gebhart/patrepeval huggingface dataset:
Framework for evaluating clustering algorithms in duplicate detection (2009)

The presence of duplicate records is a major data quality concern in large databases. To detect duplicates, entity resolution also known as duplication detection or record linkage is used as a part of the data cleaning process to identify records that potentially refer to the same real-world entity. We present the Stringer system that provides an evaluation framework for understanding what barriers remain towards the goal of truly scalable and general purpose duplication detection algorithms. In this paper, we use Stringer to evaluate the quality of the clusters (groups of potential duplicates) obtained from several unconstrained clustering algorithms used in concert with approximate join techniques. Our work is motivated by the recent significant advancements that have made approximate join algorithms highly scalable. Our extensive evaluation reveals that some clustering algorithms that have never been considered for duplicate detection, perform extremely well in terms of both accuracy and scalability.
Potentiation of the antitumor activity of methotrexate by concurrent infusion of thymidine. (1978)

An on-wafer measurement strategy for determining the driving point impedance of a planar 100 GHz double slot antenna is presented. The technique is verified by comparison with a theoretical determination of the antenna impedance
Optimal Use of Blood Products in Severely Injured Trauma Patients (2010)

Injury is the leading cause of life years lost in the United States, and uncontrolled hemorrhage is the leading cause of potentially preventable death. Traditionally, these patients have been serially resuscitated with large volumes of crystalloid and/or colloids and red blood cells, followed by smaller amounts of plasma and platelets. Transfusion data coming first from the ongoing war in Iraq and Afghanistan and followed by multiple civilian studies have brought into question this tradition-based practice. Numerous recent retrospective single and multicenter studies have associated improved outcomes with earlier and increased use of plasma and platelets. These data have stimulated significant interest in studying massively transfused trauma patients. Most clinicians have concluded that the optimal timing and quantity of blood products in the treatment of hypothermic, coagulopathic, and acidotic trauma patients are unclear. Although there are strongly held opinions and long-standing traditions in their use, there are little quality data within which to logically guide resuscitation therapy. A multicenter prospective observational study is ongoing, and randomized trials are planned. This review will address the issues raised previously and describe recent trauma patient outcome data utilizing predetermined plasma:platelet:red blood cell transfusion ratios, and possibilities for future transfusion products and research.
Genetic Analysis of the Mammalian Transforming Growth Factor-β Superfamily (2002)

Members of the TGF-beta superfamily, which includes TGF-betas, growth differentiation factors, bone morphogenetic proteins, activins, inhibins, and glial cell line-derived neurotrophic factor, are synthesized as prepropeptide precursors and then processed and secreted as homodimers or heterodimers. Most ligands of the family signal through transmembrane serine/threonine kinase receptors and SMAD proteins to regulate cellular functions. Many studies have reported the characterization of knockout and knock-in transgenic mice as well as humans or other mammals with naturally occurring genetic mutations in superfamily members or their regulatory proteins. These investigations have revealed that TGF-beta superfamily ligands, receptors, SMADs, and upstream and downstream regulators function in diverse developmental and physiological pathways. This review attempts to collate and integrate the extensive body of in vivo mammalian studies produced over the last decade.
The Major Immediate-Early Gene ie3 of Mouse Cytomegalovirus Is Essential for Viral Growth (2000)

The significance of the major immediate-early gene ie3 of mouse cytomegalovirus (MCMV) and that of the corresponding ie2 gene of human cytomegalovirus to viral replication are not known. To investigate the function of the MCMV IE3 regulatory protein, we generated two different MCMV recombinants that contained a large deletion in the IE3 open reading frame (ORF). The mutant genomes were constructed by the bacterial artificial chromosome mutagenesis technique, and MCMV ie3 deletion mutants were reconstituted on a mouse fibroblast cell line that expresses the MCMV major immediate-early genes. The ie3 deletion mutants failed to replicate on normal mouse fibroblasts even when a high multiplicity of infection was used. The replication defect was rescued when the IE3 protein was provided in trans by a complementing cell line. A revertant virus in which the IE3 ORF was restored was able to replicate with wild-type kinetics in normal mouse fibroblasts, providing evidence that the defective growth phenotype of the ie3 mutants was due to disruption of the ie3 gene. To characterize the point of restriction in viral replication that is controlled by ie3, we analyzed the pattern of expression of selective early (beta) and late (gamma) genes. While we could detect transcripts for the immediate-early gene ie1 in cells infected with the ie3 mutants, we failed to detect transcripts for representative beta and gamma genes. These data demonstrate that the MCMV transactivator IE3 plays an indispensable role during viral replication in tissue culture, implicating a similar role for the human CMV ie2 gene product. To our knowledge, the ie3 deletion mutants represent the first MCMV recombinants isolated that contain a disruption of an essential gene.
Human Neutrophil-Expressed CD28 Interacts with Macrophage B7 to Induce Phosphatidylinositol 3-Kinase-Dependent IFN-γ Secretion and Restriction of Leishmania Growth (2002)

We previously showed that CD28 is expressed on human peripheral blood neutrophils and plays an important role in CXCR-1 expression and IL-8-induced neutrophil migration. In this work we demonstrate that Leishmania major infection of macrophages results in parasite dose-dependent IL-8 secretion in vitro and in IL-8-directed neutrophil migration, as blocked by both anti-IL-8 and anti-IL-8R Abs, toward the L. major-infected macrophages. In the neutrophil-macrophage cocultures, both CTLA4-Ig, a fusion protein that blocks CD28-CD80/CD86 interaction, and a neutralizing anti-IFN-gamma Ab inhibit the anti-leishmanial function of neutrophils, suggesting that the neutrophil-macrophage interaction via CD28-CD80/CD86 plays an important role in the IFN-gamma-dependent restriction of the parasite growth. Cross-linking of neutrophil-expressed CD28 by monoclonal anti-CD28 Ab or B7.1-Ig or B7.2-Ig results in phosphatidylinositol 3-kinase association with CD28 and in wortmannin-sensitive but cyclosporin A-resistant induction and secretion of IFN-gamma. Whereas the neutrophils secrete IFN-gamma with CD28 signal alone, the T cells do not secrete the cytokine in detectable amounts with the same signal. Thus, neutrophil-expressed CD28 modulates not only the granulocyte migration but also induction and secretion of IFN-gamma at the site of infection where it migrates from the circulation.
Cutting Edge: A Short Polypeptide Domain of HIV-1-Tat Protein Mediates Pathogenesis (1999)

HIV-1 encodes the transactivating protein Tat, which is essential for virus replication and progression of HIV disease. However, Tat has multiple domains, and consequently the molecular mechanisms by which it acts remain unclear. In this report, we provide evidence that cellular activation by Tat involves a short core domain, Tat21-40, containing only 20 aa including seven cysteine residues highly conserved in most HIV-1 subtypes. Effective induction by Tat21-40 of both NF-kappaB-mediated HIV replication and TAR-dependent transactivation of HIV-long terminal repeat indicates that this short sequence is sufficient to promote HIV infection. Moreover, Tat21-40 possesses potent angiogenic activity, further underscoring its role in HIV pathogenesis. These data provide the first demonstration that a 20-residue core domain sequence of Tat is sufficient to transactivate, induce HIV replication, and trigger angiogenesis. This short peptide sequence provides a potential novel therapeutic target for disrupting the functions of Tat and inhibiting progression of HIV disease.
Identification of organic acids and other intermediates in oxidative degradation of chlorinated ethanes on titania surfaces en route to mineralization: a combined photocatalytic and radiation chemical study (1991)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTIdentification of organic acids and other intermediates in oxidative degradation of chlorinated ethanes on titania surfaces en route to mineralization: a combined photocatalytic and radiation chemical studyYun Mao, Christian Schoeneich, and Klaus Dieter AsmusCite this: J. Phys. Chem. 1991, 95, 24, 10080–10089Publication Date (Print):November 1, 1991Publication History Published online1 May 2002Published inissue 1 November 1991https://pubs.acs.org/doi/10.1021/j100177a085https://doi.org/10.1021/j100177a085research-articleACS PublicationsRequest reuse permissionsArticle Views672Altmetric-Citations156LEARN 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 options Get e-Alerts
Phase II study of docetaxel with or without plinabulin (NPI-2358) in patients with non-small cell lung cancer (NSCLC). (2010)

7592 Background: Plinabulin (NPI-2358) is a vascular disrupting agent (VDA) that acts on the cytoskeleton to destabilize tumor vascular endothelial cell cohesion with additional cytotoxic activity, leading to selective tumor vascular disruption and necrosis. As VDAs target tumor vasculature through different mechanisms than anti-VEGF pathway agents, the activity and safety profiles are different. VDAs have demonstrated intriguing activity in oncology, particularly in NSCLC where there is potential differentiation from other agents in patient subsets such as those with squamous cell carcinoma or at risk for bleeding events. Positive outcomes were seen in preclinical and early clinical studies in NSCLC with plinabulin and docetaxel, resulting in the initiation of this trial (the ADVANCE study). Methods: The trial will enroll a total of 167 patients with advanced NSCLC who have received prior chemotherapy. Patients were randomized to receive docetaxel alone or docetaxel with plinabulin. Docetaxel (75 mg/m2) was given on Day 1 and in those in the combination arm, plinabulin was added on Days 1 and 8 in 21-day cycles. Two different doses of plinabulin were tested sequentially (30 mg/m2, 20 mg/m2). Primary endpoint is overall survival; secondary endpoints include progression-free survival, response and safety. Results: Enrollment of the 110 patients in the 30 mg/m2 plinabulin dose group is complete, and continues in the 20 mg/m2 plinabulin dose group. Neutropenia was seen as expected with docetaxel. Nausea, vomiting, fatigue, fever, tumor pain, and diarrhea as consistent with plinabulin effects were seen. Of interest, the incidence of neutropenia appeared lower in the combination arm (4% vs. 27%) (consistent with preclinical studies) and the incidence of ileus appeared higher in the combination arm. Out of 64 currently evaluable patients, 6/27 (22%) in the combination arm group had a PR while 2/37 (5%) in the docetaxel arm group had PR (p = 0.04). The results indicate the safety and antitumor activity of the combination. Conclusions: The results demonstrate marked antitumor activity of the combination compared to the control arm, with an acceptable safety profile. Efficacy and safety continue to be compared in a 20 mg/m2 plinabulin dose group to determine the optimal dose to bring into phase III testing. Author Disclosure Employment or Leadership Position Consultant or Advisory Role Stock Ownership Honoraria Research Funding Expert Testimony Other Remuneration Nereus Pharmaceuticals Nereus Pharmaceuticals
Nonsteroidal antiinflammatory drugs and uncoupling of mitochondrial oxidative phosphorylation (1996)

The ability to uncouple mitochondrial oxidative phosphorylation is a common characteristic of antiinflammatory agents with an ionizable group. Modification or absence of an ionizable moiety reduces the effect on mitochondria and could lead to improved NSAID GI safety.
DNA Immunization withTrypanosoma cruziHSP70 Fused to the KMP11 Protein Elicits a Cytotoxic and Humoral Immune Response against the Antigen and Leads to Protection (2001)

Murine immunization with Trypanosoma cruzi KMP11-HSP70 fused genes but not the KMP11 gene alone elicited both an immunoglobulin G2a long-lasting humoral immune response against KMP11 protein and activation of CD8+ cytotoxic T lymphocytes specific for two KMP11 peptides containing A2 motifs. Moreover, protection against the parasite challenge was observed after immunization with the chimeric gene.
Rapid and Quantitative Cyclization of Multiple Peptide Loops onto Synthetic Scaffolds for Structural Mimicry of Protein Surfaces (2005)

No need for side-chain protection in the cyclization reaction of cysteine-containing linear peptides onto bromomethylated aromatic scaffolds (see scheme). The reaction is extremely fast and clean and runs to completion in less than 15 min at room temperature.
Ultrafine particles in concrete : Influence of ultrafine particles on concrete properties and application to concrete mix design (2010)

Ultrafine particles in concrete : Influence of ultrafine particles on concrete properties and application to concrete mix design
Expression of NeuGc on Pig Corneas and Its Potential Significance in Pig Corneal Xenotransplantation (2015)

The absence of NeuGc on GTKO aortic tissue and AECs is associated with reduced human antibody binding, and possibly will provide a better outcome in clinical xenotransplantation using vascularized organs. For clinical corneal xenotransplantation, the absence of NeuGc expression on GTKO/NeuGcKO pig corneas may not prove an advantage over GTKO corneas.
Melanoma vaccines (2000)

Remarkable advances in tumor vaccination have been made since Coley first deliberately infected cancer patients with both live and heat-killed bacteria. Melanoma is the most immunogenic solid tumor and, as such, has served as the major model for tumor vaccine investigation in both the laboratory and the clinic. Many advances in the field of melanoma vaccination have been based on an improved understanding of the cellular interaction required to induce a specific antitumor immune response. As a result of this new knowledge, many clinical trials of melanoma vaccines are now under way, and vaccines for metastatic melanoma have shown evidence of clinical effectiveness. This paper outlines the current status of melanoma vaccination.
Autofluorescence characteristics of immortalized and carcinogen-transformed human bronchial epithelial cells (2001)

Tissue autofluorescence has been explored as a potential method of noninvasive pre-neoplasia (pre-malignancy) detection in the lung. Here, we report the first studies of intrinsic cellular autofluorescence from SV40 immortalized and distinct tobacco-carcinogen-transformed (malignant) human bronchial epithelial cells. These cell lines are useful models for studies seeking to distinguish between normal and pre-neoplastic human bronchial epithelial cells. The cells were characterized via spectrofluorimetry and confocal fluorescence microscopy. Spectrofluorimetry revealed that tryptophan was the dominant fluorophore. No change in tryptophan emission intensity was observed between immortalized and carcinogen-transformed cells. Confocal autofluorescence microscopy was performed using a highly sensitive, spectrometer-coupled instrument capable of limiting emission detection to specific wavelength ranges. These studies revealed two additional endogenous fluorophores, whose excitation and emission characteristics were consistent with nicotinamide adenine dinucleotide (NADH) and flavins. In immortalized human bronchial epithelial cells, the fluorescence of these species was localized to cytoplasmic granules. In contrast, the carcinogen-transformed cells showed an appreciable decrease in the fluorescence intensity of both NADH and flavins and the punctate, spatial localization of the autofluorescence was lost. The observed autofluorescence decrease was potentially the result of changes in the redox state of the fluorophores. The random cytoplasmic fluorescence pattern found in carcinogen-transformed cells may be attributed to changes in the mitochondrial morphology. The implications of these results to pre-neoplasia detection in the lung are discussed.
Copper-Catalyzed Aerobic Enantioselective Cross-Dehydrogenative Coupling of N-Aryl Glycine Esters with Terminal Alkynes (2016)

A copper-catalyzed enantioselective cross-coupling of a Csp3-H moiety (N-aryl glycine ester) with a Csp-H component (terminal alkyne) using molecular oxygen as the terminal oxidant is described for the first time. The sustainable method provides an efficient and environmentally friendly approach to rapidly prepare a diverse array of optically active non-natural α-amino acids.
CNP production in the kidney and effects of protein intake restriction in nephrotic syndrome (2002)

C-type natriuretic peptide (CNP) possesses well-established cardiovascular properties. Although present in the mammalian kidney, CNP production in human kidney and its modulation in human renal disease remain less defined. We investigated the presence of CNP in normal human kidney and in patients with nephrotic syndrome (NS). We also addressed whether or not a low-protein diet (LPD) alters plasma CNP and urinary CNP excretion in NS. In situ hybridization studies demonstrated CNP mRNA expression in tubular cells and glomeruli of normal human kidneys. CNP immunoreactivity was positive in proximal, distal, and medullary collecting duct tubular cells in both controls and patients with NS. The ratios of plasma CNP and urinary CNP to creatinine were significantly higher in patients with NS compared with controls. Urinary CNP, but not plasma CNP, was significantly lowered in patients with NS after an LPD. Similarly, the ratios of urinary protein to creatinine and urinary albumin to creatinine, but not urinary guanosine 3',5'-cyclic monophosphate to creatinine, decreased significantly with an LPD. These data confirm and extend previous reports and demonstrate for the first time the presence of CNP in human kidney with NS. We also report increased plasma CNP concentration and urinary CNP excretion in NS patients and a significant reduction of CNP excretion with an LPD. Our findings demonstrate that CNP metabolism is altered in patients with NS and support the hypothesis that activation of renal CNP can be partially offset by an LPD. These results underscore that the beneficial effect of an LPD on protein excretion is paralleled by a substantial reduction in intrarenal CNP release.
S -nitrosation of proteins relevant to Alzheimer’s disease during early stages of neurodegeneration (2016)

Protein S-nitrosation (SNO-protein), the nitric oxide-mediated posttranslational modification of cysteine thiols, is an important regulatory mechanism of protein function in both physiological and pathological pathways. A key first step toward elucidating the mechanism by which S-nitrosation modulates a protein's function is identification of the targeted cysteine residues. Here, we present a strategy for the simultaneous identification of SNO-cysteine sites and their cognate proteins to profile the brain of the CK-p25-inducible mouse model of Alzheimer's disease-like neurodegeneration. The approach-SNOTRAP (SNO trapping by triaryl phosphine)-is a direct tagging strategy that uses phosphine-based chemical probes, allowing enrichment of SNO-peptides and their identification by liquid chromatography tandem mass spectrometry. SNOTRAP identified 313 endogenous SNO-sites in 251 proteins in the mouse brain, of which 135 SNO-proteins were detected only during neurodegeneration. S-nitrosation in the brain shows regional differences and becomes elevated during early stages of neurodegeneration in the CK-p25 mouse. The SNO-proteome during early neurodegeneration identified increased S-nitrosation of proteins important for synapse function, metabolism, and Alzheimer's disease pathology. In the latter case, proteins related to amyloid precursor protein processing and secretion are S-nitrosated, correlating with increased amyloid formation. Sequence analysis of SNO-cysteine sites identified potential linear motifs that are altered under pathological conditions. Collectively, SNOTRAP is a direct tagging tool for global elucidation of the SNO-proteome, providing functional insights of endogenous SNO proteins in the brain and its dysregulation during neurodegeneration.
Clutch-free panning and integrated pan-zoom control on touch-sensitive surfaces (2010)

International audience
BKM: a new hardware algorithm for complex elementary functions (1994)

A new algorithm for computing the complex logarithm and exponential functions is proposed. This algorithm is based on shift-and-add elementary steps, and it generalizes some algorithms by Briggs and De Lugish (1970), as well as the CORDIC algorithm. It can easily be used to compute the classical real elementary functions (sin, cos, arctan, ln, exp). This algorithm is more suitable for computations in a redundant number system than the CORDIC algorithm, since there is no scaling factor when computing trigonometric functions.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>