gebhart/patrepeval huggingface dataset:
Clinical features of Clostridium difficile-associated diarrhoea due to binary toxin (actin-specific ADP-ribosyltransferase)-producing strains (2005)

Toxins A and B are known to be the primary virulence factors of Clostridium difficile. Other potential virulence factors have been identified such as binary toxin (actin-specific ADP-ribosyltransferase toxin, or CDT). A retrospective case-control study was performed in order to identify clinical features and risk factors of C. difficile-associated diarrhoea due to binary toxin-producing strains. Each case (a patient with diarrhoea due to binary toxin-producing strain) was compared with two controls (patients with diarrhoea due to a C. difficile strain that did not produce binary toxin) matched for ward and date of hospitalization. cdtA and cdtB genes were screened by PCR. Production of CDT was studied by Western blotting using an antiserum against Ia and Ib from the Clostridium perfringens iota toxin, and the activity of the binary toxin was assessed using an ADP-ribosyltransferase assay. Twenty-six cases (14 males and 12 females) were identified in 1999 and 2000. Cases and controls did not differ significantly for sex, age, previous administration of antibiotics or frequency of endoscopic examination. Diarrhoea was community-acquired more often in cases than in controls (65.4 vs 35.7 %, P = 0.017) and more often represented the cause of hospitalization (61.5 vs 26.2 %, P = 0.003). Moreover, diarrhoea in cases was more frequently associated with abdominal pain (63.6 vs 39.4 %, P = 0.07) and with liquid stools (76.9 vs 59.5 %, P = 0.14) than in controls. These results suggest that there could be a correlation between the production of binary toxin and the severity of diarrhoea.
Loss of Stromal IMP1 Promotes a Tumorigenic Microenvironment in the Colon (2015)

The tumor-suppressive role of stromal IMP1 and its ability to modulate protumorigenic factors suggest that IMP1 status is important for the initiation and growth of epithelial tumors.
The Common Cold—Principles of Judicious Use of Antimicrobial Agents (1998)

Most children will suffer between 3 and 8 colds per year, and over half of patients seen for the common cold are given an antimicrobial prescription. Unnecessary antimicrobial therapy can be avoided by recognizing the signs and symptoms that are part of the usual course of these diseases. Controlled trials of antimicrobial treatment of the common cold are reviewed. These trials consistently fail to show that treatment changes the course or outcome. Furthermore, antimicrobial therapy for patients with viral rhinosinusitis is not an effective way to prevent bacterial complications. Mucopurulent rhinitis (thick, opaque, or discolored nasal discharge) frequently accompanies the common cold and is part of the natural course of viral rhinosinusitis. It is not an indication for antimicrobial treatment unless it persists without improvement for &amp;gt;10 to 14 days.
A longitudinal study of orthopaedic outcomes for severe factor‐VIII‐deficient haemophiliacs (1994)

Higher doses of factor per se do not necessarily produce improved orthopaedic outcomes. However, full time prophylaxis is likely to produce the best orthopaedic outcome. The most critical factor for a good orthopaedic outcome is the reduction of joint bleeds.
Mapping and binding analysis of peptides derived from the tumor-associated antigen survivin for eight HLA alleles. (2005)

There is considerable interest in developing immunotherapeutic approaches to elicit tumor-specific CTL responses in cancer patients. Epitope-based approaches aim to deliver the antigenic peptides or epitopes recognized by CTLs rather than the intact tumor antigen. Many tumor-associated proteins are nonmutated self proteins for which the dominant peptide epitopes are usually poorly immunogenic. The subdominant epitopes, however, can elicit robust T cell responses if optimized for their ability to bind to class I MHC molecules. Only the epitopes for a few tumor antigens expressed in human cancers have been defined to this level, mainly for technical reasons. The means to rapidly screen and characterize the binding of epitopes derived from complex tumor-associated antigens is an important enabling technology. Here, we have used the high-throughput technology iTopia to identify those peptides derived from the tumor-associated antigen survivin that bind 8 class I alleles. A library of overlapping nonamers spanning the length of the survivin protein was initially screened for peptides capable of binding each allele. Nineteen HLA-A*0201, zero HLA-A*0101, seven HLA-A*0301, twelve HLA-A*1101, twenty-four HLA-A*2402, six HLA-B*0702, six HLA-B*0801, and eight HLA-B*1501 binding peptides were identified based on an arbitrary cutoff. Peptides capable of binding a given allele were further characterized by their affinity for MHC class I molecules and by the rate of dissociation of the complex. This information should help guide functional studies and future epitope-based immunotherapies.
Endometrial endothelial cells are derived from donor stem cells in a bone marrow transplant recipient (2007)

Bone marrow-derived endothelial progenitors contribute to the formation of new blood vessels in the endometrium.
Reduction of doxorubicin cytotoxicity by ouabain: correlation with topoisomerase-induced DNA strand breakage in human and hamster cells. (1988)

The cardiac glycoside ouabain, which is a specific inhibitor of the Na+,K+-pump, confers dramatic protection from the cytotoxic effects of doxorubicin (Adriamycin). This effect was documented in cultured A549 cells (human lung adenocarcinoma). CCL210 cells (human fibroblasts), and V79 cells (hamster fibroblasts). Maximum protection from doxorubicin cytotoxicity was achieved using 1 microM ouabain for A549 and CCL210 cells and 300 microM ouabain for V79 cells. These concentrations correlated well with the concentrations of ouabain required to induce Na+,K+-pump blockade, which was assessed using the K+ analogue 86Rb+. This suggests that protection is mediated by pump blockade. Addition of ouabain at the same time as doxorubicin was just as protective as preincubation with ouabain for an hour, demonstrating that the ouabain acts rapidly. Ouabain treatment affected neither influx nor efflux of doxorubicin. Ouabain also had no effect on verapamil-induced inhibition of doxorubicin efflux. However, ouabain partially blocked the verapamil-induced potentiation of the cytotoxic effects of doxorubicin. Therefore, ouabain does not protect by affecting intracellular doxorubicin levels. Fluorescence microscopy showed that the ability of doxorubicin to reach the nucleus was not influenced by ouabain. Alkaline elution studies demonstrated that ouabain greatly decreased doxorubicin-induced DNA strand breakage. Protection from cytotoxicity correlated closely with this decrease in strand breakage. These studies suggest that the stabilization of DNA-topoisomerase II complexes is closely linked to the mechanism of doxorubicin cytotoxicity and that this stabilization is influenced by the intracellular ionic milieu.
Effect of cyclosporin A on human lymphocyte responses in vitro. III. CsA inhibits the production of T lymphocyte growth factors in secondary mixed lymphocyte responses but does not inhibit the response of primed lymphocytes to TCGF. (1982)

The mechanism whereby Cyclosporin A (CsA) inhibits secondary mixed lymphocyte responses was assessed. CsA added to secondary MLR cultures inhibited proliferation and induction of cytolytic lymphocyte activity. This inhibition was found to be associated with the inhibition of T lymphocyte stimulating growth factor(s) (TCGF) production in the supernatants of secondary MLR cultures. As little as 1.0 micrograms/ml of CsA added to secondary MLR cultures resulted in no measurable TCGF activity. In contrast, moderate doses of CsA (1.0, 2.5 micrograms/ml), which completely inhibited the secondary MLR response to alloantigen, did not inhibit the proliferative and CML response of alloantigen-primed lymphocytes to these stimulating growth factors. Even at high doses of CsA (20 micrograms/ml), substantial levels of proliferation (50% of control response) and CML induction (60% of control response) were observed when the primed cells were exposed to secondary MLR supernatants containing TCGF activity. It was concluded that inhibition of secondary mixed lymphocyte responses by CsA may be due in part to the inhibition of TCGF production rather than the inhibition of the effect of TCGF on mature cytotoxic T lymphocytes.
Functionally distinct subsets of human γ/δ T cells (1991)

To determine if effector subsets exist among human gamma/delta T cells, we examined the cytokine production and cytotoxic activity of gamma/delta T cell clones with different accessory molecule phenotypes, V delta and V gamma gene expression, and J gamma rearrangements. T cell clones bearing gamma/delta T cell receptor produce an array of cytokines like alpha/beta T cell clones. Individual gamma/delta T cell clones produced a characteristic array of cytokines without correlation with V delta or V gamma gene expression. However, when phenotypic subsets were considered, CD4+ gamma/delta clones produced significantly higher levels of interleukin 2 and granulocyte-monocyte colony-stimulating factor compared with CD4-CD8- and CD8+ gamma/delta clones. Similarly, when cytotoxic potential was assessed, CD4+ gamma/delta clones exhibited minimal activity when compared with CD4-CD8- and CD8+ adult peripheral blood gamma/delta clones. We conclude that functionally distinct gamma/delta T cell subsets exist and suggest that these subsets may correlate with expression of the CD4 accessory molecule.
Khmaralite, a new beryllium-bearing mineral related to sapphirine; a superstructure resulting from partial ordering of Be, Al, and Si on tetrahedral sites (1999)

Khmaralite, Ca 0.04 Mg 5.46 Fe 3+ 0.12 Fe 2+ 1.87 Al 14.26 Be 1.43 B 0.02 Si 4.80 O 40 , is a new mineral closely related to sapphirine from Khmara Bay, Enderby Land, Antarctica. It occurs in a pegmatite metamorphosed at T 820 C, P 10 kbar. The minerals surinamite, musgravite, and sillimanite associated with khmaralite at Casey Bay saturate it in BeO, and thus its BeO content could be close to the maximum possible. Optically, khmaralite is biaxial (-); at = 589 nm, = 1.725(2), = 1.740(2), = 1.741(2), 2V meas = 34.4 (1.8), v > r strong, and b. The weak superstructure reported using electron diffraction has been confirmed by single-crystal X-ray diffraction. The superstructure corresponds to a doubling of the a axis in monoclinic sapphirine-2M (P2 1 /c setting) with the following unit-cell parameters: a = 19.800(1), b = 14.371(1), c = 11.254(1) , = 125.53(1), Z = 4, D calc = 3.61 g/cm 3 . Using a simplified chemical formula of Mg 5.46 Al 14.28 Fe 2.00 Si 4.80 Be 1.46 O 40 , the fully anisotropic structure refinement of all site occupancies, including Al vs. Mg and Al vs. Si on the 16 octahedral (M) and 12 tetrahedral (T) sites respectively, establishes that the 2a superstructure results primarily from ordering in the doubled (T1 T6, T7 T12) tetrahedral chain, which is parallel to the a axis. The strongest contribution comes from Al-Si-Be ordering on the T2 (33-16-51%) vs. T8 (0-95-5%) and T3 (4-78-18%) vs. T9 (30-0-70%) sites. Thus, the sequence Al-Si-Al in sapphirine is replaced by the sequence Si-Be-Si in khmaralite; i.e., Be replaces Si on two sites and Si replaces Al on on four adjacent sites, resulting in an indirect replacement of Al by Be by the coupled substitution Be + Si = 2Al. The Be distribution in khmaralite and the strong preference for Be/Al mixing over Be/Si mixing appear to satisfy the bonding requirements of the bridging O atoms by minimizing the number of Be-O-Be and Be-O-Al linkages.
Characterization of human T lymphocytes that express the C3b receptor. (1983)

The presence of the C3b receptor (C3bR) on human peripheral blood T lymphocytes was recognized by the capacity of rabbit F(ab')2 anti-C3bR and tetramethylrhodamine isothiocyanate (TRITC)-conjugated goat F(ab')2 anti-rabbit F(ab')2 to stain 14.5 +/- 3.7% (mean +/- SEM; n = 5) of lymphocytes forming rosettes with sheep erythrocytes (E). The F(ab')2 anti-C3bR also blocked the capacity of peripheral blood lymphocytes stained with OKT11 to form rosettes with bovine E bearing C3b and immunoprecipitated a single membrane protein having a m.w. of approximately 250,000 from detergent lysates of 125I-labeled, purified T cells. Measurement by fluorescent flow cytometry of the quantitative expression of the C3bR indicated that T cells had slightly more antigenic sites/cell than did E and approximately 10-fold fewer sites than were present on B cells. The surface constituents of the peripheral blood T cells expressing the C3bR were assessed in an assay that employed simultaneously three markers: rosette formation with sheep E, TRITC staining with anti-C3bR and fluorescein isothiocyanate (FITC)-staining with a panel of monoclonal antibodies or with aggregated IgG. Among lymphocytes forming rosettes with sheep E and expressing the C3bR, 99.6 +/- 0.4%, 65.0 +/- 5.8%, 17.2 +/- 6.2%, and 15.3 +/- 5.0% of the cells expressed antigens detected by OKT3, OKT4, OKT8, and OKM1 monoclonal antibodies, respectively. Ninety-seven per cent of the C3bR-bearing T cells were also capable of specifically binding aggregated IgG, indicating the presence of Fc receptors for IgG (Fc gamma R) on these cells. The T cells expressing the C3bR had large nuclei, thin rims of basophilic cytoplasm and no azurophilic granules. Thus, the C3bR is present on some T cells, all of which have a typical lymphocyte morphology, the T3 antigen and the Fc gamma R.
Abnormalities in structure and expression of the retinoblastoma gene in small cell lung cancer cell lines and xenografts in nude mice. (1990)

The putative retinoblastoma gene (Rb) is a tumor suppressor gene which is believed to cause retinoblastomas when both alleles are inactivated, leading to lack of the encoded Mr 110,000-116,000 phosphoprotein. Inactivation of the Rb gene has also been found in several other tumor types, including small cell lung cancer (SCLC). Absence of the 4.7 kilobase mRNA has been found to be frequent in SCLC, and it has been reported that the Rb Mr 110,000-116,000 protein product is always absent, even in tumors expressing Rb mRNA. Using Western blotting technique with a monoclonal antibody directed against the Rb protein, we investigated the expression of the Mr 110,000-116,000 Rb protein in SCLC tumors grown as xenografts in nude mice and/or as cell lines. Rb messenger RNA expression was determined by Northern blotting, and gross structural gene alterations were investigated by Southern blotting. Tumors established from 23 patients were studied. Seven of the tumors did not express Rb protein, whereas expression was detectable in 13. Three tumors were not investigated for protein expression. Only two tumors expressed Rb mRNA without detectable Rb protein expression. Gross DNA alterations were found in four tumors, of which only one expressed Rb mRNA. Our results demonstrated frequent absence of Rb mRNA and protein in SCLC, but apparently normal Rb mRNA and protein were both expressed in more than one-half of the tumors.
Discriminating image senses by clustering with multimodal features (2006)

We discuss Image Sense Discrimination (ISD), and apply a method based on spectral clustering, using multimodal features from the image and text of the embedding web page. We evaluate our method on a new data set of annotated web images, retrieved with ambiguous query terms. Experiments investigate different levels of sense granularity, as well as the impact of text and image features, and global versus local text features.
Evolutionary Implications of Microbial Genome Tetranucleotide Frequency Biases (2003)

We compared nucleotide usage pattern conservation for related prokaryotes by examining the representation of DNA tetranucleotide combinations in 27 representative microbial genomes. For each of the organisms studied, tetranucleotide usage departures from expectations (TUD) were shared between related organisms using both Markov chain analysis and a zero-order Markov method. Individual strains, multiple chromosomes, plasmids, and bacteriophages share TUDs within a species. TUDs varied between coding and noncoding DNA. Grouping prokaryotes based on TUD profiles resulted in relationships with important differences from those based on 16S rRNA phylogenies, which may reflect unequal rates of evolution of nucleotide usage patterns following divergence of particular organisms from a common ancestor. By both symmetrical tree distance and likelihood analysis, phylogenetic trees based on TUD profiles demonstrate a level of congruence with 16S rRNA trees similar to that of both RpoA and RecA trees. Congruence of these trees indicates that there exists phylogenetic signal in TUD patterns, most prominent in coding region DNA. Because relationships demonstrated in TUD-based analyses utilize whole genomes, they should be considered complementary to phylogenies based on single genetic elements, such as 16S rRNA.
Matching storage organisation to usage pattern in relational data bases (1974)

A significant improvement in the performance of data base systems may be achieved by dynamically optimising the storage organisation and the access paths in accordance with the usage patterns. The principle of defined relations may be .employed to ensure that a given relational data base is tuned to match its usage pattern. This thesis describes some original contributions to the solution of the update problem of defined relations. Some methods of improving the response time without impairing the utilization of disk space have been investigated, and a generalised page replacement algorithm for the management of the data base work space is recommended. The arguments in this thesis are supported by examples drawn from existing relational data bases. As a whole, the thesis emphasises the benefits of organising the data base in a manner dictated by the activity of its users.
Mannose-Binding Lectin Deficiency Is Associated With Smaller Infarction Size and Favorable Outcome in Ischemic Stroke Patients (2011)

MBL deficiency is associated with smaller cerebral infarcts and favorable outcome in patients receiving conservative treatment. Our data suggest an important role of the lectin pathway in the pathophysiology of cerebral I/R injury and might pave the way for new therapeutic interventions.
Inactivation of Vitamin B1 by Raw Fish. (1941)

SummaryPrevious observations that a dietary deficiency disease, produced in foxes by feeding raw fish, is fundamentally a B1 avitaminosis, have been confirmed in the chick. The additional observation has been made that this condition can be reproduced in foxes which have recovered from a previous attack. Evidence obtained from experimentation in vitro confirms the observation previously made in vivo that the inactivation of vitamin B1 by raw carp occurs within the feed mixture itself. The level of inactivation depends upon the length of time that the fish is in contact with the feed mixture. Studies to standardize the conditions of the reaction are now in progress. Present evidence indicates that the reaction may be enzymatic in nature.
The methylotrophic yeast Pichia pastoris synthesizes a functionally active chromophore precursor of the plant photoreceptor phytochrome. (1996)

Induction of the expression of an algal phytochrome cDNA in the methylotrophic yeast Pichia pastoris led to time-dependent formation of photoactive holophytochrome without the addition of exogenous bilins. Both in vivo and in vitro difference spectra of this phytochromic species are very similar to those of higher plant phytochrome A, supporting the conclusion that this species possesses a phytochromobilin prosthetic group. Zinc blot analyses confirm that a bilin chromophore is covalently bound to the algal phytochrome apoprotein. The hypothesis that P. pastoris contains phytochromobilin synthase, the enzyme that converts biliverdin IX alpha to phytochromobilin, was also addressed in this study. Soluble extracts from P. pastoris were able to convert biliverdin to a bilin pigment, which produced a native difference spectrum upon assembly with oat apophytochrome A. HPLC analyses confirm that biliverdin is converted to both 3E- and 3Z-isomers of phytochromobilin. These investigations demonstrate that the ability to synthesize phytochromobilin is not restricted to photosynthetic organisms and support the hypothesis of a more widespread distribution of the phytochrome photoreceptor.
A MAP Kinase Targeted by Endotoxin and Hyperosmolarity in Mammalian Cells (1994)

Mammalian cells respond to endotoxic lipopolysaccharide (LPS) by activation of protein kinase cascades that lead to new gene expression. A protein kinase, p38, that was tyrosine phosphorylated in response to LPS, was cloned. The p38 enzyme and the product of the Saccharomyces cerevisiae HOG1 gene, which are both members of the mitogen-activated protein (MAP) kinase family, have sequences at and adjacent to critical phosphorylation sites that distinguish these proteins from most other MAP kinase family members. Both HOG1 and p38 are tyrosine phosphorylated after extracellular changes in osmolarity. These findings link a signaling pathway in mammalian cells with a pathway in yeast that is responsive to physiological stress.
A practical approach to peer-to-peer publish-subscribe (2006)

The Web has filed to fulfill its promise of delivering relevant news and information in a timely fashion. In fact, it doesn�t deliver anything on its own at all; instead, it requires its users to explicitly poll information sources. Checking for updates by pointing, clicking, and reloading Web sites, whether the sites are Slashdot, news, or online classifieds, is not only slow, inefficient, and cumbersome for users, but it places an unnecessary bandwidth burden on content providers. Recent attempts to automate this process, with the aid of feed readers, have created more problems than they have solved. A system that detects updates to content anywhere on the Web and delivers it to users via an asynchronous channel, such as an instant message, would do much to relieve the burden on users and content providers alike.
In Vitro Effects of Thiazolides on Giardia lamblia WB Clone C6 Cultured Axenically and in Coculture with Caco2 Cells (2005)

The thiazolides represent a novel class of anti-infective drugs, with the nitrothiazole nitazoxanide [2-acetolyloxy-N-(5-nitro 2-thiazolyl) benzamide] (NTZ) as the parent compound. NTZ exhibits a broad spectrum of activities against a wide variety of helminths, protozoa, and enteric bacteria infecting animals and humans. In vivo, NTZ is rapidly deacetylated to tizoxanide (TIZ), which exhibits similar activities. We have here comparatively investigated the in vitro effects of NTZ, TIZ, a number of other modified thiazolides, and metronidazole (MTZ) on Giardia lamblia trophozoites grown under axenic culture conditions and in coculture with the human cancer colon cell line Caco2. The modifications of the thiazolides included, on one hand, the replacement of the nitro group on the thiazole ring with a bromide, and, on the other hand, the differential positioning of methyl groups on the benzene ring. Of seven compounds with a bromo instead of a nitro group, only one, RM4820, showed moderate inhibition of Giardia proliferation in axenic culture, but not in coculture with Caco2 cells, with a 50% inhibitory concentration (IC50) of 18.8 microM; in comparison, NTZ and tizoxanide had IC50s of 2.4 microM, and MTZ had an IC50 of 7.8 microM. Moreover, the methylation or carboxylation of the benzene ring at position 3 resulted in a significant decrease of activity, and methylation at position 5 completely abrogated the antiparasitic effect of the nitrothiazole compound. Trophozoites treated with NTZ showed distinct lesions on the ventral disk as soon as 2 to 3 h after treatment, whereas treatment with metronidazole resulted in severe damage to the dorsal surface membrane at later time points.