gebhart/patrepeval huggingface dataset:
Structural Basis for a Ca <sup>2+</sup> -Sensing Function of the Metabotropic Glutamate Receptors (1998)

The metabotropic glutamate receptors (mGluRs) are widely distributed in the brain and play important roles in synaptic plasticity. Here it is shown that some types of mGluRs are activated not only by glutamate but also by extracellular Ca2+ (Ca2+o). A single amino acid residue was found to determine the sensitivity of mGluRs to Ca2+o. One of the receptors, mGluR1alpha, but not its point mutant with reduced sensitivity to Ca2+o, caused morphological changes when transfected into mammalian cells. Thus, the sensing of Ca2+o by mGluRs may be important in cells under physiological condition.
Database on monoclonal antibodies to Cytokeratins (2004)

Cytokeratins (CK) are being extensively used as diagnostic markers for various malignancies and other diseases, including human oral precancer and cancer, due to their tissue specific expression. CK are epithelia specific intermediate filament (IF) proteins, which are expressed in a differentiation dependent and tissue specific manner. There are about 30 polypeptides of CK expressed by different human epithelia. Each type of epithelium expresses about 4-6 polypeptides. CK polypeptides share many common epitopes, due to which the antibodies developed against CK tend to cross react. Therefore, a large number of monoclonal and polyclonal antibodies have been developed to distinguish among these proteins. Many of these antibodies are not only monospecific but are also epitope specific. These antibodies are being used in pathology laboratories for routine diagnosis using immunohistochemistry. A number of fixatives are used for fixation of tissue sections prior to the use of these antibodies. Sometimes, this leads in epitope masking. Hence, it becomes necessary to use a battery of monoclonal antibodies (MAb) for accurate diagnosis. Apart from the use of these antibodies in diagnostics, they are also being used in basic research for the study of CK function and their interactions with associated proteins and membrane proteins. In the present communication an effort has been made to make a comprehensive list of MAb to CK giving information like cross-reactivity, epitope specificity, various fixatives used, etc. along with the source of the antibodies, which will provide useful information to the users.
Stages of Infection during the Tripartite Interaction between <i>Xenorhabdus nematophila</i> , Its Nematode Vector, and Insect Hosts (2004)

Bacteria of the genus Xenorhabdus are mutually associated with entomopathogenic nematodes of the genus Steinernema and are pathogenic to a broad spectrum of insects. The nematodes act as vectors, transmitting the bacteria to insect larvae, which die within a few days of infection. We characterized the early stages of bacterial infection in the insects by constructing a constitutive green fluorescent protein (GFP)-labeled Xenorhabdus nematophila strain. We injected the GFP-labeled bacteria into insects and monitored infection. We found that the bacteria had an extracellular life cycle in the hemolymph and rapidly colonized the anterior midgut region in Spodoptera littoralis larvae. Electron microscopy showed that the bacteria occupied the extracellular matrix of connective tissues within the muscle layers of the Spodoptera midgut. We confirmed the existence of such a specific infection site in the natural route of infection by infesting Spodoptera littoralis larvae with nematodes harboring GFP-labeled Xenorhabdus. When the infective juvenile (IJ) nematodes reached the insect gut, the bacterial cells were rapidly released from the intestinal vesicle into the nematode intestine. Xenorhabdus began to escape from the anus of the nematodes when IJs were wedged in the insect intestinal wall toward the insect hemolymph. Following their release into the insect hemocoel, GFP-labeled bacteria were found only in the anterior midgut region and hemolymph of Spodoptera larvae. Comparative infection assays conducted with another insect, Locusta migratoria, also showed early bacterial colonization of connective tissues. This work shows that the extracellular matrix acts as a particular colonization site for X. nematophila within insects.
Voxelized shadow volumes (2011)

Efficient shadowing algorithms have been sought for decades, but most shadow research focuses on quickly identifying shadows on surfaces. This paper introduces a novel algorithm to efficiently sample light visibility at points inside a volume. These voxelized shadow volumes (VSVs) extend shadow maps to allow efficient, simultaneous queries of visibility along view rays, or can alternately be seen as a discretized shadow volume. We voxelize the scene into a binary, epipolar-space grid where we apply a fast parallel scan to identify shadowed voxels. Using a view-dependent grid, our GPU implementation looks up 128 visibility samples along any eye ray with a single texture fetch. We demonstrate our algorithm in the context of interactive shadows in homogeneous, single-scattering participating media.
Styrylbenzoazole derivatives for imaging of prion plaques and treatment of transmissible spongiform encephalopathies (2006)

Recent prevalence of acquired forms of transmissible spongiform encephalopathies (TSEs) has urged the development of early diagnostic measures as well as therapeutic interventions. To extend our previous findings on the value of amyloid imaging probes for these purposes, styrylbenzoazole derivatives with better permeability of blood-brain barrier (BBB) were developed and analyzed in this study. The new styrylbenzoazole compounds clearly labeled prion protein (PrP) plaques in brain specimens from human TSE in a manner irrespective of pathogen strain, and a representative compound BF-168 detected abnormal PrP aggregates in the brain of TSE-infected mice when the probe was injected intravenously. On the other hand, most of the compounds inhibited abnormal PrP formation in TSE-infected cells with IC50 values in the nanomolar range, indicating that they represent one of the most potent classes of inhibitor ever reported. BF-168 prolonged the lives of mice infected intracerebrally with TSE when the compound was given intravenously at the preclinical stage. The new compounds, however, failed to detect synaptic PrP deposition and to show pathogen-independent therapeutic efficacy, similar to the amyloid imaging probes we previously reported. The compounds were BBB permeable and non-toxic at doses for imaging and treatment; therefore, they are expected to be of practical use in human TSE.
Scheduling Problems with Two Competing Agents (2004)

We consider the scheduling problems arising when two agents, each with a set of nonpreemptive jobs, compete to perform their respective jobs on a common processing resource. Each agent wants to minimize a certain objective function, which depends on the completion times of its jobs only. The objective functions we consider in this paper are maximum of regular functions (associated with each job), number of late jobs, and total weighted completion times. We obtain different scenarios, depending on the objective function of each agent, and on the structure of the processing system (single machine or shop). For each scenario, we address the complexity of various problems, namely, finding the optimal solution for one agent with a constraint on the other agent's cost function, finding single nondominated schedules (i.e., such that a better schedule for one of the two agents necessarily results in a worse schedule for the other agent), and generating all nondominated schedules.
Electrochemical Oxidation of Mn[sup 2+] on Boron-Doped Diamond Electrodes with Bi[sup 3+] Used as an Electron Transfer Mediator (2004)

Electrochemical oxidation of Mn2+ with and without the presence of Bi3+ was studied using voltammetric and in situ spectro-electrochemical techniques at boron-doped diamond (BDD) electrodes in 1.0 M HClO4. Electrochemical oxidation of only Mn2+ resulted in the formation of mostly MnO2 with MnO4- produced as a minor product. The MnO2 film formed on the electrode surface, which is an inevitable part of Mn2+ oxidation, shows a blocking effect on the formation of MnO4-, and reduces the overall current efficiency of MnO4- production. Higher Mn2+ concentrations result in less MnO4- production due to the formation of more MnO2. The addition of Bi3+ increased the current efficiency of MnO4- production. The Bi3+ is oxidized to Bi(V), which acts as an electrocatalyst in MnO4- production. The Bi(V) oxidizes MnO2, formed on the electrode surface, to MnO4-. This increases the production of MnO4- by removing the blocking film to provide an active electrode (bare BDD) surface, which is available for further Mn2+ oxidation. (C) 2004 The Electrochemical Society.
Acid-Degradable Polymer-Caged Lipoplex (PCL) Platform for siRNA Delivery: Facile Cellular Triggered Release of siRNA (2013)

An acid-degradable polymer-caged lipoplex (PCL) platform consisting of a cationic lipoplex core and a biocompatible, pH-responsive polymer shell has been developed for the effective delivery of small interfering RNA (siRNA) through a combination of facile loading, rapid acid-triggered release, cellular internalization, and effective endosomal escape. In vitro testing of this degradable PCL delivery platform reveals ∼45- and ∼2.5-fold enhancement of enhanced green fluorescent protein knockdown in cancer cells in comparison to either free siRNA or siRNA-loaded non-acid-degradable lipoplex formulations, respectively.
Enterobacter pulveris sp. nov., isolated from fruit powder, infant formula and an infant formula production environment (2008)

Six Gram-negative, facultatively anaerobic, non-spore-forming, coccoid rod-shaped isolates were obtained from fruit powder (n=3), infant formula (n=2) and an infant formula production environment (n=1) and investigated in a polyphasic taxonomic study. Comparative 16S rRNA gene sequence analysis combined with rpoB gene sequence analysis allocated the isolates to the family Enterobacteriaceae. The highest rpoB gene sequence similarities (91.2-95.8%) were obtained with Enterobacter helveticus, Enterobacter radicincitans, Enterobacter turicensis and Enterobacter sakazakii and the phylogenetic branch formed by these species was supported by a high bootstrap value. Biochemical data revealed that the isolates could be differentiated from their nearest neighbours by their ability to utilize melibiose, sucrose, D-arabitol, mucate and 1-O-methyl-alpha-galactopyranoside and their negative reactions for D-sorbitol utilization and the Voges-Proskauer test. On the basis of the phylogenetic analyses, DNA-DNA hybridization data, and unique physiological and biochemical characteristics, it is proposed that the isolates represent a novel species of the genus Enterobacter, Enterobacter pulveris sp. nov. The type strain is 601/05(T) (=LMG 24057(T)=DSM 19144(T)).
Silicone acrylates through the hydrosilation of polyacryloyloxy functional monomers with copolymers of dimethyl and hydrogen methylsiloxanes (1993)

Abstract Silicone acrylates, as possible electron beam (EB) curable release coatings for paper, were prepared by the platinum‐catalyzed hydrosilation of polyacryloyloxy functional monomers with copolymers of dimethylsiloxane and hydrogen methylsiloxane (PDMHMS). The hydrosilation of either 1,6‐hexanediol diacrylate (HDDA) or trimethylolpropane triacrylate (TMPTA) with PDMHMS occurs to only one of the 2 or 3 available olefinic groups, respectively, as long as excess monomer is present. The amount of excess monomer needed to prevent gelation during hydrosilation or subsequent storage in excess of 1 month appears to be dependent on the hydrogen methylsiloxane content of the PDMHMS. A release coating having excellent cohesive and adhesive strength on paper was obtained by the EB curing of the product of hydrosilation of TMPTA with a PDMHMS containing 4 mol % hydrogen methylsiloxane at a dose‐to‐cure of 2 Mrad, but the aged release force was excessively high. The poor aged‐release performance was likely due to dilution of the dimethylsiloxane content of the coating with excess monomer required to stabilize the silicone acrylate. © 1993 John Wiley & Sons, Inc.
Inhibition of Tyrosinase by Protocatechuic Aldehyde (2004)

The purpose of this study was to determine the inhibitory action of protocatechuic aldehyde (PCA) on tyrosinase activity. PCA is one of the compounds found in the root of Salvia miltiorrhiza. Our study documented that PCA has a potent inhibitory effect on tyrosinase, which catalyzes the rate-limiting step of melanin biosynthesis. Although melanin biosynthesis has an essential function normally in human skin for defense against ultraviolet light of the sun, its abnormal activity as seen in pigmentation disorder could lead to serious medical problems. Our data showed that PCA, with concentrations ranging from 1 x 10(-5) M to 8 x 10(-5) M, exhibited dose-dependent inhibition of the enzyme activity with 50% of inhibition at 19.92 x 10(-6) M. A further kinetic analysis on PCA inactivation of tyrosinase activity revealed a competitive inhibition of the enzyme at the L-tyrosine binding site. The findings of our present study merit further research on the applicability of PCA as a potential agent for treatment of pigmentation disorder.
Recent trends of capillary electrophoresis‐mass spectrometry in proteomics research (2019)

Progress in proteomics research has led to a demand for powerful analytical tools with high separation efficiency and sensitivity for confident identification and quantification of proteins, posttranslational modifications, and protein complexes expressed in cells and tissues. This demand has significantly increased interest in capillary electrophoresis-mass spectrometry (CE-MS) in the past few years. This review provides highlights of recent advances in CE-MS for proteomics research, including a short introduction to top-down mass spectrometry and native mass spectrometry (native MS), as well as a detailed overview of CE methods. Both the potential and limitations of these methods for the analysis of proteins and peptides in synthetic and biological samples and the challenges of CE methods are discussed, along with perspectives about the future direction of CE-MS. @ 2019 Wiley Periodicals, Inc. Mass Spec Rev 00:1-16, 2019.
Computer security and intrusion detection (2004)

Computer attacks are now commonplace. By connecting your computer to the Internet, you increase the risk of having someone break in, install malicious programs and tools on it, and possibly use it to attack other machines on the Internet by controlling it remotely.Several major banks have been subject to attacks, in which attackers gained access into customers' accounts and viewed detailed information about the activities on these accounts. In some instances the attackers stole credit card information to blackmail e-commerce companies by threatening to sell this information to unauthorized entities. Several online trading companies and e-commerce sites were shut down temporarily due to major packet flood attacks, also known as Denial-of-Service (DoS) attacks, causing these companies to lose revenue, customer satisfaction, and trust [10]. A major software development company discovered that attackers had broken into its network and stolen the source code for future releases of its popular products. Just recently, the source code of the future flagship product belonging to a major software development company was stolen and made publicly available on the Internet.In order to combat this growing trend of computer attacks, both academic and industry groups have been developing systems to monitor networks and systems and raise alarms of suspicious activities. These systems are called Intrusion Detection Systems (IDS).
Enhanced Step Coverage of SiO<sub>2</sub> Films Sputtered in Hydrogen-Argon Mixed Gas (1980)

Step coverage of magnetron sputtered SiO 2 films prepared in 30% hydrogen-70% argon mixed gases has been investigated in comparison with that in argon only. The following results were obtained. (1) In pure argon, the step coverage profile has a vertical slope with microcrack at the step. (2) By mixing hydrogen in argon, step coverage is improved to a positive slope profile without microcracks, and the film at the step is densified.
Scheduling of tests on vehicle prototypes (2009)

In the automotive industry, a manufacturer must perform several hundreds of tests on prototypes of a vehicle before starting its mass production. These tests must be allocated to suitable prototypes and ordered to satisfy temporal constraints and various kinds of test dependencies. To reduce costs, the manufacturer is interested in using the minimum number of prototypes. We apply Constraint Programming (CP) and a hybrid approach to solve the scheduling problem. Our CP method can achieve good feasible solutions even for our largest instances within a reasonable time. In comparison with existing methods, we can improve the solutions for most of our instances and reduce the average number of required prototypes. The hybrid approach uses mixed integer linear programming (MILP) to solve the planning part and CP to find the complete schedule. Although the hybrid approach is not as robust as CP with respect to data characteristics and additional constraints, it can complement CP in finding a better lower bound.
Einleitung (2003)

Hersteller und Handel bilden die traditionellen Akteure im Distributionssystem mit der gemeinsamen Intention, potentielle Konsumenten zum Kauf der infrage stehenden Distributionsobjekte zu veranlassen.1 Die Beziehung dieser Elemente des Distributionssystems, die häufig als Marktpartner im Absatzkanal bezeichnet werden, ist jedoch in den vergangenen zwei Jahrzehnten, insbesondere im Nahrungsmittelsektor, weniger von einer partnerschaftlichen Beziehung, als vielmehr von einer zunehmend spannungsgeladenen Ausprägung ihres Leistungsgeflechts gekennzeichnet. Wesentliche Ursache dieser absatzwirtschaftlichen Dissensen stellt trotz einer gemeinsamen übergeordneten Zielsetzung die von den Herstellern praktizierte und von den Handelsunternehmen häufig kritisierte Konditionenpolitik dar, die als Teilbereich der Preispolitik einen signifikanten Einfluss auf den langfristigen Erfolg der Unternehmung ausübt.
Depth Based View Synthesis Using Graph Cuts for 3DTV (2013)

In three-dimensional television (3DTV), an interactive free viewpoint selection application has received more attention so far. This paper presents a novel method that synthesizes a free-viewpoint based on multiple textures and depth maps in multi-view camera configuration. This method solves the cracks and holes problem due to sampling rate by performing an inverse warping to retrieve texture images. This step allows a simple and accurate re-sampling of synthetic pixels. To enforce the spatial consistency of color and remove the pixels wrapped incorrectly because of inaccuracy depth maps, we propose some processing steps. The warped depth and warped texture images are used to classify pixels as stable, unstable and disoccluded pixels. The stable pixels are used to create an initial new view by weighted interpolation. To refine the new view, Graph cuts are used to select the best candidates for each unstable pixel. Finally, the remaining disoccluded regions are filled by our inpainting method based on depth information and texture neighboring pixel values. Our experiment on several multi-view data sets is encouraging in both subjective and objective results. Furthermore, our proposal can flexibly use more than two views in multi-view system to create a new view with higher quality.
Purification and characterization of MSH1, a yeast mitochondrial protein that binds to DNA mismatches. (1994)

MSH1 is a homologue of the Escherichia coli MutS gene that is proposed to play an important role in the repair and maintenance of mitochondrial DNA in Saccharomyces cerevisiae (Reenan, R.A., and Kolodner, R. D. (1992) Genetics 132, 985-1985). In this study, we demonstrate that msh1/MSH1 strains accumulate point mutations in mitochondria seven times faster than the wild-type. We also show that the MSH1 protein is targeted to the mitochondria where its mitochondrial-targeting sequence is removed. Purified MSH1 hydrolyzes ATP and recognizes DNA substrates containing nucleotide mismatches and unpaired nucleotides. The hierarchy of binding affinity of MSH1 among various mismatches is similar to that of MutS, suggesting that both proteins share a highly conserved scheme for recognizing mismatches. The specific binding of MSH1 to mismatches is more resistant to NaCl inhibition and has a slower dissociation rate as compared to the nonspecific binding to complementary DNA sequences. Our data support the idea that MSH1 plays a role in eliminating biosynthetic errors and homeologous recombination in mitochondrial genome by recognizing premutagenic DNA mismatches.
Protocol for high-sensitivity/long linear-range spectrofluorimetric DNA quantification using ethidium bromide (2007)

Ethidium bromide (EtBr) is the most widely used fluorescent dye in nucleic acid gel electrophoresis since decades. However it has been essentially forgotten in DNA quantification by spectrofluorimetry. While investigating sensitivity and dynamic range of available fluorochromes, we found that EtBr permits much more sensitive fluorimetric measurements than previously thought. We report here a revised, accurate, and easy-to-use protocol for EtBr-based DNA quantification in solution, which usefully complements the widely used indirect quantification on agarose gels.
Empirical thermal model for inverter-driven cage induction machines (1994)

The paper describes an empirical thermal model which provides an estimate of stator- and rotor-conductor temperatures in an inverter-driven cage induction machine under both transient and steady-state conditions (of heating and cooling), and under constant and variable flux control. The model is based on a widely used thermal-torque derating for inverter-driven induction machines, and features a single frequency-dependent thermal resistance and time constant for each winding. It is easily implemented in real time for online thermal protection and compensation for winding-resistance variation. The technique is demonstrated on two 7.5 kW inverter drives to give temperature estimates to within 10 deg C for both transient and steady-state operation. This accuracy is shown to be sufficient to maintain torque output to within 0.01 p.u. in both voltage-forced and current-forced inverter drives. The model can be generalised for a wide range of machine sizes, without the need for specific physical details, by assuming that induction machines are constructed of similar materials, and have similar insulation thermal limits.
Fiber parametric oscillator for the 2 μm wavelength range based on narrowband optical parametric amplification (2010)

We describe a widely tunable synchronously pumped coherent source based on the process of narrowband parametric amplification in a dispersion-shifted fiber. Using an experimental fiber with a zero-dispersion wavelength of 1590 nm and pump wavelengths of 1530 to 1570 nm yields oscillations at 1970 to 2140 nm-the longest reported wavelength for a fiber parametric oscillator. The long-wavelength oscillations are accompanied by simultaneous short-wavelength oscillations at 1200 to 1290 nm. The parametric gain is coupled to stimulated Raman scattering. For parametric oscillations close to the Raman gain peak, the two gain processes must be discriminated from each other. We devised two configurations that achieve this discrimination: one is based on the exploitation of the difference in group delay between the wavelengths where Raman and parametric gain peak, and the other uses intracavity polarization tuning.