gebhart/patrepeval huggingface dataset:
Identification and Allele-Specific Silencing of the Mutant Huntingtin Allele in Huntington's Disease Patient-Derived Fibroblasts (2008)

Huntington's disease (HD) is a dominantly inherited neurodegenerative disorder caused by the expression of mutant huntingtin protein (Htt). Suppression of Htt expression, using RNA interference, might be an effective therapy. However, if reduction of wild-type protein is not well tolerated in the brain, it may be necessary to suppress just the product of the mutant allele. We present a small interfering RNA (siRNA) that selectively reduces the endogenous mRNA for a heterozygous HD donor's pathogenic allele by approximately 80% by specifically targeting a single-nucleotide polymorphism (SNP) located several thousand bases downstream from the disease-causing mutation. In addition, we show selective suppression of endogenous mutant Htt protein, using this siRNA. We further present a method, using just a heterozygous patient's own mRNA, to determine which SNP variants correspond to the mutant allele. The method may be useful in any disorder in which a targeted SNP is far downstream from the pathogenic mutation. These results indicate that allele-specific treatment for Huntington's disease may be clinically feasible and practical.
Characterization of Adhesion Strength and Residual Stresses of HVOF Sprayed Inconel 718 for Aerospace Repair Applications (2007)

Abstract Thermally sprayed Inconel 718 coatings have been deposited by high velocity oxy-fuel (HVOF) spraying on Inconel 718 substrates. The aim of the on-going study is to understand and control the adhesion mechanisms and the residual stress state of the deposit/substrate system, in order to build up thick coatings for maintenance purposes. The coating adhesion strength was evaluated by the standard ASTM C633 tensile test. Coating shear strength was evaluated by the recently developed prEN15340 Shear Test. A modified Layer Removal Method (MLRM) test was carried out to measure residual stresses. The work is a part of an ongoing study for evaluation of relationships between process parameters, residual stress distribution and adhesion strength.
Population and Diversity of Endophytic Bacteria Associated with Medicinal Plant Curcuma zedoaria (2014)

Traditionally Curcuma zedoaria (white turmeric) known as herbal medicine which possessing many biological activities. Many endophytic bacteria live in association with their host and may play an important biological roles. The main interest of this study was to investigate the endophytic bacterial diversity associated with white turmeric. White turmerics were collected from three locations in Bogor, West Java, Indonesia. The isolation of endophytic bacteria was carried out using 4 kinds media (Nutrient Agar (NA), NA contained white turmeric extract (NAT), Water Yeast Extract Agar (WYEA), WYEA contained white turmeric extract (WYEAT)), and 2 methods of spread plate and plant piece methods. The identification of selected isolates was conducted by molecular analysis based on 16S DNA. The suitable media and method of isolation endophytic bacteria were NA and spread plate method. A total of 207 bacterial colonies were isolated from rhizomes, stems, and leaves and 73 endophytic bacteria were selected based on morphological characteristics. From them, 32% isolates from Bojong Gede, 22% isolates from Cibinong and 46% isolates from Dramaga were obtained. Endophytic bacteria were predominated 38% in the rhizomes, 32% of stems, and 30% of leaves. Based on 16S rDNA sequence analysis, the isolates were belonging to the cluster Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Firmicutes, and Actinobacteria, with twenty three different genera includes Stenothropomonas, Pseudomonas, Enterobacter, Providencia, Klebsiella, Dickeya, Pantoea, Bacillus, Acinetobacter, Citrobacter, Mycobacterium, Cellulomonas, Microbacterium, Methylobacterium, Penylobacterium, Roseomonas, Agrobacterium, Bosea, Xanthobacter, Rhizobium, Burkholderia, Ralstonia, and Alcaligenes. The plant location, age, part of plant, media and method of isolation seem to influence the endophytic bacterial communities.
Inhibition of the Ribonuclease H and DNA Polymerase Activities of HIV-1 Reverse Transcriptase by N-(4-tert-Butylbenzoyl)-2-hydroxy-1-naphthaldehyde Hydrazone (1997)

HIV-1 reverse transcriptase (RT) is multifunctional, with RNA-dependent DNA polymerase (RDDP), DNA-dependent DNA polymerase (DDDP), and ribonuclease H (RNase H) activities. N-(4-tert-Butylbenzoyl)-2-hydroxy-1-naphthaldehyde hydrazone (BBNH) inhibited both the polymerase and the RNase H activities of HIV-1 RT in vitro. IC50 values for inhibition of RDDP were 0.8-3.4 microM, depending on the template/primer (T/P) used in the assay. The IC50 for DDDP inhibition was about 12 microM, while that for inhibition of RNase H was 3.5 microM. EC50 for inhibition of HIV-1 replication in cord blood mononuclear cells was 1.5 microM. BBNH inhibition of RNase H in vitro was time-dependent, whereas inhibition of RT polymerase activities was immediate. BBNH was a linear mixed-type inhibitor of RT RDDP activity with respect to both T/P and to dNTP, whereas BBNH inhibition of RT RNase H activity was linear competitive. Protection experiments using an azidonevirapine photolabel showed that BBNH binds to the non-nucleoside RT inhibitor (NNRTI) binding pocket. Importantly, the compound inhibited recombinant RT containing mutations associated with high-level resistance to other NNRTI. While BBNH did not inhibit the DNA polymerase activities of other retroviral reverse transcriptases and DNA polymerases, the compound inhibited Escherichia coli RNase HI and the RNase H activity of murine leukemia virus RT. BBNH also inhibited HIV-1 RT RNase H in the presence of high concentrations of other non-nucleoside inhibitors with higher affinities for the NNRTI binding pocket, and of RT in which the NNRTI binding pocket had been irreversibly blocked by the azidonevirapine photolabel. We conclude that BBNH may therefore bind to two sites on HIV-1 RT. One site is the polymerase non-nucleoside inhibitor binding site and the second may be located in the RNase H domain. BBNH is therefore a promising lead compound for the development of multisite inhibitors of HIV-1 RT.
Pyrido[2,1-b]quinazolinecarboxamide derivatives as platelet activating factor antagonists (1988)

A series of N-[(heteroaryl)alkyl]pyrido[2,1-b]quinazolines were evaluated for their ability to inhibit the binding of radiolabeled platelet activating factor (PAF) to its receptor on dog platelets. The most potent compounds in this series were found to be pyrido[2,1-b]quinazoline-8-carboxamides possessing a four- or six-carbon chain between the carboxamide nitrogen atom and a 3-pyridinyl or 5-pyrimidinyl moiety. Since earlier metabolism studies with pyridoquinazolinecarboxamides suggest that the carboxamide moiety is labile to hydrolysis in vivo, attempts were made to find isosteric replacements for this group. The substitutions examined led to a loss of activity; however, insertion of a methyl group on the carbon atom alpha to the carboxamide nitrogen led to an enantioselective enhancement of potency. (R)-2-(1-Methylethyl)-N-[1-methyl-4-(3-pyridinyl)butyl]-11-oxo-11H- pyrido[2,1-b]quinazoline-8-carboxamide (34) was more potent than the corresponding S enantiomer in the PAF binding assay and was also shown to be more resistant to degradation by amidases present in whole liver homogenates obtained from guinea pig, dog, and squirrel monkey. The corresponding rac-2-(1-methylethyl)-N-[1-methyl-4-(3-pyridinyl)butyl]-11-oxo-11H- pyrido[2,1-b]quinazoline-8-carboxamide (33) was found to inhibit transient PAF-induced thrombocytopenia and decreases in blood pressure in guinea pigs after intravenous or oral administration and to have a duration of action of greater than 5 h after an oral dose of 200 mg/kg. Compound 33 thus represents the prototype of a new class of orally active PAF antagonists.
Role of architecture and molecular weight in the formation of tailor‐made ultrathin multilayers using dendritic macromolecules and click chemistry (2007)

Abstract The high efficiency and mild reaction conditions associated with the Cu(I) catalyzed cycloaddition of azides and alkynes were exploited for the covalent layer‐by‐layer synthesis of dendritic thin films on silicon wafers. The preparation of azide and alkyne‐terminated dendrimers based on bisMPA was accomplished by a divergent strategy; combinations of these monodisperse building blocks from the 2nd to the 5th generation were used for construction of the thin films. The layer‐by‐layer self assembly process proceeds under ambient conditions and was monitored by ellipsometry, XPS, and ATR‐IR, which showed extremely regular growth of the dendritic thin films. Film thickness could be accurately controlled by both the size/generation number of the dendrimers as well as the number of layers. In comparison with linear analogues, the growth of the dendritic films was significantly more controlled and defect‐free with each layer being thinner than the corresponding films prepared from the isomeric linear polymers, demonstrating the well‐defined, three‐dimensional nature of the dendritic architecture. © 2007 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 45: 2835–2846, 2007
Localization of platelet-derived growth factor beta receptor expression in the periepithelial stroma of human breast carcinoma. (1996)

Platelet-derived growth factor (PDGF) BB is secreted by most human breast carcinoma cells; however, only recently have PDGF beta receptors been demonstrated in malignant breast tissue. In the present study, the tissue localization of PDGF beta receptor expression was studied in human breast carcinoma and nonmalignant breast tissues stained using both immunofluorescence and immunoperoxidase techniques. We examined a total of 29 cases of breast carcinomas, which showed both in situ and invasive components. PDGF beta receptor staining was localized in the periepithelial stroma and was particularly intense in regions immediately adjacent to carcinoma in situ components in all tumors examined. A diffuse low level of PDGF beta receptor staining was seen throughout the stroma of eight nonmalignant breast tissues as well as of nonmalignant regions of tumor tissues. Image analysis was used to assess the coincidence of staining of PDGF beta receptor with epithelial or stromal cells in 13 of the 29 tumor tissues studied. Less than 5% of malignant ductal epithelium or myoepithelium showed PDGF beta receptor staining. Analysis with stromal cell type-specific markers indicated significant localization of PDGF beta receptor primarily within alpha smooth muscle actin-staining cells (32%) and vascular endothelial cells (41%) in the periepithelial stroma. PDGF beta receptor positivity was strongly associated with periepithelial stromal cells adjacent to the basement membrane surrounding regions of carcinoma in situ but was less intense in regions of invasive carcinoma where basement membrane was degraded. The absence of PDGF beta receptors on carcinoma cells and their presence in the surrounding stroma suggest a paracrine stimulation of adjacent stromal tissue by malignant epithelial cells in human breast tumors.
MK-1775, a small molecule Wee1 inhibitor, enhances anti-tumor efficacy of various DNA-damaging agents, including 5-fluorouracil (2010)

MK-1775 is a potent and selective small molecule Wee1 inhibitor. Previously we have shown that it abrogated DNA damaged checkpoints induced by gemcitabine, carboplatin, and cisplatin and enhanced the anti-tumor efficacy of these agents selectively in p53-deficient tumor cells. MK-1775 is currently in Phase I clinical trial in combination with these anti-cancer drugs. In this study, the effects of MK-1775 on 5-fluorouracil (5-FU) and other DNA-damaging agents with different modes of action were determined. MK-1775 enhanced the cytotoxic effects of 5-FU in p53-deficient human colon cancer cells. MK-1775 inhibited CDC2 Y15 phosphorylation in cells, abrogated DNA damaged checkpoints induced by 5-FU treatment, and caused premature entry of mitosis determined by induction of Histone H3 phosphorylation. Enhancement by MK-1775 was specific for p53-deficient cells since this compound did not sensitize p53-wild type human colon cancer cells to 5-FU in vitro. In vivo, MK-1775 potentiated the anti-tumor efficacy of 5-FU or its prodrug, capecitabine, at tolerable doses. These enhancements were well correlated with inhibition of CDC2 phosphorylation and induction of Histone H3 phosphorylation in tumors. In addition, MK-1775 also potentiated the cytotoxic effects of pemetrexed, doxorubicin, camptothecin, and mitomycin C in vitro. These studies support the rationale for testing the combination of MK-1775 with various DNA-damaging agents in cancer patients.
Epidemiological and experimental evidence for immunodeficiency affecting avian infectious bronchitis (2006)

We evaluated the effects of viral immunodeficiency on the outcome of infectious bronchitis virus (IBV) infection in chickens as a hypothetical cause for failure of adequate protection in vaccinated chickens. Initially, we investigated IBV isolations from cases of respiratory disease in association with the presence of thymic and/or bursal atrophy in 322 submissions during 1997 to 2002. Arkansas (Ark)-type IBV was most frequently isolated in spite of extensive ArkDPI vaccination in the broiler industry. The number of IBV isolations was consistently higher in broilers aged 27 to 43 days, coinciding with lymphocytic depletion of the bursa and/or thymus, providing circumstantial evidence that immunodeficiency and IBV incidence may be linked. S1 gene sequence analyses, antigenic characterizations, and challenge of susceptible chickens demonstrated that the field IBV isolates tested were closely related to vaccine strains and had low pathogenicity for chickens. We experimentally evaluated the effects of immunodeficiency caused by co-infection with chicken anaemia virus and infectious bursal disease virus on the outcome of IBV infection. Clinical signs and histological lesions were more persistent in immunodeficient chickens. Local specific IgA production was delayed and lower levels were achieved in immunodeficient chickens. At the same time, IBV RNA concentrations in tracheas and lachrymal fluids were higher and more persistent in immunodeficient chickens. Collectively, these results indicate that viral immunodeficiency most probably plays a relevant role in the epidemiology and outcome of IBV infection.
Scaffolds and biomaterials for tissue engineering: a review of clinical applications (2003)

Tissue engineering is a multidisciplinary area of research aimed at regeneration of tissues and restoration of organ function. This is achieved through implantation of cells/tissues grown outside the body or by stimulating cells to grow into an implanted matrix. In this short review, we discuss the use of biomaterials, in the form of scaffolds, for tissue engineering and review clinical applications to otorhinolaryngology-head and neck surgery.
Repeated injections of lipopolysaccharide attenuate the satiety effects of cholecystokinin (1999)

The present study examined the effects of repeated injections of lipopolysaccharide (LPS) and cholecystokinin (CCK) on both sucrose palatability and body weight. Rats received repeated injections of LPS (200 microg/kg), CCK (8 microg/kg) and/or NaCl on days 1, 4, 7 and 10. Body weight was monitored on each test day and sucrose palatability was assessed using the taste reactivity test (TRT) on days 7 and 10. Rats treated with LPS developed a rapid tolerance to the reductions in body weight; however, this tolerance did not affect sucrose palatability. Furthermore it was found that repeated exposures to LPS and CCK attenuated the typical satiety related behaviors produced in the TRT by administration of CCK. This desensitization to CCK with repeated exposures to LPS may be one of the mechanisms that could account for the rapid development of tolerance to LPS-induced hypophagia.
Addressing Personal Wealth Issues in an IPO (2006)

Business owners approaching an initial public offering typically focus their attention on the transaction9s effects on the company—often at the expense of personal wealth planning. Yet these transactions create a number of financial issues and opportunities for owners, making personal objectives an important consideration. Proper wealth planning begun well in advance of an IPO can help owners accomplish important goals, such as minimizing taxes, addressing valuation issues, and transferring assets efficiently, without slowing the transaction or diminishing its value. This article examines a variety of wealth planning issues connected to an IPO and outlines important steps owners can take to maximize the value of the transaction for themselves and their families. <b>TOPICS:</b>Wealth management, legal/regulatory/public policy
CpG island hypermethylation in progression of esophageal and gastric cancer (2005)

The upper gastrointestinal (GI) cancers have various carcinogenic pathways and precursor lesions, such as dysplasia for esophageal squamous cell carcinoma, Barrett esophagus for esophageal adenocarcinoma, and intestinal metaplasia for the intestinal-type of gastric cancer. Recently, many epigenetic events in carcinogenic pathways have been revealed, along with genomic and genetic alterations. This information has provided deeper insight into an understanding of the mechanisms of upper GI carcinogenesis. Moreover, detection methods of aberrant methylation have been applied to clinical fields to stratify high-risk groups, detect early cancer, and to predict clinical outcomes. In this review, a variety of information is summarized regarding gene hypermethylation in esophageal and gastric cancer.
Subwavelength lithography and its potential impact on design and EDA (1999)

Article Subwavelength lithography and its potential impact on design and EDA Share on Authors: Andrew B. Kahng UCLA Department of Computer Science, Los Angeles, CA UCLA Department of Computer Science, Los Angeles, CAView Profile , Y. C. Pati Numerical Technologies, Inc., Santa Clara, CA Numerical Technologies, Inc., Santa Clara, CAView Profile Authors Info & Claims DAC '99: Proceedings of the 36th annual ACM/IEEE Design Automation ConferenceJune 1999 Pages 799–804https://doi.org/10.1145/309847.310072Online:01 June 1999Publication History 18citation538DownloadsMetricsTotal Citations18Total Downloads538Last 12 Months8Last 6 weeks1 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteGet Access
Impact on the composition of the faecal flora by a new probiotic preparation: preliminary data on maintenance treatment of patients with ulcerative colitis (1999)

These results show that this probiotic preparation is able to colonize the intestine, and suggest that it may be useful in maintaining the remission in ulcerative colitis patients intolerant or allergic to 5-ASA. Controlled trials are warranted to confirm these preliminary results.
Photosensitive Tetramethylpiperidine Urethanes: Synthesis and Characterization (1994)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPhotosensitive Tetramethylpiperidine Urethanes: Synthesis and CharacterizationStefano Martina, Scott A. MacDonald, and Volker EnkelmannCite this: J. Org. Chem. 1994, 59, 12, 3281–3283Publication Date (Print):June 1, 1994Publication History Published online1 May 2002Published inissue 1 June 1994https://pubs.acs.org/doi/10.1021/jo00091a012https://doi.org/10.1021/jo00091a012research-articleACS PublicationsRequest reuse permissionsArticle Views346Altmetric-Citations9LEARN 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-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
The Genome Sequence ofMethanosphaera stadtmanaeReveals Why This Human Intestinal Archaeon Is Restricted to Methanol and H2for Methane Formation and ATP Synthesis (2005)

Methanosphaera stadtmanae has the most restricted energy metabolism of all methanogenic archaea. This human intestinal inhabitant can generate methane only by reduction of methanol with H2 and is dependent on acetate as a carbon source. We report here the genome sequence of M. stadtmanae, which was found to be composed of 1,767,403 bp with an average G+C content of 28% and to harbor only 1,534 protein-encoding sequences (CDS). The genome lacks 37 CDS present in the genomes of all other methanogens. Among these are the CDS for synthesis of molybdopterin and for synthesis of the carbon monoxide dehydrogenase/acetyl-coenzyme A synthase complex, which explains why M. stadtmanae cannot reduce CO2 to methane or oxidize methanol to CO2 and why this archaeon is dependent on acetate for biosynthesis of cell components. Four sets of mtaABC genes coding for methanol:coenzyme M methyltransferases were found in the genome of M. stadtmanae. These genes exhibit homology to mta genes previously identified in Methanosarcina species. The M. stadtmanae genome also contains at least 323 CDS not present in the genomes of all other archaea. Seventy-three of these CDS exhibit high levels of homology to CDS in genomes of bacteria and eukaryotes. These 73 CDS include 12 CDS which are unusually long (>2,400 bp) with conspicuous repetitive sequence elements, 13 CDS which exhibit sequence similarity on the protein level to CDS encoding enzymes involved in the biosynthesis of cell surface antigens in bacteria, and 5 CDS which exhibit sequence similarity to the subunits of bacterial type I and III restriction-modification systems.
CD48 expression on leukocytes in infectious diseases: Flow cytometric analysis of surface antigen (1998)

These data suggest that CD48 expression on leukocytes reflects the disease activity of infectious diseases, especially of viral infections.