gebhart/patrepeval huggingface dataset:
Diagnosis of hepatitis C virus (HCV) infection using an immunodominant chimeric polyprotein to capture circulating antibodies: reevaluation of the role of HCV in liver disease. (1992)

Structural and nonstructural regions of the HCV-encoded polyprotein have been expressed in recombinant yeast, bacteria, or insect cells and used to capture and measure reactive antibodies circulating in different individuals. The putative nucleocapsid protein (C) and nonstructural proteins 3-5 (NS3-NS5) were found to contain the most immunodominant epitopes. The NS3, NS4, and C regions were expressed in yeast in the form of a fused, chimeric polyprotein (C25) and a capture assay for reactive antibody was developed. This anti-C25 assay detects all previously identified HCV-seropositive cases and provides a substantially more sensitive diagnostic for both acute and chronic HCV infections than the current anti-C100-3 (NS4) assay. Anti-C25 was detected more frequently than anti-C100-3 in chronic, transfusion-associated non-A, non-B hepatitis patients from the United States (95% vs. 71%) and Japan (98% vs. 82%), in cryptogenic cirrhosis patients from the United States (62% vs. 28%), and in hepatitis B surface antigen-negative cases of hepatocellular carcinoma from Japan (83% vs. 63%). These data indicate that HCV has a greater role in these liver diseases than was previously thought. In volunteer United States blood donors sampled following the introduction of anti-C100-3 screening, the prevalence of anti-C25 and anti-C100-3 was 0.5% and 0.08%, respectively.
SM09A and SM09B: Romaine Lettuce Breeding Lines Resistant to Dieback and with Improved Shelf Life (2010)

Additional index words. Lactuca sativa, tomato bushy stunt virus, lettuce necrotic stunt virus, salad-cut lettuce, storage, disease resistance, marker-assisted selection SM09A and SM09B are F 8 romaine breeding lines of lettuce (Lactuca sativa L.) resistant to the dieback disease and with good shelf life. SM09B was selected from a cross between 'Darkland' and PI 491224, whereas SM09A was developed from 'Green Towers' ('Darkland' PI 491224). Resistance to the disease in both breeding lines is derived from PI 491224, a primitive romaine-type lettuce that is highly perishable when processed for salad. In replicated field trials, the two breeding lines showed complete resistance to dieback. Field observations were confirmed through the analysis of molecular markers closely linked to the dieback resistance gene Tvr1. Testing of salad-cut lettuce in modified atmosphere packaging indicated slower decay in the two breeding lines compared with other dieback-resistant romaines.
A selenophenyl bridged perylene diimide dimer as an efficient solution-processable small molecule acceptor (2014)

We report herein a new solution-processable small molecule acceptor, a selenophenyl bridged perylene diimide dimer, that gives 4.0% efficiency when employing PBDTTT-C-T as the polymer donor and a conventional cell structure.
Review: The Cct eukaryotic chaperonin subunits of Saccharomyces cerevisiae and other yeasts (1996)

All eight of the CCT1-CCT8 genes encoding the subunits of the Cct chaperonin complex in Saccharomyces cerevisiae have been identified, including three that were uncovered by the systematic sequencing of the yeast genome. Although most of the properties of the eukaryotic Cct chaperonin have been elucidated with mammalian systems in vitro, studies with S. cerevisiae conditional mutants revealed that Cct is required for assembly of microtubules and actin in vivo. Cct subunits from the other yeasts, Candida albicans and Schizosaccharomyces pombe, also have been identified from partial and complete DNA sequencing of genes. Cct8p from C. albicans, the only other completely sequenced Cct protein from a fungal species other than S. cerevisiae, is 72% and 61% similar to the S. cerevisiae and mouse Cct8 proteins, respectively.
ChemInform Abstract: Functional Mimics of Superoxide Dismutase Enzymes as Therapeutic Agents (1999)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Modulation of Activation-Loop Phosphorylation by JAK Inhibitors Is Binding Mode Dependent (2012)

Janus kinase (JAK) inhibitors are being developed for the treatment of rheumatoid arthritis, psoriasis, myeloproliferative neoplasms, and leukemias. Most of these drugs target the ATP-binding pocket and stabilize the active conformation of the JAK kinases. This type I binding mode can lead to an increase in JAK activation loop phosphorylation, despite blockade of kinase function. Here we report that stabilizing the inactive state via type II inhibition acts in the opposite manner, leading to a loss of activation loop phosphorylation. We used X-ray crystallography to corroborate the binding mode and report for the first time the crystal structure of the JAK2 kinase domain in an inactive conformation. Importantly, JAK inhibitor-induced activation loop phosphorylation requires receptor interaction, as well as intact kinase and pseudokinase domains. Hence, depending on the respective conformation stabilized by a JAK inhibitor, hyperphosphorylation of the activation loop may or may not be elicited.
Scaling laws for thermal conductivity of crystalline nanoporous silicon based on molecular dynamics simulations (2011)

This study establishes that the effective thermal conductivity keff of crystalline nanoporous silicon is strongly affected not only by the porosity fν and the system’s length Lz but also by the pore interfacial area concentration Ai. The thermal conductivity of crystalline nanoporous silicon was predicted using non-equilibrium molecular dynamics simulations. The Stillinger-Weber potential for silicon was used to simulate the interatomic interactions. Spherical pores organized in a simple cubic lattice were introduced in a crystalline silicon matrix by removing atoms within selected regions of the simulation cell. Effects of the (i) system length ranging from 13 to 130 nm, (ii) pore diameter varying between 1.74 and 5.86 nm, and (iii) porosity ranging from 8% to 38%, on thermal conductivity were investigated. A physics-based model was also developed by combining kinetic theory and the coherent potential approximation. The effective thermal conductivity was proportional to (1 − 1.5fν) and inversely proportional to the sum (Ai/4 + 1/Lz). This model was in excellent agreement with the thermal conductivity of nanoporous silicon predicted by molecular dynamics simulations for spherical pores (present study) as well as for cylindrical pores and vacancy defects reported in the literature. These results will be useful in designing nanostructured materials with desired thermal conductivity by tuning their morphology.
Effects of HIV‐1 Tat protein on human T cell proliferation (1992)

In inducing immunodeficiency in human immunodeficiency virus (HIV)-1 infection, a role for the HIV-1 Tat protein has been suggested. In addition to effects on viral transcription, the protein has been ascribed immunosuppressive functions, which were investigated in this study. Proliferation of purified T cells to CD3 monoclonal antibodies immobilized to plastic plates was inhibited up to 70% by addition of 5 micrograms/ml of the Tat protein. This inhibitory effect, however, was not observed in the presence of accessory cells. Furthermore, no effect of Tat protein could be observed on T cell proliferative responses to recall antigen which most likely is related to the presence of accessory cells in the cultures. Taken together, our results do not imply an important role for immunosuppressive effects of Tat in induction of immunodeficiency as observed in HIV infection in vivo.
Population expansion, clonal growth, and specific differentiation patterns in primary cultures of hepatocytes induced by HGF/SF, EGF and TGF alpha in a chemically defined (HGM) medium. (1996)

Mature adult parenchymal hepatocytes, typically of restricted capacity to proliferate in culture, can now enter into clonal growth under the influence of hepatocyte growth factor (scatter factor) (HGF/SF), epidermal growth factor (EGF), and transforming growth factor alpha (TGFalpha) in the presence of a new chemically defined medium (HGM). The expanding populations of hepatocytes lose expression of hepatocyte specific genes (albumin, cytochrome P450 IIB1), acquire expression of markers expressed by bile duct epithelium (cytokeratin 19), produce TGFalpha and acidic FGF and assume a very simplified morphologic phenotype by electron microscopy. A major change associated with this transition is the decrease in ratio between transcription factors C/EBPalpha and C/EBPbeta, as well as the emergence in the proliferating hepatocytes of transcription factors AP1, NFkappaB. The liver associated transcription factors HNFI, HNF3, and HNF4 are preserved throughout this process. After population expansion and clonal growth, the proliferating hepatocytes can return to mature hepatocyte phenotype in the presence of EHS gel (Matrigel). This includes complete restoration of electron microscopic structure and albumin expression. The hepatocyte cultures however can instead be induced to form acinar/ductular structures akin to bile ductules (in the presence of HGF/SF and type I collagen). These transformations affect the entire population of the hepatocytes and occur even when DNA synthesis is inhibited. Similar acinar/ductular structures are seen in embryonic liver when HGF/SF and its receptor are expressed at high levels. These findings strongly support the hypothesis that mature hepatocytes can function as or be a source of bipotential facultative hepatic stem cells (hepatoblasts). These studies also provide evidence for the growth factor and matrix signals that govern these complex phenotypic transitions of facultative stem cells which are crucial for recovery from acute and chronic liver injury.
Gene delivery to the central and peripheral nervous systems of mice using HSV1 ICP34.5 deletion mutant vectors. (1996)

Herpes simplex virus 1 (HSV1) ICP34.5 deletion mutants are avirulent upon inoculation of both the central and peripheral nervous systems of mice, but they replicate to near wild-type titres in a number of non-neuronally derived cell lines in culture. Thus these mutants might be suitable for development as safe vectors for gene transfer to the nervous system. However, the mechanism of this avirulent phenotype in neuronal cells is at present poorly understood, although it has been suggested that nonpermissive cells infected with these mutants may undergo apoptosis, the function of ICP34.5 being to prevent this response and to allow continued virus replication. If this were the case ICP34.5 null mutants might be unsuitable for gene transfer as infected cells would quickly die, limiting the expression of a transgene. Here we have inserted a beta-galactosidase marker gene into a nonessential gene of an HSV1 strain 17+ mutant in which ICP34.5 has been deleted and also into a second mutant in which the virion transactivator protein VMW65 is also inactive. While all the mutants grew to high titre in tissue culture, mice inoculated by the foot-pad or intracranial route at high titre remained healthy until the end of the experiment. Moreover, beta-galactosidase was expressed either in the brain or in the dorsal root ganglia, depending on the site of inoculation. This suggests that in vivo the absence of ICP34.5 does not prevent the expression of a transgene in neuronal tissue and indicates that non-neurovirulent mutants lacking this gene may be suitable for further development as safe vectors for gene therapy in vivo.
Surfactant protein A-deficient mice are susceptible to group B streptococcal infection (1997)

To determine the role of surfactant protein A (SP-A) in host defense, the murine SP-A locus was targeted by homologous recombination to produce mice lacking SP-A. SP-A -/- and control mice were infected with group B streptococcus (GBS) by intratracheal instillation. Pulmonary infiltration 6 and 24 h following infection was more severe in SP-A -/- than in control mice, and was associated with increased numbers of GBS in lung homogenates. Dissemination of GBS to the spleen was observed more frequently in SP-A -/- mice. Pulmonary infiltration with macrophages was similar in both groups; however, the number of bacteria associated with alveolar macrophages was decreased in the SP-A-deficient mice. There was no detectable compensatory increase in surfactant protein D, the other known pulmonary collectin, in response to GBS instillation. SP-A plays an important role in vivo, enhancing clearance of GBS from the lung and inhibiting systemic dissemination of the organism.
Activation of P2X7-mediated apoptosis Inhibits DMBA/TPA-induced formation of skin papillomas and cancer in mice (2009)

(a) P2X(7)-dependent apoptosis is an important mechanism that controls the development and progression of epidermal neoplasia in the mouse. (b) The P2X(7)-dependent apoptosis is mediated by calcium influx via P2X(7) pores, and involves the caspase-9 (mitochondrial) pathway. (c) The diminished pro-apoptotic effect of BzATP in mouse cancer keratinocytes is possibly the result of low expression of the P2X(7) receptor. (d) Activation of P2X(7)-dependent apoptosis, e.g. with BzATP could be a novel chemotherapeutic growth-preventive modality for papillomas and epithelial cancers in vivo.
Microwave phase shifter based on fibre Bragg grating (1998)

A variable delay line is presented for phased array antennas based on a fibre Bragg grating which has a uniform period and operates at constant optical wavelength. The Bragg wavelength of a localised part of the fibre grating is modified by straining the fibre, the optical carrier is reflected by the strained part of the grating and the time delay of the microwave modulating signal is determined by the position where the strain has been applied. In this initial experiment time delay variations up to 330 ps in the frequency range 1 – 14 GHz have been achieved.
Synthesis of 2,6-disubstituted pyridin-3-yl C-2′-deoxyribonucleosides through chemoselective transformations of bromo-chloropyridine C-nucleosides (2013)

2-Bromo-6-chloro- and 6-bromo-2-chloropyridin-3-yl deoxyribonucleosides were prepared by the Heck coupling of bromo-chloro-iodopyridines with TBS-protected deoxyribose glycal. Some of their Pd-catalyzed cross-coupling reactions proceeded chemoselectively at the position of the bromine, whereas nucleophilic substitutions were unselective and gave mixtures of products. The mono-substituted intermediates were used for another coupling or nucleophilic substitution giving rise to a small library of title 2,6-disubstituted pyridine C-deoxyribonucleosides. The title nucleosides did not exert antiviral or cytostatic effects.
Triple haploids in Cucurbita (1973)

Journal Article Triple haploids in Cucurbita Get access W. P. BEMIS W. P. BEMIS University of ArizonaTucson, Arizona 85721 Search for other works by this author on: Oxford Academic PubMed Google Scholar Journal of Heredity, Volume 64, Issue 2, March 1973, Pages 103–104, https://doi.org/10.1093/oxfordjournals.jhered.a108347 Published: 01 March 1973
Quantification of Gel-separated Proteins and Their Phosphorylation Sites by LC-MS Using Unlabeled Internal Standards (2005)

Protein phosphorylation plays a critical role in normal cellular function and is often subverted in disease. Although major advances have recently been made in identification and quantitation of protein phosphorylation sites by MS, current methodological limitations still preclude routine, easily usable, and comprehensive quantitative analysis of protein phosphorylation. Here we report a simple LC-MS method to quantify gel-separated proteins and their sites of phosphorylation; in this approach, integrated chromatographic peak areas of peptide analytes from proteins under study are normalized to those of a non-isotopically labeled internal standard protein spiked into the excised gel samples just prior to in-gel digestion. The internal standard intensities correct for differences in enzymatic activities and sample losses that may occur during the processes of in-gel digestion and peptide extraction from the gel pieces. We used this method of peak area measurement with an internal standard to investigate the effects of pervanadate on protein phosphorylation in the WEHI-231 B cell lymphoma cell line and to assess the role of phosphoinositide 3-kinase (PI3K) in these phosphorylation events. Phosphoproteins, isolated from total cell lysates using IMAC or by immunoprecipitation using Tyr(P) antibodies, were analyzed using this method, leading to identification of >400 proteins, several of which were found at higher levels in phosphoprotein fractions after pervanadate treatment. Pretreatment of cells with the PI3K inhibitor wortmannin reduced the phosphorylation level of certain proteins (e.g. STAT1 and phospholipase Cgamma2) while increasing the phosphorylation of several others. Peak area measurement with an internal standard was also used to follow the dynamics of PI3K-dependent and -independent changes in the post-translational modification of both known and novel phospholipase Cgamma2 phosphorylation sites. Our results illustrate the capacity of this conceptually simple LC-MS method for quantification of gel-separated proteins and their phosphorylation sites and for quantitative profiling of biological systems.
Neuroimmune interactions in allergic skin diseases (2007)

Peripheral sensory and autonomic nerves are critically involved in many pathways of the innate and adoptive immune system during allergic and atopic skin diseases. Further dissection of receptor-mediated and intracellular signal pathways will help to develop more effective therapeutic approaches for allergic and inflammatory skin diseases.
Basic electronic properties of a Si H c Si heterostructure solar cells (2004)

Basic Electronic Properties of a Si H c Si Heterostructure Solar Cells
Isolation and Properties of Two Soluble Heme Proteins in Extracts of the Photoanaerobe Chromatium (1960)

The involvement of heme proteins in photometabolism, first suggested by Hill (1, 2), seems certain from results of recent enzyme studies (3-5) and observations on systems in viva using differential spectrophotometry (6-10). Of the many heme proteins which exist in intimate association with the photoactive pigments in the functional subcellular structures of photosynthetic tissues, only three have been isolated in soluble form in sufficient amounts and purity for adequate characterization. One of these is the so-called “cytochrome f” of green plant tissues (11). The other two are variant cytochromes, one of the V type (12), and one an atypical heme protein called “RHP” (12, 13) obtained from extracts of the facultative photoheterotrophic purple bacterium, Rhodospirillum rubrum. We now report the isolation and identification of two soluble heme proteins contained in extracts of the obligate photoanaerobit purple bacterium, Chromatium. Previous studies (14, 15) have indicated the existence of both a cytochrome ‘Y-type and an RHP-type heme protein’ in partially resolved preparations (15). Some preliminary data have been published on their physicochemical properties. Complete resolution of these heme protein mixtures has been achieved so that it is now possible to characterize completely the two soluble Chromutium cytochrome components.
Characterization of chronic myeloid leukemia stem cells (2010)

Although tyrosine kinase inhibitors have redefined the care of chronic myeloid leukemia (CML), these agents have not proved curative, likely due to resistance of the leukemia stem cells (LSC). While a number of potential therapeutic targets have emerged in CML, their expression in the LSC remains largely unknown. We therefore isolated subsets of CD34(+) stem/progenitor cells from normal donors and from patients with chronic phase or blast crisis CML. These cell subsets were then characterized based on ability to engraft immunodeficient mice and expression of candidate therapeutic targets. The CD34(+)CD38(-) CML cell population with high aldehyde dehydrogenase (ALDH) activity was the most enriched for immunodeficient mouse engrafting capacity. The putative targets: PROTEINASE 3, SURVIVIN, and hTERT were expressed only at relatively low levels by the CD34(+)CD38(-)ALDH(high) CML cells, similar to the normal CD34(+)CD38(-)ALDH(high) cells and less than in the total CML CD34(+) cells. In fact, the highest expression of these antigens was in normal, unfractionated CD34(+) cells. In contrast, PRAME and WT1 were more highly expressed by all CML CD34(+) subsets than their normal counterparts. Thus, ALDH activity appears to enrich for CML stem cells, which display an expression profile that is distinct from normal stem/progenitor cells and even the CML progenitors. Indeed, expression of a putative target by the total CD34(+) population in CML does not guarantee expression by the LSC. These expression patterns suggest that PROTEINASE 3, SURVIVIN, and hTERT are not optimal therapeutic targets in CML stem cells; whereas PRAME and WT1 seem promising.
MIMO OFDM receivers for Systems with IQ imbalances (2005)

Orthogonal frequency division multiplexing (OFDM) is a widely recognized modulation scheme for high data rate communications. However, the implementation of OFDM-based systems suffers from in-phase and quadrature-phase (IQ) imbalances in the front-end analog processing. Such imbalances are caused by the analog processing of the received radio frequency (RF) signal, and they cannot be efficiently or entirely eliminated in the analog domain. The resulting IQ distortion limits the achievable operating SNR at the receiver and, consequently, the achievable data rates. The issue of IQ imbalances is even more severe at higher SNR and higher carrier frequencies. In this paper, the effect of IQ imbalances on multi-input multioutput (MIMO) OFDM systems is studied, and a framework for combating such distortions through digital signal processing is developed. An input-output relation governing MIMO OFDM systems is derived. The framework is used to design receiver algorithms with compensation for IQ imbalances. It is shown that the complexity of the system at the receiver grows from dimension (n/sub R//spl times/n/sub T/) for ideal IQ branches to (2n/sub R//spl times/2n/sub T/) in the presence of IQ imbalances. However, by exploiting the structure of space-time block codes along with the distortion models, one can obtain efficient receivers that are robust to IQ imbalances. Simulation results show significant improvement in the achievable BER of the proposed MIMO receivers for space-time block-coded OFDM systems in the presence of IQ imbalances.
Isolation and characterization of pristimerin as the antiplasmodial and antileishmanial agent of Maytenus senegalensis (Lam.) Exell. (2007)

Bioactivity directed fractionation of the chloroform extract of the root bark of Maytenus senegalensis resulted in the isolation and characterization of the quinonemethide triterpene, (20)-3-hydroxy-2-oxo-24-nor-friedela-1(10),3,5,7-tetraen-carboxylic acid-(29)-methylester (pristimerin). The structure was elucidated by spectroscopic techniques. The in vitro antiplasmodial activity of the isolated compound against chloroquine-resistant strain (Dd2) of Plasmodium falciparum was IC 50 = 0.5g/ml and its in vitro antileishmanial activity performed on promostigotes of Leishmania major was IC 50 = 6.8 0.8 g/ml while the cytotoxicity on lymphocyte proliferation model was detected at IC 50 = 6.8 0.8 g/ml.
Phase I and Pharmacokinetic Evaluation of Intravenous Hyaluronic Acid in Combination with Doxorubicin or 5-Fluorouracil (2005)

High doses of intravenous high-molecular-weight HA can be safely co-administered with clinical doses of chemotherapy without significantly altering the toxicity or pharmacokinetics of the drugs or HA.