syedzayyan/paper_mill_benchmark huggingface dataset:
Insights into Antiperovskite Ni3In1-xCuxN Multi-Crystalline Nanoplates and Bulk Cubic Particles as Efficient Electrocatalysts on Hydrogen Evolution Reaction.

Intrinsic hydrogen evolution reaction (her) activity and the mechanism of antiperovskite ni3in1-x cux n bulk cubic particles and multi-crystalline nanoplates are thoroughly investigated.Stoichiometric ni3in0.6cu0.4n reaches the best her performance, with an overpotential of 102 m v in its multi-crystalline nanoplates obtained from the ldh-derived method, and 143 m v in its bulk cubic particles from the citric method.Dft calculation reveals that ni-in or ni-cu paired on the (100) plane serve as primary active sites.The ni-cu pair exhibits stronger oh* and h* affinity that correspondingly reduce oh* and h* adsorption free energy.Introducing specific amounts of the ni-cu pair, that is in:cu = 0.6:0.4 in ni3in0.6cu0.4n, can optimize oh* and h* adsorption free energy to facilitate water dissociation in the her process, while avoiding oh* adsorption getting too strong to block active sites.Besides, ni3in0.6cu0.4n turns the water adsorption step spontaneous, which may be attributed to the shifted d-band center and polarizing effect from surface in-cu charge distribution.This work expands the scope for material design in an antiperovskite system by tailoring the chemical components and morphology for optimal reaction free energy and performance.

Journal: Small (Weinheim an der Bergstrasse, Germany) (2022)
Publication types: Journal Article
Cell Wall Integrity and Its Industrial Applications in Filamentous Fungi.

Signal transduction pathways regulating cell wall integrity (cwi) in filamentous fungi have been studied taking into account findings in budding yeast, and much knowledge has been accumulated in recent years.Given that the cell wall is essential for viability in fungi, its architecture has been analyzed in relation to virulence, especially in filamentous fungal pathogens of plants and humans.Although research on cwi signaling in individual fungal species has progressed, an integrated understanding of cwi signaling in diverse fungi has not yet been achieved.For example, the variety of sensor proteins and their functional differences among different fungal species have been described, but the understanding of their general and species-specific biological functions is limited.Our long-term research interest is cwi signaling in filamentous fungi.Here, we outline cwi signaling in these fungi, from sensor proteins required for the recognition of environmental changes to the regulation of cell wall polysaccharide synthesis genes.We discuss the similarities and differences between the functions of cwi signaling factors in filamentous fungi and in budding yeast.We also describe the latest findings on industrial applications, including those derived from studies on cwi signaling: the development of antifungal agents and the development of highly productive strains of filamentous fungi with modified cell surface characteristics by controlling cell wall biogenesis.

Journal: Journal of fungi (Basel, Switzerland) (2022)
Publication types: Journal Article;Review
Quantitative Proteomic Analysis Revealed Broad Roles ofN6-Methyladenosine in Heat Shock Response.

As optimum temperature is essential for all living organisms, heat shock represents a challenging problem for their survival.Therefore, cellular response to heat shock is among the most extensively investigated stress response pathways; however, how the human proteome responds to heat shock has not been comprehensively investigated.In this study, we employed stable isotope labeling by amino acids in cell culture (silac), together with liquid chromatography-tandem mass spectrometry (lc-ms/ms) analysis, to fulfill an in-depth analysis of the alterations in the human proteome in m14 human melanoma cells in response to heat shock stress.We found that, after heat shock, 284 and 278 out of the 4319 quantified proteins were with substantially diminished and elevated expressions, respectively.We also examined the alterations in human kinome after heat shock by using our recently developed targeted proteomic method relying on parallel-reaction monitoring.Our results showed that the expression levels of 11 and 22 kinase proteins were increased and decreased, respectively, by at least 1.5-fold upon heat shock.By interrogating publicly available rna-seq and m6a sequencing data, we observed that the elevated expression of more than 30 proteins, including chek1 and ccnd3 kinases, could occur via an m6a-mediated mechanism.Furthermore, our results from single-base elongation and ligation-based quantitative polymerase chain reaction (q pcr) amplification (select) and luciferase reporter assays revealed that heat shock gave rise to elevated m6a levels at a280 and a286 sites in the 5'-untranslated region of hsph1m rna, thereby leading to increased translation of hsph1 protein.Together, our discovery and targeted proteomic methods revealed the reprogramming of human proteome and kinome upon heat shock stress and provided insights into cellular responses toward heat shock stress.

Journal: Journal of proteome research (2021)
Publication types: Journal Article;Research Support, N.I.H., Extramural
The Catalytic Mechanism of Pdx2 Glutaminase Driven by a Cys-His-Glu Triad: A Computational Study.

The catalytic mechanism of pdx2 was studied with atomic detail employing the computational oniom hybrid qm/mm methodology.Pdx2 employs a cys-his-glu catalytic triad to deaminate glutamine to glutamate and ammonia - the source of the nitrogen of pyridoxal 5'-phosphate (plp).This enzyme is, therefore, a rate-limiting step in the plp biosynthetic pathway of malaria and tuberculosis pathogens that rely on this mechanism to obtain plp.For this reason, pdx2 is considered a novel and promising drug target to treat these diseases.The results obtained show that the catalytic mechanism of pdx2 occurs in six steps that can be divided into four stages: (i) activation of cys87, (ii) deamination of glutamine with the formation of the glutamyl-thioester intermediate, (iii) hydrolysis of the formed intermediate, and (iv) enzymatic turnover.The kinetic data available in the literature (19.1-19.5 kcal mol-1) agree very well with the calculated free energy barrier of the hydrolytic step (18.2 kcal.mol-11), which is the rate-limiting step of the catalytic process when substrate is readily available in the active site.This catalytic mechanism differs from other known amidases in three main points: i) it requires the activation of the nucleophile cys87to a thiolate; ii) the hydrolysis occurs in a single step and therefore does not require the formation of a second tetrahedral reaction intermediate, as it is proposed, and iii) glu198does not have a direct role in the catalytic process.Together, these results can be used for the synthesis of new transition state analogue inhibitors capable of inhibiting pdx2 and impair diseases like malaria and tuberculosis.

Journal: Chembiochem : a European journal of chemical biology (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Comparative analysis of aroma components and quality ofGeotrichum candidumafter space mutation breeding.

The aroma-producing strain of geotrichum candidum gdmcc60675 was taken as the research object, the composition of aroma-producing substances of g.Candidumwas studied, and the target strains of g.Candidumsuitable for food additives were screened out by mutagenesis.Methods mutants were obtained by space breeding.The colony morphology and cell morphology of the mutant strain were identified, the phylogenetic tree of the two strains was constructed, and the whole-genome sequences of the wild strain and the mutant strain were compared.The aroma components and key odor compounds of the two strains were analyzed and compared by hs-spme-gc-ms and e-nose detection, and the data were processed by using the relative odor activity value (roav) analysis method.Results a mutant strain of g.Candidumwas found with different characteristics of aroma production compared with wild-type g.Candidum.It was found that its colony morphology and cell morphology were similar.However, it was found that the aroma-producing substances produced by the two strains were different, and the key difference compound was phenyl ethyl alcohol, which also proved that the two strains were different, and the main aroma note was different.

Journal: Frontiers in microbiology (2022)
Publication types: Journal Article
Relationship Between Physical Activity Levels and Thyroid Cancer Risk: A Prospective Cohort Study in Korea.

Physical activity is a protective factor against several types of cancers.However, evidence for the association between physical activity and thyroid cancer (tc) is still inconclusive.methods:we used prospectively collected data from the korea national cancer screenee cohort, which consisted of 30,435 participants from 20 years who received health examinations at national cancer center between june 2007 and december 2014.Participants' follow-up data up to december 2019 was used to identify new tc cases.Demographic characteristics of the subjects were collected using a self-administered questionnaire.Physical activity measurement was analyzed from 15,175 participants using international physical activity questionnaire-short form.Physical activity data included frequency (days per week) and duration (minutes per day) of their exercises in three intensity levels (walking, moderate, and vigorous-intensity).The association between physical activity levels and tc risk was examined by cox proportional hazards regression models.results:we identified 234 new tc cases among 15,175 eligible participants during the follow-up period.Participants with the highest physical activity level had a reduced risk of tc (hazard ratio [hr] = 0.65 [confidence interval, ci = 0.44-0.94],p-trend = 0.028) than participants with the lowest physical activity level.The significant associations were stronger among female subjects with a body mass index ≥25 kg/m2(hr = 0.38 [ci = 0.16-0.93],p-trend = 0.034), subjects with household income >4 million won/month (hr = 0.53 [ci = 0.30-0.94],p-trend = 0.034), subjects without a first-degree family history of tc (hr = 0.66 [ci = 0.45-0.96],p-trend = 0.040), and subjects who did not drink alcohol (hr = 0.48 [ci = 0.26-0.88],p-trend = 0.018) or smoke (hr = 0.61 [ci = 0.40-0.95],p-trend = 0.030).conclusion:this prospective korean cohort study suggests that increased physical activity may be protective for development of tc.These findings require confirmation in other populations.

Journal: Thyroid : official journal of the American Thyroid Association (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Mucinous Cystic Neoplasm of Mesentery: A Case Report.

Mucinous cystic neoplasms are very rare tumours.They may originate from ovaries, pancreas or other intra-abdominal sites but they rarely originate from the mesentery.They can be asymptomatic or present as an abdominal mass or abdominal pain.We present the case of a 28-year-old woman who presented with epigastric pain and cystic mass per abdomen with a diagnosis of mesenteric cyst made on further imaging studies.Subsequent excision and histopathological analysis demonstrated the cyst to be a mucinous tumour arising from the mesocolon.Mesenteric cyst must be considered as one of the differentials in abdominal cystic lesions.

Journal: Cureus (2022)
Publication types: Case Reports;Journal Article
Kidney transplantation from expanded criteria donors: an increased risk of urinary complications - the UriNary Complications Of Renal Transplant (UNyCORT) study.

S to assess the impact of expanded criteria donors (ecd) on urinary complications in kidney transplantation.Patients and methods the uri nary complications of renal transplant (uny cort) is a cohort study based on the french prospective données informatisées et validées en transplantation/computerized and validated data in transplantation (divat) cohort.Data were extracted between 1 january 2002 and 1 january 2018 with 1-year minimum follow-up, in relation to 44 pre- and postoperative variables.Ecd status was included according to united network for organ sharing (unos) definition.The primary outcome of the uny cort study was the association between the donor's ecd/standard criteria donors (scd) status and urinary complications at 1 year in uni- and multivariate analysis.Sub-group analysis, stratified analysis on ecd/scd donor's status and transplant failure analysis were then conducted.Results between 1 january 2002 and 1 january 2018, 10 279 kidney transplants in adult recipients were recorded within the divat network.A total of 8559 (83.4%) donors were deceased donors and 1699 (16.6%) were living donors (ld).Among donation after circulatory death (dcd) donors, 224 (2.85%) were uncontrolled dcd and 93 (1.09%) were controlled dcd donors.A total of 3617 (43.9%) deceased donors were ecd.The overall urological complication rate was 16.26%.The donor's ecd status was significantly associated with an increased risk of urological complications at 1 year in multivariate analysis (odds ratio: 1.50, 95% ci 1.31-1.71; p < 0.001) and especially with stenosis and ureteric fistulae at 1 year.There is no association with ld, uncontrolled and controlled dcd.The placement of an endo-ureteric stent was beneficial in preventing urinary complications in all donors and particularly in ecd donors.Conclusion the donor's ecd status is associated with a higher likelihood of stenosis and ureteric fistulae at 1 year.Recipients of grafts from ecd donors should probably be considered for closer urological monitoring and systematic preventive measures.

Journal: BJU international (2022)
Publication types: Journal Article
Protective effect of ginsenoside Rg1 on LPS-induced apoptosis of lung epithelial cells.

Sepsis-induced acute lung injury (ali) is a life-threatening medical condition with high mortality and morbidity in the critical care units.Though, it was commonly accepted that inflammation and apoptosis of lung epithelial cells played an essential role in the pathogenesis of ali, the underlying mechanism remain unknown.In our study, we found that lps-induced cell apoptosis could be counteracted by elevated cell autophagy.In lps-treated mle-12 cells, suppression of autophagy via 3-ma could aggravate lps-induced apoptosis, while activation of autophagy via rapamycin could effectively impair the apoptosis of mle-12 cells induced by lps.In order to further discover the molecular regulation mechanism between apoptosis and autophagy in lps-treated mle-12 cells, we demonstrated that autophagy could induced the expression of nrf2, followed with the decrease of p-p65.Targeted inhibition of nrf2 could induce enlarged cell apoptosis via increasing the level of p-p65.In addition, we demonstrated that ginsenoside rg1 protected mle-12 cells from lps-induced apoptosis via augmenting autophagy and inducing the expression of nrf2.Our data implicates that activation of autophagy and nrf2 by ginsenoside rg1 may provide a preventive and therapeutic strategy for ali.

Journal: Molecular immunology (2021)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Ki67 Immunohistochemical Expression Level ≥70%, Bulky Presentation ≥7.5 cm, Meningeal Lymphomatosis, and Interim PET ΔSUVmax After 4 Treatment Cycles <71% as Parts of a Practical Scoring System to Predict Progression-Free Survival and Overall Survival in Diffuse Large B-Cell Lymphoma.

Currently, prognostic models in diffuse large b-cell lymphoma (dlbcl) fail to closely reflect patients' biological, clinical, and survival heterogeneity.We, therefore, assessed the impact of clinical, biological, immunohistochemical (ihc), baseline (0), and interim (after 2 and 4 treatment cycles) pet (pet0, pet2, and pet4) data not yet included in any scoring system on dlbcl outcome.The analysis was conducted on 89 previously untreated adult patients of the finistere observatory cohort (o.ly.fin) with documented dlbcl, recruited between january 2010 and december 2017, with progression-free survival (pfs) and overall survival (os) as primary and secondary endpoints, respectively.Seventy-eight patients were treated with rituximab, cyclophosphamide, hydroxyadriamycin, vincristine, and prednisone (r-chop), while 11 received r-dose-adjusted etoposide, prednisone, vincristine, cyclophosphamide, and hydroxyadriamycin (epoch).Patients were followed up until june 20, 2020.On multivariate analysis, ki67 ≥ 70% on ihc (k), bulky presentation ≥7.5 cm (b), meningeal lymphomatosis (m), and pet0-pet4 δsuvmax <71% (p4) were identified as strong independent predictors of pfs, and all variables but bulky disease also strongly and independently predicted os.Using these 4 parameters, we designed a scoring model named kbmp4 stratifying patients into low- (0 parameter), intermediate- (1 or 2), and high-risk (≥3) subgroups by the kaplan-meier analysis.At a median follow-up of 43 months, pfs and os were both 100% in the low-risk subgroup, 71.4 and 90.5%, respectively, in the intermediate-risk subgroup, and 0 and 55.5%, respectively, in the high-risk subgroup.Use of the kbmp4 model in clinical practice may improve accuracy in prognostic prediction and treatment decisions inde novo dlbcl patients.

Journal: Frontiers in nuclear medicine (2022)
Publication types: Journal Article
A randomized, split-face, double-blind, comparative study of the safety and efficacy of small- and large-particle hyaluronic acid fillers for the treatment of nasolabial folds.

Injections of hyaluronic acid (ha) for tissue augmentation are one of the most common aesthetic treatments performed worldwide.However, few studies have compared the safety and efficacy of small- and large-particle ha (sp-ha; lp-ha).Aim to assess and compare the safety and efficacy of sp-ha and lp-ha for the correction of nasolabial folds (nlfs).Methods a prospective, split-face, triple-blind study design was used.Ten female subjects were recruited.Patients underwent treatment at baseline, an optional touch up at week 2, and a follow-up visit at week 4.At weeks 2 and 4, a blinded reviewer assessed the patients using the global aesthetic improvement scale (gais) and wrinkle severity rating scale (wsrs); and subjects completed the patient satisfaction questionnaire (psq).At all visits, 3-dimensional imagery and ultrasonography of patients' nlfs were captured.Adverse events (aes) were evaluated by the investigator and recorded by subjects in diaries.Results the gais response rate, defined as ≥ "improved" from baseline, was between 90 (2 weeks) and 100% (1 month) for sp-ha and was 100% for lp-ha, at both visits.Paired-samples t tests revealed significant differences in the change in wsrs scores between groups, at both visits (p < .01).Differences in the clinical effect and lifting capacity of both products were observed in 3-dimensional imagery and ultrasonography.Treatment volumes varied, with 61.32% more sp-ha being required than lp-ha for achieving a ≥ one-grade wsrs improvement.There were no severe aes throughout the trial, nor aes related to the investigational device.Conclusions lp-ha demonstrates better efficacy for correcting bony resorption in the nasal pyriform region.

Journal: Journal of cosmetic dermatology (2021)
Publication types: Comparative Study;Journal Article;Randomized Controlled Trial
Obesity Pillars Roundtable: Obesity and Diversity.

The clinical implications of obesity differ, depending on race, ethnicity, and sexual orientation.Methods this roundtable discussion included 4 obesity specialists with expertise in the clinical management of obesity among diverse populations including blacks, hispanics/latinos, lesbian-gay-bisexual-transgender-questioning (lgbtq) individuals, and native-americans.Results one of the first obstacles towards overcoming disparities in managing obesity and its complications among diverse populations is understanding applicable terminology.This includes categorization terminology relative to native americans (for the purpose of assessing culture and possibly genetic predispositions), understanding the differences between black african americans and black africans, understanding the differences between the terms hispanic and latinx, and basic concepts behind different pronouns applicable to lesbian-gay-bisexual-transgender-questioning (lgbtq) individuals.After being better able to grasp the input from patients with diverse backgrounds, universal obesity assessment and management principles can be then tailored utilizing a patient-centered approach.Conclusion understanding the unique genetic, culture, and terminology regarding patients of different races, ethnicities, and sexual orientation may help clinicians better engage patients in managing obesity via utilizing a more patient-centered approach.

Journal: Obesity pillars (2022)
Publication types: Journal Article
A liquid thermal gradient refractive index lens and using it to trap single living cell in flowing environments.

A gradient refractive index (grin) lens has a great potential for on-chip imaging and detection systems because of its flat surface with reduced defects.This paper reports a liquid thermal grin lens prepared using heat conduction between only one liquid, and uses it as a tunable optical tweezer for single living cell trapping in a flowing environment.This liquid grin lens consists of a trapezoidal region in the upper layer which is used to establish a grin profile by the heat conduction between three streams of benzyl alcohol with different temperatures, and subsequently a rhombus region in the lower layer with compensation liquids to form a steady square-law parabolic refractive index profile only in transverse direction.Simulations and experiments successfully show the real-time tunability of the focusing properties.The focal length can be modulated in the range of 500 μm with the minimum focal length of 430 μm.A considerable high enhancement factor achieves 5.4 whereas the full width at half maximum is 4 μm.The response time of the grin lens is about 20 ms.Based on this enhancement, tunable optical trapping for single human embryonic kidney 293 cell in the range of 280 μm is demonstrated by varying the focal length and working distance which is difficult for solid optical tweezers.The considerable quality of this liquid grin lens indicates on-chip applications especially in high quality optical imaging, detection and cells' handling.

Journal: Lab on a chip (2017)
Publication types: Journal Article;Research Support, Non-U.S. Gov't