gebhart/patrepeval huggingface dataset:
Catalytic Key Amino Acids and UDP-Sugar Donor Specificity of a Plant Glucuronosyltransferase, UGT94B1: Molecular Modeling Substantiated by Site-Specific Mutagenesis and Biochemical Analyses (2008)

The plant UDP-dependent glucosyltransferase (UGT) BpUGT94B1 catalyzes the synthesis of a glucuronosylated cyanidin-derived flavonoid in red daisy (Bellis perennis). The functional properties of BpUGT94B1 were investigated using protein modeling, site-directed mutagenesis, and analysis of the substrate specificity of isolated wild-type and mutated forms of BpUGT94B1. A single unique arginine residue (R25) positioned outside the conserved plant secondary product glycosyltransferase region was identified as crucial for the activity with UDP-glucuronic acid. The mutants R25S, R25G, and R25K all exhibited only 0.5% to 2.5% of wild-type activity with UDP-glucuronic acid, but showed a 3-fold increase in activity with UDP-glucose. The model of BpUGT94B1 also enabled identification of key residues in the acceptor pocket. The mutations N123A and D152A decreased the activity with cyanidin 3-O-glucoside to less than 15% of wild type. The wild-type enzyme activity toward delphinidin-3-O-glucoside was only 5% to 10% of the activity with cyanidin 3-O-glucoside. Independent point mutations of three residues positioned near the acceptor B ring were introduced to increase the activity toward delphinidin-3-O-glucoside. In all three mutant enzymes, the enzymatic activity toward both acceptors was reduced to less than 15% of wild type. The model of BpUGT94B1 allowed for correct identification of catalytically important residues, within as well as outside the plant secondary product glycosyltransferase motif, determining sugar donor and acceptor specificity.
Regeneration of ischemic cardiac muscle and vascular endothelium by adult stem cells (2001)

Myocyte loss in the ischemically injured mammalian heart often leads to irreversible deficits in cardiac function. To identify a source of stem cells capable of restoring damaged cardiac tissue, we transplanted highly enriched hematopoietic stem cells, the so-called side population (SP) cells, into lethally irradiated mice subsequently rendered ischemic by coronary artery occlusion for 60 minutes followed by reperfusion. The engrafted SP cells (CD34(-)/low, c-Kit(+), Sca-1(+)) or their progeny migrated into ischemic cardiac muscle and blood vessels, differentiated to cardiomyocytes and endothelial cells, and contributed to the formation of functional tissue. SP cells were purified from Rosa26 transgenic mice, which express lacZ widely. Donor-derived cardiomyocytes were found primarily in the peri-infarct region at a prevalence of around 0.02% and were identified by expression of lacZ and alpha-actinin, and lack of expression of CD45. Donor-derived endothelial cells were identified by expression of lacZ and Flt-1, an endothelial marker shown to be absent on SP cells. Endothelial engraftment was found at a prevalence of around 3.3%, primarily in small vessels adjacent to the infarct. Our results demonstrate the cardiomyogenic potential of hematopoietic stem cells and suggest a therapeutic strategy that eventually could benefit patients with myocardial infarction.
Gastric and Intestinal Phenotypic Marker Expression in Early Differentiated-Type Tumors of the Stomach: Clinicopathologic Significance and Genetic Background (2006)

Our present findings show that phenotypic marker expression is associated with tumor aggressiveness during the early stage of gastric differentiated-type tumors. Differences in the biological behavior of tumors with different phenotypes may result from differences in the genetic backgrounds during the incipient phase of gastric tumorigenesis.
Clathrate hydrates (1993)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTClathrate hydratesPeter EnglezosCite this: Ind. Eng. Chem. Res. 1993, 32, 7, 1251–1274Publication Date (Print):July 1, 1993Publication History Published online1 May 2002Published inissue 1 July 1993https://pubs.acs.org/doi/10.1021/ie00019a001https://doi.org/10.1021/ie00019a001research-articleACS PublicationsRequest reuse permissionsArticle Views4002Altmetric-Citations849LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Fragile X syndrome: causes, diagnosis, mechanisms, and therapeutics (2012)

Fragile X syndrome (FXS) is the most frequent form of inherited intellectual disability and is also linked to other neurologic and psychiatric disorders. FXS is caused by a triplet expansion that inhibits expression of the FMR1 gene; the gene product, FMRP, regulates mRNA metabolism in the brain and thus controls the expression of key molecules involved in receptor signaling and spine morphology. While there is no definitive cure for FXS, the understanding of FMRP function has paved the way for rational treatment designs that could potentially reverse many of the neurobiological changes observed in FXS. Additionally, behavioral, pharmacological, and cognitive interventions can raise the quality of life for both patients and their families.
Fast Parallel GPU-Sorting Using a Hybrid Algorithm (2007)

Abstract — This paper presents an algorithm for fast sorting of large lists using modern GPUs. The method achieves high speed by efficiently utilizing the parallelism of the GPU throughout the whole algorithm. Initially, a parallel bucketsort splits the list into enough sublists then to be sorted in parallel using merge-sort. The parallel bucketsort, implemented in NVIDIA’s CUDA, utilizes the synchronization mechanisms, such as atomic increment, that is available on modern GPUs. The mergesort requires scattered writing, which is exposed by CUDA and ATI’s Data Parallel Virtual Machine[1]. For lists with more than 512k elements, the algorithm performs better than the bitonic sort algorithms, which have been considered to be the fastest for GPU sorting, and is more than twice as fast for 8M elements. It is 6-14 times faster than single CPU quicksort for 1-8M elements respectively. In addition, the new GPU-algorithm sorts on n log n time as opposed to the standard n(log n) 2 for bitonic sort. Recently, it was shown how to implement GPU-based radix-sort, of complexity n log n, to outperform bitonic sort. That algorithm is, however, still up to ∼ 40 % slower for 8M elements than the hybrid algorithm presented in this paper. GPU-sorting is memory bound and a key to the high performance is that the mergesort works on groups of four-float values to lower the number of memory fetches. Finally, we demonstrate the performance on sorting vertex distances for two large 3D-models; a key in for instance achieving correct transparency. I.
Interspecific Pregnancy: Barriers and Prospects (1988)

Investigations on the mechanisms that allow survival of the fetal allograft have been extended by pregnancies in which the fetus and pregnant female are from different species. Such interspecific pregnancies are useful models for the study of maternal/fetal interactions and also may assist in the preservation of endangered species. Results of experiments with three different interspecific model systems are discussed: a murine model using Mus musculus and M. caroli; an equine model involving primarily the domestic horse and donkey, but including several wild Equidae; and a bovid model that crosses genera--pregnancy between the domestic sheep and goat. Species differences are reflected in results of experiments involving the various models. An immunological barrier appears to restrict interspecific pregnancy, but how the barrier is manifested appears to differ with species. Evidence for inappropriate interaction between trophoblast and endometrium is also presented. Results of experiments aimed at overcoming barriers to interspecific reproduction are discussed.
Gene therapy clinical trials worldwide to 2012 – an update (2013)

To date, over 1800 gene therapy clinical trials have been completed, are ongoing or have been approved worldwide. Our database brings together global information on gene therapy clinical trials from official agency sources, published literature, conference presentations and posters kindly provided to us by individual investigators or trial sponsors. This review presents our analysis of clinical trials that, to the best of our knowledge, have been or are being performed worldwide. As of our June 2012 update, we have entries on 1843 trials undertaken in 31 countries. We have analysed the geographical distribution of trials, the disease indications (or other reasons) for trials, the proportions to which different vector types are used, and which genes have been transferred. Details of the analyses presented, and our searchable database are available on The Journal of Gene Medicine Gene Therapy Clinical Trials Worldwide website at: http://www.wiley.co.uk/genmed/clinical. We also provide an overview of the progress being made in clinical trials of gene therapy approaches around the world and discuss the prospects for the future.
Structural Bases of FcγR Functions (1997)

This review describes structures which determine the biological activities triggered by Fc gamma R and account for the cell-mediated functions of IgG antibodies in physiology and pathology. The binding specificity and affinity of Fc gamma R depend primarily on IgG-binding structures, in their immunoglobulin-like extracellular domains. Binding is however also influenced by subunits that associate to multichain Fc gamma R. Effector and regulatory intracytoplasmic sequences that are unique to molecules of the Fc gamma RIIB family determine the internalization properties of these receptors. Immunoreceptor Tyrosine-based Activation Motifs (ITAMs) are intracytoplasmic effector sequences shared by Fc gamma R and other receptors involved in the recognition of antigen, which trigger cell activation and internalization. Immunoreceptor Tyrosine-based Inhibition Motifs (ITIMs) are intracytoplasmic sequences, shared by Fc gamma RIIB and a growing number of negative coreceptors which negatively regulate cell activation via ITAM-bearing receptors. Altogether, these structures enable IgG antibodies to exert a variety of finely tuned biological effects during the immune response.
NAPHTHYL PHOSPHORAMIDATE DERIVATIVES OF BVdU AS POTENTIAL ANTICANCER AGENTS: DESIGN, SYNTHESIS AND BIOLOGICAL EVALUATION (2005)

The phosphoramidate technology we have developed has been recently applied to BVdU, leading to NB1011 (NewBiotics Inc., California), a novel potential anticancer compound recently entered into phase 2 of the clinical trials for colon cancer. We report in this work a new series of derivatives containing naphthol as aryl masking group on the phosphate moiety, which has shown a significant increase in anticancer activity in preliminary biological evaluations.
Effects of interactions of antibacterial drugs with each other and with 6-mercaptopurine on in vitro growth of Mycobacterium avium subspecies paratuberculosis (2009)

This in vitro study suggests that 6-mercaptopurine may be synergistic with macrolides and rifamycin derivatives against MAP. The activity of clarithromycin against MAP seems to be enhanced by rifampicin.
Comparative Efficacy of Insect Repellents against Mosquito Bites (2002)

Currently available non-DEET repellents do not provide protection for durations similar to those of DEET-based repellents and cannot be relied on to provide prolonged protection in environments where mosquito-borne diseases are a substantial threat.
Structural prerequisites for G-protein activation by the neurotensin receptor (2015)

We previously determined the structure of neurotensin receptor NTSR1 in an active-like conformation with six thermostabilizing mutations bound to the peptide agonist neurotensin. This receptor was unable to activate G proteins, indicating that the mutations restricted NTSR1 to relate agonist binding to G-protein activation. Here we analyse the effect of three of those mutations (E166A(3.49), L310A(6.37), F358A(7.42)) and present two structures of NTSR1 able to catalyse nucleotide exchange at Gα. The presence of F358(7.42) causes the conserved W321(6.48) to adopt a side chain orientation parallel to the lipid bilayer sealing the collapsed Na(+) ion pocket and linking the agonist with residues in the lower receptor part implicated in GPCR activation. In the intracellular receptor half, the bulkier L310(6.37) side chain dictates the position of R167(3.50) of the highly conserved D/ERY motif. These residues, together with the presence of E166(3.49) provide determinants for G-protein activation by NTSR1.
Moment-to-moment flight manoeuvres of the female yellow fever mosquito (Aedes aegyptiL.) in response to plumes of carbon dioxide and human skin odour (2011)

Odours are crucial cues enabling female mosquitoes to orient to prospective hosts. However, their in-flight manoeuvres to host odours are virtually unknown. Here we analyzed in 3-D the video records of female Aedes aegypti mosquitoes flying in a wind tunnel in response to host odour plumes that differed in spatial structure and composition. Following a brief (~0.03 s) encounter with CO(2), mosquitoes surged upwind and, in the absence of further encounters, counterturned without displacing upwind. These patterns resemble moth responses to encounter and loss of a filament of pheromone. Moreover, CO(2) encounters induced a highly regular pattern of counterturning across the windline in the horizontal (crosswind) and vertical planes, causing the mosquito to transect repeatedly the area where CO(2) was previously detected. However, despite the rapid changes across all three axes following an encounter with CO(2), the angular velocities remained remarkably constant. This suggests that during these CO(2)-induced surges mosquitoes stabilize flight through sensors, such as the halteres and Johnston organs, sensitive to Coriolis forces. In contrast to the instantaneous responses of the mosquito CO(2), a brief encounter with a filament of human skin odour did not induce a consistent change in mosquito flight. These differential responses were reflected in further experiments with broad plumes. A broad homogeneous plume of skin odour induced rapid upwind flight and source finding, whereas a broad filamentous plume of skin odour lowered activation rates, kinetic responses and source finding compared with homogeneous plumes. Apparently, yellow fever mosquitoes need longer continuous exposure to complex skin-odour blends to induce activation and source finding.
An inhibitor of collagenase from human amniotic fluid. Purification, characterization and action on metalloproteinases (1981)

1. An inhibitor of collagenase of apparent mol.wt. 28000 was isolated from term human amniotic fluid. 2. It is active against mammalian collagenases from a number of species and tissues as well as other mammalian metalloproteinases, but has no activity against bacterial metalloproteinases. 3. Activity is destroyed by treatment with either trypsin or 4-aminophenylmercuric acetate, by heat, and by reduction and carboxymethylation. 4. All the properties observed suggest that it is similar to the synthesized tissue inhibitor of metalloproteinases.
Clinical Assessment of Irritability, Aggression, and Apathy in Huntington and Alzheimer Disease (1990)

Thirty-one patients with Alzheimer disease (AD) and 26 patients with Huntington disease (HD) were assessed using new scales to measure apathy and irritability. An existing scale was used to assess aggression. A similar prevalence of apathy and irritability was found in the two groups. The HD patients were more aggressive than the AD patients. In a subsample of the two groups, matched for degree of cognitive impairment, the HD patients were found to be more apathetic than the AD group. Irritability was related to be the premorbid trait of "bad temper" in HD but not in AD. There was no interrelationship among the three symptoms in either group. The scales for irritability and apathy have both interrater and test-retest reliability. They are able to differentiate patients with AD and HD from normal, disease-free control subjects. The usefulness of these scales, in relation to preexisting scales, is discussed.
Paclitaxel incorporated in hydrophobically derivatized hyperbranched polyglycerols for intravesical bladder cancer therapy (2009)

Intravesical administration of mucoadhesive nanoparticulate formulations of paclitaxel might be a promising approach for instillation therapy of patients with non-muscle-invasive bladder cancer.
A Gradient Risk Sampling Method For Performance Inspection and Preventive Maintenance (2003)

Clinical engineering departments traditionally determine if equipment should undergo safety and performance inspection (SPI) and preventive maintenance (PM) by using variations of a risk assessment method described by Fennigkoh and Smith. These methods use the sum of categorical risk measures to group equipment into two levels. Equipment with risk below a specified critical risk is excluded from the equipment management plan and no (or 0%) SPI and PM is required. Equipment with risk at or exceeding the critical risk is included in the plan and a considerable fraction (typically greater than 90%) must undergo SPI and PM. The 0% and >90% criteria, traditionally regarded as PM completion ratios, are reinterpreted to be sampling fractions. The traditional methods are shown to be a limiting case of a simplified logistic function describing SPI and PM value and sampling fraction as a function of equipment risk. This leads to a risk based multi-logistic sampling model that includes a perspective of organizational benefit and risk. A simplified sampling plan that includes traditionally excluded equipment is discussed and results of a pilot study are presented. The results suggest that an appropriate value and risk based sampling plan can form the basis for an organizational value based clinical equipment management plan. Suggestions for improving equipment management plans by expanding the model and improving the definition and measurement of risk are provided. Index under:acceptance sampling; clinical equipment management; logistic regression; management, clinical equipment; performance inspection; preventive maintenance; risk analysis
Effects of organic and inorganic selenium compounds on rat mammary tumor cells (1995)

To explore cellular effects of potent organoselenium chemopreventive agents we have used a rat mammary tumor cell line. We demonstrate that 1,4-phenylenebis(methylene) selenocyanate (p-XSC) at a dose of 5 microM is a more potent inhibitor of DNA, RNA and protein synthesis as well as of mitochondrial transmembrane potential than its chemopreventive counterparts benzyl selenocyanate (BSC) and sodium selenite. These differences were also reflected in reduced growth rate by 24 and 48 hr. Cell-cycle and cell-morphology analysis revealed that higher doses of p-XSC (10 microM) caused DNA fragmentation which was accompanied with partial loss of nuclear stainability, whereas BSC caused a noticeable change in cell-cycle distribution and extensive micronucleation. Overall, our results point to cellular targets of selenium compounds which may mediate their chemopreventive activities in mammary tissues.
Advanced Glycation End Product-induced Apoptosis and Overexpression of Vascular Endothelial Growth Factor and Monocyte Chemoattractant Protein-1 in Human-cultured Mesangial Cells (2002)

Advanced glycation end products (AGE) have been implicated in the pathogenesis of glomerulosclerosis in diabetes. However, their involvement in the development of the early phase of diabetic nephropathy has not been fully elucidated. We investigated the effects of AGE on growth and on vascular endothelial growth factor (VEGF) and monocyte chemoattractant protein-1 (MCP-1) expression in human cultured mesangial cells. We prepared three immunochemically distinct AGE by incubating bovine serum albumin (BSA) with glucose, glyceraldehyde, or glycolaldehyde. When human mesangial cells were cultured with various types of AGE-BSA, viable cell numbers as well as DNA syntheses were significantly decreased. All of the AGE-BSA were found to significantly increase p53 and Bax protein accumulations and subsequently induce apoptotic cell death in mesangial cells. An antioxidant, N-acetylcysteine, significantly prevented the AGE-induced apoptotic cell death in mesangial cells. Human mesangial cells stimulated prostacyclin production by co-cultured glomerular endothelial cells. Furthermore, various types of AGE-BSA were found to up-regulate the levels of mRNAs for VEGF and stimulate the secretion of VEGF and MCP-1 proteins in mesangial cells. The results suggest that AGE disturbed glomerular homeostasis by inducing apoptotic cell death in mesangial cells and elicited hyperfiltration and microalbuminuria by stimulating the secretion of VEGF and MCP-1 proteins, thereby being involved in the pathogenesis of the early phase of diabetic nephropathy.
The pili of Pseudomonas aeruginosa strains PAK and PAO bind specifically to the carbohydrate sequence βGalNAc(1–4)βGal found in glycosphingolipids asialo‐GM1 and asialo‐GM2 (1994)

Pseudomonas aeruginosa employs pili to mediate adherence to epithelial cell surfaces. The pilus adhesin of P. aeruginosa strains PAK and PAO has been shown to bind to the glycolipid asialo-GM1 (Lee et al., 1994--accompanying article). PAK and PAO pili were examined for their abilities to bind to the synthetic beta GalNAc(1-4)beta Gal (a minimal structural carbohydrate receptor sequence of asialo-GM1 and asialo-GM2 proposed by Krivan et al., 1988a) using solid-phase binding assays. Both pili specifically bound to beta GalNAc(1-4)beta Gal. The binding of beta GalNAc(1-4)beta Gal-Biotin to the immobilized PAK and PAO pili was inhibited by corresponding free pili. The receptor binding domain of the PAK pilus resides in the C-terminal disulphide-looped region (residues 128-144) of the pilin structural subunit (Irvin et al., 1989). Biotinylated synthetic peptides corresponding the C-terminal residues 128-144 of P. aeruginosa PAK and PAO pilin molecules were shown to bind to the beta GalNAc(1-4)beta Gal-(bovine serum albumin (BSA)). The binding of biotinylated peptides to beta GalNAc(1-4)beta GAL-BSA was inhibited by PAK pili, Ac-KCTSDQDEQFIPKGCSK-OH (AcPAK(128-144)ox-OH) and Ac-ACKSTQDPMFTPKGCDN-OH (AcPAO(128-144)ox-OH) peptides. (In these peptides Ac denotes N alpha-acetylation of the N-terminus, -OH means a peptide with a free alpha-carboxyl group at the C-terminus and the 'ox' denotes the oxidation of the sulphhydryl groups of Cys-129 and Cys-142.) Both acetylated peptides were also able to inhibit the binding of beta GalNAc(1-4)beta Gal-biotin to the corresponding BSA-Peptide(128-144)ox-OH conjugates.(ABSTRACT TRUNCATED AT 250 WORDS)