gebhart/patrepeval huggingface dataset:
Exploration of associative power management with instruction governed operation for ultra-low power design (2016)

This paper explores a novel associative low power operation where instructions govern the operation of on-chip regulators in real time. Based on explicit association between long delay instruction patterns and hardware performance, an instruction based power management scheme is developed with energy models formulated for deriving the energy efficiency of the associative operation. The proposed system scheme is demonstrated using a low power microprocessor design with an integrated switched capacitor regulator in 45nm CMOS technology. Simulations on benchmark programs show a power saving of around 14% from the proposed scheme. A novel compiler optimization strategy is also proposed to further improve the energy efficiency.
In Vivo Reshaping the Catalytic Site of Nucleoside 2′-Deoxyribosyltransferase for Dideoxy- and Didehydronucleosides via a Single Amino Acid Substitution (2008)

Nucleoside 2'-deoxyribosyltransferases catalyze the transfer of 2-deoxyribose between bases and have been widely used as biocatalysts to synthesize a variety of nucleoside analogs. The genes encoding nucleoside 2'-deoxyribosyltransferase (ndt) from Lactobacillus leichmannii and Lactobacillus fermentum underwent random mutagenesis to select variants specialized for the synthesis of 2',3'-dideoxynucleosides. An Escherichia coli strain, auxotrophic for uracil and unable to use 2',3'-dideoxyuridine, cytosine, and 2',3'-dideoxycytidine as a source of uracil was constructed. Randomly mutated lactobacilli ndt libraries from two species, L. leichmannii and L. fermentum, were screened for the production of uracil with 2',3'-dideoxyuridine as a source of uracil. Several mutants suitable for the synthesis of 2',3'-dideoxynucleosides were isolated. The nucleotide sequence of the corresponding genes revealed a single mutation (G --> A transition) leading to the substitution of a small aliphatic amino acid by a nucleophilic one, A15T (L. fermentum) or G9S (L. leichmannii), respectively. We concluded that the "adaptation" of the nucleoside 2'-deoxyribosyltransferase activity to 2,3-dideoxyribosyl transfer requires an additional hydroxyl group on a key amino acid side chain of the protein to overcome the absence of such a group in the corresponding substrate. The evolved proteins also display significantly improved nucleoside 2',3'-didehydro-2',3'-dideoxyribosyltransferase activity.
Passive Noise Shaping in SAR ADC With Improved Efficiency (2017)

This brief reports a passive noise-shaping (PNS) scheme for successive approximation register (SAR) analog-to-digital converter (ADC) based on the two-step integration with passive gain and comparator gain techniques. The analysis shows that the proposed method achieves a better noise-shaping (NS) efficiency than prior arts, which enhances the noise attenuation by 14 dB. A design example is provided which further adopts the delta-sampling technique to relieve the conversion efficiency loss due to the oversampling in the NS SAR ADC. The efficiency of the proposed PNS scheme and the performance of the ADC are verified by simulation achieving a 13.2 effective number of bits with a 10-b ADC architecture and eight conversion cycles for a signal bandwidth of 2 MHz sampled at 100 MS/s. The calculated Schreier figure of merit (FoM) and Walden FoM are 176.8 dB and 16 fJ/conv.-step, respectively.
Graphene technology for RF and THz applications (2013)

This work presents recent advances in the development of graphene technology for various applications from RF to THz frequencies. First, large-scale graphene synthesis methods are reviewed. Graphene FETs suitable for RF applications are then presented along with their DC and RF characteristics. The challenges and current progress toward wafer-scale integration of graphene-based RFICs are also discussed including RFIC measurement results up to 200C. Finally, the absorption properties of graphene at THz frequencies are discussed.
Identifying blood-brain-barrier selective single-chain antibody fragments (2014)

The blood-brain barrier (BBB) represents an obstacle in targeting and delivering therapeutics to the central nervous system. In order to discover new BBB-targeting molecules, we panned a phage-displayed nonimmune human single-chain antibody fragment (scFv) library against a representative BBB model comprised of hydrocortisone-treated primary rat brain endothelial cells. Parallel screens were performed with or without pre-subtraction against primary rat heart and lung endothelial cells in an effort to identify antibodies that may have binding selectivity toward brain endothelial cells. After three rounds of screening, three unique scFvs, scFv15, scFv38, and scFv29, were identified that maintained binding to primary rat brain endothelial cells, both in phage and soluble scFv format. While scFv29 and to a lesser extent, scFv15, exhibited some brain endothelial cell specificity in tissue culture, scFv29 did not appear to bind a BBB antigen in vivo. In contrast, both scFv15 and scFv38 were capable of immunolabeling rat brain vessels in vivo and displayed brain vascular selectivity with respect to all peripheral organs tested other than heart. Taken together, scFv15 and scFv38 represent two new antibodies that are capable of binding antigens that are expressed at the BBB in vivo.
Self-clocked optical control of a self-routed photonic switch (1989)

Self-routing of 100-Mb/s data through a photonic switch is demonstrated. Individual data bits are subencoded into one of 124 destination addresses using a pulse-interval technique with 80-ps pulses. At the switch, optical processing is used to read the address of an incoming bit and to route that bit to the correct switch output without the aid of an external clock. Although the pulse-interval technique is presented in a bit-switching context, it can readily be extended to a packet-switching environment.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Optical device for the precision control of the electric field in the focus of a beam (2018)

We present a common-path optical device consisting of four optical components that produce a laser field consisting of two sub-beams with one radially polarized and the other linearly polarized. In the focus, the radially polarized sub-beam produces longitudinal polarization while the linearly polarized sub-beam produces polarization perpendicular to the propagation direction. By rotating the optical components, the orientation of the resulting electric field in the focus can be continuously varied in any direction. Estimates of the angular resolution of the device are given within the paraxial approximation.
A tale of two bacterial enteropathogens and one multivalent vaccine (2019)

Shigella and enterotoxigenic Escherichia coli (ETEC) are among the top four enteric pathogens that cause diarrheal illness in young children in developing countries and are major etiologic agents of travellers' diarrhoea. A single vaccine that could target both of these pathogens would have significant public health impact. In this review, we highlight the many pivotal contributions of Phillippe Sansonetti to the identification of molecular mechanisms of pathogenesis of Shigella that paved the way for the development of rationally designed, novel vaccines candidates. The CVD developed a series of live attenuated Shigella vaccine strains based on the most prevalent serotypes associated with disease. Shigella vaccine strains were engineered to express critical ETEC antigens to form a broadly protective Shigella-ETEC multivalent vaccine.
The Dendritic Cell-Specific Adhesion Receptor DC-SIGN Internalizes Antigen for Presentation to T Cells (2002)

Dendritic cells (DCs) capture Ags or viruses in peripheral tissue to transport them to lymphoid organs to induce cellular T cell responses. Recently, a DC-specific C-type lectin was identified, DC-specific ICAM-grabbing non-integrin (DC-SIGN), that functions as cell adhesion receptor mediating both DC migration and T cell activation. DC-SIGN also functions as an HIV-1R that captures HIVgp120 and facilitates DC-induced HIV transmission of T cells. Internalization motifs in the cytoplasmic tail of DC-SIGN hint to a function of DC-SIGN as endocytic receptor. In this study we demonstrate that on DCs DC-SIGN is rapidly internalized upon binding of soluble ligand. Mutating a putative internalization motif in the cytoplasmic tail reduces ligand-induced internalization. Detailed analysis using ratio fluorescence imaging and electron microscopy showed that DC-SIGN-ligand complexes are targeted to late endosomes/lysosomes. Moreover, ligands internalized by DC-SIGN are efficiently processed and presented to CD4+ T cells. The distinct pattern of expression of C-type lectins on DCs in situ and their nonoverlapping Ag recognition profile hint to selective functions of these receptors to allow a DC to recognize a wide variety of Ags and to process these to induce T cell activation. These data point to a novel function of the adhesion receptor DC-SIGN as an efficient DC-specific Ag receptor that can be used as a target to induce viral and antitumor immunity.
Automatic Identification of Individual <i>rpoB</i> Gene Mutations Responsible for Rifampin Resistance in Mycobacterium tuberculosis by Use of Melting Temperature Signatures Generated by the Xpert MTB/RIF Ultra Assay (2019)

Molecular surveillance of rifampin-resistant <i>Mycobacterium tuberculosis</i> can help to monitor the transmission of the disease. The Xpert MTB/RIF Ultra assay detects mutations in the rifampin resistance-determining region (RRDR) of the <i>rpoB</i> gene by the use of melting temperature (<i>T<sub>m</sub></i> ) information from 4 <i>rpoB</i> probes which can fall in one of the 9 different assay-specified <i>T<sub>m</sub></i> windows. The large amount of <i>T<sub>m</sub></i> data generated by the assay offers the possibility of an RRDR genotyping approach more accessible than whole-genome sequencing. In this study, we developed an automated algorithm to specifically identify a wide range of mutations in the <i>rpoB</i> RRDR by utilizing the pattern of the <i>T<sub>m</sub></i> of the 4 probes within the 9 windows generated by the Ultra assay. The algorithm builds a RRDR mutation-specific "<i>T<sub>m</sub></i> signature" reference library from a set of known mutations and then identifies the RRDR genotype of an unknown sample by measuring the <i>T<sub>m</sub></i> distances between the test sample and the reference <i>T<sub>m</sub></i> values. Validated using a set of clinical isolates, the algorithm correctly identified RRDR genotypes of 93% samples with a wide range of <i>rpoB</i> single and double mutations. Our analytical approach showed a great potential for fast RRDR mutation identification and may also be used as a stand-alone method for ruling out relapse or transmission between patients. The algorithm can be further modified and optimized for higher accuracy as more Ultra data become available.
ChemInform Abstract: SYNTHESIS AND REACTIONS OF CYCLOHEXA‐1,4‐DIENE‐3‐THIONES (1975)

Abstract Die Behandlung der Dienone (Ia), (IIa) und (IIIa) mit Phosphorpentasulfid in Benzol, Toluol oder Pyridin ergibt die Thioverbindungen (Ib), (IIb) und (IIIb), von denen (Ib) mit m‐Chlorperbenzoesäure zum Sulfoxid (Ic) reagiert.
ChemInform Abstract: 2,4‐DIAMINOTRIHALOPROPYLTRIAZINES DERIVED FROM Γ‐TRIHALOBUTYRONITRILES (1977)

Abstract Die aus Acetonitril (I) und Chloroform bzw. Bromoform nach einer verbesserten Methode über die Nitrile (II) erhältlichen Trihalogenbuttersäureester (III) kondensieren mit Biguanid zu den Triazinen (IV).
Identification of a novel complex between human kallikrein 2 and protease inhibitor-6 in prostate cancer tissue. (1999)

Human kallikrein (hK) 2 is an arginine-selective serine protease expressed predominantly in the prostate that has an 80% sequence identity with prostate-specific antigen. Expression of hK2 is elevated in the tumor epithelium compared to benign prostate tissue. We have purified, sequenced, and identified a novel hK2 complex in prostate tissue consisting of hK2 and a serine protease inhibitor known as protease inhibitor-6 (PI-6). This 64-kDa SDS-PAGE stable complex is elevated in the tumor and is approximately 10% of total hK2. No comparable complex of prostate-specific antigen was detected. PI-6, also known as cytoplasmic antiprotease, has been characterized as an intracellular inhibitor of trypsin and chymotrypsin-like proteases, which has high homology to plasminogen activator inhibitor 1 and 2. The physiological role of PI-6 in the prostate and its relationship to hK2 and prostate cancer are under investigation.
A wide dynamic range high linearity in-pixel data acquisition front-end for computed tomography (2009)

Computed tomography (CT) detectors require wide dynamic range (DR) and high linearity. This paper reports the design of a new CMOS pixel with in-pixel acquisition front-end for CT in a 0.35 mum CMOS process. The detector uses a synchronous partial quantization scheme to linearly expand the dynamic range with a constant potential well size. A low-power analog-to-digital converter is also designed in the pixel. HSPICE simulations verify that the designed detector is able to achieve 96 dB DR, with -104 dB total-harmonic-distortion (THD) over the dynamic range. No calibration procedure is required for the high linearity. The input-referred noise is less than 1 mV <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">rms</sub> . The frame rate of the designed detector is 2.4 k Hz.
Oligomerization of ethylene with a homogeneous sulfonated nickel ylide–aluminum alkoxide catalyst (1989)

Abstract Various organoaluminum compounds strongly affect reactivity of a sulfonated nickel ylide complex in its reactions with ethylene. The complex, if used alone, is an active single‐component catalyst for ethylene oligomerization to linear 1‐alkenes. Al(C 2 H 5 ) 3 and tetraethylaluminoxane completely deactivate the catalyst by reducing it to Ni(O). Alkylaluminum halides, such as Al(C 2 H 5 ) 2 Cl and Al(C 2 H 5 )Cl 2 , convert the nickel complex into a very active catalyst for ethylene dimerization to mixtures of butenes. Aluminum alkoxides, e.g., Al(C 2 H 5 ) 2 OC 2 H 5 , AlC 2 H 5 (OC 2 H 5 ) 2 , and Al(OC 2 H 5 ) 3 , significantly increase oligomerization activity by a factor of 20–100. The distribution of 1‐alkenes (in the C 4 C 40 + range) produced with the sulfonated nickel ylide–aluminum alkoxide catalyst follows the Flory molecular weight distribution law. The ratio of the chain termination to chain propagation rate constants is ca. 0.3 and is not temperature‐sensitive in the 50–120°C range. Kinetic analysis of the ethylene oligomerization reaction with the binary catalytic system showed that the number of active centers is proportional to the nickel complex concentration. The effective activation energy of ethylene oligomerization with the catalyst is ca. 27 kJ/mol. The oligomerization catalysts loose their activity in time. The activity decay follows the first‐order kinetic law. The rate of the decay increases with increasing temperature and is caused mainly by the intrinsic instability of active species.
Active turbulence in a gas of self-assembled spinners (2017)

Colloidal particles subject to an external periodic forcing exhibit complex collective behavior and self-assembled patterns. A dispersion of magnetic microparticles confined at the air-liquid interface and energized by a uniform uniaxial alternating magnetic field exhibits dynamic arrays of self-assembled spinners rotating in either direction. Here, we report on experimental and simulation studies of active turbulence and transport in a gas of self-assembled spinners. We show that the spinners, emerging as a result of spontaneous symmetry breaking of clock/counterclockwise rotation of self-assembled particle chains, generate vigorous vortical flows at the interface. An ensemble of spinners exhibits chaotic dynamics due to self-generated advection flows. The same-chirality spinners (clockwise or counterclockwise) show a tendency to aggregate and form dynamic clusters. Emergent self-induced interface currents promote active diffusion that could be tuned by the parameters of the external excitation field. Furthermore, the erratic motion of spinners at the interface generates chaotic fluid flow reminiscent of 2D turbulence. Our work provides insight into fundamental aspects of collective transport in active spinner materials and yields rules for particle manipulation at the microscale.
Advanced Crash Avoidance Technologies Program – Final Report of the Honda-DRI Team Volume I: Executive Summary and Technical Report (2011)

The Advanced Crash Avoidance Technologies (ACAT) program initiated by the National Highway Traffic Safety Administration had two major objectives. These are to develop a standardized Safety Impact Methodology (SIM) tool to evaluate the effectiveness of advanced technologies in mitigating specific types of vehicle crash avoidance crashes; and to develop and demonstrate objective tests that are used in the SIM to verify the safety impact of a real system. Honda and Dynamic Research Inc. (DRI) had been developing and applying such a SIM for several years and DRI with Honda's support entered into a Cooperative Agreement with NHTSA to extend the existing SIM, which provides an estimate of full systems safety benefits at the US level. Objective tests that produce quantifiable, repeatable and reproducible results were developed to ensure that a crash avoidance countermeasure meets system performance specifications, and that the results are directly linked to the safety needs and sample of technology-relevant crashes being addressed. The objective tests, which are based on dynamic reconstructions of a sub-sample of technology-relevant real crashes, include Track tests with an expert driver using automatically guided soft targets (GSTs) of an automobile and of a pedestrian; and Driving Simulator tests with a jury of 12 typical drivers, in order to evaluate driver-vehicle system response and to measure the driver's and vehicle's response characteristics to system warnings and interventions. Results from the objective tests were used to parameterize, calibrate and validate the SIM tool, which was then used to estimate US-level benefits. The delivered SIM tool includes modules for automated reconstruction of conflict and crash scenarios from available databases; definition and sampling of Technology Relevant Crash Types; dynamic simulations involving a human-vehicle-device-environmental model; and an overall safety effects estimator. An example application of the extended SIM tool and developed objective tests involved evaluation of Honda’s prototype Advanced Collision Mitigation Brake System (A-CMBS).
LEM-an approach for real time physically based soft tissue simulation (2002)

This paper presents LEM (long elements method), a new method for physically based simulation of deformable objects, suitable for real time animation and virtual environment interaction. The approach implements a static solution for elastic global deformations of objects filled with fluid based on the Pascal's principle and volume conservation. The volumes are discretised in long elements, defining meshes one order of magnitude smaller than tetrahedral or cubic meshes. The physics of the objects are modeled using bulk variables: pressure, density, volume and stress. No pre-calculations or condensations are needed. The approach is particularly interesting for soft tissue real time simulation and for graphic and haptic rendering.
Subvoxel processing: A method for reducing partial volume blurring with application to in vivo MR images of trabecular bone (2002)

Partial volume blurring precludes accurate measurement of structural dimensions in the limited-resolution regime in which image voxel size is larger than the typical structural element to be resolved. Since acquiring images at increased resolution often exacts an unacceptable signal-to-noise ratio (SNR) penalty, methods to alleviate the adverse effects of partial volume blurring are instrumental for the accurate measurement of architectural parameters in applications such as predicting the mechanical competence of trabecular bone networks. In the current work, a novel post-processing method, referred to as "subvoxel processing," is described for increasing apparent image resolution. The method is applicable to volumes of interest containing material phases of two discrete signal intensities. The principal strategy consists of subdividing voxels and assigning voxel intensities to each subvoxel on the basis of local neighborhood criteria and strict mass conservation. In the current work, the method's accuracy has been evaluated using microcomputed tomography images (22 x 22 x 22 microm(3) voxel size) of human trabecular bone. The results demonstrate that subvoxel processing is significantly more accurate than trilinear interpolation in decreasing apparent voxel size, especially in the presence of noise. In addition, the method's effectiveness is illustrated with MR images of human trabecular bone acquired in vivo at 137 x 137 x 350 microm(3) voxel size. The subvoxel-processed images are shown to have architectural features characteristic of images acquired at higher spatial resolution.
Hazard analysis and web-based tool for evaluating glint and glare from solar collector systems. (2010)

This paper extends previous work by the authors evaluating glint and glare from concentrating solar power (CSP) systems. Analytical expressions are derived that provide ranges of distances that can cause permanent eye damage (retinal burn) or temporary flash blindness resulting from specular reflections from different CSP collector systems. In addition, a web-based tool has been developed that evaluates glint and glare hazards. Both analytical and empirical evaluations are implemented by the tool. For empirical evaluations, the user uploads digital photographs of the source reflection causing glint or glare and of the sun for scaling. The web-based tool presents the potential ocular hazard, flux maps, and irradiance profiles.
Securing Augmented Reality Output (2017)

Augmented reality (AR) technologies, such as Microsoft's HoloLens head-mounted display and AR-enabled car windshields, are rapidly emerging. AR applications provide users with immersive virtual experiences by capturing input from a user's surroundings and overlaying virtual output on the user's perception of the real world. These applications enable users to interact with and perceive virtual content in fundamentally new ways. However, the immersive nature of AR applications raises serious security and privacy concerns. Prior work has focused primarily on input privacy risks stemming from applications with unrestricted access to sensor data. However, the risks associated with malicious or buggy AR output remain largely unexplored. For example, an AR windshield application could intentionally or accidentally obscure oncoming vehicles or safety-critical output of other AR applications. In this work, we address the fundamental challenge of securing AR output in the face of malicious or buggy applications. We design, prototype, and evaluate Arya, an AR platform that controls application output according to policies specified in a constrained yet expressive policy framework. In doing so, we identify and overcome numerous challenges in securing AR output.
Low dark current, long wavelength metal-semiconductor-metalphotodetectors (1996)

Dark current densities of 0.13 and 0.44 pA/µm2 at biases of 5 and 10 V, respectively, have been obtained for InAlAs/InGaAs metal-semiconductor-metal photodetectors with a 2 µm electrode width and spacing, by placing the electrode tips and contact pads on top of an insulating layer of silicon nitride. This is the lowest known dark current density reported for InAlAs/InGaAs metal-semiconductor-metal photodetectors to date.