Miracle-dz/UniFAR-FTUs huggingface dataset:
Screening of differentially expressed protein kinases in bone marrow endothelial cells and the protective effects of the p38a inhibitor SB203580 on bone marrow in liver fibrosis

Hematological abnormalities are frequently observed in patients with liver cirrhosis (LC). A previous study demonstrated that the apoptosis and damage of endothelial cells could cause the hematological abnormalities in LC. Protein kinases are one of the most important factors that regulate cell behavior, and are potential therapeutic targets for the treatment of a number of diseases. In a previous study, whole genome profiling was used to identify differentially expressed genes in human bone marrow endothelial cells treated with serum from 26 patients with LC. From this data set, the present study identified 14 differentially expressed kinase genes in human bone marrow endothelial cells in LC from the microarray data, including p38a, AKT1 and PDK1. Pathway analysis revealed that these kinase genes were enriched in certain important LC-associated pathways (e.g. MAPK and WNT signaling pathway). Literature mining revealed that p38a was associated with bone marrow apoptosis; therefore, p38a and its inhibitor, SB203580, were selected as potential therapeutic targets in the present study. The results of hematoxylin-eosin and Masson's trichrome staining of livers from a rat model of liver fibrosis (LF) that underwent ligation of the bile duct demonstrated that SB203580 reduced the degree of LF. In addition, SB203580-treated rats with LF demonstrated a significantly higher number of platelets when compared with the untreated group. Terminal deoxynucleotidyl transferase dUTP nick end labeling (TUNEL) analysis indicated that apoptosis of bone marrow tissue in rats with LF was inhibited by SB203580. In addition, the results from the immunohistochemical analysis demonstrated that SB203580 reduced the expression of von Willebrand factor and caspase 3 in the bone marrow of rats with LF. In conclusion, the results from the present study indicate that the p38a kinase inhibitor, SB203580, may exhibit a protective effect on bone marrow tissues in rats with LF. This suggests that protein kinases and their inhibitors may present novel therapeutic strategies for the treatment of hematological abnormalities in patients with LC.
Field oriented control of five-phase synchronous reluctance motor drive with flexible 3/sup rd/ harmonic current injection for high specific torque

It is shown that third harmonic current injection can produce higher shaft torque than conventional sinusoidal current regulation in five-phase synchronous reluctance machines with salient-pole rotors. This paper investigates the field oriented control (FOC) including the hysteresis-type PWM current regulator of such machines under flexible third harmonic current injection. It is concluded that the sinusoidal current injection can be viewed as a special case of combined fundamental plus third harmonic current injection with 0 percent of third harmonic current. The flexible FOC control algorithm is designed and the developed model is confirmed by the simulation results in Matlab/Simulink environment. The complete strategy has been implemented on a digital signal processor based five-phase synchronous reluctance motor drive fabricated in the authors' laboratory. The experimental results verify the developed flexible fundamental plus third harmonic FOC.
Predicting morphotropic phase boundary locations and transition temperatures in Pb- and Bi-based perovskite solid solutions from crystal chemical data and first-principles calculations

Using data obtained from first-principles calculations, we show that the position of the morphotropic phase boundary (MPB) and transition temperature at MPB in ferroelectric perovskite solutions can be predicted with quantitative accuracy from the properties of the constituent cations. We find that the mole fraction of PbTiO3 at MPB in Pb(B′B″)O3–PbTiO3, BiBO3–PbTiO3, and Bi(B′B″)O3–PbTiO3 exhibits a linear dependence on the ionic size (tolerance factor) and the ionic displacements of the B cations as found by density-functional-theory calculations. This dependence is due to competition between the local repulsion and A-cation displacement alignment interactions. Inclusion of first-principles displacement data also allows accurate prediction of transition temperatures at the MPB. The obtained structure-property correlations are used to predict morphotropic phase boundaries and transition temperatures in as yet unsynthesized solid solutions.
A fitness trade-off between seasons causes multigenerational cycles in phenotype and population size

Although seasonality is widespread and can cause fluctuations in the intensity and direction of natural selection, we have little information about the consequences of seasonal fitness trade-offs for population dynamics. Here we exposed populations of Drosophila melanogaster to repeated seasonal changes in resources across 58 generations and used experimental and mathematical approaches to investigate how viability selection on body size in the non-breeding season could affect demography. We show that opposing seasonal episodes of natural selection on body size interacted with both direct and delayed density dependence to cause populations to undergo predictable multigenerational density cycles. Our results provide evidence that seasonality can set the conditions for life-history trade-offs and density dependence, which can, in turn, interact to cause multigenerational population cycles. DOI: http://dx.doi. org/10.7554/eLife.18770. 001
Crime, unemployment and labor market programs in turbulent times

We exploit the exceptional variation in municipality-level unemployment and spending on labor market programs in Sweden during the 1990s to identify the impact of unemployment and programs on crime. We identify a statistically significant effect of unemployment on the incidence of overall crime, burglary, auto-theft and drug possession. A calculation suggests that the sharp reduction in unemployment during the later 1990s may have reduced burglary and auto-theft with 15 and 20 percent, respectively. After addressing several specification issues, we conclude that there is at best weak evidence that labor market programs – general ones and those specifically targeted to the young – help to reduce crime.
Correlation Properties and Complexity of Perioperative RR-Interval Dynamics in Coronary Artery Bypass Surgery Patients

Background Dynamic measures of heart rate variability (HRV) may uncover abnormalities that are not easily detectable with traditional time and frequency domain measures. The purpose of this study was to characterize changes in RR-interval dynamics in the immediate postoperative phase of coronary artery bypass graft (CABG) surgery using traditional and selected newer dynamic measures of HRV. Methods Continuous 24-h electrocardiograph recordings were performed in 40 elective CABG surgery patients up to 72 h postoperatively. In one half of the patients, Holter recordings were initiated 12–40 h before the surgery. Time and frequency domain measures of HRV were assessed. The dynamic measures included a quantitative and visual analysis of Poincaré plots, measurement of short- and intermediate-term fractal-like scaling exponents (&agr;1 and &agr;2), the slope (&bgr;) of the power-law regression line of RR-interval dynamics, and approximate entropy. Results The SD of RR intervals (P < 0.001) and the ultra-low-, very-low-, low-, and high-frequency power (P < 0.01, P < 0.001, P < 0.001, P < 0.01, respectively) measures in the first postoperative 24 h decreased from the preoperative values. Analysis of Poincaré plots revealed increased randomness in beat-to-beat heart rate behavior demonstrated by an increase in the ratio between short-term and long-term HRV (P < 0.001) after CABG. Average scaling exponent &agr;1 of the 3 postoperative days decreased significantly after CABG (from 1.22 ± 0.15 to 0.85 ± 0.20, P < 0.001), indicating increased randomness of short-term heart rate dynamics (i.e., loss of fractal-like heart rate dynamics). Reduced scaling exponent &agr;1 of the first postoperative 24 h was the best HRV measure in differentiating between the patients that had normal (≤ 48 h, n = 33) or prolonged (> 48 h, n = 7) intensive care unit stay (0.85 ± 0.17 vs. 0.68 ± 0.18;P < 0.05). In stepwise multivariate logistic regression analysis including typical clinical predictors, &agr;1 was the most significant independent predictor (P < 0.05) of long intensive care unit stay. None of the preoperative HRV measures were able to predict prolonged intensive care unit stays. Conclusions In the selected group of patients studied, a decrease in overall HRV was associated with altered nonlinear heart rate dynamics after CABG surgery. Current results suggest that a more random short-term heart rate behavior may be associated with a complicated clinical course. Analysis of fractal-like dynamics of heart rate may provide new perspectives in detecting abnormal cardiovascular function after CABG.
Simultaneous Decomposition of Multiple Hyperspectral Data Sets: Signal Recovery of Unknown Fluorophores in the Retinal Pigment Epithelium References and Links

Upon excitation with different wavelengths of light, biological tissues emit distinct but related autofluorescence signals. We used non-negative matrix factorization (NMF) to simultaneously decompose co-registered hyperspectral emission data from human retinal pigment epithelium/Bruch's membrane specimens illuminated with 436 and 480 nm light. NMF analysis was initialized with Gaussian mixture model fits and constrained to provide identical abundance images for the two excitation wavelengths. Spectra recovered this way were smoother than those obtained separately; fluorophore abundances more clearly localized within tissue compartments. These studies provide evidence that leveraging multiple co-registered hyperspectral emission data sets is preferential for identifying biologically relevant fluorophore information. snapshot hyperspectral image analysis of age-related macular degeneration, " in Engineering in Medicine and Nonnegative matrix factorization for rapid recovery of constituent spectra in magnetic resonance chemical shift imaging of the brain, " IEEE Trans. 2013). 6. A. Shashua and T. Hazan, " Non-negative tensor factorization with applications to statistics and computer vision, " in Blind source separation techniques for the decomposition of multiply labeled fluorescence images, " Biophys. Phospholipid meets all-trans-retinal: the making of RPE bisretinoids, " J. New insights into retinoid metabolism and cycling within the retina, " Prog. Predictive value of fundus autofluorescence for development of geographic atrophy in age-related macular degeneration, " Invest. Lack of correlation between the spatial distribution of A2E and lipofuscin fluorescence in the human retinal pigment epithelium, " Invest. Lipofuscin of human retinal pigment epithelium, " Am. J. Fluorophores of the human retinal pigment epithelium: separation and spectral characterization, " Exp. Novel lipofuscin bisretinoids prominent in human retina and in a model of recessive Stargardt disease, " J. A novel bisretinoid of retina is an adduct on glycerophosphoethanolamine, " Invest. Characterization of peroxy-A2E and furan-A2E photooxidation products and detection in human and mouse retinal pigment epithelial cell lipofuscin, " J. The all-trans-retinal dimer series of lipofuscin pigments in retinal pigment epithelial cells in a recessive Stargardt disease model, " Proc. Similar molecules spatially correlate with lipofuscin and N-retinylidene-N-retinylethanolamine in the mouse but not in the human retinal pigment epithelium, " Arch. Quantitative autofluorescence and cell density maps of the human retinal pigment epithelium, " Invest. Retinal pigment epithelial lipofuscin and melanin and choroidal melanin in human eyes, " Invest. Autofluorescence imaging of human RPE cell granules using structured illumination microscopy, " Br. Ortiz-de-Solorzano, " Efficient blind spectral unmixing of fluorescently labeled samples using multi-layer non-negative matrix factorization, " PLoS ONE 8(11), …
SLEEP DISORDERS ,E PILEPSY, AND AUTISM

The purpose of this review article is to describe the clinical data linking autism with sleep and epilepsy and to discuss the impact of treating sleep disorders in children with autism either with or without coexisting epileptic seizures. Studies are presented to support the view that sleep is abnormal in individuals with autistic spectrum disorders. Epilepsy and sleep have reciprocal relationships, with sleep facilitating seizures and seizures adversely affecting sleep architecture. The hypothesis put forth is that identifying and treating sleep disorders, which are potentially caused by or contributed to by autism, may impact favorably on seizure control and on daytime behavior. The article concludes with some practical suggestions for the evaluation and treatment of sleep disorders in this population of children with autism.
‘Membership matters’: applying Membership Categorisation Analysis (MCA) to qualitative data using Computer‐Assisted Qualitative Data Analysis (CAQDAS) Software

This paper introduces and outlines a methodology that may be unfamiliar to some qualitative researchers: Membership Categorisation Analysis (MCA). The first section of the paper explains the basic principles of MCA and why it is a valid method for exploring the power of categorisations in texts and talk. Additionally, it explains why MCA differs from other forms of qualitative data analysis. The second section begins with a discussion of why researchers might or might not use Computer‐Assisted Qualitative Data Analysis (CAQDAS) Software. Subsequently, a detailed description of how MCA was applied to qualitative data using the CAQDAS software package NVivo is outlined. To provide examples, this paper draws on a project that used MCA to analyse the interview accounts of 25 young people who had taken a Gap Year between leaving school and beginning university. The paper concludes that qualitative researchers should consider using MCA and that CAQDAS is a useful tool to aid its application.
SimCompass: Using Deep Learning Word Embeddings to Assess Cross-level Similarity

This article presents our team’s participating system at SemEval-2014 Task 3. Using a meta-learning framework, we experiment with traditional knowledgebased metrics, as well as novel corpusbased measures based on deep learning paradigms, paired with varying degrees of context expansion. The framework enabled us to reach the highest overall performance among all competing systems.
Automatic pronunciation evaluation of language learners' utterances generated through shadowing

In foreign language learning, shadowing has been used as a method for improving speaking and listening ability. In this method, learners are required to repeat a presented native utterance as closely and quickly as possible. Since learners have to follow the speaking rate of the presented utterance, their pronunciation often becomes very inarticulate and unintelligible. These features of shadowing make it very difficult to build a reliable scoring system for shadowing productions. In this paper, two techniques are proposed and investigated for automatic scoring of shadowing productions. Experiments show that good correlations are found between automatic scores and TOEIC overall proficiency scores.
Toward an Optical Brain-computer Interface based on Consciously-modulated Prefrontal Hemodynamic Activity

Toward an optical brain-computer interface based on consciously-modulated prefrontal hemodynamic activity Sarah Dianne Power Doctor of Philosophy Graduate Department of Biomaterials and Biomedical Engineering University of Toronto 2012 Brain-computer interface (BCI) technologies allow users to control external devices through brain activity alone, circumventing the somatic nervous system and the need for overt physical movement. BCIs may potentially benefit individuals with severe neuromuscular disorders who experience significant, and often total, loss of voluntary muscle control (e.g. amyotrophic lateral sclerosis, multiple sclerosis, brainstem stroke). This thesis investigates the feasibility of a practical, online optical BCI based on conscious modulation of prefrontal cortex activity through the performance of different cognitive tasks, specifically mental arithmetic (MA) and mental singing (MS). The thesis comprises five studies, each representing a step toward the realization of a practical optical BCI. The first study demonstrates the feasibility of a two-choice synchronized optical BCI based on intentional control states corresponding to MA and MS. The second study explores a more user-friendly alternative a two-choice system-paced BCI supporting a single intentional control state (either MA or MS) and a natural baseline, or “no-control (NC)”, state. The third study investigates the feasibility of a three-choice system-paced BCI supporting both MA and MS, as well as the NC state. The fourth study examines the consistency with which the relevant mental states can be differentiated over multiple sessions. The first four studies involve healthy adult participants; in the final study, the feasibility of optical BCI use by a user with Duchenne muscular dystrophy is explored.
Perception Science in the Age of Deep Neural Networks

For decades, perception was considered a unique ability of biological systems, little understood in its inner workings, and virtually impossible to match in artificial systems. But this status quo was upturned in recent years, with dramatic improvements in computer models of perception brought about by “deep learning” approaches. What does all the ruckus about a “new dawn of artificial intelligence” imply for the neuroscientific and psychological study of perception? Is it a threat, an opportunity, or maybe a little of both?
Functions of Nonmuscle Myosin II in Assembly of the Cellular Contractile System

The contractile system of nonmuscle cells consists of interconnected actomyosin networks and bundles anchored to focal adhesions. The initiation of the contractile system assembly is poorly understood structurally and mechanistically, whereas system’s maturation heavily depends on nonmuscle myosin II (NMII). Using platinum replica electron microscopy in combination with fluorescence microscopy, we characterized the structural mechanisms of the contractile system assembly and roles of NMII at early stages of this process. We show that inhibition of NMII by a specific inhibitor, blebbistatin, in addition to known effects, such as disassembly of stress fibers and mature focal adhesions, also causes transformation of lamellipodia into unattached ruffles, loss of immature focal complexes, loss of cytoskeleton-associated NMII filaments and peripheral accumulation of activated, but unpolymerized NMII. After blebbistatin washout, assembly of the contractile system begins with quick and coordinated recovery of lamellipodia and focal complexes that occurs before reappearance of NMII bipolar filaments. The initial formation of focal complexes and subsequent assembly of NMII filaments preferentially occurred in association with filopodial bundles and concave actin bundles formed by filopodial roots at the lamellipodial base. Over time, accumulating NMII filaments help to transform the precursor structures, focal complexes and associated thin bundles, into stress fibers and mature focal adhesions. However, semi-sarcomeric organization of stress fibers develops at much slower rate. Together, our data suggest that activation of NMII motor activity by light chain phosphorylation occurs at the cell edge and is uncoupled from NMII assembly into bipolar filaments. We propose that activated, but unpolymerized NMII initiates focal complexes, thus providing traction for lamellipodial protrusion. Subsequently, the mechanical resistance of focal complexes activates a load-dependent mechanism of NMII polymerization in association with attached bundles, leading to assembly of stress fibers and maturation of focal adhesions.
Aggregate Short Interest and Market Valuations

We examine some basic data on the evolution of aggregate short interest, both during the dot-com era, and at other times in history. Total short interest moves in a countercyclical fashion. For example, short interest in NASDAQ stocks actually declines as the NASDAQ index approaches its peak. Moreover, this decline does not seem to reflect a substitution away from outright short-selling and towards put options, as the ratio of put-to-call volume displays the same countercyclical tendency. The evidence suggests that: i) arbitrageurs are reluctant to bet against aggregate mispricings; and ii) short-selling does not play a particularly helpful role in stabilizing the overall stock market.
Tuning of Control Systems Over CSMA Networks

In this paper, control systems over soft real-time carrier sensing multiple access networks are considered. A precise modeling of the system is presented, and the effects of using the communication network are probabilistically characterized. The results can be used to study several control performance issues in the stochastic setting. In this paper, the expected value of a quadratic cost function is calculated, and the result is used for optimal controller tuning and performance analysis through an example.
Beyond the Usefulness of Branded Applications: Insights from Consumer–Brand Engagement and Self-construal Perspectives

Branded mobile applications (apps) present one of the most promising opportunities for marketers to reach current and potential customers, sell products or services, and facilitate customer engagement with brands. This study aims to explore how branded apps influence consumers’ brand repurchase intention and continuance usage intention. Integrating the utilitarian view from information systems research and the view of consumer–brand engagement from marketing research, a complementary engagement path alongside the utilitarian path was devised and tested in order to elucidate consumer perceptions toward branded apps. Independent self-construal and interdependent self-construal moderate relationships along the utilitarian path and engagement path, respectively. Data collected from 637 respondents support most of the proposed hypotheses. Results show that the engagement path has more influence on continuance intention and equal influence on repurchase intention when compared to the utilitarian path. Findings show that apps users have different thoughts along each of the two paths, depending on their self-construal. The study's findings also provide app designers and marketers with new perspectives on how to better design branded apps.
Universal Social Orderings ∗

We propose the concept of a universal social ordering, defined on the set of pairs of an allocation and a preference profile of any finite population. It is meant to unify evaluations and comparisons of social states with populations of possibly different sizes with various characteristics. The universal social ordering not only evaluates policy options for a given population but also compares social welfare across populations, as in international or intertemporal comparisons of living standards. It also makes it possible to evaluate policy options which affect the size of the population or the preferences of its members. We study how to extend the theory of social choice in order to select such orderings on a rigorous axiomatic basis. Key ingredients in this analysis are attitudes with respect to population size and the bases of interpersonal comparisons.