gebhart/patrepeval huggingface dataset:
Second human protein with homology to the Escherichia coli abasic endonuclease exonuclease III (2000)

There are two major apurinic/apyrimidinic (AP) endonuclease/3′-diesterase families designated after the Escherichia coli proteins exonuclease III (ExoIII) and endonuclease IV (EndoIV). These repair proteins function to excise mutagenic and cytotoxic AP sites or 3′-phosphate/phosphoglycolate groups from DNA. In mammals, the predominant repair endonuclease is Ape1, a homolog of ExoIII, whereas a mammalian homolog to EndoIV has not been identified to date. We have identified a human protein termed Ape2 that represents a subclass of the ExoIII family (exhibiting highest similarity to the Saccharomyces cerevisiae ETH1/APN2 gene product) and maintains many of the essential functional residues of the ExoIII-like proteins. The human protein is 518 amino acids with a predicted molecular mass of 57.3 kDa and a pI of 8.65. Unlike Ape1, this protein exhibited only weak ability to complement the repair defects of AP endonuclease/3′-repair-defective bacteria and yeast. Similarly, a weak, but specific, DNA-binding and incision activity for abasic site-containing substrates was observed with partially purified Ape2 protein. APE2 is located on the X chromosome at position p11.21 and consists of six exons. The transcript for APE2 is ubiquitously expressed, suggesting an important function for the encoded protein. An Ape2 green fluorescent fusion protein localized predominantly to the nucleus of HeLa cells, indicating a nuclear function; this localization was dependent on the C-terminal domain. We discuss our results in the context of the evolutionary conservation of the AP endonuclease families and their divergent activities and biological contributions. Environ. Mol. Mutagen. Environ. Mol. Mutagen. 36:312–324, 2000. Published 2000 Wiley-Liss, Inc.
Expression and activation of α<sub>v</sub>β<sub>3</sub> integrins by SDF‐1/CXC12 increases the aggressiveness of prostate cancer cells (2006)

The transition from a locally invasive phenotype to a metastatic phenotype may be primed by the elevated expression of alpha(v)beta(3) receptors. Activation and increased expression of alpha(v)beta(3) within SDF-1-rich organs may participate in metastatic localization.
Acetaminophen plasma level after oral administration in liver cirrhotic patients suffering from schistosomal infection. (1996)

Hepatosplenic schistosomal infection is a common parasitic liver disease in Egypt, resulting in the formation of granuloma followed by fibrosis which leads to the chronic liver disease. Plasma level of acetaminophen (AAP) and its glucuronide and sulfate metabolites after oral administration at a dose of 1 g was determined in liver-cirrhotic younger (9 - 25 years old) and elderly patients (45 - 65 years old) suffering from schistosomal infection. These levels of AAP and its metabolites in patient groups were compared with those in corresponding healthy subject groups. Examinations for participants in the present study by physicians indicated the more severe cirrhosis in elderly patients compared to younger patients and the formation of collateral circulation and the renal insufficiency in elderly patients. The elimination of AAP from plasma was significantly prolonged in both younger and elderly patient groups. In elderly patients plasma concentration of AAP in early stage (before the time to reach Cmax) was significantly higher, indicating the partial avoidance of first-pass metabolism due to the formation of hepatic shunt pathway. Plasma concentration of AAP-glucuronide was greatly decreased in both patient groups, whereas no significant difference in the plasma concentration of AAP-sulfate compared to those in corresponding healthy subject groups. These results will suggest that with repeated dosing of AAP special care must be taken in schistosomal patients since the elimination of AAP from plasma is remarkably reduced.
Adversarial Ranking for Language Generation (2017)

Generative adversarial networks (GANs) have great successes on synthesizing data. However, the existing GANs restrict the discriminator to be a binary classifier, and thus limit their learning capacity for tasks that need to synthesize output with rich structures such as natural language descriptions. In this paper, we propose a novel generative adversarial network, RankGAN, for generating high-quality language descriptions. Rather than training the discriminator to learn and assign absolute binary predicate for individual data sample, the proposed RankGAN is able to analyze and rank a collection of human-written and machine-written sentences by giving a reference group. By viewing a set of data samples collectively and evaluating their quality through relative ranking scores, the discriminator is able to make better assessment which in turn helps to learn a better generator. The proposed RankGAN is optimized through the policy gradient technique. Experimental results on multiple public datasets clearly demonstrate the effectiveness of the proposed approach.
Changes in the expression of annexin A5 gene during in vitro chondrocyte differentiation: Influence of cell attachment (2001)

Several lines of evidence indicate that annexin A5, a membrane-associated protein with calcium-channel activity, plays a key role in cartilage calcification during endochondral ossification. As a major constituent of cartilage matrix vesicles, which are released from microvilli of hypertrophic chondrocytes, it is involved in calcium uptake necessary for the initial stages of cartilage calcification. Little is known, however, concerning transcriptional regulation of the annexin A5 gene during chondrocyte differentiation. Here, we report on changes in annexin A5 expression by measuring mRNA and protein levels during in vitro differentiation of chick sternal chondrocytes to the hypertrophic phenotype. Terminal differentiation of mature sternal chondrocytes was achieved in the presence of sodium ascorbate in high-density cultures growing either in monolayer or over agarose as cell aggregates. Differentiation of chondrocytes to hypertrophic cells was followed by morphological analysis and by the onset of type X collagen expression. High expression levels of annexin A5 mRNA were detected in chondrocytes freshly isolated from the sterna by enzymatic digestion and subsequently in cells growing in monolayer, but annexin A5 gene transcription was rapidly downregulated when cells were grown in suspension as aggregates over agarose. However, protein levels did not decrease probably due to its low turnover rate. In suspension culture, annexin A5 mRNA reappeared after 3 weeks concomitantly with segregation of the aggregates into single cells and onset of chondrocyte hypertrophy. The downregulation of annexin A5 expression in cells growing as matrix-rich aggregates was reverted when extracellular matrix components were removed and cells were reseeded onto tissue culture plastic, suggesting that cell spreading, formation of focal contacts and stress fibers stimulated annexin A5 expression in proliferating as well as in hypertrophic chondrocytes.
Linking fast and slow positive feedback loops creates an optimal bistable switch in cell signaling (2007)

Interlinked positive feedback loops are frequently found in biological signaling pathways. It is intriguing to study the dynamics, functions, and robustness of these motifs. Using numerical simulations and theoretical analysis, here we explore the sensitiveness and robustness of positive feedback loops with various time scales. Both single and dual loops can behave as a bistable switch. We study the responses of five types of bistable switches to noisy stimuli. The noise-induced transitions between two states are discussed in detail by using energy landscape. The dual-time switch, consisting of interconnected fast and slow loops, is both sensitive to stimuli and resistant to fluctuations in stimulus. This provides a novel mechanism for creating optimal bistable switches and memory modules. Our results also suggest that the dual-time switch can act as a ubiquitous motif with sensitive robustness in biological systems.
Microwave Induced Pyrolysis of Bromine Contained Printed Circuit Board Wastes (2011)

Printed Circuit Board (PCBs) wastes are a typical kind of electronic wastes. The recycling and disposal of PCBs wastes have become an important issue. Thermal degradation via pyrolysis is considered to be a feasible disposal approach. The microwave induced pyrolysis of PCBs wastes was performed in a bench scale microwave reactor with a horizontal quartz tube. The effects of reaction conditions on the pyrolysis process and pyrolytic products were investigated under different microwave power, microwave heating time and the weight ratio of SiC to PCBs. The optimum microwave pyrolysis process conditions for disposal of PCBs were determined. The liquid and solid pyrolytic products were further analyzed. The composition and surface properties of solid pyrolytic product showed that the solid product mainly contained inorganic substance, such as Si, Ca, Mg, Al, Ti and their oxide compounds. The results of GC-MS analysis of liquid pyrolytic product showed that liquid pyrolytic product contained large amounts of compounds with aromatic structure, such as phenol, biphenyl A, etc. Some substance contains Br, N and O was also detected, such as ketone, hydroxybenzene, etc. The bromine in liquid product is related with the bromide fire retarding agent in PCBs. Phenol and biphenyl A were the main component in liquid pyrolytic product which came from the pyrolysis of epoxy resin.
A new signature scheme based on the DSA giving message recovery (1993)

In this paper we present a modification of the DSA which allows signatures with message recovery. The new public key signature scheme is then applied to create (a) an identity-based public key system without restrictions in trust and (b) a one-pass key exchange protocol with mutual authentication.
Prenatal pharmacotherapy rescues brain development in a Down’s syndrome mouse model (2013)

Intellectual impairment is a strongly disabling feature of Down's syndrome, a genetic disorder of high prevalence (1 in 700-1000 live births) caused by trisomy of chromosome 21. Accumulating evidence shows that widespread neurogenesis impairment is a major determinant of abnormal brain development and, hence, of intellectual disability in Down's syndrome. This defect is worsened by dendritic hypotrophy and connectivity alterations. Most of the pharmacotherapies designed to improve cognitive performance in Down's syndrome have been attempted in Down's syndrome mouse models during adult life stages. Yet, as neurogenesis is mainly a prenatal event, treatments aimed at correcting neurogenesis failure in Down's syndrome should be administered during pregnancy. Correction of neurogenesis during the very first stages of brain formation may, in turn, rescue improper brain wiring. The aim of our study was to establish whether it is possible to rescue the neurodevelopmental alterations that characterize the trisomic brain with a prenatal pharmacotherapy with fluoxetine, a drug that is able to restore post-natal hippocampal neurogenesis in the Ts65Dn mouse model of Down's syndrome. Pregnant Ts65Dn females were treated with fluoxetine from embryonic Day 10 until delivery. On post-natal Day 2 the pups received an injection of 5-bromo-2-deoxyuridine and were sacrificed after either 2 h or after 43 days (at the age of 45 days). Untreated 2-day-old Ts65Dn mice exhibited a severe neurogenesis reduction and hypocellularity throughout the forebrain (subventricular zone, subgranular zone, neocortex, striatum, thalamus and hypothalamus), midbrain (mesencephalon) and hindbrain (cerebellum and pons). In embryonically treated 2-day-old Ts65Dn mice, precursor proliferation and cellularity were fully restored throughout all brain regions. The recovery of proliferation potency and cellularity was still present in treated Ts65Dn 45-day-old mice. Moreover, embryonic treatment restored dendritic development, cortical and hippocampal synapse development and brain volume. Importantly, these effects were accompanied by recovery of behavioural performance. The cognitive deficits caused by Down's syndrome have long been considered irreversible. The current study provides novel evidence that a pharmacotherapy with fluoxetine during embryonic development is able to fully rescue the abnormal brain development and behavioural deficits that are typical of Down's syndrome. If the positive effects of fluoxetine on the brain of a mouse model are replicated in foetuses with Down's syndrome, fluoxetine, a drug usable in humans, may represent a breakthrough for the therapy of intellectual disability in Down's syndrome.
Metal Migration (Ag, Cu, Pb) in Encapsulated Modules and Time-to-Fail Model as a Function of the Environment and Package Properties (1982)

Metal migration occurs between biased lands and, under conditions conducive to electrocrystallization, causes dendritic growths and failure. A model, based on the physics of condensation, ionic migration and thermally activated mechanism, was verified with polymer-encapsulated modules (Ag lands) under accelerated conditions of temperature, humidity and voltage. The acceleration factors agree with the predictions. Additional results with Ag, Cu, Pb films showed that oxides and process contaminants constitute strong migration factors controlling passivation against the electrochemical process.
A novel reannotation strategy for dissecting DNA methylation patterns of human long intergenic non-coding RNAs in cancers (2014)

Despite growing consensus that long intergenic non-coding ribonucleic acids (lincRNAs) are modulators of cancer, the knowledge about the deoxyribonucleic acid (DNA) methylation patterns of lincRNAs in cancers remains limited. In this study, we constructed DNA methylation profiles for 4629 tumors and 705 normal tissue samples from 20 different types of human cancer by reannotating data of DNA methylation arrays. We found that lincRNAs had different promoter methylation patterns in cancers. We classified 2461 lincRNAs into two categories and three subcategories, according to their promoter methylation patterns in tumors. LincRNAs with resistant methylation patterns in tumors had conserved transcriptional regulation regions and were ubiquitously expressed across normal tissues. By integrating cancer subtype data and patient clinical information, we identified lincRNAs with promoter methylation patterns that were associated with cancer status, subtype or prognosis for several cancers. Network analysis of aberrantly methylated lincRNAs in cancers showed that lincRNAs with aberrant methylation patterns might be involved in cancer development and progression. The methylated and demethylated lincRNAs identified in this study provide novel insights for developing cancer biomarkers and potential therapeutic targets.
Avian Influenza H5N1 in Naturally Infected Domestic Cat (2006)

We report H5N1 virus infection in a domestic cat infected by eating a pigeon carcass. The virus isolated from the pigeon and the cat showed the same cluster as the viruses obtained during the outbreak in Thailand. Since cats are common house pets, concern regarding disease transmission to humans exists.
Phosphatidylinositol 3-Kinase Translocates to the Nucleus of Osteoblast-Like MC3T3-E1 Cells in Response to Insulin-Like Growth Factor I and Platelet-Derived Growth Factor But Not to the Proapoptotic Cytokine Tumor Necrosis Factor α (2000)

Changes in the metabolism of nuclear inositides phosphorylated in the D3 position of the inositol ring, which may act as second messengers, mainly have been linked to cell differentiation. To clarify a possible role of this peculiar class of inositides also during cell proliferation and/or apoptosis, we have examined the issue of whether or not in the osteoblast-like clonal cell line MC3T3-E1 it may be observed an insulin-like growth factor-I (IGF-I)- and platelet-derived growth factor (PDGF)-dependent nuclear translocation of an active phosphatidylinositol 3-kinase (PI 3-K). We found that both the growth factors increased rapidly and transiently both the amount and the activity of immunoprecipitable nuclear PI 3-K. Intranuclear PI 3-K exhibited a massive tyrosine phosphorylation on the p85 regulatory subunit. Moreover, by means of coimmunoprecipitation experiments, we showed the presence, in isolated nuclei, of the p110beta catalytic subunit of PI 3-K. Enzyme translocation was blocked by the specific PI 3-K inhibitor LY294002. In contrast, intranuclear translocation of PI 3-K did not occur in response to the proapoptotic cytokine tumor necrosis factor alpha (TNF-alpha). IGF-I was able to counteract the apoptotic stimulus of TNF-alpha and this was accompanied by the intranuclear translocation of PI 3-K. LY294002 inhibited both intranuclear translocation of PI 3-K and the rescuing effect of IGF-I. These findings strongly suggest that an important step in the signaling pathways that mediate both cell proliferation and survival is represented by the intranuclear translocation of PI 3-K.
Adaptive estimators for filtering noisy images (1990)

A new estimation criterion called the minimum-error minimumcorrelation (MEMC) criterion is implemented in conjunction with an adaptive windowing technique. The image statistics are calculated within the window, the dimensions of which vary depending on the local statistics. The MEMC estimator produces sharper and hence visually more pleasing restorations, while the adaptive windows tend to isolate regions of the image that are locally stationary. Since most of the error after restoration is in the vicinity of edges, a postprocessing step of filtering along the edges is applied. These image restorations are compared to both fixed and adaptive minimum mean squared error estimators.
Temporary cardiac pacing (1995)

Jan keenan offers guidance on aspects of temporary pacing and explores some nursing considerations in caring for patients with temporary pacemakers
Computation and Automata (1986)

Editor's statement Foreword G. Rozenberg Acknowledgements 1. Introduction: models of computation 2. Rudiments of language theory 3. Restricted automata 4. Turing machines and recursive functions 5. Famous decision problems 6. Computational complexity 7. Cryptography 8. Trends in automata and language theory Historical and bibliographical remarks
Performance of the BD GeneOhm Methicillin-Resistant <i>Staphylococcus aureus</i> Test before and during High-Volume Clinical Use (2007)

We evaluated the use of the BD GeneOhm MRSA real-time PCR assay (BD Diagnostics, San Diego, CA) for the detection of nasal colonization with methicillin-resistant Staphylococcus aureus (MRSA). The initial evaluation consisted of 403 paired nasal swabs and was done using the specimen preparation provided with the kit and an in-house lysis method that was specifically developed to accommodate large-volume testing using a minimal amount of personnel time. One swab was placed in an achromopeptidase (ACP) lysis solution, and the other was first used for culture and then prepared according to the kit protocol. PCR was performed on both lysates, and results were compared to those for culture. The sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) of the PCR assay were 98%, 96%, 77%, and 99.7% with the kit lysate and 98%, 95%, 75%, and 99.7% with the ACP lysate (P, not significant), respectively. The second evaluation was done after implementation of all-admission surveillance using PCR with ACP lysis and a sampling of 1,107 PCR-negative samples and 215 PCR-positive samples that were confirmed by culture. The results of this sampling showed an NPV of 99.9% and a PPV of 73.5% (prevalence, 6%), consistent with our initial findings. The BD GeneOhm MRSA assay is an accurate and rapid way to detect MRSA nasal colonization. When one is dealing with large specimen numbers, the ACP lysis method offers easier processing without negatively affecting the sensitivity or specificity of the PCR assay.
In Vivo Ventricular Gene Delivery of a β-Adrenergic Receptor Kinase Inhibitor to the Failing Heart Reverses Cardiac Dysfunction (2001)

In vivo delivery of Adeno-betaARKct is feasible in the infarcted/failing heart by coronary catheterization; expression of betaARKct results in marked reversal of ventricular dysfunction. Thus, inhibition of betaARK1 provides a novel treatment strategy for improving the cardiac performance of the post-MI heart.
Expression of GITR ligand abrogates immunosuppressive function of ocular tissue and differentially modulates inflammatory cytokines and chemokines (2006)

The glucocorticoid-induced TNF-related receptor ligand (GITRL) was previously shown to be constitutively expressed at low levels in human eye, including retinal pigment epithelial (RPE) cells. By expressing enhanced yellow fluorescent protein-tagged human GITRL in human RPE cells, we investigated the significance of expression of GITRL on human ocular tissue. Confocal immunofluorescence microscopy and flow cytometry confirmed the surface expression of GITRL on RPE cells. However, a soluble form of GITRL was also detected. Remarkably, expression of GITRL on the RPE cells abrogated RPE-mediated immunosuppression of CD3(+) T cells, implicated as a possible mechanism for ocular immune privilege. This abrogation of immunosuppression by GITRL-RPE was dependent on GITR-GITRL interaction and could not be mimicked by anti-CD28 antibody. Analysis of cytokine profiles revealed high level of TGF-beta during the immunosuppression by RPE cells while expression of GITRL abrogated the RPE cell-induced TGF-beta secretion. Expression of GITRL also stimulates secretion of an array of proinflammatory cytokines/chemokines from T cells. GITR-GITRL interaction provides a unique proinflammatory costimulation that may signal through a different pathway than that of CD28-B7 costimulation. This study implicated that GITRL could be a potential candidate for regulation of the ocular immune privilege and the balance between immune privilege and inflammation.
The reaction of imidazo[1,5‐<i>a</i>]pyridines with methyl‐ and phenyltriazolinediones and with diethyl azodicarboxylate (1995)

Abstract Imidazo[1,5‐ a ]pyridines react in one of two ways with methyl‐ and phenyl triazolinediones and diethyl azodicarboxylate to give either Michael type addition products at C‐3 or C‐1, or novel 1,2,4‐triazolines. The nature of the product depends upon the dienophile and the substitution pattern of the imidazo[1,5‐ a ]pyridine.
Identification of (<i>R</i>)-6-(1-(4-Cyano-3-methylphenyl)-5-cyclopentyl-4,5-dihydro-1<i>H</i>-pyrazol-3-yl)-2-methoxynicotinic Acid, a Highly Potent and Selective Nonsteroidal Mineralocorticoid Receptor Antagonist (2014)

A novel series of nonsteroidal mineralocorticoid receptor (MR) antagonists identified as part of our strategy to follow up on the clinical candidate PF-03882845 (2) is reported. Optimization departed from the previously described pyrazoline 3a and focused on improving the selectivity for MR versus the progesterone receptor (PR) as an approach to avoid potential sex-hormone-related adverse effects and improving biopharmaceutical properties. From this effort, (R)-14c was identified as a potent nonsteroidal MR antagonist (IC50 = 4.5 nM) with higher than 500-fold selectivity versus PR and other related nuclear hormone receptors, with improved solubility as compared to 2 and pharmacokinetic properties suitable for oral administration. (R)-14c was evaluated in vivo using the increase of urinary Na(+)/K(+) ratio in rat as a mechanism biomarker of MR antagonism. Treatment with (R)-14c by oral administration resulted in significant increases in urinary Na(+)/K(+) ratio and demonstrated this novel compound acts as an MR antagonist.