syedzayyan/paper_mill_benchmark huggingface dataset:
Fine Mapping of Two Major Quantitative Trait Loci for Rice Chalkiness With High Temperature-Enhanced Additive Effects.

Chalkiness is a crucial determinant of rice quality.During seed filling period, high temperature usually increases grain chalkiness, resulting in poor grain quality.Rice chalkiness was controlled by quantitative trait loci (qtls) and influenced by environmental conditions.In this study, we identified two single-segment substitution lines (sssls) 22-05 and 15-06 with significantly lower percentage of grain chalkiness (pgc) than recipient huajingxian 74 (hjx74) over 6 cropping seasons.Two major qtls for chalkiness,q pgc5andq pgc6, were located by substitution mapping of sssls 22-05 and 15-06, respectively.q pgc5was located in the 876.5 kb interval of chromosome 5 andq pgc6was located in the 269.1 kb interval of chromosome 6.Interestingly, the pgc of hjx74 was significantly different between the two cropping seasons per year, with 25.8% in the first cropping season (fcs) and 16.6% in the second cropping season (scs), while the pgc of sssls 22-05 and 15-06 did not significantly differ between fcs and scs.The additive effects ofq pgc5andq pgc6on chalkiness in the sssls were significantly greater in fcs than in scs.These results showed thatq pgc5andq pgc6had major effects on chalkiness and the sssl alleles were more effective in reducing chalkiness under high temperature condition in fcs.The fine-mapping of the two qtls will facilitate the cloning of genes for chalkiness and provide new genetic resources to develop new cultivars with low chalkiness even under high temperature condition.

Journal: Frontiers in plant science (2022)
Publication types: Journal Article
Deployment of olive-stone waste as a substitute growing medium component for Brassica seedling production in nurseries.

In the mediterranean region, olive-stone waste (osw) is accumulated and considered of environmental and human health constraints.In this study, osw was used for peat (p) replacement in growing media for brassica seedling production.Cauliflower, broccoli, and cabbage were seeded in growing media consisted of 0-20-40-60% osw.The mixture of osw with peat increased growing media bulk density and reduced the total pore space and available water and air at root system.A considerable amount of minerals were provided into the growing media with the osw, while their availability was increased with the raised p h values.Seed emergence percentage decreased with high ratio of osw which also increased mean emergence time.The addition of osw decreased plant height, leaf number, and fresh weight in all three examined species.The osw decreased stomatal conductance (in cauliflower and cabbage) and chlorophylls content (including broccoli).The insertion of osw affected the mineral accumulation in plants with decreases in nitrogen and sodium content and increases in potassium and calcium.Osw increased to some extent for cauliflower and broccoli or unchanged for cabbage polyphenolic content and antioxidant activity (abts, frap).Cellular damage was caused by the addition of osw by increasing the lipid peroxidation and the production of hydrogen peroxide, and as a consequence, the plant antioxidative (catalase, superoxide dismutase) enzyme metabolism increased.The current study demonstrates that up to 20% of osw can substitute peat for cauliflower, broccoli, and cabbage seedling production while cabbage was performed better under the increased osw-caused stress.

Journal: Environmental science and pollution research international (2019)
Publication types: Journal Article
Safety and feasibility of virus-specific T cells derived from umbilical cord blood in cord blood transplant recipients.

Adoptive transfer of virus-specific t cells (vsts) has been shown to be safe and effective in stem cell transplant recipients.However, the lack of virus-experienced t cells in donor cord blood (cb) has prevented the development of ex vivo expanded donor-derived vsts for recipients of this stem cell source.Here we evaluated the feasibility and safety of ex vivo expansion of cb t cells from the 20% fraction of the cb unit in pediatric patients receiving a single cb transplant (cbt).In 2 clinical trials conducted at 2 separate sites, we manufactured cb-derived multivirus-specific t cells (cb-vsts) targeting epstein-barr virus (ebv), adenovirus, and cytomegalovirus (cmv) for 18 (86%) of 21 patients demonstrating feasibility.Manufacturing for 2 cb-vsts failed to meet lot release because of insufficient cell recovery, and there was 1 sterility breach during separation of the frozen 20% fraction.Delayed engraftment was not observed in patients who received the remaining 80% fraction for the primary cbt.There was no grade 3 to 4 acute graft-versus-host disease (gvhd) associated with the infusion of cb-vsts.None of the 7 patients who received cb-vsts as prophylaxis developed end-organ disease from cmv, ebv, or adenovirus.In 7 patients receiving cb-vsts for viral reactivation or infection, only 1 patient developed end-organ viral disease, which was in an immune privileged site (cmv retinitis) and occurred after steroid therapy for gvhd.Finally, we demonstrated the long-term persistence of adoptively transferred cb-vsts using t-cell receptor-vβ clonotype tracking, suggesting that cb-vsts are a feasible addition to antiviral pharmacotherapy.

Journal: Blood advances (2019)
Publication types: Journal Article;Research Support, Non-U.S. Gov't;Research Support, N.I.H., Extramural
Combined liver transplantation and off-pump coronary artery bypass grafting: a report of two cases.

Introduction liver transplantation (lt) is the most effective treatment modality in patients with end-stage liver disease (esld).With the increased prevalence of diabetes and non-alcoholic fatty liver disease (nafld), coupled with a steady increase in the age of transplant population, liver transplant candidates are at increased risk for coronary artery disease (cad).Improvements in anesthesia, surgical experiences, and increased effectiveness of drugs have facilitated concurrent surgical interventions in transplantation, allowing for orthotopic lt to be performed in elderly patients with a high incidence of coexisting diseases, especially those of the cardiovascular system.In this study, we present two cases of combined off-pump coronary artery bypass surgery and living donor liver transplantation.Case presentation a 68-year-old male patient with esld due to chronic hepatitis c infection and multi-vessel cad, and a 65-year-old female patient with nafld cirrhosis and multi-vessel cad were referred to our institution for an lt evaluation.We performed combined living donor lt and off-pump coronary artery bypass surgery in both patients.Both the first and second patients were alive with good liver and cardiac function at the 25 and 15 months after surgery, respectively.Conclusion combined off-pump coronary artery bypass surgery and living donor lt are an alternative treatment for patients with severe cad and esld.We consider that combined coronary artery bypass graft surgery and lt can be safely performed by experienced anesthesia and surgical teams in selected patients.

Journal: Acta chirurgica Belgica (2022)
Publication types: Case Reports;Journal Article
Three-Dimensional Structure and Optimization of the Metallo-β-Lactamase Inhibitor Aspergillomarasmine A.

The aminopolycarboxylic acid aspergillomarasmine a (ama) is a natural zn2+metallophore and inhibitor of metallo-β-lactamases (mbls) which reverses β-lactam resistance.The first crystal structure of an ama coordination complex is reported and reveals a pentadentate ligand with distorted octahedral geometry.We report the solid-phase synthesis of 23 novel analogs of ama involving structural diversification of each subunit (l-asp, l-apa1, and l-apa2).Inhibitory activity was evaluated in vitro using five strains of escherichia coliproducing globally prevalent mbls.Further in vitro assessment was performed with purified recombinant enzymes and intracellular accumulation studies.Highly constrained structure-activity relationships were demonstrated, but three analogs revealed favorable characteristics where either zn2+affinity or the binding mode to mbls were improved.This study identifies compounds that can further be developed to produce more potent and broader-spectrum mbl inhibitors with improved pharmacodynamic/pharmacokinetic properties.

Journal: ACS omega (2022)
Publication types: Journal Article
Therapeutic implications of the tumor microenvironment in ovarian cancer patients receiving PD-1/PD-L1 therapy.

Epithelial ovarian cancer (eoc) ranks as the second most common cause of gynecologic cancer death.The conventional treatment for patients with eoc is postoperative therapy along with platinum chemotherapy.However, a more efficient treatment regimen is of great need for these patients diagnosed with advanced disease (figo stages iii-iv), whose survival is approximately 29%.Immunotherapy seems to be an encouraging therapeutic strategy for eoc.Given the crucial role in the complicated interactions between tumor cells and other cells, the tumor microenvironment (tme) influences the response to immunotherapy.In this review, we discuss feasible strategies for eoc immunotherapy by exploiting the reciprocity of cancer cells and the constituents of the tme.

Journal: Frontiers in immunology (2022)
Publication types: Journal Article;Review
Echogenic swirling pattern, carcinoembryonic antigen, and lactate dehydrogenase in the diagnosis of malignant pleural effusion.

The echogenic swirling pattern has a role in predicting malignant pleural effusion (mpe).However, its predictive ability is suboptimal, and its clinical utility remains to be defined.The aim of this study was to assess the diagnostic potential of the echogenic swirling pattern combined with pleural carcinoembryonic antigen (cea) and routine laboratory tests of pleural effusion in mpe.The 80 consecutive patients with underlying malignancy and pleural effusions were recruited.All patients underwent one diagnostic thoracentesis with a cytologic examination of pleural fluid.Our study showed that the sensitivity of echogenic swirling patterns in mpe diagnosis was 67.7%, specificity was 72.2%, positive predictive value (ppv) was 89.4%, and negative predictive value (npv) was 39.4%.Both cea and lactate dehydrogenase (ldh) had acceptable sensitivity (71.0% and 60.7%) and specificity (72.2% and 77.8%).Combining the echogenic swirling pattern, pleural cea, and pleural ldh, the highest sensitivity (95.2%) with a good ppv (86.8) was reached.In this clinical study, we found that combining the echogenic swirling pattern, pleural cea, and pleural ldh had a higher sensitivity and a high positive predictive value for the diagnosis of mpe.This combination is a potentially suitable method for mpe screening in cancer patients with pleural effusions.

Journal: Scientific reports (2022)
Publication types: Journal Article
Cell type-specific changes in Wnt signaling and neuronal differentiation in the developing mouse cortex after prenatal alcohol exposure during neurogenesis.

Fetal alcohol spectrum disorder (fasd) encompasses an array of effects of prenatal alcohol exposure (pae), including physical abnormalities and cognitive and behavioral deficits.Disruptions of cortical development have been implicated in multiple pae studies, with deficits including decreased progenitor proliferation, disrupted neuronal differentiation, aberrant radial migration of pyramidal neurons, and decreased cortical thickness.While several mechanisms of alcohol teratogenicity have been explored, how specific cell types in the brain at different developmental time points may be differentially affected by pae is still poorly understood.In this study, we used single nucleus rna sequencing (sn rnaseq) to investigate whether moderate pae from neurulation through peak cortical neurogenesis induces cell type-specific transcriptomic changes in the developing murine brain.Cluster analysis identified 25 neuronal cell types, including subtypes of radial glial cells (rgcs), intermediate progenitor cells (ipcs), projection neurons, and interneurons.Only wnt-expressing cortical hem rgcs showed a significant decrease in the percentage of cells after pae, with no cell types showing pae-induced apoptosis as measured by caspase expression.Cell cycle analysis revealed only a subtype of rgcs expressing the downstream wnt signaling transcription factor tcf7l2had a decreased percentage of cells in the g2/m phase of the cell cycle, suggesting decreased proliferation in this rgc subtype and further implicating disrupted wnt signaling after pae at this early developmental timepoint.An increased pseudotime score in ipc and projection neuron cell types indicated that pae led to increased or premature differentiation of these cells.Biological processes affected by pae included the upregulation of pathways related to synaptic activity and neuronal differentiation and downregulation of pathways related to chromosome structure and the cell cycle.Several cell types showed a decrease in wnt signaling pathways, with several genes related to wnt signaling altered by pae in multiple cell types.As wnt has been shown to promote proliferation and inhibit differentiation at earlier stages in development, the downregulation of wnt signaling may have resulted in premature neuronal maturation of projection neurons and their intermediate progenitors.Overall, these findings provide further insight into the cell type-specific effects of pae during early corticogenesis.

Journal: Frontiers in cell and developmental biology (2022)
Publication types: Journal Article
High-resolution structural analysis of enterovirus-reactive polyclonal antibodies in complex with whole virions.

Non-polio enteroviruses (npevs) cause serious illnesses in young children and neonates, including aseptic meningitis, encephalitis, and inflammatory muscle disease, among others.While over 100 serotypes have been described to date, vaccine only exists for ev-a71.Efforts toward rationally designed pan-npev vaccines would greatly benefit from structural biology methods for rapid and comprehensive evaluation of vaccine candidates and elicited antibody responses.Toward this goal, we introduced a cryo-electron-microscopy-based approach for structural analysis of virus- or vaccine-elicited polyclonal antibodies (p abs) in complex with whole npev virions.We demonstrated the feasibility using coxsackievirus a21 and reconstructed five structurally distinct p abs bound to the virus.The p abs targeted two immunodominant epitopes, one overlapping with the receptor binding site.These results demonstrate that our method can be applied to map broad-spectrum polyclonal immune responses against intact virions and define potentially cross-reactive epitopes.

Journal: PNAS nexus (2022)
Publication types: Journal Article
Community engagement in general practice: a qualitative study.

Community engagement is believed to be an important component of quality primary health care.We aimed to capture specific examples of community engagement by general practices, and to understand the barriers that prevent engagement.Methods we conducted 20 distinct interviews with 31 key informants from general practice and the wider community.The interviews were semi-structured around key relevant topics and were analysed thematically.Results key themes identified from the interview transcripts included an understanding of 'community', examples of community engagement and the perceived benefits and barriers to community-engaged general practice.We particularly explored aspects of community engagement with māori.Conclusions general practices in the study do not think in terms of communities, and they do not have a systematic framework for engagement.Although local champions have generated some great initiatives, most practices seemed to lack a conceptual framework for engagement: who to engage with, how to engage with them, and how to evaluate the results of the engagement.

Journal: Journal of primary health care (2019)
Publication types: Journal Article
Spatiotemporal Characteristics of Coupling and Coordination of Cultural Tourism and Objective Well-Being in Western China.

A supply of high-quality cultural tourism products effectively promotes people's happiness.This study takes the coupling and coordination relationship between cultural tourism (ct) and objective well-being (owb) in western china as the research object and constructs an index evaluation system for the development levels of cultural tourism and objective welfare, which are divided into three development stages of dysfunctional, transitional, and coordinated development and 10 coordination levels, including high-quality coordination.The entropy weight method, coupled coordination model, thiel index, standard deviation, and coefficient of variation were used to calculate the comprehensive development index and coupling coordination degree of the ct and owb systems in western china from 2007 to 2020, and then their evolution characteristics were analyzed from the perspectives of time and space.The results show the following: (1) the comprehensive development capacity of the ct and owb systems in the western region shows a relatively consistent growth trend except for 2020, the overall development capacity of objective welfare was relatively high, and the development capacity of cultural tourism was relatively low.(2) the ct and owb systems were in a state of transition from high coupling and low coordination to high coupling and high coordination, which were divided into three development stages: imbalanced stage (2007-2008), transitional stage (2009-2011), and coordinated development (2012-2020).The coordination degree has developed steadily from moderate misalignment to good coordination over time, and the diversified characteristics of coupling coordination levels are obvious.(3) the spatial equilibrium of the ct and owb systems is obvious, and the spatial difference in the western region is getting smaller, but the relative gap is widening significantly.(4) the comprehensive development capacity of the cultural tourism system should be enhanced, the spiritual needs of residents based on objective well-being should be met, and the sustainable development of the ct and owb systems.

Journal: International journal of environmental research and public health (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Pep5-based antitumor peptides containing multifunctional fragments with enhanced activity and synergistic effect.

In this study, we designed a series of hybrid peptides based on pep5-tat (p-05), comprising antitumor segment (pep5), endosomal escape segment ((llhh)3) and cell penetrating/membrane disrupting segment (tat, r9, s c182).These peptides exhibited remarkable antitumor activity towards tumor cells (hep g2, a549).Among them, the ic50values of peptide p-09 were 4.0 and 4.8 times lower than those of p-05 in hep g2 and a549 cells, respectively.It was proved that p-09 could enter tumor cells through endocytosis and direct penetration and induce the apoptosis and necrosis.The antitumor effects were attributed to the synergistic effect of membrane disruption and proteasome inhibition, which occurred during and after the cellular entry, respectively.The whole process was accompanied by excessive ros production.In vivo, p-09 exhibited enhanced ability to inhibit the growth of hep g2 subcutaneous tumor xenografts than p-05 in nude mice.In brief, this work provided valuable insights into the design of peptide-based antitumor agents with synergistic antitumor effects.

Journal: European journal of medicinal chemistry (2022)
Publication types: Journal Article
Empathy, burnout, life satisfaction, correlations and associated socio-demographic factors among Chinese undergraduate medical students: an exploratory cross-sectional study.

Medical education is widely known to be a demanding process that may cause various mental health problems, such as burnout, which can lead to lowered levels of life satisfaction among medical students.Research shows that empathy is negatively correlated with burnout, but there are few studies on the relationship among empathy, burnout and life satisfaction in medical students.The objective of the present study is to explore the correlations of empathy and burnout with life satisfaction and the associated socio-demographic factors among chinese undergraduate medical students.Methods in this cross-sectional study, 1271 undergraduate medical students (age 19.42 ± 1.34 years, 36% male) from 1st to 4th grades completed questionnaires including the interpersonal reactivity index chinese version (iri-c), the maslach burnout inventory modified chinese version (mbi-mc), the satisfaction with life scale (swls) and socio-demographic characteristics.Statistical analyses included student's t-test, one-way anova, post hoc bonferroni tests, hierarchical linear regression analysis and general linear model-univariate full factorial model.Results over four academic years, medical students' empathy levels declined, but their burnout levels almost plateaued and their life satisfaction levels witnessed an initial fall before a rebound.Empathy was correlated with students' age and grade, and burnout was associated with students' maternal education.Significant differences in life satisfaction were detected with regard to medical students' age, academic year, the number of children in the family, place of residence and parents' educational levels.Conclusions empathy explained 0.6% of the variance in life satisfaction in contrast to 13.7% of the variance explained by burnout in life satisfaction.Although empathy did not have a main effect on life satisfaction, there was an interaction effect of empathy and burnout on life satisfaction among students of high and low empathy and burnout levels.Students with high levels of empathy and low levels of burnout were most satisfied with life.Medical institutions and related authorities need to find effective measures to enhance students' empathy levels and reduce burnout to improve their life satisfaction.

Journal: BMC medical education (2019)
Publication types: Journal Article
Assessment on chronic and transgenerational toxicity of methamphetamine to Caenorhabditis elegans and associated aquatic risk through toxicity indicator sensitivity distribution (TISD) analysis.

Evidence about the adverse effects of methamphetamine (meth) on invertebrates is scarce.Hence, c.Elegans, a representative invertebrate model, was exposed to meth at environmental levels to estimate chronic and transgenerational toxicity.The results of chronic exposure were integrated into an underlying toxicity framework of meth in invertebrates (e.g., benthos) at environmentally relevant concentrations.The induction of cellular oxidative damage-induced apoptosis and fluctuation of ecologically important traits (i.e., feeding and locomotion) might be attributed by the activation of the longevity regulating pathway regulated by daf-16/foxo, and detoxification by cyp family enzymes.The adverse effects to the organism level included impaired viability and decreased fecundity.The results from transgenerational exposure elucidated the cumulative meth-induced damage in invertebrates.Finally, a new risk assessment method named toxicity indicator sensitivity distribution (tisd) analysis was proposed by combining multiple toxicity indicator test data (ecx) to derive the hazardous concentration for 10% indicators (c10) of one species.The risk quotient (rq) values calculated by measured environmental concentrations and c10in southern china, southeastern australia, and the western us crossed the alarm line (rq = 5), suggesting a need for long-term monitoring.

Journal: Environmental pollution (Barking, Essex : 1987) (2021)
Publication types: Journal Article