gebhart/patrepeval huggingface dataset:
Automated Finishing with Autofinish (2001)

Currently, the genome sequencing community is producing shotgun sequence data at a very high rate, but finishing (collecting additional directed sequence data to close gaps and improve the quality of the data) is not matching that rate. One reason for the difference is that shotgun sequencing is highly automated but finishing is not: Most finishing decisions, such as which directed reads to obtain and which specialized sequencing techniques to use, are made by people. If finishing rates are to increase to match shotgun sequencing rates, most finishing decisions also must be automated. The Autofinish computer program (which is part of the computer software package) does this by automatically choosing finishing reads. Autofinish is able to suggest most finishing reads required for completion of each sequencing project, greatly reducing the amount of human attention needed. sometimes completely finishes the project, with no human decisions required. It cannot solve the most complex problems, so we recommend that Autofinish be allowed to suggest reads for the first three rounds of finishing, and if the project still is not finished completely, a human finisher complete the work. We compared this Autofinish-Hybrid method of finishing against a human finisher in five different projects with a variety of shotgun depths by finishing each project twice--once with each method. This comparison shows that the Autofinish-Hybrid method saves many hours over a human finisher alone, while using roughly the same number and type of reads and closing gaps at roughly the same rate. Autofinish currently is in production use at several large sequencing centers. It is designed to be adaptable to the finishing strategy of the lab--it can finish using some or all of the following: resequencing reads, reverses, custom primer walks on either subclone templates or whole clone templates, PCR, or minilibraries. Autofinish has been used for finishing cDNA, genomic clones, and whole bacterial genomes (see http://www.phrap.org).
Identification and purification from bovine brain of a guanine-nucleotide-binding protein distinct from Gs, Gi and Go (1987)

A guanine-nucleotide-binding protein (G-protein) was purified from cholate extracts of bovine brain membranes by sequential DEAE-Sephacel, Ultrogel AcA-34, heptylamine-Sepharose and Sephadex G-150 chromatography. Guanosine 5'-[gamma-[35S]thio]triphosphate (GTP[35S])-binding activity copurified with a 25,000 Da peptide and a 35,000-36,000 Da protein doublet. Neither pertussis toxin nor cholera toxin catalysed the ADP-ribosylation of a protein associated with the GTP[35S]-binding activity. Photoaffinity labelling of the purified protein with 8-azido[gamma-32P]GTP indicated that the GTP-binding site resides on the 25,000 Da protein. The 35,000-36,000 Da protein doublet was electrophoretically indistinguishable from the beta-subunits of other GTP-binding proteins, and the 36,000 Da protein was recognized by antiserum to oligomeric Gt. The purified protein specifically bound 17.2 nmol of GTP[35S]/mg of protein. The Kd of the binding site for radioligand was approx. 15 nM. The brain GTP-binding protein co-migrated during SDS/polyacrylamide-gel electrophoresis with a GTP-binding protein, named Gp, purified from human placenta [Evans, Brown, Fraser & Northup (1986) J. Biol. Chem. 261, 7052-7059], and cross-reacted with antiserum raised against the placental protein, but not with antiserum raised to brain Go. SDS/polyacrylamide-gel electrophoresis of the brain and placental GTP-binding proteins in the presence of Staphylococcus aureus V8 protease yielded identical peptide maps.
Passive Cutaneous Anaphylaxis with Antibody Fragments (1963)

Pepsin-digested rabbit antibody (5S) provoked reverse passive cutaneous anaphylaxis in the guinea pig, but was somewhat less effective, mole for mole, than the native antibody. Fixation of guinea pig complement by the pepsin-digested antibody could not be demonstrated either in vitro or in vivo. Splitting of the 5S fragment into two monovalent fragments (3.5S) markedly reduced the capacity to provoke reverse passive cutaneous anaphylaxis.
Efficient expression of protein coding genes from the murine U1 small nuclear RNA promoters. (1996)

Few promoters are active at high levels in all cells. Of these, the majority encode structural RNAs transcribed by RNA polymerases I or III and are not accessible for the expression of proteins. An exception are the small nuclear RNAs (snRNAs) transcribed by RNA polymerase II. Although snRNA biosynthesis is unique and thought not to be compatible with synthesis of functional mRNA, we have tested these promoters for their ability to express functional mRNAs. We have used the murine U1a and U1b snRNA gene promoters to express the Escherichia coli lacZ gene and the human alpha-globin gene from either episomal or integrated templates by transfection, or infection into a variety of mammalian cell types. Equivalent expression of beta-galactosidase was obtained from < 250 nucleotides of 5'-flanking sequence containing the complete promoter of either U1 snRNA gene or from the 750-nt cytomegalovirus promoter and enhancer regions. The mRNA was accurately initiated at the U1 start site, efficiently spliced and polyadenylylated, and localized to polyribosomes. Recombinant adenovirus containing the U1b-lacZ chimeric gene transduced and expressed beta-galactosidase efficiently in human 293 cells and airway epithelial cells in culture. Viral vectors containing U1 snRNA promoters may be an attractive alternative to vectors containing viral promoters for persistent high-level expression of therapeutic genes or proteins.
Differences of molecular expression mechanisms among neural cell adhesion molecule 1, synaptophysin, and chromogranin A in lung cancer cells (2012)

Neural cell adhesion molecule 1 (NCAM1), synaptophysin (SYPT), and chromogranin A (CGA) are immunohistochemical markers for diagnosing lung neuroendocrine tumors (LNETs). However, the precise expression mechanisms have not been studied in enough detail. The purpose of the present study is to define the molecular mechanisms of NCAM1, SYPT, and CGA gene expressions, using cultivated lung cancer cells and focusing upon NeuroD1 (ND1), achaete-scute homolog-like 1 (ASCL1), and known transcription factors, repressor element 1 (RE1)-silencing transcription factor (REST) and c-AMP responsive element-binding protein (CREB). Promoter assays, chromatin immunoprecipitation, and transfection experiments revealed that ND1 activated NCAM1, that ASCL1 weakly upregulated SYPT expression, and that CGA expression was not regulated by ND1 or ASCL1. REST expression was restricted in non-small cell lung cancer (NSCLC) cells, and knockdown of REST could cause as much SYPT expression as in SCLC cells and weak CGA expression in NSCLC cells. However, CGA gene upregulation via CREB activation was not found in REST-lacking NSCLC cells, indicating the requirement of some additional mechanism for sufficient expression. These results suggest that NCAM1, SYPT and CGA expressions are differently regulated by neuroendocrine phenotype-specific transcription factors and provide a reason why NCAM1 and SYPT are frequently expressed in LNETs, irrespective of malignancy grade.
Characterization of space-time focusing in time-reversed random fields (2005)

This paper proposes various metrics to characterize space-time focusing resulting from application of time reversal techniques in richly scattering media. The concept and goals of time reversal are presented. Pertinent metrics describing both the time and space focusing effects are outlined. Two examples based on a model of discrete and continuous scattering media are used to illustrate how the proposed metrics vary as a function of various system and channel parameters, such as the bandwidth, delay and angle spreads, number of antennas, etc.
On the Design of Optical Systems with an Aspheric Surface (1961)

This short article is concerned with the problem of designing a correcting aspherical surface which is situated in an arbitrary position within an optical system. The method requires the solution of two first-order differential equations and seems more suitable for the use with an electronic computer than methods previously proposed by other authors. It can be considered as a differential form of a method previously proposed by E. Wolf.
Light Scattering Study of Semidilute Aqueous Systems of Chitosan and Hydrophobically Modified Chitosans (1998)

Intensity (ILS) and dynamic light scattering (DLS) experiments were performed on semidilute acid aqueous solutions of unmodified chitosan (UM-chitosan) and of hydrophobically modified chitosan (HM-chitosan) with two different degrees of C12-aldehyde substitution. Both the ILS and the DLS measurements suggest the formation of association structures. According to the ILS measurements in the range qξ > 1 (q is the wave vector and ξ is the correlation length), all the systems have a fractal structure and the fractal dimension is about 2. The time correlation data obtained from the DLS experiments revealed, for all systems, the existence of two relaxation modes, one single exponential at short times followed by a stretched exponential at longer times. The value of the slow relaxation time increases with increasing concentration and hydrophobicity. This behavior reflects the importance of intermolecular associations and hydrophobic interactions. The reduced slow relaxation time exhibits a weak temperature dependence for both UM-chitosan and HM-chitosans. The fast mode is always diffusive, while the slow mode shows an approximately q3 dependence at low concentrations and a q2 dependence, characteristic of diffusion, at higher concentrations.
Inactivation of Escherichia coli outer‐membrane phospholipase A by the affinity label hexadecanesulfonyl fluoride (1991)

The Escherichia coli outer-membrane phospholipase A (OM PLA) is a membrane-bound acyl hydrolase with a broad substrate specificity. In order to obtain more insight into the mechanism of action of this enzyme, we designed an active-site-directed inhibitor for OM PLA on the basis of the known substrate specificity as a first step in the elucidation of the catalytic mechanism of this enzyme. The inhibitor, hexadecanesulfonyl fluoride, consists of a long hydrocarbon chain for high-affinity binding by the enzyme and a sulfonyl fluoride moiety as a reactive group. The kinetics of the inactivation of OM PLA by hexadecanesulfonyl fluoride were studied in Triton X-100 micelles. Inactivation is very fast, specific and shows the same characteristics with respect to acyl specificity, pH profile and metal ion requirement as the activity of OM PLA on substrates. Incubation of OM PLA with a stoichiometric amount of hexadecanesulfonyl fluoride leads to a total and irreversible loss of enzyme activity, resulting from the sulfonylation of Ser144. This Ser144, which we suggest to be the active-site serine of OM PLA, is part of the sequence HDSNG, whereas in the water-soluble serine proteases and lipases the structural motif GXSXG is normally encountered. On the basis of the kinetics of inactivation of OM PLA by hexadecanesulfonyl fluoride, we discuss a possible catalytic mechanism of the enzyme.
Pharmacokinetics and pharmacodynamics of testosterone enanthate and dihydrotestosterone enanthate in non-human primates (1990)

The pharmacokinetics and pharmacodynamics of testosterone enanthate and dihydrotestosterone-enanthate were compared in orchidectomized cynomolgus monkeys (Macaca fascicularis) and in intact GnRH agonist-suppressed rhesus monkeys (Macaca mulatta). Following a single im injection of 32.8 mg testosterone enanthate or 32.7 mg dihydrotestosterone-enanthate, i.e. 23.6 mg of pure steroid, in the orchidectomized cynomolgus monkeys, serum testosterone and dihydrotestosterone levels rose to 400 and 800% of baseline, respectively, within 24 h. Androgen levels remained in that range for 3-5 days followed by a continuous decline until baseline values were attained after 4-5 weeks. The areas under the testosterone- and dihydrotestosterone-curves did not differ significantly 2290 +/- 340 (dihydrotestosterone-enanthate) vs 2920 +/- 485 (testosterone-enanthate) suggesting that similar amounts of steroid had been released from the respective ester preparation. Mean half-life estimates of the terminal elimination phase were 4 and 7 days for testosterone-enanthate and dihydrotestosterone-enanthate, respectively. In a second experiment rhesus monkeys received, at 4-weekly intervals, sc implantation of a biodegradable polylactic:polyglycolide rod loaded with the GnRH agonist buserelin. The last injection was given during week 20. GnRH agonist treatment suppressed serum bioactive LH, testosterone and dihydrotestosterone levels, testicular size, sperm production, and seminal carnitine content. The ejaculatory response to electrostimulation and the masturbatory behaviour were abolished. Testosterone or dihydrotestosterone injections at the same doses as above were given in week 10, 14, 17 and 20 of GnRH agonist treatment. Serum testosterone and dihydrotestosterone levels were stimulated 9- and 4-fold, respectively. Mean half-life estimates for testosterone-enanthate and dihydrotestosterone were 5 and 7 days, respectively. Both ester preparations completely restored the ejaculatory response, ejaculate size, masturbatory behaviour, and seminal carnitine levels. In conclusion, androgen substitution with dihydrotestosterone-enanthate, in equivalent doses, is as effective as testosterone-enanthate in restoring reproductive functions in hypogonadal monkeys.
Vinyl-Functionalized Poly(imidazolium)s: A Curable Polymer Platform for Cross-Linked Ionic Liquid Gel Synthesis (2014)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTVinyl-Functionalized Poly(imidazolium)s: A Curable Polymer Platform for Cross-Linked Ionic Liquid Gel SynthesisTrevor K. Carlisle, William M. McDanel, Matthew G. Cowan, Richard D. Noble*, and Douglas L. Gin*View Author Information Department of Chemical and Biological Engineering, University of Colorado, Boulder, Colorado 80309, United States*E-mail: [email protected] (R.D.N.).*E-mail: [email protected] (D.L.G.).Cite this: Chem. Mater. 2014, 26, 3, 1294–1296Publication Date (Web):January 22, 2014Publication History Received24 November 2013Revised12 January 2014Published online22 January 2014Published inissue 11 February 2014https://pubs.acs.org/doi/10.1021/cm403885rhttps://doi.org/10.1021/cm403885rrapid-communicationACS PublicationsCopyright © 2014 American Chemical SocietyRequest reuse permissionsArticle Views2853Altmetric-Citations42LEARN 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:Membranes,Monomers,Nucleic acid structure,Polymer films,Polymers Get e-Alerts
Semantic similarity between search engine queries using temporal correlation (2005)

We investigate the idea of finding semantically related search engine queries based on their temporal correlation; in other words, we infer that two queries are related if their popularities behave similarly over time. To this end, we first define a new measure of the temporal correlation of two queries based on the correlation coefficient of their frequency functions. We then conduct extensive experiments using our measure on two massive query streams from the MSN search engine, revealing that this technique can discover a wide range of semantically similar queries. Finally, we develop a method of efficiently finding the highest correlated queries for a given input query using far less space and time than the naive approach, making real-time implementation possible.
Bioavailability of two new formulations of paracetamol, comparedwith three marketed formulations, in healthy volunteers (2003)

The aim of this study was to compare the main pharmacokinetic characteristics of two new paracetamol formulations, powder sachet and tablet, with that of three commercially available paracetamol formulations: two conventional solid tablets and one effervescent tablet. Twelve healthy volunteers participated in an open, single dose (paracetamol 1,000 mg), randomized, five-way, crossover study. Formulations studied included: formulation A: 2 x 500 mg paracetamol tablets (Laboratorios Belmac S.A.); formulation B: 1 x 1,000 mg paracetamol powder sachets (Laboratorios Belmac, S.A.); formulation C: 2 x 500 mg paracetamol film-coated tablets (Panadol, SmithKline Beecham); formulation D: 2 x 500 mg paracetamol tablets (Tylenol, McNeil); and formulation E: 1 x 1,000 mg effervescent paracetamol tablets (Efferalgan, UPSA). The primary variables were area under the plasma concentration time curve extrapolated to infinity (AUC(0-infinity)), maximum plasma concentration (Cmax), and time to maximum plasma concentration (tmax). Mean AUC(0-infinity) ranged from 52.6 (B) to 56.3 microg x h/ml (D); mean Cmax varied between 17.98 (C) and 20.73 microg/ml (E); mean tmax ranged from 0.40 (E) to 0.88 h (C); and median t(1/2) varied between 2.65 (C) and 2.81 h (A). Formulations A, B and E showed significantly shorter tmax than formulation C. The tmax and Cmax values found for formulations A and B were very similar to that found for E, an effervescent tablet formulation. In conclusion, the two new formulations of paracetamol tested in this study were absorbed rapidly after a single oral dose in healthy volunteers, similar to an effervescent paracetamol formulation and significantly faster than two ordinary commercialized paracetamol tablets.
Defibrotide as a possible anti-ischemic drug. (1996)

Defibrotide is a polydeoxyribonucleotide extracted from mammalian organs (porcine) and prepared by controlled depolymerization, resulting in a single-stranded deoxyribonucleotide with a mean molecular weight of 15 to 30 kDa. Early studies of experimental pharmacology in different animal species (1981-1986) were focused on an antithrombotic effect in arteries, veins, and the microcirculation, attributed to a dose-dependent activation of fibrinolysis. More recently, a number of new data have raised interest in an "anti-ischemic" action of the substance, as suggested by its evident protective effect in different models of tissue and organ ischemia. Protection from myocardial ischemia was demonstrated in different experimental models, and several ischemic features, such as heart muscle contracture, loss of high-energy substrates, decline in beta-adrenergic receptor sensitivity, and drop in infarct-related blood flow, were successfully prevented. Similar protective effects were observed during liver and kidney ischemia and in different types of experimental shock. The mechanisms involved in the anti-ischemic properties of defibrotide have been investigated in studies of experimental and human pharmacology. The substance has been shown to modulate arachidonic acid metabolism by enhancing the production and release of prostacyclin and prostaglandin E2 from tissues and whole blood, and inhibiting leukotriene B4 generation in leukocytes. Furthermore, an effect of defibrotide on activation of polymorphonuclear leukocytes and their incorporation into thrombi was described. Favorable effects on blood rheology were also reported. In summary, defibrotide deserves attention for therapeutic trials in clinical conditions characterized by organ or tissue ischemia.
Bioceramics: From Concept to Clinic (1991)

Ceramics used for the repair and reconstruction of diseased or damaged parts of the musculo‐skeletal system, termed bioceramics, may be bioinert (alumina, zirconia), resorbable (tricalcium phosphate), bioactive (hydroxyapatite, bioactive glasses, and glass‐ceramics), or porous for tissue ingrowth (hydroxyapatite‐coated metals, alumina). Applications include replacements for hips, knees, teeth, tendons, and ligaments and repair for periodontal disease, maxillofacial reconstruction, augmentation and stabilization of the jaw bone, spinal fusion, and bone fillers after tumor surgery. Carbon coatings are thromboresistant and are used for prosthetic heart valves. The mechanisms of tissue bonding to bioactive ceramics are beginning to be understood, which can result in the molecular design of bioceramics for interfacial bonding with hard and soft tissues. Composites are being developed with high toughness and elastic modulus match with bone. Therapeutic treatment of cancer has been achieved by localized delivery of radioactive isotopes via glass beads. Development of standard test methods for prediction of long‐term (20‐year) mechanical reliability under load is still needed.
寻找茱丽叶 AUDI S5 (2007)

爱,也分了很多种:亲人爱、朋友爱、情人爱……我们在各自的角色中扮演好自己便可以更接近幸福的彼岸,当然走到爱的节点,看到凝聚爱的仙境便可以有更深感受。人们在这里寻找到一种爱的精神,对爱的向往、对爱的恪守,这就足够了。文人余秋雨先生所说的这里,我也终于有幸驾临,这就是意大利爱情圣地维罗纳,德国车厂AUDI在这里带给我一次有关现代爱情的另类诠释。
A phase II study of DT fusion protein denileukin diftitox in patients with fludarabine-refractory chronic lymphocytic leukemia. (2003)

DAB(389)IL2 produced a rapid decrease of leukemic cells in the bone marrow and peripheral blood of most chemotherapy refractory CLL patients. Most patients also tolerated DAB(389)IL2 well, without significant myelosuppression and/or immunosuppression. The prolonged progression-free interval and subjectively observed quality-of-life in responders is intriguing. The results suggest DAB(389)IL2 has biological activity in patients with B-cell CLL. Follow-up studies of combinations or altered schedules or doses to improve the response rate are warranted.
Crystal field, phonon coupling and emission shift of Mn2+ in ZnS:Mn nanoparticles (2001)

The Mn2+ emission wavelengths are at 591, 588, 581 and 570 nm, respectively, for the ∼10, ∼4.5, ∼3.5 nm sized nanoparticles and the ZnS:Mn nanoparticles formed in an ultrastable zeolite-Y. To reveal the cause for the shift, the crystal field and phonon coupling were investigated. The results show that the predominant factor for the shift is the phonon coupling, whose strength is size dependent and is determined by both the size confinement and the surface modification of the nanoparticles. Although the crystal field strength decreases with the decreasing of the particle size, its change has little contribution to the emission shift of Mn2+ in ZnS:Mn nanoparticles.