Miracle-dz/UniFAR-FTUs huggingface dataset:
Genetic association of liver X receptor beta rs2695121 polymorphism with obesity-related traits in a northeastern Iranian population

Background Liver X receptor Beta (LXRβ), located in an obesity susceptible region, has been shown to be involved in the metabolism of lipid and carbohydrates. Previous human genetic studies have suggested genetic variability of LXRβ could be associated with human obesity. Therefore, we hypothesized that LXRβ gene rs2695121 polymorphism may be associated with the risk of obesity in a northeastern Iranian population. Methods A TaqMan allelic discrimination assay was used to genotype LXRβ rs2695121 polymorphism in this cross-sectional study of 168 obese, 209 overweight and 76 normal-weight subjects recruited from Mashhad city in Iran. Logistic regression analyses were used to analyze alleles and genotypes distribution. Anthropometrics and clinical variables among different genotype carriers were compared by univariate analyses. All statistical analysis was performed using SPSS v.16. 0. Results Allelic and genotypic associations with obesity were not significant for the rs2695121 variant even after adjustment for age and gender (OR=1.17, 95% CI=0.46–2.91), p=0.586). Moreover, haplotype analysis using data from the other variant (rs17373080) of LXRβ revealed no significant association (p=0.88). However, among the clinical and metabolic parameters tested, systolic and diastolic blood pressures were found nominally associated with the genotype CT (p=0.031 and p=0.017 respectively). Conclusion This study failed to demonstrate any association between the rs2695121 variant of LXRβ and obesity neither alone nor when considered with rs17373080. However, its association with blood pressure may influence one’s susceptibility to obesity, supporting further studies in a larger population.
Activity energy expenditure and change in body composition in late life.

BACKGROUND Change in body composition, specifically loss of fat-free mass and gain in fat mass, in older adults is a major pathway leading to the onset of functional decline and physical disability. OBJECTIVE The objective was to determine the association of activity-related energy expenditure with change in body mass and composition among older men and women. DESIGN Total energy expenditure (TEE) was assessed over 2 wk by using the doubly labeled water method in 302 community-dwelling older adults aged 70-82 y. Resting metabolic rate (RMR) was measured by using indirect calorimetry, and the thermic effect of meals was estimated at 10% of TEE. Activity energy expenditure (AEE) was calculated as [TEE(0.9) - RMR]. Total body mass, fat-free mass (FFM), and fat mass (FM) were assessed by dual-energy X-ray absorptiometry annually over a mean (+/-SD) of 4.9 +/- 1.3 y. RESULTS In multivariate models adjusted for baseline age, smoking status, and race, men and women had a decline (in kg/y) in body mass (men: -0.34, 95% CI: -0.71, 0.02; women: -0.45, 95% CI: -0.71, -0.19) and FFM (men: -0.48, 95% CI: -0.67, -0.29; women: -0.14, 95% CI: -0.026, -0.03). No changes (in kg/y) were observed in FM (men: 0.14, 95% CI: -0.10, 0.38; women: -0.28, 95% CI: -0.49, -0.07). In men and women, higher AEE at baseline was associated with greater FFM. The average change in these outcomes (ie, slope), however, was similar across tertiles of AEE. CONCLUSIONS These data suggest that accumulated energy expenditure from all physical activities is associated with greater FFM, but the effect does not alter the trajectory of FFM change in late life.
Comparison of common risk stratification indices to predict outcomes among stage IV cancer patients with bowel obstruction undergoing surgery

Among patients with disseminated malignancy (DMa), bowel obstruction is common with high operative morbidity. Since preoperative risk stratification is critical, we sought to compare three standard risk indices, the American Society of Anesthesiology (ASA) classification, Charlson comorbidity index (CCI), and modified frailty index (mFI).
Low-density lipoprotein 4: a novel predictor of coronary artery disease severity

Abstract Background: Hyperlipidemia is a well established risk factor for coronary artery disease (CAD). Severe CAD has been observed in patients with normal levels of total and low-density lipoprotein (LDL) cholesterol. Small dense LDL particle subtypes (LDL3 and LDL4) have been observed to be more oxidizable and atherogenic. We aimed to identify the role of cholesterol particle subtypes in predicting CAD severity. Methods: Blood samples were obtained immediately before cardiac catheterization in 179 consecutive patients with suspected CAD. Detailed lipid profiling was performed using a VAP cholesterol test. CAD severity was categorized angiographically as no/minor CAD (<20% luminal diameter stenosis [LDS]), moderate CAD (20% to 74% LDS) and severe CAD (>75% LDS of any major coronary vessel). Results: Patients with severe CAD had significantly higher LDL4 and triglycerides, and lower total HDL, HDL2, HDL3, LDL2 and LDL3 compared to patients with no/minor CAD (p < .05 for all). Multivariate analysis showed high LDL4 as an independent predictive of severe CAD. ROC analysis showed an area under the curve of 0.62 (p < .0001) with a cut-point of >16.9 mg/dL to predict severe CAD with a sensitivity of 53% and specificity of 79%. Conclusion: Elevated LDL4 levels are associated with severe CAD. Further large-scale investigations are required to evaluate the utility of LDL4 in predicting CAD severity.
Learning Stylometric Representations for Authorship Analysis

Authorship analysis (AA) is the study of unveiling the hidden properties of authors from textual data. It extracts an author’s identity and sociolinguistic characteristics based on the reflected writing styles in the text. The process is essential for various areas, such as cybercrime investigation, psycholinguistics, political socialization, etc. However, most of the previous techniques critically depend on the manual feature engineering process. Consequently, the choice of feature set has been shown to be scenario- or dataset-dependent. In this paper, to mimic the human sentence composition process using a neural network approach, we propose to incorporate different categories of linguistic features into distributed representation of words in order to learn simultaneously the writing style representations based on unlabeled texts for AA. In particular, the proposed models allow topical, lexical, syntactical, and character-level feature vectors of each document to be extracted as stylometrics. We evaluate the performance of our approach on the problems of authorship characterization, authorship identification and authorship verification with the Twitter, blog, review, novel, and essay datasets. The experiments suggest that our proposed text representation outperforms the static stylometrics, dynamic ${n}$ -grams, latent Dirichlet allocation, latent semantic analysis, distributed memory model of paragraph vectors, distributed bag of words version of paragraph vector, word2vec representations, and other baselines.
Aggressive Behaviour Risk Assessment Tool for newly admitted residents of long‐term care homes

AIM The aim of this study was to revise the 10-item Aggressive Behaviour Risk Assessment Tool for predicting aggressive events among residents newly admitted to long-term care homes. BACKGROUND The original tool had acceptable sensitivity and specificity for identifying potentially aggressive patients in acute care medical-surgical units, but its usefulness in long-term care homes is unknown. DESIGN A retrospective cohort study design was used. METHODS All residents admitted to 25 long-term care homes in western Canada were assessed for the risk of aggression using the original tool within 24 hours of admission from January 2014 - December 2014 (n = 724). Incident reports of aggressive events occurring within 30 days of admission were collected. Multiple logistic regression and receiver operating characteristics analyses were performed. RESULTS Fifty-three residents of 724 exhibited aggressive behaviours. The demographic variable of age less than 85 years was found to be a positive predictor of aggressive events in multivariate logistic regression model and was added to the tool. The revised six-item Aggressive Behaviour Risk Assessment Tool for Long-Term Care consists of one new item, age less than 85 years and five items from the original tool: History of physical aggression, physically aggressive/threatening, anxiety, confusion/cognitive impairment and threatening to leave. The receiver operating characteristics of the revised tool with weighted scoring showed a good discriminant ability with satisfactory sensitivity and specificity at the recommended cut-off score of 4. CONCLUSION The revised six-item tool may be useful in identifying potentially aggressive residents newly admitted to long-term care homes.
Renal potassium transport: mechanisms and regulation.

The regulation of potassium metabolism involves mechanisms for the appropriate distribution between the intra- and extracellular fluid compartments and for the excretion by the kidney. Clearance and single-nephron studies show that renal excretion is determined by regulated potassium secretion and potassium reabsorption, respectively, in principal and intercalated cells of the distal nephron. Measurement of the electrochemical driving forces acting on potassium transport across individual cell membranes and characterization of several ATPases and potassium channels provide insights into the transport and regulation of renal potassium excretion.
A feedback loop comprising PRMT7 and miR-24-2 interplays with Oct4, Nanog, Klf4 and c-Myc to regulate stemness

Self-renewal and pluripotency are two fundamental characteristics of embryonic stem cells (ESCs) and are controlled by diverse regulatory factors, including pluripotent factors, epigenetic regulators and microRNAs (miRNAs). Although histone methyltransferases are key epigenetic regulators, whether and how a histone methyltransferase forms a network with miRNAs and the core pluripotent factor system to regulate ESC stemness is little known. Here, we show that the protein arginine methyltransferase 7 (PRMT7) is a pluripotent factor essential for the stemness of mouse ESCs. PRMT7 repressed the miR-24-2 gene encoding miR-24-3p and miR-24-2-5p by upregulating the levels of symmetrically dimethylated H4R3. Notably, miR-24-3p targeted the 3′ untranslated regions (UTRs) of the major pluripotent factors Oct4, Nanog, Klf4 and c-Myc, whereas miR-24-2-5p silenced Klf4 and c-Myc expression. miR-24-3p and miR-24-2-5p also targeted the 3′UTR of their repressor gene Prmt7. miR-24-3p and miR-24-2-5p induced mouse ESC differentiation, and their anti-sense inhibitors substantially reversed spontaneous differentiation of PRMT7-depleted mouse ESCs. Oct4, Nanog, Klf4 and c-Myc positively regulated Prmt7 expression. These findings define miR-24-3p and miR-24-2-5p as new anti-pluripotent miRNAs and also reveal a novel epigenetic stemness-regulatory mechanism in which a double-negative feedback loop consisting of PRMT7 and miR-24-3p/miR24-2-5p interplays with Oct4, Nanog, Klf4 and c-Myc to control ESC stemness.
The vulnerability of spinal motoneurons and soma size plasticity in a mouse model of amyotrophic lateral sclerosis

Motoneuron soma size is a largely plastic property that is altered during amyotrophic lateral sclerosis (ALS) progression. We report evidence of systematic spinal motoneuron soma size plasticity in mutant SOD1‐G93A mice at various disease stages and across sexes, spinal regions and motoneuron types. We show that disease‐vulnerable motoneurons exhibit early increased soma sizes. We show via computer simulations that the measured changes in soma size have a profound impact on the excitability of disease‐vulnerable motoneurons. This study reveals a novel form of plasticity in ALS and suggests a potential target for altering motoneuron function and survival.
Stimulation of oxygen uptake by prostaglandin E2 is oxygen dependent in perfused rat liver.

The aim of this study was to determine if the effect of prostaglandin E2(PGE2) on hepatic oxygen uptake was affected by oxygen tension. Livers from fed female Sprague-Dawley rats were perfused at normal or high flow rates (4 or 8 ml ⋅ g-1 ⋅ min-1) to vary local oxygen tension within the liver lobule. During perfusion at normal flow rates, PGE2 (5 μM) infusion increased oxygen uptake by about 50 μmol ⋅ g-1 ⋅ h-1; however, when livers were perfused at high flow rates, the increase was nearly twice as large. Simultaneously, glucose output was increased rapidly by about 50%, whereas glycolysis was decreased about 60%. When flow rate was held constant, increases in oxygen uptake due to PGE2 were proportional to oxygen delivery. Infusion of PGE2 into livers perfused at normal flow rates increased state 3 rates of oxygen uptake of subsequently isolated mitochondria by about 25%; however, rates were increased 50-75% in mitochondria isolated from livers perfused at high flow rates. Thus it is concluded that PGE2stimulates oxygen uptake via mechanisms regulated by oxygen tension in perfused rat liver. High flow rates also increased basal rates of oxygen uptake: this increase was prevented by inactivation of Kupffer cells with GdCl3. In addition, conditioned medium from Kupffer cells incubated at high oxygen tension (75% oxygen) stimulated oxygen uptake of isolated parenchymal cells by >30% and elevated PGE2production about twofold compared with Kupffer cells exposed to normal air-saturated buffer (21% oxygen). These effects were blocked completely by both indomethacin and nisoldipine. These data support the hypothesis that oxygen stimulates Kupffer cells to release mediators such as PGE2 which elevate oxygen consumption in parenchymal cells, possibly by mechanisms involving cyclooxygenase and calcium channels.
A Many-sorted Polyadic Modal Logic

This paper presents a many-sorted polyadic modal logic that generalizes some of the existing approaches. The algebraic semantics has led us to a many-sorted generalization of boolean algebras with operators, for which we prove the analogue of the J\'onsson-Tarski theorem. While the transition from the mono-sorted logic to many-sorted one is a smooth process, we see our system as a step towards deepening the connection between modal logic and program verification, since our system can be seen as the propositional fragment of Matching logic, a first-order logic for specifying and reasoning about programs.
Variational Autoencoders for Deforming 3D Mesh Models

3D geometric contents are becoming increasingly popular. In this paper, we study the problem of analyzing deforming 3D meshes using deep neural networks. Deforming 3D meshes are flexible to represent 3D animation sequences as well as collections of objects of the same category, allowing diverse shapes with large-scale non-linear deformations. We propose a novel framework which we call mesh variational autoencoders (mesh VAE), to explore the probabilistic latent space of 3D surfaces. The framework is easy to train, and requires very few training examples. We also propose an extended model which allows flexibly adjusting the significance of different latent variables by altering the prior distribution. Extensive experiments demonstrate that our general framework is able to learn a reasonable representation for a collection of deformable shapes, and produce competitive results for a variety of applications, including shape generation, shape interpolation, shape space embedding and shape exploration, outperforming state-of-the-art methods.
Exploring hydrophobicity limits of polyproline helix with oligomeric octahydroindole‐2‐carboxylic acid

The polyproline‐II helix is the most extended naturally occurring helical structure and is widely present in polar, exposed stretches and “unstructured” denatured regions of polypeptides. Can it be hydrophobic? In this study, we address this question using oligomeric peptides formed by a hydrophobic proline analogue, (2S,3aS,7aS)‐octahydroindole‐2‐carboxylic acid (Oic). Previously, we found the molecular principles underlying the structural stability of the polyproline‐II conformation in these oligomers, whereas the hydrophobicity of the peptide constructs remains to be examined. Therefore, we investigated the octan‐1‐ol/water partitioning and inclusion in detergent micelles of the oligo‐Oic peptides. The results showed that the hydrophobicity is remarkably enhanced in longer oligomeric sequences, and the oligo‐Oic peptides with 3 to 4 residues and higher are specific towards hydrophobic environments. This contrasts significantly to the parent oligoproline peptides, which were moderately hydrophilic. With these findings, we have demonstrated that the polyproline‐II structure is compatible with nonpolar media, whereas additional manipulations of the terminal functionalities feature solubility in extremely nonpolar solvents such as hexane.
Cognitive deficits including executive functioning in relation to clinical parameters in paediatric MS patients

Background A number of studies have investigated cognitive impairment in paediatric patients with multiple sclerosis (MS) but deficits regarding executive functions have not been comprehensively assessed up to now. This study was meant to explore cognitive impairment in German paediatric MS patients with a focus on deficits in executive functions and relate these to clinical disease parameters. Methods and findings Forty paediatric MS patients, which presented at the German centre for MS in childhood and adolescence, were assessed for cognitive deficits applying a very comprehensive battery of cognitive tests including the Wechsler Intelligence scale and subtests of the D-KEFS for executive functions. The performance of MS patients was compared with a group of age and sex matched healthy controls using between-subjects ANOVAs. Paediatric MS patients performed worse in tests assessing verbal comprehension and fluency, processing speed, memory, calculation skills and other executive functions. Arranged by the cognitive domain, group differences were most pronounced regarding verbal comprehension and fluency for the WISC subtests Comprehension (p = 0.000), Vocabulary (p = 0.003) and Information (p = 0.005); regarding processing speed for the written SDMT (p = 0.001) and the WISC subtest Coding (p = 0.005); regarding memory for the VLMT training (p = 0.007) and the BASIC MLT pattern learning training (p = 0.009); regarding executive functions including working memory for the WISC subtest Arithmetics (p = 0.002), the D-KEFS Design Fluency (p = 0.003) and the Corsi block tapping backward task (p = 0.003). Fluid reasoning was largely intact. Relations of cognitive performance and clinical parameters were assessed in MS patients. Disease duration was associated with a reduced performance in tests belonging to the domains verbal comprehension and fluency (WISC Vocabulary: p = 0.034, WISC Information: p = 0.015) and fluid reasoning (WISC Picture Completion: p = 0.003) as well as the WISC Working Memory Index (p = 0.047). Patients with a disease onset between 11 and 14 years performed better in fluid reasoning (WISC matrix reasoning: p = 0.024) than patients with a disease onset at an age above 14. The number of relapses negatively influenced the visual spatial memory performance (BASIC MLT pattern learning training: p = 0.009). Conclusions The distribution of cognitive deficits in a representative group German of paediatric MS patients was similar to the pattern known from other European and North-American cohorts. Paediatric MS patients do have cognitive deficits in executive functions and key qualities necessary for successful school performance. Disease duration, age of onset and the number of relapses influence cognitive performance. Cognitive screenings should be implemented on a regular basis for paediatric MS patients, enabling early intervention.
PAI1 mediates fibroblast–mast cell interactions in skin fibrosis

Fibrosis is a prevalent pathological condition arising from the chronic activation of fibroblasts. This activation results from the extensive intercellular crosstalk mediated by both soluble factors and direct cell-cell connections. Prominent among these are the interactions of fibroblasts with immune cells, in which the fibroblast–mast cell connection, although acknowledged, is relatively unexplored. We have used a Tg mouse model of skin fibrosis, based on expression of the transcription factor Snail in the epidermis, to probe the mechanisms regulating mast cell activity and the contribution of these cells to this pathology. We have discovered that Snail-expressing keratinocytes secrete plasminogen activator inhibitor type 1 (PAI1), which functions as a chemotactic factor to increase mast cell infiltration into the skin. Moreover, we have determined that PAI1 upregulates intercellular adhesion molecule type 1 (ICAM1) expression on dermal fibroblasts, rendering them competent to bind to mast cells. This heterotypic cell-cell adhesion, also observed in the skin fibrotic disorder scleroderma, culminates in the reciprocal activation of both mast cells and fibroblasts, leading to the cascade of events that promote fibrogenesis. Thus, we have identified roles for PAI1 in the multifactorial program of fibrogenesis that expand its functional repertoire beyond its canonical role in plasmin-dependent processes.
Effects of pacing parameters on entrainment of gastric slow waves in patients with gastroparesis.

The aim of this study was to investigate the effect of pacing parameters on the entrainment of gastric slow waves in patients with gastroparesis. Four pairs of cardiac pacing wires were placed on the serosal surface of the stomach in 13 patients with gastroparesis. After a baseline recording for 30 min, gastric pacing was performed in a number of sessions with different effective parameters, each lasting for 30 min. The following parameters were found to be effective for the entrainment of the gastric slow wave: a pacing frequency 10% higher than the intrinsic gastric slow wave frequency (IGF), 300 ms pulse width, and 4 mA pacing amplitude. A reduction of pacing amplitude from 4 to 2 mA and 1 mA reduced the percentage of entrainment of the gastric slow wave to 79 ± 10% and 50 ± 11%, respectively. Pacing with a pulse width of 30 or 3 ms was not able to entrain the gastric slow wave in any of the patients. An ectopic pacemaker of tachygastria found in three patients was reversed with gastric pacing. It was concluded that gastric pacing at a frequency up to 10% higher than the IGF and with an amplitude of 4 mA and a pulse width of 300 ms is able to completely entrain the gastric slow wave and normalize gastric dysrhythmias in patients with gastroparesis.