gebhart/patrepeval huggingface dataset:
Identification of Host-Targeted Small Molecules That Restrict Intracellular Mycobacterium tuberculosis Growth (2014)

Mycobacterium tuberculosis remains a significant threat to global health. Macrophages are the host cell for M. tuberculosis infection, and although bacteria are able to replicate intracellularly under certain conditions, it is also clear that macrophages are capable of killing M. tuberculosis if appropriately activated. The outcome of infection is determined at least in part by the host-pathogen interaction within the macrophage; however, we lack a complete understanding of which host pathways are critical for bacterial survival and replication. To add to our understanding of the molecular processes involved in intracellular infection, we performed a chemical screen using a high-content microscopic assay to identify small molecules that restrict mycobacterial growth in macrophages by targeting host functions and pathways. The identified host-targeted inhibitors restrict bacterial growth exclusively in the context of macrophage infection and predominantly fall into five categories: G-protein coupled receptor modulators, ion channel inhibitors, membrane transport proteins, anti-inflammatories, and kinase modulators. We found that fluoxetine, a selective serotonin reuptake inhibitor, enhances secretion of pro-inflammatory cytokine TNF-α and induces autophagy in infected macrophages, and gefitinib, an inhibitor of the Epidermal Growth Factor Receptor (EGFR), also activates autophagy and restricts growth. We demonstrate that during infection signaling through EGFR activates a p38 MAPK signaling pathway that prevents macrophages from effectively responding to infection. Inhibition of this pathway using gefitinib during in vivo infection reduces growth of M. tuberculosis in the lungs of infected mice. Our results support the concept that screening for inhibitors using intracellular models results in the identification of tool compounds for probing pathways during in vivo infection and may also result in the identification of new anti-tuberculosis agents that work by modulating host pathways. Given the existing experience with some of our identified compounds for other therapeutic indications, further clinically-directed study of these compounds is merited.
Electronic Detection of Lectins Using Carbohydrate-Functionalized Nanostructures: Graphene <i>versus</i> Carbon Nanotubes (2011)

Here we investigated the interactions between lectins and carbohydrates using field-effect transistor (FET) devices comprised of chemically converted graphene (CCG) and single-walled carbon nanotubes (SWNTs). Pyrene- and porphyrin-based glycoconjugates were functionalized noncovalently on the surface of CCG-FET and SWNT-FET devices, which were then treated with 2 μM nonspecific and specific lectins. In particular, three different lectins (PA-IL, PA-IIL, and ConA) and three carbohydrate epitopes (galactose, fucose, and mannose) were tested. The responses of 36 different devices were compared and rationalized using computer-aided models of carbon nanostructure/glycoconjugate interactions. Glycoconjugate surface coverage in addition to one-dimensional structures of SWNTs resulted in optimal lectin detection. Additionally, lectin titration data of SWNT- and CCG-based biosensors were used to calculate lectin dissociation constants (K(d)) and compare them to the values obtained from the isothermal titration microcalorimetry technique.
Multi-Aspect, Robust, and Memory Exclusive Guest OS Fingerprinting (2014)

Precise fingerprinting of an operating system (OS) is critical to many security and forensics applications in the cloud, such as virtual machine (VM) introspection, penetration testing, guest OS administration, kernel dump analysis, and memory forensics. The existing OS fingerprinting techniques primarily inspect network packets or CPU states, and they all fall short in precision and usability. As the physical memory of a VM always exists in all these applications, in this article, we present OS-SOMMELIER <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">+</sup> , a multi-aspect, memory exclusive approach for precise and robust guest OS fingerprinting in the cloud. It works as follows: given a physical memory dump of a guest OS, OS-SOMMELIER <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">+</sup> first uses a code hash based approach from kernel code aspect to determine the guest OS version. If code hash approach fails, OS-SOMMELIER <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">+</sup> then uses a kernel data signature based approach from kernel data aspect to determine the version. We have implemented a prototype system, and tested it with a number of Linux kernels. Our evaluation results show that the code hash approach is faster but can only fingerprint the known kernels, and data signature approach complements the code signature approach and can fingerprint even unknown kernels.
Scaling Relationships between Saturated Hydraulic Conductivity and Soil Physical Properties (2005)

Saturated hydraulic conductivity ( K s ) is an important soil hydraulic property that affects water flow and the transport of dissolved solutes. Obtaining sufficient and reliable K s data for large‐scale process modeling is always a challenge due to the extremely high spatial variability. The objectives of this study were (i) to determine if a monofractal or multifractal approach is needed to describe the variability in K s and its soil surrogates, and (ii) to identify which soil property best reflects the spatial distribution of K s across a wider range of scales. Saturated hydraulic conductivity and soil physical property data were collected from a 384‐m transect, located at Smeaton, SK, Canada. Observation scale variability and relationships were examined using statistical and geostatistical methods. Statistical scale‐invariance was evaluated through the Hurst scaling parameter ( H ). Multiple scale variability and relationships were studied using multifractal and joint multifractal techniques. Results indicate that for all the studied variables 0.80 < H < 0.90, suggesting a certain degree of statistical scale‐invariance and long‐range dependency. At the observation scale, the variability in K s was significantly related to sand (SA) and silt (SI) distribution ( R = 0.40 for SA and −0.39 for SI, P < 0.01; n = 128), whereas, across a wider range of scales, the variability in K s was related only to clay (CL) and organic C (OC). The result indicates scale dependent relationships between K s and soil physical properties, which implies that the success of predictive models such as pedotransfer functions (PTFs) and K s aggregation techniques depends largely on the correspondence between observation and implementation scales.
A New Mechanism of Leukemia Drug Resistance? (2007)

The resistance of leukemic blast cells to asparaginase may depend on their biochemical niche in the bone marrow.
VLSI architectures for discrete wavelet transforms (1993)

A folded architecture and a digit-serial architecture are proposed for implementation of one- and two-dimensional discrete wavelet transforms. In the one-dimensional folded architecture, the computations of all wavelet levels are folded to the same low-pass and high-pass filters. The number of registers in the folded architecture is minimized by the use of a generalized life time analysis. The converter units are synthesized with a minimum number of registers using forward-backward allocation. The advantage of the folded architecture is low latency and its drawbacks are increased hardware area, less than 100% hardware utilization, and the complex routing and interconnection required by the converters used. These drawbacks are eliminated in the alternate digit-serial architecture at the expense of an increase in the system latency and some constraints on the wordlength. In latency-critical applications, the use of the folded architecture is suggested. If latency is not so critical, the digit-serial architecture should be used. The use of a combined folded and digit-serial architecture is proposed for implementation of two-dimensional discrete wavelet transforms.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
An Anatomy of SVC for Full HD Video Streaming (2014)

The continuous developments and improvements of network infrastructure along with the growing number of modern smartphones, tablets and smart TVs have led to an increasing popularity of multimedia applications, such as video conferencing, video streaming and mobile TV. Towards delivering video stream to diverse devices over a heterogamous network, scalable video coding (SVC) has received many research attentions. SVC is an extension of H.264/AVC that allows a video streaming service provider to encode a high quality video into a number of scalable layers. The receivers of the stream may decode the video at the appropriate quality level that is suitable for their hardware/software capabilities and network connections. Nevertheless, compared to single layer H.264/AVC, the de facto standard for many commercial streaming service providers such as YouTube, SVC is not widely deployed, mostly due to its overhead in terms of bit rate and complexity. In this paper, we conduct a thorough study on the performance of SVC for full HD video streaming. Our performance analysis identifies good and bad uses of SVC, quantifies the coding overhead, and benchmarks the SVC video quality under different spatial, temporal, and quality settings. Through the use a set of carefully selected and diverse video sequences, we also identify the types of video that can benefit from SVC.
Activation of Platelet Function Through G Protein–Coupled Receptors (2006)

Because of their ability to become rapidly activated at places of vascular injury, platelets are important players in primary hemostasis as well as in arterial thrombosis. In addition, they are also involved in chronic pathological processes including the atherosclerotic remodeling of the vascular system. Although primary adhesion of platelets to the vessel wall is largely independent of G protein-mediated signaling, the subsequent recruitment of additional platelets into a growing platelet thrombus requires mediators such as ADP, thromboxane A(2), or thrombin, which act through G protein-coupled receptors. Platelet activation via G protein-coupled receptors involves 3 major G protein-mediated signaling pathways that are initiated by the activation of the G proteins G(q), G(13), and G(i). This review summarizes recent progress in understanding the mechanisms underlying platelet activation and thrombus extension via G protein-mediated signaling pathways.
Sequence Analysis and Organization of the<i>Neodiprion abietis</i>Nucleopolyhedrovirus Genome (2006)

Of 30 baculovirus genomes that have been sequenced to date, the only nonlepidopteran baculoviruses include the dipteran Culex nigripalpus nucleopolyhedrovirus and two hymenopteran nucleopolyhedroviruses that infect the sawflies Neodiprion lecontei (NeleNPV) and Neodiprion sertifer (NeseNPV). This study provides a complete sequence and genome analysis of the nucleopolyhedrovirus that infects the balsam fir sawfly Neodiprion abietis (Hymenoptera, Symphyta, Diprionidae). The N. abietis nucleopolyhedrovirus (NeabNPV) is 84,264 bp in size, with a G+C content of 33.5%, and contains 93 predicted open reading frames (ORFs). Eleven predicted ORFs are unique to this baculovirus, 10 ORFs have a putative sequence homologue in the NeleNPV genome but not the NeseNPV genome, and 1 ORF (neab53) has a putative sequence homologue in the NeseNPV genome but not the NeleNPV genome. Specific repeat sequences are coincident with major genome rearrangements that distinguish NeabNPV and NeleNPV. Genes associated with these repeat regions encode a common amino acid motif, suggesting that they are a family of repeated contiguous gene clusters. Lepidopteran baculoviruses, similarly, have a family of repeated genes called the bro gene family. However, there is no significant sequence similarity between the NeabNPV and bro genes. Homologues of early-expressed genes such as ie-1 and lef-3 were absent in NeabNPV, as they are in the previously sequenced hymenopteran baculoviruses. Analyses of ORF upstream sequences identified potential temporally distinct genes on the basis of putative promoter elements.
Near-field optics theories (1996)

The development of near-field optics theory is reviewed. We first recall that near-field optics is not limited to near-field microscopy. Broadly speaking, it concerns phenomena involving evanescent electromagnetic waves. The importance of such waves was ignored for a long time in optical and surface physics until the emergence of scanning near-field optical microscopes. Taking evanescent waves into account prevents the use of any simple approximation in the set of Maxwell's equations. The various theoretical approaches of near-field optics are discussed from the point of view of their ability to assess evanescent electromagnetic waves. We discuss the main results of the application of the various practical schemes which all rely on a numerical procedure.
ZOD Micro-Images: Colour and Black-and-White Image Reproduction from Surface Relief Grating Structures (1978)

AbstractTwo-dimensional colour pictures have been recorded as diffractive surface-relief structures in a transparent medium. They are read out in the zero diffraction order using commercially available slide projectors or microfilm viewers. Compared to conventional colour film they offer a considerable cost advantage, as they can be mass produced by hot embossing into thermoplastic sheet. Resolution up to 360 lines/mm is achieved.A colour picture is formed by three separate embossings on thermoplastic sheet material which are sandwiched together in registration. A black-and-white picture requires a single embossing. Through the use of master blanks, which correspond to unexposed film or printing plates, the preparation of the embossing master becomes a simple reliable process. NotesTrademark of RCA Corporation.paper presented at a Symposium on "Unconventional Photographic Systems", organized by the Science Committee of The Royal Photographic Society on 12-16 September 1977 in Oxford.
Monte Carlo analysis of In<inf>0.53</inf>Ga<inf>0.47</inf>as Implant-Free Quantum-Well device performance (2010)

This work reports a Monte Carlo (MC) and Drift Diffusion (DD) investigation of the IF-QW device performance. The optimisation of the output characteristics is based on the careful choice of layer thicknesses and doping concentrations. Particular attention has been paid on the improvement of the subthreshold characteristics and drive current by careful design of the overgrown regions, δ-doping on the backside of the channel and optimisation of the lateral spacer.
An Event Service Supporting Autonomic Management of Ubiquitous Systems for e-Health (2006)

An event system suitable for very simple devices corresponding to a body area network for monitoring patients is presented. Event systems can be used both for self-management of the components as well as indicating alarms relating to patient health state. Traditional event systems emphasise scalability and complex event dissemination for internet based systems, whereas we are considering ubiquitous systems with wireless communication and mobile nodes which may join or leave the system over time intervals of minutes. Issues such as persistent delivery are also important. We describe the design, prototype implementation, and performance characteristics of an event system architecture targeted at this application domain.
Picosecond time-resolved fluorescence spectroscopy of the photochromic reaction of spiropyran in Langmuir-Blodgett films (1991)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPicosecond time-resolved fluorescence spectroscopy of the photochromic reaction of spiropyran in Langmuir-Blodgett filmsTakahide Minami, Naoto Tamai, Tomoko Yamazaki, and Iwao YamazakiCite this: J. Phys. Chem. 1991, 95, 10, 3988–3993Publication Date (Print):May 1, 1991Publication History Published online1 May 2002Published inissue 1 May 1991https://pubs.acs.org/doi/10.1021/j100163a020https://doi.org/10.1021/j100163a020research-articleACS PublicationsRequest reuse permissionsArticle Views245Altmetric-Citations38LEARN 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 options Get e-Alerts
Continuous-Time Common-Mode Feedback Circuit for Applications with Large Output Swing and High Output Impedance (2008)

Motivated by the fact that no existing common- mode feedback block (CMFB) can work for the systems characterized with both high output impedance and large output swing, a new CMFB topology is introduced in this paper to accomplish this task. Various types of CMFB are studied, analyzed and simulated. Compared with other CMFBs, the proposed CMFB obtains the widest linear input range, smallest output common-mode level error, largest (full) output swing and has no interference to the system output impedance. All these properties entitle the presented CMFB circuit to suit all types of fully differential systems, especially for systems which require both high output impedance and large signal output swing.
Computer Vision-Based Video Interpretation Model for Automated Productivity Analysis of Construction Operations (2009)

Videotaping is an effective and inexpensive technique that has long been used in construction to conduct productivity analyzes. However, as schedules of modern construction projects become more and more compressed, the limitation of video-based analysis—intensive manual reviewing process—contrasts sharply with the need for effortless data analysis methods. This paper presents a study on developing a video interpretation model to interpret videos of construction operations automatically into productivity information. More specifically, this research formalizes key concepts and procedures of video interpretation within the construction domain. It focuses on designing a mechanism for furthering the crosstalk between the prior knowledge of construction operations and computer vision techniques. It uses this mechanism to guide the detection and tracking of project resources as well as work state classifications and abnormal production scenario identifications. The resulting approach has the potential to provide a common base for developing automated video interpretation procedures that can greatly improve current data collection and analyzes practices in construction. Experimental results from preliminary studies have shown the potential of the proposed video interpretation method as an improved productivity data analysis method.
Static and time-dependent shortest path through an urban environment: Time-Dependent Shortest Path (2014)

More and more problems occur with an increasing amount of transportation on the road. These problems include pollution, accidents and traffic congestion. Road traffic congestion is a significant problem in modern society. To avoid traffic jams we need to reduce the number of vehicles on the road by encouraging the use of public transportation. Travelers require individualized, dependable route information to be persuaded to use public transportation. This can be determined through the use of shortest path algorithms to determine the optimal routes for individuals. This paper aims to evaluate two k shortest path implementations (based on Dijkstra's algorithm (1959)) in a static and time dependent network.
Recombinant human antithrombin inhibits thrombin formation and interleukin 6 release in human endotoxemia (2006)

We hypothesized that infusion of recombinant human antithrombin without concomitant heparin would have dose-dependent anticoagulant properties and potentially decrease endotoxin (lipopolysaccharide [LPS])-induced cytokine production. This was a randomized, double-blind, placebo-controlled study in parallel groups enrolling 30 healthy male volunteers. The active treatment groups received infusions of recombinant human antithrombin to increase antithrombin levels to 200% and 500% before infusion of 2 ng/kg endotoxin (LPS). Infusion of antithrombin dose-dependently decreased coagulation (P < .01 by repeated-measures ANOVA): peak levels of prothrombin fragment (1.8 nmol/L [95% confidence interval (CI), 1.3-2.3 nmol/L] in the 500% antithrombin group and 4.4 nmol/L [95% CI, 2.7-6.2 nmol/L] in the placebo group at 4 hours), thrombin antithrombin complexes (12 microg/L [95% CI, 8-16 microg/L] in the 500% antithrombin group and 34 microg/L [95% CI, 20-48 microg/L] in the placebo group at 4 hours), and D-dimer (0.2 microg/L [95% CI, 0.1-0.2 microg/L] in the 500% antithrombin group and 0.5 microg/L [95% CI, 0.4-0.7 microg/L] in the placebo group). Recombinant human antithrombin decreased peak interleukin-6 levels by 40% (222 pg/mL [95% CI, 148-295 pg/mL] and 216 pg/mL [95% CI, 112-320 pg/mL] in the 500% and 200% antithrombin groups, respectively, versus 357 pg/mL [95% CI, 241-474 pg/mL] in the placebo group; P < .001 by ANOVA). Finally, infusion of recombinant human antithrombin rapidly and transiently decreased neutrophil counts (by 19% [95% CI, 8%-30%] in the 500% antithrombin group versus 6% [95% CI, 1%-10%] in the placebo group, P = .002 by Kruskal-Wallis ANOVA) and monocyte counts (by 30% [95% CI, 16%-44%] in the 500% antithrombin group and 18% [95% CI, 9%-28%] in the 200% antithrombin group versus 8% [95% CI, 5%-20%] in the placebo group, P = .04) before LPS challenge, indicating that recombinant human antithrombin directly interacts with these leukocyte subsets. In summary, recombinant human antithrombin dose-dependently inhibited tissue factor-triggered coagulation. Effects on leukocytes and inhibition of interleukin-6 release seem to represent specific pharmacodynamic properties of recombinant human antithrombin.