gebhart/patrepeval huggingface dataset:
Characterization of the developmentally regulated Bacillus subtilis glucose dehydrogenase gene (1986)

The DNA sequence of the structural gene for glucose dehydrogenase (EC 1.1.1.47) of Bacillus subtilis was determined and comprises 780 base pairs. The subunit molecular weight of glucose dehydrogenase as deduced from the nucleotide sequence is 28,196, which agrees well with the subunit molecular weight of 31,500 as determined from sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The sequence of the 49 amino acids at the NH2 terminus of glucose dehydrogenase purified from sporulating B. subtilis cells matched the amino acid sequence derived from the DNA sequence. Glucose dehydrogenase was purified from an Escherichia coli strain harboring pEF1, a plasmid that contains the B. subtilis gene encoding glucose dehydrogenase. This enzyme has the identical amino acid sequence at the NH2 terminus as the B. subtilis enzyme. A putative ribosome-binding site, 5'-AGGAGG-3', which is complementary to the 3' end of the 16S rRNA of B. subtilis, was found 6 base pairs preceding the translational start codon of the structural gene of glucose dehydrogenase. No known promoterlike DNA sequences that are recognized by B. subtilis RNA polymerases were present immediately preceding the translational start site of the glucose dehydrogenase structural gene. The glucose dehydrogenase gene was found to be under sporulation control at the trancriptional level. A transcript of 1.6 kilobases hybridized to a DNA fragment within the structural gene of glucose dehydrogenase. This transcript was synthesized 3 h after the cessation of vegetative growth concomitant to the appearance of glucose dehydrogenase.
A Solution-Phase Approach to the Synthesis of Uniform Nanowires of Crystalline Selenium with Lateral Dimensions in the Range of 10−30 nm (2000)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTA Solution-Phase Approach to the Synthesis of Uniform Nanowires of Crystalline Selenium with Lateral Dimensions in the Range of 10−30 nmByron Gates, Yadong Yin, and Younan XiaView Author Information Department of Chemistry University of Washington Seattle, Washington 98195 Cite this: J. Am. Chem. Soc. 2000, 122, 50, 12582–12583Publication Date (Web):December 1, 2000Publication History Received17 July 2000Published online1 December 2000Published inissue 1 December 2000https://pubs.acs.org/doi/10.1021/ja002608dhttps://doi.org/10.1021/ja002608drapid-communicationACS PublicationsCopyright © 2000 American Chemical SocietyRequest reuse permissionsArticle Views4522Altmetric-Citations318LEARN 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 SUBJECTS:Colloids,Nanostructures,Nanowires,Selenium,Wires Get e-Alerts
Failure of Xylitol Given Three Times a Day for Preventing Acute Otitis Media (2007)

Xylitol given regularly 3 times a day for 3 months during the respiratory infection season failed to prevent AOM.
Vitamin D insufficiency and treatment with oral vitamin D3 in northern-dwelling patients with chronic kidney disease (2009)

Vitamin D insufficiency is highly prevalent in northern-dwelling patients with stage 3-5 CKD, and is moderated by oral supplementation with 1,000 IU of vitamin D3 daily.
The solubilization of tetrameric alkaline phosphatase from human liver and its conversion into various forms by phosphatidylinositol phospholipase C or proteolysis. (1988)

When membrane-bound human liver alkaline phosphatase was treated with a phosphatidylinositol (PI) phospholipase C obtained from Bacillus cereus, or with the proteases ficin and bromelain, the enzyme released was dimeric. Butanol extraction of the plasma membranes at pH 7.6 yielded a water-soluble, aggregated form that PI phospholipase C could also convert to dimers. When the membrane-bound enzyme was solubilized with a non-ionic detergent (Nonidet P-40), it had the Mr of a tetramer; this, too, was convertible to dimers with PI phospholipase C or a protease. Butanol extraction of whole liver tissue at pH 6.6 and subsequent purification yielded a dimeric enzyme on electrophoresis under nondenaturing conditions, whereas butanol extraction at pH values of 7.6 or above and subsequent purification by immunoaffinity chromatography yielded an enzyme with a native Mr twice that of the dimeric form. This high molecular weight form showed a single Coomassie-stained band (Mr = 83,000) on electrophoresis under denaturing conditions in sodium dodecyl sulfate, as did its PI phospholipase C cleaved product; this Mr was the same as that obtained with the enzyme purified from whole liver using butanol extraction at pH 6.6. These results are highly suggestive of the presence of a butanol-activated endogenous enzyme activity (possibly a phospholipase) that is optimally active at an acidic pH. Inhibition of this activity by maintaining an alkaline pH during extraction and purification results in a tetrameric enzyme. Alkaline phosphatase, whether released by phosphatidylinositol (PI) phospholipase C or protease treatment of intact plasma membranes, or purified in a dimeric form, would not adsorb to a hydrophobic medium. PI phospholipase C treatment of alkaline phosphatase solubilized from plasma membranes by either detergent or butanol at pH 7.6 yielded a dimeric enzyme that did not absorb to the hydrophobic medium, whereas the untreated preparations did. This adsorbed activity was readily released by detergent. Likewise, alkaline phosphatase solubilized from plasma membranes by butanol extraction at pH 7.6 would incorporate into phosphatidylcholine liposomes, whereas the enzyme released from the membranes by PI phospholipase C would not incorporate. The dimeric enzyme purified from a butanol extract of whole liver tissue carried out at pH 6.6 did not incorporate. We conclude that PI phospholipase C converts a hydrophobic tetramer of alkaline phosphatase into hydrophilic dimers through removal of the 1,2-diacylglycerol moiety of phosphatidylinositol. Based on these and others' findings, we devised a model of alkaline phosphatase's conversion into its various forms.
Crystal Structure and Evolution of a Transfer RNA Splicing Enzyme (1998)

The splicing of transfer RNA precursors is similar in Eucarya and Archaea. In both kingdoms an endonuclease recognizes the splice sites and releases the intron, but the mechanism of splice site recognition is different in each kingdom. The crystal structure of the endonuclease from the archaeon Methanococcus jannaschii was determined to a resolution of 2.3 angstroms. The structure indicates that the cleavage reaction is similar to that of ribonuclease A and the arrangement of the active sites is conserved between the archaeal and eucaryal enzymes. These results suggest an evolutionary pathway for splice site recognition.
Holoenzyme proteins required for the physiological assembly and activity of telomerase (2004)

Many proteins have been implicated in the physiological function of telomerase, but specific roles of telomerase-associated proteins other than telomerase reverse transcriptase (TERT) remain ambiguous. To gain a more comprehensive understanding of catalytically active enzyme composition, we performed affinity purification of epitope-tagged, endogenously assembled Tetrahymena telomerase. We identified and cloned genes encoding four telomerase proteins in addition to TERT. We demonstrate that both of the two new proteins characterized in detail, p65 and p45, have essential roles in the maintenance of telomere length as part of a ciliate telomerase holoenzyme. The p65 subunit contains an La motif characteristic of a family of direct RNA-binding proteins. We find that p65 in cell extract is associated specifically with telomerase RNA, and that genetic depletion of p65 reduces telomerase RNA accumulation in vivo. These findings demonstrate that telomerase holoenzyme proteins other than TERT play critical roles in RNP biogenesis and function.
Recognize complex events from static images by fusing deep channels (2015)

A considerable portion of web images capture events that occur in our personal lives or social activities. In this paper, we aim to develop an effective method for recognizing events from such images. Despite the sheer amount of study on event recognition, most existing methods rely on videos and are not directly applicable to this task. Generally, events are complex phenomena that involve interactions among people and objects, and therefore analysis of event photos requires techniques that can go beyond recognizing individual objects and carry out joint reasoning based on evidences of multiple aspects. Inspired by the recent success of deep learning, we formulate a multi-layer framework to tackle this problem, which takes into account both visual appearance and the interactions among humans and objects, and combines them via semantic fusion. An important issue arising here is that humans and objects discovered by detectors are in the form of bounding boxes, and there is no straightforward way to represent their interactions and incorporate them with a deep network. We address this using a novel strategy that projects the detected instances onto multi-scale spatial maps. On a large dataset with 60, 000 images, the proposed method achieved substantial improvement over the state-of-the-art, raising the accuracy of event recognition by over 10%.
A Prospective Longitudinal Study of Cholesterol and Aggression in Patients Randomized to Clozapine, Olanzapine, and Haloperidol (2010)

1Nathan Kline Institute for Psychiatric Research, Orangeburg, NY, New York University School of Medicine, New York, NY 2Nathan Kline Institute for Psychiatric Research, Orangeburg, NY, Department of Psychiatry, Semmelweis University, Budapest, Hungary [email protected]
760. Optimized AAV-Mediated Human Factor VIII Gene Therapy in Hemophilia A Mice and Cynomolgus Macaques (2016)

In an effort to optimize expression of human coagulation VIII (hFVIII) for the treatment of hemophilia A, an extensive study was performed combining liver-specific promoter and enhancer elements with a codon-optimized human B-domain-deleted hFVIII transgene. Due to the large size of the FVIII coding sequence, there is a strong requirement for gene expression control elements to be as short as possible while retaining hepatocyte-restricted transcription. Several strong liver-specific promoters were shortened and combined, with combinations of up to three liver-specific enhancer sequences, to generate 42 enhancer/promoter combinations. These 42 liver regulatory gene cassettes were packaged into the AAVrh10 capsid and were tested in FVIII KO mice. Following intravenous (IV) administration of 1010 genome copies (GC), mice were bled every two weeks to follow hFVIII activity and antibody generation to the transgene. At week 2 post-injection, mice showed a range in hFVIII activity from 0.12-2.12 IU/ml. FVIII KO mice developed antibodies to hFVIII at week 4, and by week 8, mice in most of the 42 vector groups had detectable anti-hFVIII IgG levels. Based on the FVIII KO mouse studies and a small pilot rhesus macaque study, two of the original 42 enhancer/promoter combinations were selected for further evaluation in cynomolgus macaques, using two different Clade E capsids for expression. Each of the four vector combinations were administered IV at a dose of 1.2×1013 GC/kg into five macaques per group. With one capsid plus enhancer/promoter combination, peak expression of 37% of normal FVIII levels was seen at week 2 post-vector administration, which then plateaued at 20% of normal. While antibodies to the hFVIII were detected in the majority of macaques by week 8, antibodies remained undetectable in two animals at week 30 post-vector administration.
Maximum mutual information estimation of hidden Markov model parameters for speech recognition (2005)

A method for estimating the parameters of hidden Markov models of speech is described. Parameter values are chosen to maximize the mutual information between an acoustic observation sequence and the corresponding word sequence. Recognition results are presented comparing this method with maximum likelihood estimation.
Perfluorocarbons: Future Clinical Possibilities (1997)

Perfluorocarbons are now being used as oxygen carriers in clinical settings. Because these chemicals may have a role as a blood substitute, in organ preservation, and in the management of respiratory failure, we have reviewed some of the research leading to these applications.
Antiviral Effect of Brassinosteroids against Herpes Virus and Arenaviruses (2000)

A natural brassinosteroid and a series of synthetic derivatives were found to be good inhibitors of herpes simplex virus type 1 (HSV-1) and arenavirus replication in cell culture. The synthetic compounds tested were analogues of the 24(S) ethylbrassinone. Compounds (22 R,23 R,24S)-2alpha, 3alpha,5alpha,22,23-pentahydroxy-stigmastan-6-one and (22R,23R,24S)-3beta-bromo-5alpha,22,23-trihydroxy stigmastan-6-one were cytotoxic at concentrations of 20-40 microM. (22S,23S,24S)-2alpha,3alpha,22,23-tetrahydroxy-5alpha, stigmastan-6-one, (22R,23R,24S)-3beta-acetoxy-22,23-dihydroxy-5alpha-choles tan-6-one, (22S,23S,24S)-3beta-bromo-22,23-dihydroxy-5alpha-cholestan-6 -one and (22S,23S,24S)-3beta-bromo-5alpha,22,23-trihydroxy-stigmastan -6-one were the most active of the series against HSV-1, with selectivity index (SI) values (CC50/EC50) ranging from 10.6 to 16.5. The majority of the compounds were potent inhibitors of arenaviruses, (22S,23S,24S)-3beta-bromo-5alpha,22,23-trihydroxy-stigmastan -6-one being the most active, with SI values of 307.8 and 692.5 for Tacaribe and Junin viruses, respectively. The antiviral activity of brassinosteroid derivatives was not because of direct inactivation; time-of-addition experiments suggested that a late step in HSV-1 multiplication was affected, whereas arenaviruses remained susceptible to the compounds throughout the replicative cycle.
A new type of raspberry-like polymer composite sub-microspheres with tunable gold nanoparticles coverage and their enhanced catalytic properties (2012)

A new type of gold nanoparticles-coated composite spheres with chemically reactive poly(glycidyl methacrylate) colloids as cores is synthesized in raspberry-like fashion via a controlled assembly method. The surface coverage of the immobilized gold nanoparticles, which is controlled by the surface charge density of the poly(allylamine hydrochloride)-modified polymer spheres and the conformation of the adsorbed polyelectrolyte chains on the spheres, can be tuned with polyelectrolyte concentration, ratio of polymer spheres to gold nanoparticles, and the pH value of the solution. A double-conformation poly(allylamine hydrochloride) film structure: inner collapsed and outer extended, is proposed to explain how the polyelectrolyte concentration, ratio of polymer spheres to gold nanoparticles, and the pH value of the solution affect the adsorption amount of the gold nanoparticles on the modified polymer spheres. The obtained composite particles are stable without loss of the gold nanoparticle coatings even after applying ultrasonication, cleaning or long term nanopure water storage. These composites exhibit an excellent catalytic activity with an average turnover frequency of 250.5 mol mol−1 s−1 and the fastest reported reduction of 4-nitrophenol with sodium borohydride is achieved within 76 s.
Radionuclide Simultaneous Dual-Isotope Stress Myocardial Perfusion Study Using the ???Three Window Technique (1993)

Several methods are available for performing radionuclide stress myocardial perfusion studies. All of these methods require two separate acquisition and processing iterations, which is time-consuming and inconvenient for the patient. The authors introduce a new method using the "three window technique" that they developed to perform simultaneous dual-isotope imaging for stress myocardial perfusion studies. In addition to Tl-201 and Tc-99m windows centered at 70 KeV and 140 KeV, respectively, a third window centered at 105 KeV, representing scattered radioactivity from Tc-99m, is established. By subtracting the radioactivity in the third window from the radioactivity in the Tl-201 window, "crosstalk" interference is significantly reduced. The simultaneous dual-isotope imaging method acquires and processes resting and stress myocardial perfusion images simultaneously. It halves imaging time and doubles patient throughput, improves scheduling flexibility, and reduces patient waiting time and discomfort.
O- and S-Methyl Phosphotriester Oligonucleotides: Facile Synthesis Using N-Pent-4-enoyl Nucleoside Phosphoramidites (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTO- and S-Methyl Phosphotriester Oligonucleotides: Facile Synthesis Using N-Pent-4-enoyl Nucleoside PhosphoramiditesRadhakrishnan P. Iyer, Dong Yu, Nan-Hui Ho, Theresa Devlin, and Sudhir AgrawalCite this: J. Org. Chem. 1995, 60, 25, 8132–8133Publication Date (Print):December 1, 1995Publication History Published online1 May 2002Published inissue 1 December 1995https://pubs.acs.org/doi/10.1021/jo00130a008https://doi.org/10.1021/jo00130a008research-articleACS PublicationsRequest reuse permissionsArticle Views153Altmetric-Citations18LEARN 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 (2)»Supporting Information Supporting Information Get e-Alerts
EEL (1995)

EEL (Executable Editing Library) is a library for building tools to analyze and modify an executable (compiled) program. The systems and languages communities have built many tools for error detection, fault isolation, architecture translation, performance measurement, simulation, and optimization using this approach of modifying executables. Currently, however, tools of this sort are difficult and time-consuming to write and are usually closely tied to a particular machine and operating system. EEL supports a machine- and system-independent editing model that enables tool builders to modify an executable without being aware of the details of the underlying architecture or operating system or being concerned with the consequences of deleting instructions or adding foreign code.
MUC‐1 Epithelial Tumor Mucin‐Based Immunity and Cancer Vaccines (1995)

Many obstacles still stand in the way to eliciting an effective immune response against cancer, even though several antigens and antigenic peptides have been identified as potential tumor targets. All of them, including the MUC-1 mucin, share the caveat of being normal cellular proteins. Unlike all the others, however, MUC-1 expressed on tumors can still be considered a truly tumor-specific antigen. Its expression on normal cells is hidden from the immune system, and its aberrant glycosylation on tumors creates new epitopes recognized by the immune system. Moreover, all other tumor targets identified so far are MHC-restricted peptides that can only be recognized by patients who carry a specific HLA type, or on tumors which continue to express particular HLA alleles. MUC-1 is powerfully different. Recognized as a native molecule independent of MHC, it is a universal immunogen and a universal target, and if made effectively immunogenic, it would be expected to elicit immune responses in all patients, and against numerous MUC-1 expressing human tumors. It may, in fact, be the extraordinary solution to an extraordinary problem of cancer immunity and immunotherapy.
Persistence ofBacillus thuringiensisBerliner Insecticidal Activity on Cotton Foliage12 (1981)

Journal Article Persistence of Bacillus thuringiensis Berliner Insecticidal Activity on Cotton Foliage Get access Clayton C. Beegle, Clayton C. Beegle Cotlon Insects Research, Agricultural Research, Science and Education Administration, U.S. Department of Agriculture, Brownsville, Texas 78520 Search for other works by this author on: Oxford Academic PubMed Google Scholar Howard T. Dulmage, Howard T. Dulmage Cotlon Insects Research, Agricultural Research, Science and Education Administration, U.S. Department of Agriculture, Brownsville, Texas 78520 Search for other works by this author on: Oxford Academic PubMed Google Scholar Dan A. Wolfenbarger, Dan A. Wolfenbarger Cotlon Insects Research, Agricultural Research, Science and Education Administration, U.S. Department of Agriculture, Brownsville, Texas 78520 Search for other works by this author on: Oxford Academic PubMed Google Scholar Eduardo Martinez Eduardo Martinez Cotlon Insects Research, Agricultural Research, Science and Education Administration, U.S. Department of Agriculture, Brownsville, Texas 78520 Search for other works by this author on: Oxford Academic PubMed Google Scholar Environmental Entomology, Volume 10, Issue 3, 1 June 1981, Pages 400–401, https://doi.org/10.1093/ee/10.3.400 Published: 01 June 1981 Article history Received: 14 July 1980 Published: 01 June 1981
Estimates of integrated circuit yield components from in-line inspection data and post-process sort data (2002)

Increasing process complexity and shortening cycle times identification of defect traditional techniques such as post processing delayering are useful, such methodologies are somewhat tedious and not very amenable to statistical manipulation. A comprehensive yield management approach must utilize several pieces of information commonly available in fabs today such as end-of-process wafer sort data and in-process defect data from automated defect inspection equipment. With the help of such data the magnitude of yield loss accounted for by specific inspection steps and the relative culpability of the observed defects in causing faults are estimated. Aspects of the overlay coincidence methodology described here include partial die area inspected and multiple defects per die not covered elsewhere.