Miracle-dz/UniFAR-FTUs huggingface dataset:
Role of PheE15 Gate in Ligand Entry and Nitric Oxide Detoxification Function of Mycobacterium tuberculosis Truncated Hemoglobin N

The truncated hemoglobin N, HbN, of Mycobacterium tuberculosis is endowed with a potent nitric oxide dioxygenase (NOD) activity that allows it to relieve nitrosative stress and enhance in vivo survival of its host. Despite its small size, the protein matrix of HbN hosts a two-branched tunnel, consisting of orthogonal short and long channels, that connects the heme active site to the protein surface. A novel dual-path mechanism has been suggested to drive migration of O2 and NO to the distal heme cavity. While oxygen migrates mainly by the short path, a ligand-induced conformational change regulates opening of the long tunnel branch for NO, via a phenylalanine (PheE15) residue that acts as a gate. Site-directed mutagenesis and molecular simulations have been used to examine the gating role played by PheE15 in modulating the NOD function of HbN. Mutants carrying replacement of PheE15 with alanine, isoleucine, tyrosine and tryptophan have similar O2/CO association kinetics, but display significant reduction in their NOD function. Molecular simulations substantiated that mutation at the PheE15 gate confers significant changes in the long tunnel, and therefore may affect the migration of ligands. These results support the pivotal role of PheE15 gate in modulating the diffusion of NO via the long tunnel branch in the oxygenated protein, and hence the NOD function of HbN.
The Diagnostic Value of Transcription Factors T-bet/GATA3 Ratio in Predicting Antibody-Mediated Rejection

Background. Previous data showed that the predominance of intraglomerular T-bet or GATA3 is correlated with different mechanisms of rejection, suggesting that the ratio of T-bet/GATA3 might be used to distinguish antibody-mediated rejection (ABMR) and T-cell-mediated rejection (TCMR). Methods. We compared the intraglomerular T-bet/GATA3 ratio in ABMR and TCMR. The intragraft expression of T-bet and GATA3 was studied via immunohistochemistry. The correlation of the diagnosis of AMR with the ratio of T-bet/GATA3 was examined. Results. Both intraglomerular T-bet- and GATA3-expressing cells were increased during acute rejection. T-bet/GATA3>1 was strongly correlated with ABMR (93.3% versus 18.2%). The incidence of positive HLA-I/II antibodies and glomerulitis is significantly higher in T-bet/GATA3>1 group (P < 0.001, 0.013, resp.). The scores of peritubular capillary inflammation and glomerulitis were also higher in T-bet/GATA3>1 group (P = 0.052, P < 0.001, resp.). Nevertheless, T-bet/GATA3>1 is also correlated with C4d-negative ABMR and resistance to steroid treatment. Compared with C4d deposition, T-bet/GATA3>1 had a slight lower (90% versus 100%) specificity but a much higher (87.5% versus 68.8%) sensitivity. Conclusion. Our data suggested that intraglomerular predominance of T-bet over GATA3 might be used as diagnosis maker of ABMR in addition to C4d, especially in C4d-negative cases.
DC characteristics of dual gated large area graphene MOSFET

This work reports the DC characteristics of dual gated large area graphene metal oxide semiconductor field effect transistor (MOSFET). The sheet charge density dependent quantum capacitance is obtained self-consistently with considering the impurities concentration of the gate oxide layer. The potential profile as well as sheet charge density of graphene channel is calculated. The C-V and I-V characteristics are illustrated here. Finally, the velocity-field relation is shown.
Exploring relationships between tourism experience co-creation, life satisfaction and behavioural intentions: Empirical evidence

This paper contributes to the debate about the relationships among tourism experience co- creation, satisfaction with vacation experience, satisfaction with impact of vacation on overall life, life satisfaction and behavioural intentions. A survey was conducted on a convenience sample of 263 international tourists who visited several tourist destinations in Croatia. To test the proposed model, partial least square structural equation modelling (PLS- SEM) was employed. All six hypotheses were confirmed. It has been established that co- creation of tourism experience significantly contributes to the satisfaction of tourists staying in a destination, which has a positive effect on life satisfaction and future behavioural intentions.
Selecting Power-Optimal SBST Routines for On-Line Processor Testing

Software-based self-test (SBST) has emerged as an effective strategy for on-line testing of processors integrated in non-safety critical embedded system applications. Among the most popular applications falling in this category are the various mobile devices. However, in-field testing of processors integrated in mobile devices has the extra requirement of minimum energy consumption, since these devices are operating on battery. In this paper initially we present the parameters contributing to energy consumption in order to set the scope of the problem and make a qualitative analysis about the efficiency of the SBST routines from a low energy perspective. Then we propose a power evaluation framework based on a combination of tools from the testing and computer architecture technical areas. Utilizing this framework we evaluate for the first time the most effective structural SBST strategies in terms of energy consumption for three representative processor configurations, showing the validity of our analysis. Finally, the SBST strategies are combined and an appropriate strategy for each processor component is selected, in order to minimize overall energy consumption during on-line testing up to an order of magnitude between the best and worst case combination of test routines.
Prostaglandins and Kidney Function: A Comparison Between the Cortical and Inner Medullary Collecting Duct on Prostaglandin Production

ii TABLE OF CONTENTS.iv LIST OF FIGURES.vi LIST OF ABBREVIATIONS.vii CHAPTER 1: INTRODUCTION.1 Overview of prostaglandins.1 Kidney basics – the anatomy and physiology of the kidneys.8 Renal blood flow.8 Renal corpuscle anatomy and function.9 Prostaglandins and their effects on renal blood flow and ultrafiltration of blood.9 Prostaglandins and renin release.10 Nephron tubule anatomy and function.10 Prostaglandins and their effects on the nephron tubule.13 Collecting duct anatomy and function.13 Prostaglandins and their effects on the collecting duct.15 Differences between the cortical and inner medullary collecting duct.17 Cell lines.17 Aim of the study and hypothesis.18 CHAPTER 2: MATERIALS AND METHODS.20 Cell Culture.20 Time course experiments.20
Functional Expression of the Multidrug Resistance Protein 1 in Microglia

Brain expression of the multidrug resistance proteins (MRPs), a collection of membrane-associated ATP-dependent efflux transporters, is poorly understood. Although several studies have examined the expression of these proteins within the brain barriers (i.e., the blood-brain barrier and choroid plexus), little information is available with respect to brain parenchyma cells such as microglia and astrocytes. Because microglia are the primary brain cells infected by the human immunodeficiency virus type 1 (HIV-1), MRP1 expression within microglia may contribute to lower brain accumulation of anti-HIV drugs. To examine the expression pattern of MRP1 within microglia, we performed reverse transcriptase-polymerase chain reaction analysis and Western blotting on a rat brain microglia cell line MLS-9, and in primary cultures of rat microglia. Both rat MRP1 (rMPR1) mRNA and protein were expressed in the cell line, as well as the primary cultures. We then characterized rMRP1-mediated transport properties in MLS-9 cells using [3H]vincristine, a known MRP1 substrate. Vincristine accumulation by monolayers of MLS-9 cells increased significantly in the presence of several well established MRP1 inhibitors (MK571, genistein, sulfinpyrazone, probenecid, and indomethacin), protease inhibitors, or the ATPase inhibitor sodium azide. In addition, vincristine accumulation was significantly modulated by altering the intracellular concentration of the reduced form of glutathione, further suggesting the involvement of rMRP1-mediated transport. These results provide strong evidence that the MRP1 protein is both expressed and functional in microglia cells. They also suggest that brain parenchyma can act as a “second” barrier to drug permeability and regulate brain distribution/accumulation of various xenobiotics, including protease inhibitors.
Using Shakespeare to teach English in the digital age

This paper examines the opportunities and challenges of using Shakespeare as a teaching resource for English language learners, using as a case study an open distance learning programme aimed at engaging EFL students across diverse world contexts. The paper reviews the pedagogical design, production and dissemination of these teaching materials and in doing so discusses how points of language, issues of historical culture, and insights into modern usage can all be addressed in ways which aim to be both entertaining and instructional by reference to Shakespeare’s life and works. Additionally, it considers how the harnessing of the transmedia affordances of digital communication can create a broad, interactive experience for students, thus mixing the traditional with the cutting-edge in English language pedagogy.
RESULTS ON DELAY-DEPENDENT STABILITY CRITERIA FOR NEUTRAL SYSTEMS WITH MIXED TIME-VARYING DELAYS AND NONLINEAR PERTURBATIONS

In this paper, the problem of delay-dependent stability criteria for neutral systems with mixed time-varying delays and nonlinear perturbations is considered. Based on the new Lyapunov-Krasovskii functional, Leibniz-Newton formula, decomposition technique of coefficient matrix, utilization of zero equations, model transformation and linear matrix inequality, new delay-dependent stability criteria are established in terms of linear matrix inequalities (LMIs). Numerical examples show that the proposed criteria improve the existing results significantly with much less computational effort.
Non-Steroidal Anti-Inflammatory Drugs and Brain Inflammation: Effects on Microglial Functions

The term NSAID refers to structurally diverse chemical compounds that share the ability to inhibit the activity of the prostaglandin (PG) biosynthetic enzymes, the cyclooxygenase (COX) isoforms 1 and 2. The suppression of PG synthesis at sites of inflammation has been regarded as primarily responsible for the beneficial properties of NSAIDs, but several COX-independent effects have been described in recent years. Epidemiological studies indicate that NSAIDs are neuroprotective, although the mechanisms underlying their beneficial effect remain largely unknown. Microglial cells play a major role in brain inflammation and are often viewed as major contributors to the neurodegeneration. Therefore, microglia represent a likely target for NSAIDs within the brain. In the present review, we focused on the direct effects of NSAIDs and selective COX-2 inhibitors on microglial functions and discuss the potential efficacy in controlling brain inflammation.
Multivariate normal approximation using Stein's method and Malliavin calculus

We combine Stein's method with Malliavin calculus in order to obtain explicit bounds in the multidimensional normal approximation (in the Wasserstein distance) of functionals of Gaussian fields. Our results generalize and refine the main findings by Peccati and Tudor (2005), Nualart and Ortiz-Latorre (2007), Peccati (2007) and Nourdin and Peccati (2007b, 2008); in particular, they apply to approximations by means of Gaussian vectors with an arbitrary, positive definite covariance matrix. Among several examples, we provide an application to a functional version of the Breuer-Major CLT for fields subordinated to a fractional Brownian motion.
School and teacher determinants underlying teachers’ implementation of self-regulated learning in primary education

ABSTRACT Teaching students how to regulate their own learning has become a popular innovative practice in primary education. However, not much is known about how teacher as well as school characteristics enhance students’ self-regulated learning (SRL). This study explores whether schools differ in the way they implement SRL and what factors at the school and teacher level are related to successful classroom implementation of SRL. Survey data was gathered from 331 teachers in 44 primary schools. A comprehensive theoretical model, identifying determinants on teacher and school level related to teachers’ SRL implementation, was tested using structural equation modelling. Results indicate that teachers’ beliefs and teacher self-efficacy are strongly related to SRL implementation. At the school level, the importance of a shared SRL vision and the engagement of teachers in reflective dialogue are highlighted with implications for the role of the school leader. Recommendations for future research and considerations for teachers’ educational practice are discussed. Abbreviation: CFA: confirmatory factor analysis; CFI: comparative fit index; df: degrees of freedom; ICT: information and communication technology; JD-R: job demands-resources; M: mean; PLC: professional learning community; RMSEA: root mean square error of approximation; SD: standard deviation; SEM: structural equation modelling; SRL: self-regulated learning; SRLIT: Self-Regulated Learning Inventory for Teachers; SRLTB: Self-Regulated Learning Teacher Belief Scale; SRMR: standardized root mean residual; TLI: Tucker-Lewis index; TSES-SRL: Teacher Self-Efficacy Scale to implement Self-Regulated Learning
Fast Computation of Posterior Mode in Multi-Level Hierarchical Models

Multi-level hierarchical models provide an attractive framework for incorporating correlations induced in a response variable that is organized hierarchically. Model fitting is challenging, especially for a hierarchy with a large number of nodes. We provide a novel algorithm based on a multi-scale Kalman filter that is both scalable and easy to implement. For Gaussian response, we show our method provides the maximum a-posteriori (MAP) parameter estimates; for non-Gaussian response, parameter estimation is performed through a Laplace approximation. However, the Laplace approximation provides biased parameter estimates that is corrected through a parametric bootstrap procedure. We illustrate through simulation studies and analyses of real world data sets in health care and online advertising.
HarpiaGrid: A Reliable Grid-based Routing Protocol for Vehicular Ad Hoc Networks

Vehicular ad hoc network (VANET) is a research field attracting growing attention. Current routing protocols in VANET usually use geographic information to forward data packets to the destination. Since geographic routing is stateless, during routing forwarding, route recovery processes would be continuously initiated if any topology hole exists, resulting in serious performance degradation. In addition, if vehicle density is low in the network, there might not be vehicles available to deliver the packet. This paper proposes HarpiaGrid, a reliable grid-based routing protocol for VANETs. The protocol utilizes in-car navigators to produce geographically logical routing paths, effectively trades route discovery network overhead with insignificant computation time. In addition, by taking advantage of the information provided by gridded geographic data, transmissions are made more efficient. Moreover, in the route maintenance, a fault-tolerance procedure is designed to avoid dead paths. Simulations were conducted, and the results demonstrated that the proposed scheme is indeed more efficient and reliable than other protocols.
Use of elemental composition to predict bioavailability of dissolved organic matter in a Georgia river

The relationship between the bioavailability of dissolved organic matter (DOM) and its bulk chemical composition was examined on three dates at 10 sites on the Ogeechee River, a blackwater river in Georgia. Samples of riverine DOM were concentrated from filtered river water using reverse osmosis. In addition, particulate organic matter (POM), in the form of leaf litter, algae, and macrophytes, was leached with synthetic rainwater to obtain fresh DOM. Elemental composition, carboxylic acid content, and bacterial growth were measured on all samples. The results of this study indicate that fresh DOM in POM leachates is generally more bioavailable than riverine DOM. The bioavailability of riverine DOM appears to be greater under low discharge conditions and decreases with distance downstream. The bioavailability of all DOM samples is very well predicted (r2 = 0.93, n = 20) by an empirical equation of the form: bioavailability = a0 + a1(H:C) + a2(O:C) + a3(N:C). When compositional data are plotted on a van Krevelen diagram, it is evident that POM leachates and, to a lesser degree, DOM from headwater sites have compositions that differ little from simple mixtures of major components of biomass (lipids, sugars, proteins, and lignins). Father downstream, major diagenetic alteration of organic matter is evident from the compositions of DOM samples, whose H: C and O: C ratios are lower and higher, respectively, than for any possible mixture of biomass components. Bioavailability of DOM is closely related to the percentage of aliphatic carbon in a sample, and downstream decreases in bioavailability are mainly attributable to selective degradation of aliphatic carbon in riverine DOM.
CO2 Laser and Topical Fluoride Therapy in the Control of Caries Lesions on Demineralized Primary Enamel

This study evaluated the effect of CO2 laser irradiation and topical fluoride therapy in the control of caries progression on primary teeth enamel. 30 fragments (3 × 3 × 2 mm) from primary canines were submitted to an initial cariogenic challenge that consisted of immersion on demineralizing solution for 3 hours and remineralizing solution for 21 hours for 5 days. Fragments were randomly assigned into three groups (n = 10): L: CO2 laser (λ = 10.6 μm), APF: 1.23% acidulated phosphate fluoride, and C: no treatment (control). CO2 laser was applied with 0.5 W power and 0.44 J/cm2 energy density. Fluoride application was performed with 0.1 g for 1 minute. Cariogenic challenge was conducted for 5 days following protocol previously described. Subsurface Knoop microhardness was measured at 30 μm from the edge. Obtained data were subjected to analysis the variance (ANOVA) and Duncan test with significance of 5%. It was found that the L group showed greater control of deciduous enamel demineralization and were similar to those of APF group, while being statistically different from C group (P ≤ 0.05) that showed the lowest microhardness values. It was concluded that CO2 laser can be an additional resource in caries control progression on primary teeth enamel.
The Influence of Neighborhood Risk Factors on Parolee Recidivism in Philadelphia, Pennsylvania

Recidivism research has largely addressed individual-level attributes, neglecting the role of the neighborhood context. Following a sample of 4,851 parolees returning to the City of Philadelphia in 2007 and 2008, the current study examines the role of the neighborhood context and nonresidential land uses (both risk and protective factors) in reincarceration and time to reincarceration. Although our findings suggest limited support for the neighborhood context in explaining reincarceration, we found that the presence of beer bars and liquor outlets within walking distance of a parolee’s home increased their likelihood of reincarceration and reduced their time in the community.
Local Component Analysis

Kernel density estimation, a.k. a. Parzen windows, is a popular density estimation method, which can be used for outlier detection or clustering. With multivariate data, its performance is heavily reliant on the metric used within the kernel. Most earlier work has focused on learning only the bandwidth of the kernel (i.e., a scalar multiplicative factor). In this paper, we propose to learn a full Euclidean metric through an expectation-minimization (EM) procedure, which can be seen as an unsupervised counterpart to neighbourhood component analysis (NCA). In order to avoid overfitting with a fully nonparametric density estimator in high dimensions, we also consider a semi-parametric Gaussian-Parzen density model, where some of the variables are modelled through a jointly Gaussian density, while others are modelled through Parzen windows. For these two models, EM leads to simple closed-form updates based on matrix inversions and eigenvalue decompositions. We show empirically that our method leads to density estimators with higher test-likelihoods than natural competing methods, and that the metrics may be used within most unsupervised learning techniques that rely on such metrics, such as spectral clustering or manifold learning methods. Finally, we present a stochastic approximation scheme which allows for the use of this method in a large-scale setting.
Parental influence on begging call structure in zebra finches (Taeniopygia guttata): evidence of early vocal plasticity

Begging calls are signals of need used by young birds to elicit care from adults. Different theoretical frameworks have been proposed to understand this parent–offspring communication. But relationships between parental response and begging intensity, or between begging characteristics and proxies of a young’s need remain puzzling. Few studies have considered the adjustment of nestling begging features to previous experience as a possible explanation of these discrepancies. In this study, we tested the effect of a heterospecific rearing environment on individual developmental trajectories of the acoustic structure of nestling begging calls. Fifty-two zebra finch chicks were fostered either to Bengalese finch or to zebra finch parents, and begging calls were recorded at several stages of nestling development. Acoustic analyses revealed that the development of the spectral features of the begging calls differed between experimental conditions: chicks reared by Bengalese finches produced higher pitched and less broadband begging calls than chicks reared by conspecific parents. Differences were stronger in males than females and were not explained by differences in growth rate. We conclude that nestling begging calls can be plastic in response to social interactions with parents.
Specifying Agents in Construct

Construct is a multi-agent simulation tool that is commonly used to investigate dynamic behavior in complex socio-cultural systems. This technical report describes the parameters necessary to specify agents in the simulation, focusing especially on the features which help describe agent behavior. It also introduces a number of pre-defined agent classes, stock-agents which can be used to quickly build up a simulation. This document is intended both as an introduction to Construct model and as a reference guide for simulation experts and casual modelers.