gebhart/patrepeval huggingface dataset:
Transfer of Campylobacter pylori and Campylobacter mustelae to Helicobacter gen. nov. as Helicobacter pylori comb. nov. and Helicobacter mustelae comb. nov., Respectively (1989)

Different types of studies have shown that Campylobacter pylori does not belong in the genus Campylobacter. Ribonucleic acid sequencing has indicated that C. pylori might belong in the genus Wolinella, but we describe five major groups of taxonomic features of the genus Wolinella that differ markedly from those of C. pylori, including ultrastructure and morphology, cellular fatty acids, menaquinones, growth characteristics, and enzyme capabilities, indicating that C. pylori should not be included in the genus Wolinella. Thus, we propose the establishment of a new genus, Helicobacter, C. pylori should be transferred to this genus as Helicobacter pylori comb, nov., and H. pylori NCTC 11637 (= ATCC 43504) is the type strain. The gastric spiral organism from ferrets has been elevated recently from Campylobacter pylori subsp. mustelae to Campylobacter mustelae. We describe the similarities and differences between C. mustelae and C. pylori compared with other campylobacters, and we propose that C. mustelae should be included in the new genus Helicobacter as Helicobacter mustelae comb. nov. (type strain, ATCC 43772).
Fitness Cost of Escape Mutations in p24 Gag in Association with Control of Human Immunodeficiency Virus Type 1 (2006)

Mutational escape by human immunodeficiency virus (HIV) from cytotoxic T-lymphocyte (CTL) recognition is a major challenge for vaccine design. However, recent studies suggest that CTL escape may carry a sufficient cost to viral replicative capacity to facilitate subsequent immune control of a now attenuated virus. In order to examine how limitations can be imposed on viral escape, the epitope TSTLQEQIGW (TW10 [Gag residues 240 to 249]), presented by two HLA alleles associated with effective control of HIV, HLA-B*57 and -B*5801, was investigated. The in vitro experiments described here demonstrate that the dominant TW10 escape mutation, T242N, reduces viral replicative capacity. Structural analysis reveals that T242 plays a critical role in defining the start point and in stabilizing helix 6 within p24 Gag, ensuring that escape occurs at a significant cost. A very similar role is played by Thr-180, which is also an escape residue, but within a second p24 Gag epitope associated with immune control. Analysis of HIV type 1 gag in 206 B*57/5801-positive subjects reveals three principle alternative TW10-associated variants, and each is strongly linked to concomitant additional variants within p24 Gag, suggesting that functional constraints operate against their occurrence alone. The extreme conservation of p24 Gag and the predictable nature of escape variation resulting from these tight functional constraints indicate that p24 Gag may be a critical immunogen in vaccine design and suggest novel vaccination strategies to limit viral escape options from such epitopes.
Free radical polymerization of a sugar residue-carrying styryl monomer with a lipophilic alkoxyamine initiator: synthesis of a well-defined novel glycolipid (1998)

Controlled free radical polymerization of N-p-vinylbenzyl-2,3,5,6-tetra-O-acetyl-4-O-(2,3,4,6-tetra-O-acetyl-β-D-galactopyranosyl)-D-gluconamide (Ac-VLA) was achieved by the nitroxide-mediated free radical polymerization with a lipophilic alkoxyamine “initiator” with a dioctadecyl group in 1,2-dichloroethane at 90°C. The polymerization proceeds in a “living” fashion, providing Ac-VLA polymers with low polydispersity. The hydrolysis of the polymers results in well-defined glycopolymer-carrying amphiphiles, viz., artificial “glycolipids”.
Quantitative peptide binding motifs for 19 human and mouse MHC class I molecules derived using positional scanning combinatorial peptide libraries (2008)

These data confirm, on a large scale, including 15 human and 4 mouse class I alleles, the efficacy of the positional scanning combinatorial library approach for describing MHC class I binding specificity and identifying high affinity binding peptides. These libraries were shown to be useful for identifying specific primary and secondary anchor positions, and thereby simpler motifs, analogous to those described by other approaches. The present study also provides matrices useful for predicting high affinity binders for several alleles for which detailed quantitative descriptions of binding specificity were previously unavailable, including A*3001, A*3201, B*0801, B*1501 and B*1503.
Color constant color indexing (1995)

Objects can be recognized on the basis of their color alone by color indexing, a technique developed by Swain-Ballard (1991) which involves matching color-space histograms. Color indexing fails, however, when the incident illumination varies either spatially or spectrally. Although this limitation might be overcome by preprocessing with a color constancy algorithm, we instead propose histogramming color ratios. Since the ratios of color RGB triples from neighboring locations are relatively insensitive to changes in the incident illumination, this circumvents the need for color constancy preprocessing. Results of tests with the new color-constant-color-indexing algorithm on synthetic and real images show that it works very well even when the illumination varies spatially in its intensity and color.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Isolation of Escherichia coli O157:H7 from retail fresh meats and poultry (1987)

A total of 896 samples of retail fresh meats and poultry was assayed for Escherichia coli serogroup O157:H7 by a hydrophobic grid membrane filter-immunoblot procedure developed specifically to isolate the organism from foods. The procedure involves several steps, including selective enrichment, filtration of enrichment culture through hydrophobic grid membrane filters, incubation of each filter on nitrocellulose paper on selective agar, preparation of an immunoblot (by using antiserum to E. coli O157:H7 culture filtrate) of each nitrocellulose paper, selection from the filters of colonies which corresponded to immunopositive sites on blots, screening of isolates by a Biken test for precipitin lines from metabolites and antiserum to E. coli O157:H7 culture filtrate, and confirmation of isolates as Vero cell cytotoxic E. coli O157:H7 by biochemical, serological, and Vero cell cytotoxicity tests. E. coli O157:H7 was isolated from 6 (3.7%) of 164 beef, 4 (1.5%) of 264 pork, 4 (1.5%) of 263 poultry, and 4 (2.0%) of 205 lamb samples. One of 14 pork samples and 5 of 17 beef samples contaminated with the organism were from Calgary, Alberta, Canada, grocery stores, whereas all other contaminated samples were from Madison, Wis., retail outlets. This is the first report of the isolation of E. coli O157:H7 from food other than ground beef, and results indicate that the organism is not a rare contaminant of fresh meats and poultry.
Interleukin 10 is a potent growth and differentiation factor for activated human B lymphocytes. (1992)

Interleukin 10 (IL-10), originally identified as a TH2 helper T-cell product able to inhibit cytokine production by TH1 cells, is highly homologous to BCRF1 (viral IL-10), an open reading frame in the Epstein-Barr virus genome. Here, we show that human and viral IL-10 stimulate DNA replication of B lymphocytes activated either via their antigen receptor or via their CD40 antigen. IL-4 and IL-10 display additive effects and induce a strong increase in the number of viable cells. Moreover, IL-10 induces activated B cells to secrete large amounts of IgG, IgA, and IgM, and the combination of IL-10 and IL-4 results in the secretion of the four immunoglobulin isotypes. Thus, IL-10 may play an important role in the amplification of humoral responses.
Recent Developments in the Preparation and Chemistry of Metallacycles and Metallacages via Coordination (2015)

ADVERTISEMENT RETURN TO ISSUEPREVReviewNEXTRecent Developments in the Preparation and Chemistry of Metallacycles and Metallacages via CoordinationTimothy R. Cook*† and Peter J. Stang*‡View Author Information† Department of Chemistry, University at Buffalo, State University of New York, 359 Natural Sciences Complex, Buffalo, New York 14260, United States‡ Department of Chemistry, University of Utah, 315 S. 1400 E. Room 2020, Salt Lake City, Utah 84112, United States*E-mail: [email protected]*E-mail: [email protected]Cite this: Chem. Rev. 2015, 115, 15, 7001–7045Publication Date (Web):March 27, 2015Publication History Received2 October 2014Published online27 March 2015Published inissue 12 August 2015https://pubs.acs.org/doi/10.1021/cr5005666https://doi.org/10.1021/cr5005666review-articleACS PublicationsCopyright © 2015 American Chemical SocietyRequest reuse permissionsArticle Views22427Altmetric-Citations1536LEARN 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 SUBJECTS:Chemical structure,Ligands,Metallacycles,Metals,Self organization Get e-Alerts
Two highly related insecticidal crystal proteins of Bacillus thuringiensis subsp. kurstaki possess different host range specificities (1989)

Two genes encoding insecticidal crystal proteins from Bacillus thuringiensis subsp. kurstaki HD-1 were cloned and sequenced. Both genes, designated cryB1 and cryB2, encode polypeptides of 633 amino acids having a molecular mass of ca. 71 kilodaltons (kDa). Despite the fact that these two proteins display 87% identity in amino acid sequence, they exhibit different toxin specificities. The cryB1 gene product is toxic to both dipteran (Aedes aegypti) and lepidopteran (Manduca sexta) larvae, whereas the cryB2 gene product is toxic only to the latter. DNA sequence analysis indicates that cryB1 is the distal gene of an operon which is comprised of three open reading frames (designated orf1, orf2, and cryB1). The proteins encoded by cryB1 and orf2 are components of small cuboidal crystals found in several subspecies and strains of B. thuringiensis; it is not known whether the orf1 or cryB2 gene products are present in cuboidal crystals. The protein encoded by orf2 has an electrophoretic mobility corresponding to a molecular mass of ca. 50 kDa, although the gene has a coding capacity for a polypeptide of ca. 29 kDa. Examination of the deduced amino acid sequence for this protein reveals an unusual structure which may account for its aberrant electrophoretic mobility: it contains a 15-amino-acid motif repeated 11 times in tandem. Escherichia coli extracts prepared from cells expressing only orf1 and orf2 are not toxic to either test insect.
Type beta transforming growth factor is an inhibitor of myogenic differentiation. (1986)

We have investigated the effect of type beta transforming growth factor (TGF-beta) on the differentiation of skeletal muscle myoblasts. TGF-beta potently (ID50 approximately 10 pM) prevents established cell lines and primary cultures of rat and chicken embryo myoblasts from fusing into multinucleated myotubes. Inhibition of morphological differentiation by TGF-beta correlates with inhibition of the expression of muscle-specific mRNAs and proteins, strong induction of extracellular matrix type I collagen and fibronectin, and a marked tendency of the treated myoblasts to aggregate into densely multilayered arrays or clusters. Myogenic differentiation can resume after removal of TGF-beta from the medium. Examination of the time of action of TGF-beta shows that myoblasts stochastically reach a point beyond which they become insensitive to the inhibitory action of TGF-beta. This resistance of committed myoblasts to the inhibitory action of TGF-beta is not associated with any measurable change in the number or affinity of TGF-beta receptors in those cells. The results indicate that TGF-beta is a potent inhibitor of myogenesis and may regulate muscle development in vivo.
Activation Tagging Identifies a Conserved MYB Regulator of Phenylpropanoid Biosynthesis (2000)

Plants produce a wide array of natural products, many of which are likely to be useful bioactive structures. Unfortunately, these complex natural products usually occur at very low abundance and with restricted tissue distribution, thereby hindering their evaluation. Here, we report a novel approach for enhancing the accumulation of natural products based on activation tagging by Agrobacterium-mediated transformation with a T-DNA that carries cauliflower mosaic virus 35S enhancer sequences at its right border. Among approximately 5000 Arabidopsis activation-tagged lines, we found a plant that exhibited intense purple pigmentation in many vegetative organs throughout development. This upregulation of pigmentation reflected a dominant mutation that resulted in massive activation of phenylpropanoid biosynthetic genes and enhanced accumulation of lignin, hydroxycinnamic acid esters, and flavonoids, including various anthocyanins that were responsible for the purple color. These phenotypes, caused by insertion of the viral enhancer sequences adjacent to an MYB transcription factor gene, indicate that activation tagging can overcome the stringent genetic controls regulating the accumulation of specific natural products during plant development. Our findings suggest a functional genomics approach to the biotechnological evaluation of phytochemical biodiversity through the generation of massively enriched tissue sources for drug screening and for isolating underlying regulatory and biosynthetic genes.
Correction of scoliosis with shape-memory alloy. (1993)

Using NiTi shape-memory alloy, we devised an instrument for correction of scoliosis. Our instrument is characterized by gradual correction of the spine. Restoration power of the alloy was 25 kgcm in a rod with a diameter of 3 mm, 45 kgcm in a 4-mm rod, and 110 kgcm in a 5-mm rod. Spinal cord injuries on heating the rod were observed at an epidural temperature of 48 degrees C or more, suggesting that 48 degrees C is the critical temperature. The blood Ni concentration after implantation of the NiTi alloy rod reached a level twice normal after 6-9 hours. After 4 weeks, the Ni concentration increased 4-fold in the kidneys, 2-fold in the liver, and 10-fold in the urine. Alloy rods were attached to a scoliosis monkey and heated gradually. Scoliosis with a Cobb angle of 43 degrees was completely corrected.
Detecting DNA by field effect transistor arrays (2006)

We present electronics approach for the detection of unlabeled DNA. The biopolymers are immobilized on an array of field effect transistors integrated in silicon. Local immobilization to part of the array is achieved by direct deposition with a microspotting device and specific hybridization between complementary DNA oligonucleotides. The current voltage characteristic of the transistors is measured with the sample surface in contact with an aqueous solution. It is shown that both DNA adsorption and hybridization induce sizeable variations in the current-voltage characteristics
Expression of platelet-derived growth factor and its receptors in neuroendocrine tumors of the digestive system. (1992)

Carcinoid tumors are slowly growing neuroendocrine neoplasms which often present pronounced fibrosis around the tumor cells. We have previously shown by immunohistochemistry that carcinoid tumors express platelet-derived growth factor (PDGF) beta-receptors on surrounding stromal cells. In this report, 22 midgut carcinoids and 5 endocrine pancreatic tumors were examined for the presence of PDGF with a monoclonal antibody raised against a peptide corresponding to a part of the B-chain of PDGF which reacts strongly with the B-chain and weakly with the A-chain. They were also examined for PDGF alpha-receptors with an affinity-purified polyclonal peptide antibody and for PDGF beta-receptor with the monoclonal antibody PDGFR-B2. PDGF was expressed on tumor cells and on adjacent stroma. PDGF alpha-receptor was seen on clusters of tumor cells and occasionally on adjacent stroma, whereas beta-receptors were seen only in the stroma. Tissue sections from some of these midgut carcinoids were also investigated by in situ hybridization for mRNA of PDGF A- and B-chains as well as alpha- and beta-receptors. By in situ hybridization, abundant expression of mRNA for PDGF beta-receptor and PDGF A-chain was observed in stromal cells adjacent to carcinoid tumor cell clusters, but the mRNA expression in the tumor cells themselves was at a low level. A few clustered tumor cells and stromal cells expressed mRNA for the PDGF alpha-receptor, thus consolidating the immunohistochemical findings. mRNA for the PDGF B-chain was detected in both tumor cells and stroma, but only at low levels. Our data suggest that PDGF is involved in the growth stimulation of the carcinoid tumor cells in an autocrine fashion and in the stimulation of stromal cell growth through paracrine and possibly autocrine mechanisms. Moreover, remarkably strong immunostaining of PDGF and the PDGF alpha-receptor was seen on peripheral nerve fibers.
Synergy of Radiation Therapy and Immunotherapy in Murine Renal Cell Carcinoma (1992)

The treatment of metastatic renal cell carcinoma with immunotherapy has resulted in objective anti-tumor responses in 15-30% of patients. To enhance the therapeutic effects of immunotherapy, it is becoming evident that this approach should be combined with other treatment modalities. In this study, a spontaneously metastasizing murine renal adenocarcinoma (Renca), transplanted under the renal capsule, was treated with either radiation therapy, immunotherapy or a combination of both. In order to distinguish between the local and systemic effects of radiation therapy, total body irradiation was compared to irradiation of the tumor-bearing kidney only, or irradiation of the whole mouse with the tumor-bearing kidney shielded. Immunotherapy was administered with interleukin-2 (IL-2) alone or with IL-2 and lymphokine activated killer (LAK) cells. Combined radiation and immunotherapy induced a better anti-tumor response than either modality alone. The best response was obtained by local tumor irradiation and IL-2 therapy and resulted in a significant reduction in primary tumor size, elimination of lung metastases and a significant increase in survival.
Importance of CD8 T cell-mediated immune response during intracellular parasitic infections and its implications for the development of effective vaccines (2003)

Obligatory intracellular parasites such as Plasmodium sp, Trypanosoma cruzi, Toxoplasma gondii and Leishmania sp are responsible for the infection of hundreds of millions of individuals every year. These parasites can deliver antigens to the host cell cytoplasm that are presented through MHC class I molecules to protective CD8 T cells. The in vivo priming conditions of specific CD8 T cells during natural infection are largely unknown and remain as an area that has been poorly explored. The antiparasitic mechanisms mediated by CD8 T cells include both interferon-gamma-dependent and -independent pathways. The fact that CD8 T cells are potent inhibitors of parasitic development prompted many investigators to explore whether induction of these T cells can be a feasible strategy for the development of effective subunit vaccines against these parasitic diseases. Studies performed on experimental models supported the hypothesis that CD8 T cells induced by recombinant viral vectors or DNA vaccines could serve as the basis for human vaccination. Regimens of immunization consisting of two different vectors (heterologous prime-boost) are much more efficient in terms of expansion of protective CD8 T lymphocytes than immunization with a single vector. The results obtained using experimental models have led to clinical vaccination trials that are currently underway.
Polymorphic human somatostatin gene is located on chromosome 3. (1983)

Somatostatin is a 14-amino-acid neuropeptide and hormone that inhibits the secretion of several peptide hormones. The human gene for somatostatin SST has been cloned, and the sequence has been determined. This clone was used as a probe in chromosome mapping studies to detect the human somatostatin sequence in human-rodent hybrids. Southern blot analysis of 41 hybrids, including some containing translocations of human chromosomes, placed SST in the q21 leads to qter region of chromosome 3. Human DNAs from unrelated individuals were screened for restriction fragment polymorphisms detectable by the somatostatin gene probe. Two polymorphisms were found: (i) an EcoRI variant located at the 3' end of the gene, found in Caucasian, U.S. Black, and Asian populations with a frequency of approximately 0.10 and (ii) a BamHI variant in the intron, which occurs in Caucasians at a frequency of 0.13.
Evaluation of petroleum generation by hydrous phrolysis experimentation (1985)

Abstract Generation and expulsion of oil from organic sedimentary rocks have been achieved in the laboratory by a technique known as hydrous pyrolysis. This technique maintains a liquid water phase in contact with organic sedimentary rocks during their heating at subcritical water temperatures (less than 374 °C ). The expelled oil accumulates on the water surface and contains no measurable olefmic hydrocarbons. Hydrous pyrolysis provides a means of acquiring inform ation relating to stages, kinetics an d indices of petroleum generation that would be difficult to obtain from a study of only the natural system
Drosophila tumor suppressor PTEN controls cell size and number by antagonizing the Chico/PI3-kinase signaling pathway (1999)

The human tumor suppressor gene PTEN encodes a putative cytoskeleton-associated molecule with both protein phosphatase and phosphatidylinositol 3,4,5-trisphosphate (PIP3) 3-phosphatase activities. In cell culture, the lipid phosphatase activity of this protein is involved in regulating cell proliferation and survival, but the mechanism by which PTEN inhibits tumorigenesis in vivo is not fully established. Here we show that the highly evolutionarily conserved Drosophila PTEN homolog, DPTEN, suppresses hyperplastic growth in flies by reducing cell size and number. We demonstrate that DPTEN modulates tissue mass by acting antagonistically to the Drosophila Class I phosphatidylinositol 3-kinase, Dp110, and its upstream activator Chico, an insulin receptor substrate homolog. Surprisingly, although DPTEN does not generally affect cell fate determination, it does appear to regulate the subcellular organization of the actin cytoskeleton in multiple cell types. From these data, we propose that DPTEN has a complex role in regulating tissue and body size. It acts in opposition to Dp110 to control cell number and growth, while coordinately influencing events at the cell periphery via its effects on the actin cytoskeleton.