Miracle-dz/UniFAR-FTUs huggingface dataset:
Inter‐ and intramuscular differences in training‐induced hypertrophy of the quadriceps femoris: association with muscle activation during the first training session

The purpose of this study was to examine whether inter‐ and intramuscular differences in hypertrophy induced by resistance training correspond to differences in muscle activation during the first training session. Eleven young men completed 12 weeks of training intervention for knee extension. Before and after the intervention, T1‐weighted magnetic resonance (MR) images were recorded to determine the volume and anatomical cross‐sectional area (CSA) along the length of the individual muscles of the quadriceps femoris. The T2‐weighted MR images were also acquired before and immediately after the first training session. The T2 was calculated for each pixel within the quadriceps femoris, from which the muscle activation was evaluated as %activated volume and area. The results showed that the %activated volume after the first training session was significantly higher in the vastus intermedius than the vastus medialis. However, the relative change in muscle volume after the training intervention was significantly greater in the rectus femoris than the vasti muscles (vastus lateralis, intermedius and medialis). Within the rectus femoris, both the %activated area and relative increase in CSA were significantly greater in the distal region than the proximal region. In contrast, the %activated area and relative increase in CSA of the vasti were nearly uniform along each muscle. These results suggest that the muscle activation during the first training session is associated with the intramuscular difference in hypertrophy induced by training intervention, but not with the intermuscular difference.
Protein Kinase D Selectively Targets Cardiac Troponin I and Regulates Myofilament Ca2+ Sensitivity in Ventricular Myocytes

Protein kinase D (PKD) is a serine/threonine kinase with emerging myocardial functions; in skinned adult rat ventricular myocytes (ARVMs), recombinant PKD catalytic domain phosphorylates cardiac troponin I at Ser22/Ser23 and reduces myofilament Ca2+ sensitivity. We used adenoviral gene transfer to determine the effects of full-length PKD on protein phosphorylation, sarcomere shortening and [Ca2+]i transients in intact ARVMs. In myocytes transduced to express wild-type PKD, the heterologously expressed enzyme was activated by endothelin 1 (ET1) (5 nmol/L), as reflected by PKD phosphorylation at Ser744/Ser748 (PKC phosphorylation sites) and Ser916 (autophosphorylation site). The ET1-induced increase in cellular PKD activity was accompanied by increased cardiac troponin I phosphorylation at Ser22/Ser23; this measured approximately 60% of that induced by isoproterenol (10 nmol/L), which activates cAMP-dependent protein kinase (PKA) but not PKD. Phosphorylation of other PKA targets, such as phospholamban at Ser16, phospholemman at Ser68 and cardiac myosin-binding protein C at Ser282, was unaltered. Furthermore, heterologous PKD expression had no effect on isoproterenol-induced phosphorylation of these proteins, or on isoproterenol-induced increases in sarcomere shortening and relaxation rate and [Ca2+]i transient amplitude. In contrast, heterologous PKD expression suppressed the positive inotropic effect of ET1 seen in control cells, without altering ET1-induced increases in relaxation rate and [Ca2+]i transient amplitude. Complementary experiments in “skinned” myocytes confirmed reduced myofilament Ca2+ sensitivity by ET1-induced activation of heterologously expressed PKD. We conclude that increased myocardial PKD activity induces cardiac troponin I phosphorylation at Ser22/Ser23 and reduces myofilament Ca2+ sensitivity, suggesting that altered PKD activity in disease may impact on contractile function.
Predictors of treatment efficacy and ALT non‐normalization with sofosbuvir/ribavirin therapy for patients with hepatitis C virus genotype 2

The tolerability and efficacy of sofosbuvir and ribavirin in patients infected with hepatitis C virus (HCV) genotype 2 were investigated under actual clinical conditions. A total of 208 patients with chronic HCV genotype 2 infection were treated with sofosbuvir 400 mg and ribavirin (weight‐based dosing) for 12 weeks. Treatment discontinuation and sustained virological response 12 (SVR12) were evaluated. Moreover, factors associated with SVR12, hemoglobin decreasing to less than 10 g/dL during treatment, and alanine aminotransferase (ALT) non‐normalization after treatment were evaluated. In all patients, SVR12 responses were 96.1% (200/208). About 6 of 8 patients (3.8%) who did not achieve SVR12 were re‐treatment patients, and eight patients who did not achieve SVR all had liver cirrhosis. Multivariate analysis also identified body mass index (OR = 0.79; P < 0.001), platelet count (OR = 0.88; P = 0.003), and estimated glomerular filtration rate (eGFR) (OR = 0.96; P = 0.007) as independent contributing factors associated with hemoglobin decreasing to less than 10 g/dL during treatment, and only Mac‐2 Binding Protein Glycosylation isomer (M2BpGi) (OR = 2.46; P = 0.017) as an independent contributing factor associated with ALT non‐normalization after treatment. Cirrhotic patients may have a relatively high rate of treatment failure. In patients whose M2BpGi levels are elevated, their ALT tended to not normalize after treatment completion. These patients who did not achieve normalization of ALT after sofosbuvir plus RBV treatment need more careful observation for emergence of hepatocellular carcinoma even after achievement of SVR.
Cancer-associated fibroblasts induce epithelial-mesenchymal transition through secreted cytokines in endometrial cancer cells

Endometrial cancer (EC) is the most common malignant gynecological disease. Cancer-associated fibroblasts (CAFs) serve an important role in the development and progression of EC through epithelial-mesenchymal transition (EMT). The aim of the present study was to examine the association between CAFs and EMT, and the possible mechanisms of action. Firstly, the CAFs and normal fibroblasts (NFs) were isolated and cultured, then an immunofluorescence assay was performed to analyze the purity and level of activation of CAFs and NFs, and then the conditional medium (CM) of CAFs and NFs was prepared. Reverse transcription quantitative polymerase chain reaction (RT-qPCR) and western blotting examined the expression levels of epithelial (E)-cadherin, neural (N)-cadherin and vimentin. A Matrigel® invasion assay and wound healing assay were used to analyze the effect of the CM on invasion and migration. An ELISA assay also measured the levels of various cytokines in the CM. In addition, EMT-associated proteins in metastatic lung tissues were detected by immunohistochemical assay. The results indicated that the CM of CAFs may decrease the level of E-cadherin, and increase the levels of N-cadherin and vimentin, while increasing the levels of invasion and metastasis in EC cells. The concentration of epidermal growth factor, transforming growth factor-β, hepatic growth factor and fibroblast growth factor in the CM of CAFs increased significantly, in comparison with the NFs group (P<0.05). The exogenous growth factors induced migration and invasion of EC cells. CAFs induced lung metastasis and the EMT process in vivo. These data suggested that cancer-associated fibroblasts may induce EMT through the secreted cytokines in endometrial cancer cells.
Effect on Strength and Hardness of Clay Ceramic Substrate after Treatment Using Koalin Based Geopolymer Glaze

Geopolymerization is an alternative for ceramic industry by using clay based material such as kaolin or calcined kaolin geopolymer. Geopolymer paste is initially produced by alkaline activation of calcined kaolin with NaOH and Na2SiO3 solution), dried at 80oC for 4 hours, pulverized and sieved to fixed particle size powder. The parameters involved in this processing route (alkali concentration, kaolin or calcined kaolin to activator ratio, alkali activator ratio and heating conditions) are investigated. Geopolymeric powder is added with water to produce slurry to be coated on the surface of clay ceramic. It undergoes heat treatment at high temperature to produce glaze on the surface. Flexural strength and hardness analysis are studied. Result evidences the processing show of incresing strength value between 8-10% after treatment with geopolymer glaze and also the Vickers hardness values of geopolymers improved.
Random or Stochastic Monoallelic Expressed Genes Are Enriched for Neurodevelopmental Disorder Candidate Genes

Random or stochastic monoallelic expressed genes (StMA genes) represent a unique form of monoallelic expression where allelic choice is made at random early in development. The consequential clonal diversity provides opportunity for functional heterozygosity in tissues such as the brain, and can impact on both development and disease. We investigate the relationship of StMA expressed genes previously identified in clonal neural stem cells with the neurodevelopmental disorders autism and schizophrenia. We found that StMA genes show an overrepresentation of schizophrenia risk candidates identified by genome wide association studies from the genetic association database. Similar suggestive enrichment was also found for genes from the NHGRI genome-wide association study catalog and a psychiatric genetics consortium schizophrenia dataset although these latter more robust gene lists did not achieve statistical significance. We also examined multiple sources of copy number variation (CNV) datasets from autism and schizophrenia cohorts. After taking into account total gene numbers and CNV size, both autism and schizophrenia associated CNVs appeared to show an enrichment of StMA genes relative to the control CNV datasets. Since the StMA genes were originally identified in neural stem cells, bias due to the neural transcriptome is possible. To address this, we randomly sampled neural stem cell expressed genes and repeated the tests. After a significant number of iterations, neural stem cell expressed genes did not show an overrepresentation in autism or schizophrenia CNV datasets. Therefore, irrespective of the neural derived transcriptome, StMA genes originally identified in neural stem cells show an overrepresentation in CNVs associated with autism and schizophrenia. If this association is functional, then the regulation (or dysregulation) of this form of allelic expression status within tissues such as the brain may be a contributory risk factor for neurodevelopmental disorders and may also influence disease discordance sometimes observed in monozygotic twins.
AN EFFECTIVE UNIAXIAL TENSILE STRESS-STRAIN RELATIONSHIP FOR PRESTRESSED CONCRETE

This report evaluates the direct tensile strength and an equivalent uniaxial tensile stress-strain relationship for prestressed concrete using data from specimens tested at the University of Alberta which represent segments from the wall of a containment vessel. The | stress-strain relationship, when used in conjunction with the BOSOR5 program [4], enables prediction of the response of prestressed concrete I under any biaxial combination of compressive and/or tensile stresses. Comparisons between the experimental and analytical (B0S0R5) load' • strain response of the wall segments are also presented. It is I concluded that the BOSOR5 program is able to predict satisfactorily the response of the wall segments and multi-layered shell structures. I I I I I I i I iii
Training for Lung Ultrasound Score Measurement in Critically Ill Patients.

1.86 0.8% (mean6 SD). The exact value chosen for VANA appears not to be critical. Therefore, a moderate error in flow sensor calibration is of low importance. In future studies, EFFi should be compared with alternative parameters (e.g., VAE/VT proposed by Lucangelo and colleagues [10]). Because EFFi and VDphys/VT reflect uneven V : /Q : among lung compartments, it was expected that they correlate closely. EFFi is easier to study, as it is noninvasive and may be continuously monitored. The study is limited to small groups. However, at health, the results show a low degree of variation, as expected from absence of variability caused by disease. The total separation between health and ARDS indicates that, in mechanically ventilated patients, EFFi may be useful for monitoring of ARDS evolution. This aspect is strengthened by the fact that EFFi may automatically, continuously, and noninvasively be monitored in the individual patient, who then serves as his own standard of reference. EFFi merits further studies in broad materials covering ARDS and other diseases, performed with modern capnographic equipment. n
Influence of slag composition and temperature on the hydration and performance of slag blends in chloride environments

The use of GGBS as supplement for cements has been shown to improve the long-term strength and durability properties of concrete. In practice, while the chemical composition of GGBS from a single plant may be constant, due to the varying sources from which GGBS is obtained the chemical composition from plant to plant may vary. The wide variability in the use of GGBS as a SCM in different climates, coupled with differences in chemical composition, is bound to have impact on the performance of slag blends. This study investigated the combined influence of difference in slag composition and temperature on the performance of slag blends. Performance was evaluated in terms of strength and transport properties. Paste samples were characterised by calorimetry, TGA, XRD and SEM to follow hydration and microstructural development. Mortar samples were used to follow strength development and transport properties. All tests were carried out at temperatures of 20 and 38°C. Curing at 38°C accelerated the early hydration, but not the later hydration. This led to higher early strengths and lower later strengths, and was attributed to the coarsening of the pore structure caused by the high temperature curing. Except at the early ages at 20°C, both slag blends showed better strength performance than the reference cement. The slag blends also showed better transport properties than the reference cement, especially at 38°C, and this was attributed to their finer pore structure and higher chloride binding capacity. Of the two slags studied, the more reactive slag (slag 1) had better performance, especially at 38°C. Performance of the slag blends at 20°C was influenced mainly by the length of curing, and by the difference in chemical composition at 38°C.
Decision-support workload characteristics on a clustered database server from the OS perspective

A range of database services are being offered on clusters of workstations today to meet the demanding needs of applications with voluminous datasets, high computational and I/O requirements and a large number of users. The underlying database engine runs on cost-effective off-the-shelf hardware and software components that may not really be tailored/tuned for these applications. At the same time, many of these databases have legacy codes that may not be easy to modulate based on the evolving capabilities and limitations of clusters. An indepth understanding of the interaction between these database engines and the underlying operating system (OS) can identify a set of characteristics that would be extremely valuable for future research on systems support for these environments. To our knowledge, there is no prior work that has embarked on such a characterization for a clustered database server. Using IBM DB2 Universal Database (UDB) Extended Enterprise Edition (EEE) V7.2 Trial version and TPC-H like/sup 1/ decision support queries, this paper studies numerous issues by evaluating performance on an off-the-shelf Pentium/Linux cluster connected by Myrinet. These include detailed performance profiles of all kernel activities, as well as qualitative and quantitative insights on the interaction between the database engine and the operating system.
Epidemiology of Chronic Pancreatitis Jorge

Epidemiologic descriptions of chronic pancreatitis (CP) have changed over time. The focus of reports from 1950-1990's was to describe the clinical profile and natural history in a series of patients. Many landmark studies during this period are crucial to our understanding of the disease. In the past 25 years, studies have also focused on describing population distributions of CP, its risk based on the presence of environmental and genetic risk factors, impact of CP on quality of life, and frequency and factors that affect the evolution of acute and recurrent acute pancreatitis (RAP) to CP. In this chapter, we will review the current epidemiology of CP, and changes that have been observed over the past half-century and their potential explanations. For detailed descriptions of the role of environmental risk factors in CP, natural history of disease, and medical and surgical management, the reader is encouraged to refer to chapters of this book dedicated to these topics.
A CTP Synthase Undergoing Stage-Specific Spatial Expression Is Essential for the Survival of the Intracellular Parasite Toxoplasma gondii

Cytidine triphosphate synthase catalyzes the synthesis of cytidine 5′-triphosphate (CTP) from uridine 5′-triphosphate (UTP), the final step in the production of cytidine nucleotides. CTP synthases also form filamentous structures of different morphologies known as cytoophidia, whose functions in most organisms are unknown. Here, we identified and characterized a novel CTP synthase (TgCTPS) from Toxoplasma gondii. We show that TgCTPS is capable of substituting for its counterparts in the otherwise lethal double mutant (ura7Δ ura8Δ) of Saccharomyces cerevisiae. Equally, recombinant TgCTPS purified from Escherichia coli encodes for a functional protein in enzyme assays. The epitope-tagged TgCTPS under the control of its endogenous promoter displays a punctate cytosolic distribution, which undergoes spatial reorganization to form foci or filament-like structures when the parasite switches from a nutrient-replete (intracellular) to a nutrient-scarce (extracellular) condition. An analogous phenotype is observed upon nutrient stress or after treatment with a glutamine analog, 6-diazo-5-oxo-L-norleucine (DON). The exposure of parasites to DON disrupts the lytic cycle, and the TgCTPS is refractory to a genetic deletion, suggesting an essential requirement of this enzyme for T. gondii. Not least, this study, together with previous studies, supports that CTP synthase can serve as a potent drug target, because the parasite, unlike human host cells, cannot compensate for the lack of CTP synthase activity.
Vitamin D limits inflammation-linked microRNA expression in adipocytes in vitro and in vivo: A new mechanism for the regulation of inflammation by vitamin D

ABSTRACT Inflammation of adipose tissue is believed to be a contributing factor to many chronic diseases associated with obesity. Vitamin D (VD) is now known to limit this metabolic inflammation by decreasing inflammatory marker expression and leukocyte infiltration in adipose tissue. In this study, we investigated the impact of VD on microRNA (miR) expression in inflammatory conditions in human and mouse adipocytes, using high-throughput methodology (miRNA PCR arrays). Firstly, we identified three miRs (miR-146a, miR-150, and miR-155) positively regulated by TNFα in human adipocytes. Interestingly, the expression of these miRs was strongly prevented by 1,25(OH)2D preincubation. These results were partly confirmed in 3T3-L1 adipocytes (for miR-146a and miR-150). The ability of VD to control the expression of these miRs was confirmed in diet-induced obese mice: the levels of the three miRs were increased following high fat (HF) diet in epididymal white adipose tissue and reduced in HF diet fed mice supplemented with VD. The involvement of NF-κB signaling in the induction of these miRs was confirmed in vitro and in vivo using aP2-p65 transgenic mice. Finally, the ability of VD to deactivate NF-κB signaling, via p65 and IκB phosphorylation inhibition in murine adipocyte, was observed and could constitute a driving molecular mechanism. This study demonstrated for the first time that VD modulates the expression of miRs in adipocytes in vitro and in adipose tissue in vivo through its impact on NF-κB signaling pathway, which could represent a new mechanism of regulation of inflammation by VD.
Combination of Boundary Element Method and Finite Element Method in Diffuse Optical Tomography

This paper presents a new numerical method for optical tomography: the combined boundary element/finite element method (BEM-FEM), designed to tackle reconstructions in layered turbid media. The BEM-FEM focuses on the region of interest by creating a volume mesh and reconstructing in this region only. All other regions are treated as piecewise constant in a surface-integral approach. We validate the model in concentric spheres, with different positions of the volume-integral treated area and found it compared well with an analytical result. We then performed functional imaging of the neonate's motor cortex in vivo, in a reconstruction restricted to the brain, both with FEM and BEM-FEM. These results show the effectiveness of the BEM-FEM in situations where the organ of interest is surrounded by superficial layers.
Quantifying Reproducibility in Computational Biology: The Case of the Tuberculosis Drugome

How easy is it to reproduce the results found in a typical computational biology paper? Either through experience or intuition the reader will already know that the answer is with difficulty or not at all. In this paper we attempt to quantify this difficulty by reproducing a previously published paper for different classes of users (ranging from users with little expertise to domain experts) and suggest ways in which the situation might be improved. Quantification is achieved by estimating the time required to reproduce each of the steps in the method described in the original paper and make them part of an explicit workflow that reproduces the original results. Reproducing the method took several months of effort, and required using new versions and new software that posed challenges to reconstructing and validating the results. The quantification leads to “reproducibility maps” that reveal that novice researchers would only be able to reproduce a few of the steps in the method, and that only expert researchers with advance knowledge of the domain would be able to reproduce the method in its entirety. The workflow itself is published as an online resource together with supporting software and data. The paper concludes with a brief discussion of the complexities of requiring reproducibility in terms of cost versus benefit, and a desiderata with our observations and guidelines for improving reproducibility. This has implications not only in reproducing the work of others from published papers, but reproducing work from one’s own laboratory.