gebhart/patrepeval huggingface dataset:
Identification of a novel Nrf2-regulated antioxidant response element (ARE) in the mouse NAD(P)H:quinone oxidoreductase 1 gene: reassessment of the ARE consensus sequence (2003)

NQO1 [NAD(P)H:quinone oxidoreductase 1] has an integral role in cellular responses to oxidative stress. The expression of NQO1 is up-regulated in the mouse following challenge with electrophilic chemicals, in an Nrf2 (NF-E2 p45-related factor 2)-dependent fashion, but the molecular basis for this observation remains unexplained. Through characterization of the murine nqo1 5'-upstream region, we now show that Nrf2 regulates this gene directly via an ARE (antioxidant response element) that lies within a 24 bp region spanning nt -444 to -421. A comprehensive mutation study of this ARE revealed that it does not conform to the currently accepted ARE consensus sequence [(5'-TMAnnRTGAYnnnGCRwwww-3', with essential nucleotides shown in capitals); two cytosine residues (shown in bold in the following sequence) that have been designated 'n' previously because they were thought to be redundant (5'-gagTcA C aGTgAGt C ggCAaaatt-3') have now been found to be essential for enhancer activity; two guanines (also shown in bold) previously regarded as essential for ARE function (5'-gagTcACaGT g AGtCg g CAaaatt-3') have proven to be dispensable]. Examination of wild-type and nrf2 (-/-) mouse embryonic fibroblasts demonstrated that Nrf2 is essential for both constitutive expression of NQO1 and its induction by sulphoraphane. Electrophoretic mobility-shift and chromatin immunoprecipitation assays revealed that Nrf2 associates, in low amounts, with the nqo1 ARE under constitutive conditions, and following sulphoraphane challenge of cells, Nrf2 is recruited to the ARE in substantially greater quantities, as a heterodimer with the small Maf (musculoaponeurotic fibrosarcoma virus) protein, MafK. Also, MafK was found to bind the nqo1 ARE in an Nrf2-independent fashion, and may contribute to transcriptional repression of the oxidoreductase gene. These findings allow a model for transcriptional control of nqo1 through the ARE to be proposed. Furthermore, our results indicate that distinct AREs have differential sequence requirements, and a universally applicable consensus sequence cannot be derived.
Separation of duties as a service (2011)

We introduce the concept of Separation of Duties (SoD) as a Service, an approach to enforcing SoD requirements on workflows and thereby preventing fraud and errors. SoD as a Service facilitates a separation of concern between business experts and security professionals. Moreover, it allows enterprises to address the need for internal controls and to quickly adapt to organizational, regulatory, and technological changes. In this paper, we describe an implementation of SoD as a Service, which extends a widely used, commercial workflow system, and discuss its performance. We present a drug dispensation workflow deployed in a hospital as case study to demonstrate the feasibility and benefits of our proof-of-concept implementation.
Microfluidics-Based Plasmonic Biosensing System Based on Patterned Plasmonic Nanostructure Arrays (2021)

This review aims to summarize the recent advances and progress of plasmonic biosensors based on patterned plasmonic nanostructure arrays that are integrated with microfluidic chips for various biomedical detection applications. The plasmonic biosensors have made rapid progress in miniaturization sensors with greatly enhanced performance through the continuous advances in plasmon resonance techniques such as surface plasmon resonance (SPR) and localized SPR (LSPR)-based refractive index sensing, SPR imaging (SPRi), and surface-enhanced Raman scattering (SERS). Meanwhile, microfluidic integration promotes multiplexing opportunities for the plasmonic biosensors in the simultaneous detection of multiple analytes. Particularly, different types of microfluidic-integrated plasmonic biosensor systems based on versatile patterned plasmonic nanostructured arrays were reviewed comprehensively, including their methods and relevant typical works. The microfluidics-based plasmonic biosensors provide a high-throughput platform for the biochemical molecular analysis with the advantages such as ultra-high sensitivity, label-free, and real time performance; thus, they continue to benefit the existing and emerging applications of biomedical studies, chemical analyses, and point-of-care diagnostics.
Making trace monitors feasible (2007)

A trace monitor observes an execution trace at runtime; when it recognises a specified sequence of events, the monitor runs extra code. In the aspect-oriented programming community, the idea originatedas a generalisation of the advice-trigger mechanism: instead of matchingon single events (joinpoints), one matches on a sequence of events. The runtime verification community has been investigating similar mechanisms for a number of years, specifying the event patterns in terms of temporal logic, and applying the monitors to hardware and software. In recent years trace monitors have been adapted for use with mainstream object-oriented languages. In this setting, a crucial feature is to allow the programmer to quantify over groups of related objects when expressing the sequence of events to match. While many language proposals exist for allowing such features, until now no implementation had scalable performance: execution on all but very simple examples was infeasible. This paper rectifies that situation, by identifying two optimisations for generating feasible trace monitors from declarative specifications of the relevant event pattern. We restrict ourselves to optimisations that do not have a significant impact on compile-time: they only analyse the event pattern, and not the monitored code itself. The first optimisation is an important improvement over an earlier proposal in [2] to avoid space leaks. The second optimisation is a form of indexing for partial matches. Such indexing needs to be very carefully designed to avoid introducing new space leaks, and the resulting data structure is highly non-trivial.
ScreenLock: A Smart Display Management System for Smartphones (2013)

Smartphones are powerful mobile devices in terms of processing speed and data traffic. These devices assist users in everyday tasks and are highly personalized. To provide good use experience and low energy consumption, it is important that it behaves according to the users' current context. It is known that when a device is active, the screen is responsible for 16% of total power consumption. In Android Smartphones, screen timeout can be set to fixed value. Therefore, generic and manual approaches can make some problems arise: annoyance caused by turning-off screen in inopportune moments and unnecessary energy consumption when there is no user interaction. To solve these issues, we developed, first, a data collector to understand better user's behavior. The analysis of collected data showed that time needed for screen remain active is strongly determined by application in use. A service in Android, called Screen Lock, is proposed to learning screen timeout appropriated for each situation. Experiments were performed using Screen Lock with a dataset provided by data collector. Results show that accuracy can reach 96.6%.
Fundamental Study on the Production of Ultrapure Water VIII. Removal of Leachables from Mixed-Bed Ion Exchange Resins (1990)

Abstract A study was made concerning the removal of leachables released from mixed-bed ion exchange resins. The key concerns were to determine the optimum mixed ratio of strong acid cation exchange resins (SACERs) and strong base anion exchange resins (SBAERs), which give the minimum value of total organic carbon (TOC) released from the resin mixtures and to investigate the effect of synthetic carbonaceous adsorbents on the adsorption of the leachables. The leaching rates of the leachables from the resin mixtures were dependent on the mixed ratios of SACERs and SBAERs. The TOC value for the leachables showed a minimum for a SACER-to-SBAER volume ratio of 9:1, far different from the mixed ratio in ordinary water treatment. The release of leachables from resin mixtures was mainly due to SBAER. The carbonaceous adsorbent having a higher hydrophobic surface adsorbed the leachables well from the resin mixtures.
Overview Of Fiber Optic Research At Brown University (1990)

Research in the Laboratory for Lightwave Technology is focused on novel applications of specially designed optical fibers. Emphasis is placed on new techniques of dopant incorporation, using both MCVD (Modified Chemical Vapor Deposition) and OVD (Outside Vapor Deposition) to fabricate fibers that are primarily for non-telecommunications applications. The topics pursued are fibers for fiber lasers, nonlinear effects in fibers, in particular, second harmonic generation, fiber devices for the measurement of electric field, new techniques for the fabrication of bulk-glass gradient index lenses, fiber designs for embedded fibers for sensor elements of future "smart skin" composites, the poling of glasses to induce anisotropy or possibly optical activity, and finally, fiber designs for N x N fused taper couplers.
Interactions of pathogenic <i>Neisseria</i> with host cells. Is it possible to assemble the puzzle? (1999)

Neisseria meningitidis and Neisseria gonorrhoeae are human pathogens that have to interact with mucosa and/or cellular barriers for their life cycles to progress. Even though they both give rise to dramatically different diseases, the use of in vitro models has shown that most of the mechanisms mediating cellular interactions are common to N. meningitidis and N. gonorrhoeae. This suggests that bacterial cell interactions may be essential not only for pathogenesis but also for other aspects of the bacterial life cycle that are common to both N. meningitidis and N. gonorrhoeae. This manuscript will review the most recent developments concerning the mechanisms mediating cellular interaction of pathogenic Neisseria and will then try to put them into the perspective of pathogenesis and bacterial life cycle.
Virtual Replicas for Remote Assistance in Virtual and Augmented Reality (2015)

In many complex tasks, a remote subject-matter expert may need to assist a local user to guide actions on objects in the local user's environment. However, effective spatial referencing and action demonstration in a remote physical environment can be challenging. We introduce two approaches that use Virtual Reality (VR) or Augmented Reality (AR) for the remote expert, and AR for the local user, each wearing a stereo head-worn display. Both approaches allow the expert to create and manipulate virtual replicas of physical objects in the local environment to refer to parts of those physical objects and to indicate actions on them. This can be especially useful for parts that are occluded or difficult to access. In one approach, the expert points in 3D to portions of virtual replicas to annotate them. In another approach, the expert demonstrates actions in 3D by manipulating virtual replicas, supported by constraints and annotations. We performed a user study of a 6DOF alignment task, a key operation in many physical task domains, comparing both approaches to an approach in which the expert uses a 2D tablet-based drawing system similar to ones developed for prior work on remote assistance. The study showed the 3D demonstration approach to be faster than the others. In addition, the 3D pointing approach was faster than the 2D tablet in the case of a highly trained expert.
Influence of additives of aluminum, magnesium and calcium on synthesis and sintering of lanthanum chromite (2014)

In this paper, materials based on lanthanum chromite La1 − x A x Cr(1 − y)B y O3 doped with Ca in the A position and Al and Mg in the B position are obtained. The influence of the introduced additives on the particle size, morphology, and phase composition of powders and properties of sintered ceramic samples based on lanthanum chromite is studied. It is established that the additive of magnesium in the amount of 20 mol % promotes the best sintering of ceramics and level of properties compared to other compositions studied in this work.
Systems Biology: The synergistic interplay between biology and mathematics (2008)

Abstract Systems Biology is a nascent field that arose from the technology driven omics measurement revolution. It goes beyond mere data analysis and focuses on the biological behaviour emerging from the dynamic interactions between system components that are organized in a hierarchical and highly connected manner. Mathematical models have been used as a conceptual framework to study such systems and their impact is maximal when there is a synergistic interplay of the models with experimental data and biological domain knowledge. The review provides an introduction to the modelling process and selectively highlights manuscripts that have strong biological impact.
Interferon-β 1a and SARS Coronavirus Replication (2004)

A global outbreak of severe acute respiratory syndrome (SARS) caused by a novel coronavirus began in March 2003. The rapid emergence of SARS and the substantial illness and death it caused have made it a critical public health issue. Because no effective treatments are available, an intensive effort is under way to identify and test promising antiviral drugs. Here, we report that recombinant human interferon-beta 1a potently inhibits SARS coronavirus replication in vitro.
Dynamics of Escherichia coli Infection in Experimentally Inoculated Chickens (1997)

In order to study the dynamics of avian colibacillosis, commercial broiler chickens were inoculated with a pathogenic Escherichia coli strain (01:K1:H7) into the left caudal thoracic air sac. Chickens were euthanatized at different times from 3 to 48 hr postinoculation and examined for bacterial counts and macroscopic and microscopic lesions. The E. coli strain colonized the air sacs, lungs, and trachea and was recovered from blood and all tested extrarespiratory organs of inoculated birds. A gradual increase in bacterial counts in the trachea, lungs, air sacs, and liver was observed from 3 to 12 hr. Clinical signs and macroscopic lesions of colibacillosis were observed in all inoculated birds. Moderate to severe lesions of airsacculitis, pericarditis, perihepatitis, and splenic hypertrophy were observed. Microscopically, inflammatory cell infiltration, serious to fibrinous exudate, and cellular debris on serosal surfaces were present in the liver, spleen, and air sacs. In air sacs, heterophils were present in low numbers perivascularly 3 hr after inoculation and became more numerous by 24 hr postinoculation. Ultrastructurally, epithelial cells in the air sacs and in air capillary regions of the lung were swollen and vacuolated beginning at 3 hr postinoculation. Bacteria were adherent to and present within the epithelial cells at 3 hr postinoculation and were also seen in phagocytic cells and, rarely, in the connective tissue of these organs at 24 hr postinoculation. These results indicate that both air sacs and lungs can be the portal of entry for E. coli into the systemic circulation, probably via damaged epithelium.
Notch3 Is Necessary for Blood Vessel Integrity in the Central Nervous System (2014)

We demonstrate that Notch3 is important for survival of VSMC, and reveal a critical role for Notch3 and VSMC in blood vessel integrity and blood-brain barrier function in the mammalian vasculature.
An Adaptive Multimedia-Oriented Handoff Scheme for IEEE 802.11 WLANs (2011)

Previous studies have shown that the actual handoff schemes employed in the IEEE 802.11 Wireless LANs (WLANs) do not meet the strict delay constraints placed by many multimedia applications like Voice over IP. Both the active and the passive supported scan modes in the standard handoff procedure have important delay that affects the Quality of Service (QoS) required by the real-time communications over 802.11 networks. In addition, the problem is further compounded by the fact that limited coverage areas of Access Points (APs) occupied in 802.11 infrastructure WLANs create frequent handoffs. We propose a new optimized and fast handoff scheme that decrease both handoff latency and occurrence by performing a seamless prevent scan process and an effective next-AP selection. Through simulations and performance evaluation, we show the effectiveness of the new adaptive handoff that reduces the process latency and adds new context-based parameters. The Results illustrate a QoS delay-respect required by applications and an optimized AP-choice that eliminates handoff events that are not beneficial.
Digitize Your Body and Action in 3-D at Over 10 FPS: Real Time Dense Voxel Reconstruction and Marker-less Motion Tracking via GPU Acceleration (2013)

In this paper, we present an approach to reconstruct 3-D human motion from multi-cameras and track human skeleton using the reconstructed human 3-D point (voxel) cloud. We use an improved and more robust algorithm, probabilistic shape from silhouette to reconstruct human voxel. In addition, the annealed particle filter is applied for tracking, where the measurement is computed using the reprojection of reconstructed voxel. We use two different ways to accelerate the approach. For the CPU only acceleration, we leverage Intel TBB to speed up the hot spot of the computational overhead and reached an accelerating ratio of 3.5 on a 4-core CPU. Moreover, we implement an intensively paralleled version via GPU acceleration without TBB. Taking account all data transfer and computing time, the GPU version is about 400 times faster than the original CPU implementation, leading the approach to run at a real-time speed.
Spin extraction from a non-magnetic semiconductor (2003)

New efficient mechanism of obtaining spin polarization in_nonmagnetic_ semiconductors at arbitrary temperutures is described. The effect appears during tunneling of electrons from a nonmagnetic semiconductors (S) into ferromagnet (FM) through a Schottky barrier modified with very thin heavily doped interfacial layer. We show that electrons with a certain spin projection are extracted from S, while electrons with the opposite spins are accumulated in S. The spin density increases and spin penetration depth decreases with current.
Online Parameter Estimation for Permanent Magnet Synchronous Machines: An Overview (2021)

Online parameter estimation of permanent magnet synchronous machines is critical for improving their control performance and operational reliability. This paper provides an overview of the recent achievements of online parameter estimation of PMSMs with examples. The critical issues in parameter estimation are firstly analysed, especially the rank-deficient issue and inverter nonlinearities. Then, the state-of-the-art online parameter estimation modelling techniques are reviewed and assessed. Finally, some typical applications and examples are outlined, e.g. estimation of mechanical parameters, improvement of sensored and sensorless control performance, thermal condition monitoring, and fault diagnosis, together with future research trends.
Isolation and characterization of <i>Schizosaccharomyces pombe</i> mutants with defective NAD-dependent malic enzyme (1986)

To obtain NAD-dependent malic enzyme mutants of Schizosaccharomyces pombe, a colony color indicator screening system was developed. Mutants defective for malic acid utilization (mau mutants) are yellow, while wild-type colonies are blue on the defined bromcresol green based indicator medium. NAD-dependent malic enzyme mutants were distinguished from other mau mutants by subsequent, starch gel electrophoresis, spectrophotometry, complementation tests, and intermediate pool analysis with cell-free extracts.
Precision of noninvasive temperature measurement by diffuse reflectance spectroscopy (1995)

Diffuse reflectance spectroscopy can be used as a noninvasive probe for measurement of temperature in real time. We have measured the precision of this technique to determine the temperature of Si and GaAs substrates during semiconductor processing. Our results show that the standard deviation of the noninvasive optical technique is less than 1.5 °C for GaAs and less than 2.0 °C for Si over the temperature range 25 °C&lt;T&lt;600 °C. This standard deviation compares favorably to that for a type-K thermocouple used in the same measurements: s.d.&lt;1.5 °C. These results support the notion that noninvasive optical temperature measurement can be used in semiconductor processing with a precision approaching that of a thermocouple.
prDeep: Robust Phase Retrieval with a Flexible Deep Network (2018)

Phase retrieval algorithms have become an important component in many modern computational imaging systems. For instance, in the context of ptychography and speckle correlation imaging, they enable imaging past the diffraction limit and through scattering media, respectively. Unfortunately, traditional phase retrieval algorithms struggle in the presence of noise. Progress has been made recently on more robust algorithms using signal priors, but at the expense of limiting the range of supported measurement models (e.g., to Gaussian or coded diffraction patterns). In this work we leverage the regularization-by-denoising framework and a convolutional neural network denoiser to create prDeep, a new phase retrieval algorithm that is both robust and broadly applicable. We test and validate prDeep in simulation to demonstrate that it is robust to noise and can handle a variety of system models. A MatConvNet implementation of prDeep is available at https://github.com/ricedsp/prDeep.
Security Solutions for Cloud Computing (2015)

In the recent times, most organizations in the world have increasingly realized the importance of cloud platforms. Cloud computing is an emerging technology to store and access personal data along with business information from remote locations. One of the benefits of using cloud computing is the ability to tap into huge quantities of both structured and unstructured data. With every new technology there are certain drawbacks associated with it and cloud is no exception. Unlike others, Cloud environment also faces challenges such as Distributed denial of service (DDoS) attacks, data thefts, particularly when they are insider attacks. Increase in the number of DDoS attacks is one of the latest issues. We have studied various intrusion detection techniques that includes Cloud trace back model, use of back propagation neural network and Virtual Intrusion Detection Systems (V-IDS). Now these attacks can be prevented using the proposed Intrusion Prevention System i.e. Service-based Intrusion Prevention System in Cloud Computing (SIPSCC). A technique called fog computing can be used to detect and prevent data theft attacks by malicious insiders is studied.
Detecting Errors with Configurable Whole-program Dataflow Analysis (2002)

In this paper, we present an automatic compiler-based approach for detecting programming errors. Our system uses a configurable and scalable whole-program dataflow analysis engine driven by highlevel programmer-written annotations. We show that our system can automatically detect a wide range of programmer errors in C programs, including improper use of libraries, information leaks, and security vulnerabilities. We show that the aggressive compiler analysis that our system performs yields precise results. Further, our system detects a wide range of errors with greater scalability than previous automatic approaches. For one important class of security vulnerabilities, our system automatically finds all known errors in five medium to large C programs without producing any false positives. 1.