syedzayyan/paper_mill_benchmark huggingface dataset:
Transposon-associated epigenetic silencing during Pleurotus ostreatus life cycle.

Transposable elements constitute an important fraction of eukaryotic genomes.Given their mutagenic potential, host-genomes have evolved epigenetic defense mechanisms to limit their expansion.In fungi, epigenetic modifications have been widely studied in ascomycetes, although we lack a global picture of the epigenetic landscape in basidiomycetes.In this study, we analysed the genome-wide epigenetic and transcriptional patterns of the white-rot basidiomycete pleurotus ostreatus throughout its life cycle.Our results performed by using high-throughput sequencing analyses revealed that strain-specific dna methylation profiles are primarily involved in the repression of transposon activity and suggest that 21 nt small rnas play a key role in transposon silencing.Furthermore, we provide evidence that transposon-associated dna methylation, but not s rna production, is directly involved in the silencing of genes surrounded by transposons.Remarkably, we found that nucleus-specific methylation levels varied in dikaryotic strains sharing identical genetic complement but different subculture conditions.Finally, we identified key genes activated in the fruiting process through the comparative analysis of transcriptomes.This study provides an integrated picture of epigenetic defense mechanisms leading to the transcriptional silencing of transposons and surrounding genes in basidiomycetes.Moreover, our findings suggest that transcriptional but not methylation reprogramming triggers fruitbody development in p.Ostreatus.

Journal: DNA research : an international journal for rapid publication of reports on genes and genomes (2018)
Publication types: Journal Article
It's more than just lubrication of the skin: parents' experiences of caring for a child with ichthyosis.

The ichthyoses are a group of genetic skin disorders, characterized by excessive amounts of dry, thickened skin, which may be fragile, inelastic and prone to fissures and infection.Skin care is time consuming and demanding, and, usually performed by the parents.methods: we aimed to explore parental experience of caring for a child with ichthyosis, and collected data using semistructured interview, and thematic analysis.results: our analysis revealed four main themes: parents' and others' reactions to the child's difference, experiences with healthcare services, it's all skin care, and impact on relationships.conclusion: after birth of a child with severe ichthyosis, the parents experienced emotional distress and stigmatization due to the different appearance of the skin and healthcare professionals' lack of knowledge.Skin care caused pain in the child, was time consuming, and caused financial burdens.This study can guide healthcare professionals on where to focus future efforts in meeting the clinical and psychological needs of parents caring for a child with ichthyosis.

Journal: Health psychology and behavioral medicine (2022)
Publication types: Journal Article
Plug-and-Display Photo-Switchable Systems on Plant Virus Nanoparticles.

Light can be used to regulate protein interactions with a high degree of spatial and temporal precision.Photo-switchable systems therefore allow the development of controllable protein complexes that can influence various cellular and molecular processes.Here, we describe a plant virus-based nanoparticle shuttle for the distribution of proteins that can be released when exposed to light.Potato virus x (pvx) is often used as a presentation system for heterologous proteins and epitopes, and has ideal properties for biomedical applications such as good tissue penetration and the ability to form hydrogels that present signaling molecules and promote cell adhesion.In this study, we describe three different systems attached to the surface of pvx particles: lovtrap, bph p1/qpas1 and dronpa145n.We demonstrated the functionality of all three photo-switchable protein complexes in vitro and the successful loading and unloading of pvx particles.The new systems provide the basis for promising applications in the biomedical and biomaterial sciences.

Journal: Biotech (Basel (Switzerland)) (2022)
Publication types: Journal Article
T cell repertoire in peripheral blood as a potential biomarker for predicting response to concurrent cetuximab and nivolumab in head and neck squamous cell carcinoma.

T cell receptor (tcr) signaling profile is a fundamental property that underpins both adaptive and innate immunity in the host.Despite its potential clinical relevance, the tcr repertoire in peripheral blood has not been thoroughly explored for its value as an immunotherapy efficacy biomarker in head and neck squamous cell carcinoma (hnscc).The purpose of the present study is to characterize and compare the tcr repertoire in peripheral blood mononuclear cells (pbmc) from patients with hnscc treated with the combination of cetuximab and nivolumab.Methods we used the immuno seq assay to sequence the tcr beta (tcr-b) chain repertoire from serially obtained pbmc at baseline and during the treatments from a total of 41 patients who received the combination (nct03370276).Key tcr repertoire metrics, including diversity and clonality, were calculated and compared between patients with different therapy responses and clinical characteristics (eg, human papillomavirus (hpv) status and smoking history).Patient survival outcomes were compared according to patient groups stratified by the tcr-b clonotyping.To confirm the observed patterns in tcr spectrum, samples from patients who achieved complete response (cr) and partial response (pr) were further profiled with the immuno seq deep resolution assay.Results our data indicated that the patients who achieved cr and pr had an increased tcr sequence diversity in their baseline samples, this tendency being more pronounced in hpv-negative patients or those with a smoking history.Notably, the cr/pr group had the lowest proportion of patients with oligoclonal tcr clones (2 out of 8 patients), followed by the stable disease group (9 out of 20 patients) and lastly the progressive disease group (7 out of 10 patients).An overall trend toward favorable patient survival was also observed in the polyclonal group.Finally, we reported the shared tcr clones across patients within the same response group, as well as the shared clones by aligning immuno seq reads with tcr data retrieved from the cancer genome atlas- head and neck squamous cell carcinoma (tcga-hnsc) cohort.Conclusions our data suggest that, despite the great clinical heterogeneity of hnscc and the limited responders in the present cohort, the peripheral tcr repertoires from pretreatment pbmc may be developed as biomarkers for the benefit of immunotherapy in hnscc.

Journal: Journal for immunotherapy of cancer (2022)
Publication types: Clinical Study;Journal Article;Research Support, N.I.H., Extramural;Research Support, Non-U.S. Gov't
Exercising body but not mind: A qualitative exploration of attitudes to combining physical activity and mindfulness practice for mental health promotion.

Physical activity and mindfulness meditation can be effective for maintaining good mental wellbeing, with early-stage research suggesting even greater effectiveness in tandem.Literature is lacking on the perceptions and acceptability of these practices, particularly in a preventative context.The study aimed to explore attitudes toward mental health and its maintenance through physical activity and mindfulness meditation in the university student population.Methods semi-structured qualitative interviews were conducted with a sample of 16 students from 10 united kingdom universities (mage= 23 years,sd= 3.22) recruited through social media and stratified to have varied wellbeing symptoms, physical activity levels, and experience with mindfulness meditation.Reflexive thematic analysis was used to elicit meaning from the data.Results four main themes were constructed.Participants held a "dualist view of health," in which mental and physical aspects were seen as distinct but connected, and prioritized physical health maintenance.The "low-point paradox," where engagement is most difficult during the time of greatest need, was identified as a crucial psychological barrier across health behaviors."unfamiliarity with mindfulness practice" was common, as were misconceptions inhibiting practice.Finally, participants were intrigued by combining physical activity and mindfulness, supposing that "whole is greater than the sum of its parts," with mutual reinforcement of the two techniques cited as biggest motivating factor.Conclusion effective preventative mental health strategies for adults, including university students, should accommodate for common psychological barriers and facilitators to health maintenance behaviors, including misconceptions surrounding mindfulness, to increase acceptability.Combining physical activity and mindfulness meditation is one promising preventative approach that warrants further investigation.

Journal: Frontiers in psychology (2022)
Publication types: Journal Article
Analysis of Channel Area Fluctuation Effects of Gate-All-Around Tunnel Field-Effect Transistor.

In this manuscript, channel area fluctuation (caf) effects on turn-on voltage (von) and subthreshold swing (ss) in gate-all-around (gaa) nanowire (nw) tunnel field-effect transistor (tfet) with multi-bridge-channel (mbc) have been investigated for the first time.These variations occur because oblique etching slope makes various elliptical-shaped channels in mbc-tfet.Since tfet is promising candidates to succeed metal-oxide-semiconductor fets (mosfet), these variation effects have been compared to mosfet.Furthermore, ge homojunction tfet, one of the solutions to increase on-state current in tfet and improve ss also has been simulated using technology computer-aided design (tcad) simulation.The results would be worth reference for future study about gaa nw tfets.

Journal: Journal of nanoscience and nanotechnology (2020)
Publication types: Journal Article
Pattern of Ametropia, Presbyopia, and Barriers to the Uptake of Spectacles in Adult Patients Attending a General Hospital in Kaduna State.

The aim of the study was to assess the pattern of ametropia, presbyopia, and the barriers to the uptake of spectacles among adult patients attending hajiya gambo sawaba general hospital (hgsgh), zaria, nigeria.Materials and methods this study was a descriptive hospital-based study.The study population was selected by systematic sampling over a 3-month period (july-september, 2016).A questionnaire was administered for sociodemographic data, patients' history, and refraction.Patients with visual acuity less than 6/12 or who required at least +1.00ds to read n8 were given spectacle prescriptions and assessed after 2 months to confirm if they purchased the spectacles.Results two hundred and nine patients were assessed: 124 (59.3%) females and 85 (40.7%) males.The age ranged from 18 to 75 years with a mean of 45.5.One hundred and seventy-five (83.7%) had ametropia, 100 (47.8%) had presbyopia, and patients having both were 66 (31.6%).Astigmatism was the most common ametropia, 118 (67.4%), followed by hypermetropic astigmatism 33 (18.9%) and myopia 24 (13.7%).Only 97 (46.6%) patients purchased their spectacles, and 92 of them were using their spectacles.One hundred and twelve (52.2%) patients did not buy their spectacles, with cost being most common barrier to the uptake of spectacles.Conclusion there is a high burden of ametropia and presbyopia among patients attending hgsgh, zaria.Cost of spectacles and 'no felt need' were found to affect spectacle uptake.Health information and availability of low-cost spectacles are important strategies in reducing the burden of uncorrected ametropia and presbyopia in kaduna state.

Journal: Journal of the West African College of Surgeons (2022)
Publication types: Journal Article
Evidence of multi-decadal behavior and ecosystem-level changes revealed by reconstructed lifetime stable isotope profiles of baleen whale earplugs.

Biological time series datasets provide an unparalleled opportunity to investigate regional and global changes in the marine environment.Baleen whales are long-lived sentinel species and an integral part of the marine ecosystem.Increasing anthropogenic terrestrial and marine activities alter ocean systems, and such alterations could change foraging and feeding behavior of baleen whales.In this study, we analyzed δ13c and δ15n of baleen whale earplugs from three different species (n = 6 earplugs, n = 337 laminae) to reconstruct the first continuous stable isotope profiles with a six-month resolution.Results of our study provide an unprecedented opportunity to assess behavioral as well as ecological changes.Abrupt shifts and temporal variability observed in δ13c and δ15n profiles could be indicative of behavior change such as shift in foraging location and/or trophic level in response to natural or anthropogenic disturbances.Additionally, five out of six individuals demonstrated long-term declining trends in δ13c profiles, which could suggest influence of emission of depleted13co2from fossil fuel combustion referred to as the suess effect.After adjusting the δ13c values of earplugs for the estimated suess effect and re-evaluating δ13c profiles, significant decline in δ13c values as well as different rate of depletion suggest contribution of other sources that could impact δ13c values at the base of the food web.

Journal: The Science of the total environment (2021)
Publication types: Journal Article
Patient-reported experience with patient-reported outcome measures in adult patients seen in rheumatology clinics.

S patient-reported outcome measures (proms) are increasingly utilized in the evaluation of patients with rheumatic diseases.The aim of our study was to assess the patient experience with completing proms within rheumatology clinics, and identify patient characteristics associated with a more positive experience.Methods we conducted a retrospective cross-sectional study of adult patients seen in rheumatology clinics between 1/1/2017 and 6/30/2017.Patients were included in the study if they completed at least one patient-reported experience question following completion of proms.Patient characteristics associated with more positive experiences were identified through multivariable proportional odds models.Results 12,597 adult patients (mean age 59 ± 15; 76% female; 84% white) completed proms, as well as questions on their experience completing proms.Patients agreed/strongly agreed that prom questions were easy to understand (97%), useful (84%), helped their physician understand their health (78%), improved communication with their provider (78%) and improved control over their own care (70%).Predictors of better experience with proms included being younger, non-white, having lower income, and being a new patient.Worse self-reported health also predicted better experience with proms.Conclusion our study found a positive patient experience with proms, which is a crucial component of their successful implementation and utilization.Findings from this study suggest proms may be particularly beneficial in new patients, minorities, those with lower income, and worse self-reported quality of life.Collecting proms could provide opportunities to improve patient-provider communication and enhance control over care for rheumatology patients who could most benefit.

Journal: Quality of life research : an international journal of quality of life aspects of treatment, care and rehabilitation (2021)
Publication types: Journal Article
Novel and noninvasive methods for in-home sleep measurement and subsequent state coding in 12-month-old infants.

Research studying the role of sleep in development abounds but focuses on global aspects of sleep like quality or timing.Far fewer studies include the ultradian cycle, or patterns of rem and non-rem (nrem), because doing so is costly in time and resources.In a complete, lab-based sleep study, individuals are monitored by a technician overnight while wearing a host of sensors to capture brain activity, eye and limb movement, and cardiorespiratory rates.There is a need for creative, minimally disruptive solutions to study sleep that do not compromise the richness and accuracy of the measurements.The current pilot study parsed down the physiological measures to only movement and cardiorespiratory rates, creating a protocol simple enough for caregivers to incorporate into bedtime.Ten 12-month-old infants (+/- 3 weeks) wore an actigraph and wireless cardiorespiratory sensor for five nights of data collection.Of this, 92% were useable data.Actigraphy was analyzed with the sadeh algorithm to delineate sleep from wake.Heart rate and respiration were then used to state score visually or via an algorithm; greater variability demarcated rem from nrem.Time spent in each state was compared between scoring methods as well as to published results from age matched infants who underwent polysomnography (psg).Visually scored data, using a 1-hour viewing window, was in line with peer's psg values.To automatically state score, epoch-by-epoch cardiorespiratory and actigraphy files were produced for each minute of data collection.Heart and respiratory rates were transformed into z-scores and iterations of scoring, using increasingly greater z score thresholds, were compared to determine which identified state proportions most similar to data collected with psg.Based on these results, our novel method appears to be a feasible choice for studying the ultradian cycle.The combination of actigraphy and cardiorespiratory monitoring is uniquely advantageous because it is less resource intensive and more naturalistic, being put on by caregivers while still resulting in high rates of good data.Taken together, it is a quality option for infant researchers interested in incorporating sleep into their paradigms.

Journal: Infant behavior & development (2022)
Publication types: Journal Article;Research Support, U.S. Gov't, Non-P.H.S.;Research Support, Non-U.S. Gov't
Pharmacology of Diosmin, a Citrus Flavone Glycoside: An Updated Review.

Flavonoids are phytochemicals that are well known for their beneficial pharmacological properties.Diosmin is a flavone glycoside derived from hesperidin, a flavanone abundantly found in citrus fruits.Daflon is an oral phlebotonic flavonoid combination containing diosmin and hesperidin (9:1) that is commonly used for the management of blood vessel disorders.After oral administration, diosmin is converted to diosmetin, which is subsequently absorbed and esterified into glucuronide conjugates that are excreted in the urine.Pharmacological effects of diosmin have been investigated in several in vitro and in vivo studies, and it was found to possess anti-inflammatory, antioxidant, antidiabetic, antihyperlipidemic, and antifibrotic effects in different disease models.Diosmin also demonstrated multiple desirable properties in several clinical studies.Moreover, toxicological studies showed that diosmin has a favorable safety profile.Accordingly, diosmin is a potential effective and safe treatment for many diseases.However, diosmin exhibits inhibitory effects on different metabolic enzymes.This encourages the investigation of its potential therapeutic effect and safety in different diseases in clinical trials, while taking potential interactions into consideration.

Journal: European journal of drug metabolism and pharmacokinetics (2022)
Publication types: Journal Article;Review
Health care workers' perspectives on care for patients with injection drug use associated infective endocarditis (IDU-IE).

Despite high morbidity and mortality, patients with injection drug use associated infective endocarditis (idu-ie) lack standardized care, and experience prolonged hospitalization and variable substance use disorder (sud) management.Our study's objective was to elicit perspectives of health care workers (hcws) who deliver care to this population by understanding their perceived patient, provider, and system-level resources and barriers.Methods this qualitative study included interviews of hcws providing care to patients with idu-ie from january 2017 to december 2019 at a single midwest academic center.Based on electronic medical record queries to determine high and low rates of referral to sud treatment, hcws were selected using stratified random sampling followed by convenience sampling of non-physician hcws and a patient.Study participants were recruited via email and verbal consent was obtained.The final sample included 11 hospitalists, 3 specialists (including 2 cardiovascular surgery providers), 3 case managers, 2 social workers, 1 nurse, and 1 patient.Qualitative semi-structured interviews explored challenges and resources related to caring for this population.Qualitative data analysis (qda) minor lite was used for thematic data using an inductive approach.Results three major thematic categories emerged relative to patient-level barriers (e.g., pain control, difficult patient interactions, social determinants of health), provider-level barriers (e.g., inequity, expectations for recovery, varying levels of hope, communication style, prescribing medication for sud), and system-level barriers (e.g., repeat surgery, placement, resources for sud and mental health).The need to address underlying sud was a prominent theme.Conclusion practical steps we can take to improve treatment for this population include training and coaching hcws on a more person-centered approach to communication and transparent decision-making around pain management, surgery decisions, and expectations for sud treatment.

Journal: BMC health services research (2022)
Publication types: Journal Article
Selected predictors of parental satisfaction with child nursing care in paediatric wards in Poland-Cross-sectional study.

Assessment of parental satisfaction with child nursing is the key issue in evaluation of the care quality, enabling the adjustment of the services provided to the needs and expectations of recipients, and thus ensuring safety and achieving better long-term health effects.Aim assessment of parental satisfaction with child nursing in paediatric wards including its determinants.Material and methods the study covered 1030 parents of children hospitalised in paediatric and surgical wards of seven hospitals of different levels of health security in poland.The polish adaptation of the empathic standardised questionnaire for assessment of the level of parents' satisfaction with nursing care, developed by latour et al.And the self-constructed summary of socio-demographic data were applied in the study.Results more than 90% of respondents expressed high level of satisfaction with nurses' availability, the lowest, but still high score of respondents' satisfaction was observed for parental participation.The highest satisfaction was observed among the parents of children at the preschool, early school and puberty stage, admitted to the hospital on the elective basis, referred for diagnostic assessment and with the length of hospital stay less than 7 and longer than 28 days.Achieving preschool age was the strongest factor which increased assessment of satisfaction in most domains.Conclusions there is a need for optimising nursing care especially in the area of parental participation.The nursing care' quality improvement plan in paediatric departments should focus particularly on early childhood patients and their parents who are the most critical in satisfaction' assessment.

Journal: PloS one (2021)
Publication types: Journal Article