Miracle-dz/UniFAR-FTUs huggingface dataset:
SOD mRNA and MDA Expression in Rectus Femoris Muscle of Rats with Different Eccentric Exercise Programs and Time Points

Purpose Although superoxide dismutase (SOD) and malondialdehyde (MDA) affect Delayed Onset Muscle Soreness (DOMS), their effects are unclear in rectus femoris muscles (RFM) of rats with different eccentric exercise programs and time points. The purpose of this study is to investigate the effects of the various eccentric exercise programs at different time points on the SOD mRNA expression and MDA using rat as the animal model. Methods 248 male rats were randomly divided into 4 groups: control group (CTL, n = 8), once-only exercise group (OEG, n = 80), continuous exercise group (CEG, n = 80), and intermittent exercise group (IEG, n = 80). Each exercise group was divided into 10 subgroups that exercised 0.5 h, 6 h, 12 h, 24 h, 48 h, 72 h, 96 h, 120 h, 144 h, or 168 h. Rats were sacrificed and their SOD mRNA expression, and MDA concentrations of skeletal muscle tissue were measured. Results The specimen in all eccentric exercise programs showed increased RFM SOD1 mRNA expression levels at 0.5 h (P<0.05), and decreased RFM SOD3 mRNA expression at 0.5 h (P<0.05). The continuous eccentric exercise (CE) significantly enhanced muscle SOD2 mRNA level at 0.5 h (P<0.05). After once-only eccentric exercise (OE), SOD1, SOD2, and SOD3 mRNA expression significantly increased at 96 h, whereas MDA concentrations decreased at 96 h. After CE, the correlation coefficients of SOD1, SOD2, SOD3 mRNA expression levels and MDA concentrations were −0.814, −0.763, −0.845 (all P<0.05) at 12 h. Conclusion Regular eccentric exercise, especially CE could enhance SOD1 and SOD2 mRNA expression in acute stage and the SOD2 mRNA expression correlates to MDA concentration in vivo, which may improve the oxidative adaption ability of skeletal muscles.
Modeling spatial hole burning and mode competition in index-guided VCSELs

We have derived and implemented a simplified dynamical multi-mode model for vertical-cavity surface-emitting lasers (VCSELs) requiring minimal computing resources while remaining realistic. A set of spatially independent rate equations with a minimum of parameters is extracted from the general spatially resolved equations and reduced to dimensionless form to expose its essentials. The shape of the carrier density distribution is approximated with a linear sum of the modal shapes which are considered to be bias independent for index-guided devices. Despite this simplification the model, which can be extended to any number of laser modes, includes important effects like spatial hole burning (SHB), carrier diffusion and inhomogeneous injection and shows good agreement with spatially resolved models. We describe the reduction and nondimensionalization of the general spatially resolved equations. The implementation inside a C++ rate-equation framework is discussed and shown to provide a powerful and flexible environment to efficiently study the contribution of different factors. The effect of spatial hole burning (SHB) and mode competition on the small signal modulation response is investigated in three basic cases. The comparison between a single mode VCSEL without SHB, a single mode VCSEL including SHB and two mode VCSEL including SHB enables us to pinpoint which contributions are due to SHB and which are due to the modal competition. Finally,the possibility of using this approach to model polarization switching in VCSELs is discussed. The unavoidable small birefringence (with elasto-optic and electro-optic contributions) present in all VCSELs leads to a doubling of each mode into two orthogonal polarization states which are almost degenerate. Although small, the birefringence causes gain differences: part of which are due to frequency dependent gain and loss of the materials and part of which are due to slightly different transverse modal shapes. As these gain differences depend on the injected current, they can be one of the causes of polarization switching.
Vesicle formation by self-assembly of membrane-bound matrix proteins into a fluidlike budding domain

The shape of enveloped viruses depends critically on an internal protein matrix, yet it remains unclear how the matrix proteins control the geometry of the envelope membrane. We found that matrix proteins purified from Newcastle disease virus adsorb on a phospholipid bilayer and condense into fluidlike domains that cause membrane deformation and budding of spherical vesicles, as seen by fluorescent and electron microscopy. Measurements of the electrical admittance of the membrane resolved the gradual growth and rapid closure of a bud followed by its separation to form a free vesicle. The vesicle size distribution, confined by intrinsic curvature of budding domains, but broadened by their merger, matched the virus size distribution. Thus, matrix proteins implement domain-driven mechanism of budding, which suffices to control the shape of these proteolipid vesicles.
Preparation of photonic crystals made of air pores in anodic alumina

Photonic crystals made of air pores in anodic alumina were prepared by electrochemical oxidation of aluminium and subsequent chemical etching. Optical photographs and transmission spectra prove the existence of a photonic band gap in the optical sprectrum for this porous material. The colour of the sample and the diffraction peak position in the transmission spectra could easily be adjusted in the chemical etching process. This method could provide a possible approach to producing large-area optical photonic crystals cheaply and rapidly.
Bandwidth extension in CMOS with optimized on-chip inductors

We present a technique for enhancing the bandwidth of gigahertz broad-band circuitry by using optimized on-chip spiral inductors as shunt-peaking elements. The series resistance of the on-chip inductor is incorporated as part of the load resistance to permit a large inductance to be realized with minimum area and capacitance. Simple, accurate inductance expressions are used in a lumped circuit inductor model to allow the passive and active components in the circuit to be simultaneously optimized. A quick and efficient global optimization method, based on geometric programming, is discussed. The bandwidth extension technique is applied in the implementation of a 2.125-Gbaud preamplifier that employs a common-gate input stage followed by a cascoded common-source stage. On-chip shunt peaking is introduced at the dominant pole to improve the overall system performance, including a 40% increase in the transimpedance. This implementation achieves a 1.6-k/spl Omega/ transimpedance and a 0.6-/spl mu/A input-referred current noise, while operating with a photodiode capacitance of 0.6 pF. A fully differential topology ensures good substrate and supply noise immunity. The amplifier, implemented in a triple-metal, single-poly, 14-GHz f/sub Tmax/, 0.5-/spl mu/m CMOS process, dissipates 225 mW, of which 110 mW is consumed by the 50-/spl Omega/ output driver stage. The optimized on-chip inductors consume only 15% of the total area of 0.6 mm/sup 2/.
Manipulating the phase morphology in PPS/PA66 blends using clay

By adding a small amount of clay into poly(p-phenylene sulfide) (PPS)/polyamide 66 blends, the morphology was found to change gradually from sea–island into cocontinuity and lamellar supramolecular structure, as increasing of clay content. Clay was selectively located in the PA66 phase, and the exfoliated clay layers formed an edge-contacted network. The change of morphology is not caused by the change of volume ratio and viscosity ratio but can be well explained by the dynamic interplay of phase separation between PPS and PA66 through preferential adsorption of PA66 onto the clay layers and through layer–layer repulsion. This provides a means of manipulating the phase morphology for the immiscible polymer blends. The mechanical and tribological properties of PPS/PA66 blends with different phase morphologies (different clay contents) were studied. Both tensile and impact strength of the blends were found obviously increased by the addition of clay. The antiwear property was greatly improved for the blends with cocontinuous phase form. Our work indicates that the phase-separating behavior of polymer blends contained interacting clay can be exploited to create a rich diversity of new structures and useful nanocomposites. © 2007 Wiley Periodicals, Inc. J Appl Polym Sci 2007
Application of Modified POT Method with Volatility Model for Estimation of Risk Measures

The main aim of this paper is the presentation and empirical analysis of the new approach which combines volatility models with Peaks over Threshold method that comes from extreme value theory. The new approach is applied for estimation of risk measures (VaR and ES) in financial time series. For the empirical analysis the financial risk model evaluation was conducted. In this paper the POT method was compared with standard volatility models (GARCH and SV) in case of the conditional modeling.
A Fast Decoder for Joint Word Segmentation and POS-Tagging Using a Single Discriminative Model

We show that the standard beam-search algorithm can be used as an efficient decoder for the global linear model of Zhang and Clark (2008) for joint word segmentation and POS-tagging, achieving a significant speed improvement. Such decoding is enabled by: (1) separating full word features from partial word features so that feature templates can be instantiated incrementally, according to whether the current character is separated or appended; (2) deciding the POS-tag of a potential word when its first character is processed. Early-update is used with perceptron training so that the linear model gives a high score to a correct partial candidate as well as a full output. Effective scoring of partial structures allows the decoder to give high accuracy with a small beam-size of 16. In our 10-fold cross-validation experiments with the Chinese Tree-bank, our system performed over 10 times as fast as Zhang and Clark (2008) with little accuracy loss. The accuracy of our system on the standard CTB 5 test was competitive with the best in the literature.
PGP: parallel prokaryotic proteogenomics pipeline for MPI clusters, high-throughput batch clusters and multicore workstations

Summary: We present the first public release of our proteogenomic annotation pipeline. We have previously used our original unreleased implementation to improve the annotation of 46 diverse prokaryotic genomes by discovering novel genes, post-translational modifications and correcting the erroneous annotations by analyzing proteomic mass-spectrometry data. This public version has been redesigned to run in a wide range of parallel Linux computing environments and provided with the automated configuration, build and testing facilities for easy deployment and portability. Availability and implementation: Source code is freely available from https://bitbucket.org/andreyto/proteogenomics under GPL license. It is implemented in Python and C++. It bundles the Makeflow engine to execute the workflows. Contact: atovtchi@jcvi.org
Brain mechanisms of sympathetic activation in heart failure: Roles of the renin-angiotensin system, nitric oxide and pro-inflammatory cytokines (Review)

Patients with chronic heart failure (CHF) have an insufficient perfusion to the peripheral tissues due to decreased cardiac output. The compensatory mechanisms are triggered even prior to the occurrence of clinical symptoms, which include activation of the sympathetic nervous system (SNS) and other neurohumoral factors. However, the long-term activation of the SNS contributes to progressive cardiac dysfunction and has toxic effects on the cardiomyocytes. The mechanisms leading to the activation of SNS include changes in peripheral baroreceptor and chemoreceptor reflexes and the abnormal regulation of sympathetic nerve activity (SNA) in the central nervous system (CNS). Recent studies have focused on the role of brain mechanisms in the regulation of SNA and the progression of CHF. The renin-angiotensin system, nitric oxide and pro-inflammatory cytokines were shown to be involved in the abnormal regulation of SNA in the CNS. The alteration of these neurohumoral factors during CHF influences the activity of neurons in the autonomic regions and finally increase the sympathetic outflow. The present review summarizes the brain mechanisms contributing to sympathoexcitation in CHF.
Virtual Environments for Treating the Fear of Heights

Can virtual environments help elicit fearful feelings so they can be treated? This article shows how therapists and computer experts used them to do just that. We describe a pilot study that used virtual reality graded exposure techniques to treat acrophobia-the fear of heights. We specifically address two issues: the extent to which we were able to make subjects feel that they were actually present in height situations, and the efficacy of the treatment conducted using virtual height situations. >
Interorganizational Collaboration in Healthcare ( Langabeer ) 1 Interorganizational Collaboration in Healthcare : Insights from Cardiovascular Systems of Care

Interorganizational theories of management contend that collaboration and interdependencies between organizations can lead to distinct competitive advantages. Yet, this theory is largely rooted in the consumer goods industry (not healthcare) and has been examined primarily from the advantages provided to individual firms (not the community as a whole). In this research, we will explore the nature of collaboration between organizations in healthcare, and specifically examine evidence from the field of cardiovascular care on community outcomes emerging from a large-scale interorganizational collaboration. We present data on resulting from a six-year collaboration around the Dallas metropolitan area, which has yielded significant improvements in key outcomes for the community. We will generalize these findings to provide recommendations for interorganizational collaborations elsewhere in the healthcare industry. Background Organizations collaborate in a variety of structural ways, including strategic alliances, joint ventures, and other less formal partnerships. Management theories about interorganizational collaboration tend to focus on the resulting competitive advantages which these relationships will produce, primarily for
Animal Behavioural Studies in the Evaluation of Antidepressant Drugs

Animal behavioural models of psychiatric disorders cannot exactly simulate human psychopathology, but they can be used to evaluate the behavioural changes induced by drugs and to suggest hypotheses about the functions of the CNS and its involvement in psychiatric disorders. This should lead to a more heuristic classification of psychotropic drugs and to clarification of their therapeutic possibilities. The following animal models simulate aspects of depressive disorders and are sensitive to the antidepressant effects of drugs. (i) The forced swimming test: described as ‘behavioural despair‘ on the assumption that the animal has given up hope of escaping. (ii) The ‘restraint stress‘ test: this may indicate a failure to adapt to stress. (iii) The learned-helplessness model: exposed to uncontrollable events, animals exhibit learning performance deficit and behavioural changes, including decreased locomotor activity and loss of appetite. (iv) Waiting behaviour: improvement in the ability to wait for and/or postpone an active response; this could be related to the reported beneficial effects of antidepressants on impulsive behaviour.
Computational modelling of constrained sintering in EB-PVD thermal barrier coatings

A micromechanical model is developed to simulate the evolution of microstructure during in-service sintering and eventual inter-columnar cracking in coatings made using electron beam vapour deposition (EB-PVD) route. The coating is idealized with a discrete distribution of axisymmetric asperities across interfaces between columnar grains. The model assumes that inter-columnar sintering is driven by changes in interface free energy of columns and the potential energy of the applied stress. Much faster diffusion that occurs over the free surfaces of the asperities is neglected. It is further assumed that the rate of sintering of the contacting asperities is determined by diffusion along the interface between the contacting asperities. Time evolution of contact modulus of the coating is accounted for as a function of sintering strain. The developed macroscopic constitutive model is employed to evaluate the sensitivity of the sintering response to imperfections and examine the conditions under which inter-columnar cracks can develop within the coating.
miR-125b Regulation of Androgen Receptor Signaling Via Modulation of the Receptor Complex Co-Repressor NCOR2

Abstract Recognition of micro-RNA function and their contribution to the biology of disease has given a new insight into disease mechanisms, with these discoveries potentially improving clinical diagnostic and therapeutic options. miR-125b has been identified as an important regulator in various cancers, including prostate cancer, but the mechanism of this regulation remains incompletely understood. In these studies, the effect of castration on miR-125b serum expression was evaluated in mice, simulating androgen deprivation. Furthermore, miR-125b expression was measured by quantitative real-time polymerase chain reaction (qRT-PCR) in LNCaP prostate cancer cells treated with the antiandrogen bicalutamide. Using LNCaP cells, the effect of miR-125b modulation on apoptotic protein and NCOR2, a co-repressor of androgen receptor (AR), was examined by Western blot. A 3′-untranslated region (UTR) luciferase-binding assay was performed to confirm that miR-125b targets NCOR2. We found that surgical castration induced an initial increase in the expression of circulating miR-125b in mice, while sham surgery did not. In addition, AR blockade via bicalutamide was associated with the rapid release of miR-125b into the cell culture medium of prostate cancer cells. A previously studied target of miR-125b, a regulator in the apoptotic pathway, BAK1, could not completely account for the role of miR-125b in prostate cancer. Thus, we looked for additional targets of miR-125b and found that NCOR2, which is a repressor of AR, is a direct target of miR-125b. We found that NCOR2 protein expression was blocked by mimics of miR-125b, and a luciferase-binding assay confirmed that NCOR2 is a direct target of miR-125b. Our data provide novel evidence that miR-125b is an important regulator of the AR with specific ramification for the effectiveness of antiandrogens and other hormonal therapies in prostate cancer.
Characterization of Next Generation Commercial Surface Enhanced Raman Scattering Substrates with a 633- and 785-nm System

Abstract : The development of a sensing platform to detect and identify biological, chemical, and energetic hazards is a long-sought-after goal of the Army and other first responder communities. Surface enhanced Raman scatting (SERS) is a spectroscopic technique gaining popularity as it address many sensing needs. However, despite the many advantages of SERS, it remains a marginalized sensing technique primarily due to the challenges in fabricating a reliable, highly sensitive, reproducible nanoscale surface. In this work, we demonstrate that many of the substrate fabrication challenges have been overcome by a newly developed, commercially available, next generation Klarite SERS substrate. These substrates are fabricated similarly to the standard Klarite substrates, but due to variations in the size and spacing of the surface features, they have increased sensing capabilities. The sensitivity for detecting the model SERS analyte, trans-1,2-bi-(4-pyridyl) ethylene (BPE) using both a 633- and 785-nm laser system is demonstrated. For one of the next generation substrates, the detection limit improved by as much as 4 times for BPE (under some conditions). This improved performance may in part be attributed to physical changes to the substrate surface including an increased density of features and plasmon absorbance band locations.
DNA Vaccination Protects Mice against Challenge with Listeria monocytogenes Expressing the Hepatitis C Virus NS3 Protein

ABSTRACT The goal of this study was to develop a new surrogate challenge model for use in evaluating protective cell-mediated immune responses against hepatitis C virus (HCV) antigens. The use of recombinant Listeria monocytogenes organisms which express HCV antigens provides novel tools with which to assay such in vivo protection, as expression of immunity against this hepatotropic bacterial pathogen is dependent on antigen-specific CD8+ T lymphocytes. A plasmid DNA vaccine encoding a ubiquitin-NS3 fusion protein was generated, and its efficacy was confirmed by in vivo induction of NS3-specific, gamma interferon-secreting T cells following vaccination of BALB/c mice. These immunized mice also exhibited specific in vivo protection against subsequent challenge with a recombinant L. monocytogenes strain (TC-LNS3) expressing the NS3 protein. Notably, sublethal infection of naive mice with strain TC-LNS3 induced similar NS3-specific T-cell responses. These findings suggest that recombinant strains of L. monocytogenes expressing HCV antigens should prove useful for evaluating, or even inducing, protective immune responses against HCV antigens.
Interaction Between Viral Proteins and Caretakers — Polyomavirus as a Model

DNA repair plays an essential barrier against birth of a precancerous cell [1]. In nature history of cancer, one important characteristic is genomic instability [2]. Among tumor suppressor genes (TSG), the functions of caretakers including DNA repair genes are crucial for cellular genomic integrity. They prevent the mutation of other TSG, e.g. gatekeepers and landscapers [3]. Virueses are always more complicated than human understanding. They not only direct host replication machineries but also interact with a wide variety of cellular proteins. In the past decade, some viruses have been reported to hijack DNA repair proteins and/or collaborate DNA damage response (DDR) which favor their own life cycle or induce carcinogenesis of host cells [4, 5].
Using Machine Learning to Guide Architecture Simulation

An essential step in designing a new computer architecture is the careful examination of different design options. It is critical that computer architects have efficient means by which they may estimate the impact of various design options on the overall machine. This task is complicated by the fact that different programs, and even different parts of the same program, may have distinct behaviors that interact with the hardware in different ways. Researchers use very detailed simulators to estimate processor performance, which models every cycle of an executing program. Unfortunately, simulating every cycle of a real program can take weeks or months. To address this problem we have created a tool called SimPoint that uses data clustering algorithms from machine learning to automatically find repetitive patterns in a program's execution. By simulating one representative of each repetitive behavior pattern, simulation time can be reduced to minutes instead of weeks for standard benchmark programs, with very little cost in terms of accuracy. We describe this important problem, the data representation and preprocessing methods used by SimPoint, the clustering algorithm at the core of SimPoint, and we evaluate different options for tuning SimPoint.
Approaches to the Intelligent Subject Search

This article presents main results of the pilot study of approaches to the subject information search based on automated semantic processing of mass scientific and technical data. The authors focus on technology of building and qualification of search queries with the following filtering and ranking of search data. Software architecture, specific features of subject search and research results application are considered.