syedzayyan/paper_mill_benchmark huggingface dataset:
Genetic variants in the mTOR pathway and interaction with body size and weight gain on breast cancer risk in African-American and European American women.

Positive energy imbalance and growth factors linked to obesity promote the phosphatidylinositol 3-kinase/akt/mammalian target of rapamycin (m tor) pathway.As the obesity-breast cancer associations differ between european american (ea) and african-american (aa) women, we investigated genetic variants in the m tor pathway and breast cancer risk in these two racial groups.Methods we examined 400 single-nucleotide polymorphisms (snps) in 31 m tor pathway genes in the women's circle of health study with 1263 incident breast cancers (645 ea, 618 aa) and 1382 controls (641 ea, 741 aa).Multivariable logistic regression was performed separately within racial groups.Effect modification was assessed for measured body size and weight gain since age 20.Results in ea women, variants in frap1 rs12125777 (intron), prr5l rs3740958 (synonymous coding), and cdkal1 rs9368197 (intron) were associated with increased breast cancer risk, while variants in rptor rs9900506 (intron) were associated with decreased risk (nominal p-trend for functional and frap1 snps or p adjusted for correlated test [p act] < 0.05).For aa women, variants in rptor rs3817293 (intron), pik3r1 rs7713645 (intron), and cdkal1 rs9368197 were associated with decreased breast cancer risk.The significance for frap1 rs12125777 and rptor rs9900506 in ea women did not hold after correction for multiple comparisons.The risk associated with frap1 rs12125777 was higher among eas who had body mass index ≥30 kg/m(2) (odds ratio = 7.69, 95 % ci 2.11-28.0; p-interaction = 0.007) and gained weight ≥35 lb since age 20 (odds ratio = 3.34, 95 % ci 1.42-7.85; p-interaction = 0.021), compared to their counterparts.Conclusions the m tor pathway may be involved in breast cancer carcinogenesis differently for ea and aa women.

Journal: Cancer causes & control : CCC (2016)
Publication types: Journal Article
Identification of an early-stage Parkinson's disease neuromarker using event-related potentials, brain network analytics and machine-learning.

The purpose of this study is to explore the possibility of developing a biomarker that can discriminate early-stage parkinson's disease from healthy brain function using electroencephalography (eeg) event-related potentials (erps) in combination with brain network analytics (bna) technology and machine learning (ml) algorithms.Background currently, diagnosis of pd depends mainly on motor signs and symptoms.However, there is need for biomarkers that detect pd at an earlier stage to allow intervention and monitoring of potential disease-modifying therapies.Cognitive impairment may appear before motor symptoms, and it tends to worsen with disease progression.While erps obtained during cognitive tasks performance represent processing stages of cognitive brain functions, they have not yet been established as sensitive or specific markers for early-stage pd.Methods nineteen pd patients (disease duration of ≤2 years) and 30 healthy controls (hc) underwent eeg recording while performing visual go/no-go and auditory oddball cognitive tasks.Erps were analyzed by the bna technology, and a ml algorithm identified a combination of features that distinguish early pd from hc.We used a logistic regression classifier with a 10-fold cross-validation.Results the ml algorithm identified a neuromarker comprising 15 bna features that discriminated early pd patients from hc.The area-under-the-curve of the receiver-operating characteristic curve was 0.79.Sensitivity and specificity were 0.74 and 0.73, respectively.The five most important features could be classified into three cognitive functions: early sensory processing (p50 amplitude, n100 latency), filtering of information (p200 amplitude and topographic similarity), and response-locked activity (p-200 topographic similarity preceding the motor response in the visual go/no-go task).Conclusions this pilot study found that bna can identify patients with early pd using an advanced analysis of erps.These results need to be validated in a larger pd patient sample and assessed for people with premotor phase of pd.

Journal: PloS one (2022)
Publication types: Clinical Trial;Journal Article;Multicenter Study
The development of a web-based app employing machine learning for delirium prevention in long-term care facilities in South Korea.

Long-term care facilities (lcfs) in south korea have limited knowledge of and capability to care for patients with delirium.They also often lack an electronic medical record system.These barriers hinder systematic approaches to delirium monitoring and intervention.Therefore, this study aims to develop a web-based app for delirium prevention in lcfs and analyse its feasibility and usability.Methods the app was developed based on the validity of the ai prediction model algorithm.A total of 173 participants were selected from lcfs to participate in a study to determine the predictive risk factors for delerium.The app was developed in five phases: (1) the identification of risk factors and preventive intervention strategies from a review of evidence-based literature, (2) the iterative design of the app and components of delirium prevention, (3) the development of a delirium prediction algorithm and cloud platform, (4) a pilot test and validation conducted with 33 patients living in a lcf, and (5) an evaluation of the usability and feasibility of the app, completed by nurses (main users).Results a web-based app was developed to predict high risk of delirium and apply preventive interventions accordingly.Moreover, its validity, usability, and feasibility were confirmed after app development.By employing machine learning, the app can predict the degree of delirium risk and issue a warning alarm.Therefore, it can be used to support clinical decision-making, help initiate the assessment of delirium, and assist in applying preventive interventions.Conclusions this web-based app is evidence-based and can be easily mobilised to support care for patients with delirium in lcfs.This app can improve the recognition of delirium and predict the degree of delirium risk, thereby helping develop initiatives for delirium prevention and providing interventions.Moreover, this app can be extended to predict various risk factors of lcf and apply preventive interventions.Its use can ultimately improve patient safety and quality of care.

Journal: BMC medical informatics and decision making (2022)
Publication types: Journal Article;Review;Research Support, Non-U.S. Gov't
Impact of COVID-19 pandemic on pediatric endoscopy: A multicenter study on behalf of the SIGENP Endoscopy Working Group.

Aim of the present report was to investigate the repercussions of covid-19 pandemic on the procedural volumes and on the main indications of pediatric digestive endoscopy in italy.Methods an online survey was distributed at the beginning of december 2020 to italian digestive endoscopy centers.Data were collected comparing two selected time intervals: the first from 1st of february 2019 to 30th june 2019 and the second from 1st february 2020 to 30th june 2020.Results responses to the survey came from 24 pediatric endoscopy units.Globally, a reduction of 37.2% was observed between 2019 and 2020 periods with a significant decrease in median number of procedures (111 vs 57, p < 0.001).Both the median number of procedures performed for new diagnoses and those for follow-up purposes significantly decreased in 2020 (63 vs 36, p < 0.001 and 42 vs 21, p< 0.001, respectively).We reported a drastic reduction of procedures performed for suspected celiac disease and functional gastrointestinal disorders (55.1% and 58.0%, respectively).Diagnostic endoscopies for suspected ibd decreased of 15.5%, whereas procedures for mucosal healing (mh) assessment reduced of 48.3%.Conclusions our study provides real-world data outlining the meaningful impact of covid-19 on pediatric endoscopy practice in italy.

Journal: Digestive and liver disease : official journal of the Italian Society of Gastroenterology and the Italian Association for the Study of the Liver (2022)
Publication types: Journal Article;Multicenter Study
The Impact of Colleague Suicide and the Current State of Postvention Guidance for Affected Co-Workers: A Critical Integrative Review.

People bereaved by suicide are affected psychologically and physically and may be at greater risk of taking their own lives.Whilst researchers have explored the impact of suicide on family members and friends, the area of colleague suicide has been neglected and postvention guidance for supporting surviving colleagues is often poorly developed.This critical integrative review explored the impact of colleague suicide on surviving co-workers and reviewed postvention guidance for workplaces.Systematic searches found 17 articles that met the inclusion criteria.Articles were appraised for quality and extracted data were analysed using a thematic network method.Article quality was moderate.Two global themes were developed: impact of a colleague suicide comprised themes of 'suicide loss in the workplace'; 'professional identities and workplace roles'; 'perceptions of professional uniqueness'; and 'professional abandonment and silencing'.Postvention following a colleague suicide comprised 'individualised responses'; 'the dual function of stigma'; and 'complex pressure on managers'.A unifying global network 'after a colleague suicide' describes the relationships between all themes.A series of disconnects between existing postvention guidance and the needs of impacted workers are discussed.This review demonstrates the need for robust, systemic postvention for colleagues impacted by the complex issue of colleague suicide.

Journal: International journal of environmental research and public health (2022)
Publication types: Journal Article;Review;Research Support, Non-U.S. Gov't
Autoimmune liver diseases in systemic rheumatic diseases.

Systemic rheumatic diseases (srds) are chronic, inflammatory, autoimmune disorders with the presence of autoantibodies that may affect any organ or system.Liver dysfunction in srds can be associated with prescribed drugs, viral hepatitis, alternative hepatic comorbidities and coexisting autoimmune liver diseases (ailds), requiring an exclusion of secondary conditions before considering liver involvement.The patterns of overlap diseases depend predominantly on genetic determinants with common susceptible loci widely distributing in both disorders.In ailds, it is important to identify the overlapping srds at an early stage since such a coexistence may influence the disease course and prognosis.Commonly co-occurring srds in ailds are sjögren syndrome (ss), rheumatoid arthritis (ra) or systemic lupus erythematosus (sle) in autoimmune hepatitis (aih), and ss, ra or systemic sclerosis in primary biliary cholangitis.Owing to different disease complications and therapies, it is imperative to differentiate between sle liver involvement and sle-aih overlap disease.Therapeutic options can be personalized to control coexisting conditions of liver autoimmunity and rheumatic manifestations in aild-srd overlap diseases.The collaboration between hepatologists and rheumatologists can lead to significant advances in managing such a complex scenario.In this review, we provide a comprehensive overview on coexisting ailds in different srds and the therapeutic approach in managing these overlap diseases.

Journal: World journal of gastroenterology (2022)
Publication types: Journal Article;Review
Tobacco mosaic virus movement protein complements a Potato spindle tuber viroid RNA mutant impaired for mesophyll entry but not mutants unable to enter the phloem.

Tobacco mosaic virus movement protein (tmv mp) is essential for virus spread between cells.To accomplish its task, tmv mp binds viral rna, interacts with components of the cytoskeleton, and increases the size exclusion limit (sel) of plasmodesmata.Plasmodesmata are gated intercellular channels that allow passage of small molecules and macromolecules, including rna and protein, between plant cells.Moreover, plasmodesmata are diverse and those connecting different cell types appear to have unique mechanisms to regulate macromolecular trafficking, which likely contributes to the establishment of distinct cell boundaries.Consequently, tmv mp might be competent to mediate rna transport through some but not all plasmodesmal gates.Due to a lack of viral mutants defective for movement between specific cell types, the ability of tmv mp in this regard is incompletely understood.In contrast, a number of trafficking impaired potato spindle tuber viroid (pstvd) mutants have been identified.Pstvd is a systemically infectious non-coding rna that nevertheless can perform all functions required for replication as well as cell-to-cell and systemic spread.Previous studies have shown that pstvd employs different structure and sequence elements to move between diverse cell types in host plants, and mutants defective for transport between specific cell types have been identified.Therefore, pstvd may serve as a tool to analyze the functions of mps of viral and cellular origin.To probe the rna transport activity of tmv mp, transgenic plants expressing the protein were inoculated with pstvd mutants.Remarkably, tmv mp complemented a pstvd mutant defective for mesophyll entry but could not support two mutants impaired for phloem entry, suggesting it fails to productively interface with plasmodesmata at the phloem boundary and that additional viral and host factors may be required.Consistent with this idea, tmv co-infection, but not the combination of mp and coat protein (cp) expression, was able to complement one of the phloem entry mutants.These observations suggest that phloem loading is a critical impediment to establishing systemic infection that could involve the entire ensemble of tmv proteins.They also demonstrate a novel strategy for analysis of mps.

Journal: PLoS pathogens (2022)
Publication types: Journal Article;Research Support, U.S. Gov't, Non-P.H.S.
Optimization of the nutritional constituents for ergosterol peroxide production by Paecilomyces cicadae based on the uniform design and mathematical model.

We optimized medium components for the production of ergosterol peroxide (ep) by paecilomyces cicadae based on a mono-factor experiment, a uniform design, and a non-linear regression analysis.The maximum ep yield achieved was 256 μg/l, which was increased by 5 folds compared with that before the optimization.Structured monod model, andrews model, contois model, and aibe model were developed to describe the effects of viscosity inhibition, substrate, and production on biomass growth.The results showed that the monod model could predict biomass growth, and the effects of viscosity and substrate on the ep concentration were significantly higher compared with the effect of production.The addition of water and glycerol could decrease the viscosity inhibition and glycerol inhibition, and further increase the ep yield.The newly developed structured model was demonstrated for batch growth of p.Cicadae.

Journal: Scientific reports (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Avoiding gauge ambiguities in cavity quantum electrodynamics.

Systems of interacting charges and fields are ubiquitous in physics.Recently, it has been shown that hamiltonians derived using different gauges can yield different physical results when matter degrees of freedom are truncated to a few low-lying energy eigenstates.This effect is particularly prominent in the ultra-strong coupling regime.Such ambiguities arise because transformations reshuffle the partition between light and matter degrees of freedom and so level truncation is a gauge dependent approximation.To avoid this gauge ambiguity, we redefine the electromagnetic fields in terms of potentials for which the resulting canonical momenta and hamiltonian are explicitly unchanged by the gauge choice of this theory.Instead the light/matter partition is assigned by the intuitive choice of separating an electric field between displacement and polarisation contributions.This approach is an attractive choice in typical cavity quantum electrodynamics situations.

Journal: Scientific reports (2021)
Publication types: Journal Article
Target-enrichment sequencing yields valuable genomic data for challenging-to-culture bacteria of public health importance.

Genomic data contribute invaluable information to the epidemiological investigation of pathogens of public health importance.However, whole-genome sequencing (wgs) of bacteria typically relies on culture, which represents a major hurdle for generating such data for a wide range of species for which culture is challenging.In this study, we assessed the use of culture-free target-enrichment sequencing as a method for generating genomic data for two bacterial species: (1)bacillus anthracis,which causes anthrax in both people and animals and whose culture requires high-level containment facilities; and (2)mycoplasma amphoriforme, a fastidious emerging human respiratory pathogen.We obtained high-quality genomic data for both species directly from clinical samples, with sufficient coverage (>15×) for confident variant calling over at least 80% of the baited genomes for over two thirds of the samples tested.Higher q pcr cycle threshold (ct) values (indicative of lower pathogen concentrations in the samples), pooling libraries prior to capture, and lower captured library concentration were all statistically associated with lower capture efficiency.The ctvalue had the highest predictive value, explaining 52 % of the variation in capture efficiency.Samples with ctvalues ≤30 were over six times more likely to achieve the threshold coverage than those with a ct> 30.We conclude that target-enrichment sequencing provides a valuable alternative to standard wgs following bacterial culture and creates opportunities for an improved understanding of the epidemiology and evolution of many clinically important pathogens for which culture is challenging.

Journal: Microbial genomics (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Daidzein suppresses TGF-β1-induced cardiac fibroblast activation via the TGF-β1/SMAD2/3 signaling pathway.

Myocardial fibrosis is a concomitant bioprocess associated with many cardiovascular diseases (cvds).Daidzein is an isoflavone that has been used for the treatment of cvds.This study aimed to reveal its role in myocardial fibrosis.Our results indicate that daidzein had a nontoxic effect on cardiac fibroblasts and that tgf-β1 and tgfβri levels were gradually decreased by daidzein in a dose-dependent manner.In the current study, we show that daidzein significantly inhibited tgf-β1-induced m rna and protein expression of α-sma, collagen i, and collagen iii.Accordingly, immunofluorescence staining of α-sma was performed.Daidzein also inhibited tgf-β1-induced cardiac fibroblast proliferation and migration.Mechanistically, daidzein inhibited the tgf-β/smad signaling pathway induced by tgf-β1 in cardiac fibroblasts.Additionally, daidzein ameliorated mi-induced cardiac dysfunction and cardiac fibrosis in vivo.Based on these findings, we conclude that daidzein reduces tgf-β1-induced cardiac fibroblast activation by partially regulating the tgf-β1/smad2/3 signaling pathway.

Journal: European journal of pharmacology (2022)
Publication types: Journal Article
Management of multiple sclerosis patients in central European countries: current needs and potential solutions.

Multiple sclerosis (ms) experts in europe are facing rapidly rising demands of excellence due to the increasing complexity of ms therapy and management.A central european expert board of ms experts met to identify needs and obstacles with respect to raising quality of ms care in central and eastern european countries.There are substantial variations across countries regarding delivery of care and its cost structure, as well as access to treatment.To date, eastern european countries are often less able to afford reimbursement of immunomodulatory agents than western countries.Overall, approximately 40% of working-age patients are not working due to ms.Costs rise steeply with increasing disability; indirect costs constitute the bulk of the financial burden in patients with severe ms.Magnetic resonance imaging (mri) assessment is meanwhile obligatory as the diagnostic interface in the management of ms patients.Recommended measures directed at improving quality of care include the collection of patient data in registries, enhanced education of healthcare professionals, implementation of national strategies aiming at reducing regional variation, optimization of approval processes, and removal of administrative barriers.Local partnerships with authorities such as those that represent the interests of employees can contribute to leverage the importance of epidemiological data.The need for education extends to (neuro)radiologists who are responsible for reporting mri findings in expert quality.Dissemination of the magnetic resonance imaging in ms (magnims) protocol would be an important step in this context.Also, clinical freedom of choice is rated as essential.Physicians should have access to a range of treatment options due to the complexity of disease.Guidelines such as the upcoming ean-ectrims clinical practice guideline also aim at providing a basis for argumentation in negotiations with national health authorities.

Journal: Therapeutic advances in neurological disorders (2018)
Publication types: Journal Article;Review
A Three-Gene Signature for Predicting the Prognosis of Patients Treated with Transarterial Chemoembolization (TACE) and Identification of PD-184352 as a Potential Drug to Reverse Nonresponse to TACE.

Transarterial chemoembolization (tace) is a first-line treatment for patients with unresectable hepatocellular carcinoma (hcc).Owing to differences in its efficacy across individuals, determining the indicators of patient response to tace and finding approaches to reversing nonresponse thereto are necessary.Methods transcriptome data were obtained from the gse104580 dataset, in which patients were marked as having tace response or nonresponse.We identified differentially expressed genes (degs) and performed kyoto encyclopedia of genes and genomes (kegg) analysis.We screened genes with a prognostic value for tace in the hif-1 signaling pathway by univariate regression analysis.By using least absolute shrinkage and selection operator (lasso) cox regression, we established a multigene signature in gse14520, which we verified using a drug sensitivity test.The connectivity map (cmap) database was used to find potential drugs to reverse nonresponse to tace.Results we constructed a prognostic signature consisting of three genes (erythropoietin (epo), heme oxygenase 1 (hmox1), and serine protease inhibitor 1 (serpine1)) that we validated by drug sensitivity test.After dividing patients treated with tace into high- and low-risk groups based on this new signature, we showed that overall survival (os) of the high-risk group was significantly lower than that of the low-risk group and that the risk score was an independent predictor of os in patients treated with tace.Based on our cmap findings, we speculated that pd-184352, an inhibitor of mitogen-activated protein kinase (mek), had potential as a drug treatment to reverse nonresponse to tace.We confirmed this speculation by using pd-184352 in a cell promotion experiment in a tace environment.Conclusion we constructed a tace-specific three-gene signature that could be used to predict hcc patients' responses to and prognosis after tace treatment.Pd-184352 might have potential as a drug to improve tace efficacy.

Journal: Journal of oncology (2022)
Publication types: Journal Article