Miracle-dz/UniFAR-FTUs huggingface dataset:
Regulation of Mannose Phosphotransferase System Permease and Virulence Gene Expression in Listeria monocytogenes by the EIItMan Transporter

ABSTRACT The EIItMan phosphotransferase system (PTS) permease encoded by the mpt operon is the principal glucose transporter in Listeria monocytogenes. EIItMan participates in glucose-mediated carbon catabolite repression (CCR) and downregulation of virulence gene expression, and it is the receptor for class IIa bacteriocins. The regulation of this important protein and its roles in gene control were examined using derivatives of strain EGD-e in which the mpt operon or its regulatory genes, manR and lmo0095, were deleted. Real-time reverse transcription-PCR analysis showed that the mpt mRNA level was 10- and 100-fold lower in the lmo0095 and manR deletion strains, respectively. The manR mRNA level was higher in the mpt deletion mutant in medium lacking glucose, possibly due to disruption of a regulatory process that normally downregulates manR transcription in the absence of this sugar. Analysis of the mpt deletion mutant also showed that EIItMan participates to various degrees in glucose-mediated CCR of PTS operons. CCR of the lmo0027 gene, which encodes a β-glucoside PTS transporter, required expression of EIItMan. In contrast, genes in two mannose PTS operons (lmo0024, lmo1997, and lmo2002) were repressed by glucose even when EIItMan was not synthesized. A third mannose PTS operon, mpo, was not regulated by glucose or by the level of EIItMan. Finally, the mRNA levels for five genes in the prfA virulence gene cluster were two- to fourfold higher in the mpt deletion mutant. The results show that EIItMan participates to various extents in glucose-mediated CCR of PTS operons and makes a small, albeit significant, contribution to downregulation of virulence gene transcription by glucose in strain EGD-e.
Promoter Clearance by RNA Polymerase II Is an Extended, Multistep Process Strongly Affected by Sequence

ABSTRACT We have characterized RNA polymerase II complexes halted from +16 to +49 on two templates which differ in the initial 20 nucleotides (nt) of the transcribed region. On a template with a purine-rich initial transcript, most complexes halted between +20 and +32 become arrested and cannot resume RNA synthesis without the SII elongation factor. These arrested complexes all translocate upstream to the same location, such that about 12 to 13 bases of RNA remain in each of the complexes after SII-mediated transcript cleavage. Much less arrest is observed over this same region with a second template in which the initially transcribed region is pyrimidine rich, but those complexes which do arrest on the second template also translocate upstream to the same location observed with the first template. Complexes stalled at +16 to +18 on either template do not become arrested. Complexes stalled at several locations downstream of +35 become partially arrested, but these more promoter-distal arrested complexes translocate upstream by less than 10 nt; that is, they do not translocate to a common, far-upstream location. Kinetic studies with nonlimiting levels of nucleoside triphosphates reveal strong pausing between +20 and +30 on both templates. These results indicate that promoter clearance by RNA polymerase II is at least a two-step process: a preclearance escape phase extending up to about +18 followed by an unstable clearance phase which extends over the formation of 9 to 17 more bonds. Polymerases halted during the clearance phase translocate upstream to the preclearance location and arrest in at least one sequence context.
Transient alteration of T cell fine specificity by a strong primary stimulus correlates with T cell receptor down‐regulation

P14 mice expressing a transgenic TCR specific for the lymphocytic choriomeningitis virus glycoprotein p33 epitope were used to study the induction of CTL effector activity by a variety of ligands. Surprisingly, p33 variants which are weaker agonists for the P14 TCR than the wild‐type p33 peptide were able to induce more potent effectors with a broader range of cytolytic specificity. Similarly, low concentrations of p33 were more effective than higher concentrations. These results correlated with no or only moderate TCR down‐regulation by variants of p33 and low p33 concentrations. This phenotype observed after 18 h of culture was transient as progressive restoration of reactivity was observed at 42 or 66 h in the cultures stimulated with high p33 concentrations and this correlated with recovery of TCR surface levels. TCR down‐regulation was blocked by src family kinase inhibitors. These findings indicate that the specificity of a T cell can be fine‐tuned by the nature of the primary stimulus correlating with surface TCR level and imply an important role for src family kinases in the differential regulation of surface TCR levels upon TCR engagement by different ligand/MHC complexes.
Effect of 2'-deoxycoformycin infusion on S-adenosylhomocysteine hydrolase and the amount of S-adenosylhomocysteine and related compounds in tissues of mice.

Mice were given constant infusions of the adenosine deaminase inhibitor, 2'-deoxycoformycin, by i.p. implantation of microosmotic pumps, delivering the compound at a rate of 0.16 mg hr-1 kg-1. In accordance with published data, we observed that adenosine deaminase in most tissues was nearly completely inhibited. In addition, the S-adenosylhomocysteine hydrolase activity decreased slowly and showed a half-life in liver of about 4 hr. The rate and extent of the inactivation were highest in spleen. The amounts of adenosine, 2'-deoxyadenosine, S-adenosylhomocysteine, and S-adenosylmethionine were determined in treated animals and control animals. The tissue levels of adenosine and, to a lesser degree, S-adenosylhomocysteine and S-adenosylmethionine were critically dependent on the procedure used for processing the tissues. Lowest concentrations were observed when the organs were frozen in situ by liquid nitrogen. Treatment with 2'-deoxycoformycin induced no or a moderate increase in tissue content of adenosine and S-adenosylhomocysteine, whereas the amount of 2'-deoxyadenosine increased markedly, especially in spleen and thymus. 2'-Deoxycoformycin treatment caused an increase in adenosine and 2'-deoxyadenosine, but not S-adenosylhomocysteine, in serum of mice.
Transcription of Clumping Factor A in Attached and Unattached Staphylococcus aureus In Vitro and during Device-Related Infection

ABSTRACT Staphylococcus aureus is one of the pathogens most frequently isolated in device-related infections. S. aureus is equipped with surface-associated proteins promoting specific binding to matrix molecules. Clumping factor A (ClfA, encoded by clfA) mediates adhesion to fibrinogen. Whereas the contribution of ClfA to pathogenicity is well documented, the influence of different growth and host parameters on gene activity is unclear. To elucidate this question, we investigated clfA transcript levels in an animal model of device-related infection and in planktonic and sessile bacteria grown in vitro. Specific mRNA from the S. aureus strains Newman, Reynolds, and RN6390 was quantified by LightCycler reverse transcription-PCR. In vitro, clfA transcript levels were low in the early logarithmic growth phase, but a clear increase was observed after the late logarithmic phase. Quantities of clfA transcripts were four to six times higher in the planktonic than in the sessile bacterial subpopulations grown to the stationary phase. During infection, in strains Newman and Reynolds levels of clfA transcripts in exudates accumulating in the infected devices were lower than those in the bacteria grown in vitro to stationary phase. clfA mRNA levels in the exudates increased during the initial phase of infection and remained constant after 96 h postinoculation. In contrast to the in vitro results, quantities of clfA transcripts in the unattached bacteria of the exudates never exceeded the level of clfA transcripts in the sessile bacteria attached to glass beads. However, a clear increase in clfA quantities in the sessile bacteria was observed late in infection after 144 h. In conclusion, maximal clfA transcript levels are reached late during growth in vitro and in vivo.
Semiconductor Yield Analysis and Multi-Chip Package (MCP) Die Pairing Optimization using Statistical-Learning

In this paper we discuss the advancement and applications of Tree based classification and regression methods to semiconductor data. We begin the paper with a description of the problem, followed by an overview of the statistical-learning techniques we use in our case studies. We then describe how the challenges presented by semiconductor data were addressed with original extensions to tree-based and kernel-based methods. Next, we review four case studies: home sales price prediction, signal identification/separation, final speed bin classification and die pairing optimization for multi-chip packages (MCP). Results from the case studies demonstrate how statistical-learning addresses the challenges presented by semiconductor manufacturing data and enables improved data discovery and prediction when compared to traditional statistical approaches
evelopment of a magnetic bead fluorescence microscopy immunoassay to etect and quantify Leptospira in environmental water samples

Climate change, world population growth, and poverty have led to an increase in the incidence of leptospirosis. Leptospirosis is caused by pathogenic spirochaete bacteria that belong to the genus Leptospira. The bacteria are maintained in the renal tubules of the reservoir hosts (typically a rodent), then shed into the environment via the urine. Water is key for environmental survival and transmission, as leptospires can survive for several weeks in a moist environment. Therefore, environmental epidemiological studies are needed to study the contamination of environmental water sources. However, few such studies have been performed using cultivation of the isolates and PCR assays. But, leptospira cultivation can be easily contaminated by other organisms and takes usually several weeks. Moreover, PCR is a complex and costly analysis for the underdeveloped countries that have the highest incidence of leptospirosis. In this study, we describe two modifications of a fluorescence microscopy assay based on immuno-magnetic separation (IMS) to detect leptospires in environmental water samples that mainly differ in fluorescent dye staining. The first type uses acridine orange fluorescent dye staining combined with multiplexed IMS for sample screening. The detection limit ranged from 102 to 103 organisms per mL and largely depended on the capture efficiency (CE) of the immuno-magnetic particles. The second type uses serogroup-specific immuno-particles and direct fluorescence antibody staining (DFA) to detect leptospires; the detection limit of this second assay was approximately 101 cells per mL. Both assay types were applied to natural and experimentally infected water samples, which were also analysed with DFM and real-time PCR. Our data show that the fluorescent microscopy immunoassay successfully identified experimental leptospire contamination and was as sensitive as PCR. This modified immune-fluorescence assay may therefore enable epidemiological studies of leptospirosis. Abbreviations: IMS, immuno-magnetic separation; mIMS, multiplexed IMS; DFA, irect fluorescence antibody assay; CE, capture efficiency; AO, acridine orange; AOS, direct acridine orange staining; EPA, environmental protection agency; EMJH, llinghausen and McCullough liquid medium as modified by Johnson and Haris; BSA, bovine serum albumin; PBS, phosphate buffered saline; MAT, microscopic gglutination test; RT, room temperature; FITC, fluorescein isothiocyanate; Ct, cycleo-threshold. ∗ Corresponding author at: Institute for Innovative Learning, Mahidol University, 99, Phuttamonthon 4 Road, Nakhon Pathom 73170, Thailand. Tel. : +66 2441 9020 x1301 1309/084 004 2689; fax: +66 2441 0479. E-mail addresses: wtriampo@gmail.com, scwtr@mahidol.ac. th (W. Triampo). 001-706X/$ – see front matter © 2012 Elsevier B.V. All rights reserved. oi:10.1016/j.actatropica. 2011.12. 011 © 2012 Elsevier B.V. All rights reserved.
Enhancing STEM Motivation through Personal and Communal Values: NLP for Assessment of Utility Value in Student Writing

We present, to our knowledge, the first experiments on using NLP to measure the extent to which a writing sample expresses the writer’s utility value from studying a STEM subject. Studies in social psychology have shown that a writing intervention where a STEM student is asked to reflect on the value of the STEM subject in their personal and social life is effective for improving motivation and retention of students in STEM in college. Automated assessment of UV in student writing would allow scaling the intervention up, opening access to its benefits to multitudes of college students. Our results on biology data suggest that expression of utility value can be measured with reasonable accuracy using automated means, especially in personal essays.
Childhood disintegrative disorder: results of the DSM-IV autism field trial.

OBJECTIVE This report is concerned with the classification of children in whom an "autistic-like" syndrome develops after some years of normal development. In DSM-IV the term "childhood disintegrative disorder" (CDD) is used to describe such cases. METHOD Data collected as part of the international, multisite DSM-IV field trial for autism and related conditions were examined and cases that met DSM-IV criteria for CDD were identified. RESULTS In 16 cases the clinician had given a CDD diagnosis; in an additional 10 cases criteria for the condition were met even though this diagnosis was not given by the clinician rating the case. CONCLUSIONS The available data suggest that CDD cases can be differentiated from those with autism; these two groups appear to differ in important ways. The identification of cases of CDD may be of particular importance for research.
Financing and institutions as key elements of the future of adult education – some empirical observations

The empirical basis of this chapter is an explorative attempt of the observation and analysis of the total expenditure and basic structures of participation for adult education in Austria, compared to selected countries from different welfare regimes (Finland, Sweden, Australia, Scotland/UK). The empirical results from the estimations are widely unexpected, and they are reflected in relation to disciplinary struggles at different levels, viz. the inner Austrian discourses and more broadly the wider academic and research disciplines. A big disciplinary struggle is about how the contributions of different stakeholders relate to market failure and to adult education as a public good.
Incremental Semantic Analysis

Semantic analysis is a central part of the compilation process. The main subproblems include name analysis, type checking, and detection of static-semantic errors. In an interactive programming environment it is useful to perform the semantic analysis incrementally, keeping the staticsemantic information up to date while the program is edited. This allows advanced browsing and editing facilities to be implemented, based on the semantic information. Furthermore, incremental semantic analysis is a prerequisite for making also the rest of the compilation process incremental in order to reduce the turnaround time between editing and execution. This work is directed towards incremental semantic analysis for object-oriented programming languages. These languages have comparatively complex static-semantics which could not be adequately handled with earlier techniques such as attribute grammars. The main contribution of this work is a new technique for developing incremental semantic analyzers: Door Attribute Grammars . This technique extends standard attribute grammars by allowing objects and references to be specified as part of the attribution of a syntax tree. This extension results in space-efficient attributions for which incremental updates can be performed efficiently. In particular, the complex naming semantics of object-oriented languages can be handled in a straight forward way by attributing the tree with explicit visibility graphs built using objects and references. The price for using objects and references in an attribution is that non-local attribute dependencies are introduced which prevent incremental attribute evaluators to be generated completely automatically from the grammar. We solve this problem by splitting the grammar in two parts: one part (the main grammar) which can be treated by automatic methods, and another part (the door package) for which a manual, but systematic, implementation technique is developed. A door package can implement general aspects of a family of programming languages. To specify a new language in the supported family it suffices to write a main grammar, using the door package as a tool box. The techniques have been developed and tested in practice. A complete incrementally compiling environment has been built: Mjolner/Orm , which currently supports the major part of Simula.
Application-oriented real time algebra

Many attempts have been made to define timed process algebras as a route to formal reasoning about real-time systems. In this paper, we argue that existing timed process algebras unsuccessfully try to address all of the aspects which their untimed counterparts address (specification, design and modelling) whereas they would be more useful if they were restricted to one of these roles. Drawing on this, an application-oriented real-time algebra (AORTA) is introduced, with special features making it suitable for the design of real-time systems which may need to be formally verified.
Arc stabilization in low-frequency square-wave electronic ballast for metal halide lamps

Discharge lamps present a negative dynamic characteristic that makes necessary using a current limiting element. In high frequency resonant ballasts current limitation is performed by the output resonant tank, but in low-frequency square-wave electronic ballasts arc stabilization is accomplished by stage feeding the square wave inverter. Therefore, the design of the input converter must be made taking into account the lamp dynamic characteristic. This paper presents a new procedure for obtaining the small-signal dynamic characteristic of metal halide lamps is proposed. Using the proposed methodology the small-signal characteristic of a 70 W is obtained, this characteristic is then used for the design of an electronic ballast based on a buck-boost converter followed by a full bridge inverter. The limits for stable operation obtained are verified using a laboratory prototype.
Influence of age at weaning and nutritive value of weaning diet on growth performance and caecal traits in rabbits.

This work has been realized within the CUNISVEZZ research project financed by the Agricultural Department of the Regione Lombardia as part of the 2004 research and development plan, d.g. r. 30/04/2004 n. VII/17326. The authors wish to thank Nicoletta Cesari for her technical assistance.
March LR: a test for realistic linked faults

Many march tests have already been designed to cover faults of different fault models. The complexity of these tests arises when linked faults are taken into consideration. This paper gives an overview of the most important and commonly used fault models, including the industry's popular disturb fault model. The fault coverage of march tests is analysed in a novel way, i.e., in terms of their detection capabilities for: simple faults, and linked faults; whereby the infinite class of linked faults has been reduced to a set of realistic linked faults. Thereafter the paper presents a methodology to design tests for realistic linked faults, resulting in the new tests March LR, March LRD and March LRDD. These new tests will be shown to be more efficient and to offer a higher fault coverage than comparable existing tests.
Human cystinuria-related transporter: localization and functional characterization.

BACKGROUND Cystinuria has been proposed to be an inherited defect of apical membrane transport systems for cystine and basic amino acids in renal proximal tubules. Although the mutations of the recently identified transporter BAT1/b(0,+)AT have been related to nontype I cystinuria, the function and localization of human BAT1 (hBAT1)/b(0,+)AT have not been well characterized. METHODS The cDNA encoding hBAT1 was isolated from human kidney. Fluorescence in situ hybridization was performed to map the hBAT1 gene on human chromosomes. Tissue distribution and localization of expression were examined by Northern blot and immunohistochemical analyses. hBAT1 cDNA was transfected to COS-7 cells with rBAT cDNA, and the uptake and efflux of 14C-labeled amino acids were measured to determine the functional properties. The roles of protein kinase-dependent phosphorylation were investigated using inhibitors or activators of protein kinases. RESULTS The hBAT1 gene was mapped to 19q12-13.1 on the human chromosome, which is the locus of nontype I cystinuria. hBAT1 message was expressed predominantly in kidney. hBAT1 protein was localized in the apical membrane of proximal tubules in human kidney. When expressed in COS-7 cells with a type II membrane glycoprotein rBAT (related to b(0,+)-amino acid transporter), hBAT1 exhibited the transport activity with the properties of amino acid transport system b(0,+), which transported cystine as well as basic and neutral amino acids presumably via a substrate exchange mechanism. BAT1-mediated transport was reduced by the protein kinase A activator and enhanced by the tyrosine kinase inhibitor. CONCLUSIONS hBAT1 exhibited the properties expected for a transporter subserving the high-affinity cystine transport system in renal proximal tubules. The hBAT1 gene was mapped to the locus of nontype I cystinuria, confirming the involvement of hBAT1 in cystinuria.
Matrix Decomposition for Recommendation System

Matrix decomposition, when the rating matrix has missing values, is recognized as an outstanding technique for recommendation system. In order to approximate user-item rating matrix, we construct loss function and append regularization constraint to prevent overfitting. Thus, the solution of matrix decomposition becomes an optimization problem. Alternating least squares (ALS) and stochastic gradient descent (SGD) are two popular approaches to solve optimize problems. Alternating least squares with weighted regularization (ALS-WR) is a good parallel algorithm, which can perform independently on user-factor matrix or item-factor matrix. Based on the idea of ALS-WR algorithm, we propose a modified SGD algorithm. With experiments on testing dataset, our algorithm outperforms ALS-WR. In addition, matrix decompositions based on our optimization method have lower RMSE values than some classic collaborate filtering algorithms.