gebhart/patrepeval huggingface dataset:
Phylogenetic Relationship of the Twenty-One DNA Groups of the Genus Acinetobacter as Revealed by 16S Ribosomal DNA Sequence Analysis (1997)

The inter- and intrageneric relationships of members of the genus Acinetobacter were investigated by performing a comparative sequence analysis of PCR-amplified 16S ribosomal DNAs (rDNAs) from 21 strains representing all of the DNA groups that have been described. Phylogenetic treeing confirmed that Acinetobacter spp. form a coherent cluster within the gamma subdivision of the class Proteobacteria that includes strains with overall levels of 16S rDNA sequence similarity of more than 94%. The analysis of intrageneric relationships suggested that the majority of the strains cluster in five clearly distinguishable clusters, and this conclusion was supported by the results obtained with the different methods used for phylogenetic analysis (i.e., the maximum-likelihood, parsimony, and distance matrix methods). The first cluster contains the representatives of DNA groups 2 (Acinetobacter baumannii) and TU13, whereas the second cluster comprises representatives of DNA groups 3, "Close To TU13," and "between 1 and 3." The representatives of closely related Acinetobacter DNA groups 8 (Acinetobacter twoffii) and 9 belong to the third cluster, which includes the representative of DNA group 6 as well. The fourth cluster is formed by DNA groups BJ15, BJ16, and BJ17, and the fifth cluster comprises DNA groups 1 (Acinetobacter calcoaceticus), BJ14, 10, and 11. Within the fifth cluster the 16S rDNA sequences of DNA group 10 and 11 strains are nearly identical. The representatives of DNA groups 4 (Acinetobacter haemolyticus), 5 (Acinetobacter junii), 7 (Acinetobacter johnsonii), 12 (Acinetobacter radioresistens), TU14, and TU15 form individual branches that are not significantly affiliated with any of the five clusters identified. Apart from the clustering of the most closely related DNA groups, the general topology of the distance dendrogram revealed some discrepancy with previous DNA-DNA hybridization data, which may point to the inadequacy of comparative 16S rDNA sequence analysis for reflecting true evolutionary relationships of closely related bacterial taxa. Important, however, was the presence of unique sequence motifs in each of the 21 different DNA groups studied, which may be useful for rapid differentiation of DNA groups of the genus Acinetobacter.
Phase II Study of Sunitinib in Recurrent or Metastatic Squamous Cell Carcinoma of the Head and Neck: GORTEC 2006-01 (2009)

PURPOSE To assess the efficacy and toxicity of sunitinib monotherapy in palliative squamous cell carcinoma of the head and neck (SCCHN). PATIENTS AND METHODS Thirty-eight patients with SCCHN having evidence of progressive disease (PD) were treated with sunitinib 37.5 mg/d given continuously until PD or unacceptable toxicity. The primary end point was the rate of disease control, defined as stable disease (SD) or partial response (PR) at 6 to 8 weeks after treatment initiation (two-stage design, Simon). Dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) was performed in a subset of patients before and 6 to 8 weeks after treatment. The volume transfer constant of the contrast agent (K(trans)) was used to measure changes in the microcirculation blood flow and endothelial permeability of the tumor. Results A PR was observed in one patient, SD in 18, and PD in 19 (Response Evaluation Criteria in Solid Tumors [RECIST]), resulting in a disease control rate of 50%. Among the 18 patients with SD, there were five unconfirmed PRs and six additional minor responses. A significant decrease in K(trans) was seen in three of the four patients who received DCE-MRI monitoring. Grade 5 head and neck bleeds occurred in four patients. Local complications, including the appearance or worsening of tumor skin ulceration or tumor fistula, were recorded in 15 patients. CONCLUSION Sunitinib demonstrated modest activity in palliative SSCHN. The severity of some of the complications highlights the importance of improved patient selection for future studies with sunitinib in head and neck cancer. Sunitinib should not be used outside clinical trials in SSCHN.
Megaelectronvolt phosphorus implantation for bipolar devices (1988)

The use of megaelectronvolt phosphorus implantation in the formation of the buried layer of bipolar transistors was investigated. The main focus was on the reduction of the secondary defect density. The lowest defect density is obtained with annealing by rapid thermal processing (1150 degrees C/60 s). Results on electrical characteristics of bipolar transistors with megaelectronvolt-implanted buried layers are presented and compared with those of conventional devices.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Ueber Synthesen in der Biphenylreihe (1901)

e l t 3). Da die Halogen-Derivate
Model Predictive Control as an Energy Management Strategy for Hybrid Electric Vehicles (2009)

The energy management strategy in a hybrid electric vehicle is viewed as an optimal control problem and is solved using Model Predictve Control (MPC). The method is applied to a series hybrid electric vehicle, using a linearized model in state space formulation and a linear MPC algorithm, based on quadratic programming, to find a feasible suboptimal solution. The significance of the results lies in obtaining a real-time implementable control law. The MPC algorithm is applied using a quasi-static simulator developed in the MATLAB environment. The MPC solution is compared with the dynamic programming solution (offline optimization). The dynamic programming algorithm, which requires the entire driving cycle to be known a-priori, guarantees the optimality and is used here as the benchmark solution. The effect of the parameters of the MPC (length of prediction horizon, type of prediction) is also investigated.
Lumbar Spinal Stenosis: Therapeutic Options Review (2014)

Lumbar spinal stenosis (LSS) functionally impacts significant numbers of Americans per year. Current estimates place the number of Americans suffering from senescent lumbar spinal stenosis at 400,000. The prevalence of this disorder in patients ranging from 60 to 69 years of age is very high. Forty-seven percent of this age group have mild to moderate stenosis, and 19.7% have severe stenosis. As the baby boomer generation gets older, 10,000 individuals attain the age of 65 years every day in United States. LSS is becoming very common and will be a major healthcare issue as the population ages. Although LSS is not life threatening, it can cause substantial disability with limitations to performing daily activities, and thus, the associated negative impact on quality of life (QOL). This article reviews the pathophysiology and current treatment options for LSS, focusing on evidence-based treatment options.
Novel gene members in the Pho regulon of<i>Escherichia coli</i> (2006)

The transcriptome profiles of the wild-type and the phoB mutant strains were compared at the time point showing the highest expression levels of the phoB and phoR genes under a P-limiting condition. Among the 18 new putative genes that were found to be under the control of the PhoB transcriptional regulator, five genes that contain the consensus Pho box were identified by sequence analysis. A reporter gene assay was carried out by fusing the upstream regions of these genes to the promoterless enhanced green fluorescent protein gene, followed by expression. It was found that the expressions of the amn (AMP nucleosidase), yibD (metal ion stress response gene) and ytfK (hypothetical protein) genes were activated by PhoB. These results indicate the additional roles of PhoB as a global regulator.
Advances in the Elegance of Chemistry in Designing Dendrimers (2010)

Highly functional and monodisperse macromolecules with tailored architecture constitute the key to designing efficient and smart nanomaterials. Dendrimers offer real potential to achieve this goal, and one of the earlier challenges faced by this novel class of polymers has been addressed by the evolution of synthetic methodologies. This review provides an evaluation of the role played by chemistry in taking these macromolecules of academic relevance to practical industrial and biological applications, in a relatively short period. One can now construct dendrimers in a 'made-to-order' fashion, for numerous applications in a variety of disciplines.
FlexFET: a low-cost planar, self-aligned independent-double-gate MOSFET with flexible, dynamic threshold control (2005)

A variety of double-gate (DG) MOSFET transistor structures are being developed to permit scaling to the sub-50nm regime. However, flexible dynamic threshold voltage control is urgently needed for ultra-low-power digital circuits, novel analog/RF circuits, and dynamically reconfigurable & self-repairing circuits (Yang et al., 1997). Independently-double-gated (IDG) FinFETs have recently been reported to have highly-controllable V/sub t/ without the use of multiple masks & implants (Liu et al., 2003; Liu et al., 2004; Fried et al., 2003). However, a lithographically-defined fin width of >10nm is required to achieve /spl Delta/V/sub t/=0.8V/V. The few recently reported planar IDG MOSFETs have oversized, nonself-aligned bottom gates and/or require epitaxial channel growth (Tanaka et al., 1991; Harrison et al., 2003; Guarini et al., 2001). We introduce FlexFET, a low-cost planar IDG MOSFET, with a damascene metal topgate and an implanted JFET bottomgate that are self-aligned in a gate trench. This new device is highly scalable, due to its sub-lithographic undoped channel, nonimplanted ultrashallow SDEs, nonepi raised SD's, and "gate-last" flow. Most damascene gate processes use a dummy gate and implanted SDE junctions. FlexFET utilizes a spacer-lined gate trench (Chen et al., 2000; Matsuo et al., 2002) that is etched through implanted SD regions to self-align its implanted JFET bottomgate with its TiN topgate. The top and bottomgates are connected at opposite edges of the device by a damascene local interconnect (LI) that is embedded in the STI regions between devices, resulting in high layout density. Since the top gate is CMPed, and the SDEs are not implanted, there is no damage to the channel edges. Effectively "raised" SDs are achieved without using selective epi. Sidewall spacers narrow the gate trench opening, resulting in >180nm channel lengths, even with low-cost relaxed 350nm lithography.
Visualizing Localized Reentry With Ultra–High Density Mapping in Iatrogenic Atrial Tachycardia (2017)

The activation pattern of LR is of small stable rotational activations (carousels), and this drove 30% (7/23) of our postablation atrial tachycardias. However, this appearance is most often pseudo-reentrant and must be differentiated by interpretation of electrograms in the candidate circuit and activation in the wider surrounding region.
Approximating attack surfaces with stack traces (2015)

Security testing and reviewing efforts are a necessity for software projects, but are time-consuming and expensive to apply. Identifying vulnerable code supports decision-making during all phases of software development. An approach for identifying vulnerable code is to identify its attack surface, the sum of all paths for untrusted data into and out of a system. Identifying the code that lies on the attack surface requires expertise and significant manual effort. This paper proposes an automated technique to empirically approximate attack surfaces through the analysis of stack traces. We hypothesize that stack traces from user-initiated crashes have several desirable attributes for measuring attack surfaces. The goal of this research is to aid software engineers in prioritizing security efforts by approximating the attack surface of a system via stack trace analysis. In a trial on Windows 8, the attack surface approximation selected 48.4% of the binaries and contained 94.6% of known vulnerabilities. Compared with vulnerability prediction models (VPMs) run on the entire codebase, VPMs run on the attack surface approximation improved recall from .07 to .1 for binaries and from .02 to .05 for source files. Precision remained at .5 for binaries, while improving from .5 to .69 for source files.
Summary Abstract: Hydrogen plasma etching of semiconductors and their oxides (1982)

First Page
Fabrication of silicon-based multilevel nanostructures via scanning probe oxidation and anisotropic wet etching (2005)

A rational approach is described for fabricating multilevel silicon-based nanostructures via scanning probe oxidation (SPO) and anisotropic wet etching. Using silicon oxide nanopatterns on Si(100) and Si(110) surfaces created by SPO as masks, two-dimensional (2D) nanostructures with high aspect ratio and a variety of patterns can be formed by anisotropic wet etching with KOH. By employing a mixture of KOH solutions and isopropyl alcohol (IPA) as an alternative to KOH alone, control of the morphology of the etched silicon surfaces, crucial for further fabrication, was greatly improved. The SPO and etching processes can be continually repeated on the 2D nanostructures, permitting the formation of various multilevel silicon-based nanostructures, including a T-gate structure useful for electronic circuitry. In addition, these multilevel silicon structures can be used as nanoimprint moulds for their rapid replication.
Optodynamic simulation of β-adrenergic receptor signalling (2015)

Optogenetics has provided a revolutionary approach to dissecting biological phenomena. However, the generation and use of optically active GPCRs in these contexts is limited and it is unclear how well an opsin-chimera GPCR might mimic endogenous receptor activity. Here we show that a chimeric rhodopsin/β2 adrenergic receptor (opto-β2AR) is similar in dynamics to endogenous β2AR in terms of: cAMP generation, MAP kinase activation and receptor internalization. In addition, we develop and characterize a novel toolset of optically active, functionally selective GPCRs that can bias intracellular signalling cascades towards either G-protein or arrestin-mediated cAMP and MAP kinase pathways. Finally, we show how photoactivation of opto-β2AR in vivo modulates neuronal activity and induces anxiety-like behavioural states in both fiber-tethered and wireless, freely moving animals when expressed in brain regions known to contain β2ARs. These new GPCR approaches enhance the utility of optogenetics and allow for discrete spatiotemporal control of GPCR signalling in vitro and in vivo.
A New Non-intrusive Authentication Approach for Data Protection Based on Mouse Dynamics (2012)

Mouse-dynamics-related schemes have been shown to be feasible for user authentication systems, however, the existing approaches are either intrusive or not prompt response. Preventing unauthorized accesses to critical digital assets, namely, data stored in the file management system, is one of the major objectives of user authentication. We therefore propose a non-intrusive approach capable of verifying a user having performed a few times of file-related operations via a mouse. To evaluate the effectiveness of the proposed approach, the mouse movement of the file-related operations in Explorer, which is the most common way to search, open, save, copy, and/or delete files in Windows environments, is used for authentication. The experimental results show that the proposed approach is feasible and has three advantages: 1) it is non-intrusive, 2) it authenticates users in a short period of time, and 3) the quantity of mouse dynamics used for authentication purpose is lightweight.
Analysis of the Interaction of Platelet Collagen Receptor Glycoprotein VI (GPVI) with Collagen (2002)

Glycoprotein VI (GPVI) is a platelet-specific glycoprotein that has been indicated to react with collagen and activate platelets. Its structure was recently identified by cDNA cloning (Clemetson, J. M., Polgar, J., Magnenat, E., Wells, T. N., and Clemetson, K. J. (1999) J. Biol. Chem. 274, 29019-29024). However, the mechanism of the interaction between collagen and GPVI has not been analyzed in detail because both collagen and GPVI are insoluble molecules. In this study, we expressed the extracellular domain of GPVI as soluble forms as follows: the monomeric form (GPVIex) and the dimeric form of GPVI fused with the human immunoglobulin Fc domain (GPVI-Fc(2)). Purified GPVIex strongly inhibited convulxin (Cvx)-induced platelet aggregation but only weakly inhibited that induced by collagen-related peptide. However, only GPVI-Fc(2), and not GPVIex, inhibited collagen-induced platelet aggregation. The dimeric form of GPVI exhibits high affinity for collagen, as concluded from measurements of GPVI binding to immobilized collagen by both the enzyme-linked immunosorbent assay and surface plasmon resonance methods. GPVI-Fc(2) bound to the surface of immobilized collagen with a dissociation constant (K(D)) of 5.76 x 10(-7) m, but the binding of GPVIex was too weak to allow estimation of this parameter. Cvx did not inhibit the binding of dimeric GPVI to collagen, indicating that the binding site of GPVI to collagen was different from that to Cvx. Taken together, our data indicate that the high affinity binding site for collagen is composed from two chains of GPVI. Furthermore, they suggest that the binding sites for Cvx are different from the collagen-binding sites and do not need to be formed by two GPVI molecules. Because dimeric GPVI is the only form that shows high affinity to fibrous collagen, our results indicate that GPVI would be present as a dimeric form on the platelet. Moreover, surface plasmon resonance indicated that there is no detectable interaction between soluble collagen and GPVI, supporting our previous observation that GPVI only reacts with fibrous collagen.
A cache coherence approach for large multiprocessor systems (1988)

This paper explores the architecture of high-performance large scale multiprocessors using private caches for each processor. The caches reduce the average memory access time, but they also result in the well known cache coherence problem. Multiple copies of each memory location are allowed to exist but they must be kept consistent with each other. In this paper, we present a solution to the cache coherence problem specifically for shared bus multiprocessors that adapts dynamically to the reference pattern. Simulation results are presented that demonstrate the high level of performance relative to other protocols particularly during intervals with high levels of sharing.
Peptide conformations. 42. Conformation of side chains in peptides using heteronuclear coupling constants obtained by two-dimensional NMR spectroscopy (1987)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPeptide conformations. 42. Conformation of side chains in peptides using heteronuclear coupling constants obtained by two-dimensional NMR spectroscopyHorst Kessler, C. Griesinger, and K. WagnerCite this: J. Am. Chem. Soc. 1987, 109, 23, 6927–6933Publication Date (Print):November 1, 1987Publication History Published online1 May 2002Published inissue 1 November 1987https://pubs.acs.org/doi/10.1021/ja00257a004https://doi.org/10.1021/ja00257a004research-articleACS PublicationsRequest reuse permissionsArticle Views325Altmetric-Citations97LEARN 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
Integrating fiber Bragg grating sensors with sensor networks (2008)

Optical fiber Bragg grating sensors exhibit specialized sensing characteristics for harsh environments. The most common interrogation methods for FBGs require high resolution spectrometers that are not well suited to some embedded test situations. We have developed a compact, high speed, Ethernet-enabled interrogator that consumes less than 10 Watts. We describe the conventions used to convert from the optical domain to a sensor network, then present integrated system test data acquired from sensors in dynamic temperature and strain environments. Fiber optic system and sensor performance signal a maturity level capable of mainstream usability.
Development of Cell Cultures with Competency for Contributing to the Zebrafish Germ Line (2004)

The zebrafish is an established model for the genetic analysis of vertebrate development. Forward-genetic screens have generated thousands of mutations, and antisense-based methods have been used to transiently knockdown gene expression during embryogenesis. Although these methods have made the zebrafish a valuable system for the identification and functional characterization of developmentally important genes, one deficiency of the zebrafish model is the absence of methods to introduce targeted mutations to generate knockout lines of fish. Application of gene-targeting methods has been limited in nonmurine species due to the absence of germ-line competent embryonic stem (ES) cell lines. Recently, progress was made in addressing this problem by the derivation of zebrafish embryo cell lines that remain pluripotent and germ-line competent for multiple passages in culture. Zebrafish germ-line chimeras were generated using cultures derived from embryos at two different developmental stages, and targeted insertion of vector DNA by homologous recombination was demonstrated in both cultures. Several strategies are being used to optimize the production and identification of germ-line chimeras. The zebrafish embryo cell culture system should provide the basis of a gene-targeting approach that will complement other genetic strategies and improve the utility of the zebrafish model for studies of development and disease.