syedzayyan/paper_mill_benchmark huggingface dataset:
Valve-Like Outflow System Behavior With Motion Slowing in Glaucoma Eyes: Findings Using a Minimally Invasive Glaucoma Surgery-MIGS-Like Platform and Optical Coherence Tomography Imaging.

This study aimed to investigate anatomic relationships and biomechanics of pressure-dependent trabecular meshwork and distal valve-like structure deformation in normal and glaucoma eyes using high-resolution optical coherence tomography (hr-oct).Methods we controlled schlemm's canal (sc) pressure during imaging with hr-oct in segments of three normal (nl) and five glaucomatous (gl)ex vivoeyes.The dissected limbal wedges were studied from 15 locations (5 nl and 10 gl).A minimally invasive glaucoma surgery (migs)-like cannula was inserted into the sc lumen, whereas the other end was attached to a switch between two reservoirs, one at 0, the other at 30 mm hg.A steady-state pressure of 30 mm hg was maintained to dilate sc and collector channels (cc) during 3d volume imaging.The resulting 3d lumen surface relationships were correlated with internal structural features using an image mask that excluded tissues surrounding sc and cc.While imaging with hr-oct, real-time motion responses in sc and cc areas were captured by switching pressure from 0 to 30 or 30 to 0 mm hg.Nl vs.Gl motion differences were compared.Results lumen surface and internal relationships were successfully imaged.We identified sc inlet and outlet valve-like structures.In nl and gl, the mean sc areas measured at the steady-state of 0 and 30 mm hg were each significantly different (p< 0.0001).Synchronous changes in sc and cc lumen areas occurred in <200 ms.Measured sc area differences at the steady-state 0 and 30 mm hg, respectively, were larger in nl than gl eyes (p< 0.0001).The sc motion curves rose significantly more slowly in gl than nl (p< 0.001).Pressure waves traveled from the cannula end along the sc lumen to cc and deep intrascleral channels.Conclusion hr-oct provided simultaneous measurements of outflow pathway lumen surfaces, internal structures, and biomechanics of real-time pressure-dependent dimension changes.We identified sc inlet and outlet valve-like structures.Gl tissues underwent less motion and responded more slowly than nl, consistent with increased tissue stiffness.A migs-like shunt to sc permitted pulse waves to travel distally along sc lumen and into cc.

Journal: Frontiers in medicine (2022)
Publication types: Journal Article
Design, Preparation, and Application of Magnetic Nanoparticles for Food Safety Analysis: A Review of Recent Advances.

This review (with 126 references) aims at providing an updated overview of the recent developments and innovations of the preparation and application of magnetic nanoparticles for food safety analysis.During the past two decades, various magnetic nanoparticles with different sizes, shapes, and surface modifications have been designed, synthesized, and characterized with the prospering development of material science.Analytical scientists and food scientists are among the ones who bring these novel materials from laboratories to commercial applications.Powerful and versatile surface functional groups and high surface to mass ratios make these magnetic nanoparticles useful tools for high-efficiency capture and preconcentration of certain molecules, even when they exist in trace levels or complicated food matrices.This is why more and more methods for sensitive detection and quantification of hazards in foods are developed based on these magic magnetic tools.In this review, the principles and superiorities of using magnetic nanoparticles for food pollutant analysis are first introduced, like the mechanism of magnetic solid phase extraction, a most commonly used method for food safety-related sample pretreatment.Their design and preparation are presented afterward, alongside the mechanisms underlying their application for different analytical purposes.After that, recently developed magnetic nanoparticle-based methods for dealing with food pollutants such as organic pollutants, heavy metals, and pathogens in different food matrices are summarized in detail.In the end, some humble outlooks on future directions for work in this field are provided.

Journal: Journal of agricultural and food chemistry (2022)
Publication types: Journal Article;Review
Constrained Peptides with Fine-Tuned Flexibility Inhibit NF-Y Transcription Factor Assembly.

Protein complex formation depends on the interplay between preorganization and flexibility of the binding epitopes involved.The design of epitope mimetics typically focuses on stabilizing a particular bioactive conformation, often without considering conformational dynamics, which limits the potential of peptidomimetics against challenging targets such as transcription factors.We developed a peptide-derived inhibitor of the nf-y transcription factor by first constraining the conformation of an epitope through hydrocarbon stapling and then fine-tuning its flexibility.In the initial set of constrained peptides, a single non-interacting α-methyl group was observed to have a detrimental effect on complex stability.Biophysical characterization revealed how this methyl group affects the conformation of the peptide in its bound state.Adaption of the methylation pattern resulted in a peptide that inhibits transcription factor assembly and subsequent recruitment to the target dna.

Journal: Angewandte Chemie (International ed. in English) (2019)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Arthroscopic Excision of Bipartite Patella.

A bipartite patella usually presents as an incidental finding on radiographs because most cases are asymptomatic.However, some patients may present with pain and functional limitations.Conservative treatment is sufficient to resolve symptoms in most cases; however, a small minority of patients may require surgical management.Recent studies have reported excellent results with an arthroscopic approach.This technical note details our procedure for treating a symptomatic bipartite patella that has not resolved with conservative care.

Journal: Arthroscopy techniques (2021)
Publication types: Journal Article
Comparing Attained Weight and Weight Velocity during the First 6 Months in Predicting Child Undernutrition and Mortality.

The first 6 mo of life are critical for subsequent risk of undernutrition and mortality.The predictive abilities of attained weight at the end of each month and monthly weight velocity for undernutrition and mortality need to be compared.Objectives this study aimed to examine the predictive abilities of different weight metrics during the first 6 mo of life in predicting undernutrition and mortality.Methods this study used a cohort of infants in tanzania.Weight and length were measured monthly from birth to 18 mo of age.Three weight metrics during the first 6 mo of life were considered as predictors, including attained weight-for-age z score (waz) at the end of each month, monthly change in waz, and monthly weight velocity z score (wvz).Logistic models were used with undernutrition (at 6 or 12 mo) and mortality (over the first 18 mo) as outcomes.Auc values were compared across metrics.Results for predicting wasting at 6 mo, wvz (auc: 0.80) had a greater predictive ability than attained waz (auc: 0.76) and change in waz (auc: 0.71) during the second month of life.After 2 mo, attained waz (auc: 0.81-0.89) had greater predictive abilities than wvz (auc: 0.71-0.77) and change in waz (auc: 0.65-0.67).For predicting stunting at 6 mo, attained waz (auc: 0.75-0.79) had consistently greater predictive abilities than wvz (auc: 0.56-0.66) and change in waz (auc: 0.50-0.57).The weight metrics had similar abilities in predicting mortality, with the auc rarely reaching >0.65.Conclusions attained weight at the end of each month had greater abilities than monthly weight velocity in the same month in predicting undernutrition.Attained weight remains a useful indicator for identifying infants at greater risk of undernutrition.

Journal: The Journal of nutrition (2022)
Publication types: Journal Article;Research Support, N.I.H., Extramural
COVID-19 Convalescent Plasma and Clinical Trials: Understanding Conflicting Outcomes.

Convalescent plasma (cp) recurs as a frontline treatment in epidemics because it is available as soon as there are survivors.The covid-19 pandemic represented the first large-scale opportunity to shed light on the mechanisms of action, safety, and efficacy of cp using modern evidence-based medicine approaches.Studies ranging from observational case series to randomized controlled trials (rcts) have reported highly variable efficacy results for covid-19 cp (ccp), resulting in uncertainty.We analyzed variables associated with efficacy, such as clinical settings, disease severity, ccp sars-co v-2 (severe acute respiratory syndrome coronavirus 2) antibody levels and function, dose, timing of administration (variously defined as time from onset of symptoms, molecular diagnosis, diagnosis of pneumonia, or hospitalization, or by serostatus), outcomes (defined as hospitalization, requirement for ventilation, clinical improvement, or mortality), ccp provenance and time for collection, and criteria for efficacy.The conflicting trial results, along with both recent who guidelines discouraging ccp usage and the recent expansion of the fda emergency use authorization (eua) to include outpatient use of ccp, create confusion for both clinicians and patients about the appropriate use of ccp.A review of 30 available rcts demonstrated that signals of efficacy (including reductions in mortality) were more likely if the ccp neutralizing titer was >160 and the time to randomization was less than 9 days.The emergence of the omicron variant also reminds us of the benefits of polyclonal antibody therapies, especially as a bridge to the development and availability of more specific therapies.

Journal: Clinical microbiology reviews (2022)
Publication types: Journal Article;Review
Liquid dibromomethane under pressure: a computational study.

Molecular dynamics simulations have been performed on liquid dibromomethane at thermodynamic states corresponding to temperature in the range 268-328 k and pressure varying from 1 bar to 3000 bar.The interaction model is a simple effective two-body pair potential with atom-atom coulomb and lennard-jones interactions and molecules are rigid.Thermodynamic properties have been studied, including the isobaric thermal expansion coefficient, the isothermal compressibility, the heat capacities and the speed of sound.The simulation results exhibit a crossing of the isotherms of the isobaric thermal expansion coefficient at about 800 bar in very good agreement with the prediction of an isothermal fluctuation equation of state predicting such a crossing in the pressure range 650-900 bar, though experimental results up to 1000 bar do not find any crossing.

Journal: Physical chemistry chemical physics : PCCP (2021)
Publication types: Journal Article
Kynurenine/Aryl Hydrocarbon Receptor Modulates Mitochondria-Mediated Oxidative Stress and Neuronal Apoptosis in Experimental Intracerebral Hemorrhage.

S:oxidative stress and neuronal apoptosis play crucial roles in the pathological processes of secondary injury after intracerebral hemorrhage (ich).Aryl hydrocarbon receptor (ahr), together with its endogenous ligand kynurenine, is known to mediate free radical accumulation and neuronal excitotoxicity in central nervous systems.Herein, we investigate the pathological roles of kynurenine/ahr after ich.results:endogenous ahr knockout alleviated reactive oxygen species accumulation and neuronal apoptosis in ipsilateral hemisphere at 48 h after ich in mice.The ich insult resulted in an increase of total and nucleus ahr protein levels and ahr transcriptional activity.Inhibition of ahr provided both short- and long- term neurological benefits by attenuating mitochondria-mediated oxidative stress and neuronal apoptosis after ich in mice.Rho a-bax signaling activated mitochondrial death pathway and participated in deleterious actions of ahr.Finally, we reported that exogenous kynurenine aggravated ahr activation and mediated the brain mentioned earlier.Male animals were used in the experiments.innovation:we show for the first time that kynurenine/ahr mediates mitochondria death and free radical accumulation, at least partiallyviathe rho a/bax signaling pathway.Pharmacological antagonists of ahr and kynurenine may ameliorate neurobehavioral function and improve the prognosis of patients with ich.conclusion:kynurenine/ahr may serve as a potential therapeutic target to attenuate mitochondria-mediated oxidative stress and neuronal cells impairment in patients with ich.antioxid.Redox signal.37, 1111-1129.

Journal: Antioxidants & redox signaling (2022)
Publication types: Journal Article;Research Support, N.I.H., Extramural;Research Support, Non-U.S. Gov't
Effects of valinomycin doping on the electrical and structural properties of planar lipid bilayers supported on polyelectrolyte multilayers.

Supported lipid bilayers (slbs) on polyelectrolyte multilayers (pems) have large potential as models for developing sensor devices.Slbs can be designed with receptors and channels, which benefit from the biological environment of the lipid layers, to create a sensing interface for ions and biomarkers.Pems assembled by the layer-by-layer (lbl) technique and used as supports for a lipid bilayer enable an easy integration of the bilayer on almost any surface and device.For electrochemical sensors, lbl assembly enables nanoscale tunable separation of the lipid bilayer from the electrode surface, avoiding undesired effects of the electrode surface on the lipid bilayers.We study the fabrication of valinomycin-doped slbs on pems as a model system for biophysical studies and for selective ion sensing.Slbs are fabricated from dioleoylphosphatidylcholine (dopc) and dioleoylphosphatidylserine (dops) 50:50 vesicles doped with valinomycin, as a k+-selective carrier.Slbs were deposited on electrodes coated with poly(allyl amine hydrochloride) (pah) and poly(styrene sodium sulfonate) (pss) multilayers.Lipid bilayer formation was monitored by using quartz crystal microbalance with dissipation (qcmd) technique and atomic force microscopy (afm).Electrochemical impedance spectroscopy (eis) and potentiometric measurements were performed to assess k+selectivity over other ions and the potential of valinomycin-doped slbs for k+-sensing.

Journal: Bioelectrochemistry (Amsterdam, Netherlands) (2021)
Publication types: Journal Article
The role and regulation of Pnn in proliferative and non-dividing cells: Form embryogenesis to pathogenesis.

Pnn, a multiple functional protein, plays roles in embryonic development, cellular differentiation, tumorigenesis, and metastasis.In the past two decades, the functions of pnn in regulating rna alternative splicing, gene regulation, and cell-cell connection have been revealed.Although pnn is originally identified as a desmosome-associated protein for linking desmosome and intermediated filament, emerging evidence implies that pnn not only is a desmosome protein but also plays critical roles in the nucleus.To date, through cell biology investigation and the generation of animal models with genetic manipulation, the physiological role of pnn has been characterized in the research fields of developmental biology, tumor biology, and neuroscience.Through proteomic and molecular biology studies, transcription regulators, splicing regulators, and cytoskeletal proteins were found to interact with pnn.In addition, histopathological and biochemical evidence has pointed to an association of pnn expression level with tumorigenesis and metastasis.A previous clinical study also demonstrated a correlation between a reduced expression of pnn and human dementia.Besides, experimental studies showed a protective role of pnn against ischemic stress in astrocytes.All indicated a variety of roles of pnn in different cell types.In this review article, we introduced the role of pnn in embryogenesis and pathogenesis as well as discussed its potential clinical application.

Journal: Biochemical pharmacology (2021)
Publication types: Journal Article;Research Support, Non-U.S. Gov't;Review
Glycemic Control and the Risk of Acute Kidney Injury in Patients With Type 2 Diabetes and Chronic Kidney Disease: Parallel Population-Based Cohort Studies in U.S. and Swedish Routine Care.

Patients with diabetes and chronic kidney disease (ckd) have increased susceptibility to acute kidney injury (aki), but mechanisms are unclear.We investigated the association of glycemic control with risk of aki.Research design and methods in two observational cohorts of u.s.(geisinger health system, danville, pa) and swedish (stockholm creatinine measurements [scream] project, stockholm, sweden) adults with type 2 diabetes and confirmed ckd stages g3-g5 undergoing routine care, we evaluated associations between baseline and time-varying hemoglobin a1c(hb a1c) with the incident aki (defined as increase in creatinine ≥0.3 mg/d l over 48 h or 1.5 times creatinine over 7 days).Results in the u.s.Cohort, there were 22,877 patients (55% women) with a median age of 72 years and estimated glomerular filtration rate (e gfr) 52 m l/min/1.73 m2.In the swedish cohort, there were 12,157 patients (50% women) with a median age of 77 years and e gfr 51 m l/min/1.73 m2.During 3.1 and 2.3 years of follow-up, 7,060 and 2,619 aki events were recorded in the u.s.And swedish cohorts, respectively.The adjusted association between baseline hb a1cand aki was similar in both cohorts.Compared with baseline hb a1c6-6.9% (42-52 mmol/mol), the hazard ratio for aki in patients with hb a1c>9% (75 mmol/mol) was 1.29 (95% ci 1.18-1.41) in geisinger and 1.33 (95% ci 1.13-1.57) in the swedish cohort.Results were consistent in stratified analysis, when using death as competing risk, and when using time-varying hb a1c.Conclusions higher hb a1cwas associated with aki in adults with type 2 diabetes and ckd, suggesting that improving glycemic control may reduce the risk of aki.

Journal: Diabetes care (2020)
Publication types: Journal Article;Research Support, N.I.H., Extramural;Research Support, Non-U.S. Gov't
Antibody-Drug Conjugates in Breast Cancer: What Is Beyond HER2?

The therapeutic landscape of patients with breast cancer has changed significantly with the introduction of antibody-drug conjugates (adcs).Although human epidermal growth factor receptor 2 (her2) has been the centerpiece of adc development, potentially any surface antigen with differential expression between tumor and normal cells may be suitable for targeting with adcs.Exploration of new targets is critical to expand the fraction of patients who can benefit from adcs.Sacituzumab govitecan, an anti-trophoblast cell surface antigen 2 adc, is the only non-anti-her2 adc approved for breast cancer to date, with several novel adcs directed against novel targets (e.g., her3, liv-1) at various stages of preclinical and clinical development.The aim of this review is to provide an overview of clinical trials investigating adcs targeting novel antigens.We discuss the optimal characteristics of the target to be exploited in adcs' design and potential future challenges in the evolving field of adcs such as biomarker assessment, patient selection, and sequencing of adcs.

Journal: Cancer journal (Sudbury, Mass.) (2022)
Publication types: Review;Journal Article
Use of handheld X-ray fluorescence as a non-invasive method to distinguish between Asian and African elephant tusks.

We describe the use of handheld x-ray fluorescence, for elephant tusk species identification.Asian (n = 72) and african (n = 85) elephant tusks were scanned and we utilized the species differences in elemental composition to develop a functional model differentiating between species with high precision.Spatially, the majority of measured elements (n = 26) exhibited a homogeneous distribution in cross-section, but a more heterologous pattern in the longitudinal direction.Twenty-one of twenty four elements differed between asian and african samples.Data were subjected to hierarchical cluster analysis followed by a stepwise discriminant analysis, which identified elements for the functional equation.The best equation consisted of ratios of si, s, cl, ti, mn, ag, sb and w, with zr as the denominator.Next, bayesian binary regression model analysis was conducted to predict the probability that a tusk would be of african origin.A cut-off value was established to improve discrimination.This bayesian hybrid classification model was then validated by scanning an additional 30 asian and 41 african tusks, which showed high accuracy (94%) and precision (95%) rates.We conclude that handheld xrf is an accurate, non-invasive method to discriminate origin of elephant tusks provides rapid results applicable to use in the field.

Journal: Scientific reports (2016)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Promoter hypermethylation of the RECK gene is associated with its low expression and poor survival of esophageal squamous cell carcinoma.

The present study aimed to investigate the association between the methylation status of the reversion-inducing cysteine-rich protein with kazal motifs (reck) gene and its m rna expression levels in patients with esophageal squamous cell carcinoma (escc).The methylation status of reck was analyzed by methylation-specific polymerase chain reaction (pcr), and reck m rna expression levels were analyzed by quantitative pcr, in 310 paired escc tissues.The mean reck methylation index (mi) was 0.65 in esccs and 0.49 in non-tumor samples.There was a significant association between reck methylation and the american joint committee on cancer stage and lymph node metastasis in escc (p 0.16; mean-∆∆cq=-2.85) compared with those with hypomethylation of the reck gene (∆mi ≤0.16; mean-∆∆ct=-0.83), and there was a significant difference in the m rna expression levels of reck between those with n0-1and n2-3lymph node metastasis (p<0.0001).A significant correlation was observed between reck m rna expression levels, the mi of reck and poor postoperative survival (p=0.0003; p<0.0001).The results of the present study suggested that promoter hypermethylation may be an important factor for loss of reck m rna expression and may be an indicator of poor survival in escc.

Journal: Oncology letters (2017)
Publication types: Journal Article
Evolutionary Algorithm-Based Crystal Structure Prediction for Copper(I) Fluoride.

Despite numerous experimental studies since 1824, the binary copper(i) fluoride remains unknown.A crystal structure prediction has been carried out for cu f using the uspex evolutionary algorithm and a dispersion-corrected hybrid density functional method.In total about 5000 hypothetical structures were investigated.The energetics of the predicted structures were also counter-checked with local second-order møller-plesset perturbation theory.Herein 39 new hypothetical copper(i) fluoride structures are reported that are lower in energy compared to the previously predicted cinnabar-type structure.Cuprophilic cu-cu interactions are present in all the low-energy structures, leading to ordered cu substructures such as helical or zig-zag-type cu-cu motifs.The lowest-energy structure adopts a trigonal crystal structure with space group p3121.From an electronic point of view, the predicted cu f modification is a semiconductor with an indirect band gap of 2.3 e v.

Journal: Chemistry (Weinheim an der Bergstrasse, Germany) (2019)
Publication types: Journal Article