syedzayyan/paper_mill_benchmark huggingface dataset:
Arresting the Catalytic Arginine in Chlorite Dismutases: Impact on Heme Coordination, Thermal Stability, and Catalysis.

Chlorite dismutases (clds) are hemeb-containing oxidoreductases that can decompose chlorite to chloride and molecular oxygen.They are divided in two clades that differ in oligomerization, subunit architecture, and the hydrogen-bonding network of the distal catalytic arginine, which is proposed to switch between two conformations during turnover.To understand the impact of the conformational dynamics of this basic amino acid on heme coordination, structure, and catalysis, cld from cyanothecesp.Pcc7425 was used as a model enzyme.As typical for a clade 2 cld, its distal arginine 127 is hydrogen-bonded to glutamine 74.The latter has been exchanged with either glutamate (q74e) to arrest r127 in a salt bridge or valine (q74v) that mirrors the setting in clade 1 clds.We present the x-ray crystal structures of q74v and q74e and demonstrate the p h-induced changes in the environment and coordination of the heme iron by ultraviolet-visible, circular dichroism, and electron paramagnetic resonance spectroscopies as well as differential scanning calorimetry.The conformational dynamics of r127 is shown to have a significant role in heme coordination during the alkaline transition and in the thermal stability of the heme cavity, whereas its impact on the catalytic efficiency of chlorite degradation is relatively small.The findings are discussed with respect to (i) the flexible loop connecting the n-terminal and c-terminal ferredoxin-like domains, which differs in clade 1 and clade 2 clds and carries q74 in clade 2 proteins, and (ii) the proposed role(s) of the arginine in catalysis.

Journal: Biochemistry (2021)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Staff perspectives on the impact of COVID 19 on the delivery of specialist domestic abuse services in the UK: A qualitative study.

Domestic abuse is a significant public health issue effecting 2.4 million adults in england and wales each year.In march 2020 the world health organisation declared a global pandemic following the outbreak of covid-19.As a result, the uk moved to a period of lockdown.There is growing evidence that highlights the unintended negative consequences of lockdown, particularly in households where abuse is present.The aim of this study was to explore the experiences of frontline specialist domestic abuse staff who continued to support victims during the period of lockdown to understand the impact of covid-19 on service delivery.Ten, one to one, semi structured qualitative interviews were carried out with staff from a specialist domestic abuse service that operates in regions across the north-east of england.All participants had been involved in service delivery for a minimum of 12 months prior to march 2020 and had continued to deliver services throughout the uk initial lockdown period between march and july 2020.Each interview was transcribed verbatim, anonymised, then subjected to thematic analysis.Six themes were developed from the data covering: emergency support for victims; wider service efficiencies; victim safety; group work versus one-to-one support; criminal and family courts; and workforce development.While lockdown resulted in increased levels and severity of referrals, the switch to remote working brought a range of service efficiencies including time and money saved by negating the need to travel.Remote working also enhanced support offered to male victims and those with mental health issues but not those in rural locations with poor connectivity and those effected by the digital divide.Services should not underestimate the long-term benefits of peer support both to clients and staffs.

Journal: PLOS global public health (2022)
Publication types: Journal Article
Two-sample Mendelian randomization analysis evaluates causal associations between inflammatory bowel disease and osteoporosis.

Introduction over the past few years, multiple observational studies have speculated a potential association between inflammatory bowel disease (ibd), which includes ulcerative colitis (uc) and crohn's disease (cd), and osteoporosis.However, no consensus has been reached regarding their interdependence and pathogenesis.Herein, we sought to further explore the causal associations between them.Methods we validated the association between ibd and reduced bone mineral density in humans based on genome-wide association studies (gwas) data.To investigate the causal relationship between ibd and osteoporosis, we performed a two-sample mendelian randomization study using training and validation sets.Genetic variation data for ibd, cd, uc, and osteoporosis were derived from published genome-wide association studies in individuals of european ancestry.After a series of robust quality control steps, we included eligible instrumental variables (snps) significantly associated with exposure (ibd/cd/uc).We adopted five algorithms, including mr egger, weighted median, inverse variance weighted, simple mode, and weighted mode, to infer the causal association between ibd and osteoporosis.In addition, we evaluated the robustness of mendelian randomization analysis by heterogeneity test, pleiotropy test, leave-one-out sensitivity test, and multivariate mendelian randomization.Results genetically predicted cd was positively associated with osteoporosis risk, with ors of 1.060 (95% cis 1.016, 1.106;p= 0.007) and 1.044 (95% cis 1.002, 1.088;p= 0.039) for cd in the training and validation sets, respectively.However, mendelian randomization analysis did not reveal a significant causal relationship between uc and osteoporosis (p> 0.05).Furthermore, we found that overall ibd was associated with osteoporosis prediction, with ors of 1.050 (95% cis 0.999, 1.103;p= 0.055) and 1.063 (95% cis 1.019, 1.109;p= 0.005) in the training and validation sets, respectively.Conclusion we demonstrated the causal association between cd and osteoporosis, complementing the framework for genetic variants that predispose to autoimmune disease.

Journal: Frontiers in public health (2023)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
How Behavioral Economics and Nudges Could Help Diminish Irrationality in Suicide-Related Decisions.

People regularly make decisions that are not aligned with their own self-interests.These irrational decisions often stem from humans having bounded rationality (e.g., limited computational power), which produces reliable cognitive biases that occur outside of people's awareness and influences the decisions people make.There are many important decisions leading up to a suicide attempt, and it is likely that these same biases exist within suicide-related decisions.This article presents an argument for the likely existence of cognitive biases within suicide-related decision making and how they may influence people to make irrational decisions.In addition, this article provides new evidence for using a behavioral economic intervention-nudges-as a potential way to combat rising suicide rates.We explore how nudges can help increase means safety, disseminate suicide prevention skills/materials, diminish well-known biases (e.g., confirmation bias), and uncover biases that may be occurring when making suicide-related decisions.

Journal: Perspectives on psychological science : a journal of the Association for Psychological Science (2020)
Publication types: Journal Article
Influence of medical shortage on GP burnout: a cross-sectional study.

Burnout is a common occurrence among gps, decreasing quality of and access to care and impacting both physician and patient health.The link between burnout and low medical density has never been studied.Objectives this study aimed to assess the prevalence of burnout and its related factors, including low medical density, among gps.Method we conducted a cross-sectional survey.A self-administered questionnaire was sent to all of the 1632 gps in normandy, france, in september 2015.The maslach burnout inventory was used to assess the three burnout dimensions: emotional exhaustion (ee), depersonalization (dp) and low personal accomplishment (pa).Results in all, 501 gps sent back their questionnaire (response rate: 30.7%); 487 questionnaires were analysed.Burnout had been experienced by 43.3% of the physicians in the sample.Nearly 24% of the respondents scored high ee, 27.3% scored high dp, and 13.3% scored low pa.Low medical density [odds ratios (or): 2.16 (1.31-3.54)], and intent to quit [or: 4.40 (2.59-7.47)] were strongly linked to the three burnout dimensions.Burnout was not linked with quantitative workload.Conclusion burnout among gps was common.Low medical density and intent to quit were strong predictors of burnout.Given the current medical demographic crisis, these results highlight the relationship between burnout and medical shortage.Qualitative workload may have a more significant influence on burnout than quantitative workload.Recruiting more gps is necessary, but may prove insufficient in fighting burnout.Preventive and curative actions are required, especially in areas with low medical density.

Journal: Family practice (2019)
Publication types: Journal Article
How Do the Outcomes of Radiation-Associated Pelvic and Sacral Bone Sarcomas Compare to Primary Osteosarcomas following Surgical Resection?

Radiation-associated sarcoma of the pelvis and/or sacrum (rasb) is a rare but challenging disease process associated with a poor prognosis.We hypothesized that patients with rasb would have worse surgical and oncologic outcomes than patients diagnosed with primary pelvic or sacral bone sarcomas.This was a retrospective, multi-institution, comparative analysis.We reviewed surgically treated patients from multiple tertiary care centers who were diagnosed with a localized rasb.We also identified a comparison group including all patients diagnosed with a primary localized pelvic or sacral osteosarcoma/spindle cell sarcoma of bone (pops).There were 35 patients with localized rasb and 73 patients with pops treated with surgical resection.Patients with rasb were older than those with pops (57 years vs.38 years, p < 0.001).Patients with rasb were less likely to receive chemotherapy (71% for rasb vs.90% for pops, p = 0.01).Seventeen percent of patients with rasb died in the perioperative period (within 90 days of surgery) as compared to 4% with pops (p = 0.03).Five-year disease-specific survival (dss) (31% vs.54% p = 0.02) was worse for patients with rasb vs.Pops.There was no difference in 5-year local recurrence free survival (lrfs) or metastasis free survival (mfs).Rasb and pops present challenging disease processes with poor oncologic outcomes.Rates of perioperative mortality and 5-year dss are worse for rasb when compared to pops.

Journal: Cancers (2022)
Publication types: Journal Article
Prognostic utility of biomarker levels and clinical severity scoring in sepsis: a comparative study.

Procalcitonin (pct) is one of the best validated biomarkers in the management of sepsis.However, its prognostic utility remains poorly studied.The present study sought to assess the prognostic utility of serial pct assessments in patients with sepsis, and to compare the prognostic predictive capability of serial measurements of pct with conventional markers of inflammation and validated intensive care unit (icu) severity scoring systems.We recruited consecutive patients admitted to the medical units of a tertiary care center with suspected or proven bacterial infection and sepsis.Measurement of serum pct levels, inflammatory markers, and icu severity scores were performed at admission and repeated every 48 hours subsequently for the duration of hospital stay.99 patients with bacterial infection and sepsis were recruited and followed until death or discharge.Median serum pct level was similar between survivors and non-survivors on day 1, but was significantly lower at days 3, 5 and 7 in the survivors.The analysis found acute physiology and chronic health evaluation (apache iv) score on all days (1, 3, 5, and 7), pct on days 5 and 7, and sequential organ failure assessment score at 24 hours to have good predictive accuracy for adverse patient outcome.Pct clearance on days 3 and 5 of admission was measured and demonstrated predictive accuracy comparable to day-matched apache iv scores.While serial levels of serum pct in patients with sepsis are accurate in the prediction of adverse patient outcome, they do not offer any additional clinical benefit over existing severity of illness scores and may be cost prohibitive in resource-limited settings.While serial levels of serum pct in patients with sepsis are accurate in the prediction of adverse patient outcome, they do not offer any additional clinical benefit over existing severity of illness scores and may be cost prohibitive in resource-limited settings.

Journal: Journal of investigative medicine : the official publication of the American Federation for Clinical Research (2022)
Publication types: Journal Article
Improving surface water quality of the Yellow River Basin due to anthropogenic changes.

Understanding of how changes in diverse human activities and climate contribute to water quality dynamics is crucial for sustainable water environment management especially in the arid and semi-arid regions.This study conducted a comprehensive estimation of the surface water quality change in the yellow river basin during 2003-2017 and its responses to varied pollution sources and water volumes under socioeconomic and environmental influences.Basin-wide measurements of chemical oxygen demand (cod), ammonium nitrogen (nh+4-n) and dissolved oxygen (do) concentrations were used in trend detection.Annual anthropogenic (covering six sectors) and natural (sediment-induced, flow-in from the upstream and stored last year) pollution sources and water components (inflow, natural runoff, water consumption, reservoir storage and evaporation) were compiled for each sub-basin.Bottom-up hierarchical analysis was then performed to differentiate individual contributions.Results showed significant decreasing trends in cod and nh+4-n concentrations and increasing trends in do concentrations.The middle reaches that traverse the loess plateau however remained severely polluted with 11.3-39.0% inferior to level iii in 2017.The pollutant load played major positive contributions that gradually increased from upper to lower reaches.Declines in urban, rural and industrial pollution discharges following environmental investments and rural depopulation contributed the most: 78-96% for cod and 55-100% for nh+4-n.The total surface water volume had dilution effects in the upper and middle reaches (3-28%) and condensing effects in the lower reaches (2-37%).Precipitation and vegetation dynamics contributed slightly.The primary unfavorable factors were the growing agricultural pollution discharges and water consumption in the upper and middle reaches that also threatened the lower reaches.This study is expected to provide in-depth insights for the systematic response of regional water quality to combined human interventions and references for water quality management in other arid and semi-arid river basins worldwide.

Journal: The Science of the total environment (2022)
Publication types: Journal Article
Current View on Genetic Relationships within the Bunyamwera Serological Group.

The bunyamwera serological group includes a number of geographically widespread viruses that are related but not identical and have serological cross-reactivity.As the first group members were obtained in the pre-sequencing era, their classifications (group attribution, species differentiation) were originally based on serological reactions.At the same time, the accuracy of the typing in each case depended on the variety of viruses that the researcher had as a comparison panel.With the advent of sequencing techniques, it has become customary to use identity thresholds (nucleotide or amino acid composition) as demarcation criteria for the interspecific differentiation of viral species.Identity thresholds are determined by the international committee on taxonomy of viruses (ictv) and are regularly reviewed.Similar criteria were established for the orthobunyavirusgenus, which includes members of the bunyamwera serological group.On the basis of these criteria, the species attributions of some members of the serological group need to be clarified.For this purpose, we analyzed sequences (available in ncbi gen bank) of viruses belonging to the bunyamwera serological group in order to clarify their phylogenetic positions on the basis of the current demarcation criteria established by the ictv.

Journal: Viruses (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Developing self-care in an interdependent therapeutic relationship: patients' experiences from Norwegian psychomotor physiotherapy.

Factors causing and sustaining long-lasting musculoskeletal pain differ between patients, but must be identified in order to target treatment.During physiotherapy, there are multiple factors influencing the treatment outcome.The focus in the present study was to grasp patients' experiences of how social burdens influence the development and persistence of symptoms of muscle pain, and how the relationship with the physiotherapist influences the process of change during norwegian psychomotor physiotherapy.A phenomenological, descriptive, and retrospective design was chosen.Data were collected through focus-group interviews.Eleven patients participated.They ranged in age from 34 to 67 years.The analysis was inspired by giorgi's phenomenological method.The results identified a general, overarching structure; "caring for others and developing self-care" and the two interwoven themes "emerging awareness of overload" and "receiving care from the physiotherapist." these themes describe the essence of the experiences from the treatment process.To be recognized by the physiotherapist, both through the hands-on treatment and verbal communication, appears to be crucial for patients to develop an awareness of the factors causing and sustaining their pain problems.This awareness seemed necessary for the process of change to take place and for the patients to take more responsibility for their own care.

Journal: Physiotherapy theory and practice (2022)
Publication types: Journal Article
Training "Pivots" from the Pandemic: Lessons Learned Transitioning from In-Person to Virtual Synchronous Training in the Clinical Scholars Leadership Program.

Introduction since the inception of distance-based teaching modalities, a debate has ensued over the quality of online versus in-person instruction.Due to the covid-19 pandemic, a number of teaching environments-including leadership development trainings for post-graduate learners-have been thrust into exploring the virtual learning environment more thoroughly.One three-year leadership development program for interdisciplinary healthcare professionals transitioned three simultaneous leadership intensives from in-person to online in the spring of 2020.Methods documented changes in overall training length, session length, and session format are described.Further, evaluative data were collected from participants at both retreats via post-session surveys.Ninety-three participants attended the 2019 retreat, and 92 participants attended the 2020 virtual retreat.Quantitative data of three rating questions per session are reported: 1) overall session satisfaction, 2) participants' reported knowledge gain, and 3) participants' reported ability gain.Qualitative data were obtained via two open-ended feedback questions per session.Results in comparing pre/post scores for knowledge and ability, participants had meaningful (and in some cases higher) self-reported gains in knowledge and ability measures in the online environment, as compared to the in-person environment.Participants reported statistically significant gains in all sessions for both knowledge and ability.Qualitative data of participant feedback identified a number of positive themes similar across the in-person and virtual settings.Negative or constructive feedback of the virtual setting included time constraint issues (eg too much content in one session, a desire for more sessions overall), technical difficulties, and the loss of social connection and networking with fellow participants as compared to in-person trainings.Discussion while meaningful shifts in knowledge and ability ratings indicate that the transition to successful online learning is possible, several disadvantages remain.The preparation time for both faculty and participants was considerable, there is a need to reduce overall content in each session due to time restraints, and participants indicated feeling the loss of one-on-one connections with their peers in the training.Lessons learned of transitioning leadership training from in-person to an online experience are highlighted.

Journal: Journal of healthcare leadership (2021)
Publication types: Journal Article
Integrated application of transcriptome and metabolomics reveals potential therapeutic targets for the polarization of atherosclerotic macrophages.

The polarization of macrophages often leads to severe calcification and necrosis in aged atherosclerotic plaques, which eventually leads to poor prognosis of ischaemic cardiovascular and cerebrovascular diseases.More reliable diagnostic methods are urgently needed to discover therapeutic targets of macrophage polarization in aged atherosclerotic plaques.Metabolomics of aged plaques (n = 20) and macrophage polarization transcriptomes (n = 30) were integrated to identify metabolic therapeutic targets of macrophage polarization associated with aged plaque.Finally, metabolic inhibitors were used to verify the reliability of the target genes.Integrated multiomics analysis revealed that 6 metabolic pathways (including 21 genes) regulate macrophage polarization in aged atherosclerosis.Targeted treatment of macrophage polarization with metabolic inhibitors can effectively reduce the adverse risk of aged atherosclerosis.The combination of transcriptomics and metabolomics approaches can identify effective therapeutic targets for macrophage polarization in arteriosclerosis.

Journal: Biochimica et biophysica acta. Molecular basis of disease (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't