syedzayyan/paper_mill_benchmark huggingface dataset:
POSTOPERATIVE CHANGES AND PROGNOSTIC FACTORS OF VISUAL ACUITY, METAMORPHOPSIA, AND ANISEIKONIA AFTER VITRECTOMY FOR EPIRETINAL MEMBRANE.

To investigate postoperative changes and prognostic factors of visual impairment after vitrectomy for unilateral epiretinal membrane.Methods a prospective observational study on 45 eyes from 45 patients with unilateral idiopathic epiretinal membrane who underwent vitrectomy.Visual parameters (best-corrected visual acuity, metamorphopsia using m-charts, and aniseikonia using the new aniseikonia test) and spectral domain optical coherence tomography parameters (macular retinal layer thickness and microstructure of the outer retina) were measured preoperatively and 6 and 12 months postoperatively.Statistical analyses included linear mixed-effects models for the longitudinal changes and prognostic factors of visual parameters.Results best-corrected visual acuity and horizontal metamorphopsia improved significantly from 6 months after surgery (p < 0.001), whereas aniseikonia decreased significantly only at 12 months (p = 0.015).Vertical metamorphopsia remained unchanged.Preoperative inner nuclear layer thickness was significantly correlated with preoperative metamorphopsia.Besides baseline values, best-corrected visual acuity had no significant prognostic factors, but preoperative ellipsoid zone disruption had a negative direction of association with postoperative metamorphopsia (coefficients: -0.37 and -0.62, p = 0.015 and 0.006 for horizontal and vertical metamorphopsia, respectively), and preoperative horizontal metamorphopsia had a positive direction of association with postoperative aniseikonia (coefficient: 1.77, p = 0.002).Conclusion after vitrectomy, postoperative changes and prognostic factors for unilateral epiretinal membrane differed for best-corrected visual acuity, metamorphopsia, and aniseikonia.

Journal: Retina (Philadelphia, Pa.) (2018)
Publication types: Journal Article;Observational Study
Algorithm-driven activity-directed expansion of a series of antibacterial quinazolinones.

Activity-directed synthesis (ads) is a structure-blind, function driven approach that can drive the discovery of bioactive small molecules.In ads, arrays of reactions are designed and executed, and the crude product mixtures are then directly screened to identify reactions that yield bioactive products.The design of subsequent reaction arrays is then informed by the hit reactions that are discovered.In this study, algorithms for reaction array design were developed in which the reactions to be executed were selected from a large set of virtual reactions; the reactions were selected on the basis of similarity to reactions known to yield bioactive products.The algorithms were harnessed to design arrays of photoredox-catalysed alkylation reactions whose crude products were then screened for inhibition of growth of s.Aureus atcc29213.It was demonstrated that the approach enabled expansion of a series of antibacterial quinazolinones.It is envisaged that such algorithms could ultimately enable fully autonomous activity-directed molecular discovery.

Journal: Organic & biomolecular chemistry (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Perceptions of on-farm emergency slaughter for dairy cows in British Columbia.

Some jurisdictions permit on-farm emergency slaughter (ofes) as one end-of-life option for dairy cows and other animals that cannot be transported humanely but are deemed fit for human consumption.Anecdotal reports suggest that ofes is controversial among dairy industry professionals, but to date their perceptions of ofes have not been studied systematically.Twenty-five individual interviews and 3 focus groups with 40 dairy producers, veterinarians, and other professionals in british columbia, canada, revealed positive and negative perceptions of ofes influenced by (1) individual values, (2) the perceived operational legitimacy of ofes, and (3) concern over social responsibility and public perception of the dairy industry.Study participants valued cow welfare but were divided on whether ofes quickened or delayed death for injured animals.Views on the operational legitimacy of ofes varied because of different perceptions and concerns regarding regulatory, veterinary, and meat inspector oversight, a possible conflict of interest for veterinarians, and concerns over carcass hygiene and transport.Whereas many appreciated that ofes prevented transport of compromised cows, others saw ofes as merely a stopgap measure.Seven recommended actions could address concerns while retaining the benefits of ofes: (1) specifying precise timing parameters for ofes, (2) clarification of allowable cow conditions for ofes, (3) consultation with dairy industry professionals if ofes is to be expanded, (4) more proactive culling and the development of euthanasia protocols on farms, (5) the designation of veterinarians as the first point of contact in the ofes process, (6) veterinarian training on animal inspection and allowable conditions for ofes, and (7) the use of proper procedures and equipment during the ofes process to ensure food safety.

Journal: Journal of dairy science (2019)
Publication types: Journal Article
Data processing on a comparative evaluation of the extraction and analysis procedures for urinary phospholipid and lysophospholipid using MALDI-TOF/MS.

In this dataset we provide maldi-tof/ms spectra for the testing and application of a quantitative method using external ionization standards (ionization stds) for peak-intensity normalization.The presented data is related to our recent article entitled "a comparative evaluation of the extraction and analysis procedures for urinary phospholipid and lysophospholipid using maldi-tof/ms".Gradient dilutions of mixture containing thirteen phospho- and lysophospho-lipid species (internal stds) were mixed with constant concentration of the ionization stds and analyzed together.Peak intensities of the internal and ionization stds were picked by a homemade workflow based on open ms (steps including noise filtration, baseline subtraction and peak-picking).The peak-intensity ratios between the internal and ionization stds were linearly correlated with their concentration ratios.Using this method, the evaluation of efficiencies of six different lipid extraction methods was performed in urine samples.In summary, a free and easy-to-use method for phospholipid and lysophospholipid quantitative analysis based on maldi-tof/ms is provided in this article.

Journal: Data in brief (2019)
Publication types: Journal Article
A decadal synthesis of atmospheric emissions, ambient air quality, and deposition in the oil sands region.

This review is part of a series synthesizing peer-reviewed literature from the past decade on environmental monitoring in the oil sands region (osr) of northeastern alberta.It focuses on atmospheric emissions, air quality, and deposition in and downwind of the osr.Most published monitoring and research activities were concentrated in the surface-mineable region in the athabasca osr.Substantial progress has been made in understanding oil sands (os)-related emission sources using multiple approaches: airborne measurements, satellite measurements, source emission testing, deterministic modeling, and source apportionment modeling.These approaches generally yield consistent results, indicating os-related sources are regional contributors to nearly all air pollutants.Most pollutants exhibit enhanced air concentrations within ~20 km of surface-mining activities, with some enhanced >100 km downwind.Some pollutants (e.g., sulfur dioxide, nitrogen oxides) undergo transformations as they are transported through the atmosphere.Deposition rates of os-related substances primarily emitted as fugitive dust are enhanced within ~30 km of surface-mining activities, whereas gaseous and fine particulate emissions have a more diffuse deposition enhancement pattern extending hundreds of kilometers downwind.In general, air quality guidelines are not exceeded, although these single-pollutant thresholds are not comprehensive indicators of air quality.Odor events have occurred in communities near os industrial activities, although it can be difficult to attribute events to specific pollutants or sources.Nitrogen, sulfur, polycyclic aromatic compounds (pacs), and base cations from os sources occur in the environment, but explicit and deleterious responses of organisms to these pollutants are not as apparent across all study environments; details of biological monitoring are discussed further in other papers in this special series.However, modeling of critical load exceedances suggests that, at continued emission levels, ecological change may occur in future.Knowledge gaps and recommendations for future work to address these gaps are also presented.Integr environ assess manag 2022;18:333-360.© 2021 the authors.Integrated environmental assessment and management published by wiley periodicals llc on behalf of society of environmental toxicology & chemistry (setac).

Journal: Integrated environmental assessment and management (2022)
Publication types: Journal Article;Review
Failure to Rescue: A New Society of Thoracic Surgeons Quality Metric for Cardiac Surgery.

Failure to rescue (ftr) focuses on the ability to prevent death among patients who have postoperative complications.The society of thoracic surgeons (sts) quality measurement task force has developed a new, risk-adjusted ftr quality metric for adult cardiac surgery.Methods the study population was taken from 1118 sts adult cardiac surgery database participants including patients who underwent isolated cabg, aortic valve replacement with or without cabg, or mitral valve repair or replacement with or without cabg between january 2015 and june 2019.The ftr analysis was derived from patients who had one or more of the following complications: prolonged ventilation, stroke, reoperation, and renal failure.Data were randomly split into 70% training samples (n = 89,059) and 30% validation samples (n = 38,242).Risk variables included sts predicted risk of mortality, operative procedures, and intraoperative variables (cardiopulmonary bypass and cross-clamp times, unplanned procedures, need for circulatory support, and massive transfusion).Results overall mortality for patients undergoing any of the index operations during the study period was 2.6% (27,045 of 1,058,138), with mortality of 0.9% (8316 of 930,837), 8% (7618 of 94,918), 30.6% (8247 of 26,934), 51.9% (2661 of 5123), and 62.3% (203 of 326), respectively, among patients having none, one, two, three, or four complications.The ftr risk model calibration was excellent, as were model discrimination (c-statistic 0.806) and the brier score (0.102).Using 95% bayesian credible intervals, 62 participants (5.6%) performed worse and 53 (4.7%) performed better than expected.Conclusions a new risk-adjusted ftr metric has been developed that complements existing sts performance measures.The metric specifically assesses institutional effectiveness of postoperative care, allowing hospitals to target quality improvement efforts.

Journal: The Annals of thoracic surgery (2022)
Publication types: Journal Article
Real-World Performance of High-Flux Dialyzers in Patients With Hypoalbuminemia.

There is little research on factors that influence the choice of dialyzer in patients undergoing hemodialysis.In patients at risk for poorer outcomes, including those with hypoalbuminemia, understanding how this choice impacts clinical parameters could inform patient management.The objective of this real-world analysis was to evaluate the use and performance of four single-use (i.e., nonreuse [nr]), high-flux optiflux dialyzers with varying surface areas (f160nr [1.5 m2], f180nr [1.7 m2], f200nr [1.9 m2], and f250nr [2.5 m2]) in patients (n = 271) with baseline hypoalbuminemia (≤3.5 g/dl) receiving hemodialysis at a medium-sized dialysis organization.Thrice weekly, in-center dialysis was delivered for 6 months without adjustments to the hemodialysis prescription.Larger dialyzers were more frequently used in men, patients with higher body mass indices, and those with diabetes.Increases in serum albumin from baseline (month 1) to month 6 (p < 0.05) were observed with all dialyzer sizes.A mean increase in hemoglobin of 0.31 g/dl was also observed (p < 0.001).Among patients exhibiting increased serum albumin levels (n = 177), reductions in the neutrophil-to-lymphocyte ratio, a marker of inflammation, were observed (mean: 0.90; p < 0.001).These results support the use of high-flux dialyzers in patients with hypoalbuminemia.

Journal: ASAIO journal (American Society for Artificial Internal Organs : 1992) (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
The impact of COVID-19 lockdown stringency on loneliness in five European countries.

Rationale the coronavirus pandemic has forced governments to implement a variety of different dynamic lockdown-stringency strategies in the last two years.Extensive lockdown periods could have potential unintended consequences on mental health, at least for at-risk groups.Objective we present novel evidence on the heterogeneous direct and indirect effects of lockdown-stringency measures on individuals' perception of social isolation (i.e.Loneliness) using panel data from five european countries (germany, france, spain, italy and sweden), which tracks changes in both in-person and remote social interactions between may 2020 and march 2021.Method we combine data from the come-here panel survey (university of luxembourg) and the oxford covid-19 government response tracker (ox cgrt).We implement a dynamic mixture model in order to estimate the loneliness sub-population classes based on the severity of loneliness, as well as the evolution of social interactions.Results while loneliness is remarkably persistent over time, we find substantial heterogeneity across individuals, identifying four latent groups by loneliness severity.Group membership probability varies with age, gender, education and cohabitation status.Moreover, we note significant differences in the impact of social interactions on loneliness by degree of severity.Older people are less likely to feel lonely, but were more affected by lockdown measures, partly due to a reduction in face-to-face interactions.On the contrary, the younger, especially those living alone, report high levels of loneliness that are largely unaffected by changes in the pandemic after lockdown measures were initially implemented.Conclusions understanding the heterogeneity in loneliness is key for the identification of at-risk populations that can be severely affected by extended lockdown measures.As part of public-health crisis-response systems, it is critical to develop support measures for older individuals living alone, as well as promoting continuous remote communication for individuals more likely to experience high levels of loneliness.

Journal: Social science & medicine (1982) (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Blocking endothelial TRPV4-Nox2 interaction helps reduce ROS production and inflammation, and improves vascular function in obese mice.

Obesity induces inflammation and oxidative stress, and ultimately leads to vasodilatory dysfunction in which transient receptor potential vanilloid type 4 (trpv4) and nicotinamide adenine dinucleotide phosphate oxidase (nox2) have been reported to be involved.However, little attention has been paid to the role of the trpv4-nox2 complex in these problems.The purpose of this study was to figure out the role of the trpv4-nox2 complex in obesity-induced inflammation, oxidative stress, and vasodilatory dysfunction.Using fluorescence resonance energy transfer and immunoprecipitation assays, we found enhanced trpv4 and nox2 interactions in obese mice.Using q-pcr, fluorescent dye dihydroethidium staining, and myotonic techniques, we found that obesity caused inflammation, oxidative stress, and vasodilatory dysfunction.Using adeno-associated viruses, we found that enhancement or attenuation of trpv4-nox2 interaction altered the vaso-function.Based on these findings, we found a small-molecule drug, m12, that interrupted the trpv4-nox2 interaction, thereby reducing inflammatory factors and reactive oxygen species production and helping to restore the vasodilatory function.In summary, our results revealed a new mechanism by which obesity-induced inflammation, oxidative stress, and vasodilatory dysfunction is caused by enhanced trpv4-nox2 interactions.Using m12 to interrupt the trpv4-nox2 interaction may have anti-inflammatory and anti-oxidative stress effects and help restore vasodilatory function and thus provide a new therapeutic approach to obesity.

Journal: Journal of molecular and cellular cardiology (2021)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Gender-based differences in brain and plasma pharmacokinetics of letrozole in sprague-dawley rats: Application of physiologically-based pharmacokinetic modeling to gain quantitative insights.

Based on the discovery that the estrogen synthase aromatase (cyp19a1) is abundantly expressed in high- grade gliomas, the aromatase inhibitor, letrozole is being investigated in pre-clinical models as a novel agent against this malignancy.Here, we investigated the systemic and brain pharmacokinetics of letrozole following single and steady state dosing in both male and female sprague-dawley rats.Furthermore, we employed physiologically-based pharmacokinetic (pbpk) modeling to gain quantitative insights into the blood-brain barrier penetration of this drug.Letrozole (4 mg/kg) was administered intraperitoneally daily for 5 days (for males) and 11 days (for females) and intracerebral microdialysis was performed for brain extracellular fluid (ecf) collection simultaneously with venous blood sampling.Drug levels were measured using hplc and non-compartmental analysis was conducted employing win nonlin®.Simcyp animal simulator was used for conducting bottom-up pbpk approach incorporating the specified multi-compartment brain model.Overall, marked gender-specific differences in the systemic and brain pharmacokinetics of letrozole were observed.Letrozole clearance was much slower in female rats resulting in markedly higher plasma and brain drug concentrations.At steady state, the plasma auc 0-24 was 103.0 and 24.8 μg*h/ml and brain ecf auc 0-12 was 24.0 and 4.8 μg*h/ml in female and male rats, respectively.The pbpk model simulated brain concentration profiles were in close agreement with the observed profiles.While gender-specific differences in letrozole pk are not observed in the clinical setting, these findings will guide the dose optimization during pre-clinical investigations of this compound.The pbpk model will serve as an important clinical translational tool.

Journal: PloS one (2021)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Indirect Calorimetry as an Instrument of Research to Identify the Effect of Hypermetabolism in Critical Patients' Prognosis.

Energy expenditure (ee) evaluation in intensive care unit (icu) patients can be very challenging.Critical illness is characterized by great variability in ee, which is influenced by the disease itself and the effects of treatment.Indirect calorimetry (ic) is currently the gold standard to measure ee in intensive care unit (icu) patients.However, calorimeters are not widely available, and predictive formulas (pf) are still commonly used, leading to under or overfeeding and deleterious consequences.important metabolic changes occur and catabolism becomes prominent in critically ill patients.both hyper and hypometabolism can be observed, but hypermetabolic patients appear to have higher mortality rates compared to metabolically normal patients.This study aimed to assess hypermetabolism incidence and compare clinical outcomes between hypermetabolic and normometabolic patients in icu.Methods a single-center, retrospective, and observational study was conducted in the icu of the hospital do divino espírito santo in ponta delgada, between august 2018 and february 2021.Only invasively mechanically ventilated patients were included.Resting energy expenditure (ree) was predicted by 25 kcal/kg/day formula to obtain predicted resting energy expenditure (pree), and ree was measured by ic to obtain measured resting energy expenditure (mree).According to their metabolic state (pree/mree), patients were divided into hypermetabolic (≥1.3) and normometabolic (<1.3).To determine the limits of agreement between pree and mree, we performed a bland-altman (ba) analysis.Baseline characteristics, severity criteria, nutritional status, and main diagnosis on admission were compared.The primary outcome considered was 30-day mortality.Other outcomes such as the icu length of stay (los), in-hospital los, and length of invasive ventilation were also evaluated.Results among the 80 icu patients included in the final analysis, 67 patients were normometabolic (83.4%).Patients admitted due to pneumonia were more hypermetabolic, 8 (61.5%) vs.10 (14.9%); p<0.001.Hypermetabolism was found also in patients admitted due to sepsis/septic shock, 7 (53.8%) vs.16 (23.9%); p=0.029.Hypermetabolic patients had lower body mass index (22.5 [interquartile range (iqr): 21.5-24.9] vs.27.7 [iqr: 25.0-32.4] kg/m2; p=0.001) and higher mree (2715.0 [2399.0-3090.0] vs.1690.0 [1410.0-2190.0] kcal/day; p<0.001).Bland-altman analysis showed a mean difference of -5.6 ± 744.7 kcal/day between the pree and mree by ic.No statistically significant difference was found between the two groups, neither in 30-day mortality nor in the other outcomes considered.Conclusions hypermetabolism was not seen to present a greater risk of death in mechanically ventilated patients in icu.Lower bmi, sepsis/septic shock, and pneumonia appear to be associated with a hypermetabolic state.

Journal: Cureus (2021)
Publication types: Journal Article
Extending Treatment Intervals of R-CHOP Therapy Might Be Acceptable for Some Patients with Non-indolent Non-Hodgkin's B-cell Lymphoma.

R-chop therapy is generally performed every 3 weeks.We investigated the effects of extending the interval of r-chop therapy for > 1 week on the prognoses of patients with non-indolent non-hodgkin's b-cell lymphoma.Among the 338 patients with non-indolent non-hodgkin's b-cell lymphoma who received initial chemotherapy at our institution, we focused on 178 patients who received r-chop therapy and analyzed the outcomes of the patients stratified by the treatment intervals.The estimated 3-year overall survival (os) for the entire population was 82.1%.Patients treated at intervals of ≥ 4 weeks were significantly older, and they had significantly longer follow-up periods and lower relative dose intensity.But the estimated 3-year os was comparable to those treated at <4 weeks (83.3% vs.80.5% p=0.947).In a multivariate analysis, age and the dose of anti-cancer agents had significant impacts on os, but there was no significant relationship regarding the treatment intervals.Propensity score matching confirmed the same result.R-chop therapy every around 4 weeks could achieve relatively good survival in some selected patients with non-indolent non-hodgkin's b-cell lymphoma.

Journal: Acta medica Okayama (2022)
Publication types: Journal Article