gebhart/patrepeval huggingface dataset:
Toxigenic clostridia. (1990)

Toxigenic clostridia belonging to 13 recognized species are discussed in this review. Each species or group of organisms is, in general, introduced by presenting the historical aspects of its discovery by early investigators of human and animal diseases. The diseases caused by each species or group are described and usually discussed in relation to the toxins involved in the pathology. Morphological and physiological characteristics of the organisms are described. Finally, the toxins produced by each organism are listed, with a presentation of their biological activities and physical and biochemical characteristics. The complete amino acid sequences for some are known, and some of the genes have been cloned. The term toxin is used loosely to include the various antigenic protein products of these organisms with biological and serological activities which have served as distinguishing characteristics for differentiation and classification. Some of these factors are not truly toxic and have no known role in pathogenicity. Some of the interesting factors common to more than one species or group are the following: neurotoxins, lethal toxins, lecithinases, oxygen-labile hemolysins, binary toxins, and ADP-ribosyltransferases. Problems in bacterial nomenclature and designation of biologically active factors are noted.
Scene Registration In Aerial Image Analysis (1989)

In this paper we discuss the importance of scene registration for several tasks in the automated interpretation of aerial imagery. These tasks are structure matching, stereo matching, and stereo visualization. While the process of registration and matching has traditionally been treated as separate problems, particularily in the case of stereo matching, we describe techniques that may unify these processes.
Flow cytometric sorting of sperm: Influence on fertilization and embryo/fetal development in the rabbit (1996)

Viable, intact rabbit sperm, prepared, processed, and flow cytometrically sorted, were used in this study to determine the influence of flow sorting on fertilization and embryo development. In experiment I, flow-sorted or control (unstained and unsorted) sperm were surgically inseminated into the uterine horn of hormonally primed does (10 to 12 does per time point). At 42 hr postsurgical insemination, flushed embryos were assessed for development. Fetal development was determined at day 7, day 14, and day 21 post-surgical insemination. Embryos resulting from does surgically inseminated with control sperm at 42 hr post-insemination were observed to be at the early morula stage of development (> 16 cell), whereas embryos from does inseminated with flow sorted sperm were at the 8- to 16-cell stage. No difference was observed between treatments at day 7, 14, or 21, however, there was a significant decrease in fetus number per doe inseminated with flow-sorted sperm over time. In experiment II, mature oocytes were flushed from the oviducts of superovulated does and coincubated in vitro (IVF) with flow-sorted or control rabbit sperm. Oocytes observed at 6 hr post-coincubation exhibited swollen sperm heads in the cytoplasm, demonstrating that fertilization had occurred (2 PN + T). There was a higher percentage of fertilized oocytes by 8 hr post-coincubation for both control (31%) and flow-sorted sperm (31%) when used for IVF. By 10 and 12 hr post-coincubation, little difference was observed in the number of fertilized oocytes between sperm treatments (52% and 66% for control vs. 57 and 54% for flow-sorted, respectively). These studies demonstrate that flow-sorted sperm are capable of fertilizing mature oocytes under in vitro conditions. In addition they show that flow sorting may not negatively influence fertilization events, but likely interferes during early embryonic and fetal development.
DAVID Bioinformatics Resources: expanded annotation database and novel algorithms to better extract biology from large gene lists (2007)

All tools in the DAVID Bioinformatics Resources aim to provide functional interpretation of large lists of genes derived from genomic studies. The newly updated DAVID Bioinformatics Resources consists of the DAVID Knowledgebase and five integrated, web-based functional annotation tool suites: the DAVID Gene Functional Classification Tool, the DAVID Functional Annotation Tool, the DAVID Gene ID Conversion Tool, the DAVID Gene Name Viewer and the DAVID NIAID Pathogen Genome Browser. The expanded DAVID Knowledgebase now integrates almost all major and well-known public bioinformatics resources centralized by the DAVID Gene Concept, a single-linkage method to agglomerate tens of millions of diverse gene/protein identifiers and annotation terms from a variety of public bioinformatics databases. For any uploaded gene list, the DAVID Resources now provides not only the typical gene-term enrichment analysis, but also new tools and functions that allow users to condense large gene lists into gene functional groups, convert between gene/protein identifiers, visualize many-genes-to-many-terms relationships, cluster redundant and heterogeneous terms into groups, search for interesting and related genes or terms, dynamically view genes from their lists on bio-pathways and more. With DAVID (http://david.niaid.nih.gov), investigators gain more power to interpret the biological mechanisms associated with large gene lists.
Defining an optimal size of support for remote sensing investigations (1995)

The support is a geostatistical term used to describe the size, geometry and orientation of the space on which an observation is defined. In remote sensing, the size of support is equivalent to the spatial resolution. The relation of size of support with the precision of estimating the mean of several properties is evaluated by kriging. The authors chose three examples; estimating the dry biomass of pasture on May 6, 1988, and estimating the percentage cover of clover in the pasture and its NDVI (measured using a ground-based radiometer) on Aug. 6, 1988. The modelled experimental variograms of these properties were deregularized to estimate the punctual variograms and these functions regularized to new sizes of support. The regularized variograms were then used to estimate the kriging variances attainable by sampling on a square grid. The kriging variances were plotted against grid spacing for each new size of support and the optimal sampling strategy read from the graph. In each case, there were several optimal sampling strategies, and the final choice depended on the cost of measurement. In some cases increasing the size of support was more efficient than increasing the sampling intensity.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Cerebrovascular Changes in Chronic Hypertension (1997)

Enalapril treatment had a protective effect and attenuated vascular hypertrophy and the increase in vascular extracellular matrix proteins observed in chronic hypertension. In addition, there was reduction in the magnitude of BBB breakdown.
Intestinal and hepatic metabolism of glutamine and citrulline in humans (2007)

Glutamine plays an important role in nitrogen homeostasis and intestinal substrate supply. It has been suggested that glutamine is a precursor for arginine through an intestinal-renal pathway involving inter-organ transport of citrulline. The importance of intestinal glutamine metabolism for endogenous arginine synthesis in humans, however, has remained unaddressed. The aim of this study was to investigate the intestinal conversion of glutamine to citrulline and the effect of the liver on splanchnic citrulline metabolism in humans. Eight patients undergoing upper gastrointestinal surgery received a primed continuous intravenous infusion of [2-(15)N]glutamine and [ureido-(13)C-(2)H(2)]citrulline. Arterial, portal venous and hepatic venous blood were sampled and portal and hepatic blood flows were measured. Organ specific amino acid uptake (disposal), production and net balance, as well as whole body rates of plasma appearance were calculated according to established methods. The intestines consumed glutamine at a rate that was dependent on glutamine supply. Approximately 13% of glutamine taken up by the intestines was converted to citrulline. Quantitatively glutamine was the only important precursor for intestinal citrulline release. Both glutamine and citrulline were consumed and produced by the liver, but net hepatic flux of both amino acids was not significantly different from zero. Plasma glutamine was the precursor of 80% of plasma citrulline and plasma citrulline in turn was the precursor of 10% of plasma arginine. In conclusion, glutamine is an important precursor for the synthesis of arginine after intestinal conversion to citrulline in humans.
Molecular cloning of bovine zona pellucida glycoproteins ZPA and ZPB and analysis for sperm‐binding component of the zona (2001)

The zona pellucida, a transparent envelope surrounding the mammalian oocyte, comprises three glycoproteins, ZPA, ZPB and ZPC, and plays important roles in fertilization. We have previously reported that apparent relative molecular masses of bovine zona glycoproteins on SDS/PAGE under nonreducing conditions after removal of poly N ‐acetyllactosamine at the nonreducing portion of sugar chains with endo‐β‐galactosidase are 72 000, 58 000 and 45 000 [Noguchi, S., Yonezawa, N., Katsumata, T., Hashizume, K.,Kuwayama, M., Hamano, S., Watanabe, S. &amp; Nakano, M. (1994) Biochim . Biophys . Acta 1201 , 7–14]. The N‐terminal amino‐acid sequences and crossreactivity to antibodies specific to each porcine zona component show that the bovine components correspond to porcine ZPA, ZPB and ZPC, respectively. In this study, we deduced amino‐acid sequences of bovine ZPA and ZPB by cDNA cloning and sequencing. Identities in amino‐acid sequences between bovine and porcine counterparts were 77% for ZPA and 75% for ZPB, whereas between bovine and murine counterparts identities were 57% for ZPA and 37% for ZPB. The positions of Cys were completely conserved in bovine ZPA and ZPB compared with counterparts of other mammalian species. Bovine ZPA was processed between Ala and Asp on fertilization, suggesting that the consensus motif for the processing is Ala‐Asp‐Asp/Glu. We purified bovine zona components and examined their sperm‐binding activity with an in vitro competition assay and sperm‐bead‐binding assay. As a result, ZPB showed the strongest sperm‐binding activity among the components. ZPC also showed sperm‐binding activity and the activity per molecule was about one‐sixth that of ZPB according to the result of the sperm‐bead‐binding assay. We could not determine if ZPA has significant sperm‐binding activity, but the activity may be much lower than that of ZPB even if ZPA has significant activity. Thus, ZPB may play a major role in sperm binding in bovine zona.
Correction of complex heteroduplexes made of mouse H-2 gene sequences in Escherichia coli K-12. (1984)

We have prepared heteroduplexes between two plasmids that carry, in the same orientation, two H-2 cDNA inserts, 1.15 and 1.0 kilobase long, respectively. Their sequences encode two distinct class I transplantation antigens of the mouse and differ by 8% of their nucleotides. Molecules with a rearranged array of restriction sites were found after transformation and cloning in an Escherichia coli recA- host. Nucleotide sequences showed that the rearranged molecules derived their nucleotides from the two parental strands. Thus, correction of these complex heteroduplexes takes place in E. coli and probably involves repair mechanisms. It provides the basis for a mutational process in which several nucleotides (amino acids) can be altered in a single event. It also offers a practical means of making genetic variants. Several other implications are discussed.
Typhim Vi vaccine against typhoid fever: a clinical trial in Kenya. (1995)

Safety, tolerance and immunogenicity of the purified Vi polysaccharide vaccine (Typhim Vi) against typhoid fever was evaluated in primary school children aged 5-15 years. A total of 435 children were vaccinated, each with a single intramuscular injection in the left deltoid muscle. One hundred and ten children were randomly selected for blood samples on day 0 (pre vaccination) and day 30 (post vaccination). Vi antibodies studied by Radio immuno assay (RIA) on 97(88%) paired sera showed a seroconversion rate of 76.2% and seroprotection rate after vaccination was 74.2%, while 6.2% of children already had protective immunity before vaccination. The vaccine was well tolerated. Most commonly reported reactions were mild pain at site of injection (83%), and a few complained of mild swelling (4.6%), induration (1.1%), itching (1.1%) and headaches (1.4%). All reactions were of mild severity and disappeared within 24 to 48 hours.
PdAg Nanorings Supported on Graphene Nanosheets: Highly Methanol‐Tolerant Cathode Electrocatalyst for Alkaline Fuel Cells (2012)

Abstract Due to the high costs, slow reaction kinetics, and methanol poisoning of platinum‐based cathode catalysts, designing and exploring non‐Pt or low‐Pt cathode electrocatalysts with a low cost, high catalytic performance, and high methanol‐tolerance are crucial for the commercialization of fuel cells. Here, a facile method to fabricate a system of PdAg nanorings supported by graphene nanosheets is demonstrated; the fabrication is based on the galvanic displacement reaction between pre‐synthesized Ag nanoparticles and palladium ions. X‐ray diffraction and high‐resolution transmission electron microscopy show that the synthesized PdAg nanocrystals exhibit a ring‐shaped hollow structure with an average size of 27.49 nm and a wall thickness of 5.5 nm. Compared to the commercial Pd–C catalyst, the PdAg nanorings exhibit superior properties as a cathode electrocatalyst for oxygen reduction. Based on structural and electrochemical studies, these advantageous properties include efficient usage of noble metals and a high surface area because of the effective utilization of both the exterior and interior surfaces, high electrocatalytic performance for oxygen reduction from the synergistic effect of the alloyed PdAg crystalline phase, and most importantly, excellent tolerance of methanol crossover at high concentrations. It is anticipated that this synthesis of graphene‐based PdAg nanorings will open up a new avenue for designing advanced electrocatalysts that are low in cost and that exhibit high catalytic performance for alkaline fuel cells.
Inducible high level synthesis of mature human fibroblast interferon inEscherichia coli (1983)

We have obtained high level synthesis in Escherichia coli of mature human fibroblast interferon using a plasmid vector that was designed to allow easy coupling of a DNA coding region to the initiator AUG of the replicase gene of the RNA phage MS2 cloned downstream of phage lambda's leftward promoter. The activity of the promoter can be regulated by temperature. Induced cells accumulated the interferon up to 4% of the total cellular protein. The biological activity of the product amounted to 4 X 10(9) international units per litre of culture. The synthesis of human fibroblast interferon was shown to drastically inhibit the growth rate of the bacterial host.
The use of natural products in the treatment of inflammatory bowel disease (2008)

The use of complementary medicine among patients with inflammatory bowel disease, particularly in the form of herbal therapies is widespread in the Western world as well as in many asian countries including China and india.1 it seems that their use is continously increasing despite the fact that only a small number of controlled trials dealing with either efficacy or safety of these natural products exist. so far, there is limited controlled evidence indicating efficacy of traditional Chinese medicines, aloe vera gel, wheat grass juice, Boswellia serrata and bovine colostrum enemas in patients with ulcerative colitis.2 However, there is emerging evidence that many of these substances have the ability to modulate the immune system and disrupt the proinflammatory cascade through a variety of mechanisms, including antioxidant effects, alterations in cell signaling (in particular the nuclear factor kappaB pathway), cytokines, proinflammatory mediators, and disruption of bacterial flora.3 it must be emphasized that natural therapies are not always safe as fatal hepatic and renal failure have occurred with some preparations and interactions with conventional drugs are potentially dangerous.4
Guanidine Methods for Total RNA Preparation (1996)

Three different methods for RNA preparation using guanidine are presented in this unit--a single-step isolation method employing liquid-phase separation to selectively extract total RNA from tissues and cultured cells and two methods that rely on a CsCl step gradient to isolate total RNA.
Interleukin 6 Induces the Expression of Vascular Endothelial Growth Factor (1996)

Angiogenesis, the formation of new blood vessels, is induced by various growth factors and cytokines that act either directly or indirectly. Vascular endothelial growth factor (VEGF) is a specific mitogen for vascular endothelial cells and therefore has a central role in physiological events of angiogenesis. Interleukin-6 (IL-6) expression on the other hand is elevated in tissues that undergo active angiogenesis but does not induce proliferation of endothelial cells. We demonstrate using Northern analysis that treatment of various cell lines with IL-6 for 6-48 h results in a significant induction of VEGF mRNA. The level of induction is comparable to the documented induction of VEGF mRNA by hypoxia or cobalt chloride, an activator of hypoxia-induced genes. In addition, it is demonstrated by transient transfection assays that the effect of IL-6 is mediated not only by DNA elements at the promoter region but also through specific motif(s) located in the 5'-untranslated region (5'-UTR) of VEGF mRNA. Our results imply that IL-6 may induce angiogenesis indirectly by inducing VEGF expression. It is also shown that the 5'-UTR is important for the expression of VEGF. The 5'-UTR of VEGF is exceptionally long (1038 base pairs) and very rich in G + C. This suggests that secondary structures in the 5'-UTR might be essential for VEGF expression through transcriptional and post-transcriptional control mechanisms.
RETRACTED: Selective cell death mediated by small conditional RNAs (2010)

Cancer cells are characterized by genetic mutations that deregulate cell proliferation and suppress cell death. To arrest the uncontrolled replication of malignant cells, conventional chemotherapies systemically disrupt cell division, causing diverse and often severe side effects as a result of collateral damage to normal cells. Seeking to address this shortcoming, we pursue therapeutic regulation that is conditional, activating selectively in cancer cells. This functionality is achieved using small conditional RNAs that interact and change conformation to mechanically transduce between detection of a cancer mutation and activation of a therapeutic pathway. Here, we describe small conditional RNAs that undergo hybridization chain reactions (HCR) to induce cell death via an innate immune response if and only if a cognate mRNA cancer marker is detected within a cell. The sequences of the small conditional RNAs can be designed to accept different mRNA markers as inputs to HCR transduction, providing a programmable framework for selective killing of diverse cancer cells. In cultured human cancer cells (glioblastoma, prostate carcinoma, Ewing's sarcoma), HCR transduction mediates cell death with striking efficacy and selectivity, yielding a 20- to 100-fold reduction in population for cells containing a cognate marker, and no measurable reduction otherwise. Our results indicate that programmable mechanical transduction with small conditional RNAs represents a fundamental principle for exploring therapeutic conditional regulation in living cells.
Chemical stability of insulin. 4. Mechanisms and kinetics of chemical transformations in pharmaceutical formulation. (1992)

Insulin decomposes by a multitude of chemical reactions [1-3]. It deamidates at two different residues by entirely different mechanisms. In acid, deamidation at AsnA21 is intramolecularly catalyzed by the protonated C-terminal, whereas above pH 6 an intermediate imide formation at residue AsnB3 leads to isoAsp and Asp derivatives. The imide formation requires a large rotation around the alpha-carbon/peptide carbonyl carbon bond at B3, corresponding to a 10 A movement of the B-chain N-terminal. The main determinant for the rate of B3 deamidation, as well as for the ratio between the two products formed, is the local conformational structure, which is highly influenced by various excipients and the physical state of the insulin. An amazing thermolysin-like, autoproteolytic cleavage of the A-chain takes place in rhombohedral insulin crystals, mediated by a concerted catalytic action by several, inter-hexameric functional groups and Zn2+. Intermolecular, covalent cross-linking of insulin molecules occurs via several mechanisms. The most prominent type of mechanism is aminolysis by the N-terminals, leading to isopeptide linkages with the A-chain side-chain amides of residues GlnA15, AsnA18 and AsnA21. The same type of reaction also leads to covalent cross-linking of the N-terminal in protamine with insulin. Disulfide exchange reactions, initiated by lysis of the A7-B7 disulfide bridge, lead mainly to formation of covalent oligo- and polymers. Activation energy (Ea) for the neutral deamidation and the aminolysis reactions was found to be 80 and 119 KJ/mol, respectively.
Remote Effects in Macrolide Formation through Ring-Forming Olefin Metathesis:  An Application to the Synthesis of Fully Active Epothilone Congeners (1997)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTRemote Effects in Macrolide Formation through Ring-Forming Olefin Metathesis: An Application to the Synthesis of Fully Active Epothilone CongenersDongfang Meng, Dai-Shi Su, Aaron Balog, Peter Bertinato, Erik J. Sorensen, Samuel J. Danishefsky, Yu-Huang Zheng, Ting-Chao Chou, Lifeng He, and Susan B. HorwitzView Author Information Laboratories for Bioorganic Chemistry and Biochemical Pharmacology Sloan-Kettering Institute for Cancer Research 1275 York Avenue, New York, New York 10021 Department of Molecular Pharmacology The Albert Einstein College of Medicine Bronx, New York 10461Cite this: J. Am. Chem. Soc. 1997, 119, 11, 2733–2734Publication Date (Web):March 19, 1997Publication History Received12 December 1996Published online19 March 1997Published inissue 1 March 1997https://pubs.acs.org/doi/10.1021/ja964275jhttps://doi.org/10.1021/ja964275jrapid-communicationACS PublicationsCopyright © 1997 American Chemical SocietyRequest reuse permissionsArticle Views1032Altmetric-Citations149LEARN 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-AlertscloseSupporting Info (2)»Supporting Information Supporting Information SUBJECTS:Antineoplastic agents,Chemical synthesis,Cyclization,Olefin metathesis,Organic synthesis Get e-Alerts