gebhart/patrepeval huggingface dataset:
Insertion element IS987 from Mycobacterium bovis BCG is located in a hot-spot integration region for insertion elements in Mycobacterium tuberculosis complex strains (1991)

Most strains of the Mycobacterium tuberculosis complex carry multiple copies of an IS3-like element, and these strains are highly polymorphic with regard to the site of integration in the chromosome. In contrast, Mycobacterium bovis BCG contains a single copy of the insertion element, and in all strains this copy is integrated at the same site in the chromosome. In this study, we determined the sequence of the single-copy insertion element from M. bovis BCG, IS987, and its flanking regions. The analysis of IS987 revealed that this element was virtually identical to the sequence of IS986 from M. tuberculosis. IS987 is located in a region containing direct repeats (DRs). The cloned flanking regions contained 20 virtually identical DRs of 36 bp, each separated by 35 to 41 bp of spacer DNA. Analysis of chromosomal DNA by the polymerase chain reaction revealed the presence of a cluster of 49 DRs, and IS987 is inserted in the 30th DR. Furthermore, the DR sequences were found to occur only in species of the M. tuberculosis complex and not in nine other mycobacterial species tested. Analysis of 14 M. tuberculosis strains revealed the presence of one insertion sequence element in the DR-containing region of eight strains, two insertion sequence elements were located in the DR region of five strains, and one strain did not contain an insertion sequence element in this region. Additionally, the DR-containing regions of these 14 M. tuberculosis strains were polymorphic in length and composition. We conclude that the DR cluster is a specific, hot-spot region for integration of insertion elements in the chromosome of M. tuberculosis complex strains.
Temporospatial expression of the small HSP/αB‐crystallin in cardiac and skeletal muscle during mouse development (1997)

Although the small (22 Kd) heat shock protein/αB-crystallin functions as a major structural protein and molecular chaperone in the vertebrate lens, little is known about the protein's role in nonlenticular tissues such as the heart and skeletal muscle. Recent studies have demonstrated that αB-crystallin expression is uniquely regulated during myogenesis in vitro. We report here for the first time that the temporal and spatial expression of αB-crystallin is similarly regulated in vivo during mouse embryogenesis. Expression of αB-crystallin mRNA was detected by in situ hybridization in the primitive heart at 8.5 days post-conception (p.c.) and in the myotome of the somites at 10.5 days p.c. This tissue-restricted pattern was corroborated by immunohistochemical studies. αB-crystallin mRNA and protein expression were uniform in the developing atria and ventricles without regional differences or gradients. αB-crystallin expression was absent in the endocardial cushion, pulmonary trunk, aorta, and endothelium. Examination of muscle precursors revealed expression throughout the dorsoventral aspect of the myotomes and in developing skeletal muscle. Our findings suggest that αB-crystallin may serve pivotal roles as a structural protein and a molecular chaperone in myofiber stabilization of metabolically active tissues during early embryo-genesis. Thus, early αB-crystallin expression in myogenic lineages supports the hypothesis that the putative functions of αB-crystallin are coupled to the activation of genetic programs responsible for myogenic differentiation and cardiac morphogenesis. Dev Dyn 208:75–84, 1997. © 1997 Wiley-Liss, Inc.
mutM, a second mutator locus in Escherichia coli that generates G.C----T.A transversions (1988)

We used strains carrying specific lacZ alleles to identify a new mutator locus in Escherichia coli which generates only G.C----T.A transversions among base substitutions. The locus, mutM, mapped near the cysE locus, which is at 81 min on the genetic map.
Plant wide sensor calibration monitoring (2002)

This paper describes an autoassociative neural network (AANN) based plant wide sensor calibration monitoring system that detects sensor drifts and replaces the faulty sensor output with a best estimate of the fault free value. A network tuning paradigm has also been implemented that allows the network to function when new plant conditions are encountered. The system was tested using data from the high flux isotope reactor operated at Oak Ridge National Laboratory.
Occurrence of Yersinia enterocolitica in wild-living birds and Japanese serows (1985)

Yersinia spp. were isolated from 34 of 500 birds representing nine species. The highest isolation rate, 5 of 21 (23.8%), was found in blue magpies (Cyanopia cyanus), followed by pheasants (Phasianus colchicus tohkaidi), 5 of 33 (15.2%); gray starlings (Sturnus cineraceus), 6 of 57 (10.5%); tree sparrows (Passer montanus), 1 of 14 (7.1%); bulbuls (Hypsipetes amaurotis), 4 of 57 (7.0%); crows (Corvus levailantii or Corvus corone), 7 of 117 (6.0%); eastern turtledoves (Streptopelia orientalis), 4 of 118 (3.4%); Chinese bamboo pheasants (Bumbusicola thoracica thoracica), 1 of 36 (2.8%); and domestic pigeons (Columba livia domestica), 1 of 47 (2.1%). The isolates were identified as Yersinia enterocolitica O:3, O:4, O:4,32, O:5A, O:6,30, O:7,8, and O:14, Yersinia frederiksenii, Yersinia intermedia, and Yersinia kristensenii. Yersinia spp. were isolated from 35 of 157 wild-living Japanese serows (Capricornis cripus). The isolates were identified as Y. enterocolitica O:4, O:4,32, O:5A, O:7, O:7,8, O:9, O:14, O:18, and O:34, Y. frederiksenii, Y. intermedia, and Y. kristensenii.
The pathogenesis of septic acute renal failure (2003)

This review suggests that, on the evidence available, septic acute renal failure is more likely to be an immune or toxic state rather than simply a hemodynamic condition. The authors speculate that future insights into its pathogenesis might lead to a paradigm shift away from the concept of acute tubular necrosis, which has never been convincingly shown in sepsis, to that of acute tubular apoptosis.
SYNTHESIS OF TRIGONELLINE AND NICOTINAMIDE LINKED PRODRUGS OF 5-AMINOSALICYLIC ACID (5-ASA) WITH ANALGESIC AND ANTI-INFLAMMATORY EFFECTS (2005)

3-N-(4`-Hydroxy-3`-substituted phenyl)carbamoyl-1-methylpyridinium iodides (compds. 5b-j) and 3-carbamoyl-1-(N-(4`-hydroxy- 3`-substituted phenyl)carbamoyl) methyl pyridinium chlorides (compds. 7a-j) were synthesised and some of them were tested for their analgesic and antiinflammatory activities by hot plate test and carageenin-induced hind paw edema model, respectively. Compound 5b revealed the most potent analgesic and anti-inflammatory activities in comparison to sulfasalazine (SASP) and 5-ASA. In addition, ulcerogenicity, LD50, in-vivo and in vitro cleavage and pH stability of compound 5b were also determined.
Agent-based support for personalized information with Web search engines (1997)

The popularization of computers and the Internet has produced an explosion in the amount of information and makes it difficult to find them. In order to complement the works of Wet agents for autonomously browsing or filtering on behalf of the user, we focus on adaptive agents for providing support at query formulation and information filtering. These adaptive or learning agents make it possible to add a layer of personalization and collaboration between the users and the existing search engines. The personalization is realized by learning the user preference and using it at query formulation and filtering, while the social aspect is obtained by exchange of information between agents with similar interests.
Promoter elements in the influenza vRNA terminal structure. (1996)

The role of the partially double-stranded influenza vRNA terminal structure and its constitutive elements as a promoter signal was studied in vivo in a series of nucleotide substitution and insertion derivatives. A series of single and complementary double exchanges restoring intrastrand base pairing shows that a distal promoter element consists of a six-base pair double-stranded RNA rod in long-range complementary interaction. Within the distal element, all base pair positions are freely exchangeable, and hence no nucleotide-specific recognition could be identified. The proximal promoter element consists of nine partially complementary nucleotides at the vRNA 5' and 3' end. The nine plus six base pair panhandle rod of protein-free vRNA is interrupted by a central third element, a single unpaired nucleotide: adenosine 10 or various substitute residues, which appears to cause a bulged conformation in the overall structure. Mutagenization studies in the promoter proximal element indicate that, upon binding to polymerase, nucleotides at positions 2 and 3 interact with positions 9 and 8 within each branch (5' or 3') in short-range base pairing. In this conformation, the intermediate positions 4-7 are exposed as a single-stranded tetra-loop, which includes invariant guanosine residue 5 in the top conformational position of the 5' segment loop. Altogether, the three base paired segments in angular conjunction to each other adopt a conformation that is described in a "corkscrew model" for an activated stage of vRNA/polymerase interaction.
The Yersinia Yop virulon: a bacterial system for subverting eukaryotic cells (1997)

The Yop virulon enables Yersinia spp. (Y. pestis, Y. pseudotuberculosis and Y. enterocolitica) to survive and multiply in the lymphoid tissues of their host. It is an integrated system allowing extracellular bacteria to communicate with the host cell's cytosol by the injection of effector proteins. It is composed of the following four elements. (I) A contact or type III secretion system called Ysc, which is devoted to the secretion of Yop proteins. This secretion apparatus, comprising some 22 proteins recognizes the Yops by a short N-terminal signal that is not cleaved off during secretion. (II) A system designed to deliver bacterial proteins into eukaryotic target cells. This system is made of YopB, YopD and possibly other Yops such as LcrV. (III) A control element (YopN). (IV) A set of effector Yop proteins designed to disarm these cells or disrupt their communications (YopE, YopH, YpkA/YopO, and YopM). The whole virulon is encoded by a 70 kb plasmid designated pYV. Transcription of the genes is controlled both by temperature and by contact with a eukaryotic cell.
Environmental Chemistry of Aminopolycarboxylate Chelating Agents (2002)

Aminopolycarboxylate chelating agents are under scrutiny due to their influence on metal availability and mobility and in particular due to their persistence in the environment. In this review chelate adsorption, metal-mobilization, metal-exchange, mineral dissolution, reactive transport, photodegradation, and chemical degradation are all shown to be substantially affected by the chelated metal ion. The different reactivities of the metal-complexes have to be considered when assessing the reactions of chelating agents in the environment because they occur in natural waters predominantly in the form of metal complexes. Knowing the speciation of chelating agents in natural waters is therefore crucial for predicting their environmental fate. Despite this importance, only a few speciation measurements have been reported for natural waters, and model calculations have been frequently used instead. These calculations are, however, complicated by slow metal-exchange reactions that result in a nonequilibrium speciation and by the presence of naturally occurring ligands that compete with the chelating agents for available metals. The basis for a refined risk assessment of aminocarboxylate chelates should be the actual speciation in the natural water directly determined by analytical methods. The discussion of the influence of chelates on metal availability and fate also has to include the potential presence of other aminopolycarboxylate chelating agents besides the well-known EDTA and NTA.
Nuclear Receptor Dax-1 Represses the Transcriptional Cooperation Between GATA-4 and SF-1 in Sertoli Cells1 (2001)

A crucial step in mammalian sex differentiation is the regression of the Müllerian ducts in males. This is achieved through the action of Müllerian inhibiting substance (MIS), a key hormone produced by fetal Sertoli cells. Proper spatiotemporal expression of the MIS gene requires the concerted action of several transcription factors that include Sox9, SF-1, WT-1, GATA-4, and Dax-1. Indeed, SF-1 contributes to MIS gene expression by transcriptionally cooperating with other factors such as GATA-4 and WT-1. Dax-1 is coexpressed with SF-1 in many tissues, including the gonads, where it acts as a negative modulator of SF-1-dependent transcription. We now report that Dax-1 can repress MIS transcription in Sertoli cells by disrupting transcriptional synergism between GATA-4 and SF-1. Dax-1-mediated repression of GATA-4/SF-1 synergism did not involve direct repression of GATA-dependent transactivation, but rather, it occurred through a direct protein-protein interaction with DNA-bound SF-1. It is interesting that SF-1, Dax-1, and GATA factors are coexpressed in several tissues such as the pituitary, the adrenals, and the gonads. Because we have shown that other GATA family members also have the ability to synergize with SF-1, Dax-1 repression of GATA/SF-1 synergism may represent an important mechanism for fine-tuning the regulation of SF-1-dependent genes in multiple target tissues.
Empty space skipping and occlusion clipping for texture-based volume rendering (2004)

We propose methods to accelerate texture-based volume rendering by skipping invisible voxels. We partition the volume into sub-volumes, each containing voxels with similar properties. Sub-volumes composed of only voxels mapped to empty by the transfer function are skipped. To render the adaptively partitioned sub-volumes in visibility order, we reorganize them into an orthogonal BSP tree. We also present an algorithm that computes incrementally the intersection of the volume with the slicing planes, which avoids the overhead of the intersection and texture coordinates computation introduced by the partitioning. Rendering with empty space skipping is 2 to 5 times faster than without it. To skip occluded voxels, we introduce the concept of orthogonal opacity map, that simplifies the transformation between the volume coordinates and the opacity map coordinates, which is intensively used for occlusion detection. The map is updated efficiently by the GPU. The sub-volumes are then culled and clipped against the opacity map. We also present a method that adaptively adjusts the optimal number of the opacity map updates. With occlusion clipping, about 60% of non-empty voxels can be skipped and an additional 80% speedup on average is gained for iso-surface-like rendering.
A newly identified immunodominant membrane protein (pMB67) involved in Mycoplasma bovis surface antigenic variation (1996)

Mycoplasma bovis is a bovine pathogen able to cause systemic disease. It possesses a series of prominent, structurally related yet clearly distinguishable membrane lipoproteins on the cell surface. These variable surface proteins (Vsps) undergo highly dynamic and spontaneous changes in size and expression and are key immunogenic components. They may play a critical role as mediators of adherence to host cells and in escaping immune destruction. In this report, we define a novel, Vsp-unrelated membrane protein also associated with M. bovis surface antigenic variation. This protein has an apparent molecular mass of 67,000 Da in the type strain PG45 and was designated pMB67. Immunological and biochemical characterization of pMB67 demonstrated that it: (i) contains a specific epitope, (ii) is not modified by lipid but does contain cysteine, (iii) does not contain a Vsp-like repetitive periodic protein structure, (iv) is a predominant antigen recognized during M. bovis infections, (v) undergoes a high rate of phase variation in vitro and (vi) is size-variable. These results showed that M. bovis employs two types of specialized membrane proteins for surface diversification. The pMB67 protein may be useful in diagnostic assays and as a vaccine component.
Bug isolation via remote program sampling (2003)

We propose a low-overhead sampling infrastructure for gathering information from the executions experienced by a program's user community. Several example applications illustrate ways to use sampled instrumentation to isolate bugs. Assertion-dense code can be transformed to share the cost of assertions among many users. Lacking assertions, broad guesses can be made about predicates that predict program errors and a process of elimination used to whittle these down to the true bug. Finally, even for non-deterministic bugs such as memory corruption, statistical modeling based on logistic regression allows us to identify program behaviors that are strongly correlated with failure and are therefore likely places to look for the error.
Radical Nature of Cu-Catalyzed Controlled Radical Polymerizations (Atom Transfer Radical Polymerization) (1998)

Copper-catalyzed atom transfer radical polymerization (ATRP) is one of the most robust and precise techniques for controlling radical polymerization. The very good control of molecular weights, polydispersities, functionalities, chain composition, and topologies unusual for radical systems combined with the application of transition metals as catalysts requires more detailed mechanistic studies and proof of the radical nature of active species. The following results are in agreement with the radical nature of ATRP: reverse ATRP, chemoselectivities similar to those for conventional radical polymerization (effect of additives and inhibitors/scavengers, reactivity ratios, transfer coefficients), regioselectivities similar to those for conventional radical polymerization (low proportion of head-to-head units and expected structure of both tail and head end groups), stereoselectivities (tacticities) similar to that in conventional radical polymerization, EPR detection of X-Mtn+1 species resulting from the persistent radical effect, and confirmation of the termination by doubling molecular weights as well as cross-linking with multifunctional initiators and inimers. In addition, it seems that, in most ATRP systems, the contribution of degenerative transfer and reversible formation of organometallic intermediates is small and a halogen atom is transferred in the concerted process rather than in a two-step process with the involvement of radical anions.
Cerebral Hypoxia-Ischemia Stimulates Cytokine Gene Expression in Perinatal Rats (1995)

These results suggest that IL-1 beta and TNF-alpha may play important roles in the response of the developing brain to acute hypoxic-ischemic injury.
Modified optical frequency domain reflectometry with high spatial resolution for components of integrated optic systems (1989)

An apparatus which allows detection of scatterers and faults as well as measurement of reflections in fiber or integrated optic devices and systems with a spatial resolution in the region of 10-100 mu m is discussed. The dynamic range is sufficient to detect reflection with a reflection coefficient down to 10/sup -10/. The system uses a modified optical frequency domain reflectometry (OFDR) technique whereby signal light and local oscillator light are coupled into the waveguide under test from opposite directions. The measurement principle requires the wavelength of the light source to be swept continuously up or down. It is shown that the experimental relationship between frequency shift and waveguide length is in fairly good agreement with the theoretical estimate. Polarization-sensitive experimental results are given for reflection factors in short, side-polished polarization-maintaining fibers.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Materials for fluorescence-based optical chemical sensors (2005)

Optical chemical sensors are capable of continuously recording a chemical species and thus have found (and will find) numerous applications in areas such as the chemical industry, in biotechnology and medicine. Among the many optical methods are employed for sensing purposes, fluorescence has attracted particular attention because it is sensitive, has numerous parameters that can serve as an analytical information and knows effects unknown to other spectroscopies. The implementation of spectroscopic schemes into a useful sensing scheme has been hampered though, by the lack of appropriate materials including polymers and particles, indicator probes, molecular receptors, carriers, catalysts and fluorescent semiconductor materials. This article will address the progress made in the past years and some of the futures aspects and challenges.
Plasma glutamine and ammonia concentrations in ornithine carbamoyltransferase deficiency and citrullinaemia (2001)

A retrospective review of the plasma ammonia and glutamine concentrations during the long-term management of 7 patients with ornithine carbamoyltransferase (OCT) deficiency and three with citrullinaemia is presented. The relationship between the plasma concentrations of ammonia and glutamine is not a simple linear one and there are significant differences between the two disorders. Patients with citrullinaemia tend to have higher plasma ammonia concentrations for a given plasma glutamine concentration compared to those with OCT deficiency. The possible reasons for these differences and the implications for management are discussed.
Catheter balloon valvuloplasty of stenotic aortic valves—part II: Balloon valvuloplasty during life subsequent tissue examination (1991)

This review describes 23 patients with aortic valve stenosis who underwent balloon valvuloplasty during life and had subsequent valve tissue examined at the time of aortic valve replacement or at necropsy. Of 23 stenotic aortic valves, 17 were examined within 30 days (early) after balloon dilation. Of these 94% had nonrheumatic (nonfused commissures) etiologies for the aortic stenosis. Of the 6 valves examined after 30 days (late) (restenosis), mechanisms of restenosis involve refusion of split commissures and probable elastic recoil. Clinical prediction of the aortic stenosis etiology prior to balloon valvuloplasty may help predict short- and long-term success of the dilation procedure.
Modified mesenchymal stem cells using miRNA transduction alter lung injury in a bleomycin model (2017)

Although different preclinical models have demonstrated a favorable role for bone marrow-derived mesenchymal stem cells (B-MSC) in preventing fibrosis, this protective effect is not observed with late administration of these cells, when fibrotic changes are consolidated. We sought to investigate whether the late administration of B-MSCs overexpressing microRNAs (miRNAs) let-7d (antifibrotic) or miR-154 (profibrotic) could alter lung fibrosis in a murine bleomycin model. Using lentiviral vectors, we transduced miRNAs (let-7d or miR-154) or a control sequence into human B-MSCs. Overexpression of let-7d or miR-154 was associated with changes in the mesenchymal properties of B-MSCs and in their cytokine expression. Modified B-MSCs were intravenously administered to mice at <i>day 7</i> after bleomycin instillation, and the mice were euthanized at <i>day 14</i> Bleomycin-injured animals that were treated with let-7d cells were found to recover quicker from the initial weight loss compared with the other treatment groups. Interestingly, animals treated with miR-154 cells had the lowest survival rate. Although a slight reduction in collagen mRNA levels was observed in lung tissue from let-7d mice, no significant differences were observed in Ashcroft score and OH-proline. However, the distinctive expression in cytokines and CD45-positive cells in the lung suggests that the differential effects observed in both miRNA mice groups were related to an effect on the immunomodulation function. Our results establish the use of miRNA-modified mesenchymal stem cells as a potential future research in lung fibrosis.