Miracle-dz/UniFAR-FTUs huggingface dataset:
Systematic Review: Vitamin D and Cardiometabolic Outcomes

BACKGROUND Vitamin D may modify risk for cardiometabolic outcomes (type 2 diabetes, hypertension, or cardiovascular disease). PURPOSE To examine the association between vitamin D status, including the effect of vitamin D supplementation, and cardiometabolic outcomes in generally healthy adults. DATA SOURCES English-language studies in MEDLINE (inception to 4 November 2009) and the Cochrane Central Register of Controlled Trials (fourth quarter of 2009). STUDY SELECTION 11 reviewers screened citations to identify longitudinal cohort studies that reported associations between vitamin D status and cardiometabolic outcomes, including randomized trials of vitamin D supplementation. DATA EXTRACTION 5 independent reviewers extracted data about study conduct, participant characteristics, outcomes, and quality. Differences were resolved by consensus. DATA SYNTHESIS 13 observational studies (14 cohorts) and 18 trials were eligible. Three of 6 analyses (from 4 different cohorts) reported a lower incident diabetes risk in the highest versus the lowest vitamin D status groups. Eight trials found no effect of vitamin D supplementation on glycemia or incident diabetes. In meta-analysis of 3 cohorts, lower 25-hydroxyvitamin D concentration was associated with incident hypertension (relative risk, 1.8 [95% CI, 1.3 to 2.4]). In meta-analyses of 10 trials, supplementation nonsignificantly reduced systolic blood pressure (weighted mean difference, -1.9 mm Hg [CI, -4.2 to 0.4 mm Hg]) and did not affect diastolic blood pressure (weighted mean difference, -0.1 mm Hg [CI, -0.7 to 0.5 mm Hg]). Lower 25-hydroxyvitamin D concentration was associated with incident cardiovascular disease in 5 of 7 analyses (6 cohorts). Four trials found no effect of supplementation on cardiovascular outcomes. LIMITATIONS Studies included primarily white participants. Observational studies were heterogeneous. Several trials reported post hoc analyses. CONCLUSION The association between vitamin D status and cardiometabolic outcomes is uncertain. Trials showed no clinically significant effect of vitamin D supplementation at the dosages given. PRIMARY FUNDING SOURCE National Institute of Diabetes and Digestive and Kidney Disease, the National Institutes of Health Office of Dietary Supplements, U.S. Food and Drug Administration, Agency for Healthcare Research and Quality, and Public Health Agency of Canada.
From Volatility Transmission to Contagion between Stock Markets: The Lighting of a Nonlinear VAR Model with Structural Breaks in Variance

We develops in this paper a nonlinear vector autoregressive model to study stock market interdependences. Among the innovations of this work, we introduce a structural break in the conditional variances-covariance’s matrix of multivariate GARCH process. We consider a BEKK expand with shocks to volatility transmission across markets. The purpose of these amendments is to respond to several biases in the measurement of volatilities and correlations between markets: a primer bias is the shocks to volatility persistence over estimating; second, heteroskedasticity and omitted variables bias in market cross-correlation estimates. We use a sample of 11 markets from Europe, North America, and Asia with weekly data of market indices between 1985 and 2006. Several interesting results are obtained with this model: the reduction of shocks to volatility persistence, price and uncertainties transmission from U.S. market to European and Asian markets, regional transmission phenomenon in Europe and Asia, apart from the U.S. crash of October 1987, all crises are not always contagious. At last but not the least, it is not clear that financial liberalization isolates markets from instability and contagion, although the integration is a good tool for market efficiency. Crises and contagion phenomenon can be market equilibrating process.
RGBM: regularized gradient boosting machines for identification of the transcriptional regulators of discrete glioma subtypes

Abstract We propose a generic framework for gene regulatory network (GRN) inference approached as a feature selection problem. GRNs obtained using Machine Learning techniques are often dense, whereas real GRNs are rather sparse. We use a Tikonov regularization inspired optimal L-curve criterion that utilizes the edge weight distribution for a given target gene to determine the optimal set of TFs associated with it. Our proposed framework allows to incorporate a mechanistic active biding network based on cis-regulatory motif analysis. We evaluate our regularization framework in conjunction with two non-linear ML techniques, namely gradient boosting machines (GBM) and random-forests (GENIE), resulting in a regularized feature selection based method specifically called RGBM and RGENIE respectively. RGBM has been used to identify the main transcription factors that are causally involved as master regulators of the gene expression signature activated in the FGFR3-TACC3-positive glioblastoma. Here, we illustrate that RGBM identifies the main regulators of the molecular subtypes of brain tumors. Our analysis reveals the identity and corresponding biological activities of the master regulators characterizing the difference between G-CIMP-high and G-CIMP-low subtypes and between PA-like and LGm6-GBM, thus providing a clue to the yet undetermined nature of the transcriptional events among these subtypes.
Effects of the Porcine Oviduct-Specific Glycoprotein on Fertilization, Polyspermy, and Embryonic Development In Vitro1

Abstract This study evaluated the effects of porcine oviduct-specific glycoprotein (pOSP) on in vitro fertilization (IVF), polyspermy, and development to blastocyst. Experiment 1 evaluated the effects of various concentrations (0–100 μg/ml) of purified pOSP on fertilization parameters, including penetration, polyspermy, male pronuclear formation, and mean number of sperm penetrated per oocyte. Experiment 2 examined the ability of an anti-pOSP immunoglobulin G to inhibit the observed effects of pOSP on fertilization parameters. Experiments 3 and 4 examined various concentrations of pOSP (0–100 μg/ml) on zona pellucida solubility and sperm binding, respectively. Lastly, experiment 5 assessed the effects of various concentrations of pOSP (0–100 μg/ml) on the in vitro embryo cleavage rate and development to blastocyst. Pig oocytes matured and fertilized in vitro were used for all experiments. An effect of treatment (P < 0.05) was detected for pOSP on penetration, polyspermy, and mean number of sperm per oocyte. Concentrations for pOSP of 0–50 μg/ml had no effect on sperm penetration rates; however, compared with the control, 100 μg/ml significantly decreased the penetration rate (74% vs. 41%). Addition of 10–100 μg/ml significantly reduced the polyspermy rate compared with the control (61% vs. 24–29%). The decrease in polyspermy achieved by addition of pOSP during preincubation and IVF was blocked with a specific antibody to pOSP. No effect of treatment was observed on zona digestion time relative to the control; however, the number of sperm bound to the zona pellucida was significantly decreased by treatment (P < 0.05). Compared with the control, all concentrations of pOSP examined reduced the number of sperm bound per oocyte (45 vs. 19–34). A treatment effect (P < 0.05) was observed for pOSP on embryo development to blastocyst but not on cleavage rates. Addition of pOSP during preincubation and fertilization significantly increased postcleavage development to blastocyst, but a synergistic stimulation on development was not detected when pOSP was included during in vitro culture. These results indicate that exposure to pOSP before and during fertilization reduces the incidence of polyspermy in pig oocytes, reduces the number of bound sperm, and increases postcleavage development to blastocyst.
The power of spectral density analysis for mapping endogenous BOLD signal fluctuations

FMRI has revealed the presence of correlated low‐frequency cerebro‐vascular oscillations within functional brain systems, which are thought to reflect an intrinsic feature of large‐scale neural activity. The spatial correlations shown by these fluctuations has been their identifying feature, distinguishing them from fluctuations associated with other processes. Major analysis methods characterize these correlations, identifying networks and their interactions with various factors. However, other analysis approaches are required to fully characterize the regional signal dynamics contributing to these correlations between regions. In this study we show that analysis of the power spectral density (PSD) of regional signals can identify changes in oscillatory dynamics across conditions, and is able to characterize the nature and spatial extent of signal changes underlying changes in measures of connectivity. We analyzed spectral density changes in sessions consisting of both resting‐state scans and scans recording 2 min blocks of continuous unilateral finger tapping and rest. We assessed the relationship of PSD and connectivity measures by additionally tracking correlations between selected motor regions. Spectral density gradually increased in gray and white matter during the experiment. Finger tapping produced widespread decreases in low‐frequency spectral density. This change was symmetric across the cortex, and extended beyond both the lateralized task‐related signal increases, and the established “resting‐state” motor network. Correlations between motor regions also reduced with task performance. In conclusion, analysis of PSD is a sensitive method for detecting and characterizing BOLD signal oscillations that can enhance the analysis of network connectivity. Hum Brain Mapp 2008. © 2008 Wiley‐Liss, Inc.
Histone deacetylase dHDAC4 is involved in segmentation of the Drosophila embryo and is regulated by gap and pair‐rule genes

Summary: Histone deacetylases (HDACs) are catalytic subunits of multiprotein complexes that are targeted to specific promoters through their interaction with different transcriptional repressors causing silencing of the corresponding genes. This study describes the isolation of dHDAC4, a novel, catalytically active class II Drosophila histone deacetylase, and the analysis of its role in embryonic development. In early embryos, dHDAC4 is expressed in several phases. Initial ubiquitous expression becomes localized to an anterior domain, then evolves into a pair‐rule‐like and finally into a segment‐polarity‐like pattern. Suppression of dHDAC4 during early embryogenesis by double‐stranded RNA interference led to segmentation defects. Analysis of dHDAC4 expression in gap and pair‐rule gene mutants demonstrated that hunchback, knirps, and giant activate, while even‐skipped suppresses dHDAC4 expression. These data revealed dHDAC4 involvement in the segmentation regulatory pathway and suggested complex transcriptional regulation as a potential mechanism that controls its expression. genesis 35:31–38, 2003. © 2002 Wiley‐Liss, Inc.
Structural model of the complete poly(A) region of HIV-1 pre-mRNA

In the HIV-1 retrovirus, identical sequences encompassing the AAUAAA hexamer and the U/GU-rich downstream sequence element (DSE) that compose the core poly(A) site are present at both the 5′ and 3′ ends of the HIV-1 pre-mRNA. The AAUAAA hexamer is partly occluded by base pairing in the upper part of a semi-stable polyA hairpin. This sets the stage for regulation of HIV-1 polyadenylation, which involves reaction suppression at the 5′ end and its stimulation at the 3′ end. Efficient utilization of the 3′ core poly(A) site is promoted by major and minor upstream sequence elements (USEs) which are uniquely present at the 3′ end of the HIV-1 transcript. The structures of the HIV-1 5′ and 3′ poly(A) sites are defined by overall architecture of complete 5′ and 3′ untranslated terminal regions (UTRs). To our knowledge, there is still no structural model of a complete 3′ UTR of the HIV-1 pre-mRNA and complete 3′ poly(A) region including the USEs except the fact that the polyA and transactivation response (TAR) hairpins are present at both ends of the HIV-1 pre-mRNA. In this work, we predicted a secondary structure of the 3′ UTR of HIV-1 pre-mRNA based on our observation that the minor USEs are located in a region with a high potential to form G-quadruplex structures. We first present structural models for the major USE, complete 3′ poly(A) region, and almost entire 3′ UTR of HIV-1 pre-mRNA. Our models are built based on the mfold and UNAFold secondary structure prediction of these regions for about 1500 HIV-1 isolates of different subtypes and recombinant forms. We have demonstrated that these models are valid for most of the HIV-1 isolates studied. The proposed models include the known TAR and polyA hairpins and new structural elements containing the U-rich tract of the major USE and U/GU-rich DSE which are fully exposed and accessible to the polyadenylation machinery, which confirms the functional competence of our models.
Estimation of the domain of attraction for nonlinear autonomous systems using a bezoutian approach

One of the central subjects in modern control engineering is the investigation of stability for arbitrary given nonlinear systems. In this contribution we will introduce a novel method to compute the domain of attraction (DA) of a polynomial system using bezoutians. The presented method is able to estimate the DA for a given system linear as well as nonlinear system. It works for quadratic Lyapunov function as well as for arbitrary non linear Lyapunov functions. In this present algorithm the DA is successfully determined by an inner and outer bound. The inner bound yields an enclosure of the Lyapunov function (LF) countour line c*.
In vivo processing of Staphylococcus aureus lipase

The Staphylococcus aureus lipase gene encodes a 76-kDa protein. Extracellular lipase purified from culture supernatants is only 45 to 46 kDa, however. We show that the lipase is secreted in vivo as an 82-kDa protein with full enzymatic activity. It is then sequentially processed, both in culture and in cell-free supernatants, to a mature, 45- to 46-kDa protein. Protein sequencing demonstrates that the N-terminal region of the 82-kDa prolipase, comprising 295 amino acids, is cleaved from the central and C-terminal moieties, which contain the active site. A metallocysteine protease is probably responsible for initiating this processing. The extremely hydrophobic, mature lipase is resistant to further protease degradation and retains the full catalytic activity of the prolipase.
A generalized concordance correlation coefficient for continuous and categorical data

This paper discusses a generalized version of the concordance correlation coefficient for agreement data. The concordance correlation coefficient evaluates the accuracy and precision between two measures, and is based on the expected value of the squared function of distance. We have generalized this coefficient by applying alternative functions of distance to produce more robust versions of the concordance correlation coefficient. In this paper we extend the application of this class of estimators to categorical data as well, and demonstrate similarities to the kappa and weighted kappa statistics. We also introduce a stratified concordance correlation coefficient which adjusts for explanatory factors, and an extended concordance correlation coefficient which measures agreement among more than two responses. With these extensions, the generalized concordance correlation coefficient provides a unifying approach to assessing agreement among two or more measures that are either continuous or categorical in scale. Copyright © 2001 John Wiley & Sons, Ltd.
Bank Run Determinants in Indonesia: Bad Luck or Fundamental Factors?

Bank runs and banking crises have become global phenomena occurring repeatedly in both developed and developing countries during the last few decades. Bank runs and banking crises have increased since financial liberalization in the 1980? s and 1990? s (Davis and Karim, 2007). In Indonesia, bank runs have also occurred repeatedly. In 1992, bank runs beset a few national banks triggering the liquidation of one of the country? s national private banks. Subsequently, in 1997/1998, bank runs developed into the worst banking crisis in the history of Indonesian banking. Empirical experience can demonstrate the magnitude of costs incurred due to bank runs and the banking crisis. In Indonesia? s case, the total fiscal cost involved for the recuperation of banks and output loss due to banking crises in Indonesia during the period of 1997-2002 were 55% and 39% of gross domestic product respectively (Hanson, 2005). Considering the extent of losses precipitated by bank runs and the banking crisis, extensive studies on the determinants of bank runs are urgently required to prevent future bank runs and banking crises. This paper aims to comprehensively analyze the determinants of a bank runs, including macroeconomic conditions, bank fundamentals and the self-fulfilling prophecy factor for all banks, both during the sample period of 1990-2005 as well as during the banking crisis in 1997-1998. The study of bank run determinants uses the dynamic panel model of Arrelano-Bond. Based on monthly bank data from 1990-2005, the Arrelano-Bond dynamic panel shows that the self-fulfilling prophecy factor (bad luck), bank fundamentals -including profitability and non-performing loans- as well as macroeconomic conditions such as economic growth, inflation and real interest rates affect bank runs in Indonesia. Bank run determinants during the crisis period in 1997-1998 also display similar results to bank run determinants for the extended sample period of 1990-2005. See above See above
An Improved Peak Quantification Algorithm for Automatic Heart Rate Measurements

This paper proposes a new method improving the peak quantification algorithm (PQA) introduced by Navakatikyan, et al. In measuring a human heart rate (HR). Experiments reveal that although the PQA can accurately measure the heart rates based on electrocardiogram (ECG) waveforms, this algorithm is too complex and uses too much memory, resulting in substantial reduction in accuracy when applied such algorithm to an embedded system. The proposed improved-peak quantification algorithm (improved-PQA) can rapidly analyze the heartbeat waveforms and still accurately measure the heart rates even when it is adopted in an embedded system with a lower computational power and speed
Teacher Perceptions of Their Curricular and Pedagogical Shifts: Outcomes of a Project-Based Model of Teacher Professional Development in the Next Generation Science Standards

In this study, we conducted a model of teacher professional development (PD) on the alignment of middle and high school curricula and instruction to the Next Generation Science Standards (NGSSs), and evaluated the impact of the PD on teacher participants’ development. The PD model included a 4-day summer academy emphasizing project-based learning (PBL) in the designing of NGSS-aligned curricula and instruction, as well as monthly follow-up Professional Learning Community meetings throughout the year providing numerous opportunities for teachers to develop and implement lesson plans, share results of lesson writing and implementation (successes and challenges), provide mutual feedback, and refine curricula and assessments. Following the summer academy, six female teachers were interviewed about their current conceptualizations of NGSS, the extent of curricular shifts made that are required by NGSS, their self-perceptions regarding their level of accomplishment in curriculum writing, and the benefits of the PD in reaching their goals related to NGSS. Interviews were supplemented with an analysis of lesson plans written while participating in the PD program. The interviewed teachers suggested that they had made important conceptual and pedagogical shifts required by NGSS as they participated in the PD, and also noted a variety of challenges as they made this shift. While all teachers were relative novices at NGSS curriculum writing before the PD, most of the teachers interviewed felt that they had achieved the status of an “accomplished novice” following the summer academy. An analysis of their written lessons suggested a great range in the extent to which teachers effectively applied their understanding of NGSS to write lessons aligned to NGSS. Interviewed teachers believed that the PD model was helpful to their development as science teachers, and all reported that there were no aspects of the PD that were not helpful. Even though most teachers obtained a basic understanding and conceptualization of NGSS and PBL, their application of this understanding in their curriculum writing varied. The present study may help to inform future efforts to support teachers to align curricula and instruction to NGSS through teacher PD.
Forecasting the Jordanian stock index: modelling asymmetric volatility and distribution effects within a GARCH framework

The modelling of market returns can be especially problematical in emerging and frontier financial markets given the propensity of their returns to exhibit significant non-normality and volatility asymmetries. This paper attempts to identify which representations within the GARCH family of models can most efficiently deal with these issues. A number of different distributions (normal, Student t, GED and skewed Student) and different volatility of returns asymmetry representations (EGARCH and GJR- -GARCH) are examined. Our data set consists of daily Jordanian stock market returns over the period January 2000 – November 2014. Using both the Superior Predicative Ability (SPA) and Model Confidence Set (MCS) testing frameworks it is found that using GJR-GARCH with a skewed Student distribution most accurately and efficiently forecasts Jordanian market movements. Our findings are consistent with similar research undertaken in respect to developed markets.
Haemostatic profile in hypothyroidism as potential risk factor for vascular or thrombotic disease

The influence of thyroid failure on haemostasis is controversial, both hypocoagulable and hypercoagulable states have been reported. Since both subclinical and overt hypothyroidism have been associated with atherosclerosis, a hypercoagulable state in addition might represent a risk factor for thromboembolic disease.