syedzayyan/paper_mill_benchmark huggingface dataset:
Long-term prognostic impact of anticoagulation on patients with atrial fibrillation undergoing hemodialysis.

Introduction and objectives evidence for the efficacy and safety of oral anticoagulation with dicumarines in patients with atrial fibrillation (af) on hemodialysis is controversial.The aim of our study is to evaluate the long-term prognostic implications of anticoagulation with dicumarines in a cohort of patients with non-valvular af on a hemodialysis program due to end-stage renal disease.Methods retrospective, observational study with consecutive inclusion of 74 patients with af on hemodialysis.The inclusion period was from january 2005 to october 2016.The primary variables were all-cause mortality, non-scheduled readmissions and bleeding during follow-up.Results mean age was 75±10 years; 66.2% were men and 43 patients (58.1%) received acenocoumarol.During a median follow-up of 2.40 years (iqr=0.88-4.15), acenocoumarol showed no survival benefit [hr=0.76, 95% ci (0.35-1.66), p=0.494].However, anticoagulated patients were at increased risk of recurrent cardiovascular hospitalizations [irr=3.94, 95% ci (1.06-14.69), p=0.041].There was a trend towards an increase in repeated hospitalizations of ischemic cause in anticoagulated patients [irr=5.80, 95% ci (0.86-39.0), p=0.071].There was a statistical trend towards a higher risk of recurrent total bleeding in patients treated with acenocoumarol [irr=4.43, 95% ci (0.94-20.81), p=0.059].Conclusions in this study, oral anticoagulation with acenocoumarol in patients with af on hemodialysis did not increase survival.However, it was associated with an increased risk of hospitalizations of cardiovascular causes and a tendency to an increased risk of total bleeding.

Journal: Nefrologia (2018)
Publication types: Journal Article;Observational Study
Mass spectrometric analysis of chondroitin sulfate-linked peptides.

Chondroitin sulfate proteoglycans (cspgs) are extracellular matrix components composed of linear glycosaminoglycan (gag) side chains attached to a core protein.Cspgs play a vital role in neurodevelopment, signal transduction, cellular proliferation and differentiation and tumor metastasis through interaction with growth factors and signaling proteins.These pleiotropic functions of proteoglycans are regulated spatiotemporally by the gag chains attached to the core protein.There are over 70 chondroitin sulfate-linked proteoglycans reported in cells, cerebrospinal fluid and urine.A core glycan linker of 3-6 monosaccharides attached to specific serine residues can be extended by 20-200 disaccharide repeating units making intact cspgs very large and impractical to analyze.The current paradigm of cspg analysis involves digesting the gag chains by chondroitinase enzymes and analyzing either the protein part, the disaccharide repeats, or both by mass spectrometry.This method, however, provides no information about the site of attachment or the composition of linker oligosaccharides and the degree of sulfation and/or phosphorylation.Further, the analysis by mass spectrometry and subsequent identification of novel cspgs is hampered by technical challenges in their isolation, less optimal ionization and data analysis.Unknown identity of the linker oligosaccharide also makes it more difficult to identify the glycan composition using database searching approaches.Following chondroitinase digestion of long gag chains linked to tryptic peptides, we identified intact gag-linked peptides in clinically relevant samples including plasma, urine and dermal fibroblasts.These intact glycopeptides including their core linker glycans were identified by mass spectrometry using optimized stepped higher energy collision dissociation and electron-transfer/higher energy collision dissociation combined with hybrid database search/de novo glycan composition search.We identified 25 cspgs including three novel cspgs that have not been described earlier.Our findings demonstrate the utility of combining enrichment strategies and optimized high-resolution mass spectrometry analysis including alternative fragmentation methods for the characterization of cspgs.Supplementary information the online version contains supplementary material available at .

Journal: Journal of proteins and proteomics (2022)
Publication types: Journal Article
Ensemble Linear Subspace Analysis of High-Dimensional Data.

Regression models provide prediction frameworks for multivariate mutual information analysis that uses information concepts when choosing covariates (also called features) that are important for analysis and prediction.We consider a high dimensional regression framework where the number of covariates (p) exceed the sample size (n).Recent work in high dimensional regression analysis has embraced an ensemble subspace approach that consists of selecting random subsets of covariates with fewer thanpcovariates, doing statistical analysis on each subset, and then merging the results from the subsets.We examine conditions under which penalty methods such as lasso perform better when used in the ensemble approach by computing mean squared prediction errors for simulations and a real data example.Linear models with both random and fixed designs are considered.We examine two versions of penalty methods: one where the tuning parameter is selected by cross-validation; and one where the final predictor is a trimmed average of individual predictors corresponding to the members of a set of fixed tuning parameters.We find that the ensemble approach improves on penalty methods for several important real data and model scenarios.The improvement occurs when covariates are strongly associated with the response, when the complexity of the model is high.In such cases, the trimmed average version of ensemble lasso is often the best predictor.

Journal: Entropy (Basel, Switzerland) (2021)
Publication types: Journal Article
Meta-analysis: analysis of mechanistic pathways in the treatment of non-alcoholic steatohepatitis. Evidence from a Bayesian network meta-analysis.

And aims non-alcoholic steatohepatitis (nash) is the most common cause of liver disease.However, there is lack of comparison of efficacy between different nash drug classes.We conducted a network meta-analysis evaluating drug classes through comparing histological outcomes and targets of drugs.Approach and results medline, embase and central were searched for randomised controlled trials evaluating nash drugs in biopsy-proven nash patients.Primary outcomes included nash resolution without worsening of fibrosis, at least 2-point reduction in non-alcoholic fatty liver disease activity score (nas) without worsening of fibrosis and at least 1-point reduction in fibrosis.Treatments were classified into inflammation, energy, bile acid and fibrosis modulators.The analysis was conducted with bayesian network model and surface under the cumulative ranking curve (sucra) analysis.Among 49 included trials, treatments modulating energy (risk ratio (rr): 1.92, credible intervals (crl): 1.59-2.34) were most likely to achieve nash resolution followed by treatments modulating fibrosis (rr 1.66, crl: 0.65-4.50), bile acids (rr: 1.37, crl: 0.99-1.92) and inflammation (rr: 1.00, crl: 0.75-1.33).Energy and bile acids modulation were effective in at least 2-point nas reduction without worsening of fibrosis (rr: 1.52, crl 1.30-1.77; rr: 1.69, crl 1.41-2.03) and at least 1-point reduction in fibrosis (rr: 1.26, crl:1.05-1.49; rr: 1.54, crl: 1.20-1.97).Conclusions this network analysis demonstrates the relative superiority of drugs modulating energy pathways and bile acids in nash treatment.This guides the development and selection of drugs for combination therapies.

Journal: Alimentary pharmacology & therapeutics (2022)
Publication types: Journal Article;Meta-Analysis
Phytochemical Characterization and Biological Evaluation ofOriganum vulgareL. Essential Oil Formulated as Polymeric Micelles Drug Delivery Systems.

This study presents phytochemical characterization and biological evaluation of origanum vulgare l.Essential oil (oeo) formulated as polymeric micelles drug delivery systems as a possible non-invasive approach for the management of skin tags.Gc-ms analysis of romanian oeo revealed the identification and quantification of 43 volatile compounds (thymol and carvacrol being the main ones).The antioxidant activity was shown by four consecrated methods: cuprac, abts, orac and dpph.Oeo was incorporated by micellar solubilization into a binary hydrogel based on a pluronic f 127/l 31 block-copolymers mixture.The p h, consistency, spreadability, particle size, polydispersity index and zeta potential of the oeo-loaded poloxamer-based binary hydrogel (oeo-pb h) were investigated.Oeo-pb h was skin compatible in terms of p h and exhibited adequate spreadability and consistency.The minimal inhibitory concentrations of the tested oeo were similar to those obtained for the formulation, lower (2.5 μg/m l) for yeast and higher (40-80 μg/m l) for gram-negative bacilli.As keratinocytes are among main components of skin tags, an in vitro evaluation was conducted in order to see the effect of the formulation against ha ca t human keratinocytes.Oeo-pb h decreased ha ca t cells migration and proliferation and elicited a cytotoxic and pro-apoptotic effect in a dose- and time-dependent manner.No harmful effect on the viability of dendritic cells (dcs) was detected following the incubation with different concentrations (0-200 μg/m l) of the 5% formulation.Treatment in inflammatory dcs (+lps) indicated a decrease in cytokine production of il-6, tnf-α and il-23 but no significant effect on il-10 in any of the tested concentrations.

Journal: Pharmaceutics (2022)
Publication types: Journal Article
Postsynthetic Modification of NU-1000 for Designing a Polyoxometalate-Containing Nanocomposite with Enhanced Third-Order Nonlinear Optical Performance.

For the advancement of laser technologies and optical engineering, various types of new inorganic and organic materials are emerging.Metal-organic frameworks (mofs) reveal a promising use in nonlinear optics, given the presence of organic linkers, metal cluster nodes, and possible delocalization of π-electron systems.These properties can be further enhanced by the inclusion of solely inorganic materials such as polyoxometalates as prospective low-cost electron-acceptor species.In this study, a novel hybrid nanocomposite, namely, si w12@nu-1000 composed of si w12(h4si w12o40) and zr-based mof (nu-1000), was assembled, completely characterized, and thoroughly investigated in terms of its nonlinear optical (nlo) performance.The third-order nlo behavior of the developed system was assessed by z-scan measurements using a 532 nm laser.The effect of two-photon absorption and self-focusing was significant in both nu-1000 and si w12@nu-1000.Experimental studies suggested a much superior nlo performance of si w12@nu-1000 if compared to that of nu-1000, which can be assigned to the charge-energy transfer between si w12and nu-1000.Negligible light scattering, good stability, and facile postsynthetic fabrication method can promote the applicability of the si w12@nu-1000 nanocomposite for various optoelectronic purposes.This research may thus open new horizons to improve and enhance the nlo performance of mof-based materials through π-electron delocalization and compositing metal-organic networks with inorganic molecules as electron acceptors, paving the way for the generation of novel types of hybrid materials for prospective nlo applications.

Journal: Inorganic chemistry (2022)
Publication types: Journal Article
Negative Effects of Annealed Seed Layer on the Performance of ZnO-Nanorods Based Nitric Oxide Gas Sensor.

Nitric oxide (no) is a toxic gas, which is dangerous for human health and causes many respiratory infections, poisoning, and lung damage.In this work, we have successfully grown zn o nanorod film on annealed zn o seed layer in different ambient temperatures, and the morphology of the nanorods sensing layer that affects the gas sensing response to nitric oxide (no) gas were investigated.To acknowledge the effect of annealing treatment, the devices were fabricated with annealed seed layers in air and argon ambient at 300 °c and 500 °c for 1 h.To simulate a vertical device structure, a silver nanowire electrode covered in zn o nanorod film was placed onto the hydrothermal grown zn o nanorod film.We found that annealing treatment changes the seed layer's grain size and defect concentration and is responsible for this phenomenon.The i-v and gas sensing characteristics were dependent on the oxygen defects concentration and porosity of nanorods to react with the target gas.The resulting as-deposited zn o seed layer shows better sensing response than that annealed in an air and argon environment due to the nanorod morphology and variation in oxygen defect concentration.At room temperature, the devices show good sensing response to no concentration of 10 ppb and up to 100 ppb.Shortly, these results can be beneficial in the no breath detection for patients with chronic inflammatory airway disease, such as asthma.

Journal: Sensors (Basel, Switzerland) (2022)
Publication types: Journal Article
Systemic Inflammation and Activation of Haemostasis Predict Poor Prognosis and Response to Chemotherapy in Patients with Advanced Lung Cancer.

Systemic inflammation and activation of haemostasis are common in patients with lung cancer.Both conditions support tumour growth and metastasis.Therefore, inflammatory and haemostatic biomarkers might be useful for prediction of survival and therapy response.Patients with unresectable/metastatic lung cancer initiating 1st-line chemotherapy (n= 277, 83% non-small cell lung cancer) were followed in a prospective observational cohort study.A comprehensive panel of haemostatic biomarkers (d-dimer, prothrombin fragment 1+2, soluble p-selectin, fibrinogen, coagulation factor viii, peak thrombin generation), blood count parameters (haemoglobin, leucocytes, thrombocytes) and inflammatory markers (neutrophil-lymphocyte ratio, lymphocyte-monocyte ratio, platelet-lymphocyte ratio, c-reactive protein) were measured at baseline.We assessed the association of biomarkers with mortality, progression-free-survival (pfs) and disease-control-rate (dcr).A biomarker-based prognostic model was derived.Selected inflammatory and haemostatic biomarkers were strong and independent predictors of mortality and therapy response.The strongest predictors (d-dimer, lmr, crp) were incorporated in a unified biomarker-based prognostic model (1-year overall-survival (os) by risk-quartiles: 79%, 69%, 51%, 24%; 2-year-os: 53%, 36%, 23%, 8%; log-rankp< 0.001).The biomarker-based model further predicted shorter pfs and lower dcr.In conclusion, inflammatory and haemostatic biomarkers predict poor prognosis and treatment-response in patients with advanced lung cancer.A biomarker-based prognostic score efficiently predicts mortality and disease progression beyond clinical characteristics.

Journal: Cancers (2020)
Publication types: Journal Article
Genetics of Gene Expression in the Aging Human Brain Reveal TDP-43 Proteinopathy Pathophysiology.

Here, we perform a genome-wide screen for variants that regulate the expression of gene co-expression modules in the aging human brain; we discover and replicate such variants in the tmem106b and rbfox1 loci.The tmem106b haplotype is known to influence the accumulation of tar dna-binding protein 43 k da (tdp-43) proteinopathy, and the haplotype's large-scale transcriptomic effects include the dysregulation of lysosomal genes and alterations in synaptic gene splicing that are also seen in the pathophysiology of tdp-43 proteinopathy.Further, a variant near grn, another tdp-43 proteinopathy susceptibility gene, shows concordant effects with the tmem106b haplotype.Leveraging neuropathology data from the same participants, we also show that tmem106b and apoe-amyloid-β effects converge to alter myelination and lysosomal gene expression, which then contributes to tdp-43 accumulation.These results advance our mechanistic understanding of the tmem106b tdp-43 risk haplotype and uncover a transcriptional program that mediates the converging effects of apoe-amyloid-β and tmem106b on tdp-43 aggregation in older adults.

Journal: Neuron (2020)
Publication types: Journal Article;Research Support, N.I.H., Extramural;Research Support, Non-U.S. Gov't
Acute epiglottitis is a rare clinical presentation of coronavirus disease 2019: a case report.

In humans, coronavirus disease 2019 (covid-19) has a variable presentation ranging from mild self-limiting respiratory tract infections to severe acute respiratory distress syndrome.Methods: we present the case of a patient who developed acute epiglottitis after surgery for an intracranial tumour and was subsequently diagnosed with covid-19.Results a 58-year-old female patient developed acute-onset respiratory distress on day 6 after intracranial surgery.Neck computed tomography revealed near-total airway obstruction due to severe edoema of the epiglottis and periepiglottis.The patient's sars-co v-2 polymerase chain reaction test was positive.Viral respiratory tract panel and sputum and blood cultures were negative.She completed the antiviral and antibacterial treatment regimens recommended by the chest disease department.Conclusions we conclude that epiglottitis can be an unusual manifestation of covid-19.

Journal: Infectious diseases (London, England) (2022)
Publication types: Case Reports;Journal Article
Comparison of fracture resistance of endodontically treated maxillary first premolar with mesio-occlusal-distal access restored with composite resin, fiber post, and prefabricated metal posts restored with/without full-coverage metal crowns.

A myriad of materials and procedures have been recommended for restoring the root-filled teeth with significant loss of tooth structure and the most common method being the use of "posts." material and methods a mesio-occluso-distal preparation was done on eighty intact maxillary first premolars, followed by access preparation and cleaning and shaping with rotary files.All samples were obturated and divided into four groups (n= 20).In group 1, 3-mm gutta-percha was removed and restored using composite resin; group 2 - group 1 + crowns; group 3 - prefabricated fiber post + crowns; and group 4 - prefabricated metal post + crowns.All the groups were subdivided into eight groups (n= 10), fractured with 90° vertical and 45° oblique loading by a universal testing machine.Statistical analysis fracture resistance was analyzed and compared by means of two-factorial two-way analysis of variance and scheffe'spost hoctest.Results under 90° loading, the fracture load of teeth restored with the nayyar's composite resin core and crown was greatest.Under 45° loading, the fracture load of teeth restored with prefabricated metallic posts was significantly (p< 0.05) less than that in other groups.Under 45° load, group with fiber post exhibited significantly (p< 0.05) more number of favorable fractures than other groups.Conclusion under the conditions of vertical and oblique loadings, fiber post and composite resin core with a full-coverage crown is the most effective restorative modality for protecting the remaining tooth structure in pulpless teeth.

Journal: Journal of conservative dentistry : JCD (2021)
Publication types: Journal Article
Psychological complications in patients with acromegaly: relationships with sex, arthropathy, and quality of life.

Current treatment of acromegaly restores a normal life expectancy in most cases.So, the study of persistent complications affecting patients' quality of life (qo l) is of paramount importance, especially motor disability and depression.In a large cohort of acromegalic patients we aimed at establishing the prevalence of depression, to look for clinical and sociodemographic factors associated with it, and to investigate the respective roles (and interactions) of depression and arthropathy in influencing qo l.Methods one hundred and seventy-one acromegalic patients (95 women and 76 men, aged 20-85 years) among those recruited in a cross-sectional italian multicentric study were investigated.Each patient filled in three validated questionnaires: acro qo l, womac (measuring articular pain, stiffness and functionality), and aims (evaluating articular symptoms and depression).Results a very high (up to 28%) depression rate was detected in acromegalic subjects.Two patients showing pathological aims depression scores, committed suicide during the three years observational period.In our population poor psychological status was significantly associated with female sex.Furthermore, a significant strong correlation was found between aims depression score and womac score.Both depression and arthropathy-related motor disability turned out to independently contribute with similar strength to the impairment of qo l.Conclusions we report a high prevalence of depression in acromegaly, which is associated with female sex and arthropathy.Both depression and arthropathy strongly and independently contribute to the impaired qo l of patients.Our study shows that assessment and monitoring of psychological status is mandatory in acromegaly, also suggesting an inexpensive tool for this assessment.

Journal: Endocrine (2022)
Publication types: Journal Article
Perinatal unusual rhabdomyoma location - case report and systematic reviews of the literature.

To report a case of prenatal diagnosis of cardiac rhabdomyoma (cr) and neonatal surgical treatment as well as undertaking a systematic review of the literature to determine most frequent localization of cr, common signs and symptoms, associated pathologies, incidence of surgery, and prognoses for cr.methods:we conducted systematic review of the literature on cr that were diagnosed and treated in the perinatal period, searching for english language articles in the pub med/medline database that were published within the past 20 years, using the following search terms: "cardiac rhabdomyoma"; "neonates"; "newborn"; "surgery".results:eighty-two studies were selected, but only 46 studies met the inclusion criteria.After birth, the majority of newborns were asymptomatic; however, murmurs and arrhythmia were also the two most prevalent signs of cr.The most prevalent location was the ventricles, corresponding to 40.3% of all cases, with 53% of these having a rhabdomyoma in the left ventricle.The incidence of multiple tumors was 56%, and in those cases the location of tumors was also most common in the ventricles.Tuberous sclerosis was the most commonly associated pathology, being present in 72% of cases of cr.Surgical treatment occurred in 27% of cases, and 3% of cases required surgery and prostaglandin.Regarding the perinatal outcome, 6% of cases resulted in fetal or neonatal death.conclusion:cr are benign tumors which tend to spontaneously regress during early childhood but may have unfavorable outcomes in the presence of obstructive lesions and arrhythmias.Surgery is generally necessary in symptomatic patients.

Journal: The journal of maternal-fetal & neonatal medicine : the official journal of the European Association of Perinatal Medicine, the Federation of Asia and Oceania Perinatal Societies, the International Society of Perinatal Obstetricians (2021)
Publication types: Case Reports;Journal Article;Systematic Review