gebhart/patrepeval huggingface dataset:
A Diverse and Versatile Regiospecific Synthesis of Tetrasubstituted Alkylsulfanylimidazoles as p38α Mitogen-Activated Protein Kinase Inhibitors (2018)

An alternative strategy for the synthesis of 1-aryl- and 1-alkyl-2-methylsulfanyl-4-(4-fluorophenyl)-5-(pyridin-4-yl)imidazoles as potential p38α mitogen-activated protein kinase inhibitors is reported. The regioselective <i>N</i>-substitution of the imidazole ring was achieved by treatment of α-aminoketones with different aryl or alkyl isothiocyanates. In contrast to previously published synthesis routes starting from 2-amino-4-methylpyridine, the presented route is characterized by a higher flexibility and a lower number of steps. This strategy was also applied to access 1-alkyl-2-methylsulfanyl-5-(4-fluorophenyl)-4-(pyridin-4-yl)imidazoles in six steps starting from 2-chloro-4-methylpyridine.
Transperineal Management for Postoperative and Radiation Rectourethral Fistulas (2012)

Rectal sphincter preserving transperineal repair is a successful surgical method to repair postoperative and energy ablative rectourethral fistulas. An interposition muscle flap should be considered in the setting of energy ablative rectourethral fistulas to increase successful outcomes.
Automated mass spectrometric analysis of urinary and plasma serotonin (2010)

Serotonin emerges as crucial neurotransmitter and hormone in a growing number of different physiologic processes. Besides extensive serotonin production previously noted in patients with metastatic carcinoid tumors, serotonin now is implicated in liver cell regeneration and bone formation. The aim was to develop a rapid, sensitive, and highly selective automated on-line solid-phase extraction method coupled to high-performance liquid chromatography-tandem mass spectrometry (XLC-MS/MS) to quantify low serotonin concentrations in matrices such as platelet-poor plasma and urine. Fifty microliters plasma or 2.5 microL urine equivalent were pre-purified by automated on-line solid-phase extraction, using weak cation exchange. Chromatography of serotonin and its deuterated internal standard was performed with hydrophilic interaction chromatography. Mass spectrometric detection was operated in multiple reaction monitoring mode using a quadrupole tandem mass spectrometer with positive electrospray ionization. Serotonin concentrations were determined in platelet-poor plasma of metastatic carcinoid patients (n = 23) and healthy controls (n = 22). Urinary reference intervals were set by analyzing 24-h urine collections of 120 healthy subjects. Total run-time was 6 min. Intra- and inter-assay analytical variation were <10%. Linearity in the 0-7300 micromol/L calibration range was excellent (R(2) > 0.99). Quantification limits were 30 and 0.9 nmol/L in urine and plasma, respectively. Platelet-poor serotonin concentrations in metastatic carcinoid patients were significantly higher than in controls. The urinary reference interval was 10-78 micromol/mol creatinine. Serotonin analysis with sensitive and specific XLC-MS/MS overcomes limitations of conventional HPLC. This enables accurate quantification of serotonin for both routine diagnostic procedures and research in serotonin-related disorders.
The Drosophila SH2B Family Adaptor Lnk Acts in Parallel to Chico in the Insulin Signaling Pathway (2009)

Insulin/insulin-like growth factor signaling (IIS) plays a pivotal role in the regulation of growth at the cellular and the organismal level during animal development. Flies with impaired IIS are developmentally delayed and small due to fewer and smaller cells. In the search for new growth-promoting genes, we identified mutations in the gene encoding Lnk, the single fly member of the SH2B family of adaptor molecules. Flies lacking lnk function are viable but severely reduced in size. Furthermore, lnk mutants display phenotypes reminiscent of reduced IIS, such as developmental delay, female sterility, and accumulation of lipids. Genetic epistasis analysis places lnk downstream of the insulin receptor (InR) and upstream of phosphoinositide 3-kinase (PI3K) in the IIS cascade, at the same level as chico (encoding the single fly insulin receptor substrate [IRS] homolog). Both chico and lnk mutant larvae display a similar reduction in IIS activity as judged by the localization of a PIP(3) reporter and the phosphorylation of protein kinase B (PKB). Furthermore, chico; lnk double mutants are synthetically lethal, suggesting that Chico and Lnk fulfill independent but partially redundant functions in the activation of PI3K upon InR stimulation.
Controlled Resonances for Sensing and Biology (2013)

The detection of tiny magnetic fields emanating for example from small number of nuclear and electronic spins in biological environments holds the promise for a wide variety of applications. The presence of environmental noise presents a key obstacle on the path towards this goal. Considering a single colour center in diamond I will explain how resonance conditions can be exploited to achieve the dual of goal of sensing minute fields while protecting against environmental noise. Connections to quantum effects in biology will be drawn where similar resonance conditions are being exploited to achieve optimal performance and novel function. Finally I will proceed to explain how these tools can be used to construct a novel room temperature quantum simulator on the basis of nuclear or electron spin arrays in diamond.
Segment modeling alternatives for continuous speech recognition (1995)

This dissertation presents alternative parametric statistical models of phoneticallybased segments for use in continuous speech recognition (CSR). A categorization of segment modeling approaches is proposed according to two characteristics: the assumed form of the probability distribution and the representation chosen for segment observations. The question of distribution form divides models into two groups: those based on conditional probability densities of feature given label and those using a posteriori probabilities of label given feature. The second characteristic concerns whether a model uses a variable or fixed-length representation of observed speech segments. The choices for both characteristics have important implications, particularly for context modeling and score normalization. In this work, specific segment models are developed in order to understand the benefits and limitations that follow from these choices.
Involvement of reactive oxygen species in the cytotoxic effect of acid-electrolyzed water (2014)

Acid-electrolyzed water (AEW) is commonly used as a disinfectant in the agricultural and medical fields. Although several studies have been conducted to examine its toxicity in vitro and in vivo, the cytotoxic mechanism of AEW has never been verified. The purpose of the present study was to elucidate the underlying mechanism by which AEW exerts its in vitro cytotoxic effect. Mouse fibroblasts treated with AEW experienced dilution rate-dependent cytotoxic effects in the 100% confluent phase as well as in the mitotic phase. The levels of intracellular reactive oxygen species (ROS) increased significantly in fully-confluent cells treated with undiluted and four times diluted AEW. In both of these treatments, cytotoxicity was also observed. It is thus concluded that the in vitro cytotoxicity of AEW is attributable to increased intracellular ROS. Additionally, the ROS responsible for these effects appears to be, at least in part, hydroxyl radical because the increase in intracellular ROS was attenuated by post-treatment with dimethyl sulfoxide, a hydroxyl radical scavenger, and with the antioxidant polyphenol, proanthocyanidin.
Isolation of a calcium‐sensitive, 35,000‐dalton microfilament‐ and liposome‐binding protein from ascites tumor cell microvilli: Identification as monomeric calpactin (1987)

Microvilli isolated from the MAT-C1 ascites subline of the 13762 rat mammary adenocarcinoma contain a major calcium-sensitive microfilament-binding protein, AMV-p35 (ascites microvillar p35). Association of AMV-p35 with microfilament cores during Triton X-100 extraction of the microvilli is half-maximal at 0.1-0.2 mM calcium. The protein, which comprises 6% of the total microvillar protein, can be isolated from microfilament cores prepared in the presence of calcium by extraction with EGTA and purification by ion-exchange chromatography. Alternatively, the protein can be isolated from Triton extracts of microvilli prepared in the absence of calcium by precipitation with calcium, solubilization of the precipitate with EGTA, and chromatography on an ion-exchange column. AMV-p35 binds to phosphatidylserine liposomes and F-actin with half-maximal calcium concentrations of about 10 microM and 0.2 mM, respectively. Treatment of AMV-p35 with chymotrypsin yields a 33,000-dalton fragment, behavior similar to the tyrosine kinase substrates calpactins I and II and lipocortins I and II. Immunoblot analyses using antibodies directed against calpactin I, lipocortin I, and lipocortin II showed strong reactivity of AMV-p35 with anti-calpactin I and anti-lipocortin II, but little reactivity toward anti-lipocortin I. The close relationship between AMV-p35 and calpactin I was verified by amino acid sequence analyses of peptides isolated from cyanogen bromide digests of AMV-p35. By gel filtration and velocity sedimentation analyses purified AMV-p35 is a 35,000-dalton monomer. Moreover, AMV-p35 extracted directly from microvilli in Triton/EGTA also behaves as a 35,000-dalton menomer. These findings indicate that AMV-p35 is closely related to the pp60src kinase substrate calpactin I (p36). However, AMV-p35 occurs in the microvilli as a monomer rather than as the heterotetrameric calpactin found in several other cell types.
Sonoluminescence as the PeTa Radiation, Part Two (2017)

This paper is a continuation of one published in this journal nine months ago. The two papers present a model of cavitational luminescence (CL), multi-bubble sonoluminescence (MBSL), one-bubble sonoluminescence (OBSL), and laser-induced bubble luminescence (LIBL). The basis of this model is the PeTa (Perel’man-Tatartchenko) effect, a nonequilibrium characteristic radiation under first-order phase transitions, especially vapour condensation. In this model, the main role is given to the liquid, where the evaporation, condensation, flash, and subsequent collapse of bubbles occur. The instantaneous vapour condensation inside the bubble is a reason for the CL/MBSL/OBSL/LIBL. Apparently, the dissolved gases and other impurities in the liquid are responsible for peaks that appear at the background of the main spectrum. They are most likely excited by a shock wave occurred during the collapse. This paper, in contrast to the previous one, presents a slightly expanded model that explains additional experimental data concerning especially the LIBL spectrum. As a result, today we are not aware of any experimental data that would contradict the PeTa model, and we continue to assert that there is no mystery to the CL/MBSL/OBSL/LIBL phenomena, as well as no reason to hope that they can be used for high-temperature chemical reactions, and even more so for a thermonuclear ones.
Multi-operator access to a network management system (2002)

This paper reports on research that has been performed into a Java and CORBA based Network Management System (NMS). The research involved the building of a prototype system which used a CORBA object abstraction layer to model network elements with a Java-based operator interface layered on top. The operator interface is a graphical user interface (GUI) through which the network may be monitored and controlled. This implies that the data displayed by the operator interface should be able to be both viewed and edited as the operator desires. The system had to allow for multiple distributed operator interfaces being used simultaneously and asynchronously. One of the major issues that this work focussed on was the mechanism by which the operator interfaces would be able to maintain consistency between the data displayed by the distributed operator interfaces while still providing efficient read and write access to the data. An overview of the NMS architecture is described initially, before focussing on the high level requirements of the work that was done. The design and implementation of the approach that was adopted is then explained and discussed in the context of the requirements. A prototype implementation of the architecture using the approach was developed for a simple SDH application. This paper discusses the efficiency of the approach as it is implemented in the prototype and the areas where the design can be extended. The paper concludes that the approach used fulfils the defined requirements whilst still keeping a simple, extendable architecture.
53rd National Meeting of the Italian Society of Biochemistryand Molecular Biology (SIB)andNational Meeting of Chemistry of Biological Systems – Italian Chemical Society (SCI - Section CSB) (2008)

The 53rd National Congress of the Italian Society of Biochemistry and Molecular Biology (SIB), which will be held in Riccione from 23 to 26 September, is characterised by the elevated scientific level and interdisciplinary interest of the numerous sessions in which it is organised. The Scientific Programme comprises three joint Symposia of the SIB and the Chemistry of Biological Systems section of the Italian Chemistry Society (SCI) on Molecular Systems Biology, Chemistry of Nucleic Acids, Protein and Drug Structure, and Environmental Biotechnology. These Symposia address groundbreaking arguments, making the joint interest of the two societies particularly fascinating; the joint organisation of these events in fact signals the shared intention to proceed along the path of scientific exchange. The topics of the other sessions have been chosen by the Scientific Committee on the basis of their scientific relevance and topicality, with particular attention paid to the selection of the speakers. The SIB sessions will range from Signal Transduction and Biomolecular Targets, Protein Misfolding and its Relationship with Disease, Emerging Techniques in Biochemistry, Gene Silencing, Redox Signalling and Oxidative Stress, Lipids in Cell Communication and Signal Transduction, Mitochondrial Function and Dysfunction.
Synergistic Antifungal Activities of Bafilomycin A <sub>1</sub> , Fluconazole, and the Pneumocandin MK-0991/Caspofungin Acetate (L-743,873) with Calcineurin Inhibitors FK506 and L-685,818 against <i>Cryptococcus neoformans</i> (2000)

Cryptococcus neoformans is an opportunistic fungal pathogen that causes life-threatening infections of the central nervous system. Existing therapies include amphotericin B, fluconazole, and flucytosine, which are limited by toxic side effects and the emergence of drug resistance. We recently demonstrated that the protein phosphatase calcineurin is required for growth at 37 degrees C and virulence of C. neoformans. Because calcineurin is the target of potent inhibitors in widespread clinical use, cyclosporine and FK506 (tacrolimus), it is an attractive drug target for novel antifungal agents. Here we have explored the synergistic potential of combining the calcineurin inhibitor FK506 or its nonimmunosuppressive analog, L-685,818, with other antifungal agents and examined the molecular basis of FK506 action by using genetically engineered fungal strains that lack the FK506 target proteins FKBP12 and calcineurin. We demonstrate that FK506 exhibits marked synergistic activity with the H(+)ATPase inhibitor bafilomycin A(1) via a novel action distinct from calcineurin loss of function. FK506 also exhibits synergistic activity with the pneumocandin MK-0991/caspofungin acetate (formerly L-743,873), which targets the essential beta-1,3 glucan synthase, and in this case, FK506 action is mediated via FKBP12-dependent inhibition of calcineurin. Finally, we demonstrate that FK506 and fluconazole have synergistic activity that is independent of both FKBP12 and calcineurin and may involve the known ability of FK506 to inhibit multidrug resistance pumps, which are known to export azoles from fungal cells. In summary, our studies illustrate the potential for synergistic activity of a variety of different drug combinations and the power of molecular genetics to define the mechanisms of drug action, as well as identify a novel action of FK506 that could have profound implications for therapeutic or toxic effects in other organisms, including humans.
Deep-Hole Traps in p-Type GaAs<sub>1-x</sub>Bi<sub>x</sub> Grown by Molecular Beam Epitaxy (2011)

Deep-level transient spectroscopy measurements reveal deep-hole traps with activation energies of 0.43 and 0.23 eV in p-type GaAs 1- x Bi x samples with x = 1.2 and 3.4%, respectively, grown at 370 °C by molecular beam epitaxy. In spite of low-temperature growth, the deep-level trap concentration is suppressed on the order of 10 15 cm -3 , suggesting that Bi atoms contribute to the enhancement of migration to prevent the formation of point defects. The possible origin of the hole traps is discussed in connection with arsenic antisite, As Ga , and bismuth antisite, Bi Ga .
Location Effect on Incidence of Citrus Tristeza Virus in Hawaii (1991)

Forty-one of 45 samples from various locations on the Islands of Oahu, Maui, and Hawaii indexed positive for citrus tristeza virus (CTV) infection by enzyme-linked immunosorbent assay (ELISA). High rates of infection were also observed in young, virus-free trees planted in experimental plots in the Hilo area. In contrast, navel orange trees in a large, isolated commercial grove near South Point, Hawaii, had a low incidence of infection after 4 yr of field exposure. A gradual increase in infection was noted in the subsequent 3 yr. The isolation of the planting from large numbers of infected trees, plus lack of the efficient aphid vector, Toxoptera citricidus Kirk, in the grove, and prevailing on-shore winds may account for the low incidence of infection. Proper location may markedly reduceincidence of CTVinnewplantings, eveninareas withgenerally high potential for naturalspread.
The physics of determining chip reliability (2001)

We have indicated the necessity for using statistical models to determine the reliability of deep-submicron MOSFETs. We have presented a methodology by which the reliability can be determined from short-time tests if the defect generation statistics are linked to variations in defect activation energies. We have shown that enhanced latent failures follow from our model for deep-submicron MOSFETs. Therefore, more stringent reliability standards are required, which can be validated by the use of short-time tests. Our model provides the means to calculate these novel reliability demands quantitatively.
Mutation Testing: An Artificial Immune System Approach (2003)

Through time, many software engineering fundamentals change such as programming languages, paradigms and development teams. These changes affect test suites; if these suites do not evolve, they will wear out. Mutation testing is a computationally expensive, fault-based testing method. By using high quality test data however, only a minimal number of mutations are required, allowing changes in the development environment. Initially however, test data is rarely of high quality. To improve it necessitates more mutations. The focus of this conceptual paper is the adoption of an immune system metaphor as the basis for an alternative mutation testing system. It is envisaged that such a system, through careful monitoring of program development, will be able to provide a minimal set of effective mutations and test cases; a vaccine which can be applied to the software development process to help protect it from errors.
Probing biological light-harvesting phenomena by optical cavities (2012)

We propose a driven optical cavity quantum electrodynamics (QED) setup aimed at directly probing energy transport dynamics in photosynthetic biomolecules. We show that detailed information concerning energy transfer paths and delocalization of exciton states can be inferred (and exciton energies estimated) from the statistical properties of the emitted photons. This approach provides us with a spectroscopic tool to interrogate biological systems in terms of quantum optical phenomena which have usually been studied in solid-state or atomic systems (e.g., semiconductor quantum dots and trapped atoms) and which are now extended to a broader range of spectroscopy experiments.
Local motion feature aided ground moving target tracking with GMTI and HRR measurements (2005)

Tracking ground moving targets with ground moving target indicator (GMTI) measurements only could face a potential problem of losing tracks or track mingling, if the targets move together within the range of GMTI sensing uncertainty for an extended period of time. We propose a remedy for this problem by using local motion features extracted from high resolution range (HRR) profiles to assist data association. Unlike other HRR features, the new local motion features carry both spatial and temporal information and are ideal for feature aided tracking. A probabilistic logic based tracker is developed for local motion feature aided tracking.
AVPRO-LBR5, an Initial Design Software Suite with Scantling Optimization Capabilities (2003)

peer reviewed
Spin Hall effect goes electrical (2010)

electrically could make an obscure but intriguing effect more accessible to research.
Efficacy and potential clinical applications of pentaglobin®, an IgM-enriched immunoglobulin concentrate suitable for intravenous infusion (1999)

Our data suggest that infusion of well characterised immunoglobulin preparations might be beneficial for patients with severe infections. This is highly relevant in view of the high pathogenicity of bacteria that cause infections in patients in hospital and the continually increasing antibiotic resistance (particularly methicillin-resistant S. aureus).
Learning from the World Wide Web: Using Organizational Profiles in Information Searches (2000)

An international association advancing the multidisciplinary study of informing systems. Founded in 1998, the Informing Science Institute (ISI) is a global community of academics shaping the future of informing science.
Compressed Indexes for Fast Search of Semantic Data (2020)

The sheer increase in volume of RDF data demands efficient solutions for the triple indexing problem, that is to devise a compressed data structure to compactly represent RDF triples by guaranteeing, at the same time, fast pattern matching operations. This problem lies at the heart of delivering good practical performance for the resolution of complex SPARQL queries on large RDF datasets. In this work, we propose a trie-based index layout to solve the problem and introduce two novel techniques to reduce its space of representation for improved effectiveness. The extensive experimental analysis, conducted over a wide range of publicly available real-world datasets, reveals that our best space/time trade-off configuration substantially outperforms existing solutions at the state-of-the-art, by taking 30-60 percent less space and speeding up query execution by a factor of 2 - 81×.