gebhart/patrepeval huggingface dataset:
Effects of Mutations of RAD50, RAD51, RAD52, and Related Genes on Illegitimate Recombination in Saccharomyces cerevisiae (1996)

To examine the mechanism of illegitimate recombination in Saccharomyces cerevisiae, we have developed a plasmid system for quantitative analysis of deletion formation. A can1 cyh2 cell carrying two negative selection markers, the CAN1 and CYH2 genes, on a YCp plasmid is sensitive to canavanine and cycloheximide, but the cell becomes resistant to both drugs when the plasmid has a deletion over the CAN1 and CYH2 genes. Structural analysis of the recombinant plasmids obtained from the resistant cells showed that the plasmids had deletions at various sites of the CAN1-CYH2 region and there were only short regions of homology (1-5 bp) at the recombination junctions. The results indicated that the deletion detected in this system were formed by illegitimate recombination. Study on the effect of several rad mutations showed that the recombination rate was reduced by 30-, 10-, 10-, and 10-fold in the rad52, rad50, mre11, and xrs2 mutants, respectively, while in the rad51, 54, 55, and 57 mutants, the rate was comparable to that in the wild-type strain. The rad52 mutation did not affect length of homology at junction sites of illegitimate recombination.
Discovery of a 2,4-Diamino-7-aminoalkoxyquinazoline as a Potent and Selective Inhibitor of Histone Lysine Methyltransferase G9a (2009)

SAR exploration of the 2,4-diamino-6,7-dimethoxyquinazoline template led to the discovery of 8 (UNC0224) as a potent and selective G9a inhibitor. A high resolution X-ray crystal structure of the G9a-8 complex, the first cocrystal structure of G9a with a small molecule inhibitor, was obtained. The cocrystal structure validated our binding hypothesis and will enable structure-based design of novel inhibitors. 8 is a useful tool for investigating the biology of G9a and its roles in chromatin remodeling.
Exploitation of a new flagellatropic phage ofErwiniafor positive selection of bacterial mutants attenuated in plant virulence: towards phage therapy (2009)

To isolate and characterize novel bacteriophages for the phytopathogen, Erwinia carotovora ssp. atroseptica (Eca), and to isolate phage-resistant mutants attenuated in virulence.A novel flagellatropic phage was isolated on the potato-rotting bacterial species, Eca, and characterized using electron microscopy and restriction analysis. The phage, named PhiAT1, has an icosahedral head and a long, contractile tail; it belongs to the Myoviridae family. Partial sequencing revealed the presence of genes with homology to those of coliphages T4, T7 and Mu. Phage-resistant transposon mutants of Eca were isolated and studied in vitro for a number of virulence-related phenotypes; only motility was found to be affected. In vivo tuber rotting assays showed that these mutants were attenuated in virulence, presumably because the infection is unable to spread from the initial site of inoculation.The Eca flagellum can act as a receptor for PhiAT1 infection, and resistant mutants are enriched for motility and virulence defects.PhiAT1 is the first reported flagellatropic phage found to infect Eca and has enabled further study of the virulence of this economically important phytopathogen.
In vivo kinetic degradation analysis and biocompatibility of aliphatic polyester polyurethanes (2010)

Polyester polyurethanes incorporating polyhedral oligosilsesquioxane (POSS) as the crystalline hard block were evaluated for biocompatibility and degradation over 24 weeks in vivo. In vitro studies were also used to predict the onset of mass loss. The molecular weight of each sample was found to decrease quickly over an 8 week period and then became constant due to the nondegrading POSS hard block. Kinetic analysis of the initial molecular weight change indicated that the degradation rate was dependent on the soft block composition. Crystallinity, melting temperature, and heat of fusion of the polyurethanes were found to increase during degradation as the amorphous polyester soft segments were hydrolyzed. The histological analysis of each polymer demonstrated rapid resolution of the acute and chronic inflammatory responses and the development of expected, normal foreign body reaction, consisting of adherent macrophages and foreign body giant cells on the surface of the polymers, and fibrous capsule formation around the polymer. No acute and/or chronic inflammation was seen after 3 weeks, indicating that the polymers in film form and biodegraded form, that is, particles, were biocompatible and did not elicit inflammatory responses expected for toxic or nonbiocompatible materials.
The PRY/SPRY/B30.2 Domain of Butyrophilin 1A1 (BTN1A1) Binds to Xanthine Oxidoreductase (2009)

Butyrophilin 1A1 (BTN1A1) and xanthine oxidoreductase (XOR) are highly expressed in the lactating mammary gland and are secreted into milk associated with the milk fat globule membrane (MFGM). Ablation of the genes encoding either protein causes severe defects in the secretion of milk lipid droplets, suggesting that the two proteins may function in the same pathway. Therefore, we determined whether BTN1A1 and XOR directly interact using protein binding assays, surface plasmon resonance analysis, and gel filtration. Bovine XOR bound with high affinity in a pH- and salt-sensitive manner (KD=101+/-31 nM in 10 mM HEPES, 150 mM NaCl, pH 7.4) to the PRY/SPRY/B30.2 domain in the cytoplasmic region of bovine BTN1A1. Binding was stoichiometric, with one XOR dimer binding to either two BTN1A1 monomers or one dimer. XOR bound to BTN1A1 orthologs from mice, humans, or cows but not to the cytoplasmic domains of the closely related human paralogs, BTN2A1 or BTN3A1, or to the B30.2 domain of human RoRet (TRIM 38), a protein in the TRIM family. Analysis of the protein composition of the MFGM of wild type and BTN1A1 null mice showed that most of the XOR in mice lacking BTN1A1 was released from the MFGM in a soluble form when the milk lipid droplets were disrupted to prepare membrane, compared with wild-type mice, in which most of the XOR remained membrane-bound. Thus BTN1A1 functions in vivo to stabilize the association of XOR with the MFGM by direct interactions through the PRY/SPRY/B30.2 domain. The potential significance of BTN1A1/XOR interactions in the mammary gland and other tissues is discussed.
Thermodegradable polyurethanes having azo groups in the main chains. 1. Synthesis and thermal properties (1993)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTThermodegradable polyurethanes having azo groups in the main chains. 1. Synthesis and thermal propertiesYukio Shimura and Dajun ChenCite this: Macromolecules 1993, 26, 19, 5004–5008Publication Date (Print):September 1, 1993Publication History Published online1 May 2002Published inissue 1 September 1993https://pubs.acs.org/doi/10.1021/ma00071a003https://doi.org/10.1021/ma00071a003research-articleACS PublicationsRequest reuse permissionsArticle Views199Altmetric-Citations16LEARN 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
Characterisation of two highly oncogenic strains of Marek's disease virus12 (1982)

The RB-1B and ALA-8 strains of Marek's disease (MD) virus, which were isolated from chickens with MD and which had been vaccinated with the herpesvirus of turkeys (HVT), were evaluated for their oncogenic potential in genetically susceptible (P-line) and resistant (N-line, PDRC) chickens. RB-1B and ALA-8 were both highly oncogenic, causing a high incidence of MD in both susceptible and resistant birds. Vaccination of P-line birds with SB-1 or HVT did not protect satisfactorily against RB-1B. However, a bivalent vaccine consisting of SB-1 and HVT enhanced protection significantly. HVT alone, and the bivalent vaccine, protected PDRC and N-line chickens well against RB-1B, but SB-1 was less protective in PDRC birds. HVT protected equally well against challenge with ALA-8 and the standard JM-10 strain. Differences in the pathogenesis of viral infection could not be detected among ALA-8, RB-1B and JM-10 between 4-7 days post-infection (d.p.i.). However, after d.p.i. 12 RB-1B caused significantly higher levels of viral internal antigen and virus isolation rates than did JM-10 in the same genetic strain. Prior vaccination prevented the expression of ALA-8 at 5 and 20 d.p.i., but not that of RB-1B. Pathogenetic events such as expression of VIA or level of virus infection appeared to be directly related to the level of protection observed in challenged birds.
Identification of a yeast artificial chromosome clone encoding an accessory factor for the human interferon gamma receptor: evidence for multiple accessory factors. (1993)

Human chromosomes 6 and 21 are both necessary to confer sensitivity to human interferon gamma (Hu-IFN-gamma), as measured by the induction of human HLA class I antigen. Human chromosome 6 encodes the receptor for Hu-IFN-gamma, and human chromosome 21 encodes accessory factors for generating biological activity through the Hu-IFN-gamma receptor. A small region of human chromosome 21 that is responsible for encoding such factors was localized with hamster-human somatic cell hybrids carrying an irradiation-reduced fragment of human chromosome 21. The cell line with the minimum chromosome 21-specific DNA is Chinese hamster ovary 3x1S. To localize the genes further, 10 different yeast artificial chromosome clones from six different loci in the vicinity of the 3x1S region were fused to a human-hamster hybrid cell line (designated 16-9) that contains human chromosome 6q (supplying the Hu-IFN-gamma receptor) and the human HLA-B7 gene. These transformed 16-9 cells were assayed for induction of class I HLA antigens upon treatment with Hu-IFN-gamma. Here we report that a 540-kb yeast artificial chromosome encodes the necessary species-specific factor(s) and can substitute for human chromosome 21 to reconstitute the Hu-IFN-gamma-receptor-mediated induction of class I HLA antigens. However, the factor encoded on the yeast artificial chromosome does not confer antiviral protection against encephalomyocarditis virus, demonstrating that an additional factor encoded on human chromosome 21 is required for the antiviral activity.
Natural Microbial Community Compositions Compared by a Back-Propagating Neural Network and Cluster Analysis of 5S rRNA (1997)

The community compositions of free-living and particle-associated bacteria in the Chesapeake Bay estuary were analyzed by comparing banding patterns of stable low-molecular-weight RNA (SLMW RNA) which include 5S rRNA and tRNA molecules. By analyzing images of autoradiographs of SLMW RNAs on polyacrylamide gels, band intensities of 5S rRNA were converted to binary format for transmission to a back-propagating neural network (NN). The NN was trained to relate binary input to sample stations, collection times, positions in the water column, and sample types (e.g., particle-associated versus free-living communities). Dendrograms produced by using Euclidean distance and average and Ward's linkage methods on data of three independently trained NNs yielded the following results. (i) Community compositions of Chesapeake Bay water samples varied both seasonally and spatially. (ii) Although there was no difference in the compositions of free-living and particle-associated bacteria in the summer, these community types differed significantly in the winter. (iii) In the summer, most bay samples had a common 121-nucleotide 5S rRNA molecule. Although this band occurred in the top water of midbay samples, it did not occur in particle-associated communities of bottom-water samples. (iv) Regardless of the season, midbay samples had the greatest variety of 5S rRNA sizes. The utility of NNs for interpreting complex banding patterns in electrophoresis gels was demonstrated.
User-Modulated Impedance Control of a Prosthetic Elbow in Unconstrained, Perturbed Motion (2008)

Humans use the agonist-antagonist structure of their muscles to simultaneously determine both the motion and the stiffness of their joints. Designing this feature into an artificial limb may prove advantageous. To evaluate the performance of an artificial limb capable of modulating its impedance, we have created a compact series elastic actuator that has the same size and similar weight as commercially available electric prosthetic elbows. The inherent compliance in series elastic actuators ensure their safety to the user, even at high speeds, while creating a high-fidelity force actuator ideally suited for impedance control. This paper describes three serial studies that build on each other. The first study presents modeling of the actuator to ensure stability in the range of impedance modulation and empirically tests the actuator to validate its ability to modulate impedance. The actuator is found to be stable and accurate over a wide range of impedances. In the second study, four subjects are tested in a preliminary experiment to answer basic questions necessary to implement user-modulated impedance control. Findings include the superiority of velocity control over position control as the underlying motion paradigm and the preference for high stiffness and non-negative inertia. Based on the findings of the second study, the third study evaluates the performance of 15 able-bodied subjects for two tasks, using five different impedance paradigms. Impedance modulation, speed, and error were compared across paradigms. The results indicate that subjects do not actively modulate impedance if it is near a preferred baseline. Fixed impedance and viscosity modulation provide the most accurate control.
The OAuth 2.0 Authorization Framework draft-ietf-oauth-v2-28 (2012)

The OAuth 2.0 authorization framework enables a third-party application to obtain limited access to an HTTP service, either on behalf of a resource owner by orchestrating an approval interaction between the resource owner and the HTTP service, or by allowing the third-party application to obtain access on its own behalf. This specification replaces and obsoletes the OAuth 1.0 protocol described in RFC 5849.
Efficient stream sequence matching algorithms for handheld devices on time-series stream data (2006)

In recent years, real-time processing of a large amount of infinite stream data becomes a hot research issue. For handheld devices, minimization of CPU operations is the most important factor in performance. In this paper, we propose the efficient algorithms that extract sequences similar to the given query sequence from the time-series stream such as network traffic data, stock prices, and sensor data. First, we formally define the stream sequence matching that finds similar sequences from the time-series stream. Second, we propose an efficient window-based approach by using the window construction mechanism of traditional subsequence matching methods. Third, we provide the notion of a window MBR and propose two different stream sequence matching algorithms based on the notion. Fourth, we formally prove correctness of the proposed algorithms by presenting the related theorems. Last, through extensive analysis and experiments, we show that our approach improves performance significantly compared with the naive approach. Experimental results show that our window-based approach improves performance by tens to hundreds of times over the naive approach. Overall, we believe that our methods would be very suitable for handheld devices as the embedded algorithms.
PieceMaker: selection of DNA fragments for selector-guided multiplex amplification (2005)

We describe PieceMaker, a software tool for the design of applications of selector probes-oligonucleotide probes that direct circularization of target nucleic acid molecules. Such probes can be combined in parallel to circularize a selection of fragments from restriction digested total genomic DNA. These fragments can then be amplified in a single PCR using a common primer pair, yielding substrates for subsequent analyses, such as parallel genotyping or sequencing. However, designing multiplex selector assays is a laborious task. The PieceMaker program alleviates this problem by selecting restriction enzymes to generate suitable fragments for selection, and generating the output data required to design the selector probes.
Efficient synthesis of 3,5‐functionalized isoxazoles and isoxazolines via 1,3‐dipolar cycloaddition reactions of 1‐propargyl‐ and 1‐allylbenzotriazoles (2000)

Abstract 3‐Aryl‐5‐(benzotriazol‐1‐ylmethyl)‐ 10a‐f and 3‐ p ‐methoxyphenyl‐5‐(α‐benzotriazol‐1‐yl‐α‐ethoxymethyl)‐isoxazole (13) were prepared in high yields by 1,3‐dipolar cycloadditions of 1‐propargyl‐benzotriazole (5) and (α‐ethoxypropargyl)benzotriazole (8), respectively, with nitrite oxides 3a‐f (prepared in situ from benzohydroximoyl chlorides 2a‐f). The benzotriazol‐1‐ylmethyl moiety was further elaborated by sequential lithiation and reaction with aldehydes, alkyl halides and Michael acceptors. Similar 1,3‐cycloadditions using 1‐allylbenzotriazole (6) and 1‐(α‐ethoxyallyl)benzotriazole (7) afforded 3,5‐substituted isoxazolines 11b, f and 12 in excellent yields.
BAD Dephosphorylation and Decreased Expression of MCL-1 Induce Rapid Apoptosis in Prostate Cancer Cells (2013)

PTEN loss and constitutive activation of the PI3K signaling pathway have been associated with advanced androgen-independent prostate cancer. PTEN-deficient prostate cancer C42Luc cells survive in serum-free media and show relative resistance to apoptosis even in the presence of the PI3K inhibitor ZSTK474. Yet, when ZSTK474 is combined with the translation inhibitor cycloheximide, C42Luc cells undergo apoptosis within 6 hours. We identified dephosphorylation of BAD (Bcl2-associated death promoter) as a main apoptosis-regulatory molecule downstream from PI3K, and loss of MCL-1 (Myeloid cell leukemia -1) as a major target of cycloheximide. The combination of MCL-1 knockdown and expression of phosphorylation-deficient mutant BAD2SA is sufficient to trigger rapid apoptosis in prostate cancer cells. These results establish the mechanism for the synergistic induction of apoptosis by the combination of a PI3K inhibitor and of a protein synthesis inhibitor in PTEN-deficient prostate cancer cells.
'DYNAMIC', STATISTICALLY-ADJUSTED DESCRIPTIONS: A BETTER TOOL FOR COMPARING CULTIVARS, USING SWEDE (BRASSICA NAPUS L. VAR. NAPOBRASSICA (L.) RCHB.) AS AN EXAMPLE. (1996)

ISHS ISHS Brassica Symposium - IX Crucifer Genetics Workshop 'DYNAMIC', STATISTICALLY-ADJUSTED DESCRIPTIONS: A BETTER TOOL FOR COMPARING CULTIVARS, USING SWEDE (BRASSICA NAPUS L. VAR. NAPOBRASSICA (L.) RCHB.) AS AN EXAMPLE.
Electroless deposition of CoO thin films (1999)

The influence of various preparation conditions such as bath composition, film growth and heat treatment conditions on the properties of chemical bath deposited cobalt II oxide thin films has been studied. The interference fringes on the transmission spectra were used to calculate the refractive index and the average thickness of the films. The effects of surface roughness of the films on the interference extrema are also analysed. The maximum film thickness obtainable in a single deposition cycle is about 700 nm. X-ray diffractometry, energy-dispersive analysis of x-ray fluorescence and electrical resistivity measurements were also used for the characterization of the films. The properties of the deposited films are similar to those of hot-sprayed and sol-gel and baked films but film deposition is simpler and more cost effective than via solution growth procedures.
EFFECTS OF KETAMINE ON EXPLICIT AND IMPLICIT SUICIDAL COGNITION: A RANDOMIZED CONTROLLED TRIAL IN TREATMENT-RESISTANT DEPRESSION (2014)

Intravenous ketamine produces rapid reductions in suicidal cognition over and above active placebo. Further study is warranted to test ketamine's antisuicidal effects in higher-risk samples.
Nuclear transplantation using bovine primordial germ cells from male fetuses (1995)

The developmental potential of nuclei of bovine gonial cells was investigated by nuclear transfer. Gonial cells were collected from male fetuses at about 175 days post coitum (p.c.). They were fused with enucleated oocytes; reconstituted embryos were cultured in vitro for 7 days. Embryos reaching the compacted morula or blastocyst stage were either fixed for cell counting or transferred into recipients. Out of 115 oocyte-gonia fusions, 101 (87.8%) gave rise to cleaved embryos at Day 3 and 26 (22.6%) had reached the 8-cell stage. At Day 7, 1 (1%) developed to the morula stage and 5 (4%) reached the blastocyst stage. Three blastocysts were fixed and showed normal cell numbers (135; 90; 76 cells). Three blastocysts and one morula were transferred in four recipients; two recipients were pregnant at Day 21 but only one was positive at Day 35 p.c.; this last one aborted around Day 40 p.c. No conceptus was collected. These results indicate that gonial cell nuclei can be partially reprogrammed; they are able to develop into blastocysts and to initiate gestation. However, more experiments will be necessary to prove the nuclear totipotency of bovine gonial cells.
Development and optimization of quantitative PCR for the diagnosis of invasive aspergillosis with bronchoalveolar lavage fluid (2008)

The Aspergillus qPCR assay detected Aspergillus DNA in 76.9% of subjects with proven or probable IPA when the concentrated BAL fluid pellet fraction was used for diagnosis. There was no benefit from analyzing the BAL supernatant fraction. Use of both extraction and amplification controls provided optimal quality control for interpreting qPCR results and therefore may increase our understanding of the true potential of qPCR for the diagnosis of IPA.
Cardiac glycosides. 7. Sugar stereochemistry and cardiac glycoside activity (1986)

Digitoxigenin alpha-L-, beta-L-, alpha-D-, and beta-D-glucosides; alpha-L-, beta-L-, alpha-D-, and beta-D-mannosides; and alpha-L- and beta-L-rhamnosides were stereoselectively synthesized from the corresponding sugar tetrabenzyl trichloroacetimidates. The Na+,K+-ATPase receptor inhibitory activities of these glycosides (as a measure of receptor binding) were compared with those of digitoxigenin, digitoxigenin 6'-hydroxy-beta-D-digitoxoside, digitoxigenin beta-D-galactoside, and digitoxigenin beta-D-digitoxoside. The observed activities reveal that a given sugar substituent may have a role in binding of some glycoside stereoisomers, but not others. With alpha-L- and possibly beta-L-rhamnosides, the 5'-CH3 and 4'-OH appear to have a predominant role in binding to the Na+,K+-ATPase receptor. Addition of a 6'-OH to form the corresponding mannosides dramatically disrupts the effect of both the 5'-CH3 and 4'-OH in prompting receptor binding of the alpha-L isomer. However, with the beta-L isomer, some influence of 4'-OH, 3'-OH, and 2'-OH binding remains. With beta-D-glycosides, binding via the "5'-CH3 site" appears to be of little importance and addition of a 6'-OH diminishes activity only slightly. With these beta-D-glycosides, an equatorial 4'-OH, axial 3'-OH, and equatorial 2'-OH groups appear to contribute to binding.