gebhart/patrepeval huggingface dataset:
Phenotypic analysis of TNFR1-deficient mice and characterization of TNFR1-deficient fibroblasts in vitro. (1994)

In order to analyse the physiological relevance of the 55 kDa tumor necrosis factor receptor 1 (TNFR1) and its role in various TNF related pathological conditions, such as septic shock, we have generated mice by gene targeting deficient for TNFR1 expression. The TNFR1-deficient mice are unable to cope with Listeria monocytogenes infections but mount an apparently normal immune response when challenged with Vaccinia or LCMV viruses. They are resistant to the lethal effects of lipopolysaccharide (LPS) after sensitization with D-galactosamine (D-GalN) but remain sensitive to very high doses of LPS given alone. We have analyzed functions relevant to inflammatory processes, such as adhesion, secondary factor release, and proliferation in fibroblasts derived from these mice. We show that the TNFR1 virtually monopolises TNF-mediated signaling in all these situations and that the 75 kDa TNFR2 seems to be largely restricted to an accessory role, which is compatible with the previously established "ligand passing" hypothesis.
HER2 as a Prognostic Factor in Breast Cancer (2001)

HER2 amplification/overexpression is a marker of poor prognosis in breast cancer. The prognostic impact of HER2 positivity is lower in node-negative compared with node-positive women. The only significant, independent prognostic factors in breast cancer are node status, HER2 status and menopausal status. HER2-positive tumors also contain p53 abnormalities, tend to be hormone receptor and bcl-2 negative, have lymphoid infiltration (LI) and a high mitotic index. Patients with LI who are HER2 positive have a better prognosis than those who are HER2 negative, whereas HER2-positive patients without LI have a significantly worse prognosis than HER2-negative patients. Morphological and biological alterations appear to identify two categories of breast tumor. Two hypotheses may explain the progression to two tumor types: (1) atypical ductal hyperplasia (ADH) is a precursor of ductal carcinoma in situ (DCIS), which is a precursor of invasive ductal carcinoma (IDC); or (2) ADH is a precursor of HER2-negative IDC whereas DCIS is a precursor of HER2-positive IDC. The second theory fits well with two breast cancer subsets and the characteristics of ADH and DCIS. The first type of IDC occurs in older patients, progresses slowly due to estrogen dependency but is aggressive long term. The other type progresses rapidly, is HER2 positive and is more likely to occur in young patients.
Quantum annealing (2014)

Brief description on the state of the art of some local optimization methods: Quantum annealing Quantum annealing (also known as alloy, crystallization or tempering) is analogous to simulated annealing but in substitution of thermal activation by quantum tunneling. The class of algorithmic methods for quantum annealing (dubbed: 'QA'), sometimes referred by the italian school as Quantum Stochastic Optimization ('QSO'), is a promising metaheuristic tool for solving local search problems in multivariable optimization contexts.
π-Extended <i>C</i><sub>2</sub>-Symmetric Double NBN-Heterohelicenes with Exceptional Luminescent Properties (2019)

Two novel B,N-embedded double heterohelicenes, <b>Ph-NBNDH</b> and <b>Naph-NBNDH</b>, with intensively twisted quasi-<i>C</i><sub>2</sub> symmetrical structures are synthesized for the first time via a highly regioselective intramolecular Scholl reaction. The π-extended skeletons render them with exceptional physical properties, such as the highest fluorescence quantum yields up to 0.83 among multiple helicenes. Moreover, the isolated (<i>M,M</i>)- and (<i>P,P</i>)-enantiomers of <b>Naph-NBNDH</b> deliver intense circularly polarized luminescence. As the emitting layer, <b>Ph-NBNDH</b> exhibits strong electroluminescence at high working voltage.
Mapping tissue inhomogeneity in acute myocarditis: a novel analytical approach to quantitative myocardial edema imaging by T2-mapping (2015)

The proposed cut-off values for maxT2 and madSD in the setting of ACM allow edema detection with high sensitivity and specificity and therefore have the potential to overcome the hurdles of T2-mapping for its integration into clinical routine.
Stereoselective Synthesis of Fluoro-homoneplanocin A as a Potential Antiviral Agent (2012)

Fluoro-homoneplanocin A (4) was synthesized from d-ribose, via the enyne ring-closing metathesis of 9, the stereoselective opening of epoxide 23a with fluoride, and a simultaneous oxidation–elimination reaction. The key intermediate 8 is expected to serve as a versatile intermediate for the synthesis of carbanucleosides.
Evaluation of Syncardia Total Artificial Heart Using Device Thrombogenicity Emulator (2011)

The thrombogenicity of the left ventricle of the temporary Total Artificial Heart (TAH-t) (SynCardia Systems, Inc. Tucson, AZ) was evaluated using our device thrombogenicity emulator (DTE) methodology [1] that integrates advanced numerical modeling of the whole device combined with experimental measurements of platelet activity. The ejection phase of the cardiac cycle, including diaphragm motion, was modeled with fully-coupled fluid structure interaction (FSI) simulation. Stress loading histories of several thousand platelet trajectories were extracted from these simulations and collapsed into quantitative probability density function (PDF) distributions that represent the TAH-t thrombogenic footprint. Representative stress-loading waveforms with substantially higher stress accumulation (high propensity to cause platelet activation) were replicated in computer controlled hemodynamic shearing device (HSD), where the effect on platelet activation was measured with a modified prothrombinase assay. By determining the platelet stress accumulation distribution, the thrombogenic signature unique to specific TAH design from the results, this methodology facilitates virtual evaluation and optimization of various designs.
Flux networks in metabolic graphs (2009)

A metabolic model can be represented as a bipartite graph comprising linked reaction and metabolite nodes. Here it is shown how a network of conserved fluxes can be assigned to the edges of such a graph by combining the reaction fluxes with a conserved metabolite property such as molecular weight. A similar flux network can be constructed by combining the primal and dual solutions to the linear programming problem that typically arises in constraint-based modelling. Such constructions may help with the visualization of flux distributions in complex metabolic networks. The analysis also explains the strong correlation observed between metabolite shadow prices (the dual linear programming variables) and conserved metabolite properties. The methods were applied to recent metabolic models for Escherichia coli, Saccharomyces cerevisiae and Methanosarcina barkeri. Detailed results are reported for E. coli; similar results were found for other organisms.
Effects of mitogens and other agents on rat mesangial cell proliferation, pH, and Ca2+ (1990)

We investigated effects of various agents on proliferation, intracellular pH (pHi), and intracellular calcium [( Ca2+]i) of rat mesangial cells (MCs) in early passages (2-5). Serum-starved MCs incubated in HCO3- were exposed to one of the following: fetal calf serum (FCS), serotonin, angiotensin II (ANG II), arginine vasopressin (AVP), bombesin (Bom), bradykinin (BK), epidermal growth factor (EGF), epinephrine (Epi), interleukin 1 (IL-1), norepinephrine (NE), neuropeptide Y, oxytocin, substance P (SP), platelet-derived growth factor, or 12-O-tetradecanoylphorbol-13-acetate (TPA). We assessed DNA synthesis from [3H]thymidine uptake during exposure to test agent. All agents except ANG II, NE, Bom, and SP were mitogenic. When MCs were incubated in a HCO3(-) -free N-2-hydroxyethylpiperazine-N'-2-ethanesulfonic acid-buffered medium, maximal mitogenic responses to FCS, AVP, and EGF were 41, 44, and 55% (P less than 0.01) lower, respectively, than those in presence of HCO3-. In absence of HCO3-, agents other than BK and IL-1 produced a biphasic pHi response characterized by a transient acidification followed by a prolonged alkalinization that was both Na(+)-dependent and amiloride-sensitive. In presence of HCO3-, agents produced only a small and gradual acidification, except for IL-1 and Epi. Addition of all agonists except IL-1, EGF, and TPA produced significant transient increases in [Ca2+]i, the magnitudes of which were similar in HCO3- and non-HCO3- buffers. These results demonstrate that, in presence of HCO3-, agents (i.e., NE and ANG II) can produce typical [Ca2+]i transients and still not cause MC proliferation. Conversely, an agent may cause proliferation without eliciting a short-term change in either [Ca2+]i or pHi (i.e., IL-1), a change in [Ca2+]i but not pHi (i.e., Epi), or a change in pHi but not [Ca2+]i (i.e., TPA). Thus, at least for MCs, proliferation in HCO3- can be dissociated from early agonist-induced changes in pHi and [Ca2+]i.
<i>Thermoacoustics: A Unifying Perspective for Some Engines and Refrigerators </i> (2003)

I am thrilled by the power density and efficiency recently achieved by thermoacoustic engines and refrigerators, and I am fascinated by some of the latest developments in thermoacoustics.'' With that sentence, Dr. G. W. Swift begins a textbook that employs 21st century pedagogical tools to introduce students and researchers to a 21st century technology. In addition to a logical and complete development of this multidisciplinary subject, the 300-page textbook includes a CD-ROM with computerized animations and DELTAE software, with its own 200-page manual in searchable PDF format.
Uplink Buffer Status Reporting for Delay Constrained Flows in 3GPP Long Term Evolution (2009)

Scheduling of uplink data by the network typically requires that the buffer status information from each User Equipment (UE) is available at the network to ensure that the air interface resources are not wasted. The presence of delay constrained flows or radio bearers at the UE may impose a constraint that the delay information be available at the network in addition to the size of buffer data. In this paper, we discuss the different uplink buffer status reporting schemes considered in 3GPP Long Term Evolution (LTE) and the current agreement. We propose modified limited feedback buffer status reporting schemes for delay-constrained radio bearers. Using simulation results, we illustrate that delay information at the network is important for scheduling real-time flows without dropping packets.
Whole genome sequencing of Halomonas sp. SUBG004 isolated from Little Rann of Kutch, a desert of India (2015)

A salt tolerant strain, designated as SUBG004, was isolated from the desert of India, Little Rann of Kutch. The organism is a Gram-negative, facultatively anaerobic and rod shaped bacterium. Chemotaxonomic and phylogenetic properties were consistent with its classification in the genus Halomonas. Here we report the whole genome sequence of Halomonas sp. SUBG004 deposited in DDBJ/EMBL/GenBank under accession number JPEU0100000 which provides insights for salt stress adaptation through betaine synthesis.
Fast Diffraction-Pattern Matching For Object Detection And Recognition In Digital Holograms (2013)

Publication in the conference proceedings of EUSIPCO, Marrakech, Morocco, 2013
Aromatic substitution. 48. Boron trifluoride catalyzed nitration of aromatics with silver nitrate in acetonitrile solution (1981)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAromatic substitution. 48. Boron trifluoride catalyzed nitration of aromatics with silver nitrate in acetonitrile solutionGeorge A. Olah, Alexander P. Fung, Subhash C. Narang, and Judith A. OlahCite this: J. Org. Chem. 1981, 46, 17, 3533–3537Publication Date (Print):August 1, 1981Publication History Published online1 May 2002Published inissue 1 August 1981https://pubs.acs.org/doi/10.1021/jo00330a032https://doi.org/10.1021/jo00330a032research-articleACS PublicationsRequest reuse permissionsArticle Views2242Altmetric-Citations30LEARN 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
Synthesis and Properties of [1-(3,5-dimethyl-4-iodoisoxazole)-2-(2-methyl-(5-ethynyl)trimethylsilane-3-thienyl)perfluorocyclopentene (2014)

A photochromic diarylethene of [1-(3,5-dimethyl-4-iodoisoxazole)-2-(2-methyl-(5-ethynyl) trimethylsilane-3-thienyl) perfluorocyclopentene ( 1o ) was synthesized and characterized. Its properties, including photochromic behavior and fluorescent properties have been investigated. Upon irradiation with UV light with the extended response time, the diarylethene underwent a ring opening reaction to produce closed forms and color change in solution. The results showed the compound exhibited good photochromism in acetonitrile solution. The kinetic experiments showed that the cyclization and cycloreversion processes were zeroth and first order reaction, respectively. Moreover, diarylethene 1o also exhibited obviously fluorescence switches along with the photochromism.
Thin-film Mo-Si interaction (1979)

Previous results of single-crystal Si-Mo interaction indicate that MoSi2, the phase predicted by the Walser-Bené theory, is the first silicide to form at the Si-Mo interface. We now report that in thin-film Si-Mo diffusion couples either MoSi2 or a combination of Mo3Si/Mo5Si3 forms at the interface. These two results have never been observed to occur in the same sample, indicating a bistable growth mechanism. We believe this growth to be triggered by the initial interface which is modified by sample preparation conditions. Interdiffusion and reaction of Mo with amorphous Si is also found to be slower than with crystalline Si.
Direct and controllable nitric oxide delivery into biological media and living cells by a pin-to-hole spark discharge (PHD) plasma (2011)

Nitric oxide has great potential for improving wound healing through both inflammatory and vascularization processes. Nitric oxide can be produced in high concentrations by atmospheric pressure thermal plasmas. We measured the physical characteristics and nitric oxide production of a pin-to-hole spark discharge (PHD) plasma, as well as plasma-produced nitric oxide delivery into liquid and endothelial cells. The plasma temperature was calculated as 9030 ± 320 K by the Boltzmann method, which was adequate to produce nitric oxide, although the average gas temperature was near room temperature. The plasma produced significant UV radiation and hydrogen peroxide, but these were prevented from reaching the cells by adding a straight or curved tube extension to the plasma device. Plasma-produced nitric oxide in gas reached 2000 ppm and rapidly diffused into liquid and cells. Cells remained viable following plasma treatment and showed a linear increase in cGMP concentration with plasma treatment, indicating an intracellular functional response to PHD plasma NO. These data suggest that this plasma may provide a novel method for delivering NO locally and directly for enhanced wound healing.
JDBC checker: a static analysis tool for SQL/JDBC applications (2004)

In data-intensive applications, it is quite common for the implementation code to dynamically construct database query strings and execute them. For example, a typical Java servlet Web service constructs SQL query strings and dispatches them over a JDBC connector to an SQL-compliant database. The servlet programmer enjoys static checking via Java's strong type system. However, the Java type system does little to check for possible errors in the dynamically generated SQL query strings. For example, a type error in a generated selection query (e.g., comparing a string attribute with an integer) can result in an SQL runtime exception. Currently, such defects must be rooted out through careful testing, or (worse) might be found by customers at runtime. In this paper, we describe JDBC Checker, a sound static analysis tool to verify the correctness of dynamically generated query strings. We have successfully applied the tool to find known and unknown defects in realistic programs using JDBC. We give a short description of our tool in this paper.
Statin Therapy in Acute Coronary Syndromes (2002)

Randomized trials have established that statin treatment reduces coronary events in primary prevention and in patients with stable coronary artery disease. In unstable coronary artery disease, however, the pathophysiological background is distinct, and the potential benefits of statin therapy have not been evaluated until recently. Data from animal models and clinical studies indicate that statin treatment can influence a spectrum of molecular and cellular mechanisms that are intimately related to the pathogenesis of acute coronary syndromes; these include the reduction of circulating levels of atherogenic lipoproteins (very low density lipoprotein, very low density lipoprotein remnants, intermediate density lipoprotein, and low density lipoprotein) and thus of arterial lipid deposition and the attenuation of inflammation, modulation of thrombogenesis and thrombolysis, improvement of endothelial dysfunction, and reduction of ischemia/reperfusion injury. Indeed, findings from prospective and observational studies have demonstrated that statin treatment significantly improves clinical outcome after acute coronary syndromes. Therefore, early initiation of statin therapy after an acute coronary event not only enhances adherence to treatment but also preempts the occurrence of new events. In this review, we discuss recent important developments in our knowledge of the clinical evidence of the beneficial effects of early statin therapy in acute coronary syndromes and the biological mechanisms that underlie them.
Overexpression of <i>AtCPS</i> and <i>AtKS</i> in Arabidopsis Confers Increased <i>ent</i>-Kaurene Production But No Increase in Bioactive Gibberellins (2003)

The plant growth hormone gibberellin (GA) is important for many aspects of plant growth and development. Although most genes encoding enzymes at each step of the GA biosynthetic pathway have been cloned, their regulation is less well understood. To assess how up-regulation of early steps affects the biosynthetic pathway overall, we have examined transgenic Arabidopsis plants that overexpress either AtCPS or AtKS or both. These genes encode the enzymes ent-copalyl diphosphate synthase (CPS) and ent-kaurene synthase, which catalyze the first two committed steps in GA biosynthesis. We find that both CPS and CPS/ent-kaurene synthase overexpressors have greatly increased levels of the early intermediates ent-kaurene and ent-kaurenoic acid, but a lesser increase of later metabolites. These overexpression lines do not exhibit any GA overdose morphology and have wild-type levels of bioactive GAs. Our data show that CPS is limiting for ent-kaurene production and suggest that conversion of ent-kaurenoic acid to GA12 by ent-kaurenoic acid oxidase may be an important rate-limiting step for production of bioactive GA. These results demonstrate the ability of plants to maintain GA homeostasis despite large changes in accumulation of early intermediates in the biosynthetic pathway.
Seismic screening of rock stiffness and fluid softening using rock-physics attributes (2015)

Abstract We have developed a methodology to create easy-to-implement rock-physics attributes that can be used to screen for reservoir sandstones and hydrocarbon pore fill from seismic inversion data. Most seismic attributes are based on the empirical relationships between reservoir properties and seismic observables. We have honored the physical properties of the rocks by defining attributes that complied with calibrated rock-physics models. These attributes included the fluid saturation sensitive curved pseudo-elastic impedance (CPEI) and the rock stiffness/lithology attribute pseudo-elastic impedance for lithology (PEIL). We found that the CPEI attribute correlated nicely with saturation and resistivity, whereas the PEIL attribute in practice was a scaled version of the shear modulus and correlated nicely with porosity. We determined the use of these attributes on well log and seismic inversion data from the Norwegian Sea, and we successfully screened out reservoir rocks filled with either water or hydrocarbons.
Ebola Virus VP40 Late Domains Are Not Essential for Viral Replication in Cell Culture (2005)

Ebola virus particle formation and budding are mediated by the VP40 protein, which possesses overlapping PTAP and PPXY late domain motifs (7-PTAPPXY-13). These late domain motifs have also been found in the Gag proteins of retroviruses and the matrix proteins of rhabdo- and arenaviruses. While in vitro studies suggest a critical role for late domain motifs in the budding of these viruses, including Ebola virus, it remains unclear as to whether the VP40 late domains play a role in Ebola virus replication. Alteration of both late domain motifs drastically reduced VP40 particle formation in vitro. However, using reverse genetics, we were able to generate recombinant Ebola virus containing mutations in either or both of the late domains. Viruses containing mutations in one or both of their late domain motifs were attenuated by one log unit. Transmission and scanning electron microscopy did not reveal appreciable differences between the mutant and wild-type viruses released from infected cells. These findings indicate that the Ebola VP40 late domain motifs enhance virus replication but are not absolutely required for virus replication in cell culture.
Dynamics and control of state-dependent networks for probing genomic organization (2011)

A state-dependent dynamic network is a collection of elements that interact through a network, whose geometry evolves as the state of the elements changes over time. The genome is an intriguing example of a state-dependent network, where chromosomal geometry directly relates to genomic activity, which in turn strongly correlates with geometry. Here we examine various aspects of a genomic state-dependent dynamic network. In particular, we elaborate on one of the important ramifications of viewing genomic networks as being state-dependent, namely, their controllability during processes of genomic reorganization such as in cell differentiation.
Comparison of Total Lumbosacral Flexion and True Lumbar Flexion Measured by a Dual Inclinometer Technique (1994)

Our results suggest that total lumbosacral flexion may be as equally relevant as true lumbar flexion in the measurement of trunk mobility in the clinical examination of patients with chronic low back pain. Regarding their relationship to self-reported disability, total flexion seems to be more relevant to outcome after intensive rehabilitation.