gebhart/patrepeval huggingface dataset:
The Genome of a Pathogenic Rhodococcus: Cooptive Virulence Underpinned by Key Gene Acquisitions (2010)

We report the genome of the facultative intracellular parasite Rhodococcus equi, the only animal pathogen within the biotechnologically important actinobacterial genus Rhodococcus. The 5.0-Mb R. equi 103S genome is significantly smaller than those of environmental rhodococci. This is due to genome expansion in nonpathogenic species, via a linear gain of paralogous genes and an accelerated genetic flux, rather than reductive evolution in R. equi. The 103S genome lacks the extensive catabolic and secondary metabolic complement of environmental rhodococci, and it displays unique adaptations for host colonization and competition in the short-chain fatty acid-rich intestine and manure of herbivores--two main R. equi reservoirs. Except for a few horizontally acquired (HGT) pathogenicity loci, including a cytoadhesive pilus determinant (rpl) and the virulence plasmid vap pathogenicity island (PAI) required for intramacrophage survival, most of the potential virulence-associated genes identified in R. equi are conserved in environmental rhodococci or have homologs in nonpathogenic Actinobacteria. This suggests a mechanism of virulence evolution based on the cooption of existing core actinobacterial traits, triggered by key host niche-adaptive HGT events. We tested this hypothesis by investigating R. equi virulence plasmid-chromosome crosstalk, by global transcription profiling and expression network analysis. Two chromosomal genes conserved in environmental rhodococci, encoding putative chorismate mutase and anthranilate synthase enzymes involved in aromatic amino acid biosynthesis, were strongly coregulated with vap PAI virulence genes and required for optimal proliferation in macrophages. The regulatory integration of chromosomal metabolic genes under the control of the HGT-acquired plasmid PAI is thus an important element in the cooptive virulence of R. equi.
β-Galactosidase Enzymatic Activity as a Molecular Probe to Detect Specific Antibodies (1996)

The main antigenic region of foot-and-mouth disease virus serotype C1, also called site A, has been inserted in zones of the beta-galactosidase important for the stabilization of the active site, causing important changes in the Km and the specific activity of the resulting enzymes. The peptide is displayed at the surface of the recombinant proteins and, in all the cases, presents a good antigenicity. Among the recombinant proteins constructed, in proteins M278VP1 and M275SVP1 the peptide is inserted in a large loop of the beta-galactosidase (amino acids 272-288) involved in the formation of the activating interface. In these constructs, the binding of the specific antibodies directed to the foreign peptide causes an increase of the beta-galactosidase activity up to about 200%. This phenomenon has been proved using monoclonal antibodies and also using polyclonal sera generated against the peptide. Different hypothesis of the mechanism of modulation upon antibody binding are discussed. This insertion site seems to be sensitive enough to enzymatic modulation mediated by antibody binding. We propose further exploring this insertion site as a tool for a rapid detection of specific antibodies in a quick and simple homogeneous assay based on the colorimetric determination of beta-galactosidase activity.
Metalation of Pyrazinethiocarboxamides. Metalation of Diazines XXVI (1999)

Some new pyrazinethiocarboxamides were synthesized and metalated with LTMP in tetrahydrofuran.The reaction of these lithio derivatives with various ele~~ophiles gave access to a large range of 2,s-disubstituted pyrazines.This unexpected regioselectivity was established by application of gradient enhanced HMBC sequence for the observation of long range 'H-I% heteronuclear couplings at natural abundance.Following our studies on the metalation of x-deficient heterocycles we have recently investigated the use of sulfur derivatives as ortho-directing group (0.D.G) in these series.'.2It was found that sulfoxides, sulfones and sulfamides were good ortho-directing groups.Another type of sulfur derivatives is based on the thiocarbonyl group contained in dithioesters: thiocarboxamides or thioamides.In the benzene series, ~s c h w e n d ~ obtained good results with thiocarboxamides so we tested these O.D.G. in the pyrazine series.These thiocarboxamides were, to our knowledge, never tested before as O.D.G. in the diazine series and some were still unknown.Metalation could be a new and versatile way of functionalization of these compounds.Some pyrazinethiocarboxamides have tuberculostatic and antimycobacterial properties5~' and some pyridinylthioacetamides have antiulcer a c t i ~i t y .~. ~ Synthesis of thiocarboxamides was mainly performed following four different ways: thionation of carboxamides with sulfur derivatives of phosphorous (P& Lawesson's reagent ( L. R. ) ),I0-'' reaction of an organometallic derivative with an i~othioc~anate,~.'~.'~ reaction of an m i n e derivative with sulfur ( S ~) , ' , I ~~~* reaction of an amine with a sulfine group.'9In order to obtain the pyrazinethiocarboxamides, the two first methods were tcsted.16* 72 8 MelSiCI** S i M e , 17 98 *: Product (16) was the 3,5-disubstituted product **: Metalation was performed by the in situ trapping method The metalation of compound (5) followed by the reaction with various electrophiles led to only one product.This complete regioselectivity must be ensured by an unambiguous attribution o f the substitution position.The accurate attribution of the 'H NMR signals in the pyrazine series has always been a problem due in general to the close vicinity of the signals for Hs and H6.In our case a coupling constant of 1.1 Hz was observed and could he attributed to a '1 coupling constant between HI and H6.However, in order to determine unambiguously the site of metalation, a structure elucidation of compound (1 1) has been canied out by applying gradient enhanced HMBC sequence, such as a method using long range 'H-"N heteronuclear coupling at natural abundance.This method has been previously described by Martin to determine the structure of a l k a l ~i d s , ~~~~' and more recently used to determine the structure of quinazoline derivative^.'^
Effect of Carbon Dioxide on Diaphragmatic Function in Human Beings (1984)

We studied the effects of acute changes in the partial pressure of arterial carbon dioxide on diaphragmatic contractility and performance in four normal men. To study contractility we measured the ability of the diaphragm to generate pressure at a given level of excitation by determining the relation between the electrical activity of the diaphragm and transdiaphragmatic pressure during a voluntary quasi-isometric inspiratory effort carried out at different levels of end-tidal carbon dioxide. Our results show that contractility was reduced with hypercapnia (when end-tidal carbon dioxide was 7.5 per cent or higher), although hypocapnia (end-tidal carbon dioxide, 3 per cent) had no effect on diaphragmatic contractility. We also studied the development of diaphragmatic fatigue before and during carbon dioxide breathing. Subjects were studied at the same diaphragmatic tension-time index, a value analogous to the more familiar myocardial tension-time index, while the same inspiratory flow was maintained. Electromyographic signs of fatigue appeared at a lower tension-time index during hypercapnia than during normocapnia, indicating that endurance is diminished during hypercapnia. These findings show that acute respiratory acidosis equivalent to an arterial carbon dioxide tension of about 54 mm Hg decreases the contractility and endurance time of the diaphragm in human beings.
Extension of base mispairs byTaqDNA polymerase: implications for single nucleotide discrimination in PCR (1992)

Thermus aquaticus (Taq) DNA polymerase was used to measure the extension efficiency for all configurations of matched and mismatched base pairs at template-primer 3'-termini. The transition mispairs, A(primer).C, C.A, G.T, and T.G were extended 10(-3) to 10(-4)-fold less efficiently than their correctly paired counterparts. Relative efficiencies for extending transversion mispairs were 10(-4) to 10(-5) for T.C and T.T, about 10(-6) for A.A, and less than 10(-6) for G.A, A.G, G.G and C.C. The transversion mispair C(primer).T was extended with high efficiency, about 10(-2) compared to a correct A.T basepair. The unexpected ease of extending the C.T mismatch was not likely to have been caused by primer-template misalignment. Taq polymerase was observed to bind with similar affinities to each of the correctly paired and mispaired primer-template 3'-ends. Thus, the failure of Taq polymerase to extend mismatches efficiently appears to be an intrinsic property of the enzyme and not due to an inability to bind to 3'-terminal mispairs. For almost all of the mispairs, C.T being the exception, Taq polymerase exhibits about 100 to 1000-fold greater discrimination against mismatch extension compared to avian myeloblastosis reverse transcriptase and HIV-1 reverse transcriptase which extend most mismatched basepairs permissively. Relative mismatch extension efficiencies for Taq polymerase were measured at 45 degrees C, 55 degrees C and 70 degrees C and found to be independent of temperature. The mispair extension data should be important in designing experiments using PCR to distinguish between sequences that vary by a single nucleotide.
Biofilms and urethral catheter infections (1991)

The perennial problem of recurrent urinary tract infections in people with indwelling urethral catheters causes great distress, discomfort, morbidity and even mortality. Anne Mulhall discusses the significance of biofilms on the surfaces of catheters and indicates that they pose a profound clinical problem. The need for continued research and increased effort from scientists and practitioners in the search for new and safer synthetic materials are emphasised.
Rapid Genome Divergence at Orthologous Low Molecular Weight Glutenin Loci of the A and Am Genomes of Wheat[W] (2003)

To study genome evolution in wheat, we have sequenced and compared two large physical contigs of 285 and 142 kb covering orthologous low molecular weight (LMW) glutenin loci on chromosome 1AS of a diploid wheat species (Triticum monococcum subsp monococcum) and a tetraploid wheat species (Triticum turgidum subsp durum). Sequence conservation between the two species was restricted to small regions containing the orthologous LMW glutenin genes, whereas >90% of the compared sequences were not conserved. Dramatic sequence rearrangements occurred in the regions rich in repetitive elements. Dating of long terminal repeat retrotransposon insertions revealed different insertion events occurring during the last 5.5 million years in both species. These insertions are partially responsible for the lack of homology between the intergenic regions. In addition, the gene space was conserved only partially, because different predicted genes were identified on both contigs. Duplications and deletions of large fragments that might be attributable to illegitimate recombination also have contributed to the differentiation of this region in both species. The striking differences in the intergenic landscape between the A and A(m) genomes that diverged 1 to 3 million years ago provide evidence for a dynamic and rapid genome evolution in wheat species.
Lost in translation: an assessment and perspective for computational microRNA target identification (2009)

Supplementary data are available at Bioinformatics online.
Effects of ionotropic glutamate receptor antagonists on rat dural artery diameter in an intravital microscopy model (2010)

Although GYKI52466 has not been tested clinically, our data suggest that it would not inhibit migraine via vascular mechanisms. Similarly, the antimigraine efficacy of LY466195 seems unrelated to vascular CGRP-mediated pathways and/or receptors. In contrast, the cranial vascular effects of ketamine and MK801 may represent a therapeutic mechanism, although the same mechanism might contribute, peripherally, to cardiovascular side effects.
A myriad of miRNA variants in control and Huntington’s disease brain regions detected by massively parallel sequencing (2010)

Huntington disease (HD) is a neurodegenerative disorder that predominantly affects neurons of the forebrain. We have applied the Illumina massively parallel sequencing to deeply analyze the small RNA populations of two different forebrain areas, the frontal cortex (FC) and the striatum (ST) of healthy individuals and individuals with HD. More than 80% of the small-RNAs were annotated as microRNAs (miRNAs) in all samples. Deep sequencing revealed length and sequence heterogeneity (IsomiRs) for the vast majority of miRNAs. Around 80-90% of the miRNAs presented modifications in the 3'-terminus mainly in the form of trimming and/or as nucleotide addition variants, while the 5'-terminus of the miRNAs was specially protected from changes. Expression profiling showed strong miRNA and isomiR expression deregulation in HD, most being common to both FC and ST. The analysis of the upstream regulatory regions in co-regulated miRNAs suggests a role for RE1-Silencing Transcription Factor (REST) and P53 in miRNAs downregulation in HD. The putative targets of deregulated miRNAs and seed-region IsomiRs strongly suggest that their altered expression contributes to the aberrant gene expression in HD. Our results show that miRNA variability is a ubiquitous phenomenon in the adult human brain, which may influence gene expression in physiological and pathological conditions.
ChemInform Abstract: BORON DIFFUSION IN SILICON‐CONCENTRATION AND ORIENTATION DEPENDENCE, BACKGROUND EFFECTS, AND PROFILE ESTIMATION (1975)

Abstract B ist ein bekanntes p‐Dotierungsmittel für Si‐Anordnungen.
DRAM Circuit Design: Fundamental and High-Speed Topics (2007)

A modern, comprehensive introduction to DRAM for students and practicing chip designers Dynamic Random Access Memory (DRAM) technology has been one of the greatestdriving forces in the advancement of solid-state technology. With its ability to produce high product volumes and low pricing, it forces solid-state memory manufacturers to work aggressively to cut costs while maintaining, if not increasing, their market share. As a result, the state of the art continues to advance owing to the tremendous pressure to get more memory chips from each silicon wafer, primarily through process scaling and clever design. From a team of engineers working in memory circuit design, DRAM Circuit Design gives students and practicing chip designers an easy-to-follow, yet thorough, introductory treatment of the subject. Focusing on the chip designer rather than the end user, this volume offers expanded, up-to-date coverage of DRAM circuit design by presenting both standard and high-speed implementations. Additionally, it explores a range of topics: the DRAM array, peripheral circuitry, global circuitry and considerations, voltage converters, synchronization in DRAMs, data path design, and power delivery. Additionally, this up-to-date and comprehensive book features topics in high-speed design and architecture and the ever-increasing speed requirements of memory circuits. The only book that covers the breadth and scope of the subject under one cover, DRAM Circuit Design is an invaluable introduction for students in courses on memory circuit design or advanced digital courses in VLSI or CMOS circuit design. It also serves as an essential, one-stop resource for academics, researchers, and practicing engineers.
Understanding the intracellular effect of enhanced nutrient feeding toward high titer antibody production process (2010)

One of the major goals in cell culture process development for therapeutic antibody production is to develop methods to reach high titer in classical fed-batch processes. This goal is often achieved through the optimizations of expression vector, cell line, media and cell culture process controls to increase cell specific productivity, viable cell density, and culture longevity. During process optimization for a selected production cell line, cell specific productivity (qP) can vary significantly with culture conditions. Therefore, identifying strategies to maintain maximal specific productivity throughout the entire fed-batch culture and to eliminate cellular/process bottlenecks that prevent high levels of antibody production would be crucial for further advancements in this area. In this work, specific productivity was increased and maintained at high level throughout the course of the culture by the optimization of feed media and feeding strategy. Through the enhancement of nutrient feeding, final titer was increased by 2.5-fold from the platform fed-batch process and reached 7.5 g/L. In addition, further insight upon possible cellular bottlenecks in high yield antibody production was obtained by comparing the levels of heavy chain (HC) and light chain (LC) mRNA and the levels of intracellular antibody between the non-optimized and optimized feeding processes. The mRNA levels of the two processes were measured and exhibited no significant difference suggesting that transcription is not the bottleneck. When intracellular antibody level was studied, the relatively constant level of HC, LC, and intact antibody between days 9 and 14 suggested that translation could be the rate-limiting step under the non-optimized nutrient feeding condition due to the dramatic drop of qP to roughly zero which correlated with the depletion of tyrosine as one of the key amino acids for protein synthesis. Finally, accumulation of unassembled HC but not intact antibody was observed at days 14-18 under the enhanced feeding condition, implying that folding and assembly may be the bottleneck toward the end of the culture.
Spontaneous Spatial Alignment of Polymer Cylindrical Nanodomains on Silicon Nitride Gratings (2002)

We report a simple method to align lying-down cylindrical domains of PS-b-PMMA in the trough regions of 555 nm deep silicon nitride gratings without the aid of an external orientation field. This alignment is perpendicular to the orientation of the grating lines and essentially spans the width of the grating trough. The proposed mechanism involves polymer flow and confinement in small dimensions. Also, regularly spaced bumps of almost uniform size can be formed on the crest regions of the support grating. The thickness dependence of PS-b-PMMA thin film surface morphology is also utilized to generate micron-scale periodic structures on 115 nm deep gratings. These experiments to align microdomains with controlled nanometer-scale spacing can be extended to generate self-organizing nanofabricated surfaces.
5G Ultra-Reliable Vehicular Communication (2015)

Applications enabled by Cooperative Intelligent Transport Systems (C-ITS) represent a major step towards making the road transport system safer and more efficient (green), and thus suited for a sustainable future. Wireless communication between vehicles and road infrastructure is an enabler for high-performance C-ITS applications. State-of-the-art communication systems for supporting low-latency C-ITS applications are based on IEEE 802.11 medium access control (MAC) and physical (PHY) layers. In this paper, we argue that a well-designed 5G system can complement or even replace these systems. We will review the C-ITS application requirements and explain how these are well aligned with the foreseen generic 5G service of ultra-reliable machine-type communication (uMTC). Key technology components suitable for constructing the uMTC service are identified: reliable service composition (RSC) and device-to-device (D2D) links for all-to-all broadcast communication, operational at high mobility and with varying degree of network assistance. Important problems for future studies, including radio-resource management, medium access control, and physical layer challenges, are discussed.
Rationaler Pluralismus : zu Reschers Habermas-Kritik (1994)

L'A. expose les conceptions de la raison de Rescher et Habermas, et les compare en particulier sur la question de la pluralite des valeurs, du contextualisme
不花钱玩家有肉吃《征途2》福利大讲堂 (2011)

游戏中也能得到福利？游戏中也能夭降淇福？游戏中也能幸运中奖？没错．在《征途2》的游戏世界里，不花钱就能获得福利和幸运奖励的活动比比皆是．今天我就带你走进《征途2》福利社会。一起对《征途2》的福利活动进行大揭密。
16 kbps wideband speech coding technique based on algebraic CELP (1991)

The application of algebraic code excited linear prediction (ACELP) coding to wideband speech is presented. An algebraic codebook with a 20 bit address can be used without any storage requirements and, more importantly, with a very efficient search procedure which allows for real-time implementation. The authors describe an efficient procedure for searching such a large codebook deploying a focused search strategy, where less than 0.1% of the codebook is searched with performance very close to that of a full search. High-quality speech at a bit rate of 13 kbps was obtained.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Immunocytochemical localization of parathyroid hormone-like peptide in the rat fetus. (1991)

Studies of parathyroid hormone-like peptide (PLP) have demonstrated that PLP gene expression is inducible by serum, growth factors, and cycloheximide. Rapid induction of PLP gene expression has also been observed following the induction of cell differentiation. These features of PLP gene expression are consistent with a role for PLP in the regulation of cell growth and differentiation. To understand the biology of PLP in developing cells and tissues, we have studied the distribution of PLP gene expression in the fetal and neonatal rat. PLP was localized by immunocytochemistry to skin, vascular smooth muscle, skeletal muscle, heart, liver, kidney, lung, and gastrointestinal tract in Day 14 fetal rat. By Day 18 PLP immunopositivity was also detected in both fetal pituitary and adrenal medulla, as well as in endocrine pancreas. Whereas few PLP-immunopositive cells were detected in Day 14 brain, scattered areas of PLP immunopositivity were evident in Day 18 brain, in regions such as the choroid plexus. Immunostaining for PLP was also detected in Day 18 tissues that were positive on Day 14. The pattern of staining in fetal testis, where PLP was strongly localized to seminiferous tubules, differed from adult testis, where PLP was localized predominantly in Leydig cells. PLP was localized to the hepatocytes but not to the hematopoietic elements in fetal liver. Neonatal hepatocytes were weakly PLP immunopositive, and PLP was not detected in adult rat liver. Northern blot analysis demonstrated the presence of a single 1.4-kilobase PLP mRNA transcript in fetal brain, liver, heart, lung, and intestine. The results of these studies demonstrate that the PLP gene is widely expressed in a diverse number of fetal rat tissues. The cellular and tissue localization of PLP immunopositivity remains fairly constant in the transition from fetal to neonatal and adult tissues except in the testis, where a cellular switch in PLP-producing cells occurs, and the liver, where PLP gene expression is progressively extinguished postnatally.