syedzayyan/paper_mill_benchmark huggingface dataset:
Application of a Statistical and Linear Response Theory to Multi-Ion Na+Conduction in NaChBac.

Biological ion channels are fundamental to maintaining life.In this manuscript we apply our recently developed statistical and linear response theory to investigate na+ conduction through the prokaryotic na+ channel na ch bac.This work is extended theoretically by the derivation of ionic conductivity and current in an electrochemical gradient, thus enabling us to compare to a range of whole-cell data sets performed on this channel.Furthermore, we also compare the magnitudes of the currents and populations at each binding site to previously published single-channel recordings and molecular dynamics simulations respectively.In doing so, we find excellent agreement between theory and data, with predicted energy barriers at each of the four binding sites of ∼4,2.9,3.6, and 4k t.

Journal: Entropy (Basel, Switzerland) (2021)
Publication types: Journal Article
Immune sunrise: from the immunome to the cancer immune landscape.

The complex dynamics of the tumor-immune interaction during tumor progression have been characterized by integrating genomic and proteomic experiments.The immunome, a reference compendium of markers for the majority of immune cell subpopulations was used to describe the immune landscape in cancer.The immune contexture is at the cornerstone in the success of cancer immunotherapies.Markers with the highest clinical relevance were summarized as the consensus immunoscore.This immune evaluation refines the prognosis of the patients and the chemotherapy decision-making process and was introduced as essential and desirable diagnostic criteria into three major international guidelines.

Journal: Oncoimmunology (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
GC/MS-Based Urine Metabolomics Study on the Ameliorative Effect ofXanthoceras sorbifoliaExtract on Alzheimer's Disease in Mice.

The cause of alzheimer's disease, the most common type of dementia today, is still unclear, and in current research, there are no drugs that work relatively well.Therefore, the study for new drugs to treat alzheimer's disease is an urgent research need.Research on the improvement of alzheimer's disease with extracts of xanthoceras sorbifoliahas been increasing in recent years, but the mechanism is not fully understood.The experiments were conducted to validate the model and analyze the treatment effect through d-galactose and aβ25-35induced dementia model mice, using the morris water maze, to detect the learning behavior and brain tissue section to observe the hippocampal tissue structure of mice.We performed a nontargeted metabolomic analysis of the urine obtained from different groups of mice using gas chromatography-mass spectrometry.Fourteen potential biomarkers were identified in the mice's urine, outlining five metabolic pathways of interest.It was shown that the extracts of xanthoceras sorbifoliamay exert protective effects on mice in dementia models through energy metabolism, neuroinflammation, and antioxidants.This study reveals the potential pathogenesis of alzheimer's disease and the possible therapeutic mechanism of xanthoceras sorbifolia, suggests relevant biomarkers, and provides an additional basis for the clinical application of xanthoceras sorbifolia.

Journal: Evidence-based complementary and alternative medicine : eCAM (2022)
Publication types: Journal Article
Masking Ability of the Combined Application of Opaquers and Resin Composite on Discolored Backgrounds.

The aim of this study was to evaluate the masking ability of a combined application of opaquers and resin composite over discolored backgrounds: a3, a3.5, c2, c3, and c4.The groups were divided according to the opaquer brand, the number of opaquer coats (one or two), and the thickness of the resin composite layer (0.5 or 1.0 mm).The color measurements were made by a reflectance spectrophotometer (sp60, ex-rite).The color difference between the opaquer + resin composite + background and a reference background was calculated using the ciede2000 formula.Anova and tukey's post hoc test (α=0.05) were used to analyze the δe00 mean values.A bivariate analysis was used to determine the association between dependent and independent variables.The masking ability was rated by the δe00 visual thresholds of acceptability and perceptibility (excellent match: δe00 ≤ 0.8; acceptable match: 0.8 5.4).The mean δe00 values ranged from 0.5 to 5.52.Masking ability was affected by the opaquer brand, thickness of the resin composite layer, and background shades.Most of the combinations that achieved either excellent or acceptable masking ability were obtained with combinations composed of one or two coats of opaquer and a 1.0-mm-thick resin composite layer for all backgrounds except c4.Acceptable results were also obtained for combinations with 0.5-mm-thick resin composite over c2, a3, and a3.5 backgrounds.

Journal: Operative dentistry (2022)
Publication types: Journal Article
Stability of maxillary anterior teeth after 2 years of retention in adolescents: a randomized controlled trial comparing two bonded and a vacuum-formed retainer.

Retention of the maxillary anterior teeth is commonly recommended to maintain the teeth in their corrected positions.Both fixed and removable retention methods are used, but the certainty of evidence is low.Objective to evaluate post-treatment changes in irregularity of the maxillary six anterior teeth and single tooth contact point discrepancy (cpd) of three different retention methods.Trial design three-arm parallel group single-centre randomized controlled trial.Materials and methods ninety patients, 54 girls and 36 boys, were recruited to the study.The inclusion criteria were adolescent patients treated with fixed appliances at least in the maxilla.After gaining informed consent from the patient and their custodians, the patients were randomized to one of three groups: bonded retainer 13-23, bonded retainer 12-22, and removable vacuum-formed retainer (vfr) covering the maxillary teeth including the second molars.The randomization, prepared by an independent person, used blocks of 30.The primary outcomes were changes in single cpd and little's irregularity index (lii) measured on digitalized three-dimensional study casts before and after 2-year retention.The study casts were anonymized before assessment and the changes were blinded for the assessor.Data were evaluated on an intention-to-treat basis.Thus, all randomized patients were incorporated into the final analysis.Results the lii and cpds increased slightly in all three groups without any statistically significant differences between the groups.The vfr group showed a small intercanine width increase and some more changes of canine rotations than in the other groups.Harms no harm was observed in any subjects and none of the patients needed retreatment.Limitations the trial was a single-centre study and short-term changes were evaluated.Conclusions all three retention methods showed equally effective retention capacity and all the changes found in the three groups were small and considered clinically insignificant.Thus, the null hypothesis was confirmed.All three methods can be recommended.Trial registration nct04616755.

Journal: European journal of orthodontics (2021)
Publication types: Journal Article;Randomized Controlled Trial;Research Support, Non-U.S. Gov't
Endophytic fungus Phomopsis sp. as a source of 3-nitropropionic acid with larvicidal activity against Aedes aegypti (Linnaeus 1762, Diptera: Culicidae).

Aedes aegypti is the primary vector of viruses, such as zika, chikungunya, yellow fever, and dengue.In this context, a biomonitored chemical study was conducted to evaluate the activity of the crude extract of the endophytic fungus phomopsis sp.Against the larvae of aedes aegypti.Methods crude extract, fractions, and isolated substances were evaluated in in-vitro assays against third-stage larvae of aedes aegypti.Results we isolated 3-nitropropionic acid with an lc50 of 15.172 ppm and lc90 of 18.178 ppm after 24 hours of larval exposure.Conclusions the results indicated that 3-nitropropionic acid exerted larvicidal activity.

Journal: Revista da Sociedade Brasileira de Medicina Tropical (2022)
Publication types: Journal Article
ERS International Congress 2021: highlights from the Epidemiology and Environment Assembly.

In this article, early career members of the epidemiology and environment assembly of the european respiratory society (ers) summarise a selection of four sessions from the society's 2021 virtual congress.The topics covered focus on chronic respiratory disease epidemiology, the health effects of tobacco and nicotine, and the respiratory health impact of environmental exposures and climate change.While the burden of chronic respiratory diseases such as copd is expected to increase in the next decades, research on modifiable risk factors remains key.The tobacco and nicotine research presented here focuses on recent evolutions in cigarette alternatives, including vaping and the use of heated tobacco products, and changes in behaviours related to the coronavirus disease 2019 pandemic.The 2021 world health organization air quality guidelines were also a major topic of the congress.Despite their benefits, challenges remain in driving and implementing environmental health policies to take into account the respiratory effects observed at very low air pollution concentrations, as well as the impact of climate change on environmental exposures.

Journal: ERJ open research (2022)
Publication types: Journal Article
Aging as a Productive Process: A Critical Analysis of Aging Policy in Newfoundland and Labrador, Canada.

There has been a growing focus on healthy aging in the political agenda.Discourses contained within policy documents have the potential to shape our notions of healthy aging and well-being.This comprehensive critical document analysis of provincial aging policies in newfoundland and labrador (2006-2015) contributes to a larger research study exploring aging women's notions of health and the body in relation to the aging process.The findings highlight how healthy aging discourses focus on the concept of productivity and how a certain type of health is required for ongoing contribution.The paper concludes by arguing that if healthy aging is framed around one's ability to remain productive, notions of health will remain limited to an externalized measure of output versus subjective experience of well-being.

Journal: Journal of aging & social policy (2022)
Publication types: Journal Article
Polystyrene microplastics induced oxidative stress, inflammation and necroptosis via NF-κB and RIP1/RIP3/MLKL pathway in chicken kidney.

Microplastics (mps) are a novel environment pollutant widespread among the natural environment, also causing damage to aquatic animals and mammals.However, their effects on the kidney of poultry are still unclear.In this study, chickens were exposure to the different doses of ps-mps (1, 10, 100 mg/l) for six weeks, with 1 mg/l being the environmental concentration.The effects of ps-mps on renal tissue damage in chicken were analyzed.Our results suggested that mps exposure causes mitochondrial morphology and dysbiosis (mfn1/2, opa1, drp1), mitochondrial structural damage by triggering imbalance in mitochondrial dynamics.Antioxidant enzyme (sod, cat, mda, gsh, t-aoc) activity was significantly altered, which in turn caused oxidative stress.H&e staining results showed damage and inflammation of chicken kidney.Mechanistically, the inflammation featured by activated nf-κb p65 and increased expression of pro-inflammatory factors (tnfα, i nos, il-1β and il-6).Moreover, ps-mps intake induced necroptosis through activated rip1/rip3/mlkl signaling pathway.In conclusion, our study was the first to show that oral intake of ps-mps induced inflammation and necroptosis in chicken kidney and the differences in damage were linked to the concentration of ps-mps.The purpose of this study provided theoretical support for the environmental risk assessment of ps-mps.

Journal: Toxicology (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
The First Total Synthesis of the Lipid Mediator PD2n-3 DPA.

The resolution of inflammation is governed by the active biosynthesis of specialized pro-resolving mediators using ω-6 and ω-3 polyunsaturated fatty acids as substrates.These mediators act as resolution agonists and display several interesting bioactivities.Pd2n-3 dpais an oxygenated polyunsaturated fatty acid biosynthesized from n-3 docosapentaenoic acid belonging to the specialized pro-resolving lipid mediator family named protectins.The protectins exhibit anti-inflammatory properties and pro-resolving bioactivities.These endogenously produced compounds are of interest as leads in resolution pharmacology and drug development.Herein, together with its nmr, ms, and uv data, a stereoselective total synthesis of pd2n-3 dpais presented.

Journal: Journal of natural products (2020)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Prediction of Recombination Spots Using Novel Hybrid Feature Extraction Method via Deep Learning Approach.

Meiotic recombination is the driving force of evolutionary development and an important source of genetic variation.The meiotic recombination does not take place randomly in a chromosome but occurs in some regions of the chromosome.A region in chromosomes with higher rate of meiotic recombination events are considered as hotspots and a region where frequencies of the recombination events are lower are called coldspots.Prediction of meiotic recombination spots provides useful information about the basic functionality of inheritance and genome diversity.This study proposes an intelligent computational predictor called i rspots-dnn for the identification of recombination spots.The proposed predictor is based on a novel feature extraction method and an optimized deep neural network (dnn).The dnn was employed as a classification engine whereas, the novel features extraction method was developed to extract meaningful features for the identification of hotspots and coldspots across the yeast genome.Unlike previous algorithms, the proposed feature extraction avoids bias among different selected features and preserved the sequence discriminant properties along with the sequence-structure information simultaneously.This study also considered other effective classifiers named support vector machine (svm), k-nearest neighbor (knn), and random forest (rf) to predict recombination spots.Experimental results on a benchmark dataset with 10-fold cross-validation showed that i rspots-dnn achieved the highest accuracy, i.e., 95.81%.Additionally, the performance of the proposed i rspots-dnn is significantly better than the existing predictors on a benchmark dataset.The relevant benchmark dataset and source code are freely available at: rspot_dnn/tree/master/i rspot_dnn.

Journal: Frontiers in genetics (2020)
Publication types: Journal Article
Identification of shared tumor epitopes from endogenous retroviruses inducing high-avidity cytotoxic T cells for cancer immunotherapy.

Human endogenous retroviruses (hervs) represent 8% of the human genome.Herv products may represent tumor antigens relevant for cancer immunotherapy.We developed a bioinformatic approach to identify shared cd8+t cell epitopes derived from cancer-associated hervs in solid tumors.Six candidates among the most commonly shared hla-a2 epitopes with evidence of translation were selected for immunological evaluation.In vitro priming assays confirmed the immunogenicity of these epitopes, which induced high-avidity cd8+t cell clones.These t cells specifically recognize and kill hla-a2+tumor cells presenting herv epitopes on hla molecules, as demonstrated by mass spectrometry.Furthermore, epitope-specific cd8+t cells were identified by dextramer staining among tumor-infiltrating lymphocytes from hla-a2+patients with breast cancer.Last, we showed that herv-specific t cells lyse patient-derived organoids.These shared virus-like epitopes are of major interest for the development of cancer vaccines or t cell-based immunotherapies, especially in tumors with low/intermediate mutational burden.

Journal: Science advances (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Pressure-induced coupled structural-electronic transition in SnS2under different hydrostatic environments up to 39.7 GPa.

A series ofin situhigh-pressure raman spectroscopy and electrical conductivity experiments have been performed to investigate the vibrational and electrical transport properties of sn s2under non-hydrostatic and hydrostatic environments.Upon compression, an coupled structural-electronic transition in sn s2occurred at 30.2 gpa under non-hydrostatic conditions, which was evidenced by the splitting of the egmode and the discontinuities in raman shifts, raman full width at half maximum (fwhm) and electrical conductivity.However, the coupled structural-electronic transition took place at a higher pressure of 33.4 gpa under hydrostatic conditions, which may be due to the influence of the pressure medium.Furthermore, our first-principles theoretical calculations results revealed that the bandgap energy of sn s2decreased slowly with increasing pressure and it closed in the pressure range of 30-40 gpa, which agreed well with our raman spectroscopy and electrical conductivity results.Upon decompression, the recoverable raman peaks and electrical conductivity indicated that the coupled structural-electronic transition was reversible, which was further confirmed by our hrtem observations.

Journal: RSC advances (2022)
Publication types: Journal Article
Comparison of performances of infliximab biosimilars CT-P13 versus SB2 in the treatment of inflammatory bowel diseases: a real-life multicenter, observational study in Italy.

To compare the performances of infliximab (ifx) biosimilar ct-p13 and sb2 in the treatment of inflammatory bowel diseases (ibd) outpatients in italy.Research design and methods three hundred and eighty ibd outpatients were retrospectively evaluated.The primary endpoint was to compare the two ifx biosimilars in terms of reaching and maintenance of remission at any timepoint.Results 197 patients with ulcerative colitis (uc) and 183 patients with crohn's disease (cd) treated with ct-p13 or sb2 and having a median (iqr) follow-up of 12 (6-36) months were compared: 230 (60.5%) were naïve to anti-tnfα, 20 (5.26%) were switched from ifx originator or from ifx ct-p13 to ifx sb2.Clinical remission was achieved in 133 (67.5%) uc patients and in 164 (89.6%) cd patients (p < 0.000), with no differences between ct-p13 and sb2 in the rate of remission in uc (p = 0.667) and cd (p = 0.286).Clinical response, steroid-free remission, rate of surgery, mucosal healing (mh) in uc, switching from ifx originator or from other biosimilar, and safety were similar.Higher mh rate was obtained in cd patients treated with ct-p13 (p = 0.004).Conclusion this first comparative study found that both ifx biosimilars ct-p13 and sb2 are effective and safe in managing ibd outpatients.

Journal: Expert opinion on biological therapy (2022)
Publication types: Journal Article;Multicenter Study;Observational Study
Nursing students' sense perception of communication in psychiatric hospital.

To analyze the sense perception of nursing students in the learning of communication in a psychiatric hospital.Method qualitative, exploratory and descriptive, from representative drawings of the communication perceived by the body senses of 23 nursing students, and recorded enunciation of the remarkable experiences after the end of the practical activities.The data were analyzed according to thematic content.Results the heart captures perceptions, favoring interpersonal relationships; smelling shows care lacking in hospitalization; vision monopolizes the impressions of reality, making the movements static; hearing is exercised in the amplitude to listen; touching demarcates limitations of contact and interaction; and tasting, as social sense, seeks to overcome the obstacles to take care.Conclusion the learning of communication was significant, making the psychiatric hospital a space to listen to what is inside, to find in the emotions and rationalities the sensations that can be inside and outside the tension nodes that interfere in the perceptions.

Journal: Revista brasileira de enfermagem (2018)
Publication types: Journal Article
Utility of cardiac magnetic resonance in the diagnosis of suspected "MINOCA": a case series and literature review.

Myocardial infarction with nonobstructive coronary artery (minoca) is a common condition in clinical practice with multiple specific causes, such as plaque rupture, plaque erosion, and epicardial coronary vasospasm.There must be an ischemic mechanism responsible for the myocyte injury and an exclusion of nonischemic mechanisms that can mimic myocardial infarction, and then a diagnosis of minoca can be made.Cardiac magnetic resonance (cmr) plays an essential role in the diagnosis and differential diagnosis of minoca, which cannot only exclude myocarditis, takotsubo syndrome, and cardiomyopathies, but also provide imaging confirmation of acute myocardial infarction.In this study, we presented 2 typical cases with the clinical presentation of acute myocardial infarction but normal or nonobstructive epicardial coronary arteries.Further cmr examinations showed different patterns of late gadolinium enhancement (lge) in these 2 cases, one case with subendocardial lge of the anterolateral wall and the other one with subepicardial lge of the lateral wall, which indicated 2 different mechanisms for the myocyte injury.Subsequently, these 2 patients received different treatment regimens and were discharged with improved symptoms.In conclusion, cmr should be a mandatory test in patients with suspected minoca, because it can not only make a clear diagnosis, but also play an important role in guiding clinical decision-making.

Journal: Radiology case reports (2022)
Publication types: Case Reports;Journal Article
3-Ketosphinganine provokes the accumulation of dihydroshingolipids and induces autophagy in cancer cells.

Although several reports describe the metabolic fate of sphingoid bases and their analogs, as well as their action and that of their phosphates as regulators of sphingolipid metabolizing-enzymes, similar studies for 3-ketosphinganine (ksa), the product of the first committed step in de novo sphingolipid biosynthesis, have not been reported.In this article we show that 3-ketosphinganine (ksa) and its dideuterated analog at c4 (d2ksa) are metabolized to produce high levels of dihydrosphingolipids in hgc27, t98g and u87mg cancer cells.In contrast, either direct c1 o-phosphorylation or n-acylation of d2ksa to produce dideuterated ketodihydrosphingolipids does not occur.We also show that cells respond to d2ksa treatment with induction of autophagy.Time-course experiments agree with sphinganine, sphinganine 1-phosphate and dihydroceramides being the mediators of autophagy stimulated by d2ksa.Enzyme inhibition studies support that inhibition of des1 by 3-ketobases is caused by their dihydroceramide metabolites.However, this effect contributes to increasing dihydrosphingolipid levels only at short incubation times, since cells respond to long time exposure to 3-ketobases with des1 overexpression.The translation of these overall effects into cell fate is discussed.

Journal: Molecular bioSystems (2016)
Publication types: Journal Article;Research Support, Non-U.S. Gov't