syedzayyan/paper_mill_benchmark huggingface dataset:
Treatment advocate tactics to expand access to antiviral therapy for HIV and viral hepatitis C in low- to high-income settings: making sure no one is left behind.

Introduction worldwide, 71 million people are infected with hepatitis c virus (hcv), which, without treatment, can lead to liver failure or hepatocellular carcinoma.Hcv co-infection increases liver- and aids-related morbidity and mortality among hiv-positive people, despite art.A 12-week course of hcv direct-acting antivirals (daas) usually cures hcv - regardless of hiv status.However, patents and high prices have created access barriers for people living with hcv, especially people who inject drugs (pwid).Inadequate access to and coverage of harm reduction interventions feed the co-epidemics of hiv and hcv; as a result, the highest prevalence of hcv is found among pwid, who face additional obstacles to treatment (including stigma, discrimination and other structural barriers).The hiv epidemic occurred during globalization of intellectual property rights, and highlighted the relationship between patents and the high prices that prevent access to medicines.Indian generic manufacturers produced affordable generic hiv treatment, enabling global scale-up.Unlike hiv, donors have yet to step forward to fund hcv programmes, although daas can be mass-produced at a low and sustainable cost.Unfortunately, although voluntary licensing agreements between originators and generic manufacturers enable low-income (and some lower-middle income countries) to buy generic versions of hiv and hcv medicines, most middle-income countries with large burdens of hcv infection and hiv/hcv co-infection are excluded from these agreements.Our commentary presents tactics from the hiv experience that treatment advocates can use to expand access to daas.Discussion a number of practical actions can help increase access to daas, including new research and development (r&d) paradigms; compassionate use, named-patient and early access programmes; use of trips flexibilities such as compulsory licences and patent oppositions; and parallel importation via buyers' clubs.Together, these approaches can increase access to antiviral therapy for people living with hiv and viral hepatitis in low-, middle- and high-income settings.Conclusions the hiv example provides helpful parallels for addressing challenges to expanding access to hcv daas.Hcv treatment access - and harm reduction - should be massively scaled-up to meet the needs of pwid, and efforts should be made to tackle stigma and discrimination, and stop criminalization of drug use and possession.

Journal: Journal of the International AIDS Society (2018)
Publication types: Journal Article
Apheresis physician well-being during the COVID-19 pandemic: Results of a survey.

The covid-19 pandemic has placed additional stressors on physician lives.In this study, we report findings from a survey conducted among attending physician (ap) members of the american society for apheresis (asfa) to elucidate the status of their well-being during the covid-19 pandemic as well as resources provided or actions taken by their institutions and themselves personally to maintain or improve their well-being.Study design and methods a 17-question, voluntary, irb-approved survey regarding well-being was distributed to the asfa ap members between august 26, 2020 and september 16, 2020.The descriptive analyses were reported as number and frequency of respondents for each question.Non-parametric chi-square tests, anova, and paired t-tests were performed to determine differences in categorical variables, changes in well-being scores, and compare time points, respectively.Results based on the responses of 70 attending level physicians representing the united states (u.s., 53, 75.7%) and outside the u.s.(17, 24.3%), the following were observed: (1) covid-19 negatively affects the well-being of a sub-population of aps, (2) neither institutional nor individual measures to improve well-being completely resolved the problem of decreased ap well-being during the pandemic, and (3) personal actions may be superior to institutional resources.Conclusion there is a widespread decline in ap well-being during the covid-19 pandemic that was not adequately improved by institutional or personal resources/actions taken.Institutions and physicians must work together to implement strategies including resources and actions that could further improve ap physician well-being during a public health crisis.

Journal: Transfusion (2021)
Publication types: Clinical Trial;Journal Article
Plasma Cell-Free DNA Predicts Survival and Maps Specific Sources of Injury in Pulmonary Arterial Hypertension.

Cell-free dna (cf dna) is a noninvasive marker of cellular injury.Its significance in pulmonary arterial hypertension (pah) is unknown.Methods plasma cf dna was measured in 2 pah cohorts (a, n=48; b, n=161) and controls (n=48).Data were collected for reveal 2.0 (registry to evaluate early and long-term pah disease management) scores and outcome determinations.Patients were divided into the following reveal risk groups: low (≤6), medium (7-8), and high (≥9).Total cf dna concentrations were compared among controls and pah risk groups by 1-way analysis of variance.Log-rank tests compared survival between cf dna tertiles and reveal risk groups.Areas under the receiver operating characteristic curve were estimated from logistic regression models.A sample subset from cohort b (n=96) and controls (n=16) underwent bisulfite sequencing followed by a deconvolution algorithm to map cell-specific cf dna methylation patterns, with concentrations compared usingttests.Results in cohort a, median (interquartile range) age was 62 years (47-71), with 75% female, and median (interquartile range) reveal 2.0 was 6 (4-9).In cohort b, median (interquartile range) age was 59 years (49-71), with 69% female, and median (interquartile range) reveal 2.0 was 7 (6-9).In both cohorts, cf dna concentrations differed among patients with pah of varying reveal risk and controls (analysis of variance p≤0.002) and were greater in the high-risk compared with the low-risk category (p≤0.002).In cohort b, death or lung transplant occurred in 14 of 54, 23 of 53, and 35 of 54 patients in the lowest, middle, and highest cf dna tertiles, respectively.Cf dna levels stratified as tertiles (log-rank:p=0.0001) and reveal risk groups (log-rank:p<0.0001) each predicted transplant-free survival.The addition of cf dna to reveal improved discrimination (area under the receiver operating characteristic curve, 0.72-0.78;p=0.02).Compared with controls, methylation analysis in patients with pah revealed increased cf dna originating from erythrocyte progenitors, neutrophils, monocytes, adipocytes, natural killer cells, vascular endothelium, and cardiac myocytes (bonferroni adjusted p<0.05).Cf dna concentrations derived from erythrocyte progenitor cells, cardiac myocytes, and vascular endothelium were greater in patients with pah with high-risk versus low-risk reveal scores (p≤0.02).Conclusions circulating cf dna is elevated in patients with pah, correlates with disease severity, and predicts worse survival.Results from cf dna methylation analyses in patients with pah are consistent with prevailing paradigms of disease pathogenesis.

Journal: Circulation (2022)
Publication types: Journal Article;Research Support, N.I.H., Intramural
Evans Calcaneal Osteotomy: Assessment of Multiplanar Correction.

Flatfoot deformity consists of collapse of the medial arch, forefoot abduction, increased talonavicular uncoverage, and hindfoot valgus.Although numerous soft tissue and bony procedures have been proposed to correct each plane of deformity, there is a lack of objective data in the literature quantifying the amount of structural correction.The purpose of this study was to quantify the multiplanar deformity correction of the lateral column lengthening osteotomy (evans) on hindfoot alignment through objective, reproducible, radiographic measurements.We retrospectively reviewed 45 evans calcaneal osteotomy procedures in 24 female (53%) and 21 male (47%) feet performed on 40 patients (5 bilateral).The mean follow-up was 53 weeks (range, 32-116).The mean age at the time of surgery was 35 years (range, 11-73).Statistically significant improvement in radiographic alignment was found in the calcaneal inclination angle, tibial-calcaneal angle, tibial-calcaneal position, and the anteroposterior talo-first metatarsal angle (p < .0001 for all).Although a direct correlation between graft size and degree of angular correction was not observed, it should be noted the calcaneal graft size (mean, 11.8 mm) and the amount of hindfoot valgus correction (mean, 12.6°) appear to be clinically related.The results of this study support that the evans calcaneal osteotomy corrects the hindfoot alignment in 3 planes as evidenced by our multiplanar radiographic measurements.

Journal: The Journal of foot and ankle surgery : official publication of the American College of Foot and Ankle Surgeons (2022)
Publication types: Journal Article
Advanced Metal-Organic Frameworks-Based Catalysts in Electrochemical Sensors.

Developing efficient catalysts is vital for the application of electrochemical sensors.Metal-organic frameworks (mofs), with high porosity, large specific surface area, good conductivity, and biocompatibility, have been widely used in catalysis, adsorption, separation, and energy storage applications.In this invited review, the recent advances of a novel mof-based catalysts in electrochemical sensors are summarized.Based on the structure-activity-performance relationship of mof-based catalysts, their mechanism as electrochemical sensor, including metal cations, synthetic ligands, and structure, are introduced.Then, the mof-based composites are successively divided into metal-based, carbon-based, and other mof-based composites.Furthermore, their application in environmental monitoring, food safety control, and clinical diagnosis is discussed.The perspective and challenges for advanced mof-based composites are proposed at the end of this contribution.

Journal: Frontiers in chemistry (2022)
Publication types: Journal Article;Review
Mutations in the John Cunningham virus VP1 gene could predispose to the development of progressive multifocal leukoencephalopathy in multiple sclerosis patients undergoing treatment with natalizumab.

Patients with multiple sclerosis (ms) undergoing treatment with natalizumab (ntz) are at risk of developing progressive multifocal leukoencephalopathy (pml) due to the reactivation of john cunningham (jc) virus.A relevant characteristic among pml cases is the development of single nucleotide mutations in the vp1 gene of the causal jc virus.The identification of such mutations in timely manner can provide valuable information for ms management.Objective to identify mutations along the jc virus vp1 gene in ms patients undergoing treatment with ntz, and correlate them with anti-jc virus antibody index.Methods eighty-eight ms patients, one hundred twenty controls, and six patients with diagnosis of human immunodeficiency virus (hiv) with and without secondary pml were included.Jc virus was identified in peripheral blood mononuclear cells and cerebrospinal fluid by pcr.Amplification and sequencing of the entire length of the vp1 gene were performed in all positive clinical samples.Results in ms cases no mutations were observed in the jc virus vp1 gene, but it was positive in hiv controls with pml.Interestingly, the jc virus vp1 gene sequence derived from the hiv patients exhibited a non-silent substitution in position 186 (g → c), leading to an amino acid change (lys → asp).We did not find correlation between anti-jc virus antibody index and dna viral detection.Conclusions .The identification of single nucleotide mutants in the jc virus vp1 gene might be an early predictive marker to pml for efficient patient treatment and follow-up.

Journal: Multiple sclerosis and related disorders (2021)
Publication types: Journal Article
Molecular characterization of antimicrobial susceptibility of Salmonella isolates: First identification of a plasmid carrying qnrD or oqxAB in Taiwan.

/purpose the aim of this study is to characterize antibiotic-nonsusceptible salmonella isolates in taiwan.Methods a total of 76 salmonella isolates showing lower susceptibility to cephalosporins or quinolones were identified from 1416 clinical isolates from 1999 to 2008.Minimal inhibitory concentrations for selected antimicrobial agents were tested by the agar dilution method.Antibiotic resistance-related genes were determined by polymerase chain reaction (pcr) combined with sequencing.Southern blotting, conjugation tests, and transformation tests were used to characterize plasmid-mediated quinolone resistance (pmqr) determinants.Results the observed nonsusceptible phenotypes of 76 isolates were against cefoxitin (57.9%), cefotaxime (43.4%), ceftazidime (40.8%), ceftriaxone (42.1%), cefepime (5.3%), ciprofloxacin (80.3%), and levofloxacin (81.6%).Among 44 cephalosporin-resistant isolates, tem-1, cmy-2, cmy-14, ctx-m-3-like and ctx-m-15-like determinants were present in 31 (70.5%), 32 (72.7%), 1 (2.3%), 1 (2.3%), and 1 (2.3%) of isolates, respectively.Pcr screening for pmqr genes of 62 quinolone-nonsusceptible isolates revealed the presence of qnr s, qnr d, aac(6')-ib-cr, and oqx ab in 3 (4.8%), 2 (3.2%), 1 (1.6%), and 10 (16.1%) isolates, respectively.Among 36 isolates showing high resistance to quinolones, s83f/d87n and s83f/d87g amino acid substitutions of gyr a were found in 29 (80.6%) and 6 (16.7%) isolates, respectively.Moreover, among quinolone highly resistant isolates, eight (22.2%) of isolates showed over-expression of the paβn-sensitive efflux pump.Transformants and transconjugants harboring qnr d- or oqx ab-plasmids showed decreased susceptibility to quinolones.Conclusion gyr a mutations are the major mechanisms associated with quinolone-resistant salmonella isolates in taiwan.Overproduction of efflux pump genes and the presence of qnr and oqx ab play additional roles in reduced susceptibility to quinolones.

Journal: Journal of microbiology, immunology, and infection = Wei mian yu gan ran za zhi (2017)
Publication types: Journal Article
Relationship between foot morphology, muscle strength, and physical performance test in women aged 65 years and older: a cross-sectional study.

Hallux valgus is a foot deformity that may affect gait, thus increasing the risk of falls among older people.We investigated the relationship between foot morphology, muscle strength, and physical performance.Methods in this study, community-dwelling older people aged ≥65 years were included.A three-dimensional footprint automatic measurement apparatus was used to measure the hallux valgus angle, arch height ratio, and heel-floor angle.Furthermore, the toe flexor strength and ankle plantar flexion strength were measured.Physical performance tests included the five-repetition sit-to-stand test, one-leg standing time, maximal step length, functional reach test, and 5-m fastest walking time (walking time).The relationship between the hallux valgus angle and foot morphology and muscle strength was examined.In addition, factors affecting physical performance testing were assessed.Two-group comparisons, correlation, and multiple comparisons were used for statistical analyses.Results of the 133 women (age 77.7 ± 6.2 years), 57 had hallux valgus and 76 had no hallux valgus.There was a significant difference in the arch height ratio and heel-floor angle between women with and without hallux valgus (p < 0.001).A correlation was found between the hallux valgus angle and the heel-floor angle (r = 0.468, p < 0.001) and arch height ratio (r = - 0.337, p < 0.001), respectively.Multiple regression analysis showed that the hallux valgus angle was related to functional reach (β = - 0.162, p = 0.042), and toe flexor strength was related to five-repetition sit-to-stand (β = - 0.182, p = 0.036), maximal step length (β = 0.328, p < 0.001), and walking time (β = - 0.219, p = 0.006).Conclusions a relationship was found between the hallux valgus angle, arch height rate, and inward inclination angle of the calcaneus.Functional reach was predicted based on the hallux valgus angle, whereas the five-repetition sit-to-stand, maximal step length, and walking time were predicted based on toe flexor strength.Hallux valgus predicted not only the forefoot but also the foot morphology and was related to physical performance.From the perspective of motor function and fall prevention, efforts should be made to better understand and prevent the onset and progression of hallux valgus.

Journal: BMC musculoskeletal disorders (2022)
Publication types: Journal Article
Disabled Throwing Shoulder: 2021 Update: Part 2-Pathomechanics and Treatment.

The purpose of this paper is to provide updated information for sports healthcare specialists regarding the disabled throwing shoulder (dts).A panel of experts, recognized for their experience and expertise in this field, was assembled to address and provide updated information on several topics that have been identified as key areas in creating the dts spectrum.Each panel member submitted a concise presentation on one of the topics within these areas, each of which were then edited and sent back to the group for their comments and consensus agreement in each area.Part two presents the following consensus conclusions and summary findings regarding pathomechanics and treatment, including (1) internal impingement results from a combination of scapular protraction and humeral head translation; (2) the clinically significant labral injury that represents pathoanatomy can occur at any position around the glenoid, with posterior injuries most common; (3) meticulous history and physical examination, with a thorough kinetic chain assessment, is necessary to comprehensively identify all the factors in the dts and clinically significant labral injury; (4) surgical treatment should be carefully performed, with specific indications and techniques incorporating low profile implants posterior to the biceps that avoid capsular constraint; (5) rehabilitation should correct all kinetic chain deficits while also developing high-functioning, throwing-specific motor patterns and proper distribution of loads and forces across all joints during throwing; and (6) injury risk modification must focus on individualized athlete workload to avoid overuse.Level of evidence: v, expert opinion.

Journal: Arthroscopy : the journal of arthroscopic & related surgery : official publication of the Arthroscopy Association of North America and the International Arthroscopy Association (2022)
Publication types: Journal Article
DriverFuse: An R package for analysis of next-generation sequencing datasets to identify cancer driver fusion genes.

We developed the driver fuse package to integrate orthogonal data types such as structural variants (sv) and copy number variations (cnv) to characterize fusion genes in cancer datasets.A fusion gene is reported as a driver or passenger fusion gene, based on mapping sv and cnv profiles.Driver fuse generates a fusion plot of fusion genes with their mapping sv, cnv profile, domain architecture and classification of its role in cancer.The analysis facilitates discrimination of driver fusions from passenger fusions.To demonstrate the utility of driver fuse, we analyzed two datasets, one each for ccle (cancer cell line encyclopedia) for lung cancer and hcc1395bl for breast cancer.The analysis validates the driver fusion genes that are already reported for the datasets.Thus, driver fuse is a valuable tool for studying the driver fusion genes in cancers, enabling the identification of recurrent complex rearrangements that provide intuitive insights into disease driver events.

Journal: PloS one (2022)
Publication types: Journal Article
Bending Vibration Characteristics of a Novel Piezoelectric Composite Trilaminar Vibrator.

In this work, the bending vibration characteristics of the 2-2 piezoelectric composite trilaminar vibrator are studied by the finite element simulation and experiment.The simulation results show that the trilaminar vibrator has lower resonant frequency and larger vibration displacement under the fixed boundary condition compared with that of the free boundary condition, and its performance is relatively good.Then, the 2-2 piezoelectric composite and piezoelectric ceramic trilaminar vibrators are fabricated and their performances are tested under the fixed boundary condition.The experimental and simulation results show that the vibrator has pure bending vibration characteristics in the frequency band of 1.2-1.4 k hz, especially the 2-2 piezoelectric composite vibrator, which has lower frequency, higher electromechanical coupling coefficient and larger bending vibration displacement; thus, the 2-2 piezoelectric composite trilaminar vibrator is a better choice for the fabrication of a low-frequency transducer.

Journal: Materials (Basel, Switzerland) (2021)
Publication types: Journal Article
Presymptomatic macrophage targeting has a long-lasting therapeutic effect on treatment termination in a mouse model of Charcot-Marie-Tooth 1.

Macrophage-mediated inflammation is a potent driver of disease progression in mouse models of charcot-marie-tooth (cmt) 1 diseases.This leads to the possibility to consider these cells as therapeutic targets to dampen disease outcome in the so far non-treatable neuropathies.As a pharmacological proof-of-principle study, long-term targeting of nerve macrophages with the orally applied csf-1 receptor specific kinase (c-fms) inhibitor plx5622 showed a substantial alleviation of the neuropathy in distinct cmt1 mouse models.However, regarding translational options, clinically relevant questions emerged regarding treatment onset, duration and termination.Corroborating previous data, we here show that in a model for cmt1b, peripheral neuropathy was substantially alleviated after early continuous plx5622 treatment in cmt1b mice, leading to preserved motor function.However, late-onset treatment failed to mitigate histopathological and clinical features, despite a similar reduction in the number of macrophages.Surprisingly, in cmt1b mice, terminating early plx5622 treatment at six months was still sufficient to preserve motor function at 12 months of age, suggesting a long-lasting, therapeutic effect of early macrophage depletion.This novel and unexpected finding may have important translational implications, since we here show that continuous macrophage targeting appears not to be necessary for disease alleviation, provided that the treatment starts within an early, critical time window.

Journal: Experimental neurology (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't