gebhart/patrepeval huggingface dataset:
Rapid Extraction of Genome DNA from Avian Blood (2010)

[Objective] To establish a novel method for extracting genome DNA from avian blood sample by silica membrane.[Method] The extraction of genome DNA from EDTA and Heparin anticoagulated chicken blood were performed by the silica membrane adsorption method and phenol-chloroform extraction method.A pair of 2.7 kb primer was designed,synthesized and used to check the genomic templates for influencing on PCR amplification efficiency by different extraction methods.[Result] The yield and quality of genomic DNA extracted by the silica membrane adsorption method was better than that extracted by the traditional phenol/chloroform extraction method.Moreover,through using the genomic DNA of silica membrane adsorption method as template of Polymerase Chain Reaction(PCR),the influences of anticoagulants on the amplification efficiency were eliminated.[Conclusion] Silica membrane adsorption method lays the foundation for simple and rapid extraction of high quality genome DNA from avian blood.
Structures of the CCR5 N Terminus and of a Tyrosine-Sulfated Antibody with HIV-1 gp120 and CD4 (2007)

The CCR5 co-receptor binds to the HIV-1 gp120 envelope glycoprotein and facilitates HIV-1 entry into cells. Its N terminus is tyrosine-sulfated, as are many antibodies that react with the co-receptor binding site on gp120. We applied nuclear magnetic resonance and crystallographic techniques to analyze the structure of the CCR5 N terminus and that of the tyrosine-sulfated antibody 412d in complex with gp120 and CD4. The conformations of tyrosine-sulfated regions of CCR5 (alpha-helix) and 412d (extended loop) are surprisingly different. Nonetheless, a critical sulfotyrosine on CCR5 and on 412d induces similar structural rearrangements in gp120. These results now provide a framework for understanding HIV-1 interactions with the CCR5 N terminus during viral entry and define a conserved site on gp120, whose recognition of sulfotyrosine engenders posttranslational mimicry by the immune system.
Tyrosine phosphorylation of CD45 phosphotyrosine phosphatase by p50csk kinase creates a binding site for p56lck tyrosine kinase and activates the phosphatase. (1994)

Src family protein tyrosine kinases (PTKs) play an essential role in antigen receptor-initiated lymphocyte activation. Their activity is largely regulated by a negative regulatory tyrosine which is a substrate for the activating action of the CD45 phosphotyrosine phosphatase (PTPase) or, conversely, the suppressing action of the cytosolic p50csk PTK. Here we report that CD45 was phosphorylated by p50csk on two tyrosine residues, one of them identified as Tyr-1193. This residue was not phosphorylated by T-cell PTKs p56lck and p59fyn. Tyr-1193 was phosphorylated in intact T cells, and phosphorylation increased upon treatment with PTPase inhibitors, indicating that this tyrosine is a target for a constitutively active PTK. Cotransfection of CD45 and csk into COS-1 cells caused tyrosine phosphorylation of CD45 in the intact cells. Tyrosine-phosphorylated CD45 bound p56lck through the SH2 domain of the kinase. Finally, p50csk-mediated phosphorylation of CD45 caused a severalfold increase in its PTPase activity. Our results show that direct tyrosine phosphorylation of CD45 can affect its activity and association with Src family PTKs and that this phosphorylation could be mediated by p50csk. If this is also true in the intact cells, it adds a new dimension to the physiological function of p50csk in T lymphocytes.
Parameters guiding selection of best embryos for transfer after cryopreservation: a reappraisal (2002)

The results of our study suggest that the most important factor to predict further embryo development is the total number of blastomeres in transferred embryos, however they are obtained (good survival and/or resumption of mitosis).
The Twin-arginine Signal Peptide of PhoD and the TatAd/Cd Proteins of Bacillus subtilis Form an Autonomous Tat Translocation System (2002)

The bacterial twin-arginine translocation (Tat) pathway has been recently described for PhoD of Bacillus subtilis, a phosphodiesterase containing a twin-arginine signal peptide. The expression of phoD is co-regulated with the expression of tatA(d) and tatC(d) genes localized downstream of phoD. To characterize the specificity of PhoD transport further, translocation of PhoD was investigated in Escherichia coli. By using gene fusions, we analyzed the particular role of the signal peptide and the mature region of PhoD in canalizing the transport route. A hybrid protein consisting of the signal peptide of beta-lactamase and mature PhoD was transported in a Sec-dependent manner indicating that the mature part of PhoD does not contain information canalizing the selected translocation route. Pre-PhoD, as well as a fusion protein consisting of the signal peptide of PhoD (SP(PhoD)) and beta-galactosidase (LacZ), remained cytosolic in the E. coli. Thus, SP(PhoD) is not recognized by E. coli transport systems. Co-expression of B. subtilis tatA(d)/C(d) genes resulted in the processing of SP(PhoD)-LacZ and periplasmic localization of LacZ illustrating a close substrate specificity of the TatA(d)/C(d) transport system. While blockage of the Sec-dependent transport did not affect the localization of SP(PhoD)-LacZ, translocation and processing was dependent on the pH gradient of the cytosolic membrane. Thus, the minimal requirement of a functional Tat-dependent protein translocation system consists of a twin-arginine signal peptide-containing Tat substrate, its specific TatA/C proteins, and the pH gradient across the cytosolic membrane.
Motor blockade and absence of local nerve toxicity induced by liposomal bupivacaine injected into the brachial plexus of rabbits. (1995)

Bupivacaine has been encapsulated into multilameller liposomes in order to reduce its systemic toxicity and to lengthen its action. Low, constant and sustained plasma levels have been observed after epidural injection and brachial plexus administration to rabbits. The present experiment was performed in order to study the motor block effect and the possible neurotoxicity of bupivacaine encapsulated in multilamellar liposomes applied in vivo to intact peripheral nerve bundles. Five milliliters of sterile solutions containing 0.75% bupivacaine encapsulated in 42.5 and 85 mg of lipids (phosphatidylcholine and cholesterol in a molar ratio 4:3) were administered to 4 rabbits at the level of the brachial plexus. A motor blockade of the forelimb lasting for 10 hours was measured immediately after injection of the liposomal drug. Light microscopic analyses of the nerves after 2 and 7 days revealed weak inflammatory perineural infiltration. Electron microscopy showed no changes of the myelin sheaths and no alteration of unmyelinated fibers. It may be concluded that the pharmacologically active liposomal formulation of bupivacaine did not induce alterations of the nerve tissues.
Further evidence to support the melanocytic origin of MDA-MB-435 (2002)

These results strongly suggest that MDA-MB-435 is indeed of melanoma origin.
Photo- and radiation-induced chemical generation and reactions of styrene radical cations in polar and non-polar solvents (1995)

Radical cations of the substituted styrenes (M)1–10 have been produced by pulse radiolysis of solutions of M in cyclohexane. The monomer radical cations, M˙+, are formed by fast electron transfer from the solute, M, to the solvent radical cation produced by the ionizing radiation. The decay of M˙+ proceeds by an ion–molecule reaction with the parent styrene (dimerization; k= 0.6–1.0 × 1010 dm3 mol–1 s–1) resulting in head-to-head connected distonic dimer radical cations which show properties of carbenium ions. At high styrene concentrations a trimerization which represents the start of the free cationic polymerization takes place with a rate constant of ca. 106 dm3 mol–1 s–1. In aqueous or alcoholic solutions, radical cations were generated by direct two-photon ionization (indicated by the presence of the solvated electron) of the styrenes or by reactions with strong oxidants, such as SO4˙– and Tl2+, generated by laser UV photolysis as well as by pulse radiolysis. Only for 4-methoxystyrene 6 and trans-anethole 7 could the (monomeric) radical cations be directly observed in the nanosecond to millisecond range. In the other cases, the radical cations decay within the sub-nanosecond timescale by reaction with H2O forming β-hydroxybenzyl type radicals.
ChemInform Abstract: Reduction of Chlorate and Perchlorate Ions at an Active Titanium Electrode. (1986)

Abstract The electrochemical reduction of Cl0 4 ‐ at an active Ti electrode in aqueous 1.0 M HClO 4 yielding C1′ occurs by oxygen atom transfer to the Ti surface and not by a pathway involving catalysis by soluble Ti corrosion products.
Discovery of Potent Antagonists of the Interaction between Human Double Minute 2 and Tumor Suppressor p53 (2000)

ADVERTISEMENT RETURN TO ISSUEPREVLetterNEXTDiscovery of Potent Antagonists of the Interaction between Human Double Minute 2 and Tumor Suppressor p53Carlos García-Echeverría, Patrick Chène, Marcel J. J. Blommers, and Pascal FuretView Author Information Oncology Research and Core Technologies, Novartis Pharma Inc., CH-4002 Basel, Switzerland Cite this: J. Med. Chem. 2000, 43, 17, 3205–3208Publication Date (Web):August 5, 2000Publication History Received8 December 1999Published online5 August 2000Published inissue 1 August 2000https://pubs.acs.org/doi/10.1021/jm990966phttps://doi.org/10.1021/jm990966prapid-communicationACS PublicationsCopyright © 2000 American Chemical SocietyRequest reuse permissionsArticle Views1940Altmetric-Citations211LEARN 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-AlertscloseSupporting Info (1)»Supporting Information Supporting Information SUBJECTS:Conformation,Hydrophobicity,Monomers,Peptides and proteins,Screening assays Get e-Alerts
Surface simplification using quadric error metrics (1997)

Many applications in computer graphics require complex, highly detailed models. However, the level of detail actually necessary may vary considerably. To control processing time, it is often desirable to use approximations in place of excessively detailed models. We have developed a surface simplification algorithm which can rapidly produce high quality approximations of polygonal models. The algorithm uses iterative contractions of vertex pairs to simplify models and maintains surface error approximations using quadric matrices. By contracting arbitrary vertex pairs (not just edges), our algorithm is able to join unconnected regions of models. This can facilitate much better approximations, both visually and with respect to geometric error. In order to allow topological joining, our system also supports non-manifold surface models. CR Categories: I.3.5 [Computer Graphics]: Computational Geometry and Object Modeling—surface and object representations
Estimating and comparing time‐dependent areas under receiver operating characteristic curves for censored event times with competing risks (2013)

The area under the time-dependent ROC curve (AUC) may be used to quantify the ability of a marker to predict the onset of a clinical outcome in the future. For survival analysis with competing risks, two alternative definitions of the specificity may be proposed depending of the way to deal with subjects who undergo the competing events. In this work, we propose nonparametric inverse probability of censoring weighting estimators of the AUC corresponding to these two definitions, and we study their asymptotic properties. We derive confidence intervals and test statistics for the equality of the AUCs obtained with two markers measured on the same subjects. A simulation study is performed to investigate the finite sample behaviour of the test and the confidence intervals. The method is applied to the French cohort PAQUID to compare the abilities of two psychometric tests to predict dementia onset in the elderly accounting for death without dementia competing risk. The 'timeROC' R package is provided to make the methodology easily usable.
Effects of body reverse pulse bias on geometric component of charge pumping current in FD SOI MOSFETs (2002)

The geometry-dependent component in charge pumping current (I/sub cp/) is well known as the undesirable factor causing the overestimated interface state density in FD SOI devices (Brugler and Jespers, 1969; Groeseneken et al, 1984; Li and Ma, 1995). In this work, the effects of the body reverse pulse bias on the geometric component of I/sub cp/ in fully depleted (FD) SOI MOSFETs are described. The majority carriers of the high resistivity body region can be completely removed by a reverse pulse applied to the body. As a result, the geometry-dependent component is suppressed. This method also suppresses the reduction of effective channel length which takes place when using a DC reverse bias.
A Convergence Theorem for Competitive Bidding with Differential Information (1979)

IN THIS PAPER we investigate the properties of the winning bid in a sealed bid tender auction where each player has private information. We find that it is possible for the winning bid to converge in probability to the true value of the object at auction, even though no bidder knows the true value. Necessary and sufficient conditions for this phenomenon are derived, extending and generalizing certain of Wilson's results [3]. We study an auction in which a seller offers to sell at the highest bid an item of unknown value V. The kth bidder receives a private signal Sk (for k = 1, 2,.. .) and submits a bid without knowledge of the other signals. A finitely additive probability measure P reflects the bidders' unanimous beliefs about V and the signals. Conditional on V, the signals are independent and identically distributed. The signals take their values in some space &'. With n bidders, a bidding strategy for k is a function Pnk: 9' -> R. k's strategy specifies that upon receiving the signal Sk, he shall bid Pnk(Sk).2 Thus the winning
Molecular genetic methods for diagnosis and antibiotic resistance detection of mycobacteria from clinical specimens (2004)

Mycobacteria comprise a diverse group of bacteria that are widespread in nature, some of which cause significant disease in humans. Members of the Mycobacterium tuberculosis complex (MTBC) are the most important human pathogens of the genus Mycobacterium. Traditional methods for detection and identification of mycobacteria include microscopy, culture and phenotypic tests. These methods either lack sensitivity, specificity, or are time consuming. Advances in the field of molecular biology have provided rapid diagnostic tools that have reduced the turnaround times for detecting MTBC and drug resistance in cultures and directly in clinical specimens from weeks to days. This review discusses the molecular genetic techniques for detecting and identifying MTBC as well as drug resistance of mycobacteria in clinical specimens.
A formal method for computer design verification (1982)

A formal computer design verification method based on Floyd's inductive assertion technique[9] is presented as an alternative or at least a supplement to simulation. The semantics of a register transfer language is defined formally. It specifies how machine variables and time change. Hardware descriptions in this language may contain assertions. The formal definition of the language can then be used for automatic verification of logical correctness and realtime performance of the design.
Osteoporosis in Men with Hyperprolactinemic Hypogonadism (1986)

To ascertain the effects of chronic hyperprolactinemia and testosterone deficiency on skeletal integrity in men, we measured forearm bone density and hormone concentrations in 18 men aged 30 to 79 who had prolactin-secreting pituitary tumors. We also measured vertebral bone density in 12 of the men. Patients with hyperprolactinemia had significant decreases in both forearm (p less than 0.001) and vertebral bone density (p = 0.003) compared with age-matched controls. Cortical osteopenia was significantly related to the duration of hyperprolactinemia (p less than 0.01) but not to the absolute levels of prolactin or androgens. Seven patients had longitudinal follow-up measurements of forearm bone density. Normalization of serum levels of prolactin or testosterone was associated with an increase in forearm bone density (p less than 0.05). These data show that chronic hyperprolactinemia and testosterone deficiency in men have deleterious and previously unrecognized extragonadal effects that may be alleviated after normalization of hormone concentrations.
Studies of the prothrombin activation pathway utilizing radioimmunoassays for the F2/F1 + 2 fragment and thrombin--antithrombin complex (1982)

We have evaluated the efficacy of utilizing radioimmunoassays (RIAs) for prothrombin activation fragments (F2/F1 + 2) and for thrombin-- antithrombin complex (TAT) in purified systems and in whole blood. During venipuncture, appropriate anticoagulants were employed in order to prevent the generation of thrombin and factor Xa. The RIAs were shown to be specific for F2/F1 + 2 as well as TAT and did not interact with other plasma components. Initially, thrombin generation was studied in a purified human system of prothrombin, antithrombin, factor Xa, and factor V as well as phospholipid and Ca++. Under these conditions, the kinetics of F2/F1 + 2 and TAT generation were virtually superimposable. However, when factor V was omitted from the reaction mixture, a significantly greater amount of F2/F1 + 2 as compared to TAT was observable. Subsequently, prothrombin activation was monitored during the spontaneous coagulation of freshly drawn blood. Throughout the entire course of thrombin generation, the observable rate of formation of F2/F1 + 2 was considerably greater than that of TAT. We have examined the levels of F2/F1 + 2 and TAT in normal individuals. Our studies indicate that the concentrations of F1 + 2 and TAT average 1.97 nM and 2.32 nM, respectively. We have also quantitated the concentrations of F2/F1 + 2 and TAT in patients with disseminated intravascular coagulation. In these individuals, the levels of both components are elevated. However, the ratio of F1 + 2 to TAT ranges from 2.37 to 5.55. Thus, we conclude that under in vivo conditions, prothrombin activation is characterized by the accumulation of a stable precursor, such as prethrombin-2, and that this phenomenon may be related to an alteration of factor V function.
ACO for a new TSP in region coverage (2005)

An unmanned reconnaissance aerial vehicle mounted sensor of footprint with a small area /spl omega//sub s//sup 2/ is used to cover critical airbase structures for damage assessment. The region of coverage interest is modeled with a closed union of a minimal set of interior disjoint rectangles of width /spl omega//sub i/ = /spl omega//sub s/. We wish to find a minimum-length flight path for complete coverage for the nonholonomic vehicle. We prove that our minimization problem is a traveling salesman problem (TSP) that is symmetric, non-Euclidean and satisfies the triangular inequality. We compare our modeling primitive with two simple primitives commonly used for representing coverage regions. An ant colony optimization heuristic for solving the TSP is presented.
Antigen-driven but not lipopolysaccharide-driven IL-12 production in macrophages requires triggering of CD40 (1997)

We demonstrated that two distinct pathways exist for the induction of IL-12 in APC. The first pathway for IL-12 production occurred during responses to T cell-dependent Ags such as OVA and required triggering of CD40 molecules on the APC. IL-12 production in this T cell-dependent system increased in direct proportion to Ag concentration and required TCR ligation but not CD28 costimulation. The second pathway occurred when bacterial products such as LPS or heat-killed Listeria monocytogenes were used to activate macrophages to produce IL-12 in the complete absence of T cells. In this second pathway, IL-12 production was completely independent of CD40 triggering. In both pathways, the presence of IFN-gamma was not required for induction of IL-12 synthesis when splenic adherent cells (SAC) from normal mice were used. However, addition of IFN-gamma to cultures of Th2 T cells and SAC increased IL-12 production two- to fivefold, and addition of rTNF-alpha with IFN-gamma further enhanced IL-12 production. The addition of TNF-alpha in the absence of IFN-gamma, however, had no effect on IL-12 production in the T cell-dependent pathway. Similarly, addition of TNF-alpha in the presence or the absence of IFN-gamma to cultures of LPS or heat-killed Listeria and SAC did not increase IL-12 production, but addition of IFN-gamma alone greatly enhanced IL-12 production, consistent with the idea that bacterial stimuli induce significant quantities of endogenous TNF-alpha production. These results indicate that the requirements for the induction of IL-12 production in T cell-dependent and T cell-independent responses differs mainly with regard to CD40 triggering. Furthermore, these results suggest that IL-12 production can be induced by bacterial products in patients with hyper-IgM syndrome who lack CD40 ligand expression and in those treated with soluble gp39 to interrupt CD40-CD40 ligand interactions.
Quantitative optimization of solid freeform deposition of aqueous hydrogels (2013)

Many soft tissues exhibit complex anatomical geometry that is challenging to replicate for regenerative medicine applications. Solid freeform fabrication (SFF) has emerged as an attractive approach for creating 3D tissues, but a detailed understanding of how specific fabrication parameters affect accuracy and viability has not been established to date. In this study, we evaluate the effects of printing parameters of the Fab@Home 3D printing system on accuracy using alginate, photocrosslinkable polyethylene-glycol diacrylate (PEG-DA) and gelatin as commonly used model hydrogel materials. Print accuracy and resolution along the length, width and height were determined based on quantitative image analysis. The effects of extrusion parameters on cell viability were assessed using porcine aortic valve interstitial cells (PAVIC) as a model cell type. We observed that pressure, pathheight and pathspace all significantly affected print accuracy and resolution. Printing conditions did not affect PAVIC viability within the ranges applied. We predicted that optimal pressure, pathheight and pathspace values would be increased linearly with increasing nozzle diameter, and we confirmed that the predicted values generate accurate 3D geometries while poorly chosen parameters yield inaccurate, unpredictable geometries. This systematic optimization strategy therefore improves the accuracy of 3D printing platforms for biofabrication and tissue engineering applications.