syedzayyan/paper_mill_benchmark huggingface dataset:
A conserved mechanism for regulating replisome disassembly in eukaryotes.

Replisome disassembly is the final step of eukaryotic dna replication and is triggered by ubiquitylation of the cdc45-mcm-gins (cmg) replicative helicase1-3.Despite being driven by evolutionarily diverse e3 ubiquitin ligases in different eukaryotes (scfdia2in budding yeast1, cul2lrr1in metazoa4-7), replisome disassembly is governed by a common regulatory principle, in which ubiquitylation of cmg is suppressed before replication termination, to prevent replication fork collapse.Recent evidence suggests that this suppression is mediated by replication fork dna8-10.However, it is unknown how scfdia2and cul2lrr1discriminate terminated from elongating replisomes, to selectively ubiquitylate cmg only after termination.Here we used cryo-electron microscopy to solve high-resolution structures of budding yeast and human replisome-e3 ligase assemblies.Our structures show that the leucine-rich repeat domains of dia2 and lrr1 are structurally distinct, but bind to a common site on cmg, including the mcm3 and mcm5 zinc-finger domains.The lrr-mcm interaction is essential for replisome disassembly and, crucially, is occluded by the excluded dna strand at replication forks, establishing the structural basis for the suppression of cmg ubiquitylation before termination.Our results elucidate a conserved mechanism for the regulation of replisome disassembly in eukaryotes, and reveal a previously unanticipated role for dna in preserving replisome integrity.

Journal: Nature (2021)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Simplified Analysis and Expanded Profiles of Avenanthramides in Oat Grains.

Uniquely, oats contain avenanthramides (avas), a group of phenolic alkaloids, exhibiting many health benefits.Ava analysis involves extraction with alcohol-based solvents and hplc separation with uv and/or mass spectrometer detectors.There are many reported methods to extract avas.Almost all entail multiple extractions.The whole procedure is time- and labor-intensive.Furthermore, most quantifications are limited to three common avas (2f, 2p, 2c).The present study compared three extraction methods (all at 50 °c) for their effects on ava concentrations and composition (% relative to total ava) of oat grains.These included triplicate extractions with 80% ethanol containing 10 m m phosphate buffer (p h 2.0) (a), triplicate extractions with 80% ethanol (b), and a single extraction with 80% ethanol (c), while keeping solid/total solvent ratio at 1/60 (g/m l) and total extraction time of 60 min.Results showed that 80% buffered ethanol gave significantly lower ava contents than 80% ethanol, while single and triplicate extractions with 80% ethanol produced the same extractability.However, the extraction method had no effect on ava composition.Using 0.25 g sample size instead of 0.5 g saved extractants by half, without affecting ava measurements.Consequently, a simplified method of extraction was developed, featuring method c.The present study also expanded profiling individual avas beyond ava 2c, 2p and 2f.Other avas identified and semi-quantified included 5p, 4p, 3f/4f, and 2pd.The simplified analysis was validated by measuring 16 selected oat grain samples.Some of these grains had relatively high contents of 4p, 3f/4f and 2pd, which have been considered minor avas previously.

Journal: Foods (Basel, Switzerland) (2022)
Publication types: Journal Article
Prevalence and predictors of heated tobacco product use and its relationship with attempts to quit cigarette smoking among Korean adolescents.

Introduction heated tobacco products (htps) have been available in the korean market since june 2017.In this study, we examined the prevalence and predictors of htp use among korean adolescents and the association between htp and electronic cigarette (ec) use and attempts to quit conventional cigarette (cc) smoking.Methods we analysed the data of a representative sample (n=60 040) of 13-18-year-old middle-school and high-school students in korea who had participated in the 14th korea youth risk behavior web-based survey in 2018.Results the prevalence of ever htp use among korean adolescents was 2.9% (men: 4.4%, women: 1.2%), a year after the introduction of htps in the korean market.Furthermore, 81.3% of the 1568 ever htp users were triple users of htps, ecs and ccs.Multivariate analysis revealed that ever htp use was greater among men, higher-grade students, current cc and/or ec users and risky alcohol drinkers.Among current cc smokers, ever users of ecs (28%-30%) and ever htp users and current ec users (48%) were more likely to have attempted to quit cc smoking than those who had never used htps and ecs.However, there were fewer htp and/or ec ever users among ever cc smokers who successfully quit smoking.Conclusions many adolescents, especially cc and ec users, had already used htps shortly after the introduction of htps in korea.The use of newer types of tobacco products is associated with lower odds of abstinence from ccs; therefore, it is important to protect adolescents from them.

Journal: Tobacco control (2021)
Publication types: Journal Article
Under-coding of dementia and other conditions indicates scope for improved patient management: A longitudinal retrospective study of dementia patients in Australia.

Under-coding of dementia during hospitalisation results in an inability to identify all patients with dementia using hospital administrative data.Clinical coding can be viewed as a proxy for management; therefore, under-coding indicates dementia was not considered in the patient's management.While under-coding of dementia is well established, there is sparse evidence on whether dementia is coded in subsequent hospitalisations among patients with a known diagnosis.Objective (a) to describe patterns of dementia coding over 5 years after a first-coded (i.e.Index) admission for dementia; (b) to identify factors associated with clinical coding of dementia; and (c) to identify patient subgroups at risk of not being coded to inform future interventions to improve hospital identification and management of dementia.Method retrospective study of longitudinal hospital data from 1 july 2006 to 30 june 2015 for 7919 patients hospitalised during the 5 years' post-index admission for dementia in a regional local health district of new south wales, australia.Results dementia was coded in 63.9% of admissions in the 12 months following index admission for dementia; this decreased to 53.7% after 5 years.Patients were 20% more likely to have dementia actively managed when it co-occurred with delirium.Under-coding varied across conditions, with dementia more likely to be coded in admissions for falls and pneumonitis, and less likely for heart failure, pneumonia and urinary tract infection (uti).Conclusion the frequency with which dementia was not coded highlights opportunities to improve identification and management of dementia through dementia-specific care, enhanced clinical protocols, and interventions focused around heart failure, pneumonia and uti admissions.

Journal: Health information management : journal of the Health Information Management Association of Australia (2022)
Publication types: Journal Article
Understanding the psychological impacts of responding to a terrorist incident.

Responding to a mass casualty event can cause significant distress, even for highly trained medical and emergency services personnel.Objective the purpose of the study was to understand more about first responders' perspectives about their participation in major incident responses, specifically how and which individual and system factors contributed to their preparedness or may have enabled or hindered their response.The aim of the work was to improve preparedness and response for future incidents.Methods this study reports a detailed analysis of qualitative interview data from frontline staff who responded to a large mass casualty terrorist incident in the uk in 2017.Data highlighted the psychological distress caused by responding to terrorist events and thus became the focus of further, detailed analysis.Results participants (n= 21) articulated in their own words the psychological distress experienced by many of the first responders to the event.Participants reported that they were not prepared to deal with psychological impact associated with this mass casualty terrorist incident and their role in the response, and that follow-up support was inconsistent.Multiple factors were identified as potentially increasing psychological distress.Social support provided by peers and organizational debriefs were identified as two most common support mechanisms.Organizational support was identified as inconsistent.Conclusions this research contributes to the literature the voices of first responders to uk terrorist incidents, building on existing findings while further contributing unique contextual perspectives.This research reinforces the importance of psychosocial support for those who respond to these tragic incidents, and offers a number of recommendations for organizational preparedness for future events.Abbreviations a&e: accident and emergency; eprr: emergency preparedness, resilience and response; erd: emergency response department; hepe: health emergency preparedness exercise; phe: public health england; phe regg: public health england research ethics and governance group; mci: mass casualty incident; nhs: national health service.

Journal: European journal of psychotraumatology (2021)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Infantile hepatic hemangiomas associated with high-output cardiac failure and pulmonary hypertension.

Infantile hepatic hemangioma (ihh) is a rare endothelial cell neoplasm, which may be concurrent with severe complications and result in poor outcomes.Moreover, the coexistence of ihh and congenial heart disease is even rarer.Case presentation we present a 10-day-old male born with ihh associated with patent ductus arteriosus (pda), atrial septal defect (asd) and pulmonary hypertension.Moreover, we reviewed a series of studies of ihh-associated high-output cardiac failure between 1974 and 2018, and summarized the treatment outcomes.Conclusions infantile hepatic hemangioma (ihh) has been known to induce high-output heart failure.There is no literature to summarize the severity of its impact on heart, which can lead to a high mortality rate.When ihh is detected by ultrasound, the heart should be evaluated to facilitate treatment.The outcomes of ihh associated with heart failure are good.

Journal: BMC cardiovascular disorders (2019)
Publication types: Case Reports;Research Support, Non-U.S. Gov't;Journal Article
A stand-alone structured educational programme after myocardial infarction: a randomised study.

Acute myocardial infarction (mi) is a major clinical manifestation of coronary artery disease.Post-mi morbidity and mortality can be reduced by lifestyle changes and aggressive risk factor modification.These changes can be applied more effectively if the patient is actively involved in the process.The hypothesis of this study was that an educational programme in post-mi patients could lead to reduced incidence of cardiovascular events.Methods post-mi patients were prospectively randomised into two groups.Patients in the intervention arm were scheduled to attend an 8-week-long educational programme on top of usual treatment, while controls received optimal treatment.The primary endpoint was the composite of all-cause death, mi, cerebrovascular event and unscheduled hospitalisation for cardiovascular causes.Endpoint adjudication was blinded.Results 329 patients (238 men) were included, with a mean follow-up time of 17±4 months.In the primary analysis, mean primary end point-free survival time was 597 days (95% ci 571 to 624) in controls, compared with 663 days (95% ci 638 to 687) in the intervention group (p<0.001).The hr in the univariate cox regression analysis was 0.48 (95% ci 0.32 to 0.73; p=0.001).The raw rates of the primary endpoint were 20.8% (6 deaths, 13 mis, 2 strokes and 14 hospitalisations) vs 36.6% (8 deaths, 22 mis, 7 strokes and 22 hospitalisations), respectively (or 0.46, 95% ci 0.28 to 0.74; p=0.002).Conclusion these results suggest that a relatively short adult education programme offered to post-mi patients has beneficial effects, resulting in reduced risk of cardiovascular events.Trial registration number nct04007887.

Journal: Heart (British Cardiac Society) (2021)
Publication types: Journal Article
A passive mechanism for decoupling energy storage and return in ankle-foot prostheses: A case study in recycling collision energy.

Individuals with lower limb amputation experience reduced ankle push-off work in the absence of functional muscles spanning the joint, leading to decreased walking performance.Conventional energy storage and return (esr) prostheses partially compensate by storing mechanical energy during midstance and returning this energy during the terminal stance phase of gait.These prostheses can provide approximately 30% of the push-off work performed by a healthy ankle-foot during walking.Novel prostheses that return more normative levels of mechanical energy may improve walking performance.In this work, we designed a decoupled esr (desr) prosthesis which stores energy usually dissipated at heel-strike and loading response, and returns this energy during terminal stance, thus increasing the mechanical push-off work done by the prosthesis.This decoupling is achieved by switching between two different cam profiles that produce distinct, nonlinear torque-angle mechanics.The cams automatically interchange at key points in the gait cycle via a custom magnetic switching system.Benchtop characterization demonstrated the successful decoupling of energy storage and return.The desr mechanism was able to capture energy at heel-strike and loading response, and return it later in the gait cycle, but this recycling was not sufficient to overcome mechanical losses.In addition to its potential for recycling energy, the desr mechanism also enables unique mechanical customizability, such as dorsiflexion during swing phase for toe clearance, or increasing the rate of energy release at push-off.

Journal: Wearable technologies (2021)
Publication types: Journal Article
Controlling the surface charge of simple viruses.

The vast majority of plant viruses are unenveloped, i.e., they lack a lipid bilayer that is characteristic of most animal viruses.The interactions between plant viruses, and between viruses and surfaces, properties that are essential for understanding their infectivity and to their use as bionanomaterials, are largely controlled by their surface charge, which depends on p h and ionic strength.They may also depend on the charge of their contents, i.e., of their genes or-in the instance of virus-like particles-encapsidated cargo such as nucleic acid molecules, nanoparticles or drugs.In the case of enveloped viruses, the surface charge of the capsid is equally important for controlling its interaction with the lipid bilayer that it acquires and loses upon leaving and entering host cells.We have previously investigated the charge on the unenveloped plant virus cowpea chlorotic mottle virus (ccmv) by measurements of its electrophoretic mobility.Here we examine the electrophoretic properties of a structurally and genetically closely related bromovirus, brome mosaic virus (bmv), of its capsid protein, and of its empty viral shells, as functions of p h and ionic strength, and compare them with those of ccmv.From measurements of both solution and gel electrophoretic mobilities (ems) we find that the isoelectric point (p i) of bmv (5.2) is significantly higher than that of ccmv (3.7), that virion ems are essentially the same as those of the corresponding empty capsids, and that the same is true for the p is of the virions and of their cleaved protein subunits.We discuss these results in terms of current theories of charged colloidal particles and relate them to biological processes and the role of surface charge in the design of new classes of drug and gene delivery systems.

Journal: PloS one (2021)
Publication types: Journal Article;Research Support, Non-U.S. Gov't;Research Support, U.S. Gov't, Non-P.H.S.
21stCentury FOX: Toward Gene Therapy for the Regulatory T Cell Deficiency Syndrome IPEX.

Ipex is a fatal x-linked autoimmune disorder that results from mutations in the canonical regulatory t cell transcription factor foxp3.In this issue of cell stem cell, masiuk et al.(2019) demonstrate an effective and potentially durable approach to eliminate the ipex phenotype in murine models.

Journal: Cell stem cell (2019)
Publication types: Journal Article;Comment
Sputum Metabolites Associated with Nontuberculous Mycobacterial Infection in Cystic Fibrosis.

Nontuberculous mycobacterial (ntm) pulmonary infections in people with cystic fibrosis (cf) are associated with significant morbidity and mortality and are increasing in prevalence.Host risk factors for ntm infection in cf are largely unknown.We hypothesize that the airway microbiota represents a host risk factor for ntm infection.In this study, 69 sputum samples were collected from 59 people with cf; 42 samples from 32 subjects with ntm infection (14 samples collected before incident ntm infection and 28 samples collected following incident ntm infection) were compared to 27 samples from 27 subjects without ntm infection.Sputum samples were analyzed with 16s r rna gene sequencing and metabolomics.A supervised classification and correlation analysis framework (sparse partial least-squares discriminant analysis [s pls-da]) was used to identify correlations between the microbial and metabolomic profiles of the ntm cases compared to the ntm-negative controls.Several metabolites significantly differed in the ntm cases compared to controls, including decreased levels of tryptophan-associated and branched-chain amino acid metabolites, while compounds involved in phospholipid metabolism displayed increased levels.When the metabolome and microbiome data were integrated by s pls-da, the models and component ordinations showed separation between the ntm and control samples.While this study could not determine if the observed differences in sputum metabolites between the cohorts reflect metabolic changes that occurred as a result of the ntm infection or metabolic features that contributed to ntm acquisition, it is hypothesis generating for future work to investigate host and bacterial community factors that may contribute to ntm infection risk in cf.importancehost risk factors for nontuberculous mycobacterial (ntm) infection in people with cystic fibrosis (cf) are largely unclear.The goal of this study was to help identify potential host and bacterial community risk factors for ntm infection in people with cf, using microbiome and metabolome data from cf sputum samples.The data obtained in this study identified several metabolic profile differences in sputum associated with ntm infection in cf, including 2-methylcitrate/homocitrate and selected ceramides.These findings represent potential risk factors and therapeutic targets for preventing and/or treating ntm infections in people with cf.

Journal: mSphere (2022)
Publication types: Journal Article
Airway inflammatory profile among cleaning workers from different workplaces.

Cleaning workers represent a significant proportion of the active population worldwide, with poor remuneration, particularly in developing countries.Despite this, they remain a relatively poorly studied occupational group.They are constantly exposed to agents that can cause symptoms and respiratory problems.This study aimed to evaluate upper airway inflammation in professional cleaning workers in three different occupational settings by comparing nasal cytology inflammation and clinical profiles.Methods we performed a cross-sectional study on the prevalence of upper airway inflammation and symptoms of asthma/rhinitis related to cleaning work, according to workplace.A total of 167 participants were divided into four groups: hospital, university, housekeeper and control.A nasal swab was collected for upper airway inflammation evaluation.Clinical profiles and respiratory symptom employee evaluations were performed using specific questionnaires (european community respiratory health survey-ecrs and the international study of asthma and allergies in childhood-isaac).Results cleaning workers showed increased neutrophils and lymphocytes; the hospital and university groups showed increased macrophages compared to the housekeeper and control groups.The hospital and housekeeper groups showed increased eosinophils when they performed cleaning services for up to one year and reported having more asthma symptoms than the control group.Cleaning workers showed increased rhinitis symptoms.The university group showed increased rhinitis symptoms aggravated by the workplace compared with the hospital and housekeeper groups.Cleaning workers showed an increased affirmative response when directly asked about rhinitis symptoms compared to the control group.Conclusions cleaning workers showed airway inflammation, asthma symptoms and rhinitis, regardless of the occupational environment to which they were exposed, as well as showed increased rhinitis and asthma symptoms.Hospital cleaning workers showed increased macrophages, lymphocytes and eosinophils compared to the others.The length of time spent performing cleaning work was not related to nasal inflammation or respiratory symptoms in this population.However, there were differences in workplaces.Registered on clinical trials.gov.Trial registration number nct03311048.Registration date: 10.16.2017.Retrospectively registered.

Journal: BMC pulmonary medicine (2022)
Publication types: Clinical Study;Journal Article
Delayed prosthetic seroma: a localized inflammatory response to COVID vaccination and infection?

We present a patient whom we believe developed a late abdominal mesh collection in response to covid-19 m rna vaccination booster and covid-19 infection.A polypropylene mesh was placed during her right breast reconstruction operation 2 years ago where she underwent a right transverse abdominis rectus muscle (tram) free flap.She recovered uneventfully from this operation.This lady, though vaccinated, developed respiratory symptoms and tested positive for covid-19 infection 3 days after her booster injection.She then noticed right-sided abdominal swelling 3 days after the onset of respiratory symptoms.She only presented 1 month later due to a 7-day history of pain at the site of abdominal swelling.A computed tomography scan confirmed the presence of a seroma, and she underwent ultrasound-guided percutaneous drainage.A covid antigen rapid test of the fluid returned positive, though the pcr swab returned negative.There have been no published reports of periprosthetic mesh seroma after covid-19 vaccination or infection to date.We wanted to share our experience so that other surgeons may be aware of this potential presentation given the current ongoing pandemic.Level of evidence: level v, risk/prognostic.

Journal: European journal of plastic surgery (2023)
Publication types: Journal Article