syedzayyan/paper_mill_benchmark huggingface dataset:
Evaluation of commotio retinae in orbital fractures.

This study aimed to evaluate the mechanisms of injury and types of orbital fractures and their relation to concurrent commotio retinae.Methods this retrospective study evaluated the records of patients with orbital fractures whose diagnoses had been confirmed by computer tomography between july 2017 and september 2019.Patient demographics, the circumstances of injury, ophthalmic examination results, and radiological findings were tabulated.Statistical analysis of the data used two-tailed student's t-tests, chi-squared tests, and odds ratio calculations.Statistical significance was set at p<0.05.Results of the 204 patients with orbital fractures included in this study, 154 (75.5%) were male.The mean age was 42.1 years.Orbital fractures involving one orbital wall (58.8%) were more common than those affecting multiple walls (41.2%).The majority of fractures affected the inferior wall (60.3%), with the medial walls being the next most frequently affected (19.6%).The most common cause of injury was assault (59.3%), and the second most common was falls (24%).Commotio retinae was observed in 20.1% of orbital fracture cases and was most associated with injuries caused by assault (or=5.22, p<0.001) and least associated with those caused by falls (or=0.06, p<0.001).Eye movement restrictions were more common in central than peripheral commotio (or=3.79, p=0.015) and with medial wall fractures than fractures to other orbital walls (or=7.16, p<0.001).The odds of commotio were not found to be higher in patients with multi-walled orbital fractures than in those with single-walled fractures (p=0.967).Conclusions in the study population, assault was the most common cause of orbital fractures and resulted in commotio retinae than other causes.Ophthalmologists should be aware of the likelihood of commotio retinae in patients with orbital fractures resulting from assault, regardless of the extent of the patient's injuries.

Journal: Arquivos brasileiros de oftalmologia (2022)
Publication types: Journal Article
TAZ promotes osteogenic differentiation of mesenchymal stem cells line C3H10T1/2, murine multi-lineage cells lines C2C12, and MEFs induced by BMP9.

Bone morphogenetic protein 9 (bmp9), also named as growth differentiation factor 2 (gdf-2), is the strongest cytokine that promotes osteogenic differentiation in the bmp family, and has broad clinical application value.Nevertheless, the mechanism of bmp9 promotes osteogenic differentiation remain unclear.Taz, a transcriptional co-activator, has great effects on cell proliferation, differentiation, and stem cell self-renewal.In this research, we investigated the effects of taz in bmp9-induced osteogenic differentiation of mesenchymal stem cell line c3h10t1/2 (mscs) and murine multi-lineage cell lines c2c12 and mefs (mmcs) and explored its possible mechanisms.This study has found that bmp9 induces the expression of taz and promotes its nuclear translocation.Meanwhile, our study found that ad-taz and tm-25659, a taz agonist, can enhance the osteogenic differentiation of mscs and mmcs induced by bmp9.Conversely, ad-si-taz and verteporfin, an inhibitor of taz, have the contradictory effect.Likewise, the promotion of taz to the bmp9-induced ectopic bone formation in vivo was confirmed by the subcutaneous transplantation of mscs in nude mice.Furthermore, we have detected that taz might increase the levels of the phosphorylation of smad1/5/8, p38, erk1/2, and jnk induced by bmp9.Additionally, we also found that taz increased the total protein level of β-catenin induced by bmp9.In summary, our results strongly indicated that taz will promote the osteogenic differentiation in mscs and mmcs induced by bmp9 through multiple signal pathways.

Journal: Cell death discovery (2022)
Publication types: Journal Article
Biscuit consumption and diabetic retinopathy incidence in adults in the United States.

Foods have a considerable influence on human health and were directly related to glycemic control for diabetes patients.However, little is known about the effects of biscuits, a traditional food consumed in large amounts in several countries, on diabetic retinopathy.This study aimed to explore the association between biscuit consumption and diabetic retinopathy prevalence in adults of the united states population.Methods a cross-sectional study with 1904 participants from the national health and nutrition examination survey database were included in this population-based, cross-sectional study.The association between different consumption frequencies of biscuit and diabetic retinopathy prevalence was evaluated using a binary logistic regression model.Trend test, stratified and interaction analyses were also performed.Results after possible confounders including sex, age, ethnicity, education, marital status, family poverty income ratio, smoking and alcohol consumption habit, fasting blood glucose level, hemoglobin a1c level, diagnosis of diabetes, insulin use, blood pressure, body mass index were adjusted, the participants who consumed biscuit 1-11 times a year, 1-3 times a month, and more than once a week had a 139.8% (95% confidence interval, 1.003-5.734), 182.1% (95% confidence interval, 1.106-7.191), and 236.2% (95% confidence interval, 1.335-9.844) higher risk of diabetic retinopathy prevalence, respectively, compared with those who never ate biscuit.For male, non-hispanic, and overweight (body mass index ≥ 25 kg/m2) subgroups, the trend test demonstrated that the diabetic retinopathy prevalence significantly elevated with increased frequency of biscuit consumption (ptrend= 0.021, 0.009, and 0.002, respectively).The interaction analysis suggested that no aforementioned confounders played an interactive role in the relationship between biscuit consumption and diabetic retinopathy prevalence.Conclusions the risk of diabetic retinopathy was positively associated with biscuit consumption.Moreover, for male, non-hispanic, or overweight individuals, the risk of diabetic retinopathy significantly increased with the frequency of biscuit consumption.

Journal: Diabetology & metabolic syndrome (2022)
Publication types: Journal Article
Antibody-free profiling of transcription factor occupancy during early embryogenesis by FitCUT&RUN.

Key transcription factors (tfs) play critical roles in zygotic genome activation (zga) during early embryogenesis, whereas genome-wide occupancies of only a few factors have been profiled during zga due to the limitation of cell numbers or the lack of high-quality antibodies.Here, we present fit cut&run, a modified cut&run method, in which an fc fragment of immunoglobulin g is used for tagging, to profile tf occupancy in an antibody-free manner and demonstrate its reliability and robustness using as few as 5000 k562 cells.We applied fit cut&run to zebrafish undergoing embryogenesis to generate reliable occupancy profiles of three known activators of zebrafish zga: nanog, pou5f3, and sox19b.By profiling the time-series occupancy of nanog during zebrafish zga, we observed a clear trend toward a gradual increase in nanog occupancy and found that nanog occupancy prior to the major phase of zga is important for the activation of some early transcribed genes.

Journal: Genome research (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
A Novel Hierarchical Clustering Approach for Joint Analysis of Multiple Phenotypes Uncovers Obesity Variants Based on ARIC.

Genome-wide association studies (gwass) have successfully discovered numerous variants underlying various diseases.Generally, one-phenotype one-variant association study in gwass is not efficient in identifying variants with weak effects, indicating that more signals have not been identified yet.Nowadays, jointly analyzing multiple phenotypes has been recognized as an important approach to elevate the statistical power for identifying weak genetic variants on complex diseases, shedding new light on potential biological mechanisms.Therefore, hierarchical clustering based on different methods for calculating correlation coefficients (hcdc) is developed to synchronously analyze multiple phenotypes in association studies.There are two steps involved in hcdc.First, a clustering approach based on the similarity matrix between two groups of phenotypes is applied to choose a representative phenotype in each cluster.Then, we use existing methods to estimate the genetic associations with the representative phenotypes rather than the individual phenotypes in every cluster.A variety of simulations are conducted to demonstrate the capacity of hcdc for boosting power.As a consequence, existing methods embedding hcdc are either more powerful or comparable with those of without embedding hcdc in most scenarios.Additionally, the application of obesity-related phenotypes from atherosclerosis risk in communitiesviaexisting methods with hcdc uncovered several associated variants.Among these,uqcc1-rs1570004 is reported as a significant obesity signal for the first time, whose differential expression in subcutaneous fat, visceral fat, and muscle tissue is worthy of further functional studies.

Journal: Frontiers in genetics (2022)
Publication types: Journal Article
Band Alignments, Electronic Structure, and Core-Level Spectra of Bulk Molybdenum Dichalcogenides (MoS2, MoSe2, and MoTe2).

A comprehensive study of bulk molybdenum dichalcogenides is presented with the use of soft and hard x-ray photoelectron (sxps and haxpes) spectroscopy combined with hybrid density functional theory (dft).The main core levels of mo s2, mo se2, and mo te2are explored.Laboratory-based x-ray photoelectron spectroscopy (xps) is used to determine the ionization potential (ip) values of the mo x2series as 5.86, 5.40, and 5.00 e v for mo se2, mo se2, and mo te2, respectively, enabling the band alignment of the series to be established.Finally, the valence band measurements are compared with the calculated density of states which shows the role of p-d hybridization in these materials.Down the group, an increase in the p-d hybridization from the sulfide to the telluride is observed, explained by the configuration energy of the chalcogen p orbitals becoming closer to that of the valence mo 4d orbitals.This pushes the valence band maximum closer to the vacuum level, explaining the decreasing ip down the series.High-resolution sxps and haxpes core-level spectra address the shortcomings of the xps analysis in the literature.Furthermore, the experimentally determined band alignment can be used to inform future device work.

Journal: The journal of physical chemistry. C, Nanomaterials and interfaces (2022)
Publication types: Journal Article
Associations between parental involvement at bedtime and young children's evening cortisol and nighttime sleep.

Parents are theorized to play an important role in helping young children to downregulate arousal to achieve sufficient and good-quality sleep.To my knowledge, however, the links between parenting and children's physiological arousal at bedtime and subsequent nighttime sleep have not been empirically tested.The present study examined 3- to 6-year-old children's evening cortisol levels as a pathway linking parental involvement at bedtime to children's nighttime sleep duration and quality.Fifty-one children (53% male, 47% female; 80% white, 18% biracial, 2% black) and their families participated.Parental involvement (presence, contact, quiet activities) was assessed by raters from video recordings of one night of bedtime.Children's evening cortisol levels were measured from saliva samples taken at bedtime by parents across three nights.Children's nighttime sleep (minutes, efficiency) was determined from an actigraph worn the same three nights.Path analyses controlling for child and family demographics provided support for three significant indirect effects: lower child evening cortisol acted as a pathway linking greater parental presence at bedtime to more child nighttime sleep minutes and higher sleep efficiency, and lower child evening cortisol also linked greater parental contact at bedtime to higher sleep efficiency.Among this low-risk sample, the findings suggest that encouraging parental involvement in young children's bedtime routine may promote healthy sleep by way of reduced child physiological arousal.

Journal: Developmental psychobiology (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Emerging Cholesterol Modulators for Atherosclerotic Cardiovascular Disease.

Experimental and clinical studies have conclusively demonstrated that lowering elevated low-density lipoprotein cholesterol levels results in fewer major adverse cardiac events.Over the past few decades, statins have become the mainstay of lipid-lowering therapy, contributing significantly to the reduction of lipids, and providing patients with a cost-effective approach.However, with growing evidence in support of combination therapies providing increased benefits to certain patient populations, such as those intolerant to statins, there is an urgent need to investigate the safety and efficacy of alternative lipid-lowering drugs.In this paper, we review the current alternative and adjuvant cholesterol targeting agents.We further discuss the clinical trials that have evaluated the safety and efficacy of these alternative and adjuvant therapies as well as their implications for practical use.These drugs target levels of low-density lipoprotein cholesterol, high-density lipoprotein cholesterol, or lipoprotein(a) as treatments for hyperlipidemia and atherosclerotic cardiovascular disease.

Journal: The American journal of the medical sciences (2022)
Publication types: Journal Article;Review
Glycaemic control of Asian patients with type-2 diabetes mellitus on tiered up-titration of metformin monotherapy: A one-year real-world retrospective longitudinal study in primary care.

S to determine the glycaemic control and associated factors among patients with type-2 diabetes mellitus on tiered metformin monotherapy over one-year.Methods adult asian patients on metformin monotherapy with tiered dosage up-titration (low < 500 mg/day; medium 500-<1000 mg/day and high ≥ 1000 mg/day) are divided into four sub-cohorts based on their baseline hb a1c < 7%(c<7); 7%-<8%(c7-<8); 8%-<9%(c8-<9) and ≥ 9%(c≥9).The hb a1c absolute reduction, time to reach glycaemic control (hb a1c < 7%), and time from glycaemic control to failure (hb a1c ≥ 7%) after the dosage up-titration were the outcomes.Results among 5503 eligible patients (mean age = 64.9 years, 45.6% males and 74.6% chinese), the hb a1c absolute reduction after the up-titration at three months are 0%, 0.4%-0.6%, 0.8%-1.2% and 2.0%-2.1% for c<7,c7-<8,c8-<9and c≥9respectively.The median time (months) to attain glycaemic control for low, medium and high dosage up-titration were 4, 3, 3(c7-<8); 12, 7, 4(c8-<9); na, 7, 7(c≥9).Within twelve months after the goal attainment, 36.2%(c<7), 48.8%(c7-<8), 52.7%(c8-<9) and 45.3%(c≥9) of patients had treatment failure.Conclusions the results show that the baseline hb a1c and tiered metformin dosage up-titration are associated with disproportionate hb a1c reduction, time to glycaemic control and time from glycaemic control to failure.

Journal: Diabetes research and clinical practice (2022)
Publication types: Journal Article
Loss of NPPA-AS1 promotes heart regeneration by stabilizing SFPQ-NONO heteromer-induced DNA repair.

The role of long non-coding rna (lnc rna) in endogenous cardiac regeneration remains largely elusive.The mammalian cardiomyocyte is capable of regeneration for a brief period after birth.This fact allows the exploration of the roles of critical lnc rnas in the regulation of cardiac regeneration.Through a cardiac regeneration model by apical resection (ar) of the left ventricle in neonatal mice, we identified an lnc rna named natriuretic peptide a antisense rna 1 (nppa-as1), which negatively regulated cardiomyocyte proliferation.In neonates, nppa-as1 deletion did not affect heart development, but was sufficient to prolong the postnatal window of regeneration after ar.In adult mice, nppa-as1 deletion improved cardiac function and reduced infarct size after myocardial infarction (mi), associated with a significant improvement in cardiomyocyte proliferation.Further analysis showed that nppa-as1 interacted with dna repair-related molecule splicing factor, proline- and glutamine-rich (sfpq).A heteromer of sfpq and non-pou domain-containing octamer-binding protein (nono) was required for double-strand dna break repair, but nppa-as1 was competitively bound with sfpq due to the overlapped binding sites of sfpq and nono.Nppa-as1 deletion promoted the binding of sfpq-nono heteromer, decreased dna damage, and activated cardiomyocyte cell cycle re-entry.Together, loss of nppa-as1 promoted cardiomyocyte proliferation by stabilizing sfpq-nono heteromer-induced dna repair and exerted a therapeutic effect against mi in adult mice.Consequently, nppa-as1 may be a novel target for stimulating cardiac regeneration to treat mi.

Journal: Basic research in cardiology (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Fish toxicity testing for identification of thyroid disrupting chemicals.

Identification of thyroid disrupting chemicals (tdcs), one of the most studied types of endocrine disruptors (eds), is required according to eu regulations on industrial chemicals, pesticides, and biocides.Following that requirement, the use of fish as a unique non-mammalian model species for identification of eds may be warranted.This study summarized and evaluated effects of tdcs on fish thyroid sensitive endpoints including thyroid hormones, thyroid related gene expression, immunostaining for thyroid follicles, eye size and pigmentation, swim bladder inflation as well as effects of tdcs on secondary sex characteristics, sex ratio, growth and reproduction.Changes in thyroid sensitive endpoints may reflect the balanced outcome of different processes of the thyroid cascade.Thyroid sensitive endpoints may also be altered by non-thyroid molecular or endocrine pathways as well as non-specific factors such as general toxicity, development, stress, nutrient, and the environmental factors like temperature and p h.Defining chemical specific effects on thyroid sensitive endpoints is important for identification of tdcs.Application of the aop (adverse outcome pathway) concept could be helpful for defining critical events needed for testing and identification of tdcs in fish.

Journal: Environmental pollution (Barking, Essex : 1987) (2021)
Publication types: Journal Article;Review
Potential role of exercise echocardiography and right heart catheterization in the detection of early pulmonary vascular disease in patients with systemic sclerosis.

Pulmonary vascular disease represents one of the most frequent complications in systemic sclerosis leading to increased mortality.The recognition and appropriate clinical management of early pulmonary vascular disease could significantly improve the prognosis of affected patients.Early pulmonary vascular disease is characterized by the histological signs of pulmonary vascular remodeling, mildly increased mean pulmonary arterial pressure (21-24 mm hg) at rest, abnormal pulmonary hemodynamics during exercise, decreased exercise capacity, and a high risk for development of pulmonary arterial hypertension.Pulmonary hemodynamics can be investigated during exercise by echocardiography or by right heart catheterization both representing important clinical tools for the screening and confirmation of early pulmonary vascular disease.Further studies are needed to better understand the clinical course of systemic sclerosis patients with early pulmonary vascular disease and to define the characteristics of patients that will or will not profit from pulmonary arterial hypertension treatment.

Journal: Journal of scleroderma and related disorders (2019)
Publication types: Journal Article;Review
Trends and Outcomes of Cranioplasty Alone Versus Single-Stage Composite Scalp and Calvarial Reconstruction.

Cranioplasty is a critical intervention to restore the calvarium using autologous or alloplastic materials with single-stage composite scalp and calvarial reconstruction reserved for complex cases.This study aims to identify 30-day outcomes in scalp and calvarial reconstruction using the american college of surgeons national surgical quality improvement program database.Methods the authors conducted a retrospective analysis of the 2010 to 2018 american college of surgeons national surgical quality improvement program database.Adult patients who underwent cranioplasty were identified using current procedural terminology coding and included by exposure type (autologous, alloplastic, composite, or other).Subjects with missing exposure or outcome data were excluded.Primary outcome was 30-day reoperation, whereas secondary outcomes were 30-day unplanned readmission and transfusion.Univariate analysis was completed to assess differences in demographics, comorbidities, and postoperative complications.Multivariable logistic regression was used to control for confounders.Results in total, 1719 patients underwent cranioplasty (mean age 54.7 ± 15.3 years, 43.5% male), including 169(9.8%) autologous, 1303(75.8%) alloplastic, 32(1.9%) composite, and 215(12.5%) other procedures.Cranioplasty procedures were associated with 30-day complication and mortality rate of 16.5% and 2.4%, respectively.Composite cranioplasty was associated with decreased 30-day reoperation (adjusted odds ratios 0.11, 95% confidence interval 0.014-0.94, p = 0.044).There was no statistically significant difference in readmission between cranioplasty groups.Alloplastic cranioplasty was associated with decreased odds of postoperative transfusion (adjusted odds ratios 0.47, 95% confidence interval 0.27â0.84, p = 0.01).Conclusions cranioplasty is an increasingly common procedure.Alloplastic cranioplasty is associated with decreased 30-day transfusion requirement, whereas single-stage composite reconstruction is a viable option and associated with decreased 30-day reoperation with no difference in readmission.

Journal: The Journal of craniofacial surgery (2022)
Publication types: Journal Article
Progress and promise of antisense oligonucleotide therapeutics for central nervous system diseases.

Antisense oligonucleotide (aso) drugs are an emerging class of therapeutics that have recently demonstrated progress and promise to treat diseases of the central nervous system (cns).Asos for a variety of targets and mechanisms are currently being investigated in clinical trials and pre-clinically for a number of cns diseases.This review examines the available data regarding central aso delivery, distribution, pharmacokinetics, pharmacodynamics and therapeutic opportunities.This article is part of the special issue entitled "beyond small molecules for neurological disorders".

Journal: Neuropharmacology (2017)
Publication types: Journal Article;Review