gebhart/patrepeval huggingface dataset:
Automatic pool allocation (2005)

This paper describes Automatic Pool Allocation , a transformation framework that segregates distinct instances of heap-based data structures into seperate memory pools and allows heuristics to be used to partially control the internal layout of those data structures. The primary goal of this work is performance improvement, not automatic memory management, and the paper makes several new contributions. The key contribution is a new compiler algorithm for partitioning heap objects in imperative programs based on a context-sensitive pointer analysis, including a novel strategy for correct handling of indirect (and potentially unsafe) function calls. The transformation does not require type safe programs and works for the full generality of C and C++. Second, the paper describes several optimizations that exploit data structure partitioning to further improve program performance. Third, the paper evaluates how memory hierarchy behavior and overall program performance are impacted by the new transformations. Using a number of benchmarks and a few applications, we find that compilation times are extremely low, and overall running times for heap intensive programs speed up by 10-25% in many cases, about 2x in two cases, and more than 10x in two small benchmarks. Overall, we believe this work provides a new framework for optimizing pointer intensive programs by segregating and controlling the layout of heap-based data structures.
Intranasal Delivery of an IgA Monoclonal Antibody Effective against Sublethal H5N1 Influenza Virus Infection in Mice (2010)

Highly pathogenic avian H5N1 influenza viruses are endemic in poultry in Asia and pose a pandemic threat to humans. Since the deployment of vaccines against a pandemic strain may take several months, adequate antiviral alternatives are needed to minimize the effects and the spread of the disease. Passive immunotherapy is regarded as a viable alternative. Here, we show the development of an IgA monoclonal antibody (DPJY01 MAb) specific to H5 hemagglutinin. The DPJY01 MAb showed a broad hemagglutination inhibition (HI) profile against Asian H5N1 viruses of clades 0, 1.0, 2.1, 2.2, and 2.3 and also against H5 wild bird influenza viruses of the North American and Eurasian lineages. DPJY01 MAb displayed also high neutralization activity in vitro and in vivo. In mice, DPJY01 MAb provided protection via a single dose administered intranasally before or after inoculation with a sublethal dose of H5N1 viruses of clades 1.0 and 2.2. Pretreatment with 50 mg of DPJY01 MAb kg of body weight at either 24, 48, or 72 h before highly pathogenic H5N1 virus (A/Vietnam/1203/2004 [H5N1]) inoculation resulted in complete protection. Treatment with 50 mg/kg at either at 24, 48, or 72 h after H5N1 inoculation provided 100%, 80%, and 60% protection, respectively. These studies highlight the potential use of DPJY01 MAb as an intranasal antiviral treatment for H5N1 influenza virus infections.
Hormone-dependent Transactivation by the Human Androgen Receptor Is Regulated by a dnaJ Protein (1995)

Genetic studies were performed to examine the role of eukaryotic dnaJ protein, Ydj1p, in the regulated activation of human androgen receptor (hAR) after heterologous expression in Saccharomyces cerevisiae. Hormone-dependent activation of hAR was measured as a function of lacZ reporter gene expression, which was defective in ydj1-151 and ydj1-2 delta null mutant strains compared to the wild type. This defect was not due to receptor misfolding, since hAR in both wild type and mutant strains had a similar capacity to bind hormone. The target for Ydj1p action was determined to be the hAR hormone binding domain since an N-terminal fragment lacking this region was constitutively active in both wild type and ydj1-151 mutant strains. These data correlate hormone dependence of hAR activation with a requirement for Ydj1p function and are consistent with a role for dnaJ proteins in signal transduction by steroid hormone receptors.
Bone marrow-derived dendritic cells pulsed with a tumor-specific peptide elicit effective anti-tumor immunity against intracranial neoplasms (1998)

Although the central nervous system (CNS) is often regarded as an immunologically privileged site, it is well established that specific CNS immunoreactivity can be generated through peripheral vaccination with CNS antigens. Dendritic cells (DC) are potent antigen presenting cells of hematopoietic origin that have emerged as a promising tool for cancer immunotherapy capable of evoking significant anti-tumor immunity when pulsed with tumor-associated peptides. To explore a role for DC-based immunization strategies for the treatment of CNS tumors, we developed a brain tumor model using the C3 sarcoma cell line which expresses the tumor-specific, major histocompatibility complex (MHC) class I-restricted peptide epitope E7(49-57). Syngeneic C57Bl/6 mice receiving intravenous (i.v.) injections of bone marrow-derived DCs pulsed with E7 peptide were effectively protected against a subsequent intracerebral challenge with C3 tumor cells. More importantly, this systemic immunization strategy was effective in a therapy model as 67% of animals (10 of 15) with established (day 7) intracerebral C3 tumors treated with 3 weekly injections of E7 peptide-pulsed DCs achieved a long-term survival (>90 days) while no control animals survived beyond day 41. In vivo depletion of CD8+ cells, but not CD4+ or asialo-GM1+ cells, abrogated the efficacy of E7 peptide-pulsed DC therapy of established tumors, indicating a pivotal role of specific CD8+ T-cell responses in mediating the anti-tumor effect. Our findings support the hypothesis that effective CNS anti-tumor immunoreactivity can be generated with DC-based tumor vaccines.
Human Invariant NKT Cells Are Required for Effective In Vitro Alloresponses (2005)

NKT cells are a small subset of regulatory T cells conserved in humans and mice. In humans they express the Valpha24Jalpha18 invariant chain (hence invariant NKT (iNKT) cells) and are restricted by the glycolipid-presenting molecule CD1d. In mice, iNKT cells may enhance or inhibit anti-infectious and antitumor T cell responses but suppress autoimmune and alloreactive responses. We postulated that iNKT cells might also modulate human alloreactive responses. Using MLR assays we demonstrate that in the presence of the CD1d-presented glycolipid alpha-galactosylceramide (alphaGC) alloreactivity is enhanced (37 +/- 12%; p < 0.001) in an iNKT cell-dependent manner. iNKT cells are activated early during the course of the MLR, presumably by natural ligands. In MLR performed without exogenous ligands, depletion of iNKT cells significantly diminished the alloresponse in terms of proliferation (58.8 +/- 24%; p < 0.001) and IFN-gamma secretion (43.2 +/- 15.2%; p < 0.001). Importantly, adding back fresh iNKT cells restored the reactivity of iNKT cell-depleted MLR to near baseline levels. CD1d-blocking mAbs equally reduced the reactivity of the iNKT cell-replete and -depleted MLR compared with IgG control, indicating that the effect of iNKT cells in the in vitro alloresponse is CD1d-dependent. These findings suggest that human iNKT cells, although not essential for its development, can enhance the alloreactive response.
Effect of growth factors on the activation of human Tenon’s capsule fibroblasts (2003)

The present investigation strongly supports the hypothesis that PDGF-isoforms are major stimulators of proliferation of Tenon's capsule fibroblasts after glaucoma filtering surgery while TGF-beta-isoforms are essential for the transformation of Tenon's capsule fibroblasts into myofibroblasts.
Major Histocompatibility Complex (MHC) Genes and Disease Resistance in Fish (2019)

Fascinating about classical major histocompatibility complex (MHC) molecules is their polymorphism. The present study is a review and discussion of the fish MHC situation. The basic pattern of MHC variation in fish is similar to mammals, with MHC class I versus class II, and polymorphic classical versus nonpolymorphic nonclassical. However, in many or all teleost fishes, important differences with mammalian or human MHC were observed: (1) The allelic/haplotype diversification levels of classical MHC class I tend to be much higher than in mammals and involve structural positions within but also outside the peptide binding groove; (2) Teleost fish classical MHC class I and class II loci are not linked. The present article summarizes previous studies that performed quantitative trait loci (QTL) analysis for mapping differences in teleost fish disease resistance, and discusses them from MHC point of view. Overall, those QTL studies suggest the possible importance of genomic regions including classical MHC class II and nonclassical MHC class I genes, whereas similar observations were not made for the genomic regions with the highly diversified classical MHC class I alleles. It must be concluded that despite decades of knowing MHC polymorphism in jawed vertebrate species including fish, firm conclusions (as opposed to appealing hypotheses) on the reasons for MHC polymorphism cannot be made, and that the types of polymorphism observed in fish may not be explained by disease-resistance models alone.
Minimum drift architectures for 3-layer scalable DTV decoding (1998)

This paper describes new techniques for implementing a low-cost video decoder that can decode an HDTV bitstream and display the signal at lower resolutions. Two key algorithms are discussed: downconversion and low-resolution motion compensation. In the proposed scheme, incoming blocks are subject to a down-conversion process within the decoding loop, hence motion compensation is performed from the downconverted images. The filters used for down-conversion are based on the concept of frequency synthesis, and the filters used to perform the low-resolution motion compensation are determined by an optimal least squares solution. Using these algorithms, three different architectures that provide equal quality with varying system level complexity are presented; the first is directly derived from the initial model of the low-resolution decoder, another attempts to reduce the amount of computation for the IDCT, while another addresses the concerns regarding the amount of interface with an existing decoder structure. All of the above systems are hierarchical with regard to the logic used for filtering and scalable in the amount of memory which is required to reconstruct each output layer. Our simulation results demonstrate that high quality video can be provided at lower-resolutions with significant memory savings.
Precocene II Metabolism in Insects: Synthesis of Potential Metabolites and Identification of Initial in Vitro Biotransformation Products (1980)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPrecocene II Metabolism in Insects: Synthesis of Potential Metabolites and Identification of Initial in Vitro Biotransformation ProductsDavid M. Soderlund, Angel Messeguer, and William S. BowersCite this: J. Agric. Food Chem. 1980, 28, 4, 724–731Publication Date (Print):July 1, 1980Publication History Published online1 May 2002Published inissue 1 July 1980https://pubs.acs.org/doi/10.1021/jf60230a053https://doi.org/10.1021/jf60230a053research-articleACS PublicationsRequest reuse permissionsArticle Views137Altmetric-Citations86LEARN 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
Multilevel Diode-Clamped Converter for Photovoltaic Generators With Independent Voltage Control of Each Solar Array (2008)

In photovoltaic (PV) power systems where a set of series-connected PV arrays (PVAs) is connected to a conventional two-level inverter, the occurrence of partial shades and/or the mismatching of PVAs leads to a reduction of the power generated from its potential maximum. To overcome these problems, the connection of the PVAs to a multilevel diode-clamped converter is considered in this paper. A control and pulsewidth-modulation scheme is proposed, capable of independently controlling the operating voltage of each PVA. Compared to a conventional two-level inverter system, the proposed system configuration allows one to extract maximum power, to reduce the devices voltage rating (with the subsequent benefits in device-performance characteristics), to reduce the output-voltage distortion, and to increase the system efficiency. Simulation and experimental tests have been conducted with three PVAs connected to a four-level three-phase diode-clamped converter to verify the good performance of the proposed system configuration and control strategy.
The Role of Growth Factors for Disease and Therapy in Diseases of the Head and Neck (2003)

Growth factors are a large family of polypeptide molecules that regulate cell division in many tissues by autocrine or paracrine mechanisms. Depending on what receptors are activated, growth factors can initiate mitogenic, antiproliferative, or trophic effects, that is, growth factors act as positive or negative modulators of cell proliferation. Therefore, growth factors do not only play an important role in embryonic development and adult tissue homeostasis, but also in pathological situations like infection, wound healing, and tumorigenesis. Consequently, the application of growth factors, or vice versa the application of substances which are directed against growth factors like antigrowth factor antibodies, may have therapeutic applications. This review provides a brief account of what we know regarding growth factors in otorhinolaryngology, particularly in the field of otology, wound healing, oncology, peripheral nerve regeneration, and rhinology.
Characterization of monoclonal antibodies B1 and B3 that react with mucinous adenocarcinomas. (1991)

B1 and B3 are two newly isolated monoclonal antibodies that react uniformly with the surface of many mucinous carcinomas of the colon, stomach, and ovary but with a limited number of normal tissues, among which are glands of the stomach, epithelia of the trachea and bladder, differentiated epithelium of the esophagus, and small bowel mucin. They also react uniformly with many human tumor cell lines, including MCF7, MDA-MB-468, and HTB20 (breast), A431 (epidermoid), HT29 (colon), HTB33 (cervical), and DU145 (prostate). Immunoprecipitation experiments indicate that B1 and B3 react with epitopes present on a large number of glycoproteins, ranging in molecular weight from greater than 200,000 to less than 40,000. Using a panel of 37 different carbohydrate residues attached to albumin to form neoglycoproteins, it was found that B1 reacts with Ley and H-type 2 and B3 reacts with Ley, di-Lex, and tri-Lex antigens. Thus, each antibody reacts with a distinct portion of a carbohydrate residue. Because of the limited reactivity of these antibodies with normal tissues, they merit evaluation in the treatment of cancer.
The Fractional Extraction and Quantitative Determination of Pectic Substances in Grapes and Musts (1979)

A sensitive and specific procedure is described for the fractional extraction and quantitative determination of pectic substances in grape berries and musts. The fractionation procedure involves the progressive extraction of the alcohol insoluble solids by water (when the high methoxyl pectins are extracted), ammonium oxalate (when the low methoxyl pectins are extracted) and cold alkali (which solubilizes the protopectin). The anhydrogalacturonic acid content of the three fractions is then determined quantitatively by heating the extract with concentrated sulfuric acid and sodium tetraborate and forming a chromogen with m-hydroxydiphenyl. The absorbance of the solutions is then compared to that obtained from standard solutions of galacturonic acid subjected to the same procedure. The advantages of this method over the commonly used carbazole method are demonstrated, and the reproducibility of both methods is presented. It is recommended that the procedure described herein be adopted for the routine determination of pectic substances in grapes.
Cross-Protection by B Subunit-Whole Cell Cholera Vaccine Against Diarrhea Associated with Heat-Labile Toxin-Producing Enterotoxigenic Escherichia coli: Results of a Large-Scale Field Trial (1988)

The B subunit (BS) of cholera toxin and that of the heat-labile enterotoxin (LT) of enterotoxigenic Escherichia coli (ETEC) are antigenically similar. We therefore assessed whether a combined cholera toxin BS/whole-cell (BS-WC) oral vaccine against cholera conferred cross-protection against LT-producing ETEC (LT-ETEC) diarrhea in a randomized, double-blind field trial among rural Bangladeshi children and women. The 24,770 persons who ingested two or more doses of BS-WC vaccine were compared with 24,842 controls who took two or more doses of killed whole-cell (WC) oral cholera vaccine. Sixty-seven percent fewer episodes of LT-ETEC diarrhea were noted in the BS-WC group than in the WC group during short-term (three-month) follow-up (P less than .01), but no reduction was evident during the ensuing nine months. Short-term protection was particularly notable against LT-ETEC diarrhea causing life-threatening dehydration (protective efficacy, 86%; P less than .05).
Activation of the heat shock response in a primary cellular model of motoneuron neurodegeneration-evidence for neuroprotective and neurotoxic effects (2009)

Pharmacological up-regulation of heat shock proteins (hsps) rescues motoneurons from cell death in a mouse model of amyotrophic lateral sclerosis. However, the relationship between increased hsp expression and neuronal survival is not straightforward. Here we examined the effects of two pharmacological agents that induce the heat shock response via activation of HSF-1, on stressed primary motoneurons in culture. Although both arimoclomol and celastrol induced the expression of Hsp70, their effects on primary motoneurons in culture were significantly different. Whereas arimoclomol had survival-promoting effects, rescuing motoneurons from staurosporin and H(2)O(2) induced apoptosis, celastrol not only failed to protect stressed motoneurons from apoptosis under same experimental conditions, but was neurotoxic and induced neuronal death. Immunostaining of celastrol-treated cultures for hsp70 and activated caspase-3 revealed that celastrol treatment activates both the heat shock response and the apoptotic cell death cascade. These results indicate that not all agents that activate the heat shock response will necessarily be neuroprotective.
Laura Brown, Homeless Dogs and Melancholy Apes: Humans and Other Animals in the Modern Literary Imagination (2011)

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NATURAL KILLER CELLS IN ANTIVIRAL DEFENSE: Function and Regulation by Innate Cytokines (1999)

Natural killer (NK) cells are populations of lymphocytes that can be activated to mediate significant levels of cytotoxic activity and produce high levels of certain cytokines and chemokines. NK cells respond to and are important in defense against a number of different infectious agents. The first indications for this function came from the observations that virus-induced interferons alpha/beta (IFN-alpha and -beta) are potent inducers of NK cell-mediated cytotoxicity, and that NK cells are important contributors to innate defense against viral infections. In addition to IFN-alpha/beta, a wide range of other innate cytokines can mediate biological functions regulating the NK cell responses of cytotoxicity, proliferation, and gamma interferon (IFN-gamma) production. Certain, but not all, viral infections induce interleukin 12 (IL-12) to elicit NK cell IFN-gamma production and antiviral mechanisms. However, high levels of IFN-alpha/beta appear to be unique and/or uniquely dominant in the context of viral infections and act to regulate other innate responses, including induction of NK cell proliferation in vivo and overall negative regulation of IL-12 production. A detailed picture is developing of particular innate cytokines activating NK cell responses and their consorted effects in providing unique endogenous milieus promoting downstream adaptive responses, most beneficial in defense against viral infections.
Characterization of translational initiation sites inE. coli (1982)

We characterize the Shine and Dalgarno sequence of 124 known gene beginnings. This information is used to make "rules" which help distinguish gene beginning from other sites in a library of over 78,000 bases of mRNA. Gene beginnings are found to have information besides the initiation codon and Shine and Dalgarno sequence which can be used to make better "rules".
Lung reperfusion injury is reduced by inhibiting a CD18-dependent mechanism. (1993)

CD18 designates a component of a leukocyte surface glycoprotein complex that mediates endothelial adherence. To determine whether interference with CD18-dependent leukocyte adhesion modifies reperfusion injury, we transplanted 16 canine left lungs after 4-hour preservation with modified Euro-Collins solution. Anti-canine CD18 monoclonal antibody (R15.7, 1 mg/kg, intravenously) was administered to eight lung recipients 5 minutes before reperfusion; eight control recipients were not treated. Ventilation was identical in donor-recipient pairs (tidal volume, 600 ml; fraction of inspired oxygen, 0.53; positive end-expiratory pressure, 5 cm H2O). Respiratory and inert gas exchange and hemodynamics were assessed in left lung donors one-half hour after right lung exclusion and in allograft recipients at 0.5, 1.5, 2.5, 3.5, and 6.0 hours after transplantation and right lung exclusion. Reperfusion injury was evident in both recipient groups at 6 hours after transplantation, but inert gas shunt was lower in monoclonal antibody-treated dogs (13% +/- 6%) than in controls (30% +/- 17%, p < 0.05); comparisons of arterial blood gases in monoclonal antibody recipients (PaO2, 209 +/- 83 mm Hg; PaCO2, 45 +/- 7 mm Hg) and controls (PaO2, 108 +/- 54, p < 0.05; PaCO2, 64 +/- 25, p < 0.05) at 6 hours indicated that monoclonal antibody administration distinctly improved respiratory gas transfer. Gravimetric lung water was less in monoclonal antibody recipients (5.78 +/- 1.01 ml/kg) than in controls (8.02 +/- 1.90 ml/kg, p < 0.05), but lung compliance at 6 hours was equally reduced in monoclonal antibody recipients (40 +/- 9 ml/cm H2O) and in controls (39 +/- 7 ml/cm H2O, p = not significant). Pulmonary vascular resistance doubled immediately after transplantation but was identical in monoclonal antibody-treated dogs (890 +/- 168 dynes.sec.cm-5) and in controls (874 +/- 162 dynes.sec.cm-5, p = not significant) at 6 hours. We conclude that inhibition of CD18-dependent leukocyte function attenuates the development of both shunt and abnormal respiratory gas exchange in lung reperfusion injury. Significant physiologic abnormalities occurred despite R15.7 treatment and may represent inadequate preservation or the effect of CD18-independent adhesion mechanisms.
Alteration of Met protooncogene product expression and prognosis in breast carcinomas. (1999)

Our studies suggest that in a subpopulation of node-negative breast cancer patients, either high or low levels of Met in tumor tissue relative to normal tissue is an indicator of poor overall survival (P = .0068). Thus, Met expression could be useful for identifying node-negative patients who could benefit from adjuvant therapy.