gebhart/patrepeval huggingface dataset:
Coordinate Regulation of Phospholipid Biosynthesis and Secretory Pathway Gene Expression in XBP-1(S)-induced Endoplasmic Reticulum Biogenesis (2007)

Development of the expansive endoplasmic reticulum (ER) present in specialized secretory cell types requires X-box-binding protein-1 (Xbp-1). Enforced expression of XBP-1(S), a transcriptional activator generated by unfolded protein response-mediated splicing of Xbp-1 mRNA, is sufficient to induce proliferation of rough ER. We previously showed that XBP-1(S)-induced ER biogenesis in fibroblasts correlates with increased production of phosphatidylcholine (PtdCho), the primary phospholipid of the ER membrane, and enhanced activities of the choline cytidylyltransferase (CCT) and cholinephosphotransferase enzymes in the cytidine diphosphocholine (CDP-choline) pathway of PtdCho biosynthesis. Here, we report that the level and synthesis of CCT, the rate-limiting enzyme in the CDP-choline pathway, is elevated in fibroblasts overexpressing XBP-1(S). Furthermore, overexpression experiments demonstrated that raising the activity of CCT, but not cholinephosphotransferase, is sufficient to augment PtdCho biosynthesis in fibroblasts, indicating that XBP-1(S) increases the output of the CDP-choline pathway primarily via its effects on CCT. Finally, fibroblasts overexpressing CCT up-regulated PtdCho synthesis to a level similar to that in XBP-1(S)-transduced cells but exhibited only a small increase in rough ER and no induction of secretory pathway genes. The more robust XBP-1(S)-induced ER expansion was accompanied by induction of a wide array of genes encoding proteins that function either in the ER or at other steps in the secretory pathway. We propose that XBP-1(S) regulates ER abundance by coordinately increasing the supply of membrane phospholipids and ER proteins, the key ingredients for ER biogenesis.
Cytokines in chronic inflammatory arthritis. VI. Analysis of the synovial cells involved in granulocyte-macrophage colony-stimulating factor production and gene expression in rheumatoid arthritis and its regulation by IL-1 and tumor necrosis factor-alpha (1991)

Granulocyte-macrophage CSF (GM-CSF) is a potent stimulator of macrophages and neutrophils and is produced by rheumatoid arthritis (RA) synovium. We now report studies that identify some of the synovial cells and cytokines responsible for local GM-CSF production and gene expression in RA. GM-CSF was assayed by ELISA in supernatants from cultured RA fibroblast-like synoviocytes stimulated with various cytokines (IL-1 beta, TNF-alpha, macrophage-CSF, IFN-gamma, IL-6, and TGF-beta). Immunoreactive GM-CSF was detected in IL-1 beta and TNF-alpha-stimulated cultures, but not in cells cultured in medium or stimulated with any of the other cytokines. IL-1 and TNF-alpha had a synergistic effect on GM-CSF production. GM-CSF gene expression by fibroblast-like synoviocytes was analyzed by ribonuclease protection assay, Northern blot analysis, and in situ hybridization. Both IL-1 beta and TNF-alpha induced GM-CSF mRNA accumulation, with a maximum effect after 4 h of stimulation. We then studied GM-CSF production by macrophage-like synoviocytes (MLS) isolated from fresh synovial specimens by flow microfluorimetry. Fresh MLS spontaneously secreted the cytokine and exogenous IL-1 beta or TNF-alpha had no effect. After 1 wk in culture, additional stimulation with IL-1 beta or TNF-alpha was required for GM-CSF production. Finally, in situ hybridization performed on freshly isolated subpopulations of synovial cells, identified GM-CSF RNA transcripts in MLS.
OS-Directed Throttling of Processor Activity for Dynamic Power Management (1999)

In this individual participant meta-analysis, we found no evidence for an association between breast milk n-3 LC PUFAs and BP.
Design, synthesis, cytotoxic properties and preliminary DNA sequencing evaluation of CPI--N-methylpyrrole hybrids. Enhancing effect of a trans double bond linker and role of the terminal amide functionality on cytotoxic potency. (1996)

In an approach to the design and exploration of the properties of cyclopropylindole (CPI)-lexitropsin conjugates as potential anticancer agents. CPI--N-methylpyrroles of two separate classes have been synthesized and characterized. These comprise structures (i) in which the N-methylpyrrole moiety bears amide groups of different sizes and (ii) in which both flexible and rigid linkers are introduced between the CPI and N-methylpyrrole units. The extent and the relative rates of DNA cleavage following alkylation and thermal treatment by these CPI conjugates were determined by an agarose gel mobility shift assay. The DNA sequence preferences of the seven new agents were also determined in a preliminary study by high-resolution polyacrylamide gel electrophoresis and contrasted with that of CC-1065. The CPI--N-methylpyrrole agents avoid the major alkylation sites of CC-1065, but all alkylate the minor CC-1065 site of 5'AATA and exhibit a consensus sequence of 5'-N.A/T.A/T.A. The cytotoxicities of these compounds were determined against KB human tumor cells in vitro. Compound 6, bearing a 4-butyramide group in the N-methylpyrrole, is 100 times more potent that 7 which lacks an amide group, while 10 which bears a rigid trans double bond linker is 1000 times more potent than its flexible ethyl-linked counterpart.
Changing pattern of expression of the epidermal growth factor receptor and transforming growth factor alpha in the progression of prostatic neoplasms. (1995)

The autocrine/paracrine interaction of the epidermal growth factor receptor (EGFr) and transforming growth factor alpha (TGF-alpha) has been implicated in prostate cancer cell growth and proliferation. To evaluate the role of EGFr and TGF-alpha in prostate cancer progression, we studied the immunohistochemical staining pattern of EGFr and TGF-alpha in malignant primary and hormone-independent metastatic prostate lesions. The specimens evaluated included 37 primary carcinomas (34 hormone-naive and 3 hormone-refractory tumors) and 22 metastases. For each specimen, the pattern of expression was evaluated and staining reactivities graded from 0-3, with 0 representing no staining and 3 representing homogeneous and intense staining. Primary malignant prostate epithelial cells in areas with discrete gland formation showed strong EGFr immunostaining, while stromal cells were generally nonreactive. In untreated primary tumors, TGF-alpha expression was primarily in the stroma, while epithelial cells were weakly positive in several cases. Malignant epithelial cells adjacent to neural elements that stained positive for TGF-alpha was frequently observed. A homogeneous staining pattern for EGFr was noted in 17 (89%) of 19 evaluable androgen-independent-refractory metastases, while TGF-alpha expression was found in 14 (78%) of 18 evaluable cases. Overall, 14 of 18 androgen-independent metastases coexpressed the receptor and the ligand. These results suggest that, unlike primary prostate tumors where a paracrine relationship between EGFr and TGF-alpha appears to predominate, the potential for autocrine stimulation may exist in the majority of metastatic androgen-independent tumors. Furthermore, the changing pattern of expression as the disease evolves from the localized hormone-naive to metastatic androgen-independent condition suggests that strategies aimed at blocking this growth factor pathway may be of therapeutic importance for androgen-independent disease.
Fluorinated Polyhedral Oligomeric Silsesquioxanes (F‐POSS) (2008)

Water-repellent: Fluorinated polyhedral oligomeric silsesquioxanes (POSS) are produced by facile, single-step, base-catalyzed condensation of trialkoxy silanes. The octameric fluorinated polyhedra are soluble, thermally stable, and hydrophobic, exhibiting static water contact angles up to 154°. The fluorodecyl POSS is believed to be the most hydrophobic crystalline solid known. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2002/2008/z705355_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Quantitative near‐infrared spectroscopy discriminates between mitochondrial myopathies and normal muscle (1999)

Five patients with chronic progressive external ophthalmoplegia (CPEO) and 27 healthy controls were examined by near-infrared spectroscopy (NIRS) for the noninvasive and direct quantitative measurement of muscle oxygen consumption and forearm blood flow. NIRS measurements were obtained in rest and during static isometric handgrip exercise at 10% of the maximum voluntary contraction (MVC) force. A significantly decreased oxygen consumption at rest as well as during exercise was found in patients with CPEO. Our results suggest that NIRS is able to discriminate between CPEO patients and healthy controls, which makes NIRS a valuable tool in the diagnostic workup of patients suspected to have a mitochondrial myopathy.
Effect of DNA-damaging agents on isolated spleen cells and lung fibroblasts from the mouse mutant "wasted," a putative animal model for ataxia-telangiectasia. (1986)

Spleen cells from control and wasted (wst) mice, a putative animal model for the human genetic disease ataxia-telangiectasia, were tested for inhibition of replicative (semiconservative) DNA synthesis after treatments with bleomycin, gamma-irradiation, 4-nitroquinoline 1-oxide, and ultraviolet irradiation. The wasted cells were found to be more resistant than control cells to the first three treatments, but equally sensitive to ultraviolet light. Bleomycin-stimulated repair synthesis in spleen cells was also studied by the CsCl/bromodeoxyuridine method and found to be similar in cells from wasted and control animals. Similarly, no differences in sensitivity to killing by gamma-rays, as manifested by relative cloning efficiencies, were demonstrated between primary lung fibroblasts from mutant and control mice. We concluded that observed defects in DNA repair in wasted cells are not identical to those reported in human cells from ataxia-telangiectasia patients.
From Genes to Proteins (2003)

The availability of the complete genome sequences of several organisms allows the comparative analysis of genomes, a branch of bioinformatics known as genomics. With this approach, much can be learned about the biology of organisms that are difficult to culture, even when few, if any, of their proteins have been isolated and studied directly. We have focused our interest on Rickettsia conorii, an obligate intracellular bacterium responsible for Mediterranean spotted fever, a disease endemic in southern Europe. While bioinformatic annotation of the complete genome of this bacteria has allowed identification of 1,374 genes, a large number of them remain functionally uncharacterized. The final goal of many experiments in molecular biology is to use biological systems to synthesize the protein encoded by the gene being studied. Because three-dimensional structures are more resilient to evolution and change than amino acid sequences, structure determination of some open reading frames should also exhibit structural similarity to previously described protein families. We have thus initiated a systematic expression and structure determination program for the proteins encoded by rickettsial genes of interest. We have cloned different genes of R. conorii by recombinational cloning (GATEWAY), Invitrogen) a method that uses in vitro site-specific recombination to accomplish a directional cloning of PCR products and the subsequent automatic subcloning of the DNA segment into new vector backbones at high efficiency. The constructions in p-Dest17 yielded several clones able to express recombinant proteins with a C-terminal histidine tag. Expression of corresponding proteins was then performed using a cell-free protein expression system (Rapid Translation System, RTS, Roche Diagnostics). The recombinational cloning approach coupled to RTS provides an approach to rapid optimization of protein expression and is very useful to express rickettsial proteins. Moreover, this system is able to overcome some of the limitations encountered with rickettsial proteins highly toxic for E. coli or insect cells.
A methodology of Benefit Segmentation for the Internet Shopping Mall Users (2004)

As a lot of the Internet shopping malls continue to obtain competitive advantage a turbulent electronic in marketplace. decision support need for analyzing the benefit segmentation, one of market segmentation methods. is becoming essential. In this sense, we suggest a conjoint analysis-driven benefit segmentation method where legacy website and its log data are used With applying our proposed methodology to an illustrative real world Internet shopping mall, we acquired robust and stimulating results which could be utilized for building a more effective marketing strategy for the Internet shopping mall
Chroma Intra Prediction Based on Inter-Channel Correlation for HEVC (2013)

In this paper, we investigate a new inter-channel coding mode called LM mode proposed for the next generation video coding standard called high efficiency video coding. This mode exploits inter-channel correlation using reconstructed luma to predict chroma linearly with parameters derived from neighboring reconstructed luma and chroma pixels at both encoder and decoder to avoid overhead signaling. In this paper, we analyze the LM mode and prove that the LM parameters for predicting original chroma and reconstructed chroma are statistically the same. We also analyze the error sensitivity of the LM parameters. We identify some LM mode problematic situations and propose three novel LM-like modes called LMA, LML, and LMO to address the situations. To limit the increase in complexity due to the LM-like modes, we propose some fast algorithms with the help of some new cost functions. We further identify some potentially-problematic conditions in the parameter estimation (including regression dilution problem) and introduce a novel model correction technique to detect and correct those conditions. Simulation results suggest that considerable BD-rate reduction can be achieved by the proposed LM-like modes and model correction technique. In addition, the performance gain of the two techniques appears to be essentially additive when combined.
<title>Explosives-related chemical concentrations in surface soils over buried land mines</title> (2002)

Night Vision Electronic Sensors Directorate (NVESD) has initiated a program for land mine sensor development based upon explosives-related chemical (ERC) detection. As part of the NVESD ERC sensor program, we have sampled soils surrounding buried land mines at the experimental mine lanes, U.S. Army Test Site, with the assistance of the Army Corps of Engineers, Cold Regions Research and Engineering Laboratory. Our goal has been to quantify concentrations of explosive related chemicals found in surface soils above and around nine types of buried land mines and to study their fate over time. This paper will describe the field tests conducted post-DARPA Dog Nose Program, the sampling and analysis protocol and the conclusions drawn from these tests.
Role of the IL-33-ST2 axis in sepsis (2017)

Sepsis remains a major clinical problem with high morbidity and mortality. As new inflammatory mediators are characterized, it is important to understand their roles in sepsis. Interleukin 33 (IL-33) is a recently described member of the IL-1 family that is widely expressed in cells of barrier tissues. Upon tissue damage, IL-33 is released as an alarmin and activates various types of cells of both the innate and adaptive immune system through binding to the ST2/IL-1 receptor accessory protein complex. IL-33 has apparent pleiotropic functions in many disease models, with its actions strongly shaped by the local microenvironment. Recent studies have established a role for the IL-33-ST2 axis in the initiation and perpetuation of inflammation during endotoxemia, but its roles in sepsis appear to be organism and model dependent. In this review, we focus on the recent advances in understanding the role of the IL-33/ST2 axis in sepsis.
Neutrophils, but Not Lymphocytes or Monocytes, Infiltrate Maternal Systemic Vasculature in Women with Preeclampsia (2008)

1) A significantly greater number of neutrophils adhered to endothelium and infiltrated into the intimal space in the maternal systemic vasculature of preeclamptic women than in that of normal pregnant women or normal non-pregnant women; 2) No significant difference in lymphocyte infiltration was observed among the patient groups, and lymphocytes were present in much lower numbers than-neutrophils; 3) Monocytes/macrophages were found in fat tissue but not in vessels. We speculate that neutrophils are the class of leukocytes that cause the majority of vascular cell dysfunction in women with preeclampsia.
Mitochondrial dependence of nerve growth factor-induced mechanical hyperalgesia (2011)

Mitochondria are present at high concentration at the site of sensory transduction in the peripheral terminals of nociceptors. Because nerve growth factor (NGF), which induces nociceptor sensitization by acting on the high-affinity tropomyosin receptor kinase A (TrkA) receptor, also produces local recruitment of mitochondria in DRG neurons, we evaluated the role of mitochondria in NGF-induced mechanical hyperalgesia. Inhibition of 3 major mitochondrial functions-oxidation of nutrients, adenosine triphosphate (ATP) production, and generation of reactive oxygen species--markedly attenuated NGF-induced mechanical hyperalgesia in the rat. Disruption of microtubules, which are required for the trafficking and subcellular localization of mitochondria, also attenuated NGF-induced hyperalgesia. Our results suggest a contribution of mitochondrial localization and function to NGF-dependent pain syndromes.
Alkali Metal CO2 Sorbents and the Resulting Metal Carbonates: Potential for Process Intensification of Sorption-Enhanced Steam Reforming (2016)

Sorption-enhanced steam reforming (SESR) is an energy and cost efficient approach to produce hydrogen with high purity. SESR makes it economically feasible to use a wide range of feedstocks for hydrogen production such as methane, ethanol, and biomass. Selection of catalysts and sorbents plays a vital role in SESR. This article reviews the recent research aimed at process intensification by the integration of catalysis and chemisorption functions into a single material. Alkali metal ceramic powders, including Li<sub>2</sub>ZrO<sub>3</sub>, Li<sub>4</sub>SiO<sub>4</sub> and Na<sub>2</sub>ZrO<sub>3</sub> display characteristics suitable for capturing CO<sub>2</sub> at low concentrations (<15% CO<sub>2</sub>) and high temperatures (>500 °C), and thus are applicable to precombustion technologies such as SESR, as well as postcombustion capture of CO<sub>2</sub> from flue gases. This paper reviews the progress made in improving the operational performance of alkali metal ceramics under conditions that simulate power plant and SESR operation, by adopting new methods of sorbent synthesis and doping with additional elements. The paper also discusses the role of carbonates formed after in situ CO<sub>2</sub> chemisorption during a steam reforming process in respect of catalysts for tar cracking.
Anatomical localization of protease‐activated receptor‐1 and protease‐mediated neuroglilal crosstalk on peri‐synaptic astrocytic endfeet (2011)

We studied the localization, activation and function of protease-activated receptor 1 (PAR-1) at the CNS synapse utilizing rat brain synaptosomes and slices. Confocal immunofluoresence and transmission electron microscopy in brain slices with pre-embedding diaminobenzidine (DAB) immunostaining found PAR-1 predominantly localized to the peri-synaptic astrocytic endfeet. Structural confocal immunofluorescence microscopy studies of isolated synaptosomes revealed spherical structures stained with anti-PAR-1 antibody which co-stained mainly for glial-filament acidic protein compared with the neuronal markers synaptophysin and PSD-95. Immunoblot studies of synaptosomes demonstrated an appropriate major band corresponding to PAR-1 and activation of the receptor by a specific agonist peptide (SFLLRN) significantly modulated phosphorylated extracellular signal-regulated kinase. A significant membrane potential depolarization was produced by thrombin (1 U/mL) and the PAR-1 agonist (100 μM) and depolarization by high K(+) elevated extracellular thrombin-like activity in the synaptosomes preparation. The results indicate PAR-1 localized to the peri-synaptic astrocytic endfeet is most likely activated by synaptic proteases and induces cellular signaling and modulation of synaptic electrophysiology. A protease mediated neuron-glia pathway may be important in both physiological and pathological regulation of the synapse.
Unstructured queries based on mobile user context (2012)

Purpose Many mobile devices today are equipped with diversified sensors that enable the acquisition of rich user context (e.g. GPS location, phone activity) for application utilization. With the growing usage of mobile devices in daily life, the problem of conveniently and promptly searching a piece of content that a user has viewed on his/her device before becomes more and more crucial. This paper aims to propose a context‐based query processing framework called UCQP that supports unstructured queries for content search in a user's access history. Design/methodology/approach Beyond the keywords related to the content properties, a context query in the framework is specified with freeform phrases that describe high‐level mobile contexts of the user at a previous time when the user viewed the searched content. Findings Experimental results on a prototype system of the framework illustrate its good accuracy and small response time. Originality/value To tolerate the incompleteness and inaccuracy in user query texts caused by fading human memory, the authors develop several semantic query parsers that are tailored for different types of contexts using natural language processing and information retrieval techniques. The authors further propose a similarity model to rank the multiple result contents of a query by comparing context entities specified in the query and historical context values associated with each result.
Eliprodil stimulates CNS myelination (1999)

Although the molecular mechanism mediating the effect of the sigma-receptor agonist on myelination remains to be elucidated, these results strongly suggest that neuroprotective molecules may be of therapeutic interest in demyelinating diseases such as MS.
Tetrahedron beam computed tomography (TBCT): a new design of volumetric CT system (2009)

Volumetric CT imaging systems usually comprise a point x-ray source and a 2D detector. Flat panel imager (FPI)-based cone beam CT (CBCT) has become an important online imaging modality for image-guided radiotherapy and intervention. However, due to excessive scatter photons and inferior detector performance, the image quality of current CBCT is significantly inferior to diagnostic fan-beam CT. We propose a novel tetrahedron beam computed tomography (TBCT) imaging system which consists of a linear scan x-ray source and a linear x-ray detector array. The linear x-ray tube and detector array are aligned perpendicular and parallel to the rotation plane, respectively. The x-ray beams are narrowly collimated into fan beams and focused on the linear detector array. The linear detector and linear x-ray source form a 'tetrahedron' volume instead of a 'cone' volume. TBCT is similar to CBCT in image reconstruction geometry; however, its image quality will be significantly superior to that of CBCT due to its scatter rejection mechanism and the use of high-performance discrete x-ray detectors. In this paper, we describe the design of the TBCT system for image-guided radiotherapy and some results of preliminary studies.