Miracle-dz/UniFAR-FTUs huggingface dataset:
Construction and Characterization of a Nonproliferative El Tor Cholera Vaccine Candidate Derived from Strain 638

ABSTRACT In recent clinical assays, our cholera vaccine candidate strain,Vibrio cholerae 638 El Tor Ogawa, was well tolerated and immunogenic in Cuban volunteers. In this work we describe the construction of 638T, a thymidine auxotrophic version of improved environmental biosafety. In so doing, the thyAgene from V. cholerae was cloned, sequenced, mutated in vitro, and used to replace the wild-type allele. Except for its dependence on thymidine for growth in minimal medium, 638T is essentially indistinguishable from 638 in the rate of growth and morphology in complete medium. The two strains showed equivalent phenotypes with regard to motility, expression of the celAmarker, colonization capacity in the infant mouse cholera model, and immunogenicity in the adult rabbit cholera model. However, the ability of this new strain to survive environmental starvation was limited with respect to that of 638. Taken together, these results suggest that this live, attenuated, but nonproliferative strain is a new, promising cholera vaccine candidate.
ERROR ANALYSIS AND DISFLUENCY MODELING IN THE SWITCHBOARD DOMAIN

When analyzing the baseline system, we discovered that a word missing from the lattice tends to cause up to 3 word errors, and that such errors are hard to eradicate even with extremely powerful language models. We quanti ed the loss incurred when working from N -best lists as opposed to lattices, and consequently decided to use 1000-best lists. We learned that doubling the amount of language training data is likely to reduce the word error rate by no more than 2%. We experimented with rank histograms as an alternative measure of modeling progress. We found that a mismatch between segmentation information in the training and test data is a signi cant problem, and that it can be overcome to some extent by hypothesizing boundaries; linguistic boundries were found to be more informative than acoustic ones. Segment based error analysis revealed surprisingly that disuent segments are no more error prone than non-dis uent ones, and long segments are no more erroneous than short ones. Finally, word based error analysis yielded a list of features strongly correlated with word error.
Residual vector quantisation-based iris image compression

Research in iris image compression was triggered by its wide application in biometric recognition system. Iris has become one of the three biometric identification technologies (other than fingerprint and face recognition) internationally standardised by International Civil Aviation Organization (ICAO) for use in future passports. In this paper, a novel approach has been proposed for compressing iris images and its performance has been found to outclass standard compression algorithms.
Erwinia asparaginase after allergy to E. coli asparaginase in children with acute lymphoblastic leukemia

Escherichia coli asparaginase is an important component of treatment for childhood acute lymphoblastic leukemia (ALL); however, hypersensitivity develops in up to 30% of patients. We assessed the nadir enzyme activity and tolerability of Erwinia asparaginase, an alternative preparation, in E. coli asparaginase‐allergic patients.
Development of a Novel, Ultra-rapid Biosensor for the Qualitative Detection of Hepatitis B Virus-associated Antigens and Anti-HBV, Based on “Membrane-engineered” Fibroblast Cells with Virus-Specific Antibodies and Antigens

A novel miniature cell biosensor detection system for the detection of Hepatis B virus (HBV)-associated antigens and anti-HBV is described. The biosensor is based on “membrane-engineered” Vero fibroblast cells immobilized in an alginate matrix. The membrane-engineering process involved the electroinsertion of anti-HBV specific antibodies (anti-HBs, anti-HBe) or antigens (HBsAg) in the membranes of the Vero cells. The attachment of a homologous antigen to the electroinserted antibody (or, respectively, of the antibody to the electroinserted antigen) triggered specific changes to the cell membrane potential that were measured by appropriate microelectrodes, according to the principle of the Bioelectric Recognition Assay (BERA). The sensor was used for screening 133 clinical blood serum samples according to a double-blind protocol. Considerably higher sensor responses were observed against HBV-positive samples, compared with responses against negative samples or samples positive for heterologous hepatitis viruses such as Hepatitis C (HCV) virus. Detection of anti-HBs antibodies was made possible by using a biosensor based on immobilized Vero cells bearing the respective antigen (HBsAg). The observed response was rapid (45 sec) and quite reproducible. Fluorescence microscopy observations showed that attachment of HBV particles to cells membrane-engineered with anti-HBs was associated with a decrease of [Ca2+]cyt. The perspectives for using the novel biosensor as a qualitative, rapid screening, high throughput assay for HBV antigens and anti-HBs in clinical samples is discussed.
Impact of computerised provider order entry system on nursing workflow, patient safety, and medication errors: perspectives from the front line

There is a paucity of research on the impact of computerised provider order entry (CPOE) system on the front line staff. We assessed nurses perspectives of the impact of CPOE system implementation on their workflow, patient safety and medication errors in a Saudi Arabian hospital. We conducted a cross-sectional survey involving 112 nurses between April and May 2012. The workflow was easy to manage for nurses who rated CPOE training as of good quality (p = 0.001) and they found that CPOE helped in reducing medication errors (p = 0.001). The nurses who rated CPOE training as of good quality also stated that patient safety was better with CPOE implementation and its use (p < 0.05). Provision of adequate CPOE training improves nurses' perception of the system's role in their workflow, patient safety and medication errors, and is critical in the success of CPOE use and its long-term adoption.
Perturbations in B cell responsiveness to CD4+ T cell help in HIV-infected individuals

HIV infection induces a wide array of B cell dysfunctions. We have characterized the effect of plasma viremia on the responsiveness of B cells to CD4+ T cell help in HIV-infected patients. In HIV-negative donors, B cell proliferation correlated with CD154 expression on activated CD4+ T cells and with the availability of IL-2, whereas in HIV-infected viremic patients, reduced B cell proliferation was observed despite normal CD154 expression on activated CD4+ T cells. Reduced triggering of B cells by activated CD4+ T cells was clearly observed in HIV-infected viremic patients compared with aviremic patients with comparable CD4+ T cell counts, and a dramatic improvement in B cell function was observed in patients whose plasma viremia was controlled by effective antiretroviral therapy. The degree of B cell dysfunction in viremic patients correlated strongly with the inability of B cells to express CD25 in response to activated CD4+ T cells, resulting in an inability to mount a normal proliferative response to IL-2. Similar defects in responsiveness to IL-2 were observed in the B cells of HIV-infected viremic patients in the context of B cell receptor stimulation. These data provide new insight into the mechanisms associated with ineffective humoral responses in HIV disease.
Modeling and Experimental Analyses Reveals Signaling Plasticity in a Bi-Modular Assembly of CD40 Receptor Activated Kinases

Depending on the strength of signal dose, CD40 receptor (CD40) controls ERK-1/2 and p38MAPK activation. At low signal dose, ERK-1/2 is maximally phosphorylated but p38MAPK is minimally phosphorylated; as the signal dose increases, ERK-1/2 phosphorylation is reduced whereas p38MAPK phosphorylation is reciprocally enhanced. The mechanism of reciprocal activation of these two MAPKs remains un-elucidated. Here, our computational model, coupled to experimental perturbations, shows that the observed reciprocity is a system-level behavior of an assembly of kinases arranged in two modules. Experimental perturbations with kinase inhibitors suggest that a minimum of two trans-modular negative feedback loops are required to reproduce the experimentally observed reciprocity. The bi-modular architecture of the signaling pathways endows the system with an inherent plasticity which is further expressed in the skewing of the CD40-induced productions of IL-10 and IL-12, the respective anti-inflammatory and pro-inflammatory cytokines. Targeting the plasticity of CD40 signaling significantly reduces Leishmania major infection in a susceptible mouse strain. Thus, for the first time, using CD40 signaling as a model, we show how a bi-modular assembly of kinases imposes reciprocity to a receptor signaling. The findings unravel that the signalling plasticity is inherent to a reciprocal system and that the principle can be used for designing a therapy.
A pattern matching framework for software architecture recovery and restructuring

The paper presents a framework for software architecture recovery and restructuring. The user specifies a high level abstraction view of the system using a structured pattern language. A pattern matching engine provides an optimal match between the given pattern and a decomposition of the legacy system entities by satisfying the inter/intramodule constraints defined by the pattern. The data mining technique Apriori is used by the matching engine to reveal meaningful data and control flow properties of the target system and limit the search space. A branch and bound search algorithm using a score function, models the constraints in the pattern as a Valued Constraint Satisfaction Problem (VCSP), and assists in searching for an optimal match between the given pattern and the target system.
Blood cardioplegia with N-acetylcysteine may reduce coronary endothelial activation and myocardial oxidative stress.

OBJECTIVES The aim of this prospective study was to compare the efficacy of intermittent antegrade blood cardioplegia with or without n-acetylcysteine (NAC) in reducing myocardial oxidative stress and coronary endothelial activation. METHODS Twenty patients undergoing elective isolated coronary artery bypass graft surgery were randomly assigned to receive intermittent antegrade blood cardioplegia (32 degrees C-34 degrees C) with (NAC group) or without (control group) 300 mg of NAC. For these 2 groups we compared clinical outcome, hemodynamic evolution, systemic plasmatic levels of troponin I, and plasma concentrations of malondialdehyde (MDA) and soluble vascular adhesion molecule 1 (sVCAM-1) from coronary sinus blood samples. RESULTS Patient demographic characteristics and operative and postoperative data findings in both groups were similar. There was no hospital mortality. Comparing the plasma levels of MDA 10 min after the aortic cross-clamping and of sVCAM-1 30 min after the aortic cross-clamping period with the levels obtained before the aortic clamping period, we observed increases of both markers, but the increase was significant only in the control group (P= .039 and P= .064 for MDA; P= .004 and P= .064 for sVCAM-1). In both groups there was a significant increase of the systemic serum levels of troponin I compared with the levels observed before cardiopulmonary bypass (P< .001), but the differences between the groups were not significant (P= .570). CONCLUSIONS Our investigation showed that NAC as an additive to blood cardioplegia in patients undergoing on-pump coronary artery bypass graft surgery may reduce oxidative stress and the resultant coronary endothelial activation.
An editing-defective aminoacyl-tRNA synthetase is mutagenic in aging bacteria via the SOS response

Mistranslation in bacterial and mammalian cells leads to production of statistical proteins that are, in turn, associated with specific cell or animal pathologies, including death of bacterial cells, apoptosis of mammalian cells in culture, and neurodegeneration in the mouse. A major source of mistranslation comes from heritable defects in the editing activities of aminoacyl-tRNA synthetases. These activities clear errors of aminoacylation by deacylation of mischarged tRNAs. We hypothesized that, in addition to previously reported phenotypes in bacterial and mammalian systems, errors of aminoacylation could be mutagenic and lead to disease. As a first step in testing this hypothesis, the effect of an editing defect in a single tRNA synthetase on the accumulation of mutations in aging bacteria was investigated. A striking, statistically significant, enhancement of the mutation rate in aging bacteria was found. This enhancement comes from an increase in error-prone DNA repair through induction of the bacterial SOS response. Thus, mistranslation, as caused by an editing-defective tRNA synthetase, can lead to heritable genetic changes that could, in principle, be linked to disease.
Mouse interleukin-1 receptor antagonist induced by Actinobacillus actinomycetemcomitans lipopolysaccharide blocks the effects of interleukin-1 on bone resorption and osteoclast-like cell formation

We have reported that P388D1 cell line murine macrophages stimulated with lipopolysaccharide (LPS) from Actinobacillus actinomycetemcomitans release interleukin-1 (IL-1) inhibitor. The IL-1 inhibitor was purified from conditioned media of P388D1 cells stimulated with A. actinomycetemcomitans LPS for 72 h to homogeneity by a four-step procedure: acetic acid extraction from conditioned media; Bio-Gel P-60 gel filtration chromatography; DEAE-Sepharose CL-6B column chromatography; and reverse-phase high-performance liquid chromatography on a C18 hydrophobic support. The purified IL-1 inhibitor gave a single band of protein with a molecular mass of 26 kDa on sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The purified IL-1 inhibitor was a heat- and acid-stable protein that was inactivated by digestion with trypsin and reduction with dithiothreitol. This inhibitory factor suppressed the proliferation of C3H/HeJ mouse thymocytes and the proliferation of IL-1-dependent cell lines, D10.G4. 1 and RPMI 1788, induced by IL-1. However, this inhibitor did not affect the proliferation of IL-2-dependent CTLL-2 cells induced by IL-2, the proliferation of C3H/HeJ mouse thymocytes stimulated with a mitogenic dose of concanavalin A, and the proliferation of IL-6-dependent B9 cells induced by IL-6. Furthermore, the IL-1 inhibitor significantly blocked stimulation of bone resorption in organ cultures of newborn mouse calvaria and inhibited the osteoclast-like cell formation in mouse marrow cultures. A monoclonal antibody prepared against the purified IL-1 inhibitor reacted with mouse recombinant IL-1 receptor antagonist (rIL-1ra), and a polyclonal antibody to mouse rIL-1ra reacted with the IL-1 inhibitor by Western blot (immunoblot) analysis. These results indicate that the IL-1 inhibitor is an identical molecule to rIL-1ra, suggesting that the IL-1 inhibitor (IL-1ra) released by macrophages stimulated with LPS from A. actinomycetemcomitans may play an important mediative role in the development of periodontal disease.
Evaluation of Methionine Content in a High-Fat and Choline-Deficient Diet on Body Weight Gain and the Development of Non-Alcoholic Steatohepatitis in Mice

Aim Non-alcoholic steatohepatitis (NASH) is a globally recognized liver disease. A methionine- and choline-deficient diet is used to induce NASH in mice; however, this diet also causes severe body weight loss. To resolve this issue, we examined the effects of methionine content in a high-fat and choline-deficient (HFCD) diet on body weight and the development of NASH in mice. Methods C57BL/6J mice (male, 10 weeks of age) were fed an L-amino acid rodent (control) diet, high-fat (HF) diet, or HFCD diet containing various amounts of methionine (0.1–0.6% (w/w)) for 12 weeks. Plasma lipid levels, hepatic lipid content and inflammatory marker gene expression were measured, and a pathological analysis was conducted to evaluate NASH. Results The 0.1% methionine in HFCD diet suppressed body weight gain, which was lower than that with control diet. On the other hand, the 0.2% methionine in HFCD diet yielded similar body weight gains as the control diet, while more than 0.4% methionine showed the same body weight gains as the HF diet. Liver weights and hepatic lipid contents were the greatest with 0.1% methionine and decreased in a methionine dose-dependent manner. Pathological analysis, NAFLD activity scores and gene expression levels in the liver revealed that 0.1% and 0.2% methionine for 12 weeks induced NASH, whereas 0.4% and 0.6% methionine attenuated the induction of NASH by HFCD diet. However, the 0.2% methionine in HFCD diet did not induce insulin resistance, despite the body weight gain. Conclusions The 0.2% methionine in HFCD diet for 12 weeks was able to induce NASH without weight loss.
Genome-Wide Association Study Meta-Analysis Reveals Transethnic Replication of Mean Arterial and Pulse Pressure Loci

We conducted a genome-wide association study meta-analysis of mean arterial pressure and pulse pressure among 26 600 East Asian participants (stage 1) followed by replication study of up to 28 783 participants (stage 2). For novel loci, statistical significance was determined by a P<5.0×10–8 in joint analysis of stage 1 and stage 2 data. For loci reported by the previous mean arterial and pulse pressure genome-wide association study meta-analysis in Europeans, evidence of transethnic replication was determined by consistency in effect direction and a Bonferroni-corrected P<1.4×10–3. No novel loci were identified by the current study. Five independent mean arterial pressure variants demonstrated robust evidence for transethnic replication including rs17249754 at ATP2B1 (P=7.5×10–15), rs2681492 at ATP2B1 (P=3.4×10–7), rs11191593 at NT5C2 (1.1×10–6), rs3824755 at CYP17A1 (P=1.2×10–6), and rs13149993 at FGF5 (P=2.4×10–4). Two additional variants showed suggestive evidence of transethnic replication (consistency in effect direction and P<0.05), including rs319690 at MAP4 (P=0.014) and rs1173771 at NPR3 (P=0.018). For pulse pressure, robust evidence of replication was identified for 2 independent variants, including rs17249754 at ATP2B1 (P=1.2×10–5) and rs11191593 at NT5C2 (P=1.1×10–3), with suggestive evidence of replication among an additional 2 variants including rs3824755 at CYP17A1 (P=6.1×10–3) and rs2681492 at ATP2B1 (P=9.0×10–3). Replicated variants demonstrated consistency in effect sizes between East Asian and European samples, with effect size differences ranging from 0.03 to 0.24 mm Hg for mean arterial pressure and from 0.03 to 0.21 mm Hg for pulse pressure. In conclusion, we present the first evidence of transethnic replication of several mean arterial and pulse pressure loci in an East Asian population.
Optimal mass distribution for a passive dynamic biped with upper body considering speed, efficiency and stability

This paper reports how mass distribution can affect the stability, efficiency and speed of a passive dynamic biped with upper body. To investigate the optimal mass distribution, we extend the simplest walking model with upper body, round feet and hip actuation. The mechanical parameters, including mass and the center of mass, are optimized by particle swarm optimization method. In addition, the effects of the hip torque on the walking characteristics are studied. Simulation results indicate that optimized mass distribution can improve walking characteristics of the passivity-based biped.
A platform for secure IP integration in Xilinx Virtex FPGAs

Advancements in silicon, software and IP support have made Field Programmable Gate Arrays (FPGAs) a highly flexible solution for many applications. With the growing number of companies providing IP support for FPGAs, IP license violations by over-deployment of IP into more devices than originally licensed remains a major concern for IP owners. In this paper we present a solution for secure IP exchange and configuration based on the Dynamic Partial Reconfiguration (DPR) feature in Xilinx FPGAs. Our system deploys DPR to integrate encrypted hard-macro IP cores into identifiable FPGA devices. These IP cores are configured using a proposed partial bitstream relocation technique to allow for a flexible design flow. We present a proof-of-concept implementation of a secure internal reconfiguration engine on a Xilinx Virtex-6 FPGA.
Prion liposomes.

Perhaps the novelty and insolubility of the scrapie agent have been the two factors which contributed most to the confusing and tortuous history of this particle. Scrapie is a degenerative neurological disease of sheep and goats [1-4]. Although scrapie can be transmitted to animals by inoculation with extracts of diseased tissue, whether infection features in the spread of natural scrapie is unclear [3-10]. Some investigators proposed that natural scrapie is a genetic disease and that its transmissibility is incidental [3,8] while others have argued vehemently that natural scrapie is an infectious disease [9,10]. Seven diseases, four in animals and three in humans, are thought to be caused by prions. The animal prion diseases are scrapie, transmissible mink encephalopathy [11], chronic wasting disease of mule deer and elk [12] and bovine spongiform encephalopathy [13,14]. The human prion diseases are kuru [15], Creutzfeldt-Jakob disease (CJD) [16] and Gerstmann-Straussler syndrome (GSS) [17], which illustrate the transmissible, sporadic and familial manifestations of these disorders [18-20]. Consistent with some of the observations on natural scrapie noted above, GSS and familial CJD are the only known human diseases which appear to be both inherited and transmissible [18,21-24]. Recent genetic linkage studies provide the best evidence, to date, that GSS is a genetic disorder in which infectious prions are produced [18]. An alternative hypothesis, for which there are few supporting data, is that prions are ubiquitous infectious pathogens causing CJD sporadically across the earth at a rate of one case per million population and GSS in all individuals carrying a mutation in one allele of their PrP gene [18-21,25,26]. Our genetic linkage results with GSS raise the possibility that sporadic CJD arises from a somatic mutation [5,18,25]. While many exciting and provocative areas of prion research have evolved over the past 5 years, it is neither the intent nor province of this review to chronicle all these developments. Many other reviews [5,19,27-32] and books [33,34] provide more broad coverage of the subject. Instead, this review is intended to focus primarily on the recent advances in prion research that have come from the application of liposome technology.
Integrated Covert Channel Countermeasure Model in MLS Networks

Our country needs specially appointed data transmission between different security level networks in government. In this paper, we put forward a model of warden, which is deployed between these networks and used to counteract the overall covert channels. We use 2-type Turing machine to handle input and unrestricted grammar to generate output, this will eliminate all covert channels in packet header. We use union of automata to filtrate and modify application content. Four kinds of filters are described for different aspects. We then propose a 3-host prototype to testify our model. The two side hosts strip packet header. The centre host uses policy configured in advance to do limited-output filtration on content. For the practical access emulation by file transfer protocol, the prototype successfully reduced the overall covert channel capacity and the anticipated result is achieved.