bluuebunny/crossref_metadata_2025_split huggingface dataset:
MAP3K19 regulatory variation in populations with African ancestry is associated with severe COVID-19
Authors: Cheng Zhong-shan , Cai Yi , Zhang Ke , Zhang Jingxuan , Gui Allen , Luo Yu-Si , Zhou Jie , DeVeale Brian 
Published: November 2022

Abstract
Ancestry impacts the likelihood of hospitalization due to severe acute respiratory syndrome coronavirus 2 (SARS-CoV2). To identify ancestry-linked genetic risk variants associated with COVID-19 hospitalization, we performed an integrative analysis of two genome-wide association studies (GWASs) evaluating genetic variation among ancestrally diverse cohorts. We resolved four single nucleotide polymorphisms (SNPs) that are more frequent in COVID-19 hospitalized patients with non-European ancestry than the general population. Among them, the COVID-19 risk SNP rs16831827 shows the largest difference in allele frequency between African and European populations. The minor allele frequency of rs16831827*T was significantly higher in hospitalized COVID-19 patients with African ancestry. SNP rs16831827 also associates with COVID-19 hospitalization in an independent GWAS from the UK Biobank wherein both the hospitalized and control patients are entirely of African ancestry. rs16831827 is an expression quantitative trait locus (eQTL) of MAP3K19. Apart from rs16831827, two rare SNPs of MAP3K19, rs186150828 and rs192473276, were also significantly associated with COVID-19 hospitalization among African populations in the Regeneron COVID-19 hospitalization GWAS (p < 5x10-7). MAP3K19 expression is induced during ciliogenesis and most abundant in ciliated tissues including the lung and testis. Multiple COVID-19 related single-cell RNA sequencing data revealed that MAP3K19 is highly expressed in nasal multiciliated epithelial cells, nasopharyngeal ciliated cells, and airway ciliated cells. The COVID-19 hospitalization risk allele rs16831827*T is associated with reduced MAP3K19 expression. Hence, rs16831827 may increase the risk of severe COVID-19 by reducing baseline MAP3K19 expression.
Comparison of visual performance between bifocal and extended-depth-of-focus intraocular lenses
Authors: Tabuchi Hitoshi , Tanabe Hirotaka , Shirakami Tomoki , Takase Kosuke , Shojo Tomohiro , Yamauchi Tomofusa 
Published: November 2022

Abstract
We compared the visual performance of a bifocal intraocular lens (IOL) (ZMB00) and an extended-depth-of-focus (EDOF) IOL (ZXR00V) by evaluating postoperative parameters at 10 weeks after the last surgery in cataract patients who underwent bilateral ZMB00 or ZXR00V implantation between 2011 and 2020. The right and left lenses were implanted within 3 months of each other. The study enrolled 1536 eyes from 768 patients; the ZMB00 group comprised 1326 eyes of 663 patients (age: 67.0 ± 7.8 years; female/male, 518/145), and the ZXR00V group comprised 210 eyes of 105 patients (age: 67.8 ± 6.9 years; female/male, 39/66). A linear mixed-effects model using data for both eyes, with strict adjustments for sex, age, subjective refraction spherical equivalent, subjective refraction cylinder, corneal astigmatism, axial length, corneal higher-order aberrations and pupil diameter, ensured statistical validity. Uncorrected near visual acuity, corrected near visual acuity, and near spectacle independence were significantly better in the ZMB00 group (p < 0.00068, Wald test) than in the ZXR00V group. Contrast sensitivity (visual angle of the test target: 4.0°/2.5°/1.6°/1.0°/0.7°) and contrast sensitivity with glare (4.0°/2.5°/1.6°/1.0°/0.7°) were significantly better in the ZXR00V group (p < 0.00068, Wald test) than in the ZMB00 group. Uncorrected intermediate visual acuity, contrast sensitivity with glare (6.3°), and the 25-item National Eye Institute Visual Function Questionnaire (VFQ-25) scores for General Vision were slightly but significantly better in the ZXR00V group than in the ZMB00 group (p < 0.05, Wald test). At high-performance levels, the two IOL groups had different characteristics regarding various visual performance parameters.
On the calibration of the cohesive strength for cohesive zone models in finite element analyses
Authors: Linke Max , Lammering Rolf 
Published: November 2022

Abstract
Cohesive zone models are commonly used to numerically model fracture phenomena on the microscale. Typical fracture processes are described experimentally via the Double Cantilever Beam test and the End Notched Flexure test on the macroscale. Analytical solutions, e.g. the LEFM-based beam theory, are used to evaluate these tests and to validate numerical models. However, some input parameters of cohesive zone models, i.e. cohesive stiffness and cohesive strength, are independent of the analytical solutions. In particular, the cohesive strength has a significant effect on the accuracy of the numerical model compared to the analytical solution and thus needs to be calibrated. This work extends the available literature by fitting the numerical to the analytical solution through calibration of the cohesive strength by using more suitable and generally applicable criteria. It considers the deformation, the applied load and the crack length of the specimen. The latter has been neglected so far in the existing literature. Via a parametric study, the derived criteria are minimised to find the best fit to the analytical solution. In addition, the effect of all input parameters and of the numerical element size on the calibrated cohesive strength is investigated. The obtained information can be used to qualify numerical models with coarse meshes to accurately compute fracture processes. Further, it provides a comprehensive understanding of the cohesive strength as a modelling parameter.
Using vibration data to classify conditions in disk stack separators
Authors: Merkelbach Silke , Afroze Lameya , Janssen Nils , von Enzberg Sebastian , Kühn Arno , Dumitrescu Roman 
Published: November 2022

Mounting sensors in disk stack separators is often a major challenge due to the operating conditions. However, a process cannot be optimally monitored without sensors. Virtual sensors can be a solution to calculate the sought parameters from measurable values. We measured the vibrations of disk stack separators and applied machine learning (ML) to detect whether the separator contains only water or whether particles are also present. We combined seven ML classification algorithms with three feature engineering strategies and evaluated our model successfully on vibration data of an experimental disk stack separator. Our experimental results demonstrate that random forest in combination with manual feature engineering using domain specific knowledge about suitable features outperforms all other models with an accuracy of 91.27 %.
Effect Of Introducing P-Fluorophenylalanine And Multiple Tryptophan Residues In A 13-Residue Antibacterial Peptide
Authors: Bikshapathy Erugurala , Sitaram Narasimhaiah , Nagaraf Ramakrishnan 
Published: November 2022

Abstract:
The effect of introducing tryptophan residues and p-fluorophenylalanine on the biological activities of the 13-residue antibacterial peptide PKLLTKFLKSWIG was investigated. Introduction of one and two Trp residues and replacement of Try and Phe by p-fluorophenylalanine resulted in enhanced antimicrobial activity as compared to the parent peptide
Unfolding and Disassociation of the FlgM/ σ28 Complex are Thermodynamically Coupled
Authors: Daughdrill G. W. 
Published: November 2022

Abstract:
FlgM and cr28 regulate the transcription of flagella and chemotaxis genes in E. coli and S. typhimurium. In an attempt to determine the strength of the interaction between FlgM and cr28 thermal unfolding studies were performed using circular dichroism spectroscopy (CD). A single, cooperative, melting transition was observed for the FlgM/cr28 complex suggesting that unfolding and disassociation of the complex occur simultaneously.
Inverse Peptide Synthesis In Solution Using Free Amino Acids As Amino Components
Authors: V Mitin Yu. , M.G Ryadnov 
Published: November 2022

Abstract:
We have realized inverse peptide synthesis in order to exclude deprotection reaction at every synthesis stage. This became possible using high solubility of free amino acids in dimethylformamide containing Ba(ClO4h, Ca(ClO4h or Ca(NO3)i. The developed method was tested on synthesis of(Leu5]-enkephaline, pentapeptide (1- 5) of cholecystokinin, pentapeptide (1-5) of indolicidin, hexapeptide of phekellistatin 7 and caeridin 1.1
Molecular Dynamics Simulation Of The Bzip Domain Of The C-Jun Homodimer
Authors: Jung Seunho , Choi Yong-Hoon , Yang Chul-Hak , Kim Hyun-Won 
Published: November 2022

Abstract:
Molecular dynamics simulation of the bZIP domain of the c-Jun homodimer has been performed. The conformational analyses of leucine zipper domain showed high consistency to the solution structure obtained from NMR spectroscopy [2]. The basic domain of homodimer exhibited a Gaussian distributed inter-domain wagging motion. Constant wagging motion of the basic domain was proposed to "grope" for DNA major grooves to recognize a specific sequence
Shuffling Alghorithm For Protein Design
Authors: Zielenkiewicz Piotr , Kaczanowski Szymon , Kierzek Andrzej M. 
Published: November 2022

Abstract:
A new algorithm producing a large number of divergent sequences which can adopt a defined structure is proposed. The algorithm can be applied to proteins of any size. This is achieved by constraining the amino acid composition to the native one and minimising the pseudoenergy function by "shuffling" the sequence. The algorithm is tested by sequence design for five different protein structures. Modelling by homology with the use of resultant sequences produces "proper" protein structures as judged using several different methods
The Risk Factors of Acute Coronary Syndrome in Young Women:
A Systematic Review and Meta-Analysis
Authors: Siagian Sisca Natalia , Christianto Christianto , Angellia Phoniex , Holiyono Ho Indra 
Published: November 2022

Background:
Acute coronary syndrome (ACS) has been one of the leading causes of
mortality in the world. Despite common understanding regarding ACS as an older population’s or
man's disease, the number of young women affected by this condition is increasing. Many studies
have assessed the risk factors of ACS, but only a few studies focused on this subpopulation. Therefore,
this systematic review and meta-analysis aim to evaluate the risk factors predisposing to ACS
in the young women population.

Methods:
Nine online databases were screened from the date of inception to September 2021,
where the acquired studies were evaluated using the PRISMA statement. The inclusion criteria
were a case control study with women age cut-off of <50 years. The risk factors of acute coronary
syndrome were analyzed using a random-effect model, expressed as summary statistics of odds ratio
(OR) for categorical variable and standard mean difference (SMD) for continuous data with
normal distribution, with 95% confidence interval (CI). Quality assessment was conducted using
the STROBE statement.

Results:
Seven studies with the total of 7042 patients met the inclusion criteria of this metaanalysis.
Diabetes mellitus, high BMI, obesity, hypercholestrolemia, hypertension, smoking, and
family history significantly increased acute coronary syndrome risk in young women. Other risks
such as heavy alcohol consumption, oral contraceptive use, and postmenopausal state were associated
with higher risk of ACS.

Conclusion:
The independent risk factors which are strongly related to ACS in young women were
diabetes mellitus, hypertension, and hypercholesterolemia with odd ratios of 6.21, 5.32, and 4.07.
Other risk factors which may be associated with an increased risk of ACS in young women were
heavy alcohol consumption, oral contraceptive use, and postmenopausal state. Health promotion
and effective intervention on this specific population regarding these risk factors can decrease
young female cardiovascular morbidity and mortality as well as improved quality of life of women.
Computational Search for Potential COVID-19 Drugs from Ayurvedic Medicinal Plants to Identify Potential Inhibitors against SARS-CoV-2 Targets
Authors: Alagarsamy V. , Solomon V. Raja , Sundar P. Shyam , Kulkarni Vishaka S. , Sulthana M.T. , Aishwarya A. Dharshini , Narendhar B. , Murugesan S. 
Published: November 2022

Background:To date, very few small drug molecules are used for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that has been discovered since the epidemic commenced in November 2019. SARS-CoV-2 RdRp and spike protein are essential targets for drug development amidst whole variants of coronaviruses.Objective:This study aims to discover and recognize the most effective and promising small molecules against SARS-CoV-2 RNA-dependent RNA polymerase (RdRp) and spike protein targets through molecular docking screening of 39 phytochemicals from five different Ayurveda medicinal plants.Methods:The phytochemicals were downloaded from PubChem, and SARS-CoV-2 RdRp and spike protein were taken from the protein data bank. The molecular interactions, binding energy, and ADMET properties were analyzed.Results:Molecular docking analysis identified some phytochemicals, oleanolic acid, friedelin, serratagenic acid, uncinatone, clemaphnol A, sennosides B, trilobine and isotrilobine from ayurvedic medicinal plants possessing greater affinity against SARS-CoV-2-RdRp and spike protein targets. Two molecules, namely oleanolic acid and sennosides B, with low binding energies, were the most promising. Furthermore, based on the docking score, we carried out MD simulations for the oleanolic acid and sennosides B-protein complexes.Conclusion:Molecular ADMET profile estimation showed that the docked phytochemicals were safe. The present study suggested that active phytochemicals from medicinal plants could inhibit RdRp and spike protein of SARS-CoV-2.
Prevalence and Transmission of Multi Drug Resistance Gene in Staphylococcus
aureus
Authors: Patra Bijayata , Chakraborty Tamalika , Ghosh Sutripto 
Published: November 2022

Abstract:
Antibiotics are antimicrobial substances that are commonly used to treat humans, ani-mals, and fish, as well as to research susceptibility patterns in a variety of bacteria. With the rising number of diseases and the emergence of new infections, many drugs for humans, animals, fish, and plants are being developed. However, with the development of pharmaceuticals came the advent of a phenomenon known as drug resistance, which has alarmed scientists and researchers all around the world. The building of resistance in genes that code for specific drugs, plasmids, or transposons, the action of multidrug efflux pumps, changes in chromosomal genes, or the Staphylococci cassette chromosome can all produce it. Staphylococcus aureus, the most common Gram-positive bacteria, has a multidrug-resistant phenotype that reveals its pathogenicity. Staphylococcus sp. possesses a variety of transmissible genes that cause them to be resistant to treatments such as antibiotics. The discovery of antibiotics by Alexander Fleming has long been a boon in the fight against bacterial illnesses. Drug-resistant bacteria have emerged as a result of antibiotic overuse and suboptimal us-age, attracting the attention of scientists throughout the world. Therefore, as a first step in combat-ing drug-resistant bacteria, it is obvious that widespread efforts to curb antibiotic abuse are required. This review focuses on and brings to society the prevalence of different multidrug resistant genes in Staphylococcus aureus and their transmission.
A Comprehensive Review of Quba and Its Correlation with Dermatophytosis
Authors: Shahid Arisha , Quamri Mohd Aleemuddin , Riyazuddin Mohd 
Published: November 2022

Background:
In the Unani text, the disease described by the name Quba matches the conventional description of Dermatophytosis, commonly referred to as Tinea or Ringworm. Although there is a slight variation in the disease etiology and pathogenesis, the clinical picture and the individual manifestations are by and large the same. This review elaborates on the Unani description of dermatophytosis (Quba) and highlights the relationship between the two entities.

Methods:
This review article was compiled after surfing thoroughly the available classical Unani literature and published articles in reputed journals.

Result:
This article comprehensively analyses both Quba and dermatophytosis as per their etiology, pathogenesis, clinical manifestations and management. Dermatophytosis is a superficial fungal infection whereas Quba is identified to be caused by viscid humours (Ghaleez Ratubaat) and morbid matter (Fasid Mawaad). As per the Unani principles of treatment, the disease Quba is treated using purgatives of black bile (Mukhrij Sauda), resolvent (Muhallil), and moderator (Muaddil) drugs along with some physical modalities like Leeching (Irsale Alaq) and Venesection (Fas’d), which is entirely different from the conventional treatment modality which includes the fungistatic and fungicidal antifungal agents for systemic as well as topical use

Conclusion:
This article tries to elaborate on various aspects of the disease Quba and dermatophytosis and to establish a correlation between the two terms. It also puts forth a potential alternative to the conventional treatment of dermatophytosis (Quba), provided by the Unani system of medicine.
Medical Text Simplification Using Reinforcement Learning (TESLEA): Deep Learning–Based Text Simplification Approach
Authors: Phatak Atharva , Savage David W , Ohle Robert , Smith Jonathan , Mago Vijay 
Published: November 2022

Background
In most cases, the abstracts of articles in the medical domain are publicly available. Although these are accessible by everyone, they are hard to comprehend for a wider audience due to the complex medical vocabulary. Thus, simplifying these complex abstracts is essential to make medical research accessible to the general public.

Objective
This study aims to develop a deep learning–based text simplification (TS) approach that converts complex medical text into a simpler version while maintaining the quality of the generated text.

Methods
A TS approach using reinforcement learning and transformer–based language models was developed. Relevance reward, Flesch-Kincaid reward, and lexical simplicity reward were optimized to help simplify jargon-dense complex medical paragraphs to their simpler versions while retaining the quality of the text. The model was trained using 3568 complex-simple medical paragraphs and evaluated on 480 paragraphs via the help of automated metrics and human annotation.

Results
The proposed method outperformed previous baselines on Flesch-Kincaid scores (11.84) and achieved comparable performance with other baselines when measured using ROUGE-1 (0.39), ROUGE-2 (0.11), and SARI scores (0.40). Manual evaluation showed that percentage agreement between human annotators was more than 70% when factors such as fluency, coherence, and adequacy were considered.

Conclusions
A unique medical TS approach is successfully developed that leverages reinforcement learning and accurately simplifies complex medical paragraphs, thereby increasing their readability. The proposed TS approach can be applied to automatically generate simplified text for complex medical text data, which would enhance the accessibility of biomedical research to a wider audience.
Prehabilitation Before Gastrointestinal Cancer Surgery: Protocol for an Implementation Study
Authors: Raso Kristy-Lee , Suen Michael , Turner Jane , Khatri Sonia , Lin Yanlan , Wildbore Carolyn , Becerril-Martinez Guillermo , Le Page Philip , Tan Sim Yee , Egger Sam , Vardy Janette 
Published: November 2022

Background
Surgery remains the standard curative treatment for early-stage colorectal and upper gastrointestinal cancer. Reduced preoperative functional capacity, nutritional status, and psychological well-being are associated with poor postoperative outcomes. Prehabilitation aims to improve preoperative functional reserves through physical, nutritional, and psychological interventions. Yet, how it transitions from a trial setting to being integrated into a real-world health setting is unknown.

Objective
The primary aim is to evaluate the implementation of a multimodal (supervised exercise, nutrition, and nursing support) prehabilitation program into standard care for patients with gastrointestinal cancer (colorectal and upper gastrointestinal cancer) scheduled for curative intent surgery. The secondary aim is to determine the impact of a multimodal prehabilitation program on functional capacity, nutritional and psychological status, and surgical outcomes.

Methods
This is an implementation study that will investigate a multimodal prehabilitation intervention, in a nonblinded, nonrandomized, single-group, pre-post design. Patients diagnosed with colorectal and upper gastrointestinal cancer scheduled for potentially curative intent surgery at Concord Repatriation General Hospital, with ≥14 intervention days prior to surgery and are medically cleared to exercise will be eligible. The study will be evaluated using the Reach, Effectiveness, Adoption, Implementation, and Maintenance Evaluation Framework.

Results
The protocol was approved in December 2019 by the Concord Repatriation General Hospital Human Research Ethics Committee (reference number 2019/PID13679). Recruitment commenced in January 2020. In response to the COVID-19 pandemic, recruitment was paused in March 2020 and reopened in August 2020 with remote or telehealth intervention adaptations. Recruitment ended on December 31, 2021. Over the 16-month recruitment period, a total of 77 participants were recruited.

Conclusions
Prehabilitation represents an opportunity to maximize functional capacity and improve surgical outcomes. The study will provide guidance and contribute to the evidence on the integration of prehabilitation into standard care using adaptive models of health care delivery including telehealth.

Trial Registration
Australian and New Zealand Clinical Trials Registry ACTR 12620000409976; https://anzctr.org.au/Trial/Registration/TrialReview.aspx?id=378974&isReview=true

International Registered Report Identifier (IRRID)
RR1-10.2196/41101
Association of Estimated Glomerular Filtration Rate With Progression of Albuminuria in Individuals With Type 2 Diabetes
Authors: Hanai Ko , Mori Tomomi , Yamamoto Yui , Yoshida Naoshi , Murata Hidekazu , Babazono Tetsuya 
Published: November 2022

OBJECTIVE
To elucidate the association of glomerular filtration rate (GFR) at baseline with subsequent progression of albuminuria in individuals with type 2 diabetes.

RESEARCH DESIGN AND METHODS
This was a single-center retrospective cohort study of 6,618 Japanese adults with type 2 diabetes and urinary albumin-to-creatinine ratio of &lt;300 mg/g, comprising 2,459 women and 4,159 men with a mean (± SD) age of 60 ± 12 years. The exposure was baseline estimated GFR (eGFR) (mL/min/1.73 m2), treated as a categorical variable and classified into five categories: ≥90, 75–90, 60–75, 45–60, and &lt;45, as well as a continuous variable. The outcome was progression of albuminuria category (i.e., from normoalbuminuria to micro- or macroalbuminuria or from micro- to macroalbuminuria). Hazard ratios (HRs) for the outcome were estimated using the multivariable Cox proportional hazards model. In the analysis treating baseline eGFR as a continuous variable, the multivariable-adjusted restricted cubic spline model was used.

RESULTS
During the median follow-up period of 6.3 years, 1,190 individuals reached the outcome. When those with a baseline eGFR of 75–90 mL/min/1.73 m2 were considered the reference group, HRs (95% CIs) for the outcome in those with a baseline eGFR of ≥90, 60–75, 45–60, or &lt;45 mL/min/1.73 m2 were 1.38 (1.14–1.66), 1.34 (1.14–1.58), 1.81 (1.50–2.20), or 2.37 (1.84–3.05), respectively. Furthermore, the inverse J-shaped curve was more clearly shown by the spline model.

CONCLUSIONS
This study of Japanese adults with type 2 diabetes suggests that both high and low GFRs are implicated in the pathogenesis of albuminuria progression.