childbirth; Screening
Online: 27 January 2022 (13:21:05 CET)
Background: Perinatal anxiety and related disorders are common (20%), distressing and impairing. Fear of childbirth (FoB) is a common type of perinatal anxiety associated with negative mental health, obstetrical, childbirth and child outcomes. Screening can facilitate treatment access for those most in need. Objectives: The purpose of this research was to evaluate the accuracy of the Childbirth Fear Questionnaire (CFQ) and the Wijma Delivery Expectations Questionnaire (W-DEQ) of FoB as screening tools for specific phobia, FoB. Methods: A total of 659 English-speaking pregnant women living in Canada and over the age of 18 were recruited to the study. Participants completed an online survey of demographic, current pregnancy, and reproductive history information, as well as the CFQ and the W-DEQ, and a telephone interview to assess specific phobia FoB. Results: Symptoms meeting full and subclinical diagnostic criteria for specific phobia, FoB were reported by 3.3% and 7.1% of participants, respectively. The W-DEQ met or exceeded the criteria for a “good enough” screening tool across several analyses, whereas the CFQ only met these criteria in one analysis, and came close in three others. Conclusions: The W-DEQ demonstrated high performance as a screening tool for specific phobia, FoB, with accuracy superior to that of the CFQ. Additional research, to ensure the stability of these findings, is needed.
ARTICLE | doi:10.20944/preprints202105.0308.v1
Subject: Biology, Anatomy & Morphology Keywords: Indonesia; biodiversity; novel antibiotics; drug screening; bioactivity; gene cluster networking; GNPS
Online: 13 May 2021 (14:05:00 CEST)
Indonesia is one of the most biodiverse countries in the world and a promising resource for novel natural compound producers. Actinomycetes produce about two-thirds of all clinically used antibiotics. Thus, exploiting Indonesia’s microbial diversity for actinomycetes may lead to the discovery of novel antibiotics. A total of 422 actinomycete strains were isolated from three different unique areas in Indonesia and tested for their antimicrobial activity. Nine potent bioactive strains were prioritized for further drug screening approaches. The nine strains were cultivated in different solid and liquid media and a combination of genome mining analysis and mass spectrometry (MS)-based molecular networking was employed to identify potential novel compounds. By correlating secondary metabolite gene cluster data with MS-based molecular networking results, we identified several gene cluster-encoded biosynthetic products from the nine strains, including naphthyridinomycin, amicetin, echinomycin, tirandamycin, antimycin, and desferrioxamine B. Besides, eight putative ion clusters and numerous gene clusters were detected that could not be associated with any known compound, indicating that the strains can produce novel secondary metabolites. Our results demonstrate that sampling of actinomycetes from unique and biodiversity-rich habitats, such as Indonesia, along with a combination of gene cluster networking and molecular networking approaches, accelerates natural product identification.
ARTICLE | doi:10.20944/preprints202009.0019.v2
Subject: Life Sciences, Biochemistry Keywords: mass spectrometry; OSMAC approach; natural products; silent BGC activation; bioinformatics; screening
Online: 23 December 2020 (11:19:38 CET)
Over the past decade, the One Strain Many Compounds (OSMAC) approach has been established for silent gene cluster activation and elicitation of secondary metabolite production, but so far the full secondary metabolome of a biosynthetically promising bacterium has not been elucidated yet. Here, we investigate the ability of seven categories of OSMAC conditions to enhance the diversity of new mass features from bacterial strains with little literature coverage but high biosynthetic potential. The strains Bacillus. amyloliquefaciens DSM7, Corallococcus. coralloides DSM2259, Pyxidicoccus. fallax HKI727, Rhodococcus. jostii DSM44719, and Streptomyces. griseochromogenes DSM40499 were selected after genome mining with antiSMASH. After cultivation under OSMAC conditions, the generated extracts were subjected to LC-MS and MZmine analysis to determine new mass features and evaluate the tested culture conditions. 4 predicted compounds, bacillibactin, desferrioxamine B, myxochelin A, and surfactin, were identified and up to 147 new mass features were detected in the generated extracts, which greatly surpasses the number of predicted gene clusters. Among the new mass features are bioactive compounds that were so far unreported for the strains such as cyclo-(Tyr-Pro) from DSM7 and nocardamin from DSM2259. Furthermore, the tested culture conditions were evaluated regarding their suitability for the generation of new mass features from the selected strains and promising new starting points for further screenings are postulated. Especially culture conditions with little prior literature coverage are responsible for the activation of predicted gene clusters
ARTICLE | doi:10.20944/preprints202011.0560.v1
Subject: Biology, Anatomy & Morphology Keywords: HCMV; protein-protein interactions; small molecules; ppUL44; PAP; pUL54; antivirals; screening
Online: 23 November 2020 (08:29:23 CET)
Human cytomegalovirus (HCMV) is a leading cause of severe diseases in immunocompromised individuals, including AIDS and transplanted patients, and in congenitally infected newborns. The utility of available drugs is limited by poor bioavailability, toxicity, and emergence of resistant strains. Therefore, it is crucial to identify new targets of therapeutic intervention. Among the latter, viral protein-protein interactions are becoming increasingly attractive. Since dimerization of HCMV DNA polymerase processivity factor ppUL44 plays an essential role in the viral life cycle being required for oriLyt-dependent DNA replication, we performed an in silico screening and selected 18 small molecules (SMs) potentially interfering with ppUL44 homodimerization. Antiviral assays using recombinant HCMV TB40-UL83-YFP in the presence of the selected SMs led to the identification of four active compounds. The most active one, B3, also efficiently inhibited AD169 in plaque reduction assays and impaired replication of an AD169-GFP reporter virus and its ganciclovir-resistant counterpart to a similar extent. As assessed by Western blotting experiments, treatment of infected cells with B3 specifically reduced viral gene expression starting from 48 h post infection, consistent with activity on viral DNA synthesis. Therefore, inhibition of ppUL44 dimerization could represent a new class of HCMV inhibitors, complementary to those targeting the DNA polymerase catalytic subunit or the viral terminase complex.
ARTICLE | doi:10.20944/preprints202010.0463.v1
Subject: Social Sciences, Accounting Keywords: Geographic Information Systems; Women’s Health; Cancer Screening; Breast Cancer; Health Programs
Online: 22 October 2020 (12:36:12 CEST)
The National Breast and Cervical Cancer Early Detection Program (NBCCEDP) of Minnesota, “Sage”, provides breast cancer screening to uninsured women. We introduce a novel mapping technique, spatially adaptive filters (SAFs), to estimate utilization of Sage screening in Minnesota. Sage screenings (N = 74,712) were geocoded. The eligible population was modeled with the RTI synthetic population dataset. Between 2011 and 2015, 36,979 women a year were Sage eligible. Utilization was highly variable across Minnesota (M = 37.2%, range 0% - 131%, SD = 18.7%). This replicable approach modeled utilization rates to the neighborhood-level, allowing Sage to prioritize locations and engage communities.
ARTICLE | doi:10.20944/preprints202007.0558.v2
Subject: Chemistry, Medicinal Chemistry Keywords: COVID-19; protein protein interactions; virtual screening; docking; molecular dynamics; zinc
Online: 2 September 2020 (09:48:48 CEST)
The outbreak of COVID-19, the disease caused by SARS-CoV-2, continues to affect millions of people around the world. The absence of a globally distributed effective treatment makes the exploration of new mechanisms of action a key step to address this situation. Stabilization of non-native Protein-Protein Interactions (PPIs) of the nucleocapsid protein of MERS-CoV has been reported as a valid strategy to inhibit viral replication. In this study, the applicability of this unexplored mechanism of action against SARS-CoV-2 is analyzed. During our research, we were able to find three inducible interfaces of SARS-CoV-2 N protein NTD, compare them to the previously reported MERS-CoV stabilized dimers, and identify those residues that are responsible for their formation. A drug discovery protocol implemented consisting of docking, molecular dynamics and MM-GBSA enabled us to find several compounds that might be able to exploit this mechanism of action. In addition, a common catechin skeleton was found among many of these molecules, which might be useful for further drug design. We consider that our findings could motivate future research in the fields of drug discovery and design towards the exploitation of this previously unexplored mechanism of action against COVID-19.
ARTICLE | doi:10.20944/preprints202008.0713.v1
Subject: Chemistry, Food Chemistry Keywords: NMR; alcoholic beverages; ethanol; methanol; acetaldehyde; screening; validation; food control; PULCON
Online: 31 August 2020 (06:21:35 CEST)
Due to legal regulations, the rise of globalised (online) commerce and the need for public health protection, the analysis of spirits (alcoholic beverages > 15 % vol) is a task with growing importance for governmental and commercial laboratories. In this article a newly developed method using nuclear magnetic resonance (NMR) spectroscopy for the simultaneous determination of 15 substances relevant for the quality and authenticity assessment of spirits is described. The new method starts with a simple and rapid sample preparation and does not need an internal standard. For each sample a group of 1H-NMR spectra is recorded, among them a 2D spectrum for analyte identification and 1D spectra with suppression of solvent signals for quantification. Using the Pulse Length Based Concentration Determination (PULCON) method, concentrations are calculated from curve fits of the characteristic signals for each analyte. The optimisation of the spectra, their evaluation and the transfer of the results are done fully automatically. Glucose, fructose, sucrose, acetic acid, citric acid, formic acid, ethyl acetate, ethyl lactate, acetaldehyde, ethanol, methanol, n-propanol, isobutanol, isopentanol, 2-phenylethanol and 5-(hydroxymethyl)furfural (HMF) can be quantified with an overall accuracy better than 8 %. This new NMR-based targeted quantification method enables the simultaneous and efficient quantification of relevant spirits ingredients in their typical concentration ranges in one process with good accuracy. It has proven to be a reliable method for all kinds of spirits in routine food control.
ARTICLE | doi:10.20944/preprints202008.0423.v1
Subject: Biology, Agricultural Sciences & Agronomy Keywords: gene editing; mutagenesis; genetically modified; GMO; crop breeding; RNP; genetic screening
Online: 20 August 2020 (04:34:55 CEST)
CRISPR-Cas9 technology allows the modification of DNA sequences in vivo at the location of interest. Although CRISPR-Cas9 can produce genomic changes that do not require DNA vector carriers, the use of transgenesis for stable integration of DNA coding for gene-editing tools into plant genomes is still the most used approach and it can generate unintended transgenic integrations, while Cas9 prolonged expression can increase cleavage at off-target sites. In addition, the selection of genetically modified cells from millions of treated cells, especially plant cells, is still challenging. These downfalls can be avoided with the delivery of preassembled ribonucleoprotein complexes (RNPs) composed of purified recombinant enzyme Cas9 and in vitro- transcribed guide RNA (gRNA) molecules in a protoplast system. We therefore aimed to develop the first DNA-free protocol for gene-editing in maize and introduced RNPs into their protoplasts with PEG 4000. We performed effective transformation of maize protoplasts using different gRNAs sequences targeting the inositol phosphate kinase gene and applying two different exposure times to RNPs. Using low-cost Sanger sequencing protocol, we observed an efficiency rate of 0.85 up to 5.85%, which is equivalent to DNA-free protocols used in other plant species. A positive correlation was displayed between exposure time and mutation frequency. Mutation frequency was gRNA sequence- and exposure time-dependent. In summary, we demonstrated the suitability of RNP transfection as an effective screening platform for gene-editing in maize. This efficient and relatively easy assay method for selection of gRNA suitable for editing of gene of interest will be highly useful for genome editing in maize, since genome size and GC-content are large and high in maize genome, respectively. Nevertheless, the large amplitude of mutations at target site requires scrutiny when checking mutations at off-target sites and potential safety concerns.
REVIEW | doi:10.20944/preprints202008.0382.v1
Subject: Medicine & Pharmacology, Nutrition Keywords: nutritional screening; nutritional risk; nutritional assessment; malnutrition; elderly; COVID-19; coronavirus
Online: 18 August 2020 (11:03:10 CEST)
Coronavirus disease 2019 (COVID-19) is associated with high risk of malnutrition, primarily in elderly people; assessing nutritional risk using appropriate screening tools is critical. This systematic review identified applicable tools and assessed their measurement properties. Literature was searched in the MEDLINE, Embase, and LILACS databases. Four studies conducted in China met the eligibility criteria. Sample sizes ranged from six to 182, and participants’ ages from 65 to 87 years. Seven nutritional screening and assessment tools were used: the Nutritional Risk Screening 2002 (NRS-2002), Mini Nutritional Assessment (MNA), MNA-short form (MNA-sf), Malnutrition Universal Screening Tool (MUST), Nutritional Risk Index (NRI), Geriatric NRI (GNRI), and modified Nutrition Risk in the Critically ill (mNUTRIC) score. Nutritional risk was identified in 27.5% to 100% of participants. The NRS-2002, MNA, MNA-sf, NRI, and MUST demonstrated high sensitivity; the MUST had better specificity. The MNA and MUST demonstrated better criterion validity. The MNA-sf demonstrated better predictive validity for poor appetite and weight loss; the NRS-2002 demonstrated better predictive validity for prolonged hospitalization. mNUTRIC score demonstrated good predictive validity for hospital mortality. Most instruments demonstrate high sensitivity for identifying nutritional risk, but none are acknowledged as the best for nutritional screening in elderly COVID-19 patients.
ARTICLE | doi:10.20944/preprints202007.0495.v1
Subject: Chemistry, Medicinal Chemistry Keywords: In silico target prediction; dihydrochalcones; SEA; SwissTargetPrediction; SuperPred; polyphamracology; virtual screening
Online: 21 July 2020 (13:43:40 CEST)
Natural products comprise a rich reservoir for innovative drug leads and are a constant source of bioactive compounds. To find pharmacological targets for new or already known natural products using modern computer-aided methods is a current endeavor in drug discovery. Nature’s treasures, however, could be used more effectively. Yet, reliable pipelines for large scale target prediction of natural products are still rare. We have developed an in silico workflow consisting of four independent, stand-alone target prediction tools and evaluated its performance on dihydrochalcones (DHCs) – a well-known class of natural products. Thereby, we revealed four previously unreported protein targets for DHCs, namely 5-lipoxygenase, cyclooxygenase-1, 17β- hydroxysteroid dehydrogenase 3, and aldo-keto reductase 1C3. Moreover, we provide a thorough strategy on how to perform computational target prediction and guidance on using the respective tools.
COMMUNICATION | doi:10.20944/preprints202004.0062.v1
Subject: Medicine & Pharmacology, General Medical Research Keywords: COVID-19; FDA approved drugs; High Throughput Virtual Screening; Sincalide; Pentagastrin.
Online: 6 April 2020 (14:09:04 CEST)
In the end of December 2019, a new strain of coronavirus was identified in the Wuhan city of Hubei province in China. Within a shorter period of time, an unprecedented outbreak of this strain was witnessed over the entire Wuhan city. This novel coronavirus strain was later officially renamed as COVID-19 (Coronavirus disease 2019) by the World Health Organization. The mode of transmission had been found to be human-to-human contact and hence resulted in a rapid surge across the globe where more than 1,100,000 people have been infected with COVID-19. In the current scenario, finding potent drug candidates for the treatment of COVID-19 has emerged as the most challenging task for clinicians and researchers worldwide. Identification of new drugs and vaccine development may take from a few months to years based on the clinical trial processes. To overcome the several limitations involved in identifying and bringing out potent drug candidates for treating COVID-19, in the present study attempts were made to screen the FDA approved drugs using High Throughput Virtual Screening (HTVS). The COVID-19 main protease (COVID-19 Mpro) was chosen as the drug target for which the FDA approved drugs were initially screened with HTVS. The drug candidates that exhibited favorable docking score, energy and emodel calculations were further taken for performing Induced Fit Docking (IFD) using Schrodinger’s GLIDE. From the flexible docking results, the following four FDA approved drugs Sincalide, Pentagastrin, Ritonavir and Phytonadione were identified. In particular, Sincalide and Pentagastrin can be considered potential key players for the treatment of COVID-19 disease.
ARTICLE | doi:10.20944/preprints202003.0372.v1
Subject: Chemistry, Medicinal Chemistry Keywords: COVID-19; SARS-CoV-2; Marine natural product; Virtual screening; Docking
Online: 25 March 2020 (08:23:57 CET)
The current emergency due to the worldwide spread of the COVID-19 caused by the new SARS-CoV-2 is a great concern for global public health. Already in the past, the outbreak of severe acute respiratory syndrome (SARS) in 2003 and Middle Eastern respiratory syndrome (MERS) in 2012 demonstrates the potential of coronaviruses to cross-species borders and further underlines the importance of identifying new-targeted drugs. An ideal antiviral agent should target essential proteins involved in the lifecycle of SARS-CoV. Currently, some HIV protease inhibitors (i.e., Lopinavir) are proposed for the treatment of COVID-19, although their effectiveness was not yet assessed. The main protease (Mpro) provides a highly validated pharmacological target for the discovery and design of inhibitors. We identified potent Mpro inhibitors employing computational techniques that entail the screening of a Marine Natural Product (MNP) library. MNP library was screened by hyphenated pharmacophore model, and molecular docking approaches. Molecular dynamics and re-docking further confirmed the results obtained by structure-based techniques and allowed to highlight some crucial aspects. Seventeen potential SARS-CoV-2 Mpro inhibitors have been identified among the natural substances of marine origin. As these compounds were extensively validated by a consensus approach and by molecular dynamics, the likelihood that at least one of these compounds could be bioactive is excellent.
ARTICLE | doi:10.20944/preprints201908.0285.v1
Subject: Medicine & Pharmacology, Dentistry Keywords: oral health , pre-diabetic, diabetic, oral systemic, screening, H1A1c, Findrisk , periodontal
Online: 27 August 2019 (11:58:44 CEST)
Pre-diabetes is a serious health condition where blood sugar levels are higher than normal, but not high enough yet to be diagnosed as type 2 diabetes. Pre-diabetes puts one at an increased risk of developing type 2 diabetes and heart disease Methodology: A cross-sectional study was carried out on 384 patients aged 20-70 years old, attending the dental clinics to assess the risk for diabetes, using the FINDRISC questionnaire, HbA1c blood test and a periodontal examination. Results: The mean age of participants was 38.90±10.74. 32.3% were categorized as no risk, 46.6% low risk, while 19% and 2.1% moderate and high risk of developing diabetes respectively. Tests for serum HbA1c Level showed 46.1 % had normal HbA1c followed by 18.0% and 3.6 % were pre-diabetic and diabetic respectively. 19.3% of participants had periodontal pockets measuring more than 4mm and 15.9% measuring more than 6mm. Conclusion: The study has proven to be useful in identifying patients at high-risk of developing diabetes. Controlling and managing periodontal disease could be a new aspect to include in the standards for diabetes care. Dental settings could be a successful platform to carry out the screening and risk stratification of pre-diabetic patients.
ARTICLE | doi:10.20944/preprints201907.0150.v1
Subject: Biology, Other Keywords: dual-channel sensor; efficient capture; lung cancer biomarker; lung cancer screening
Online: 10 July 2019 (11:37:13 CEST)
Lung cancer remains the leading cancer killer worldwide. Early diagnosis can effectively increase the patient cure rate but existing diagnostic methods limit early lung cancer diagnosis. Therefore, development of a simple but efficient lung cancer screening method is important to improvement of both the diagnosis rate and the survival rate of lung cancer patients. In this study, ten photosensitive materials with high sensitivity and high specificity were screened accurately to construct a microarray sensor that can rapidly identify six types of lung cancer biomarkers in exhaled breath. Results from hierarchical cluster analysis (HCA), principal component analysis (PCA) and difference maps showed that the classification of the analytes agreed with structure similarity laws. The detection results from parallel experiments and structurally similar analytes, in turn, cluster into a group; the fingerprints of the different analytes have specific response regions. The well-screened sensor chip fabrication workload and cost were both reduced by approximately two thirds, while the microfluidic device sensitivity and stability increased by approximately 1.3 times their corresponding values before optimization. The dual-channel device also offers real-time contrast detection and synchronous parallel detection functions and has potential application prospects for use in extensive screening of high-risk populations for lung cancer.
ARTICLE | doi:10.20944/preprints201806.0192.v1
Subject: Life Sciences, Biotechnology Keywords: β4-galactosyltransferase 4; transcriptional mechanism; sensor cells; colon cancer; drug screening
Online: 12 June 2018 (12:51:07 CEST)
The increased expression of β4-galactosyltransferase (β4GalT) 4 was closely associated with poor prognosis of colon cancer. Recently, we showed that the expression of the β4GalT4 gene is regulated by the 0.17 kb core promoter region containing one binding site for Specificity protein 1 (Sp1). To develop a novel screening method for anti-colon cancer drugs, two sensor cell lines having the luciferase gene under the control of two β4GalT4 gene promoters that differed in length were established from SW480 human colon cancer cells. The hGT4-0.17-sensor cells possessed the luciferase reporter driven by the 0.17 kb promoter, while the hGT4-0.3-sensor cells possessed the luciferase reporter driven by the 0.3 kb promoter containing one binding site each for colon cancer-related transcription factors including activator protein 2, E2F, caudal-related homeobox transcription factors, and Runt-related transcription factors besides Sp1. Upon treatment with mitogen-activated protein kinase inhibitor U0126, the promoter activities of the hGT4-0.3-sensor cells decreased significantly, while those of the hGT4-0.17-sensor cells unchanged. These results suggest that the responsiveness to U0126 differs between two sensor cell lines due to the different regulation of the luciferase reporters. This study provides the novel screening method for anti-colon cancer drugs by the combination of two sensor cell lines.
ARTICLE | doi:10.20944/preprints201711.0199.v2
Subject: Life Sciences, Microbiology Keywords: human papillomavirus; HPV; cervical cancer; cancer screening; self-sampling; vaginal microbiome
Online: 1 December 2017 (07:19:13 CET)
In most industrialized countries, screening programs for cervical cancer have shifted from cytology (Pap smear or ThinPrep) alone on clinician-obtained samples to the addition of screening for human papillomavirus (HPV), its main causative agent. For HPV testing, self-sampling instead of clinician-sampling has proven to be equally accurate, in particular for assays that use nucleic acid amplification techniques. In addition, HPV testing of self-collected samples in combination with a follow-up Pap smear in case of a positive result is more effective in detecting precancerous lesions than a Pap smear alone. Self-sampling for HPV testing has already been adopted by some countries, while others have started trials to evaluate its incorporation into national cervical cancer screening programs. Self-sampling may result in more individuals willing to participate in cervical cancer screening, because it removes many of the barriers that prevent women, especially those in low socioeconomic and minority populations, from participating in regular screening programs. Several studies have shown that the majority of women who have been underscreened but who tested HPV-positive in a self-obtained sample, will visit a clinic for follow-up diagnosis and management. Additionally, a self-collected sample can also be used for vaginal microbiome analysis, which can provide additional information about HPV infection persistence as well as vaginal health in general.
ARTICLE | doi:10.20944/preprints201706.0022.v1
Subject: Chemistry, General & Theoretical Chemistry Keywords: HPPD inhibitors; pharmacophore model; molecule docking; HipHop model; virtual screening; ChemDiv
Online: 5 June 2017 (05:16:39 CEST)
p-Hydroxyphenylpyruvate dioxygenase (HPPD) is not only the useful molecular target in treating life-threatening tyrosinemia type I, but also an important target for chemical herbicides. A combined in silico structure-based pharmacophore and molecular docking based virtual screening were performed to identify novel potential HPPD inhibitors. The complex based pharmacophore model (CBP) with 0.721 of ROC used for screening compound showed remarkable ability to retrieve known active ligands from decoy molecule. The ChemDiv database was screened using CBP-Hypo2 as a 3D query, and the best-fit hits subjected to molecular docking with two methods of LibDock and CDOCKER in Accelrys Discovery Studio 2.5(DS 2.5) to discern interactions with key residues at the active site of HPPD. 4 Compounds with top rank in HipHop model and well-known binding model were finally chosen as identification of lead compounds with potentially inhibitory effects on active site of target. The results provided powerful insight to the development of novel HPPD inhibitors herbicides using computational techniques.
ARTICLE | doi:10.20944/preprints201610.0016.v1
Subject: Medicine & Pharmacology, Oncology & Oncogenics Keywords: molecular dynamics simulation; virtual screening; molecular docking; prostate cancer; caveolin-1
Online: 7 October 2016 (12:09:06 CEST)
Caveolin-1 (Cav-1) is 22 kDa caveolae protein, acts as a scaffold within caveolar membranes. It interacts with alpha subunits of G-protein and thereby regulates their activity. Earlier studies reported elevated or up-regulated levels of caveolin-1 in the serum of prostate cancer patients. Secreted Cav-1 promotes angiogenesis, cell proliferation and anti-apoptotic activities in prostate cancer patients. Cav-1 upregulation is mainly related to prostate cancer metastasis. Keeping above facts in view, the present study was designed to explore Cav-1 as a target for prostate cancer therapy using computational approach. Molecular docking, structural base molecular modelling and molecular dynamics simulations were performed to investigate Cav-1 inhibitors. A predictive model was generated and validated to establish a stable structure. ZINC database of biogenic compounds was used for induced fit docking (IFD) and high throughput virtual screening. The H-bond interactions of the compounds with active site residues of Cav-1 were estimated by IFD and 100 ns long molecular dynamic simulations. The reported compounds showed significant binding and thus can be considered as potent therapeutic inhibitors of Cav-1. This study provides a valuable insight into biochemical interactions of Cav-1 for therapeutic applications and warrants for experimental validation of the predicted ‘active(s)’.
ARTICLE | doi:10.20944/preprints202208.0126.v1
Subject: Chemistry, Applied Chemistry Keywords: Eugenol; Essential oils; Nanoencapsulation; Biopesticides; Insecticides; Odorant binding proteins; Inverted virtual screening
Online: 5 August 2022 (14:43:22 CEST)
The eugenol derivative, ethyl 4-(2-methoxy-4-(oxiran-2-ylmethyl)phenoxy)butanoate 1, with promising insecticidal capability was encapsulated in liposomal formulations of egg-phosphatidylcholine/cholesterol (Egg-PC:Ch) 70:30 and of 100% dioleoylphosphatidylglycerol (DOPG). Compound-loaded Egg-PC:Ch liposomes exhibit small hydrodynamic diameters (below 100 nm), high encapsulation efficiency (88.8% ± 2.7%), higher stability and a more efficient compound release, being chosen for assays in Sf9 insect cells. Compound 1 elicited a loss of cell viability up to 80% after 72h of incubation. Relevantly, encapsulation maintained the toxicity of compound 1 towards insect cells, while it lowered toxicity towards human cells, thus showing the selectivity of the system. Structure based inverted virtual screening was used to predict the most likely targets and molecular dynamics simulations and free energy calculations were used to demonstrate that this molecule can form a stable complex with insect odorant binding proteins and/or acetylcholinesterase.
ARTICLE | doi:10.20944/preprints202203.0151.v1
Subject: Medicine & Pharmacology, Nutrition Keywords: vitamins; micronutrients; deficiencies; screening; general population; lifestyle; prevention; vitamin d; vitamin b12
Online: 10 March 2022 (14:11:38 CET)
Maintaining an adequate micronutrient status can be achieved by following a complete, diverse diet. Yet, food trends in Western countries show suboptimal consumption of healthy nutrients. In this study we explored the prevalence of vitamin and mineral imbalances in a general population cohort of Dutch adults, and evaluated the effect of a digital lifestyle program on the nutritional status and nutrition health behaviors of these individuals. A micronutrient panel was measured in 348 participants, alongside a dietary assessment. One-hundred users subsequently underwent a remeasurement. We identified at least one nutritional imbalance in 301 individuals (86.5%). 80% improved and normalized B6, 67% improved folate, 70% improved B12, and 86% improved vitamin D. Iron abnormalities were corrected in 75% of participants. In conclusion, this study found micronutrient deficiencies of easily obtainable vitamins through diet or supplementation such as B vitamins and vitamin D were more prevalent than expected in a Dutch population. This can partly be explained by an insufficient consumption of food groups rich in B vita-mins. Our preliminary results in those remeasured after a digitally-enabled lifestyle intervention show these imbalances can be corrected with adequate behavioral support in a “food as medicine” approach complemented with supplementation where needed.
ARTICLE | doi:10.20944/preprints202105.0344.v1
Subject: Medicine & Pharmacology, Allergology Keywords: Familial hypercholesterolemia; identification; implementation outcomes; cascade screening; cascade testing; chatbots; direct contact
Online: 14 May 2021 (14:49:21 CEST)
Guided by the Conceptual Model of Implementation Research, we explored the acceptability, appropriateness, and feasibility of: 1) automated screening approaches utilizing existing health data to identify those who require subsequent diagnostic evaluation for familial hypercholesterolemia (FH) and 2) family communication methods including chatbots and direct contact to communicate information about inherited risk for FH. Focus groups were conducted with 22 individuals with FH (2 groups) and 20 clinicians (3 groups). These were recorded, transcribed, and analyzed using deductive (coded to implementation outcomes) and inductive (themes based on focus group discussions) methods. All stakeholders described these initiatives as: 1) acceptable and appropriate to identify individuals with FH and communicate risk with at-risk relatives; and 2) feasible to implement in current practice. Stakeholders cited current initiatives, outside of FH (e.g., pneumonia protocols, colon cancer and breast cancer screenings), that gave them confidence for successful implementation. Stakeholders described perceived obstacles, such as nonfamiliarity with FH, that could hinder implementation and potential solutions to improve systematic uptake of these initiatives. Automated health data screening, chatbots, and direct contact approaches may be useful for patients and clinicians to improve FH diagnosis and cascade screening.
ARTICLE | doi:10.20944/preprints202101.0303.v1
Subject: Medicine & Pharmacology, Allergology Keywords: Controlling Nutritional Status Score; Hemorrhagic stroke; Nutrition screening; Prognosis; Modified Rankin Scale
Online: 15 January 2021 (16:08:15 CET)
Controlling Nutritional Status (CONUT) Score is useful for the nutritional screening. We aimed to explore whether the CONUT score may predict a 3-month functional outcome in hemorrhagic stroke (AHS). Totally, 349 patients with incident AHS were consecutively recruited, and their malnutrition risks were determined using a high CONUT score of ≥ 2. Poor functional outcomes were defined as the modified Rankin Scale (mRS) score of ≥ 3 at 3 months. A total of 328 patients (mean age, 60.4 ± 12.83 years; 66.8% male) were included, 172 (52.40%) patients at malnutrition risk and 104 (31.7%) patients with a poor prognosis. High-CONUT patients had lower total lymphocyte counts and total cholesterol levels than low-CONUT patients (p < 0.001 and p = 0.012). At 3-month post discharge, patients with malnutrition risk had higher hospitalization costs (p = 0.021), lower Barthel Index (p = 0.001), and more infectious complications (p = 0.002) than those without, and there was a greater risk for poor functional outcomes in the high-CONUT compared with the low-CONUT patients at admission (adjusted odds ratio: 2.32, 95% confidence interval: 1.28-4.17). High-CONUT scores predict a 3-month poor prognosis in AHS, which may help identify the AHS patients who need additional nutritional managements.
ARTICLE | doi:10.20944/preprints202012.0264.v1
Subject: Physical Sciences, General & Theoretical Physics Keywords: Unified field; space-time film; soliton-particle; gravitation; dark matter; gravitational screening
Online: 10 December 2020 (13:58:28 CET)
The scalar field of space-time film is considered as unified fundamental field. The field model under consideration is the space-time generalization of the model for a two-dimensional thin film. The force and metrical interactions between solitons are considered. These interactions correspond to the electromagnetic and gravitational interactions respectively. The metrical interaction and its correspondence to the gravitational one are considered in detail. The practical applications of this approach are discussed.
REVIEW | doi:10.20944/preprints202008.0461.v1
Subject: Medicine & Pharmacology, Nutrition Keywords: eating disorders; anorexia nervosa; bulimia nervosa; personality traits; screening tools; Covid-19
Online: 20 August 2020 (13:11:08 CEST)
This article aims to review the screening and diagnostic tools for eating disorders (ED). Eating disorders represent a complex pathology defined by an imbalance between hunger and satiety, installed in an emotional, traumatic, or conflictive context. Recently, the emphasis regarding ED is focused on the link between genetics, mental pathology, and the somatic and metabolic phenotype and early detection. Early detection and intervention can assure a better recovery and can improve a lot the quality of life of these patients. Methods: We selected ten articles of central importance on the topic in a systematic search on eight databases, articles selected on the type of scales, and size of the study. Results: We identified eight questionnaire scales used in large trials in ED disorders in the scanned literature, choose because we consider it the most accurate and the ones that evaluate best the pathology and the elements that are important as specific traits in ED. There are interview-type scales and self-administered scales. Interview scales are characterized by assessments of symptoms and diagnosis, while self-administered assess particular traits and the possibility of further development of eating disorders. The majority of the scales evaluated were described and used in adult populations. From all the scales assessed and analyzed, only three are described at the child population – it is EAT-26 (> 16 years), EDI-3 (>13 years), and ANSOCQ (> 13 years). Conclusions: It is essential to develop specific scales for people under 18 years of age, given the increasing incidence of ED among children and the need for early detection and appropriate intervention. Early detection of ED in children implies a simple and accurate evaluation at the primary care level or in schools, as the course of the disease can be subclinical for several years. Moreover, the need for accurate scales and telemedicine testing and diagnosis is of high importance during the COVID-19 pandemic as youth are at particular risk being psychologically affected due to disrupted education and social interactions - at a critical time.
ARTICLE | doi:10.20944/preprints202003.0024.v1
Subject: Medicine & Pharmacology, Allergology Keywords: SARS-CoV-2; nonstructural proteins (NSP); NSP12; NSP7; NSP8; virtual screening; inhibitor
Online: 2 March 2020 (03:11:33 CET)
A novel coronavirus (SARS-CoV-2) that is initially found to trigger human severe respiratory illness in Wuhan City of China in 2019, has killed 2,718 people in China by February 26, 2020, and which has been recognized as a public health emergency of international concern as well. And the virus has spread to more than 38 countries around the world. However, the drug has not yet been officially licensed or approved to treat SARS-Cov-2 infection. NSP12-NSP7-NSP8 complex of SARS-CoV-2, essential for viral replication and transcription, is generally regarded as a potential target to fight against the virus. According to the NSP12-NSP7-NSP8 complex (PDB ID: 6NUR) structure of SARS, two homologous models were established for virtual screening in the present study, namely NSP12-NSP7 interface model and NSP12-NSP8 interface model. Seven compounds (Saquinavir, Tipranavir, Lonafarnib, Tegobuvir, Olysio, Filibuvir, and Cepharanthine) were selected for binding free energy calculations based on virtual screening and docking scores. All seven compounds can combine well with NSP12-NSP7-NSP8 in the homologous model, providing drug candidates for the treatment and prevention of SARS-CoV-2.
ARTICLE | doi:10.20944/preprints202002.0178.v1
Subject: Medicine & Pharmacology, Pharmacology & Toxicology Keywords: DILIrank; DILI; drug hepatotoxicity; QSAR; nested cross-validation; virtual screening; in silico
Online: 14 February 2020 (02:24:04 CET)
Drug induced liver injury (DILI) remains one of the challenges in the safety profile of both authorized drugs and candidate drugs and predicting hepatotoxicity from the chemical structure of a substance remains a challenge worth pursuing, being also coherent with the current tendency for replacing non-clinical tests with in vitro or in silico alternatives. In 2016 a group of researchers from FDA published an improved annotated list of drugs with respect to their DILI risk, constituting “the largest reference drug list ranked by the risk for developing drug-induced liver injury in humans”, DILIrank. This paper is one of the few attempting to predict liver toxicity using the DILIrank dataset. Molecular descriptors were computed with the Dragon 7.0 software, and a variety of feature selection and machine learning algorithms were implemented in the R computing environment. Nested (double) cross-validation was used to externally validate the models selected. A number of 78 models with reasonable performance have been selected and stacked through several approaches, including the building of multiple meta-models. The performance of the stacked models was slightly superior to other models published. The models were applied in a virtual screening exercise on over 100,000 compounds from the ZINC database and about 20% of them were predicted to be non-hepatotoxic.
ARTICLE | doi:10.20944/preprints201907.0258.v1
Subject: Medicine & Pharmacology, Oncology & Oncogenics Keywords: GPR15, pan-cancer, TCGA, cancer immunity, differential gene expression, prognosis, virtual screening
Online: 23 July 2019 (11:15:19 CEST)
G protein-coupled receptor 15 (GPR15, also known as BOB) is an extensively studied orphan GPCR involving HIV infection, colonic inflammation and smoking-related diseases. Recently, GPR15 was deorphanized and its corresponding natural ligand demonstrated an ability of inhibiting cancer cell growth. However, no study reported the potential role of GPR15 in a pan-cancer manner. Using large-scale publicly available data from the Cancer Genome Atlas (TCGA) and the Genotype-Tissue Expression (GTEx) databases, we found that GPR15 expression is significantly lower in colon adenocarcinoma (COAD) than in normal tissues. And among 33 cancer types, GPR15 expression is significantly correlated with the prognoses of COAD, neck squamous carcinoma (HNSC), lung adenocarcinoma (LUAD) positively and stomach adenocarcinoma (STAD) negatively. This study also revealed that commonly upregulated gene set in the high GPR15 expression group (stratified via median) of COAD, HNSC, LUAD and STAD are enriched in immune systems, indicating that GPR15 might be considered as a potential target for cancer immunotherapy. Furthermore, we modelled the 3D structure of GPR15 and conducted the structure-based virtual screening. The top 8 hits compounds were screened and then subjected to molecular dynamics (MD) simulation for stability analysis. Our study provided novel insights into the role of GPR15 in a pan-cancer manner and discovered a potential hit compound for GPR15 antagonists.
REVIEW | doi:10.20944/preprints201906.0002.v1
Subject: Medicine & Pharmacology, Oncology & Oncogenics Keywords: patient-derived xenograft; immunocompromised mice; precision medicine; drug screening; cancer; cell line
Online: 3 June 2019 (04:47:14 CEST)
Patient-derived xenograft (PDX) models are created by engraftment of patients’ tumor tissues into immunocompetent mice. Since PDX model keep the characteristics of primary patient’s tumor such as gene expression profiles and drug sensitivity, it now becomes most reliable in vivo human cancer model. The engraftment rate are increased with the introduction of NOD/Scid based immunocompromised mice, especially, NK cell defective NOD strains such as NOD/Scid/IL2Rγnu (NOG/ NSG) mice and NOD/Scid/Jak3null (NOJ) mice. Success ratio differs from the origin of tumor: Gastrointestinal tumors tend to higher success rate and breast cancer is lower. Subcutaneous transplantation is most popular method to establish PDX, but some tumor needs orthotropic or renal capsule transplantation, and human hormone treatment is needed to establish hormone dependent cancers such as prostate and breast cancer. PDX library with patient’s clinical data, gene-expression patterns, mutational status, drug responsiveness and tumor architecture will be the powerful tool for developing specific biomarker and novel individualized therapy and establishing precision cancer medicine.
ARTICLE | doi:10.20944/preprints201810.0381.v1
Subject: Chemistry, Medicinal Chemistry Keywords: Biginelli reaction; dihydropyrimidin-2-thiones; synthesis, virtual screening, drug design; LaSOM 282
Online: 17 October 2018 (09:34:06 CEST)
The Biginelli reaction is a highly versatile reaction, which leads to dihydropyrimidinones/thiones. This scaffold is reported as being a privileged structure due to its ability to interact with biological targets. Synthesis of ethyl 4-(2-fluorophenyl)-6-methyl-2-thioxo-1-(p-tolyl)-1,2,3,4-tetrahydropyrimidine-5-carboxylate was achieved through the Biginelli reaction using a functionalized thiourea. In silico studies demonstrated that the compound title showed good potential for interacting with ecto-5’-nucleotidase, which has been considered as a target in designs for anti-cancer drugs.
ARTICLE | doi:10.20944/preprints201808.0020.v1
Subject: Medicine & Pharmacology, Obstetrics & Gynaecology Keywords: expanded carrier screening; prenatal diagnosis; pregnancy management; clinical utility; at-risk couple
Online: 1 August 2018 (12:07:35 CEST)
Purpose: Expanded carrier screening (ECS) informs couples of their risk of having offspring affected by certain genetic conditions. Limited data exists assessing the actions and reproductive outcomes of at-risk couples (ARCs). We describe the impact of ECS on planned and actual pregnancy management in the largest sample of ARCs studied to date. Methods: Couples who elected ECS and were found to be at high risk of having a pregnancy affected by at least one of 176 genetic conditions were invited to complete a survey about their actions and pregnancy management. Results: Three hundred ninety-one ARCs completed the survey. Among those screened before becoming pregnant, 77% planned or pursued actions to avoid having affected offspring. Among those screened during pregnancy, 37% elected prenatal diagnostic testing (PNDx) for that pregnancy. In subsequent pregnancies that occurred in both the preconception and prenatal screening groups, PNDx was pursued in 29%. The decision to decline PNDx was most frequently based on the fear of procedure-related miscarriage, as well as the belief that termination would not be pursued in the event of a positive diagnosis. Conclusions: ECS results impacted couples’ reproductive decision-making and led to altered pregnancy management that effectively eliminates the risk of having affected offspring.
ARTICLE | doi:10.20944/preprints201807.0427.v1
Subject: Chemistry, Medicinal Chemistry Keywords: Pharmacophore; 3D-QSAR; virtual screening; D3R selective antagonist; molecular docking; CNS-like
Online: 23 July 2018 (14:09:10 CEST)
The dopamine D3 receptor is an important CNS target for the treatment of a variety of neurological diseases. Selective dopamine D3 receptor antagonists modulate the improvement of psychostimulant addiction and relapse. In this study, five and six featured pharmacophore models of D3R antagonists were generated and evaluated with the post-hoc score combining two survival scores of active and inactive. Among Top 10 models, APRRR215 and AHPRRR104 were chosen based on the coefficient of determination (APRRR215: R2training = 0.80; AHPRRR104: R2training = 0.82) and predictability (APRRR215: Q2test = 0.73, R2predictive = 0.82; AHPRRR104: Q2test = 0.86, R2predictive = 0.74) of their 3D-quantitative structure–activity relationship models. Pharmacophore-based virtual screening of a large compound library from eMolecules (> 3 million compounds) using two optimal models expedited the search process 100-fold speed increase compared to the docking-based screening (HTVS scoring function in Glide) and identified a series of hit compounds having promising novel scaffolds. After the screening, docking scores, as an adjuvant predictor, were added to two fitness scores (from the pharmacophore models) and predicted Ki (from PLSs of the QSAR models) to improve accuracy. Final selection of the most promising hit compounds were also evaluated for CNS-like properties as well as expected D3R antagonism.
REVIEW | doi:10.20944/preprints201608.0054.v1
Subject: Biology, Other Keywords: influenza virus; antiviral agent; proteomics; phosphoproteomics; metabolomics; transcriptomics; genomics; virtual ligand screening
Online: 5 August 2016 (12:41:07 CEST)
Human influenza A viruses (IAVs) cause global pandemics and epidemics. These viruses evolve rapidly, making current treatment options ineffective. To identify novel modulators of IAV-host interactions, we re-analyzed our recent transcriptomics, metabolomics, proteomics, phosphoproteomics, and genomics/virtual ligand screening data. We identified 713 potential modulators targeting 200 cellular and two viral proteins. Anti-influenza activity for 48 of them has been reported previously, whereas the antiviral efficacy of the remaining 665 is unknown. Studying anti-influenza efficacy, immuno-modulating properties and potential resistance of these compounds or their combinations may lead to the discovery of novel modulators of IAV-host interactions, which might be more effective than the currently available anti-influenza therapeutics.