syedzayyan/paper_mill_benchmark huggingface dataset:
Neurodevelopmental outcome of children with congenital heart disease.

Congenital heart disease (chd) constitutes the most common congenital malformation, with moderate or severe chd occurring in around 6 in 1000 live births.Due to advances in medical care, survival rates have increased significantly.Thus, the majority of children with chd survive until adolescence and adulthood.Children with chd requiring cardiopulmonary bypass surgery are at risk for neurodevelopmental impairments in various domains, including mild impairments in cognitive and neuromotor functions, difficulties with social interaction, inattention, emotional symptoms, and impaired executive function.The prevalence for these impairments ranges from 20% to 60% depending on age and domain ("high prevalence-low severity").Domains are often affected simultaneously, leading to school problems with the need for learning support and special interventions.The etiology of neurodevelopmental impairments is complex, consisting of a combination of delayed intrauterine brain development and newly occurring perioperative brain injuries.Mechanisms include altered intrauterine hemodynamic flow as well as neonatal hypoxia and reduced cerebral blood flow.The surgical procedure and postoperative phase add to this cascade of factors interfering with normal brain development.Early identification of children at high risk through structured follow-up programs is mandated to provide individually tailored early interventions and counseling to improve developmental health.

Journal: Handbook of clinical neurology (2019)
Publication types: Journal Article;Review
Monophasic Pulsed Current Stimulation of Duty Cycle 10% Promotes Differentiation of Human Dermal Fibroblasts into Myofibroblasts.

Many clinical trials have shown the therapeutic effects of electrical stimulation (es) in various conditions.Our previous studies showed that es (200 μa and 2 hz) promotes migration and proliferation of human dermal fibroblasts (hdfs).However, the effective duty cycle and the effect of es on myofibroblast differentiation are unclear.This study aimed to investigate the relationship between duty cycle and myofibroblast differentiation.Methods hdfs were subjected to es (200 μa and 2 hz) for 24 h with the duty cycle adapted at 0% (control), 10%, 50%, or 90%.Α-smooth muscle actin (sma) and transforming growth factor (tgf)-β1 m rna and α-sma protein expressions were assessed.Collagen gel contraction was observed for 48 h after es initiation and the gel area was measured.Cell viability and p h of culture medium were analyzed for cytotoxicity of the es.Results cell viabilities were decreased in the 50% and the 90% groups but es did not influence on p h of culture media.Es with a duty cycle of 10% significantly promoted the m rna expression of α-sma and tgf-β1.Α-sma protein expression in the 10% group was also significantly higher than that of the control group.Collagen gel subjected to es with a duty cycle of 10% was contracted.Conclusion duty cycle can influence on myofibroblast differentiation and es with a duty cycle 10% is the effective for wound healing.

Journal: Physical therapy research (2021)
Publication types: Journal Article
Vps21 Directs the PI3K-PI(3)P-Atg21-Atg16 Module to Phagophores via Vps8 for Autophagy.

Phosphatidylinositol 3-phosphate (pi(3)p) serves important functions in endocytosis, phagocytosis, and autophagy.Pi(3)p is generated by vps34 of the class iii phosphatidylinositol 3-kinase (pi3k) complex.The vps34-pi3k complex can be divided into vps34-pi3k class ii (containing vps38, endosomal) and vps34-pi3k class i (containing atg14, autophagosomal).Most pi(3)ps are associated with endosomal membranes.In yeast, the endosomal localization of vps34 and pi(3)p is tightly regulated by vps21-module proteins.At yeast phagophore assembly site (pas) or mammalian omegasomes, pi(3)p binds to wd-repeat protein interacting with phosphoinositide (wipi) proteins to further recruit two conjugation systems, atg5-atg12·atg16 and atg8-pe (lc3-ii), to initiate autophagy.However, the spatiotemporal regulation of pi(3)p during autophagy remains obscure.Therefore, in this study, we determined the effect of vps21 on localization and interactions of vps8, vps34, atg21, atg8, and atg16 upon autophagy induction.The results showed that vps21 was required for successive colocalizations and interactions of vps8-vps34 and vps34-atg21 on endosomes, and atg21-atg8/atg16 on the pas.In addition to disrupted localization of the pi3k complex ii subunits vps34 and vps38 on endosomes, the localization of the pi3k complex i subunits vps34 and atg14, as well as atg21, was partly disrupted from the pas invps21∆ cells.The impaired pi3k-pi(3)p-atg21-atg16 axis invps21∆ cells might delay autophagy, which is consistent with the delay of early autophagy when atg21 was absent.This study provides the first insight into the upstream sequential regulation of the pi3k-pi(3)p-atg21-atg16 module by vps21 in autophagy.

Journal: International journal of molecular sciences (2022)
Publication types: Journal Article
Spatial Variability in COVID-19 Mortality.

Covid-19 emerged as a global pandemic in the spring of 2020.Since that time, the disease has resulted in approximately 150 million cases and 3 million deaths worldwide.However, there is significant spatial variation in the rate of mortality from covid-19.Here, we briefly explore spatial variations in covid-19 mortality by country groupings and propose possible explanations for the differences observed.Specifically, we find that there is a statistically significant difference in covid-19 mortality between countries grouped into categories based on (1) developed, primarily western diets and healthcare systems; (2) "scandinavian" countries with advanced healthcare systems and generally anti-inflammatory diets, and (3) developing countries.We do not infer causality but believe that the observed associations provide hypotheses for future research investigations.Moreover, our results add further evidence to support additional exploration of vitamin d exposure/status and covid-19 mortality.

Journal: International journal of environmental research and public health (2021)
Publication types: Journal Article
Characterization of non-specific lipid transfer protein (nsLtp) gene families in the Brassica napus pangenome reveals abundance variation.

Brassica napus is an important agricultural species, improving stress resistance was one of the main breeding goals at present.Non-specific lipid transfer proteins (ns ltps) are small, basic proteins which are involved in some biotic or abiotic stress responses.B.Napus is susceptible to a variety of fungal diseases, so identify the bn ltps and their expression in disease responses is very important.The common reference genome of b.Napus does not contain all b.Napus genes because of gene presence/absence variations between individuals.Therefore, it was necessary to search for candidate bn ltp genes in the b.Napus pangenome.Results in the present study, the bn ltp genes were identified throughout the pangenome, and different bn ltp genes were presented among varieties.Totally, 246 bn ltp genes were identified and could be divided into five types (1, 2, c, d, and g).The classification, phylogenetic reconstruction, chromosome distribution, functional annotation, and gene expression were analyzed.We also identified potential cis-elements that respond to biotic and abiotic stresses in the 2 kb upstream regions of all bn ltp genes.Rna sequencing analysis showed that the bn ltp genes were involved in the response to sclerotinia sclerotiorum infection.We identified 32 bn ltps linked to blackleg resistance quantitative trait locus (qtl).Conclusion the identification and analysis of ltp genes in the b.Napus pangenome could help to elucidate the function of bn ltp family members and provide new information for future molecular breeding in b.Napus.

Journal: BMC plant biology (2022)
Publication types: Journal Article
A Three-Dimensional Lead Halide Perovskite-Related Ferroelectric.

Three-dimensional (3d) organic-inorganic lead halides represented by [ch3nh3]pb i3perovskite have attracted great interest for their diverse functional properties and promising optoelectronic applications.However, 3d lead halides are still very rare and their ferroelectricity remains controversial.Here, we report an unprecedented 3d lead halide perovskite-related ferroelectric [2-trimethylammonioethylammonium]pb2cl6([tmaea]pb2cl6), which contains a 3d lead chloride framework of corner- and edge-sharing pb cl6octahedral, with the [tmaea]+cations occupying the voids of the framework.[tmaea]pb2cl6shows a ferroelectric-to-paraelectric phase transition with the curie temperature as high as 412 k, a typical ferroelectric hysteresis loop at 293 k with a spontaneous polarization of 1 μc/cm2, and a clear ferroelectric domain switching.To the best of our knowledge, [tmaea]pb2cl6is the first 3d lead halide showing such an excellent ferroelectricity.Additionally, it also exhibits a semiconducting property with a direct band gap of 3.43 e v.This finding enriches the family of 3d hybrid lead halides and inspires the exploration of 3d lead halide ferroelectrics.

Journal: Journal of the American Chemical Society (2020)
Publication types: Journal Article
Changes in the T-helper 1 and 2 cell populations during pregnancy in tacrolimus-treated women with repeated implantation failure and recurrent pregnancy loss.

Tacrolimus has received considerable attention as a treatment approach for infertility associated with maternal-foetal immune abnormalities, such as repeated implantation failure (rif) and recurrent pregnancy loss (rpl).This study examined the changes in t-helper (th) 1 and 2 cell populations during pregnancy in peripheral blood of tacrolimus-treated rif patients who delivered a liveborn infant from august 2012 to february 2020 at the national centre for child health and development.A total of 58 eligible study subjects were divided into two groups according to the presence of a history of rpl: (i) rif-alone group (n= 31); and (ii) rif-plus-rpl group (n= 27).In a flow cytometric analysis, the th1/th2 cell ratios were significantly higher before pregnancy than after pregnancy, and during the first trimester than the second trimester in the rif-alone group (p= 0.0071 andp= 0.0087, respectively).However, no significant differences were present in the rif-plus-rpl group.Although the th1 immunity was suppressed under tacrolimus treatment in both groups, a delayed reduction in the th1 cell percentage after initiation of treatment was observed in the rif-plus-rpl group.In conclusion, the cellular immune alterations in tacrolimus-treated patients with rif were different depending on the presence or absence of a history of rpl.

Journal: Human fertility (Cambridge, England) (2022)
Publication types: Journal Article
Mobile Health App for Tuberculosis Screening and Compliance to Undergo Chest X-ray Examination Among Presumptive Cases Detected by the App in Myanmar: Usability Study.

In myanmar, the use of a mobile app for tuberculosis (tb) screening and its operational effect on seeking tb health care have not been evaluated yet.Objective this study aims to report the usability of a simple mobile app to screen tb and comply with chest x-ray (cxr) examination of presumptive cases detected by the app.Methods a new "tb-screen" app was developed from a google sheet based on a previously published algorithm.The app calculates a tb risk propensity score from an individual's sociodemographic characteristics and tb clinical history and suggests whether the individual should undergo a cxr.The screening program was launched in urban slum areas soon after the covid-19 outbreak subsided.A standard questionnaire was used to assess the app's usability rated by presumptive cases.Compliance to undergo cxr was confirmed by scanning the referral quick response (qr) code via the app.Results raters were 453 presumptive cases detected by the app.The mean usability rating score was 4.1 out of 5.Compliance to undergo cxr examination was 71.1% (n=322).Active tb case detection among cxr compliances was 7.5% (n=24).One standard deviation (sd) increase in the app usability score was significantly associated with a 59% increase in the odds to comply with cxr (β=.464) after adjusting for other variables (p<.001).Conclusions this simple mobile app got a high usability score rated by 453 users.The mobile app usability score successfully predicted compliance to undergo cxr examination.Eventually, 24 (7.5%) of 322 users who were suspected of having tb by the mobile app were detected as active tb cases by cxr.The system should be upscaled for a large trial.

Journal: JMIR formative research (2022)
Publication types: Journal Article
A Model of Depression in University Faculty, Staff, and Health Care Workers Using an Automated Mental Health Screening Tool.

This study aimed to examine relationships among worked hours, stress, sleep hours, burnout, posttraumatic stress disorder (ptsd), anxiety, and depression reported by academic medical center employees.Methods employees completed an anonymous electronic mental health survey with automated feedback that included self-help and professional local resources.Data were analyzed using structural equation modeling.Results eighty percent of participants reported ( n = 693) medium/high stress, 58% reported burnout, 37%/26% screened positive for anxiety/depression, and 14% reported ptsd.Structural equation modeling attained highly significant coefficients ( p < 0.05) and excellent goodness of fit, with strong stress and ptsd positive direct associations with anxiety, burnout, and depression.The model explained 58% of variation in depression scores.A clinician only model demonstrated stronger ptsd effects, but no work hours effects.Conclusion workplace self-screening tools can guide employee mental health self-assessment, self-help programs, and professional resources, while also informing targets for employer programs.

Journal: Journal of occupational and environmental medicine (2022)
Publication types: Journal Article
Sarcopenia in Persons Living with HIV under Antiretroviral Therapy: Literature Review.

The epidemiological profile of people living with hiv (plwh) has expressively changed since the introduction of antiretroviral therapy (art), from a high mortality rate to a profile similar to those living with chronic diseases.Despite the advances and effectiveness of art, there are still various challenges to overcome, and we highlight the increased risk of sarcopenia in plwh.This review study aims to (i) explore the pathophysiological background of sarcopenia in plwh under the different existing art and (ii) develop a mini-systematic review searching epidemiological studies investigating sarcopenia prevalence in plwh.As our main findings: we established the risk of sarcopenia development, under a sequential path involving hiv, art, immune activation, low-grade systemic inflammation, metabolic disorders, and changes in protein synthesis and breakdown in skeletal muscle tissue; some art drugs, mainly reverse transcriptase inhibitors and protease inhibitors, contribute to critical metabolic changes, lowering the autophagy, increasing mitochondrial dysfunction and insulin resistance, which favor the development of inflammation and muscle protein breakdown.There is still insufficient data to discuss the effects of the new generation drugs, namely integrase inhibitors and fusion inhibitors, on skeletal muscle.More studies are needed to better clarify these relationships.

Journal: AIDS reviews (2022)
Publication types: Journal Article;Review
Moderating effects of social support on the relationship between substance use disorders and HIV viral load and medication adherence among Black women living with HIV in the United States.

Substance use may predict lower rates of antiretroviral therapy (art) adherence and viral suppression among black women living with hiv (bwlwh).We assessed how perceived social support (pss) moderates the relationship between substance use disorder (sud) and viral load (vl) and art adherence.119 bwlwh provided information on pss, sud, alcohol use disorder (aud) and adherence (via wisepill).Higher pss from friends (β= -.263,p= .008) and significant others (β= -.219,p= .025) predicted lower vl.Sud predicted low wisepill adherence (a) in the past week (β= -.273,p= .035) and past two weeks (β= -.273,p= .033) only for women low in pss from friends, and (b) in the past two weeks only for women low in total pss (β= -.294,p= .024).Ironically, for women high in total pss, sud predicted higher adherence in the past four weeks (β= .360,p= .006).Adherence and vl may be bolstered by understanding the role of various forms of pss and suds.

Journal: AIDS care (2022)
Publication types: Journal Article;Research Support, N.I.H., Extramural
Effects of Early TACE Refractoriness on Survival in Patients with Hepatocellular Carcinoma: A Real-World Study.

To investigate the effect of early transarterial chemoembolization (tace) refractoriness on hepatocellular carcinoma (hcc) patient survival and to explore whether viable lesions > 50% after two consecutive tace treatments negatively affect the prognosis of hcc patients.Patients and methods from january 2014 to august 2017, 323 hcc patients who received tace as the initial treatment were analyzed.Tace refractoriness was diagnosed according to the japan society of hepatology 2021 version.Propensity score matching (psm) was used to create a 1:1 matched group (nonrefractoriness vs refractoriness).To determine survival outcomes and prognostic factors, the kaplan-meier method and cox proportional hazards model were used.Results in total, 51.1% of patients developed early tace refractoriness (n = 165).After psm, 120 patients from each group were matched and analyzed.The median overall survival (os) time of the early tace refractoriness group was significantly shorter than that of the nonrefractory group [21 months (95% ci: 15.7-26.3) vs 34 months (95% ci: 27.5-40.5),p= 0.002].Thirty-eight patients with viable lesions >50% after two consecutive tace procedures were identified and matched with patients of non-refractoriness.No significant difference in median os was observed [35 months (95% ci: 21.6-48.5) vs 31 months (95% ci: 25.4-36.6),p= 0.611].Multivariate analysis revealed that the bclc stage, tumor size, tumor capsule, tumor distribution, α-fetoprotein level (afp), and early tace refractoriness were independent risk factors for prognosis in hcc patients.Conclusion early tace refractoriness may shorten the os of hcc patients.However, viable lesions >50% after two consecutive tace treatments did not impair the survival of patients.It may be inappropriate to consider these patients as having developed tace refractoriness.

Journal: Journal of hepatocellular carcinoma (2022)
Publication types: Journal Article
Functional genomics of OCTN2 variants informs protein-specific variant effect predictor for Carnitine Transporter Deficiency.

Genetic variants in slc22a5, encoding the membrane carnitine transporter octn2, cause the rare metabolic disorder carnitine transporter deficiency (ctd).Ctd is potentially lethal but actionable if detected early, with confirmatory diagnosis involving sequencing of slc22a5.Interpretation of missense variants of uncertain significance (vuss) is a major challenge.In this study, we sought to characterize the largest set to date (n= 150) of octn2 variants identified in diverse ancestral populations, with the goals of furthering our understanding of the mechanisms leading to octn2 loss-of-function (lof) and creating a protein-specific variant effect prediction model for octn2 function.Uptake assays with14c-carnitine revealed that 105 variants (70%) significantly reduced transport of carnitine compared to wild-type octn2, and 37 variants (25%) severely reduced function to less than 20%.All ancestral populations harbored lof variants; 62% of green fluorescent protein (gfp)-tagged variants impaired octn2 localization to the plasma membrane of human embryonic kidney (hek293t) cells, and subcellular localization significantly associated with function, revealing a major lof mechanism of interest for ctd.With these data, we trained a model to classify variants as functional (>20% function) or lof (<20% function).Our model outperformed existing state-of-the-art methods as evaluated by multiple performance metrics, with mean area under the receiver operating characteristic curve (auroc) of 0.895 ± 0.025.In summary, in this study we generated a rich dataset of octn2 variant function and localization, revealed important disease-causing mechanisms, and improved upon machine learning-based prediction of octn2 variant function to aid in variant interpretation in the diagnosis and treatment of ctd.

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;Research Support, N.I.H., Extramural
Influence of intermittent fasting on prediabetes-induced neuropathy: Insights on a novel mechanistic pathway.

S peripheral neuropathy (pn) is correlated with obesity and metabolic syndrome.Intermittent fasting (if) has been described as the cornerstone in the management of obesity; however, its role in prediabetic complications is not well elucidated.Cytochromes p450 monooxygenases (cyp450) are major sources of reactive oxygen species (ros) that orchestrate the onset and development of diabetic complications.One of the cyp-metabolites, expoxyecosatetraenoic acids (eets), are considered to be negative regulators of ros production.In this study, we elucidated the role of if on ros production and investigated its influence on prediabetes-induced pn.Methods c57/bl6 control mice, prediabetic, prediabetic that underwent alternate day fasting with different diet composition, and prediabetic mice treated with eet-metabolizing s eh-inhibitor, auda.Body mass composition, metabolic, behavioral, and molecular tests were performed.Results high-fat diet (hfd) led to an increase in nadph-induced ros production; that was due to an alteration in the epoxygenase pathway assessed by the decrease in cyp1a1/1a2 expression.If reinstated the homeostatic levels of eets in hfd-fed mice.Moreover, treatment with auda mimicked the beneficial effect observed with if.Conclusion if and eets bioavailability have a protective role in prediabetes-induced pn, suggesting a novel interventional strategy in the management of prediabetes and its associated complications.

Journal: Metabolism open (2022)
Publication types: Journal Article
Unexpected Movement of the Esophagus across the Aorta.

Tumor regression throughout treatment would induce organ movement, but little is known of this in the esophagus.To achieve successful tumor regression, radiation therapy requires several weeks of radiation to be delivered accurately to the tumor.Usually, a 5-10 mm margin is allowed for set-up error and internal organ motion.Our case exhibited an unexpectedly large movement of the esophagus across the aorta with tumor regression that extended outside the margin and thus outside the radiotherapy field.These movements may affect subsequent invasive procedures or treatment during cancer therapy.After the unexpected large movement of the esophagus due to tumor regression, we revised the radiotherapy plan to reflect the new esophageal position.This implied that regular imaging and close monitoring are required during treatment of esophageal cancer.

Journal: Diagnostics (Basel, Switzerland) (2022)
Publication types: Journal Article