Miracle-dz/UniFAR-FTUs huggingface dataset:
MULTIPLE PAR AND E4BP4 bZIP TRANSCRIPTION FACTORS IN ZEBRAFISH: DIVERSE SPATIAL AND TEMPORAL EXPRESSION PATTERNS

Circadian rhythms of physiology and behavior are generated by an autonomous circadian oscillator that is synchronized daily with the environment, mainly by light input. The PAR subfamily of transcriptional activators and the related E4BP4 repressor belonging to the basic leucine zipper (bZIP) family are clock-controlled genes that are suggested to mediate downstream circadian clock processes and to feedback onto the core oscillator. Here, the authors report the characterization of these genes in the zebrafish, an increasingly important model in the field of chronobiology. Five novel PAR and six novel e4bp4 zebrafish homolog genes were identified using bioinformatic tools and their coding sequences were cloned. Based on their evolutionary relationships, these genes were annotated as ztef2, zhlf1 and zhlf2, zdbp1 and zdbp2, and ze4bp4-1 to -6. The spatial and temporal mRNA expression pattern of each of these factors was characterized in zebrafish embryos in the context of a functional circadian clock and regulation by light. Nine of the factors exhibited augmented and rhythmic expression in the pineal gland, a central clock organ in zebrafish. Moreover, these genes were found to be regulated, to variable extents, by the circadian clock and/or by light. Differential expression patterns of multiple paralogs in zebrafish suggest multiple roles for these factors within the vertebrate circadian clock. This study, in the genetically accessible zebrafish model, lays the foundation for further research regarding the involvement and specific roles of PAR and E4BP4 transcription factors in the vertebrate circadian clock mechanism. (Author correspondence: yoavg@tauex.tau.ac.il)
Non-interactive Privacy-preserving k-NN Classifier

Machine learning tasks typically require large amounts of sensitive data to be shared, which is notoriously intrusive in terms of privacy. Outsourcing this computation to the cloud requires the server to be trusted, introducing a non-realistic security assumption and high risk of abuse or data breaches. In this paper, we propose privacy-preserving versions of the k-NN classifier which operate over encrypted data, combining orderpreserving encryption and homomorphic encryption. According to our experiments, the privacy-preserving variant achieves the same accuracy as the conventional k-NN classifier, but considerably impacts the original performance. However, the performance penalty is still viable for practical use in sensitive applications when the additional security properties provided by the approach are considered. In particular, the cloud server does not need to be trusted beyond correct execution of the protocol and computes the algorithm over encrypted data and encrypted classes. As a result, the cloud server never learns the real dataset values, the number of classes, the query vectors or their classification.
Characterization of the apelin-1860 T > C polymorphism in Turkish coronary artery disease patients and healthy individuals

To evaluate the association between the apelin -1860T>C polymorphism and plasma apelin levels in Turkish patients with coronary artery disease (CAD). A total of 276 individuals were enrolled in the present study, including 158 patients with CAD and 118 individuals without CAD as controls. The presence of the apelin -1860T>C gene polymorphism and plasma apelin levels were determined using polymerase chain reaction/restriction fragment length polymorphism and enzyme-linked immunosorbent assay, respectively. Significance was set at p≤0.05 for all statistical analyses. The genotype and allele frequencies of interested genes were significantly different between groups (χ2=10.2; df=2; p=0.006 and χ2=13.4; df=1; p=0.000, respectively). Frequency of CC genotype and the C allele of -1860T>C site was significantly higher in CAD patients compared to healthy controls. We found that individuals with the TC and CC genotypes were associated with an increased risk of CAD when compared with the TT genotype in CAD patients, and the adjusted ORs (95% CI) were 6.50 (1.27-33.0) and 6.39 (1.77-23.0), respectively. Plasma apelin levels were significantly lower in CAD patients compared to control group. Apelin level of CAD patient group having CC genotype of -1860T>C site was significantly lower compared to those having TT genotypes, but it was not statistically significant (p > 0.05). The homozygous CC genotype of apelin gene is associated with high risk of CAD. Apelin gene polymorphism -1860T>C is a significant predictor of predisposition to CAD in in Turkish population. Keyword: Apelin -1860T>C gene, coronary artery disease, polymorphism
Crystal Structure of the YchF Protein Reveals Binding Sites for GTP and Nucleic Acid

ABSTRACT The bacterial protein encoded by the gene ychF is 1 of 11 universally conserved GTPases and the only one whose function is unknown. The crystal structure determination of YchF was sought to help with the functional assignment of the protein. The YchF protein from Haemophilus influenzae was cloned and expressed, and the crystal structure was determined at 2.4 Å resolution. The polypeptide chain is folded into three domains. The N-terminal domain has a mononucleotide binding fold typical for the P-loop NTPases. An 80-residue domain next to it has a pronounced α-helical coiled coil. The C-terminal domain features a six-stranded half-barrel that curves around an α-helix. The crablike three-domain structure of YchF suggests the binding site for a double-stranded nucleic acid in the cleft between the domains. The structure of the putative GTP-binding site is consistent with the postulated guanine specificity of the protein. Fluorescence measurements have demonstrated the ability of YchF to bind a double-stranded nucleic acid and GTP. Taken together with other experimental data and genomic analysis, these results suggest that YchF may be part of a nucleoprotein complex and may function as a GTP-dependent translation factor.
Suppression of interleukin-2 production by macrophages in genetically susceptible mice infected with Leishmania major

Spleen cells from BALB/c mice infected with 2 X 10(7) L. major promastigotes and developing progressive disease produced significantly lower levels of interleukin-2 (IL-2) in response to concanavalin A stimulation than did spleen cells from uninfected mice. In contrast, spleen cells from sublethally irradiated and infected mice, which were able to contain lesion development, produced significantly higher levels of IL-2. The increase in IL-2 production closely paralleled lesion regression. Mice protectively immunized by four intravenous injections with lethally irradiated promastigotes also produced enhanced levels of IL-2, which were sustained after challenge infection. In contrast, spleen cells from BALB/c mice given four s.c. injections of irradiated promastigotes produced high levels of IL-2 before but not after infection. These mice eventually produced levels of IL-2 indistinguishable from those of unimmunized mice with progressive disease. There is thus an inverse relation between disease progression and the ability of spleen cells to produce IL-2. Spleen cells from mice with uncontrolled disease not only produced lower levels of IL-2 but also impaired IL-2 production by normal spleen cells. The ability to inhibit IL-2 was abrogated by passing the cells through a Sephadex G-10 column, removal of plastic adherent cells, and removal of carbonyl iron-ingesting cells. Furthermore, Sephadex G-10 column-treated and plastic adherent, nonspecific esterase-positive spleen cells from mice with progressive disease were able to suppress IL-2 production by normal splenic T cells. The suppressive activity of the adherent cells was not affected by treatment with anti-Thy-1.2 antibody and complement. In contrast, adherent spleen cells from uninfected mice were devoid of such suppressor activity. The depressed IL-2 production by spleen cells from progressively infected mice could be restored to that of normal spleen cells by the addition of indomethacin to the culture. There was however, no correlation between IL-2 production and IL-1 activity in infected or immunized BALB/c mice. Thus, it appears that the suppression of IL-2 production is mediated by prostaglandins elaborated by macrophages from chronically infected mice.
Analysis of employee training needs in information technology industry

Information technology industry is the fastest booming and high-gross profit making industry in the world. The employability size of this industry is no wonder very high and covers a major proportion of the service sector. This industry is the perfect model of individual skills, team-cohesion and organisational success hence it is a complete role-model industry to visualise both people-oriented and work-oriented approach at the same time. This paper will put forward all essential skills like communication, team-work, critical thinking, etc. needed most at the time of employability and will try to find the way to make the training of these soft skills more effective. The data has been collected from few IT companies by interviewing different sets of people working at different levels. It is of high importance to every person in this industry to acquire adequate soft skills as it's the parameter to judge the whole personality.
Reduced-Order Models of Series Resonant Inverters in Induction Heating Applications

From the controller design framework, a simple analytical model that captures the dominant behavior in the range of interest is the optimal. When modeling resonant circuits, complex mathematical models are obtained. These high-order models are not the most suitable for controller design. Although some assumptions can be made for simplifying these models, variable frequency operation or load uncertainty can make these premises no longer valid. In this study, a systematic modeling order reduction technique, slowly varying amplitude and phase (SVAP), is considered for obtaining simpler analytical models of resonant inverters. SVAP gives identical results as the classical model-order residualization technique from automatic control theory. A slight modification of SVAP, slowly varying amplitude derivative and phase (SVADP) is applied in this paper to obtain a better validity range. SVADP is validated for a half-bridge series resonant inverter and for a high-order plant, a dual-half bridge series resonant inverter giving analytical second-order transfer functions for both topologies. Simulation and experimental results are provided to show the validity range of the reduced-order models.
Assessment of pathological speech prosody based on automatic stress detection and phrasing approaches

Automatic classification methods are frequently used in early diagnosis of different diseases that affect speech production. These methods can also be applied to identify speech samples from patients affected by Parkinson's disease (PD) or depressive disorder (DD). This paper is interested in applying automatic stress detection and prosodic phrasing approaches on pathological speech samples in order to assess to what extent these tools can be useful either in characterizing in an unsupervised manner the prosodic attributes of pathological samples from individuals affected by PD and DD, or classifying samples as belonging to healthy or non-healthy individuals. We formulated hypotheses in connection with the duration of phonological phrases and the number of words grouped by them. We also briefly analyzed the phrase distributions. Our results show that healthy and pathological samples can be separated from each other by means of these prosodic analysers, and deep neural network or support vector machine based classifiers built on top of them.
Enzymatic Synthesis and Functional Characterization of Bioactive Microcin C-Like Compounds with Altered Peptide Sequence and Length

ABSTRACT Escherichia coli microcin C (McC) consists of a ribosomally synthesized heptapeptide attached to a modified adenosine. McC is actively taken up by sensitive Escherichia coli strains through the YejABEF transporter. Inside the cell, McC is processed by aminopeptidases, which release nonhydrolyzable aminoacyl adenylate, an inhibitor of aspartyl-tRNA synthetase. McC is synthesized by the MccB enzyme, which terminally adenylates the MccA heptapeptide precursor MRTGNAN. Earlier, McC analogs with shortened peptide lengths were prepared by total chemical synthesis and were shown to have strongly reduced biological activity due to decreased uptake. Variants with longer peptides were difficult to synthesize, however. Here, we used recombinant MccB to prepare and characterize McC-like molecules with altered peptide moieties, including extended peptide lengths. We find that N-terminal extensions of E. coli MccA heptapeptide do not affect MccB-catalyzed adenylation and that some extended-peptide-length McC analogs show improved biological activity. When the peptide length reaches 20 amino acids, both YejABEF and SbmA can perform facilitated transport of toxic peptide adenylates inside the cell. A C-terminal fusion of the carrier maltose-binding protein (MBP) with the MccA peptide is also recognized by MccB in vivo and in vitro, allowing highly specific adenylation and/or radioactive labeling of cellular proteins. IMPORTANCE Enzymatic adenylation of chemically synthesized peptides allowed us to generate biologically active derivatives of the peptide-nucleotide antibiotic microcin C with improved bioactivity and altered entry routes into target cells, opening the way for development of various McC-based antibacterial compounds not found in nature.
RFS-SLAM robot: An experimental platform for RFS based occupancy-grid SLAM

This paper describes the implementation of a miniature open-source and cost-effective SLAM-robot, utilizing a novel occupancy-grid SLAM algorithm based on the concept of random-finite-sets (RFS). This robotic platform is remotely controlled to move and scan unknown environments using a differential drive system algorithm, sending instantaneous position feedback to the remote operator. The mobile robot utilizes a LIDAR-Lite 2 laser range finder to map the environment while simultaneously estimating its position and orientation within the map. Even though there are many mobile robots that implement this behavior, the main advantage in this proposed robotic platform is modeling of LIDAR measurements at each scan as a RFS. This model provides robustness against the random count of received returns, due to false and missed detections, allowing the use of an inexpensive LIDAR sensor and commercial off the shelf hardware.
Injury- and Use-Related Plasticity in Adult Auditory Cortex

After restricted cochlear lesions in adult animals the frequency selectivity of neurons in the cortical region deprived of its normal input by the lesion is changed such that the region is occupied by expanded representations of adjacent (perilesion) frequencies. These changes reflect a dynamic process of reorganization (plasticity) and are not explicable as passive consequences of the lesion. Analogous plasticity of cortical frequency selectivity and organization is seen following behavioural training that enhances the significance of particular acoustic stimuli. The occurrence of injury- and use-related auditory cortical plasticity gives rise to a number of questions relating to the mechanisms involved, the perceptual consequences and functional significance of such plastic changes, and their implications for the central processing of input from prosthetic devices. Evidence relating to these issues is briefly summarized in this review, and the directions of future research are considered.
Desempenho muscular e equilíbrio postural em idosas frágeis residentes na comunidade

Introducao: o envelhecimento humano e um processo fisiologico que gera alteracoes nos diversos sistemas do organismo. No sistema musculoesqueletico, a principal mudanca gerada e o decrescimo da forca muscular, que nos membros inferiores, compromete a habilidade de responder rapidamente e com forca suficiente para prevenir quedas, levando a alteracoes no equilibrio postural. Atualmente, muitos p esquisadores tem estudado a fragilidade humana, que e definida como uma sindrome de carater multifatorial, em que ocorre um excesso de vulnerabilidade aos estressores, com reducao na habilidade de manter ou regular a homeostasia. Estas caracteristicas estao diretamente relacionadas a funcao fisica. Objetivo: analisar parâmetros do desempenho muscular e equilibrio postural entre idosas frageis e pre-frageis, e compara-los com os criterios do fenotipo de fragilidade propostos por Fried et al 2001. Metodologia: 39 idosas frageis comunitarias, acima de 65 anos, foram avaliadas quanto aos parâmetros do desempenho muscular do membro inferior atraves do dinamometro isocinetico, e do equilibrio postural na Escala de Equilibrio de Berg e na Baropodometria Computadorizada. Resultados: houve diferenca significativa na forca dos flexores-plantares, e flexores e extensores do joelho, na oscilacao ântero-posterior com olhos abertos e nos escores do Berg entre os grupos. Foi observada correlacao entre a forca e o equilibrio. Conclusao: os resultados sugerem que idosas frageis apresentam alteracoes no desempenho muscular e equilibrio mais significativas do que as pre-frageis. Correlacoes entre desempenho muscular e deficits de equilibrio estao presentes nessas idosas, todavia outras variaveis estao envolvidas na manutencao do equilibrio postural
Development of New Insulin-like Growth Factor-1 Receptor Kinase Inhibitors Using Catechol Mimics*

Because insulin-like growth factor-1 (IGF-1) and its receptor play a pivotal role in many cancers, it is an attractive target for the design of inhibitors. Here we present a new family of bioisostere inhibitors, based on the structure of AG 538. AG 538 is a substrate-competitive inhibitor of the IGF-1 receptor (IGF-1R), with an IC50 = 61 nM in a cell-free kinase assay (Blum, G., Gazit, A., and Levitzki, A. (2000) Biochemistry 39, 15705–15712). AG 538 is a low molecular weight compound containing two catechol rings, which are sensitive to oxidation in cells. We have therefore prepared and examined catechol bioisosteres of AG 538. These AG 538 bioisosteres possess similar biological properties to AG 538; they inhibit IGF-1R by a substrate-competitive mechanism and are non-competitive vis à vis ATP. They inhibit IGF-1R kinase activity in the sub-micromolar concentration range in cell-free assays. IGF-1 induced IGF-1R autophosphorylation; IRS-1 phosphorylation and protein kinase B activation are inhibited at a low micromolar concentration range when applied to intact cells. These inhibitors also block the formation of colonies in soft agar by prostate and breast cancer cells. The ability to replace catechol groups with a moiety that is more stable in cells may aid in developing non-catechol-containing substrate-competitive inhibitors targeted toward IGF-1R and possibly against other protein-tyrosine kinases.
MLSD Bounds and Receiver Designs for Clipped OFDM Channels

We derive tight closed-form approximations of symbol and bit error probability on maximum-likelihood sequence detection (MLSD) of Nyquist-rate and oversampled OFDM systems over the AWGN, flat and frequency-selective quasi-static Rayleigh fading channels. Contrary to common knowledge, we show that on a frequency-selective channel, clipping at the transmitter leads to achievable frequency-diversity and performance gain over unclipped systems with MLSD. We derive closed-form expressions of the diversity and the performance gain over the no-clipping case, as well as the optimal clipping ratio for a given system. We show that such diversity and performance gain are a result of both clipping and channel frequency-selectivity, and they do not occur on the AWGN and flat fading channels.We also present a new near-optimum detection algorithm that achieves the MLSD performance bound with a few iterations for the clipped OFDM systems with both high and low clipping levels on the AWGN and flat Rayleigh fading channels. For the frequency selective channel, we present a receiver design that utilizes the advantage of clipping to some extent. We consider rectangular QAM signaling in this paper.
Variation in hydration status within the normative range is associated with urinary biomarkers of systemic oxidative stress in Guatemalan preschool children.

BACKGROUND Researchers have increasingly sought noninvasive methods to determine health and nutritional status in humans. Easy and painless to collect, human urine is a source of noninvasive biomarkers. OBJECTIVE We aimed to explore the relation between systemic oxidative stress biomarkers excreted in urine and urinary osmolality (Uosm). DESIGN The current trial was a descriptive, cross-sectional study. We collected seventy-eight samples of 24-h urine in preschoolers who were attending daycare centers in the Western Highlands province of Quetzaltenango, Guatemala. After we measured the total urine volume (Uvol), the aliquot was stored for the later determination of Uosm as a hydration biomarker and to measure 15-isoprostane F2t (F2-Iso) and 8-hydroxydeoxyguanosine (8-OHdG) as biomarkers of cellular oxidation with the use of ELISA assay kits in Spain. Descriptive statistics and linear [Spearman rank-order (rs)] and nonlinear (goodness-of-fit) correlations were performed. RESULTS Twenty-four hour Uvols ranged from 65 to 1670 mL, whereas the Uosm varied between 115 and 1102 mOsm/kg. With respect to oxidative biomarkers, the 24-h urinary output of F2-Iso and 8-OHdG had median values of 748 and 2793 ng/d, respectively. The Uvol correlated inversely and significantly with the concentrations of both oxidative biomarkers (F2-Iso rs = -0.603, P < 0.001; 8-OHdG rs = -0.433, P < 0.001), whereas the Uosm was correlated in a direct manner (F2-Iso rs = 0.541, P < 0.001; 8-OHdG rs = 0.782, P < 0.001) when analyzed as a concentration. Associations were weaker when they were analyzed as the total 24-h production. CONCLUSIONS Preschool children from the Western Highlands of Guatemala show strong correlations between hydration status measured through the use of Uosm and biomarkers of oxidative stress in urine. Thus, a relatively superior hydration status is associated with a quantitative reduction in urinary excretion of systemic oxidation products. This trial was registered at clinicaltrials.gov as NCT02203890.