syedzayyan/paper_mill_benchmark huggingface dataset:
Automated Diagnosis of COVID-19 Using Deep Supervised Autoencoder With Multi-View Features From CT Images.

Accurate and rapid diagnosis of coronavirus disease 2019 (covid-19) from chest ct scans is of great importance and urgency during the worldwide outbreak.However, radiologists have to distinguish covid-19 pneumonia from other pneumonia in a large number of ct scans, which is tedious and inefficient.Thus, it is urgently and clinically needed to develop an efficient and accurate diagnostic tool to help radiologists to fulfill the difficult task.In this study, we proposed a deep supervised autoencoder (dsae) framework to automatically identify covid-19 using multi-view features extracted from ct images.To fully explore features characterizing ct images from different frequency domains, dsae was proposed to learn the latent representation by multi-task learning.The proposal was designed to both encode valuable information from different frequency features and construct a compact class structure for separability.To achieve this, we designed a multi-task loss function, which consists of a supervised loss and a reconstruction loss.Our proposed method was evaluated on a newly collected dataset of 787 subjects including covid-19 pneumonia patients, other pneumonia patients, and normal subjects without abnormal ct findings.Extensive experimental results demonstrated that our proposed method achieved encouraging diagnostic performance and may have potential clinical application for the diagnosis of covid-19.

Journal: IEEE/ACM transactions on computational biology and bioinformatics (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
A systematic review to identify research priority setting in Black and minority ethnic health and evaluate their processes.

Black, asian and minority ethnic communities suffer from disproportionately poorer health than the general population.This issue has been recently exemplified by the large numbers of infection rates and deaths caused by covid-19 in bame populations.Future research has the potential to improve health outcomes for these groups.High quality research priority setting is crucial to effectively consider the needs of the most vulnerable groups of the population.Objective the purpose of this systematic review is to identify existing research priority studies conducted for bame health and to determine the extent to which they followed good practice principles for research priority setting.Method included studies were identified by searching medline, cinnahl, psych info, psychology and behavioral sciences collection, as well as searches in grey literature.Search terms included "research priority setting", "research prioritisation", "research agenda", "black and minority ethnic", "ethnic group".Studies were included if they identified or elicited research priorities for bame health and if they outlined a process of conducting a research prioritisation exercise.A checklist of nine common themes of good practice in research priority setting was used as a methodological framework to evaluate the research priority processes of each study.Results out of 1514 citations initially obtained, 17 studies were included in the final synthesis.Topic areas for their research prioritisation exercise included suicide prevention, knee surgery, mental health, preterm birth, and child obesity.Public and patient involvement was included in eleven studies.Methods of research prioritisation included workshops, delphi techniques, surveys, focus groups and interviews.The quality of empirical evidence was diverse.None of the exercises followed all good practice principles as outlined in the checklist.Areas that were lacking in particular were: the lack of a comprehensive approach to guide the process; limited use of criteria to guide discussion around priorities; unequal or no representation from ethnic minorities, and poor evaluation of their own processes.Conclusions research priority setting practices were found to mostly not follow good practice guidelines which aim to ensure rigour in priority setting activities and support the inclusion of bame communities in establishing the research agenda.Research is unlikely to deliver useful findings that can support relevant research and positive change for bame communities unless they fulfil areas of good practice such as inclusivity of key stakeholders' input, planning for implementation of identified priorities, criteria for deciding on priorities, and evaluation of their processes in research priority setting.

Journal: PloS one (2021)
Publication types: Journal Article;Research Support, Non-U.S. Gov't;Systematic Review
Environmentally Improved Coherent Light Harvesting.

Coherence-enhanced light harvesting has not been directly observed experimentally, despite theoretical evidence that coherence can significantly enhance light-harvesting performance.The main experimental obstacle has been the difficulty in isolating the effect of coherence in the presence of confounding variables.Recent proposals for externally controlling coherence by manipulating the light's degree of polarization showed that coherent efficiency enhancements would be possible, but they were restricted to light-harvesting systems weakly coupled to their environment.Here, we show that increases in system-bath coupling strength can amplify coherent efficiency enhancements, rather than suppress them.This result dramatically broadens the range of systems that could be used to conclusively demonstrate coherence-enhanced light harvesting or to engineer coherent effects into artificial light-harvesting devices.

Journal: The journal of physical chemistry letters (2021)
Publication types: Journal Article
Expertise of Surgeons Publishing Novel Techniques in theJournal of Wrist Surgery.

Introduction recent efforts to standardize reporting of surgeon experience in novel technique publications have recommended reporting of tang level of expertise (loe).question/purpose the aim of this study was to document trends in loe reporting for novel technique articles published in the journal of wrist surgeryand evaluate whether author experience affects novel research outcomes.methods a total of 261 articles published from 2018 to 2020 were reviewed.Articles describing novel surgical techniques were included and examined for tang loe.Author variables were collected online.results eight percent (21/261) of articles discussed novel surgical techniques and one reported loe.Nearly half (47.6%) of articles did not conduct statistical analysis.Four (19.0%) reported insignificant statistical results and 7 (33.3%) reported significant findings.All significant statistical findings were positive.Number of prior related publications by the senior author did not affect new technique result significance (p= 0.34).discussion from 2018 to 2020, only one article documented loe.Authors' variables, including number of prior related publications, were not correlated with significant results in their new publications.This may suggest that an author's established experience in a novel technique, quantified by prior publications on the topic, does not make one more likely to achieve significantly better or worse outcomes in their reviewed journal of wrist surgerystudy.conclusions tang loe is an important way for readers to classify expertise and should be reported, and potentially modified to better define contributing variables.

Journal: Journal of wrist surgery (2022)
Publication types: Journal Article
Inhibition of regulator of G protein signaling 10, aggravates rheumatoid arthritis progression by promoting NF-κB signaling pathway.

Rheumatoid arthritis (ra) is the most common inflammatory arthropathy, with evidence pointing to an immune-mediated etiology that propagates chronic inflammation.Although targeted immune therapeutics and aggressive treatment strategies have substantially improved, a complete understanding of the associated pathological mechanisms of the disease remains elusive.This study aimed at investigating whether regulator of g protein signaling 10 (rgs10) could affect rheumatoid arthritis (ra) pathology by regulating the immune response.A dba/j1 mouse model of ra was established and evaluated for disease severity.Rgs10 expression was inhibited by adeno-associated virus in vivo.Moreover, small interfering rna was used to downregulate rgs10 expression in raw 264.7 cells in vitro.Results showed that rgs10 inhibition augmented ra severity, and attenuated the increase in expression of inflammatory factors.Furthermore, activated nf-κb signaling pathways were detected following rgs10 inhibition.These results revealed that rgs10 inhibition directly aggravated the ra pathological process by activating the nf-κb signaling pathway.Therefore, rgs10 is a promising novel therapeutic target for ra treatment with a potential clinical impact.

Journal: Molecular immunology (2021)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Fat-restricted low-glycemic index diet controls weight and improves blood lipid profile: A pilot study among overweight and obese adults in Southwest China.

Evidence from trials demonstrating the benefits and risks of low-glycemic index and fat-restricted diets in weight loss and blood lipid profile changes is unclear.This study aimed to assess the implemented and effects of a fat-restricted low-glycemic index diet on weight control and blood lipid profile changes in in overweight/obese southwest chinese individualst.this prospective pilot study enrolled overweight/obese subjects at the people's hospital of sichuan province between february and july 2019.The daily energy intake was reduced by 300 to 500 kcal according to the participant's weight and activity level, with low-glycemic index carbohydrate- and fat-energy ratios < 45% and 25% to 30%, respectively.Participants received guidance for 3 months by telephone follow-up, internet interaction, or we chat.Changes in weight, body composition, and blood profile were measured.a total of 254 patients were finally analyzed, including 101 males and 153 females.After adjusting for potential confounders, weight (p < .001), body mass index (p < .001), waist circumference (p < .001), waist-hip ratio (p < .001), body fat percentage (p < .001), visceral fat area (p < .001), basal metabolism (p = .002), cholesterol (p < .001), and triglycerides (p < .001) were significantly reduced after the 3-month intervention.The above indexes showed no significant differences between men and women.regardless of gender, fat-restricted low-glycemic index diet might be helpful for controlling weight and lowering blood cholesterol and triglycerides in overweight/obese individuals in southwest china.

Journal: Medicine (2021)
Publication types: Journal Article;Observational Study
Acellular Dermal Matrix Mimicking a New Retroareolar Mass After Central Pillar Neonipple Reconstruction.

Acellular dermal matrix (adm) is an increasingly popular alloplastic cadaveric dermis used to enhance postmastectomy reconstruction.Acellular dermal matrix can be used as a nipple-shaped cylinder in central pillar nipple reconstruction to help maintain long-term projection.We report a unique presentation of adm mimicking a retroareolar mass after central pillar neonipple reconstruction.A 49-year-old woman with a history of invasive ductal carcinoma underwent delayed nipple reconstruction after lumpectomy and oncoplastic closure using an inframammary v-y advancement flap.the nipple reconstruction was performed using pretattoo and articulated tab flaps.A rolled tube of acellular dermal matrix was placed in the central aspect of the neonipple reconstruction for projection.At 4 months postoperative, a screening mammogram and ultrasound noted a new retroareolar mass classified as birads 4 necessitating a breast biopsy.Biopsy revealed portions of fibrous connective tissue consistent with partially incorporated acellular dermal matrix allograft.There was no evidence of malignancy.To mitigate the risk of future radiographic or clinical misinterpretation of adm in nipple reconstruction, the placement of radiopaque markers such as microclips on the adm implant could be a useful adjunct.Radiologists and surgeons should include adm artifact in their differential diagnosis of radiologic imaging when evaluating a new mass in the proximity of prior adm placement in neonipple reconstruction of the breast.

Journal: Annals of plastic surgery (2022)
Publication types: Case Reports;Journal Article
Psychophysical assessments of olfaction after endoscopic unilateral resection with post-operative radiotherapy in olfactory neuroblastomas.

Endoscopic resection with post-operative radiotherapy has been included in the standard therapeutic options for olfactory neuroblastomas (onbs).Recent publications have indicated the feasibility of olfactory preservation after endoscopic unilateral resection of onbs.This study validated residual olfaction using the psychophysical assessment, t & t olfactometer, in patients who underwent endoscopic unilateral resection with post-operative radiotherapy.A single-institutional retrospective review was performed to identify patients who underwent endoscopic unilateral resection of onbs with olfaction monitoring using t & t olfactometer between 2009 and 2020.T & t olfactometry was performed before surgery, after surgery, before radiotherapy, and after completion of radiotherapy.Four patients (one female and three males) were identified.The mean observation period was 41.9 months, and all patients showed no evidence of disease.Three patients exhibited residual olfactory function with two patients having normal or pre-operative level olfaction, although t & t olfactometer results showed a temporary increase in recognition thresholds after surgery.As consequence, endoscopic unilateral resection can achieve satisfactory olfactory preservation in patients with early-stage onbs.

Journal: Auris, nasus, larynx (2022)
Publication types: Case Reports;Validation Study;Journal Article
Assessment of Sulphate and Iron Contamination and Seasonal Variations in the Water Resources of a Damodar Valley Coalfield, India: A Case Study.

The aim of the present study was to assess the sulphate [formula: see text] and iron (fe) contamination and seasonal variations in the water resources (groundwater, surface water, and mine water) of the west bokaro coalfield region, india.One hundred and twenty-four water resources samples were collected from the coalfield during the post- and pre-monsoon seasons.The concentrations of [formula: see text] were determined using ion chromatography and fe concentrations were analyzed using inductively coupled plasma mass spectrometry.A statistical analysis was used to easily understand the seasonal variations of the elements in the water resources of the area.The concentrations of [formula: see text] and fe in the water resources were higher in the pre-monsoon season than in the post-monsoon season, irrespective of location.The water resources of the coalfield were contaminated with high concentrations of [formula: see text] and fe, and would require suitable treatment before drinking, domestic and industrial uses.

Journal: Bulletin of environmental contamination and toxicology (2018)
Publication types: Journal Article
Reliability and agreement of the Nine Hole Peg Test in patients with unilateral spastic cerebral palsy.

Upper extremity involvement is one of the most common motor impairments in children with unilateral spastic cerebral palsy (cp).One tool for the assessment of manual function in cp is the nine hole peg test (nhpt).However, the reliability of the nhpt in patients with unilateral cp is unknown.This study aimed to analyze the intra-rater inter-session reliability of the nhpt in unilateral spastic cp, for its use in clinical practice and research.A total of 27 participants with spastic unilateral cp were included.Reliability was verified by the intraclass correlation coefficient (icc), standard error of measurement, and minimum detectable change.The agreement was analyzed by the bland-altman method.An excellent intra-rater reliability was observed for the non-affected side (icc = 0.94) and the affected side (icc = 0.96).The minimal detectable change was 4 and 12 s for the non-affected and affected side, respectively.There were no significant biases between repetitions.Conclusions: the nhpt showed excellent intra-rater inter-session reliability in patients with spastic unilateral cp.In addition, the test shows adequate agreement and proportionally small errors to assess manual dexterity.What is known: • the nine hole peg test (nhpt) is widely used to assess dexterity in patients with neurological conditions.• the nhpt has demonstrated appropriate measurement properties in healthy children and adults with neurological conditions.What is new: • the nhpt presents excellent reliability, small measurement errors, and adequate agreement for the assessment of patients with cerebral palsy.• the measurement error of the nhpt in unilateral cerebral palsy may be up to 13% of the total time to perform it.

Journal: European journal of pediatrics (2022)
Publication types: Journal Article
Pharmacogenetics of Praziquantel Metabolism: Evaluating the Cytochrome P450 Genes of Zimbabwean Patients During a Schistosomiasis Treatment.

Schistosomiasis is a parasitic disease infecting over 236 million people annually, with the majority affected residing on the african continent.Control of this disease is reliant on the drug praziquantel (pzq), with treatment success dependent on an individual reaching pzq concentrations lethal to schistosomes.Despite the complete reliance on pzq to treat schistosomiasis in africa, the characterization of the pharmacogenetics associated with pzq metabolism in african populations has been sparse.We aimed to characterize genetic variation in the drug-metabolising cytochrome p450 enzymes (cyps) and determine the association between each variant and the efficacy of pzq treatment in zimbabwean patients exposed to schistosoma haematobiuminfection.Genomic dna from blood samples of 114 case-control zimbabweans infected with schistosomes were sequenced using the cyp1a2,cyp2c9,cyp2c19,cyp2d6,cyp3a4, and cyp3a5genes as targets.Bioinformatic tools were used to identify and predict functional effects of detected single nucleotide polymorphisms (snps).A random forest (rf) model was then used to assess snps most predictive of pzq efficacy, with a misclassification rate of 29%.Snps were detected across all six genes, with 70 snps identified and multiple functional changes to the cyp enzymes predicted.Only four snps were significantly associated with pzq efficacy using χ2tests, with rs951840747 (or: 3.61,p= 0.01) in the cyp1a2gene having the highest odds of an individual possessing this snp clearing infection, and rs6976017 (or: 2.19,p= 0.045) of cyp3a5determined to be the most predictive of pzq efficacyviathe rf.Only the rs28371702 (cc) genotype (or: 2.36,p= 0.024) of cyp2d6was significantly associated with an unsuccessful pzq treatment.This study adds to the genomic characterization of the diverse populations in africa and identifies variants relevant to other pharmacogenetic studies crucial for the development and usage of drugs in these populations.

Journal: Frontiers in genetics (2022)
Publication types: Journal Article
Self-injury in autism spectrum disorder: an effect of serotonin transporter gene promoter variants.

Self-injurious behavior in autism spectrum disorder (asd) has been associated with lower whole blood serotonin levels and the role of serotonin transporter gene promoter region (5httlpr) polymorphisms is of interest because of their effects on transporter functioning.This study examined the association between self-injurious behavior in asd and allelic frequencies of 5httlpr.Sixty-four children and adolescents with asd who were not taking serotonergic medication at the time of the assessment were included in the analysis.Self-injury was assessed using the autism diagnostic interview-revised (adi-r) and whole blood serotonin levels were measured using high-pressure liquid chromatography (hplc) with fluorometic detection.Dna was extracted from saliva and pcr amplified with fluorescent primers.Self-injury significantly increased with the number of la alleles of the 5httlpr and decreased with the number of lg alleles.Self-injury in asd may be associated with a specific genotype of the serotonin transporter gene promoter region.Future studies should continue to explore subgroups to clarify the underlying clinical and genetic heterogeneity in asd.

Journal: Psychiatry research (2014)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Proteinopathy and Longitudinal Cognitive Decline in Parkinson Disease.

And objectives people with parkinson disease (pd) commonly experience cognitive decline, which may relate to increased α-synuclein, tau, and β-amyloid accumulation.This study examines whether the different proteins predict longitudinal cognitive decline in pd.Methods all participants (pd n = 152, controls n = 52) were part of a longitudinal study and completed a lumbar puncture for csf protein analysis (α-synuclein, total tau [tau], and β-amyloid42[β-amyloid]), a β-amyloid pet scan, and/or provided a blood sample for apoegenotype (ε4+, ε4-), which is a risk factor for β-amyloid accumulation.Participants also had comprehensive, longitudinal clinical assessments of overall cognitive function and dementia status, as well as cognitive testing of attention, language, memory, and visuospatial and executive function.We used hierarchical linear growth models to examine whether the different protein metrics predict cognitive change and multivariate cox proportional hazard models to predict time to dementia conversion.Akaike information criterion was used to compare models for best fit.Results baseline measures of csf β-amyloid predicted decline for memory (p= 0.04) and overall cognitive function (p= 0.01).apoegenotypes showed a significant group (ε4+, ε4-) effect such that ε4+ individuals declined faster than ε4- individuals in visuospatial function (p= 0.03).Baseline β-amyloid pet significantly predicted decline in all cognitive measures (allp≤ 0.004).Neither baseline csf α-synuclein nor tau predicted cognitive decline.All 3 β-amyloid--related metrics (csf, pet,apoe) also predicted time to dementia.Models with β-amyloid pet as a predictor fit the data the best.Discussion presence or risk of β-amyloid accumulation consistently predicted cognitive decline and time to dementia in pd.This suggests that β-amyloid has high potential as a prognostic indicator and biomarker for cognitive changes in pd.

Journal: Neurology (2022)
Publication types: Journal Article;Research Support, N.I.H., Extramural;Research Support, Non-U.S. Gov't
Trace Level Quantification of 4-Methyl-1-nitrosopiperazin in Rifampicin Capsules by LC-MS/MS.

Rifampicin is a first-line anti-tuberculosis drug.However, in august 2020, the presence of 1-methyl-4-nitrosopiperazine (mnp), a nitrosamine impurity, was detected by the united stated food and drug administration (us fda) in rifampicin capsules.Consequently, the development of efficient methods for the detection of mnp is an important objective.In this study, the mnp present in rifampicin capsules was detected using lc-ms/ms.A total of 27 batches from nine manufacturers in the chinese market were tested, with mnp (0.33-2.36 ppm) being detected in all samples at levels exceeding the maximum acceptable intake limit of 0.16 ppm initially set by the fda.However, after considering the associated benefits and risks, the fda-approved limit was revised to 5 ppm; hence, all the samples examined herein exhibited mnp levels well below the required limit.Furthermore, the results of forced degradation experiments suggest that mnp is formed by the thermal degradation of rifampicin.

Journal: Frontiers in chemistry (2022)
Publication types: Journal Article