syedzayyan/paper_mill_benchmark huggingface dataset:
Prediction of treatment outcome in burning mouth syndrome patients using machine learning based on clinical data.

The purpose of this study is to apply a machine learning approach to predict whether patients with burning mouth syndrome (bms) respond to the initial approach and clonazepam therapy based on clinical data.Among the patients with the primary type of bms who visited the clinic from 2006 to 2015, those treated with the initial approach of detailed explanation regarding home care instruction and use of oral topical lubricants, or who were prescribed clonazepam for a minimum of 1 month were included in this study.The clinical data and treatment outcomes were collected from medical records.Extreme gradient-boosted decision trees was used for machine learning algorithms to construct prediction models.Accuracy of the prediction models was evaluated and feature importance calculated.The accuracy of the prediction models for the initial approach and clonazepam therapy was 67.6% and 67.4%, respectively.Aggravating factors and psychological distress were important features in the prediction model for the initial approach, and intensity of symptoms before administration was the important feature in the prediction model for clonazepam therapy.In conclusion, the analysis of treatment outcomes in patients with bms using a machine learning approach showed meaningful results of clinical applicability.

Journal: Scientific reports (2021)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Total Synthesis of an All-1,2-cis-Linked Repeating Unit from theAcinetobacter baumanniiD78 Capsular Polysaccharide.

Chemical synthetic efforts have resulted in the preparation of the assigned tetrasaccharide repeating subunit from the acinetobacter baumannii kl4-associated capsular polysaccharide.A convergent synthetic strategy hinging on a 1,2-cis-selective [2+2] glycosylation to generate the fully protected tetrasaccharide was key to the success of this synthesis.

Journal: Organic letters (2022)
Publication types: Journal Article;Research Support, U.S. Gov't, Non-P.H.S.
A Non-Volatile Tunable Ultra-Compact Silicon Photonic Logic Gate.

Logic gates, as one of the most important basic units in electronic integrated circuits (eics), are also equally important in photonic integrated circuits (pics).In this study, we proposed a non-volatile, ultra-compact all-photonics logic gate.The footprint is only 2 μm × 2 μm.We regulate the phase change of optical phase change materials(o-pcms) sb2se3to switch the function of the logic gate.The sb2se3possess a unique non-volatile optical phase change function; therefore, when sb2se3is in the crystalline or amorphous state, our device can work as xor gate or and gate, and our designed logic '1' and logic '0' contrasts reach 11.8 d b and 5.7 d b at 1550 nm, respectively.Compared with other traditional optical logic gates, our device simultaneously has non-volatile characteristics, tunability, and additionally an ultra-small size.These results could fully meet the needs of fusion between pics and eics, and developing truly chip-scale optoelectronic logic solution.

Journal: Nanomaterials (Basel, Switzerland) (2022)
Publication types: Journal Article
Identification of Robust Protein Associations With COVID-19 Disease Based on Five Clinical Studies.

Multiple studies have investigated the role of blood circulating proteins in covid-19 disease using the olink affinity proteomics platform.However, study inclusion criteria and sample collection conditions varied between studies, leading to sometimes incongruent associations.To identify the most robust protein markers of the disease and the underlying pathways that are relevant under all conditions, it is essential to identify proteins that replicate most widely.Here we combined the olink proteomics profiles of two newly recruited covid-19 studies (n=68 and n=98) with those of three previously published covid-19 studies (n=383, n=83, n=57).For these studies, three olink panels (inflammation and cardiovascular ii & iii) with 253 unique proteins were compared.Case/control analysis revealed thirteen proteins (ccl16, ccl7, cxcl10, ccl8, lgals9, cxcl11, il1rn, ccl2, cd274, il6, il18, mertk, ifnγ, and il18r1) that were differentially expressed in covid-19 patients in all five studies.Except ccl16, which was higher in controls, all proteins were overexpressed in covid-19 patients.Pathway analysis revealed concordant trends across all studies with pathways related to cytokine-cytokine interaction, il18 signaling, fluid shear stress and rheumatoid arthritis.Our results reaffirm previous findings related to a covid-19 cytokine storm syndrome.Cross-study robustness of covid-19 specific protein expression profiles support the utility of affinity proteomics as a tool and for the identification of potential therapeutic targets.

Journal: Frontiers in immunology (2021)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Elevated parathyroid hormone levels in older women treated for osteoporosis using denosumab.

Primary care physicians (pcps) often struggle with elevated serum intact parathyroid hormone (i pth) in osteoporotic patients on antiresorptive treatment, specifically, denosumab.As i pth and calcium levels need to be within normal ranges to receive the next dose of denosumab, continuously high serum i pth may necessitate additional tests to rule out pathological causes.We aimed to determine factors associated with i pth elevation in a cohort of postmenopausal women receiving osteoporosis treatment.Method a cross-sectional analysis of electronic medical records of patients 50 years and older who visited a geriatric osteoporosis clinic between october 1, 2014 and december 31, 2019, was conducted.We divided patients into 3 categories: not currently on treatment, on bisphosphonates or on denosumab.Percentage change in i pth levels from baseline to 1 year follow-up was the outcome measure.Other variables used are age, body mass index, chronic co-morbidities, 25oh-vitamin d, calcium, tsh, glomerular filtration rate and femoral neck bmd.Linear regression models were used to assess independent associations between treatment group and i pth changes.Results mean (sd) age of 173 participants in our study was 78 (± 10) years, and 71% were caucasian.At follow-up, mean percent change of i pth was 13.47 ± 62.76, 30.35 ± 61.17, and 39.60 ± 35.51 in the "no treatment", "bisphosphonate" and "denosumab" groups, respectively.Age was a predictor of elevated percent change of i pth in the denosumab group.Conclusion increasing age is associated with i pth elevations in osteoporotic patients on denosumab.In the absence of any pathology, continuation of denosumab may be safe in lowering fracture risk.However, a larger study may be required to confirm this.

Journal: European geriatric medicine (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Moderators of long-term treatment outcome when comparing two group interventions for adolescents with ADHD: who benefits more from DBT-based skills training?

Psychosocial interventions for adolescents with attention-deficit/hyperactivity disorder (adhd), targeting emotional dysregulation and impulsive behaviors, have been requested, but the heterogeneity within this group makes it unlikely that there is one treatment that fits all.The aim of this study was to identify which adolescents with adhd might have an effect from a structured skills training group (sstg) based on dialectical behavioral therapy, by exploring pre-treatment characteristics as potential moderators of long-term treatment outcome.Methods this study was based on follow-up data from a randomized controlled trial comparing the sstg (n = 71) to a psychoeducational control intervention (n = 57) for adolescents with adhd (15-18 years old).Clinical characteristics (sex, age, medication status, adhd presentation, severity of adhd symptom, psychiatric comorbidity, impairment of emotional dysregulation and functional impairment) were explored as potential moderators of pre-treatment to follow-up change in adhd symptoms and functional impairment.Moderation analyses were performed using the process macro for spss.Results three moderators (severity of hyperactivity/impulsivity, conduct problems and impairment of emotional dysregulation) were identified in regard to the outcome self-rated change in adhd symptoms.Participants with elevated pre-scores on these variables had a better effect of the sstg than of the psychoeducational control intervention.No moderators were found in regard to the parental-rated outcomes.Conclusions the sstg seems to be beneficial for adolescents with adhd who perceive pronounced symptoms of hyperactivity/impulsivity, conduct problems and emotional dysregulation.Our findings need to be confirmed in future trials evaluating dialectical behavioral therapy-based skills training for adolescents with adhd, where these moderators could be used as criteria for inclusion or stratification.Trial registration , retrospectively registered.

Journal: BMC psychiatry (2022)
Publication types: Randomized Controlled Trial;Journal Article;Research Support, Non-U.S. Gov't
Differences in the effects of BMI on bone microstructure between loaded and unloaded bones assessed by HR-pQCT in Japanese postmenopausal women.

S the relationship between weight-related load and bone mineral density (bmd)/bone microstructure under normal load conditions using high-resolution peripheral quantitative computed tomography (hr-p qct) remains unconfirmed.The study aims to investigate the differences in effect of body mass index (bmi) on bmd/bone microstructure of loaded and unloaded bones, respectively, in japanese postmenopausal women.Methods fifty-seven postmenopausal women underwent hr-p qct on the tibia and radius.Correlation analysis, principal component (pc) analysis, and hierarchical multiple regression were performed to examine the relationship between bmi and hr-p qct parameters.Results several microstructural parameters of the tibia and radius correlated with bmi through a simple correlation analysis, and these relationships remained unchanged even with an age-adjusted partial correlation analysis.Pc analysis was conducted using seven bone microstructure parameters.The first pc (pc1) reflected all parameters of trabecular and cortical bone microstructures, except for cortical porosity, whereas the second pc (pc2) reflected only cortical bone microstructure.Hierarchical multiple regression analysis indicated that bmi was more strongly related to bmd/bone microstructure in the tibia than in the radius.Furthermore, bmi was associated with trabecular/cortical bmd, and pc1 (not pc2) of the tibia and radius.Thus, bmi was strongly related to the trabecular bone microstructure rather than the cortical bone microstructure.Conclusions our data confirmed that bmi is associated with volumetric bmd and trabecular bone microstructure parameters in the tibia and radius.However, although bmi may be more related to hr-p qct parameters in the tibia than in the radius, the magnitude of association is modest.

Journal: Osteoporosis and sarcopenia (2021)
Publication types: Journal Article
Serum Level of Galectin-3 in Early Detection of Acute Pancreatitis.

Acute pancreatitis (ap) is a common cause of hospital admissions.Diagnosing ap in patients presenting to emergency departments remains a challenge for physicians.Thus, we aimed to evaluate the diagnostic accuracy of galectin-3 to find a new and effective method for detecting ap.Methods in this prospective cross-sectional study, 43 patients with a manifestation of ap were enrolled.The serum levels of galectin-3 were measured at admission and 48 hours later and compared between the groups of patients with and without ap.Results serum levels of galectin-3 at admission and after 48 hours were significantly higher in ap cases compared with non-ap individuals.The area under the curve (auc) for galectin-3 was 73.1%, which revealed a good accuracy in predicting the ap diagnosis.Conclusion serum levels of galectin-3 at admission and after 48 hours were significantly higher in ap cases, and their diagnostic value was acceptable in the detection of ap.

Journal: Middle East journal of digestive diseases (2021)
Publication types: Journal Article
PHLPP1 deficiency ameliorates cardiomyocyte death and cardiac dysfunction through inhibiting Mcl-1 degradation.

Myocardial infarction (mi), ischemia-reperfusion injury or chemotherapy can trigger excessive loss of terminally differentiated cardiomyocytes, leading to the development of heart failure.Whereas apoptosis has been considered to be the major form of cell death in various myocardial damage, the means by which to reduce cardiomyocyte loss are limited, and the mechanism that underlies cardiomyocyte apoptosis need to be further investigated.Ph domain leucine-rich repeat protein phosphatase1 (phlpp1) belongs to a novel family of ser/thr protein phosphatases that functions as a tumor suppressor.Here, we identified phlpp1 as an important pro-apoptosis factor of cardiomyocytes in response to pathogenic stresses.The conditional phlpp1 deficiency in cardiomyocytes alleviated myocardial ischemic injury, improved cardiac function and inhibited myocardial fibrosis, in turn preventing adverse cardiac remodeling and heart failure after mi.The conditional phlpp1 deficiency in cardiomyocytes also attenuated doxorubicin (dox)-induced myocardial injury, suppressed the inflammation and fibrosis in cardiac tissues, and protected from cardiac dysfunction.Mechanically, phlpp1 bound the anti-apoptosis protein myeloid cell leukemia sequence 1 (mcl-1) in cardiomyocytes.Thr163 phosphorylation of mcl-1 was reported to slow mcl-1 protein turnover.We further found that phlpp1 deficiency enhanced thr163 phosphorylation of mcl-1, inhibited mcl-1 degradation and maintained mcl-1 protein expression level in myocardium and cardiomyocytes upon mi or dox treatment.Phlpp1 could directly dephosphorylate thr163 of mcl-1.Thus, phlpp1 promotes cardiomyocyte death and cardiac dysfunction through binding and enhancing mcl-1 degradation under ischemic or toxic injury conditions, which sheds new light on the development of potential therapies to control cardiomyocyte loss.

Journal: Cellular signalling (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Current and Future Prospects for Gene Therapy for Rare Genetic Diseases Affecting the Brain and Spinal Cord.

In recent years, gene therapy has been raising hopes toward viable treatment strategies for rare genetic diseases for which there has been almost exclusively supportive treatment.We here review this progress at the pre-clinical and clinical trial levels as well as market approvals within diseases that specifically affect the brain and spinal cord, including degenerative, developmental, lysosomal storage, and metabolic disorders.The field reached an unprecedented milestone when zolgensma® (onasemnogene abeparvovec) was approved by the fda and ema forin vivoadeno-associated virus-mediated gene replacement therapy for spinal muscular atrophy.Shortly after ema approved libmeldy®, anex vivogene therapy with lentivirus vector-transduced autologous cd34-positive stem cells, for treatment of metachromatic leukodystrophy.These successes could be the first of many more new gene therapies in development that mostly target loss-of-function mutation diseases with gene replacement (e.g., batten disease, mucopolysaccharidoses, gangliosidoses) or, less frequently, gain-of-toxic-function mutation diseases by gene therapeutic silencing of pathologic genes (e.g., amyotrophic lateral sclerosis, huntington's disease).In addition, the use of genome editing as a gene therapy is being explored for some diseases, but this has so far only reached clinical testing in the treatment of mucopolysaccharidoses.Based on the large number of planned, ongoing, and completed clinical trials for rare genetic central nervous system diseases, it can be expected that several novel gene therapies will be approved and become available within the near future.Essential for this to happen is the in depth characterization of short- and long-term effects, safety aspects, and pharmacodynamics of the applied gene therapy platforms.

Journal: Frontiers in molecular neuroscience (2021)
Publication types: Journal Article;Review
Mass photometry reveals SARS-CoV-2 spike stabilisation to impede ACE2 binding through altered conformational dynamics.

Here we show using mass photometry how proline substitutions, commonly used for sars-co v-2 spike stabilisation in vaccine design, directly affects ace2 receptor interactionsviadynamics of open and closed states.Conformational changes and ace2 binding were influenced by spike variant and temperature, but independent of site-specific n-glycosylation.

Journal: Chemical communications (Cambridge, England) (2022)
Publication types: Journal Article
BAP1 phosphorylation-mediated Sp1 stabilization plays a critical role in cathepsin K inhibition-induced C-terminal p53-dependent Bax upregulation.

Cathepsin k inhibitor (odanacatib; odn) and cathepsin k knockdown (si rna) enhance oxaliplatin-induced apoptosis through p53-dependent bax upregulation.However, its underlying mechanisms remain unclear.In this study, we elucidated the mechanism behind enhancement of oxaliplatin-induced apoptosis by odn.We also investigated the molecular mechanisms of odn-induced bax upregulation.Here, we demonstrated that odn-induced bax upregulation required p53, but it was independent of p53 transcriptional activity.Various mutants of the dna-binding domain of p53 induced bax upregulation in odn-treated cells.P53 functional domain analysis showed that the c-terminal domain of p53 participates in the physical interaction and stabilization of sp1, a major transcription factor of bax.We screened a specific si rna encoding 50 deubiquitinases and identified that bap1 stabilizes sp1.The knockdown or catalytic mutant form of bap1 abolished the odn-induced upregulation of sp1 and bax expression.Mechanistically, odn induced bap1 phosphorylation and enhanced sp1-bap1 interaction, resulting in sp1 ubiquitination and degradation.Interestingly, odn-induced bap1 phosphorylation and dna damage were modulated by the production of mitochondrial reactive oxygen species (ros).Mitochondrial ros scavengers prevented dna damage, bap1-mediated sp1 stabilization, and bax upregulation by odn.Bap1 downregulation by si rna inhibited apoptosis induced by the combined treatment of odn and oxaliplatin/etoposide.Therefore, sp1 is a crucial transcription factor for odn-induced bax upregulation, and sp1 stabilization is regulated by bap1.

Journal: Redox biology (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Dietary Postbiotics Reduce Cytotoxicity and Inflammation Induced by Crystalline Silica in an In Vitro RAW 264.7 Macrophage Model.

Crystalline silica (c si o2) particles are naturally existing environmental toxicants.Exposure to c si o2could cause local or systemic inflammation and aggregate inflammation-associated diseases.Dietary postbiotics are reported to possess anti-inflammatory activities; however, their effects on c si o2-triggered inflammation are unknown.Here, we investigate the impact of postbiotics from lacticaseibacillus rhamnosus(lgg),limosilactobacillus reuteri(l.reu), and bifidobacterium animalissubsp.lactis bb12 (bb12) on c si o2-induced cytotoxicity and il-1 cytokines in vitro using macrophages.The postbiotics used in this study were cell-free fractions of a probiotic growth medium collected at different time points.The in vitro model used was the wild-type murine macrophage raw 264.7 cell line stably transfected with the inflammasome adapter protein, asc.Our results indicate that all the postbiotics could reduce c si o2-induced cytotoxicity in the wild-type and asc macrophages and the effects were od-dependent.Following priming with a lipopolysaccharide, c si o2treatment resulted in robust inflammasome activation in asc, as reflected by the il-1β release.These responses were minimal or absent in the wild-type raw cells.All the postbiotics decreased the release of il-1β from asc; however, only lgg and bb12 reduced the il-1β secretion from wild-type cells.Only the l.reu postbiotics reduced the il-1α release from asc.We conclude that the postbiotics from lgg, bb12, and l.reu can protect macrophages against c si o2-induced cytotoxicity and suppress il-1β activation.

Journal: Foods (Basel, Switzerland) (2022)
Publication types: Journal Article
An integrative proteomics method identifies a regulator of translation during stem cell maintenance and differentiation.

Detailed characterization of cell type transitions is essential for cell biology in general and particularly for the development of stem cell-based therapies in regenerative medicine.To systematically study such transitions, we introduce a method that simultaneously measures protein expression and thermal stability changes in cells and provide the web-based visualization tool proteo tracker.We apply our method to study differences between human pluripotent stem cells and several cell types including their parental cell line and differentiated progeny.We detect alterations of protein properties in numerous cellular pathways and components including ribosome biogenesis and demonstrate that modulation of ribosome maturation through sbds protein can be helpful for manipulating cell stemness in vitro.Using our integrative proteomics approach and the web-based tool, we uncover a molecular basis for the uncoupling of robust transcription from parsimonious translation in stem cells and propose a method for maintaining pluripotency in vitro.

Journal: Nature communications (2021)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Marine zooplankton dynamics after a major mining dam rupture in the Doce River, southeastern Brazil: Rapid response to a changing environment.

Zooplankton were sampled five days after the tailings from the samarco dam rupture reached the ocean in the coastal region at the mouth of the doce river.This was one of the largest environmental disasters in brazilian history, and the impacts on the marine biota are not yet fully understood.This study aimed to evaluate the zooplankton community short term responses to the metal enrichment after the tailings reached the coastal region in different scenarios.Our results showed an acute impact on the zooplankton community, which peaked in abundance (222,958.60 ind/m3) and decreased in diversity (h' = 1.23) near the river mouth.Two copepod species, parvocalanus sp.And oithona nana, composed up to 61% of the total abundance and they were correlated with concentrations of fe, pb, cu and zn in particulate fraction.These species feed opportunistically on nanophytoplankton, which dominated the autotroph community, possibly in response to the iron enrichment caused by the mud flow.A shift on zooplankton species composition was also observed.During the first three days, we found the presence of oceanic species in the 20 and 30 m isobaths during an incomplete upwelling event, which directly correlated with the presence of calanoides carinatus.However, only three days later, following a cold front passage and consequent increase of water turbidity, those species were already absent, and the zooplankton community was significantly altered (permanova, df = 1, pseudo-f = 9.2247, p = .001).Zooplankton responded quickly to the environmental changes detected during our sampling period and proved to be key factors in costal monitoring, especially in dynamic oceanographic areas such as the doce river coastal region.

Journal: The Science of the total environment (2020)
Publication types: Journal Article