gebhart/patrepeval huggingface dataset:
Mapping a Conformational Epitope of Hemagglutinin A Using Native Mass Spectrometry and Ultraviolet Photodissociation (2020)

As the importance of effective vaccines and the role of protein therapeutics in the drug industry continue to expand, alternative strategies to characterize protein complexes are needed. Mass spectrometry (MS) in conjunction with enzymatic digestion or chemical probes has been widely used for mapping binding epitopes at the molecular level. However, advances in instrumentation and application of activation methods capable of accessing higher energy dissociation pathways have recently allowed direct analysis of protein complexes. Here we demonstrate a workflow utilizing native MS and ultraviolet photodissociation (UVPD) to map the antigenic determinants of a model antibody-antigen complex involving hemagglutinin (HA), the primary immunogenic antigen of the influenza virus, and the D1 H1-17/H3-14 antibody which has been shown to confer potent protection to lethal infection in mice despite lacking neutralization activity. Comparison of sequence coverages upon UV photoactivation of HA and of the HA·antibody complex indicates the elimination of some sequence ions that originate from backbone cleavages exclusively along the putative epitope regions of HA in the presence of the antibody. Mapping the number of sequence ions covering the HA antigen versus the HA·antibody complex highlights regions with suppressed backbone cleavage and allows elucidation of unknown epitopes. Moreover, examining the observed fragment ion types generated by UVPD demonstrates a loss in diversity exclusively along the antigenic determinants upon MS/MS of the antibody-antigen complex. UVPD-MS shows promise as a method to rapidly map epitope regions along antibody-antigen complexes as novel antibodies are discovered or developed.
Scaling Requirements for Presence in SIP/SIMPLE (2009)

The document provides a set of requirements for enabling inter-domain
scaling in presence for SIP/SIMPLE.
Energy Detection with Diversity Reception (2017)

We characterize the performance of energy detector (ED) over square-law, square-law selection, and switch-and-stay diversity combining schemes. The exact average probabilities of a miss (Pm), and a false alarm (Pf) are derived in closed-form. To derive Pm for versatile Nakagami-m and Rician fading channels, a twofold approach, using the probability density function (PDF) and the moment generating function (MGF), is applied. Using the PDF method, the achievable diversity order over the Nakagami-m channel is derived. However, this method becomes intractable when analyzing Pm of the aforementioned combiners in Rician channels, but the MGF method can handle this case. Our analysis helps to quantify the performance gains of ED due to diversity reception. Theoretical derivations are verified through numerical Monte-Carlo simulation results.
Optimal Power-Area Polar Decoder Design based on Iterative Decomposition Technique (2019)

Polar codes have a very good error correcting capacity compared to turbo and LDPC codes of similar length. They are the first to attain the channel capacity. The aim of the proposed work is to design an Area and Power optimal 2b SC polar decoder exhibiting reduced area and power without degrading the latency by iterative decomposition technique. The targeted performances in decoder architecture are achieved by novel reformulation of F-node, G-node and P-nodes.
Isoprenoid Biosynthesis of the Apicoplast as Drug Target (2006)

In Plasmodium falciparum the biosynthesis of isoprenoids is achieved by the mevalonate-independent 1-deoxy-d-xylulose 5-phosphate (DOXP) pathway. The enzymes of the DOXP pathway are localised inside the plastid-like organelle (apicoplast). Fosmidomycin inhibits DOXP reductoisomerase, the second enzyme of this pathway. The antimalarial activity of fosmidomycin was established in vitro and in a rodent malaria model. Fosmidomycin alone or in combination with clindamycin was evaluated for the treatment of acute uncomplicated P. falciparum malaria in early phase II studies. Fosmidomycin monotherapy led to a fast parasite and fever clearance but was inefficient in radical elimination of the parasites. With the fosmidomycin-clindamycin combinations the cure ratio on day 28 was 100 % (10/10) with treatment durations of 5 and 4 days. The cure ratio was 90 % (9/10) with treatment duration of 3 days.
Track Chair's Report: Convergence of Distributed Clouds, Grids and their Management CDCGM 2017 (2017)

This track started in 2009 with opening remarks from the Chair observing that the computing cloud evolution depends on research efforts from the infrastructure providers creating next generation hardware that is service friendly, service developers that embed business service intelligence in the computing infrastructure to create distributed business workflow execution services and service providers who assure service delivery on a massive scale with global interoperability. The state of the art architecture and evolution of the cloud at that time was already increasing datacenter complexity by piling up new layers of management over the many layers that already exist. Since then, the scale of distributed applications and their management have taken a new dimension demanding tolerance to wild fluctuations both in workloads and available computing resource pools. There are many calls to go cloud native and architect applications using the many services provided by the cloud providers such as Amazon Web Services. On the other hand, there are also calls for avoiding vendor lock-in by going multi-cloud and becoming cloud agnostic. In this conference there is a new paper that proposes cloud agnostic approach with globally interoperable cloud network using private or public network while reducing the complexity of Virtual machine image motion across clouds. In addition, there are 7 papers describing advances in current distributed and cloud computing practices dealing with quality of service, adaptive algorithms and software defined network architectures.
Effect of early‐strengthening of RC beams using UHPC layers on their performance against reinforcement corrosion (2023)

Abstract In the present work, the effect of early‐strengthening of reinforced concrete (RC) beam specimens using layers of ultra‐high performance concrete (UHPC) on their performance against reinforcement corrosion was examined. A number of fifteen RC beam specimens were prepared, one beam specimen uncorroded and unstrengthened was considered as a control beam, two beams were corroded and unstrengthened, and twelve corroded and strengthened beam specimens that were divided into two groups. RC beam specimens of the first group were corroded continuously to cause total theoretically targeted mass losses of the steel rebars and then strengthened using UHPC layers. RC beams of the second group were also corroded to the same degrees but in two steps. In the first step, the beams were corroded to cause a portion of targeted theoretical mass losses. Then the beams were strengthened in the same way as the beams of the first group and then subjected to second‐step accelerated reinforcement corrosion to achieve finally the same degrees of total theoretical mass losses as that of the first group. The corroded and strengthened beam specimens were exposed to flexural testing, and then the corroded rebars extracted from the beams were used to conduct gravimetric tests to determine the actual values of the mass losses due to accelerated corrosion. The gravimetric and flexural tests' results were used mainly to observe the influence of early‐strengthening on the actual mass loss and the flexural behavior of the tested beam specimens. Results showed a significant reduction in the values of the actual mass loss and better flexural behavior due to the early‐strengthening of the corroded beams. An analytical model, developed and validated using the data collected from the experimental tests, can be utilized to predict the ultimate load‐carrying capacities of the corroded strengthened RC beam specimens.
Language Learning Disabilities (2003)

Developmental language learning impairments affect 10 to 20% of children and increase their risk of later literacy problems (dyslexia) and psychiatric disorders. Both oral- and written-language impairments have been linked to slow neural processing, which is hypothesized to interfere with the perception of speech sounds that are characterized by rapid acoustic changes. Research into the etiology of language learning impairments not only has led to improved diagnostic and intervention strategies, but also has raised fundamental questions about the neurobiological basis of speech, language, and reading, as well as hemispheric lateralization.
Polygenic Risk Scores for Atherosclerotic Cardiovascular Disease in the Asia-Pacific Region (2021)

Approximately one-half of the phenotypic susceptibility to atherosclerotic cardiovascular disease (ASCVD) has a genetic basis. Although individual allelic variants generally impart a small effect on risk for ASCVD, an emerging body of data has shown that the aggregation and weighting of many of these genetic variations into "scores" can further discriminate an individual's risk beyond traditional risk factors alone. Consistent with the theory of population genetics, such polygenic risk scores (PRS) appear to be ethnicity specific because their elements comprise single-nucleotide variants that are always ethnicity specific. The currently available PRS are derived predominantly from European ancestry and thus predictably perform less well among non-European participants, a fact that has implications for their use in the Asia-Pacific region. This paper describes the current state of knowledge of PRS, the available data that support their use in this region, and highlights the needs moving forward to safely and effectively implement them in clinical care in the Asia-Pacific region.
ULTRAFAST SPECTROSCOPY OF TRANSITION METAL NANORODS (2008)

Author Institution: Chemistry Division, Naval Research Laboratory, Washington, DC 20375; Chemistry Department, United States Naval Academy, Annapolis, MD 21402
A 10-bit area-efficient SAR ADC with re-usable capacitive array (2012)

In this paper, an area-efficient successive approximation register (SAR) analog-to-digital converter (ADC) with a dithering V <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">ref</inf> is proposed. It reuses the capacitive array with the reconfiguration of V <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">ref</inf> to V <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">ref</inf> ± ΔV for reducing dramatically the ADC's area. The 2n resolution is achieved by the n bit SAR-ADC. To verify the proposed scheme, the proposed SAR ADC is implemented in a TSMC 0.18 μm 1P6M CMOS process with a supply voltage of 1.8V. The simulation results show that the capacitor area is reduced by 96% compared with the conventional 10-bit SAR-ADC. The ENOB of the proposed architecture is 9.767 bit when operating at 14MS/s.
Effect of Band-Edge Interface Traps and Transition Region Mobility on Transport in 4H-SiC MOSFETs (2010)

We present physics based models for the occupation of interface traps and the mobility of the transition layer found in 4H-SiC MOSFETs and extract values for the same using combined numerical simulation and experimental characterization. The Si-C-O transition layer found in 4H-SiC MOS devices is electrically modeled as having a doping dependent mobility that is different from the regular bulk 4H-SiC bulk mobility. Compared to the high intrinsic bulk mobility of 4H-SiC, the transition layer intrinsic mobility was extracted to be approximately 165cm2/Vs. The occurrence of the excessive high density of interface traps near the conduction band edge led us to develop a new model for the occupation of traps lying inside the conduction band itself. Due to the conduction band trap densities being comparable to the conduction band electron states, a non-zero probability exists for their occupation, which causes the occupied trap densities to be very high in strong inversion. Detailed numerical simulations and corroboration with experiment have been performed to calibrate the models and extract physical parameter values.
Degenerate parametric amplification in an optoelectronic GaAs CPW-to-slotline ring resonator (1997)

Nonlinear optical-microwave mixing is performed in an uniplanar CPW-to-slotline ring resonator on a semi-insulating GaAs substrate, in which a Schottky photodetector is monolithically integrated as a coupling gap. The parametric amplification effect of the mixer occurs when the capacitive reactance of the detector is modulated. In this structure, a parametric amplification gain of 20 dB, without the applied bias in the radio frequency (RF) signal, is obtained. This microwave optoelectronic mixer can be used in fiber-optic communication links.
Restriction of self‐antigen presentation to cytolytic T lymphocytes by mouse peptide pumps (1995)

Transport of an immunogenic self-peptide from the second domain of the mouse major histocompatibility complex (MHC) H-2Kd class I molecule is blocked at the TAP1-TAP2 peptide pump level due to its amino acid sequence and is not presented to cytolytic T lymphocytes (CTL). We demonstrate that first, TAP1-TAP2 pumps can restrict antigen presentation by selecting against internal peptide motifs which are not involved in peptide binding to MHC class I molecules. Second, some molecules targeted to the endoplasmic reticulum are processed for MHC class I presentation in the cytosol. Third, some abundantly expressed immunogenic self-peptides are cytosolically sequestered. The advantage for the host, in terms of the peripheral T cell repertoire is that the spared CTL can be used to recognize foreign antigens. It is, however, anticipated that this advantage will be exploited by pathogens to evade immune surveillance by similar strategies.
An Unexpected [1,5]-H Shift in the Synthesis of Nitroanilines (2002)

Addition of methyl acetoacetate to 2-nitrovinamidinium hexafluorophosphate salts leads to the formation of anilines or phenols in good to\nexcellent yields depending on the alkylamine substituents. Small substituents, e.g., pyrrolidine, lead to the formation of anilines while large\nsubstituents, e.g., &lt;i&gt;N&lt;/i&gt;,&lt;i&gt;N&lt;/i&gt;-diisopropyl, exclusively give phenols. Labeling studies implicate a [1,5]-H shift proceeding with excellent isotopic fidelity.
How sight and touch are combined depends on viewing geometry (2010)

We studied how the brain combines information from sight and touch in size perception. Contrary to earlier views that sight always dominates touch, recent evidence shows that the more visual information is corrupted by external noise, the more perceived size depends on touch. We asked whether touch information affects size perception when size is hard to measure visually. In a 2-IFC procedure, each interval contained two planes. Observers indicated the interval containing the more widely separated planes. Visual stimuli were depicted with stereograms, and touch (haptic) stimuli with force-feedback devices (PHANToMs). The planes were presented in three orientations: (1) perpendicular to the line of sight so the separation had to be judged from disparity-specified depth alone, (2) parallel to the line of sight so the separation could be judged from 2-D separation, and (3) 45 deg relative to the line of sight. Observers made size discriminations for these orientations with vision alone (V task), touch alone (T task), and with vision and touch together (VT task). In the VT task, the visual and haptic sizes were the same in one interval and differed in the other. We found that the just-discriminable separation in the V task depended on the planes orientation: it was significantly higher when they were perpendicular as opposed to parallel to the line of sight. Performance in the T task did not depend on orientation. Because the visual estimates varied with orientation and the touch estimates did not, optimal use of the two sources of information predicts visual dominance in the parallel orientation and more touch influence in the perpendicular orientation. Results in the VT task were very consistent with this prediction. Thus, the brain combines information from sight and touch in a way that depends on stimulus orientation. This is evidence that the weights given to sight and touch vary according to the relative reliabilities of the two information sources.
Small Shielded Bluetooth Module Equipped with Slot Antenna on the Surface (2018)

In this paper, a land grid array-type ultra-small shielded module that has a 2.4 GHz slot antenna is presented. Slots are patterned on both an interposer and a shield layer. The slots are connected at the side of the interposer and compose the slot antenna. A large part of the slot antenna is formed on the shield deposited on the surface of the module. The slot on the interposer is short and occupy a small area, therefore the slot antenna allows the area of the interposer to be reduced. In addition to that the slot antenna reduces the keep-out zone in which no wires can be laid out on the board. It is because the area of the slot on the interposer is small. A prototype of the module with a Bluetooth Low Energy chip was fabricated. The volume of the prototype is 5.25 × 9.0 × 1.0 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sup> . The keep-out zone of the module is 9.0 mm2. The module has received Japanese modular approval certification because it contains all the elements for wireless communication except for a power supply.
Insertion/Isomerization Polymerization of 1,5-Hexadiene:  Synthesis of Functional Propylene Copolymers and Block Copolymers (2002)

Polymerization of 1,5-hexadiene with a bis(phenoxyimine) titanium catalyst system is reported. The microstructure of the polymer contains the expected methylene-1,3-cyclopentane units as well as the unexpected 3-vinyl tetramethylene units. A mechanism for formation of this polymer is proposed. This unusual reaction is also employed in the synthesis of vinyl-functional polypropylene copolymers and block copolymers with low polydispersity indices.
A Sustainability Challenge (2012)

The essential primer and reference for all environmental professionals and the organizations they work for * Comprehensive practical guidance on policy, management, performance and evaluation * Written by leading international experts in each field Environment and sustainable development issues are now key concerns for all but the smallest organizations and apply to all sectors -- private, public and third sector -- requiring a growing army of environmental professionals to manage them. This volume provides the basic resource needed by organizations and the managers they employ on the issues and on the management tools, performance measures and communication strategies available. Leading experts on each topic provide focused explanations and clear practical guidance, as well as setting out the context and the key environmental and management drivers.
Erratum: ‘‘Ferroelectric thin films with polarization gradients normal to the growth surface’’ [Appl. Phys. Lett. 67, 721 (1995)] (1995)

First Page
Structural Model of the HIV-1 Tat(46–58)-TAR Complex (1998)

The trans-activator protein (Tat) of human immunodeficiency virus type 1 (HIV-1) binds to an uridine-rich bulge of an RNA target (TAR; trans-activation responsive element) predominantly via its basic sequence domain. The structure of the Tat(46-58)-TAR complex has been determined by a novel modeling approach relying on structural information about one crucial arginine residue and crosslink data. The strategy described here solely uses this experimental data without additional "modeling" assumptions about the structure of the complex in order to avoid human bias. Model building was performed in a fashion similar to structure calculations from nuclear magnetic resonance (NMR)-spectroscopic data using restrained molecular dynamics. The resulting set of structures of Tat(46-58) in its complex with TAR reveals that all models have converged to a common fold, showing a backbone root mean square deviation (RMSD) of 1.36A. Analysis of the calculated structures suggests that HIV-I Tat forms a hairpin loop in its complex with TAR that shares striking similarity to the hairpin formed by the structure of the bovine immunodeficiency virus Tat protein after TAR binding as determined by NMR studies. The outlined approach is not limited to the Tat-TAR complex modeling, but is also applicable to all molecular complexes with sufficient biochemical and biophysical data available.
Silicon Metal-oxide-semiconductor Quantum Dots for Single-electron Pumping (2015)

As mass-produced silicon transistors have reached the nano-scale, their behavior and performances are increasingly affected, and often deteriorated, by quantum mechanical effects such as tunneling through single dopants, scattering via interface defects, and discrete trap charge states. However, progress in silicon technology has shown that these phenomena can be harnessed and exploited for a new class of quantum-based electronics. Among others, multi-layer-gated silicon metal-oxide-semiconductor (MOS) technology can be used to control single charge or spin confined in electrostatically-defined quantum dots (QD). These QD-based devices are an excellent platform for quantum computing applications and, recently, it has been demonstrated that they can also be used as single-electron pumps, which are accurate sources of quantized current for metrological purposes. Here, we discuss in detail the fabrication protocol for silicon MOS QDs which is relevant to both quantum computing and quantum metrology applications. Moreover, we describe characterization methods to test the integrity of the devices after fabrication. Finally, we give a brief description of the measurement set-up used for charge pumping experiments and show representative results of electric current quantization.
Vericiguat in patients with coronary artery disease and heart failure with reduced ejection fraction (2022)

In this post hoc study, CAD was associated with more CVD and HFH in patients with HFrEF and worsening HF. Vericiguat was beneficial and safe regardless of concomitant CAD.
REsource LOcation And Discovery (RELOAD) Base Protocol (2014)

This specification defines REsource LOcation And Discovery (RELOAD), a peer-to-peer (P2P) signaling protocol for use on the Internet. A P2P signaling protocol provides its clients with an abstract storage and messaging service between a set of cooperating peers that form the overlay network. RELOAD is designed to support a P2P Session Initiation Protocol (P2PSIP) network, but can be utilized by other applications with similar requirements by defining new usages that specify the Kinds of data that need to be stored for a particular application. RELOAD defines a security model based on a certificate enrollment service that provides unique identities. NAT traversal is a fundamental service of the protocol. RELOAD also allows access from &amp;quot;client &amp;quot; nodes that do not need to route traffic or store data for others. Status of This Memo This is an Internet Standards Track document. This document is a product of the Internet Engineering Task Force (IETF). It represents the consensus of the IETF community. It has received public review and has been approved for publication by the