gebhart/patrepeval huggingface dataset:
The mannose‐specific lectins from ramsons (<i>Allium ursinum</i> L.) are encoded by three sets of genes (1993)

Lectin cDNA clones encoding the two mannose-binding lectins from ramsons (allium ursinum L.) bulbs, AUAI and AUAII (AUA, Allium ursinum agglutinin), were isolated and characterized. Sequence comparison of the different cDNA clones isolated revealed three types of lectin clones called LECAUAG0, LECAUAG1 and LECAUAG2, which besides the obvious differences in their sequences also differ from each other in the number of potential glycosylation sites within the C-terminal peptide of the lectin precursor. In vivo biosynthesis studies of the ramson lectins have shown that glycosylated lectin precursors occur in the organelle fraction of radioactively labeled ramson bulbs. Despite the similarities between the A. ursinum and the A. sativum (garlic) lectins at the protein level, molecular cloning of the two ramson lectins has shown that the lectin genes in A. ursinum are organized differently. Whereas in A. sativum the lectin polypeptides of the heterodimeric ASAI are encoded by one large precursor, those of the heterodimeric AUAI lectin are derived from two different precursors. These results are confirmed by Northern blot hybridization of A. ursinum RNA which, after hybridization with a labeled lectin cDNA, reveals only one band of 800 nucleotides in contrast to A. sativum RNA which yields two bands of 1400 and 800 nucleotides. Furthermore it is shown that the two mannose-binding lectins are differentially expressed.
Temperature and Trinexapac-Ethyl Effects on Bermudagrass Growth, Dormancy, and Freezing Tolerance (2002)

Applications of the plant growth regulator (PGR) trinexapac-ethyl [4-(cyclopropyl-α-hydroxymethylene)-3,5-dioxocyclohexane carboxylic acid ethylester] (TE) can delay winter dormancy in ‘Tifway’ bermudagrass (Cynodon dactylon var. dactylon), which suggests a response to TE when temperatures are suboptimum for bermudagrass growth. The purpose of this study was to investigate the interactive role of temperature and TE in bermudagrass growth responses, dormancy, and freezing tolerance. Trinexapac-ethyl (0.11 kg a.i. ha−1) was applied in two growth chamber experiments, and across a 2-yr period in the field. Results indicated that TE reduced vertical shoot growth and increased stolon production, turf density, and quality when applied at high temperatures (35–36°C). While TE effectively reduced vertical shoot growth at low (20–22°C) temperatures, little impact on stolon development was observed under these conditions. Autumn applications of TE when temperatures were cool (≈25°C) at the time of application led to decreased turfgrass density and quality. These responses may explain the effectiveness of using TE to aid in bermudagrass transition to overseeded cool-season grasses and were probably due to the limited ability of bermudagrass to recover from initial post-application growth reduction and observed leaf chlorosis. Observed delayed autumn dormancy due to summer applications of TE and accelerated dormancy due to late-season applications did not conclusively relate to the freezing tolerance of bermudagrass.
In silico CD4+, CD8+ T-cell and B-cell immunity associated immunogenic epitope prediction and HLA distribution analysis of Zika virus (2017)

Zika virus (ZIKV) is a mosquito-borne flavivirus distributed all over Africa, South America and Asia. The infection with the virus may cause acute febrile sickness that clinically resembles dengue fever, yet there is no vaccine, no satisfactory treatment, and no means of evaluating the risk of the disease or prognosis in the infected people. In the present study, the efficacy of the host's immune response in reducing the risk of infectious diseases was taken into account to carry out immuno-informatics driven epitope screening strategy of vaccine candidates against ZIKV. In this study, HLA distribution analysis was done to ensure the coverage of the vast majority of the population. Systematic screening of effective dominant immunogens was done with the help of Immune Epitope & ABCPred databases. The outcomes suggested that the predicted epitopes may be protective immunogens with highly conserved sequences and bear potential to induce both protective neutralizing antibodies, T & B cell responses. A total of 25 CD4+ and 16 CD8+ peptides were screened for T-cell mediated immunity. The predicted epitope "TGLDFSDLYYLTMNNKHWLV" was selected as a highly immunogenic epitope for humoral immunity. These peptides were further screened as non-toxic, immunogenic and non-mutated residues of envelop viral protein. The predicted epitope could work as suitable candidate(s) for peptide based vaccine development. Further, experimental validation of these epitopes is warranted to ensure the potential of B- and T-cells stimulation for their efficient use as vaccine candidates, and as diagnostic agents against ZIKV.
Cardiac and metabolic effects of hypothermia and inhaled hydrogen sulfide in anesthetized and ventilated mice* (2010)

In anesthetized and mechanically ventilated mice, inhaled hydrogen sulfide did not amplify the systemic hemodynamic and cardiac effects of hypothermia alone. The increased aerobic glucose oxidation together with the reduced responsiveness of cellular respiration to exogenous cytochrome-c stimulation suggest that, during hypothermia, inhaled hydrogen sulfide improved the yield of mitochondrial respiration, possibly via the maintenance of mitochondrial integrity. Hence, inhaled hydrogen sulfide may offer metabolic benefit during therapeutic hypothermia.
Synthesis of azacyclic compounds by an aminium radical route: orbital overlap requirements (1976)

Model compounds of Δ 4,5 -, Δ 5,6 -, and Δ 6,7 -alkenylnitrosamines were synthesized and photolyzed to generate the corresponding alkenylaminium radicals. The Δ 5,6 -alkenylaminium radicals underwent efficient intramolecular addition leading to the exclusive formation of pyrrolidine derivatives, the yield of which was lower if the steric strain and hindrance were severe in the cyclization transition state. The Δ 6,7 -alkenylaminium radical cyclized inefficiently to piperidine derivatives and the Δ 4,5 -alkenylaminium radicals did not appear to cyclize; in both cases other pathways having lower activation energies, such as elimination and hydrogen abstraction, predominated. Evidence that the direction of cyclization is controlled by the degree of p-orbital overlap, but not by stability of the developing products, in the transition state is presented. The stereochemical factors associated with the overlap determined the yields of the cyclization products. This is in excellent agreement with the fact that the transition state of cyclization is reached at an early stage in the reaction coordinate. Metal ion catalyzed or radical initiated decomposition of some alkenyl chloramines were found either to cyclize to a mixture of pyrrolidine and piperidine derivatives or to undergo no cyclization.
Abstract 3645: Low level somatic variant detection by Sanger sequencing of formalin-fixed paraffin-embedded (FFPE) samples (2016)

Abstract Deleterious sequence variants play an important role in the initiation and progression of many different cancer types. The detection of germline variants by the gold standard Sanger sequencing has been well established, however, the detection of somatic mutations, especially in heterogeneous tumor samples where variants may be present at a lower level, has been more challenging. To facilitate analysis of somatic mutations in tumor samples, we have developed Sanger sequencing panels that cover the entire coding regions of specific genes implicated in tumorigenesis (e.g. TP53, KRAS and NRAS). We have also developed companion software, Minor Variant Finder (MVF), that facilitates detection of low levels of somatic mutations in Sanger sequencing studies. To demonstrate the workflow of these panels with MVF, we analyzed DNA from lung cancer FFPE samples. We initially determined variants of TP53 and KRAS in these samples using Ion Torrent™ Personal Genome Machine (PGM™) next generation sequencing (NGS). We confirmed the identity and variant allele frequency of these variants by Sanger sequencing coupled with MVF. Furthermore, we were able to confirm these results in 1 ng, 0.5 ng or 0.1 ng of DNA from these samples. Finally, we made serial dilutions of one of these samples to establish limit of detection (LOD). We show that this workflow can detect as little as 3% of a minor variant in an FFPE sample. Sanger sequencing is the gold standard for confirmation of minor variants detected by NGS. In this study, we show that Sanger sequencing of limited number of targets, in conjunction with the MVF software, can also be an ideal first line screening choice for tumor FFPE samples where limited amount of DNA is available. For Research Use only - Not for use in diagnostic procedures. Citation Format: Arpad Gerstner, Edgar Schreiber, Stephen Jackson, Kamini Varma. Low level somatic variant detection by Sanger sequencing of formalin-fixed paraffin-embedded (FFPE) samples. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 3645.
Information technology governance by design: investigating hybrid configurations and integration mechanisms (2000)

This study aims to enrich and expand the conceptualization of IT governance by identifying the diversity of hybrid configurations and integration mechanisms and exploring the IT performance effects. While literature describes the prevailing configurations for formally allocating IT decision-making authority, previous studies have not addressed the complexity of hybrid configurations, the required integration mechanisms, and the associated performance effects. Building forth on organization theory, a conceptual framework is developed for conducting multiple comparative case study research in the financial services industry. The findings indicate that as companies experience increased uncertainty and complexity, and adopt multi-focused strategies, IT governance designs are more hybrid with increased coordination needs. A federal configuration for IT governance by itself is not related to improved IT performance. IT performance effectiveness is associated with both hybrid configuration and complex integration mechanisms. The implications for research and practice are discussed.
A functional high‐content miRNA screen identifies miR‐30 family to boost recombinant protein production in CHO cells (2014)

The steady improvement of mammalian cell factories for the production of biopharmaceuticals is a key challenge for the biotechnology community. Recently, small regulatory microRNAs (miRNAs) were identified as novel targets for optimizing Chinese hamster ovary (CHO) production cells as they do not add any translational burden to the cell while being capable of regulating entire physiological pathways. The aim of the present study was to elucidate miRNA function in a recombinant CHO-SEAP cell line by means of a genome-wide high-content miRNA screen. This screen revealed that out of the 1, 139 miRNAs examined, 21% of the miRNAs enhanced cell-specific SEAP productivity mainly resulting in elevated volumetric yields, while cell proliferation was accelerated by 5% of the miRNAs. Conversely, cell death was diminished by 13% (apoptosis) or 4% (necrosis) of all transfected miRNAs. Besides these large number of identified target miRNAs, the outcome of our studies suggest that the entire miR-30 family substantially improves bioprocess performance of CHO cells. Stable miR-30 over expressing cells outperformed parental cells by increasing SEAP productivity or maximum cell density of approximately twofold. Our results highlight the application of miRNAs as powerful tools for CHO cell engineering, identified the miR-30 family as a critical component of cell proliferation, and support the notion that miRNAs are powerful determinants of cell viability.
Structural and Functional Consequences of Antigenic Modulation of Red Blood Cells With Methoxypoly(Ethylene Glycol) (1999)

We previously showed that the covalent modification of the red blood cell (RBC) surface with methoxypoly(ethylene glycol) [mPEG; MW approximately 5 kD] could significantly attenuate the immunologic recognition of surface antigens. However, to make these antigenically silent RBC a clinically viable option, the mPEG-modified RBC must maintain normal cellular structure and functions. To this end, mPEG-derivatization was found to have no significant detrimental effects on RBC structure or function at concentrations that effectively blocked antigenic recognition of a variety of RBC antigens. Importantly, RBC lysis, morphology, and hemoglobin oxidation state were unaffected by mPEG-modification. Furthermore, as shown by functional studies of Band 3, a major site of modification, PEG-binding does not affect protein function, as evidenced by normal SO4- flux. Similarly, Na+ and K+ homeostasis were unaffected. The functional aspects of the mPEG-modified RBC were also maintained, as evidenced by normal oxygen binding and cellular deformability. Perhaps most importantly, mPEG-derivatized mouse RBC showed normal in vivo survival ( approximately 50 days) with no sensitization after repeated transfusions. These data further support the hypothesis that the covalent attachment of nonimmunogenic materials (eg, mPEG) to intact RBC may have significant application in transfusion medicine, especially for the chronically transfused and/or allosensitized patient.
Effects of Mobile-Phase Composition and Temperature on the Selectivity of Poly(<i>N</i>-isopropylacrylamide)-Bonded Silica Gel in Reversed-Phase Liquid Chromatography (1998)

We developed a simple preparation method for poly(N-isopropylacrylamide) (poly(NIPAM))-bonded silica using a water-organic two-phase system to directly copolymerize N-isopropylacrylamide with 3-(methacryloxy)propyl moieties on the silica surfaces. The stationary phase showed a phase transition with the change in temperature or in methanol content, resulting in notable changes in selectivity which cannot be expected with alkyl-type stationary phases. The packing material showed an increase in retention and column efficiency with the increase in temperature between 30 and 40 °C or in methanol content between 10 and 20%. The temperature-responsive properties were reduced with the increase in methanol content of the mobile phase and lost at 40% or higher. Significant changes in retention selectivity by the addition of methanol were observed for benzene derivatives below the transition temperature of poly(NIPAM). The preferential retention of hydrogen bond acceptors was observed at low temperatures in the mobile phase of low methanol content, while dominant contribution of the hydrophobic interaction to the retention of solutes was observed at the higher temperature in aqueous mobile phase or at the higher methanol concentration. The temperature increase brought about similar changes in retention behavior of the poly(NIPAM)-bonded silica packing materials to the addition of methanol to the mobile phase.
Enantioselective ester hydrolyses employing Rhizopus nigricans. A method of preparing and assigning the absolute stereochemistry of cyclic alcohols (1984)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTEnantioselective ester hydrolyses employing Rhizopus nigricans. A method of preparing and assigning the absolute stereochemistry of cyclic alcoholsMasaji Kasai, Kenichi Kawai, Mitsuru Imuta, and Herman ZifferCite this: J. Org. Chem. 1984, 49, 4, 675–679Publication Date (Print):February 1, 1984Publication History Published online1 May 2002Published inissue 1 February 1984https://pubs.acs.org/doi/10.1021/jo00178a020https://doi.org/10.1021/jo00178a020research-articleACS PublicationsRequest reuse permissionsArticle Views217Altmetric-Citations34LEARN 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
Development of Pneumatic Over-the-Wing Powered-Lift Technology Part II: Aeroacoustics (2009)

A current NASA project being conducted by Georgia Tech Research Institute (GTRI) and teammate California Polytechnic State University involves the development of pneumatic Circulation Control (CC) wings integrated with engines located over the wing (OTW) to improve the powered high-lift and cruise performance of Cruise Efficient STOL (CESTOL) aircraft. The emphasis of the aerodynamic/acoustic technology portion of this program is the development of an integrated system to provide very high lift when needed for STOL plus the interchange of high drag (low thrust recovery) for approach with high thrust recovery for takeoff and climb, all with a minimum of mechanical complexity. An equally important consideration for commercial transport aircraft is the noise associated with the powered-lift engines and the blown wings. A separate paper (Part I) focuses on the aerodynamic and propulsion integration issues. The present paper focuses on the acoustic issues associated with this integration (Part II). Several key design parameters are varied to understand their impact on far field noise. Key among these are the relative placement of the exhaust nozzle exit from the surface of the wing and its distance to the trailing edge. Results point towards two fundamental conclusions: 1) the efficacy of using the wing as a noise shield is largely dependent on the chord length. This is because the nature of jet noise is that the peak source location is some 5-7 jet diameters downstream of the nozzle exit; 2) the additional “scrubbing” noise source of a high speed jet in contact with a hard wall (the wing upper surface) is a significant noise source. Thus, placing the engine on a pylon some distance above the wing surface is preferable to the so-called highly integrated D-nozzle design. Placing the engine off the wing is also consistent with good cruise performance, however it runs counter to good take-off and approach design performance for powered-lift configurations.
Capacitance Super Multiplier for Sub-Hertz Low-Pass Integrated Filters (2017)

This brief addresses the design of tunable integrated low-pass filters for sub-Hertz frequencies. The required very large time constants are obtained by using the transconductance of MOS transistors with extremely low bias current and integrated capacitors whose value is augmented by a novel super multiplier circuit. Simulations at the transistor level using a 65-nm CMOS technology verify the effectiveness of the proposed techniques. It is shown that cut-off frequencies of 0.3 Hz require about 150 nA and 7 pF per single pole.
Code Division Multiple Access (2010)

An alternative to frequency division and time division multiple access schemes is provided by code division multiple access (CDMA), which permits multiple users to transmit simultaneously over a channel while occupying the same frequency band. This is effected by assigning a unique code or signature to each user. As we will see, CDMA offers several advantages. Various schemes have been devised to generate the codes; this chapter will introduce the fundamentals of direct-sequence spread spectrum CDMA (DS-CDMA).
Effects of Nicotine Patch vs Varenicline vs Combination Nicotine Replacement Therapy on Smoking Cessation at 26 Weeks (2016)

<h3>Importance</h3> Smoking cessation medications are routinely used in health care; it is vital to identify medications that most effectively treat this leading cause of preventable mortality. <h3>Objective</h3> To compare the efficacies of varenicline, combination nicotine replacement therapy (C-NRT), and the nicotine patch for 26-week quit rates. <h3>Design, Setting, and Participants</h3> Three-group randomized intention-to-treat clinical trial occurring from May 2012 to November 2015 among smokers recruited in the Madison, Wisconsin, and Milwaukee, Wisconsin, communities; 65.5% of smokers offered the study (2687/4102) refused participation prior to randomization. <h3>Interventions</h3> Participants were randomized to one of three 12-week open-label smoking cessation pharmacotherapy groups: (1) nicotine patch only (n = 241); (2) varenicline only (including 1 prequit week; n = 424); and (3) C-NRT (nicotine patch + nicotine lozenge; n = 421). Six counseling sessions were offered. <h3>Main Outcomes and Measures</h3> The primary outcome was carbon monoxide–confirmed self-reported 7-day point-prevalence abstinence at 26 weeks. Secondary outcomes were carbon monoxide–confirmed self-reported initial abstinence, prolonged abstinence at 26 weeks, and point-prevalence abstinence at weeks 4, 12, and 52. <h3>Results</h3> Among 1086 smokers randomized (52% women; 67% white; mean age, 48 years; mean of 17 cigarettes smoked per day), 917 (84%) provided 12-month follow-up data. Treatments did not differ on any abstinence outcome measure at 26 or 52 weeks, including point-prevalence abstinence at 26 weeks (nicotine patch, 22.8% [55/241]; varenicline, 23.6% [100/424]; and C-NRT, 26.8% [113/421]) or at 52 weeks (nicotine patch, 20.8% [50/241]; varenicline, 19.1% [81/424]; and C-NRT, 20.2% [85/421]). At 26 weeks, the risk differences for abstinence were, for patch vs varenicline, −0.76% (95% CI, −7.4% to 5.9%); for patch vs C-NRT, −4.0% (95% CI, −10.8% to 2.8%); and for varenicline vs C-NRT, −3.3% (95% CI, −9.1% to 2.6%). All medications were well tolerated, but varenicline produced more frequent adverse events than did the nicotine patch for vivid dreams, insomnia, nausea, constipation, sleepiness, and indigestion. <h3>Conclusions and Relevance</h3> Among adults motivated to quit smoking, 12 weeks of open-label treatment with nicotine patch, varenicline, or C-NRT produced no significant differences in biochemically confirmed rates of smoking abstinence at 26 weeks. The results raise questions about the relative effectiveness of intense smoking pharmacotherapies. <h3>Trial Registration</h3> clinicaltrials.gov Identifier:NCT01553084