gebhart/patrepeval huggingface dataset:
Gene Sequence and Mapping Data from Marek's Disease Virus and Herpesvirus of Turkeys: Implications for Herpesvirus Classification (1988)

Purified DNAs from Marek's disease virus (MDV) and the herpesvirus of turkeys (HVT) were randomly sheared and cloned into the M13 bacteriophage. Two-hundred and ten MDV and 130 HVT clones were sequenced to give representative samples of the genome sequences. The predicted amino acid sequences from these gammaherpes-viruses were compared to known sequences from other herpesviruses using computer analysis. Thirty-five MDV and 24 HVT genes were identified by comparison with varicella-zoster virus (VZV), an alphaherpesvirus. However, only 14 MDV and seven HVT genes, giving generally lower homology scores, were found by comparison with Epstein-Barr virus (EBV), a gammaherpesvirus, indicating that MDV and HVT sequences bear greater similarity to VZV than to EBV sequences. A number of sequences were mapped by hybridizing labelled M13 clones to Southern blots of restriction fragments of MDV or HVT DNA. The results were consistent with the MDV and HVT genomes being collinear with VZV.
Female Sex Hormones Regulate Macrophage Function After Trauma-Hemorrhage and Prevent Increased Death Rate From Subsequent Sepsis (2002)

These findings suggest that female sex hormones play a critical role in maintaining immune responses after trauma-hemorrhage by suppressing the elaboration of tumor necrosis factor-alpha and prevent the increased lethality from subsequent sepsis. Thus, female sex hormones may be a useful adjunct in preventing trauma-induced immunodepression and increased susceptibility to subsequent sepsis.
Cloning and expression of a cDNA encoding homospermidine synthase from Senecio vulgaris (Asteraceae) in Escherichia coli (1999)

The enzyme homospermidine synthase catalyzes the NAD+-dependent conversion of 2 mol putrescine into homospermidine. Instead of putrescine, spermidine can substitute for the first putrescine moiety in plants, in which case diaminopropane instead of ammonia is released. The enzyme facilitates the formation of the 'uncommon' polyamine homospermidine which is an important precursor in the biosynthesis of pyrrolizidine alkaloids. The first plant homospermidine synthase was purified to apparent chemical homogenity from the root tissue culture Senecio vernalis (Asteraceae) (Böttcher et al. 1994, Can. J. Chem. 72, 80-85; Ober 1997, Dissertation). Four endopeptidase LysC fragments were sequenced from the purified protein. With the aid of degenerate primers against these peptides, a cDNA encoding homospermidine synthase was now cloned and characterized from Senecio vulgaris. The nucleotide sequence of the cloned cDNA revealed an open reading frame of 1155-base pairs containing 385 amino acids with a predicted Mr of 44500. GenBank research revealed that the deduced amino acid sequence shows 59% identity to human deoxyhypusine synthase. The homospermidine synthase encoding cDNA was subcloned into the expression vector pet15b and overexpressed in E. coli. The recombinant enzyme formed upon expression catalyzed homospermidine synthesis.
Chemokine receptor CCR2 is expressed by human multiple myeloma cells and mediates migration to bone marrow stromal cell-produced monocyte chemotactic proteins MCP-1, -2 and -3 (2003)

The restricted bone marrow (BM) localisation of multiple myeloma (MM) cells most likely results from a specific homing influenced by chemotactic factors, combined with the proper signals for growth and survival provided by the BM microenvironment. In analogy to the migration and homing of normal lymphocytes, one can hypothesise that the BM homing of MM cells is mediated by a multistep process, involving the concerted action of adhesion molecules and chemokines. In this study, we report that primary MM cells and myeloma derived cell lines (Karpas, LP-1 and MM5.1) express the chemokine receptor CCR2. In addition, we found that the monocyte chemotactic proteins (MCPs) MCP-1, -2 and -3, three chemokines acting as prominent ligands for CCR2, are produced by stromal cells, cultured from normal and MM BM samples. Conditioned medium (CM) from BM stromal cells, as well as MCP-1, -2 and -3, act as chemoattractants for human MM cells. Moreover, a blocking antibody against CCR2, as well as a combination of neutralizing antibodies against MCP-1, -2 and -3, significantly reduced the migration of human MM cells to BM stromal cell CM. The results obtained in this study indicate the involvement of CCR2 and the MCPs in the BM homing of human MM cells.
Efficacy and Antivascular Effects of EphA2 Reduction With an Agonistic Antibody in Ovarian Cancer (2006)

EA5 in combination with paclitaxel decreased tumor growth in an orthotopic ovarian cancer mouse model through antiangiogenic mechanisms associated with reduced levels of VEGF and phosphorylated Src. Humanized antibody constructs against EphA2 are worthy of future study.
Algorithms for self-synchronizing ciphers (2003)

Necessary conditions are determined for a self-synchronizing steam cipher algorithm to be secure. The stream cipher encryption hardware considered consists of a keystream generator, an exclusive-OR gate to combine the keystream and the binary coded message stream, and circuits to establish initial cryptographic synchronization. The security of the system is based on the use of secret cryptographic keys which must be transmitted to the receiver in advance over a secure route. It is shown that the algorithm (when expressed as a logic function) should be correlation-immune, permutation-immune, and nonlinear in its arguments. An example of a 125-stage 7th-order correlation-immune function is given, and its resistance to cryptanalysis is evaluated.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Cardioprotective Function of the Long Pentraxin PTX3 in Acute Myocardial Infarction (2008)

Thus, PTX3 plays a nonredundant, regulatory, cardioprotective role in acute myocardial infarction in mice. Our results suggest that modulation of the complement cascade contributes to the cardioprotective function of PTX3.
Mucin synthesis. I. Detection in canine submaxillary glands of an N-acetylglucosaminyltransferase which acts on mucin substrates. (1980)

Canine submaxillary gland microsomes have been shown to catalyze the following reaction: UDP-GlcNAc + Gal beta 1-3GalNAc-X leads to Gal beta 1-3(GlcNAc)GalNAc-X + UDP where X is porcine or ovine submaxillary mucin polypeptide or a low molecular weight substituent. This activity was shown by mixed substrate experiments to be different from two other previously described glycoprotein N-acetylglucosaminyltransferases acting on N-glycosyl oligosaccharides and is the first N-acetylglucosaminyltransferase shown to act on mucin substrates. The transferase-catalyzed reaction proceeds at 70 to 80% of the optimum rate in the absence of added divalent cation or in the presence of 10 mM EDTA. The enzyme appeared to be unstable at 37 degrees C, but the reaction rate remained constant for at least 2 h at 25 degrees C. The enzyme showed a pH optimum of 7.0 and was stimulated 4-fold by 0.125% Triton X-100. Methylation analysis of product formed either with mucin acceptor or Gal beta 1-3GalNAc-alpha-O-benzyl indicated GlcNAc transfer to either carbon 4 or carbon 6 of the GalNAc residue of the acceptors.
A Novel Kinetic Analysis to Calculate Nucleotide Affinity of Proofreading DNA Polymerases: (1995)

Amino acids Tyr254 and Tyr390 of phi 29 DNA polymerase belong to one of the most conserved regions in eukaryotic-type DNA polymerases. In this paper we report a mutational study of these two residues to address their role in nucleotide selection. This study was carried out by means of a new kinetic analysis that takes advantage of the competition between DNA polymerization and 3'-->5' exonuclease activity to measure the Km values for correct and incorrect nucleotides in steady-state conditions. This method is valid for any 3'-->5' exonuclease-containing DNA polymerase, without any restriction concerning catalytic rates of nucleotide incorporation. The results showed that the discrimination factor achieved by phi 29 DNA polymerase in the nucleotide binding step of DNA polymerization is 2.4 x 10(3), that is, a wrong nucleotide is bound with a 2.4 x 10(3)-fold lower affinity than the correct one. Mutants Y254F, Y390F, and Y390S showed discrimination values of 7.0 x 10(2), > 1.9 x 10(3), and 2.9 x 10(2), respectively. The reduced accuracy of nucleotide binding produced by mutations Y254F and Y390S lead us to propose that phi 29 DNA polymerase residues Tyr254 and Tyr390, highly conserved in eukaryotic-type DNA polymerases, are involved in nucleotide binding selection, thus playing a crucial role in the fidelity of DNA replication. Comparison of the discrimination factors of mutants Y390S and Y390F strongly suggests that the phenyl ring of Tyr390 is directly involved in checking base-pairing correctness of the incoming nucleotide.
In vitroandin vivocharacterization of A‐796260: a selective cannabinoid CB2receptor agonist exhibiting analgesic activity in rodent pain models (2007)

These results further confirm the therapeutic potential of CB2 receptor-selective agonists for the treatment of pain. In addition, they demonstrate that A-796260 may be a useful new pharmacological compound for further studying CB2 receptor pharmacology and for evaluating its role in the modulation of pain.
Efficient algorithms for local and global accessibility shading (1994)

This paper discusses the use of two different approaches for computing the “accessibility” of a surface. These metrics characterize how easily a surface may be touched by a spherical probe. The paper also presents various acceleration techniques for accessibility. The idea of surface accessibility is extended to include “global accessibility” which measures the ability of a spherical probe to enter a structure from outside as well as to fit locally on the surface. The visual effect of shading using accessibility is shown to resemble the patina on certain tarnished surfaces which have then been cleaned.
N'-Acyl and N'-nitroso pyridine alkaloids in alkaloid lines of burley tobacco during growth and air-curing (1989)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTN'-Acyl and N'-nitroso pyridine alkaloids in alkaloid lines of burley tobacco during growth and air-curingRoger A. Andersen, Pierce D. Fleming, Harold R. Burton, Thomas R. Hamilton-Kemp, and Tommy G. SuttonCite this: J. Agric. Food Chem. 1989, 37, 1, 44–50Publication Date (Print):January 1, 1989Publication History Published online1 May 2002Published inissue 1 January 1989https://pubs.acs.org/doi/10.1021/jf00085a011https://doi.org/10.1021/jf00085a011research-articleACS PublicationsRequest reuse permissionsArticle Views167Altmetric-Citations10LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Copper Binding to Rabbit Liver Metallothionein (1995)

Circular dichroism and ultraviolet absorption spectral data have been used to probe the binding mechanism for formation and the structure of the copper(I)-thiolate binding clusters in rabbit liver metallothionein during addition of Cu+ to aqueous solutions of Zn7-metallothionein 2 and Cd5Zn2-metallothionein 2. Mammalian metallothionein binds metals in two binding sites, namely the alpha and beta domains. Spectral data which probe the distribution of Cu(I) between the two binding domains clearly show that both the site of binding (alpha or beta), and the structures of the specific metal-thiolate clusters formed, are dependent on temperature and on the nature of the starting protein (either Zn7-metallothionein or Cd5Zn2-metallothionein). CD spectra acquired during the addition of Cu+ to Zn7-metallothionein show that Cu+ replace the bound Zn(II) in a domain-distributed manner with complete removal of the Zn(II) after addition of 12 Cu+. Spectral and metal analyses prove that a series of Cu(I)-metallothionein species are formed by a non-cooperative metal-binding mechanism with a continuum of Cu(I):metallothionein stoichiometries. Observation of a series of spectral saturation points signal the formation of distinct optically active Cu(I)-thiolate structures for the Cu9Zn2-metallothionein, Cu12-metallothionein, and the Cu15-metallothionein species. These data very clearly show that for Cu(I) binding to Zn7-metallothionein, there are several key Cu(I):metallothionein stoichiometric ratios, and not just the single value of 12. The CD spectra up to the Cu12-metallothionein species are defined by bands located at 255(+) nm and 280(-) nm. Interpretation of the changes in the CD and ultraviolet absorption spectral data recorded between 3 degrees C and 52 degrees C as Cu+ is added to Zn-metallothionein show that copper-thiolate cluster formation is strongly temperature dependent. These changes in spectral properties are interpreted in terms of kinetic versus thermodynamic control of the metal-binding pathways as Cu+ binds to the protein. At low temperatures (3 degrees C and 10 degrees C) the spectral data indicate a kinetically controlled mechanism whereby an activation barrier inhibits formation of ordered copper-thiolate structures until formation of Cu12-metallothionein. At higher temperatures (> 30 degrees C) the activation barrier is overcome, allowing formation of new Cu(I)-thiolate clusters with unique spectral properties, especially at the Cu9Zn2-metallothionein point. The CD spectra also show that a Cu15-metallothionein species with a well-defined, three-dimensional structure forms at all temperatures, characterized by a band near 335 nm, indicating the presence of diagonal Cu(I).(ABSTRACT TRUNCATED AT 250 WORDS)
Prediction of Chemical Carcinogenicity in Rodents from in Vitro Genetic Toxicity Assays (1987)

Four widely used in vitro assays for genetic toxicity were evaluated for their ability to predict the carcinogenicity of selected chemicals in rodents. These assays were mutagenesis in Salmonella and mouse lymphoma cells and chromosome aberrations and sister chromatid exchanges in Chinese hamster ovary cells. Seventy-three chemicals recently tested in 2-year carcinogenicity studies conducted by the National Cancer Institute and the National Toxicology Program were used in this evaluation. Test results from the four in vitro assays did not show significant differences in individual concordance with the rodent carcinogenicity results; the concordance of each assay was approximately 60 percent. Within the limits of this study there was no evidence of complementarity among the four assays, and no battery of tests constructed from these assays improved substantially on the overall performance of the Salmonella assay. The in vitro assays which represented a range of three cell types and four end points did show substantial agreement among themselves, indicating that chemicals positive in one in vitro assay tended to be positive in the other in vitro assays.
Risks and complications of prolonged parenteral antibiotic treatment in children with acute osteoarticular infections. (2003)

This study aimed at assessing the prevalence of complications encountered during prolonged intravenous antibiotic (AB) therapy when treating acute osteoarticular (OA) infections in children. We reviewed retrospectively 60 paediatric patients treated in our department between 1988 and 1998 for acute osteoarticular infections (27 with acute haematogenous osteomyelitis, 25 with septic arthritis and 8 with septic osteoarthritis). C-reactive protein, erythrocyte sedimentation rate (ESR), and full blood count were monitored during the entire treatment. Body temperature was recorded three times per day until the fever subsided, and then daily during the remaining hospitalisation. Finally, we listed complications related to the antibiotic therapy and those linked to the presence of a venous catheter. Seventeen allergic reactions to drugs were recorded during the intravenous AB therapy. This complications occurred on average after 24.4 +/- 4.4 days of treatment. The clinical manifestations most often encountered were a delayed rise in temperature and cutaneous symptoms. Blood tests showed an isolated increase in the ESR and eosinophilia (> 1000 eosinophils/ml). Four venous catheters had to be removed, in two cases owing to their obstruction and in two cases owing to an infection. Prolonged intravenous AB therapy is not without complications due to its duration and its mode of administration. Drug allergies to AB constitute a major complication of the treatment. They may render the treatment of subsequent infections problematic and expose these patients to major allergic reactions if they accidentally encounter the molecule incriminated. Moreover, the anaesthetics required to insert a central venous catheter and the need to leave it in place for a prolonged duration constitute another source of potential complications. The duration of i.v. AB therapy could therefore be shortened if the clinical and biological evolution is favourable and the pathogen is identified.
Medical Management of Antimicrobial‐Associated Diarrhea and Colitis (1982)

Gastrointestinal complications, including diarrhea, may occur with virtually all antimicrobial agents. Such diarrhea may represent either a common, nonspecific adverse effect, or it may be one of the manifestations of antimicrobial-associated colitis (AAC), a potentially fatal complication. Clostridium difficile and a cytotoxin neutralized by Clostridium sordellii antitoxin has been isolated from the stools of nearly all patients with antibiotic-associated pseudomembranous colitis, many patients with AAC, and approximately 20% of those with antimicrobial-induced diarrhea. Demonstration that C. difficile is responsible for cytotoxin production has allowed for specific therapy for these disorders. General treatment measures include discontinuation of the causative antimicrobial agent(s), bowel rest, and supportive care with fluids, electrolytes and colloids, if necessary. Antiperistaltic agents and corticosteroids are not recommended. Various antimicrobials demonstrate potential efficacy in treating AAC in humans. Oral vancomycin is the most widely tested and is currently the treatment of choice. It achieves high concentrations in the feces and is very active against C. difficile in doses of 125-500 mg by mouth every six hours. Other potentially useful but inadequately tested antimicrobials include metronidazole (500 mg by mouth every eight hours) and bacitracin (25,000 units by mouth every six hours). Tetracycline has been employed with some success in nonspecific antibiotic-associated diarrhea, although it is as yet untested in humans with AAC and may induce diarrhea itself. Both miconazole and rifampin are highly effective against C. difficile in vitro but have not been evaluated in AAC. Anion-exchange resins bind the cytotoxin found in stools of patients with AAC. Cholestyramine has been used with variable response in oral doses of 4 g every six to eight hours. Since these resins may also bind vancomycin, resulting in lowered vancomycin concentrations in the stool, combination therapy should be used cautiously. With specific therapy directed against the toxin and aggressive supportive therapy, surgical intervention is rarely necessary. More recently, investigations have been directed at using bacterial preparations to suppress C. difficile by restoring the normal flora. The development of immunological agents (i.e., vaccines, toxoids, antitoxins) for the prevention or treatment of AAC would be a significant advance in therapy.
Men＇s health is evolving (2008)

Andrology (AJA ) 的亚洲杂志以快步正在成长并且由于王一飞教授， AJA 的主编，和 AJA 编辑职员的努力工作的领导在 andrology 的领域里成为领先的杂志之一。当时，它在芝加哥是 2006 的春天 AJA 的科学编辑丹金·伦女士首先在 Andrology (ASA ) 年度会议考虑在人的健康上出版一期特刊的第 31 美国协会走近我们。我们被邀请尊敬是为这期特刊的客人编辑。当 AJA 的编辑主任郑勤珠女士得出了细节并且在佛罗里达坦帕在第 32 ASA 年度会议会见了我们时，我们贡献者与许多讨论了潜在的话题。我们很高兴由国际性地公认的当局与贡献介绍优异文章的这期。
Altered Hippocampal Transcript Profile Accompanies an Age-Related Spatial Memory Deficit in Mice (2004)

We have carried out a global survey of age-related changes in mRNA levels in the C57BL/6NIA mouse hippocampus and found a difference in the hippocampal gene expression profile between 2-month-old young mice and 15-month-old middle-aged mice correlated with an age-related cognitive deficit in hippocampal-based explicit memory formation. Middle-aged mice displayed a mild but specific deficit in spatial memory in the Morris water maze. By using Affymetrix GeneChip microarrays, we found a distinct pattern of age-related change, consisting mostly of gene overexpression in the middle-aged mice, suggesting that the induction of negative regulators in the middle-aged hippocampus could be involved in impairment of learning. Interestingly, we report changes in transcript levels for genes that could affect synaptic plasticity. Those changes could be involved in the memory deficits we observed in the 15-month-old mice. In agreement with previous reports, we also found altered expression in genes related to inflammation, protein processing, and oxidative stress.
Natural Language Processing with Python (2009)

This book offers a highly accessible introduction to natural language processing, the field that supports a variety of language technologies, from predictive text and email filtering to automatic summarization and translation. With it, you'll learn how to write Python programs that work with large collections of unstructured text. You'll access richly annotated datasets using a comprehensive range of linguistic data structures, and you'll understand the main algorithms for analyzing the content and structure of written communication. Packed with examples and exercises, Natural Language Processing with Python will help you: Extract information from unstructured text, either to guess the topic or identify named entities Analyze linguistic structure in text, including parsing and semantic analysis Access popular linguistic databases, including WordNet and treebanks Integrate techniques drawn from fields as diverse as linguistics and artificial intelligence This book will help you gain practical skills in natural language processing using the Python programming language and the Natural Language Toolkit (NLTK) open source library. If you're interested in developing web applications, analyzing multilingual news sources, or documenting endangered languages -- or if you're simply curious to have a programmer's perspective on how human language works -- you'll find Natural Language Processing with Python both fascinating and immensely useful.