jimnoneill/paper-to-field-training huggingface dataset:
Identification of Genetic Risk Factors of Severe COVID-19 Using Extensive Phenotypic Data: A Proof-of-Concept Study in a Cohort of Russian Patients

The COVID-19 pandemic has drawn the attention of many researchers to the interaction between pathogen and host genomes. Over the last two years, numerous studies have been conducted to identify the genetic risk factors that predict COVID-19 severity and outcome. However, such an analysis might be complicated in cohorts of limited size and/or in case of limited breadth of genome coverage. In this work, we tried to circumvent these challenges by searching for candidate genes and genetic variants associated with a variety of quantitative and binary traits in a cohort of 840 COVID-19 patients from Russia. While we found no gene- or pathway-level associations with the disease severity and outcome, we discovered eleven independent candidate loci associated with quantitative traits in COVID-19 patients. Out of these, the most significant associations correspond to rs1651553 in MYH14p = 1.4 × 10−7), rs11243705 in SETX (p = 8.2 × 10−6), and rs16885 in ATXN1 (p = 1.3 × 10−5). One of the identified variants, rs33985936 in SCN11A, was successfully replicated in an independent study, and three of the variants were found to be associated with blood-related quantitative traits according to the UK Biobank data (rs33985936 in SCN11A, rs16885 in ATXN1, and rs4747194 in CDH23). Moreover, we show that a risk score based on these variants can predict the severity and outcome of hospitalization in our cohort of patients. Given these findings, we believe that our work may serve as proof-of-concept study demonstrating the utility of quantitative traits and extensive phenotyping for identification of genetic risk factors of severe COVID-19.

Topic: SARS-CoV-2 and COVID-19 Research
Subfield: Infectious Diseases
Field: Medicine
Domain: Health Sciences
Machine Learning in FTIR Spectrum for the Identification of Antibiotic Resistance: A Demonstration with Different Species of Microorganisms

Recent studies introduced the importance of using machine learning algorithms in research focused on the identification of antibiotic resistance. In this study, we highlight the importance of building solid machine learning foundations to differentiate antimicrobial resistance among microorganisms. Using advanced machine learning algorithms, we established a methodology capable of analyzing the FTIR structural profile of the samples of Streptococcus pyogenes and Streptococcus mutans (Gram-positive), as well as Escherichia coli and Klebsiella pneumoniae (Gram-negative), demonstrating cross-sectional applicability in this focus on different microorganisms. The analysis focuses on specific biomolecules—Carbohydrates, Fatty Acids, and Proteins—in FTIR spectra, providing a multidimensional database that transcends microbial variability. The results highlight the ability of the method to consistently identify resistance patterns, regardless of the Gram classification of the bacteria and the species involved, reinforcing the premise that the structural characteristics identified are universal among the microorganisms tested. By validating this approach in four distinct species, our study proves the versatility and precision of the methodology used, in addition to bringing support to the development of an innovative protocol for the rapid and safe identification of antimicrobial resistance. This advance is crucial for optimizing treatment strategies and avoiding the spread of resistance. This emphasizes the relevance of specialized machine learning bases in effectively differentiating between resistance profiles in Gram-negative and Gram-positive bacteria to be implemented in the identification of antibiotic resistance. The obtained result has a high potential to be applied to clinical procedures.

Topic: Spectroscopy Techniques in Biomedical and Chemical Research
Subfield: Biophysics
Field: Biochemistry, Genetics and Molecular Biology
Domain: Life Sciences
Stabilization of the integrase‐DNA complex by Mg<sup>2+</sup> ions and prediction of key residues for binding HIV‐1 integrase inhibitors

ABSTRACT The HIV‐1 integrase is an attractive target for the therapeutics development against AIDS, as no host homologue of this protein has been identified. The integrase strand transfer inhibitors (INSTIs), including raltegravir, specifically target the second catalytic step of the integration process by binding to the DDE motif of the catalytic site and coordinating Mg 2+ ions. Recent X‐ray crystallographic structures of the integrase/DNA complex from prototype foamy virus allowed to investigate the role of the different partners (integrase, DNA, Mg 2+ ions, raltegravir) in the complex stability using molecular dynamics (MD) simulations. The presence of Mg 2+ ions is found to be essential for the stability, whereas the simultaneous presence of raltegravir and Mg 2+ ions has a destabilizing influence. A homology model of HIV‐1 integrase was built on the basis of the X‐ray crystallographic information, and protein marker residues for the ligand binding were detected by clustering the docking poses of known HIV‐1 integrase inhibitors on the model. Interestingly, we had already identified some of these residues to be involved in HIV‐1 resistance mutations and in the stabilization of the catalytic site during the MD simulations. Classification of protein conformations along MD simulations, as well as of ligand docking poses, was performed by using an original learning method, based on self‐organizing maps. This allows us to perform a more in‐depth investigation of the free‐energy basins populated by the complex in MD simulations on the one hand, and a straightforward classification of ligands according to their binding residues on the other hand. Proteins 2014; 82:466–478. © 2013 Wiley Periodicals, Inc.

Topic: HIV/AIDS drug development and treatment
Subfield: Infectious Diseases
Field: Medicine
Domain: Health Sciences
SWAT-Driven Exploration of Runoff Dynamics in Hyper-Arid Region, Saudi Arabia: Implications for Hydrological Understanding

Hydrological modeling plays a vital role in water-resource management and climate-change studies in hyper-arid regions. In the present investigation, surface runoff was estimated by a Soil and Water Assessment Tool (SWAT) model for Wadi Al-Aqul, Saudi Arabia. The Sequential Uncertainty Fitting version 2 (SUFI-2) technique in SWAT-CUP was adopted for the sensitivity analysis, calibration, and validation of the SWAT model’s components. The observational runoff data were scarce and only available from 1979 to 1984; such data scarcity is a common problem in hyper-arid regions. The results show good agreement with the observed daily runoff, as indicated by a Pearson Correlation Coefficient (r) of 0.86, a regression (R2) of 0.76, and a Nash–Sutcliffe coefficient (NSE) of 0.61. Error metrics, including the Mean Absolute Error (MAE) and Root Mean Square Error (RMSE), were notably low at 0.05 and 0.58, respectively. In the daily validation, the model continued to perform well, with a correlation of 0.76 and regression of 0.58. As a new approach, fitted parameters of daily calibration were incorporated into the monthly simulation, and they demonstrated an even better performance. The correlation coefficient (regression) and Nash–Sutcliffe were found to be extremely high during the calibration period of the monthly simulation, reaching 0.97 (0.95) and 0.73, respectively; meanwhile, they reached 0.99 (0.98) and 0.63 in the validation period, respectively. The sensitivity analysis using the SUFI-2 algorithm highlighted that, in the streamflow estimation, the Curve Number (CN) was found to be the most responsive parameter, followed by Soil Bulk Density (SOL_BD). Notably, the monthly results showed a higher performance than the daily results, indicating the inherent capability of the model in regard to data aggregation and reducing the impact of random fluctuations. These findings highlight the applicability of the SWAT model in predicting runoff and its implication for climate-change studies in hyper-arid regions.

Topic: Hydrology and Watershed Management Studies
Subfield: Water Science and Technology
Field: Environmental Science
Domain: Physical Sciences
Treatment of canine parvoviral enteritis with interferon‐omega in a placebo‐controlled field trial

The clinical efficacy of a recombinant feline interferon (IFN) (type omega) was evaluated under field conditions for the treatment of dogs with parvoviral enteritis. In this multicentric, double‐blind, placebo‐controlled trial, 94 dogs from one to 28 months old were randomly assigned to two groups which were treated intravenously either with IFN (2·5 million units/kg) or placebo once a day for three consecutive days, and monitored for clinical signs and mortality for 10 days. Each dog received individual supportive treatment. The data from 92 interpretable cases (43 IFN‐treated and 49 placebo) showed that the clinical signs of the IFN‐treated animals improved significantly in comparison with the control animals, and that there were only three deaths in the IFN group compared with 14 deaths in the placebo group (P=0·0096) corresponding to a 4·4‐fold reduction. Alternative analyses of the data taking into account the prior vaccination status of the dogs against canine parvovirus suggested that the IFN therapy resulted in a 6·4‐fold reduction in mortality (P=0·044) in the unvaccinated cohort, a significant reduction when compared with the vaccinated cohort.

Topic: Virus-based gene therapy research
Subfield: Genetics
Field: Biochemistry, Genetics and Molecular Biology
Domain: Life Sciences
CCDC 249229: Experimental Crystal Structure Determination

An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.

Topic: Crystallization and Solubility Studies
Subfield: Materials Chemistry
Field: Materials Science
Domain: Physical Sciences
1-Phenylethynylpyrene (1-PEPy) as Refined Excimer Forming Alternative to Pyrene: Case of DNA Major Groove Excimer

1-Phenylethynylpyrene fluorochrome was studied as meta- and para-derivatives of arabino-uridine-2'-carbamates in ss and dsDNA. 1-PEPy showed red-shifted emission and increased fluorescence quantum yield compared to pyrene. Although 1-PEPy has very short excited lifetime (<2.5 ns), it is able to form inter- and intrastrand excimers on DNA, probably resulting from spatial preorganization of two dye molecules.

Topic: Advanced biosensing and bioanalysis techniques
Subfield: Molecular Biology
Field: Biochemistry, Genetics and Molecular Biology
Domain: Life Sciences
Senam Osteoarthritis Bersama Untuk Menjaga Kebugaran Fisik dalam Rangka WPTD di SMK 7 Semarang

Geriatrics is a branch of gerontology that studies the level of health in the elderly from various aspects, including: promotive, preventive, curative and rehabilitative which includes physical, mental and social health. In principle, geriatrics strives for a happy and useful old age. Throughout the world today, the number of elderly people is estimated to be more than 629 million people, and in 2025 it is projected that the number of elderly people will reach 1.2 billion. Indonesia is a country that has a fairly high number of elderly people. In 2010 the number of elderly aged 65 years and over was 11 million, and it is projected that in 2020 the number of elderly will increase by 7.2%. Even the United States Census Bureau estimates that Indonesia will experience the largest increase in elderly citizens in the world in 2025, namely 414%. The increasing number of elderly will affect the welfare of the elderly (Ministry of Welfare of the Republic of Indonesia. 2012). The increase in the elderly population is of course accompanied by the risk of various degenerative diseases such as diabetes mellitus, coronary heart disease, osteoarthritis, neuromuscular disease and lung disease. Around 50-80% of elderly people aged more than 65 years will experience more than one chronic disease. This is related to the fact that the older you get, the more health problems you experience. One way to improve the quality of life for the elderly is to do physical exercise. Physical exercise can maintain or improve flexibility, cardiopulmonary endurance, agility, strength and balance. Several studies show that physical exercise has a consistent effect in reducing the risk of falls in healthy older adults. Kuptniratsaikul's research in 2009-2010 showed that simple balance exercises carried out by elderly people with a history of falls could reduce the incidence of falls in the elderly and significantly improve body balance. A 2017 Cuevas meta-analysis study showed that balance training programs showed the greatest effect in reducing the risk of falls in the elderly. For elderly people who are not yet able to do balance exercises independently, they need professional assistance

Topic: Sports and Physical Education Research
Subfield: Physical Therapy, Sports Therapy and Rehabilitation
Field: Health Professions
Domain: Health Sciences
Environmental air pollution and chronic rhinosinusitis: A systematic review

Abstract Objective Chronic rhinosinusitis (CRS) is a highly prevalent and burdensome disease. The pathophysiology is not fully elucidated, but environmental pollutants have been suggested to impact the inflammatory component of the disease process. This review aims to summarize the role of environmental pollution in CRS onset and disease severity. Methods A systematic review was performed following Preferred Reporting Items for Systematic Reviews and Meta‐Analyses guidelines. PubMed, EMBASE, Cochrane Library, Web of Science, and Scopus databases were queried in August 2021. Original articles reporting on air pollution exposure in CRS were included. Other forms of sinonasal disease were excluded. Results Literature search produced 11,983 articles, of which 10 met inclusion criteria. Outcomes evaluated included incidence/prevalence, disease severity, quality of life, and histopathologic/microbial changes. Air pollutant exposure was associated with higher odds of CRS, particularly with particulate matter (PM) exposure. Increasing air pollution exposure was also associated with worsened disease severity and detectable histopathologic changes. Impact on quality of life was less clear. Conclusion Air pollution (particularly PM) is correlated with CRS incidence/prevalence and disease severity, with evidence of histopathologic changes in CRS tissue samples. Further research is warranted to better understand the mechanisms by which air pollution components may cause CRS and type 2 inflammation. Level of Evidence 3a

Topic: Sinusitis and nasal conditions
Subfield: Otorhinolaryngology
Field: Medicine
Domain: Health Sciences
[Clinical efficacy of ceftizoxime in the treatment and prevention of infectious inflammatory diseases].

The activity of doxycycline and tetracycline against natural strains of the plague microbe of different origin was studied in vitro. The MICs of doxycycline and tetracycline for the majority of the strains were 0.8 and 3.2 micrograms/ml respectively. The efficacy of doxycycline and tetracycline in the prophylaxis and treatment of experimental plague infection was studied comparatively on albino mice. Doxycycline proved to be superior to tetracycline. By using short-term schemes of the treatment and longer intervals between the drug administrations it was shown that doxycycline had a prolonged action. Moreover, the injectable doxycycline was found to be superior to the oral one. The high efficacy of doxycycline in the treatment of the albino mice with experimental plague infection was confirmed by the pathohistological findings. The pathomorphological changes in the animals were limited by local affections in the site of the contamination and the regional lymph nodes followed by the development of infiltration foci.

Topic: Yersinia bacterium, plague, ectoparasites research
Subfield: Genetics
Field: Biochemistry, Genetics and Molecular Biology
Domain: Life Sciences
Clinical Evaluation of Concentrated Red Cells

Concentrated red cells, depleted of all or almost all visible plasma, and then stored at 4°C for as long as 28 days, were administered as therapeutic transfusions. The 24-hour survival was over 70 per cent and was not affected by the degree of concentration. In four of six Group A1, B or A1B recipients, a positive direct antiglobulin test was observed immediately after transfusion of Group O cells with residual plasma, and the red cells in these samples agglutinated in the Auto-Analyzer without added antibody. However, the survival of the recipient's red cells was normal. Our data suggest that the removal of damaged red cells during transfusion was influenced by the state of the recipient's health; seriously ill patients exhibited an ineffective removal mechanism, where-as otherwise healthy recipients with accidental injuries removed the irreversibly damaged red cells promptly.

Topic: Erythrocyte Function and Pathophysiology
Subfield: Physiology
Field: Medicine
Domain: Health Sciences
International Collaboration Among Social Science Scholars: Opportunities to Bridge Institutional Goals of Internationalization with Faculty Research Agendas

Faculty of universities throughout the world form scholarly networks to exchange ideas, research, and build a knowledge infrastructure that supports the scholarly activities for their subject discipline. Merton describes this phenomenon in his theory of the Sociology of Knowledge as a social organization of scientific research in which “groups organize around distinct subject orientation (Merton, 1968).” Many higher education scholars have written about the ongoing challenges that universities face in their efforts to internationalize. Although internationalization is a common institutional priority, many universities are unable to accomplish the unilateral involvement of their faculty in international initiatives. One strategy aimed at increasing faculty participation in international initiatives involves bridging individual research agendas with the institutional mission to internationalize (Childress, 2010). The ultimate goal of this research was to inform the development of institutional policies and programs aimed at encouraging faculty to participate in collaborative research projects with their international colleagues. This research was focused on individual social science scholars who were involved in international collaborative research projects that resulted in a co-authored article. One aspect of the research concentrated on understanding the scholar’s motivation for participating in the international collaboration. Additionally, the research gathered data related to university research policies including funding for participation in international collaborative projects and the value of participation in international collaborations related to the tenure and promotion review. This research incorporated the cross sectional survey design of quantitative methodology. The unit of analysis was an individual social science scholar involved in a specific international collaborative research project that resulted in a co-authored article published in a scholarly journal. Descriptive statistics along with an explanatory regression model were developed. The results of this study may be used to develop institutional research policy aimed at expanding faculty research activities associated with international research collaboration and co-authorship thereby enabling universities to advance towards their institutional missions and goals related to internationalization.

Topic: Higher Education Governance and Development
Subfield: Political Science and International Relations
Field: Social Sciences
Domain: Social Sciences
1145 Health-related quality of life after adjuvant radiotherapy for breast cancer: a comparaison between two radiation schedules

<h3>Introduction/Background</h3> Hypofractionated radiotherapy (HFRT) carried out in 15 daily fractions, is currently the standard for breast cancer. Following the results of the Fast-Foward trial, the number of fractions could be reduced to five in selected patients. The aim of the study was to compare quality of life (QoL) among breast cancer patients undergoing HFRT versus ultrahypofractionated RT (UHFRT). <h3>Methodology</h3> One hundred patients treated with adjuvant RT to the breast or the chest wall, were included. Fifty patients received HFRT 40Gy/15fractions/3weeks + a boost of 13.35 Gy in 5 fractions and fifty patients received UHFRT 26Gy/5fractions/1 week + a boost of 10Gy in 5 fractions. After a median follow up of 8 months, QoL was assessed using the EORTC QoL questionnaire (QLQ-C30) complemented by the breast cancer specific module (QLQBR23). <h3>Results</h3> The median age of our patients was 63 years.. The average global health status was 63,17 for patients treated with UHFRT and 67 for patients treated with HPRT. (p=0,7). Patients treated with the two radiation schedules had positive body image; 95,1 in UHFRT group and 93,1 in HFRT group (p=0,5). The perspective scores in UHFRT and HFRT groups were respectively 81,9 and 97,3 (p=0,5). The scores of sexual functioning in UHFRT and HFRT groups was respectively 83,6 vs 74,3 (p=0.05). The scores relative to breast and arms symptoms in UHFRT and HFRT groups were respectively 11,2 vs 10,8 (p=0,7) and 10,2 vs 10,8 (p=0,9). <h3>Conclusion</h3> QoL scores in UHFRT for breast cancer were comparable to moderate HFRT. Patients in both groups had positive body image. Patients in UHFRT group showed less deterioration of sexual functioning (p=0,05). Our results support the benefits of UHFRT and recommend its wider use in eligible women, especially in a context of shortage of RT units. <h3>Disclosures</h3> No conflict of interest to disclose.

Topic: Breast Cancer Treatment Studies
Subfield: Cancer Research
Field: Biochemistry, Genetics and Molecular Biology
Domain: Life Sciences
Exciton complexes in ZnSe/BeTe type-II single quantum wells

We have attempted spatially‐resolved photoluminescence (PL) measurements to ZnSe/BeTe type‐II single quantum wells. We have found anomalous PL extended spatially to an order of 300 μm. The spatial extension grew with decreasing temperature. The results were unable to explain by a simple exciton diffusion model. The exciton complexes as a result of high density excitation could be responsible for the striking spatial propagation.

Topic: Semiconductor Quantum Structures and Devices
Subfield: Atomic and Molecular Physics, and Optics
Field: Physics and Astronomy
Domain: Physical Sciences
Library Carpentry: Towards a New Professional Dimension (Part III – Data Reconciliation, Named Entity Recognition and Advanced Utilities)

Data reconciliation and Named Entity Recognition (NER) are closely related concepts to the domain of data carpentry in general and library carpentry in particular. In this context, the part III of the three-part series on library carpentry (part I &amp; II have been published in April &amp; June issues of this journal) is an attempt to apply library carpentry methods in the core areas of information organization in a library of any type or size along with additional utilities like cross-linking of data sources, automatic translation, sentiment analysis and so on. A total of five case studies are included in this research study covering these areas with a focus on do-by-yourself mode.

Topic: Data Quality and Management
Subfield: Management Science and Operations Research
Field: Decision Sciences
Domain: Social Sciences