gebhart/patrepeval huggingface dataset:
Characterization of a New Plasmid-Like Prophage in a Pandemic Vibrio parahaemolyticus O3:K6 Strain (2009)

Vibrio parahaemolyticus is a common food-borne pathogen that is normally associated with seafood. In 1996, a pandemic O3:K6 strain abruptly appeared and caused the first pandemic of this pathogen to spread throughout many Asian countries, America, Europe, and Africa. The role of temperate bacteriophages in the evolution of this pathogen is of great interest. In this work, a new temperate phage, VP882, from a pandemic O3:K6 strain of V. parahaemolyticus was purified and characterized after mitomycin C induction. VP882 was a Myoviridae bacteriophage with a polyhedral head and a long rigid tail with a sheath-like structure. It infected and lysed high proportions of V. parahaemolyticus, Vibrio vulnificus, and Vibrio cholerae strains. The genome of phage VP882 was sequenced and was 38,197 bp long, and 71 putative open reading frames were identified, of which 27 were putative functional phage or bacterial genes. VP882 had a linear plasmid-like genome with a putative protelomerase gene and cohesive ends. The genome does not integrate into the host chromosome but was maintained as a plasmid in the lysogen. Analysis of the reaction sites of the protelomerases in different plasmid-like phages revealed that VP882 and PhiHAP-1 were highly similar, while N15, PhiKO2, and PY54 made up another closely related group. The presence of DNA adenine methylase and quorum-sensing transcriptional regulators in VP882 may play a specific role in this phage or regulate physiological or virulence-associated traits of the hosts. These genes may also be remnants from the bacterial chromosome following transduction.
Ultrahigh-Speed, Swept-Source Optical Coherence Tomography Angiography in Nonexudative Age-Related Macular Degeneration with Geographic Atrophy (2015)

Purpose To investigate ultrahigh-speed, swept-source optical coherence tomography (SSOCT) angiography for visualizing vascular changes in eyes with nonexudative age-related macular degeneration (AMD) with geographic atrophy (GA). Design Observational, prospective, cross-sectional study. Participants A total of 63 eyes from 32 normal subjects and 12 eyes from 7 patients with nonexudative AMD with GA. Methods A 1050-nm, 400-kHz A-scan rate SSOCT system was used to perform volumetric optical coherence tomography angiography (OCTA) of the retinal and choriocapillaris (CC) vasculatures in normal subjects and patients with nonexudative AMD with GA. Optical coherence tomography angiography using variable interscan time analysis (VISTA) was performed to assess CC alteration and differentiate varying degrees of CC flow impairment. Main Outcome Measures Qualitative comparison of retinal and CC vasculatures in normal subjects versus those in patients with a clinical diagnosis of nonexudative AMD with GA. Results In all 12 eyes with GA, OCTA showed pronounced CC flow impairment within the region of GA. In 10 of the 12 eyes with GA, OCTA with VISTA showed milder CC flow impairment extending beyond the margin of GA. Of the 5 eyes exhibiting foveal-sparing GA, OCTA showed CC flow within the region of foveal sparing in 4 of the eyes. Conclusions The ability of ultrahigh-speed, swept-source OCTA to noninvasively visualize alterations in the retinal and CC vasculatures makes it a promising tool for assessing nonexudative AMD with GA. Optical coherence tomography angiography using VISTA can distinguish varying degrees of CC alteration and flow impairment and may be useful for elucidating disease pathogenesis, progression, and response to therapy.
An investigation of monolithic colliding-pulse mode-locked semiconductor lasers (1996)

Summary form only given. We report on the operation of monolithic colliding-pulse (CPM) semiconductor lasers. Our lasers are passively mode-locked lasers consisting of a strip-loaded waveguide structure fabricated on four quantum well GaAs/AlGaAs semiconductor material nominally emitting at a wavelength of 870 nm. CPM action is achieved in these lasers by reverse biasing of an electrically isolated section in the center of the laser cavity that forms a saturable absorber.
Serpine1 negatively regulates Th1 cell responses in experimental autoimmune encephalomyelitis (2023)

Abstract Th1 cells are critical in experimental autoimmune encephalomyelitis (EAE). Serpine1 has been posited as an inhibitor of IFN γ from T cells though its role in autoimmunity remains unclear. Here, we show that Serpine1 knockout (KO) mice develop EAE of enhanced severity relative to wild-type (WT) controls. Serpine1 overexpression represses Th1 cell cytokine production and pathogenicity, while Serpine1-KO:2D2 Th1 cells transfer EAE of increased severity in comparison to WT 2D2 Th1 cells. Notably, polarized Serpine1-KO Th1 cells display delayed expression of the Th1-specific inhibitory receptor, Tim-3. Serpine1-KO:Tim-3-Tg Th1 cells, which transgenically over-express Tim-3, showed increased expression of IFN γ and reduced expression of the checkpoint molecules Lag-3 and PD-1 relative to WT Tim-3-Tg counterparts. Further, Serpine1 deficiency restored the EAE phenotype of Tim-3-Tg mice that normally develop mild disease. Together, we identify Serpine1 as a negative regulator of Th1 cells. Key points Serpine1 inhibits EAE in a T cell-dependent manner. Serpine1 is upregulated in Th1 cells and inhibits their pathogenicity. Serpine1 promotes expression and function of Th1-specific inhibitory receptor Tim-3.
Temperature Dependence of the Carrier Lifetime in 4H-SiC Epilayers (2010)

The temperature dependence of the carrier lifetime was measured in n-type 4H-SiC epilayers of varying Z1/2 deep defect concentrations and layer thicknesses in order to investigate the recombination processes controlling the carrier lifetime in low- Z1/2 material. The results indicate that in more recently grown layers with lower deep defect concentrations, surface recombination tends to dominate over carrier capture by other bulk defects. Low-injection lifetime measurements were also found to provide a convenient method to assess the surface band bending and surface trap density in samples with a significant surface recombination rate.
Design of metasurface-backed printed dipoles (2016)

In this paper, novel metasurface-backed dipoles are proposed. The dipoles are printed on a thin substrate the bottom of which is designed to get the characteristics of artificial magnetic conductor(AMC) for acceptable antenna performances. The structure is exemplified to resonate at 2.4 GHz as a relatively low frequency. The properties of the proposed AMC-backed dipoles are investigated in terms of the size, return loss, antenna efficiency and the like, Also, it is shown that the problems of the PEC-backed dipoles can be solved by the method.
Protocols for the Design of Kinase‐focused Compound Libraries (2017)

Protocols for the design of kinase-focused compound libraries are presented. Kinase-focused compound libraries can be differentiated based on the design goal. Depending on whether the library should be a discovery library specific for one particular kinase, a general discovery library for multiple distinct kinase projects, or even phenotypic screening, there exists today a variety of in silico methods to design candidate compound libraries. We address the following scenarios: 1) Datamining of SAR databases and kinase focused vendor catalogues; 2) Predictions and virtual screening; 3) Structure-based design of combinatorial kinase inhibitors; 4) Design of covalent kinase inhibitors; 5) Design of macrocyclic kinase inhibitors; and 6) Design of allosteric kinase inhibitors and activators.
Comparison of the Anticoagulant and Antithrombotic Effects of YM-75466, a Novel Orally-Active Factor Xa Inhibitor, and Warfarin in Mice (1998)

The anticoagulant and antithrombotic effects of YM-75466 (N-[4-[(1-acetimidoyl-4-piperidyl)oxy]phenyl]-N-[(7-amidino-2-naph thyl)methyl]sulfamoyl acetic acid monomethanesulfonate), a novel orally-active factor Xa (FXa) inhibitor, and warfarin were compared in mice. Both agents were orally administered in all studies. In ex vivo studies, the peak effects of YM-75466 occurred 1 hr after administration while the peak of warfarin activity occurred 18 hr after administration. At each peak, both YM-75466 and warfarin prolonged coagulation time dose-dependently. The dose response curve of warfarin for prothrombin time was steeper than that of YM-75466. In a thromboplastin-induced thromboembolism model, administration of 30 mg/kg YM-75466 or 3 mg/kg warfarin significantly improved the lethality ratio. In blood loss studies, YM-75466 did not increase blood loss from the tail even at 30 mg/kg, while warfarin markedly increased blood loss at 3 mg/kg. Agents that interfere with warfarin action did not interfere with YM-75466 action. In conclusion, this study shows that YM-75466 has advantages over warfarin: i) rapid onset of anticoagulant activity, ii) wide therapeutic range, iii) little effect on bleeding and iv) lack of drug interaction with agents that interfere with warfarin. These results suggest that YM-75466 may be promising as a novel oral anticoagulant agent.
High-field level-crossing and Stark studies of the A 2Σ+ state of OD (1973)

We have carried out a high-field level-crossing experiment on the ν = 0, N=1, J=3/2 ot the OD A 2Σ+ state. A precise measurement of the magnetic fields at which three crossovers are observed permits a determination of the three hyperfine constants b = 110.4 ± 2.6 MHz, c = 22 ± 14 MHz, and eQq = 0.09 ± 0.05 MHz (3σ). In addition, we have applied a static electric field parallel to the magnetic field and observed a shift in the location of the high-field level crossings from which we calculate the dipole moment of this excited state to be 1.72 ± 0.10 D (3σ). A comparison of these structural parameters is made with ab initio calculations.
Carbonization of Disclike Molecules in Porous Alumina Membranes: Toward Carbon Nanotubes with Controlled Graphene‐Layer Orientation (2005)

Graphitic carbon nanotubes that comprise graphene layers aligned perpendicular to the tube axis (see image; arrow indicates tube axis) were obtained by stepwise carbonization of preorganized disclike molecules in a porous alumina template. The alignment, size, wall thickness, and shape of the tubes were all controlled by this method. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2002/2005/z460986_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Mechanism of inactivation of .gamma.-aminobutyric acid aminotransferase by 3-hydrazinopropionic acid (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTMechanism of inactivation of .gamma.-aminobutyric acid aminotransferase by 3-hydrazinopropionic acidRichard B. Silverman and Gregory T. OlsonCite this: J. Org. Chem. 1995, 60, 19, 6232–6234Publication Date (Print):September 1, 1995Publication History Published online1 May 2002Published inissue 1 September 1995https://pubs.acs.org/doi/10.1021/jo00124a053https://doi.org/10.1021/jo00124a053research-articleACS PublicationsRequest reuse permissionsArticle Views82Altmetric-Citations-LEARN 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
An Analytical Model of eMMC Key Performance Indicators (2015)

Embedded Multi Media Card (eMMC) has become the mainstream embedded storage system for mobile devices like Smartphones and Tablets and it is gaining traction in other products (e.g. Wearables) and segments (e.g. Automotive). eMMC devices are complex embedded systems that include one or more Flash NAND chips and a microcontroller with a specific Firmware (FW). Estimating eMMC key performance indicators (KPIs) since the early stage of the product definition is paramount to identify potential gaps, and give prompt feedbacks to development teams. In this paper a sound theoretical framework for estimating eMMC system metrics is introduced. The mathematical model takes into account the most relevant architectural parameters of NANDs, microcontroller and FW.
Software diversity: security, entropy and game theory (2012)

Although many have recognized the risks of software monocultures, it is not currently clear how much and what kind of diversity would be needed to address these risks. Here we attempt to provide insight into this issue using a simple model of hosts and vulnerabilities connected in a bipartite graph. We use this graph to compute diversity metrics as Renyi entropy and to formulate an anti-coordination game to understand why computer host owners would choose to diversify. Since security isn't the only factor considered when choosing software in the real world, we propose a slight variation of the popular security wargame Capture the Flag that can serve as a testbed for understanding the utility of diversity as a defense strategy.
Toward Conductive Mesocrystalline Assemblies: PbS Nanocrystals Cross-Linked with Tetrathiafulvalene Dicarboxylate (2015)

We use the organic semiconductor tetrathiafulvalene dicarboxylate (TTFDA) to assemble PbS nanocrystals into conductive mesocrystals. Density functional theory calculations predict a size-tunable, near-resonant alignment between the PbS 1Sh state and the TTFDA HOMO with the potential to form a conductive channel for holes. We test this hypothesis with transport measurements on TTFDA-functionalized PbS nanocrystals of different sizes and find a pronounced modulation of the field-effect hole mobilities. Photothermal deflection spectroscopy reveals unchanged Urbach energies after ligand exchange, whereas further surface modification by colloidal-atomic layer deposition leads to a strong increase in the density of in-gap states. Hole transport in PbS-TTFDA is unusually robust against such surface modification. Our structural analysis of the mesocrystals suggests that TTFDA induces a defined interparticle spacing, the orientation of atomic lattices, and the angle within the mesocrystal unit cell. The results of this work pave the way toward conductive mesocrystalline assemblies of hybrid semiconductor nanostructures with size-tunable transport properties.
Androgen-Dependent Regulation of Her-2/neu in Prostate Cancer Cells (2006)

The mechanisms underlying the progression of prostate cancer to a state of resistance to hormone ablation remain poorly understood. Here, we have investigated the relationship between androgen receptor (AR) and Her-2/neu in prostate cancer cells. Overexpression of Her-2/neu (c-ErbB2) activates the AR pathway and confers a survival and growth advantage to prostate cancer cells in an androgen-deficient milieu. In vitro, the absence of androgens or AR blockade induced Her-2/neu protein expression and phosphorylation. In contrast, upon readministration of androgens, Her-2/neu mRNA, protein, and phosphorylation levels decreased linearly with increasing concentrations of dihydrotestosterone as LNCaP cells reentered the cell cycle. In vivo, induction of Her-2/neu by castration in orthotopically injected LNCaP cells resulted in a progressive increase in prostate-specific antigen secretion into the mouse serum, indicating that Her-2/neu-mediated, AR-dependent transcription occurs following castration and results in tumor cell growth. Finally, selection of LNCaP cells stably transfected with short hairpin RNA specific for AR resulted in Her-2/neu overexpression. Similarly, knockdown of Her-2/neu led to induction of AR. However, when Her-2/neu and AR were simultaneously targeted, we observed cell death, whereas surviving cells retained low level expression of Her-2/neu. Thus, induction and activation of Her-2/neu occurs in an androgen-depleted environment or as a result of AR inactivation, promoting ablation-resistant survival of prostate cancer cells. These data provide the biochemical rationale to target Her-2/neu in hormone-refractory prostate cancer.
ChemInform Abstract: A GENERAL SYNTHESIS OF α‐VINYL‐α‐AMINO ACIDS (1979)

Abstract Aus den Iminen (I) erhält man durch Behandlung mit Li‐bis‐silylamid (II) und Alkylierungsmitteln (III) die Substitutionsprodukte (IV), die zu den Vinyl‐aminosäurederivaten (V) bzw. (VI) hydrolysiert werden können.
A compound-heterozygous Marfan patient: two defective fibrillin alleles result in a lethal phenotype. (1994)

We describe here the identification of defined mutations in both alleles of the fibrillin gene (FBN1) in a compound-heterozygote Marfan syndrome (MFS) child who had a very severe form of MFS resulting in death from cardiac failure at the age of 4 mo. The nonconsanguineous parents were both affected with MFS. The father's heterozygous point mutation has earlier been reported to result in W217G substitution, the mother was here shown to carry a heterozygous point mutation resulting in G2627R substitution, and the child had inherited both these mutations. The mutant FBN1 alleles were demonstrated to be transcribed with equal efficiency compared with the normal alleles, but metabolic labeling of fibroblast cultures from the child and both parents showed reduced biosynthesis and secretion of profibrillin. Also, the respective amounts of fibrillin in cell-culture media and extracellular-matrix extracts were markedly diminished, particularly in the cell cultures from father and child. In addition, immunofluorescence analysis of the cell cultures of all three family members revealed a drastically reduced amount of microfibrils, and virtually no visible fibrils could be seen in the case of the compound-heterozygote child. These findings demonstrate incomplete dominance of fibrillin mutations and underline the fatal consequences of the complete absence of normal fibrillin molecules in the microfibrils.
GPR40 partial agonists and AgoPAMs: Differentiating effects on glucose and hormonal secretions in the rodent (2017)

GPR40 agonists are effective antidiabetic agents believed to lower glucose through direct effects on the beta cell to increase glucose stimulated insulin secretion. However, not all GPR40 agonists are the same. Partial agonists lower glucose through direct effects on the pancreas, whereas GPR40 AgoPAMs may incorporate additional therapeutic effects through increases in insulinotrophic incretins secreted by the gut. Here we describe how GPR40 AgoPAMs stimulate both insulin and incretin secretion in vivo over time in diabetic GK rats. We also describe effects of AgoPAMs in vivo to lower glucose and body weight beyond what is seen with partial GPR40 agonists in both the acute and chronic setting. Further comparisons of the glucose lowering profile of AgoPAMs suggest these compounds may possess greater glucose control even in the presence of elevated glucagon secretion, an unexpected feature observed with both acute and chronic treatment with AgoPAMs. Together these studies highlight the complexity of GPR40 pharmacology and the potential additional benefits AgoPAMs may possess above partial agonists for the diabetic patient.
Critical Issues for MOS Based Power Devices in 4H-SiC (2009)

In this paper, we present the effects of MOS channel processing on the threshold voltage and the MOS field effect mobility of 4H-SiC MOSFETs. By increasing the p-well doping concentration by two orders of magnitude, the threshold voltage could be shifted positive from 0V to 5 V when a thermal oxide layer with NO post oxidation anneal was used as the gate dielectric layer. However, a severe degradation of MOS field effect mobility, decreasing from 37 cm2/Vs to 5 cm2/Vs, was also observed. Using a different processing technique, which uses a deposited oxide layer with an NO anneal, a threshold voltage of 7.5 V and a MOS field effect mobility of 15 cm2/Vs could be achieved. A 10 kV, 1 A power DMOSFET was demonstrated with this technique. A DMOSFET turn-off voltage of 5.25 V was measured at room temperature, which shifted to 3.0 V at 250oC, providing acceptable noise margins throughout the operating temperature range.
Tensile Properties and Plastic Strain Distribution in a Metastable Cr-Mn-N Duplex Stainless Steel (2016)

The effect of stress-induced martensite on the work hardening behavior of ferrite-austenite duplex stainless steels has been investigated. A precise grid marker method was utilized to observe the plastic strain distribution in each phase during the tensile tests. Two kinds of duplex stainless steels containing 22Cr-5Mn-0.34N and 20Cr-5Mn-0.25N were employed. Stress-induced martensitic transformation did not occur in 22Cr-5Mn-0.34N steel while it occurred in 20Cr-5Mn-0.25N steel. The former uniform elongation is 0.33, but the latter is 0.61, indicating that the transformation-induced plasticity (TRIP) is apparent in the latter steel with metastable austenite due to the low nitrogen content. The precise grid marker method revealed the inhomogeneous plastic deformation in both steels. Particularly, a large difference of plastic strain was observed between the areas of newly formed martensite and the austenite adjacent to the martensite, although the plastic strain due to the martensitic transformation itself was not clearly detected. Vickers hardness tests were performed, and it was clarified not only that austenite phase is harder than ferrite phase but also that stress-induced martensite is harder than residual austenite. Based on these results, the contribution of the stress-induced martensite to the work hardening behavior in the duplex stainless steel was discussed from the view point of load transfer from the soft phase to the hard phase, i.e., the internal stress induced between the two phases.
An X-Band Low Noise InP-HBT VCO with Separate Optimized Varactor Layers (2007)

A Colpitts 8 GHz InP heterojunction bipolar transistor (HBT) monolithic voltage controlled oscillator (VCO) with separate varactor layers is presented. The separate and optimized varactor layers were grown underneath the transistor layers. A broad tuning range of 12%, low phase noise of -94 dBc/Hz at 100 KHz offset frequency, and high linearity of 2% were demonstrated. The VCO power consumption was 30 mW while providing -3 dBm output power. The over all chip size is 1.3times0.8 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> .
ChemInform Abstract: Hydrogen Bond Controlled Aggregation of Guanidinium‐Carboxylate Derivatives in the Solid State. (2002)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.