syedzayyan/paper_mill_benchmark huggingface dataset:
Head and Neck Squamous Cell Carcinoma in Elderly Patients: Role of Radiotherapy and Chemotherapy.

Head and neck squamous cell carcinomas (hnscc) constitute the sixth most common malignancy worldwide, with approximately 25-40% of the diagnosed patients older than 70 years.Hnscc patients are often frail and frequently have multiple comorbidities due to their unhealthy lifestyle, and evidence suggests that older patients may receive less aggressive and suboptimal treatment than younger patients with the same disease status.The aim of this review is to depict and summarize the evidence regarding the different strategies that can be used in the clinical management of elderly hnscc patients.Key references were derived from a pub med query.Hand searching and clinicaltrials.gov were also used.This paper contains a narrative report and a critical discussion of clinical approaches in the context of elderly hnscc.

Journal: Cancers (2022)
Publication types: Journal Article;Review
Educational Outcomes of Childhood Survivors of Critical Illness-A Population-Based Linkage Study.

S major postintensive care sequelae affect up to one in three adult survivors of critical illness.Large cohorts on educational outcomes after pediatric intensive care are lacking.We assessed primary school educational outcomes in a statewide cohort of children who survived picu during childhood.Design multicenter population-based study on children less than 5 years admitted to picu.Using the national assessment program-literacy and numeracy database, the primary outcome was educational achievement below the national minimum standard (nms) in year 3 of primary school.Cases were compared with controls matched for calendar year, grade, birth cohort, sex, socioeconomic status, aboriginal and torres strait islander status, and school.Multivariable logistic regression models to predict educational outcomes were derived.Setting tertiary picus and mixed icus in queensland, australia.Patients children less than 5 years admitted to picu between 1998 and 2016.Interventions not applicable.Measurements and main results year 3 primary school data were available for 5,017 picu survivors (median age, 8.0 mo at first picu admission; interquartile range, 1.9-25.2).Picu survivors scored significantly lower than controls across each domain (p < 0.001); 14.03% of picu survivors did not meet the nms compared with 8.96% of matched controls (p < 0.001).In multivariate analyses, socioeconomic status (odds ratio, 2.14; 95% ci, 1.67-2.74), weight (0.94; 0.90-0.97), logit of pediatric index of mortality-2 score (1.11; 1.03-1.19), presence of a syndrome (11.58; 8.87-15.11), prematurity (1.54; 1.09-2.19), chronic neurologic conditions (4.38; 3.27-5.87), chronic respiratory conditions (1.65; 1.24-2.19), and continuous renal replacement therapy (4.20; 1.40-12.55) were independently associated with a higher risk of not meeting the nms.Conclusions in this population-based study of childhood picu survivors, 14.03% did not meet nmss in the standardized primary school assessment.Socioeconomic status, underlying diseases, and severity on presentation allow risk-stratification to identify children most likely to benefit from individual follow-up and support.

Journal: Critical care medicine (2022)
Publication types: Journal Article;Multicenter Study;Research Support, Non-U.S. Gov't
Software Architecture Patterns for Extending Sensing Capabilities and Data Formatting in Mobile Sensing.

Mobile sensing—that is, the ability to unobtrusively collect sensor data from built-in phone and attached wearable sensors—have proven to be a powerful approach to understanding the behavior, well-being, and health of people in their everyday life.Different platforms for mobile sensing have been presented and significant knowledge on how to facilitate mobile sensing has been accumulated.However, most existing mobile sensing platforms only support a fixed set of mobile phone and wearable sensors which are `built into’ the platform’s generic `study app’.This creates some fundamental challenges for the creation and approval of application-specific mobile sensing studies, since there is little support for adapting the sensing capabilities to what is needed for a specific study.Moreover, most existing platforms use their own proprietary data formats and there is no standardization in how data are collected and in what formats.This poses some fundamental challenges to realizing the vision of using mobile sensing in health applications, since mobile sensing data collected across different phones and studies cannot be compared, thus hampering generalizability and reproducibility across studies.This paper presents two software architecture patterns enabling (i) dynamic extension of mobile sensing to incorporate new sensing capabilities, such as collecting data from a wearable sensor, and (ii) handling real-time transformation of data into standardized data formats.These software patterns are derived from our work on carp mobile sensing (cams), which is a cross-platform (android/i os) software architecture providing a reactive and unified programming model that emphasizes extensibility.This paper shows how the framework uses the two software architecture patterns to add sampling support for an electrocardiography (ecg) device and support data transformation into the new open m health (omh) data format.The paper also presents data from a small study, demonstrating the robustness and feasibility of using cams for data collection and transformation in mobile sensing.

Journal: Sensors (Basel, Switzerland) (2022)
Publication types: Journal Article
Automatic identification of scientific publications describing digital reconstructions of neural morphology.

Motivation the increasing number of peer-reviewed publications constitutes a challenge for biocuration.For example, neuro morpho.org, a sharing platform for digital reconstructions of neural morphology, must evaluate more than 6000 potentially relevant articles per year to identify data of interest.Here, we describe a tool that uses natural language processing and deep learning to assess the likelihood of a publication to be relevant for the project.Results the tool automatically identifies articles describing digitally reconstructed neural morphologies with high accuracy.Its processing rate of 900 publications per hour is not only amply sufficient to autonomously track new research, but also allowed the successful evaluation of older publications backlogged due to limited human resources.The number of bio-entities found since launching the tool almost doubled while greatly reducing manual labor.The classification tool is open source, configurable, and simple to use, making it extensible to other biocuration projects.Availability relevancy.Contact ascoli@gmu.edu.Supplementary information supplementary information, tool installation, and api usage are available at

Journal: bioRxiv : the preprint server for biology (2023)
Publication types: Preprint;Journal Article
Using saturated absorption for superresolution laser scanning transmission microscopy.

We improved the three-dimensional spatial resolution of laser scanning transmission microscopy by exploiting the saturated absorption of dye molecules.The saturated absorption is induced by the high-intensity light irradiation and localises the signal within the centre of the focal spot.Our numerical calculation indicates that the spatial resolution in transmission imaging is significantly improved for both lateral and axial directions using nonlinear transmitted signals induced by saturated absorption.We experimentally demonstrated the improvement of the three-dimensional resolution by observing fine structures of stained rat kidney tissues, which were not able to be visualised by conventional laser scanning transmission microscopy.

Journal: Journal of microscopy (2022)
Publication types: Journal Article
Worker adjustment to unexpected occupational risk: Evidence from COVID-19.

We study the link between the revelation of a hitherto non-existent occupational risk - mortality due to the covid-19 pandemic in 2020 - and subsequent worker behaviour.We link occupation-specific data on covid-19 mortality to individual level data sets.We find that wages did not adjust, but workers started leaving high-risk occupations during 2020.These effects are stronger for workers not affected by lockdowns or working from home orders and for those considered to be clinically vulnerable to covid-19 and are not driven by negative health shocks or employer-initiated separations.Occupation-level results suggest that employment began to rebound in 2021.

Journal: European economic review (2022)
Publication types: Journal Article
Facile preparation of all-cellulose composites from softwood, hardwood, and agricultural straw cellulose by a simple route of partial dissolution.

In this study, we report a novel, facile, and green method that was used for creating a new all-cellulose composite (acc) based on inorganic molten salt solvent.Three representatively native fibers from softwood (pinus kesiya), hardwood (eucalyptus globulus), and agricultural straw (zea mays) were selected to verify the effect of the method.The welded sheets were thoroughly characterized and compared.Cellulose sheets from the pine exhibited excellent mechanical properties (σb 16.94 mpa) and thermal stability (tmax265 °c) after the welding process, while the corn stalk sheets displayed more robust and thermostable features than the eucalyptus.The welding technique using inorganic metal salt hydrate provides a promising and convenient route to obtain firm sheet-materials with micro- or nano-structures from nature fibers.

Journal: Carbohydrate polymers (2021)
Publication types: Journal Article
Chromatin Mechanisms Driving Cancer.

The change in cell state from normal to malignant is driven fundamentally by oncogenic mutations in cooperation with epigenetic alterations of chromatin.These alterations in chromatin can be a consequence of environmental stressors or germline and/or somatic mutations that directly alter the structure of chromatin machinery proteins, their levels, or their regulatory function.These changes can result in an inability of the cell to differentiate along a predefined lineage path, or drive a hyperactive, highly proliferative state with addiction to high levels of transcriptional output.We discuss how these genetic alterations hijack the chromatin machinery for the oncogenic process to reveal unique vulnerabilities and novel targets for cancer therapy.

Journal: Cold Spring Harbor perspectives in biology (2022)
Publication types: Journal Article;Review
Serial transplantation unmasks galectin-9 contribution to tumor immune escape in the MB49 murine model.

Mechanisms of tumor immune escape are quite diverse and require specific approaches for their exploration in syngeneic tumor models.In several human malignancies, galectin-9 (gal-9) is suspected to contribute to the immune escape.However, in contrast with what has been done for the infiltrating cells, the contribution of gal-9 produced by malignant cells has never been demonstrated in an animal model.Therefore, we derived isogenic clones-either positive or negative for gal-9-from the mb49 murine bladder carcinoma cell line.A progressive and consistent reduction of tumor growth was observed when gal-9-ko cells were subjected to serial transplantations into syngeneic mice.In contrast, tumor growth was unaffected during parallel serial transplantations into nude mice, thus linking tumor inhibition to the enhancement of the immune response against gal-9-ko tumors.This stronger immune response was at least in part explained by changing patterns of response to interferon-γ.One consistent change was a more abundant production of cxcl10, a major inflammatory factor whose production is often induced by interferon-γ.Overall, these observations demonstrate for the first time that serial transplantation into syngeneic mice can be a valuable experimental approach for the exploration of novel mechanisms of tumor immune escape.

Journal: Scientific reports (2021)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Study of Ageing in Complex Interface Interaction Tasks: Based on Combined Eye-Movement and HRV Bioinformatic Feedback.

Human-computer interaction tends to be intelligent and driven by technological innovation.However, there is a digital divide caused by usage barriers for older users when interacting with complex tasks.To better help elderly users efficiently complete complex interactions, a smart home's operating system's interface is used as an example to explore the usage characteristics of elderly users of different genders.This study uses multi-signal physiological acquisition as a criterion.The results of the study showed that: (1) older users are more attracted to iconic information than textual information.(2) when searching for complex tasks, female users are more likely to browse the whole page before locating the job.(3) female users are more likely to browse from top to bottom when searching for complex tasks.(4) female users are more likely to concentrate when performing complex tasks than male users.(5) males are more likely to be nervous than females when performing complex tasks.

Journal: International journal of environmental research and public health (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Quantification of large and middle proteins of hepatitis B virus surface antigen (HBsAg) as a novel tool for the identification of inactive HBV carriers.

Among individuals with chronic hepatitis b, those with hepatitis b e-antigen (hbe ag)-negative chronic hepatitis (chb) can be difficult to distinguish from those with hbe ag-negative chronic hbv infection, also referred to as inactive hbv carriers (ics), but both require different medical management.The level of hbv surface antigen (hbs ag) has been proposed as a marker to discriminate between chronic infection and hepatitis stages.Hbs ag consists of large, middle and small hbs.The aim of this study was to determine whether the composition of hbs ag improved the identification of ics among hbs ag-positive subjects with different phases of hbv infections.Design hbv large surface proteins (lhbs) and hbv middle surface proteins (mhbs) were quantified in serum samples from 183 clinically well-characterised untreated patients with acute (n=14) hbv infection, ics (n=44), chbs (n=46), chronic hbe ag-positive phase (n=68) and hepatitis delta coinfection (n=11) using an elisa, with well-defined monoclonal antibodies against the pre s1 domain (lhbs) and the pre s2-domain (mhbs).A western blot analysis was used to verify the quantitation of the components of hbs ag.Total hbs ag was quantified using a modified commercially available assay (hbs ag v.6.0, enzygnost, siemens, erlangen).Results the composition of hbs ag showed specific patterns across different phases of hepatitis b.Individuals in the ic phase had significantly lower proportions of lhbs and mhbs than patients in acute or chronic phases irrespective of their hbv e-antigen status (p<0.0001) or hbs ag level.Both lhbs and mhbs ratios better predicted the ic phase than total hbs ag levels.Conclusion quantification of mhbs, particularly lhbs represents a novel tool for the identification of the ic stage.

Journal: Gut (2018)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Brominated flame retardants and organochlorine pesticides and incidence of uterine leiomyomata: A prospective ultrasound study.

Uterine leiomyomata (ul) are hormone-responsive benign neoplasms.Brominated flame retardants and organochlorine pesticides (ocps) can disrupt hormones involved in ul etiology.Methods the study of environmental, lifestyle, and fibroids is a detroit-area prospective cohort of 1693 black women 23-35 years of age.At baseline and approximately every 20 months for 5 years, women completed questionnaires and underwent transvaginal ultrasounds.Using a case-cohort study design, we selected 729 ul-free participants at baseline and analyzed baseline plasma samples for polybrominated diphenyl ethers (pbdes), a polybrominated biphenyl ether (pbb-153), and ocps.We used cox proportional hazard models to estimate hazard ratios (hrs) and 95% confidence intervals (cis).Results compared with total pbde plasma concentrations <50th percentile, adjusted hrs for the 50th-74th, 75th-89th, and ≥90th percentiles were 1.00 (95% ci = 0.68, 1.47), 1.04 (95% ci = 0.63, 1.68), and 0.85 (95% ci = 0.48, 1.50), respectively.Hrs for pbb-153 plasma concentrations were generally similar to total pbde plasma concentrations.Compared with total ocp plasma concentrations <50th percentile, hrs for the 50th-74th, 75th-89th, and ≥90th percentiles were 0.86 (95% ci = 0.57, 1.29), 0.73 (95% ci = 0.43, 1.22), and 0.58 (95% ci = 0.32, 1.04), respectively.Hrs for individual pbdes and ocps were similar to their respective totals.Conclusion we found little support for an association between brominated flame retardant plasma concentrations and ul incidence, and some evidence of lower ul incidence with the highest ocp plasma concentrations.

Journal: Environmental epidemiology (Philadelphia, Pa.) (2021)
Publication types: Journal Article
Urological issues following gender reassignment surgery.

It has been estimated that 0.2% of the uk population identifies as transgender.For those who seek gender reassignment, the pathway can involve the expertise of multiple disciplines, including primary care, psychology, endocrinology and speech and language therapy.A small but significant number of the transgender population will also elect to undergo gender-affirming genital surgery in order to achieve gender congruence.In the uk, very few specialist centres provide genital gender-affirming surgery for trans-men and women.The population accessing these services spans the entire uk, and with such geographical dispersion, trans-patients with uro-genital complications after surgery in both the short and long term are likely to present locally, with initial assessment/management often conducted in a non-specialist setting.This article aims to help familiarise nurses with genital gender reassignment/affirming surgery and the resultant altered anatomy.It explores the urological issues trans-men and women may experience as a consequence of surgery.

Journal: British journal of nursing (Mark Allen Publishing) (2017)
Publication types: Journal Article
Association of +1923C > T, -1112C > T and +2044A > G Polymorphisms in IL-13 Gene with Susceptibility to Pediatric Asthma: A Systematic Review and Meta-Analysis.

Previous studies have provided conflicting evidence implicating the il-13 polymorphism and pediatric asthma.Thus, we performed a meta-analysis to combine and analyze the available studies to provide more accurate conclusions.methods:a comprehensive retrieval in pub med, embase, web of science, and cnki was performed up to february 05, 2020.results:a total of 39 case-control studies including 15 studies with 4,968 cases and 7,091 controls were on +1923 c > t, ten studies with 3,175 cases and 2,983 controls on -1112 c > t, and 14 studies with 4,476 cases and 5,121 controls on +2044 a > g were selected.Pooled data showed that the il-13 + 1923 c > t, -1112 c > t and +2044 a > g polymorphisms were significantly associated with risk of pediatric asthma.The il-13 + 1923 c > t (asians and africans), -1112 c > t (caucasians) and +2044 a > g (asians) polymorphisms were more frequently associated in these ethnic groups.conclusions:our pooled data indicated that il-13 + 1923 c > t, -1112 c > t and +2044 a > g polymorphisms were correlated with risk of pediatric asthma.

Journal: Fetal and pediatric pathology (2022)
Publication types: Journal Article;Meta-Analysis;Systematic Review
Associations of conflict and migration on childhood cognitive development in Ethiopia: Evidence from a longitudinal study.

Migration has substantial consequences on the wellness of affected households, thereby exposing children to circumstances that are detrimental for healthy cognitive development.This study evaluates the relationship between conflict and migration during conception or early childhood and childhood cognitive development outcomes among families in ethiopia.We hypothesized that migration is associated with worse cognitive development outcomes among children and that this association is mediated by educational disparities and caregiver psychological distress.Methods the study used longitudinal data of children enrolled in the young lives study (yls) conducted in ethiopia during 2002 (age 1), 2006-2007 (age 5), and 2009-2010 (age 8).We used multivariate linear and logistic regression to analyze the association between migration on cognitive development during middle childhood.Household migration and caregiver psychological distress were measured during round 1, type of education was measured at round 2, and cognitive development was measured at round 3.Results results of the multivariate regression analysis showed that migrant children achieved lower scores on a test of verbal intelligence after controlling for sex, ethnicity, religion, and caregiver distress (β: -8.09; 95% ci: -15.33, -0.85).Results of the mediation analysis show that the type of schooling that children attended, but not caregiver psychological distress, mediated the association between migration and cognitive development.Migrant children were more likely to attend private schools, which buffered the association between migration and lower cognitive development.Conclusions this study suggests that migration is a key determinant of childhood cognitive development among migrated populations.More research is needed to build the evidence base to support interventions for this growing, underserved population.

Journal: Journal of child psychology and psychiatry, and allied disciplines (2022)
Publication types: Journal Article
Modelling and Characterisation of Residual Stress of SiC-Ti3C2TxMXene Composites Sintered via Spark Plasma Sintering Method.

This article presents an attempt to determine the effect of the mxene phase addition and its decomposition during sintering with the use of the spark plasma sintering method on mechanical properties and residual stress of silicon carbide based composites.For this purpose, the unreinforced silicon carbide sinter and the silicon carbide composite with the addition of 2 wt.% of ti3c2txwere tested.The results showed a significant increase of fracture toughness and hardness for composite, respectively 36% and 13%.The numerical study involving this novel method of modelling shows the presence of a complex state of stress in the material, which is related to the anisotropic properties of graphitic carbon structures formed during sintering.An attempt to determine the actual values of residual stress in the tested materials using raman spectroscopy was also made.These tests showed a good correlation with the constructed numerical model and confirmed the presence of a complex state of residual stress.

Journal: Materials (Basel, Switzerland) (2022)
Publication types: Journal Article
Social Autonomy and Family-Based Informed Consent.

The western focus on personal autonomy as the normative basis for securing persons' consent to their treatment renders this autonomy-based approach to informed consent vulnerable to the charge that it is based on an overly atomistic understanding of the person.This leads to a puzzle: how does this generally-accepted atomistic understanding of the person fits with the emphasis on familial consent that occurs when family members are provided with the opportunity to veto a prospective donor's wish to donate after she has died and her organs are being considered for harvesting?It is argued in this paper that this charge can be met and this puzzle dissolved once it is recognized that autonomy is an inherently social concept.

Journal: The Journal of medicine and philosophy (2019)
Publication types: Journal Article