syedzayyan/paper_mill_benchmark huggingface dataset:
Struct2Graph: a graph attention network for structure based predictions of protein-protein interactions.

Development of new methods for analysis of protein-protein interactions (ppis) at molecular and nanometer scales gives insights into intracellular signaling pathways and will improve understanding of protein functions, as well as other nanoscale structures of biological and abiological origins.Recent advances in computational tools, particularly the ones involving modern deep learning algorithms, have been shown to complement experimental approaches for describing and rationalizing ppis.However, most of the existing works on ppi predictions use protein-sequence information, and thus have difficulties in accounting for the three-dimensional organization of the protein chains.Results in this study, we address this problem and describe a ppi analysis based on a graph attention network, named struct2graph, for identifying ppis directly from the structural data of folded protein globules.Our method is capable of predicting the ppi with an accuracy of 98.89% on the balanced set consisting of an equal number of positive and negative pairs.On the unbalanced set with the ratio of 1:10 between positive and negative pairs, struct2graph achieves a fivefold cross validation average accuracy of 99.42%.Moreover, struct2graph can potentially identify residues that likely contribute to the formation of the protein-protein complex.The identification of important residues is tested for two different interaction types: (a) proteins with multiple ligands competing for the same binding area, (b) dynamic protein-protein adhesion interaction.Struct2graph identifies interacting residues with 30% sensitivity, 89% specificity, and 87% accuracy.Conclusions in this manuscript, we address the problem of prediction of ppis using a first of its kind, 3d-structure-based graph attention network (code available at ).Furthermore, the novel mutual attention mechanism provides insights into likely interaction sites through its unsupervised knowledge selection process.This study demonstrates that a relatively low-dimensional feature embedding learned from graph structures of individual proteins outperforms other modern machine learning classifiers based on global protein features.In addition, through the analysis of single amino acid variations, the attention mechanism shows preference for disease-causing residue variations over benign polymorphisms, demonstrating that it is not limited to interface residues.

Journal: BMC bioinformatics (2022)
Publication types: Journal Article
Restoring Superconductivity in the Quantum Metal Phase of NbSe2Using Dissipative Coupling.

Localization arguments forbid the appearance of a metallic ground state in two dimensions.Yet, a large variety of disordered superconductors are known to manifest an anomalous metal phase in the zero temperature limit.While previous observations were confined to noncrystalline "dirty" superconductors, the recent observation of the so-called bose metal phase in crystalline thin flakes of nb se2has sparked off intense debate.While the exact nature of this phase remains unknown, it is thought that quantum fluctuations play a decisive role in bose metal physics.In this work, we study the response of the anomalous metal phase in thin flakes of nb se2to dissipative coupling.We evince a dramatic quenching of the bose metal phase when dissipative coupling is strong, fully restoring a zero resistance superconducting state in the entire region of the magnetic field (h)-temperature (t) phase diagram where the bose metal phase is otherwise observed.The suppression of the bose metal phase by dissipative coupling is possible only in a quantum system where dissipation can directly affect system thermodynamics.Our observation of a dissipative phase transition in two-dimensional nb se2firmly establishes the quantum nature of the anomalous metal phase in this class of "clean" superconductors.

Journal: Nano letters (2019)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Epidemiology of gastroenteropancreatic neuroendocrine neoplasms in Krakow and Krakow district in 2007-2011.

Introduction gastroenteropancreatic neuroendocrine neoplasms (gepnen) are rare and heterogeneous tumours with variable biology.The aim of this study was to evaluate the epidemiology of gepnen in the population of krakow and krakow district in 2007-2011.Material and methods the database of the chair and department of endocrinology, jagiellonian university medical college, comprising the data on nen cases collected from the endocrinology department, university hospital in krakow and from independent sources: surgery, pathology, and endocrinology departments located in the krakow area, was searched for cases of gepnen patients living in krakow and krakow district, diagnosed between 2007 and 2011.Eighty-eight such patients (39 males, 49 females, median age at diagnosis 59 ± 17 years) were identified and characterised.Results the mean follow-up time was 2.67 ± 1.6 years.The most frequent primary location of gepnen was small intestine (20%), followed by the appendix (18%), stomach (16%), pancreas (16%), rectum (15%), and colon (15%).Neng1 predominated (64%) in the analysed group.Most well-differentiated gepnen (63%) were diagnosed at stage i; however, 18% of them were diagnosed at stage iv.Metastases at diagnosis were found in 31% of patients.The gepnen incidence rate in 2007-2011 was 2.1/100000 inhabitants/year, without significant increase during the studied period.Conclusions gepnen incidence and epidemiology in the population of krakow and krakow district is similar to the incidence observed in most european countries.Registers are important tools to evaluate gepnen epidemiology.(endokrynol pol 2017; 68 (1): 42-46).

Journal: Endokrynologia Polska (2017)
Publication types: Journal Article
Transcranial alternating brain stimulation at alpha frequency reduces hemispatial neglect symptoms in stroke patients.

/objective non-invasive brain stimulation techniques such as transcranial alternating current stimulation (t acs) may help alleviate attention deficits in stroke patients with hemispatial neglect by modulating oscillatory brain activity.We applied high-definition (hd)-t acs at alpha frequency over the contralesional hemisphere to support unilateral oscillatory alpha activity and correct for the pathologically altered attention bias in neglect patients.Methods we performed a within-subject, placebo-controlled study in which sixteen stroke patients with hemispatial neglect underwent 10 hz (alpha) as well as sham (placebo) stimulation targeting the contralesional posterior parietal cortex.Attentional bias was measured with a computerized visual detection paradigm and two standard paper-and-pencil neglect tests.Results we revealed a significant shift of attentional resources after alpha-hd-t acs, but not sham t acs, toward the ipsilateral and thus contralesional hemifield leading to a reduction in neglect symptoms, measured with a computerized visual detection paradigm and a widely used standard paper and pencil neglect tests.Conclusions we showed a significant alpha-hd-t acs-induced shift of attentional resources toward the contralesional hemifield, thus leading to a reduction in neglect symptoms.Importantly, hd-t acs effects persisted after the stimulation itself had ended.This t acs protocol, based on intrinsic oscillatory processes, may be an effective and well-tolerated treatment option for neglect.

Journal: International journal of clinical and health psychology : IJCHP (2022)
Publication types: Journal Article
Psychosocial consequences of receiving false-positive colorectal cancer screening results: a qualitative study.

The objective of this study was to investigate the psychosocial consequences of receiving false-positive colorectal cancer (crc) screening results, following a positive immunochemical faecal occult blood test.design, setting, and subjects:we conducted a qualitative study with four semi-structured focus group interviews with 16 participants aged 50-74, all of whom had received a false-positive result in the national danish crc screening programme.We selected, recruited, and grouped participants to ensure maximum variation, and to enable a level of confidence to speak openly about experiences of screening.We subjected interview data, audio-recordings, and transcripts to a strategy of qualitative analysis called systematic text condensation.results:we identified four main themes which described the psychosocial consequences of false-positive crc screening results: anxiety; discomfort; changed self-perception and behaviour; and considerations on participation in screening.Each of these themes covered a wide range of experiences which were relevant to the informants and broadly shared by them in many aspects.conclusions:receiving false-positive results from crc screening can lead to negative psychosocial consequences such as changes in self-perception and anxiety: some participants may experience subsequent relief, others not.These negative psychosocial consequences might persist over time.implications:negative psychosocial consequences from false-positive crc screening results may result in a greater use of general practitioner services by healthy people who need reassurance or further tests.More research using condition-specific measures is required to further understand the degree and potential persistence of psychosocial consequences of false-positive results from crc screening.Key points participants who receive false-positive colorectal cancer (crc) screening results may experience negative psychosocial consequences e.g.Anxiety and subsequent relief.Participants who receive false-positive crc screening results may experience discomfort during the screening process.Participants who receive false-positive crc screening results may experience longer term changes of self-perception.Participants who receive false-positive crc screening results may experience ambivalence about the offered diagnostic down-stream procedures including colonoscopy.

Journal: Scandinavian journal of primary health care (2019)
Publication types: Journal Article
Health risk assessment and source apportionment of polycyclic aromatic hydrocarbons associated with PM10and road deposited dust in Ahvaz metropolis of Iran.

The objective of this study was to compare the characteristics of polycyclic aromatic hydrocarbons (pahs) in pm10and road dust samples, as well as to identify and quantify the contributions of each source profile using the positive matrix factorization (pmf) receptor model.Health risk assessment was carried out using toxic equivalency factors and incremental lifetime cancer risk (ilcr), which quantitatively estimate the exposure risk for age-specific groups.Pm10samples were collected on ptfe filters in the metropolitan area of ahvaz.Road dust samples were also collected from all over the urban areas with different land uses.Total pah concentrations in pm10and road dust samples were 0.5-25.5 ng/m3and 49.3-16,645 μg/kg, respectively.Pyrene was the highest pah in the pm10profile, whereas fluoranthene became the highest pah in the road dust.Abundance of benzo[ghi]perylene at pm10and road dust samples suggested a source indicator for traffic emissions.The results demonstrate that in 36.5% of samples, pm10concentrations exceed the maximum concentration level recommended by epa.A multiple linear regression model was used to estimate the influence of meteorological parameters (temperature, wind speed, and relative humidity) on buildup of pahs.All of pah species show higher concentrations during the cold and typical days rather than the dust event days and warm periods.Pmf analysis showed that vehicular emissions (50.6%) and industrial activities (especially steel industries) (30.4%) were first two sources of pahs bounded with pm10, followed by diesel emissions (11.6%) and air-soil exchange (7.4%).For road dust samples, three common sources were also identified: vehicular traffic (48%), industrial activities (42.3%), and petrogenic sources (9.7%), in line with that of diagnostic molecular ratios results.According to the results of health risk assessment model, the ilcr of exposure to pahs associated with pm10and road-deposited dust was higher than the guidelines of usepa, indicating high carcinogenic risk.

Journal: Environmental geochemistry and health (2019)
Publication types: Journal Article
Pd/Fe2O3with Electronic Coupling Single-Site Pd-Fe Pair Sites for Low-Temperature Semihydrogenation of Alkynes.

Dispersing single palladium atoms on a support is promising to minimize the usage of palladium and improve the selectivity for alkyne semihydrogenation, but its activity is often very low as a result of unfavorable h2activation.Here, we load palladium onto α-fe2o3(012) to construct highly active and stable single-site pd-fe pairs with luxuriant d-electron domination near the fermi level driven by strong electronic coupling and prove that pd-fe pairs cooperatively adsorb h2and dissociate an h─h bond, whereas solo pd sites enable preferential desorption of c═c intermediate, thus achieving both high activity and high selectivity for alkyne hydrogenation.This catalyst exhibits state-of-the-art performance in purifying acetylene of ethylene stream, with 99.6% and 100% conversion and 96.7% and 94.7% selectivity at 353 and 393 k, respectively, and excellent stability with negligible activity decay after a 200 h test.This single-site pair inherits the advantage but overcomes the weakness of both pd ensemble and single pd atoms, enabling ultralow-pd-loading catalysts for selective hydrogenation.

Journal: Journal of the American Chemical Society (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Comparison of Dietary Behaviors and the Prevalence of Metabolic Syndrome in Single- and Multi-Person Households among Korean Adults.

Changes in household dynamics in korea, such as the transition from multi- to single-person households, have led to changes in individuals' dietary behavior patterns and health status.Thus, this study aimed to compare dietary behaviors and determine the prevalence of metabolic syndrome (met s) as well as explore factors associated with met s according to household type among korean adults.Using data from the korea national health and nutrition examination survey 2014-2018, we included 21,944 korean adults with available health examination and dietary recall data.Based on self-reported information, individuals were divided into two household types: single- and multi-person households.We used multivariable logistic regression to estimate the adjusted odds ratios (aors) and 95% confidence intervals (cis) for met s and its components after adjusting for potential covariates.Among the study population, 9.19% and 90.81% lived in single-person and multi-person households, respectively.Individuals in single-person households had a higher energy intake overall and a greater percentage of energy from animal protein; total, saturated, and monounsaturated fats; and animal source foods and a lower percentage of energy from carbohydrates, plant protein, and plant source foods than those from multi-person households (all,p< 0.05).Individuals living in single-person rather than multi-person households were more likely to consume milk/dairy products, alcoholic and non-alcoholic beverages, oils/fats, and others but were less likely to consume vegetables/mushrooms, fruits, seaweeds, and fish/shellfish (all,p< 0.05).Living alone was associated with higher energy intake from main meals and foods prepared away from home but a lower dietary variety score and fewer total main meals consumed (all,p< 0.05).Skipping breakfast, frequent eating out, food insecurity, and met s combination phenotypes significantly differed by household type.Individuals living alone had higher odds of met s (aor: 1.14, 95% ci: 1.02-1.29), abdominal obesity (aor: 1.14, 95% ci: 1.01-1.28), elevated blood pressure (aor: 1.28, 95% ci: 1.12-1.47), and elevated fasting blood glucose (aor: 1.18, 95% ci: 1.05-1.33) than those living with others.Compared with those in multi-person households, individuals in single-person households tend to have health and dietary behaviors that increase vulnerability to met s; therefore, establishing health care strategies and nutrition policies according to household type is necessary.

Journal: Healthcare (Basel, Switzerland) (2021)
Publication types: Journal Article
Accurate quantification of phosphorus intergranular segregation in iron by STEM-EDX.

This study describes a method to quantify phosphorus grain boundary segregation by energy dispersive x-ray spectroscopy in scanning transmission electron microscope (stem-edx).A "box-type method" is employed, removing the long-discussed problems of interaction volume and the beam broadening effect.The proposed methodology also introduces a novel way of subtracting the spectrum background to remove the influence of coherent bremsstrahlung and spurious peaks.A fe-p model alloy was used to compare the box method to the quantification results previously obtained by atom probe tomography on two high angle grain boundaries.The results are specifically reported in surface concentration (atom/nm2) to avoid additional hypotheses and allow the results between the two techniques to be directly compared.The measurements show that the box-type method can accurately measure phosphorus intergranular segregation in iron.

Journal: Micron (Oxford, England : 1993) (2022)
Publication types: Journal Article
Association between epidemiological and clinico-pathological features of breast cancer with prognosis, family history, Ki-67 proliferation index and survival in Tunisian breast cancer patients.

Breast cancer has different epidemio-clinical characteristics in middle east and north-african populations compared to those reported in the western countries.The aim of this study is to analyze the epidemiological and clinico-pathological features of breast cancer in tunisia and to determine prognostic factors with special interest to family history, ki-67 proliferation index and comorbidity.We retrospectively reviewed epidemiological and clinico-pathological data from patients' medical records, treated in the medical oncology department at abderrahmane mami hospital, in the period 2011-2015.Data has been collected on 602 breast cancer patients and analyzed using spss software v.23.0.Our study showed high fractions of young breast cancer patients and cases with dense breasts.The most prevalent comorbidities observed in the studied cohort were cardiovascular diseases and diabetes.Familial breast cancer was found in 23.3% of cases and was associated with younger age at diagnosis (p 20% was significantly associated with early age at diagnosis, lymph node involvement (p = 0.002), advanced tumor grade (p<0.001) and high risk of relapse (p = 0.007).Ki-67 cut-off 30% predicted survival in luminal cases.Survival was worse in patients with triple negative breast cancer compared to non-triple negative breast cancer, inflammatory breast cancer compared to non-inflammatory breast cancer, moderately to poorly differentiated tumors compared to well-differentiated tumors and with positive lymph nodes compared to p n0 (p<0.05).Our study showed new insights into epidemiological and clinico-pathological characteristics of breast cancer that are not well explored in tunisian population.Considering our findings along with the implementation of electronic health record system may improve patient health care quality and disease management.

Journal: PloS one (2022)
Publication types: Journal Article
Evaluation of the potential complication of interstitial lung disease associated with antifibrotic drugs using data from databases reporting spontaneous adverse effects.

Interstitial lung disease (ild), as an adverse effect of certain drugs, leads to inflammation and damage in the walls of the alveoli, making it difficult for the alveoli to take up oxygen.Interstitial pneumonia with no identifiable cause is called idiopathic interstitial pneumonia (iip), and, among the major iips, idiopathic pulmonary fibrosis (ipf) is diagnosed in about half of patients.Current treatment options are limited, among which the antifibrotic drugs nintedanib (ofev) and pirfenidone (pirespa) are the first-line drugs.In this study, we investigated the incidence of ild possibly caused by antifibrotic agents using data from the japanese adverse drug event report (jader) database, a database of spontaneous adverse event reports published by the pharmaceuticals and medical devices agency (pmda), and the us food and drug administration (fda) adverse event reporting system (faers), published by the fda.We used the faers and jader to detect the signals of adverse events on the basis of reporting odds ratios.The relationship between indications and adverse events was clarified by separating indications and adverse events using the spontaneous adverse event reporting database with novel drug involvement.Regarding the involvement of nintedanib and pirfenidone in the development of ild, jader and faers showed signals for both nintedanib and pirfenidone as suspect drugs, and no signals for nintedanib or pirfenidone as concomitant drug interactions were detected.We highlight this because there are only a few effective drugs for ipf, and effective and safe drug therapies should be implemented by taking into consideration drug-induced ild.

Journal: Clinical and translational science (2022)
Publication types: Journal Article
Apoptosis induced by synthetic compounds containing a 3,4,5-trimethoxyphenyl fragment against lymphoid immature neoplasms.

T-cell acute lymphoblastic leukemia is an aggressive hematological malignancy originating from the malignant transformation of progenitor t cells at different stages of development.The treatment causes severe adverse effects and is associated with relapses and high morbidity and mortality rates.The present study aimed to evaluate the cytotoxic activity of 28 new compounds containing 3,4,5-trimethoxyphenyl analogues on hematological neoplastic cells lines.Cytotoxicity screening by the mtt method revealed that compound 1d was the most promising.Cell viability of neoplastic cells decreased in a concentration- and time-dependent manner, with compound 1d not causing hemolysis or reducing peripheral blood mononuclear cells viability, suggesting a selective cytotoxicity.We also suggested that compound 1d induced apoptotic-like cell death with mitochondrial involvement in jurkat cells.

Journal: Biochemistry and cell biology = Biochimie et biologie cellulaire (2019)
Publication types: Journal Article
Exact Distribution of Threshold Crossing Times for Protein Concentrations: Implication for Biological Timekeeping.

Stochastic protein accumulation up to some concentration threshold sets the timing of many cellular physiological processes.Here we obtain the exact distribution of first threshold crossing times of protein concentration, in either laplace or time domain, and its associated cumulants: mean, variance, and skewness.The distribution is asymmetric, and its skewness nonmonotonically varies with the threshold.We study lysis times of e.Coli cells for holin gene mutants of bacteriophage-λ and find a good match with theory.Mutants requiring higher holin thresholds show more skewed lysis time distributions as predicted.The theory also predicts a linear relationship between infection delay time and host doubling time for lytic viruses, that has recently been experimentally observed.

Journal: Physical review letters (2022)
Publication types: Journal Article