gebhart/patrepeval huggingface dataset:
Role of intestinal microflora in chronic inflammation and ulceration of the rat colon. (1994)

Bacteria and their products stimulate inflammatory responses. The effects of different antimicrobial regimens (amoxicillin/clavulanic acid, tobramycin, imipenem, vancomycin, metronidazole) were investigated on the course of experimental colitis induced by trinitrobenzenesulphonic acid (TNB) in the rat. On day 7 and 21 after the induction of colitis, matched groups of control and antibiotic treated rats were subjected to colonic dialysis to measure eicosanoid release, and killed for morphological assessment of the colonic lesions (macro and microscopic scores). Stool samples were cultured. Selective antibiotic treatment against Gram positive, Gram negative or anaerobic bacteria had no effect on colonic lesion scores. By contrast, certain broad spectrum antibiotics (amoxicillin/clavulanic acid or the association of imipenem plus vancomycin) significantly reduced macro and microscopic scores. Rats receiving these antibiotics did not develop chronic colitis as shown by the virtual absence of colonic strictures, adhesions, fibrosis, and granulomas. On day 21 after TNB, the intracolonic release of prostaglandin E2, thromboxane B2, and leukotriene B4 was significantly higher in control than in antibiotic treated rats. Control stool cultures showed abundant colony forming units of both aerobic and anaerobic bacteria. Amoxicillin/clavulanic acid and imipenem plus vancomycin induced appreciable reductions in luminal bacteria. In conclusion, certain broad spectrum antibiotics prevent chronic colitis. The normal colonic flora seems to play an important pathogenetic part in the progression of inflammatory colonic lesions to chronicity.
Nuclear matrix attachment regions antagonize methylation-dependent repression of long-range enhancer-promoter interactions (1999)

The immunoglobulin intragenic mu enhancer region acts as a locus control region that mediates transcriptional activation over large distances in germ line transformation assays. In transgenic mice, but not in transfected tissue culture cells, the activation of a variable region (V(H)) promoter by the mu enhancer is dependent on flanking nuclear matrix attachment regions (MARs). Here, we examine the effects of DNA methylation, which occurs in early mouse development, on the function of the mu enhancer and the MARs. We find that methylation of rearranged mu genes in vitro, before transfection, represses the ability of the mu enhancer to activate the V(H) promoter over the distance of 1.2 kb. However, methylation does not affect enhancer-mediated promoter activation over a distance of 150 bp. In methylated DNA templates, the mu enhancer alone induces only local chromatin remodeling, whereas in combination with MARs, the mu enhancer generates an extended domain of histone acetylation. These observations provide evidence that DNA methylation impairs the distance independence of enhancer function and thereby imposes a requirement for additional regulatory elements, such as MARs, which facilitate long-range chromatin remodeling.
The Tec Family Tyrosine Kinase Btk Regulates RANKL-induced Osteoclast Maturation (2008)

A spontaneous mutation in Bruton's tyrosine kinase (Btk) induces a defect in B-cell development that results in the immunodeficiency diseases X-linked agammaglobulinemia in humans and X-linked immunodeficiency (Xid) in mice. Here we show an unexpected role of Btk in osteoclast formation. When bone marrow cells derived from Xid mice were stimulated with receptor activator of NF-kappaB ligand, an osteoclast differentiation factor, they did not completely differentiate into mature multinucleated osteoclasts. Moreover, we found that the defects appeared to occur at the stage in which mononuclear preosteoclasts fuse to generate multinucleated cells. Supporting this notion, macrophages from Xid mice also failed to form multinucleated foreign body giant cells. The fusion defect of the Xid mutant osteoclasts was caused by decreased expression of nuclear factor of activated T cells c1 (NFATc1), a master regulator of osteoclast differentiation, as well as reduced expression of various osteoclast fusion-related molecules, such as the d2 isoform of vacuolar H(+)-ATPase V0 domain and the dendritic cell-specific transmembrane protein. This deficiency was completely rescued by the introduction of a constitutively active form of NFATc1 into bone marrow-derived macrophages. Our data provide strong evidence that Btk plays a critical role in osteoclast multinucleation by modulating the activity of NFATc1.
An emerging medium: interactive three-dimensional digital video (2002)

This paper describes a new visual medium called interactive 3D digital video. 3D digital video displays motion pictures of real-world events from the view of a virtual camera controlled by the viewer during playback. For 3D video to become of practical use, sophisticated data manipulation, management and processing capabilities are required. These tasks are daunting, given the amount and complexity of data involved. Furthermore, due to the hybrid nature of the 3D video data, no standardized representation and coding schemes are available. We explore these issues and present an overview of a functional system called immersive video. For real events such as basketball games, immersive video analyzes and composites recorded multiviewpoint videos to create a full 3D version of the event which is then encoded and stored for immersive playback. While replaying this 3D digital movie, viewers are able to explore the scene continuously from any perspective. We describe the steps we have taken toward using the Internet infrastructure and a client-server configuration to allow World Wide Web users to interactively view any of our experimental 3D videos including a one minute staged karate demonstration captured by six video cameras. Applications of this new medium include telepresence, interactive video and television, video-based virtual environments, and immersive feature films.
The Topographical and Neuroanatomical Distribution of Neurofibrillary Tangles and Neuritic Plaques in the Cerebral Cortex of Patients with Alzheimer's Disease (1991)

The distribution of neurofibrillary tangles (NFTs) and neuritic plaques (NPs) was mapped in 39 cortical areas of 11 brains of patients with Alzheimer's disease (AD). Whole hemisphere blocks were embedded in polyethylene glycol (Carbowax), sectioned coronally, and stained with thioflavin S and thionin. The densities of NFTs and NPs were assessed using a numerical rating scale for each area. Scores were grouped by type of cortex and by lobe for statistical analysis. Highly significant differences were obtained. For example, limbic periallocortex and allocortex had more NFTs than any other type of cortex. In descending order, the density of NFTs was as follows: periallocortex (area 28) greater than allocortex (subiculum/CA1 zones of hippocampal formation, area 51) greater than corticoid areas (accessory basal nucleus of amygdala, nucleus basalis of Meynert) greater than proisocortex (areas 11, 12, 24, 23, anterior insula, 38, 35) greater than nonprimary association cortex (32, 46, superior temporal sulcus, 40, 39, posterior parahippocampal cortex, 37, 36) greater than primary sensory association cortex (7, 18, 19, 22, 21, 20) greater than agranular cortex (44-5, 8, 6, 4) greater than primary sensory cortex (41-2, 3-1-2, 17). The laminar distribution of NFTs tended to be selective, involving primarily layers III and V of association areas and layers II and IV of limbic periallocortex. There were far more NFTs in both limbic and temporal lobes than in frontal, parietal, and occipital lobes. In general, NPs were more evenly distributed throughout the cortex, with the exceptions of limbic periallocortex and allocortex, which had notably fewer NPs than other cortical areas. Temporal and occipital lobes had the highest NP densities, limbic and frontal lobes had the lowest, and parietal lobe was intermediate. No significant left-right hemispheric differences for NFT or NP densities were found across the population, and there was no relationship between duration of illness and densities of NFTs or NPs. The regional and laminar distribution of NFTs (and, to a lesser degree, that of NPs) suggests a consistent pattern of vulnerability within the cerebral cortices that seems correlated to the hierarchies of cortico-cortical connections. The higher-order association cortices, especially those in the anterior and ventromedial sectors of temporal lobe, are the most vulnerable, while other cortices appear less vulnerable to a degree commensurate with their connectional "distance" (i.e., synapses removed) from the limbic areas.
Mapping the fine specificity of a cytolytic T cell response to HIV-1 nef protein. (1990)

Epitope mapping of a MHC class I-restricted cytotoxic T cell response to nef, a regulatory protein of HIV, was performed with fresh PBMC from HIV-seropositive donors and target cells pulsed with a panel of overlapping peptides of the nef protein. These nef-specific CTL recognized a synthetic peptide of 10 residues derived from a nonamphipathic, highly conserved region of the nef protein in association with the HLA A3.1 molecule. Using human cell transfectants expressing mutations of the A3 molecule, we demonstrated that the amino acid at position 152 of the A3.1 molecule appears to be critical for detection of this response. Thus, rapid analysis of the epitopes of HIV proteins stimulating CTL responses can be achieved using a combination of fresh donor PBMC and target cells pulsed with synthesized peptides.
Design and Testing of β-Actin Primers for RT-PCR that Do Not Co-amplify Processed Pseudogenes (1997)

Quantitative reverse transcription polymerase chain reaction (RT-PCR) is being used increasingly as an alternative to Northern blots analysis or RNase protection assays for quantitation of gene expression. To quantify different samples, measurements are often normalized using the expression of so-called "housekeeping" genes, such as cytoplasmic beta-actin or glyceraldehyde-3-phosphate dehydrogenase. This approach can produce false results because the presence of processed pseudogenes in the genome, which are related to some of the commonly used transcripts of housekeeping genes, leads to co-amplification of contaminating genomic DNA. By yielding amplification products of the same or similar size as the reverse-transcribed target, mRNA quantitation of expression is prone to error. In this paper, we report the results of using three sets of beta-actin primers for RT-PCR in the presence and absence of genomic DNA. In addition, we propose two new pairs of oligonucleotide primers that specifically amplify the human and rat beta-actin reverse-transcribed mRNA but not pseudogene sequences. These primers are especially suitable for quantitation of mRNA in small tissue samples (e.g., biopsies), where DNase digestion is not feasible, and therefore DNA contamination cannot be avoided.
A biomechanical study of the aponeurotic inguinal hernia repair. (1994)

The aponeurotic inguinal hernia repair is essentially a union of the aponeuroses of the external oblique and transversus abdominis muscles in the groin. Its tension-free status and resistance to intra-abdominal stress were measured in a biomechanical study. Comparative studies were made with the American Bassini procedure. Suture tensions were measured at three sites in six aponeurotic repairs and the mean tension was 3.9 +/- 2.9 grams, which was within the accuracy of the combined transducer and recorder measurement. Similar measurements in six American Bassini operations registered 633 +/- 230 grams mean tension. A relaxing incision in the Bassini repair reduced but did not eliminate tension. Mean tension figures remained at 401 +/- 198 grams. Specimens of external oblique aponeuroses in six random patients were tested, counter to their parallel fibers, in a tensiometer. The thickness of the specimens varied from 0.21 to 1.2 millimeters. The tissue mean stress capacity under tension was 4.1 +/- 1.9 x 10(6) pascals with a range of 2.5 to 6.5 x 10(6) pascals. An analysis was made of the impact of intra-abdominal pressure at five possible sites of failure in the aponeurotic repair. Established values of suture bite tissue tear resistance and our values of external oblique aponeurosis stress tension were used to calculate the resistance of the aponeurotic repair to established values of intra-abdominal pressure. The maximum reported intra-abdominal pressure is 26.6 kilopascals. In this series, the largest reconstructed inguinal floor was 5 square centimeters and supported a load of 1,360 grams force. There was a safety margin of 2.4 against a failure of tissue of minimal thickness (0.2 millimeter) in the aponeurotic repairs when subjected to maximum intra-abdominal pressure. With average thickness of specimen (0.45 millimeter) there was a safety margin of 5.4. The 2-0 polypropylene suture had a requirement of 1,590 grams force maximum knot pull strength, which was much greater than our measured tensions. The added suture-line tension created by the assumed intra-abdominal pressure with sutures spaced one-half centimeter apart was calculated to be 65 grams force. This figure is well below the reported tensions of 5,300 and 9,100 grams force resisting tissue pull through failure in the external oblique and transversus aponeurosis, respectively. The transversalis aponeurosis component of the repair had shown in the proceeding study a tensile strength greater than the external oblique aponeurosis, and by analogy, a competence to resist intra-abdominal pressure.(ABSTRACT TRUNCATED AT 400 WORDS)
Preparation of Pregnane-17α,21-diol-3,11,20-trione Acetate (1949)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPreparation of Pregnane-17α,21-diol-3,11,20-trione AcetateL. H. SarettCite this: J. Am. Chem. Soc. 1949, 71, 7, 2443–2444Publication Date (Print):July 1, 1949Publication History Published online1 May 2002Published inissue 1 July 1949https://pubs.acs.org/doi/10.1021/ja01175a061https://doi.org/10.1021/ja01175a061research-articleACS PublicationsRequest reuse permissionsArticle Views92Altmetric-Citations27LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
IL-11 Selectively Inhibits Aeroallergen-Induced Pulmonary Eosinophilia and Th2 Cytokine Production (2000)

IL-11 is a pleiotropic cytokine that induces tissue remodeling with subepithelial fibrosis when expressed in the airway. Its effects on the Th2-dominated airway inflammation that is characteristic of asthma, however, are poorly understood. To characterize the effects of IL-11 on Th2 tissue inflammation, we compared the inflammatory responses elicited by OVA in sensitized mice in which IL-11 is overexpressed in a lung-specific fashion (CC10-IL-11) with that in transgene- wild-type littermate controls. Transgene- and CC10-IL-11 transgene+ mice had comparable levels of circulating Ag-specific IgE after sensitization. OVA challenge of sensitized transgene- mice caused airway and parenchymal eosinophilic inflammation, Th2 cell accumulation, and mucus hypersecretion with mucus metaplasia. Exaggerated levels of immunoreactive endothelial cell VCAM-1, mucin (Muc) 5ac gene expression and bronchoalveolar lavage and lung IL-4, IL-5, and IL-13 protein and mRNA were also noted. In contrast, OVA challenge in CC10-IL-11 animals elicited impressively lower levels of tissue and bronchoalveolar lavage inflammation, eosinophilia, and Th2 cell accumulation, and significantly lower levels of VCAM-1 and IL-4, IL-5, and IL-13 mRNA and protein. IL-11 did not cause a comparable decrease in mucus hypersecretion, Muc 5ac gene expression, or the level of expression of RANTES, monocyte chemoattractant protein-2, or monocyte chemoattractant protein-3. In addition, IL-11 did not augment IFN-gamma production demonstrating that the inhibitory effects of IL-11 were not due to a shift toward Th1 inflammation. These studies demonstrate that IL-11 selectively inhibits Ag-induced eosinophilia, Th2 inflammation, and VCAM-1 gene expression in pulmonary tissues.
Highly Functionalized Organomagnesium Reagents Prepared through Halogen–Metal Exchange (2003)

Organomagnesium reagents occupy a central position in synthetic organic and organometallic chemistry. Recently, the halogen-magnesium exchange has considerably extended the range of functionalized Grignard reagents available for synthetic purposes. Functional groups such as esters, nitriles, iodides, imines, or even nitro groups can be present in a wide range of aromatic and heterocyclic organomagnesium reagents. Also various highly functionalized alkenyl magnesium species can be prepared. These recent developments as well as new applications of organomagnesium reagents in cross-coupling reactions and amination reactions will be covered in this Review.
Secreted production of collagen‐inspired gel‐forming polymers with high thermal stability in Pichia pastoris (2011)

Previously, we have shown that gel-forming triblock proteins, consisting of random coil middle blocks and trimer-forming (Pro-Gly-Pro)(9) end blocks, are efficiently produced and secreted by the yeast Pichia pastoris. These end blocks had a melting temperature (T(m)) of ∼41°C (at 1.1 mM of protein). The present work reveals that an increase of T(m) to ∼74°C, obtained by extension of the end blocks to (Pro-Gly-Pro)(16), resulted in a five times lower yield and partial endoproteolytic degradation of the protein. A possible cause could be that the higher thermostability of the longer (Pro-Gly-Pro)(16) trimers leads to a higher incidence of trimers in the cell, and that this disturbs secretion of the protein. Alternatively, the increased length of the proline-rich (Pro-Gly-Pro)(n) domain may negatively influence ribosomal translation, or may result in, for example, hydrophobic aggregation or membrane-active behavior owing to the greater number of closely placed proline residues. To discriminate between these possibilities, we studied the production of molecules with randomized end blocks that are unable to form triple helices. The codon- and amino acid composition of the genes and proteins, respectively, remained unchanged. As these nontrimerizing molecules were secreted intact and at high yield, we conclude that the impaired secretion and partial degradation of the triblock with (Pro-Gly-Pro)(16) end blocks was triggered by the occurrence of intracellular triple helices. This degradation was overcome by using a yapsin 1 protease disruptant, and the intact secreted polymer was capable of forming self-supporting gels of high thermal stability.
Dressed Qubits (2003)

Inherent gate errors can arise in quantum computation when the actual system Hamiltonian or Hilbert space deviates from the desired one. Two important examples we address are spin-coupled quantum dots in the presence of spin-orbit perturbations to the Heisenberg exchange interaction, and off-resonant transitions of a qubit embedded in a multilevel Hilbert space. We propose a ``dressed qubit'' transformation for dealing with such inherent errors. Unlike quantum error correction, the dressed qubit method does not require additional operations or encoding redundancy, is insensitive to error magnitude, and imposes no new experimental constraints.
Extended constituent-to-dependency conversion for English (2007)

Proceedings of the 16th Nordic Conference &#13;\nof Computational Linguistics NODALIDA-2007.&#13;\nEditors: Joakim Nivre, Heiki-Jaan Kaalep, Kadri Muischnek and Mare Koit.&#13;\nUniversity of Tartu, Tartu, 2007.&#13;\nISBN 978-9985-4-0513-0 (online)&#13;\nISBN 978-9985-4-0514-7 (CD-ROM)&#13;\npp. 105-112.
Expression of matrix metalloproteinase-2 and -9 during early human wound healing. (1994)

During wound healing, MMP-9 is suggested to be involved in keratinocyte migration and granulation tissue remodelling. Expression of MMP-2 remains stable during wound healing.
Visual opinion analysis of customer feedback data (2009)

Today, online stores collect a lot of customer feedback in the form of surveys, reviews, and comments. This feedback is categorized and in some cases responded to, but in general it is underutilized - even though customer satisfaction is essential to the success of their business. In this paper, we introduce several new techniques to interactively analyze customer comments and ratings to determine the positive and negative opinions expressed by the customers. First, we introduce a new discrimination-based technique to automatically extract the terms that are the subject of the positive or negative opinion (such as price or customer service) and that are frequently commented on. Second, we derive a Reverse-Distance-Weighting method to map the attributes to the related positive and negative opinions in the text. Third, the resulting high-dimensional feature vectors are visualized in a new summary representation that provides a quick overview. We also cluster the reviews according to the similarity of the comments. Special thumbnails are used to provide insight into the composition of the clusters and their relationship. In addition, an interactive circular correlation map is provided to allow analysts to detect the relationships of the comments to other important attributes and the scores. We have applied these techniques to customer comments from real-world online stores and product reviews from web sites to identify the strength and problems of different products and services, and show the potential of our technique.
Propane Respiration Jump-Starts Microbial Response to a Deep Oil Spill (2010)

The Deepwater Horizon event resulted in suspension of oil in the Gulf of Mexico water column because the leakage occurred at great depth. The distribution and fate of other abundant hydrocarbon constituents, such as natural gases, are also important in determining the impact of the leakage but are not yet well understood. From 11 to 21 June 2010, we investigated dissolved hydrocarbon gases at depth using chemical and isotopic surveys and on-site biodegradation studies. Propane and ethane were the primary drivers of microbial respiration, accounting for up to 70% of the observed oxygen depletion in fresh plumes. Propane and ethane trapped in the deep water may therefore promote rapid hydrocarbon respiration by low-diversity bacterial blooms, priming bacterial populations for degradation of other hydrocarbons in the aging plume.