gebhart/patrepeval huggingface dataset:
Cytokine Effects on Glutamate Uptake by Human Astrocytes (2000)

Glutamate uptake by astrocytes has been postulated to play a neuroprotective role during brain inflammation. Using primary human fetal astrocyte cultures, we investigated the influence of selected cytokines on glutamate uptake activity. Interleukin (IL)-1beta and tumor necrosis factor-alpha dose-dependently inhibited astrocyte glutamate uptake, whereas interferon (IFN)-gamma alone stimulated this activity. The nitric oxide synthase inhibitor, N(G)-monomethyl-L-arginine, blocked IL-1beta-mediated inhibition of glutamate uptake, suggesting involvement of nitric oxide in the effect of IL-1beta. IL-1 receptor antagonist protein totally reversed the inhibitory effect of cytokines, suggesting a critical role of IL-1beta. The anti-inflammatory cytokine IFN-beta blocked cytokine (IL-1beta plus IFN-gamma)-induced inhibition of glutamate uptake with a corresponding reduction in nitric oxide generation. Taken together, these findings suggest that proinflammatory cytokines inhibit astrocyte glutamate uptake by a mechanism involving nitric oxide, and that IFN-beta may exert a therapeutically beneficial effect by blocking cytokine-induced nitric oxide production in inflammatory diseases of the brain.
Automatic speech recognition : the development of the SPHINX system (1988)

1. Introduction.- 2. Hidden Markov Modeling of Speech.- 3. Task and Databases.- 4. The Baseline SPHINX System.- 5. Adding Knowledge.- 6. Finding a Good Unit of Speech.- 7. Learning and Adaptation.- 8. Summary of Results.- 9. Conclusion.- Appendix I. Evaluating Speech Recognizers.- I.1. Perplexity.- I.2. Computing Error Rate.- Appendix H. The Resource Management Task.- II.1. The Vocabulary and the SPHINX Pronunciation Dictionary.- II.2. The Grammar.- II.3. Training and Test Speakers.- Appendix III. Examples of SPHINX Recognition.- References.
A novel transforming growth factor beta response element controls the expression of the connective tissue growth factor gene. (1996)

We reported previously that transforming growth factor beta (TGF-beta) selectively induced high levels of connective tissue growth factor (CTGF) mRNA and protein in human skin fibroblasts. In this study, we investigated the molecular mechanism for TGF-beta regulation of CTGF gene expression. Northern blot and run-on transcription assays indicate that TGF-beta directly activates transcription of the CTGF gene. Fragments of the 5'flanking region of the human CTGF gene were linked to luciferase reporter constructs. TGF-beta induced a 25-30 fold increase in luciferase activity in NIH/3T3 fibroblasts that had been transfected with this construct compared with nontreated cells after 24 h incubation. Other growth factors, such as platelet derived growth factor or fibroblast growth factor, caused only a 2-3-fold induction. This response to TGF-beta occurred only in human skin fibroblasts, fetal bovine aortic smooth muscle cells, and NIH/3T3 fibroblasts but not in the epithelial cell lines tested. Analysis of deletion mutants indicated that an important TGF-beta regulatory element is located between positions -162 and -128 of the CTGF promoter sequence. A fragment of the promoter containing this region conferred TGF-beta induction to a SV40 enhanceriess promoter. Methylation interference and competition gel shift assays mapped a unique 13-nucleotide sequence delineating a novel TGF-beta cis-regulatory element. Point mutations in this region result in a complete loss of the TGF-beta induction, identifying this sequence as a new TGF-beta response element.
Molecular phenotype of airway side population cells (2004)

Lung epithelial-specific stem cells have been localized to discrete microenvironments throughout the adult conducting airway. Properties of these cells include pollutant resistance, multipotent differentiation, and infrequent proliferation. Goals of the present study were to use Hoechst 33342 efflux, a property of stem cells in other tissues, to purify and further characterize airway stem cells. Hoechst 33342 effluxing lung cells were identified as a verapamil-sensitive side population by flow cytometry. Lung side population cells were further subdivided on the basis of hematopoietic (CD45 positive) or nonhematopoietic (CD45 negative) origin. Nonhematopoietic side population cells were enriched for stem cell antigen-1 reactivity and expressed molecular markers specific to both airway and mesenchymal lineages. Analysis of the molecular phenotype of airway-derived side population cells indicates that they are similar to neuroepithelial body-associated variant Clara cells. Taken together, these data suggest that the nonhematopoietic side population isolated from lung is enriched for previously identified airway stem cells.
Characterization of the zinc binding site of bacterial phosphotriesterase. (1992)

The bacterial phosphotriesterase has been found to require a divalent cation for enzymatic activity. This enzyme catalyzes the detoxification of organophosphorus insecticides and nerve agents. In an Escherichia coli expression system significantly higher concentrations of active enzyme could be produced when 1.0 mM concentrations of Mn2+, Co2+, Ni2+, and Cd2+ were included in the growth medium. The isolated enzymes contained up to 2 equivalents of these metal ions as determined by atomic absorption spectroscopy. The catalytic activity of the various metal enzyme derivatives was lost upon incubation with EDTA, 1,10-phenanthroline, and 8-hydroxyquinoline-5-sulfonic acid. Protection against inactivation by metal chelation was afforded by the binding of competitive inhibitors, suggesting that at least one metal is at or near the active site. Apoenzyme was prepared by incubation of the phosphotriesterase with beta-mercaptoethanol and EDTA for 2 days. Full recovery of enzymatic activity could be obtained by incubation of the apoenzyme with 2 equivalents of Zn2+, Co2+, Ni2+, Cd2+, or Mn2+. The 113Cd NMR spectrum of enzyme containing 2 equivalents of 113Cd2+ showed two resonances at 120 and 215 ppm downfield from Cd(ClO4)2. The NMR data are consistent with nitrogen (histidine) and oxygen ligands to the metal centers.
Binding Interactions between Long Noncoding RNA HOTAIR and PRC2 Proteins (2013)

Long noncoding RNAs (lncRNAs) play a key role in the epigenetic regulation of cells. Many of these lncRNAs function by interacting with histone repressive proteins of the Polycomb group (PcG) family, recruiting them to gene loci to facilitate silencing. Although there are now many RNAs known to interact with the PRC2 complex, little is known about the details of the molecular interactions. Here, we show that the PcG protein heterodimer EZH2-EED is necessary and sufficient for binding to the lncRNA HOTAIR. We also show that protein recognition occurs within a folded 89-mer domain of HOTAIR. This 89-mer represents a minimal binding motif, as further deletion of nucleotides results in substantial loss of affinity for PRC2. These findings provide molecular insights into an important system involved in epigenetic regulation.
TheMycobacterium tuberculosisPhagosome in Human Macrophages Is Isolated from the Host Cell Cytoplasm (2002)

Knowledge of whether Mycobacterium tuberculosis resides within a relatively impermeable membrane-bound vacuole or is free within the cytoplasm within its host cell is central to an understanding of the immunobiology of this intracellular parasite but is a matter of controversy. To explore this issue, we assessed the accessibility of medium-size protein molecules (Fab fragments of 50,000 Da) to M. tuberculosis within human macrophages. We infected the macrophages with wild-type or green fluorescent protein-expressing M. tuberculosis, microinjected Fab fragments directed against a major surface antigen of M. tuberculosis into the host cell, and assayed the accessibility of the bacteria to the Fab fragments by both immunofluorescence microscopy and immunogold electron microscopy. Whereas microinjected intact immunoglobulin G molecules against cytoplasmic early endosomal antigen 1 readily stained this antigen, microinjected Fab fragments against M. tuberculosis did not stain the bacterium within its phagosome. In contrast, microinjected Fab fragments against Listeria monocytogenes, an intracellular bacterium known to permeabilize its phagosomal membrane, strongly stained this bacterium. Our study shows that M. tuberculosis resides in an isolated phagosome that is relatively impermeable to cytoplasmic constituents.
Dual temperature and strain sensor using a combined fiber Bragg grating and fluorescence intensity ratio technique in Er3+-doped fiber (2003)

A prototype dual temperature–strain point sensor has been demonstrated by combining a short length of erbium-doped fiber in close proximity to a fiber Bragg grating. By measurement of the green fluorescence intensity ratio in erbium (Er3+) and the Bragg wavelength shift of a fiber Bragg grating the temperature and strain are deduced. Calibrations reveal that the sensitivity of the fluorescence intensity ratio in Er3+-doped fiber to strain is near zero. Three alternative analysis methods were used; the conventional matrix method, and two variations of a technique that provides a better fit to the fluorescence intensity ratio temperature data using a quadratic. The quadratic methods considered two cases of the strain dependence of the fluorescence intensity ratio, namely, zero and linear. The matrix method showed standard deviations of 2.2 °C and 20.6 με, while the quadratic fit with a linear strain dependence yielded 1.0 °C and 22.9 με over temperature and strain ranges of 18–150 °C and 350–2534 με, respectively.
The Effect of Inactivated <i>Lactobacillus</i> LB Fermented Culture Medium on Symptom Severity: Observational Investigation in 297 Patients with Diarrhea-Predominant Irritable Bowel Syndrome (2011)

This observational investigation shed new light on patients with IBS-D, the HRQOL of which is altered by a fecal incontinence rate twice as high as that of the general population. Correlation with diet is confirmed by 1 out of 2 patients reporting poor tolerance of fiber and dairy products. Nutritional management should thus be part of these patients' treatment. Inactivated Lactobacillus LB plus fermented culture medium is a probiotic drug that has been used by physicians for a long time to treat patients with diarrhea. Strongly concentrated, it has no side effects and seems to help these patients. Due to a strong placebo effect in patients with this pathology, however, a controlled study is necessary to confirm this result.
Relation of Hexanal in Vapor Above Stored Potato Granules to Subjective Flavor Estimates (1964)

SUMMARY Influence of air storage of commercial potato granules at 22°C was determined by gas chromatography and flavor tests by judges. Increases in hexanal content of the vapor above the reconstituted product at 93°C followed subjective flavor estimates closely. Sixty‐five percent of the judges distinguished between air‐packed granules and a control sample packaged in nitrogen atmosphere after approximately three months (5% level of significance). During this time, hexanal concentration above the reconstituted air‐packed granules increased from 0.2 to 2.5 ppm. By the end of the fourth month, when hexanal had increased to 8.5 ppm, almost all of the judges detected flavor deterioration.
Robotics in Surgery (2003)

Bann, Simon BSc (Hons), MB, BS, FRCS*, **; Khan, Mansoor BSc (Hons), MB, BS, AFRCS, MRCS*; Hernandez, Juan MD*; Munz, Yaron MD*; Moorthy, Krishna MB, BS, FRCS*; Datta, Vivek BSc, MB, BS, FRCS*; Rockall, Timothy MB, BS, FRCS*; Darzi, Ara MB, BS, FRCS, FRCSI, FACS* Author Information
Interleukin-1 in Ischemia-Reperfusion Acute Lung Injury (1997)

Interleukin-1 (IL-1) is a proinflammatory cytokine produced by blood-borne and resident inflammatory lung tissue involved in the thrombotic occlusion of the pulmonary microcirculation and the increase of the vascular permeability following a wide variety of injuries and sepsis. The locally accentuated, organ-related activation of this cytokine seems to be responsible for the development of acute lung injury. The present study was conducted to determine if IL-1beta was produced in an ischemia-reperfusion (I/R) rat model subjected to lung injury. We measured sequential perfusate levels of IL-1beta by ELISA and we measured IL-1 gene expression in the rat lung tissue by a reverse-transcriptase polymerase chain reaction method. Little IL-1beta gene expression was observed in normal rat lung tissue. Perfusate IL-1beta slightly increased 2 h after induced ischemia and 3 h after reperfusion. IL-1beta gene expression rapidly increased as early as 30 min after ischemia and continued to increase for up to 120 min. IL-1beta gene expression was dramatically upregulated during reperfusion after cessation of ischemia, reached a peak at 1 h, and then gradually decreased (2 to 3 h) to near baseline levels. During ischemia, the increased IL-1 gene expression was not significantly different between the ventral and dorsal sites of the lung. However, IL-1 gene expression markedly increased on the dorsal part (the dependent site for a rat in a supine position) after reperfusion. From these results, it appears that IL-1 may have an important role in I/R lung injury.
Control of starch branching in barley defined through differential RNAi suppression of starch branching enzyme IIa and IIb (2010)

The roles of starch branching enzyme (SBE, EC 2.4.1.18) IIa and SBE IIb in defining the structure of amylose and amylopectin in barley (Hordeum vulgare) endosperm were examined. Barley lines with low expression of SBE IIa or SBE IIb, and with the low expression of both isoforms were generated through RNA-mediated silencing technology. These lines enabled the study of the role of each of these isoforms in determining the amylose content, the distribution of chain lengths, and the frequency of branching in both amylose and amylopectin. In lines where both SBE IIa and SBE IIb expression were reduced by >80%, a high amylose phenotype (>70%) was observed, while a reduction in the expression of either of these isoforms alone had minor impact on amylose content. The structure and properties of the high amylose starch resulting from the concomitant reduction in the expression of both isoforms of SBE II in barley were found to approximate changes seen in amylose extender mutants of maize, which result from lesions eliminating expression of the SBE IIb gene. Amylopectin chain length distribution analysis indicated that both SBE IIa and SBE IIb isoforms play distinct roles in determining the fine structure of amylopectin. A significant reduction in the frequency of branches in amylopectin was noticed only when both SBE IIa and SBE IIb were reduced, whereas there was a significant increase in the branching frequency of amylose when SBE IIb alone was reduced. Functional interactions between SBE isoforms are suggested, and a possible inhibitory role of SBE IIb on other SBE isoforms is discussed.
Influence ofMycobacterium aviumsubsp.paratuberculosison Colitis Development and Specific Immune Responses during Disease (2007)

The granulomatous and intramural inflammation observed in cases of inflammatory bowel diseases (IBD) and veterinary Johne's disease suggests that Mycobacterium avium subsp. paratuberculosis is a causative agent. However, an incomplete understanding of the immunological steps responsible for the pathologies of IBD makes this conclusion uncertain. Sera from interleukin-10-deficient (IL-10(-/-)) mice with spontaneous colitis displayed significantly higher M. avium subsp. paratuberculosis-specific immunoglobulin G2a antibody responses than did sera from similar mice without disease. Pathogen-free IL-10(-/-) mice received control vehicle or the vehicle containing heat-killed or live M. avium subsp. paratuberculosis. Mucosal CD4(+) T cells from the mice that developed colitis proliferated and secreted higher levels of gamma interferon and tumor necrosis factor alpha after ex vivo stimulation with a Vbeta11(+) T-cell receptor-restricted peptide from the MPT59 antigen (Ag85B) than those secreted from cells from mice before the onset of colitis. The data from this study provide important information regarding the mechanisms of colitis in IL-10(-/-) mice, which are driven in part by Ag85B-specific T cells. The data suggest a plausible mechanism of Ag-specific T-cell responses in colitis driven by potent Ags conserved in Mycobacterium species.
The Design of Scaffolds for Use in Tissue Engineering. Part I. Traditional Factors (2001)

In tissue engineering, a highly porous artificial extracellular matrix or scaffold is required to accommodate mammalian cells and guide their growth and tissue regeneration in three dimensions. However, existing three-dimensional scaffolds for tissue engineering proved less than ideal for actual applications, not only because they lack mechanical strength, but they also do not guarantee interconnected channels. In this paper, the authors analyze the factors necessary to enhance the design and manufacture of scaffolds for use in tissue engineering in terms of materials, structure, and mechanical properties and review the traditional scaffold fabrication methods. Advantages and limitations of these traditional methods are also discussed.
Modulation of Cell Signaling Networks after CTLA4 Blockade in Patients with Metastatic Melanoma (2010)

clinicaltrials.gov; Registration numbers NCT00090896 and NCT00471887.
Evidence for a transcriptional activation function of BRCA1 C-terminal region (1996)

Mutations in BRCA1 account for 45% of families with high incidence of breast cancer and for 80-90% of families with both breast and ovarian cancer. BRCA1 protein includes an amino-terminal zinc finger motif as well as an excess of negatively charged amino acids near the C terminus. In addition, BRCA1 contains two nuclear localization signals and localizes to the nucleus of normal cells. While these features suggest a role in transcriptional regulation, no function has been assigned to BRCA1. Here, we show that the C-terminal region, comprising exons 16-24 (aa 1560-1863) of BRCA1 fused to GAL4 DNA binding domain can activate transcription both in yeast and mammalian cells. Furthermore, we define the region comprising exons 21-24 (aa 1760-1863) as the minimal transactivation domain. Any one of four germ-line mutations in the C-terminal region found in patients with breast or ovarian cancer (Ala-1708-->Glu, Gln-1756 C+, Met-1775-->Arg, Tyr-1853 ->Stop), had markedly impaired transcription activity. Together these data underscore the notion that one of the functions of BRCA1 may be the regulation of transcription.
Heat Shock Up-Regulates lmp2 and lmp7 and Enhances Presentation of Immunoproteasome-Dependent Epitopes (2006)

The heat shock response is a canonical regulatory pathway by which cellular stressors such as heat and oxidative stress alter the expression of stress-responsive genes. Some of these stress-responsive genes (heat shock proteins and MHC class I (MHC I)-related chains) play a significant role in the immune system. In this study, we have investigated the impact of stimulating the heat shock response on genes involved in the MHC I presentation pathway. We report that two inducible subunits of the proteasome, lmp2 and lmp7, are transcriptionally up-regulated by heat shock in cells of mouse and human origin. Furthermore, heat-shocked cells show enhanced presentation of the immunoproteasome-dependent MHC I antigenic epitopes NP(118-126) of lymphocytic choriomeningitis virus and E1B(192-200) of adenovirus, but not immunoproteasome-independent epitopes such as tumor Ag AH1 and SV40 large T Ag epitope II(223-231). These findings show a novel immunological sequel to the cellular response to stress that may play a key role during fever or other homeostatic perturbations.
The Created Kind: Noah's Doves, Ravens, and Their Descendants (1998)

The purpose of this paper is to look at the Biblical kind, focussing on the only two known kinds to be on the Ark, the dove and the raven. They give an opportunity to clearly identify the way in which a biblical kind has developed into races in the Post-Flood era. The two bird groups are considered with reference to hybridisation records, karyotypes and genetic variation. A fundamental concept to this paper is the respective authorship of Genesis, Deuteronomy and Leviticus. There is therefore a brief review of the role of Moses, as the editor of documents handed down from the Patriarchs.
Overexpression of Matrix Metalloproteinases in Lung Tissue of Patients with Primary Spontaneous Pneumothorax (2014)

MMP-2, MMP-9, MMP-7 and TIMP-2 were upregulated in PSP lesions. These results suggest that an imbalance between the expression of proteases and antiproteases may be involved in the pathogeneses of PSP.
A programmable analog neural network chip (2003)

Analog VLSI implementations of adaptive systems, either of the traditional variety or the more complex types frequently found in neural network models of learning, require variable analog weights which are compact and have substantial resolution. The authors have designed a chip in ordinary 1.25- mu m CMOS which stores analog weights as charge on MOS capacitors. The weights, of which there are 1104 per chip, can be updated in parallel along a vector in weight space, allowing for efficient implementations of gradient descent algorithms. The chips are organized as 46*24 matrix multipliers with voltage inputs and current outputs.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
From Club Drug to Orphan Drug: Sodium Oxybate (Xyrem) for the Treatment of Cataplexy (2003)

Narcolepsy, a rare disease with a prevalence of 0.05% in the general population, affects an estimated 140,000 patients in the United States. Patients have been able to lead fuller personal and professional lives since the Food and Drug Administration approved sodium oxybate (Xyrem) in 2002 for treatment of cataplexy in patients with narcolepsy. Previously, gamma-hydroxybutyrate (GHB), the active ingredient of sodium oxybate, had been a substance of abuse, most notoriously as a date-rape drug. Public Law 106-172, the date-rape prohibition act enacted in 2000, was modified to allow the drug to be legally administered for medical purposes. Because of the apprehension regarding the risk of possible drug diversion after the approval of sodium oxybate and concerns about safety, the Xyrem Risk Management Program was created. This program has been successful in satisfying the needs of patients and physicians while ensuring responsible distribution of the drug.