gebhart/patrepeval huggingface dataset:
Functional Genomics Reveals the Induction of Inflammatory Response and Metalloproteinase Gene Expression during Lethal Ebola Virus Infection (2011)

Ebola virus is the etiologic agent of a lethal hemorrhagic fever in humans and nonhuman primates with mortality rates of up to 90%. Previous studies with Zaire Ebola virus (ZEBOV), mouse-adapted virus (MA-ZEBOV), and mutant viruses (ZEBOV-NP(ma), ZEBOV-VP24(ma), and ZEBOV-NP/VP24(ma)) allowed us to identify the mutations in viral protein 24 (VP24) and nucleoprotein (NP) responsible for acquisition of high virulence in mice. To elucidate specific molecular signatures associated with lethality, we compared global gene expression profiles in spleen samples from mice infected with these viruses and performed an extensive functional analysis. Our analysis showed that the lethal viruses (MA-ZEBOV and ZEBOV-NP/VP24(ma)) elicited a strong expression of genes 72 h after infection. In addition, we found that although the host transcriptional response to ZEBOV-VP24(ma) was nearly the same as that to ZEBOV-NP/VP24(ma), the contribution of a mutation in the NP gene was required for a lethal phenotype. Further analysis indicated that one of the most relevant biological functions differentially regulated by the lethal viruses was the inflammatory response, as was the induction of specific metalloproteinases, which were present in our newly identify functional network that was associated with Ebola virus lethality. Our results suggest that this dysregulated proinflammatory response increased the severity of disease. Consequently, the newly discovered molecular signature could be used as the starting point for the development of new drugs and therapeutics. To our knowledge, this is the first study that clearly defines unique molecular signatures associated with Ebola virus lethality.
The alpha-glucosidase I inhibitor castanospermine alters endothelial cell glycosylation, prevents angiogenesis, and inhibits tumor growth. (1995)

The development of drugs that target the tumor neovasculature may hold promise in inhibiting tumor growth. Experiments in vivo with castanospermine, an inhibitor of the glucosidases that convert protein N-linked high mannose carbohydrates to complex oligosaccharides, resulted in significant inhibition of tumor growth in nude mice. Angiogenesis to basic fibroblast growth factor in castanospermine-treated C57/BL mice was similarly reduced. Endothelial cell proliferation, invasion of basement membrane, and differentiation are crucial steps during neovascularization. In vitro differentiation models using Matrigel and postconfluent cultures of endothelial cells were used to study the effects of glycosidase inhibitors on endothelial cell behavior. FACS analysis of cell surface oligosaccharides using either Concanavalin A or L-phytohemagglutinin lectins confirmed an increase in high mannose groups and a decrease in tri- and tetra antennary beta-linked galactose-N-acetylglucosamine on mannose residues of Asn-linked oligosaccharides upon drug treatment. Castanospermine and the glucosidase inhibitor N-methyldeoxynojirimycin prevented the morphological differentiation of endothelial cells in vitro. These compounds did not alter the proliferation of cultured endothelial cells or their ability to attach to various extracellular matrix molecules. However, the cells showed a reduced ability to migrate and to invade basement membrane gels in vitro and an increased tendency to form aggregates that was inhibitable by D-mannose. These studies suggest that certain cell surface oligosaccharides are required for angiogenesis and that glucosidase inhibitors that alter these structures on endothelial cells are able to inhibit tumor growth.
FR-900520 and FR-900523, novel immunosuppressants isolated from a Streptomyces. II. Fermentation, isolation and physico-chemical and biological characteristics. (1988)

FR-900520 and FR-900523, novel neutral macrolide immunosuppressants, were isolated from the cultured broth of Streptomyces hygroscopicus subsp. yakushimaensis No. 7238. Their molecular formulae were determined as C43H69NO12 and C42H67NO12, respectively. The compounds suppressed immune response in vitro. IC50 values of FR-900520 and FR-900523 for mouse mixed lymphocyte reaction were 0.55 nM and 1.6 nM, respectively. FR-900520, the major component, clearly prolonged skin allograft survival in rats.
Femtosecond laser-assisted microstructuring of silicon for novel detector, sensing and display technologies (2003)

Summary form only given. Arrays of sharp, conical microstructures are obtained by texturing the surface of a silicon wafer using femtosecond laser-assisted chemical etching. The one step, maskless texturing process drastically changes the optical, material and electronic properties of the original silicon wafer. These properties make microstructured silicon viable for use in a wide range of commercial devices including solar cells, infrared photodetectors, chemical and biological sensors, and field emission devices. We describe the unique optical and electronic properties of microstructured silicon, discuss the formation process of the conical microstructures, and review the chemical and structural make-up of the surface that are responsible for the novel optoelectronic properties. We also deal with future directions for this technique including structuring of new materials, incorporation of new ambient gases, and better control over the position and density of the microstructures themselves.
Cyclodextrin alleviates neuronal storage of cholesterol in Niemann‐Pick C disease without evidence of detectable blood–brain barrier permeability (2013)

Abstract Niemann‐Pick type C disease is an inherited autosomal recessive neurodegenerative disorder characterised by the accumulation of unesterified cholesterol and sphingolipids within the endosomal/lysosomal compartments. It has been observed that the administration of hydroxypropyl‐β‐cyclodextrin (HPBCD) delays onset of clinical symptoms and reduces accumulation of cholesterol and gangliosides within neuronal cells. It was assumed that HPBCD exerts its action by readily entering the CNS and directly interacting with neurones and other brain cells to facilitate removal of stored cholesterol from the late endosomal/lysosomal compartment. Here, we present evidence that refutes this hypothesis. We use two well established techniques for accurately measuring brain uptake of solutes from blood and show that there is no significant crossing of HPBCD into the brain. The two techniques are brain in situ perfusion and intraperitoneal injection followed by multi‐time‐point regression analysis. Neither study demonstrates significant, time‐dependent uptake of HPBCD in either adult or neonatal mice. However, the volume of distribution available to HPBCD (0.113 ± 0.010 ml/g) exceeds the accepted values for plasma and vascular volume of the brain. In fact, it is nearly three times larger than that for sucrose (0.039 ± 0.006 ml/g). We propose that this indicates cell surface binding of HPBCD to the endothelium of the cerebral vasculature and may provide a mechanism for the mobilisation and clearance of cholesterol from the CNS.
High‐Efficiency Organic‐Dye‐ Sensitized Solar Cells Controlled by Nanocrystalline‐TiO2 Electrode Thickness (2006)

A mesoscopic bilayer TiO2 film used as an electron collector in conjunction with an acetonitrile- or ionic liquid-based electrolyte greatly improves the performance of dye-sensitized solar cells (see figure). The thickness of the nanocrystalline TiO2 film affects the photovoltaic characteristics, particularly for the ionic-liquid-based electrolyte, owing to a limitation of the photocurrent by the diffusion of I3– ions.
A newly identified fatty alcohol oxidase gene is mainly responsible for the oxidation of long-chain ω-hydroxy fatty acids inYarrowia lipolytica (2014)

Nine potential (fatty) alcohol dehydrogenase genes and one alcohol oxidase gene were identified in Yarrowia lipolytica by comparative sequence analysis. All relevant genes were deleted in Y. lipolytica H222ΔP which is lacking β-oxidation. Resulting transformants were tested for their ability to accumulate ω-hydroxy fatty acids and dicarboxylic acids in the culture medium. The deletion of eight alcohol dehydrogenase genes (FADH, ADH1-7), which may be involved in ω-oxidation, led only to a slightly increased accumulation of ω-hydroxy fatty acids, whereas the deletion of the fatty alcohol oxidase gene (FAO1), which has not been described yet in Y. lipolytica, exhibited a considerably higher effect. The combined deletion of the eight (fatty) alcohol dehydrogenase genes and the alcohol oxidase gene further reduced the formation of dicarboxylic acids. These results indicate that both (fatty) alcohol dehydrogenases and an alcohol oxidase are involved in ω-oxidation of long-chain fatty acids whereby latter plays the major role. This insight marks the first step toward the biotechnological production of long-chain ω-hydroxy fatty acids with the help of the nonconventional yeast Y. lipolytica. The overexpression of FAO1 can be further used to improve existing strains for the production of dicarboxylic acids.
Importance of Heat Transfer by Radiation in Li-Ion Batteries during Thermal Abuse (1999)

As much as 50% of the heat transferred from a cell to the environment during oven exposure testing could be by radiation. The effectiveness of radiation heat transfer depends on the emissivity of the outermost surface of the cell, normally the label. We show that the tolerance of cells to thermal abuse is dramatically improved when suitable labels are used on the cell. Selecting labels with the highest possible emissivity will lead to cells with the greatest thermal tolerance. A comparison between labels on commercial cells suggests that major manufacturers are not aware of these advantages and that the inherent safety of the technology in the marketplace can be easily improved. ©2000 The Electrochemical Society
A Review on Applications of Liposomes in Textile Processing (2008)

This review discusses the properties of liposomes and their role in the textile process, including textile preparation and dyeing. Liposomes have a surface activity effect due to a hydrophilic head group and hydrophobic hydrocarbon tail. Its preparations do not tend to foam, which advantageously distinguishes them from other textile auxiliaries. According to the carrier role of liposomes, they can be used in several textile processes such as textile finishing and dyeing with several types of dyes and fibers. Each application is discussed in this review paper. Several types of dyes are encapsulated by liposomes in the dyeing process and their presence indicates that they have retardant and leveling effects according to their gradual release of dyes. In addition, the presence of liposomes in the textile process can improve the mechanical properties of textile products, resulting in better wash fastness properties and leveling effect and handle properties. The best character of liposomes is a reduction in temperature of process resulting to save energy and they are environment degradable materials.
Chemical Chaperones Reduce ER Stress and Restore Glucose Homeostasis in a Mouse Model of Type 2 Diabetes (2006)

Endoplasmic reticulum (ER) stress is a key link between obesity, insulin resistance, and type 2 diabetes. Here, we provide evidence that this mechanistic link can be exploited for therapeutic purposes with orally active chemical chaperones. 4-Phenyl butyric acid and taurine-conjugated ursodeoxycholic acid alleviated ER stress in cells and whole animals. Treatment of obese and diabetic mice with these compounds resulted in normalization of hyperglycemia, restoration of systemic insulin sensitivity, resolution of fatty liver disease, and enhancement of insulin action in liver, muscle, and adipose tissues. Our results demonstrate that chemical chaperones enhance the adaptive capacity of the ER and act as potent antidiabetic modalities with potential application in the treatment of type 2 diabetes.
TGF‐β2 Induces Maturation of Immature Human Intestinal Epithelial Cells and Inhibits Inflammatory Cytokine Responses Induced Via the NF‐κB Pathway (2011)

Conditioning with TGF-β2 attenuates the subsequent inflammatory cytokine response in immature human IECs by inhibiting signaling in the NF-κB pathway. The immunomodulatory potential of breast milk may in part be mediated by TGF-β2, which may provide a novel means of supporting intestinal immune maturation in neonates.
Sequence Specificity of C‐Terminal Src Kinase (Csk) (1997)

An eicosapeptide encompassing the C-terminal tail of c-Src (Tyr527) which is conserved in most Src-related protein kinases, is phosphorylated by C-terminal Src kinase (CSK) and by the two Src-related protein kinases c-Fgr and Lyn, with similar kinetic constants. Two related peptides reproducing the C-terminal segments of c-Src mutants defective in CSK phosphorylation [MacAuley, A., Okada, M., Nada, S., Nakagawa, H. & Cooper, J. A. (1993) Oncogene 8, 117-124] AFLEDSCTGTEPLYQRGENL (mutant number 28) and AFLEDNFTGTKPQYHPGENL (mutant number 29), proved a better and a much worse substrates, respectively than the wild-type peptide, with either CSK or the two Src kinases. By changing individual residues in the best peptide substrate, it was shown that the main element responsible for its improved phosphorylation is leucine at position -1 (instead of glutamine), while lysine at position -3 (instead of glutamate) has a detrimental effect, possibly accounting for the negligible phosphorylation of peptide derived from mutant number 29. By contrast to most peptide substrates, including the Src C-terminal peptides, which exhibit relatively high K(m) values, a polyoma-virus-middle-T-antigen-(mT)-derived peptide with tyrosine embedded in a highly hydrophobic sequence (EEEPQFEEIPIYLELLP) exhibits with CSK a quite low K(m) value (63 microM). Consistent with this, the optimal sequence selected by CSK in an oriented peptide library is XXXIYMFFF. This is different from sequences selected by Lyn (DEEIYEELX) and c-Fgr (XEEIYGIFF), although they all share a high selection for a hydrophobic residue at n-1. In sharp contrast, TPKIIB/p38syk, related to the catalytic domain of p72syk, selects acidic residues at nearly all positions, n-1 included. These data support the notion that the features determining the specific phosphorylation of the C-terminal tyrosine residue of Src do not reside in the primary structure surrounding the target tyrosine. They also show that this site does not entirely fulfil the optimal consensus sequence recognized by CSK, disclosing the possibility that as yet unrecognized CSK targets structurally unrelated to the C-terminal tyrosine residue of Src kinases may exist.
Transcriptional regulation in human bladder cancer cells by RalA and RalB via both independent and overlapping pathways (2006)

4276 The monomeric GTPases RalA and RalB have been shown to contribute to human tumorigenesis and cancer progression in a number of ways. In some cases, RalA and RalB appear to have overlapping roles, but for at least two phenotypes, colony formation in soft agar and motility, they have been shown to act antagonistically. RalA and RalB have been shown to regulate a small set of transcription factors - NF-kappaB, the forkhead protein FoxO4, ZONAB - although in some cases, the specificity of transcriptional regulation of RalA vs. RalB remains unclear. What also remains unclear is the relevance of transcriptional regulation mediated by RalA and/or RalB to their roles in human cancer. Here, we studied the importance of RalA and/or RalB to trancriptional regulation in the human bladder cancer cell line, UMUC-3, by combining siRNA depletion Ral with gene expression analysis via microarray. RalA knockdown resulted in significant up-regulation of 95 genes (> 2 fold) and down-regulation of 156 genes (
Gene Transfer Into Intact Sugarcane Cells Using Microprojectile Bombardment (1991)

A microprojectile accelerator has been constructed and used to bombard cultured sugarcane tissues with GUS reporter gene constructs. Design features useful to minimise target tissue damage and variation between shots are described. Transient expression of GUS occurred in pEmuGN-bombarded cells of nonregenerable suspension culture as well as in regenerable embryogenic callus of commercial sugarcane cultivar 463, and in suspension cultures capable of regeneration to plants. Parameters yielding transient GUS expression in up to 1055 cells per bombardment in homogeneous suspension cultures of sugarcane have been established with a mean of 206 expressing cells per bombardment over a series of 8 independent experiments. Approximately 4% of these transiently expressing cells continued to express GUS for extended periods, indicating probable stable transformation of intact cells of the commercial sugarcane cultivar. Microprojectile bombardment appears the most promising of the available gene transfer techniques for practical genetic transformation of sugarcane because most commercial cultivars readily form regenerable callus suitable for bombardment.
Differential Induction of Colitis and Gastritis in HLA-B27 Transgenic Rats Selectively Colonized withBacteroides vulgatusorEscherichia coli (1999)

Resident bacteria play an important role in initiating and perpetuating gastrointestinal inflammation. We previously demonstrated that six commensal bacteria including Bacteroides vulgatus caused more aggressive colitis and gastritis in HLA-B27 transgenic rats than did the other five bacteria without B. vulgatus. This study compared the degree of gastrointestinal inflammation in gnotobiotic HLA-B27 transgenic rats monoassociated with either B. vulgatus or Escherichia coli. Gnotobiotic transgenic rats raised in Trexler isolators were selectively colonized with either B. vulgatus or E. coli. Control rats were either germfree or colonized with six common commensal bacteria (Streptococcus faecium, E. coli, Streptococcus avium, Eubacterium contortum, Peptostreptococcus productus, and B. vulgatus [DESEP-B]). After 1 month, all the rats were killed and tissues were prepared for histologic and biochemical evaluation. Colitis induced by B. vulgatus monoassociation was almost equal to that in DESEP-B-colonized rats and was significantly more severe than E. coli-induced colitis, which was absent by histological testing and mild by colonic myeloperoxidase and interleukin-1beta concentration determinations. However, gastritis was detectable only in DESEP-B-associated rats. These studies suggest that not all resident bacteria have equal proinflammatory capabilities, since B. vulgatus alone is more active than E. coli alone in inducing colitis, and that colitis and gastritis result from different luminal bacterial stimuli.
Device independence and the Web (2002)

Device manufacturers, users, and authors have differing needs and expectations when it comes to Web content. Web software and hardware manufacturers naturally try to differentiate their products by supporting a special combination of capabilities, but few can expect Web authors to create content for their product alone. Users, however, do expect to access the same content from any device with similar capabilities. Even when device capabilities differ, users might still want access to an adapted version of the content. Due to device differences, the adaptation might not produce an identical presentation, but device-independence principles suggest it should be sufficiently functional to let users interact with it successfully. Web application authors cannot afford to create multiple content versions for each of the growing range of device types. Authors would rather create their content once, and adapt it to different devices-but they also want to retain control of presentation quality. Device independence is about trying to satisfy these differing needs, spanning the delivery path between author and user by way of diverse manufacturers' devices. The field's continued evolution within the broader Web standards framework aims to find solutions that are beneficial for all.
Biotin Reagents for Antibody Pretargeting. 5. Additional Studies of Biotin Conjugate Design To Provide Biotinidase Stability (2001)

An investigation was conducted in which the stabilities of four structurally different biotin derivatives were assessed with regard to biotinamide bond hydrolysis by the enzyme biotinidase. The biotin derivatives studied contained an extra methylene in the valeric acid chain of biotin (i.e., homobiotin), or contained conjugated amino acids having hydroxymethylene, carboxylate, or acetate functionalities on a methylene alpha to the biotinamide bond. The biotinidase hydrolysis assay was conducted on biotin derivatives that were radioiodinated at high specific activity, and then subjected to diluted human serum at 37 degrees C for 2 h. After incubation, assessment of biotinamide bond hydrolysis by biotinidase was readily achieved by measuring the percentage of radioactivity that did not bind with avidin. As controls, an unsubstituted biotin derivative which is rapidly cleaved by biotinidase and an N-methyl-substituted biotin derivative which is stable to biotinidase cleavage were included in the study. The results indicate that increasing the distance from the biotin ring structure to the biotinamide bond by one methylene only decreases the rate of biotinidase cleavage, but does not block it. The data obtained also indicate that placing a hydroxymethylene, carboxylate, or acetate alpha to the biotinamide bond is effective in blocking the biotinamide hydrolysis reaction. These data, in combination with data previously obtained, which indicate that biotin derivatives containing hydroxymethylene or carboxylate moieties retain the slow dissociation rate of biotin from avidin and streptavidin [Wilbur, D. S., et al. (2000) Bioconjugate Chem. 11, 569-583], strongly support incorporation of these structural features into biotin derivatives being used for in vivo targeting applications.
Quantitative Magnetic Resonance Imaging Analysis of Neovasculature Volume in Carotid Atherosclerotic Plaque (2003)

Dynamic contrast-enhanced MRI provides an indication of the extent of neovasculature within carotid atherosclerotic plaque. MRI therefore provides a means for prospectively studying the link between neovasculature and plaque vulnerability.
New Methods of Treatment for Renal Allotransplant Using the Baboon as a Primate Experimental Model (1969)

No AccessJournal of Urology1 Nov 1969New Methods of Treatment for Renal Allotransplant Using the Baboon as a Primate Experimental Model J.N. deKlerk, G.P. Murphy, J.J.W. van Zyl, J.A. van Zyl, H.W. Weber, H.D. Brede, and W.W. Scott J.N. deKlerkJ.N. deKlerk More articles by this author , G.P. MurphyG.P. Murphy Current address: Department of Urology, Roswell Park Memorial Institute, Buffalo, New York 14203 More articles by this author , J.J.W. van ZylJ.J.W. van Zyl More articles by this author , J.A. van ZylJ.A. van Zyl More articles by this author , H.W. WeberH.W. Weber More articles by this author , H.D. BredeH.D. Brede More articles by this author , and W.W. ScottW.W. Scott More articles by this author View All Author Informationhttps://doi.org/10.1016/S0022-5347(17)62192-XAboutPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookLinked InTwitterEmail © 1969 by The American Urological Association Education and Research, Inc.FiguresReferencesRelatedDetails Volume 102Issue 5November 1969Page: 532-540 Advertisement Copyright & Permissions© 1969 by The American Urological Association Education and Research, Inc.MetricsAuthor Information J.N. deKlerk More articles by this author G.P. Murphy Current address: Department of Urology, Roswell Park Memorial Institute, Buffalo, New York 14203 More articles by this author J.J.W. van Zyl More articles by this author J.A. van Zyl More articles by this author H.W. Weber More articles by this author H.D. Brede More articles by this author W.W. Scott More articles by this author Expand All Advertisement PDF downloadLoading ...