gebhart/patrepeval huggingface dataset:
The GeneCards Suite: From Gene Data Mining to Disease Genome Sequence Analyses (2016)

GeneCards, the human gene compendium, enables researchers to effectively navigate and inter-relate the wide universe of human genes, diseases, variants, proteins, cells, and biological pathways. Our recently launched Version 4 has a revamped infrastructure facilitating faster data updates, better-targeted data queries, and friendlier user experience. It also provides a stronger foundation for the GeneCards suite of companion databases and analysis tools. Improved data unification includes gene-disease links via MalaCards and merged biological pathways via PathCards, as well as drug information and proteome expression. VarElect, another suite member, is a phenotype prioritizer for next-generation sequencing, leveraging the GeneCards and MalaCards knowledgebase. It automatically infers direct and indirect scored associations between hundreds or even thousands of variant-containing genes and disease phenotype terms. VarElect's capabilities, either independently or within TGex, our comprehensive variant analysis pipeline, help prepare for the challenge of clinical projects that involve thousands of exome/genome NGS analyses. © 2016 by John Wiley & Sons, Inc.
Bankruptcy prediction for credit risk using neural networks: A survey and new results (2001)

The prediction of corporate bankruptcies is an important and widely studied topic since it can have significant impact on bank lending decisions and profitability. This work presents two contributions. First we review the topic of bankruptcy prediction, with emphasis on neural-network (NN) models. Second, we develop an NN bankruptcy prediction model. Inspired by one of the traditional credit risk models developed by Merton (1974), we propose novel indicators for the NN system. We show that the use of these indicators in addition to traditional financial ratio indicators provides a significant improvement in the (out-of-sample) prediction accuracy (from 81.46% to 85.5% for a three-year-ahead forecast).
CD-MOF: A Versatile Separation Medium (2016)

Porous metal-organic frameworks (MOFs) have been studied in the context of a wide variety of applications, particularly in relation to molecular storage and separation sciences. Recently, we reported a green, renewable framework material composed of γ-cyclodextrin (γ-CD) and alkali metal salts--namely, CD-MOF. This porous material has been shown to facilitate the separation of mixtures of alkylaromatic compounds, including the BTEX mixture (benzene, toluene, ethylbenzene, and the regioisomers of xylene), into their pure components, in both the liquid and gas phases, in an energy-efficient manner which could have implications for the petrochemical industry. Here, we report the ability of CD-MOF to separate a wide variety of mixtures, including ethylbenzene from styrene, haloaromatics, terpinenes, pinenes and other chiral compounds. CD-MOF retains saturated compounds to a greater extent than their unsaturated analogues. Also, the location of a double bond within a molecule influences its retention within the extended framework, as revealed in the case of the structural isomers of pinene and terpinine, where the isomers with exocyclic double bonds are more highly retained than those with endocyclic double bonds. The ability of CD-MOF to separate various mono- and disubstituted haloaromatic compounds appears to be controlled by both the size of the halogen substituents and the strength of the noncovalent bonding interactions between the analyte and the framework, an observation which has been confirmed by molecular simulations. Since CD-MOF is a homochiral framework, it is also able to resolve the enantiomers of chiral analytes, including those of limonene and 1-phenylethanol. These findings could lead to cheaper and easier-to-prepare stationary phases for HPLC separations when compared with other chiral stationary phases, such as CD-bonded silica particles.
Effects of High Process-Zone Stress in Shale Stimulation Treatments (2009)

Abstract Over the last few years shale plays across North America have received significant attention because of their revenue potential and the supplementary reserves they add to the U.S. natural-gas reserves. However, the flow capacity (i.e., permeability) of these shales is very low and, therefore, requires some sort of stimulation to make them economically viable. Problems during stimulation treatments can lead to "pressure outs" and screenouts. One of the main reasons that lead to "pressure outs" is high process-zone stress (PZS). With high PZS, the chance for pressuring out is higher than screenout (i.e., one can still flush the job at lower rates provided the sand has not settled in the wellbore). The purpose of this work is to show the effects of high PZS in shale stimulation treatments and the associated production from such zones. Examples are presented from three shale wells in the Rocky Mountain region. Well A provides examples from the Gothic and Hovenweep shales, while Well B consists of an example from the Mancos shale. A Diagnostic Fracture-Injection Test (DFIT) was performed in the Gothic and Hovenweep shales before the stimulation treatment, and the results obtained point to very high PZS. History-match analysis of the Gothic and Upper or Main Hovenweep stimulation treatments using a grid-oriented, fully functional three-dimensional (3D) fracture simulator confirmed the same. Solutions are provided to overcome this effect and successfully "place" the stimulation treatment. However, the production associated with such high PZS zones is not very encouraging. Well A is temporarily abandoned because of poor production, and the Mancos shale well with high PZS (Well B) is one of the poor producers in the field. Finally, another example (Well C) from a successful Mancos test is also included in this work to show the difference in production between high- and low-PZS zones. This paper discusses methods for early identification of high-PZS shale zones to possibly avoid stimulation treatments in order to pay more attention to the low-PZS zones that require stimulation.
Theory of four-point alternating current potential drop measurements on a metal half-space (2006)

An analytic expression describing the complex voltage measured between the pickup points of a four-point probe, in contact with the surface of a half-space conductor, is derived. The driving current is assumed to be time harmonic. There are two contributions to the measured voltage. One arises from the potential drop due to electric current flowing in the conductor. The other arises from induction in the loop of the pickup circuit. Both terms are obtained by integrating analytic expressions for the electric field, derived previously, along appropriate paths. Theory is compared with experimental data for co-linear and rectangular arrangements of the probe points, and very good agreement is obtained.
Association of the HLA‐A2, CW2, B27, S31, DR2 Haplotype with Ankylosing Spondylitis. A Possible Role of NON‐B27 Factors in the Disease (1993)

With the aim of searching for HLA haplotypes and non-B27 allele frequency variations in Sardinian AS patients, HLA-A, B, Cw, DR, DQ and Bf, C4A and C4B typing and haplotype assignment was carried out in the families of 25 AS patients and in 44 healthy individuals, all B27 heterozygotes. In the AS patients a significant increase of the A2, Cw2, B27, DR2, DQ1 haplotype was found. This depends only partially on the linkage disequilibrium existing in the Sardinian population between B27 and the other alleles of this haplotype, and rather seems to be due to a primary association of Cw2 and DR2 alleles with AS. Preliminary data seem to show that this haplotype bears the S31 complotype and the DRB1*1601 allele both in the AS patients and in the healthy controls. The pathogenetic implications of these findings are discussed.
Safety and efficacy of reduced dose Brucella abortus strain- 19 vaccine in non-pregnant zebu cattle (Bos indicus) heifers (2016)

In India, brucellosis a re-emerging disease, is of public health and economic concern to dairy industry. Brucella abortus strain-19 vaccine is recommended as most effective vaccine for cattle and buffaloes, however application of full dose is restricted in adults due to persistence of antibody response that interfere with serological diagnosis. In the present study 120 seronegative female cattle (60 calves and 60 young heifers each in a group) were subjected for vaccination. In each age group, 40 animals were vaccinated subcutaneously with a reduced dose of B. abortus S-19 vaccine, 10 animals with standard dose and 10 animals served as controls. Animals were observed for local or systemic reactions after vaccination as well as during study period. Blood samples were collected on day 0, 21, 60, 90 post-vaccination for antibody response and cell mediated immunity (CMI). The study revealed that the reduced dose vaccine is safe with satisfactory humoral and CMI response comparable to that of the standard dose, in both the age groups of animals when administered subcutaneously. It was concluded that the B. abortus S-19 reduced dose vaccine is safe and effective in the young and non-pregnant cattle up to the age of 30 months.
Novel mechanisms for activated protein C cytoprotective activities involving noncanonical activation of protease-activated receptor 3 (2013)

The direct cytoprotective activities of activated protein C (APC) on cells convey therapeutic, relevant, beneficial effects in injury and disease models in vivo and require the endothelial protein C receptor (EPCR) and protease activated receptor 1 (PAR1). Thrombin also activates PAR1, but its effects on cells contrast APC's cytoprotective effects. To gain insights into mechanisms for these contrasting cellular effects, protease activated receptor 3 (PAR3) activation by APC and thrombin was studied. APC cleaved PAR3 on transfected and endothelial cells in the presence of EPCR. Remarkably, APC cleaved a synthetic PAR3 N-terminal peptide at Arg41, whereas thrombin cleaved at Lys38. On cells, APC failed to cleave R41Q-PAR3, whereas K38Q-PAR3 was still cleaved by APC but not by thrombin. PAR3 tethered-ligand peptides beginning at amino acid 42, but not those beginning at amino acid 39, conveyed endothelial barrier-protective effects. In vivo, the APC-derived PAR3 tethered-ligand peptide, but not the thrombin-derived PAR3 peptide, blunted vascular endothelial growth factor (VEGF)-induced vascular permeability. These data indicate that PAR3 cleavage by APC at Arg41 can initiate distinctive APC-like cytoprotective effects. These novel insights help explain the differentiation of APC's cytoprotective versus thrombin's proinflammatory effects on cells and suggest a unique contributory role for PAR3 in the complex mechanisms underlying APC cytoprotective effects.
Status of Fuel Cells and the Challenges Facing Fuel Cell Technology Today (2010)

The Department of Energy (DOE) Hydrogen Program supports research and development that has substantially improved the state-of-the-art in fuel cell technology, especially with regard to the major technical hurdles to fuel cell commercialization - durability, performance, and cost of fuel cell components and systems. In particular, membrane and catalyst structure and composition have been found to be critical in obtaining improved performance and durability. For example, advancements in alloy catalysts, novel catalyst supports, and mechanically-stabilized membranes have led to single-cell membrane electrode assemblies (MEAs) with platinum metal group loadings approaching the DOE 2015 MEA target that have a lifetime of 7,300 hours under voltage cycling, showing the potential to meet the DOE 2010 automotive fuel cell stack target of 5,000 hours (equivalent to 150,000 miles). In addition, improvements in the performance of alloy catalysts and membranes have helped improve overall performance and reduce the modeled cost of an 80-kW direct hydrogen fuel cell system for transportation projected to a volume of 500,000 units per year to $73/kW. While component research enabled such advances, innovation in characterization and analysis techniques has improved researchers' understanding of the processes that affect fuel cell performance and durability. An improved understanding of these processes will be key to making further progress in eliminating cost, durability, and performance challenges that remain for fuel cell technology.
Buffer Management for Reducing Packet-in Messages in OpenFlow Networks (2019)

The interaction between the control plane and data plane can lead to an additional performance penalty in OpenFlow networks. The performance penalty is very severe in large networks and packet bursts make the penalty worse. Upon arrival of a burst, the controller receives many flow installation requests in a very short time. In such cases, the controller may become the bottleneck of the OpenFlow network. Therefore, it is very important to avoid overload of the controller. In this paper, we focus on bursts of packet-in messages in OpenFlow networks. We build a queueing model for bursts of packet-in messages and present a method that decreases the number of packet-in messages using buffers in OpenFlow switches. The mismatched packets are stored in the buffers of the switches and are sent to the controller at a lower rate. We evaluate our method by queueing analysis and simulation. The results show that the bursts of packet-in messages decrease the performance of OpenFlow networks and the proposed method can reduce this effect.
Electro-Osteograms of Long Bones of Immature Rabbits (1971)

Direct current potentials in the humerus, femur, and tibia of the growing rabbit showed a consistent pattern of change: the diaphysis was electropositive in relation to the metaphysis. The growing epiphysis and epiphyseal line were identified electrically. Variations in bone contour, ridges, tuberosities, and points of muscle attachments did not alter the polarity of the bone.
Synthesis and Properties of Oligoribonucleotide Analogs Having Formacetal Internucleoside Linkages (1997)

ADVERTISEMENT RETURN TO ISSUEPREVNoteNEXTSynthesis and Properties of Oligoribonucleotide Analogs Having Formacetal Internucleoside LinkagesEriks Rozners and Roger StrömbergView Author Information Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, S-10691 Stockholm, Sweden, and Laboratory of Organic and Bioorganic Chemistry, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-17177 Stockholm, Sweden Cite this: J. Org. Chem. 1997, 62, 6, 1846–1850Publication Date (Web):March 21, 1997Publication History Received6 November 1996Published online21 March 1997Published inissue 1 March 1997https://pubs.acs.org/doi/10.1021/jo962080ohttps://doi.org/10.1021/jo962080obrief-reportACS PublicationsCopyright © 1997 American Chemical SocietyRequest reuse permissionsArticle Views382Altmetric-Citations22LEARN 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:Biopolymers,Genetics,Oligomers,Protective groups,Stability Get e-Alerts
Enantioselective organocatalytic phospha-Michael reaction of α,β-unsaturated aldehydes (2011)

The enantioselective organocatalytic phospha-Michael reaction of α,β-unsaturated aldehydes with diaryl phosphine oxides is explored for the first time using (S)-2-(diphenyl(trimethylsilyloxy)methyl)pyrrolidine as a catalyst. It afforded 1,4-addition adducts in good to excellent yields with up to 99% ee.
Synthesis, Characterization, and Explosive Properties of the Nitrogen-Rich Borazine [H<sub>3</sub>N<sub>3</sub>B<sub>3</sub>(N<sub>3</sub>)<sub>3</sub>] (1999)

The azidoborazines [Me(3)N(3)B(2)(Me)(2)B(N(3))] and [H(3)N(3)B(3)(N(3))(3)] were prepared from the combination of Me(3)SiN(3) and the chloroborazines [Me(3)N(3)B(2)(Me)(2)BCl] and (H(3)N(3)B(3)Cl(3)). The compounds have been characterized by analytical and spectroscopic methods. The molecular structure of [H(3)N(3)B(3)(N(3))(3)] has been confirmed by single-crystal X-ray diffraction techniques: triclinic space group P&onemacr; with a = 8.579(1) Å, b = 9.182(1) Å, c = 12.043(1) Å, alpha = 104.62(1) degrees, beta = 90.26(1) degrees, gamma = 110.74(1) degrees, and Z = 4. The thermal behavior of the azides have been examined by TGA/DTA. The explosion sensitivity of [H(3)N(3)B(3)(N(3))(3)], which contains 82.58% nitrogen by weight, has been accessed by drop weight impact, spark, and friction tests. These measurements indicate that [H(3)N(3)B(3)(N(3))(3)] is a relatively sensitive explosive. The Staudinger reactivity of the azides with Ph(3)P was examined, and [H(3)N(3)B(3)(N(3))(3)] was found to produce [Ph(3)P=NH(2)](N(3)). The molecular structure of this compound was determined by single-crystal X-ray diffraction techniques: orthorhombic space group P2(1)2(1)2(1) with a = 10.649(2) Å, b = 11.737(3) Å, c = 13.364(4) Å, alpha = beta = gamma = 90 degrees, Z = 4.
Characterization of antigens for Q fever serodiagnostics (2010)

The aim of this study was to identify candidate proteins for serodiagnostics of Q fever by monoclonal antibodies (MAbs), and to clone, express, and purify the selected proteins for use as antigens in ELISA. The reactivity of three MAbs to Coxiella burnetii (C. b.) Nine Mile strain and one MAb to Priscilla strain was tested using SDS-PAGE, 2-D gel electrophoresis, immunoblot analysis, and mass spectrometry. Three immunoreactive Q fever-specific proteins discriminated by MAbs, namely the CBU_0937 protein, outer membrane Com1 (CBU_1910) protein, and elongation factor Tu (CBU_0236) were identified. Successful PCR-amplification, cloning, expression, and purification of the recombinant proteins Com1 and CBU_0937 allowed their use for the screening of sera from patients with Q fever endocarditis (18) or acute Q fever (16) in ELISA. The recombinant protein CBU_0937 with unknown biological function proved to be a more applicable diagnostic tool for Q fever ELISA as compared to the Com1 protein.
Fast Visualization of Gaussian Density Surfaces for Molecular Dynamics and Particle System Trajectories (2012)

We present an efficient algorithm for computation of surface representations enabling interactive visualization of large dynamic particle data sets. Our method is based on a GPU-accelerated data-parallel algorithm for computing a volumetric density map from Gaussian weighted particles. The algorithm extracts an isovalue surface from the computed density map, using fast GPU-accelerated Marching Cubes. This approach enables interactive frame rates for molecular dynamics simulations consisting of millions of atoms. The user can interactively adjust the display of structural detail on a continuous scale, ranging from atomic detail for in-depth analysis, to reduced detail visual representations suitable for viewing the overall architecture of molecular complexes. The extracted surface is useful for interactive visualization, and provides a basis for structure analysis methods.
Realtime MicroCloud-based flow aggregation for fixed and mobile networks (2013)

Monitoring of large distributed networks requires the deployment of several probes at different network locations where traffic to be analyzed is flowing. Each probe analyzes the traffic and sends the monitoring data toward a centralized management station often using protocols such as NetFlow and IPFIX. As each probe monitors a part of the traffic, the data collector has the responsibility of merging data coming from all the probes and correlate information. This task adds extra load on collectors and prevents traffic information to be available until it has been correlated, thus preventing (near) realtime traffic monitoring. This paper describes how the microcloud architecture can be used to provide real-time traffic monitoring and correlation on large distributed environments where monitoring traffic is analyzed by several probes that collectively concur to the monitoring task. This work has been successfully validated on using this architecture for monitoring the. It DNS ccTLD and a large 3G mobile network with million of users.
DNA-Bound Proteins Contribute Much More Than Soluble Intracellular Compounds to the Intrinsic Protection against Radiation-Induced DNA Strand Breaks in Human Cells (1991)

To assess the role of soluble intracellular compounds and DNA-bound proteins in the intrinsic protection against radiation-induced DNA strand breaks, the alkaline unwinding technique was applied to cellular, nuclear, and nucleoid monolayers. It was found that, when the soluble intracellular compounds were removed from human fibroblasts by permeabilization (nuclear monolayers) and irradiated in a phosphate buffer containing 150 mM monovalent cations (Na+ and K+) and 0.8 mM MgCl2, the frequency of radiation-induced DNA strand breaks increased twofold. Removal of both soluble intracellular compounds and DNA-bound proteins from the cells by a pretreatment with 2 M NaCl (nucleoid monolayers) resulted in a 100-fold increase in the frequency of strand-break induction by gamma radiation. Expressed as percentage of total intrinsic protection against radiation-induced DNA strand breaks, DNA-bound protein contributed 99% compared to 1% by soluble intracellular compounds. Using a different experimental approach it was found that the radioprotective capacity of soluble intracellular compounds was equivalent to about 5 mM dimethyl sulfoxide (DMSO) and DNA-bound proteins to about 70 mM DMSO. It is concluded that DNA-bound proteins play a much greater role than soluble intracellular compounds in the intrinsic protection against radiation-induced DNA strand breaks in cultured human cells.
Emulation of biological networks in reconfigurable hardware (2011)

Models of biological networks have been studied through simulations using a number of software tools. However, the intrinsic disparity between the sequential nature of microprocessor architecture used in software-based simulations and the highly parallel nature of biological systems may result in prohibitively long simulation times. In this work, we adopt an alternative approach to simulation of biological systems using hardware-based emulation. Our results on Boolean network models show that such an approach can provide speedup of 17,000X when compared to existing software simulation approaches.