gebhart/patrepeval huggingface dataset:
Evidence for synthesis of scrapie prion proteins in the endocytic pathway. (1992)

Infectious scrapie prions are composed largely, if not entirely, of an abnormal isoform of the prion protein (PrP) which is designated PrPSc. A chromosomal gene encodes both the cellular prion protein (PrPC) as well as PrPSc. Pulse-chase experiments with scrapie-infected cultured cells indicate that PrPSc is formed by a post-translational process. PrP is translated in the endoplasmic reticulum, modified as it passes through the Golgi, and is transported to the cell surface. Release of nascent PrP from the cell surface by phosphatidylinositol-specific phospholipase C or hydrolysis with dispase prevented PrPSc synthesis. At 18 degrees C, the synthesis of PrPSc was inhibited under conditions that other investigators report a blockage of endosomal fusion with lysosomes. Our results suggest that PrPSc synthesis occurs after PrP transits from the cell surface. Whether all of the PrP molecules have an equal likelihood to be converted into PrPSc or only a distinct subset is eligible for conversion remains to be established. Identifying the subcellular compartment(s) of PrPSc synthesis should be of considerable importance in defining the molecular changes that distinguish PrPSc from PrPC.
Sphingolipids regulate [Mg<sup>2+</sup>]<sub>o</sub> uptake and [Mg<sup>2+</sup>]<sub>i</sub> content in vascular smooth muscle cells: potential mechanisms and importance to membrane transport of Mg<sup>2+</sup> (2010)

Sphingolipids have a variety of important signaling roles in mammalian cells. We tested the hypothesis that certain sphingolipids and neutral sphingomyelinase (N-SMase) can regulate intracellular free magnesium ions ([Mg2+]i) in vascular smooth muscle (VSM) cells. Herein, we show that several sphingolipids, including C2-ceramide, C8-ceramide, C16-ceramide, and sphingosine, as well as N-SMase, have potent and direct effects on content and mobilization of [Mg2+]i in primary cultured rat aortic smooth muscle cells. All of these sphingolipid molecules increase, rapidly, [Mg2+]i in these vascular cells in a concentration-dependent manner. The increments of [Mg2+]i, induced by these agents, are derived from influx of extracellular Mg2+ and are extracellular Ca2+ concentration-dependent. Phospholipase C and Ca2+/calmodulin/Ca2+-ATPase activity appear to be important in the sphingolipid-induced rises of [Mg2+]i. Activation of certain PKC isozymes may also be required for sphingolipid-induced rises in [Mg2+]i. These novel results suggest that sphingolipids may be homeostatic regulators of extracellular Mg2+ concentration influx (and transport) and [Mg2+]i content in vascular muscle cells.
Regulation of nuclear factor of activated T cells by phosphotyrosyl-specific phosphatase activity: a positive effect on HIV-1 long terminal repeat–driven transcription and a possible implication of SHP-1 (2001)

Although protein tyrosine phosphatase (PTP) inhibitors used in combination with other stimuli can induce interleukin 2 (IL-2) production in T cells, a direct implication of nuclear factor of activated T cells (NFAT) has not yet been demonstrated. This study reports that exposure of leukemic T cells and human peripheral blood mononuclear cells to bis-peroxovanadium (bpV) PTP inhibitors markedly induce activation and nuclear translocation of NFAT. NFAT activation by bpV was inhibited by the immunosuppressive drugs FK506 and cyclosporin A, as well as by a specific peptide inhibitor of NFAT activation. Mobility shift assays showed specific induction of the NFAT1 member by bpV molecules. The bpV-mediated NFAT activation was observed to be important for the up-regulation of the human immunodeficiency virus 1 (HIV-1) long terminal repeat (LTR) and the IL-2 promoter; NFAT1 was demonstrated to be particularly important in bpV-dependent positive action on HIV-1 LTR transcription. The active participation of p56(lck), ZAP-70, p21(ras), and calcium in the bpV-mediated signaling cascade leading to NFAT activation was confirmed, using deficient cell lines and dominant-negative mutants. Finally, overexpression of wild-type SHP-1 resulted in a greatly diminished activation of NFAT by bpV, suggesting an involvement of SHP-1 in the regulation of NFAT activation. These data were confirmed by constitutive NFAT translocation observed in Jurkat cells stably expressing a dominant-negative version of SHP-1. The study proposes that PTP activity attenuates constitutive kinase activities that otherwise would lead to constant NFAT activation and that this activation is participating in HIV-1 LTR stimulation by PTP inhibition.
Astroglial Differentiation of Cortical Precursor Cells Triggered by Activation of the cAMP-Dependent Signaling Pathway (1999)

In the developing brain, differentiation of neural precursors into neurons or glial cells occurs in response to neurotrophic factors acting on the cell surface. Intracellular signaling mechanisms that relay information to initiate differentiative responses of neural precursor cells are poorly understood. To investigate whether stimulation of the cAMP-dependent signaling pathway participates in differentiative responses of cells in the developing CNS, we performed experiments using both conditionally immortalized neural precursor cells (RC2.E10 cells) and primary cultures of cells from developing rat cortex. Initially, we determined that RC2.E10 cells retain phenotypic features of neural precursors after inactivation of the immortalizing oncogene, a temperature-sensitive mutant of the simian virus 40 large-T antigen (SV40T). We found that, once SV40T is inactivated, RC2.E10 cells cease to divide and die. However, RC2. E10 cells can proliferate in the presence of basic fibroblast growth factor. In addition, they express nestin, a marker of neural precursor cells. Both RC2.E10 cells and primary cortical precursor cells undergo astroglial differentiation in response to cAMP stimulation by treatment with 8-bromo-cAMP. In both cases, cAMP-induced astrocyte differentiation is characterized by morphological changes, stimulation of glial fibrillary acidic protein expression, downregulation of nestin expression, and decreased proliferation. No increases in the expression of neuronal or oligodendrocytic markers were observed. Our results support the notion that the developing CNS contains neural precursor cells with the capacity of undergoing astrocyte differentiation in response to increased intracellular cAMP concentrations.
Linguistic model based on the generative topological information space (1980)

Based on the structuralism, we propose a generative semantic model which has a topological information space generative grammar as basic rules. In this model a semantic map which is called a topological information space, is generated by the grammar, and the space can express implications and similarities among concepts. In the syntax, a syntactic generative grammar is defined based on the space grammar, and a mapping from the map to the language is defined. The mapping is composed of two mappings: one is a meaning affix mapping Φ which maps a conceptual area in the space to a token in the language, and the other is an operator mapping ψ which maps a generative rule in semantics to a rewriting rule in syntax. By these mappings, a derivation tree in semantics is mapped to a derivation tree in syntax, and vice versa.An algebraic system on the space is defined, and an algebraic system on the sentences is derived by the (Φ, ψ) -mappings. English will be analyzed according to this model and the algebraic systems on them.Finally an information processing model is described based on the model. The information processing in a natural language is carried out in the following steps: recognizing the inputs, parsing, interpreting, deducing, updating them, and outputting. These processes are discussed in details.
Importance of Ring Puckering versus Interstrand Hydrogen Bonds for the Conformational Stability of Collagen (2011)

Mismatch is fine: Proline derivatives with a ring pucker mismatching that of natural collagen but with favorable torsional angles along the peptide chain are readily tolerated within the collagen triple helix (see picture). In contrast, a competition between intramolecular and interstrand H bonds destabilizes the collagen triple helix.
Design study of a gate valve with respect to maintainability (1991)

A common problem experienced in the process industries is leakage through gate valves. This paper proposes a gate valve design which features a novel arrangement of replaceable seats which are not held in place by fasteners. A 100mm nominal bore valve has been modified to the design proposed and has been subjected to timed maintenance trials followed by pressure testing. This experimental work has demonstrated that the design proposed is sound and that the valve seats can be replaced quickly with a minimum skill requirement. The valve has the potential to reduce plant downtime in applications where seat wear is a frequent problem. (A)
Oral sodium phosphate solution is a superior colonoscopy preparation to polyethylene glycol with bisacodyl (2000)

Colonoscopy preparation with sodium phosphate solution is better tolerated and more effective than polyethylene glycol with bisacodyl.
Effect of Al/Si substitution on the structure and luminescence properties of CaSrSiO<sub>4</sub>:Ce<sup>3+</sup> phosphors: analysis based on the polyhedra distortion (2015)

The polyhedra distortion originating from the variation of [(Si,Al)O<sub>4</sub>] induced a red-shift of the Ce<sup>3+</sup> emission in CaSrSi<sub>1−x</sub>Al<sub>x</sub>O<sub>4</sub>:Ce<sup>3+</sup>,Li<sup>+</sup> phosphors.
5'-noncoding region sacR is the target of all identified regulation affecting the levansucrase gene in Bacillus subtilis (1986)

The regulation of the levansucrase gene sacB was studied in Bacillus subtilis strains. Fusions were constructed in which genes of cytoplasmic proteins such as lacZ were placed immediately downstream from sacR, the regulatory region located upstream from sacB. These fusions were introduced in mutants affected in sacB regulation. In all cases the marker gene was affected in the same way as sacB by the genetic context. This result is of particular interest for the sacU pleiotropic mutations, which affect sacB expression and other cellular functions such as the synthesis of several exocellular enzymes. We also showed that strains harboring sacU+ or sacU-hyperproducing alleles contained different amounts of sacB mRNA, which was proportional to their levansucrase secretion. We concluded that the sacU gene does not affect sacB expression at the level of secretion but acts on a target within sacR. We discuss the possibility that sacU acts on a part of sacR, a homologous copy of which was found upstream from the gene of another sacU-dependent secreted enzyme of B. subtilis, beta-glucanase.
Pro Internet Explorer 8 & 9 Development: Developing Powerful Applications for The Next Generation of IE (2010)

This book is an in-depth guide to writing applications that embrace and extend the new features and capabilities of Windows Internet Explorer 8 and 9. With solid instruction, hands-on examples, and expert insight direct from the source into extending the browser, youll learn how to create and maintain powerful applications for Microsofts next-generation Internet platform. Join author Matthew Crowley as you discover how to take advantage of new features like accelerators, Web Slices, and search providers, and create intense web experiences for the browser that ships by default with the popular Windows 7 operating system. If youre interested in creating and shipping high-quality, feature-rich applications for the Web, Pro Internet Explorer 8 and 9 Development is the only resource you need. What youll learn Understand the architecture and design of Internet Explorer. Build browser-based extensions such as ActiveX controls, toolbars, explorer bars, browser helper objects, and pluggable protocols. Extend existing web services with accelerators, Web Slices, and search providers. Enhance applications using Internet Explorer APIs, COM objects, and controls. Design extensions that integrate with Windows security features. Debug applications designed for Internet Explorer. Address compatibility and upgrade scenarios for applications. Utilize powerful tools for enhancing extension development. Master best practices in constructing world-class applications. Who this book is for Intermediate to advanced developers will get the most from this book. This book assumes that the reader is familiar with HTML, JavaScript, and CSS. Later sections require the reader have some understanding of C++ and/or C#. This book, while geared toward code-minded individuals, is also meant for a larger segment of the web community. Potential readers include Project managers seeking a new idea for development and deployment Product planners looking to create new features based-on Internet Explorers development framework Hobbyists interested in web browsers and Internet programming
Interferon Production by Cultured Human Trophoblasts and Choriocarcinoma Cell Lines Induced by Sendai Virus (1990)

Human term-placental trophoblasts in primary culture were studied for an interferon (IFN) response when challenged with Sendai virus and compared to three choriocarcinoma cell lines, placental fibroblasts and placental macrophages. Normal trophoblasts were high producers and released both IFN-alpha and IFN-beta. In contrast, one choriocarcinoma cell line was a low producer and all malignant lines produced only IFN-beta. Circulating monocytes produce IFN-alpha but placental macrophages secreted IFN-beta and some IFN-alpha, suggesting that IFN production may be dependent on the stage of differentiation. A role for trophoblast IFNs in protection of the foetus against virus infections is proposed.
Surface acoustic wave substrates for gas sensing applications (2002)

The bulk of the previous research on surface acoustic wave (SAW) gas sensors has focused on the sensing film itself and on gas-film interactions. Very little has been done to optimize the SAW substrate for gas sensing applications. The fact that many films are known to be more sensitive to target gases at certain temperatures other than room temperature has not been factored into substrate selection. In order to identify temperature stable substrates, a systematic search of various orientations of quartz has been made. Theoretical calculations show that the rotated Y-cut of quartz offers temperature compensated cuts over a broad range of temperatures. Each orientation in this cut has a parabolic temperature variation in /spl Delta//spl tau///spl tau/, where /spl tau/ is the delay time from the input to the output of the SAW device, with a unique turnover temperature (the temperature where /spl Delta//spl tau///spl tau/ is constant). These turnover temperatures range from -35/spl deg/C to well over 500/spl deg/C. Experimental data on selected rotated Y-cuts in quartz have exhibited satisfactory agreement with the theory. Finally, an H/sub 2/S sensor with an optimum operating temperature of 200/spl deg/C has been fabricated using 27/spl deg/ rotated Y-cut quartz. The stability of this sensor is shown to be superior to SAW gas sensors using YZ-LiNbO/sub 3/ substrates.
Species-specific assessment of pain in laboratory animals. (2003)

Pain has been defined by the International Association for the Study of Pain as "an unpleasant sensory and emotional experience associated with actual or potential damage or described in terms of such damage". However, the ability to describe the concept of pain is difficult largely because pain is an individualized and subjective experience. What one person finds painful, another may not; what relieves pain for one may not do so for another. Awareness of pain management has become an important health issue for humans and animals. To effectively manage pain, it is crucial to be able to identify it, and identification of pain in animals can be especially problematic. Recognition and alleviation of pain in animals used in biomedical research and teaching is an important goal, both from a humane and regulatory perspective. This paper will: 1) review current literature regarding pain assessment using pain scales and 2) describe how an institutional care and use committee (IACUC) has implemented an effective pain scoring system to allow for an objective, accurate, and humane assessment of pain experienced by animals used in biomedical research.
End-User Construction and Configuration of Distributed Multimedia Applications (1996)

Distributed multimedia applications supported by a global electronic infrastructure have tremendous potential for providing users with customized communication and computation environments. Since communication and computation requirements vary by context and change dynamically, it is unlikely that off-the-shelf applications will anticipate the needs of all users. Therefore, empowering end-users to create their own customized applications for both communication and computation is an important challenge. This dissertation presents several mechanisms that enable end-users to create and configure distributed multimedia applications, including end-users construction direct manipulation graphical users interface (GUIs) and application management of distributed multimedia applications over the Internet.
Crystallization Behavior of Asymmetric PLLA/PDLA Blends (2011)

The effects of the addition of poly(D-lactide) (PDLA) on the crystallization behavior of poly(L-lactide)(PLLA) were investigated by means of differential scanning calorimetry (DSC) and temperature-dependent X-ray diffraction(XRD). When the blends were cooled from different temperatures (250, 240, and 190 °C) at the rate of cooling of 5 °C/min, stereocomplex (sc) crystallites could stay at diverse states. Accordingly, the stereocomplexes acted as a nucleation agent exerting distinct effects on PLLA crystallization. The speculated mechanisms of the stereocomplex formation and the effectiveness as a nucleating agent are schematically described. Moreover, temperature-dependent XRD was carried out to further investigate the melt-crystallization behavior of PLLA/PDLA blends in real time. Temperature-dependent XRD results indicated that even at 240 °C the stereocomplex crystallites in all blend samples existed clearly, which could not be detected by DSC. These XRD results further suggest that the onset T(c) values for the PLLA α-form crystals formation were 160, 120, 140, and 160 °C, respectively, for neat PLLA, PLLA/PDLA 95/5, 90/10, and 80/20 as well as 70/30 samples.
Small RNAs Control Sodium Channel Expression, Nociceptor Excitability, and Pain Thresholds (2010)

To examine the role of small RNAs in peripheral pain pathways, we deleted the enzyme Dicer in mouse postmitotic damage-sensing neurons. We used a Nav1.8-Cre mouse to target those nociceptors important for inflammatory pain. The conditional null mice were healthy with a normal number of sensory neurons and normal acute pain thresholds. Behavioral studies showed that inflammatory pain was attenuated or abolished. Inflammatory mediators failed to enhance excitability of Nav1.8+ sensory neurons from null mutant mice. Acute noxious input into the dorsal horn of the spinal cord was apparently normal, but the increased input associated with inflammatory pain measured using c-Fos staining was diminished. Microarray and quantitative real-time reverse-transcription PCR (qRT-PCR) analysis showed that Dicer deletion lead to the upregulation of many broadly expressed mRNA transcripts in dorsal root ganglia. By contrast, nociceptor-associated mRNA transcripts (e.g., Nav1.8, P2xr3, and Runx-1) were downregulated, resulting in lower levels of protein and functional expression. qRT-PCR analysis also showed lowered levels of expression of nociceptor-specific pre-mRNA transcripts. MicroRNA microarray and deep sequencing identified known and novel nociceptor microRNAs in mouse Nav1.8+ sensory neurons that may regulate nociceptor gene expression.
Sustained metabolic scope. (1990)

Sustained metabolic rates (SusMR) are time-averaged metabolic rates that are measured in free-ranging animals maintaining constant body mass over periods long enough that metabolism is fueled by food intake rather than by transient depletion of energy reserves. Many authors have suggested that SusMR of various wild animal species are only a few times resting (basal or standard) metabolic rates (RMR). We test this conclusion by analyzing all 37 species (humans, 31 other endothermic vertebrates, and 5 ectothermic vertebrates) for which SusMR and RMR had both been measured. For all species, the ratio of SusMR to RMR, which we term sustained metabolic scope, is less than 7; most values fall between 1.5 and 5. Some of these values, such as those for Tour de France cyclists and breeding birds, are surely close to sustainable metabolic ceilings for the species studied. That is, metabolic rates higher than 7 times RMR apparently cannot be sustained indefinitely. These observations pose several questions: whether the proximate physiological causes of metabolic ceilings reside in the digestive tract's ability to process food or in each tissue's metabolic capacity; whether ceiling values are independent of the mode of energy expenditure; whether ceilings are set by single limiting physiological capacities or by coadjusted clusters of capacities (symmorphosis); what the ultimate evolutionary causes of metabolic ceilings are; and how metabolic ceilings may limit animals' reproductive effort, foraging behavior, and geographic distribution.
Revealing Novel Telomere Proteins Using in Vivo Cross-linking, Tandem Affinity Purification, and Label-free Quantitative LC-FTICR-MS (2010)

Telomeres are DNA-protein structures that protect chromosome ends from the actions of the DNA repair machinery. When telomeric integrity is compromised, genomic instability ensues. Considerable effort has focused on identification of telomere-binding proteins and elucidation of their functions. To date, protein identification has relied on classical immunoprecipitation and mass spectrometric approaches, primarily under conditions that favor isolation of proteins with strong or long lived interactions that are present at sufficient quantities to visualize by SDS-PAGE. To facilitate identification of low abundance and transiently associated telomere-binding proteins, we developed a novel approach that combines in vivo protein-protein cross-linking, tandem affinity purification, and stringent sequential endoprotease digestion. Peptides were identified by label-free comparative nano-LC-FTICR-MS. Here, we expressed an epitope-tagged telomere-binding protein and utilized a modified chromatin immunoprecipitation approach to cross-link associated proteins. The resulting immunoprecipitant contained telomeric DNA, establishing that this approach captures bona fide telomere binding complexes. To identify proteins present in the immunocaptured complexes, samples were reduced, alkylated, and digested with sequential endoprotease treatment. The resulting peptides were purified using a microscale porous graphite stationary phase and analyzed using nano-LC-FTICR-MS. Proteins enriched in cells expressing HA-FLAG-TIN2 were identified by label-free quantitative analysis of the FTICR mass spectra from different samples and ion trap tandem mass spectrometry followed by database searching. We identified all of the proteins that constitute the telomeric shelterin complex, thus validating the robustness of this approach. We also identified 62 novel telomere-binding proteins. These results demonstrate that DNA-bound protein complexes, including those present at low molar ratios, can be identified by this approach. The success of this approach will allow us to create a more complete understanding of telomere maintenance and have broad applicability.