syedzayyan/paper_mill_benchmark huggingface dataset:
Prevalence of low computed tomography-measured skeletal muscle index and handgrip strength in a general medical population.

Sarcopenia is defined as the loss of muscle mass and function and has been associated with worsened outcomes, including disability and mortality.The aim of this study was to describe the prevalence of sarcopenia in patients who had an abdominal computed tomography (ct) scan completed within 7 days of hospital admission.Methods a retrospective study was conducted.Adult patients admitted to either the general medical or surgical floor were included.Muscle function was assessed using handgrip strength (hgs, kg), completed within the first 48 hours of admission.Skeletal muscle index (smi, kg/m2) at the third lumber region was calculated among patients who had an abdominal ct scan completed within 7 days of admission.Sarcopenia was identified by the combination of low smi and hgs.The primary outcome was the percentage of patients diagnosed with sarcopenia.Results a total of 1318 patients were admitted; 11% (n = 141) had an abdominal ct scan completed within 7 days of admission.Only race and prevalence of malnutrition were different between patients who did and did not have a ct completed.The overall prevalence of sarcopenia was 13% (n = 18/141).Additionally, 39% of the sample was at risk for sarcopenia, with either low smi (n = 13/141) or low hgs (n = 42/141).Conclusions overall prevalence of sarcopenia was low, but more than one-third of patients had either low smi or low hgs.Minimal differences were observed between patients who did and did not have an abdominal ct scan completed upon admission.

Journal: Nutrition in clinical practice : official publication of the American Society for Parenteral and Enteral Nutrition (2022)
Publication types: Journal Article
Microarray expression and functional analysis of circular RNAs in the glomeruli of NZB/W F1 mice with lupus nephritis.

The present study applied a circular rna (circ rna) microarray to examine the circ rna expression profiles in the glomeruli of nzb/w f1 mice with lupus nephritis (ln) during the pathogenesis of the disease.Glomeruli from two groups of female nzb/w f1 mice of the same age with either severe or mild ln were isolated by perfusion with dynabeads.A microarray analysis was then performed to evaluate the differentially expressed circ rnas of the glomeruli in the two groups, which were then confirmed by reverse transcription-quantitative pcr (rt-q pcr) assays.In addition, using a biomathematical strategy, the differentially-expressed circ rnas were identified in severe ln when compared with mild ln, and the commonly expressed circ rna species among these profiles were optimized via competing endogenous rna (ce rna) analysis.The predicted micro rnas (mi rnas/mi rs) as downstream targets of circ rnas and upstream regulators of m rnas were verified by rt-q pcr and the final circ rna-mi rna-m rna network was constructed to identify the circ rna that was a pathogenic link in ln.The present study obtained 116 differentially expressed circ rnas, including 41 up- and 75 downregulated circ rnas, in severe ln when compared with mild ln, and 12 circ rnas were confirmed by rt-q pcr.The most significant difference was in the expression of mmu_circ rna_34428 (p<0.001) when comparing severe and mild ln glomeruli.A network of mmu_circ rna_34428-targeted mi rna-gene interactions was subsequently constructed, including mi r-338-3p, mi r-670-3p, mi r-3066-5p, mi r-210-5p and their corresponding m rna targets.To the best of our knowledge, the present study elucidated, for the first time, circ rna profiling and the circ rna-mi rna interactions in the development of ln in female nzb/w f1 mice.The results revealed that mmu_circ rna_34428 could serve an important role in ln progression; however, the present study did not elucidate the functions of this circ rna or others in ln progression.

Journal: Experimental and therapeutic medicine (2019)
Publication types: Journal Article
Therapeutic administration of etoposide coincides with reduced systemic HMGB1 levels in macrophage activation syndrome.

Macrophage activation syndrome (mas) is a potentially fatal complication of systemic inflammation.Hmgb1 is a nuclear protein released extracellularly during proinflammatory lytic cell death or secreted by activated macrophages, nk cells, and additional cell types during infection or sterile injury.Extracellular hmgb1 orchestrates central events in inflammation as a prototype alarmin.Tlr4 and the receptor for advanced glycation end products operate as key hmgb1 receptors to mediate inflammation.Methods standard elisa and cytometric bead array-based methods were used to examine the kinetic pattern for systemic release of hmgb1, ferritin, il-18, ifn-γ, and mcp-1 before and during treatment of four children with critical mas.Three of the patients with severe underlying systemic rheumatic diseases were treated with biologics including tocilizumab or anakinra when mas developed.All patients required intensive care therapy due to life-threatening illness.Add-on etoposide therapy was administered due to insufficient clinical response with standard treatment.Etoposide promotes apoptotic rather than proinflammatory lytic cell death, conceivably ameliorating subsequent systemic inflammation.Results this therapeutic intervention brought disease control coinciding with a decline of the increased systemic hmgb1, ifn-γ, il-18, and ferritin levels whereas mcp-1 levels evolved independently.Conclusion systemic hmgb1 levels in mas have not been reported before.Our results suggest that the molecule is not merely a biomarker of inflammation, but most likely also contributes to the pathogenesis of mas.These observations encourage further studies of hmgb1 antagonists.They also advocate therapeutic etoposide administration in severe mas and provide a possible biological explanation for its mode of action.

Journal: Molecular medicine (Cambridge, Mass.) (2021)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Optimal Brassinosteroid Levels Are Required for Soybean Growth and Mineral Nutrient Homeostasis.

Brassinosteroids (brs) are steroid phytohormones that are known to regulate plant growth and nutrient uptake and distribution.However, how brs regulate nutrient uptake and balance in legume species is not fully understood.Here, we show that optimal br levels are required for soybean (glycine max l.) seedling growth, as treatments with both 24-epicastasterone (24-epi cs) and the br biosynthesis inhibitor propiconazole (ppz) inhibit root growth, including primary root elongation and lateral root formation and elongation.Specifically, 24-epi cs and ppz reduced the total phosphorus and potassium levels in the shoot and affected several minor nutrients, such as magnesium, iron, manganese, and molybdenum.A genome-wide transcriptome analysis identified 3774 and 4273 differentially expressed genes in the root tip after brassinolide and ppz treatments, respectively.The gene ontology (go) analysis suggested that genes related to "dna-replication", "microtubule-based movement", and "plant-type cell wall organization" were highly responsive to the brassinolide and ppz treatments.Furthermore, consistent with the effects on the nutrient concentrations, corresponding mineral transporters were found to be regulated by br levels, including the gm pht1s,gm kts, gm vit2,gm zips, and gm mot1genes.Our study demonstrates that optimal br levels are important for growth and mineral nutrient homeostasis in soybean seedlings.

Journal: International journal of molecular sciences (2021)
Publication types: Journal Article
Comparison of enzymatic activities in different Candida species isolated from women with vulvovaginitis.

Introduction comparing the activities of secreted enzymes in different fungal species can improve our understanding of their pathogenic role.Secretion of various enzymes by candida species has been considered for determination of their virulence in different candida infections including vulvovaginitis.Aims the aim of this study was to determine and compare the activity of secreted enzymes in candidia strains isolated from women suspected to vulvovaginal candidiasis (vvc) and referred to some health centers in khuzestan, southwestern iran.Patients and methods the vaginal secretion samples were taken by swap from 250 suspected women with symptoms of vulvovaginal candidiasis and cultured on chromagar candida medium.Identification of the isolated candida from culture positive samples performed by the color of colonies and some standard mycological procedures.Activities of phospholipase, hemolysin-α, hemolysin-β, esterase and proteinase were measured in vitro by standard laboratory protocols.The enzymatic activity index (eai) was calculated for each enzyme in accordance to relevant protocols.Results totally in eighty cases (32%), a candida strain was isolated which found to be as 52 (65%) candida albicans; 12 (15%) c.Glabrata; 10 (12.5%) c.Dubliniensis; 4 (5%) c.Krusei, c.Tropicalis and c.Parapsilosis species (each=1; 1.3%).Among c.Albicans strains, 89.1% produced all studied enzymes, while 86% of c.Glabrata strains failed to produce proteinase and phospholipase.The eais in decreasing order were as hemolysin-β=0.2895, hemolysin-α=0.5420, esterase=0.5753, proteinase=0.7413, and phospholipase=0.7446, respectively.Activity of phospholipase, esterase and proteinase secreted by c.Albicans and c.Dubliniensis were significantly more than those released by c.Glabrata and c.Krusei, while 86% of c.Glabrata strains did not show esterase activity.On the other hand, the activity rates of hemolysin α and β among all studied isolates were almost similar.Conclusion in the present study, the prevalence of vvc among investigated women was higher than the previous report from khuzestan but c.Albicans has yet remained the predominant agent of vvc in this area.Given to the eai, the virulence of c.Albicans in vvc can be mediated by phospholipase, esterase and proteinases.

Journal: Journal de mycologie medicale (2017)
Publication types: Comparative Study;Journal Article
5-HT3Aserotonin receptor in the gastrointestinal tract: the link between immune system and enteric nervous system in the digestive form of Chagas disease.

Chagas disease is caused by trypanosoma cruzi and remains one of the most neglected diseases in latin america.One of its clinical forms is chagas megacolon.Despite being known for more than half a century, detailed causes are still obscure.Recent evidence indicates a close relationship between the immune system and the enteric nervous system in the etiology of chagasic megacolon pathology.It is believed that low expression of the 5-ht3aserotonin receptor on lymphocytes could be linked to megacolon development.To test this hypothesis, this work investigated the distribution of cd4, cd8, and cd20 lymphocytes and their 5-ht3areceptor expression.The results demonstrated that chagas patients without megacolon present a higher expression of the 5-ht3areceptor in all analyzed lymphocytes compared with chagas patients with megacolon.These data suggest that the high expression of this receptor may lead to immunomodulation and prevent the development of chagas megacolon.

Journal: Parasitology research (2019)
Publication types: Journal Article
A Novel Method for Intelligibility Assessment of Nonlinearly Processed Speech in Spaces Characterized by Long Reverberation Times.

Assessment of speech intelligibility is a complex task that requires taking into account a number of factors such as different perception of each speech sub-bands by the human hearing sense or different physical properties of each frequency band of a speech signal.Currently, the state-of-the-art method used for assessing the quality of speech transmission is the speech transmission index (sti).It is a standardized way of objectively measuring the quality of, e.g., an acoustical adaptation of conference rooms or public address systems.The wide use of this measure and implementation of this method on numerous measurement devices make sti a popular choice when the speech-related quality of rooms has to be estimated.However, the sti measure has a significant drawback which excludes it from some particular use cases.For instance, if one would like to enhance speech intelligibility by employing a nonlinear digital processing algorithm, the sti method is not suitable to measure the impact of such an algorithm, as it requires that the measurement signal should not be altered in a nonlinear way.Consequently, if a nonlinear speech enhancing algorithm has to be tested, the sti-a standard way of estimating speech transmission cannot be used.In this work, we would like to propose a method based on the sti method but modified in such a way that it makes it possible to employ it for the estimation of the performance of the nonlinear speech intelligibility enhancement method.The proposed approach is based upon a broadband comparison of cumulated energy of the transmitted envelope modulation and the received modulation, so we called it broadband sti (b sti).Its credibility with regard to signals altered by the environment or nonlinear speech changed by a dsp algorithm is checked by performing a comparative analysis of ten selected impulse responses for which a baseline value of sti was known.

Journal: Sensors (Basel, Switzerland) (2022)
Publication types: Journal Article
Population pharmacokinetics of edoxaban and its main metabolite in a dedicated renal impairment study.

A model characterizing the population pharmacokinetics (pk) of edoxaban and its major metabolite, m4, following a single oral dose of 15 mg administered to subjects with varying kidney function was developed.Thirty-two subjects contributed with edoxaban plasma, edoxaban urine, and m4 plasma concentrations.Edoxaban urine concentrations allowed estimation of renal clearance, and high contribution of renal to total clearance enabled estimation of absolute oral bioavailability.A 2-compartment model with delayed absorption and elimination parameterized as renal clearance linearly related to creatinine clearance (clcr ) and nonrenal clearance forming m4 described edoxaban pk.The pk of m4 was described with a 1-compartment model.For a typical subject (70 kg; clcr , 100 m l/min) bioavailability, clearance, and central and peripheral volume of distribution for edoxaban was estimated to 72.3%, 21.0 l/h, 95.4 l, and 54.3 l, respectively.For both edoxaban and m4, the model predicted systemic exposure to increase 57.0%, 35.0%, and 11.6% in a subject having clcr of 30, 50, and 80 m l/min, respectively, compared with a subject having a clcr of 100 m l/min.Concentration ratios (m4 over edoxaban) were predicted to vary with time after dose, but with minor influence of kidney function and body weight.Results were in agreement with previous analyses.

Journal: Journal of clinical pharmacology (2015)
Publication types: Controlled Clinical Trial;Journal Article;Research Support, Non-U.S. Gov't
Role of lactic acid bacteria and yeasts in sourdough fermentation during breadmaking: Evaluation of postbiotic-like components and health benefits.

Sourdough (sd) fermentation is a traditional biotechnological process used to improve the properties of baked goods.Nowadays, sd fermentation is studied for its potential health effects due to the presence of postbiotic-like components, which refer to a group of inanimate microorganisms and/or their components that confer health benefits on the host.Some postbiotic-like components reported in sd are non-viable microorganisms, short-chain fatty acids, bacteriocins, biosurfactants, secreted proteins/peptides, amino acids, flavonoids, exopolysaccharides, and other molecules.Temperature, p h, fermentation time, and the composition of lactic acid bacteria and yeasts in sd can impact the nutritional and sensory properties of bread and the postbiotic-like effect.Manyin vivostudies in humans have associated the consumption of sd bread with higher satiety, lower glycemic responses, increased postprandial concentrations of short-chain fatty acids, and improvement in the symptoms of metabolic or gastrointestinal-related diseases.This review highlights the role of bacteria and yeasts used for sd, the formation of postbiotic-like components affected by sd fermentation and the baking process, and the implications of functional sd bread intake for human health.There are few studies characterizing the stability and properties of postbiotic-like components after the baking process.Therefore, further research is necessary to develop sd bread with postbiotic-related health benefits.

Journal: Frontiers in microbiology (2022)
Publication types: Journal Article;Review
MAS-related G protein-coupled receptors X (MRGPRX): Orphan GPCRs with potential as targets for future drugs.

Mas-related g protein-coupled receptors (gpcrs) of subfamily x, designated mrgprx, are primate-specific orphan receptors that belong to the δ-branch of rhodopsin-like, class a gpcrs.Four distinct subtypes exist, mrgprx1, -2, -3, and -4, mrgprx2 having the lowest degree of similarity with the others.Due to their expression on sensory neurons and immune cells, and their roles in pain perception and transmission, itch, inflammation, immune defense, pseudo-allergic reactions, wound healing, and possibly cancer, they have recently attracted much attention as novel drug targets.In particular mrgprx2 was identified as an important mast cell receptor, responsible for anaphylactoid drug reactions and involved in skin and mucosal diseases, e.g.Urticaria, atopic dermatitis, rosacea, and allergic rhinitis.A major hurdle has been the lack of animal models for studying these primate-specific receptors.However, recently humanized mice have been created.Moreover, a mouse ortholog of mrgprx2, mrgprb2, was identified, both receptors having a certain degree of similarity.Mrgprx1 and -2 can be activated by various peptides and small (partly peptidomimetic) molecules.Mrgprx2 is additionally activated by a very broad range of basic molecules, positively charged at physiologic p h value of 7.4, including many drugs.Mrgprx4 is activated by small acidic molecules including bile acids.For mrgprx3, no ligands have been reported yet.Antagonists with reasonable potency and selectivity have been described for mrgprx1, and few antagonists also for mrgprx2, but not for the other subtypes.The recent elucidation of cryogenic electron microscopy structures of mrgprx2 and -4 is expected to facilitate and advance drug development for these receptors.Currently, research on mrgprx is still in its infancy, and exciting discoveries can be awaited.These receptors have great potential as future drug targets.

Journal: Pharmacology & therapeutics (2022)
Publication types: Journal Article;Review
Parity and the Resolution of Value Conflicts in Design.

Recent developments in theories for responsible innovation have focused on the importance of actively accounting for values in our technological designs.Leading among these theories is that of value sensitive design (vsd) which attempts to guide the design process on the basis of evaluative analysis.However, values often come into conflict and vsd has been criticized for not providing a proper method to resolve such inevitable conflicts.This paper examines three such methods and argues that although each has its merits, they all fail to account for a common source of value conflicts known as value incommensurability.Drawing on literature from the field of axiology, this paper argues that by incorporating the evaluative relation of 'parity' each of these three methods, and the vsd framework in general, will be able to properly understand the relation which holds between conflicting design options stemming from the incommensurable of values and be able to guide designers in making rational decision in the face of such conflicts.

Journal: Science and engineering ethics (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Osteopontin and galectin-3 as biomarkers of maladaptive right ventricular remodeling in pulmonary hypertension.

This study assessed the utility of osteopontin (opn) and galectin-3 (gal-3) as biomarkers of maladaptive right ventricular remodeling in pulmonary hypertension (ph).materials & methods:we examined plasma levels of opn and gal-3 in patients with ph (n = 62), dilated cardiomyopathy (n = 34), left ventricular hypertrophy (lvh; n = 47), and controls without right ventricle (rv) or lv abnormalities (n = 38).results:opn and gal-3 levels were higher in ph, dilated cardiomyopathy and lvh than in the controls.Opn concentrations in ph patients with maladaptive rv were significantly higher than in those with adaptive rv.Gal-3 did not differentiate between adaptive and maladaptive rv remodeling in ph.Opn and gal-3 levels did not correlate with parameters of lv remodeling.conclusion:opn is a potential biomarker of rv maladaptation.

Journal: Biomarkers in medicine (2021)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Microcirculation-guided treatment improves tissue perfusion and hemodynamic coherence in surgical patients with septic shock.

Severe sepsis and septic shock may impair microcirculatory perfusion and cause organ dysfunction.The aim of this pilot study was to assess a new microcirculation-guided resuscitation strategy in patients with septic shock undergoing emergency abdominal surgery.Methods a microcirculation-guided treatment algorithm was developed and applied intraoperatively following restoration of systemic hemodynamics.Sublingual microcirculation was monitored with sidestream dark field (sdf +) imaging technique.The primary objective was to investigate the change in de backer score, consensus proportion of perfused vessels (consensus ppv), and consensus ppv (small) and its association with venous-to-arterial carbon dioxide difference (v-a pco2).Results thirteen consecutive patients were included in the study.Microcirculation-guided resuscitation resulted in an increase of 0.49 mm-1in the de backer score (p < 0.001), an increase of 2.28% in the consensus ppv (p < 0.001), and an increase of 2.26% in the consensus ppv (small) (p < 0.001) for every 30 min of additional intraoperative time.All microcirculation variables were negatively correlated with v-a pco2(rho = - 0.656, adj-p < 0.001; rho = - 0.623; adj-p < 0.001; rho = - 0.597, adj-p < 0.001, respectively) at each intraoperative time point.Lactate levels were negatively correlated with consensus ppv (rho = - 0.464; adj-p = 0.002) and consensus ppv (small) (rho = - 0.391, adj-p < 0.001).Survival at 30 days, 90 days, and 1 year were 76.9%, 76.9%, and 61.5%, respectively.Conclusions the intraoperative use of microcirculation-guided resuscitation strategy may improve tissue perfusion and hemodynamic coherence in patients with septic shock.

Journal: European journal of trauma and emergency surgery : official publication of the European Trauma Society (2022)
Publication types: Journal Article