syedzayyan/paper_mill_benchmark huggingface dataset:
The performance of soluble CD163 as a non-invasive biomarker of liver damage in chronically HCV and HCV/HIV infected subjects.

Macrophage activation plays a key role in liver disease progression.Soluble cd163 (s cd163) is a specific macrophage activation biomarker useful for clinical estimating damage severity and predicting outcome in different liver conditions.S cd163 performance as a non-invasive marker of liver damage was evaluated in plasma samples at time of biopsy in 120 patients with different hepatic conditions (56 hcv, 20 hcv/hiv, 10 hbv and 34 mafld).S cd163 values were compared with those of healthy donors and analyzed related to histological damage.S cd163 together with other clinical parameters were used to create a logistical regression model to predict significant fibrosis.Only patients with viral hepatitis showed higher s cd163 values compared to the control group (hcv p<0.0001; hcv/hiv p<0.0001; hbv p = 0.0003), but no significant differences regarding fibrosis stages were observed.The proposed model predicts fibrosis severity using the logarithm s cd163 concentration, platelet count and age, it demonstrated to be a good marker for the hcv monoinfected group (auroc 0.834) and an excellent one for the hcv/hiv co-infected group (auroc 0.997).Moreover, the model displayed a diagnostic performance similar to fib-4 in hcv cases and fib-4 and apri in hcv/hiv coinfected cases, and it even managed to correctly classify some cases that had been misclassified.The proposed model is able to determine, in a non-invasive way, the liver fibrosis stage of hcv and hcv/hiv patients, so after validation, it could be used in a complementary way in the clinical practice whenever apri and fib-4 failed to determine damage severity in hcv and hcv/hiv cases.

Journal: PloS one (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Drying Behavior of Bulgur and Its Effect on Phytochemical Content.

The objective of this study was to determine the influence of two types of dryers (hot air oven and vacuum dryer) and the yellow berry percentage (1.75%, 36.25%, 43.25%) on the drying process and phytochemical content of bulgur.Results showed that the midilli model successfully described the moisture diffusion during drying at 60 °c in all bulgur samples, where an increase in yellow berry percentage generated an increase in moisture content.Effective diffusion coefficient (deff) increased significantly (p≤ 0.05) from 7.05 × 10-11to 7.82 × 10-11(m2.s-1) and from 7.73 × 10-11to 7.82 × 10-11(m2.s-1) for the hot air oven and vacuum dryer, respectively.However, it decreased significantly with a decrease of yellow berry percentage.It was concluded that the vacuum dryer provided faster and more effective drying than the hot air oven.Total polyphenol (tpc), total flavonoid (tfc), and yellow pigment contents (ypc) of bulgur were investigated.Tpc ranged between 0.54 and 0.64 (mg gae/g dm); tfc varied from 0.48 to 0.61 (mg qe/g dm).The ypc was found to be between 0.066 and 0.079 (mg ß-carotene/100g dm).Yellow berry percentage positively and significantly affected the tpc, tfc, and ypc contents due to the hard separation of the outer layers from the starchy grain during the debranning step.

Journal: Foods (Basel, Switzerland) (2022)
Publication types: Journal Article
Effect of Ascorbic Acid on Cardiac Surgery-Associated Acute Kidney Injury Incidence.

S acute kidney injury (aki) is associated with higher perioperative mortality and morbidity.Oxidative stress has been proposed as a cause of postoperative aki.Ascorbic acid (aa) supplementation was suggested as a novel and promising antioxidant.The aim of this study was to evaluate the capability of aa to reduce the incidence of postoperative aki in cardiac surgery patients.Methods a prospective randomized trial was conducted in patients scheduled for on-pump cardiac surgery.Subjects in the aa group received 2 g of aa intravenously during the induction of anesthesia, 2 g before aortic cross-clamp removal and 1 g every 8 hours for five postoperative days (the jerica protocol).Postoperatively, the patients were monitored for aki and other complications.Malondialdehyde levels were monitored in a subpopulation of 100 patients to evaluate the effect of aa on oxidative stress level.Results the aa and control group consisted of 163 and 169 patients, respectively.The groups were well matched for baseline demographics and had similar intraoperative characteristics.The incidence of aki in the aa and control group was 20.9 and 28.4%, respectively (p= 0.127).The estimated glomerular filtration rate did not differ between the study groups in the entire postoperative period.There was a trend toward higher malondialdehyde values with statistical significance on postoperative day 1 and lower in-hospital mortality in the aa group (0.6 vs.4.1%,p= 0.067).Conclusion our results do not support the effectiveness of aa supplementation in reducing the incidence of postoperative aki in on-pump cardiac surgery patients.Clinical registration number this study was registered with the isrctn registry under the trial registration number isrctn98572043.

Journal: The Thoracic and cardiovascular surgeon (2022)
Publication types: Journal Article;Randomized Controlled Trial
Sex differences in the human brain: a roadmap for more careful analysis and interpretation of a biological reality.

The presence, magnitude, and significance of sex differences in the human brain are hotly debated topics in the scientific community and popular media.This debate is largely fueled by studies containing strong, opposing conclusions: either little to no evidence exists for sex differences in human neuroanatomy, or there are small-to-moderate differences in the size of certain brain regions that are highly reproducible across cohorts (even after controlling for sex differences in average brain size).Our commentary uses the specific comparison between two recent large-scale studies that adopt these opposing views-namely the review by eliot and colleagues (2021) and the direct analysis of ~ 40k brains by williams and colleagues (2021)-in an effort to clarify this controversy and provide a framework for conducting this research.First, we review observations that motivate research on sex differences in human neuroanatomy, including potential causes (evolutionary, genetic, and environmental) and effects (epidemiological and clinical evidence for sex-biased brain disorders).We also summarize methodological and empirical support for using structural mri to investigate such patterns.Next, we outline how researchers focused on sex differences can better specify their study design (e.g., how sex was defined, if and how brain size was adjusted for) and results (by e.g., distinguishing sexual dimorphisms from sex differences).We then compare the different approaches available for studying sex differences across a large number of individuals: direct analysis, meta-analysis, and review.We stress that reviews do not account for methodological differences across studies, and that this variation explains many of the apparent inconsistencies reported throughout recent reviews (including the work by eliot and colleagues).For instance, we show that amygdala volume is consistently reported as male-biased in studies with sufficient sample sizes and appropriate methods for brain size correction.In fact, comparing the results from multiple large direct analyses highlights small, highly reproducible sex differences in the volume of many brain regions (controlling for brain size).Finally, we describe best practices for the presentation and interpretation of these findings.Care in interpretation is important for all domains of science, but especially so for research on sex differences in the human brain, given the existence of broad societal gender-biases and a history of biological data being used justify sexist ideas.As such, we urge researchers to discuss their results from simultaneously scientific and anti-sexist viewpoints.

Journal: Biology of sex differences (2022)
Publication types: Letter;Meta-Analysis;Review;Research Support, N.I.H., Intramural;Research Support, N.I.H., Extramural;Comment
Lipid Metabolic Disorder Induced by Pyrethroids in Nonalcoholic Fatty Liver Disease ofXenopus laevis.

Pyrethroids, an effective and widely used class of pesticides, have attracted considerable concerns considering their frequent detection in environmental matrices.However, their potential health risks to amphibians remain unclear.In our study, female xenopus laeviswere exposed to 0, 0.06, and 0.3 μg/l typical pyrethroid,cis-bifenthrin (cis-bf), for 3 months.Elevated activities of both aspartate aminotransferase (ast) and alanine aminotransferase (alt) were observed, indicating an ongoing liver injury.Furthermore, exposure tocis-bf led to hyperlipidemia and lipid accumulation in the liver of xenopus.The targeted lipidomic analysis further revealed that treatment withcis-bf perturbed liver steroid homeostasis, as evidenced by the enriched lipids in the steroid biosynthesis pathway.Consistent with the targeted lipidomic result, treatment withcis-bf changed the liver transcriptome profile with induction of 808 and 1230 differentially expressed genes.Kyoto encyclopedia of genes and genomes analysis underlined the adverse effects ofcis-bf exposure on steroid biosynthesis, primary bile acid biosynthesis, and the ppar signaling pathway in the xenopusliver.Taken together, our study revealed that exposure tocis-bf at environmentally relevant concentrations resulted in lipid metabolic disorder associated with nonalcoholic fatty liver disease of x.Laevis, and our results provided new insight into the potential long-term hazards of pyrethroids.

Journal: Environmental science & technology (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Prevalence and prognosis of increased pancreatic enzymes in patients with COVID-19: A systematic review and meta-analysis.

Introduction the prevalence of increased pancreatic enzymes (elevated serum amylase and/or lipase) and its relationship to clinical outcomes in patients with coronavirus disease 2019 (covid-19) infection is not known.Methods a systematic review and meta-analysis of relevant studies reporting prevalence and impact of increased pancreatic enzymes (defined as an elevation in amylase and/or lipase levels above the upper limit of normal [uln] value) in covid-19 was undertaken.Results a total of 36,496 patients from 21 studies were included for this meta-analysis.The overall prevalence and mortality for increased pancreatic enzymes (>uln) in covid-19 were 25.4% (95% ci, 15.8%-36.2%) and 34.6% (95% ci, 25.5%-44.4%), respectively.The overall prevalence and mortality for increased pancreatic enzymes (>3 × uln) were 6.1% (95% ci, 3.6%-9.2%) and 39.2% (95% ci, 18.7%-61.6%), respectively.Patients with increased pancreatic enzymes, including elevated serum lipase or amylase of either type, had worse clinical outcomes, including need for icu admission, mechanical ventilation and mortality.Discussion increased pancreatic enzymes is frequent and may exacerbate the consequences of covid-19 infection.

Journal: Pancreatology : official journal of the International Association of Pancreatology (IAP) ... [et al.] (2022)
Publication types: Journal Article;Meta-Analysis;Systematic Review
Influence of strain, age, origin, and anesthesia on the cardioprotective efficacy by local and remote ischemic conditioning in an ex vivo rat model.

Local ischemic preconditioning (ipc) and remote ischemic conditioning (ric) induced by brief periods of ischemia and reperfusion protect against ischemia-reperfusion injury.Methods we studied the sensitivity to ir-injury and the influence of strain, age, supplier, and anesthesia upon the efficacy of ipc and ric in 7- and 16-weeks-old sprague-dawley and wistar rats from three different suppliers.The influence of sedation with a hypnorm and midazolam mixture (rodent mixture) and pentobarbiturate was compared.Results ipc attenuated infarct size in both 7-weeks-old sprague-dawley (48.4 ± 17.7% vs.20.3 ± 6.9, p < 0.001) and 7-weeks-old wistar (55.6 ± 10.9% vs.26.8 ± 5.0%, p < 0.001) rats.Infarct size was larger in 16-weeks-old sprague-dawley rats, however, ipc still lowered infarct size (78.8 ± 9.2% vs.58.3 ± 12.3%, p < 0.01).Ric reduced infarct sizes in 7-weeks-old sprague-dawley (75.3 ± 11.8% vs.58.6 ± 8.9%, p < 0.05), but not in 7-weeks-old wistar rats (31.7 ± 17.6% and 24.0 ± 12.6%, p = 0.2).In 16-weeks-old sprague-dawley rats, ric did not induce protection (76.4 ± 5.5% and 73.2 ± 14.7%, p = 0.6).However, ric induced protection in 16-weeks-old wistar rats (45.2 ± 8.5% vs.14.7 ± 10.8%, p < 0.001).Ric did not reduce infarct size in 7-weeks-old sprague-dawley rats from charles river (62.0 ± 13.5% and 69.4 ± 10.4% p = 0.3) or 16-weeks-old wistar rats from janvier (50.7 ± 11.3 and 49.2 ± 16.2, p = 0.8).There was no difference between sedation with rodent mixture or pentobarbiturate.Conclusion the cardioprotective effect of ipc is consistent across rat strains independent of age, strain, and supplier.Ric seems to be less reproducible, but still yields protection across different rat strains.However, age, animal supplier, and anesthetics may modulate the sensitivity of ir-injury and the response to ric.

Journal: Physiological reports (2021)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Aggregation and Degradation of White Phosphorus Mediated by N-Heterocyclic Carbene Nickel(0) Complexes.

The reaction of zerovalent nickel compounds with white phosphorus (p4) is a barely explored route to binary nickel phosphide clusters.Here, we show that coordinatively and electronically unsaturated n-heterocyclic carbene (nhc) nickel(0) complexes afford unusual cluster compounds with p1, p3, p5and p8units.Using [ni(imes)2] [imes=1,3-bis(2,4,6-trimethylphenyl)imidazolin-2-ylidene], electron-deficient ni3p4and ni3p6clusters have been isolated, which can be described as superhypercloso and hypercloso clusters according to the wade-mingos rules.Use of the bulkier nhc complexes [ni(ipr)2] or [(ipr)ni(η6-toluene)] [ipr=1,3-bis(2,6-diisopropylphenyl)imidazolin-2-ylidene] affords a closo-ni3p8cluster.Inverse-sandwich complexes [(nhc)2ni2p5] (nhc=imes, ipr) with an aromatic cyclo-p5-ligand were identified as additional products.

Journal: Angewandte Chemie (International ed. in English) (2020)
Publication types: Journal Article
Experimental Study on Early Strength and Hydration Heat of Spodumene Tailings Cemented Backfill Materials.

Spodumene tailing is the associated solid waste of extracting lithium from spodumene.With the increase in the global demand for lithium resources, its emissions increase yearly, which will become a key factor restricting the economic development of the mining area.Mechanical and hydration reactions, as well as the microstructure of early cstb, are studied under different tailings-cement ratios (tcr) and solid mass concentration (sc) conditions.The results show that the uniaxial compressive strength of early cstb has a negative exponential correlation with the decrease in tcr and a positive correlation with the increase in sc: when the age of cstb increases to 7 days, the strength increases with the rise in sc in an exponential function, and the sensitivity of strength to tcr is higher than that of sc.Compared to other tailings cemented backfill materials, the addition of spodumene tailings reduces the sulfate ion concentration and leads to a new exothermic peak (i.e., the third exothermic peak) for the hydration exotherm of cstb.Additionally, with the increase in tcr or decrease in sc, the height of the third exothermic peak decreases and the occurrence time is advanced.At the same time, the duration of induction phase was prolonged, the period of acceleration phase was shortened, and the total amount of heat released was significantly increased.The decrease in tcr or the increase in sc led to the rise in the number of hydration products which can effectively fill the internal pores of cstb, enhance its structural compactness, and increase its compressive strength.The above study reveals the influence of tcr and sc on the early strength, hydration characteristics, and microstructure of cstb and provides an essential reference for the mix design of underground backfill spodumene tailings.

Journal: Materials (Basel, Switzerland) (2022)
Publication types: Journal Article
Morphological and functional abnormalities of hippocampus in APC1638T/1638Tmice.

In the present study, we examined morphology and function of hippocampus in the apc1638t/1638tmouse.Expression levels of the apc m rna and protein were both identical in the hippocampus of the apc+/+and apc1638t/1638tmice.The dentate gyrus of the apc1638t/1638thippocampus was thicker, and has more densely-populated granule cells in the apc1638t/1638tmouse hippocampus.Immunoelectron microscopy revealed co-localization of apc with alpha-amino-3- hydroxy-5-methyl- isoxazole-4-propionate receptor (ampa-r) and with psd-95 at post-synapse in the apc+/+hippocampus, while apc1638t was co-localized with neither ampa-r nor psd-95 in the apc1638t/1638thippocampus.By immunoprecipitation assay, full-length apc expressed in the apc+/+mouse was co-immunoprecipitated with ampa-r and psd-95.In contrast, apc1638t expressed in the apc1638t/1638tmouse was not co-immunoprecipitated with ampa-r and psd-95.In the hippocampal ca1 region of the apc1638t/1638tmouse, c-fos expression after electric foot shock was decreased compared with the apc+/+mouse.The present study showed some abnormalities on morphology of the hippocampus caused by a truncated apc (apc1638t).Also, our findings suggest that failure in apc binding to ampa-r and psd-95 may bring about less activities of hippocampal neurons in the apc1638t/1638tmouse.

Journal: Medical molecular morphology (2021)
Publication types: Journal Article
Whole genome resequencing of four Italian sweet pepper landraces provides insights on sequence variation in genes of agronomic value.

Sweet pepper (capsicum annuum l.) is a high value crop and one of the most widely grown vegetables belonging to the solanaceae family.In addition to commercial varieties and f1hybrids, a multitude of landraces are grown, whose genetic combination is the result of hundreds of years of random, environmental, and farmer selection.High genetic diversity exists in the landrace gene pool which however has scarcely been studied, thus bounding their cultivation.We re-sequenced four pepper inbred lines, within as many italian landraces, which representative of as many fruit types: big sized blocky with sunken apex ('quadrato') and protruding apex or heart shaped ('cuneo'), elongated ('corno') and smaller sized sub-spherical ('tumaticot').Each genomic sequence was obtained through illumina platform at coverage ranging from 39 to 44×, and reconstructed at a chromosome scale.About 35.5k genes were predicted in each inbred line, of which 22,017 were shared among them and the reference genome (accession 'cm334').Distinctive variations in mi rnas, resistance gene analogues (rgas) and susceptibility genes (s-genes) were detected.A detailed survey of the snp/indels occurring in genes affecting fruit size, shape and quality identified the highest frequencies of variation in regulatory regions.Many structural variations were identified as presence/absence variations (pavs), notably in resistance gene analogues (rgas) and in the capsanthin/capsorubin synthase (ccs) gene.The large allelic diversity observed in the four inbred lines suggests their potential use as a pre-breeding resource and represents a one-stop resource for c.Annuum genomics and a key tool for dissecting the path from sequence variation to phenotype.

Journal: Scientific reports (2020)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
2D metal-organic framework for stable perovskite solar cells with minimized lead leakage.

Despite the notable progress in perovskite solar cells, maintaining long-term operational stability and minimizing potentially leaked lead (pb2+) ions are two challenges that are yet to be resolved.Here we address these issues using a thiol-functionalized 2d conjugated metal-organic framework as an electron-extraction layer at the perovskite/cathode interface.The resultant devices exhibit high power conversion efficiency (22.02%) along with a substantially improved long-term operational stability.The perovskite solar cell modified with a metal-organic framework could retain more than 90% of its initial efficiency under accelerated testing conditions, that is continuous light irradiation at maximum power point tracking for 1,000 h at 85 °c.More importantly, the functionalized metal-organic framework could capture most of the pb2+leaked from the degraded perovskite solar cells by forming water-insoluble solids.Therefore, this method that simultaneously tackles the operational stability and lead contamination issues in perovskite solar cells could greatly improve the feasibility of large-scale deployment of perovskite photovoltaic technology.

Journal: Nature nanotechnology (2020)
Publication types: Journal Article
Aqueous Lumican Correlates with Central Retinal Thickness in Patients with Idiopathic Epiretinal Membrane: A Proteome Study.

Idiopathic epiretinal membrane (i erm) is a pathological fibrocellular change in the vitreoretinal junction over the macular area; however, possible pathogenic mechanisms remain unclear.Changes in the differential protein composition of the aqueous humor (ah) may represent potential molecular changes associated with i erm.To gain new insights into the molecular mechanisms of i erm pathology, a sensitive label-free proteomics analysis was performed to compare ah protein expressions in patients with cataracts with or without i erm.This study employed nanoflow ultra-high-performance liquid chromatography-tandem mass spectrometry to investigate protein compositions of the ah obtained from individual human cataract eyes from 10 patients with i erm and 10 age-matched controls without i erm.Eight proteins were differentially expressed between the i erm and control samples, among which six proteins were upregulated and two were downregulated.A gene ontology (go) analysis revealed that i erm was closely associated with several biological processes, such as immunity interactions, cell proliferation, and extracellular matrix remodeling.Additionally, multiple proteins, including lumican, cyclin-dependent kinase 13, and collagen alpha-3(vi) chain, were correlated with the central retinal thickness, indicating a multifactorial response in the pathogenic process of i erm.Changes in the ah level of lumican between i erm and control samples were also confirmed by an enzyme-linked immunosorbent assay.In conclusion, several pathological pathways involved in i erm were identified in the ah by a proteomic analysis, including immune reactions, cell proliferation, and remodeling of the extracellular matrix.Lumican is a potential aqueous biomarker for predicting i erm development and monitoring its progression.More clinical parameters also need to be identified to complete the analysis, and those could provide additional targets for treating and preventing i erm.

Journal: Disease markers (2022)
Publication types: Journal Article
Numerical Study on Heat-Transfer Characteristics of Convection Melting in Metal Foam under Sinusoidal Temperature Boundary Conditions.

Convection melting in metal foam under sinusoidal temperature boundary conditions is numerically studied in the present study.A multiple-relaxation-time lattice boltzmann method, in conjunction with the enthalpy approach, is constructed to model the melting process without iteration steps.The effects of the porosity, phase deviation, and periodicity parameter on the heat-transfer characteristics are investigated.For the cases considered in this work, it is found that the effects of the phase deviation and periodicity parameter on the melting rate are weak, but the melting front can be significantly affected by the sinusoidal temperature boundary conditions.

Journal: Entropy (Basel, Switzerland) (2022)
Publication types: Journal Article