syedzayyan/paper_mill_benchmark huggingface dataset:
Hierarchical Ridge Regression for Incorporating Prior Information in Genomic Studies.

There is a great deal of prior knowledge about gene function and regulation in the form of annotations or prior results that, if directly integrated into individual prognostic or diagnostic studies, could improve predictive performance.For example, in a study to develop a predictive model for cancer survival based on gene expression, effect sizes from previous studies or the grouping of genes based on pathways constitute such prior knowledge.However, this external information is typically only used post-analysis to aid in the interpretation of any findings.We propose a new hierarchical two-level ridge regression model that can integrate external information in the form of "meta features" to predict an outcome.We show that the model can be fit efficiently using cyclic coordinate descent by recasting the problem as a single-level regression model.In a simulation-based evaluation we show that the proposed method outperforms standard ridge regression and competing methods that integrate prior information, in terms of prediction performance when the meta features are informative on the mean of the features, and that there is no loss in performance when the meta features are uninformative.We demonstrate our approach with applications to the prediction of chronological age based on methylation features and breast cancer mortality based on gene expression features.

Journal: Journal of data science : JDS (2022)
Publication types: Journal Article
ESTIMATION OF PREDICTORS AND DEVELOPMENT OF PROGNOSTIC MODEL FOR COMORBID COURSE OF DIABETES MELLITUS AND ISCHEMIC HEART DISEASE.

The aim: to determine predictors and develop the model of prognosis of comorbidity of ischemic heart disease and type 2 diabetes mellitus.Patients and methods materials and methods: 126 patients were involved in the study and divided into three groups.Main group involved 70 patients with comorbid t2dm and ihd; comparison group included 36 ihd-only patients; 20 patients were included into control group.Results results: predictors of comorbid t2dm and ihd included titin (or = 0.001 [95.0 % ci 0.001-0.105], р = 0.021); i and ii grade hypertension (respectively or = 28.993 [95.0 % cі 1.595-526.940], р = 0.023 and or = 19.050 [95.0 % cі 1.078-336.620], р = 0.044); left ventricle hypertrophy (or = 3.169 [95.0 % cі 1.103-3.108], р = 0.032); very low density cholesterol level (or = 49.032 [95.0 % cі 4.155-578.644], р = 0.022); and stenocardia symptoms in significant physical load (or = 6.199 [95.0 % cі 1.129-34.039], р = 0.036).Conclusion conclusions: developed model can be used in prediction of comorbid course of t2dm in patients with ihd for early diagnosis of cardiovascular complications in such patients.

Journal: Wiadomosci lekarskie (Warsaw, Poland : 1960) (2022)
Publication types: Journal Article
Methods for Assessment of the Glomerular Filtration Rate in Laboratory Animals.

The glomerular filtration rate (gfr), as the benchmark of renal function, has been widely used in clinical practice and basic medical research.Currently, most researchers still rely on endogenous markers, such as plasma creatinine, blood urea nitrogen, and cystatin c, to evaluate renal function in laboratory animals.While inexpensive and simple to use, methods based on endogenous markers are often inaccurate and susceptible to several internal physiological factors.Thus, it is necessary to establish a method to precisely assess the gfr, especially when detecting early changes in gfr during acute kidney injury, and hyperfiltration usually caused by pregnancy or diabetic nephropathy.In addition, laboratory animals have higher tolerance for invasive procedures than humans, allowing novel technologies to be applied on them for gfr monitoring.In recent years, significant progress has been made in developing new methods to assess gfr in animals.However, no publication has reviewed these techniques.Summary this article summarized the majority of methods used to assess the gfr in animals in recent decades and discussed their working principles, workflows, advantages, and limitations, providing a wealth of reference and information for researchers interested in studying the kidney function in animals and developing techniques to monitor the gfr.

Journal: Kidney diseases (Basel, Switzerland) (2022)
Publication types: Journal Article;Review
Organic chloramines formation from algal organic matters: Insights from Fourier transform-ion cyclotron resonance mass spectrometry.

Release of algal organic matter (aom) from algae poses great threats to drinking water safety.As organic nitrogen in aom is relatively higher compared to natural organic matter (nom), the organic chloramine formation during chlorination cause overestimation of effective chlorine, which may lead to a biological risk.This study compared the organic chloramine formation from aom and nom, and confirmed that aom tend to form more organic chloramines during chlorination.Furthermore, it was found that hydrophilic fraction and high molecular weight (>100 k da) fraction of aom generated major organic chloramines due to a high content of protein.Based on the results of fourier transform ion cyclotron resonance mass spectrometry (ft-icr ms), spearman's rank correlation was used to analyze the relationship between molecular composition of aom and organic chloramine formation.Notably, molecules with high correlation to organic chloramine formation located in a triangle region of van krevelen diagram, which is a typical area of peptides.Therefore, it indicates that the precursors of organic chloramine in aom are mainly proteins/peptides, and appropriate treatment processes (e.g., biological treatment or membrane filtration) should be addressed to effectively remove the precursors before chlorination.

Journal: Water research (2021)
Publication types: Journal Article
Special Anaesthetic Considerations for Brain Tumour Surgery in Children.

Brain tumours are among the most common neoplasm in children.Therefore, paediatric anaesthesiologists face the challenge of neurosurgical interventions in all age groups.To minimize perioperative mortality and morbidity, a comprehensive understanding of age-dependent differences in anatomy and cerebrovascular physiology is a mandatory prerequisite.Advances in subspeciality training in paediatric neurosurgery and paediatric anaesthesia may improve clinical outcomes and advance communication between the teams.

Journal: Children (Basel, Switzerland) (2022)
Publication types: Journal Article;Review
Respiratory and C4-photosynthetic NAD-malic enzyme coexist in bundle sheath cell mitochondria and evolved via association of differentially adapted subunits.

In plant mitochondria, nicotinamide adenine dinucleotide-malic enzyme (nad-me) has a housekeeping function in malate respiration.In different plant lineages, nad-me was independently co-opted in c4 photosynthesis.In the c4 cleome species, gynandropsis gynandra and cleome angustifolia, all nad-me genes (nad-meα, nad-meβ1, and nad-meβ2) were affected by c4 evolution and are expressed at higher levels than their orthologs in the c3 species tarenaya hassleriana.In t.Hassleriana, the nad-me housekeeping function is performed by two heteromers, nad-meα/β1 and nad-meα/β2, with similar biochemical properties.In both c4 species, this role is restricted to nad-meα/β2.In the c4 species, nad-meα/β1 is exclusively present in the leaves, where it accounts for most of the enzymatic activity.Gynandropsis gynandra nad-meα/β1 (gg nad-meα/β1) exhibits high catalytic efficiency and is differentially activated by the c4 intermediate aspartate, confirming its role as the c4-decarboxylase.During c4 evolution, nad-meβ1 lost its catalytic activity; its contribution to the enzymatic activity results from a stabilizing effect on the associated α-subunit and the acquisition of regulatory properties.We conclude that in bundle sheath cell mitochondria of c4 species, the functions of nad-me as c4 photosynthetic decarboxylase and as a housekeeping enzyme coexist and are performed by isoforms that combine the same α-subunit with differentially adapted β-subunits.

Journal: The Plant cell (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Jorge Lobo's disease with malignant degeneration to squamous cell carcinoma: case report.

Jorge lobo's disease (jld) is a chronic, granulomatous fungal infection caused by the traumatic implantation of the fungus lacazia loboi in the cutaneous and subcutaneous tissues, with the presence of isolated nodular and coalescent keloidal lesions.Malignant degeneration is rare.This case report describes a 64-year-old male patient with jld for 30-years who showed a change in the aspect of a lesion in the left lower limb.Histopathological examination confirmed the progression to well-differentiated squamous cell carcinoma (ssc).Jld is highly prevalent in tropical and subtropical regions, requiring monitoring concerning the transformation into ssc in long-term lesions.

Journal: Anais brasileiros de dermatologia (2022)
Publication types: Case Reports;Journal Article
Photoluminescence enhancement study in a Bi-doped Cs2AgInCl6double perovskite by pressure and temperature-dependent self-trapped exciton emission.

Here, we report a halide precursor acid precipitation method to synthesize cs2ag in1-x bix cl6(x= 0, 0.02, 0.04, 0.08, 0.16, 0.32, 0.64, and 1) microcrystals.Cs2ag in cl6and bi derivative double perovskites show broadband white light emissionviaself-trapped excitons (stes) and have achieved the highest internal quantum efficiency of up to 52.4% atx= 0.08.Synchrotron x-ray diffraction confirmed the linear increase of lattice parameters and cell volume with bi3+substitution at in3+sites.Absorbance, photocurrent excitation, and photoluminescence excitation spectra are used to observe possible transitions from the valence to the conduction band or free exciton (fe) states as well as transitions within local bi3+states.The broadband photoluminescence is quenchedviaa single nonradiative process with an activation energy δe= 1490 cm-1for cs2ag in0.92bi0.08cl6.Under normal conditions, we observed ste emission, but applying external pressure alters the electronic structure such that at elevated pressure, the only emissionviathe fe state is observed.We anticipate that structure, temperature and pressure-dependent photoluminescence studies will help the future use of a single-source lead-free double perovskite for white light-emitting diode applications.

Journal: Dalton transactions (Cambridge, England : 2003) (2022)
Publication types: Journal Article
Resonant Annihilation and Positron Bound States in Benzene.

Positrons attach to molecules in vibrationally resonant two-body collisions that result in greatly enhanced annihilation rates.Measurements of annihilation as a function of positron energy are presented for benzene using a cryogenic, trap-based beam.They establish a positron binding energy of 132±3 me v to test state-of-the-art theoretical calculations, and they exhibit many unexpected resonances, likely due to combination and overtone vibrational modes.The relationship of these results to the unique π-bonded structure of benzene is discussed.

Journal: Physical review letters (2022)
Publication types: Journal Article
Palliative care models for patients living with advanced cancer: a narrative review for the emergency department clinician.

Eighty-one percent of persons living with cancer have an emergency department (ed) visit within the last 6 months of life.Many cancer patients in the ed are at an advanced stage with high symptom burden and complex needs, and over half is admitted to an inpatient setting.Innovative models of care have been developed to provide high quality, ambulatory, and home-based care to persons living with serious, life-limiting illness, such as advanced cancer.New care models can be divided into a number of categories based on either prognosis (e.g., greater than or less than 6 months), or level of care (e.g., lower versus higher intensity needs, such as intravenous pain/nausea medication or frequent monitoring), and goals of care (e.g., cancer-directed treatment versus symptom-focused care only).We performed a narrative review to (1) compare models of care for seriously ill cancer patients in the ed and (2) examine factors that may hasten or impede wider dissemination of these models.

Journal: Emergency cancer care (2022)
Publication types: Journal Article;Review
Systematic review reveals urgent need to homogenize endpoints choices and definitions in marginal zone lymphomas trials.

Marginal zone lymphoma (mzl) is a heterogeneous disease and has various end-point measures.Our aim was to describe the endpoints used in trials involving patients with mzl.We searched over the last 35 years via pub med, the cochrane library, clinicaltrials.govandclinicaltrialsregister.eu for published and registered clinical trials using the keyword "marginalzone lymphoma." we excluded studies focusing on pediatric populations, cutaneous mzl and on use of allogenic stem cell transplant.Endpoints were reviewed as well as their influencing factors and their definitions.Among 1192 references q7 dentified by initial screening, 309 references were included (111 published, 198 registered), with 213 (69%) phase 2, 65 (21%) phase 1/2 and 31 (10%) phase 3 trials.The majority were open-label (n1⁄4295, 95%) non-randomized (n1⁄4256, 83%) trials, concerned all subtypes of mzls at once (n1⁄4239, 77%), and were often merged with non-mzl patients (n1⁄4232, 75%).Among phase 1/2 and 2 trials, overall/complete response rate (orr/crr) (n1⁄4196, 70.5%) and progression-free survival (pfs,n1⁄428, 10.1%) were the most used primary endpoints; in phase 3 trials pfs was the most used primary endpoint (n1⁄418, 58.1%; orr/crr n1⁄46, 19.4%, p<0.001).Overall, the most frequent secondary endpoints were overall survival (os, n1⁄4153, 50%), pfs (n1⁄4142, 46%) and orr/crr (n1⁄4116, 38%).Distribution was similar when considering trials with only patients with mzl.Endpoints definitions were inconsistent across published trials (up to 9 definitions per endpoint).Trials involving patients with mzl showed marked heterogeneity both in the choice and definitions of primary and secondary endpoints, thus hampering comparability between trials.

Journal: Leukemia & lymphoma (2022)
Publication types: Journal Article;Systematic Review;Research Support, Non-U.S. Gov't
Impacts of COVID-19 on individuals' mobility behavior in Pakistan based on self-reported responses.

The covid-19 pandemic has been extremely disturbing mobility behavior due to travel restrictions and perceived covid-19 threats.Recently, researchers from developed countries have shown interest in quantifying the impacts of the covid-19 on individuals' mobility; however, similar research themes in lower income developing countries like pakistan have not been sufficiently explored.Therefore, the objectives of the study are; 1) to explore the changes in self-reported individual's mobility behavior-trip frequencies by mode and by purpose in three covid-19 severity periods; 2) to quantify the effects of respondents' personal (i.e., age, gender, education, and living place), and perceived details (i.e., safety perceptions, the covid-19 threat perceptions) on the change in mobility behavior in the covid-19 severity change; 3) to analyze the willingness to use public transportation in the post-pandemic period.Methods a web-based questionnaire survey was conducted from september 2020 to november 2020, resulting in 565 responses.Descriptive analysis, random parameter bivariate probit modeling, and structural equation modeling are adopted to achieve the objectives.Results the results reflect the change in individuals' mobility behavior in three severity periods of covid-19, including before outbreak, during the most serious period, and after the most serious period.A substantial reduction in individuals' mobility was observed during the most serious period, which is recovering back to normal.The results also indicate the relationship of individuals' personal and perceived characteristics with the change in mobility in covid-19 severity changes from before-to-serious and from the serious-to-after most serious period.Conclusion the covid-19 pandemic has been affecting individuals' mobility behavior in pakistan.The study's findings provide insightful information for the transportation agencies to better prepare for sustainable transportation management in the post-pandemic era.

Journal: Journal of transport & health (2021)
Publication types: Journal Article
Epidemiological analysis of lower limb revascularization for peripheral arterial disease over 12 years on the public healthcare system in Brazil.

Worldwide, peripheral arterial disease (pad) is a disorder with high morbidity, affecting more than 200 million people.Objectives our objective was to analyze surgical treatment for pad provided on the brazilian public healthcare system over 12 years using publicly available data.Methods the study was conducted with analysis of data available on the brazilian health ministry's database platform, assessing distributions of procedures and techniques over the years and their associated mortality and costs.Results a total of 129,424 procedures were analyzed (performed either for claudication or critical ischemia, proportion unknown).The vast majority of procedures were endovascular (65.49%) and this disproportion exhibited a rising trend (p<0.001).There were 3,306 in-hospital deaths (mortality of 2.55%), with lower mortality in the endovascular group (1.2% vs.5.0%, p=0.008).The overall governmental expenditure on these procedures was u$ 238,010,096.51, and endovascular procedures were on average significantly more expensive than open surgery (u$ 1,932.27 vs.U$ 1,517.32; p=0.016).Conclusions lower limb revascularizations were performed on the brazilian public healthcare system with gradually increasing frequency from 2008 to 2019.Endovascular procedures were vastly more common and were associated with lower in-hospital mortality rates, but higher procedure costs.

Journal: Jornal vascular brasileiro (2022)
Publication types: Journal Article
Special Issue: Cholinergic Control of Inflammation.

Inflammation caused by infection, tissue trauma, and disease states such as arthritis and inflammatory bowel disease is perceived by the central nervous system (cns) through different routes that, by means of neural reflex circuits, regulate the immune system response [...].

Journal: International journal of molecular sciences (2022)
Publication types: Editorial
MHD mixed convective stagnation point flow of nanofluid past a permeable stretching sheet with nanoparticles aggregation and thermal stratification.

Using a thermally stratified water-based nanofluid and a permeable stretching sheet as a simulation environment, this research examines the impact of nanoparticle aggregation on mhd mixed convective stagnation point flow.Nanoparticle aggregation is studied using two modified models: the krieger-dougherty and the maxwell-bruggeman.The present problem's governing equations were transformed into a solvable mathematical model utilizing legitimate similarity transformations, and numerical solutions were then achieved using shooting with runge-kutta fehlberg (rkf) technique in mathematica.Equilibrium point flow toward permeable stretching surface is important for the extrusion process because it produces required heat and mass transfer patterns and identifies and clarifies fragmented flow phenomena using diagrams.Nanoparticle volume fraction was shown to have an impact on the solutions' existence range, as well.Alumina and copper nanofluids have better heat transfer properties than regular fluids.The skin friction coefficients and nusselt number, velocity, temperature profiles for many values of the different parameters were obtained.In addition, the solutions were shown in graphs and tables, and they were explained in detail.A comparison of the current study's results with previous results for a specific instance is undertaken to verify the findings, and excellent agreement between them is observed.

Journal: Scientific reports (2022)
Publication types: Journal Article
Clinicopathological analysis and outcomes of inflammatory myofibroblastic tumours of the urinary bladder.

S to describe clinical, imaging, and histopathological characteristics of inflammatory myofibroblastic tumour (imt) of the urinary bladder and provide initial management and surveillance recommendations.Patients and methods we identified patients with imt of the bladder treated at our facility from 1998 to 2020.Categorical variables were analysed with chi-square and fisher's exact tests and continuous variables with the mann-whitney u-test.Kaplan-meier analysis was performed for recurrence-free survival.Results imt was diagnosed in 35 patients with median (interquartile range [iqr]) follow-up of 20 (11.5-68.5) months.At initial diagnosis 86% were clinically organ-confined, 9% locally advanced, and 5% metastatic.Majority of patients (92%) had residual disease on re-staging transurethral resection (tur).Of the 15 patients with organ-confined disease managed initially with tur alone, five (33%) recurred at a median (iqr) of 5 (3.0-5.5) months from initial diagnosis.Presentation with visible haematuria was associated with recurrence (100% in recurrence vs 40% in non-recurrence groups, p = 0.044).There were no patients who developed a recurrence beyond 6 months after diagnosis.Partial or radical cystectomy was required in 23% and 9% of patients, respectively.One patient presented with metastatic disease associated with anaplastic lymphoma kinase (alk) translocation and achieved a durable complete remission with 7 months of crizotinib therapy.Conclusions no patient with imt treated with aggressive endoscopic management developed recurrences beyond 6 months.There were additionally no recurrences noted after definitive radical or partial cystectomy.These data support organ sparing therapy with aggressive endoscopic management and short-term surveillance in patients with localised imt, with extirpative surgery reserved for refractory cases.

Journal: BJU international (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't