gebhart/patrepeval huggingface dataset:
Aspartic Acid Homozygosity at Codon 57 of HLA-DQ β Is Associated with Susceptibility to Pulmonary Tuberculosis in Cambodia (2006)

After infection with Mycobacterium tuberculosis, clinical disease usually remains latent, contained by the host immune response. Although polymorphisms of HLA loci have been hypothesized to play a major role in the breakdown of latency, a functional link has not been established. Molecular-based HLA-typing methods were used to test the association of sets of HLA alleles encoding an aspartic acid at codon 57 of the HLA-DQ beta-chain (HLA-DQ beta57-Asp) with susceptibility to tuberculosis in a cohort of 436 pulmonary tuberculosis patients and 107 healthy controls from Cambodia. HLA class II null cells were transduced with HLA-DQ beta57-Asp or HLA-DQ beta57-Ala and evaluated for their ability to bind peptides from two immunogenic M. tuberculosis specific proteins, ESAT-6 and CFP-10. In this study, we report a highly significant association between progressive pulmonary tuberculosis and homozygosity for HLA-DQ beta57-Asp alleles. The presence of HLA-DQ beta57-Asp resulted in a significantly reduced ability to bind a peptide from the central region of the ESAT-6 protein. Furthermore, when this peptide was presented by an HLA-DQ beta57-Asp allele, Ag-specific IFN-gamma production from CD4+ T cells from tuberculosis patients was significantly less than when this peptide was presented by an HLA-DQ-beta allele encoding an alanine at codon 57. Multiple genetic loci and ethnic-specific factors are likely involved in the human immune response to tuberculosis. The data presented here provide a functional explanation for a highly significant association between an HLA polymorphism and tuberculosis in a highly characterized group of patients with susceptibility to progressive tuberculosis infection in Cambodia.
Paper and Board Pigment Coating Raw Materials – A Review of some Recent Innovative Novelties (2012)

The intention of this paper is to review of some recent innovative novelties about paper and board pigment coating raw materials. First an overview is given of “traditional” coating raw materials and the coating process. Then new starch based pigments and binders as well as novel plastic pigments are reviewed regarding their effect on coated paper properties. Finally it is concluded that further innovations and research are needed.
Convex relaxations of structured matrix factorizations (2013)

We consider the factorization of a rectangular matrix $X $ into a positive linear combination of rank-one factors of the form $u v^\top$, where $u$ and $v$ belongs to certain sets $\mathcal{U}$ and $\mathcal{V}$, that may encode specific structures regarding the factors, such as positivity or sparsity. In this paper, we show that computing the optimal decomposition is equivalent to computing a certain gauge function of $X$ and we provide a detailed analysis of these gauge functions and their polars. Since these gauge functions are typically hard to compute, we present semi-definite relaxations and several algorithms that may recover approximate decompositions with approximation guarantees. We illustrate our results with simulations on finding decompositions with elements in $\{0,1\}$. As side contributions, we present a detailed analysis of variational quadratic representations of norms as well as a new iterative basis pursuit algorithm that can deal with inexact first-order oracles.
The Admid System: Generation of Recombinant Adenoviruses by Tn7-Mediated Transposition in <i>E. coli</i> (2000)

A new system has been developed for generating recombinant adenoviruses by Tn7-mediated transposition in E. coli. Low copy number E. coli plasmids containing a full-length adenoviral genome with lacZattTn7 replacing E1 have been constructed. The adenovirus plasmid or admid, as well as high copy number progenitors, were stably maintained in E. coli strain DH10B. Several transfer vectors containing a mammalian expression cassette flanked by Tn7R and Tn7L were used as donors to transpose the mini-Tn7 into the E1 region of the adenoviral genome. Transposed recombinant admids are readily identified by their beta-galactosidase phenotype. Transfection of admid DNA into producer cells resulted in the efficient production of infectious adenovirus. This easy-to-use, efficient system generates pure, clonal stocks of recombinant adenovirus without successive rounds of plaque purification.
In Situ Method Correlating Raman Vibrational Characteristics to Chemical Expansion via Oxygen Nonstoichiometry of Perovskite Thin Films (2019)

Effective integration of perovskite films into devices requires knowledge of their electro-chemomechanical properties. Raman spectroscopy is an excellent tool for probing such properties as the films' vibrational characteristics couple to the lattice volumetric changes during chemical expansion. While lattice volumetric changes are typically accessed by analyzing Raman shifts as a function of pressure, stress, or temperature, such methods can be impractical for thin films and do not capture information on chemical expansion. An in situ Raman spectroscopy technique using an electrochemical titration cell to change the oxygen nonstoichiometry of a model perovskite film, Sr(Ti,Fe)O<sub>3-</sub> <sub>y</sub> , is reported and the lattice vibrational properties are correlated to the material's chemical expansion. How to select an appropriate Raman vibrational mode to track the evolution in oxygen nonstoichiometry is discussed. Subsequently, the frequency of the oxygen stretching mode around Fe<sup>4+</sup> is tracked, as it decreases during reduction as the material expands and increases during reoxidation as the material shrinks. This methodology of oxygen pumping and in situ Raman spectroscopy of oxide films enables future in operando measurements even for small material volumes, as is typical for applications of films as electrodes or electrolytes utilized in electrochemical energy conversion or memory devices.
Rutaecarpine, a Quinazolinocarboline Alkaloid, Inhibits Prostaglandin Production in RAW264.7 Macrophages (2001)

In order to delineate the mechanism involved in the anti-inflammatory activity of rutaecarpine, its effects on the production of prostaglandin (PG) and therein involved enzymes were examined. Rutaecarpine reduced the production of PGE(2) in RAW264.7 cells treated with lipopolysaccharide (LPS) in a dose dependent manner when added to the culture media at the time of stimulation. However, the inhibition of total cellular cyclooxygenase (COX) activity under the same experimental condition was observed only at high concentrations of rutaecarpine. Rutaecarpine did not affected the levels of COX-2 mRNA and protein in macrophages stimulated with LPS. Calcium ionophore A23187 induced-PG production and [(3)H]-arachidonic acid release were significantly decreased by the pretreatment of rutaecarpine for 30 minutes. With the same treatment schedule, however, rutaecarpine failed to alter the activities of cellular COX-1 and COX-2. Collectively, our data suggest that anti-inflammatory effect of rutaecarpine is, at least in part, ascribed to the diminution of PG production through inhibition of arachidonic acid release albeit the nature of its effects on PLA(2) activity remains to be elaborated.
Using accent-specific pronunciation modelling for improved large vocabulary continuous speech recognition (1997)

A method of modelling accent-specific pronunciation variations is presented. Speech from an unseen accent group is phonetically transcribed such that pronunciation variations may be derived. These context-dependent variations are clustered in decision trees which are used as a model of the pronunciation variation associated with this new accent group. The trees are then used to build a new pronunciation dictionary for use during the recognition process. Experiments are presented, based on Wall Street Journal and WSJCAM0 corpora, for the recognition of American speakers using a British English recogniser. Speaker independent as well as speaker dependent adaptation scenarios are presented, giving up to 20% reduction in word error rate. A linguistic analysis of the pronunciation model is presented and finally the technique is combined with maximum likelihood linear regression, a well proven acoustic adaptation technique, yielding further improvement.
Silencing Onion Lachrymatory Factor Synthase Causes a Significant Change in the Sulfur Secondary Metabolite Profile   (2008)

Through a single genetic transformation in onion (Allium cepa), a crop recalcitrant to genetic transformation, we suppressed the lachrymatory factor synthase gene using RNA interference silencing in six plants. This reduced lachrymatory synthase activity by up to 1,544-fold, so that when wounded the onions produced significantly reduced levels of tear-inducing lachrymatory factor. We then confirmed, through a novel colorimetric assay, that this silencing had shifted the trans-S-1-propenyl-l-cysteine sulfoxide breakdown pathway so that more 1-propenyl sulfenic acid was converted into di-1-propenyl thiosulfinate. A consequence of this raised thiosulfinate level was a marked increase in the downstream production of a nonenzymatically produced zwiebelane isomer and other volatile sulfur compounds, di-1-propenyl disulfide and 2-mercapto-3,4-dimethyl-2,3-dihydrothiophene, which had previously been reported in trace amounts or had not been detected in onion. The consequences of this dramatic simultaneous down- and up-regulation of secondary sulfur products on the health and flavor attributes of the onion are discussed.
Chronic Medical Conditions and Risk of Sepsis (2012)

Individuals with chronic medical conditions are at increased risk of future sepsis events.
Fault diagnosis in turbine engines using unsupervised neural networks technique (2004)

A fault diagnosis system based on the neural networks clustering technique is developed for a mid-sized jet propulsion engine. The currently recorded data set for this engine has several limitations in its quality, which results in the lack of information required for the incipient fault detection and wide coverage of failure modes. Using the residuals of core speed, exhausted gas temperature and fuel flow, the developed system is designed to diagnose the failures related to combustor liner, bleed band, and exhausted gas temperature (EGT) sensor rake. The fault diagnosis system reports not only the machine condition but also the belief factor convincing the diagnostic decisions. In this work the actual flight data collected in the field is used to develop and validate the system, and the results are shown for the test on five engines which had experienced three different failures. The presented system is implemented in the form of web-based service and has demonstrated its robustness by isolating the failures successfully in the field.
Locally adaptive detection algorithm for forward-looking ground-penetrating radar (2010)

This paper proposes an effective anomaly detection algorithm for a forward-looking ground-penetrating radar (FLGPR). One challenge for threat detection using FLGPR is its high dynamic range in response to different kinds of targets and clutter objects. The application of a fixed threshold for detection often yields a large number of false alarms. We propose a locally-adaptive detection method that adjusts the detection criteria automatically and dynamically across different spatial regions, which improves the detection of weak scattering targets. The paper also examines a spectrum-based classifier. This classifier rejects false alarms (FAs) by classifying each alarm location based on its spatial frequency-spectrum. Experimental results for the improved detection techniques are demonstrated by field data measurements from a US Army test site.
Amino-substituted sulfonium salts. Synthesis and stereochemistry (1978)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAmino-substituted sulfonium salts. Synthesis and stereochemistryAlan H. Cowley, Donald J. Pagel, and Michael L. WalkerCite this: J. Am. Chem. Soc. 1978, 100, 22, 7065–7066Publication Date (Print):October 1, 1978Publication History Published online1 May 2002Published inissue 1 October 1978https://pubs.acs.org/doi/10.1021/ja00490a049https://doi.org/10.1021/ja00490a049research-articleACS PublicationsRequest reuse permissionsArticle Views151Altmetric-Citations22LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Synthesis and adrenergic properties of new duplicated analogs of methoxamine. (1991)

New duplicated analogs of the alpha 1-selective agonist methoxamine and of its cyclic derivative 5,8-dimethoxy-1,2,3,4-tetrahydro-2-naphthylamine have been synthesized and tested for their adrenergic properties. All the compounds prepared, presenting a polymethylene spacer of varying length between two units of the active structure, turned out to be completely devoid of any alpha-stimulating activity. Surprisingly, some of them showed a marked beta-adrenergic agonistic effect, being the most interesting compound active at nanomolar concentration.
Cu<sup>2+</sup> Colorimetric Sensing and Fluorescence Enhancement and Hg<sup>2+</sup> Fluorescence Diminution in “Scorpionate”-like Tetrathienyl-Substituted Boron−Dipyrrins (2007)

Four novel tetrathienyl-substituted boron-dipyrrin-type (BODIPY-type) complexes, 3-(R')-4,4-di(R')-8-R-4-bora-3a,4a-diaza-s-indacene (4a, R = 2-T, R' = 2-T; 4b, R = 3-T, R' = 2-T; 5a, R = 2-T, R' = 3-T; 5b, R = 3-T, R' = 3-T; T = thienyl) have been prepared and fully characterized to explore patterns of stoichiometric Mn+ recognition in solution. Treatment of the respective parent BF2 dipyrrin with 2- or 3-thienyllithium gave the unexpected asymmetric tetrathienyl-substituted products in 8.5-35% yield. Compounds 4a and 4b bear a neutral "scorpionate"-like [SSS] tridentate binding pocket. Extensive NMR and UV-vis spectroscopic studies were performed on 4a-5b; 5a, 4b, and 5b were structurally characterized. The PhiF values for 4a-5b all decrease compared to the BF2-containing parent molecules (0.00058, 0.012, 0.00090, and 0.0051, respectively), with lambda(abs,max) values (epsilon, M(-1) cm(-1)) of 563 (44,000), 553 (29,000), 539 (33,000), and 531 (44,000) nm, respectively, and Stokes' shifts of 25-36 nm. Upon treatment with metal ion (Ca2+, Cs+, Mn2+, Co2+, Cu2+, Ag+, Zn2+, Cd2+, Hg2+, Pb2+) perchlorate salts, the solution of 4b undergoes rapid pink-to-clear switch-off behavior upon Cu2+ addition (10 microM scale) with smaller effects seen for 4a. Further, there were 2- to 19-fold Cu2+ fluorescence enhancements for these ligands. Cu2+- and Hg2+-L (L = 4a-5b) binding was modeled, and response patterns for Mn+-L 1:1 molar solutions upon Cu2+ addition were measured. Upon treatment with Hg2+, all ligand solutions show a significant fluorescence decrease accompanied by minor absorption increases. The UV-vis spectroscopic detection limit for Cu2+ and Hg2+ is approximately 270 ppb and approximately 1.7 ppm, respectively; the naked eye detection limit for Cu2+ with 4b (1.0 x 10(-5) M) is approximately 23 microM. DFT calculations gave HOMO-LUMO gaps of 478 (4a), 462 (4b), 448 (5a), and 442 nm (5b). Molecular orbital diagrams for 4a-5b revealed that the HOMO and LUMO electron density is distributed onto the 3-position-thienyl group and to a lesser degree the B(thienyl)2 moiety.
Prediction of engraftment after autologous peripheral blood progenitor cell transplantation: CD34, colony‐forming unit–granulocyte‐macrophage, or both? (2007)

For prediction of hematologic recovery after autologous PBPC transplantation, determination of CFU-GM dose does not add to the predictive value of the CD34+ dose.
How to Run an Automated Transportation System (1972)

The synchronous longitudinal guidance (SLG) approach to allocating guideway space and controlling traffic in a ground transportation network is described in this paper. The transportation system considered is one in which completely automated vehicles follow deterministic position-time profiles during their travel through the network. The key feature in the SLG approach is a dynamic scheduling algorithm which allocates guideway space to vehicles in such a way that the capacity of critical points (or bottlenecks) in the network is not exceeded. This guarantees that traffic flows smoothly through the entire network and that queues are confined to the entrances. Two scheduling algorithms are Identified in this paper. The basic slot allocation algorithm used in processing vehicle trip requests is outlined first. Then the more general cycle allocation algorithm, which is suitable for control of large networks, is described. The results of a computer simulation of a network run using the latter algorithm are summarized, and the required auxiliary SLG functions of entrance and exit control, merge control, and safety assurance are discussed briefly.
Monolithic analog READ-ONLY memory for character generation (1971)

Two novel circuit techniques are used. One is a compact analog memory element that is able to store a pair of coordinate values; eighty such elements can be placed on a 65/spl times/65 mil die. The other is a scanning technique that utilizes a resistive ladder network coupled to an array of common- emitter transistors, having obvious applications in other areas, for example as an analog-digital converting technique.
Abstract 93: COSMIC: The catalogue of somatic mutations in cancer receives full genome variant annotations (2010)

Abstract COSMIC, the Catalogue Of Somatic Mutations In Cancer (http://www.sanger.ac.uk/cosmic), is one of the most comprehensive web systems describing the impact of somatic mutations in human cancer. The information is sourced directly from the published scientific literature and the Cancer Genome Project's high throughput sequencing laboratories at the Wellcome Trust Sanger Institute UK (CGP), allowing a high data quality to be maintained. The v44 release (Nov. 2009) contained the curation of 8336 papers covering 71 known cancer genes by point mutation and 30 by gene fusion. The mutation data for all these genes is being maintained up-to-date and new genes are regularly added to this list. Additionally, 4871 genes and 2764 samples have been scrutinized by the CGP laboratories. As cancer genetics moves toward the analysis of whole genomes, COSMIC is being updated to handle and display these data and increase the functionality of the website. With the rapid development of sequencing technologies, the quantity of data that can be put into COSMIC is increasing fast. We have extended our curation process to include large exome-wide candidate gene screens, recently including the first such screen from Sjoblom et al (2006), and the first TCGA screen (2008) with other large scale screening datasets being curated. In addition, whole-genome screens are becoming available with many non-coding variations. From the CGP laboratories, we already have two low-coverage genome rearrangement screens in COSMIC and this will rapidly expand, beginning with the imminent release of rearrangement scans in a set of 24 breast tumours. High-coverage genome analyses are also beginning to become available; with full genome coverage, the majority of somatic mutations in a tumour can be identified and COSMIC is being prepared to receive and display this data. With the inclusion of these new data, the COSMIC website has evolved to allow more easy access to required data. New specialization filters are in place to provide methods to search for subsets of COSMIC data in the usual user-friendly web pages. More extensive investigations can be performed using the new COSMIC Biomart, an industry-standard data mining system allowing access through web pages or programmatic interfaces. As the inclusion of new genomic data accelerates and the systems through which it can be accessed evolve, COSMIC is well placed to remain a central resource in human cancer genetics. Note: This abstract was not presented at the AACR 101st Annual Meeting 2010 because the presenter was unable to attend. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 93.
Adaptive Quantization Matrices for HD and UHD Resolutions in Scalable HEVC (2016)

High Efficiency Video Coding (HEVC), and its standardized extensions including Scalable HEVC (SHVC), contains a feature to enable default or custom Quantization Matrices (QMs). The default intra QM technique in HEVC, originally designed for the JPEG standard [1, 2], is based on a perceptual Human Visual System (HVS) Contrast Sensitivity Function (CSF) approach and its associated Modulation Transfer Function (MTF) [3]. Visual Display Units (VDUs), capable of displaying video data at High Definition (HD) and Ultra HD (UHD) display resolutions, are frequently utilized in a vast variety of technological domains. Compression artifacts caused by quantization, which are not noticeable in low display resolution environments, are clearly visible on HD and UHD video data and VDUs.
Sleepiness and Ethanol Effects on Simulated Driving (1994)

Twelve healthy young men were assessed in each of four experimental conditions presented in a Latin Square design: 8-hr time in bed (TIB) and placebo, 4-hr TIB and placebo, 8-hr TIB and ethanol, and 4-hr TIB and ethanol. After consuming ethanol (0.6 g/kg) or placebo (0900-0930 hr) with 20% supplements at 1030 and 1100 hr, subjects were tested for sleepiness (Multiple Sleep Latency Test at 1000, 1200, 1400, and 1600 hr) and divided attention (1030 hr) performance on day 1, and for simulated driving and divided attention (1000-1200 and 1400-1600 hr) performance on day 2. In the morning testing, with breath ethanol concentrations (BECs) averaging 0.049%, sleepiness was increased, divided attention reaction times increased (on both days), and simulated driving performance was disturbed in the ethanol and 4-hr TIB relative to placebo. Similarly in the afternoon, with BECs averaging 0.013%, the ethanol and 4-hr TIB condition increased sleepiness and disrupted divided attention and simulated driving performance. The results show that sleepiness and low-dose ethanol combine to impair simulated automobile driving, an impairment that extends beyond the point at which BEC reaches zero. They provide a possible explanation for the incidence of alcohol-related automobile accidents at low BECs.
Adaptive array processing using the Davies beamformer (1986)

The paper presents and analyses a simple and fast adaptive array based on the Davies null-steering beamformer [1]. The use of perturbation algorithms on this beamformer is investigated. The convergence time constants and misadjustment are derived. It is shown that, if the feedback factors for these algorithms are appropriately normalised, the time constants can be roughly equalised, resulting in fast convergence behaviour.