Miracle-dz/UniFAR-FTUs huggingface dataset:
Mechanism of N10‐formyltetrahydrofolate synthetase derived from complexes with intermediates and inhibitors

N10‐formyltetrahydrofolate synthetase (FTHFS) is a folate enzyme that catalyzes the formylation of tetrahydrofolate (THF) in an ATP dependent manner. Structures of FTHFS from the thermophilic homoacetogen, Moorella thermoacetica, complexed with (1) a catalytic intermediate—formylphosphate (XPO) and product—ADP; (2) with an inhibitory substrate analog–folate; (3) with XPO and an inhibitory THF analog, ZD9331, were used to analyze the enzyme mechanism. Nucleophilic attack of the formate ion on the gamma phosphate of ATP leads to the formation of XPO and the first product ADP. A channel that leads to the putative formate binding pocket allows for the binding of ATP and formate in random order. Formate binding is due to interactions with the gamma‐phosphate moiety of ATP and additionally to two hydrogen bonds from the backbone nitrogen of Ala276 and the side chain of Arg97. Upon ADP dissociation, XPO reorients and moves to the position previously occupied by the beta‐phosphate of ATP. Conformational changes that occur due to the XPO presence apparently allow for the recruitment of the third substrate, THF, with its pterin moiety positioned between Phe384 and Trp412. This position overlaps with that of the bound nucleoside, which is consistent with a catalytic mechanism hypothesis that FTHFS works via a sequential ping‐pong mechanism. More specifically, a random bi uni uni bi ping‐pong ter ter mechanism is proposed. Additionally, the native structure originally reported at a 2.5 Å resolution was redetermined at a 2.2 Å resolution.
Preparation of nickel oxide/graphene aerogel composites and its electrochemical performance for supercapacitor

In this paper, nickel oxide/graphene aerogel composites (NiO/GA) have been synthesized by a simple solvothermal route starting with graphene oxide (GO). The morphology, composition and microstructure of the as-obtained samples are systematically characterized by Fourier Transform infrared spectroscopy (FTIR), X-ray diffraction (XRD) and field emission scanning electron microscopy (FESEM). Moreover, the electrochemical performances of composites were evaluated by cyclic voltammogram (CV) and galvanostatic charge-discharge. The nickel oxide was electrochemically deposited into the highly porous GA to form NiO/GA composites. NiO/GA electrodes exhibit excellent electrochemical performance with a maximum specific capacitance of 489.9 F g-1 at the charge/discharge current density of 1 A g-1 in 2 M KOH electrolyte.
High-throughput analysis of tissue-based biomarkers in digital pathology

By simultaneously processing a large number of tissue samples, the tissue microarray (TMA) technology allows standardized screening of protein expression using immunohistochemistry thereby providing a very efficient way for tissue-based biomarker analysis. Nowadays, whole slide imaging is becoming standard in digital pathology and enables image sharing, archiving and also processing. In this paper, we present methods for processing TMA images in order to correctly identify the numerous tissue samples and to register images from consecutive TMA sections.
Linkage and association with the NOS2A locus on chromosome 17q11 in multiple sclerosis

A large body of research supports a multifactorial cause in multiple sclerosis (MS), with an underlying genetic susceptibility likely acting in concert with undefined environmental exposures. Here, we used a highly efficient multilocus genotyping assay to study single nucleotide polymorphisms representing variation in 34 genes from inflammatory pathways in a well‐characterized MS familial data set. Evidence of transmission distortion was present for several polymorphisms. Results for the NOS2A locus (exon 10 C/T, D346D) on chromosome 17q11 remained significant after correction for multiple testing and were reproduced in a second independent African American MS data set. In addition, linkage to a NOS2A promoter region polymorphism, (CCTTT)n, was present in a third data set of multicase MS families. Our results provide strong evidence for linkage and association to a new candidate disease gene on chromosome 17q11 in MS and suggest that variation within NOS2A or a nearby locus contributes to disease susceptibility. Ann Neurol 2004
Stratégies de prévention de la malnutrition chez les personnes âgées en perte d'autonomie à domicile

La vulnerabilite des personnes âgees a des carences energetiques et nutritionnelles est particulierement manifeste chez celles qui souffrent de maladies chroniques ou d'incapacites. Nos etudes aupres de 290 personnes âgees en perte d'autonomie fonctionnelle recourant aux services communautaires d'aide a domicile ont mis en lumiere des apports energetiques tres faibles et une prevalence elevee de carences d'apports de plusieurs elements nutritifs. La baisse des apports alimentaires est un facteur primaire de la deterioration de l'etat nutritionnel qui, chez les personnes âgees, est tres rapide, difficilement reversible, et entraine inevitablement une degradation de l'etat de sante et de l'autonomie. Dans cette population, les efforts de prevention devraient etre diriges vers la surveillance alimentaire et le depistage des personnes a risque d'apports inadequats. La surveillance alimentaire sera discutee en termes d'implantation et de praticabilite sur le terrain. Les processus de developpement et de validation d'un outil de depistage specifique a cette population, a l'usage des intervenants du milieu, seront egalement presentes. Ainsi, l'identification precoce des personnes a risque permettra aux programmes de soutien a domicile de mettre en place des interventions nutritionnelles destinees a promouvoir la sante, l'autonomie et, en consequence, le maintien des personnes vieillissantes dans leur milieu naturel.
Quantitative microvessel density: A staging and prognostic marker for human prostatic carcinoma

Accurate methods of predicting pathologic stage and malignant potential of carcinoma of the prostate are lacking. Such advances would represent major additions to our ability to recommend therapy and offer prognostic information. Quantitation of microvessel density (MVD) has been shown in a number of organ systems to predict tumor aggressiveness.
Pareto-improving Risk selection in Social Health Insurance

Social health insurance traditionally imposes mandatory membership in a single pool in the aim of improving the welfare of high risks. However, this creates two problems, inefficiency of a monopolistic scheme and insufficient adaptation to individual preferences. Competition combined with a risk adjustment scheme can be used to improve efficiency. In the presence of preference heterogeneity, risk selection may improve adaptation to individual preferences, resulting in Pareto improvement over the pooling contract. This is shown to be possible both under perfect and imperfect risk adjustment.
Inefficient formation of a complex among CXCR4, CD4 and gp120 in U937 clones resistant to X4 gp120-gp41-mediated fusion.

Certain subclones (designated as minus clones) of the promonocytic U937 cell line do not support efficient infection and fusion mediated by T cell line adapted (TCLA) X4 HIV-1 gp120-gp41 (Env) although the CXCR4 and CD4 concentrations at their surfaces are similar to those at the surfaces of clones susceptible to HIV-1 entry (plus clones) (H. Moriuchi et al., J. Virol. 71, 9664-9671, 1997). To test the hypothesis that inefficient formation of gp120-CD4-CXCR4 complexes could contribute to the mechanism of resistance to Env-mediated fusion in the minus clones, we incubated plus and minus cells with HIV-1 LAI gp120 and coimmunoprecipitated CD4 by using anti-CXCR4 antibodies. The gp120 induced inefficient coimmunoprecipitation of CD4 in the minus clones but not in the plus ones. Overexpression of CD4 resulted in significant restoration of the minus clones' susceptibility to fusion in parallel with an increase in the amount of the gp120-CD4-CXCR4 complexes. These results not only suggest that the resistance to TCLA X4 HIV-1 entry in the U937 minus clones is due to the inability of these cells to efficiently form complexes among CD4, gp120, and CXCR4, but also provide a direct evidence for the correlation between fusion and the cell surface concentration of the complexes among CXCR4, CD4, and gp120. These data and similar recent observations in macrophages suggest that inefficient complex formation among CXCR4, CD4, and gp120 could be a general mechanism of cell resistance to gp120-gp41-mediated fusion and a major determinant of HIV-1 evolution in vivo.
Supramolecular Domains in Mixed Peptide Self‐Assembled Monolayers on Gold Nanoparticles

Self‐organization in mixed self‐assembled monolayers of small molecules provides a route towards nanoparticles with complex molecular structures. Inspired by structural biology, a strategy based on chemical cross‐linking is introduced to probe proximity between functional peptides embedded in a mixed self‐assembled monolayer at the surface of a nanoparticle. The physical basis of the proximity measurement is a transition from intramolecular to intermolecular cross‐linking as the functional peptides get closer. Experimental investigations of a binary peptide self‐assembled monolayer show that this transition happens at an extremely low molar ratio of the functional versus matrix peptide. Molecular dynamics simulations of the peptide self‐assembled monolayer are used to calculate the volume explored by the reactive groups. Comparison of the experimental results with a probabilistic model demonstrates that the peptides are not randomly distributed at the surface of the nanoparticle, but rather self‐organize into supramolecular domains.
On the discrete-time modeling and control of synchronous generators by means of variational integrators and sliding modes

This work deals with the discrete-time modeling and control design for synchronous generators by means of a variational integrator and sliding modes. First, a continuous non-conservative Lagrangian is formulated for the plant, then, the respective discrete Lagrangian is determined. Based on this, discrete-time rules are derived for synchronous generators. Second, a sliding-mode controller is proposed for the velocity stabilization of the system, and a nonlinear observer is designed for the non-measurable states. Simulations show the good performance of the synchronous generator when closed-loop with the novel discrete-time controller.
Diverse Transcriptional Response of CD4+ T Cells to Stromal Cell-Derived Factor (SDF)-1: Cell Survival Promotion and Priming Effects of SDF-1 on CD4+ T Cells1

Stromal cell-derived factor (SDF)-1 is a ligand for the chemokine receptor CXCR4 which is broadly expressed in lymphocytes, but the effects of SDF-1 on T cells are largely unknown. When examined using complementary DNA microarray, up-regulation of genes which are associated with DNA repair, detoxification, apoptosis, cell morphology, cell adhesion, and signal transduction was seen in CD4+ T cells upon SDF-1 exposure. SDF-1 was shown to promote CD4+ T cell survival through the phosphatidylinositol 3-kinase (PI3K)- and mitogen-activated protein kinase (MAPK)-cascades without cell cycle progression. The proapoptotic Bcl-2 antagonistic of cell death protein was also seen inactivated by the SDF-1-mediated activation of MAPK-extracellular signal-regulated kinases (MEK)-extracellular signal-regulated kinase-ribosomal S6 kinases- and PI3K-pathways. Moreover, the genes known to be associated with cell survival were up-regulated upon SDF-1 exposure and were linked to the MAPK-MEK and PI3K-pathways. Thus, SDF-1 promotes cell survival by two mechanisms: posttranslational inactivation of the cell death machinery and an increased transcription of cell survival-related genes. SDF-1 also primed resting CD4+ T cells for cytokine- and TCR-mediated stimuli. These data suggest that the SDF-1-mediated cell survival combined with its priming function would set T cells to respond to immunologic challenges.
Genome Sequence Analysis of Mycoplasma sp. HU2014, Isolated from Tissue Culture

ABSTRACT The draft genome sequence of a novel Mycoplasma strain, designated Mycoplasma sp. HU2014, has been determined. The genome comprises 1,084,927 nucleotides and was obtained from a mycoplasma-infected culture of chicken DT40 cells. Phylogenetic analysis places this taxon in a group comprising the closely related species Mycoplasma yeatsii and Mycoplasma cottewii.
Enhanced Endurance Performance by Periodization of Carbohydrate Intake: "Sleep Low" Strategy.

PURPOSE We investigated the effect of a chronic dietary periodization strategy on endurance performance in trained athletes. METHODS Twenty-one triathletes (V˙O2max: 58.7 ± 5.7 mL·min(-1)·kg(-1)) were divided into two groups: a "sleep-low" (SL) (n = 11) and a control (CON) group (n = 10) consumed the same daily carbohydrate (CHO) intake (6 g·kg(-1)·d(-1)) but with different timing over the day to manipulate CHO availability before and after training sessions. The SL strategy consisted of a 3-wk training-diet intervention comprising three blocks of diet-exercise manipulations: 1) "train-high" interval training sessions in the evening with high-CHO availability, 2) overnight CHO restriction ("sleeping-low"), and 3) "train-low" sessions with low endogenous and exogenous CHO availability. The CON group followed the same training program but with high CHO availability throughout training sessions (no CHO restriction overnight, training sessions with exogenous CHO provision). RESULTS There was a significant improvement in delta efficiency during submaximal cycling for SL versus CON (CON, +1.4% ± 9.3%; SL, +11% ± 15%, P < 0.05). SL also improved supramaximal cycling to exhaustion at 150% of peak aerobic power (CON, +1.63% ± 12.4%; SL, +12.5% ± 19.0%; P = 0.06) and 10-km running performance (CON, -0.10% ± 2.03%; SL, -2.9% ± 2.15%; P < 0.05). Fat mass was decreased in SL (CON, -2.6 ± 7.4; SL, -8.5% ± 7.4% before; P < 0.01), but not lean mass (CON, -0.22 ± 1.0; SL, -0.16% ± 1.7% PRE). CONCLUSION Short-term periodization of dietary CHO availability around selected training sessions promoted significant improvements in submaximal cycling economy, as well as supramaximal cycling capacity and 10-km running time in trained endurance athletes.
Quantitative and Qualitative Alterations of Heparan Sulfate in Fibrogenic Liver Diseases and Hepatocellular Cancer

Heparan sulfate (HS), duetoits abilitytointeract with a multitude of HS-binding factors, is involved in a variety of physiological and pathological processes. Remarkably diverse fine structure of HS, shaped by non-exhaustive enzymatic modifications, influences the interaction of HS with its partners. Here we characterized the HS profile of normal human and rat liver, as well as alterations of HS related to liver fibrogenesis and carcinogenesis, by using sulfation-specific antibodies. The HS immunopattern was compared with the immunolocalization of selected HS proteoglycans. HS samples from normal liver and hepatocellular carcinoma (HCC) were subjected to disaccharide analysis. Expression changes of nine HS-modifying enzymes in human fibrogenic diseases and HCC were measured by quantitative RT-PCR. Increased abundance and altered immunolocalization of HS was paralleled by elevated mRNA levels of HS-modifying enzymes in the diseased liver. The strong immunoreactivity of the normal liver for 3-O-sulfated epitope further increased with disease, along with upregulation of 3-OST-1. Modest 6-O-undersulfation of HCC HS is probably explained by Sulf overexpression. Our results may prompt further investigation of the role of highly 3-O-sulfated and partially 6-O-desulfated HS in pathological processes such as hepatitis virus entry and aberrant growth factor signaling in fibrogenic liver diseases and HCC.
No Consensus in Sight: An Analysis of Ten Years of Family Business Definitions in Empirical Research Studies

Family business (FB) scholars often criticize the fact that FB research has not yet developed a commonly accepted definition of what constitutes an FB. At the same time, the literature lacks empirical evidence for this claim. Hence, we collected all empirical FB research articles published between 2002 and 2011 in the five leading FB research journals to examine the types of FB definitions used in the literature and to determine how their usage relates to bibliographical and methodological contextual factors. The resulting 238 articles were analyzed in terms of their underlying approaches to defining FBs. Our paper provides empirical support for the notion that FB research has not yet found a commonly accepted definition of FB. Most definitions can be classified as being rooted in the components-of-involvement approach (44% of all evaluated articles), in the essence approach (21%), or in a combination of the two (33%). We also find that the type of FB definition used in empirical research in our sample is significantly associated with the publication outlet, the continent of data collection, the number of authors and the stock market listing status of analyzed firms.
GDP, railway freight, inflation & population density: An econometric quadrangular study in Indian context (1960–2009)

The main purpose of this study is to ascertain the existence of a relationship (if any) between GDP, Inflation, population density and freight carried by Indian railways. The paper explores the nexus between Indian GDP, Railway freight, inflation and population density, with a view of understanding the causality relationship in the backdrop of Indian economic growth over a period of fifty years (1960–2009) using cointegration and Granger causality test. Detection of stationarity in the series was carried out using the Augmented Dickey-Fuller test (ADF) and Phillips-Perron(PP) Unit root test and stationarity outcomes indicated GDP & Inflation data to be stationary and Population density & Railway Freight to be non stationary at 5% level of significance. The paper reveals unidirectional causality from GDP to Population density and also from GDP to railway freight, whereas bidirectional causality is found to exist between railway freight and population-density. Thus, these test findings confirm the existence of a positive relation between GDP and Indian railway freight for the period (1960–2009).
A Novel Multidimensional Approach to Integrate Big Data in Business Intelligence

The huge amount of information available and its heterogeneity has surpassed the capacity of current data management technologies. Dealing with huge amounts of structured and unstructured data, often referred as Big Data, is a hot research topic and a technological challenge. In this paper, the authors present an approach aimed to enable OLAP queries over different, heterogeneous, data sources. Their approach is based on a MapReduce paradigm, which integrates different formats into the recent RDF Data Cube format. The benefits of their approach are that it is capable of querying different sources of information, while maintaining at the same time, an integrated, comprehensive view of the data available. The paper discusses the advantages and disadvantages, as well as the implementation challenges that such approach presents. Furthermore, the approach is evaluated in detail by means of a case study.
Perks and public provisions: Effects of yardstick competition on local government fiscal behavior in the Philippines

Using a panel dataset from cities and municipalities in the Philippines in 2001, 2004 and 2007, we investigate whether yardstick competition -- measured here as the average spending and revenues of surrounding jurisdictions in the same province -- influence local government fiscal decisions. For local governments with incumbents facing effective term limits, the effects of the yardstick variables are generally nil. For those with incumbents who are eligible for another term, the average total expenditures of surrounding jurisdictions seem to influence the LGU to re-allocate its budget for social and economic services that directly benefit the constituents towards overhead outlays that benefit more the office holders. Local revenue mobilization is stimulated by greater revenue mobilization and dampened by higher average spending in other localities. Central fiscal transfers increase outlays for overheads and for social and economic services These suggests that while the particular yardstick variables used here may have induced reactions from local governments, the resulting changes in fiscal decisions may not have necessarily improved the constituents' welfare. What seems necessary is comparison on those public provisions that promote welfare rather than just total expenditures or revenues per se.
Dealing with censored data from contingent valuation surveys: Symmetrically-trimmed least squares estimation

The purpose of this paper is to explore the use of a consistent and robust estimator when estimating a willingness to pay (WTP) equation using the censored data collected by a contingent valuation survey.1 Mitchell and Carson's payment card format [11; 12] strongly encourages the respondent to give a WTP value that is zero or greater, because payment cards do not normally include any negative values. But some respondents who answer with a zero WTP may in fact have negative WTP. As a simple example, if people are asked about improving a salt water pond's water quality to the point that shellfish taken from it would be edible, there may be individuals in the sample who use the pond for other recreational activities that would be hindered by the presence of people shellfishing. In addition, anyone who enjoys quietness around and on the pond also might want to be paid a certain amount to allow the ponds to be made shellfishable. In brief, not every "public effect" on net is a good to every affected person, but anticipating the varieties of reasons for negative valuation is at least difficult if not impossible. This was true in our research aimed
Molecular cloning and characterization of acrA and acrE genes of Escherichia coli

The DNA fragment containing the acrA locus of the Escherichia coli chromosome has been cloned by using a complementation test. The nucleotide sequence indicates the presence of two open reading frames (ORFs). Sequence analysis suggests that the first ORF encodes a 397-residue lipoprotein with a 24-amino-acid signal peptide at its N terminus. One inactive allele of acrA from strain N43 was shown to contain an IS2 element inserted into this ORF. Therefore, this ORF was designated acrA. The second downstream ORF is predicted to encode a transmembrane protein of 1,049 amino acids and is named acrE. Genes acrA and acrE are probably located on the same operon, and both of their products are likely to affect drug susceptibilities observed in wild-type cells. The cellular localizations of these polypeptides have been analyzed by making acrA::TnphoA and acrE::TnphoA fusion proteins. Interestingly, AcrA and AcrE share 65 and 77% amino acid identity with two other E. coli polypeptides, EnvC and EnvD, respectively. Drug susceptibilities in one acrA mutant (N43) and one envCD mutant (PM61) have been determined and compared. Finally, the possible functions of these proteins are discussed.