gebhart/patrepeval huggingface dataset:
Adsorption of biometals to monosodium titanate in biological environments (2005)

Monosodium titanate (MST) is an inorganic sorbent/ion exchanger developed for the removal of radionuclides from nuclear wastes. We investigated the ability of MST to bind Cd(II), Hg(II), Au(III), or the Au-organic compound auranofin to establish the utility of MST for applications in environmental decontamination or medical therapy (drug delivery). Adsorption isotherms for MST were determined at pH 7-7.5 in water or phosphate-buffered saline. The extent of metal binding was determined spectroscopically by measuring the concentrations of the metals in solution before and after contact with the MST. Cytotoxic responses to MST were assessed using THP1 monocytes and succinate dehydrogenase activity. Monocytic activation by MST was assessed by TNFalpha secretion (ELISA) with or without lipopolysaccharide (LPS) activation. MST adsorbed Cd(II), Hg(II), and Au(III) under conditions similar to those in physiological systems. MST exhibited the highest affinity for Cd(II) followed by Hg(II) and Au (III). MST (up to 100 mg/L) exhibited only minor (<25% suppression of succinate dehydrogenase) cytotoxicity and did not trigger TNFalpha secretion nor modulate LPS-induced TNFalpha secretion from monocytes. MST exhibits high affinity for biometals with no significant biological liabilities in these introductory studies. MST deserves further scrutiny as a substance with the capacity to decontaminate biological environments or deliver metals or metal compounds for therapeutic applications.
Cloning, functional organization, transcript studies, and phylogenetic analysis of the complete nitrogenase structural genes (nifHDK2) and associated genes in the archaeon Methanosarcina barkeri 227 (1996)

Determination of the nucleotide sequence of the nitrogenase structural genes (nifHDK2) from Methanosarcina barkeri 227 was completed in this study by cloning and sequencing a 2.7-kb BamHI fragment containing the 3' end of nifK2 and 1,390 bp of the nifE2-homologous genes. Open reading frame nifK2 is 1,371 bp long including the stop codon TAA and encodes a polypeptide of 456 amino acids. Phylogenetic analysis of the deduced amino acid sequences of the nifK2 and nifE2 gene products from M. barkeri showed that both genes cluster most closely with the corresponding nif-1 gene products from Clostridium pasteurianum, consistent with our previous analyses of nifH2 and nifD2. The nifE gene product is known to be homologous to that of nifD, and our analysis shows that the branching pattern for the nifE proteins resembles that for the nifD product (with the exception of vnfE from Azotobacter vinelandii), suggesting that a gene duplication occurred before the divergence of nitrogenases. Primer extension showed that nifH2 had a single transcription start site located 34 nucleotides upstream of the ATG translation start site for nifH2, and a sequence resembling the archaeal consensus promoter sequence [TTTA(A/T)ATA] was found 32 nucleotides upstream from that transcription start site. A tract of four T's, previously identified as a transcription termination site in archaea, was found immediately downstream of the nifK2 gene, and a potential promoter was located upstream of the nifE2 gene. Hybridization with nifH2 and nifDK2 probes with M. barkeri RNA revealed a 4.6-kb transcript from N2-grown cells, large enough to harbor nifHDK genes and their internal open reading frames, while no transcript was detected from NH4(+)-grown cells. These results support a model in which the nitrogenase structural genes in M. barkeri are cotranscribed in a single NH4(+)-repressed operon.
Injection Well-Producer Well Combinations in THAI 'Toe-To-Heel Air Injection' (2002)

Abstract THAI – ‘Toe-to-Heel Air Injection’ is a new, short-distance displacement process, that achieves high recovery efficiency by virtue of its stable operation and ability to produce mobilised oil directly into an active section of the horizontal producer well, just ahead of the combustion front. THAI, therefore, avoids the pitfalls inherent in most conventionally operated in situ combustion (ISC) processes, which employ vertical injection-vertical producer wells to achieve longdistance displacement. However, the problem of achieving efficient ignition and start-up still requires critical attention, in order to ensure optimal process operation. A series of 3-D tests on heavy Wolf Lake crude (10.5 °API) and Athabasca Tar Sand Bitumen (8 °API) were made using well configurations: vertical (VI) or horizontal injection (HI) and horizontal producer (HP) wells in direct line drive (VIHP, HIHP); staggered line drive (VI2HP) and line drive (2VIHP). Experimentally, the horizontal injector configuration (HIHP) was found to be the most efficient for achieving rapid start-up, i.e. the shortest time to achieve stable combustion front propagation. However, injection of air via a horizontal well is not a very practical design for field operation. The single vertical injector configuration (VI2HP) was slow to achieve stable operation, due to the development of a much smaller ignition zone, initially, compared with the HIHP configuration. When hot air was used for ignition, the time delay for oil production is related to the reservoir temperature. When the initial temperature in the sandpack was 15°C, then a vertical injector, placed high in the sandpack, combined with a horizontal producer well (VIHP) achieved slower start-up than VI2HP for post-steam flood THAI, with the initial sandpack at 100°C. All of the tests achieved very high oil recoveries, averaging greater than 80% OOIP, except in the VIHP test. The recovery in the latter case was only 70% OOIP due to the loss of air injectivity during later stages of the combustion. Significantly, THAI also preserves the very substantial thermal upgrading which occurs in the mobile oil zone, averaging an increase of 6 to 8 API points.
Scheduling of event-triggered controllers on a shared network (2008)

We consider a system where a number of independent, time-triggered or event-triggered control loops are closed over a shared communication network. Each plant is described by a first-order linear stochastic system. In the event-triggered case, a sensor at each plant frequently samples the output but attempts to communicate only when the magnitude of the output is above a threshold. Once access to the network has been gained, the network is busy for T seconds (corresponding to the communication delay from sensor to actuator), after which the control action is applied to the plant. Using numerical methods, we compute the minimum-variance control performance under various common MAC-protocols, including TDMA, FDMA, and CSMA (with random, dynamic-priority, or static-priority access). The results show that event-triggered control under CSMA gives the best performance throughout.
Using multiple-point statistics to build geologically realistic reservoir models: the MPS/FDM workflow (2008)

Abstract Building geologically realistic reservoir models that honour well data and seismic-derived information remains a major challenge. Conventional variogram-based modelling techniques typically fail to capture complex geological structures while object-based techniques are limited by the amount of conditioning data. This paper presents new reservoir facies modelling tools that improve both model quality and efficiency relative to traditional geostatistical techniques. Geostatistical simulation using Multiple-Point Statistics (MPS) is an innovative depositional facies modelling technique that uses conceptual geological models as training images to integrate geological information into reservoir models. Replacing the two-point statistic variogram with multiple-point statistics extracted from a training image enables to model non-linear facies geobody shapes such as sinuous channels, and to capture complex spatial relationships between multiple facies. In addition, because the MPS algorithm is pixel-based, it can handle a large amount of conditioning data, including many wells, seismic data, facies proportion maps and curves, variable azimuth maps, and interpreted geobodies, thus reducing the uncertainty in facies spatial distribution. Facies Distribution Modelling (FDM) is a new technique to generate facies probability cubes from user-digitized depositional maps and cross-sections, well data, and vertical facies proportion curves. Facies probability cubes generated by FDM are used as soft constraints in MPS geostatistical modelling. They are critical, especially with sparse well data, to ensure that the spatial distribution of the simulated facies is consistent with the depositional facies interpretation of the field. A workflow combining MPS and FDM has been successfully used in Chevron to model important oilfield assets in both shallow- and deep-water depositional environments. Sedimentary environments can be characterized by a succession of deposition of elements, or rock bodies, through time. These elements are traditionally grouped into classes, commonly named ‘depositional facies’, based on their lithology, petrophysical properties, and biological structures. For example, the typical depositional facies encountered in fluvial environments are high permeability sand channels, with levées and crevasse splays, having a more variable range of permeability and net-to-gross ratio, within a background of low permeability shaley facies.
Increased brain expression of GPNMB is associated with genome wide significant risk for Parkinson’s disease on chromosome 7p15.3 (2017)

Genome wide association studies (GWAS) for Parkinson's disease (PD) have previously revealed a significant association with a locus on chromosome 7p15.3, initially designated as the glycoprotein non-metastatic melanoma protein B (GPNMB) locus. In this study, the functional consequences of this association on expression were explored in depth by integrating different expression quantitative trait locus (eQTL) datasets (Braineac, CAGEseq, GTEx, and Phenotype-Genotype Integrator (PheGenI)). Top risk SNP rs199347 eQTLs demonstrated increased expressions of GPNMB, KLHL7, and NUPL2 with the major allele (AA) in brain, with most significant eQTLs in cortical regions, followed by putamen. In addition, decreased expression of the antisense RNA KLHL7-AS1 was observed in GTEx. Furthermore, rs199347 is an eQTL with long non-coding RNA (AC005082.12) in human tissues other than brain. Interestingly, transcript-specific eQTLs in immune-related tissues (spleen and lymphoblastoid cells) for NUPL2 and KLHL7-AS1 were observed, which suggests a complex functional role of this eQTL in specific tissues, cell types at specific time points. Significantly increased expression of GPNMB linked to rs199347 was consistent across all datasets, and taken in combination with the risk SNP being located within the GPNMB gene, these results suggest that increased expression of GPNMB is the causative link explaining the association of this locus with PD. However, other transcript eQTLs and subsequent functional roles cannot be excluded. This highlights the importance of further investigations to understand the functional interactions between the coding genes, antisense, and non-coding RNA species considering the tissue and cell-type specificity to understand the underlying biological mechanisms in PD.
An artwork design verification system (1975)

Manual and semi-automatic methods of Integrated circuit layout are prone to errors which are often detected only after a sample chip has been fabricated. This paper describes two design verification programs that detect and identify such errors earlier in the design cycle through comparing a designer's logic description with the finished mask artwork. These programs are part of an integrated CAD system developed at RCA laboratories.
Design, Synthesis, and Biological Evaluation of Pyrrolo[2,1-<i>c</i>][1,4]benzodiazepine and Indole Conjugates as Anticancer Agents (2006)

A series of novel pyrrolo[2,1-c][1,4]benzodiazepine (PBD) hybrids linked with indole carboxylates is described. These compounds were prepared by linking C-8 of 3 (DC-81) with an indole 2-carbonyl moiety (9) through carbon chain linkers to afford PBD hybrid agents 17-21 in good yields. Preliminary in vivo tests show that these hybrid agents have potent antitumor activity. The cytotoxic studies of the hybrid agents on human melanoma A2058 cells indicate most of the hybrids induced higher cytotoxicity, better DNA-binding ability, an increase in the apoptotic sub-G1 population, and a significant reduction in deltapsi(mt) relative to compound 3. In addition, DNA flow cytometric analysis shows that hybrids actively induce a marked loss of cells from the G2/M phase of the cell cycle, which progresses to early apoptosis as detected by flow cytometry after double-staining with annexin V and propidium iodide (PI). Thus, we suggest that the hybrid agents are potent inducers of cell apoptosis in A2058 cells.
Control of Kernel Weight and Kernel Water Relations by Post-flowering Source-sink Ratio in Maize (2003)

The maize (Zea mays L.) kernel undergoes large changes in water content during its development. Whether such changes regulate the pattern of kernel development or are simply a consequence of it has not yet been established because other factors, such as assimilate supply, can also affect the rate and duration of kernel growth. This study was conducted to determine whether variation in kernel weight (KW) in response to source-sink treatments is mediated by a change in kernel water relations. Two hybrids were sown at three stand densities (one, eight and 18 plants m-2), and kernel numbers were restricted to control the post-flowering source-sink ratio within each stand density. Kernel development and water relations [water content, water potential (psiw), osmotic potential (psis) and turgor] were monitored throughout grain filling. Final KW varied from 253 to 372 mg per kernel in response to source-sink treatments. For both genotypes, variation in KW was a result of a change in kernel growth rate (r2 = 0.91; P < 0.001) and not in the duration of kernel filling. Final KW was closely correlated with maximum kernel water content (r2 = 0.94; P < 0.001) achieved during rapid dry matter accumulation. However, variation in KW was not reflected in kernel water status parameters (psiw, psis or turgor), which remained fairly stable across treatments. These results indicate that maximum water content provides an easily quantifiable measure of kernel sink capacity in maize. Kernel water status parameters may affect the duration of grain filling, but have no discernible impact on kernel growth rate.
Preparation and reactions of 1-(tert-butyldimethylsilyl)-3-lithioindole. Regioselective synthesis of 3-substituted indoles (1994)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPreparation and reactions of 1-(tert-butyldimethylsilyl)-3-lithioindole. Regioselective synthesis of 3-substituted indolesMercedes Amat, Sabine Hadida, Swargam Sathyanarayana, and Joan BoschCite this: J. Org. Chem. 1994, 59, 1, 10–11Publication Date (Print):January 1, 1994Publication History Published online1 May 2002Published inissue 1 January 1994https://pubs.acs.org/doi/10.1021/jo00080a004https://doi.org/10.1021/jo00080a004research-articleACS PublicationsRequest reuse permissionsArticle Views1580Altmetric-Citations59LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Induction of Left-Handed Helical Arrangement of 4-Nitrobenzyl Ester Residues in Cast Film from Poly(L-Glutamate) by Using a Cationic Bilayer Forming Compound (1991)

Abstract Poly(γ-4-nitrobenzyl L-glutamate) provided S-chirality with strong exciton coupling in cast film by using dihexadecylammonium bromide (2C16N+2C1) as an additive. The X-ray and IR spectra showed that the main chain formed helices. The addition of 2C16N+2C1 induced a left-handed helical conformation of the main chain, along which the chromophoric residues were helically arranged.
Cloning and Sequence of the Human Gene for P450cl7 (Steroid 17α-Hydroxylase/17,20 Lyase): Similarity with the Gene for P450c21 (1987)

P450c17 is a single cytochrome P450 enzyme mediating both 17 alpha-hydroxylase and 17,20 lyase activities in the biosynthesis of steroid hormones. We have cloned and sequenced the human P450XVIIA1 gene lying on chromosome 10, which encodes P450c17. The gene spans 6569 bp and is divided into eight exons by seven introns. This intron/exon structure closely resembles that of the P450XXI genes encoding P450c21 (steroid 21-hydroxylase), which contain 10 exons, except that the introns dividing exons 1 and 2 and exons 4 and 5 in the P450XXI gene are absent in the P450XVII gene. Furthermore, computer modeling studies indicate the conformations of P450c17 and P450c21 are very similar. The structures of the P450XXVII and P450XXI genes are very different from other classes of P450 genes. Although the production of P450c17 is under different hormonal, ontogenic, and tissue-specific controls in various types of steroidogenic cells, the adrenal and testis transcribe the P450XVIIA1 gene into P450c17 mRNAs having the same cap sites. S1 nuclease protection experiments locate the principal cap sites as a G residue lying 22 bases 3' to an atypical TTTAAA promoter, and 82 bases 3' to a typical CAAT box. The 5'-flanking DNA contains sequences similar to consensus sequences regulated by cAMP and glucocorticoids.
Ray tracing using Huygens' principle (1997)

PreviousNext No AccessSEG Technical Program Expanded Abstracts 1997Ray tracing using Huygens' principleAuthors: Orhan YilmazM. Turhan TanerOrhan YilmazSeismic Research Corporation and M. Turhan TanerSeismic Research Corporationhttps://doi.org/10.1190/1.1885782 SectionsAboutPDF/ePub ToolsAdd to favoritesDownload CitationsTrack CitationsPermissions ShareFacebookTwitterLinked InRedditEmail Permalink: https://doi.org/10.1190/1.1885782FiguresReferencesRelatedDetailsCited ByEstimation of Green's functions in complex mediaX. R. Staal and D. J. Verschuur8 August 2011 SEG Technical Program Expanded Abstracts 1997ISSN (print):1052-3812 ISSN (online):1949-4645Copyright: 1997 Pages: 2067 publication data© 1997 Copyright © 1997 Society of Exploration GeophysicistsPublisher:Society of Exploration Geophysicists HistoryPublished: 10 Feb 2005 CITATION INFORMATION Orhan Yilmaz and M. Turhan Taner, (1997), "Ray tracing using Huygens' principle," SEG Technical Program Expanded Abstracts : 1794-1797. https://doi.org/10.1190/1.1885782 Plain-Language Summary PDF DownloadLoading ...
Fingerprint attack against touch-enabled devices (2012)

Oily residues left by tapping fingers on a touch screen may breach user privacy. In this paper, we introduce the fingerprint attack against touch-enabled devices. We dust the touch screen surface to reveal fingerprints, and use an iPhone camera to carefully photograph fingerprints while striving to remove the virtual image of the phone from the fingerprint image. We then sharpen the fingerprints in an image via various image processing techniques and design effective algorithms to automatically map fingerprints to a keypad in order to infer tapped passwords. Extensive experiments were conducted on iPad, iPhone and Android phone and the results show that the fingerprint attack is effective and efficient in inferring passwords from fingerprint images. To the best of our knowledge, we are the first using fingerprint powder on touch screen and inferring passwords from fingerprints. Video at http://www.youtube.com/watch?v=vRUbJIcV9vg shows the dusting process on iPhone and video at http://www.youtube.com/watch?v=6jS6KroER3Y shows the dusting process on iPad. After dusting, password characters for login are clearly disclosed.
Using <scp>MUMmer</scp> to Identify Similar Regions in Large Sequence Sets (2003)

The MUMmer sequence alignment package is a suite of computer programs designed to detect regions of homology in long biological sequences. Version 2.1 makes several improvements to the package, including: increased speed and reduced memory requirements; the ability to handle both protein and DNA sequences; the ability to handle multiple sequence fragments; and new algorithms for clustering together basic matches. The system is particularly efficient at comparing highly similar sequences, such as alternative versions of fragment assemblies or closely related strains of the same bacterium.
Chemically Modified Peptides Targeting the PDZ Domain of GIPC as a Therapeutic Approach for Cancer (2012)

GIPC (GAIP-interacting protein, C terminus) represents a new target class for the discovery of chemotherapeutics. While many of the current generation of anticancer agents function by directly binding to intracellular kinases or cell surface receptors, the disruption of cytosolic protein-protein interactions mediated by non-enzymatic domains is an underdeveloped avenue for inhibiting cancer growth. One such example is the PDZ domain of GIPC. Previously we developed a molecular probe, the cell-permeable octapeptide CR1023 (N-myristoyl-PSQSSSEA), which diminished proliferation of pancreatic cancer cells. We have expanded upon that discovery using a chemical modification approach and here report a series of cell-permeable, side chain-modified lipopeptides that target the GIPC PDZ domain in vitro and in vivo. These peptides exhibit significant activity against pancreatic and breast cancers, both in cellular and animal models. CR1166 (N-myristoyl-PSQSK(εN-4-bromobenzoyl)SK(εN-4-bromobenzoyl)A), bearing two halogenated aromatic units on alternate side chains, was found to be the most active compound, with pronounced down-regulation of EGFR/1GF-1R expression. We hypothesize that these organic acid-modified residues extend the productive reach of the peptide beyond the canonical binding pocket, which defines the limit of accessibility for the native proteinogenic sequences that the PDZ domain has evolved to recognize. Cell permeability is achieved with N-terminal lipidation using myristate, rather than a larger CPP (cell-penetrating peptide) sequence. This, in conjunction with optimization of targeting through side chain modification, has yielded an approach that will allow the discovery and development of next-generation cellular probes for GIPC PDZ as well as for other PDZ domains.