syedzayyan/paper_mill_benchmark huggingface dataset:
New-Onset Atrial Fibrillation in Sepsis: A Narrative Review.

Atrial fibrillation (af) is a frequently identified arrhythmia during the course of sepsis.The aim of this narrative review is to assess the characteristics of patients with new-onset af related to sepsis and the risk of stroke and death, to understand if there is a need for anticoagulation.We searched for studies on af and sepsis on pub med, the cochrane database, and web of science, and 17 studies were included.The mean incidence of new-onset af in patients with sepsis was 20.6% (14.7% in retrospective studies and 31.6% in prospective).Risk factors for new-onset af included advanced age, white race, male sex, obesity, history of cardiopulmonary disease, heart or respiratory failure, and higher disease severity score.In-hospital mortality was higher in patients with than in those without new-onset af in 10 studies.In four studies the overall intensive care unit and hospital mortality rates were comparable between patients with and without new-onset af, while three other studies did not provide mortality data.One study reported on the in-hospital incidence of stroke, which was 2.6 versus 0.69% in patients with or without new-onset af, respectively.Seven of the studies provided follow-up data after discharge.In three studies, new-onset af was associated with excess mortality at 28 days, 1 year, and 5 years after discharge of 34, 21, and 3% patients, respectively.In two studies, the mortality rate was comparable in patients with and without new-onset af.Postdischarge stroke was reported in five studies, whereof two studies had no events after 30 and 90 days, one study showed a nonsignificant increase in stroke, and two studies demonstrated a significant increase in risk of stroke after new-onset af.The absolute risk increase was 0.6 to 1.6%.Large prospective studies are needed to better understand the need for anticoagulation after new-onset af in sepsis.

Journal: Seminars in thrombosis and hemostasis (2021)
Publication types: Journal Article;Review
Epidemiology of Congenital Rubella Syndrome Related to the 2012-2013 Rubella Epidemic in Japan.

This study assessed the epidemiological characteristics of 45 congenital rubella syndrome cases in japan following the 2012-2013 rubella epidemic.Rubella still poses significant health burdens and the uptake of rubella-containing vaccines among women of childbearing age should be improved.

Journal: Journal of the Pediatric Infectious Diseases Society (2022)
Publication types: Journal Article
A Novel Multi-Feature Fusion Method for Classification of Gastrointestinal Diseases Using Endoscopy Images.

The first step in the diagnosis of gastric abnormalities is the detection of various abnormalities in the human gastrointestinal tract.Manual examination of endoscopy images relies on a medical practitioner's expertise to identify inflammatory regions on the inner surface of the gastrointestinal tract.The length of the alimentary canal and the large volume of images obtained from endoscopic procedures make traditional detection methods time consuming and laborious.Recently, deep learning architectures have achieved better results in the classification of endoscopy images.However, visual similarities between different portions of the gastrointestinal tract pose a challenge for effective disease detection.This work proposes a novel system for the classification of endoscopy images by focusing on feature mining through convolutional neural networks (cnn).The model presented is built by combining a state-of-the-art architecture (i.e., efficient net b0) with a custom-built cnn architecture named effimix.The proposed effimix model employs a combination of squeeze and excitation layers and self-normalising activation layers for precise classification of gastrointestinal diseases.Experimental observations on the hyper kvasir dataset confirm the effectiveness of the proposed architecture for the classification of endoscopy images.The proposed model yields an accuracy of 97.99%, with an f1 score, precision, and recall of 97%, 97%, and 98%, respectively, which is significantly higher compared to the existing works.

Journal: Diagnostics (Basel, Switzerland) (2022)
Publication types: Journal Article
Diversity and similarity of wheat powdery mildew resistance among three allelic functional genes at the Pm60 locus.

Cultivated wheat is continually exposed to various pathogens.Blumeria graminis f.Sp.Tritici (bgt) causes powdery mildew disease and significant yield loss.Pm60 was cloned from triticum urartu and confers race-specific powdery mildew resistance in wheat.Pm60a and pm60b are allelic variants of pm60 and have two leucine-rich repeat motifs deletions and insertions, respectively, which were detected in other t.Urartu accessions.Through map-based cloning, virus-induced gene silencing, and stable transformation assays, we demonstrated that pm60a and pm60b conferred bgt e09 resistance resembling that provided by pm60.However, the homozygous pm60a (but not pm60 or pm60b) transformants driven by the native promoters lacked race-specific resistance when they were inoculated with bgt e18.As all three t.Urartu accessions contained the three foregoing alleles, they had high resistance to bgt e18.Pyramiding pm60a with either of the allelic genes in f1plants did not cause mutual allele suppression or interference with bgt e18 resistance.Deletion (but not insertion) of the two leucine-rich repeat motifs in pm60a substantially narrowed the resistance spectrum.In t.Urartu accession pi428210, we identified another locus adjacent to pm60a and resistant to bgt e18.Characterization of the alleles at the pm60 locus revealed their diversity and similarity and may facilitate wheat breeding for resistance to powdery mildew disease caused by b.Graminis f.Sp.Tritici.

Journal: The Plant journal : for cell and molecular biology (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Bacillus subtilis plays a role in the inhibition of transporter ABCB1 in Caco-2 cells.

S the mechanism of drug-resistant epilepsy has been incompletely understood, and the transporter hypothesis is one of the most cited theories.The association between gut microbiome and epilepsy is increasingly recognized but the mechanism remains unclear.We hypothesize that gut microbiome plays a role of pharmacokinetics of antiseizure medicines (asms) through transporters at the host-microbe interface.This study aimed to screen the key subspecies of gut microbiota related to drug-resistant epilepsy and explore their effects on the asms resistance mechanism through the regulation of transporter atp-binding cassette b1 (abcb1).Methods three groups of participants were designed, 10 drug-resistant epilepsy patients (dr group), 10 non-drug-resistant epilepsy patients (ndr group), and 19 healthy controls (control group).Fresh stool samples were collected.Based on the 16s r rna sequencing results of their fecal samples, we selected the bacillus subtilis (b.Subtilis) to explore its effect on the asms efflux mediated by transporter abcb1 whose expression were detected through quantitative pcr and western blot analysis in caco-2 cell model.Further, we conducted the rhodamine 123 accumulation assay to evaluate the activity of the transporter abcb1 in caco-2 cell and the high-performance liquid chromatography (hplc) to measure the concentrations of asms.Results we found that the phylum firmicutes were enriched in the patients with drug-resistant epilepsy (70.82%) and picked up b.Subtilis as the key type of bacteria relevant to drug-resistant epilepsy.The b.Subtilis not only downregulated the expression level and the efflux activity of abcb1 in caco-2 cells treated with asms (p < 0.01), but also reduced the carbamazepine efflux in the caco-2 cells (p < 0.05).Conclusion our study identified b.Subtilis as the key bacterial type associated with patients affected by drug-resistant epilepsy and revealed that it also ameliorated resistance to asms by downregulating the transporter abcb1.

Journal: Epilepsy research (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Increased risk of severe course of pemphigus in patients with pemphigus-associated alopecia: a prospective observational study.

Pemphigus-associated alopecia is considered rare, and has not been studied in detail.Aim to evaluate the clinical and immunological characteristics of patients with pemphigus-associated alopecia.Methods this prospective observational study included 80 consecutive patients with histopathologically and immunopathologically confirmed pemphigus, of whom 11 (13.8%) were found to have pemphigus-associated alopecia.Alopecia was observed in 11/52 patients with pemphigus and scalp involvement: [0/28 (35.7%) with pemphigus vulgaris and 1/24 (4.2%) with pemphigus foliaceus.The clinical and immunological characteristics of these patients were analysed.Results patients with pemphigus-associated alopecia had a significantly higher pemphigus disease area index total activity score compared with patients who had no pemphigus-associated alopecia (21.8 ± 18.6 and 11.0 ± 20.5, respectively; p = 0.02).Mean serum anti-desmoglein (dsg)1 antibody concentration was 141.8 ± 66.9 u/m l and 60.0 ± 52.6 u/m l, respectively (p = 0.03), and mean serum anti-dsg3 concentration was 126.6 ± 36.7 u/m l and 67.4 ± 52.5 u/m l, respectively (p = 0.03).The values for achieving serological remission were 10% and 70%, respectively (p = 0.02).Conclusions pemphigus-associated alopecia is a marker of severe disease and a treatment-resistant disease course.

Journal: Clinical and experimental dermatology (2019)
Publication types: Journal Article;Observational Study
Microfluidic quantification and separation of yeast based on surface adhesion.

Fungal adhesion is fundamental to processes ranging from infections to food production to bioengineering.Yet, robust, population-scale quantification methods for yeast surface adhesion are lacking.We developed a microfluidic assay to discriminate and separate genetically-related yeast strains based on adhesion strength, and to quantify effects of ionic strength and substrate hydrophobicity on adhesion.This approach will enable the rapid screening and fractionation of yeast based on adhesive properties for genetic protein engineering, anti-fouling surfaces, and a host of other applications.

Journal: Lab on a chip (2019)
Publication types: Journal Article;Research Support, Non-U.S. Gov't;Research Support, U.S. Gov't, Non-P.H.S.
Pseudosterins A-C, Three 1-Ethyl-3-formyl-β-carbolines fromPseudostellaria heterophyllaand Their Cardioprotective Effects.

Pseudostellaria heterophyllais used in china not only as a functional food but also as an herb to tonify the spleen, enhance immunity, and treat palpitation.Our previous investigation showed that a fraction enriched in glycosides obtained from the roots of p.Heterophyllapossessed pronounced protective effects on h9c2 cells against co cl2-induced hypoxic injury.However, the active compounds responsible for the observed effects were still unknown.In the current investigation, pseudosterins a-c (1-3), three new alkaloids with a 1-ethyl-3-formyl-β-carboline skeleton, together with polydatin, have been isolated from the active fraction.Their structures were elucidated on the basis of spectroscopic analysis and quantum chemical calculations.The four compounds showed cardioprotective effects against sodium hydrosulfite-induced hypoxia-reoxygenation injury in h9c2 cells, with the three alkaloids being more potent.This is also the first report of alkaloids with a β-carboline skeleton isolated from p.Heterophyllaas cardioprotective agents.

Journal: Molecules (Basel, Switzerland) (2021)
Publication types: Journal Article
Are direct restorations an effective treatment strategy in the management of root caries lesions?

Data sources pub med, cochrane library/embase and web of science.study selection randomised controlled trials and non-randomised trials reporting success or failure rates of direct restorative materials for managing root caries lesions and in vitro studies assessing performance of restorations for root caries lesions published between september 1990 and october 2021 and written in english were included.data extraction and synthesis data was extracted by one reviewer and quality assessment of the included clinical studies performed using the cochrane risk-of-bias in non-randomised studies of interventions tools.Restoration success, survival and failure rates were presented for each included study with no data synthesis.results a total of 11 clinical studies and 31 in vitro studies were included.Restoration failure rates ranged from 14-55% at 24-60 months.Success rates of atraumatic restorative technique (art) ranged from 65-87% at 12-60 months.conclusion there is a lack of high-quality evidence to provide a recommendation on the most appropriate restorative material for restoring root caries lesions.The survival rate of art and conventional techniques are comparable and art could be an optional treatment where conventional treatment is challenging.

Journal: Evidence-based dentistry (2022)
Publication types: Journal Article;Review
Oropharyngeal Oxygen Concentration Is Dependent on the Oxygen Mask System and Sampling Location.

Numerous oxygen delivery systems are used to treat hypoxemia.It is unknown if fio2at the lips predicts oropharyngeal fio2for various oxygen mask systems.We tested whether fio2measurements differed between the lips and oropharynx, and whether this difference depends on the mask system.Methods ten healthy volunteers had one sampling catheter positioned at the lips and another catheter in the oropharynx.Fio2was sampled at each location while the subjects breathed normal tidal volumes with oxygen at 15 l/min via 4 delivery devices: a simple mask, a non-rebreather mask, a face mask with a diffuser that concentrates and directs o2toward the mouth and nose (mask with diffuser), and a closed mask with a jackson-rees circuit.Data were analyzed by using a linear mixed model to account for subject crossover in the repeated measures design.Results fio2levels differed significantly for the 4 delivery mask systems (p< .001) and by sampling catheter location (p< .001).Differences in mean fio2between the lips and the oropharynx were observed for the mask with diffuser (difference 0.30, 95% ci 0.25-0.36;p< .001), and non-rebreather mask (difference 0.09, 95% ci 0.04-0.15;p= .001).The mean fio2at the oropharynx was highest for the closed mask (0.97, 95% ci 0.92-1.00), followed by the non-rebreather mask (0.76, 95% ci 0.72-0.81), simple mask (0.62, 95% ci 0.58-0.67), and the mask with diffuser (0.51, 95% ci 0.46-0.56).At the lips, the mean fio2was highest for the closed mask (0.97, 95% ci 0.92-1.00), followed by the non-rebreather mask (0.86, 95% ci 0.81- 0.90), oxy mask (0.81, 95% ci 0.76-0.86), and simple mask (0.67, 95% ci 0.62-0.71).Conclusions with high oxygen flows and normal tidal volume breathing, fio2measurements obtained at the oropharynx or at the lips depended on the device used, with the mask with diffuser showing the most significant discrepancies.Fio2measures at the oropharynx and the lips were only consistent for the closed mask system.(clinical trials.gov registration nct02523586.).

Journal: Respiratory care (2020)
Publication types: Clinical Trial;Journal Article
Hands-On Training Courses for Cervical Cancer Screening, Diagnosis, and Treatment Procedures in Low- and Middle-Income Countries.

In 2018, there were approximately 570,000 new cases of cervical cancer worldwide.More than 85% of cases occurred in low- and middle-income countries (lmics), primarily because of poor access to screening and a limited number of medical providers trained to diagnose and treat cervical precancerous lesions.Our objective was to provide locally arranged, hands-on training courses for medical providers in lmics to learn to perform cervical cancer screening, diagnosis, and treatment procedures.The courses included didactic lectures and hands-on training stations using low-cost simulation models developed by bioengineers and students at rice university in houston, tx, united states, and the malawi polytechnic in blantyre, malawi.The hands-on training stations included visual inspection with acetic acid (via), colposcopy, cervical biopsy, endocervical curettage, loop electrosurgical excision procedure (leep), and thermal ablation.Provider pre- and postcourse confidence levels in performing the procedures were evaluated.From february 2017 to january 2020, we arranged 15 hands-on training courses in seven cities across six countries (el salvador, mozambique, trinidad and tobago, lesotho, malawi, and nepal).Overall, there were 506 participants.The average number of participants per course was 38 (range 19-92).The participants included doctors, nurses, and midwives.The course duration varied from 1 to 3 days.Increased confidence in performing via, colposcopy and cervical biopsy, ablation, and leep was reported by 69%, 71%, 61%, and 76% of participants, respectively.Our findings suggest that locally arranged, hands-on cervical cancer prevention training courses in lmics can improve provider confidence in performing cervical cancer screening, diagnosis, and treatment procedures.These courses are part of a larger strategy to build local capacity for delivering and improving cervical cancer prevention services in lmics.

Journal: JCO global oncology (2022)
Publication types: Journal Article;Research Support, N.I.H., Extramural;Research Support, Non-U.S. Gov't
Hospital report cards: Quality competition and patient selection.

Hospital 'report cards' policies involve governments publishing information about hospital quality.Such policies often aim to improve hospital quality by stimulating competition between hospitals.Previous empirical literature lacks a comprehensive theoretical framework for analysing the effects of report cards.We model a report card policy in a market where two hospitals compete for patients on quality under regulated prices.The report card policy improves the accuracy of the quality signal observed by patients.Hospitals may improve their published quality scores by costly quality improvement or by selecting healthier patients to treat.We show that increasing information through report cards always increases quality and only sometimes induces selection.Report cards are more likely to increase patient welfare when quality scores are well risk-adjusted, where the cost of selecting patients is high, and the cost of increasing quality is low.

Journal: Journal of health economics (2021)
Publication types: Journal Article
Investigational MET inhibitors to treat Renal cell carcinoma.

Introduction: renal cell carcinoma (rcc) consists of distinct clinical and biologic entities, with an urgent need for novel therapies targeting histology-specific molecular drivers of cancer growth.The met pathway is now being targeted by multiple novel agents in clinical development.This review highlights the upcoming role of met inhibition in the treatment of rcc.areas covered: the hgf-met axis is now recognized as playing a vital role in the growth of papillary histology and in driving vegf inhibitor resistance.The heterogeneity of met alterations influences sensitivity to met inhibition and we need predictive biomarkers for improving patient selection.In this review, we highlight the role of the met pathway in both clear cell and non-clear cell rcc and provide a comprehensive review of preclinical and early clinical data on multiple drugs targeting the met pathway.expert opinion: met alterations can act as primary or secondary drivers of tumor growth in rcc and represents a viable therapeutic target.Combination strategies of vegf and met inhibitors could lead to sustained and deep responses even in non-met driven rcc by inhibiting pathways of vegf resistance.Addition of checkpoint inhibitors to met inhibition has also demonstrated promising signs of early efficacy.

Journal: Expert opinion on investigational drugs (2019)
Publication types: Journal Article;Review
A 30-Year Study of Impacts, Recovery, and Development of Critical Effect Sizes for Endocrine Disruption in White Sucker (Catostomus commersonii) Exposed to Bleached-Kraft Pulp Mill Effluent at Jackfish Bay, Ontario, Canada.

Jackfish bay is an isolated bay on the north shore of lake superior, canada that has received effluent from a large bleached-kraft pulp mill since the 1940s.Studies conducted in the late 1980s found evidence of reductions in sex steroid hormone levels in multiple fish species living in the bay, and increased growth, condition and relative liver weights, with a reduction in internal fat storage, reduced gonadal sizes, delayed sexual maturation, and altered levels of circulating sex steroid hormones in white sucker (catostomus commersonii).These early studies provided some of the first pieces of evidence of endocrine disruption in wild animals.Studies on white sucker have continued at jackfish bay, monitoring fish health after the installation of secondary waste treatment (1989), changes in the pulp bleaching process (1990s), during facility maintenance shutdowns and during a series of facility closures associated with changing ownership (2000s), and were carried through to 2019 resulting in a 30-year study of fish health impacts, endocrine disruption, chemical exposure, and ecosystem recovery.The objective of the present study was to summarize and understand more than 75 physiological, endocrine, chemical and whole organism endpoints that have been studied providing important context for the complexity of endocrine responses, species differences, and challenges with extrapolation.Differences in body size, liver size, gonad size and condition persist, although changes in liver and gonad indices are much smaller than in the early years.Population modeling of the initial reproductive alterations predicted a 30% reduction in the population size, however with improvements over the last couple of decades those population impacts improved considerably.Reflection on these 30 years of detailed studies, on environmental conditions, physiological, and whole organism endpoints, gives insight into the complexity of endocrine responses to environmental change and mitigation.

Journal: Frontiers in endocrinology (2021)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Potential Roles of Exercise-Induced Plasma Metabolites Linking Exercise to Health Benefits.

Regular exercise has a myriad of health benefits.An increase in circulating exercise factors following exercise is a critical physiological response.Numerous studies have shown that exercise factors released from tissues during physical activity may contribute to health benefitsviaautocrine, paracrine, and endocrine mechanisms.Myokines, classified as proteins secreted from skeletal muscle, are representative exercise factors.The roles of myokines have been demonstrated in a variety of exercise-related functions linked to health benefits.In addition to myokines, metabolites are also exercise factors.Exercise changes the levels of various metabolitesviametabolic reactions.Several studies have identified exercise-induced metabolites that positively influence organ functions.Here, we provide an overview of selected metabolites secreted into the circulation upon exercise.

Journal: Frontiers in physiology (2020)
Publication types: Journal Article;Review