gebhart/patrepeval huggingface dataset:
The Identification of Protein-Protein Interactions of the Nuclear Pore Complex of Saccharomyces cerevisiae Using High Throughput Matrix-assisted Laser Desorption Ionization Time-of-Flight Tandem Mass Spectrometry (2002)

Mass spectrometry has become the technology of choice for detailed identification of proteins in complex mixtures. Although electrophoretic separation, proteolytic digestion, mass spectrometric analysis of unseparated digests, and database searching have become standard methods in widespread use, peptide sequence information obtained by collision-induced dissociation and tandem mass spectrometry is required to establish the most comprehensive and reliable results. Most tandem mass spectrometers in current use employ electrospray ionization. In this work a novel tandem mass spectrometer employing matrix-assisted laser desorption ionization-time-of-flight/time-of-flight operating at 200 Hz has been used to identify proteins interacting with known nucleoporins in the nuclear pore complex of Saccharomyces cerevisiae. Proteins interacting with recombinant proteins as bait were purified from yeast extracts and then separated by one-dimensional SDS-PAGE. Although peptide mass fingerprinting is sometimes sufficient to identify proteins, this study shows the importance of employing tandem mass spectrometry for identifying proteins in mixtures or as covalently modified forms. The rules for incorporating these features into MS-Tag are presented. In addition to providing an evaluation of the sensitivity and overall quality of collision-induced dissociation spectra obtained, standard conditions for ionization and fragmentation have been selected that would allow automatic data collection and analysis, without the need to adjust parameters in a sample-specific fashion. Other considerations essential for successful high throughput protein analysis are discussed.
A New Eight Switch Seven Level Boost Active Neutral Point Clamped (8S-7L-BANPC) Inverter (2020)

A new boost Active-Neutral-Clamped (ANPC) voltage boosting inverters are appealing for low dc-link voltage demand. Recent boost ANPC topology has demonstrated a 1.5 times voltage gain, but the number of switches has a higher number. This paper proposed an improved boost ANPC topology with 1.5 voltage gain using the least number of switches. Further, the number of conducting switches has been reduced remarkably which enhances the system efficiency. The seven-level (7L) output voltage levels are achieved using a floating capacitor with self-voltage balancing capability. The proposed topology has been analyzed and compared to the ANPC topologies proposed in recent years. For the validation of the theoretical aspect of the proposed topology, the experimental findings have been compiled in the paper.
Inhibition of Soluble Tumor Necrosis Factor Prevents Chemically Induced Carcinogenesis in Mice (2016)

TNF is a potent promoter of carcinogenesis and potentially important target for cancer prevention. TNF is produced as functionally distinct transmembrane and soluble molecules (tmTNF and sTNF, respectively), but their individual roles in carcinogenesis are unexplored. We investigated the participation of tmTNF and sTNF in chemically induced carcinogenesis in mice. We found that injection of XPro1595, a dominant-negative TNF biologic (DN-TNF) and specific antagonist of sTNF, decreased tumor incidence and growth, and prolonged survival of 3-methylcholanthrene (MCA)-injected mice. Similar results were obtained following the exclusion of both TNF forms by either TNF-receptor 2-Fc fusion protein (TNFR2-Fc) treatment or TNF gene deletion. In addition, gene deletion of TNFR1, which is preferentially triggered by sTNF, was temporarily blocked, whereas gene deletion of TNFR2, which is preferentially triggered by tmTNF, enhanced MCA-induced carcinogenesis. Concomitantly with carcinogenesis induction, MCA increased circulating IL1α, accumulation of myeloid-derived suppressor cells (MDSC), STAT3 phosphorylation, and immunosuppression in the spleen. In sharp contrast, DN-TNF treatment dramatically decreased IL1α and increased the essential immunoregulatory cytokines IL1β, IL12p70, and IL17 in the peripheral blood of MCA-injected mice. In addition, MDSC accumulation, STAT3 phosphorylation, and immunosuppression in MCA-injected mice were prevented by DN-TNF treatment, TNFR2-Fc treatment, and/or gene deletion of TNF or TNFR1, but not deletion of TNFR2. These findings reveal that sTNF is both an essential promoter of carcinogenesis and a pivotal regulator of MDSCs, and indicate that sTNF could be a significant target for cancer prevention and therapy. Cancer Immunol Res; 4(5); 441-51. ©2016 AACR.
High Performance Photoinitiating Systems for Holography Recording: Need for a Full Control of Primary Processes (2014)

Optimization of holography recording in photopolymers was studied from the point of view of a quite general process, that is, the photogeneration of radicals. On the basis of a dye/coinitiator photoinitiating system, the effect of primary events and their relative efficiency was investigated with respect to the final overall properties, such as the diffraction efficiency. Quenching of the dye excited states by the borate salts coinitiators exhibits important differences depending on the dye used (Rose Bengal or Safranine O). Keeping in mind that both singlet and triplet states of the dyes can react, and taking into account the viscosity of the matrix, a method to evaluate the overall quantum yield of radicals released is proposed. It is found that this quantum yield well correlates with the maximum rate of photopolymerization. More interestingly, the dose required to obtain a given diffraction efficiency was found to be also governed by the radical quantum yield, showing that the final property is directly governed by primary events. This shed some light on the efficiency of photochemical pathway to generate radicals for use in organic or polymer areas.
Image completion with structure propagation (2005)

In this paper, we introduce a novel approach to image completion, which we call structure propagation. In our system, the user manually specifies important missing structure information by extending a few curves or line segments from the known to the unknown regions. Our approach synthesizes image patches along these user-specified curves in the unknown region using patches selected around the curves in the known region. Structure propagation is formulated as a global optimization problem by enforcing structure and consistency constraints. If only a single curve is specified, structure propagation is solved using Dynamic Programming. When multiple intersecting curves are specified, we adopt the Belief Propagation algorithm to find the optimal patches. After completing structure propagation, we fill in the remaining unknown regions using patch-based texture synthesis. We show that our approach works well on a number of examples that are challenging to state-of-the-art techniques.
Monolithic silicon optoelectronic biochips (2002)

This work presents results on protein detection through a monolithically integrated silicon optoelectronic transducer. Also, we demonstrate the enabling technologies for developing high probe density optical biochips that can be read out without the need of external optical components. Experimental results are presented that demonstrate sensitive protein detection using biotin and protein coated chips as well as probe patterning using biocompatible photoresist.
Novel multiwavelength and ultralow-noise modelocked semiconductor lasers for networking, instrumentation, and signal processing (2003)

Modelocked semiconductor diode lasers are used as compact sources for multiwavelength generation. The generation of multiple wavelengths can be grouped into 2 general categories: 1) multiple continuous wave, phase locked optical frequencies, or 2) multiple, synchronized modelocked wavelength channels. Applications of these sources are demonstrated in areas of optical sampling, access networks, and arbitrary waveform generation.
Enhanced differential power processor for PV systems: Resonant switched-capacitor gyrator converter with local MPPT (2014)

This paper introduces an enhanced differential power processor topology and principle of operation for photovoltaic systems (PV) that is based on switched-capacitor technology, featuring local maximum power point tracking (MPPT) capability, zero current switching (ZCS), high efficiency over wide operation range, and reduced size. The new converter operates as a voltage-dependent current-source and is regulated by dead-time or frequency control. Local MPPT on the individual PV elements is realized and the operation is demonstrated by simulation and experiments. Differential power processing operation is verified on 100W prototypes, demonstrating ultimate improvement in the power harvesting capability of above 90% and up to 99% out of the available power in the string, under different insolation levels.
Thermal Design Methodology for Low Flow Rate Single-Phase and Two-Phase Micro-Channel Heat Sinks (2007)

This study provides a systematic thermal design methodology for both single-phase and two-phase micro-channel heat sinks under a fixed liquid coolant flow rate. The parameters relevant to heat sink design are grouped into geometrical parameters, operating parameters, and thermal/fluid parameters. The objective of the proposed thermal design methodology is to determine micro-channel dimensions leading to the most desirable heat sink performance corresponding to a given dissipative heat flux and liquid coolant flow rate. An acceptable design region is first identified which encompasses all possible micro-channel dimensions corresponding to the prescribed dissipative heat flux and liquid coolant flow rate. Heat sink performance maps are then constructed within the acceptable design region. Finally, micro-channel dimensions yielding most desirable heat sink performance can be selected using the performance maps.
Carbonylation of Vinyl Aromatics:  Convenient Regioselective Synthesis of 2-Arylpropanoic Acids (1999)

Various substituted and nonsubstituted 2-arylpropanoic acids have been synthesized in high turnovers with high regioselectivity by palladium-catalyzed carbonylation of vinyl aromatics. Both terminal and internal olefins are carbonylated, though hindered olefins are less reactive. In all the cases high yields and high selectivity are observed. Olefins with electron-withdrawing para substituents gave the highest regioselectivity in the formation of the corresponding 2-arylpropanoic acids.
True 3D seismic visualization and interpretation (2000)

PreviousNext No AccessSEG Technical Program Expanded Abstracts 2000True 3D seismic visualization and interpretationAuthors: John GrismoreJacquelyn SingletonDennis NeffJesse LaytonErik KeskulaJohn GrismorePhillips Petroleum Company, Bartlesville, Oklahoma, Jacquelyn SingletonPhillips Petroleum Company, Bartlesville, Oklahoma, Dennis NeffPhillips Petroleum Company, Bartlesville, Oklahoma, Jesse LaytonPhillips Petroleum Company, Bartlesville, Oklahoma, and Erik KeskulaPhillips Petroleum Company, Bartlesville, Oklahomahttps://doi.org/10.1190/1.1816127 SectionsAboutPDF/ePub ToolsAdd to favoritesDownload CitationsTrack CitationsPermissions ShareFacebookTwitterLinked InRedditEmail Permalink: https://doi.org/10.1190/1.1816127FiguresReferencesRelatedDetails SEG Technical Program Expanded Abstracts 2000ISSN (print):1052-3812 ISSN (online):1949-4645Copyright: 2000 Pages: 2484 publication data© 2000 Copyright © 2000 Society of Exploration GeophysicistsPublisher:Society of Exploration Geophysicists HistoryPublished Online: 04 Jan 2005 CITATION INFORMATION John Grismore, Jacquelyn Singleton, Dennis Neff, Jesse Layton, and Erik Keskula, (2000), "True 3D seismic visualization and interpretation," SEG Technical Program Expanded Abstracts : 578-581. https://doi.org/10.1190/1.1816127 Plain-Language Summary PDF DownloadLoading ...
A robust dynamic voltage scaling scheme for FPGAs with IR drop compensation (2017)

Dynamic Voltage Scaling (DVS) has been shown to yield dramatic power savings in modern FPGAs. Because each user-specific hardware design has unique critical paths, the hardware reconfigurability of FPGAs renders the implementation of DVS much more challenging compared to CPUs. A promising FPGA DVS scheme relies on a two-step, offline self-characterization of the minimum supply voltage of the critical paths versus frequency and temperature. It does not, however, account for the resistive voltage drops in the power distribution network during regular operation. As a result, voltage guard-bands are necessary, reducing the power savings. In this paper, a self-calibration method is demonstrated to directly measure the on-chip voltage using a calibrated Delay-Line ADC (DL-ADC). The temperature dependent resistance between the dc-dc converter feedback point and the on-chip critical path is accurately extracted and used in regular DVS mode to compensate the voltage drop according to the load current. The new DVS scheme is demonstrated on an Altera Cyclone IV 60-nm FPGA with a digitally controlled dc-dc converter.
Treatment of neuromyelitis optica: state-of-the-art and emerging therapies (2014)

Neuromyelitis optica (NMO) is an autoimmune disease of the CNS that is characterized by inflammatory demyelinating lesions in the spinal cord and optic nerve, potentially leading to paralysis and blindness. NMO can usually be distinguished from multiple sclerosis (MS) on the basis of seropositivity for IgG antibodies against the astrocytic water channel aquaporin-4 (AQP4). Differentiation from MS is crucial, because some MS treatments can exacerbate NMO. NMO pathogenesis involves AQP4-IgG antibody binding to astrocytic AQP4, which causes complement-dependent cytotoxicity and secondary inflammation with granulocyte and macrophage infiltration, blood-brain barrier disruption and oligodendrocyte injury. Current NMO treatments include general immunosuppressive agents, B-cell depletion, and plasma exchange. Therapeutic strategies targeting complement proteins, the IL-6 receptor, neutrophils, eosinophils and CD19--all initially developed for other indications--are under clinical evaluation for repurposing for NMO. Therapies in the preclinical phase include AQP4-blocking antibodies and AQP4-IgG enzymatic inactivation. Additional, albeit currently theoretical, treatment options include reduction of AQP4 expression, disruption of AQP4 orthogonal arrays, enhancement of complement inhibitor expression, restoration of the blood-brain barrier, and induction of immune tolerance. Despite the many therapeutic options in NMO, no controlled clinical trials in patients with this condition have been conducted to date.
Enhanced annealing of GaAs solar cell radiation damage (1981)

Solar cells are degraded by radiation damage in space. Investigations have been conducted concerning possibilities for annealing this radiation damage in GaAs solar cells, taking into account the conditions favoring such annealing. It has been found that continuous annealing as well as the combination of injection annealing with thermal annealing can lead to recovery from radiation damage under particularly favorable conditions in GaAs solar cells. The damage caused by both electrons and protons in GaAs solar cells can be substantially reduced by annealing at temperatures as low as 150 C, under appropriate conditions. This possibility makes the GaAs solar cells especially attractive for long space missions, or for missions in severe radiation environments. Attention is given to results concerning periodic thermal annealing, continuous annealing, and injection annealing combined with thermal annealing.
Recent Developments on KCNQ Potassium Channel Openers (2005)

During the past five years, several members of the KCNQ potassium channel gene family have been identified with a high degree of CNS specificity. Within the KCNQ family, the combination of the KCNQ2/KCNQ3 proteins, and the KCNQ5/KCNQ3 arrangement has been identified as the molecular correlates of the different M-currents. Several lines of evidence are emerging demonstrating the importance of these channels in regulating neuronal excitability; for example, determination of the excitability threshold, firing properties, and responsiveness of neurons to synaptic inputs. Recent studies have shown that KCNQ openers have potential for the treatment of several CNS disorders characterized by neuronal hyperexcitability, such as migraine, epilepsy and neuropathic pain. This article reviews the recent developments of KCNQ potassium channel openers.
RAPID DETECTION OF MALARIA INFECTION IN VIVO BY LASER DESORPTION MASS SPECTROMETRY (2004)

Rapid diagnosis leading to effective treatment is essential to control escalating infectious diseases such as malaria. Malaria pigment (hemozoin) detection by laser desorption mass spectometry (LDMS) was recently shown to be a sensitive (<10 parasites/muL) technique for detecting Plasmodium falciparum parasites cultured in human blood. To examine the use of LDMS in a rapid new malaria screening assay, we followed the time course of P. yoelii infections in mice in parallel with light microscopy and a colorimetric hemozoin assay. Hemozoin was detected by LDMS in 0.3 muL of blood within two days of infection independently of the inoculating dose of 10(6), 10(4), or 10(2) parasite-infected erythrocytes. Microscopy and colorimetric hemozoin determinations lagged the LDMS detection of infections by 2-4 and 3-5 days, respectively, except at the highest inoculation dose. The LDMS detection of hemozoin is a potentially more rapid screen than light microscopy for detecting malaria infection in this mouse model at parasitemias <0.1%.
RESCU: Dynamic Hybrid Packet-Loss Recovery for Video Transmission over the Internet- (2015)

The current Internet is not reliable; packet loss rates are frequently high, and varying over time. Transmitting high-quality interactive video over the Internet is challenging because the quality of com-pressed video is very susceptible to packet losses. Loss of pack-ets belonging to a video frame manifests itself not only in the re-duced quality of that frame but also in the propagation of that dis-tortion to successive frames. This error propagation problem is inherent in many motion-based video codecs due to the interde-pendence of encoded video frames. This paper presents a dynamic loss recovery scheme, called RESCU, to address the error prop-agation problem. In this new scheme, picture coding patterns are dynamically adapted to current network conditions in order to max-imize the effectiveness of hybrid transport level recovery (employ-ing both forward error correction and retransmission) i reducing error propagation. Since RESCU does not introduce any playout delay at the receiver, it is suitable for interactive video communica-tion. An experimental study based on actual Internet transmission traces representing various network conditions shows that dynamic hybrid RESCU exhibits better er or resilience and incurs much less bit overhead than existing error recovery techniques such as NEW-PRED and Intra-H.261.
Reducing Spread Spectrum Image Steganography (SSIS) Extraction Errors With Feedback-Driven Adjustment (2002)

Abstract : Steganographic techniques are useful to hide information in various types of common multimedia data for covert communication. Spread Spectrum Image Steganography (SSIS) is a data-hiding/hidden-communication method that uses digital imagery as a cover signal. This report examines the error sources in SSIS, their impact on payload throughput, and ways of minimizing these errors. We present a method that employs a feedback-driven adjustment to anticipate extraction errors and compensate for them without adversely affecting the detectability of the stegomessage. The technique, which is performed by the transmitter, does not require any additional effort on the part of the recipient We also describe an experiment using multiple cover images to evaluate the change in error rate as a function of varying input values along with modifications to the SSIS message embedding process. In conclusion, we propose enhancements to the feedback process, enabling it to be used not only for error reduction, but also as a means of limiting the detectability of a stegomessage.
A content-based centrality metric for collaborative caching in information-centric fogs (2017)

Information-Centric Fog Computing enables a multitude of nodes near the end-users to provide storage, communication, and computing, rather than in the cloud. In a fog network, nodes connect with each other directly to get content locally whenever possible. As the topology of the network directly influences the nodes' connectivity, there has been some work to compute the graph centrality of each node within that network topology. The centrality is then used to distinguish nodes in the fog network, or to prioritize some nodes over others to participate in the caching fog. We argue that, for an Information-Centric Fog Computing approach, graph centrality is not an appropriate metric. Indeed, a node with low connectivity that caches a lot of content may provide a very valuable role in the network. To capture this, we introduce a content-based centrality (CBC) metric which takes into account how well a node is connected to the content the network is delivering, rather than to the other nodes in the network. To illustrate the validity of considering content-based centrality, we use this new metric for a collaborative caching algorithm. We compare the performance of the proposed collaborative caching with typical centrality based, non-centrality based, and non-collaborative caching mechanisms. Our simulation implements CBC on three instances of large scale realistic network topology comprising 2, 896 nodes with three content replication levels. Results shows that CBC outperforms benchmark caching schemes and yields a roughly 3x improvement for the average cache hit rate.
Mismatch Correction for Free-breathing PET and Deep-inspiration Breath-holding CT in PET/CT Imaging (2017)

CT images acquired during deep-inspiration breath-holding (DIBH) have higher image quality than free-breathing (FB) CT images as they are free from respiratory motion artifacts. However, there exists significant mismatch between DIBH CT images and FB PET images since the displacement of organs in the thorax and abdomen at DIBH is significantly larger than that during regular FB. Our goal is to correct for the large mismatch between FB PET and DIBH CT in PET/CT imaging. The list-mode PET data were divided into four equal-count frames using amplitude based data-driven respiratory gating technique. Frame 1 and Frame 4 corresponded to end-expiration and end-inspiration respectively, and they were reconstructed using OSEM image reconstruction algorithm. To avoid attenuation-activity mismatch artifacts, the attenuation map used in attenuation correction was modified by filling the lung region with attenuation coefficient of soft tissue. 3D motion vector field from Frame 4 to Frame 1 was calculated from the reconstructed PET images using B-spline image registration algorithm. Assuming the respiratory motion during FB is consistent during FB and DIBH, the motion vector field from DIBH to end-inspiration phase is modeled by scaling the calculated respiratory motion from Frame 4 to Frame 1. The scalar was determined by maximizing the mutual information between transformed DIBH attenuation map and PET image at Frame 4. DIBH attenuation map was transformed using the scaled motion vector field from Frame 4 to Frame 1 to obtain attenuation map at Frame 4. Attenuation maps for other frames were obtained by transforming attenuation map at Frame 4 using corresponding motion vector fields. The method was applied to clinical patient data acquired using DIBH CT and FB PET protocol. While DIBH attenuation map creates significant mismatch artifacts in PET images, the proposed method was able to generate attenuation maps matching FB PET frames and reduce mismatch artifacts.