syedzayyan/paper_mill_benchmark huggingface dataset:
Inner core composition paradox revealed by sound velocities of Fe and Fe-Si alloy.

Knowledge of the sound velocity of core materials is essential to explain the observed anomalously low shear wave velocity (vs) and high poisson's ratio (σ) in the solid inner core.To date, neither vsnor σ of fe and fe-si alloy have been measured under core conditions.Here, we present vsand σ derived from direct measurements of the compressional wave velocity, bulk sound velocity, and density of fe and fe-8.6 wt%si up to ~230 gpa and ~5400 k.The new data show that neither the effect of temperature nor incorporation of si would be sufficient to explain the observed low vsand high σ of the inner core.A possible solution would add carbon (c) into the solid inner core that could further decrease vsand increase σ.However, the physical property-based fe-si-c core models seemingly conflict with the partitioning behavior of si and c between liquid and solid fe.

Journal: Nature communications (2022)
Publication types: Journal Article
Multi-ionic interaction with magnesium doped hydroxyapatite-zeolite nanocomposite porous polyacrylonitrile polymer bead in aqueous solution and spiked groundwater.

Removal of multi-ionic contaminants from water resources has been a major challenge faced during the treatment of water for drinking and industrial applications.In the present study, varying composition of magnesium doped hydroxyapatite (mg-hap) and zeolite nanocomposite embedded porous polymeric beads were synthesized using solvent displacement method and its sorption efficiency towards multi-ion contaminant (such as ag, al, as, ba, be, cd, co, cr, cu, mn, ni, pb, se, tl, th, u, v and zn) was investigated in aqueous solution and spiked groundwater.The prepared beads were characterized using suitable techniques like high-resolution transmission electron microscopy (hrtem), scanning electron microscopy (sem), and brunauer-emmett-teller (bet) equation.The surface area and pore radius of the beads varied from 6.996 to 66.469 m2/g and 1.698-3.960 nm respectively according to the composition of the bead.The control bead without nanocomposite showed maximum surface area.Multi-ion adsorptions onto beads were confirmed using an inductively coupled plasma-optical emission spectrophotometer (icp-oes) and x-ray photoelectron spectrophotometer (xps).The sorption efficiency was high at p h 5 owing to its anionic surface charge leading to an increase in affinity towards the cations.For validating field application, selected high performance beads were tested in multi-ion spiked groundwater.The results indicated that the mg-hap nanocomposite bead dominate all the other bead compositions with more than 90% removal efficiency for most of the multi-ion contaminants.The feasible adsorption mechanism has been discussed.This adsorption study revealed that the mg-hap nanocomposite bead is a promising material that is cost-effective, non-toxic, biodegradable, eco-friendly and highly efficient towards the removal of multi-ionic contaminants from groundwater.

Journal: Environmental pollution (Barking, Essex : 1987) (2022)
Publication types: Journal Article
Fetal Tissue-Derived Mast Cells (MC) as Experimental Surrogate for In Vivo Connective Tissue MC.

Bone-marrow-derived mast cells are matured from bone marrow cells in medium containing 20% fetal calf serum (fcs), interleukin (il)-3 and stem-cell factor (scf) and are used as in vitro models to study mast cells (mc) and their role in health and disease.In vivo, however, bm-derived hematopoietic stem cells account for only a fraction of mc; the majority of mc in vivo are and remain tissue resident.In this study we established a side-by-side culture with bmmc, fetal skin mc (fsmc) or fetal liver mc (flmc) for comparative studies to identify the best surrogates for mature connective tissue mc (ctmc).All three mc types showed comparable morphology by histology and mc phenotype by flow cytometry.Heterogeneity was detected in the transcriptome with the most differentially expressed genes in fsmc compared to bmmc being hdcand tpsb2.Expression of st2 was highly expressed in bmmc and fsmc and reduced in flmc, diminishing their secretion of type 2 cytokines.Higher granule content, stronger response to fcεri activation and significantly higher release of histamine from fsmc compared to flmc and bmmc indicated differences in mc development in vitro dependent on the tissue of origin.Thus, tissues of origin imprint mc precursor cells to acquire distinct phenotypes and signatures despite identical culture conditions.Fetal-derived mc resemble mature ctmc, with fsmc being the most developed.

Journal: Cells (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Association between higher serum uric acid levels and plasma N-terminal pro-B-type natriuretic peptide concentrations in patients with coronary artery disease and without overt heart failure.

The association between serum uric acid (sua) and n-terminal pro-b-type natriuretic peptide (nt-pro bnp) concentrations in patients with coronary artery disease (cad) is unclear.Methods we retrospectively studied 171 patients with suspected or established cad and without overt heart failure who were consecutively admitted to our division of cardiology from february to august 2016.Plasma nt-pro bnp concentrations were measured using a chemiluminescent immunoassay method.A conventional echocardiography and coronary angiogram were also performed in all patients.Results patients in the 3rd sua tertile had higher median plasma nt-pro bnp concentrations compared with those belonging to 2nd or 1st sua tertile, respectively (443 [iqr: 222-1381] vs.224 [99-487] vs.162 [68-307] pg/m l; p < 0.001).After adjustment for age, sex, body mass index, hypertension, diabetes, chronic kidney disease, prior ischemic heart disease, prior heart failure, medication use, and left ventricular ejection fraction (lvef), patients belonging to the 3rd sua tertile had an increased risk of higher plasma nt-pro bnp concentrations (adjusted-standardized beta coefficient: 0.310, p < 0.001).Almost identical results were found when patients treated with allopurinol (n = 14), or those with prior hf (n = 8) were excluded from the analyses.Conclusions these results show that increased sua levels are strongly associated with higher plasma nt-pro bnp concentrations in patients with suspected or established cad and without overt heart failure, independent of established cardiovascular risk factors, lvef, medication use and other potential confounders.

Journal: International journal of cardiology (2022)
Publication types: Journal Article
Genetic Fine-Mapping of a Quantitative Trait Locus (QTL) Associated with Embryogenic Tissue Culture Response and Plant Regeneration Ability in Maize (Zea maysL.).

Embryogenic and regenerable tissue cultures are widely utilized in plant transformation, clonal propagation, and biological research applications.Germplasm utilized in those applications are limited, however, due to genotype-dependent culture response.The goal of this study was to identify genomic regions controlling embryogenic and regenerable tissue culture response in the globally important crop, maize ( l.), toward the long-term objective of developing approaches for genotype-independent plant genetic engineering and clonal propagation systems.An inbred maize line, wcic2, nearly-isogenic to reference inbred b73, was developed by phenotypic selection and molecular marker analysis.Wcic2 has over 50x increase in tissue culture response relative to the recurrent parent, b73.This line was used to genetically fine-map a region on chromosome 3 controlling embryogenic and regenerable tissue culture response to a 23.9 mb region.Wcic2 and derivatives will be useful materials to enable maize research in a genetic background similar to b73, and our genetic mapping results will advance research to identify causal genes controlling somatic embryo formation and plant regeneration in maize.

Journal: The plant genome (2018)
Publication types: Journal Article;Research Support, U.S. Gov't, Non-P.H.S.
Origins of DNA methylation defects in Wilms tumors.

Wilms tumor is an embryonic renal cancer that typically presents in early childhood and accounts for 7% of all paediatric cancers.Different genetic alterations have been described in this malignancy, however, only a few of them are associated with a majority of wilms tumors.Alterations in dna methylation, in contrast, are frequent molecular defects observed in most cases of wilms tumors.How these epimutations are established in this tumor is not yet completely clear.The recent identification of the molecular actors required for the epigenetic reprogramming during embryogenesis suggests novel possible mechanisms responsible for the dna methylation defects in wilms tumor.Here, we provide an overview of the dna methylation alterations observed in this malignancy and discuss the distinct molecular mechanisms by which these epimutations can arise.

Journal: Cancer letters (2019)
Publication types: Journal Article;Research Support, Non-U.S. Gov't;Review
Elucidation of SARS-Cov-2 Budding Mechanisms through Molecular Dynamics Simulations of M and E Protein Complexes.

Sars-co v-2 and other coronaviruses pose major threats to global health, yet computational efforts to understand them have largely overlooked the process of budding, a key part of the coronavirus life cycle.When expressed together, coronavirus m and e proteins are sufficient to facilitate budding into the er-golgi intermediate compartment (ergic).To help elucidate budding, we ran atomistic molecular dynamics (md) simulations using the feig laboratory's refined structural models of the sars-co v-2 m protein dimer and e protein pentamer.Our md simulations consisted of m protein dimers and e protein pentamers in patches of membrane.By examining where these proteins induced membrane curvaturein silico, we obtained insights around how the budding process may occur.Multiple m protein dimers acted together to induce global membrane curvature through protein-lipid interactions while e protein pentamers kept the membrane planar.These results could eventually help guide development of antiviral therapeutics that inhibit coronavirus budding.

Journal: The journal of physical chemistry letters (2021)
Publication types: Journal Article
Genome-wide association studies dissect the G × E interaction for agronomic traits in a worldwide collection of safflowers (Carthamus tinctoriusL.).

Genome-wide association studies were conducted using a globally diverse safflower (carthamus tinctorius l.) genebank collection for grain yield (yp), days to flowering (df), plant height (ph), 500 seed weight (sw), seed oil content (ol), and crude protein content (pr) in four environments (sites) that differed in water availability.Phenotypic variation was observed for all traits.Yp exhibited low overall genetic correlations (r goverall) across sites, while sw and ol had highr goveralland high pairwise genetic correlations (r gij) across all pairwise sites.In total, 92 marker-trait associations (mtas) were identified using three methods, single locus genome-wide association studies (gwas) using a mixed linear model (mlm), the bayesian multi-locus method (bayes r), and meta-gwas.Mtas with large effects across all sites were detected for ol, sw, and pr, and mtas specific for the different water stress sites were identified for all traits.Five mtas were associated with multiple traits; 4 of 5 mtas were variously associated with the three traits of sw, ol, and pr.This study provided insights into the phenotypic variability and genetic architecture of important safflower agronomic traits under different environments.Supplementary information the online version contains supplementary material available at .

Journal: Molecular breeding : new strategies in plant improvement (2022)
Publication types: Journal Article
Surgical results of chronic thromboembolic pulmonary endarterectomy in our recently developed program.

In this case series, we aimed to present our diagnostic workup, surgical management, and results of the patients who underwent pulmonary endarterectomy.Methods in this case series, a total of 26 patients (8 males, 18 females; median age: 58 years; range, 34 to 67 years) who were evaluated by a multidisciplinary team and were diagnosed with chronic thromboembolic pulmonary hypertension who underwent pulmonary endarterectomy in our clinic between november 2015 and december 2019 were included.Pulmonary endarterectomy procedure was performed in all cases under cardiopulmonary bypass and total circulatory arrest.The results of the procedures were analyzed retrospectively.Results perioperative complications were observed in seven patients (26.9%) and in-hospital mortality rate caused by perioperative complications was 15.38%.At one-year of postoperative follow-up, the mean systolic pulmonary artery pressure decreased from 78±22 mm hg to 41±20 mm hg, pulmonary vascular resistance decreased from 698±10 dyn·s·cm-5 to 235±10 dyn·s·cm-5, 6-min walk distance increased from 345±10 m to 460±10 m and, arterial oxygen saturation increased from 85±3.5% to 95±4%.New york heart association functional class improvement from class iii-iv to class i-ii was observed in most patients, and one-year mortality rate was 19.23%.Conclusion we suggest that patients diagnosed chronic thromboembolic pulmonary hypertension should be referred to cardiac surgery centers for pulmonary thromboendarterectomy, early before irreversible arteriopathy occurs.

Journal: Turk gogus kalp damar cerrahisi dergisi (2021)
Publication types: Journal Article
Post-transcriptional regulatory feedback encodes JAK-STAT signal memory of interferon stimulation.

Immune cells fine tune their responses to infection and inflammatory cues.Here, using live-cell confocal microscopy and mathematical modelling, we investigate interferon-induced jak-stat signalling in innate immune macrophages.We demonstrate that transient exposure to ifn-γ stimulation induces a long-term desensitisation of stat1 signalling and gene expression responses, revealing a dose- and time-dependent regulatory feedback that controls jak-stat responses upon re-exposure to stimulus.We show that ifn-α/β1 elicit different level of desensitisation from ifn-γ, where cells refractory to ifn-α/β1 are sensitive to ifn-γ, but notvice versa.We experimentally demonstrate that the underlying feedback mechanism involves regulation of stat1 phosphorylation but is independent of new m rna synthesis and cognate receptor expression.A new feedback model of the protein tyrosine phosphatase activity recapitulates experimental data and demonstrates jak-stat network's ability to decode relative changes of dose, timing, and type of temporal interferon stimulation.These findings reveal that stat desensitisation renders cells with signalling memory of type i and ii interferon stimulation, which in the future may improve administration of interferon therapy.

Journal: Frontiers in immunology (2022)
Publication types: Journal Article
Toward Understanding Whether Interactive Surface Area Could Direct Ordered Macroscopic Supramolecular Self-Assembly.

The mismatching phenomena are ubiquitous in complex and advanced self-assembly, such as hierarchical assembly, macroscopic supramolecular assembly, and so on.Recently, for macroscopic supramolecular assembly, the strategy of maximizing the interactive surface area was used and supposed to handle this problem; however, now there is little understanding of whether interactive surface area is the dominant factor to guide the assembly patterns.Herein by taking millimeter cylinder building blocks with different diameter/height (d/h) ratios as model systems, we have investigated the interactive-surface-area-dependent assembling behaviors in macroscopic supramolecular assembly.The results showed that the increasing d/h ratio of cylinders contributed to selectivity of face-to-face assembled pattern over face-to-side or side-to-side geometries, thus having improved the ordering degree of the assembled structures; however, the mismatching phenomena could not be totally avoided due to high colliding chances in kinetics and the thermally favorable stability of these structures.We further confirmed the above hypothesis by in situ measurements of interactive forces of building blocks with different assembled patterns.This work of macroscopic supramolecular assembly provides an in situ visible platform, which is significant to clarify the influences of interactive surface area on the assembly behaviors.

Journal: Langmuir : the ACS journal of surfaces and colloids (2016)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Cognitive Abilities Explain Wording Effects in the Rosenberg Self-Esteem Scale.

There is consensus that the 10 items of the rosenberg self-esteem scale(rses) reflect wording effects resulting from positively and negatively keyed items.The present study examined the effects of cognitive abilities on the factor structure of the rses with a novel, nonparametric latent variable technique calledlocal structural equation models.In a nationally representative german large-scale assessment including 12,437 students competing measurement models for the rses were compared: a bifactor model with a common factor and a specific factor for all negatively worded items had an optimal fit.local structural equation modelsshowed that the unidimensionality of the scale increased with higher levels of reading competence and reasoning, while the proportion of variance attributed to the negatively keyed items declined.Wording effects on the factor structure of the rses seem to represent a response style artifact associated with cognitive abilities.

Journal: Assessment (2020)
Publication types: Comparative Study;Journal Article
Lived Experiences of Recovered COVID-19 Patients after Hospitalization: A Phenomenological Research.

The deadly novel coronavirus disease 19 (covid-19) epidemic has sickened and killed millions of people around the world.Accordingly, iran has had the second highest incidence rate of covid-19 deaths in the world.Because this disease affects all individual, familial, and social aspects, there is not enough information about experiences of covid-19 patients.However, these experiences could be a missing link in explaining their attitudes, beliefs, and concerns for improving care and treatment processes during and after the disease.Materials and methods descriptive phenomenological research was conducted in 2020 to explain experiences of 21 covid-19 patients after post-hospitalization recovery.Semi-structured interviews were used as the data collection tool via purposeful sampling, which were continued until data saturation and analyzed using colaizzi's seven-step method.Results the main theme of "value of health" and the seven categories of (1) inefficient self-care, (2) overcoming the catastrophic crisis, (3) the shadow of death, (4) coping behaviors and resilience, (5) the need for support and accountability, (6) sympathy, and (7) new insights as well as 38 main codes were extracted.The patients' general explanation in the early stages of the disease, recovery, and subsequent periods included transition from the crisis to new insights into physical, mental, sexual, familial, and economic dimensions that finally led to the review value and concept of their life.Conclusions the findings of this study can be used to fulfil care and treatment needs of the patients, their families as well as caregivers, psychologists, counselors, health planners, and managers presently and in the future for similar diseases.

Journal: Iranian journal of nursing and midwifery research (2022)
Publication types: Journal Article
Ceftolozane/Tazobactam In-Vitro Activity against Clinical Isolates from Complicated Intra-Abdominal Infection Patients in Three Indonesian Referral Hospitals.

Complicated intra-abdominal infections (c iais) lead to high morbidity and mortality, especially if poorly managed.However, indonesia's microbial pattern and susceptibility data are limited, especially for new antibiotics.Ceftolozane/tazobactam (c/t) is reported to be a new potent antibiotic against various pathogens.Thus, we aim to investigate c/t in vitro activity against clinical isolates from c iai patients.This prospective cross-sectional study was conducted in three major referral hospitals in indonesia, including dr.Cipto mangunkusumo hospital (jakarta), dr.Kariadi hospital (semarang), and dr.Soetomo hospital (surabaya), enrolling those diagnosed with c iais.Blood specimens were collected before or after at least 72 h of the last antibiotic administration.Meanwhile, tissue biopsy/aspirate specimens were collected intraoperatively.These specimens were cultured, followed by a susceptibility test for specific pathogens.The minimum inhibitory concentration (mic) of isolates was determined according to clsi m100.Two-hundred-and-eighty-four patients were enrolled from 2019-2021.Blood culture was dominated by gram-positive bacteria (gpb, n = 25, 52.1%), whereas abdominal tissue culture was dominated by gram-negative bacteria (gnb, n = 268, 79.5%).The three most common organisms were gnb, including e.Coli,k.Pneumoniae, and p.Aeruginosa.C/t was susceptible in 96.7%, 70.2%, and 94.1% of the e.Coli,k.Pneumoniae, and p.Aeruginosaisolates, respectively.In addition, c/t also remained active against esblenterobacteralesand carbapenem-non-susceptible p.Aeruginosa.Overall, c/t demonstrates a high potency against gnb isolates and can be considered an agent for carbapenem-sparing strategy for c iai patients as the susceptibility is proven.

Journal: Antibiotics (Basel, Switzerland) (2022)
Publication types: Journal Article
Strategies for Glycoengineering Therapeutic Proteins.

Almost all therapeutic proteins are glycosylated, with the carbohydrate component playing a long-established, substantial role in the safety and pharmacokinetic properties of this dominant category of drugs.In the past few years and moving forward, glycosylation is increasingly being implicated in the pharmacodynamics and therapeutic efficacy of therapeutic proteins.This article provides illustrative examples of drugs that have already been improved through glycoengineering including cytokines exemplified by erythropoietin (epo), enzymes (ectonucleotide pyrophosphatase 1, enpp1), and ig g antibodies (e.g., afucosylated gazyva®, poteligeo®, fasenratm, and uplizna®).In the future, the deliberate modification of therapeutic protein glycosylation will become more prevalent as glycoengineering strategies, including sophisticated computer-aided tools for "building in" glycans sites, acceptance of a broad range of production systems with various glycosylation capabilities, and supplementation methods for introducing non-natural metabolites into glycosylation pathways further develop and become more accessible.

Journal: Frontiers in chemistry (2022)
Publication types: Journal Article;Review