gebhart/patrepeval huggingface dataset:
NBI‐5788, an altered MBP83‐99 peptide, induces a T‐helper 2–like immune response in multiple sclerosis patients (2000)

We assessed the immune response induced in multiple sclerosis (MS) patients who had received NBI-5788, an altered peptide ligand (APL) designed from an immunodominant region (83–99) of the neuroantigen myelin basic protein (MBP) (5, 10, or 20 mg subcutaneously weekly for 4 weeks). The mean frequency of NBI-5788–responsive T cells (stimulation index > 3) in MS patients treated with the APL was 35.8 ± 12.8% (n = 7) compared with a mean frequency of 6.2 ± 1.3% (n = 7) for the untreated patients. The mean frequency of whole MBP–responsive T cells in MS patients treated with the APL was not significantly different from that of untreated patients (16.4 ± 5.7% vs 18.0 ± 6.3%, respectively). NBI-5788–reactive T-cell lines generated from NBI-5788–treated patients exhibited an increased frequency of cross-reactivity with MBP peptide 83–99 compared with NBI-5788–reactive lines from control MS patients. Cytokine secretion by APL-reactive T-cell lines from NBI-5788–treated MS patients was more frequently T-helper 2–like compared with T-cell lines from untreated MS patients. These results demonstrate that subcutaneous administration of a soluble APL based on the MBP peptide 83–99 in MS patients can induce an APL-reactive immune response in which T lymphocytes cross-reactive with the immunodominant neuroantigen MBP secrete anti-inflammatory cytokines. The significant heterogeneity in immune response between individuals indicates the need for clinical laboratory correlation during the course of therapeutic trials. Ann Neurol 2000;48:758–765
Novel Carboxamide-Based Allosteric MEK Inhibitors: Discovery and Optimization Efforts toward XL518 (GDC-0973) (2012)

The ERK/MAP kinase cascade is a key mechanism subject to dysregulation in cancer and is constitutively activated or highly upregulated in many tumor types. Mutations associated with upstream pathway components RAS and Raf occur frequently and contribute to the oncogenic phenotype through activation of MEK and then ERK. Inhibitors of MEK have been shown to effectively block upregulated ERK/MAPK signaling in a range of cancer cell lines and have further demonstrated early evidence of efficacy in the clinic for the treatment of cancer. Guided by structural insight, a strategy aimed at the identification of an optimal diphenylamine-based MEK inhibitor with an improved metabolism and safety profile versus PD-0325901 led to the discovery of development candidate 1-({3,4-difluoro-2-[(2-fluoro-4-iodophenyl)amino]phenyl}carbonyl)-3-[(2S)-piperidin-2-yl]azetidin-3-ol (XL518, GDC-0973) (1). XL518 exhibits robust in vitro and in vivo potency and efficacy in preclinical models with sustained duration of action and is currently in early stage clinical trials.
<title>Optoacoustic effects during Er:YAG laser ablation in hard dental tissue</title> (1994)

Optoacoustic method is a very useful tool for studying laser induced processes in hard dental tissues. In principle, the method can also be used for on-line monitoring of laser drilling. Our study, however, shows that at high laser energies the optoacoustic energy is not proportional to the volume of the ablated hard dental tissue. In addition, the optoacoustic signal depends critically on the presence of water on the tooth surface. These observations must be taken into account when attempting to use the optoacoustic method for on-line monitoring of the laser drilling process.
An interactive graphical approach to module generator development (2002)

A design-by-example methodology is applied to a library of highly parameterized design-rule-independent SSI/MSI module generators. This graphical approach is far more intuitive than working procedurally. It reduces the software expertise required to develop generators, and reduces the generator development effort by 50%. In addition, generators can be modified and debugged graphically, greatly reducing the cost of generator maintenance.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Electroless Deposition of Nanoscale Copper Patterns via Microphase-Separated Diblock Copolymer Templated Self-Assembly (1999)

By use of an ultrathin film of microphase-separated poly(styrene-block-methyl methacrylate) as a template, nanometer-scale patterns of tetraalkylammonium passivated palladium colloids can be generated. This pattern serves, in turn, as the template for the electroless deposition of semicontinuous 20 nm wide copper nanostructures, which is approximately a factor of 2 smaller than feature sizes that can be generated by state-of-the-art lithographic processes.
Rapid Entry into Mono-, Bi-, and Tricyclic β-Lactam Arrays via Alkene Metathesis (1998)

4-Acetoxy-2-azetidinone and (3R,4R)-4-acetoxy-3-[(1R)-1-(tert-butyldimethylsilyl)-oxyethyl]-2-azetidinone were converted into 4-alkenyloxy-, 4-(N-allyltoluene-4-sulfonamido)-, 4-(allylthio)-, and 4-alkenyl-2-azetidinone systems. In addition, 4-acetoxy-2-azetidinone and (3R,4R)-4-acetoxy-3-[(1R)-1-(tert-butyldimethylsilyl)-oxyethyl]-2-azetidinone were converted into β-lactam dienes via sequential C-4 substitution using unsaturated alcohols, allyl mercaptan, N-allyltoluene-4-sulfonamide, and allyl(chloro)dimethylsilane followed by N-allylation. Crossed metathesis of β-lactam alkenes with styrene partners and ring closing metathesis of β-lactam dienes using the Schrock [(CF3)2MeCO]2Mo(CHCMe2Ph)(NC6H3-2,6-iso-Pr2) (1) or Grubbs Cl2(Cy3P)2RuCHPh (2) carbenes gave diverse monocyclic and bicyclic β-lactam systems including derivatives of 1-azabicyclo[4.2.0]octan-8-one, 1-azabicyclo[5.2.0]nonan-9-one and its 6-thia, 6-aza, and 6-oxa analogues, 7-oxa-1-azabicyclo[6.2.0]octan-10-one, 8-oxa-1-azabicyclo[7.2.0]octan-11-one, and 9-oxa-1-azabicyclo[8.2.0]octan-12-one. Ring-closing enyne metathesis and tandem ring-closing enyne and diene metathetic reactions were used to produce bicyclic β-lactam conjugated dienes as exemplified by the conversion of (3S,4R)-(−)-3-[(1R)-(tert-butyldimethylsilyl)oxyethyl]-1-(5-oxa-oct-7-en-2-yn-1-yl)-4-(2-propenyl)azetidin-2-one (83) into (6R,7S)-(+)-7-[(1R)-(tert-butyldimethylsilyl)oxyethyl]-3-[(2,5-dihydro)-3-furanyl]-1-azabicyclo[4.2.0]oct-3-en-8-one (98).
Real-Time Dynamic Power Management through Device Forbidden Regions (2008)

Dynamic power management (DPM) techniques are crucial in minimizing the overall energy consumption in real-time embedded systems. The timing constraints of real-time applications and non-trivial time/energy transition overheads introduce significant challenges, as the device sleep intervals should be longer than a minimum threshold (called the break-even time) to ensure energy-efficiency. In this paper, we present a novel approach to the real-time DPM problem by explicitly enforcing long device sleep intervals for different devices, called device forbidden regions. We focus on the application of our technique to task systems with rate-monotonic priorities, and develop our algorithm DFR-RMS. Our solution includes a static component where the duration and frequency of forbidden regions are determined through the extended time-demand analysis to preserve the temporal correctness of all the tasks, while enhancing the energy savings. Then, we present a sophisticated on-line component which interacts with existing prediction-based DPM schemes to realize the full potential of device forbidden regions. Further, our scheme can be used with or without dynamic voltage scaling (DVS). Our experimental evaluation hints that significant energy gains can be obtained, when compared to the existing prediction-based techniques. Another contribution of this research effort is to show that the general problem of generating feasible schedules for preemptive periodic real-time tasks where all device sleep intervals are longer than the device break-even times is NP-hard in the strong sense.
A Wily Recruiter in the Battle Against Toxic β Amyloid Aggregation (2004)

In Alzheimer's disease (AD), large, abnormal clumps of a peptide called β amyloid surround and clog the insides of neurons. These clumps are suspect because they kill cultured neurons, and several human mutations associated with early-onset AD are linked to problematic β amyloid. Hoping to retard the disease, researchers have tried using drugs to block such clumping, but with little success until recently.
Black-Box Attacks against RNN based Malware Detection Algorithms (2017)

Recent researches have shown that machine learning based malware detection algorithms are very vulnerable under the attacks of adversarial examples. These works mainly focused on the detection algorithms which use features with fixed dimension, while some researchers have begun to use recurrent neural networks (RNN) to detect malware based on sequential API features. This paper proposes a novel algorithm to generate sequential adversarial examples, which are used to attack a RNN based malware detection system. It is usually hard for malicious attackers to know the exact structures and weights of the victim RNN. A substitute RNN is trained to approximate the victim RNN. Then we propose a generative RNN to output sequential adversarial examples from the original sequential malware inputs. Experimental results showed that RNN based malware detection algorithms fail to detect most of the generated malicious adversarial examples, which means the proposed model is able to effectively bypass the detection algorithms.
A low energy plasma flood gun using RF plasma formation (2003)

A plasma flood gun (PFG) system useful for 300 mm wafer has been developed by using an RF plasma for the medium current implanter EXCEED2300. To produce low energy electrons, the electron energy is filtered by magnetic fields. To eliminate dose shift, a low flow rate of Xe gas is adopted. A linear geometry of the plasma production source chamber improves the spatial uniformity of the plasma flooding across the 300 mm wafer. The metal contamination and the maintenance time are also greatly improved with the RF plasma formation.
3. UNDERSTANDING DATA BETTER WITH BAYESIAN AND GLOBAL STATISTICAL METHODS (1997)

To understand their data better, astronomers need to use statistical tools that are more advanced than traditional \freshman lab" statistics.As an illustration, the problem of combining apparently incompatible measurements of a quantity (the Hubble constant, e.g.) is presented from both the traditional, and a more sophisticated Bayesian, perspective.Explicit formulas are given for both treatments.
An overview of utilizing CO2 for accelerated carbonation treatment in the concrete industry (2022)

Accelerated carbonation treatment as an effective approach of reducing the carbon footprint in the concrete industry is being investigated extensively. Such carbonation treatment converts gaseous CO2 into carbonate minerals (or mineral CO2 sequestration). The present review provided a state-of-the-art summary on the relevant carbonation strategies that have been investigated, with a special focus on identifying the remaining industrial challenges and critical research gaps that need further investigation. Key parameters affecting pre-carbonation treatments of recycled concrete aggregates, fly ash, and slag were examined systematically, including chemical compositions and particle sizes of the materials, temperature, pressure, and CO2 concentration. The CO2 uptake capacity and efficiency of the materials were compared with each other, and the environmental impact of pre-carbonation treatment of fly ash and slag was approximated. After carbonation treatment, the incorporation of those carbonated materials in cement-based composites was assessed. It was found that the rising CO2 uptake of ingredient materials subjected to pre-carbonation treatment does not necessarily benefit the mechanical properties of the cement-based composites with the carbonated materials. For a specific material, there may exist a CO2 uptake threshold over which high CO2 uptake tends to be deleterious, e.g. for the mechanical properties. In terms of the influence of accelerated carbonation curing on the compressive strength of cement-based composites at early ages, both positive and negative influences were identified. Corresponding mechanisms behind such contrary influences were critically discussed. It was noted that over-intensified early-age carbonation curing could compromise the strength properties of cement-based composites both in the short and long terms.
Hydrogenation of polyunsaturated fatty acids by human colonic bacteria (1999)

Emulsions of the fatty acids linoleic (C18:2 n-6), alpha-linolenic (C18:3 n-3) and arachidonic acid (C20:4 n-6) were incubated for 4 h under anaerobic conditions with human faecal suspensions. Linoleic acid was significantly decreased (P < 0.001) and there was a significant rise (P < 0.05) in its hydrogenation product, stearic acid. Linolenic acid was also significantly decreased (P < 0.01), and significant increases in C18:3 cis-trans isomers (P < 0.01) and linoleic acid (P < 0.05) were seen. With each acid, there were non-significant increases in acids considered to be intermediates in biohydrogenation. The study provides evidence that bacteria from the human colon can hydrogenate C18 essential polyunsaturated fatty acids. However, with arachidonic acid there was no evidence of hydrogenation.
Large-format and multispectral QWIP infrared focal plane arrays (2003)

The next generation of infrared (IR) focal plane arrays (FPAs) will need to be a significant improvement in capability over those used in present-day second generation FLIRs. The Army's Future Combat System requires that the range for target identification be greater than the range of detection for an opposing sensor. To accomplish this mission, the number of pixels on the target must be considerably larger than that possible with 2nd generation FLIR. Therefore, the 3rd generation FLIR will need to be a large format staring FPA with more than 1000 pixels on each side. In addition, a multi-spectral capability will be required to allow operability in challenging ambient environments, discriminate targets from decoys, and to take advantage of the smaller diffraction blur in the MWIR for enhanced image resolution. We report on laboratory measurements of a large format (1024 x 1024 pixels) single-color LWIR IR FPA made using the corrugated quantum well infrared photodetector (QWIP) structure by the ARL/NASA team. The pixel pitch is 18 μm and the spectral response peaks at 8.8 μm with a 9.2 μm cutoff. We report on recent results using a MWIR/LWIR QWIP FPA to image the boost phase of a launch vehicle for missile defense applications and a LWIR/LWIR FPA designed specifically for detecting the disturbed soil associated with buried land mines. Finally, we report on the fabrication of a new read-out integrated circuit (ROIC) specifically designed for multi-spectral operation.
On‐line SERS Detection of Single Bacterium Using Novel SERS Nanoprobes and A Microfluidic Dielectrophoresis Device (2014)

The integration of novel surface-enhanced Raman scattering (SERS) nanoprobes and a microfluidic dielectrophoresis (DEP) device is developed for rapid on-line SERS detection of Salmonella enterica serotype Choleraesuis and Neisseria lactamica. The SERS nanoprobes are prepared by immobilization of specific antibody onto the surface of nanoaggregate-embedded beads (NAEBs), which are silica-coated, dye-induced aggregates of a small number of gold nanoparticles (AuNPs). Each NAEB gives highly enhanced Raman signals owing to the presence of well-defined plasmonic hot spots at junctions between AuNPs. Herein, the on-line SERS detection and accurate identification of suspended bacteria with a detection capability down to a single bacterium has been realized by the NAEB-DEP-Raman spectroscopy biosensing strategy. The practical detection limit with a measurement time of 10 min is estimated to be 70 CFU mL(-1) . In comparison with whole-cell enzyme-linked immunosorbent assay (ELISA), the SERS-nanoprobe-based biosensing method provides advantages of higher sensitivity and requiring lower amount of antibody in the assay (100-fold less). The total assay time including sample pretreatment is less than 2 h. Hence, this sensing strategy is promising for faster and effective on-line multiplex detection of single pathogenic bacterium by using different bioconjugated SERS nanoprobes.
Multilocus Sequence Typing of <i>Klebsiella pneumoniae</i> Nosocomial Isolates (2005)

A multilocus sequence typing (MLST) scheme was developed for Klebsiella pneumoniae. Sequences of seven housekeeping genes were obtained for 67 K. pneumoniae strains, including 19 ceftazidime- and ciprofloxacin-resistant isolates. Forty distinct allelic profiles were identified. MLST data were validated against ribotyping and showed high (96%) discriminatory power. The MLST approach provides unambiguous data useful for the epidemiology of K. pneumoniae isolates.
A novel prokaryotic <i>trans</i>‐2‐enoyl‐CoA reductase from the spirochete <i>Treponema denticola</i> (2007)

An NADH-dependent trans-2-enoyl-CoA reductase (EC1.1.1.36) from the Gram negative spirochete Treponema denticola was identified, expressed and biochemically characterized. The recombinant protein is a monomeric enzyme with a molecular mass of 44 kDa with a specific activity of 43+/-4.8 U/mg (micromol mg(-1)min(-1)) and K(m) value of 2.7 microM for crotonoyl-CoA. This NADH-dependent trans-2-enoyl-CoA reductase represents the first enzymatically characterized member of a prokaryotic protein family involved in a fatty acid synthesis pathway that is distinct from the familiar fatty acid synthase system.
Electrical conductivity imaging using MRI measurement of the magnetic field vector (2009)

Current density and electrical conductivity imaging research at the University of Toronto is reviewed. Methods for imaging live animals at low frequency are described and contrasted with EIT and other MRI based techniques. New work on imaging at radio frequencies is presented and future work directions are discussed. It is concluded that low frequency methods are mature and ready for application in small animals and that radio frequency methods will soon have application in small animals.
Optimizing the Gait of a Humanoid Robot Towards Human-like Walking. (2009)

Abstract — Achieving a stable, human-like gait with a humanoid robot is a challenging problem. While several rather simple as well as more complex techniques exist to generate stable walking patterns, only little attention has been paid towards the resemblance to the human gait. Popular gaits, for example, apply the strategy to bend the knees and to swing the torso in lateral direction in order to ensure stability. As a result, the walking patterns do not look very human-like. However, human resemblance is an important aspect whenever robots are designed to interact naturally with humans. In this paper, we present techniques to optimize an initial, stable gait of a humanoid robot with respect to human resemblance. To acquire walking data of a human, we use a full-body motion capture system. We propose four different optimizing algorithms that work at joint angle basis and use the joint angle difference as measure of similarity. Experimental results carried out with a HOAP-2 robot in simulation demonstrate that we can adapt the robot’s initial gait so that it is significantly more human-like. I.
Application of the tangential radiographic technique for evaluating pipe system erosion/corrosion (1989)

The tangential radiographic technique is frequently used for the detection and evaluation of metal loss associated with pipe system erosion/corrosion. In tangential radiography, a view of the pipe's cross section, including a view of the pipe wall, is projected upon the film, enabling direct measurement of the remaining pipe wall thickness. The extremities of the pipe wall cross section projected onto the film may be defined by a line drawn from the source to the film through a tangent point on the pipe's outside diameter (OD) and from the source to the film through a tangent point on the pipe's inside diameter (ID). The thickest portion of the pipe through which the radiation passes is therefore a chord bisected by the ID tangent point. The cross section of the pipe wall that appears on the film is approximately that which occurs perpendicular to the center of the chord. The source-to-film distance (SED), film type, and exposure density all significantly influence the accuracy of tangential radiography. A search of existing literature reveals that information is relatively sparse concerning how these three variables interact with one another. This paper explores these variables and provides guidelines for optimizing the accuracy of this useful more » radiographic technique. « less
Wake structures behind plunging airfoils - A comparison of numerical and experimental results (1996)

Comparisons are made between numerically and experimentally produced wake structures behind airfoils undergoing rapid, oscillatory plunging motions. Numerical simulations are performed using an unsteady panel code. Inviscid, incompressible ows about arbitrary moving airfoils are computed with the unsteady wake approximated by discrete point vortices, tracked using a Lagrangian mesh scheme. Numerically computed results are visualized using an interactive, graphical-animation interface. Experimental data are obtained from a low-speed water tunnel. Two-color dye injection is used to visualize unsteady wake structures, and velocity data are acquired using laser doppler velocimetry. Comparisons of vortex location agree well with linear theory for low amplitude motions. For large amplitude, high frequency motions, results diverge from linear theory, but wakes from the two approaches compare well with each other, including highly non-linear, non-symmetric wakes obtained for high amplitude, high frequency motions. Computed velocity pro les and integrated thrust coe cients for both approaches agree well.
From Two-Dimensional Colloidal Self-Assembly to Three-Dimensional Nanolithography (2011)

A number of "top-down" lithographic and "bottom-up" self-assembly methods have been developed to fabricate three-dimensional (3D) nanostructures to support the recent advances in nanotechnology. But they are limited by a number of factors such as fabrication cost, pattern resolution, and/or flexibility of geometry. Here we present a 3D nanolithography process that utilizes self-assembled nanospheres to create a periodic array of focal spots, which are then replicated across multiple depth in a transparent medium according to the Talbot effect. The Talbot field then exposes a pattern onto the underlying photoresist, recording the 3D intensity distribution. We have demonstrated designable complex 3D periodic structures with 80 nm minimum feature size, roughly one-fourth of the operating wavelength. This approach combines 2D colloidal self-assembly and 3D phase lithography, is robust, cost-effective, and widely applicable to nanoscale research and manufacturing.
Reversal of multidrug resistance to cancer chemotherapy (1993)

In the past few years, the role of membrane-bound transport genes in human disease has been increasingly recognized and understood. Of these genes, the p170 membrane glycoprotein may function as an outward transport pump for many cancer chemotherapeutic drugs associated with the multidrug resistance phenotype. This article reviews the different classes of the current major modulators of multidrug resistance.