gebhart/patrepeval huggingface dataset:
Anticoagulant Dysfunction of Human Arg352Trp-Activated Protein C Caused by Defective Factor Va Inactivation (2001)

The dysfunctional mutant R352W-protein C was found in two patients with venous thrombosis. The mutant R352A-protein C was constructed to define the contribution of charge/size of the residue at 352 on protein C (chymotrypsin numbering 187). Compared with wild type-protein C, R352W-protein C showed no difference in activation by thrombin-thrombomodulin or alpha-thrombin. However, R352W-activated protein C (APC) anticoagulant activity (aPTT assay) was reduced to approximately 65%. Although the catalytic efficiency of R352W-APC towards the oligopeptide substrate S-2366 was unperturbed, factor Va and R506Q-factor Va were not efficiently inactivated by R352W-APC compared with wild type-APC. R352A-APC showed reduced anticoagulant activity and reduced efficiency in factor Va inactivation and in factor VIIIa-inactivation in the presence of protein S. These observations suggest that the dysfunction of R352W-APC in factor Va inactivation may be one of the mechanisms leading to venous thrombosis in affected patients and that R352 plays an important role in the physiological functioning of APC.
The Remote Sensing Of Eye Disorders Utilizing The Retinal Reflex Photometer (1986)

An optical device capable of detecting ocular disease states by remote sensing is described. Photometric analysis of images is explained. The clinical implications are noted for management of ocular disease in man.
Contaminations Occurring in Fungal PCR Assays (1999)

Successful in vitro amplification of fungal DNA in clinical specimens has been reported recently. In a collaboration among five European centers, the frequency and risk of contamination due to airborne spore inoculation or carryover contamination in fungal PCR were analyzed. The identities of all contaminants were specified by cycle sequencing and GenBank analysis. Twelve of 150 PCR assays that together included over 2,800 samples were found to be contaminated (3.3% of the negative controls were contaminated during the DNA extraction, and 4.7% of the PCR mixtures were contaminated during the amplification process). Contaminants were specified as Aspergillus fumigatus, Saccharomyces cerevisiae, and Acremonium spp. Further analysis showed that commercially available products like zymolyase powder or 10x PCR buffer may contain fungal DNA. In conclusion, the risk of contamination is not higher in fungal PCR assays than in other diagnostic PCR-based assays if general precautions are taken.
A Cobalt-Based Catalyst for the Hydrogenation of CO<sub>2</sub> under Ambient Conditions (2013)

Because of the continually rising levels of CO2 in the atmosphere, research for the conversion of CO2 into fuels using carbon-neutral energy is an important and current topic in catalysis. Recent research on molecular catalysts has led to improved rates for conversion of CO2 to formate, but the catalysts are based on precious metals such as iridium, ruthenium and rhodium and require high temperatures and high pressures. Using established thermodynamic properties of hydricity (ΔGH(-)) and acidity (pKa), we designed a cobalt-based catalyst system for the production of formate from CO2 and H2. The complex Co(dmpe)2H (dmpe is 1,2-bis(dimethylphosphino)ethane) catalyzes the hydrogenation of CO2, with a turnover frequency of 3400 h(-1) at room temperature and 1 atm of 1:1 CO2:H2 (74,000 h(-1) at 20 atm) in tetrahydrofuran. These results highlight the value of fundamental thermodynamic properties in the rational design of catalysts.
On triazoles XVIII. . an unexpected rearrangement observed during the reaction of 5‐amino‐1,2,4‐triazoles with <i>N</i>‐heterocyclic β‐oxo‐esters (1989)

Abstract In the course of the synthesis of pyrido[4,3‐ d ]‐1,2,4‐triazolo[1,5‐a]pyrimidine derivatives 3c representing a novel ring system an unexpected rearrangement of the intermediate enamines to yield 5 was observed. A mechanism of the formation of 5 was suggested. The isomeric pyrido[4,3‐ e ]‐1,2,4‐triazolo[1,5‐ a ]pyrimidine derivatives 4c containing also a new ring system were obtained, too. The structure of products obtained was proved with the help of their uv, cmr and X‐ray spectra.
An efficient calcium phosphate nanoparticle-based nonviral vector for gene delivery (2011)

Background: Smaller nanoparticles facilitate the delivery of DNA into cells through endocytosis and improve transfection efficiency. The aim of this study was to determine whether protamine sulfate-coated calcium phosphate (PS-CaP) could stabilize particle size and enhance transfection efficiency. Methods: pEGFP-C1 green fluorescence protein was employed as an indicator of transfection efficiency. Atomic force microscopy was used to evaluate the morphology and the size of the particles, and an MTT assay was introduced to detect cell viability and inhibition. The classical calcium phosphate method was used as the control. Results: Atomic force microscopy images showed that the PS-CaP were much smaller than classical calcium phosphate particles. In 293 FT, HEK 293, and NIH 3T3 cells, the transfection efficiency of PS-CaP was higher than for the classical calcium phosphate particles. The difference in efficiencies implies that the smaller nanoparticles may promote the delivery of DNA into cells through endocytosis and could improve transfection efficiency. In addition, PS-CaP could be used to transfect HEK 293 cells after one week of storage at 4°C with a lesser extent of efficiency loss compared with classical calcium phosphate, indicating that protamine sulfate may increase the stability of calcium phosphate nanoparticles. The cell viability inhibition assay indicated that both nanoparticles show similar low cell toxicity. Conclusion: PS-CaP can be used as a better nonviral transfection vector compared with classical calcium phosphate. Keywords: transfection efficiency, particle size, protamine sulfate, stability
The Physiology of the Fibrinolytic System. (1993)

There are many publications on the biochemical aspects of fibrinolysis and therapeutic effects of thrombolytic drugs in occlusive vessel diseases such as myocardial infarction, cerebrovascular thrombosis and venous thrombosis predisposing to pulmonary embolism. Fibrinolysis is, however, physiological phenomenon, which is constantly operating together with the coagulation system to secure the sufficient blood flow to peripheral organs or tissues. We have examined effects of various physiological parameters on the fibrinolytic enzyme system, which will be reviewed together with results reported from other laboratories.
Cell Adhesion Regulates Expression of the Androgen Receptor and Coregulators in Different Prostate Cancer Cells (2007)

Prostate cancer cells adhere to a tumor basement membrane, while secretoryepithelial cells reside in a suprabasal cell compartment. Since tumor cells are derived fromsuprabasal epithelial cells, they experience de-novo substratum adhesion in the context ofoncogenesis. We therefore analyzed whether cell-matrix adhesion could affect the proteinexpression and activity of the AR. In this study, AR protein expression declined uponsuspension of BPH-1-AR cells, but not in PC-3-AR cells shown by Western blot. In a timecourse study, BPH-1 cell lost AR expression within 6 hours, and the synthetic androgen,R1881 reduced the loss of AR expression. We further explored the mechanism of AR loss insuspended BPH-1 cells. BPH-1-AR cells underwent apoptosis (anoikis) when suspended for2 - 5 hours. Suspension did not induce significant apoptosis or decreasing of AR expressionin PC-3 cells. Inhibition of apoptosis in suspended BPH-1-AR cells, either by expression ofBcl-2 or Bcl-xl or by treatment with Z-VAD, a caspase inhibitor, prevented loss of ARprotein. In contrast, the calpain protease inhibitor , ALLN, accelerated the loss of AR proteinexpression. Additionally, cell-matrix adhesion changed the expression of coregulators of ARin the mRNA level of prostate cancer cells. Our results demonstrate that AR proteinexpression was reduced through activation of cell death pathways, and thus indirectly through cell suspension in BPH-AR cells. The activity of AR can also be regulated by adhesion in PC-3-AR and LNCaP cells through affecting the coregulators level.
<title>Single-layer silicon-on-insulator MEMS gyroscope for wide dynamic range and harsh environment applications</title> (2001)

The Army Aviation and Missile Command (AMCOM), Morgan Research Corporation, and Aegis Research Corporation are developing an SOI-based vibratory-rate z-axis MEMS gyroscope utilizing force-feedback control, and intended for wide dynamic range and harsh environment applications. Rate sensing in small diameter ballistic missile guidance units requires a rate resolution of less than 1 degree(s)/hr over a range of -3000 to +3000 degree(s)/sec, resulting in a dynamic range of 10<SUP>7</SUP>. In addition, the devices must operate through military specifications on temperature (-55 degree(s)C to +125 degree(s)C) and vibration (1000 g at 5 - 15 kHz). This paper presents modeling, simulation, and fabrication efforts, as well as initial test data, for an SOI-based rate sensor intended for this application. The prototyped gyroscope is a single layer structure consisting of a proof mass placed in a three-fold mode-decoupled symmetric suspension. The device is fabricated in a cost-effective and highly-controllable Silicon-on-Insulator (SOI) process for in-plane inertial devices. The mechanical structure is integrated in a vacuum-sealed hermetic package with a separate CMOS readout ASIC. At the present time, the device has undergone two design iterations, with the most recent just completed.
Kinetics and mechanism of aliphatic amine oxidation by aqueous (batho)2CuII (1992)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTKinetics and mechanism of aliphatic amine oxidation by aqueous (batho)2CuIIFengjiang Wang and Lawrence M. SayreCite this: J. Am. Chem. Soc. 1992, 114, 1, 248–255Publication Date (Print):January 1, 1992Publication History Published online1 May 2002Published inissue 1 January 1992https://pubs.acs.org/doi/10.1021/ja00027a032https://doi.org/10.1021/ja00027a032research-articleACS PublicationsRequest reuse permissionsArticle Views1325Altmetric-Citations48LEARN 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
Effect of glycosaminoglycans on the preimplantation development of embryos derived from in vitro fertilization and somatic cell nuclear transfer (2003)

The purpose of this study was to evaluate the effect of glycosaminoglycans (GAGs) added to the culture medium on the developmental competence of bovine embryos derived from in vitro fertilization (IVF) and from somatic cell nuclear transfer (SCNT). In vitro-matured oocytes were either inseminated with 1 x 10(6) spermatozoa mL(-1) or enucleated and reconstructed with bovine adult ear fibroblasts by SCNT. The embryos were then cultured in modified synthetic oviduct fluid (mSOF) containing 8 mg mL(-1) bovine serum albumin (BSA) (control mSOF) or control mSOF supplemented with various GAGs (hyaluronic acid, heparin or chondroitin sulfate) in a dose-dependent manner (0.1, 0.5 or 1.0 mg mL(-1)). Developmental competence was evaluated by monitoring the numbers of 2-cell embryos, 8-16-cell embryos and blastocysts. The mean cell number of flattened blastocysts stained with 5 microM bisbenzimide on Day 8 was counted. The percentage of blastocyst formation (IVF and SCNT embryos) from cleaved embryos was significantly higher (P < 0.05) in control mSOF supplemented with 0.5 mg mL(-1) hyaluronic acid (45% and 47%), heparin (40% and 47%) or chondroitin sulfate (38% and 44%) compared with control mSOF (30-31% and 30-33%). When compared with the efficacy of 0.5 mg mL(-1) GAGs, no significant differences were observed in the developmental competence of both IVF and SCNT embryos. Supplementing control mSOF with 0.5 mg mL(-1) GAGs had no effect on the cell number of IVF embryos. In contrast, supplementing 0.5 mg mL(-1) of hyaluronic acid, heparin or chondroitin sulfate to control mSOF significantly (P < 0.05) increased the numbers of total cells (93-98 v. 88 cells) and trophectoderm (TE) cells (64-66 v. 55 cells), and decreased the inner cell mass (ICM) to TE cell ratio (48.2-49.8 v. 61.3) in SCNT blastocysts compared with embryos in control mSOF. In conclusion, supplementation of culture media with GAGs may improve the development of bovine IVM-IVF and SCNT embryos to the blastocyst stage. The GAGs increased the quality of blastocysts by increasing total cell numbers in the SCNT embryos.
Privacy in the Smart City—Applications, Technologies, Challenges, and Solutions (2017)

Many modern cities strive to integrate information technology into every aspect of city life to create so-called smart cities. Smart cities rely on a large number of application areas and technologies to realize complex interactions between citizens, third parties, and city departments. This overwhelming complexity is one reason why holistic privacy protection only rarely enters the picture. A lack of privacy can result in discrimination and social sorting, creating a fundamentally unequal society. To prevent this, we believe that a better understanding of smart cities and their privacy implications is needed. We therefore systematize the application areas, enabling technologies, privacy types, attackers, and data sources for the attacks, giving structure to the fuzzy term “smart city.” Based on our taxonomies, we describe existing privacy-enhancing technologies, review the state of the art in real cities around the world, and discuss promising future research directions. Our survey can serve as a reference guide, contributing to the development of privacy-friendly smart cities.
Structures of Rat Cytosolic PEPCK:  Insight into the Mechanism of Phosphorylation and Decarboxylation of Oxaloacetic Acid<sup>,</sup> (2007)

The structures of the rat cytosolic isoform of phosphoenolpyruvate carboxykinase (PEPCK) reported in the PEPCK-Mn2+, -Mn2+-oxaloacetic acid (OAA), -Mn2+-OAA-Mn2+-guanosine-5'-diphosphate (GDP), and -Mn2+-Mn2+-guanosine-5'-tri-phosphate (GTP) complexes provide insight into the mechanism of phosphoryl transfer and decarboxylation mediated by this enzyme. OAA is observed to bind in a number of different orientations coordinating directly to the active site metal. The Mn2+-OAA and Mn2+-OAA-Mn2+GDP structures illustrate inner-sphere coordination of OAA to the manganese ion through the displacement of two of the three water molecules coordinated to the metal in the holo-enzyme by the C3 and C4 carbonyl oxygens. In the PEPCK-Mn2+-OAA complex, an alternate bound conformation of OAA is present. In this conformation, in addition to the previous interactions, the C1 carboxylate is directly coordinated to the active site Mn2+, displacing all of the waters coordinated to the metal in the holo-enzyme. In the PEPCK-Mn2+-GTP structure, the same water molecule displaced by the C1 carboxylate of OAA is displaced by one of the gamma-phosphate oxygens of the triphosphate nucleotide. The structures are consistent with a mechanism of direct in-line phosphoryl transfer, supported by the observed stereochemistry of the reaction. In the catalytically competent binding mode, the C1 carboxylate of OAA is sandwiched between R87 and R405 in an environment that would serve to facilitate decarboxylation. In the reverse reaction, these two arginines would form the CO2 binding site. Comparison of the Mn2+-OAA-Mn2+GDP and Mn2+-Mn2+GTP structures illustrates a marked difference in the bound conformations of the nucleotide substrates in which the GTP nucleotide is bound in a high-energy state resulting from the eclipsing of all three of the phosphoryl groups along the triphosphate chain. This contrasts a previously determined structure of PEPCK in complex with a triphosphate nucleotide analogue in which the analogue mirrors the conformation of GDP as opposed to GTP. Last, the structures illustrate a correlation between conformational changes in the P-loop, the nucleotide binding site, and the active site lid that are important for catalysis.
Competitive STDP-Based Spike Pattern Learning (2009)

Recently it has been shown that a repeating arbitrary spatiotemporal spike pattern hidden in equally dense distracter spike trains can be robustly detected and learned by a single neuron equipped with spike-timing-dependent plasticity (STDP) (Masquelier, Guyonneau, & Thorpe, 2008). To be precise, the neuron becomes selective to successive coincidences of the pattern. Here we extend this scheme to a more realistic scenario with multiple repeating patterns and multiple STDP neurons "listening" to the incoming spike trains. These "listening" neurons are in competition: as soon as one fires, it strongly inhibits the others through lateral connections (one-winner-take-all mechanism). This tends to prevent the neurons from learning the same (parts of the) repeating patterns, as shown in simulations. Instead, the population self-organizes, trying to cover the different patterns or coding one pattern by the successive firings of several neurons, and a powerful distributed coding scheme emerges. Taken together, these results illustrate how the brain could easily encode and decode information in the spike times, a theory referred to as temporal coding, and how STDP could play a key role by detecting repeating patterns and generating selective response to them.
Crystal structures of Mycobacterium tuberculosis RecA and its complex with ADP-AlF4: implications for decreased ATPase activity and molecular aggregation (2000)

Sequencing of the complete genome of Mycobacterium tuberculosis, combined with the rapidly increasing need to improve tuberculosis management through better drugs and vaccines, has initiated extensive research on several key proteins from the pathogen. RecA, a ubiquitous multifunctional protein, is a key component of the processes of homologous genetic recombination and DNA repair. Structural knowledge of MtRecA is imperative for a full understanding of both these activities and any ensuing application. The crystal structure of MtRecA, presented here, has six molecules in the unit cell forming a 6(1) helical filament with a deep groove capable of binding DNA. The observed weakening in the higher order aggregation of filaments into bundles may have implications for recombination in mycobacteria. The structure of the complex reveals the atomic interactions of ADP-AlF(4), an ATP analogue, with the P-loop-containing binding pocket. The structures explain reduced levels of interactions of MtRecA with ATP, despite sharing the same fold, topology and high sequence similarity with EcRecA. The formation of a helical filament with a deep groove appears to be an inherent property of MtRecA. The histidine in loop L1 appears to be positioned appropriately for DNA interaction.
Neural networks for web content filtering (2002)

With the proliferation of harmful Internet content such as pornography, violence, and hate messages, effective content-filtering systems are essential. Many Web-filtering systems are commercially available, and potential users can download trial versions from the Internet. However, the techniques these systems use are insufficiently accurate and do not adapt well to the ever-changing Web. To solve this problem, we propose using artificial neural networks to classify Web pages during content filtering. We focus on blocking pornography because it is among the most prolific and harmful Web content. However, our general framework is adaptable for filtering other objectionable Web material.
Substrate Bias Effect on the Magnetic Properties of Fe-Ta-N Films (1993)

The effects of substrate bias on the magnetic properties and structure of Fe-TaN films deposited by a new sputtering method were investigated. Films sputtered using an rf bias of less than 80 W exhibit good soft magnetic properties and have a fine-grained microstructure consisting of α-Fe and TaN. The direction of the in-plane magnetic anisotropy of the films changes with the bias applied to the substrate. For films prepared at an rf bias of over 100 W, the soft magnetic properties deteriorate due to the change in the fine-grain microstructure from bcc-Fe to fcc-γ'-Fe <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">4</sub> N(Ta). Sputtered FeTaN/SiO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> multi-layered films were also prepared with a substrate bias; in these films, the anisotropy direction of each FeTaN layer was different from that of adjacent FeTaN layers. The resulting multilayered films are isotropic with high permeability and excellent frequency response. Hence, they are suitable for use as laminated head core materials.
Degradation of PBS-based copolymers and impacts on the growth of winter wheat. (2011)

[Objective] The degradation properties of PBS-based copolymers and impacts on the growth of winter wheat were studied.[Method] Seeds of winter wheat were sown and cultivated in soil,and mixed with equal amounts of PBS,PBS-co-HS and PBS-co-BA,to investigate the degradation of polymers in soil and effects of the degradation intermediates and degradation products on seed germination and the growth of winter wheat during the continuous process of degradation.[Result] The results showed that the copolymers had better biodegradation properties than PBS in Lou Soil in Shaanxi Province under the same condition;polymer treatments had not affected the germination percentage and plant height of the winter wheat but contributed to the improvement of plant biomass.[Conclusion] These results suggested that the degradation and degradation products of PBS,PBS-co-HS and PBS-co-BA had not affected the growth of plants in soil environment for temporary.