gebhart/patrepeval huggingface dataset:
Role of SH-PTP2, a protein-tyrosine phosphatase with Src homology 2 domains, in insulin-stimulated Ras activation. (1994)

SH-PTP2 is a nontransmembrane human protein-tyrosine phosphatase that contains two Src homology 2 (SH2) domains and binds to insulin receptor substrate 1 (IRS-1) via these domains in response to insulin. The expression of a catalytically inactive mutant of SH-PTP2 (containing the mutation Cys-459-->Ser) in Chinese hamster ovary cells that overexpress human insulin receptors (CHO-IR cells) markedly attenuated insulin-stimulated Ras activation. Expression of mutant SH-PTP2 also inhibited MAP kinase activation in response to insulin but not in response to 12-O-tetradecanoyl phorbol-13-acetate. In contrast, the insulin-induced association of phosphoinositide 3-kinase activity with IRS-1 was not affected by the expression of inactive SH-PTP2. Furthermore, the expression of mutant SH-PTP2 had no effect on the binding of Grb2 to IRS-1, on the tyrosine phosphorylation of Shc, or on the formation of the complex between Shc and Grb2 in response to insulin. However, the amount of SH-PTP2 bound to IRS-1 in insulin-treated CHO-IR cells expressing mutant SH-PTP2 was greater than that observed in CHO-IR cells overexpressing wild-type SH-PTP2. Recombinant SH-PTP2 specifically dephosphorylated a synthetic phosphopeptide corresponding to the sequence surrounding Tyr-1172 of IRS-1, a putative binding site for SH-PTP2. Additionally, phenylarsine oxide, an inhibitor of protein-tyrosine phosphatases, inactivated SH-PTP2 in vitro and increased the insulin-induced association of SH-PTP2 with IRS-1. These results suggest that SH-PTP2 may regulate an upstream element necessary for Ras activation in response to insulin and that this upstream element may be required for the Grb2- or Shc-dependent pathway. Furthermore, these results are consistent with the notion that SH-PTP2 may bind to IRS-1 through its SH2 domains in response to insulin and dephosphorylate the phosphotyrosine residue to which it binds, thereby regulating its association with IRS-1.
Diversity of Sulfate-Reducing Bacteria in Oxic and Anoxic Regions of a Microbial Mat Characterized by Comparative Analysis of Dissimilatory Sulfite Reductase Genes (1999)

Sequence analysis of genes encoding dissimilatory sulfite reductase (DSR) was used to identify sulfate-reducing bacteria in a hypersaline microbial mat and to evaluate their distribution in relation to levels of oxygen. The most highly diverse DSR sequences, most related to those of the Desulfonema-like organisms within the delta-proteobacteria, were recovered from oxic regions of the mat. This observation extends those of previous studies by us and others associating Desulfonema-like organisms with oxic habitats.
A sequential vector selection algorithm for controllable bandwidth motion description encoding (2002)

The paper presents a method for controlling the bandwidth given to the motion description in motion-compensated video coding by restricting the number of motion vectors used. A new algorithm, called the metric method, for selecting the vectors is presented. This approach produces predicted images that are a close approximation of the optimal that can be achieved for a fixed number of vectors with relatively little additional computational cost. Results show that, in a video codec, the metric method produces lower overall errors than the standard approach of sending one vector per block, and is better than the histogram method previously used to select the vectors.
Tuning of Silver Catalyst Mesostructure Promotes Selective Carbon Dioxide Conversion into Fuels (2016)

Abstract An electrode's performance for catalytic CO 2 conversion to fuels is a complex convolution of surface structure and transport effects. Using well‐defined mesostructured silver inverse opal (Ag‐IO) electrodes, it is demonstrated that mesostructure‐induced transport limitations alone serve to increase the turnover frequency for CO 2 activation per unit area, while simultaneously improving reaction selectivity. The specific activity for catalyzed CO evolution systematically rises by three‐fold and the specific activity for catalyzed H 2 evolution systematically declines by ten‐fold with increasing mesostructural roughness of Ag‐IOs. By exploiting the compounding influence of both of these effects, we demonstrate that mesostructure, rather than surface structure, can be used to tune CO evolution selectivity from less than 5 % to more than 80 %. These results establish electrode mesostructuring as a powerful complementary tool for tuning both catalyst selectivity and efficiency for CO 2 conversion into fuels.
Protein tyrosine kinase inhibitors decrease induction of nitric oxide synthase activity in lipopolysaccharide-responsive and lipopolysaccharide-nonresponsive murine macrophages. (1993)

We investigated tumoricidal activation and induction of nitric oxide synthase (NOS) activity in macrophages from LPS-responsive (C3H/HeN) and -unresponsive mice (C3H/HeJ). Macrophages were incubated in vitro with a synthetic lipopeptide or with LPS and IFN-gamma. LPS and IFN-gamma activated C3H/HeN but not C3H/HeJ macrophages to lyse B16 melanoma cells. In contrast, lipopeptide and IFN-gamma activated macrophages from both strains of mice. Genistein, a specific inhibitor of protein tyrosine kinase, significantly blocked tumoricidal activation of macrophages from both strains of mice. Genistein did not affect tumor cell binding but significantly inhibited the production of nitric oxide. Genistein, herbimycin A, and tyrphostin inhibited the induction of NOS activity in macrophages from both strains of mice. These data suggest that protein tyrosine kinase activity is involved in the signal transduction pathway of LPS and other synthetic bacterial-related immunomodulators at a point preceding triggering of macrophage tumoricidal activation and expression of inducible NOS activity.
Radioimmunoassay of insulin-like growth factor-binding protein-6 in human serum and other body fluids (1992)

A radioimmunoassay has been established for the insulin-like growth factor-binding protein, IGFBP-6, isolated from a human transformed fibroblast cell-line. The binding proteins IGFBP-I and IGFBP-3 did not cross-react, but both IGF-I and IGF-II markedly inhibited IGFBP-6 tracer binding to antiserum. This inhibition, greater for IGF-II than for IGF-I, was fully reversed by the addition of IGFBP-3 to sequester the IGFs. After fractionation of human serum and follicular fluid samples by gel chromatography, interference in the radioimmunoassay by fractions corresponding to the 150 kDa IGF-IGFBP complex could be eliminated by IGFBP-3. The equivalent fractions from cerebrospinal fluid and amniotic fluid fractionation did not interfere in the assay. The mean IGFBP-6 level in adult human serum was 0.221 +/- 0.110 mg/l, with values significantly higher in men than women, and slightly decreased in pregnancy. Similar values were seen in umbilical cord serum and in amniotic and follicular fluid samples, while the mean level in cerebrospinal fluid was slightly lower, 0.152 +/- 0.049 mg/l. This assay will facilitate studies on the regulation of IGFBP-6 production, and its role as an IGF carrier.
Mechanisms of Atomic Layer Deposition on Substrates with Ultrahigh Aspect Ratios (2008)

Atomic layer deposition (ALD) appears to be uniquely suited for coating substrates with ultrahigh aspect ratios (> or similar 10(3)), including nanoporous solids. Here, we study the ALD of Cu and Cu3N on the inner surfaces of low-density nanoporous silica aerogel monoliths. Results show that Cu depth profiles in nanoporous monoliths are limited not only by Knudsen diffusion of heavier precursor molecules into the pores, as currently believed, but also by other processes such as the interaction of precursor and reaction product molecules with pore walls. Similar behavior has also been observed for Fe, Ru, and Pt ALD on aerogels. On the basis of these results, we discuss design rules for ALD precursors specifically geared for coating nanoporous solids.
Purification and characterization of Lewy bodies from the brains of patients with diffuse Lewy body disease. (1996)

Lewy bodies (LBs) are the pathological hallmarks of degenerating neurons in the brains of patients with Parkinson's disease and diffuse Lewy body disease. We developed a novel purification procedure for LBs using sucrose density separation followed by fluorescence-activated particle sorting, and we raised > 15 monoclonal antibodies to LBs purified from diffuse Lewy body disease brains. The monoclonal antibody that stained the largest number of LBs most intensely did not recognize ubiquitin in free or monoubiquitinated forms nor the ubiquitin conjugating enzymes, but it did react with polyubiquitin chains as well as with high molecular weight polyubiquitinated LB-derived proteins. Thus, these results suggest that LBs contain polyubiquitin chains. Although polyubiquitination of LB proteins may trigger ubiquitin-proteasome proteolytic pathways, the incomplete activation of these pathways could play a mechanistic role in the formation of LBs in neurodegenerative diseases.
Two Techniques to Enhance the Performance of Memory Consistency Models. (1991)

The memory consistency model supported by a multiprocessor directly affects its performance. Thus, several attempts have been made to relax the consistency models to allow for more buffering and pipelining of memory accesses. Unfortunately, the potential increase in performance afforded by relaxing the consistency model is accompanied by a more complex programming model. This paper introduces two general implementation techniques that provide higher performance for all the models. The first technique involves prefetching values for accesses that are delayed due to consistency model constraints. The second technique employs speculative execution to allow the processor to proceed even though the consistency model requires the memory accesses to be delayed. When combined, the above techniques alleviate the limitations imposed by a consistency model on buffering and pipelining of memory accesses, thus significantly reducing the impact of the memory consistency model on performance. 1 Intro...
NMR solution structure of the human prion protein (2000)

The NMR structures of the recombinant human prion protein, hPrP(23-230), and two C-terminal fragments, hPrP(90-230) and hPrP(121-230), include a globular domain extending from residues 125-228, for which a detailed structure was obtained, and an N-terminal flexibly disordered "tail." The globular domain contains three alpha-helices comprising the residues 144-154, 173-194, and 200-228 and a short anti-parallel beta-sheet comprising the residues 128-131 and 161-164. Within the globular domain, three polypeptide segments show increased structural disorder: i.e., a loop of residues 167-171, the residues 187-194 at the end of helix 2, and the residues 219-228 in the C-terminal part of helix 3. The local conformational state of the polypeptide segments 187-193 in helix 2 and 219-226 in helix 3 is measurably influenced by the length of the N-terminal tail, with the helical states being most highly populated in hPrP(23-230). When compared with the previously reported structures of the murine and Syrian hamster prion proteins, the length of helix 3 coincides more closely with that in the Syrian hamster protein whereas the disordered loop 167-171 is shared with murine PrP. These species variations of local structure are in a surface area of the cellular form of PrP that has previously been implicated in intermolecular interactions related both to the species barrier for infectious transmission of prion disease and to immune reactions.
Expression of glypican 3 GPC3 in embryonal tumors (2000)

Embryonal tumors, such as neuroblastoma, medulloblastoma and Wilms' tumor, have their peak incidence in the first 4 years of life.These neoplasias exhibit genetic and clinical heterogeneity, but little is known about their molecular pathogenesis.Application of the differential-display PCR approach led to the identification of a gene, glypican 3 (GPC3), that is differentially expressed in cancer cells.Expression of this gene is usually limited to fetal mesodermal tissue, and its inactivation has been found to be responsible for the X-linked Simpson-Golabi-Behmel overgrowth syndrome.Here, we show that GPC3 mRNA is present in several neuroblastomas and all Wilms' tumors tested to date but not in medulloblastoma.GPC3 was not expressed in normal kidney tissues obtained from the corresponding Wilms' tumor patients, suggesting that in these cancer cells expression was not repressed (or was activated).No correlation was found between expression of GPC3 and the known indicator of neuroblastoma prognosis MYCN mRNA.However, all samples that expressed GPC3 also expressed IGF-II, coding for a growth factor important in the survival and growth of many cancer types.Although the biological significance of this relationship remains unclear, our results suggest that GPC3 may be implicated in the development of embryonal tumors through a signaling pathway that appears to involve IGF-II.
Probing structural factors stabilizing antisense oligonucleotide duplexes: NMR studies of a DNA.cntdot.DNA duplex containing a formacetal linkage (1992)

The duplex formed by annealing the formacetal backbone modified dodecamer d-(CGCGTTOCH2OTTGCGC) to its complementary strand, d(GCGCAAAACGCG) (duplex I), has been studied by NMR techniques and analyzed with reference to its unmodified counterpart (duplex II). Comparison of parameters such as 2D cross-peak intensities, coupling constants, and spectral patterns indicates that structural perturbations caused by the incorporation of the formacetal linkage are minimal and localized to the central T4.A4 block. Duplex I adopts a B-type helical conformation with regular Watson-Crick base pairing and normal minor groove width. The methylene group is accommodated along the phosphate backbone in a conformation similar to that of the PO2 group found in the B-form DNA family. The central T6-T7 base pairs of duplex I melt simultaneously with the duplex, indicating a cooperative transition to single strands. Although the formacetal linkage affects global melting, as evidenced by a 3 degree C reduction in Tm for duplex I with respect to duplex II, the present study indicates that this is not the result of localized premelting at the formacetal site of duplex I but rather reflects the subtle interplay of several structural and energy factors which need to be further explored.
Zur Kenntnis des Diglycerideinflusses auf das Kristallisationsverhalten von Fetten (1991)

Abstract Insbesondere nach lipasekatalysierter Umesterung verbleiben größere Mengen an Diglyceriden im Fett. Die Auswertung vorliegender Arbeiten ergibt, daß Diglyceride die Kristallisationseigenschaften von Fetten beeinflussen können. Dabei scheinen 1,3(2,3)‐Diglyceride Phasenumwandlungsgeschwindigkeiten stärker zu verändern als die isomeren 1,3‐Diglyceride. Bisherige Untersuchungen konzentrierten sich dabei insbesondere auf die Phasenübergänge α → β′ von Palmöl und Salfett sowie β′ → β von hydriertem Rapsöl. Als Diglyceride kamen vorwiegend Gemische zum Einsatz, deren Fettsäure‐ und Isomerenverteilung häufig nicht bekannt war.
Antagonizing HMGB1 inhibits proteinuria in a murine model of lupus-like disease (131.24) (2007)

Abstract High mobility group box 1 (HMGB1) is an abundant chromatin protein that acts like an inflammatory cytokine when it is released by dying or stimulated cells. Elevated levels are detected at sites of inflammation in a number of autoimmune disorders including SLE. In addition, HMGB1 has been shown to contribute to the activation of plasmacytoid dendritic cells as well as B cells, cell types that are implicated in the pathogenesis of SLE. To address the role of HMGB1 in experimental lupus, we investigated the protective efficacy of a fully humanized mAb (IA-4, which recognizes both mouse and human HMGB1) in an IFNα-accelerated lupus model. In this model, adenovirus IFNα-treated NZB/W F1 mice exhibit 90–100% proteinuria incidence at 4–6 weeks post-treatment. The functionality of IA-4 has been demonstrated in vitro by its ability to inhibit rHMGB1-induced IL-6 secretion in human PBMC (IC50 = 0.9 nM). Prophylactic administration of the anti-HMGB1 mAb IA-4 at 10 mg/kg significantly inhibited the proteinuria severity score at seven weeks (65% inhibition; p&amp;lt;0.05 compared to an isotype control). Consistent with the proteinuria data, histopathological assessment of the kidney also revealed protection with IA-4 treatment. Despite its protection in nephritis, IA-4 treatment showed no detectable effect on serum levels of IFN-α and autoantibodies against dsDNA or SSA/Ro. Taken together, these data suggest that HMGB1 is a critical effector molecule in lupus nephritis and that anti-HMGB1 treatment may provide a potential therapeutic benefit for the treatment of SLE.
Association and linkage analyses of RGS4 polymorphisms in schizophrenia (2002)

Gene expression analyses of postmortem cerebral cortex suggest that transcription of the regulator of G-protein signaling 4 (RGS4) is decreased in a diagnosis-specific manner in subjects with schizophrenia. To evaluate the possible role of RGS4 in the pathogenesis of schizophrenia, we conducted genetic association and linkage studies using samples ascertained independently in Pittsburgh and New Delhi and by the NIMH Collaborative Genetics Initiative. Using the transmission disequilibrium test, significant transmission distortion was observed in the Pittsburgh and NIMH samples. Among single-nucleotide polymorphisms (SNPs) spanning approximately 300 kb, significant associations involved four SNPs localized to a 10 kb region at RGS4, but the associated haplotypes differed. A trend for transmission distortion was also present in the Indian sample for haplotypes incorporating the same SNPs. Consistent with the linkage/association observed from the family-based tests, samples with affected siblings (NIMH, India) showed higher levels of allele sharing, identical by descent, at RGS4. When the US patients were contrasted to two population-based control samples, however, no significant differences were observed. To check the specificity of the transmission bias, we therefore examined US families with bipolar I disorder (BD1) probands. This sample also showed a trend for transmission distortion, and differed significantly from the population-based controls for the four-SNP haplotypes tested in the other samples. The transmission distortion is unlikely to be due to chance, but its mechanism and specificity require further study. Our results illustrate the potential power of combining gene expression profiling and genomic analyses to identify susceptibility genes for genetically complex disorders.
Optical cosine transform using phase conjugation technique (1991)

An optical cosine transform system is designed using computer generated holograms and a phase-conjugate mirror which can provide segmented transform images fulfilling the specification laid down by the CCITT H.261 recommendation on Video Audiovisual Services. The system is evaluated using computer simulations.
Vascular endothelial growth factor increases hydraulic conductivity of isolated perfused microvessels (1996)

These experiments report the first direct measurement of microvessel permeability coefficients after exposure to vascular endothelial growth factor (VEGF). The Landis technique was extended to enable measurement of the resistance of the microvessel wall to water flow, hydraulic conductivity (Lp), on the same microvessel in the frog mesentery during the initial exposure to VEGF (acute) and 24 and 72 h after initial exposure (chronic). Control measurements of Lp showed no change either acutely or chronically. Exposure to 1 nM VEGF rapidly and transiently increased microvessel Lp within 30 s (to 7.8-fold greater than baseline values) and returned to control within 2 min. The baseline Lp was fivefold greater after 24 h than the initial baseline as a result of VEGF perfusion and returned to its original value after 72 h. These experiments confirm the hypothesis that VEGF acts both acutely (over a period of a few minutes) and chronically (over a few hours) to increase microvascular permeability.
Net analyte signal with floating reference theory in non-invasive blood glucose sensing by near-infrared spectroscopy (2012)

Based on the floating reference theory, a new method for extracting the net analyte signal (NAS) is proposed. The noise background subspace is spanned by spectra at the floating radial reference point, and then, the spectra at the measurement point are projected on the subspace. Thereafter, the glucose concentrations in intralipid solutions are investigated through Monte Carlo simulation and experiments, and the partial least squares (PLS) models with and without NAS analysis are built. The root mean square errors of calibration and prediction reach to 28.87% and 27.33%, respectively. The results confirm the existence of information induced by glucose concentration variations as well as the validity of the floating reference theory.
Monoclonal antibodies, immunogenicity, and associated infusion reactions. (2005)

The increasing use of monoclonal antibodies as treatment modalities for a number of immune mediated and malignant diseases has yielded great promise. In using this approach, however, we have encountered problems, in terms of infusion reactions. Two forms of reactions have been identified: acute and delayed; they appear to be related to the presence of antibodies to the monoclonal antibodies (against murine or human components). The reactions are largely not anaphylactic (IgE mediated), making it possible to re-treat patients using specific protocols. These protocols are detailed in this overview.