syedzayyan/paper_mill_benchmark huggingface dataset:
Single-cell analysis reveals immune landscape in kidneys of patients with chronic transplant rejection.

Rationale:single-cell rna sequencing (sc rna-seq) has provided an unbiased assessment of specific profiling of cell populations at the single-cell level.Conventional renal biopsy and bulk rna-seq only average out the underlying differences, while the extent of chronic kidney transplant rejection (cktr) and how it is shaped by cells and states in the kidney remain poorly characterized.Here, we analyzed cells from cktr and matched healthy adult kidneys at single-cell resolution.methods:high-quality transcriptomes were generated from three healthy human kidneys and two cktr biopsies.Unsupervised clustering analysis of biopsy specimens was performed to identify fifteen distinct cell types, including major immune cells, renal cells and a few types of stromal cells.Single-sample gene set enrichment (ss gsea) algorithm was utilized to explore functional differences between cell subpopulations and between cktr and normal cells.results:natural killer t (nkt) cells formed five subclasses, representing cd4+ t cells, cd8+ t cells, cytotoxic t lymphocytes (ctls), regulatory t cells (tregs) and natural killer cells (nks).Memory b cells were classified into two subtypes, representing reverse immune activation.Monocytes formed a classic cd14+ group and a nonclassical cd16+ group.We identified a novel subpopulation [myofibroblasts (myo f)] in fibroblasts, which express collagen and extracellular matrix components.The cktr group was characterized by increased numbers of immune cells and myo f, leading to increased renal rejection and fibrosis.conclusions:by assessing functional differences of subtype at single-cell resolution, we discovered different subtypes that correlated with distinct functions in cktr.This resource provides deeper insights into cktr biology that will be helpful in the diagnosis and treatment of cktr.

Journal: Theranostics (2020)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Mitral valve plasty in a patient with multiple cerebral cavernous malformations: A case report.

Cerebral cavernous malformations (ccms) are blood vessel malformations, often untreated if asymptomatic.However, upon cardiac surgery with cardiopulmonary bypass, cerebral edema/hemorrhage may occur.We successful performed mitral valve plasty for a case of severe mitral regurgitation with multiple ccms.Preoperative head magnetic resonance imaging and strict perioperative management are important.

Journal: Clinical case reports (2022)
Publication types: Case Reports;Journal Article
Microbial metagenomes and metatranscriptomes during a coastal phytoplankton bloom.

Metagenomic and metatranscriptomic time-series data covering a 52-day period in the fall of 2016 provide an inventory of bacterial and archaeal community genes, transcripts, and taxonomy during an intense dinoflagellate bloom in monterey bay, ca, usa.The dataset comprises 84 metagenomes (0.8 terabases), 82 metatranscriptomes (1.1 terabases), and 88 16s r rna amplicon libraries from samples collected on 41 dates.The dataset also includes 88 18s r rna amplicon libraries, characterizing the taxonomy of the eukaryotic community during the bloom.Accompanying the sequence data are chemical and biological measurements associated with each sample.These datasets will facilitate studies of the structure and function of marine bacterial communities during episodic phytoplankton blooms.

Journal: Scientific data (2019)
Publication types: Dataset;Journal Article;Research Support, Non-U.S. Gov't;Research Support, U.S. Gov't, Non-P.H.S.
Glucagon-Like Peptide-1 Receptor Agonists in Type 2 Diabetes Mellitus and Cardiovascular Disease: The Past, Present, and Future.

Type 2 diabetes mellitus (t2dm) is associated with high cardiovascular morbidity and mortality, and cardiovascular diseases are the leading causes of death and disability in people with t2dm.Unfortunately, therapies strictly aimed at glycemic control have poorly contributed to a significant reduction in the risk of cardiovascular events.On the other hand, randomized controlled trials have shown that five glucagon-like peptide-1 receptor agonists (glp-1 ras) and one exendin-based glp-1 ra reduced atherosclerotic cardiovascular events in patients with diabetes at high cardiovascular risk.Furthermore, a meta-analysis including these six agents showed a reduction in major adverse cardiovascular events as well as all-cause mortality compared with placebo, regardless of structural homology.Evidence has also shown that some drugs in this class have beneficial effects on renal outcomes, such as preventing the onset of macroalbuminuria.In addition to lowering blood pressure, these drugs also favorably impacted on body weight in large randomized controlled trials as in real-world studies, a result considered a priority in t2dm management; these and other factors may justify the benefits of glp-1 ras upon the cardiovascular system, regardless of glycemic control.Finally, studies showed safety with a low risk of hypoglycemia and no increase in pancreatitis events.Given these benefits, glp-1 ras were preferentially endorsed in the guidelines of the european and american societies for patients with these conditions.This narrative review provides a current and comprehensive overview of glp-1 ras as cardiovascular and renal protective agents, far beyond their use as glucose-lowering drugs, supporting their effectiveness in treating patients with t2dm at high cardiovascular risk.

Journal: American journal of cardiovascular drugs : drugs, devices, and other interventions (2022)
Publication types: Journal Article;Meta-Analysis;Review
Retrieval Practice in Memory- and Language-Impaired Populations: A Systematic Review.

Neurological conditions, such as multiple sclerosis and stroke, may impair memory and language.A technique called retrieval practice (rp) may improve memory and language outcomes in such clinical populations.The rp effect refers to the finding that retrieving information from memory leads to better long-term retention than restudying the same information.Although the benefits of rp have been repeatedly observed in healthy populations, less is known about its potential applications in cognitive rehabilitation in clinical populations.Here we review the rp literature in populations with acquired memory and language impairments.Method systematic searches for studies published before january 2020 were conducted on elsevier, psyc articles, psyc info, pubmed, web of science, and wiley online library, with the terms "retrieval practice"/"testing effect" and "cognitive rehabilitation".In addition, backward and forward snowballing were used to allow the identification of important publications missed by the initial search.Studies were included if they were peer-reviewed, empirical work in which memory or language outcome measures were compared between an rp condition and a re-exposure-control condition in patients with acquired memory or language impairments.Results sixteen articles fulfilled the inclusion criteria.Studies from memory-impaired samples were relatively homogeneous with respect to experimental protocols and materials and favored rp over control conditions.The results were mostly positive despite short retention intervals and predominantly single-session designs.Similarly, studies from language-impaired samples focused on naming impairments in patients with aphasia and also favored rp over name repetition.Conclusion the results indicate that rp is a viable technique for cognitive rehabilitation.

Journal: Archives of clinical neuropsychology : the official journal of the National Academy of Neuropsychologists (2020)
Publication types: Journal Article
Incidentally detected Vieussens' arterial ring-to-pulmonary trunk fistula in a patient with aortic stenosis.

We report a case of a 45-year-old man with severe aortic stenosis where computed tomography angiography incidentally revealed a fistulous communication between the conal branches of the right coronary artery and anterior interventricular artery and the left anterolateral aspect of the pulmonary trunk with a conglomerate of nondilated tortuous vessels along the anterior surface of right ventricular outflow tract.

Journal: Journal of cardiac surgery (2022)
Publication types: Case Reports;Journal Article
Radiotherapy: An immune response modifier for immuno-oncology.

The ability of radiotherapy to enhance antigenicity and adjuvanticity of an irradiated tumor has stimulated the interest for its combination with immuno-oncology agents.However, radiotherapy often generates multiple layers of host responses which likely depends on the tumor biology, the immune cell infiltration and the induction of immunosuppressive signals post radiotherapy.Consequently, translation of preclinical findings to the clinic is more convoluted than anticipated which underscore the need to decipher molecular and cellular mechanisms elicited by radiotherapy.Here we review pro-inflammatory and immunosuppressive mechanisms triggered by radiotherapy that impact the outcome of antigen specific t cell killing and discuss how radiation-induced immunostimulatory mechanisms can be exploited to reactivate the host's immune system, especially in the context of immunotherapy.

Journal: Seminars in immunology (2021)
Publication types: Journal Article;Research Support, Non-U.S. Gov't;Review
Changing Patterns in Midwestern Farm Trauma: A Retrospective Comparative Analysis.

S the objective is to determine if injury patterns on agricultural workplaces have changed over time.Methods retrospective chart review of farm trauma in fargo, nd, from 2006 to 2020.Results were compared to historical results from la crosse, wi, from 1978 to 1983.Patient charts with icd location and external cause code relating to "farm" were included in the study.Frequencies and relative percentages were computed for each categorical variable.Chi-square tests were performed to determine which categories were significantly different from one another.Results injuries on farms from 395 patients from 2006 to 2020 were compared to injuries from 375 patients from 1978 to 1983.Average age of patients in 2006-2020 was 48 compared to 36 for 1978-1983.There were fewer iss 1-9, more iss 10-24, and similar iss > 25 from 2006 to 2020 compared to 1978-1983.Falls doubled in 2006-2020, 132 compared to 67 in 1978-1983.Injuries from tractors were fewer in 2006-2020, and 63 compared to 89 in 1978-1983.Neurological injuries almost doubled in 2006-2020 compared to 1978-1883, 126 and 61, respectively.All the aforementioned temporal differences were statistically significant with pvalue < .0001.There were 9 deaths from 2006 to 2020 and 8 deaths from 1978 to 1983.Conclusion injuries on farms today occur in older patients with higher injury severity scores and are more likely to have neurological injuries compared to data from 1978 to 1983.These changing patterns in injuries can help to provide education, direct farm safety programs, and help triage resources to critical access hospitals that care for this patient population.

Journal: The American surgeon (2022)
Publication types: Journal Article
MERCI: a machine learning approach to identifying hydroxychloroquine retinopathy using mfERG.

Hydroxychloroquine (hcq) is an anti-inflammatory drug in widespread use for the treatment of systemic auto-immune diseases.Vision loss caused by retinal toxicity is a significant risk associated with long term hcq therapy.Identifying patients at risk of developing retinal toxicity can help prevent vision loss and improve the quality of life for patients.This paper presents updated reference thresholds and examines the diagnostic accuracy of a machine learning approach for identifying retinal toxicity using the multifocal electroretinogram (mf erg).Methods a retrospective study of patients referred for mf erg testing to detect hcq retinopathy.A consecutive series of all patients referred to kensington vision and research centre between august 2017 and july 2020 were considered eligible.Eyes suspect for other ocular pathology including widespread retinal disease and advanced macular pathology unrelated to hcq or with poor quality mf erg recordings were excluded.All patients received mf erg testing and ocular coherence tomography (oct) imaging.Presence of hcq retinopathy was based on ring ratio analysis using clinical reference thresholds established at kvrc coupled with structural features observed on oct, the clinical reference standard.A support vector machine (svm) using selected features of the mf erg was trained.Accuracy, sensitivity and specificity are reported.Results 1463 eyes of 748 patients were included in the study.Svm model performance was assessed on 293 eyes from 265 patients.55 eyes from 54 patients were identified as demonstrating hcq retinopathy based on the clinical reference standard, 50 eyes from 49 patients were identified by the svm.Our svm achieves an accuracy of 85.3% with a sensitivity of 90.9% and specificity of 84.0%.Conclusions machine learning approaches can be applied to mf erg analysis to identify patients at risk of retinopathy caused by hcq therapy.

Journal: Documenta ophthalmologica. Advances in ophthalmology (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Effect of Dentin Desensitizer Containing Novel Bioactive Glass on the Permeability of Dentin.

The objective of this study was to evaluate the effect of novel bioactive glass (bag)-containing desensitizers on the permeability of dentin.Experimental dentin desensitizers containing 3 wt% bag with or without acidic functional monomers (10-mdp or 4-meta) were prepared.A commercial desensitizer, seal & protect (snp), was used as a control.To evaluate the permeability of dentin, real-time dentinal fluid flow (dff) rates were measured at four different time points (demineralized, immediately after desensitizer application, after two weeks in simulated body fluid (sbf), and post-ultrasonication).The dff reduction rate (δdff) was also calculated.The surface changes were analyzed using field emission scanning electron microscopy (fe-sem).Raman spectroscopy was performed to analyze chemical changes on the dentin surface.The δdff of the desensitizers containing bag, bag with 10-mdp, and bag with 4-meta significantly increased after two weeks of sbf storage and post-ultrasonication compared to the snp at each time point (p < 0.05).Multiple precipitates were observed on the surfaces of the three bag-containing desensitizers.Raman spectroscopy revealed hydroxyapatite (hap) peaks on the dentin surfaces treated with the three bag-containing desensitizers.Novel bag-containing dentin desensitizers can reduce the dff rate about 70.84 to 77.09% in the aspect of reduction of dff through the hap precipitations after two weeks of sbf storage.

Journal: Materials (Basel, Switzerland) (2022)
Publication types: Journal Article
Ultrafast end-to-end protein structure prediction enables high-throughput exploration of uncharacterized proteins.

Deep learning-based prediction of protein structure usually begins by constructing a multiple sequence alignment (msa) containing homologs of the target protein.The most successful approaches combine large feature sets derived from msas, and considerable computational effort is spent deriving these input features.We present a method that greatly reduces the amount of preprocessing required for a target msa, while producing main chain coordinates as a direct output of a deep neural network.The network makes use of just three recurrent networks and a stack of residual convolutional layers, making the predictor very fast to run, and easy to install and use.Our approach constructs a directly learned representation of the sequences in an msa, starting from a one-hot encoding of the sequences.When supplemented with an approximate precision matrix, the learned representation can be used to produce structural models of comparable or greater accuracy as compared to our original dmpfold method, while requiring less than a second to produce a typical model.This level of accuracy and speed allows very large-scale three-dimensional modeling of proteins on minimal hardware, and we demonstrate this by producing models for over 1.3 million uncharacterized regions of proteins extracted from the bfd sequence clusters.After constructing an initial set of approximate models, we select a confident subset of over 30,000 models for further refinement and analysis, revealing putative novel protein folds.We also provide updated models for over 5,000 pfam families studied in the original dmpfold paper.

Journal: Proceedings of the National Academy of Sciences of the United States of America (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Development of High-Resolution Dedicated PET-Based Radiomics Machine Learning Model to Predict Axillary Lymph Node Status in Early-Stage Breast Cancer.

Of the report accurate clinical axillary evaluation plays an important role in the diagnosis and treatment planning for early-stage breast cancer (bc).This study aimed to develop a scalable, non-invasive and robust machine learning model for predicting of the pathological node status using dedicated-pet integrating the clinical characteristics in early-stage bc.Materials and methods a total of 420 bc patients confirmed by postoperative pathology were retrospectively analyzed.18f-fluorodeoxyglucose (18f-fdg) mammi-pet, ultrasound, physical examination, lymph-pet, and clinical characteristics were analyzed.The least absolute shrinkage and selection operator (lasso) regression analysis were used in developing prediction models.The characteristic curve (roc) of the area under receiver-operator (auc) and de long test were used to evaluate and compare the performance of the models.The clinical utility of the models was determined via decision curve analysis (dca).Then, a nomogram was developed based on the model with the best predictive efficiency and clinical utility and was validated using the calibration plots.Results a total of 290 patients were enrolled in this study.The auc of the integrated model diagnosed performance was 0.94 (95% confidence interval (ci), 0.91-0.97) in the training set (n= 203) and 0.93 (95% ci, 0.88-0.99) in the validation set (n= 87) (bothp< 0.05).In clinical n0 subgroup, the negative predictive value reached 96.88%, and in clinical n1 subgroup, the positive predictive value reached 92.73%.Conclusions the use of a machine learning integrated model can greatly improve the true positive and true negative rate of identifying clinical axillary lymph node status in early-stage bc.

Journal: Cancers (2022)
Publication types: Journal Article
Family and Friends Support and Hope in Chinese Adolescents: The Mediating Effects of Self-Esteem.

Structural modeling was used to investigate presumed antecedents of hope in a community-based sample of chinese adolescents.Specifically, we evaluated the mediating role of self-esteem in the link between social support from family and friends and individual differences in hope.The multidimensional scale of perceived social support, rosenberg self-esteem scale, and children's hope scale were administered to 1,654 adolescent students (781 boys and 873 girls) from chinese senior high schools.Social support from family and friends correlated equally with hope levels of participants, demonstrating the importance of both sources of support.Self-esteem fully mediated the relationship between family support and hope and partially (23.6%) mediated the relationship between friends support and hope.Results support a social-cognitive model of the origins of hope among adolescents.Findings also suggest implications for the design of hope-promoting environments for adolescents that extend beyond a focus on the individual to incorporate more comprehensive systemic components, including social support from family and friends.[journal of psychosocial nursing and mental health services, 60(7), 39-46.].

Journal: Journal of psychosocial nursing and mental health services (2022)
Publication types: Journal Article
Wearing high heels with an appropriate height is protective for pelvic floor function.

Wearing high-heeled shoes is a common phenomenon among women.However, the association between wearing high heels and pelvic floor function is largely unknown.Our aim was to evaluate the effects of wearing different height shoes on pelvic floor function and to analyze the influencing factors.Methods this was a population-based, cross-sectional study performed in general hospitals with a pelvic floor subspecialty in some cities of china.All participants completed a urogenital distress inventory (udi-6) questionnaire that consisted of demographic data, information about wearing shoes, and information about pelvic floor function (udi-6).One-way anova was carried out to compare the differences among 4 groups according to the heel height ( 7 cm groups).Multivariate logistic regression was performed to identify the factors influencing the effect of wearing 3-5 cm high-heeled shoes on pelvic floor function.Results in total, 1,263 participants finished the questionnaire and full data were collected.The 4 groups were comparable for clinical data, and participants who wore 3-5 cm high-heeled shoes had the lowest udi-6 scores.Multivariate analysis revealed that the number of hours (≥8 h) wearing high heels per day and the thickness diameter (≥3 cm) of the heel were important factors affecting the protective effect of wearing 3-5 cm high-heeled shoes on pelvic floor function.Conclusions wearing heeled shoes with a 3-5 cm heel height and ≥3 cm thickness for a long period of time is good for the pelvic floor function of women.

Journal: Translational andrology and urology (2021)
Publication types: Journal Article
Sex differences in motor unit behaviour: A review.

The lack of systematic investigations on sex-related differences in motor unit behaviour poses a challenge in understanding and optimizing health and performance in males and females.Limited investigations revealed that sex differences in motor unit behaviour might be present in human muscles.This review summarizes the current knowledge on sex differences in motor unit behaviour and potential factors that may contribute to these differences.We show significant under-representation of female participants in motor unit studies and a limited number of studies investigating sex differences in motor unit behaviour.We place the current insights within the context of methodological limitations and outline several recommendations and future directions to improve female representation in this research area.We conclude that there is an urgent need to gather more data in females and investigate sex differences in motor unit behaviour.The knowledge gained could be used to develop sex-specific approaches to improve neuromuscular performance and rehabilitation.

Journal: Journal of electromyography and kinesiology : official journal of the International Society of Electrophysiological Kinesiology (2022)
Publication types: Journal Article;Review