gebhart/patrepeval huggingface dataset:
UDP-glucuronic Acid:Anthocyanin Glucuronosyltransferase from Red Daisy (Bellis perennis) Flowers (2004)

In contrast to the wealth of biochemical and genetic information on vertebrate glucuronosyltransferases (UGATs), only limited information is available on the role and phylogenetics of plant UGATs. Here we report on the purification, characterization, and cDNA cloning of a novel UGAT involved in the biosynthesis of flower pigments in the red daisy (Bellis perennis). The purified enzyme, BpUGAT, was a soluble monomeric enzyme with a molecular mass of 54 kDa and catalyzed the regiospecific transfer of a glucuronosyl unit from UDP-glucuronate to the 2''-hydroxyl group of the 3-glucosyl moiety of cyanidin 3-O-6''-O-malonylglucoside with a kcat value of 34 s(-1) at pH 7.0 and 30 degrees C. BpUGAT was highlyspecific for cyanidin 3-O-glucosides (e.g. Km for cyanidin 3-O-6''-O-malonylglucoside, 19 microM) and UDP-glucuronate (Km, 476 microM). The BpUGAT cDNA was isolated on the basis of the amino acid sequence of the purified enzyme. Quantitative PCR analysis showed that transcripts of BpUGAT could be specifically detected in red petals, consistent with the temporal and spatial distributions of enzyme activity in the plant and also consistent with the role of the enzyme in pigment biosynthesis. A sequence analysis revealed that BpUGAT is related to the glycosyltransferase 1 (GT1) family of the glycosyltransferase superfamily (according to the Carbohydrate-Active Enzymes (CAZy) data base). Among GT1 family members that encompass vertebrate UGATs and plant secondary product glycosyltransferases, the highest sequence similarity was found with flavonoid rhamnosyltransferases of plants (28-40% identity). Although the biological role (pigment biosynthesis) and enzymatic properties of BpUGAT are significantly different from those of vertebrate UGATs, both of these UGATs share a similarity in that the products produced by these enzymes are more water-soluble, thus facilitating their accumulation in vacuoles (in BpUGAT) or their excretion from cells (in vertebrate UGATs), corroborating the proposed general significance of GT1 family members in the metabolism of small lipophilic molecules.
Bioelectric perturbations of bone. Research directions and clinical applications. (1984)

Bioelectric perturbation of living hard tissue produces clinically useful effects. It is being used effectively in the treatment of intractable orthopedic problems such as nonunion and avascular necrosis. Dental applications of this phenomenon are still in the early stages of research and development. Barring untoward circumstances, this form of local growth control may be used as an adjunct to localized bone induction therapy such as in the treatment of periodontal diseases, bone grafting or implantation of biocompatible products. It also appears to show promise in enhancing the rate of tooth movement or the stability of anchor teeth. The mechanism for these perturbation-induced changes in cells has not been explained. This is an active area of research with many implications for helping the clinician understand the molecular biology of hard-tissue cell proliferation, migration and differentiation.
Antisense DNA delivery in vivo: liver targeting by receptor-mediated uptake. (1994)

These findings have significant implications for the targeted delivery of therapeutic antisense molecules to the liver.
HGF as a renotrophic and anti-fibrotic regulator in chronic renal disease (2008)

Hepatocyte growth factor (HGF) and Met/HGF receptor play roles in dynamic growth and morphogenesis during development and regeneration of organs, including the kidney. In the kidney, HGF targets different types of cells, while its biological actions depend on a target cell type. During the earlier stages of chronic renal failure, renal HGF expression increased, but in later stages HGF expression decreased, associated with manifestation of chronic renal failure. When anti-HGF IgG was administered into mice with chronic renal failure, renal dysfunction and fibrosis were accelerated, indicating a role of endogenous HGF to suppress chronic renal failure. For myofibroblasts, a key cell type in tissue fibrosis, HGF exerted biological activities, including (i) inhibition of growth, (ii) suppression of fibrogenic cytokine expression, and (iii) enhancement of matrix metalloproteinases involved in subsequent apoptosis. In models of glomerular and tubulo-interstitial fibrosis, administration of HGF or HGF gene therapy improved renal fibrosis and dysfunction. Since insufficient production of HGF is causative for renal fibrosis, supplementation with HGF represents a new approach to inhibit or improve chronic renal failure.
Induction of latency‐associated peptide (transforming growth factor‐β1) expression on CD4+ T cells reduces Toll‐like receptor 4 ligand‐induced tumour necrosis factor‐α production in a transforming growth factor‐β‐dependent manner (2011)

CD4(+) T cells expressing the latent form of transforming growth factor-β [latency-associated peptide (LAP) (TGF-β(1))] play an important role in the modulation of immune responses. Here, we identified a novel peptide ligand (GPC(81-95) ) with an intrinsic ability to induce membrane-bound LAP (TGF-β(1)) expression on a subpopulation of human CD4(+) T cells (using flow cytometry; ranging from 0·8% to 2·6%) and stimulate peripheral blood mononuclear cells to release LAP (TGF-β(1) ) (using ELISPOT assay; ranging from 0·03% to 0·16%). In spite of this low percentage of responding cells, GPC(81-95) significantly reduced Toll-like receptor 4 ligand-induced tumour necrosis factor-α production in a TGF-β(1) - and CD4(+) T-cell-dependent manner. The results demonstrate that GPC(81-95) is a useful tool to study the functional properties of a subpopulation of LAP (TGF-β(1))(+) CD4(+) T cells and suggest a pathway that can be exploited to suppress inflammatory response.
Wafer inspection as alternative approach to mask defect qualification (2007)

Defect inspection is one of the major challenges in the manufacturing process of photomasks. The absence of any printing defect on patterned mask is an ultimate requirement for the mask shop, and an increasing effort is spent in order to detect and subsequently eliminate these defects. Current DUV inspection tools use wavelengths five times or more larger than the critical defect size on advanced photomasks. This makes the inspectability of high-end mask patterns (including strong OPC and small SRAF's) and sufficient defect sensitivity a real challenge. The paper evaluates the feasibility of inspecting the printed wafer as an alternative way for the high-sensitivity defect inspection of photomasks. Defects originating in the mask can efficiently be filtered as repeated defects in the various dies on wafer. Using a programmed-defect mask of 65-nm technology, a reliable detection of the printing defects was achieved with an optimized inspection process. These defects could successfully be traced back to the photomask in a semi-automated process in order to enable a following repair step. This study shows that wafer inspection is able to provide a full defect qualification of advanced photomasks with the specific advantage of assessing the actual printability of arbitrary defects.
2-Azaadamantane N-Oxyl (AZADO) and 1-Me-AZADO:  Highly Efficient Organocatalysts for Oxidation of Alcohols (2006)

Development of a stable nitroxyl radical class of catalysts, 2-azaadamantane N-oxyl (AZADO) and 1-Me-AZADO, for highly efficient oxidation of alcohols is described. AZADO and 1-Me-AZADO exhibit superior catalytic proficiency to TEMPO, converting various sterically hindered alcohols to the corresponding carbonyl compounds in excellent yields.
How Not to Lie with Visualization (1996)

H ow data are represented visually has a pow- erful effect on the perception and interpretation of the structure in those data.In Fig. I, four representations of a magnetic-resonance-imaging (MRI) scan of a human head are shown.The only difference between these images is the mapping of color to data values, yet the four representations look very different.Furthermore, the inferences an analyst would draw from these representations
Endophenotypes in the Genetic Analyses of Mental Disorders (2005)

Common mental disorders such as schizophrenia, bipolar disorder, and severe major depression are highly heritable, but differ from single-gene (Mendelian) diseases in that they are the end products of multiple causes. Although this fact may help explain their prevalence from an evolutionary perspective, the complexity of the causes of these disorders makes identification of disease-promoting genes much more difficult. The "endophenotype" approach is an alternative method for measuring phenotypic variation that may facilitate the identification of susceptibility genes for complexly inherited traits. Here we examine the endophenotype construct in context of psychiatric genetics. We first develop an evolutionary theoretical framework for common mental disorders and differentiate them from simpler, single-gene disorders. We then provide a definition and description of endophenotypes, elucidating several features that will make a proposed endophenotype useful in psychiatric genetic research and evaluating the methods for detecting and validating such endophenotypes. We conclude with a review of recent results in the schizophrenia literature that illustrate the usefulness of endophenotypes in genetic analyses of mental disorders, and discuss implications of these findings for models of disease causation and nosology. Given that in mental disorders as in behavior generally, the pathways from genotypes to phenotypes are circuitous at best, discernment of endophenotypes more proximal to the effects of genetic variation will aid attempts to link genes to disorders.
Drosophila ribosomal protein S3 contains an activity that cleaves DNA at apurinic/apyrimidinic sites. (1994)

A rat cDNA-encoding ribosomal protein S3 was used to clone the S3 homolog in Drosophila melanogaster. The Drosophila gene was in turn used to construct fusions between S3 and glutathione S-transferase that were overexpressed in Escherichia coli, purified on affinity columns, and subsequently used for antibody production and biochemical analysis. Antibody specific for S3 was originally tested to determine the subcellular location of S3 by Western (immunoblot) analysis. As expected, the S3 antigen was found associated with purified preparations of ribosomes, but notably the protein was also observed in the nucleus where it was found to be tightly associated with the nuclear matrix. This result, combined with the fact that S3 contains a nuclear localization signal and that the protein shares some homology to a yeast nuclease gene, suggested that S3 might possibly have a role in DNA metabolism. Tests were initially performed to see if S3 contained DNase activity, where it was subsequently determined that the protein specifically cleaved DNA containing an apurinic/apyrimidinic site via a beta-elimination reaction. The DNase activity was inactivated by antibody to S3, indicating that the apurinic/apyrimidinic lyase activity was associated with the Drosophila S3 protein. Taken together, these results suggest that S3 is among a growing class of multifunctional proteins with roles in transcription/translation and DNA repair.
<title>High-performance camera calibration algorithm</title> (1993)

The paper addresses a new high performance camera calibration algorithm for 3-D computer vision systems, which is named as DLTEA-II. In this algorithm, the lens distortion model is modified by considering the difference of pixel size in digital images, so as to make the model more suitable for the correction of lens distortion in the digital image case. The camera model and revised lens distortion parameters are solved by DLT (Direct Linear Transformation) method. A third-order polynomial to fit image residual errors is used for compensating systematic errors in the algorithm, which improves camera calibration accuracy further. In order to reduce the effect of image location errors to camera calibration, we explore the LOG zero-crossing detection and subpixel location algorithms to detect the control points in the digital image. Experiments show that a stereo vision system with off-the-shelf CCD cameras (resolution 512 by 512) and TV lenses (f equals 16 mm or 25 mm) calibrated by DLTEA-II has the average relative accuracy of 1/10000 over the field of view (300 mm by 300 mm) and over the depth (0.8 m approximately 0.9 m). The image residual error is less than 0.1 pixel. The experiment results with using lenses of different focal lengths are also reported, in which most of average accuracy is about 1/8000 approximately 1/10000.
[Tumor-oriented anti-cancer agent with estrogen as a carrier]. (1988)

Tumor oriented anticancer agents with estrogen as a carrier have been extensively studied since 1950's. Only Estracyt and bestrabucil have been evaluated to be useful in clinical trials. Although the use of estrogen as a carrier for anticancer agents aimed at the development of the anticancer drug for the receptor mediated chemotherapy, these two drugs did not show any affinity to estrogen receptor. The history tells us that the development of anticancer agents for the estrogen receptor mediated chemotherapy is extremely difficult. Estracyt is reported to exert its anticancer effect on prostate cancer through the specific binding to the estramustine binding protein (EMBP) which is present only in the prostate gland and cancer. Bestrabucil shows the selective uptake by the various malignant cells and is indicated that bestrabucil exerts its anti-cancer effects on various malignant tumors including breast cancer and hematopoietic malignancy, through the affinity to malignant cells. The mechanism is unknown and to be elucidated.
A dietary fibre supplement in the treatment of mild hypertension. A randomized, double-blind, placebo-controlled trial (1992)

A dietary fibre supplement can lower DBP in mildly hypertensive patients independent of changes in body weight.
An overview of trellis coded modulation research in COST 231 (2002)

This paper gives an overview of the studies accomplished by COST 231 members on the subject of trellis coded modulation (TCM). We establish first the interest of TCM for mobile systems by examining its bandwidth efficiency and potential performance. Then, we give simulation results concerning co-channel interference, the interleaving delay constraint, post detection diversity and frequency hopping.
Lhx2 expression in hematopoietic progenitor/stem cells in vivo causes a chronic myeloproliferative disorder and altered globin expression. (2003)

These observations suggest that constitutive expression of Lhx2 in hematopoietic cells causes CMD, and also that a novel cell-autonomous mechanism can contribute to anemia.
An optical differential 8-PSK modulator using cascaded QPSK modulators (2009)

A new optical D8PSK modulator implementation is proposed. The proposed scheme removes the need for precise driving signal voltage control. Simulation results show the scheme enables modulation signal generation with more relaxed EO bandwidth requirements.
Microbial Adhesion and Biofilm Formation on Ureteral Stents in Vitro and in Vivo (1992)

Thirty ureteral stents, inserted for 5 to 128 days following extracorporeal shock wave lithotripsy, were examined for the presence of bacterial biofilms. Of these, 90% had adherent pathogens (44% mixed organisms) on the stents, 45% of which were present in low numbers (10(1)-10(2) per 1 cm3 section) and 55% were in small and large microcolony biofilms (> 2 x 10(2)-10(7)). The organisms were recovered from the stents even though urine culture was only positive in 27% of patients. Of the organisms isolated, 77% were Gram positive cocci, 15% Gram negative rods and 8% Candida. No blockage of the stents occurred. All of the patients had received antimicrobial therapy post-insertion, and in 15 cases biofilms were found while on treatment. None of the patients received therapy for urinary tract infections while the stent remained in place. In vitro experiments demonstrated the ability of Escherichia coli, Proteus mirabilis, Staphylococcus epidermidis and Enterococcus faecalis uropathogens to adhere and form biofilms on ureteral stents within 24 hours. Clearly, bacterial biofilms do occur on ureteral stents and urinary culture may not detect their presence. The high recovery rate of Gram positive organisms may indicate a preferential adhesion to the biomaterial surface. The findings also indicate that unlike biofilm formation on many other prosthetic implants, colonization with Gram positive organisms on ureteral stents does not necessarily coincide with the development symptomatic infection.
THERAPEUTIC IMMUNOLOGY (1996)

Austen, K. Frank MD; Burakoff, Steven J. MD; Rosen, Fred S. MD; Strom, Terry B. MD; Robinson, John A. MD Author Information
A Versatile Route to Porous Solids: Organic-Inorganic Hybrid Materials Assembled through Hydrogen Bonds (1999)

Square-planar and octahedral complexes of Ni<sup>II</sup> and Pt<sup>II</sup> link through head-to-head hydrogen bonds to form porous frameworks with large cavities that are suitable for inclusion of guest molecules. A series of four different complexes with pyridine-based ligands (in the center of the picture) are described, which contain either counterions or small molecules in channels. A=hydrogen-bond acceptor, D=hydrogen-bond donor, M=metal ion.
Deep Ordinal Ranking for Multi-Category Diagnosis of Alzheimer's Disease using Hippocampal MRI data (2017)

Increasing effort in brain image analysis has been dedicated to early diagnosis of Alzheimer's disease (AD) based on neuroimaging data. Most existing studies have been focusing on binary classification problems, e.g., distinguishing AD patients from normal control (NC) elderly or mild cognitive impairment (MCI) individuals from NC elderly. However, identifying individuals with AD and MCI, especially MCI individuals who will convert to AD (progressive MCI, pMCI), in a single setting, is needed to achieve the goal of early diagnosis of AD. In this paper, we propose a deep ordinal ranking model for distinguishing NC, stable MCI (sMCI), pMCI, and AD at an individual subject level, taking into account the inherent ordinal severity of brain degeneration caused by normal aging, MCI, and AD, rather than formulating the classification as a multi-category classification problem. The proposed deep ordinal ranking model focuses on the hippocampal morphology of individuals and learns informative and discriminative features automatically. Experiment results based on a large cohort of individuals from the Alzheimer's Disease Neuroimaging Initiative (ADNI) indicate that the proposed method can achieve better performance than traditional multi-category classification techniques using shape and radiomics features from structural magnetic resonance imaging (MRI) data.
Hypoxia down-regulates placenta growth factor, whereas fetal growth restriction up-regulates placenta growth factor expression: molecular evidence for "placental hyperoxia" in intrauterine growth restriction. (1999)

Early placental development occurs in an environment of relative hypoxia. Hypoxia promotes angiogenesis and up-regulates vascular endothelial growth factor (VEGF) expression while it down-regulates placenta growth factor (PIGF) that possess 53% homology with VEGF. Morphological studies show poor placental vascular development and an increase in the mitotic index of cytotrophoblasts in intrauterine growth restriction (IUGR). We hypothesized that the reported relatively high oxygen level in the intervillous space in contact with IUGR placental villi will limit angiogenesis by changes in VEGF and PIGF expression and function. Western immunoblot analysis demonstrates a diametric expression of PIGF and VEGF proteins throughout pregnancy with PIGF levels increasing and VEGF levels decreasing, consistent with placental oxygenation. In IUGR placentae, the ratio of PIGF/GAPDH mRNA was increased by 2.3-fold (p < 0.03) and PIGF protein levels were also increased, (p < 0.05) as compared with gestationally-matched normal placentae. PIGF mRNA and protein were localized to the trophoblast bilayer and villous mesenchyme of the human placenta throughout gestation. In vitro studies demonstrated that increasing oxygen tension (hyperoxia) up-regulated PIGF protein in term placental villous explants, whereas hypoxic culture of a term trophoblast choriocarcinoma cell line (BeWo) down-regulated PIGF mRNA and protein and VEGFR-1 (Flt-1) autophosphorylation. The addition of PIGF-1 to a spontaneously transformed first trimester cytotrophoblast cell line stimulated DNA synthesis while PIGF-2 had little effect. VEGF and PIGF exert their biological actions by means of a common receptor VEGFR-1. In the first trimester trophoblast cells, PIGF-1 increased the association of phosphorylated extracellular signal-related kinase (ERK) with VEGFR-1 immunoprecipitates while both PIGF-1 and PIGF-2 also potentiated endogenous VEGF mediated association of phosphorylated extracellular related kinase (ERK) with VEGFR-2 (KDR). More importantly, the addition of PIGF-1 had little effect while PIGF-2 inhibited cell growth in cultured endothelial cells derived from human umbilical vein. Nitric oxide (NO) is reported to promote angiogenesis and PIGF-2 inhibited the basal release of NO from the first trimester trophoblast. The tissue expression and functional studies support the hypothesis of "placental hyperoxia" in early-onset IUGR because hypoxia down-regulates trophoblast PIGF levels, PIGF expression is increased in IUGR, and PIGF-2 inhibits endothelial cell growth. Taken together, these changes provide a cellular explanation for the observed poor angiogenesis in the pathogenesis of IUGR and show that the two PIGF isoforms may modulate trophoblast and endothelial cell function differently, possibly through potentiation of VEGF mediated activation of VEGF-2.
WDM network modeling: probability analysis of optical crosstalk accumulation and network performance confidence limits (2000)

We present a novel method to study impairments in wavelength division multiplexing (WDM) networks by using probability theory to simulate the wavelength channel assignment and the flow of signals through the network, and also to calculate confidence limits for acceptable network performance. We apply the method to study the accumulation of homodyne beat noise in order to gauge accurate and realistic component crosstalk requirements for optical switches. We include the effects of laser wavelength referencing error and drift in our model, and show that it is possible to relax the requirements to within realistic specifications.
Synthesis and Antifungal Activities of Some New Substituted 1,2,4-Triazoles and Related Compounds (1984)

Organic Chemistry Division Medicinal and Economic Plants Division Regional Research Laboratory, Jorhat-785 006 <em>Manuscript received 2 November 1983, accepted 26 May 1984</em> A series of 3-(2,4-dichlorophenyl)-4-aryl-5-mercapto 1,2,4-triazoles (4a-1) have been synthesised from the corresponding 1-(2,4-dichlorobenzoyl)-4-aryl thiosemicarbazides (3a-1) by cyclization with sodium hydroxide. Methyl thioether derivatives of some of the triazoles were prepared by methylation of the mercapto groups. All the compounds were screened for their fungitoxic properties against.\(\mathcal{Alternaria tenuis}\) and \(\mathcal{Curvularia verruciformis}\). A few of the compounds showed good activities.