gebhart/patrepeval huggingface dataset:
The <i>Arabidopsis</i> CORONATINE INSENSITIVE1 Protein Is a Jasmonate Receptor  (2009)

Jasmonates play a number of diverse roles in plant defense and development. CORONATINE INSENSITIVE1 (COI1), an F-box protein essential for all the jasmonate responses, interacts with multiple proteins to form the SCF(COI1) E3 ubiquitin ligase complex and recruits jasmonate ZIM-domain (JAZ) proteins for degradation by the 26S proteasome. To determine which protein directly binds to jasmonoyl-isoleucine (JA-Ile)/coronatine (COR) and serves as a receptor for jasmonate, we built a high-quality structural model of COI1 and performed molecular modeling of COI1-jasmonate interactions. Our results imply that COI1 has the structural traits for binding JA-Ile or COR. The direct binding of these molecules with COI1 was further examined using a combination of molecular and biochemical approaches. First, we used the immobilized jasmonate approach to show that the COI1 protein in crude leaf extracts can bind to the jasmonate moiety of JA-Ile. Second, we employed surface plasmon resonance technology with purified COI1 and JAZ1 protein to reveal the interaction among COI1, JA-Ile, and JAZ1. Finally, we used the photoaffinity labeling technology to show the direct binding of COR with purified insect-expressed COI1. Taken together, these results demonstrate that COI1 directly binds to JA-Ile and COR and serves as a receptor for jasmonate.
Low-Molecular-Weight Heparin versus a Coumarin for the Prevention of Recurrent Venous Thromboembolism in Patients with Cancer (2003)

In patients with cancer and acute venous thromboembolism, dalteparin was more effective than an oral anticoagulant in reducing the risk of recurrent thromboembolism without increasing the risk of bleeding.
Replicative cultures of adult human and rhesus monkey liver epithelial cells. (1989)

Exploratory experiments indicate that media containing lipids, phosphoethanolamine, epidermal growth factor, insulin, cholera toxin, bovine pituitary extract, chemically denatured serum, and triiodothyronine will support replicative cultures of normal liver epithelial cells obtained from adult Rhesus monkey and human donors. In addition, we have extended the culture population doubling potential of the human liver epithelial cells by their transfection with a plasmid containing the SV40 virus T-antigen gene. The T-antigen gene-containing cells continued to express albumin through 40 population doublings. Finally, results of preliminary experiments suggest that it may be possible to induce human liver epithelial cells to undergo differentiation to hepatocyte-like cells either by injecting them into the spleen of an athymic nude mouse or by incorporating them into a collagen "tissue equivalent" matrix.
Status of rod consolidation (1985)

Two of the factors that need to be taken into account with rod consolidation are (1) the effects on rods from their removal from the fuel assembly and (2) the effects on rods as a result of the consolidation process. Potential components of both factors are described in the report. Discussed under (1) are scratches on the fuel rod surfaces, rod breakage, crud, extended burnup, and possible cladding embrittlement due to hydrogen injection at BWRs. Discussed under (2) are the increased water temperature (less than 10/sup 0/C) because of closer packing of the rods, formation of crevices between rods in the close-packed mode, contact with dissimilar metals, and the potential for rapid heating of fuel rods following the loss of water from a spent fuel storage pool. Another factor that plays an important role in rod consolidation is the cost of disposal of the nonfuel-bearing components of the fuel assembly. Also, the dose rate from the components - especially Inconel spacer grids - can affect the handling procedures. Several licensing issues that exist are described. A list of recommendations is provided. 98 refs., 5 figs., 5 tabs.
Model-based tests of truisms (2002)

Software engineering (SE) truisms capture broadly-applicable principles of software construction. The trouble with truisms is that such general principles may not apply in specific cases. This paper tests the specificity of two SE truisms: (a) increasing software process level is a desirable goal; and (b) it is best to remove errors during the early parts of a software lifecycle. Our tests are based on two well-established SE models: (1) Boehm et.al.'s COCOMO II cost estimation model; and (2) Raffo's discrete event software process model of a software project life cycle. After extensive simulations of these models, the TAR2 treatment learner was applied to find the model parameters that most improved the potential performance of the real-world systems being modelled. The case studies presented here showed that these truisms are clearly sub-optimal for certain projects since other factors proved to be far more critical. Hence, we advise against truism-based process improvement. This paper offers a general alternative framework for model-based assessment of methods to improve software quality: modelling + validation + simulation + sensitivity. That is, after recording what is known in a model, that model should be validated, explored using simulations, then summarized to find the key factors that most improve model behavior.
Investigations of Coronatine Biosynthesis. Elucidation of the Mode of Incorporation of Pyruvate into Coronafacic Acid (1996)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTInvestigations of Coronatine Biosynthesis. Elucidation of the Mode of Incorporation of Pyruvate into Coronafacic AcidRonald J. Parry, Sao Jiralerspong, Sunil Mhaskar, Lawrence Alemany, and Robert WillcottView Author Information Department of Chemistry, Wiess School of Natural Sciences Rice University, Houston, Texas 77251 University of Texas, Medical Branch Galveston, Texas 77550Cite this: J. Am. Chem. Soc. 1996, 118, 3, 703–704Publication Date (Web):January 24, 1996Publication History Received30 October 1995Published online24 January 1996Published inissue 1 January 1996https://pubs.acs.org/doi/10.1021/ja9536330https://doi.org/10.1021/ja9536330rapid-communicationACS PublicationsCopyright © 1996 American Chemical SocietyRequest reuse permissionsArticle Views295Altmetric-Citations23LEARN 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 SUBJECTS:Alkyls,Carbon,Coupling reactions,Organic compounds,Precursors Get e-Alerts
Prefusion Rearrangements Resulting in Fusion Peptide Exposure in Semliki Forest Virus (2003)

Semliki Forest virus (SFV), like many enveloped viruses, takes advantage of the low pH in the endosome to convert into a fusion-competent configuration and complete infection by fusion with the endosomal membrane. Unlike influenza virus, carrying an N-terminal fusion peptide, SFV represents a less-well understood fusion principle involving an endosequence fusion peptide. To explore the series of events leading to a fusogenic configuration of the SFV, we exposed the virus to successive acidification, mimicking endosomal conditions, and followed structural rearrangements at probed sensor surfaces. Thus revealed, the initial phase involves a transient appearance of a non-linear neutralizing antibody epitope in the fusion protein, E1. Concurrent with the disappearance of this epitope, a set of masked sequences in proteins E1 and E2 became exposed. When pH reached 6.0-5.9 the virion transformed into a configuration of enlarged diameter with the fusion peptide optimally exposed. Simultaneously, a partly hidden sequence close to the receptor binding site in E2 became fully uncovered. At this presumably fusogenic stage, maximally 80 fusion peptide-identifying antibody Fab fragments could be bound per virion, i.e. one ligand per three copies of the fusion protein. The phenomena observed are discussed in terms of alphavirus structure and reported functional domains.
Keratinocyte Gene Transfer and Gene Therapy (1996)

Gene therapy has moved beyond the pre-clinical stage to the treatment of a variety of inherited and acquired diseases. For such therapy to be successful, genes must be efficiently delivered to target cells and gene products must be expressed for prolonged periods of time without toxic effects to the host. This may be achieved by means of an in vivo strategy where genes are transferred directly into a host cell, or by means of an ex vivo approach through which cells are removed, cultured, targeted for gene delivery, and grafted back to the host. Several obstacles continue to delay safe and effective clinical application of gene therapy in a variety of target cells. The limited survival of transplanted cells, transient expression of transferred genes, and difficulties in targeting stem cells are technical issues requiring further investigation. Epidermal and oral keratinocytes are potential vehicles for gene therapy. Several features of these tissues can be utilized to achieve delivery of therapeutic gene products for local or systemic delivery. These qualities include: (1) the presence of stem cells; (2) the cell-, strata-, and site-specific regulation of keratinocyte gene expression; (3) tissue accessibility; and (4) secretory capacity. Such features can be exploited by the use of gene therapy strategies to facilitate: (1) identification, enrichment, and targeting of stem cells to ensure the continued presence of the transferred gene; (2) high-level and persistent transgene expression using keratinocyte-specific promoters; (3) tissue access needed for culture and grafting for ex vivo therapy and direct in vivo gene transfer; (4) secretion of transgene product for local or systemic delivery; and (5) monitoring of genetically modified tissue and removal if treatment termination is required. Optimal gene therapy strategies are being tested in a variety of tissues to treat dominant and recessive genetic disorders as well as acquired diseases such as neoplasia and infectious disease. This experience provides a basis for the application of such clinical studies to a spectrum of diseases effecting epidermal and oral keratinocytes. Gene therapy is in an early stage yet holds great promise for its ultimate clinical application.
Synthesis and research of the optimum conditions for the optical monitoring of non-quarter-wave multilayers (1993)

Many optical filtering problems require the use of assemblies of layers with thicknesses that bear no obvious relationship to each other. Here we present the results obtained for a number of examples in which optical monitoring is performed with a change of control wavelengths for each layer of the stack. For this, it is necessary to determine for each layer the different wavelengths that provide an extremum of transmittance when the required thickness is achieved. We show that this leads, in some cases, to making the benefit of error compensation analogous to the well-known method used in the production of quarter-wave stacks. Because ion-assisted deposition and ion-plating techniques are suitable from the point of view of refractive-index reproducibility, optical monitoring can be used at a good level of performance. However, the production of high-quality optical thin films needs more than just the choice of a monitoring process. In particular, problems of uniformity are critical for high-performance coatings. Here we show how uniformity can be determined for each material involved.
Using electrical resistance to evaluate the chip seal curing process (2017)

Chip seals are among the most cost-effective surface treatments available for pavement preventive maintenance. However, frequent issues associated with asphalt emulsion early mechanical strength development, resulting in premature surface treatment failure, have led to the need to improve the characterisation of the chip seal curing process. As such, the use of an electrical resistance measurement has been studied to develop a sound construction methodology that prevents common failures that occur soon after construction. This paper presents a novel approach, based on electrical resistance measurements, to determine when a chip seal has developed enough binder adhesive strength to bond to the existing pavement while keeping the aggregate chips in place. The electrical resistance measurements provide a rapid, non-destructive indication of the amount of curing that has occurred. By implementing this methodology the user can determine when a chip seal has gained sufficient mechanical strength to allow for brooming or opening to unrestricted traffic without an undue loss of cover aggregate. Laboratory and full-scale field trials were conducted using a variety of materials. The electrical properties of the fresh seal coats were quantified by employing a handheld electrical device with a two-point probe resistance measurement. The experimental results suggest that chip seal systems have gained significant mechanical strength when the initial electrical resistance measurement increases by a factor of 10. As a result, this study establishes that electrical resistance measurements can be used to determine when a fresh chip seal has sufficiently cured to withstand the shear forces of brooms and uncontrolled traffic. The implementation of the technique could potentially impact chip seal construction quality, as well as service life performance.
Efficient, Broadband and Compact Metal Grating Couplers for Silicon-on-Insulator Waveguides (2007)

Metal grating couplers for Silicon-on-Insulator waveguides are proposed. A silver grating coupler with 33% coupling efficiency is designed. A gold grating coupler prototype is fabricated using Focused Ion Beams demonstrating over 10% coupling efficiency.
Will the Real Philosophers Please Stand, and Take Heed! (1983)

(1983). Will the Real Philosophers Please Stand, and Take Heed! The Journal of Environmental Education: Vol. 14, No. 3, pp. 41-42.
Supercritical Fluid—Adsorbate—Adsorbent Systems (1988)

Supercritical fluid (SCF) extraction of vegetable oils from a seed matrix may require the incorporation of an adsorbent bed to remove odoriferous compounds from the recycle gas stream. In this study, an elution pulse chromatographic technique has been developed which allows the determination of breakthrough volumes (BTV) for an array of odor-causing sorbates on Tenax-TA, XAD resins, and activated carbon adsorbents. Data taken over a 100-400 atmosphere range at three different temperatures indicate that the adsorbent retention capacity is rapidly lost at pressures beyond 200 atmospheres. In specific cases with the synthetic polymer sorbents, the supercritical carbon dioxide changes the sorption capacity of the resin phase by altering the physical morphology of the sorbent. Differential heat of adsorption measurements suggest that modification of the gas-solid interface by the supercritical fluid is enhancing migration of the sorbates through the column bed. Calculations incorporating the derived BTV data base illustrate how conditions can be altered to improve trapping efficiency by varying the fluid pressure, temperature, flow rate, and sorbent charge.
Doubling up the Horses in Midstream: Enhancing U.S. Patent Dispute Resolution by the PTO's Adoption of the JPO's Hantei Request System (2008)

For entities seeking to preempt or defend against adverse claims of infringement, navigating the present U.S. patent dispute resolution system is a thorny path.Judicial standing requirements hinder a potential defendant from fully assessing its risks before making and placing in jeopardy certain investments or assuming negotiation costs, thereby increasing its accountability, the financial stakes, and the probability of retaliation.While the standing doctrine has become more favorable to would-be licensees over time, a readily accessible opining mechanism for infringement would usher in still more benefits, including those unachievable through either litigation or conventional forms of alternative dispute resolution.Although the United States Patent and Trademark Office currently lacks Congressional authorization, the agency, due to its familiarity with patent claims and technical expertise, would be a prime candidate for administering such an advisory determination procedure, comparable to the Hantei Request System offered by the Japanese Patent Office.Moreover, the domestic implementation of this system by the PTO will not suffer the same disadvantages endemic to Japan's legal system.
CUG Start Codon Generates Thioredoxin/Glutathione Reductase Isoforms in Mouse Testes (2009)

Mammalian cytosolic and mitochondrial thioredoxin reductases are essential selenocysteine-containing enzymes that control thioredoxin functions. Thioredoxin/glutathione reductase (TGR) is a third member of this enzyme family. It has an additional glutaredoxin domain and shows highest expression in testes. Herein, we found that human and several other mammalian TGR genes lack any AUG codons that could function in translation initiation. Although mouse and rat TGRs have such codons, we detected protein sequences upstream of them by immunoblot assays and direct proteomic analyses. Further gene engineering and expression analyses demonstrated that a CUG codon, located upstream of the sequences previously thought to initiate translation, is the actual start codon in mouse TGR. The use of this codon relies on the Kozak consensus sequence and ribosome-scanning mechanism. However, CUG serves as an inefficient start codon that allows downstream initiation, thus generating two isoforms of the enzyme in vivo and in vitro. The use of CUG evolved in mammalian TGRs, and in some of these organisms, GUG is used instead. The newly discovered longer TGR form shows cytosolic localization in cultured cells and is expressed in spermatids in mouse testes. This study shows that CUG codon is used as an inefficient start codon to generate protein isoforms in mouse.
Metal Injection Molding of Ti-Mo-Al Mixed Powder. (1994)

The injection molding process (MIM)for the Ti-15Mo-3Al alloys has been studied by using the mixed powder consisting of Ti.Mo and TiAl. The average size of these powders was 38 μm. 1.24μm and 9.4μm, respectively. The results obtained were as follows.1) The kneading, molding and debinding (in the first stage)processes were successfully performed even in the air.2) The compacts debound at 210°C in the air, followed by debinding at 500-550°C in a vacuum, were densified to a relative density of 97% or more after sintering for 3 hours at 1296°C in a high vacuum.3) Many precipitated TiC partic]es were observed in these sintered compacts. which were not observed for the compacts obtained by conventional P/M process.
Zirconium Alkoxide Catalyzed Oxidation of Phenols, Alcohols, and Amines (1997)

The development of the zirconium alkoxide catalyzed oxygenation and dehydrogenation is described. Mono-, di- and tri-nuclear phenols are selectively oxidized to the corresponding ortho-quinones. Oxygenation also takes place with 2-alkylated phenols yielding highly functionalized α-hydroxy ketones. A very fast dehydrogenation of benzylic alcohols to the corresponding aldehydes and ketones occurs with the system Zr(O-n-Pr)4/hydroperoxide. Non-activated alcohols are also readily oxidized using the more active Zr(O-t-Bu)4/hydroperoxide or Zr(O-t-Bu)4/chloral system, higher reaction temperatures, and rigorous trapping of water with powdered molecular sieves. Silyl enol ethers are converted to the α-chloro ketones with the system ClTi(O-i-Pr)3/hydroperoxide and phenols are selectively halogenated in the para-position by the same system. Electron-donor as well as electron-acceptor substituted anilines are oxidized in good yields to the corresponding nitro compounds with the Zr(O-t-Bu)4/hydroperoxide system.
Conflict of Law Rules Between China and Taiwan and Their Significance (2008)

Kuo for their helpful comments on earlier versions.I alone bear all responsibilities and welcome suggestions and criticisms.1 The meaning of the two words China and Taiwan is a politically contested issue.In this paper, China and Taiwan are used as shorthand for the People's Republic of China and the Republic of China respectively.The problems between China and Taiwan are sometimes called the "cross-strait" problems, both because they are separated by the Taiwan Strait, and because the word "cross-strait" does not itself implicate the nation-state status.Translations of Chinese and Taiwanese materials are my own
Quantification of Uncertainty in Reserve Estimation From Decline Curve Analysis of Production Data for Unconventional Reservoirs (2008)

Decline curve analysis is the most commonly used technique to estimate reserves from historical production data for the evaluation of unconventional resources. Quantifying the uncertainty of reserve estimates is an important issue in decline curve analysis, particularly for unconventional resources since forecasting future performance is particularly difficult in the analysis of unconventional oil or gas wells. Probabilistic approaches are sometimes used to provide a distribution of reserve estimates with three confidence levels (P10, P50, and P90) and a corresponding 80% confidence interval to quantify uncertainties. Our investigation indicates that uncertainty is commonly underestimated in practice when using traditional statistical analyses. The challenge in probabilistic reserve estimation is not only how to appropriately characterize probabilistic properties of complex production data sets, but also how to determine and then improve the reliability of the uncertainty quantifications. In this paper, we present an advanced technique for the probabilistic quantification of reserve estimates using decline curve analysis. We examine the reliability of the uncertainty quantification of reserve estimates by analyzing actual oil and gas wells that have produced to near-abandonment conditions, and also show how uncertainty in reserve estimates changes with time as more data become available. We demonstrate that our method provides a more reliable probabilistic reserve estimation than other methods proposed in the literature. These results have important impacts on economic risk analysis and on reservoir management.
Polymorphism of the Cell Wall-Anchoring Domain of the Autolysin-Adhesin AtlE and Its Relationship to Sequence Type, as Revealed by Multilocus Sequence Typing of Invasive and Commensal <i>Staphylococcus epidermidis</i> Strains (2006)

We sequenced the adhesin-cell wall-anchoring domain of the atlE gene of 49 invasive and commensal Staphylococcus epidermidis strains. We identified 22 alleles, which could be separated into two main groups: group 1 (alleles 1 and 6 to 16, 32/49 strains) and group 2 (alleles 2 to 5 and 17 to 22, 17/49 strains). Allele 1 (the type strain sequence) was by far the most prevalent (21 of 49 strains). Multilocus sequence typing showed a clear relationship between the atlE allele and the sequence type (ST), with the "nosocomial" ST27 clone and closely related STs expressing group 1 alleles.