gebhart/patrepeval huggingface dataset:
Assembly of the TCR/CD3 complex: CD3ε/δ and CD3ε/γ dimers associate indistinctly with both TCRα and TCRβ chains. Evidence for a double TCR heterodimer model (1998)

The TCR/CD3 complex is composed of six subunits which are expressed on the cell surface in a coordinate fashion after assembly in the endoplasmic reticulum (ER). The TCR/CD3 complex is assembled after a series of pairwise interactions involving the formation of dimers of CD3 epsilon with either CD3 gamma or CD3 delta. These dimers assemble with TCR alpha and TCR beta chains, and finally, the CD3 zeta homodimer is added to allow export of the full complex from the ER. A model has been proposed suggesting that during assembly the CD3 epsilon/CD3 gamma dimer interacts exclusively with TCR beta and the CD3 epsilon/CD3 delta dimer with TCR alpha to form a complex with a single TCR alpha/beta heterodimer. We show in this study, by immunoprecipitation and two-dimensional gel electrophoresis, that in the human T cell line Jurkat as well as in total human thymocytes, this preferential interaction does not occur and instead, the CD3 epsilon/CD3 gamma and CD3 epsilon/CD3 delta dimers associate with both TCR chains simultaneously and indistinctly. These data are confirmed by the analysis of the TCR alpha-negative T cell line MOLT-4 in which TCR beta is found separately associated with CD3 epsilon/CD3 gamma and with CD3 epsilon/CD3 delta dimers. Indirectly, our results support a model of stoichiometry in which two TCR alpha/beta heterodimers are present in a TCR/CD3 complex. Furthermore, immunoprecipitation with anti-CD3 gamma and anti-CD3 delta antibodies from 1% NP40 and 1% Brij96 cell lysates showed that these subunits form independent partial complexes which are cross-linked through the CD3 zeta homodimer. This suggests that CD3 zeta mediates the interaction between both TCR alpha/beta heterodimers contained in the double TCR complex. Further proof for this hypothesis is obtained after analysis of a Jurkat cell transfectant containing a point mutation in the transmembrane domain of TCR beta that impairs the association of CD3 zeta. In this mutant cell line, unlike a control line with wild-type TCR beta, the CD3 gamma- and CD3 delta-containing complexes were found completely independent. Altogether, these results support a model of TCR/CD3 assembly and stoichiometry in which two TCR-alpha/beta heterodimers form two hemicomplexes containing either CD3 epsilon/gamma or CD3 epsilon/delta dimers which become associated via the CD3 zeta homodimer.
The Stereospecific Synthesis of Spectinomycin (1980)

Spectinomycin (1) is an aminocyclitol antibiotic marketed by The Upjohn Company as the dihydrochloride salt under the name of Trobicin®. It is a broad spectrum antibiotic of moderate potency which has become especially important for the treatment of penicillin-resistant strains of gonorrhoeae. Spectinomycin does not have the oto- and nephrotoxicity which is usually associated with the 2-deoxystreptamine containing aminocyclitols. The structure of spectinomycin was determined at Upjohn by Wiley, Hoeksema, and Argoudelis (1, 2). This structure (1), shown on Figure 1, is unique among the aminocyclitols in that it contains a glycosylated actinamine ring which is cyclized to form a third ring by hemiketal formation. Spectinomycin (1) has nine asymmetric centers. It also has a carbonyl group at C-3' and two masked carbonyl groups at C-1' and C-2'. This electrophilic portion of the molecule is sensitive to mild base which causes benzylic acid type rearrangement to give actinospectinoic acid (2).
Computing with Granular Information: Fuzzy Sets and Fuzzy Relations (2005)

The chapter serves as a focused introduction to fuzzy sets and their calculus. The paradigm of fuzzy sets is also cast in the framework of granular computing where fuzzy sets are sought as examples of information granules. Discussed are operations on fuzzy sets (including their realizations in terms of t- and s-norms), properties of fuzzy relations and a general processing paradigm supported by fuzzy sets.
Optimal Production of a Novel Furan Fatty Acid from 7,10-dihydroxy-8(E)- octadecenoic Acid by Heat Treatment (2013)

As a specialty oil, furan fatty acids have gained special attentions since they are known to play important roles in biological systems including human. Although several studies reported chemical synthesis of furan fatty acids, their synthesis consisted of complicated chemical multistep with chemical catalysts. Recently, a simple one-step heat treatment method was developed to produce a novel furan fatty acid, 7,10-epoxy-octadeca-7,9-dienoic acid (7,10-EODA) from a dihydroxyl fatty acid 7,10-dihydroxy-8(E)-octadecenoic acid (DOD). In this report we studied about optimization of environmental conditions for the maximum production of 7,10-EODA from DOD by heat treatment. Production of 7,10-EODA was maximized at over 85℃ for at least over 48 hour in hexane. Solvent volume for maximum production should be over 300 mL per 10 mg DOD.
Editorial: Closing the Collection on Photovoltaic Energy Conversion (2023)

This Collection represents the state of the art and likely future developments in the physics of photovoltaic energy conversion.The collection consists of 12 articles, including reviews, invited papers, and contributed papers.The aim of photovoltaic energy conversion is to harvest the energy in sunlight to generate electricity or fuel.While silicon photovoltaic technology has been very well established and commercially successful for electricity generation, there have been significant efforts in novel approaches that may eventually outperform silicon technology in various aspects, including efficiency and cost.Fuel generation through solar-energy harvesting has not yet reached a level of commercial success similar to that of silicon photovoltaic technology.However, there are significant connections between the physics of photovoltaic electricity and fuel generation, and exploiting these connections may lead to further progress in solar-energy harvesting and storable clean energy in general.Future improvements to photovoltaic energy conversion require advanced control of photons, electrons, and photonelectron interactions.On the photon side, in this Collection several papers discuss the development of thermophotovoltaics, which allow direct conversion of thermal radiation to electricity.This area has witnessed significant advances in experimentally demonstrated efficiencies in recent years, and represents a key approach in overcoming the Shockley-Queisser limit that bounds the efficiency of silicon photovoltaic cells.The utilization of optical nonreciprocity, which is essential in reaching the ultimate efficiency limit of solar-energy harvesting, is also discussed.On the electron side, several papers investigate the control of electron transport, and highlight physics considerations in emerging photovoltaic material systems.Aspects of electron-photon interactions, which manifest themselves in luminescent processes, are also described.One of the papers reports a promising photocatalytic semiconductor with strong excitonic effects for water splitting.We hope that this Collection is useful in motivating future efforts in this crucially important area.In closing, we thank
An Efficient Monte Carlo Approach to Optimization (1998)

A highly efficient Monte Carlo algorithm for global optimization has been developed which accepts beneficial moves, rejects all detrimental ones, picks a new step size at random from a guided range, and samples a new region of the response surface using a randomly generated directional search technique. The step size guide is the modified Heaviside function: r = r0 0 < m ≤ nn), r = r/2 + 1/r (nn < m ≤ 3nn), and r = {r/2 + 1/r} sin(2r0r) (m > 3nn), where m is the number of frustrated steps and nn a decision parameter. This approach quickly steps through local optima. Two strategies have been evolved leading to solutions for both the highly intractable modified n-dimensional shekel function and COSn, the “cosine function”. The strategies are efficient: starting from the point (10,10), an average of only 187 steps (successful and otherwise) taking a total of 0.22 shekels of time were required to find the minimum of the COS2 function to three significant figures with a success rate of 987/1000. In the case of COS4 the current calculations started from {xi = 10} and found the global minimum to three significant figures in 864 steps and 1.80 shekels with a success rate of 999/1000. COS100 has also been solved. In almost all comparisons with currently accepted methods, considerable efficiencies are achieved, and, more importantly, global optimization could be implemented in all test cases.
Surface Complexation Modeling for Improved Oil Recovery (2012)

Abstract Coordination chemistry models of oil adhesion to sandstones and calcite allow more precise testing of wettability alteration theories. The primary electrostatic bonds calculated to link oil to most sandstones are oil -NH+ and kaolinite edge &amp;gt;Al-OH2+ sites at pH &amp;lt; 5.5, and oil -COOCa+ and kaolinite edge &amp;gt;Al:Si-O- sites at pH &amp;gt; 5.5; −NH+ and −COOCa+ can also exchange onto basal planes. Low salinity waterfloods should break −NH+ — &amp;gt;AlOH2+ bonds at pH &amp;lt; 5.5 and low salinity, low Ca+2 waterfloods are calculated to eliminate −COOCa+ — &amp;gt;Al:Si-O- bonds at pH &amp;gt; 5.5. Oil is calculated to link electrostatically to calcite through oil − COO- and &amp;gt;CaOH2+ sites, and to a lesser extent through oil −NH+ and calcite &amp;gt;CO3- sites. Sulfate- rich floods are calculated to eliminate &amp;gt;CaOH2+ charge through sulfate sorption. Divalent cation (Ca+2 and Mg+2) – rich floods are calculated to reverse −COO- charge through sorption.
Cellular structures with interconnected microchannels (2023)

A method for fabricating a cellular tritium breeder component includes obtaining a reticulated carbon foam skeleton comprising a network of interconnected ligaments. The foam skeleton is then melt-infiltrated with a tritium breeder material, for example, lithium zirconate or lithium titanate. The foam skeleton is then removed to define a cellular breeder component having a network of interconnected tritium purge channels. In an embodiment the ligaments of the foam skeleton are enlarged by adding carbon using chemical vapor infiltration (CVI) prior to melt-infiltration. In an embodiment the foam skeleton is coated with a refractory material, for example, tungsten, prior to melt infiltration.
Impact of HCV genotype on treatment regimens and drug resistance: a snapshot in time (2016)

The introduction of highly potent direct-acting antivirals (DAAs) has revolutionized hepatitis C virus treatment. Nevertheless, viral eradication worldwide remains a challenge also in the era of DAA treatment, because of the high associated costs, high numbers of undiagnosed patients, high re-infection rates in some risk groups and suboptimal drug efficacies associated with host and viral factors as well as advanced stages of liver disease. A correct determination of the HCV genotype allows administration of the most appropriate antiviral regimen. Additionally, HCV genetic sequencing improves our understanding of resistance-associated variants, either naturally occurring before treatment, acquired by transmission at HCV infection, or emerging after virological failure. Because treatment response rates, and the prevalence and development of drug resistance variants differ for each DAA regimen and HCV genotype, this review summarizes treatment opportunities per HCV genotype, and focuses on viral genetic sequencing to guide clinical decision making. Although approval of the first pan-genotypic DAA-only regimen is expected soon, HCV genetic sequencing will remain important because when DAA therapies fail, genotyping and resistance testing to select a new active DAA combination will be essential. Copyright © 2016 John Wiley & Sons, Ltd.
ChemInform Abstract: Photoassisted Catalytic Dissociation of H2O to Produce Hydrogen on Partially Reduced α‐Fe2O3. (1987)

Abstract The photoproduction of H 2 from H 2 O has been investigated using undoped Fe 2 O 3 powders or polycrystalline pellets which are clearly shown to act as catalyst.
Static and dynamic appointment scheduling to improve patient access time (2017)

Appointment schedules for outpatient clinics have great influence on efficiency and timely access to health care services. The number of new patients per week fluctuates, and capacity at the clinic varies because physicians have other obligations. However, most outpatient clinics use static appointment schedules, which reserve capacity for each patient type. In this paper, we aim to optimise appointment scheduling with respect to access time, taking fluctuating patient arrivals and unavailabilities of physicians into account. To this end, we formulate a stochastic mixed integer programming problem, and approximate its solution invoking two different approaches: (1) a mixed integer programming approach that results in a static appointment schedule, and (2) Markov decision theory, which results in a dynamic scheduling strategy. We apply the methodologies to a case study of the surgical outpatient clinic of the Jeroen Bosch Hospital. We evaluate the effectiveness and limitations of both approaches by discrete event simulation; it appears that allocating only 2% of the capacity flexibly already increases the performance of the clinic significantly.
A Fast Estimation on Motion Compensation using an Affine Transformation. (1997)

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Silicon etch rate enhancement by traces of metal (1999)

We report the effect of nickel and tungsten contamination on the etch behavior of silicon. This is studied in a molecular beam setup, where silicon is etched by XeF2 and Ar+ ions. The etch process is directly monitored by the SiF4 reaction products which leave the surface. The effect of contamination appears very pronounced after the ion beam is switched off: it leads to a temporary enhancement of the spontaneous etch rate on a time scale of 500 s. With traces of contamination on the order of 0.01 ML, the etch rate may be enhanced by a factor of 2 for W and somewhat less for Ni. It is concluded that the contamination moves into the silicon by diffusion to vacancies created by the Ar+ ions. For 1 keV Ar+ ions the contamination moves to a depth of 25 Å, comparable to the penetration depth of the ions. After etching a 170 Å thick layer, the catalytic effect of contamination is reduced to less than 5%. A simple model, which describes the measured effect of contamination very well, indicates that only 3% of the contamination is removed when a monolayer of silicon is etched away. Besides this catalytic effect there are indications that contamination can also lower the etch rate under certain conditions, because of the formation of silicides. From the measurements no conclusions could be drawn about the underlying mechanism of etch rate enhancement.
[Effect of Zero Valent Iron on the Horizontal Gene Transfer of Tetracycline Resistance Genes During Anaerobic Sludge Digestion Process]. (2018)

The problem of bacterial resistance has become an important issue in the area of global ecological safety and human health. Waste sludge is an important reservoir and discharge source for antibiotic resistance genes (ARGs). In this study, the quantities of seven tetracycline resistance genes (TC-ARGs), including <i>tetA, tetC, tetG, tetM, tetO, tetW</i>, and <i>tetX</i>, as well as those of class 1 integron (<i>intI1</i>) genes, during anaerobic sludge digestion process were comprehensively quantified by quantitative PCR (qPCR). The effects of different doses of zero valent iron (Fe<sup>0</sup>) on the decrease and increase in the quantities of TC-ARGs and <i>intI1</i> genes were investigated. The influence of plasmid conjugation on the horizontal gene transfer (HGT) of the target TC-ARGs was preliminarily analyzed. The correlations between the quantities of TC-ARGs and <i>intI1</i> gene have been discussed. The results showed that the quantities of TC-ARGs and <i>intI1</i> genes decreased in different degrees during anaerobic sludge digestion, and the abundance of <i>tetX</i> gene was reduced by 2.4 orders of magnitude. When Fe<sup>0</sup> was added, no significant reduction in the quantities of TC-ARGs and <i>intI1</i> genes was observed. However, as the addition of Fe<sup>0</sup> increased, the quantities of TC-ARGs and <i>intI1</i> genes increased correspondingly, as compared to those in the control group. The results obtained from the quantities of TC-ARGs carried by plasmid DNA showed that plasmid conjugation probably promoted the HGT of TC-ARGs. A positive significant correlation was found between the quantities of <i>tetG</i> and <i>intI1</i> genes, indicating that <i>intI1</i> might play an important role in the evolution of <i>tetG</i> during sludge anaerobic digestion process.
Atmospheric chemistry and air quality (1975)

Before proceeding to a discussion of recent developments and advances in the research areas of atmospheric chemistry and air quality it will be useful to describe briefly the subjects with which we are dealing. Atmospheric chemistry is a mixture of traditional subjects from chemistry and from meteorology. Its practitioners range from chemists with an interest in the atmosphere to meteorologists working on atmospheric composition. At the core is a small group trained or experienced in both fields who are often members of both the American Meteorological Society and the American Chemical Society and feel comfortable in both communities. As a subject, atmospheric chemistry has theoreticians, experimentalists, bureaucrats, and politicians like any other branch of science.
LOW TEMPERATURE CRACKING OF MODIFIED AC MIXES IN ALASKA. VOLUME I: FINAL REPORT; VOLUME II: APPENDIX A; AND VOLUME III: APPENDICES B-H (1997)

Low temperature cracking is a major distress mode in Alaskan pavements due to the extreme temperature conditions that range, in some instances, from about -50 deg C in winter to 40 deg C in summer. The use of asphalt modifiers in Alaskan pavements occurred over the past 15 years. These modifiers include SBR polymers, SBS polymers, ULTRAPAVE and CRM (both the dry process, PlusRide, and the wet process). Field observations and laboratory studies in Alaska and elsewhere, indicate that the use of these modifiers would improve the low temperature cracking resistance of pavements. The degree these modifiers provide for Alaskan pavements needs to be evaluated. The objectives of this research were: 1) To characterize asphalt and polymer modified asphalt mixes from a number of selected sites using Strategic Highway Research Program (SHRP) Superpave PG grading system, thermal stress restrained specimen test (TSRST), and Superpave IDT laboratory tests on field specimens; 2) To compare low temperature cracking performance using field surveys; 3) To verify the applicability of SHRP Superpave thermal cracking; and 4) To assess the preliminary economic benefits from using polymer modified asphalts. Results of this study indicate in general significant improvement in the low temperature cracking resistance when polymer modifiers are used. The corresponding reduction in crack sealing costs are estimated to be between 30% and 40%. Minimum air and pavement temperature correlations were developed using field data covering Alaska's climatic zones. Contour maps for Alaskan roads corresponding to 50% and 98% reliability minimum pavement temperature were developed. Design recommendations to minimize low temperature cracking and estimate crack progression with age were established.
Design and Synthesis of Lactams Derived from Mucochloric and Mucobromic Acids as Pseudomonas aeruginosa Quorum Sensing Inhibitors (2018)

Bacterial infections, particularly hospital-acquired infections caused by <i>Pseudomonas aeruginosa</i>, have become a global threat with a high mortality rate. Gram-negative bacteria including <i>P. aeruginosa</i> employ <i>N</i>-acyl homoserine lactones (AHLs) as chemical signals to regulate the expression of pathogenic phenotypes through a mechanism called quorum sensing (QS). Recently, strategies targeting bacterial behaviour or QS have received great attention due to their ability to disarm rather than kill pathogenic bacteria, which lowers the evolutionary burden on bacteria and the risk of resistance development. In the present study, we report the design and synthesis of <i>N</i>-alkyl- and <i>N</i>-aryl 3,4 dichloro- and 3,4-dibromopyrrole-2-one derivatives through the reductive amination of mucochloric and mucobromic acid with aliphatic and aromatic amines. The quorum sensing inhibition (QSI) activity of the synthesized compounds was determined against a <i>P. aeruginosa</i> MH602 reporter strain. The phenolic compounds exhibited the best activity with 80% and 75% QSI at 250 µM and were comparable in activity to the positive control compound Fu-30. Computational docking studies performed using the LasR receptor protein of <i>P. aeruginosa</i> suggested the importance of hydrogen bonding and hydrophobic interactions for QSI.
Novel Effects of Chromosome Y on Cardiac Regulation, Chromatin Remodeling, and Neonatal Programming in Male Mice (2013)

Little is known about the functions of chromosome Y (chrY) genes beyond their effects on sex and reproduction. In hearts, postpubertal testosterone affects the size of cells and the expression of genes differently in male C57BL/6J than in their C57.Y(A) counterparts, where the original chrY has been substituted with that from A/J mice. We further compared the 2 strains to better understand how chrY polymorphisms may affect cardiac properties, the latter being sexually dimorphic but unrelated to sex and reproduction. Genomic regions showing occupancy with androgen receptors (ARs) were identified in adult male hearts from both strains by chromatin immunoprecipitation. AR chromatin immunoprecipitation peaks (showing significant enrichment for consensus AR binding sites) were mostly strain specific. Measurements of anogenital distances in male pups showed that the biologic effects of perinatal androgens were greater in C57BL/6J than in C57.Y(A). Although perinatal endocrine manipulations showed that these differences contributed to the strain-specific differences in the response of adult cardiac cells to testosterone, the amounts of androgens produced by fetal testes were not different in each strain. Nonetheless, chrY polymorphisms associated in newborn pups' hearts with strain-specific differences in genomic regions showing either AR occupancy, accessible chromatin sites, or trimethylation of histone H3 Lysine 4 marks, as well as with differential expression of 2 chrY-encoded histone demethylases. In conclusion, the effects of chrY on adult cardiac phenotypes appeared to result from an interaction of this chromosome with the organizational programming effects exerted by the neonatal testosterone surge and show several characteristics of being mediated by an epigenetic remodeling of chromatin.
Generation and Characterization of a Defined Mutant of Streptococcus suis Lacking Suilysin (2001)

A defined allelic-replacement mutant of the sly gene, encoding a thiol-activated cytolysin, from a European isolate of Streptococcus suis serotype 2 was generated and characterized. Unlike the parental strain, it is nonhemolytic, noncytotoxic for cultured macrophage-like cells, avirulent in a mouse infection model, yet only slightly attenuated in a porcine model of systemic infection.