Miracle-dz/UniFAR-FTUs huggingface dataset:
Pour some sugar on it: the expanding world of bacterial protein O‐linked glycosylation

Protein glycosylation was once considered as an eccentricity of a few bacteria. However in the recent years multiple O‐glycosylation mechanisms have been identified in bacterial species from the most diverse genera, including various important human pathogens. This review focuses on summarizing the structural diversity, the various pathways and the physiological roles of this post‐translational protein modification. We propose a classification of O‐glycosylation based on the requirement of an oligosaccharyltransferase (OTase). OTase‐dependent glycosylation utilizes an oligosaccharide synthesized on a lipid carrier that is transferred to proteins en bloc by an OTase. Multiple proteins, including the pilins, are glycosylated using this mechanism. OTase‐independent glycosylation refers to the pathway in which glycosyltransferases sequentially add monosaccharides onto the target proteins. This pathway is employed for glycosylation of flagella and autotransporters. Both systems play key roles in pathogenesis. Exploiting glycosylation machineries it is now possible to generate glycoconjugates made of different proteins attached to polysaccharides derived from LPS or capsule biosynthesis. These recombinant glycoproteins can be exploited for vaccines and diagnostics of bacterial infections. Furthermore, O‐glycosylation systems are promising targets for antibiotic development. Technological advances in MS and NMR will facilitate the discovery of novel glycosylation systems. Likely, the O‐glycosylation pathways we currently know constitute just the tip of the iceberg of a still largely uncharacterized bacterial glycosylation world.
Direct Divergence Approximation between Probability Distributions and Its Applications in Machine Learning

Approximating a divergence between two probability distributions from their samples is a fundamental challenge in statistics, information theory, and machine learning. A divergence approximator can be used for various purposes, such as two-sample homogeneity testing, change-point detection, and class-balance estimation. Furthermore, an approximator of a divergence between the joint distribution and the product of marginals can be used for independence testing, which has a wide range of applications, including feature selection and extraction, clustering, object matching, independent component analysis, and causal direction estimation. In this paper, we review recent advances in divergence approximation. Our emphasis is that directly approximating the divergence without estimating probability distributions is more sensible than a naive twostep approach of first estimating probability distributions and then approximating the divergence. Furthermore, despite the overwhelming popularity of the Kullback-Leibler divergence as a divergence measure, we argue that alternatives such as the Pearson divergence, the relative Pearson divergence, and the L2-distance are more useful in practice because of their computationally efficient approximability, high numerical stability, and superior robustness against outliers.
Antecedents and consequences of upward and downward social comparisons

Purpose – The purpose of this paper is to extend and test a theory of uncertainty and directional social comparisons. Prior studies have posited that uncertainty leads to increased upward and downward social comparisons. The authors ' view is that uncertainty affects upward and downward comparisons differentially. They test their theory in the Chinese workplace, and focus specifically on employees’ comparisons of career progress. Workplace consequences of social comparisons are also investigated. Design/methodology/approach – The authors achieve their objectives by collecting data from respondents in China that measure uncertainty, directional social comparisons, organizational commitment and job satisfaction. They use a longitudinal design to assess causality. Findings – This paper found that perceived organizational support, an antecedent that lowers uncertainty in the workplace, is related to upward social comparison, whereas psychological entitlement, an uncertainty-raising antecedent, is related to d.
A Functional NSP4 Enterotoxin Peptide Secreted from Rotavirus-Infected Cells

ABSTRACT Previous studies have shown that the nonstructural glycoprotein NSP4 plays a role in rotavirus pathogenesis by functioning as an enterotoxin. One prediction of the mechanism of action of this enterotoxin was that it is secreted from virus-infected cells. In this study, the media of cultured (i) insect cells infected with a recombinant baculovirus expressing NSP4, (ii) monkey kidney (MA104) cells infected with the simian (SA11) or porcine attenuated (OSU-a) rotavirus, and (iii) human intestinal (HT29) cells infected with SA11 were examined to determine if NSP4 was detectable. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis–Western blotting, immunoprecipitation and N-terminal amino acid sequencing identified, in the early media from virus-infected cells, a secreted, cleavage product of NSP4 with an apparent molecular weight of 7,000 that represented amino acids 112 to 175 (NSP4 aa112–175). The secretion of NSP4 aa112–175 was not affected by treatment of cells with brefeldin A but was abolished by treatment with nocodazole and cytochalasin D, indicating that secretion of this protein occurs via a nonclassical, Golgi apparatus-independent mechanism that utilizes the microtubule and actin microfilament network. A partial gene fragment coding for NSP4 aa112–175 was cloned and expressed using the baculovirus-insect cell system. Purified NSP4 aa112–175 increased intracellular calcium mobilization in intestinal cells when added exogenously, and in insect cells when expressed endogenously, similarly to full-length NSP4. NSP4 aa112–175 caused diarrhea in neonatal mice, as did full-length NSP4. These results indicate that NSP4 aa112–175 is a functional NSP4 enterotoxin peptide secreted from rotavirus-infected cells.
Structural domains of the avian erythroblastosis virus erbB protein required for fibroblast transformation: dissection by in-frame insertional mutagenesis

Avian erythroblastosis virus (AEV) induces erythroblastosis and fibrosarcomas. The viral erbB protein is required for AEV-mediated oncogenesis. To explore the structural aspects of the v-erbB polypeptide necessary for its oncogenic function, we created a series of small in-frame insertions in different domains of the v-erbB oncogene. AEV genomes bearing lesions within the v-erbB kinase domain demonstrated a drastically decreased ability to transform avian fibroblasts, establishing a functional role for this structurally conserved oncogene domain. In contrast, mutations in the extracellular domain, between the transmembrane region and the kinase domain, or at the extreme C terminus of the v-erbB protein had no effect on AEV-mediated fibroblast transformation. One lesion within the v-erbB kinase domain, a 10-amino acid insertion, produced a temperature-sensitive mutant capable of fibroblast transformation at 36 degrees C but not at 41 degrees C, suggesting that small in-frame insertions have general utility for the in vitro creation of conditional mutants.
Ehrlichia canis-like agent isolated from a man in Venezuela: antigenic and genetic characterization

We report the first isolation and molecular and antigenic characterization of a human ehrlichial species in South America. A retrospective study was performed with serum specimens from 6 children with clinical signs suggestive of human ehrlichiosis and 43 apparently healthy adults who had a close contact with dogs exhibiting clinical signs compatible with canine ehrlichiosis. The evaluation was performed by the indirect fluorescent-antibody assay with Ehrlichia chaffeensis Arkansas, Ehrlichia canis Oklahoma, and Ehrlichia muris antigens. The sera from two apparently healthy humans were positive by the indirect fluorescent-antibody assay for all three antigens. Of the three antigens, samples from humans 1 and 2 showed the highest antibody titers against E. chaffeensis and E. muris, respectively. The remaining serum samples were negative for all three antigens. One year later examination of a blood sample from subject 1 revealed morulae morphologically resembling either E. canis, E. chaffeensis, or E. muris in monocytes in the blood smear. The microorganism, referred to here as Venezuelan human ehrlichia (VHE), was isolated from the blood of this person at 4 days after coculturing isolated blood leukocytes with a dog macrophage cell line (DH82). The organism was also isolated from mice 10 days after intraperitoneal inoculation of blood leukocytes from subject 1. Analysis by electron microscopy showed that the human isolate was ultrastructurally similar to E. canis, E. chaffeensis, and E. muris. When the virulence of VHE in mice was compared with those of E. chaffeensis, E. canis, and E. muris, only VHE and E. muris induced clinical signs in BALB/c mice at 4 and 10 days, respectively, after intraperitoneal inoculation. VHE was reisolated from peritoneal exudate cells of the mice. Only E. chaffeensis- and E. muris-infected mice developed significant splenomegaly. Western immunoblot analysis showed that serum from subject 1 reacted with major proteins of the VHE antigen of 110, 80, 76, 58, 43, 35, and 34 kDa. Human serum against E. chaffeensis reacted strongly with 58-, 54-, 52-, and 40-kDa proteins of the VHE antigen. Anti-E. canis dog serum reacted strongly with 26- and 24-kDa proteins of VHE. In contrast, anti-E. sennetsu rabbit and anti-E. muris mouse sera did not react with the VHE antigen. Serum from subject 1 reacted with major proteins of 90, 64, or 47 kDa of the E. chaffeensis, E. canis, and E. muris antigens. This reaction pattern suggests that this serum sample was similar to serum samples from E. chaffeensis-infected human patients in Oklahoma. The base sequence of the 16S rRNA gene of VHE was most closely related to that of E. canis Oklahoma. On the basis of these observations, we suggest that VHE is a new strain or a subspecies of E. canis which may cause asymptomatic persistent infection in humans.
Delayed Development of Nervous System in Mice Homozygous for Disrupted Microtubule-associated Protein 1B (MAP1B) Gene

Microtubule-associated protein 1B (MAP1B), one of the microtubule-associated proteins (MAPs), is a major component of the neuronal cytoskeleton. It is expressed at high levels in immature neurons during growth of their axons, which indicates that it plays a crucial role in neuronal morphogenesis and neurite extension. To better define the role of MAP1B in vivo, we have used gene targeting to disrupt the murine MAP1B gene. Heterozygotes of our MAP1B disruption exhibit no overt abnormalities in their development and behavior, while homozygotes showed a slightly decreased brain weight and delayed nervous system development. Our data indicate that while MAP1B is not essential for survival, it is essential for normal time course development of the murine nervous system. These conclusions are very different from those of a previous MAP1B gene–targeting study (Edelmann, W., M. Zervas, P. Costello, L. Roback, I. Fischer, A. Hammarback, N. Cowan, P. Davis, B. Wainer, and R. Kucherlapati. 1996. Proc. Natl. Acad. Sci. USA. 93: 1270–1275). In this previous effort, homozygotes died before reaching 8-d embryos, while heterozygotes showed severely abnormal phenotypes in their nervous systems. Because the gene targeting event in these mice produced a gene encoding a 571–amino acid truncated product of MAP1B, it seems likely that the phenotypes seen arise from the truncated MAP1B product acting in a dominant-negative fashion, rather than a loss of MAP1B function.
Association between somatic cell count after first parturition and cumulative milk yield in dairy cows

The aim was to assess the association between the somatic cell count of parity 1 cows between 5 and 30 days in milk (SCC1), and subsequent cumulative milk yield over approximately two years for cows in English and Welsh dairy herds. The dataset included records from 43,461 cows in 2111 herds, from 2004 to 2006. Cumulative milk yield was the model outcome, and a random effect was included to account for variation between herds. The model fitted the data well and was used to make predictions of cumulative milk yield, based on SCC1. A unit increase in the natural logarithm of SCC1/1000 was associated with a median decrease in cumulative milk yield of 482 kg, over a median study period of 868 days.
Seroprevalence of Hepatitis‐B infection amongst Taiwanese university students 18 years following the commencement of a national Hepatitis‐B vaccination program

In Taiwan, the nation‐wide Hepatitis‐B virus (HB) vaccination program was first launched in July 1984 and was directed to those infants born to hepatitis B surface antigen (HBsAg) carrier mothers in Taiwan. From July 1986 onwards, all infants born in Taiwan were immunized against HB. This study examined the HB‐infection status amongst students at a Taiwanese university 18 years subsequent to the implementation of universal HB vaccination. A total of 1,969 new university entrants in 2005 were grouped into 1 of 3 distinct birth cohorts according to their HB‐vaccination schedule (cohort‐1 students born prior to July 1, 1984; cohort‐3 students born subsequent to June 30, 1986) and were examined for their serum HBsAg, antibody to hepatitis B surface antigen (anti‐HBs), and antibody to hepatitis B core antigen (anti‐HBc) status. Immunity arising from vaccination was defined as an anti‐HBs level 10 mIU/ml. We observed a trend toward a decreasing anti‐HBc‐positive rate and a decreasing HBsAg carrier rate from, respectively, 26.5 and 8.7% for cohort‐1 to 4.7 and 1.7% for cohort‐3 students. The prevalence of students featuring seronegativity for all three HB markers increased from 12.3% for cohort‐1 to 48.8% for cohort‐3 individuals. Amongst the 1,695 subjects revealing seronegativity for HBsAg and anti‐HBc, their anti‐HBs level was analyzed according to their birth year. The prevalence of students featuring a non‐protective anti‐HBs level increased from 11.9% for birth‐year 1984 individuals to 48.2% for birth‐year 1987 students. The introduction of HB vaccine has effectively reduced the transmission of HBV infection in Taiwan, 18 years subsequent to the commencement of the universal HB‐vaccination program. A “waning‐off” effect of anti‐HBs seropositivity acquired from the HB vaccination program has also been observed. J. Med. Virol. 79:138–143, 2007. © 2006 Wiley‐Liss, Inc.
Book Review: Working Class: Challenging Myths about Blue-collar Labor

When approaching Jeff Torlina’s book Working Class: Challenging Myths about Blue-collar Labor, the reader must make an essential assumption about the sociopolitical landscape in which this work is taken up: That the general demeanor of those academics working in the social sciences toward the manual, blue-collar working class is essentially where it was in 1972, during the publication of a similar title by Sennett and Cobb, The Hidden Injuries of Class. Fortunately for Torlina’s audience, the general attitudes of social scientists, policy makers, those working in the media, and the general public, all seem to be conveniently frozen in time and apparently hover somewhere between standing united against a blue-collar working class, and ignoring them/treating them as though they don’t exist. We know this is true in part, thanks to an aside in Torlina’s conclusion that informs us an ‘‘anonymous reviewer questioned the importance of interviews with workers in decline’’ (p. 188) and another claimed the book lacked relevance. Thus lies the cojoined state of the working class and the academy in the early part of the twenty-first century’s second decade. He knowingly takes up the challenge handed out in Sennett and Cobb’s 1972 classic, which ended on this note:
Silent infarcts in children with sickle cell anemia and abnormal cerebral artery velocity.

BACKGROUND A substantial minority of neurologically normal children with sickle cell disease have lesions consistent with cerebral infarction as seen on magnetic resonance imaging (MRI). OBJECTIVES To determine if transfusion therapy affects the rate at which silent infarcts develop and to evaluate the contribution of MRI of the brain to stroke prediction by transcranial Doppler (TCD) ultrasonography. STUDY DESIGN Children with elevated TCD ultrasonographic velocity were randomized to receive long-term transfusion therapy or standard care. Magnetic resonance imaging of the brain was obtained at randomization, annually, and with clinical neurologic events. The risk for new silent lesions and/or stroke was compared for each treatment arm. RESULTS Among the 37% of subjects with silent infarcts, those receiving standard care were significantly more likely to develop new silent lesions or stroke than were those who received transfusion therapy. For subjects receiving standard care, those with lesions at baseline were significantly more likely to develop stroke or new silent lesions than those whose MRI studies showed no abnormality. CONCLUSIONS Transfusion therapy lowers the risk for new silent infarct or stroke for children having both abnormal TCD ultrasonographic velocity and silent infarct. However, those with both abnormalities who are not provided transfusion therapy are at higher risk for developing a new silent infarct or stroke than are those whose initial MRI showed no abnormality. The finding of a silent infarct reinforces the need for TCD ultrasonographic screening and consideration of transfusion therapy if the abnormalities are seen. Similarly, elevated TCD ultrasonographic velocity warrants MRI of the brain because children with both abnormalities seem to be at increased risk for developing new silent infarct or stroke.
Master System and Network Engineering University of Amsterdam Anomaly Detection on Internet Content Filter Data Testing the effectiveness of statistical anomaly detection on user-agents

The goal of this research was to find out what the effectiveness of statistical anomaly detection on user-agent strings is. To increase effectiveness, a method was created to perform statistical analysis on the user-agents by splitting these into elements. By splitting the user-agent into multiple elements and checking these elements for anomalies, small differences in user-agents that would often occur could be removed. This helped to remove false positives that were not interesting. Next, a scoring mechanism was used to score IP-addresses based on the amount of anomalous user-agent elements in their user-agent string. The more anomalous elements originated from an IP, the higher the score. Plotting the host scores showed clear outliers when hosts are scored based on their user-agents. Outliers were often created by traffic from mobile phones, which mostly connected through proxies. Another found outlier was a host with a browser hijacker installed. Performing this form of anomaly detection proves useful on a network where hosts are uniform. Networks with more variation in hosts (more mobile devices) create a larger amount of unique user-agents. This happens because of application using a unique user-agent when sending traffic to servers.
Journal of Theoretical and Applied Information Technology Sizing of Dg Unit Operated at Optimal Power Factor to Reduce Losses in Radial Distribution. a Case Study

Distributed generators are very much beneficial in reducing the losses effectively compared to other methods of loss reduction . In this paper optimal size of DG unit operated at optimal power factor is dealt. DG unit placement using fuzzy logic and sizing of DG at any power factor is calculated using analytical method. Voltage and power loss reduction indices of distribution system nodes are modeled by fuzzy membership functions. Fuzzy inference system containing a set of rules is used to determine the DG unit placement. DG units are placed at buses with the highest suitability index. Simulation results show that optimal DG unit placement and sizing at 0.8 power factor is very efficient. Single DG unit of optimum size operated at 0.8 power factor is sufficient in reducing losses and improving voltage regulation effectively within the specified voltage constraints.
Sodium Channelopathy Underlying Familial Sick Sinus Syndrome With Early Onset and Predominantly Male Characteristics

Background—Sick sinus syndrome (SSS) is a common arrhythmia often associated with aging or organic heart diseases but may also occur in a familial form with a variable mode of inheritance. Despite the identification of causative genes, including cardiac Na channel (SCN5A), the pathogenesis and molecular epidemiology of familial SSS remain undetermined primarily because of its rarity. Methods and Results—We genetically screened 48 members of 15 SSS families for mutations in several candidate genes and determined the functional properties of mutant Na channels using whole-cell patch clamping. We identified 6 SCN5A mutations including a compound heterozygous mutation. Heterologously expressed mutant Na channels showed loss-of-function properties of reduced or no Na current density in conjunction with gating modulations. Among 19 family members with SCN5A mutations, QT prolongation and Brugada syndrome were associated in 4 and 2 individuals, respectively. Age of onset in probands carrying SCN5A mutations was significantly less (mean±SE, 12.4±4.6 years; n=5) than in SCN5A-negative probands (47.0±4.6 years; n=10; P<0.001) or nonfamilial SSS (74.3±0.4 years; n=538; P<0.001). Meta-analysis of SSS probands carrying SCN5A mutations (n=29) indicated profound male predominance (79.3%) resembling Brugada syndrome but with a considerably earlier age of onset (20.9±3.4 years). Conclusions—The notable pathophysiological overlap between familial SSS and Na channelopathy indicates that familial SSS with SCN5A mutations may represent a subset of cardiac Na channelopathy with strong male predominance and early clinical manifestations.
Summing the Instanton Series in N = 2 Superconformal Large-N QCD

We consider the multi-instanton collective coordinate integration measure in = 2 supersymmetric SU(N) gauge theory with NF fundamental hypermultiplets. In the large-N limit, at the superconformal point where NF = 2N and all VEVs are turned off, the k-instanton moduli space collapses to a single copy of AdS5 × S1. The resulting k-instanton effective measure is proportional to N1/2g4k(6), where k(6) is the partition function of = (1,0) SYM theory in six dimensions reduced to zero dimensions. The multi-instanton can in fact be summed in closed form. As a hint of an AdS/CFT duality, with the usual relation between the gauge theory and string theory parameters, this precisely matches the normalization of the charge-k D-instanton measure in type IIB string theory compactified to six dimensions on K3 with a vanishing two-cycle.
Scaled-Boundary Finite Element Solution Method for Inverse Heat Conduction Problem

The scaled boundary finite element method is a semi analytical fundamental solution-less boundary-element method which links to both finite elements and boundary elements. In this study coupling of scaled boundary finite element method (SBFEM) and genetic algorithm (GA) is used to solve inverse heat conduction problem (IHCP) in a two dimensional steady state square plate. Inverse heat conduction methods can be used to determine heat flux and temperatures on an inaccessible surface of a wall by measuring the temperature on an accessible boundary. Herein, IHCP is aimed to estimate unknown heat flux at the boundary. Temperature difference between calculated and exact values at the middle of the plate is considered as objective function. Validation of SBFEM results is proved by comparing temperature distributions which are determined using finite element method. According to accuracy of the SBFEM and low computational cost is an efficient method for IHC problems.