gebhart/patrepeval huggingface dataset:
Deep Feature Selection: Theory and Application to Identify Enhancers and Promoters (2016)

Sparse linear models approximate target variable(s) by a sparse linear combination of input variables. Since they are simple, fast, and able to select features, they are widely used in classification and regression. Essentially they are shallow feed-forward neural networks that have three limitations: (1) incompatibility to model nonlinearity of features, (2) inability to learn high-level features, and (3) unnatural extensions to select features in a multiclass case. Deep neural networks are models structured by multiple hidden layers with nonlinear activation functions. Compared with linear models, they have two distinctive strengths: the capability to (1) model complex systems with nonlinear structures and (2) learn high-level representation of features. Deep learning has been applied in many large and complex systems where deep models significantly outperform shallow ones. However, feature selection at the input level, which is very helpful to understand the nature of a complex system, is still not well studied. In genome research, the cis-regulatory elements in noncoding DNA sequences play a key role in the expression of genes. Since the activity of regulatory elements involves highly interactive factors, a deep tool is strongly needed to discover informative features. In order to address the above limitations of shallow and deep models for selecting features of a complex system, we propose a deep feature selection (DFS) model that (1) takes advantages of deep structures to model nonlinearity and (2) conveniently selects a subset of features right at the input level for multiclass data. Simulation experiments convince us that this model is able to correctly identify both linear and nonlinear features. We applied this model to the identification of active enhancers and promoters by integrating multiple sources of genomic information. Results show that our model outperforms elastic net in terms of size of discriminative feature subset and classification accuracy.
Knowledge-aware and conversational recommender systems (2018)

More and more precise and powerful recommendation algorithms and techniques have been proposed over the last years able to effectively assess users' tastes and predict information that would probably be of interest for them. Most of these approaches rely on the collaborative paradigm (often exploiting machine learning techniques) and do not take into account the huge amount of knowledge, both structured and non-structured ones, describing the domain of interest for the recommendation engine. The aim of knowledge-aware and conversational recommender systems is to go beyond the traditional accuracy goal and to start a new generation of algorithms and interactive approaches which exploit the knowledge encoded in ontological and logic-based knowledge bases, knowledge graphs as well as the semantics emerging from the analysis and exploitation of semi-structured textual sources.
Shewanella oneidensis MR-1 Uses Overlapping Pathways for Iron Reduction at a Distance and by Direct Contact under Conditions Relevant for Biofilms (2005)

We developed a new method to measure iron reduction at a distance based on depositing Fe(III) (hydr)oxide within nanoporous glass beads. In this "Fe-bead" system, Shewanella oneidensis reduces at least 86.5% of the iron in the absence of direct contact. Biofilm formation accompanies Fe-bead reduction and is observable both macro- and microscopically. Fe-bead reduction is catalyzed by live cells adapted to anaerobic conditions, and maximal reduction rates require sustained protein synthesis. The amount of reactive ferric iron in the Fe-bead system is available in excess such that the rate of Fe-bead reduction is directly proportional to cell density; i.e., it is diffusion limited. Addition of either lysates prepared from anaerobic cells or exogenous electron shuttles stimulates Fe-bead reduction by S. oneidensis, but iron chelators or additional Fe(II) do not. Neither dissolved Fe(III) nor electron shuttling activity was detected in culture supernatants, implying that the mediator is retained within the biofilm matrix. Strains with mutations in omcB or mtrB show about 50% of the wild-type levels of reduction, while a cymA mutant shows less than 20% of the wild-type levels of reduction and a menF mutant shows insignificant reduction. The Fe-bead reduction defect of the menF mutant can be restored by addition of menaquinone, but menaquinone itself cannot stimulate Fe-bead reduction. Because the menF gene encodes the first committed step of menaquinone biosynthesis, no intermediates of the menaquinone biosynthetic pathway are used as diffusible mediators by this organism to promote iron reduction at a distance. CymA and menaquinone are required for both direct and indirect mineral reduction, whereas MtrB and OmcB contribute to but are not absolutely required for iron reduction at a distance.
Quasiparticle lifetimes and tunneling times in a superconductor-insulator-superconductor tunnel junction with spatially inhomogeneous electrodes (1994)

The low-energy quasiparticle scattering and recombination lifetimes for a proximity sandwich of two superconductors S and S' with different bulk energy gaps, are calculated as a function of the spatial coordinate and temperature. The spatial dependence of the order parameter and density of states are calculated on the basis of a microscopic model of the proximity effect, based on the Usadel equations, for dirty superconductors in thermal equilibrium. A zero boundary resistance between S and S' and a Boltzmann-like energy distribution of the excess quasiparticles are assumed. In the case of a small diffusion time constant an effective quasiparticle relaxation rate into and excitation rate out of the reduced gap region in the SS' sandwich are obtained as a function of (finite, but low) temperature and strength of the proximity effect, determined by the parameter ${\ensuremath{\gamma}}_{\mathit{m}}$, by averaging over the energies and positions of the quasiparticles. In the same way effective tunneling times for electrons and holes tunneling out of the trap in the SS' sandwich to the other electrode of an SS'IS''S junction are determined as a function of temperature, voltage, and ${\ensuremath{\gamma}}_{\mathit{m}}$.
Defining the biological basis of radiomic phenotypes in lung cancer (2017)

Medical imaging can visualize characteristics of human cancer noninvasively. Radiomics is an emerging field that translates these medical images into quantitative data to enable phenotypic profiling of tumors. While radiomics has been associated with several clinical endpoints, the complex relationships of radiomics, clinical factors, and tumor biology are largely unknown. To this end, we analyzed two independent cohorts of respectively 262 North American and 89 European patients with lung cancer, and consistently identified previously undescribed associations between radiomic imaging features, molecular pathways, and clinical factors. In particular, we found a relationship between imaging features, immune response, inflammation, and survival, which was further validated by immunohistochemical staining. Moreover, a number of imaging features showed predictive value for specific pathways; for example, intra-tumor heterogeneity features predicted activity of RNA polymerase transcription (AUC = 0.62, p=0.03) and intensity dispersion was predictive of the autodegration pathway of a ubiquitin ligase (AUC = 0.69, p<i><</i>10<sup>-4</sup>). Finally, we observed that prognostic biomarkers performed highest when combining radiomic, genetic, and clinical information (CI = 0.73, p<10<sup>-9</sup>) indicating complementary value of these data. In conclusion, we demonstrate that radiomic approaches permit noninvasive assessment of both molecular and clinical characteristics of tumors, and therefore have the potential to advance clinical decision-making by systematically analyzing standard-of-care medical images.
Two Modes of Self-Coordinating Edge-over-Edge Zn(II) Porphyrin Dimerization:  A Structural and Spectroscopic Comparison (1996)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTTwo Modes of Self-Coordinating Edge-over-Edge Zn(II) Porphyrin Dimerization: A Structural and Spectroscopic Comparison†Robert T. Stibrany, Jayasree Vasudevan, Spencer Knapp, Joseph A. Potenza, Tom Emge, and Harvey J. SchugarView Author Information Department of Chemistry, Rutgers The State University of New Jersey New Brunswick, New Jersey 08855 Cite this: J. Am. Chem. Soc. 1996, 118, 16, 3980–3981Publication Date (Web):April 24, 1996Publication History Received1 November 1995Published online24 April 1996Published inissue 24 April 1996https://pubs.acs.org/doi/10.1021/ja9536734https://doi.org/10.1021/ja9536734rapid-communicationACS PublicationsCopyright © 1996 American Chemical SocietyRequest reuse permissionsArticle Views643Altmetric-Citations92LEARN 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 (3)»Supporting Information Supporting Information SUBJECTS:Absorption,Monomers,Oligomers,Pyridines,Pyrroles Get e-Alerts
Optimization of fatty alcohol biosynthesis pathway for selectively enhanced production of C12/14 and C16/18 fatty alcohols in engineered Escherichia coli (2012)

To our knowledge, this is the first report on selective production of C12/14 and C16/18 alcohols by microbial fermentation. This work achieved high-specificity production of both C12/14 and C16/18 alcohols. The encouraging 598.6 mg/L of fatty alcohols represents the highest titer reported so far. In addition, the 101.5 mg/L 89.2% C16/18 alcohol suggests an important breakthrough in C16/18 alcohol production. A more detailed optimization of the expression level of fatty alcohol biosynthesis pathway may contribute to a further improvement of fatty alcohol production.
Reactions of platinum(II) aqua complexes. 3. Multinuclear (nitrogen-15, platinum-195, carbon-13, and proton) NMR study of reactions of aqua and hydroxo complexes with glycine and (methylimino)diacetic acid (1985)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTReactions of platinum(II) aqua complexes. 3. Multinuclear (nitrogen-15, platinum-195, carbon-13, and proton) NMR study of reactions of aqua and hydroxo complexes with glycine and (methylimino)diacetic acidTrevor G. Appleton, John R. Hall, and Stephen F. RalphCite this: Inorg. Chem. 1985, 24, 5, 673–677Publication Date (Print):February 1, 1985Publication History Published online1 May 2002Published inissue 1 February 1985https://pubs.acs.org/doi/10.1021/ic00199a008https://doi.org/10.1021/ic00199a008research-articleACS PublicationsRequest reuse permissionsArticle Views196Altmetric-Citations58LEARN 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
Substrate crosstalk reduction using SOI technology (1997)

This work analyzes both by simulations and measurements the substrate crosstalk performances of various Silicon-On-Insulator (SOI) technologies, and compares them to those of normal bulk CMOS process. The influence of various parameters, such as substrate resistivity, buried oxide thickness and distance between devices, is investigated. The use of capacitive guard rings is proposed, and their effectiveness is demonstrated. A simple RC model has been developed to allow a deep understanding of these phenomena as well as to simplify future studies of more complex systems. The superiority of high-resistivity SIMOX substrates over standard SOI and bulk is finally demonstrated.
VEHICLE-TO-VEHICLE AND ROAD-SIDE SENSOR COMMUNICATION FOR ENHANCED ROAD SAFETY (2008)

We propose a hybrid ITS safety architecture that combines vehicle-to-vehicle communication and vehicle-to-roadside sensor communication. Opposed to dedicated roadside units, which require major investments for purchase, installation and maintenance, roadside wireless sensor and networking technology represents a cost-effective solution and can leverage the deployment of the system as a whole. Among the various services of the hybrid communication system, the paper introduces accident prevention and post-accident investigation. We present a system and protocol architecture with a fully distributed concept for efficient and secure storage of sensor data. For deployment, this architecture will likely be combined with an alternative approach using dedicated road-side units as a centralized network element for communication and data storage. For the proposed system, we describe the main components (radio, networking and services, security). Finally, we describe our prototype implementation and experimental testbed featuring hardware and software platforms for vehicle on-board units and sensor nodes.
A day at a time: Predicting smoking lapse from daily urge. (1997)

Smokers who recently quit (N = 214) monitored smoking urges for up to 26 days after quitting. Computers administered 4-5 assessments daily at random times; participants rated urges on waking and when they experienced temptation episodes. Urge intensity after cessation did not generally exceed urges reported during baseline ad lib smoking. Urge intensity and temptation frequency consistently declined over the quit period. Controlling for urge intensity at baseline, all daily urge intensity measures predicted lapse the following day in proportional hazards survival analyses. Average duration of temptation episodes also predicted lapses; frequency of temptation did not. To isolate the effect of day-to-day variations in urges, participants' nicotine dependence and urge intensity on quit day were controlled for. Only urge intensity at waking still predicted lapse risk; this was not because of this measured being closer in time to the day's lapses. Among lapsers, urge intensity at waking and in temptations rose preceding a lapse.
Purification and characterization of a kanamycin nucleotidyltransferase from plasmid pUB110-carrying cells of Bacillus subtilis (1980)

The nucleotidyltransferase encoded by plasmid pUB110 was purified to greater than 95% purity with a 33% yield. The enzyme is a monomeric protein with a molecular weight of 34,000. The optimum pH for activity is 5, and the optimum MgCl2 concentration for activity is 18 mM. The enzyme, which is synthesized constitutively, is stable for several weeks at 4 degrees C. This enzyme would appear to be a good model gene product for the development of a pUB110 deoxyribonucleic acid-dependent in vitro protein-synthesizing system from Bacillus subtilis.
Methyl Jasmonate Induced Production of Taxol in Suspension Cultures of Taxus cuspidata: Ethylene Interaction and Induction Models (1996)

Suspension cultures of Taxus cuspidata were challenged with various concentrations and combinations of methyl jasmonate and ethylene. Taxol productivity increased 19-fold when T. cuspidata suspension cultures were exposed to 5 ppm ethylene and 10 microM methyl jasmonate. This increase was 15-fold when either 0 or 10 ppm ethylene was combined with 10 microM methyl jasmonate. The induction of taxol occurred within 51 h after elicitation and would reduce fermentation times and costs. Ethylene concentration at 50 ppm had an inhibitory effect on taxol production but not on phosphate uptake rate, suggesting independent regulation of taxol and physiological functions of the cell. A simple induction model is proposed to explain the action and effects of both ethylene and methyl jasmonate with regard to receptor binding and regulatory systems in plants.
Eye gesture recognition on portable devices (2012)

Hand-held portable devices have received only little attention as a platform in the eye tracking community so far. This is mainly due to their -- until recently -- limited sensing capabilities and processing power. In this work-in-progress paper we present the first prototype eye gesture recognition system for portable devices that does not require any additional equipment. The system combines techniques from image processing, computer vision and pattern recognition to detect eye gestures in the video recorded using the built-in front-facing camera. In a five-participant user study we show that our prototype can recognise four different continuous eye gestures in near real-time with an average accuracy of 60% on an Android-based smartphone (17.6% false positives) and 67.3% on a laptop (5.9% false positives). This initial result is promising and underlines the potential of eye tracking and eye-based interaction on portable devices.
Large optical cavity AlGaAs buried heterostructure window lasers (1982)

Large optical cavity buried heterostructure window lasers in which only the transparent AlGaAs waveguiding layers, and not the active layer, extend to the laser mirrors have been fabricated. These lasers have threshold currents and differential quantum efficiencies comparable to those of regular large optical cavity buried heterostructure lasers in which the active region extends to the laser mirrors, however the window lasers have been operated under pulsed conditions at three times the power at which otherwise identical lasers without windows degrade by catastrophic mirror damage.
Towards the automated social analysis of situated speech data (2008)

We present an automated approach for studying fine-grained details of social interaction and relationships. Specifically, we analyze the conversational characteristics of a group of 24 individuals over a six-month period, explore the relationship between conversational dynamics and network position, and identify behavioral correlates of tie strengths within a network. The ability to study conversational dynamics and social networks over long time scales, and to investigate their interplay with rigor, objectivity, and transparency will complement the traditional methods for scientific inquiry into social dynamics. They may also enable socially aware ubiquitous computing systems that are cognizant of and responsive to the user's engagement with her social environment.
Angiogenesis inhibition as a therapeutic strategy in non-small cell lung cancer (NSCLC). (2015)

In many cancers, including non-small cell lung cancer (NSCLC), tumor angiogenesis pathways have been identified as important therapeutic targets. Angiogenesis is essential in the process of primary tumor growth, proliferation and metastasis. One of the best characterized group of protein factors for angiogenesis include the members of the vascular endothelial growth factor (VEGF) family, consisting of VEGF-(A-D), and placenta growth factor (PIGF). Targeting tumor angiogenesis has been approached through two primary methods, monoclonal antibodies that block VEGF-vascular endothelial growth factor receptor (VEGFR) binding or small molecule tyrosine kinase inhibitors (TKIs) that inhibit the downstream VEGFR mediated signaling. Many TKIs inhibit multiple pro-angiogenic and pro-proliferative pathways such as the mitogen activated protein (MAP) kinase pathway. Bevacizumab and ramucirumab, monoclonal antibodies targeting VEGF and the VEGFR, respectively, have each led to improvements in overall survival (OS) for NSCLC when added to standard first and second line chemotherapy, respectively. Small incremental gains seen with both bevacizumab and ramucirumab may be further improved upon by incorporating novel agents and treatment strategies, and many additional trials are ongoing.
Impact of a Single Intravenous Administration of Nicorandil Before Reperfusion in Patients With ST-Segment–Elevation Myocardial Infarction (2005)

The addition of intravenous nicorandil to PCI leads to beneficial clinical outcomes and prevents cardiovascular events of long duration and death in patients with ST-segment-elevation myocardial infarction.
Ovoinhibitor introns specify functional domains as in the related and linked ovomucoid gene. (1987)

We have isolated cDNA clones and determined the gene structure of chicken ovoinhibitor, a seven domain Kazal serine proteinase inhibitor. Using RNA blot hybridization analysis, the gene was identified initially as a region 9-23 kilobases upstream of the gene for the related inhibitor ovomucoid. Ovoinhibitor RNA appears in oviduct and liver. cDNA clones were identified by screening an oviduct cDNA library with a nick-translated DNA restriction fragment which contained an exon of the gene. The mature protein sequence derived from a cDNa clone is in excellent agreement with that which we obtained from direct sequencing of purified ovoinhibitor. The protein-sequencing strategy is reported. The P1 amino acids of the Kazal domains are consistent with the known broad inhibitory specificity of ovoinhibitor. The gene is about 10.3 kilobases in length and consists of 16 exons. Each Kazal domain is encoded by two exons. Like ovomucoid, introns fall between the coding sequences of the ovoinhibitor domains, an arrangement which may have facilitated domain duplication. The intradomain intron occurs in an identical position in all of the ovoinhibitor and ovomucoid Kazal domains, suggesting that this intron was present in the primordial inhibitor gene. We discuss the location of the intradomain intron in relation to the known structure of four Kazal inhibitors and suggest a scheme for the evolution of the ovoinhibitor gene.
Why workflows break &#x2014; Understanding and combating decay in Taverna workflows (2012)

Workflows provide a popular means for preserving scientific methods by explicitly encoding their process. However, some of them are subject to a decay in their ability to be re-executed or reproduce the same results over time, largely due to the volatility of the resources required for workflow executions. This paper provides an analysis of the root causes of workflow decay based on an empirical study of a collection of Taverna workflows from the myExperiment repository. Although our analysis was based on a specific type of workflow, the outcomes and methodology should be applicable to workflows from other systems, at least those whose executions also rely largely on accessing third-party resources. Based on our understanding about decay we recommend a minimal set of auxiliary resources to be preserved together with the workflows as an aggregation object and provide a software tool for end-users to create such aggregations and to assess their completeness.