gebhart/patrepeval huggingface dataset:
Significance of Microbiota in Obesity and Metabolic Diseases and the Modulatory Potential by Medicinal Plant and Food Ingredients (2017)

Metabolic syndrome is a cluster of three or more metabolic disorders including insulin resistance, obesity, and hyperlipidemia. Obesity has become the epidemic of the twenty-first century with more than 1.6 billion overweight adults. Due to the strong connection between obesity and type 2 diabetes, obesity has received wide attention with subsequent coining of the term "diabesity." Recent studies have identified unique contributions of the immensely diverse gut microbiota in the pathogenesis of obesity and diabetes. Several mechanisms have been proposed including altered glucose and fatty acid metabolism, hepatic fatty acid storage, and modulation of glucagon-like peptide (GLP)-1. Importantly, the relationship between unhealthy diet and a modified gut microbiota composition observed in diabetic or obese subjects has been recognized. Similarly, the role of diet rich in polyphenols and plant polysaccharides in modulating gut bacteria and its impact on diabetes and obesity have been the subject of investigation by several research groups. Gut microbiota are also responsible for the extensive metabolism of polyphenols thus modulating their biological activities. The aim of this review is to shed light on the composition of gut microbes, their health importance and how they can contribute to diseases as well as their modulation by polyphenols and polysaccharides to control obesity and diabetes. In addition, the role of microbiota in improving the oral bioavailability of polyphenols and hence in shaping their antidiabetic and antiobesity activities will be discussed.
Sede del Archivo Histórico Comarcal. Vilafranca del Penedès (2002)

El proceso de proyecto debe considerar de antemano la relacion del nuevo edificio con la topografia preexistente, con la que establecera una relacion dialectica que condicionara de manera sustancial la organizacion arquitectonica general. La edificacion que se proyecta es entendida como resultado de la yuxtaposicion de tres elementos basicos: una gran cubierta longitudinal, que protege todos los integrantes del conjunto, el volumen absolutamente hermetico y cerrado del deposito documental y un cuerpo lineal que se desarrolla a lo largo de su fachada posterior. La apariencia que ofrece el conjunto asi ordenado se ve enfatizada por la utilizacion de recursos y materiales de evidente condicion industrial y tecnologica.
Hepatitis C epitopes from phage-displayed cDNA libraries and improved diagnosis with a chimeric antigen (2000)

A novel method for cloning DNase I fragments into bacteriophage display vector fUSE2 was used to create libraries expressing hepatitis C virus (HCV) protein fragments on the phage surface. Selection by panning with a mixture of sera from five HCV-seropositive individuals enabled identification of antigenic determinants in NS3 (amino acids 1,383-1,415), NS4 (amino acids 1, 930-1,938), and NS5 (amino acids 2,088-2,104). The NS3 result is the most accurate location to date of a major conformational determinant that cannot be mimicked by short peptides. Any expressed sequence from the phage library can be excised with Bgl II and cloned directly into the Bgl II site of an appropriate plasmid for bacterial expression. This enables production of chimeric proteins containing multiple antigenic determinants, illustrated by co-expression of the NS4P (amino acids 1,930-1,938) epitope with an NS4N fragment (amino acids 1,644-1,812) containing at least three linear HCV epitopes. When used to screen 35 individual HCV-positive sera by enzyme-linked immunosorbent assay (ELISA), the chimeric antigen detected eight more positives than NS4N alone and gave increased immunoreactivity with others. This approach of identifying antigenic regions by phage display and then co-expressing them as chimeric proteins may be generally applicable to the production of improved diagnostic antigens and recombinant vaccines.
Effects of interferons on the expression of the proto‐oncogene her‐2 in human ovarian carcinoma cells (1992)

The over-expression of the proto-oncogene HER-2 (c-erbB-2/neu) in ovarian, endometrial and mammary carcinoma is an important indicator for poor prognosis. We have previously shown in 3 out of 4 ovarian carcinoma cell lines an interferon-gamma (IFN-gamma)-mediated reduction in HER-2 specific protein and RNA levels. The oncogene expression was lowered only in the ovarian carcinoma cell lines but not in 3 IFN-gamma-sensitive human breast cancer cell lines. We extended our observations also to IFN type I, alpha and omega. The expression of the oncogene was measured by both the p185HER-2 ELISA and in selected cases by a living cell radioimmunoassay using the monoclonal antibody (MAb) 4D5 against the extracellular domain. Both IFN types reduced the expression of HER-2 in the ovarian carcinoma cell lines OVCAR-3, HTB-77, 2774 and SKOV-6, and in the SKUT-2 endometrial carcinoma cells. In contrast, SKOV-8 human ovarian carcinoma cells were sensitive for both IFN types regarding proliferation, but only IFN-gamma reduced proto-oncogene expression. In the SKBR-3 human mammary carcinoma cells, neither IFN type had an effect on HER-2 expression. The antibodies 4D5, 7C2, 3E8, and 3H4 which bind to the extracellular domain of p185HER-2 protein specifically inhibited anchorage-independent growth of SKBR-3 and HTB-77 cells. Expression of the oncogene HER-2 is the leading prognostic factor in ovarian cancer. Its modulation might represent a mechanism by which IFNs inhibit cell proliferation.
Resuscitation from hemorrhagic shock: recovery of oxygen carrying capacity or perfusion? Efficacy of new plasma expanders (2007)

SUMMARY Potential shortages and perceived issues with the biosafety of blood have strengthened interest in the search for alternatives to blood. Currently available plasma expanders are effective in recovering pressure by volume expansion but are not safely deployed beyond the transfusion trigger. Conventional reasoning indicates that this limitation relates to oxygen carrying capacity reaching the threshold where it no longer can satisfy the metabolic demand of the organism; however, recent findings show that this limitation is also determined by other physical factors such as their viscosity and colloidal osmotic pressure. These fluid transport properties have a strong influence on the maintenance of microvascular perfusion and function in conditions of extreme hemodilution that obtain when resuscitation is continued beyond the transfusion trigger with plasma expanders. This realization leads to the possibility of developing new plasma expanders whose physical properties enhance microvascular function compensating for the decreased intrinsic oxygen carrying capacity in extreme hemodilution via enhanced microvascular perfusion. This review presents experimental, systemic and microvascular findings obtained using polyethylene glycol conjugated albumin solutions in extreme hemodilution and shock resuscitation in the hamster window chamber model, concluding that plasma expanders of this type can be effectively used beyond the transfusion trigger.
YB-1 Relocates to the Nucleus in Adenovirus-infected Cells and Facilitates Viral Replication by Inducing E2 Gene Expression through the E2 Late Promoter (2002)

The adenovirus early proteins E1A and E1B-55kDa are key regulators of viral DNA replication, and it was thought that targeting of p53 by E1B-55kDa is essential for this process. Here we have identified a previously unrecognized function of E1B for adenovirus replication. We found that E1B-55kDa is involved in targeting the transcription factor YB-1 to the nuclei of adenovirus type 5-infected cells where it is associated with viral inclusion bodies believed to be sites of viral transcription and replication. We show that YB-1 facilitates E2 gene expression through the E2 late promoter thus controlling E2 gene activity at later stages of infection. The role of YB-1 for adenovirus replication was demonstrated with an E1-minus adenovirus vector containing a YB-1 transgene. In infected cells, AdYB-1 efficiently replicated and produced infectious progeny particles. Thus, adenovirus E1B-55kDa protein and the host cell factor YB-1 act jointly to facilitate adenovirus replication in the late phase of infection.
Preparation of Fluoroadamantane Acids and Amines:  Impact of Bridgehead Fluorine Substitution on the Solution- and Solid-State Properties of Functionalized Adamantanes (2000)

Functionalized adamantanes are utilized as medicinal therapeutics and a practical route to novel bridgehead fluorinated adamantylamines and acids including fully fluorinated 3,5,7-tri-fluoroadamantane-1-carboxylic acid 1 and 3,5,7-trifluoroadamantane-1-amine 2 is described. Potassium permanganate-mediated bridgehead hydroxylation followed by DAST fluorination was utilized to sequentially insert bridgehead fluorine atoms. 13C NMR chemical shifts of mono-, di-, and trifluoroadamantylamines, acids and carbamates reveal long-range fluorine-mediated electronic effects within the adamantane framework, most notably by substrates bearing three bridgehead fluorine atoms. The impact of multiple bridgehead fluorine substitution on structure (X-ray crystallography) and on physicochemical parameters such as acidity (pKa) and lipophilicity (log P) which are important for the design of medicinal therapeutics is assessed.
Aggregation of huntingtin in yeast varies with the length of the polyglutamine expansion and the expression of chaperone proteins (2000)

Huntington's disease (HD) is an inherited neurodegenerative disorder caused by polyglutamine (polyQ) expansions in the huntingtin (Ht) protein. A hallmark of HD is the proteolytic production of an N-terminal fragment of Ht, containing the polyQ repeat, that forms aggregates in the nucleus and cytoplasm of affected neurons. Proteins with longer polyQ repeats aggregate more rapidly and cause disease at an earlier age, but the mechanism of aggregation and its relationship to disease remain unclear. To provide a new, genetically tractable model system for the study of Ht, we engineered yeast cells to express an N-terminal fragment of Ht with different polyQ repeat lengths of 25, 47, 72, or 103 residues, fused to green fluorescent protein. The extent of aggregation varied with the length of the polyQ repeat: at the two extremes, most HtQ103 protein coalesced into a single large cytoplasmic aggregate, whereas HtQ25 exhibited no sign of aggregation. Mutations that inhibit the ubiquitin/proteasome pathway at three different steps had no effect on the aggregation of Ht fragments in yeast, suggesting that the ubiquitination of Ht previously noted in mammalian cells may not inherently be required for polyQ length-dependent aggregation. Changing the expression levels of a wide variety of chaperone proteins in yeast neither increased nor decreased Ht aggregation. However, Sis1, Hsp70, and Hsp104 overexpression modulated aggregation of HtQ72 and HtQ103 fragments. More dramatically, the deletion of Hsp104 virtually eliminated it. These observations establish yeast as a system for studying the causes and consequences of polyQ-dependent Ht aggregation.
Conversion of visual to instrumental measurement of yellowness (1981)

Abstract Yellowness is the result of a tendency of many materials (especially organic) to absorb more light in the blue end than in the rest of the visible spectrum. For approximately 100 years, yellowness of materials has been rated by visual comparisons with either standardized glasses or standardized solutions of reagent grade chemicals. Since 1942, paints, textiles, plastics and many other materials have been rated for yellowness by photoelectric measurements based on the spectral response characteristics of the normal human eye. Four of the long‐established and widely used visual scales for yellowness are related herein to four of the newer and more precise photo‐electric tristimulus scales. The four visual scales are Lovibond, Hazen, Gardner and FAC. The tristimulus scales are ASTM D1925, ASTM E313, Hunter b and CIELAB b * . These interrelations between scales were actually developed more than 20 years ago by Ron Stillman of the AOCS, but his data were so voluminous that no opportunity for their publication was ever found.
Autoantibodies Associated with Psychiatric Disorders (2006)

Growing evidence suggests that autoantibodies to neuronal or endothelial targets in psychiatric disorders exist and may be pathogenic. This review describes and discusses the possible role of autoantibodies related to the psychiatric manifestations in autoimmune diseases, autoantibodies related to the psychiatric disorders present in post-streptococcal diseases, celiac disease, chronic fatigue syndrome and substance abuse, and autoantibodies related to schizophrenia and autism, disorders now considered of autoimmune origin.
Mutagenesis of Pseudomonas exotoxin in identification of sequences responsible for the animal toxicity. (1990)

Pseudomonas exotoxin (PE) is composed of three structural domains that are responsible for cell recognition, membrane translocation, and ADP-ribosylation. The deletion of the cell recognition domain (domain Ia) of PE results in a molecule that does not bind to target cells and has low toxicity in mice (Hwang, J., FitzGerald, D.J.P., Adhya, S., and Pastan, I. (1987) Cell 48, 129-136). To determine the specific sequences required for cell binding as well as cell and animal toxicity, a series of domain I mutants was constructed. Using a T7 promoter-based expression system and an OmpA signal sequence, large amounts of the various mutant toxins were secreted into the periplasm from which they were easily purified in milligram quantities. The data indicate that amino acids at positions 246, 247, and 249 have an important role in the toxicity of PE. Conversion of these amino acids to glutamic acid or glycine but not to lysine or deletion of amino acids 241-250 diminishes the toxicity of PE. When combined with a mutation at position 57 a molecule is created that has very low toxicity against cultured cells or in mice.
Fluidic Self-Assembly of Microstructures Using a Blade-Coating Technique: Influence of Volume of Water Droplets on Probability of Microstructure Placement (2012)

Fluidic self-assembly (FSA) is a promising technique for fabricating devices that are composed of large numbers of small electronic components. We have previously proposed a printing method that utilizes the FSA principle. In our method, by simply blade-coating first water and then a dispersion liquid of microstructures on a substrate, the microstructures are automatically placed on pre-patterned hydrophilic areas by means of water/solvent interfacial force. To improve the placement probability of microstructures on the intended hydrophilic areas, in the present study we investigate the influence of the volume of water droplets on the probability of microstructure placement. We prepared various sizes of hydrophilic patterns on a glass substrate to vary the volume of water droplets in hydrophilic areas, and placed square SiO2 plates, measuring 50 ×50 ×0.3 µm3, using FSA. The probability and accuracy of placement was evaluated using a high-speed microscope, and the results were interpreted using a simple model based on capture coefficients and the collision cross section of the water droplets. We verified that the model closely fitted the experimentally obtained probability of placement as observed using the high-speed microscope. We found that the capture coefficient increased with increasing area of the water droplet. These results indicate that the size of the hydrophilic area is one key to improving the probability and accuracy of our placement technique.
Orf virus-encoded interleukin-10 stimulates the proliferation of murine mast cells and inhibits cytokine synthesis in murine peritoneal macrophages (2002)

Orf virus (ORFV) is the type species of the parapoxvirus genus and produces cutaneous pustular lesions in sheep, goats and humans. The genome encodes a polypeptide with remarkable homology to interleukin-10 (IL-10), particularly ovine IL-10, and also to IL-10-like proteins encoded by Epstein-Barr virus (EBV) and equine herpesvirus. IL-10 is a pleiotropic cytokine that can exert either immunostimulatory or immunosuppressive effects on many cell types. We have expressed and purified C-terminal FLAG and His(6)-tagged versions of ORFV-IL-10 and shown that ORFV-IL-10 costimulates murine mast cells (MC/9) and inhibits tumour necrosis factor-alpha synthesis in activated mouse peritoneal macrophages. Our results demonstrate that although ORFV-IL-10 is structurally similar to EBV-IL-10 it has evolved a different spectrum of activities. EBV-IL-10 does not stimulate the proliferation of thymocytes or mast cells whereas ORFV-IL-10 has both of these activities. Recent studies show that the critical difference in molecular structure of human IL-10 and EBV-IL-10, which may be the basis of their functional differences, is linked to a single amino acid substitution. Consistent with the activity spectrum reported here for ORFV-IL-10, the viral gene encodes the critical amino acid seen in human IL-10. Although the ORFV-IL-10 gene has clearly undergone significant evolutionary change at the nucleotide level compared with ovine IL-10, it has largely retained the polypeptide structure and functional characteristics of its ovine counterpart, suggesting that mutations of the gene to a potentially more potent immunosuppressive form may compromise the co-existence of host and virus.
The almanac projects: seasons experienced through the material world (2012)

This paper explores the almanac as a medium for enacting a vital materialist practice. It begins by asking: what elements do we incorporate into the ways we think about weather, climates and seasons? What other possibilities exist if we consider weather and seasons that include non-human perspectives? What are the implications of these ways of thinking? I draw upon Jane Bennett’s “vital materialism” in considering the experience of seasons as human and non-human assemblages of activity. I present my own almanac projects as an active and creative engagement with the living and non-living worlds participating in seasonal changes. The paper argues that the almanac as a medium has the potential to make perceptible an inclusive and encompassing ecology that constitutes our multifaceted experience of the seasons.
Calcium-dependent potentiation of store-operated calcium channels in T lymphocytes. (1996)

The depletion of intracellular Ca2+ stores triggers the opening of Ca2+ release-activated Ca2+ (CRAC) channels in the plasma membrane of T lymphocytes. We have investigated the additional role of extracellular Ca2+ (Ca02+) in promoting CRAC channel activation in Jurkat leukemic T cells. Ca2+ stores were depleted with 1 microM thapsigargin in the nominal absence of Ca02+ with 12 mM EGTA or BAPTA in the recording pipette. Subsequent application of Ca02+ caused ICRAC to appear in two phases. The initial phase was complete within 1 s and reflects channels that were open in the absence of Ca02+. The second phase consisted of a severalfold exponential increase in current amplitude with a time constant of 5-10 s; we call this increase Ca(2+)-dependent potentiation, or CDP. The shape of the current-voltage relation and the inferred single-channel current amplitude are unchanged during CDP, indicating that CDP reflects an alteration in channel gating rather than permeation. The extent of CDP is modulated by voltage, increasing from approximately 50% at +50 mV to approximately 350% at -75 mV in the presence of 2 mM Ca02+. The voltage dependence of CDP also causes ICRAC to increase slowly during prolonged hyperpolarizations in the constant presence of Ca02+. CDP is not affected by exogenous intracellular Ca2+ buffers, and Ni2+, a CRAC channel blocker, can cause potentiation. Thus, the underlying Ca2+ binding site is not intracellular. Ba2+ has little or no ability to potentiate CRAC channels. These results demonstrate that the store-depletion signal by itself triggers only a small fraction of capacitative Ca2+ entry and establish Ca2+ as a potent cofactor in this process. CDP confers a previously unrecognized voltage dependence and slow time dependence on CRAC channel activation that may contribute to the dynamic behavior of ICRAC.
Extraction of Oxidized and Reduced Forms of Uranium from Contaminated Soils:  Effects of Carbonate Concentration and pH (2005)

Uranium may present in soil as precipitated, sorbed, complexed, and reduced forms, which impact its mobility and fate in the subsurface soil environment. In this study, a uranium-contaminated soil was extracted with carbonate/ bicarbonate at varying concentrations (0-1 M), pHs, and redox conditions in an attempt to evaluate their effects on the extraction efficiency and selectivity for various forms of uranium in the soil. Results indicate that at least three differentforms of uranium existed in the contaminated soil: uranium(VI) phosphate minerals, reduced U(IV) phases, and U(VI) complexed with soil organic matter. A small fraction of U(VI) could be sorbed onto soil minerals. The mechanism involved in the leaching of U(VI) by carbonates appears to involve three processes which may act concurrently or independently: the dissolution of uranium(VI) phosphate and other mineral phases, the oxidation-complexation of U(IV) under oxic conditions, and the desorption of U(VI)-organic matter complexes at elevated pH conditions. This study suggests that, depending on site-specific geochemical conditions, the presence of small quantities of carbonate/bicarbonate could result in a rapid and greatly increased leaching and the mobilization of U(VI) from the contaminated soil. Even the reduced U(IV) phases (only sparingly soluble in water) are subjected to rapid oxidation and therefore potential leaching into the environment.
NADPH oxidase is implicated in the pathogenesis of oxidative phosphorylation dysfunction in mice fed a high-fat diet (2016)

The aim of this study was to evaluate the role of NADPH oxidase (NADPHox) in the pathogenesis of oxidative phosphorylation (OXPHOS) dysfunction as found in mice fed a high-fat diet (HFD). C57BL/6J mice were distributed in four groups: WT/SCD: six wild-type (WT) mice fed a standard chow diet (SCD); WT/HFD, six WT mice fed a HFD; NOX2(-/-)/SCD, six NADPHox-deficient mice on a SCD; (4) NOX2(-/-)/HFD, six NADPHox-deficient mice on a HFD. After 32 weeks, we studied the liver for: histology; OXPHOS complex activity; fully assembled OXPHOS complexes and their subunits; gene expression of OXPHOS subunits; oxidative and nitrosative stress; and oxidative DNA damage. In the liver of WT/HFD mice, we found a significant decreased in the activity of all OXPHOS complexes, in fully assembled complexes, in the amount of OXPHOS subunits, and in gene expression of mitochondrial DNA-encoded subunits. 8-hydroxy-2'-deoxyguanosine was only increased in mitochondrial DNA. The liver of NOX(-/-)/HFD mice showed mild steatosis but no non-alcoholic steatohepatitis (NASH) lesions were found. OXPHOS activity, OXPHOS subunits, and assembly of subunits into OXPHOS complexes were normal in these mice. We conclude that this study shows that NADPH deficiency protects mice from developing OXPHOS dysfunction and NASH caused by a HFD.