gebhart/patrepeval huggingface dataset:
Detection of Methicillin-Resistant Staphylococcus aureus (MRSA) in Blood with the EVIGENE MRSA Detection Kit (2003)

A total of 200 blood cultures containing putative staphylococci were analyzed by a commercial gene probe hybridization assay (EVIGENE; Statens Serum Institut, Copenhagen, Denmark), and 18 were identified as methicillin-resistant Staphylococcus aureus (MRSA) positive. Of these, 17 were positive by PCR and 16 were positive by culture. Detailed analysis of the discrepant results showed that the EVIGENE kit allowed specific identification of MRSA in blood cultures without any of the drawbacks associated with PCR.
Experience With Bevacizumab in the Management of Epithelial Ovarian Cancer (2007)

Müllerian duct adenocarcinomas, in particular epithelial ovarian cancers, continue to represent a major source of female cancer-related morbidity and mortality, despite advances in surgical management and innovations in cytotoxic chemotherapy. Angiogenesis-targeted therapy seems to be appropriate for exploration in these disease processes based on a wealth of evidence from preclinical and molecular epidemiology studies. Bevacizumab is a prototypical agent neutralizing vascular endothelial growth factor (VEGF), a critical angiogenic promoter related to tumor progression, malignant effusions, and prognosis in ovarian cancer. Phase II trials have demonstrated the activity of bevacizumab as a single agent and in combination with other modalities such as low-dose metronomic cyclophosphamide. Historical studies have supported these observations. Unique toxicities have been ascribed to the administration of bevacizumab and other anti-VEGF molecules for patients with this disease and other solid tumors. Although most of these toxicities (such as proteinuria, hypertension, and bleeding) are generally mild, and are either self-limiting or controllable, other adverse effects, though uncommon, may be serious (these include arterial thromboembolism, wound healing complications, and GI perforation or fistulae). Phase III trials are now in progress to determine the role of this drug in primary therapy as an adjunct to platinum-taxane chemotherapy. This article reviews the background and rationale for anti-VEGF therapy of ovarian cancer, summarizes efficacy and safety data from phase II trials and historical studies of bevacizumab in this disease, introduces the implementation of bevacizumab in phase III front-line trials, examines controversial aspects related to anti-VEGF therapy, and proposes future directions regarding bevacizumab and other angiogenic growth factor-targeted therapeutics.
Protein sequence alignments: a strategy for the hierarchical analysis of residue conservation (1993)

An algorithm is described for the systematic characterization of the physico-chemical properties seen at each position in a multiple protein sequence alignment. The new algorithm allows questions important in the design of mutagenesis experiments to be quickly answered since positions in the alignment that show unusual or interesting residue substitution patterns may be rapidly identified. The strategy is based on a flexible set-based description of amino acid properties, which is used to define the conservation between any group of amino acids. Sequences in the alignment are gathered into subgroups on the basis of sequence similarity, functional, evolutionary or other criteria. All pairs of subgroups are then compared to highlight positions that confer the unique features of each subgroup. The algorithm is encoded in the computer program AMAS (Analysis of Multiply Aligned Sequences) which provides a textual summary of the analysis and an annotated (boxed, shaded and/or coloured) multiple sequence alignment. The algorithm is illustrated by application to an alignment of 67 SH2 domains where patterns of conserved hydrophobic residues that constitute the protein core are highlighted. The analysis of charge conservation across annexin domains identifies the locations at which conserved charges change sign. The algorithm simplifies the analysis of multiple sequence data by condensing the mass of information present, and thus allows the rapid identification of substitutions of structural and functional importance.
Long-Term Effects of Pravastatin on Plasma Concentration of C-reactive Protein (1999)

Among survivors of myocardial infarction on standard therapy plus placebo, CRP levels tended to increase over 5 years of follow-up. In contrast, randomization to pravastatin resulted in significant reductions in this inflammatory marker that were not related to the magnitude of lipid alterations observed. Thus, these data further support the potential for nonlipid effects of this agent.
Human Ribosomal RNA Genes: Orientation of the Tandem Array and Conservation of the 5′ End (1988)

The multiple copies of the human ribosomal RNA genes (rDNA) are arranged as tandem repeat clusters that map to the middle of the short arms of chromosomes 13, 14, 15, 21, and 22. Concerted evolution of the gene family is thought to be mediated by interchromosomal recombination between rDNA repeat units, but such events would also result in conservation of the sequences distal to the rDNA on these five pairs of chromosomes. To test this possibility, a DNA fragment spanning the junction between rDNA and distal flanking sequence has been cloned and characterized. Restriction maps, sequence data, and gene mapping studies demonstrate that (i) the rRNA genes are transcribed in a telomere-to-centromere direction, (ii) the 5' end of the cluster and the adjacent non-rDNA sequences are conserved on the five pairs of chromosomes, and (iii) the 5' end of the cluster is positioned about 3.7 kb upstream from the transcription initiation site of the first repeat unit. The data support a model of concerted evolution by interchromosomal recombination.
A molecular analysis of mouse development from 8 to 10 dayspost coitumdetects changes only in embryonic globin expression (1987)

The pattern of protein synthesis in 8-, 9- and 10-day post coitum (p.c.) mouse embryos was examined by 2-D gel electrophoresis of [35S]methionine-labelled proteins. Of the 600-800 polypeptides detected only one, a 14 X 10(3) Mr (14K) protein, was found to accumulate over this period. To isolate cDNA clones that potentially encode this protein, 32P-labelled cDNA was synthesized from 9 and 10 days p.c. embryo poly(A) +RNA, and used for the differential screening of an 8.5-day p.c. mouse embryo cDNA library cloned in lambda gt10. Six clones that hybridized strongly to the 10-day probe were purified and their inserts subcloned into plasmid vectors. Cross hybridization and restriction mapping of these inserts indicate that they fall into four distinct groups. Each of these hybridize with transcripts of approximately 600 nucleotides, which accumulate in the embryo from 9 to 10 days p.c. Expression was barely detectable in adult tissues and restricted to liver and spleen. Expression of one of these clones, 10.1, was examined by in situ hybridization of 35S-labelled RNA probes to 8.5-12.5 day p.c. embryo sections. Strong hybridization was observed in yolk sac blood islands, fetal liver and embryonic erythrocytes, suggesting that 10.1A encodes an erythrocyte-specific protein. DNA sequence analysis indicates that the four classes of cDNA were derived from transcripts of the alpha 1, zeta, beta h1 and epsilon globin genes. Labelling of 10-day p.c. erythrocyte proteins with [35S]methionine, followed by 2-D gel electrophoresis, clearly demonstrates that the most abundant polypeptide migrates to the same position as the 14K protein which accumulates from 8 to 10 days p.c. Thus the only abundant transcripts and corresponding proteins that change over a period of profound morphogenetic change correspond to globins of the newly established blood system.
T-DNA OF THE AGROBACTERIUM TI AND RI PLASMIDS (1982)

The study of T-DNA transmission from Agrobacterium Ti or Ri plasmid into the genomes of higher plant cells has revealed much about the consequences of transformation. It is now clear that the transformed phenotype is caused by hormonal changes produced directly or indirectly by T-DNA genes. The opine synthases are enzymes encoded in T-DNA that function in the plant cell. Our level of understanding of T-DNA-encoded functions is already sufficient to reveal clear and feasible ways to exploit T-DNA as a gene vector. What remains to challenge the crown gall investigator are many questions of fundamental importance: What is the mechanism of the seemingly illegitimate recombination between T-DNA and plant DNA, and is this process catalyzed by bacterial or host plant enzymes, or both? Do T-DNA genes encode enzymes that catalyze biosynthesis of auxin- and cytokinin-active substances? What gene in T-DNA confers immunity to A. tumefaciens, and what is its mode of action? Does T-DNA insert into random or specific sites in the host plant genome? Did T-DNA derive from plant genetic information or has prokaryotic DNA arrived at functional eukaryotic gene structure by convergent evolution? Although there is keen interest in T-DNA as a vector for genetic engineering, it holds equal interest as a unique interface between the biology of prokaryotes and eukaryotes.
Modulation of Adipose Tissue Development by Pharmacological Inhibition of PAI-1 (2006)

Our results indicate that a small molecule inactivator of PAI-1 can neutralize glucose-stimulated increases in PAI-1 in human preadipocyte cultures, reduce adipocyte differentiation, and prevent the development of diet-induced obesity. These data suggest the pharmacological inhibition of PAI-1 could be beneficial in diseases associated with expansion of adipose tissue mass.
AN INTELLIGENT AGENT FOR WEB ADVERTISEMENTS (2002)

The rapid growth of Internet users attracts advertisers to post their advertisements in Internet. The probabilistic selection algorithm was not satisfactory; while other advertising agents are unable to guarantee the quality due to insufficient and unstable user information. This paper describes a new advertising agent based on user information. The users' interests are discovered by the Order Pattern Mining algorithm first, then the Gaussian curve transformation is applied to represent their profiles. For the advertisements, we use the keywords from different categories to construct the advertisement profiles as Gaussian curves also. This allows us to select advertisements based on the intersections of the different profiles according to users' preferences in an effective and efficient mechanism. A prototype of the Intelligent Advertising Agent has been developed with Java and Oracle. From our evaluations, we observed that about 70% of the test cases are successful in making predictions which generated the most favorable category that the users are interested.
Macromolecular carbonyls in human stratum corneum: a biomarker for environmental oxidant exposure? (1998)

The presence of stratum corneum carbonyls may serve as an intrinsic dosimeter for environmental oxidative damage to skin. To investigate the accumulation of carbonyls in human stratum corneum, skin was tape-stripped, then tapes were sequentially incubated with 2,4-dinitrophenyl hydrazine (DNPH), rat anti-DNP, mouse anti-rat IgG conjugated with alkaline phosphatase, p-nitrophenyl phosphate and absorbance (405 nm) measured and carbonyls estimated. Stratum corneum exposed in vitro to oxidants: hypochlorous acid (1, 10, 100 mM), ozone (0, 1, 5, 10 ppm for 2 h) or UV light (280-400 nm; 0, 4, 88, or 24 J/cm2) contained increased carbonyls. Furthermore, stratum corneum carbonyls were elevated in tanned compared with untanned sites: dorsal hand (0.43 +/- 0.06 nmol/cm2) vs. lower arm (0.32 +/- 0.04, mean +/- S.E.M., n = 11; P < 0.003) and lower back (0.26 +/- 0.02) vs. buttock (0.21 +/- 0.02; n = 6, P < 0.01) indicating in vivo oxidative damage.
Rapid Identification of Emerging Pathogens: Coronavirus (2005)

We describe a new approach for infectious disease surveillance that facilitates rapid identification of known and emerging pathogens. The process uses broad-range polymerase chain reaction (PCR) to amplify nucleic acid targets from large groupings of organisms, electrospray ionization mass spectrometry for accurate mass measurements of PCR products, and base composition signature analysis to identify organisms in a sample. We demonstrate this principle by using 14 isolates of 9 diverse Coronavirus spp., including the severe acute respiratory syndrome-associated coronavirus (SARS-CoV). We show that this method could identify and distinguish between SARS and other known CoV, including the human CoV 229E and OC43, individually and in a mixture of all 3 human viruses. The sensitivity of detection, measured by using titered SARS-CoV spiked into human serum, was approximate, equals1 PFU/mL. This approach, applicable to the surveillance of bacterial, viral, fungal, or protozoal pathogens, is capable of automated analysis of >900 PCR reactions per day.
Sharing of worldwide distributed carbohydrate-related digital resources: online connection of the Bacterial Carbohydrate Structure DataBase and GLYCOSCIENCES.de (2007)

Functional glycomics, the scientific attempt to identify and assign functions to all glycan molecules synthesized by an organism, is an emerging field of science. In recent years, several databases have been started, all aiming to support deciphering the biological function of carbohydrates. However, diverse encoding and storage schemes are in use amongst these databases, significantly hampering the interchange of data. The mutual online access between the Bacterial Carbohydrate Structure DataBase (BCSDB) and the GLYCOSCIENCES.de portal, as a first reported attempt of a structure-based direct interconnection of two glyco-related databases is described. In this approach, users have to learn only one interface, will always have access to the latest data of both services, and will have the results of both searches presented in a consistent way. The establishment of this connection helped to find shortcomings and inconsistencies in the database design and functionality related to underlying data concepts and structural representations. For the maintenance of the databases, duplication of work can be easily avoided, and will hopefully lead to a better worldwide acceptance of both services within the community of glycoscienists. BCSDB is available at http://www.glyco.ac.ru/bcsdb/ and the GLYCOSCIENCES.de portal at http://www.glycosciences.de/.
Characterization of the blood group Kell (K1) antigen with a human monoclonal antibody (1989)

A human monoclonal anti-Kell (K1) antibody secreted by an Epstein-Barr virus (EBV)-transformed B-cell line was used for binding studies and immunopurification of the K1 blood group antigen. The 125I-labeled antibody bound to 4 to 5 x 10(3) and 2.5 to 3 x 10(3) antigenic sites on K1K1 and K1K2 erythrocytes, respectively, with an affinity constant of 5 x 10(8) mol/L-1. Immunoprecipitation analysis showed that the K1 antigen is carried by a 93 Kd glycoprotein containing several cysteine residues, and approximately six N-glycosidically linked sugar chains but no detectable O-linked sugar. A minor labeled component of 32 Kd was also immunoprecipitated from K1K1 RBCs but the 93- and 32-Kd components were absent from K2K2 and Kell null erythrocytes. Under nonreducing conditions, three bands were detected at 200 (weak), 120, and 93 Kd. We suggest that the 120-Kd component represents a heterodimer of the 93- and 32-Kd proteins covalently linked by disulfide bridge(s). The 93-Kd glycoprotein is a transmembrane component which interacts with the membrane skeleton but is distinct from band 3 as shown by one-dimensional peptide mapping. The site density of K1 antigen blood group on Gerbich-negative RBCs (Ge:-2,-3) was threefold lower than on K1K1 erythrocytes, but the qualitative properties of the 93-Kd component were not modified.
Alpha-toxin of Staphylococcus aureus. (1991)

Alpha-toxin, the major cytotoxic agent elaborated by Staphylococcus aureus, was the first bacterial exotoxin to be identified as a pore former. The protein is secreted as a single-chain, water-soluble molecule of Mr 33,000. At low concentrations (less than 100 nM), the toxin binds to as yet unidentified, high-affinity acceptor sites that have been detected on a variety of cells including rabbit erythrocytes, human platelets, monocytes and endothelial cells. At high concentrations, the toxin additionally binds via nonspecific absorption to lipid bilayers; it can thus damage both cells lacking significant numbers of the acceptor and protein-free artificial lipid bilayers. Membrane damage occurs in both cases after membrane-bound toxin molecules collide via lateral diffusion to form ring-structured hexamers. The latter insert spontaneously into the lipid bilayer to form discrete transmembrane pores of effective diameter 1 to 2 nm. A hypothetical model is advanced in which the pore is lined by amphiphilic beta-sheets, one surface of which interacts with lipids whereas the other repels apolar membrane constitutents to force open an aqueous passage. The detrimental effects of alpha-toxin are due not only to the death of susceptible targets, but also to the presence of secondary cellular reactions that can be triggered via Ca2+ influx through the pores. Well-studied phenomena include the stimulation of arachidonic acid metabolism, triggering of granule exocytosis, and contractile dysfunction. Such processes cause profound long-range disturbances such as development of pulmonary edema and promotion of blood coagulation.(ABSTRACT TRUNCATED AT 250 WORDS)
The nicking endonuclease N.BstNBI is closely related to Type IIs restriction endonucleases MlyI and PleI (2001)

N.BstNBI is a nicking endonuclease that recognizes the sequence GAGTC and nicks the top strand preferentially. The Type IIs restriction endonucleases PleI and MlyI also recognize GAGTC, but cleave both DNA strands. Cloning and sequencing the genes encoding each of these three endonucleases discloses significant sequence similarities. Mutagenesis studies reveal a conserved set of catalytic residues among the three endonucleases, suggesting that they are closely related to each other. Furthermore, PleI and MlyI contain a single active site for DNA cleavage. The results from cleavage assays show that the reactions catalyzed by PleI and MlyI are sequential two step processes. The double-stranded DNA is first nicked on one DNA strand and then further cleaved on the second strand to form linear DNA. Gel filtration analysis shows that MlyI dimerizes in the presence of a cognate DNA and Ca(2+) whereas N.BstNBI remains a monomer, implicating dimerization as a requisite for the second strand cleavage. We suggest that N.BstNBI, MlyI and PleI diverged from a common ancestor and propose that N.BstNBI differs from MlyI and PleI in having an extremely limited second strand cleavage activity, resulting in a site-specific nicking endonuclease.
Parabacteroides chartae sp. nov., an obligately anaerobic species from wastewater of a paper mill (2011)

A bacterial strain, designated NS31-3(T), was isolated from the wastewater of a paper mill. Cells of the isolate were obligately anaerobic, non-pigmented, non-motile, Gram-negative, short rods (0.7-1.0 × 1.4-2.5 µm). The isolate was able to grow on media containing 20% bile salts. API 20A tests showed that acid was produced from glucose, lactose, sucrose, maltose, D-xylose, L-arabinose, cellobiose, D-mannose, D-melezitose, D-raffinose, D-trehalose, D-mannitol, salicin and D-sorbitol. The main fermentation products from PYG broth were lactic acid, propionic acid, formic acid and acetic acid. Chemotaxonomic analysis showed that the major fatty acids were anteiso-C(15:0), C(15:0) and iso-C(17:0) 3-OH and the predominant respiratory quinones were MK-9 and MK-10. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain NS31-3(T) was related to members of genus Parabacteroides (91.2-93.2% sequence similarity); the isolate had the closest affinity with Parabacteroides merdae JCM 9497(T). The G+C content of the genomic DNA was 37.2 mol%. On the basis of phenotypic, chemotaxonomic and phylogenetic analysis, strain NS31-3(T) represents a novel species of the genus Parabacteroides, for which the name Parabacteroides chartae sp. nov. is proposed. The type strain is NS31-3(T) (=JCM 17797(T) =DSM 24967(T)).
Content Adaptive Representations of Omnidirectional Videos for Cinematic Virtual Reality (2015)

Cinematic virtual reality provides an immersive visual experience by presenting omnidirectional videos of real-world scenes. A key challenge is to develop efficient representations of omnidirectional videos in order to maximize coding efficiency under resource constraints, specifically, number of samples and bitrate. We formulate the choice of representation as a multi-dimensional, multiple-choice knapsack problem and show that the resulting representations adapt well to varying content. We also show that separation of the sampling and bit allocation constraints leads to a computationally efficient solution using Lagrangian optimization with only minor performance loss. Results across images and videos show significant coding gains over standard representations.
IP protection of DSP algorithms for system on chip implementation (2000)

Silicon technology has now advanced to the point that there is a serious mismatch in the time taken to design advanced silicon-based systems and the time to market for any new product or product derivative. To obviate this delay, a new paradigm is emerging based on intellectual property (IP) exchange, where designers and differing companies share subsystems (virtual cores) between themselves to reduce design time to acceptable levels. To this end, over 150 companies including all the major players formed the Virtual Socket Interface Alliance in March 1997. The protection of IP has become a serious issue as intercompany subsystem design exchange becomes more commonplace. This paper presents new techniques to protect the IP of virtual cores that implement digital signal processing (DSP) algorithms. The approach involves embedding codewords into the design of fundamental signal processing algorithms such as digital filters and the DFT in such a way that proof of authorship can be retained, and, if required, easily identified. The techniques discussed can be adapted to protect other fundamental DSP algorithms such as convolution and correlation. The protection of IP via watermarking techniques is increasingly being applied at all levels of design. It is particularly advantageous if such techniques are applied at the highest abstraction levels in the design flow, and if such techniques are applied at basic algorithm level, they become very difficult to detect at lower levels of system design.