Miracle-dz/UniFAR-FTUs huggingface dataset:
Role of novel gyrA mutations in the suppression of the fluoroquinolone resistance genotype of vaccine strain Salmonella Typhimurium vacT (gyrA D87G).

OBJECTIVES This study was aimed at characterizing the gyrA locus and determining its impact on fluoroquinolone susceptibility, DNA supercoiling degree and growth rate of Salmonella Typhimurium live vaccine strain vacT in comparison with its parent M415. Furthermore, the role of multiple drug resistance efflux in the susceptibility of vacT to fluoroquinolones and macrolides was investigated. METHODS DNA sequences were determined for genes gyrA, gyrB, parC and parE of M415 and three consecutive mutants Nal2ori, Nal2passage and vacT. The impact of gyrA mutations on the fluoroquinolone susceptibilities and relative DNA supercoiling degrees was investigated by a complementation assay using wild-type gyrA (gyrA+) and a reporter gene system, respectively. Doubling times of the strains and MICs of different antibiotics in the absence and presence of an efflux pump inhibitor (EPI) were determined. RESULTS Besides the gyrA mutation D87G, two novel mutations (G75A and A866S) were identified in the three mutants and a third novel mutation W59R in vacT. Fluoroquinolone susceptibilities and DNA supercoiling degrees of all three mutants were reduced compared with those of M415. Introduction of the gyrA+ allele restored fluoroquinolone susceptibilities of the two intermediate strains to the wild-type level; however, for vacT, MICs of fluoroquinolones were reduced below those of M415. VacT had a higher susceptibility to macrolides and the EPI compared with M415. CONCLUSIONS The data point to a combination of at least one non-gyrA mutation and novel gyrA mutation(s) as the basis for the unusual fluoroquinolone susceptibility of vacT.
On the relation between dissipativity and discounted dissipativity

In this paper, we consider a recently introduced notion of discounted strict dissipativity which is of interest, e.g., in the context of discounted optimal control and economic model predictive control. We consider the question whether (standard) strict dissipativity implies discounted strict dissipativity for discounting factors close enough to one. While in general, this need not be the case, we show that it is indeed true under certain regularity conditions.
Study on the Measurement Method and Safety Design of Ultrasonic Cleaning Equipment

To the question that it was hard to measure and verify the safety design rationality of the performance parameters for the ultrasonic cleaning machine, the destructive effect mechanism of the ultrasonic cleaning was analyzed. It was indicated that the cleaning power and time were the two main factors for damaging the insulating layer of the cleaning objects. The measuring technology was presented by aluminum foil, and it analyzed feasibility and an area assessment method for the measurement method by aluminum foil. The practical long time test of the motor demonstrated that the measurement method by aluminum foil can provide safety design data support and experimental verification to the performance parameters design of the ultrasonic cleaning machine.
What a difference a tag cloud makes: effects of tasks and cognitive abilities on search results interface use

The goal of this study is to expand our understanding of the relationships between selected tasks, cognitive abilities and search result interfaces. The underlying objective is to understand how to select search results presentation for tasks and user contexts. Twenty-three participants conducted four search tasks of two types and used two interfaces (List and Overview) to refine and examine search results. Click-through data were recorded. This controlled study employed a mixed model design with two within-subject factors (task and interface) and two between-subject factors (two cognitive abilities: memory span and verbal closure). Quantitative analyses were carried out by means of the statistical package SPSS. Specifically, multivariate analysis of variance with repeated measures and non-parametric tests were performed on the collected data. The overview of search results appeared to have benefited searchers in several ways. It made them faster; it facilitated formulation of more effective queries and helped to assess search results. Searchers with higher cognitive abilities were faster in the Overview interface and in less demanding situations (on simple tasks), while at the same time they issued about the same number of queries as lower-ability searchers. In more demanding situations (on complex tasks and in the List interface), the higher ability searchers expended more search effort, although they were not significantly slower than the lower ability people in these situations. The higher search effort, however, did not result in a measurable improvement of task outcomes for high-ability searchers. These findings have implications for the design of search interfaces. They suggest benefits of providing result overviews. They also suggest the importance of considering cognitive abilities in the design of search results’ presentation and interaction.
Hippocampal Administration of Levothyroxine Impairs Contextual Fear Memory Consolidation in Rats

Thyroid hormone (TH) receptors are highly distributed in the hippocampus, which plays a vital role in memory processes. However, how THs are involved in the different stages of memory process is little known. Herein, we used hippocampus dependent contextual fear conditioning to address the effects of hippocampal THs on the different stages of fear memory. First, we found that a single systemic levothyroxine (LT4) administration increased the level of free triiodothyronine (FT3) and free tetraiodothyroxine (FT4) not only in serum but also in hippocampus. In addition, a single systemic LT4 administration immediately after fear conditioning significantly impaired fear memory. These results indicated the important role of hippocampal THs in fear memory process. To further confirm the effects of hippocampal THs on the different stages of fear memory, LT4 (0.4 μg/μl, 1 μl/side) was injected bilaterally into hippocampus. Rats given LT4 into hippocampus before training or tests had no effect on the acquisition or retrieval of fear memory, however rats given LT4 into hippocampus either immediately or 2 h after training showed being significantly impaired fear memory, which demonstrated LT4 administration into hippocampus impairs the consolidation but has no effect on the acquisition and retrieval of fear memory. Furthermore, hippocampal injection of LT4 did not affect rats’ locomotor activity, thigmotaxis and THs level in prefrontal cortex (PFC) and serum. These findings may have important implications for understanding mechanisms underlying contribution of THs to memory disorders.
A Hybrid System for Authentication Service

This paper studies a hybrid system of the public key infrastructure (PKI) and the identity based cryptosystem (IBC). In the hybrid system, an organization runs a private key generator (PKG) and requests a certificate authority to vouch the binding of the PKG's parameters and the organization's distinguished name. Then an authentication scenario is considered where a member of an organization is authenticated by an application server. The whole design pays attention to scalability and adopts caches and password-based protocols for a scalable service and an easy deployment.
CMC-UMC: a framework for the verification of abstract service-oriented properties

CMC and UMC are two prototypical instantiations of a common logical verification framework for the analysis of functional properties of service-oriented systems. The service-oriented SocL logic is used to describe the required system properties. Computational models of the system can be built either using the COWS specification language or designing the system as a collection of interacting UML state machines, and an on-the-fly model checker can be used to verify the satisfaction of the requirements and possibly to generate counterexamples or witnesses for them. An automotive case study is used to illustrate the overall framework.
ADEPT: a computer program for prediction of protein antigenic determinants

ADEPT, a program that can be used for prediction of protein antigenic determinants from the amino acid sequence alone for the cases of humoral and cellular immune response, is described. Most methods presently utilized for this purpose are implemented in the program along with some original parameters for the case of humoral immune response. There is also a possibility to combine several methods for the case of humoral immune response, which provides a means to create new predictive methods. ADEPT also includes a literature-derived database of proteins in the SWISS-PROT standard with experimentally determined antigenic determinants, so the predictive ability of new methods can be assessed within the program and corresponding statistical information is calculated. ADEPT may be useful for solving various tasks involving the delineation of antigenic regions on proteins or characterization of peptide fragments, arising, for example, in protein engineering (e.g. selection of protein portions most suitable for insertion of peptide sequences that are antigenically active or possessing other desired characteristics), and in particular for construction of vaccines containing B- and/or T-cell epitopes, as well as for other problems of medico-biological research.
Cloning and Functional Characterization of Novel Variants and Tissue-Specific Expression of Alternative Amino and Carboxyl Termini of Products of Slc4a10

Previous studies have shown that the electroneutral Na+/HCO3 − cotransporter NBCn2 (SLC4A10) is predominantly expressed in the central nervous system (CNS). The physiological and pathological significances of NBCn2 have been well recognized. However, little is known about the tissue specificity of expression of different NBCn2 variants. Moreover, little is known about the expression of NBCn2 proteins in systems other than CNS. Here, we identified a set of novel Slc4a10 variants differing from the originally described ones by containing a distinct 5′ untranslated region encoding a new extreme amino-terminus (Nt). Electrophysiology measurements showed that both NBCn2 variants with alternative Nt contain typical electroneutral Na+-coupled HCO3 − transport activity in Xenopus oocytes. Luciferase reporter assay showed that Slc4a10 contains two alternative promoters responsible for expression of the two types of NBCn2 with distinct extreme Nt. Western blotting showed that NBCn2 proteins with the original Nt are primarily expressed in CNS, whereas those with the novel Nt are predominantly expressed in the kidney and to a lesser extent in the small intestine. Due to alternative splicing, the known NBCn2 variants contain two types of carboxyl-termini (CT) differing in the optional inclusion of a PDZ-binding motif. cDNA cloning showed that virtually all NBCn2 variants expressed in epithelial tissues contain, but the vast majority of those from the neural tissues lack the PDZ-binding motif. We conclude that alternative transcription and splicing of Slc4a10 products are regulated in a tissue-specific manner. Our findings provide critical insights that will greatly influence the study of the physiology of NBCn2.
Urinary Bisphenol A and Hypertension in a Multiethnic Sample of US Adults

Background. Bisphenol A (BPA) is a common chemical used in the manufacture of polycarbonate plastics and epoxy resins, with >93% of US adults having detectable BPA levels in urine. Recent animal studies have suggested that BPA exposure may have a role in several mechanisms involved in the development of hypertension, including weight gain, insulin resistance, thyroid dysfunction, endothelial dysfunction, and oxidative stress. However, no previous human study has examined the association between markers of BPA exposure and hypertension. Methods. We examined urinary BPA levels in 1380 subjects from the National Health and Nutritional Examination Survey 2003-2004. Main outcome-of-interest was hypertension, defined as blood pressure-reducing medication use and/or blood pressures >140/90 mm of Hg (n = 580). Results. We observed a positive association between increasing levels of urinary BPA and hypertension independent of confounding factors such as age, gender, race/ethnicity, smoking, body mass index (BMI), diabetes mellitus and total serum cholesterol levels. Compared to tertile 1 (referent), the multivariate-adjusted odds ratio (95% confidence interval) of hypertension associated with tertile 3 was 1.50 (1.12−2.00); P-trend = 0.007. The association was consistently present in subgroup analyses by race/ethnicity, smoking status, BMI, and diabetes mellitus. Conclusions. Urinary BPA levels are associated with hypertension, independent of traditional risk factors.
Formation of DNA adducts in wild-type and transgenic mice expressing human sulfotransferases 1A1 and 1A2 after oral exposure to furfuryl alcohol

Furfuryl alcohol (FFA) is present in many heat-treated foods as a result of its formation via dehydration of pentoses. It is also used legally as a flavouring agent. In an inhalation study conducted in the National Toxicology Program, FFA showed some evidence of carcinogenic activity in rats and mice. FFA was generally negative in conventional genotoxicity assays, which suggests that it may be a non-genotoxic carcinogen. However, it was recently found that FFA is mutagenic in Salmonella strains expressing appropriate sulfotransferases (SULTs), such as human or mouse SULT1A1. The same DNA adducts that were formed by FFA in these strains, mainly N 2-((furan-2-yl)methyl)-2′-deoxyguanosine (N 2-MF-dG), were also detected in tissues of FFA-exposed mice and even in human lung specimens. In the present study, a single oral dose of FFA (250mg/kg body weight) or saline was administered to FVB/N mice and transgenic mice expressing human SULT1A1/1A2 on the FVB/N background. The transgenic mice were used, since human and mouse SULT1A1 substantially differ in substrate specificity and tissue distribution. DNA adducts were studied in liver, kidney, proximal and distal small intestine as well as colon, using isotope-dilution ultra performance liquid chromatography (UPLC–MS/MS). Surprisingly, low levels of adducts that may represent N 2-MF-dG were detected even in tissues of untreated mice. FFA exposure enhanced the adduct levels in colon and liver, but not in the remaining investigated tissues of wild-type (wt) mice. The situation was similar in transgenic mice, except that N 2-MF-dG levels were also strongly enhanced in the proximal small intestine. These different results between wt and transgenic mice may be attributed to the fact that human SULT1A1, but not the orthologous mouse enzyme, is strongly expressed in the small intestine.
Antiviral responses of human Leydig cells to mumps virus infection or poly I:C stimulation

BACKGROUND The immuno-privileged status of the testis is essential to the maintenance of its functions, and innate immunity is likely to play a key role in limiting harmful viral infections, as demonstrated in the rat. In men mumps virus infects Leydig cells and has deleterious effects on testosterone production and spermatogenesis. The aim of this study was to test whether mumps virus infection of isolated human Leydig cells was associated with an inhibition of their innate antiviral defences. METHODS Leydig cell production of mRNA and protein for interferons (IFNs) and of three antiviral proteins—2′5′ oligoadenylate synthetase (2′5′OAS), double-stranded RNA-activated protein kinase (PKR) and MxA—was investigated, in the absence or presence of mumps virus or viral stimuli including poly I:C, a mimetic of RNA viruses replication product. RESULTS Stimulated or not, human Leydig cells appeared unable to produce routinely detectable IFNs α, β and γ. Although the level of PKR remained unchanged after stimulation, the expression of 2′5′OAS and MxA was enhanced following either mumps virus or poly I:C exposure (P < 0.05 versus control). CONCLUSIONS Overall, our results demonstrate that mumps virus replication in human Leydig cells is not associated with a specific inhibition of IFNs or 2′5′OAS, MxA and PKR production and that these cells display relatively weak endogenous antiviral abilities, as opposed to their rat counterparts.
Feature Descriptors: A Review of Multiple Cues Approaches

Feature descriptors have been playing an important role in many computer vision problems, such as image matching and object recognition. While classic descriptors using texture or shape as a single cue of descriptive information have been proved to be successful, recently, several approaches have been proposed introducing the combination of multiple cues to increase descriptive power and robustness. In this paper, we review the methodology of the most recent and popular multiple cues descriptors, and evaluate them with respect to their application and robustness to the variance of conditions.
Identification of Novel Variants in LTBP2 and PXDN Using Whole-Exome Sequencing in Developmental and Congenital Glaucoma

Background Primary congenital glaucoma (PCG) is the most common form of glaucoma in children. PCG occurs due to the developmental defects in the trabecular meshwork and anterior chamber of the eye. The purpose of this study is to identify the causative genetic variants in three families with developmental and primary congenital glaucoma (PCG) with a recessive inheritance pattern. Methods DNA samples were obtained from consanguineous families of Pakistani ancestry. The CYP1B1 gene was sequenced in the affected probands by conventional Sanger DNA sequencing. Whole exome sequencing (WES) was performed in DNA samples of four individuals belonging to three different CYP1B1-negative families. Variants identified by WES were validated by Sanger sequencing. Results WES identified potentially causative novel mutations in the latent transforming growth factor beta binding protein 2 (LTBP2) gene in two PCG families. In the first family a novel missense mutation (c.4934G>A; p.Arg1645Glu) co-segregates with the disease phenotype, and in the second family a novel frameshift mutation (c.4031_4032insA; p.Asp1345Glyfs*6) was identified. In a third family with developmental glaucoma a novel mutation (c.3496G>A; p.Gly1166Arg) was identified in the PXDN gene, which segregates with the disease. Conclusions We identified three novel mutations in glaucoma families using WES; two in the LTBP2 gene and one in the PXDN gene. The results will not only enhance our current understanding of the genetic basis of glaucoma, but may also contribute to a better understanding of the diverse phenotypic consequences caused by mutations in these genes.
Estimation of a Ramsay-Curve Item Response Theory Model by the Metropolis–Hastings Robbins–Monro Algorithm

In Ramsay curve item response theory (RC-IRT) modeling, the shape of the latent trait distribution is estimated simultaneously with the item parameters. In its original implementation, RC-IRT is estimated via Bock and Aitkin’s EM algorithm, which yields maximum marginal likelihood estimates. This method, however, does not produce the parameter covariance matrix as an automatic byproduct on convergence. In turn, researchers are limited in when they can employ RC-IRT, as the covariance matrix is needed for many statistical inference procedures. The present research remedies this problem by estimating the RC-IRT model parameters by the Metropolis–Hastings Robbins–Monro (MH-RM) algorithm. An attractive feature of MH-RM is that the structure of the algorithm makes estimation of the covariance matrix convenient. Additionally, MH-RM is ideally suited for multidimensional IRT, whereas EM is limited by the “curse of dimensionality. ” Based on the current research, when RC-IRT or similar IRT models are eventually generalized to include multiple latent dimensions, MH-RM would appear to be the logical choice for estimation.
Using Amino-Labeled Nucleotide Probes for Simultaneous Single Molecule RNA-DNA FISH

Using amino-labeled oligonucleotide probes, we established a simple, robust and low-noise method for simultaneous detection of RNA and DNA by fluorescence in situ hybridization, a highly useful tool to study the large pool of long non-coding RNAs being identified in the current research. With probes either chemically or biologically synthesized, we demonstrate that the method can be applied to study a wide range of RNA and DNA targets at the single-cell and single-molecule level in cellular contexts.
Parallel and Distributed Systems Report Series On Assessing Measurement Accuracy in BitTorrent Peer-to-Peer File-Sharing Networks

The BitTorrent peer-to-peer file-sharing network is currently one of the dominant Internet applications. Understanding the characteristics of BitTorrent through real-world measurements is key to improve the quality of service for tens of millions of BitTorrent users, but the complexity and scale of BitTorrent make a single, complete measurement impractical. Thus, an increasing number of real measurements have employed diverse sampling techniques to study the BitTorrent network. However, there is no study that investigates the accuracy of the findings of the different measurement techniques used in practice. To address this gap, in this work we propose a thorough investigation of the accuracy of BitTorrent measurement techniques. To this end, we first introduce a taxonomy of inaccuracy sources. We then investigate the effect of these sources using 15 long-term BitTorrent datasets collected from 9 BitTorrent communities between 2004 and 2009. We find that most reported measurements are based on techniques that can lead to inaccurate characterization of system properties. Wp 1 http://www.pds. ewi.tudelft. nl/∼iosup/ B. Zhang et al. Wp BitTorrent BitTorrent Measurement AccuracyWp PDS
Cellulose microfibrils: A novel method of preparation using high shear refining and cryocrushing

Abstract This paper describes a novel technique to produce cellulose microfibrils through mechanical methods. The technique involved a combination of severe shearing in a refiner, followed by high-impact crushing under liquid nitrogen. Fibers treated in this way were subsequently either freeze-dried or suspended in water. The fibers were characterized using SEM, TEM, AFM, and high-resolution optical microscopy. In the freeze-dried batch, 75% of the fibrils had diameters of 1 μm and below, whereas in the water dispersed batch, 89% of the fibrils had diameters in this range. The aspect ratio of the microfibrils ranged between 15 and 55 for the freeze-dried fibrils, and from 20 to 85 for the fibrils dispersed in water. These measurements suggest that the microfibrils have the potential to produce composites with high strength and stiffness for high-performance applications. The microfibrils in water were compounded with polylactic acid polymer to form a biocomposite. Laser confocal microscopy showed that the microfibrils were well dispersed in the polymer matrix.