gebhart/patrepeval huggingface dataset:
Novel Genes Related to Ceftriaxone Resistance Found among Ceftriaxone-Resistant Neisseria gonorrhoeae Strains Selected <i>In Vitro</i> (2016)

The emergence of ceftriaxone-resistantNeisseria gonorrhoeaeis currently a global public health concern. However, the mechanism of ceftriaxone resistance is not yet fully understood. To investigate the potential genes related to ceftriaxone resistance inNeisseria gonorrhoeae, we subcultured six gonococcal strains with increasing concentrations of ceftriaxone and isolated the strains that became resistant. After analyzing several frequently reported genes involved in ceftriaxone resistance, we found only a single mutation inpenA(A501V). However, differential analysis of the genomes and transcriptomes between pre- and postselection strains revealed many other mutated genes as well as up- and downregulated genes. Transformation of the mutatedpenAgene into nonresistant strains increased the MIC between 2.0- and 5.3-fold, and transformation of mutatedftsXincreased the MIC between 3.3- and 13.3-fold. Genes encoding the ABC transporters FarB, Tfq, Hfq, and ExbB were overexpressed, whilepilM,pilN, andpilQwere downregulated. Furthermore, the resistant strain developed cross-resistance to penicillin and cefuroxime, had an increased biochemical metabolic rate, and presented fitness defects such as prolonged growth time and downregulated PilMNQ. In conclusion, antimicrobial pressure could result in the emergence of ceftriaxone resistance, and the evolution of resistance ofNeisseria gonorrhoeaeto ceftriaxone is a complicated process at both the pretranscriptional and posttranscriptional levels, involving several resistance mechanisms of increased efflux and decreased entry.
Credit Card Fraud Detection using Machine Learning Algorithms (2019)

Credit card frauds are easy and friendly targets. E-commerce and many other online sites have increased the online payment modes, increasing the risk for online frauds. Increase in fraud rates, researchers started using different machine learning methods to detect and analyse frauds in online transactions. The main aim of the paper is to design and develop a novel fraud detection method for Streaming Transaction Data, with an objective, to analyse the past transaction details of the customers and extract the behavioural patterns. Where cardholders are clustered into different groups based on their transaction amount. Then using sliding window strategy [1], to aggregate the transaction made by the cardholders from different groups so that the behavioural pattern of the groups can be extracted respectively. Later different classifiers [3],[5],[6],[8] are trained over the groups separately. And then the classifier with better rating score can be chosen to be one of the best methods to predict frauds. Thus, followed by a feedback mechanism to solve the problem of concept drift [1]. In this paper, we worked with European credit card fraud dataset.
Visual Transduction and Non-Visual Light Perception (2008)

Remarkable advances have contributed to revolutionizing the study of vertebrate vision. The first step to identifying objects and establishing spatial relationships is the visual transduction cascade,
Fully Convolutional Attention Localization Networks: Efficient Attention Localization for Fine-Grained Recognition (2016)

Fine-grained recognition is challenging mainly because the inter-class differences between fine-grained classes are usually local and subtle while intra-class differences could be large due to pose variations. In order to distinguish them from intra-class variations, it is essential to zoom in on highly discriminative local regions. In this work, we introduce a reinforcement learning-based fully convolutional attention localization network to adaptively select multiple task-driven visual attention regions. We show that zooming in on the selected attention regions significantly improves the performance of fine-grained recognition. Compared to previous reinforcement learning-based models, the proposed approach is noticeably more computationally efficient during both training and testing because of its fully-convolutional architecture, and it is capable of simultaneous focusing its glimpse on multiple visual attention regions. The experiments demonstrate that the proposed method achieves notably higher classification accuracy on three benchmark fine-grained recognition datasets: Stanford Dogs, Stanford Cars, and CUB-200-2011.
The ARTS web server for aligning RNA tertiary structures (2006)

RNA molecules with common structural features may share similar functional properties. Structural comparison of RNAs and detection of common substructures is, thus, a highly important task. Nevertheless, the current available tools in the RNA community provide only a partial solution, since they either work at the 2D level or are suitable for detecting predefined or local contiguous tertiary motifs only. Here, we describe a web server built around ARTS, a method for aligning tertiary structures of nucleic acids (both RNA and DNA). ARTS receives a pair of 3D nucleic acid structures and searches for a priori unknown common substructures. The search is truly 3D and irrespective of the order of the nucleotides on the chain. The identified common substructures can be large global folds with hundreds and even thousands of nucleotides as well as small local motifs with at least two successive base pairs. The method is highly efficient and has been used to conduct an all-against-all comparison of all the RNA structures in the Protein Data Bank. The web server together with a software package for download are freely accessible at http://bioinfo3d.cs.tau.ac.il/ARTS.
Logistical computing and internetworking: middleware for the use of storage in communication (2005)

The Logistical Computing and Internetworking (LoCI) project is a reflection of the way that the next generation internetworking fundamentally changes our definition of high performance wide area computing. A key to achieving this aim is the development of middleware that can provide reliable, flexible, scalable, and cost-effective delivery of data with quality of service (QoS) guarantees to support high performance applications of all types. The LoCI effort attacks this problem with a simple but innovative strategy. At the base of the LoCI project is a richer view of the use of storage in communication and information sharing.
Synthesis of Isoxazolopyridobicyclooxacalix[4]arenes: A New Family of Heteracalixarene Systems (2008)

Abstract A new family of isoxazolopyridobicyclooxacalix[4]arenes was obtained by reaction of dichloroisoxazolopyridines with phloroglucinol. X‐ray crystallography and density functional calculations were used for their structural determination and evaluation of their chemical properties. Their role as metal chelators was studied by mass spectrometry. This new family of heteracalixarenes is of potential interest for host–guest interactions. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2008)
Synthesis of perfluoroalkylether triazine elastomers (1980)

A method of perfluoroalkylether triazine elastomer synthesis is described. To form an elastomer, the resultant polymer is heated in a closed oven at slightly reduced pressures for 1-day periods at 100, 130 and 150 C. A high-molecular-weight perfluoroalkylether triazine elastomer is produced that exhibits thermal and oxidative stability. This material is potentially useful in applications such as high-temperature seals, 'O' rings, and wire enamels.
Broadband generation of tunable Josephson radiation at microwave frequencies (1977)

Radiation with an integrated power of about 10−12 W has been obtained from a microbridge Josephson junction. The output can be continuously tuned between 2 and 12 GHz. The frequency and current dependence of radiated power and linewidth are in disagreement with the resistively shunted junction model.
Detection of orbital angular momentum using a photonic integrated circuit (2016)

Orbital angular momentum (OAM) state of photons offer an attractive additional degree of freedom that has found a variety of applications. Measurement of OAM state, which is a critical task of these applications, demands photonic integrated devices for improved fidelity, miniaturization, and reconfiguration. Here we report the design of a silicon-integrated OAM receiver that is capable of detecting distinct and variable OAM states. Furthermore, the reconfiguration capability of the detector is achieved by applying voltage to the GeSe film to form gratings with alternate states. The resonant wavelength for arbitrary OAM state is demonstrated to be tunable in a quasi-linear manner through adjusting the duty cycle of the gratings. This work provides a viable approach for the realization of a compact integrated OAM detection device with enhanced functionality that may find important applications in optical communications and information processing with OAM states.
Using Punctuation Schemes to Characterize Strategies for Querying over Data Streams (2007)

Many systems and strategies have been proposed for processing nonterminating data streams. Each approach has advantages and disadvantages, including the kinds of queries that can be executed. We present a framework for characterizing the kinds of queries that can be executed over streams based on a notion of compact sets from topology. We first apply our framework to queries over punctuated data streams. Previous work on punctuations focused primarily on the behavior of individual query operators. We use our framework to determine if an entire query can benefit from punctuations available from stream sources. We then consider other common strategies proposed in the literature for executing queries over streams, and we discuss how our framework can characterize the kinds of queries each strategy can answer.
Role of Nuclear Ca <sup>2+</sup> /Calmodulin-Stimulated Phosphodiesterase 1A in Vascular Smooth Muscle Cell Growth and Survival (2006)

In response to biological and mechanical injury, or in vitro culturing, vascular smooth muscle cells (VSMCs) undergo phenotypic modulation from a differentiated "contractile" phenotype to a dedifferentiated "synthetic" one. This results in the capacity to proliferate, migrate, and produce extracellular matrix proteins, thus contributing to neointimal formation. Cyclic nucleotide phosphodiesterases (PDEs), by hydrolyzing cAMP or cGMP, are critical in the homeostasis of cyclic nucleotides that regulate VSMC growth. Here, we demonstrate that PDE1A, a Ca2+-calmodulin-stimulated PDE preferentially hydrolyzing cGMP, is predominantly cytoplasmic in medial "contractile" VSMCs but is nuclear in neointimal "synthetic" VSMCs. Using primary VSMCs, we show that cytoplasmic and nuclear PDE1A were associated with a contractile marker (SM-calponin) and a growth marker (Ki-67), respectively. This suggests that cytoplasmic PDE1A is associated with the "contractile" phenotype, whereas nuclear PDE1A is with the "synthetic" phenotype. To determine the role of nuclear PDE1A, we examined the effects loss-of-PDE1A function on subcultured VSMC growth and survival using PDE1A RNA interference and pharmacological inhibition. Reducing PDE1A function significantly attenuated VSMC growth by decreasing proliferation via G1 arrest and inducing apoptosis. Inhibiting PDE1A also led to intracellular cGMP elevation, p27Kip1 upregulation, cyclin D1 downregulation, and p53 activation. We further demonstrated that in subcultured VSMCs redifferentiated by growth on collagen gels, cytoplasmic PDE1A regulates myosin light chain phosphorylation with little effect on apoptosis, whereas inhibiting nuclear PDE1A has the opposite effects. These suggest that nuclear PDE1A is important in VSMC growth and survival and may contribute to the neointima formation in atherosclerosis and restenosis.
Training Person-Specific Gaze Estimators from User Interactions with Multiple Devices (2018)

Learning-based gaze estimation has significant potential to enable attentive user interfaces and gaze-based interaction on the billions of camera-equipped handheld devices and ambient displays. While training accurate person- and device-independent gaze estimators remains challenging, person-specific training is feasible but requires tedious data collection for each target device. To address these limitations, we present the first method to train person-specific gaze estimators across multiple devices. At the core of our method is a single convolutional neural network with shared feature extraction layers and device-specific branches that we train from face images and corresponding on-screen gaze locations. Detailed evaluations on a new dataset of interactions with five common devices (mobile phone, tablet, laptop, desktop computer, smart TV) and three common applications (mobile game, text editing, media center) demonstrate the significant potential of cross-device training. We further explore training with gaze locations derived from natural interactions, such as mouse or touch input.
<title>Optical fiber-based wave-mixing probe</title> (1997)

A fiber-based wave-mixing probe is presented as a simple spectroscopic measurement tool with minimum optical alignment requirements for trace-concentration analytes. For a multi-photon nonlinear laser-induced grating method to become widely accessible, the optical setup must be compact, easy to align and portable. We demonstrate a significant improvement in the forward-scattering (self-diffraction) wave-mixing optical setup using optical fibers for both laser input and signal output interfaces. There is considerable flexibility inherent in the design, since the wave-mixing probe can be used in multiple configurations. Wave-mixing spectroscopy is presented as an effective and sensitive analytical method for trace analysis, offering advantages such as detection in very small sample volumes, remote and in-situ analyses, and convenient and efficient alignment enhancements obtained by the use of optical fibers.
Document image classification combining textual and visual features. (2016)

This research contributes to the problem of classifying document images. The main addition of this thesis is the exploitation of textual and visual features through an approach that uses Convolutional Neural Networks.\nThe study uses a combination of Optical Character Recognition and Natural Language Processing algorithms to extract and manipulate relevant text concepts from document images.\nSuch content information are embedded within document images, with the aim of adding elements which help to improve the classification results of a Convolutional Neural Network.\nThe experimental phase proves that the overall document classification accuracy of a Convolutional Neural Network trained using these text-augmented document images, is considerably higher than the one achieved by a similar model trained solely on classic document images, especially when different classes of documents share similar visual characteristics. The comparison between our method and state-of-the-art approaches demonstrates the effectiveness of combining visual and textual features.\nAlthough this thesis is about document image classification, the idea of using textual and visual features is not restricted to this context and comes from the observation that textual and visual information are complementary and synergetic in many aspects.
Molecular Characterization of an Anchor Protein (AKAPCE) That Binds the RI Subunit (RCE) of Type I Protein Kinase A from Caenorhabditis elegans (1998)

Classical A kinase anchor proteins (AKAPs) preferentially tether type II protein kinase A (PKAII) isoforms to sites in the cytoskeleton and organelles. It is not known if distinct proteins selectively sequester regulatory (R) subunits of type I PKAs, thereby diversifying functions of these critical enzymes. In Caenorhabditis elegans, a single type I PKA mediates all aspects of cAMP signaling. We have discovered a cDNA that encodes a binding protein (AKAPCE) for the regulatory subunit (RCE) of C. elegans PKAICE. AKAPCE is a novel, highly acidic RING finger protein composed of 1,280 amino acids. It binds RI-like RCE with high affinity and neither RIIalpha nor RIIbeta competitively inhibits formation of AKAPCE.RCE complexes. The RCE-binding site was mapped to a segment of 20 amino acids in an N-terminal region of AKAPCE. Several hydrophobic residues in the binding site align with essential Leu and Ile residues in the RII-selective tethering domain of prototypic mammalian AKAPs. However, the RCE-binding region in AKAPCE diverges sharply from consensus RII-binding sites by inclusion of three aromatic amino acids, exclusion of a highly conserved Leu or Ile at position 8 and replacement of C-terminal hydrophobic amino acids with basic residues. AKAPCE.RCE complexes accumulate in intact cells.
Kinase Domain Mutants of Bcr-Abl Exhibit Altered Transformation Potency, Kinase Activity, and Substrate Utilization, Irrespective of Sensitivity to Imatinib (2006)

Kinase domain (KD) mutations of Bcr-Abl interfering with imatinib binding are the major mechanism of acquired imatinib resistance in patients with Philadelphia chromosome-positive leukemia. Mutations of the ATP binding loop (p-loop) have been associated with a poor prognosis. We compared the transformation potency of five common KD mutants in various biological assays. Relative to unmutated (native) Bcr-Abl, the ATP binding loop mutants Y253F and E255K exhibited increased transformation potency, M351T and H396P were less potent, and the performance of T315I was assay dependent. The transformation potency of Y253F and M351T correlated with intrinsic Bcr-Abl kinase activity, whereas the kinase activity of E255K, H396P, and T315I did not correlate with transforming capabilities, suggesting that additional factors influence transformation potency. Analysis of the phosphotyrosine proteome by mass spectroscopy showed differential phosphorylation among the mutants, a finding consistent with altered substrate specificity and pathway activation. Mutations in the KD of Bcr-Abl influence kinase activity and signaling in a complex fashion, leading to gain- or loss-of-function variants. The drug resistance and transformation potency of mutants may determine the outcome of patients on therapy with Abl kinase inhibitors.
Automated data analysis solutions to silicon debug (2009)

Since pre-silicon functional verification is insufficient to detect all design errors, re-spins are often needed due to malfunctions that escape into the silicon. This paper presents an automated software solution to analyze the data collected during silicon debug. The proposed methodology analyzes the test sequences to detect suspects in both the spatial and the temporal domain. A set of software debug techniques are proposed to analyze the acquired data from the hardware testing and provide suggestions for the setup of the test environment in the next debug session. A comprehensive set of experiments demonstrate its effectiveness in terms of run-time and resolution.
Evaluation of left ventricular regional function by strain rate imaging in children at acute stage of Kawasaki disease (2014)

Objective To investigate the value of left ventricular regional function by strain rate imaging on children at acute stage of Kawasaki disease.Methods Fifty nine children at acute stage of Kawasaki disease and forty five normal children were enrolled in our experiment.The main left ventricular systolic function was examined.The segments were examined using the strain rate imaging to obtain regional peak systolic strain rate (SRs),peak early diastolic strain rate (SRe).Results The main left ventricular systolic function wasn' t decreased compared with the normal control (P ＞ 0.05).The SRs and SRe of some segments of children at acute stage of Kawasaki disease was decreased compared with the normal control (P ＜ 0.05 or ＜ 0.01).Conclusions The leftventricular regional function,especially the diastolic dysfunction,in children at acute stage of Kawasaki disease are impaired.Strain rate imaging is a sensitive and especially method in evaluation the region function of children at acute stage of Kawasaki disease.

Key words: 
Echocardiography;  Kawasaki disease;  Strain rate imaging
An evaluation of the incorporation of a semantic network into a multidimensional retrieval engine (2003)

This paper describes a new method for incorporating a hierarchical category dimension into an Information Retrieval framework. The approach is to use the synonym sets and the hyponym ("is-a") relations defined within Wordnet in order to derive a conceptual hierarchical category dimension. The hierarchical nature of a category dimension not only provides an overview of a set of documents but also facilitates the effectiveness and the efficiency of searching documents. An evaluation is performed on two different types of models and the multidimensional approach shows a significant reduction in the number of page accesses over a large document collection.
A new method to characterize conformality of BARC coatings (2005)

In the semiconductor manufacturing industry, a bottom anti-reflective coating (BARC) is used to minimize thin film interference effects by reducing reflected light. As substrate topography becomes more complex with efforts to design more complex circuits, the effect of reflected radiation becomes more critical. The degree of conformality of the BARC coating plays an important role in lithography performance, which in turn affects the design of plasma etching processes. In this study, we propose a new method to measure the BARC coating conformality. The relationship between film thickness and horizontal distance from the step can be described by an exponential function. We found this profile is related to the properties of the coating material, such as molecular weight, the composition of formulation, the polymer structure, Tg of the polymer, thermal flow capability, and the crosslinking reaction, but is independent of step height, step width, and BARC thickness. The pitch affects the shape of the coating profile only when the spacing of features is smaler than a threshold that is related to coating material properties. The curvature of the profile indicates the uniformity of BARC thickness across the topography, which is a very good parameter to quantitatively describe the conformality of BARC coatings. Studies on Brewer Science BARC products confirm that the proposed conformality measuring method is in excellent agreement with observations. This method offers the option to separately consider the effects of coating processing, topography type, film thickness, and inherent material properties. It affords the predictability of BARC behavior for coatings that cover different topographies.
<b>Strategies for Rapid Response to Emerging Foodborne Microbial Hazards</b>1 (1997)

The foodborne outbreak paradigm has shifted. In the past, an outbreak affected a small local population, had a high attack rate, and involved locally prepared food products with limited distribution. Now outbreaks involve larger populations and may be multistate and even international; in many the pathogenic organism has a low infective dose and sometimes is never isolated from the food product. Delay in identifying the causative agent can allow the outbreak to spread, increasing the number of cases. Emergency intervention should be aimed at controlling the outbreak, stopping exposure, and perhaps more importantly, preventing future outbreaks. Using epidemiologic data and investigative techniques may be the answer. Even with clear statistical associations to a contaminated food, one must ensure that the implicated organism could logically and biologically have been responsible for the outbreak.
In Vivo Targeting of Inflammation-Associated Myeloid-Related Protein 8/14 Via Gadolinium Immunonanoparticles (2012)

Targeted imaging with aMrp-NP demonstrates enhancement of plaque with binding to inflammatory cells and reduction in inflammation. This strategy has promise as a theranostic approach for atherosclerosis.