gebhart/patrepeval huggingface dataset:
NP-MuScL: Unsupervised Global Prediction of Interaction Networks from Multiple Data Sources (2013)

Inference of gene interaction networks from expression data usually focuses on either supervised or unsupervised edge prediction from a single data source. However, in many real world applications, multiple data sources, such as microarray and ISH (in situ hybridization) measurements of mRNA abundances, are available to offer multiview information about the same set of genes. We propose ISH to estimate a gene interaction network that is consistent with such multiple data sources, which are expected to reflect the same underlying relationships between the genes. NP-MuScL casts the network estimation problem as estimating the structure of a sparse undirected graphical model. We use the semiparametric Gaussian copula to model the distribution of the different data sources, with the different copulas sharing the same precision (i.e., inverse covariance) matrix, and we present an efficient algorithm to estimate such a model in the high-dimensional scenario. Results are reported on synthetic data, where NP-MuScL outperforms baseline algorithms significantly, even in the presence of noisy data sources. Experiments are also run on two real-world scenarios: two yeast microarray datasets and three Drosophila embryonic gene expression datasets, where NP-MuScL predicts a higher number of known gene interactions than existing techniques.
Identification of TBK1 complexes required for the phosphorylation of IRF3 and the production of interferon β (2017)

The double-stranded RNA mimetic poly(I:C) and lipopolysaccharide (LPS) activate Toll-like receptors 3 (TLR3) and TLR4, respectively, triggering the activation of TANK (TRAF family member-associated NF-κB activator)-binding kinase 1 (TBK1) complexes, the phosphorylation of interferon regulatory factor 3 (IRF3) and transcription of the interferon β (IFNβ) gene. Here, we demonstrate that the TANK-TBK1 and optineurin (OPTN)-TBK1 complexes control this pathway. The poly(I:C)- or LPS-stimulated phosphorylation of IRF3 at Ser396 and production of IFNβ were greatly reduced in bone marrow-derived macrophages (BMDMs) from TANK knockout (KO) mice crossed to knockin mice expressing the ubiquitin-binding-defective OPTN[D477N] mutant. In contrast, IRF3 phosphorylation and IFNβ production were not reduced significantly in BMDM from OPTN[D477N] knockin mice and only reduced partially in TANK KO BMDM. The TLR3/TLR4-dependent phosphorylation of IRF3 and IFNβ gene transcription were not decreased in macrophages from OPTN[D477N] crossed to mice deficient in IκB kinase ε, a TANK-binding kinase related to TBK1. In contrast with the OPTN-TBK1 complex, TBK1 associated with OPTN[D477N] did not undergo phosphorylation at Ser172 in response to poly(I:C) or LPS, indicating that the interaction of ubiquitin chains with OPTN is required to activate OPTN-TBK1 in BMDM. The phosphorylation of IRF3 and IFNβ production induced by Sendai virus infection were unimpaired in BMDM from TANK KO × OPTN[D477N] mice, suggesting that other/additional TBK1 complexes control the RIG-I-like receptor-dependent production of IFNβ. Finally, we present evidence that, in human HACAT cells, the poly(I:C)-dependent phosphorylation of TBK1 at Ser172 involves a novel TBK1-activating kinase(s).
Quantifying Generalization from Trial-by-Trial Behavior of Adaptive Systems that Learn with Basis Functions: Theory and Experiments in Human Motor Control (2003)

During reaching movements, the brain's internal models map desired limb motion into predicted forces. When the forces in the task change, these models adapt. Adaptation is guided by generalization: errors in one movement influence prediction in other types of movement. If the mapping is accomplished with population coding, combining basis elements that encode different regions of movement space, then generalization can reveal the encoding of the basis elements. We present a theory that relates encoding to generalization using trial-by-trial changes in behavior during adaptation. We consider adaptation during reaching movements in various velocity-dependent force fields and quantify how errors generalize across direction. We find that the measurement of error is critical to the theory. A typical assumption in motor control is that error is the difference between a current trajectory and a desired trajectory (DJ) that does not change during adaptation. Under this assumption, in all force fields that we examined, including one in which force randomly changes from trial to trial, we found a bimodal generalization pattern, perhaps reflecting basis elements that encode direction bimodally. If the DJ was allowed to vary, bimodality was reduced or eliminated, but the generalization function accounted for nearly twice as much variance. We suggest, therefore, that basis elements representing the internal model of dynamics are sensitive to limb velocity with bimodal tuning; however, it is also possible that during adaptation the error metric itself adapts, which affects the implied shape of the basis elements.
Self-tuning control for rotational speed of slider-crank mechanism (2009)

This paper proposes a self-tuning control method based on generalized minimum variance control for rotational speed control of a slider-crank mechanism. Dynamic characteristics of the slider-crank mechanism significantly changes depending on the wheel rotational angle. Thus, to achieve a good control performance, it is necessary for the plant parameters to be identified at the each section divided into six by the wheel angle. This kind of control based on the local modeling is useful not only for such a slider-crank mechanism but also for highly-accurate positioning control systems with significant nonlinearity. The validity of the proposed method is verified through simulations and experiments.
User Intent in Multimedia Search (2016)

Today's multimedia search engines are expected to respond to queries reflecting a wide variety of information needs from users with different goals. The topical dimension (“what” the user is searching for) of these information needs is well studied; however, the intent dimension (“why” the user is searching) has received relatively less attention. Specifically, intent is the “immediate reason, purpose, or goal” that motivates a user to query a search engine. We present a thorough survey of multimedia information retrieval research directed at the problem of enabling search engines to respond to user intent. The survey begins by defining intent, including a differentiation from related, often-confused concepts. It then presents the key conceptual models of search intent. The core is an overview of intent-aware approaches that operate at each stage of the multimedia search engine pipeline (i.e., indexing, query processing, ranking). We discuss intent in conventional text-based search wherever it provides insight into multimedia search intent or intent-aware approaches. Finally, we identify and discuss the most important future challenges for intent-aware multimedia search engines. Facing these challenges will allow multimedia information retrieval to recognize and respond to user intent and, as a result, fully satisfy the information needs of users.
Neuroglycan C, a Novel Membrane-spanning Chondroitin Sulfate Proteoglycan That Is Restricted to the Brain (1995)

Monoclonal antibodies were raised to membrane-bound proteoglycans derived from rat brain, and four monoclonal antibodies that recognized a 150-kDa chondroitin sulfate proteoglycan with a core glycoprotein of 120 kDa were obtained. Immunohistological study revealed that the proteoglycan was associated with developing neurons. We screened rat brain cDNA libraries using the four monoclonal antibodies and isolated overlapping cDNA clones that encoded the entire core protein of 514 amino acids plus a 30-residue signal peptide. The deduced amino acid sequence suggested an integral membrane protein divided into five structurally different domains: an N-terminal domain to which chondroitin sulfate chains might be attached, a basic amino acid cluster consisting of seven arginine and two lysine residues, a cysteine-containing domain, a membrane-spanning segment, and a C-terminal cytoplasmic domain of 95 amino acids. On Northern blots, the cDNA hybridized with a single mRNA of 3.1 kilobases that was detectable in brains of neonatal and adult rats but not in kidney, liver, lung, and muscle of either. The sequence of the proteoglycan did not exhibit significant homology to any other known protein, indicating that the proteoglycan, designated neuroglycan C, is a novel integral membrane proteoglycan.
Rubber disk passive monitor for benzene dosimeter (1981)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTRubber disk passive monitor for benzene dosimeterMichael V. Sefton, Ennio L. Mastracci, and John L. MannCite this: Anal. Chem. 1981, 53, 3, 458–461Publication Date (Print):March 1, 1981Publication History Published online1 May 2002Published inissue 1 March 1981https://pubs.acs.org/doi/10.1021/ac00226a016https://doi.org/10.1021/ac00226a016research-articleACS PublicationsRequest reuse permissionsArticle Views44Altmetric-Citations3LEARN 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
English (1992)

The rise in the use of the English language as the language for international scientific communication in the 20th century is traced. Brief overviews are provided of world languages, artificial languages, language style in scientific communication, and English for Specific Purposes. Possible reasons for the increase in the use of English and a survey of recent research in language use in scientific communication are presented.
Targeting histone lysine demethylases — Progress, challenges, and the future (2014)

N-Methylation of lysine and arginine residues has emerged as a major mechanism of transcriptional regulation in eukaryotes. In humans, N(ε)-methyllysine residue demethylation is catalysed by two distinct subfamilies of demethylases (KDMs), the flavin-dependent KDM1 subfamily and the 2-oxoglutarate- (2OG) dependent JmjC subfamily, which both employ oxidative mechanisms. Modulation of histone methylation status is proposed to be important in epigenetic regulation and has substantial medicinal potential for the treatment of diseases including cancer and genetic disorders. This article provides an introduction to the enzymology of the KDMs and the therapeutic possibilities and challenges associated with targeting them, followed by a review of reported KDM inhibitors and their mechanisms of action from kinetic and structural perspectives.
Parasites of the German Cockroach (Blattella germanica L.) in New York City (1970)

Two nematode and 7 protozoan parasites were found in the first survey of parasites in the German cockroach, Blattella germanica L. 1785 in New York City. It is the first report of Hammerschmidtiella diesingi (Thelastomidae: Nematoda) and Endolimax blattae (Endamoebidae: Protozoa) from B. germanica. Parasites of cockroaches have been reported from throughout the world (Macadow, 1931; Chitwood, 1932; Semans, 1943; Armer, 1944; MacKinnon, 1961; Hoyte, 1961; Jenkins, 1964; and Guthrie and Tindall, 1968). There have been, however, no studies of the parasites of the common German cockroach (Blattella germanica L.) in New York City. A parasitologic survey of this species in New York City was recently completed. MATERIALS AND METHODS One hundred five (105) cockroaches, adults and nymphs of all stages, were collected from 4 apartments situated between the second and sixth floors of typical middle-class, multiple family dwellings in Manhattan. Roaches were collected with forceps, at night, from the outer surface of interior sink and toilet pipes, and placed in glass bottles. They were anesthetized with ether, and examined under a dissecting microscope (40 X ) for ectoparasites. Each roach was then dissected and separate crush preparations made of adipose tissue, hindgut, midgut, foregut, and Malpighian tubules. The diluent employed was 0.6% saline; the slides were examined under 100 X magnification using a compound microscope. Protozoans isolated were preserved with Schaudinn's fluid and stained with Heidenhain's iron hematoxylin. Nematode species were preserved in Kahle's fixative, identified, and then sent to Mrs. M. B. Chitwood (Beltsville Parasitological Laboratory, USDA) for confirmation.
Multiple sequence alignment algorithm based on a dispersion graph and ant colony algorithm (2009)

In this article, we describe a representation for the processes of multiple sequences alignment (MSA) and used it to solve the problem of MSA. By this representation, we took every possible aligning result into account by defining the representation of gap insertion, the value of heuristic information in every optional path and scoring rule. On the basis of the proposed multidimensional graph, we used the ant colony algorithm to find the better path that denotes a better aligning result. In our article, we proposed the instance of three-dimensional graph and four-dimensional graph and advanced a special ichnographic representation to analyze MSA. It is yet only an experimental software, and we gave an example for finding the best aligning result by three-dimensional graph and ant colony algorithm. Experimental results show that our method can improve the solution quality on MSA benchmarks.
Growth of epitaxial silica on vicinal Si(001) surfaces during thermal oxidation in O<sub>2</sub> (1989)

Abstract Reflection high-energy electron diffraction (RHEED) and high-resolution transmission electron microscopy (HRTEM) show that, when vicinal Si(001) surfaces, cut with a 5° tilt about [110], are thermally oxidized in very dry O2, an epitaxial crystalline phase of oxide grows along [110] ledges. X-ray photoemission confirms that the oxide is stoichiometric SiO2, This crystalline SiO2 is not a standard phase of silica. We show that it can have a cubic Bravais cell (ao=8·8 Å). We propose simple models derived from β-cristobalite, coherent with the projected Si positions given by HRTEM. Structure factors are calculated and compared with the RHEED diagrams of oxide grown on both Si(001) vicinal surfaces and ‘rough’ Si surfaces of various orientations. Finally we discuss the process involved in the growth of very thin oxide films.
Chemistry of Borabenzene:  Efficient and General Synthesis of New Neutral Borabenzene−Ligand Complexes (1996)

An array of neutral borabenzene−ligand complexes (ligand = pyridine, 2,6-lutidine, NEt3, PMe3, CN-t-Bu) have been synthesized in three straightforward steps from commercially available 1-(trimethylsilyl)-1,4-pentadiyne. An X-ray crystal structure of borabenzene−PMe3 is reported.
Highly Flexible Row and Column Redundancy and Cycle Time Adaptive Read Data Path for Double Data Rate Synchronous Memories (2005)

This paper describes two circuit techniques useful for the design of high density and high speed low cost double data rate memories. One is a highly flexible row and column redundancy circuit which allows the division of flexible row redundancy unit into multiple column redundancy unit for higher flexibility, with a new test mode circuit which enables the use of the finer pitch laser fuse. Another is a compact read data path which allows thp smooth data flow without wait time in the high frequency operation with less area penalty. These circuit techniques achieved the compact chip size with the cell efficiency of 60.6% and the high bandwidth of 400MHz operation with CL=2.5.
Systems approach to Information Security Governance: An imperative need for sustainability of enterprises (2011)

In most of the current or past Information Security Governance programs for enterprises', the approaches used are poor. These approaches do not provide or deal with the systemic view of enterprises' information security governance and the emergent issues for its sustenance. In this paper, the author proposes two system models of enterprise information security governance based on systems thinking concepts. The first model, InfoSGov is used for assessing the current state of Enterprises' Information security governance and the second model, GovInfoS is used for proposing the future state and its sustenance. The application of these models in a large telecom enterprise using the qualitative tools developed, is provided. It has demonstrated the practical use of the models and tools for assessment and sustenance of the enterprise with respect to information security governance.
Estrategias y políticas antitabaco: la estrategia ausente (2017)

Globally, smoking represents the leading risk factor for early death and disability worldwide. Since 1990, smoking has claimed more than 7 million lives each year and its contribution to the burden of disease globally continues to grow, with greater emphasis on lower income countries. The negative effects of smoking extend far beyond individual and collective health, as billions of dollars lost in productivity and health expenditures are related to tobacco use (1,2)
CD4 T Lymphocyte Activation in Acute Severe Asthma (1991)

The expression of activation molecules on peripheral-blood CD4 and CD8 T lymphocytes and the serum concentrations of two products of activated T lymphocytes [interferon-gamma (IFN-gamma) and soluble interleukin-2 receptor (sIL-2R)] were measured in patients with acute severe asthma (ASA) and controls. Significantly higher percentages of CD4+ cells from patients with ASA expressed IL-2R, HLA-DR and VLA-1 as compared to controls (p less than 0.01). In contrast, CD8+ cells from both asthmatics and controls did not express IL-2R and VLA-1, and their expression of HLA-DR in asthmatics was not increased. Serum concentrations of IFN-gamma and sIL-2R were significantly elevated in patients with ASA as compared to control groups (p less than 0.01). Concentrations decreased as the patients improved clinically following therapy. Significant correlations were observed between the improvements in airways obstruction and (1) the decreases in the percentages of peripheral-blood IL-2R+ T lymphocytes and (2) the decreases in serum concentrations of sIL-2R. These observations suggest that CD4 T lymphocyte activation is important in the pathogenesis of ASA.
The systematic errors in the random coincidence estimation using a delayed window (2009)

With the advance of new technology, PET systems nowadays have much higher sensitivities than before with the adoption of faster scintillators, faster electronics, larger solid angle detectors and full 3D data collection mode. All of these lead to the increasing of the random coincidences that will affect the image quality. Accurate random correction is important for the quantitative imaging in PET applications. Delayed window method is widely used for random coincidences estimation. However, this method is not mathematically accurate. The difference between the delayed window randoms and the prompt window randoms can be significant under certain conditions. We studied the details of these differences using Monte Carlo simulations since this is the only way to separate the real random events from the true and scattered events. Three phantoms are used in the study, including the NEMA1994 20-cm long phantom, NEMA2001 70-cm long phantom and a 10-cm long, 1-cm diameter small cylinder phantom. The PET system used in this study is a 12-module LYSO camera with 20-cm axial FOV and 54-cm ring diameter to simulate a brain PET system. Two policies for the multiple events handling are used: reject-all-multiples, and take-all-goods. Random rates and NECR as the function of activities from prompt window and delayed window are obtained. The simulation results show that 1) The take-all-goods policy will underestimate the randoms rate and the reject-all-multiples will overestimate the randoms, which results overestimation of NECR for take-all-goods policy and underestimation of NECR for reject-all-multiples policy; 2) The discrepancy is more significant for smaller phantom than bigger phantom. This study demonstrates the intrinsic discrepancy for random coincidence estimation by the delayed window method. When the phantom is relatively small compared to the FOV dimension of the PET system, the discrepancy is big enough to produce non-negligible errors.
Joint PP and PS Stratigraphic Inversion for Prestack Time Migrated Multicomponent Data (2005)

P16 JOINT PP AND PS STRATIGRAPHIC INVERSION FOR PRESTACK TIME MIGRATED MULTICOMPONENT DATA Summary 1 The goal of this paper is to improve the determination of a target zone located in a slowly laterally varying background by jointly inverting PP and PS waves available in prestack time migrated multicomponent data while taking into account a priori information (well log data geological knowledge...) in the inversion process: an optimal elastic model is estimated together with an optimal correspondence between PP and PS events. The methodology and results are illustrated on a 2D realistic synthetic example. Introduction YOHAN AGULLO* DANIELE MACE KARINE
Doubling of the Bands in Overdoped<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mrow><mml:msub><mml:mrow><mml:mrow><mml:msub><mml:mrow><mml:mi>Bi</mml:mi></mml:mrow><mml:mrow><mml:mn>2</mml:mn></mml:mrow></mml:msub></mml:mrow><mml:mrow><mml:msub><mml:mrow><mml:mi>Sr</mml:mi></mml:mrow><mml:mrow><mml:mn>2</mml:mn></mml:mrow></mml:msub></mml:mrow><mml:mrow><mml:msub><mml:mrow><mml:mi>CaCu</mml:mi></mml:mrow><mml:mrow><mml:mn>2</mml:mn></mml:mrow></mml:msub></mml:mrow><mml:mi>O</mml:mi></mml:mrow><mml:mrow><mml:mn>8</mml:mn><mml:mo>+</mml:mo><mml:mi mathvariant="italic">δ</mml:mi></mml:mrow></mml:msub></mml:mrow></mml:math>: Evidence for<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mi mathvariant="italic">c</mml:mi></mml:math>-Axis Bilayer Coupling (2001)

We present high resolution angle resolved photoemission data of the bilayer superconductor Bi(2)Sr(2)CaCu(2)O(8+delta) (Bi2212) showing a clear doubling of the near E(F) bands. This splitting approaches zero along the (0,0)-->(pi,pi) nodal line and is not observed in single layer Bi(2)Sr(2)CuO(6+delta) (Bi2201), indicating that the splitting is due to the long sought after bilayer splitting effect. The splitting has a magnitude of approximately 75 meV near the middle of the zone, extrapolating to about 110 meV near the (pi,0) point. The existence of these two bands also helps to clear up the recent controversy concerning the topology of the Fermi surface.
[Therapeutic effects of borneol-walnut oil in the treatment of purulent otitis media]. (1990)

170 patients were treated with borneol-walnut oil of various concentrations, and the controls (108 patients) were treated with neomycin compound. As a result, the total effective rates were 98.06% and 84.26% respectively (P less than 0.001). This indicated that the therapeutic effects of borneol-walnut oil for the treatment of purulent otitis media were superior to that of neomycin compound. The most optimal concentration of borneol-walnut oil was 20% through clinical and laboratory observations. Due to its simple composition, significant therapeutic effects and nontoxic reactions, the borneol-walnut oil has been proved a promising external remedy for the treatment of purulent otitis media.