gebhart/patrepeval huggingface dataset:
Phenotypic and molecular diversity among landraces of snapmelon (Cucumis melo var. momordica) adapted to the hot and humid tropics of eastern India (2009)

We present here the first comprehensive genetic characterization of snapmelon landraces from the humid tropics of eastern India. The genetic diversity among 42 snapmelon landraces collected from four agro-ecological regions of eastern India (eight agro-ecological subregions) was assessed by measuring variation at 16 simple sequence repeat (SSR) marker loci, at various traits including plant habit and fruit type, yield (two associated traits), disease resistance and biochemical composition (total soluble solids, ascorbic acid, carotenoids and titrable acidity). Differences between accessions were observed in a number of plant and fruit traits. Snapmelon germplasm with high acidity, elevated carotenoid content and resistance to cucumber mosaic virus were identified in the collection. The SSR analysis indicated that there is a high level of genetic variability within snapmelon germplasm. Comparison of the genetic variability between snapmelons of eastern India and melons from north, south and central regions of India and reference accessions of melon from Spain, France, Japan, Korea, Maldives, Iraq, Zambia, Israel using SSRs showed that Indian snapmelon germplasm is not closely related to melon accessions from other parts of the world and that there are regional differences between Indian melon accessions. Eastern India snapmelon has unique traits, so it is important that more germplasm from this region is sampled and preserved.
Synthesis and Biochemical Characterization of N1-, N2-, and N7-Guanosine Adducts of Butadiene Monoxide (1996)

1,3-Butadiene is a known rodent carcinogen, but the molecular mechanisms of its carcinogenicity are poorly understood. Butadiene monoxide (BM), a known mutagenic metabolite of 1,3-butadiene, was previously shown to react with guanosine to yield two N7-guanine adducts. In the present study, eight guanosine adducts of BM were purified and characterized as diastereomeric pairs of N7-(2-hydroxy-3-buten-1-yl)guanosine (G-1 and G-3), N7-(1-hydroxy-3-buten-2-yl)guanosine (G-2 and G-5), N2-(1-hydroxy-3-buten-2-yl)guanosine (G-4 and G-7), and N1-(1-hydroxy-3-buten-2-yl)guanosine (G-6 and G-8) on the basis of stability studies and analyses by UV, 1H NMR, and fast atom bombardment mass spectrometry. While the N7-adducts exhibited half-lives of approximately 50 (G-1 and G-3) and 90 h (G-2 and G-5) upon incubation for 192 h in 100 mM phosphate buffer (pH 7.4) at 37 degrees C, the N1- and N2-adducts remained stable. When guanosine was reacted with excess BM in phosphate buffer (pH 7.4) at 37 degrees C, adduct formation exhibited pseudo-first-order kinetics, with the N7-adducts being formed approximately 10-fold more favorably than the N1- and N2-adducts. When incubations were carried out at lower BM concentrations, the N7-adducts remained the major detectable adducts, but the N2-adducts were also detectable at equimolar BM and guanosine concentrations, and the N1-adducts were detectable at a 5-fold molar excess of BM. These results, which provide clear evidence that guanosine can be alkylated at multiple sites following 1,3-butadiene exposure, may aid in the development of useful biomarkers for exposure to 1,3-butadiene. The results may also contribute to a better understanding of the molecular mechanisms of 1,3-butadiene-induced carcinogenicity.
Design optimization of beta- and photovoltaic conversion devices (1976)

This report presents the theoretical and experimental results of an LLL Electronics Engineering research program aimed at optimizing the design and electronic-material parameters of beta- and photovoltaic p-n junction conversion devices. To meet this objective, a comprehensive computer code has been developed that can handle a broad range of practical conditions. The physical model upon which the code is based is described first. Then, an example is given of a set of optimization calculations along with the resulting optimized efficiencies for silicon (Si) and gallium-arsenide (GaAs) devices. The model we have developed, however, is not limited to these materials. It can handle any appropriate material--single or polycrystalline-- provided energy absorption and electron-transport data are available. To check code validity, the performance of experimental silicon p-n junction devices (produced in-house) were measured under various light intensities and spectra as well as under tritium beta irradiation. The results of these tests were then compared with predicted results based on the known or best estimated device parameters. The comparison showed very good agreement between the calculated and the measured results.
Thioridazine Pharmacokinetic-Pharmacodynamic Parameters “Wobble” during Treatment of Tuberculosis: a Theoretical Basis for Shorter-Duration Curative Monotherapy with Congeners (2013)

Phenothiazines are being repurposed for treatment of tuberculosis. We examined time-kill curves of thioridazine and first-line drugs against log-growth-phase and semidormant bacilli under acidic conditions and nonreplicating persistent Mycobacterium tuberculosis. While both the potency and the efficacy of first-line drugs declined dramatically as M. tuberculosis replication rates decreased, those of thioridazine improved. The mutation prevalence to 3 times the thioridazine MIC was <1 × 10(-11), better than for ≥2 first-line drugs combined. Hollow fiber system studies revealed that the relationship between sterilizing effect and pharmacodynamic indices (PDI) was characterized by an r(2) of 0.88 for peak/MIC, an r(2) of 0.47 for the area under the concentration-time curve (AUC) to MIC, and an r(2) of 0.14 for the cumulative percentage of a 24-h period that the drug concentration exceeds the MIC under steady-state pharmacokinetic conditions (%TMIC) at the end of the first week. However, the PDI linked to effect "wobbled" as the duration of therapy increased, so that by the fourth week the r(2) was 0.88 for AUC/MIC, 0.78 for %TMIC, and 0.72 for peak/MIC. This "wobble" has implications on general pharmacokinetic/pharmacodynamic theory, whereby efficacy is linked to only one of the three PDIs in deterministic models. The potency changed 8.9-fold from the first to the fourth weeks. The non-protein-bound AUC/MIC associated with maximal kill at the end of therapy was 50.53 (protein binding = 99.5%). This thioridazine exposure was calculated to extinguish all three M. tuberculosis metabolic populations in human lungs in only 42.9 days of monotherapy. However, this concentration exceeds the 2- to 8-mg/liter thioridazine concentration in serum known to be lethal to humans. Therefore, the way forward for phenothiazine monotherapy that also reduces therapy duration is via synthesis of less toxic congeners.
Selective Targeting of CTNNB1-, KRAS- or MYC-Driven Cell Growth by Combinations of Existing Drugs (2015)

The aim of combination drug treatment in cancer therapy is to improve response rate and to decrease the probability of the development of drug resistance. Preferably, drug combinations are synergistic rather than additive, and, ideally, drug combinations work synergistically only in cancer cells and not in non-malignant cells. We have developed a workflow to identify such targeted synergies, and applied this approach to selectively inhibit the proliferation of cell lines with mutations in genes that are difficult to modulate with small molecules. The approach is based on curve shift analysis, which we demonstrate is a more robust method of determining synergy than combination matrix screening with Bliss-scoring. We show that the MEK inhibitor trametinib is more synergistic in combination with the BRAF inhibitor dabrafenib than with vemurafenib, another BRAF inhibitor. In addition, we show that the combination of MEK and BRAF inhibitors is synergistic in BRAF-mutant melanoma cells, and additive or antagonistic in, respectively, BRAF-wild type melanoma cells and non-malignant fibroblasts. This combination exemplifies that synergistic action of drugs can depend on cancer genotype. Next, we used curve shift analysis to identify new drug combinations that specifically inhibit cancer cell proliferation driven by difficult-to-drug cancer genes. Combination studies were performed with compounds that as single agents showed preference for inhibition of cancer cells with mutations in either the CTNNB1 gene (coding for β-catenin), KRAS, or cancer cells expressing increased copy numbers of MYC. We demonstrate that the Wnt-pathway inhibitor ICG-001 and trametinib acted synergistically in Wnt-pathway-mutant cell lines. The ERBB2 inhibitor TAK-165 was synergistic with trametinib in KRAS-mutant cell lines. The EGFR/ERBB2 inhibitor neratinib acted synergistically with the spindle poison docetaxel and with the Aurora kinase inhibitor GSK-1070916 in cell lines with MYC amplification. Our approach can therefore efficiently discover novel drug combinations that selectively target cancer genes.
Electronically Tuned Chiral Ruthenium Porphyrins: Extremely Stable and Selective Catalysts for Asymmetric Epoxidation and Cyclopropanation. (2004)

Abstract For Abstract see ChemInform Abstract in Full Text.
Study and Field Application of Multiround Profile Control for Injection Wells (2012)

Abstract In this article, multi-round profile control in heterogeneous reservoir through plate models and parallel sand pack experiments are developed. It is confirmed that there is a decreasing effect with increasing round in multiround profile control for injection wells and 5 decline mechanisms are obtained from physical simulation experiments. At the same time, the related improvement technology for the previous problem was also proposed. This technology was applied in the South Tuo 11 block of the Shengtuo oilfield with good effect.
Cellular immune responses to recombinant heat shock protein 70 from Histoplasma capsulatum (1996)

Heat shock protein (hsp) 70 from several microbes is antigenic in mammals. In this study we sequenced and expressed the gene encoding this protein from Histoplasma capsulatum to study its immunological activity. The deduced amino acid sequence of the gene demonstrated 71 and 76% identity to hsp7O from humans and Saccharomyces cerevisiae, respectively. A cDNA was synthesized by reverse transcription-PCR and was expressed in Escherichia coli. Recombinant protein reacted with a mouse monoclonal antibody raised against human hsp7O. Splenocytes from C57BL/6 mice immunized with recombinant hsp7O emulsified in adjuvant, but not yeast cells, reacted in vitro to the antigen. Recombinant hsp7O elicited a cutaneous delayed-type hypersensitivity response in mice immunized with protein or with viable yeast cells. Mice were injected with recombinant hsp7O and challenged intranasally with a sublethal inoculum of yeast cells. Vaccination did not confer protection in this model. Thus, recombinant hsp7O can induce a cell-mediated immune response but does not induce a protective response.
High-confidence measurement of solid/liquid surface energy in a pure material (1975)

Abstract A new method for measuring solid/liquid surface energies, with a total systematic and random error of well under 10%, is described. The surface energies are derived from measurements of grain-boundary grooves in solid/liquid interfaces which are maintained in shallow temperature gradients. The gradients are established by an axial heater wire in a cylindrical specimen chamber. Applying the method to highly-purified succinonitrile, a solid/liquid surface energy of 8·94±0·5 erg/cm2 was determined. This corresponds to 37% of the heat of fusion per surface molecule.
Ceramic Nanofibers and Their Applications (2018)

Ceramic materials are normally hard and inert and therefore well known for their excellent mechanical and thermal properties, as well as excellent resistance against corrosion and chemical erosion. Among the different approaches, electrospinning is a simple and versatile technique for preparing the various types of nanofibers with controlled morphology and structure on an industrial scale and has the merits of simplicity, high efficiency, low cost, and high reproducibility. This chapter examines different types of ceramic nanofibers developed by the electrospinning technique with their prospective applications in the various fields. Electrospinning is a technique to synthesized polymeric nanofibers by applying a high electric field to a polymeric solution. Monolithic fibers are synthesized by electrospinning a solution composed of only a single polymer without any additives. The electrospun fiber has a core-shell morphology in which core and shell are separately distinguishable when observed under an electron microscope. It is possible to isolate the core from the shell.
Assembling 2D blocks into 3D chips (2011)

Three-dimensional ICs promise to significantly extend the scale of system integration and facilitate new-generation electronics. However, progress in commercial 3D ICs has been slow. In addition to technology-related difficulties, industry experts cite the lack of a commercial 3D EDA tool-chain and design standards, high risk associated with a new technology, and high cost of transition from 2D to 3D ICs. To streamline the transition, we explore design styles that reuse existing 2D Intellectual Property (IP) blocks in 3D ICs. Currently, these design styles severely limit the placement of Through-Silicon Vias (TSVs) and constrain the reuse of existing 2D IP blocks in 3D ICs. To overcome this problem, we develop a methodology for using TSV islands and novel techniques for clustering nets to connect 2D IP blocks through TSV islands. Our empirical validation demonstrates 3D integration of traditional 2D circuit blocks without modifying their layout for this context.
Abstract LB-056: Quantitative mass spectrometry analysis of immune checkpoint protein expression and N-glycosylation in human melanoma (2017)

Abstract Quantitative assessment of key proteins that control the tumor-immune interface is one of the most formidable analytical challenges in immunotherapeutics. We developed an targeted mass spectrometry (MS) platform to quantify programmed cell death-1 (PD-1), programmed cell death 1 ligand 1 (PD-L1), and programmed cell death 1 ligand 2 (PD-L2) at fmol/microgram protein levels in formalin fixed, paraffin-embedded sections from 22 human melanomas. PD-L1 abundance ranged 50-fold, from approximately 0.03 to 1.5 fmol/microgram protein and the PRM data were largely concordant with total PD-L1-positive cell content, as analyzed by immunohistochemistry (IHC) with the E1L3N antibody. PD-1 was measured at levels up to 20-fold lower than PD-L1, but the abundances were not significantly correlated (r2 = 0.062, p = 0.264). PD-1 abundance was weakly correlated (r2 = 0.3057, p = 0.009) with the fraction of lymphocytes/histiocytes in sections. PD-L2 was measured from 0.03 to 1.90 fmol/microgram protein and the ratio of PD-L2 to PD-L1 abundance ranged from 0.03 to 2.58. In 8 samples, PD-L2 was present at more than half the level of PD-L1, which suggests that PD-L2, a higher affinity PD-1 ligand, is sufficiently abundant to contribute to T-cell downregulation. We also identified five branched mannose and N-acetylglucosamine glycans at PD-L1 position N192 in all 22 samples. Extent of PD-L1 glycan modification varied by approximately 10-fold and the melanoma with the highest PD-L1 protein abundance and most abundant glycan modification yielded a very low PD-L1 IHC estimate, thus suggesting that N-glycosylation may affect IHC measurement and PD-L1 function. Additional PRM analyses quantified immune checkpoint/co-regulator proteins LAG3, IDO1, TIM-3, VISTA and CD40, which all displayed distinct expression independent of PD-1, PD-L1 and PD-L2. Targeted MS can provide a next-generation analysis platform to advance cancer immuno-therapeutic research and diagnostics. (Supported by NIH grant U24CA159988) Citation Format: Carlos Morales Betanzos, Hyoungjoo Lee, Paula I. Gonzalez Ericsson, Justin M. Balko, Douglas B. Johnson, Lisa J. Zimmerman, Daniel C. Liebler. Quantitative mass spectrometry analysis of immune checkpoint protein expression and N-glycosylation in human melanoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr LB-056. doi:10.1158/1538-7445.AM2017-LB-056
Toward improved tumor targeting for image guided neurosurgery with intra-operative parametric search using distributed and grid computing (2008)

We describe a high-performance distributed software environment for real-time nonrigid registration during Image- Guided Neurosurgery (IGNS). The implementation allows to perform volumetric non-rigid registration of MRI data within two minutes of computation time, and can enable large-scale parametric studies of the registration algorithm. We explore some of the parameters of the non-rigid registration, and evaluate their impact on registration accuracy using ground truth. The results of the evaluation motivate running the registration process within the Grid environment, particularly when searching for optimal parameters of intraoperative registration. Based on the results of our evaluation, distributed parametric searching of optimal registration settings can significantly improve the registration accuracy in some regions of the brain, as compared to the accuracy achieved using the default parameters.
Construction of morally correct actions: in the stories of violence during the war in Bosnia and Herzegovina (2015)

This article is based on different types of empirical material, especially recorded interviews, carried out with 27 survivors of the war in northwestern Bosnia and Herzegovina, and field observations. The focus lies on analyzing interviewees’ and field notes description of war-time violence and also analyzing discursive patterns that contribute in constructing the phenomenon “war violence”. This study shows that narratives on the phenomenon “war violence” depict a decay of pre-war social order. The use of violence during the war is described as organized and ritualized, which implies that the use of violence became a norm in society, rather than the exception. The narratives on the phenomenon “war violence” produce and reproduce the image of human suffering and slaughter. Those subjected to violence are portrayed in a de-humanized fashion and branded as suitable to be exposed to it. In these stories, morally correct actions are constructed as a contrast to the narratives on war violence. In these descriptions, the perpetrator is depicted as a dangerous, evil, and ideal enemy. He is portrayed as a real and powerful yet alien criminal who is said to pose a clear threat to the social order existing before the war.
Origen and Augustine (2022)

Abstract Neither of these early Christian titans gladly suffers reduction to simple analysis, not as individuals and much less in tandem. But juxtaposition sheds light on intriguing complexes of convergence and divergence. Ambrose drew Augustine to Nicene Christianity through Origen’s exegesis. Origen the grammarian and Augustine the rhetor explored the same christologically shaped biblical terrain from different if congruent angles. Both saw Christian life developmentally, though each valued the beginning stage of faith differently. Origen expected purity and holiness from the visible Church, while Augustine allowed saints and sinners to mix for the sake of love. Origen saw eschatological punishment as temporary and pedagogical, inclining toward ultimate salvation, while Augustine thought unending penal justice serves God’s glory. Other differences regarding divine foreknowledge, free will, grace, and Judaism derive from their contrasting readings of Paul. Yet Origen’s enduring influence on Augustine is detectable in the bishop’s pastoral work.
On the efficacy of anthracene isomers for triplet transmission from CdSe nanocrystals (2016)

The effect of isomeric substitutions on the transmitter for triplet energy transfer (TET) between nanocrystal (NC) donor and molecular acceptor is investigated. Each isomeric acceptor is expected to bind in a unique orientation with respect to the NC donor. We see that this orbital overlap drastically affects the transmission of triplets. Here, two functional groups, the carboxylic acid and dithiocarbamate, were varied between the 1-, 2- and 9-positions of the anthracene ring to give three ACA and three ADTC isomers. These six anthracene isomers served as transmitters for triplets between CdSe NC sensitizers and 9,10-diphenylanthracene annihilators for photon upconversion. The photon upconversion quantum yield (QY) is the highest for 9-ACA (12%), lowest for 9-ADTC (0.1%), around 3% for both 1-ACA and 1-ADTC, and about 1% for the 2-isomers. These trends in QYs are reflected in the rates of TET given by ultrafast transient absorption spectroscopy where a maximum of 3.8 × 10<sup>7</sup> s<sup>-1</sup> for 9-ACA was measured. Molecular excited state energy levels were measured both in solution and polymer hosts to correlate structure to TET. This work confirms that anthracene excited states levels are very sensitive to molecular substitution, which in combination with orbital overlap, critically affect Dexter-based TET.
Double-plane-wave reverse time migration in the frequency domain (2016)

ABSTRACT We have developed an efficient, accurate, and flexible plane-wave migration algorithm in the frequency domain by using a compressed and coupled-plane-wave data set, known as the double-plane-wave (DPW) data set. The DPW data set obtained by slant stacking of seismic shot profiles over source and receiver/offset represents seismic data in a fully decomposed plane-wave domain, which is called the DPW domain. A new DPW migration algorithm is derived under the Born approximation in the frequency domain, and it is referred to as the frequency-domain DPW reverse time migration (RTM). Frequency plane-wave Green’s functions need to be constructed and used during the migration. Time dips in shot profiles help to estimate the range of plane-wave decomposition. Therefore, the number of frequency plane-wave Green’s functions required for migration is limited. Furthermore, frequency plane-wave Green’s functions can be used for imaging each set of plane waves — either source or receiver/offset plane waves. As a result, the computational burden of computing Green’s function is substantially reduced; this results in increasing the migration efficiency. A selected range of plane-wave components can be migrated independently to image specific targets. Ray-parameter common-image gathers can be generated after migration without extra effort. The algorithm was tested on several synthetic data sets to show its feasibility and usefulness. The frequency-domain DPW RTM can also include anisotropy by constructing plane-wave Green’s function in anisotropic media.