syedzayyan/paper_mill_benchmark huggingface dataset:
Determinants of Directionality and Efficiency of the ATP Synthase FoMotor at Atomic Resolution.

Fosubcomplex of atp synthase is a membrane-embedded rotary motor that converts proton motive force into mechanical energy.Despite a rapid increase in the number of high-resolution structures, the mechanism of tight coupling between proton transport and motion of the rotary c-ring remains elusive.Here, using extensive all-atom free energy simulations, we show how the motor's directionality naturally arises from the interplay between intraprotein interactions and energetics of protonation of the c-ring.Notably, our calculations reveal that the strictly conserved arginine in the a-subunit (r176) serves as a jack-of-all-trades: it dictates the direction of rotation, controls the protonation state of the proton-release site, and separates the two proton-access half-channels.Therefore, arginine is necessary to avoid slippage between the proton flux and the mechanical output and guarantees highly efficient energy conversion.We also provide mechanistic explanations for the reported defective mutations of r176, reconciling the structural information on the fomotor with previous functional and single-molecule data.

Journal: The journal of physical chemistry letters (2022)
Publication types: Journal Article
New paradigm for teaching scientific writing in STEM.

Written and oral communication are skills graduate students often request training in and supervisors often bemoan the lack of.We describe an approach to address this training gap using an instructional model that integrates experienced research-active pis with an expert in the study and teaching of technical writing.

Journal: Trends in biochemical sciences (2022)
Publication types: Journal Article
Molecular machinery regulating mitochondrial calcium levels: The nuts and bolts of mitochondrial calcium dynamics.

Mitochondria play vital role in regulating the cellular energetics and metabolism.Further, it is a signaling hub for cell survival and apoptotic pathways.One of the key determinants that calibrate both cellular energetics and survival functions is mitochondrial calcium (ca2+) dynamics.Mitochondrial ca2+regulates three ca2+-sensitive dehydrogenase enzymes involved in tricarboxylic acid cycle (tca) cycle thereby directly controlling atp synthesis.On the other hand, excessive ca2+concentration within the mitochondrial matrix elevates mitochondrial reactive oxygen species (m ros) levels and causes mitochondrial membrane depolarization.This leads to opening of the mitochondrial permeability transition pore (m ptp) and release of cytochrome c into cytosol eventually triggering apoptosis.Therefore, it is critical for cell to maintain mitochondrial ca2+concentration.Since cells can neither synthesize nor metabolize ca2+, it is the dynamic interplay of ca2+handling proteins involved in mitochondrial ca2+influx and efflux that take the center stage.In this review we would discuss the key molecular machinery regulating mitochondrial ca2+concentration.We would focus on the channel complex involved in bringing ca2+into mitochondrial matrix i.e.Mitochondrial ca2+uniporter (mcu) and its key regulators mitochondrial ca2+uptake proteins (micu1, 2 and 3), mcu regulatory subunit b (mcub), essential mcu regulator (emre) and mitochondrial ca2+uniporter regulator 1 (mcur1).Further, we would deliberate on major mitochondrial ca2+efflux proteins i.e.Mitochondrial na+/ca2+/li+exchanger (nclx) and leucine zipper ef hand-containing transmembrane1 (letm1).Moreover, we would highlight the physiological functions of these proteins and discuss their relevance in human pathophysiology.Finally, we would highlight key outstanding questions in the field.

Journal: Mitochondrion (2021)
Publication types: Journal Article;Research Support, Non-U.S. Gov't;Review
Applications of Artificial Intelligence to Predict Oil Rate for High Gas-Oil Ratio and Water-Cut Wells.

Measuring oil production rates of individual wells is important to evaluate a well's performance.Multiphase flow meters (mpfms) and test separators have been used to estimate well production rates.Due to economic and technical issues with mpfms, especially for high gas-oil ratio (gor) reservoirs, the use of a choke formula for estimating well production rate is still popular.The objective of this study is to implement different artificial intelligence (ai) techniques to predict the oil rate through wellhead chokes.Support-vector machine (svm) and random forests (rf) were used to generate different models to predict the production rates for high gor and wc wells.A set of data (548 wells) was obtained from oil fields in the middle east.Gor varied from 1000 to 9351 scf/stb, and wc ranged from 1 to 60%.Around 300 wells were flowing under critical flow conditions, while the rest were subcritical.Hence, two cases were studied using each ai model.Seventy percent of the data was used to train both rf and svm models, while 30% of the data was used to test and validate these models.The developed rf and svm models were then compared against the previous empirical formulas.The rf model in both critical and subcritical flow conditions was able to perfectly match the actual oil rates.Svm was able to predict the general trend for the oil rates but missed some of the sharp changes in the oil rate trend.The average absolute percent error (aape) values in the subcritical flow for svm and rf were 1.7 and 0.7%, respectively, while in the critical flow, the aape values were 1.4 and 0.75% for svm and rf models, respectively.Svm and rf models outperform the published formulas by 34%.The results from this study will help to estimate the real-time oil and gas rates based on the available data from wellhead chokes without the need for field intervention.

Journal: ACS omega (2021)
Publication types: Journal Article
Modelling the atmospheric dispersion of radiotracers in small-scale, controlled detonations: validation of dispersion models using field test data.

A series of modelling exercises, based on field tests conducted in the czech republic, were carried out by the 'urban' working groups as part of the international atomic energy agency's environmental modelling for radiation safety ii, modelling and data for radiological impact assessment (modaria) i and modaria ii international data compilation and model validation programmes.In the first two of these programmes, data from a series of field tests involving dispersion of a radiotracer,99m tc, from small-scale, controlled detonations were used in a comparison of model predictions with field measurements of deposition.In the third programme, data from a similar field test, involving dispersion of140la instead of99m tc, were used.Use of longer-lived140la as a radiotracer allowed a greater number of measurements to be made over a greater distance from the dispersion point and in more directions than was possible for the earlier tests involving shorter-lived99m tc.The modelling exercises included both intercomparison of model predictions from several participants and comparison of model predictions with the measured data.Several models (hot spot, lasair, addam/csa-erm, plus some research models) were used in the comparisons, which demonstrated the challenges of modelling dispersion of radionuclides from detonations and the need for appropriate meteorological measurements.

Journal: Journal of radiological protection : official journal of the Society for Radiological Protection (2022)
Publication types: Journal Article
Prevalence of Refractive Error, Presbyopia, and Spectacle Coverage in Bogotá, Colombia: A Rapid Assessment of Refractive Error.

Significance uncorrected refractive error is the leading cause of visual impairment; therefore, reducing its prevalence is important worldwide.For two decades, there has not been a comprehensive assessment of refractive error in latin america.Purpose the purpose of this study was to determine the current prevalence of refractive error, presbyopia, spectacle coverage, barriers to uptake refractive services, and spectacle correction in people 15 years and older in bogotá, colombia.Methods a cross-sectional community-based survey was conducted using 50 randomly selected clusters from 10 districts of bogotá reflecting the socioeconomic status of the city.Respondents 15 years and older were interviewed and underwent standardized clinical eye examinations.Prevalence of uncorrected refractive error, spectacle coverage, and visual impairment were standardized to 2015 age-sex population distribution of bogotá and further analyzed.Results a total of 2886 subjects (90% of 3206 eligible subjects) participated in the study; 39.1% were male and 60.9% were female in the age range of 15 to 96 years, with a median age of 46 years (interquartile range, 45 to 54 years).Age- and sex-standardized prevalence of visual impairment was 19.3% (95% confidence interval [ci], 17.8 to 20.8%).Prevalence of uncorrected refractive error was 12.5% (95% ci, 11.3 to 13.7%).Prevalence of presbyopia among participants 35 years and older was 55.2% (95% ci, 52.9 to 57.4%).Spectacle coverage was 50.9% for distance vision, and it was 33.9% for presbyopia.Main barrier to spectacle uptake was a limitation in affording spectacles because of economic factors (29.5%).Conclusions this study provides a current estimate of refractive error using the rapid assessment of refractive error for colombia and the latin american region.The prevalence of uncorrected refractive error and presbyopia was high, and the barriers to spectacle uptake were higher in the lowest socioeconomic strata.The results obtained in the present study will help in making evidence-based decisions related to eye care service delivery in colombia.

Journal: Optometry and vision science : official publication of the American Academy of Optometry (2019)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Effects of Time-Restricted Feeding on Supramaximal Exercise Performance and Body Composition: A Randomized and Counterbalanced Crossover Study in Healthy Men.

Using a crossover design, we explored the effects of both short- and long-term time-restricted feeding (trf) vs.Regular diet on wingate (wn t) performance and body composition in well-trained young men.Twelve healthy male physical education students were included (age: 22.4 ± 2.8 years, height: 174.0 ± 7.1 cm, body mass: 73.6 ± 9.5 kg, body mass index: 24.2 ± 2.0 kg/m2).The order of dieting was randomized and counterbalanced, and all participants served as their own controls.Trf was limited to an 8-h eating window and non-trf involved a customary meal pattern.Participants performed wn t tests and body composition scans at baseline, post-one and post-four weeks of the assigned diet.Before testing, participants were asked to fill out a dietary record over four consecutive days and were instructed to continue their habitual training throughout the study.Energy intake and macronutrient distribution were similar at baseline in both conditions.Wn t mean power and total work output increased post-four weeks of trf.Both conditions were similarly effective in increasing fat-free mass after four weeks of intervention.However, there was no correlation between change in fat-free mass and wn t mean power after trf.Trf did not elicit any changes in wn t performance or body composition one week post-intervention.Thus, long-term trf can be used in combination with regular training to improve supramaximal exercise performance in well-trained men.

Journal: International journal of environmental research and public health (2021)
Publication types: Journal Article;Randomized Controlled Trial;Research Support, Non-U.S. Gov't
Variation of dissolved organic matter during excess sludge reduction in microbubble ozonation system.

Sewage sludge is the major by-product of wastewater treatment plants, and about 30% readily biodegradable organic matters might be reused through the mass reduction process, which could be also reduced the disposal fee.In this study, the microbubble ozonation (mb-o3) was employed to improve the oxidation efficiency for sludge solubilization.At 160 mg o3/g ss, the maximum mixed liquor suspended solids (mlss) reduction ratio was 37.5% and the protein and polysaccharide contents increased to 31.6 and 138.6 mg/l, respectively.It was proposed that aromatic protein and soluble microbial in sludge were oxidized preferentially by mb-o3, and the dissolved organic matter (dom) fractions (mainly humic-acid-like substances) exhibited low degradability according to the variations of fluorescence excitation-emission spectrum coupled with fluorescence regional integration.Mb-o3could enhance the settleability, but deteriorate sludge dewaterability at low dosage (< 160 mg o3/g ss) due to a reduction in particle size from 61.7 to 47.5 μm.Mb-o3has a good performance on the mass reduction of sludge through the improvement of the radical generated.

Journal: Environmental science and pollution research international (2021)
Publication types: Journal Article
Accurately Defining the Incidence and Associations of 90-Day Complications after Urethroplasty: Adverse Impact of Patient Comorbidities, Preoperative Bacteriuria and Prior Urethroplasty.

The purpose of this study was to determine the incidence of 90-day complications after urethroplasty and identify factors associated with them.Materials and methods a single-institution, 2-surgeon retrospective review was performed on patients undergoing urethroplasty from august 2003-june 2020.Variables included the incidence, type and clavien-dindo grade of complications, patient age, individual comorbidities, comorbidity component of the charlson comorbidity index (cci), smoking status, obesity (body mass index ≥35 kg/m2), bacteriuria, type of urethroplasty, stricture etiology, length, location, prior endoscopic procedures, previous urethroplasty and preoperative suprapubic catheterization.The primary outcome was the incidence of significant 90-day complications defined as clavien grade ≥2.Descriptive statistics were used to summarize the results and binary logistic regression was used to examine the factors associated with 90-day complications.Results of the 1,611 patients included in the analysis, 90-day complications (clavien ≥2) occurred in 7.9% (128/1,611) and were wound related (3.5%), urinary tract infection (3.4%), cardiovascular (0.4%), catheter-related (0.2%), hematuria (0.1%) or retention (0.1%).On univariable binary logistic regression stricture location (p=0.04), stricture length (p=0.009), cci (p <0.0001), prior urethroplasty (p=0.01) and bacteriuria (p=0.002) were associated with complications, while age (p=0.3), etiology (p=0.2), smoking (p=0.2), obesity (p=0.3), failed endoscopic treatment (p=0.8), indwelling suprapubic catheter (p=0.7) and type of urethroplasty (p=0.09) were not.On multivariable analysis, increasing cci (odds ratio 1.31, 95% ci 1.10-1.56; p=0.003), prior urethroplasty (or 1.86, 95% ci 1.09-3.17; p=0.02) and preoperative bacteriuria (or 1.67, 95% ci 1.14-2.45; p=0.009) remained associated with 90-day complications.Conclusions patients with increased comorbidities, prior urethroplasty and preoperative bacteriuria are at higher risk for complications after urethroplasty and should be counseled accordingly in a shared decision-making model of care.

Journal: The Journal of urology (2022)
Publication types: Journal Article
Combined Corneal Transplant, Glaucoma Drainage Implantation, and Pars Plana Vitrectomy Outcomes in a Pediatric Population.

The combination of glaucoma drainage device (gdi), pars plana vitrectomy (ppv), and corneal transplantation is well reported in adults.However, little is known about the outcomes of such combined procedures in pediatric patients.We present a retrospective, single-center study to evaluate the safety and outcomes of concurrent gdi and/or ppv with corneal transplantation in patients 18 years and younger.Methods retrospective chart review of pediatric patients (aged 0-18 years) who received either corneal transplants or keratoprosthesis in combination with at least 1 additional procedure (either gdi and/or ppv) at the illinois eye and ear infirmary, chicago, il, between 2003 and 2017.Primary outcomes included vision, intraocular pressure, and cup-to-disc ratio (c/d).Secondary outcomes included the number of repeat surgeries and intraoperative and postoperative complications.Results thirty-six patients were included with a mean age of 8.4 years and an average follow-up of 49.7 months.Nineteen patients received corneal surgery, gdi, and ppv; 4 received corneal and gdi surgery; and 13 received corneal and ppv surgery.Of the 19 patients with all 3 procedures, 48% experienced an increase in vision with an average improvement of 0.9 lines at the last follow-up.Intraocular pressure decreased by an average of -7.2 mm hg for all groups.Fifty-three percent of all patients experienced complications.Conclusions combined keratoplasty, gdi, and ppv seems to be effective in the management of complex pediatric eye disease.However, owing to the high risk of complications in this vulnerable patient population, careful consideration must be taken when determining a patient's surgical candidacy for combined cornea/glaucoma/retina procedures.

Journal: Cornea (2022)
Publication types: Journal Article
Descriptive or injunctive: How do restaurant customers react to the guidelines of COVID-19 prevention measures? The role of psychological reactance.

In this study, we employed an experimental design to empirically test how restaurant customers react differently to normative appeals (descriptive vs.Injunctive) relating to covid-19 prevention measures through freedom threat and negative cognition.We conductedt-tests, serial mediation, moderation, and moderated serial mediation analysis to test the hypotheses using spss 23.0 and process macro v.3.5 (model 6 and model 85).Injunctive normative appeal causes an increase in freedom and a less favorable attitude than descriptive normative appeals.The findings also demonstrate the serial-mediated effect of freedom threat and negative cognition on attitude.Furthermore, the effectiveness of normative appeals depends on an individual's age.This study contributes to the academic literature on hospitality by applying psychological reactance theory and testing the model within a restaurant context.It also discusses the implications of its findings for consumers and restaurant managers.

Journal: International journal of hospitality management (2021)
Publication types: Journal Article
Focus on function: Therapies for adults with attention-deficit/hyperactivity disorder.

Attention-deficit/hyperactivity disorder (adhd) is a common disorder affecting people of all ages, and is characterized by inattention, hyperactivity, and impulsivity.Adults frequently have less hyperactivity or impulsivity but struggle more with inattentiveness and restlessness.Adults also may have comorbid psychiatric conditions and substance use issues that can make adhd challenging to detect and treat.If left untreated, adhd may harm the patient's quality of life.This article examines therapies for treating adults with adhd.

Journal: JAAPA : official journal of the American Academy of Physician Assistants (2022)
Publication types: Journal Article
Sparse Index Clones via the sortedℓ1- Norm.

Index tracking and hedge fund replication aim at cloning the return time series properties of a given benchmark, by either using only a subset of its original constituents or by a set of risk factors.In this paper, we propose a model that relies on the sorted l1penalized estimator, called slope, for index tracking and hedge fund replication.We show that slope is capable of not only providing sparsity, but also to form groups among assets depending on their partial correlation with the index or the hedge fund return times series.The grouping structure can then be exploited to create individual investment strategies that allow building portfolios with a smaller number of active positions, but still comparable tracking properties.Considering equity index data and hedge fund returns, we discuss the real-world properties of slope based approaches with respect to state-of-the art approaches.

Journal: Quantitative finance (2022)
Publication types: Journal Article
Prevalence of Mycobacterium bovis infection in traditionally managed cattle at the wildlife-livestock interface in South Africa in the absence of control measures.

Cattle are the domestic animal reservoir for mycobacterium bovis (m.Bovis) which also affects other domestic animals, several wildlife species and humans leading to tuberculosis.The study area is in a resource-poor community that is surrounded by several game parks, where m.Bovis infection has been previously diagnosed in wildlife.A cross-sectional study was carried out to determine the prevalence of m.Bovis infection in 659 cattle from a total of 192 traditionally managed herds using the bovigam® interferon gamma assay (ifn-γ).Infection was confirmed by post mortem examination and m.Bovis isolation from three test-positive cattle.Genotyping of the m.Bovis isolates was done using spoligotyping and vntr (variable number of tandem repeats typing).The apparent m.Bovis prevalence rate in cattle at animal level was 12% with a true population prevalence of 6% (95% confidence interval (c.i) 3.8 to 8.1) and a herd prevalence of 28%.Spoligotyping analysis revealed that the m.Bovis isolates belonged to spoligotype sb0130 and were shared with wildlife.Three vntr profiles were identified among the sb0130 isolates from cattle, two of which had previously been detected in buffalo in a game reserve adjacent to the study area.The apparent widespread presence of m.Bovis in the cattle population raises a serious public health concern and justifies further investigation into the risk factors for m.Bovis transmission to cattle and humans.Moreover, there is an urgent need for effective b tb control measures to reduce infection in the communal cattle and prevent its spread to uninfected herds.

Journal: Veterinary research communications (2019)
Publication types: Journal Article
All-trans retinoic acid enhances temozolomide-induced autophagy in human glioma cells U251 via targeting Keap1/Nrf2/ARE signaling pathway.

The present study evaluated the retinoic acid (ra) enhancement of temozolomide (tmz) effects on the human glioma cells u251 and explored its underlying molecular mechanism.The cell growth was detected using the mtt assay and the cell cycle was assessed by flow cytometry.Cell apoptosis was analyzed by annexin v/propidium iodide staining, and the cell morphology was evaluated using transmission electron microscopy (tem).Additionally, reverse transcription-pcr and western blot analysis were applied to detect the m rna and protein levels.The ra treatment in combination with tmz in the human u251 cells further inhibited cells growth, arresting cell cycle progression at the g0/g1 phase, and significantly induced apoptosis of u251 cells.After the ra+tmz treatment of u251 cells, autophagy associated proteins beclin 1 and lc3b were significantly increased, and the tem analysis were consistent with autophagy protein levels.Moreover, keap1/nrf2/are expression was downregulated significantly, indicating the involvement in the mechanisms that ra treatment could enhance the tmz effects on u251 cells.Ra treatment in combination with tmz may provide some experimental evidence for the possible effect of ra+tmz against the growth and the proliferation of glioma cells.Therefore, the ra+tmz administration may have potential utility for glioblastoma treatment.

Journal: Oncology letters (2017)
Publication types: Journal Article