gebhart/patrepeval huggingface dataset:
Sequence requirements of the HIV-1 protease flap region determined by saturation mutagenesis and kinetic analysis of flap mutants (1997)

The retroviral proteases (PRs) have a structural feature called the flap, which consists of a short anti-parallel beta-sheet with a turn. The flap extends over the substrate binding cleft and must be flexible to allow entry and exit of the polypeptide substrates and products. We analyzed the sequence requirements of the amino acids within the flap region (positions 46-56) of the HIV-1 PR. The phenotypes of 131 substitution mutants were determined using a bacterial expression system. Four of the mutant PRs with mutations in different regions of the flap were selected for kinetic analysis. Our phenotypic analysis, considered in the context of published structures of the HIV-1 PR with a bound substrate analogs, shows that: (i) Met-46 and Phe-53 participate in hydrophobic interactions on the solvent-exposed face of the flap; (ii) Ile-47, Ile-54, and Val-56 participate in hydrophobic interactions on the inner face of the flap; (iii) Ile-50 has hydrophobic interactions at the distance of both the delta and gamma carbons; (iv) the three glycine residues in the beta-turn of the flap are virtually intolerant of substitutions. Among these mutant PRs, we have identified changes in both kcat and Km. These results establish the nature of the side chain requirements at each position in the flap and document a role for the flap in both substrate binding and catalysis.
Neural Substrates of Decision Making in Adults With Attention Deficit Hyperactivity Disorder (2003)

The findings suggest that the neural circuits engaged during decision making differ in subjects with ADHD and healthy comparison subjects. This difference may explain observed deficits in motivated behaviors in ADHD. A better understanding of the nature of these deficits could ultimately be applied to refine treatment strategies for ADHD.
CD6-Depleted Allogeneic Bone Marrow Transplantation for Acute Leukemia in First Complete Remission (1997)

The appropriate timing of bone marrow transplantation (BMT) for adults with acute myelogenous leukemia (AML) and acute lymphoblastic leukemia (ALL) is controversial. Although allogeneic transplantation results in a lower risk of disease recurrence than intensive chemotherapy alone, overall outcome following BMT may not be improved due to the higher incidence of therapy-related fatal complications, frequently as a result of the development of graft-versus-host disease (GVHD). Selective T-cell depletion of donor marrow can reduce the incidence of GVHD and thereby limit transplant-related toxicity. Herein we report the risk of GVHD, incidence of transplant related mortality (TRM), likelihood of disease relapse, and overall survival in adult patients undergoing BMT with CD6 depleted allogeneic marrow for acute leukemia in first remission. Forty-one consecutive allogeneic transplants were performed on patients with acute leukemia and high-risk features (28 AML, 13 ALL) using T12 monoclonal antibody and complement to remove CD6+ T cells from donor marrow. No pre- or posttransplant immune suppressive medications for GVHD prophylaxis were administered. The actuarial estimated risk of grade 2 to 4 acute GVHD was 15% in patients receiving HLA identical grafts. Chronic GVHD developed in five patients. The estimated risk of TRM for patients in first complete remission was 5% at Day +100 and 16% at 2 years. Fatalities attributable to infection with cytomegalovirus or Epstein-Barr virus occurred in only three patients. Estimated probabilities of relapse, overall survival, and event-free survival at 4 years were 25%, 71%, and 63%, respectively. No significant differences in GVHD, TRM, relapse rate, or survival was observed for patients with AML compared with those with ALL. Allogeneic transplantation with CD6 depleted bone marrow is effective in consolidating remissions of high-risk patients with acute leukemia in first remission without excessive toxicity.
Absolute configuration determination of chiral molecules in the solution state using vibrational circular dichroism (2003)

Advances in the measurement, calculation, and application of vibrational circular dichroism (VCD) for the determination of absolute configuration are described. The purpose of the review is to provide an up-to-date perspective on the capability of VCD to solve problems of absolute stereochemistry for chiral molecules primarily in the solution state. The scope of the article covers the experimental methods needed for the accurate measurement of VCD spectra and the theoretical steps required to systematically deduce absolute configuration. Determination of absolute configuration of a molecule by VCD requires knowledge of its conformation or conformational distribution, and hence VCD analysis necessarily provides solution-state conformation information, in many cases available by no other method, as an additional benefit. Comparisons of the advantages and limitations of VCD relative to other available chiroptical methods of analysis are also presented.
Compensation of Interchannel Crosstalk Induced by Optical Fiber Nonlinearity in Carrier Phase-Locked WDM System (2007)

A scheme that compensates the waveform distortion induced by nonlinear interchannel crosstalk such as four-wave mixing (FWM) and cross-phase modulation as well as self-phase modulation in phase-locked wavelength-division-multiplexing transmission systems is proposed. Reduction of FWM-induced waveform distortion by controlling the phase relationship between neighbouring channels and its cancellation by precompensation is successfully demonstrated
Characteristics of an in vitro system of thymocyte positive selection. (1994)

We investigated the phenotypic changes accompanying maturation of CD4+CD8+ thymocytes in the presence of thymic stomal cells in vitro. Many of the features that are characteristic of positive selection in vivo, such as an ordered down-regulation of CD4 or CD8 together with up-regulation of the TCR-alpha beta complex, also occurred in vitro. Transient expression of CD69 was also observed, together with activation of IL-2 and IL-4 cytokine genes, providing further evidence that positive selection in vitro involves a pattern of gene regulation comparable to that seen in vivo.
Motion vector derivation of deformable block (2012)

Motion estimation (ME) plays an important role in most video encoding systems since it could significantly affect coding performance. However, both the next generation video coding standard High Efficiency Video Coding (HEVC) and the current video coding standard H.264/MPEG-4 AVC employ block matching motion estimation (BMME) which is based on translation motion model. This makes it difficult to represent the complex motion accurately such as rotation, zoom, and etc. In this paper, we propose an adjacent-block-based prediction model to improve the prediction performance of a deformable block. Based on this model, the motion information of each 4×4 block, i.e. the minimum partition (MP) in a coding unit (CU) of HEVC, is derived from the motion information of the nearest neighbors to the four corners of current prediction unit (PU). We integrate our method into HEVC as an additional choice of its merge mode. Simulation results show that our proposed method has better performance compared to HM4.0, the BD bit rate saving is up to 15.4%, while the encoding and decoding complexities are almost the same.
Applying a multitarget rational drug design strategy: the first set of modulators with potent and balanced activity toward dopamine D3 receptor and fatty acid amide hydrolase (2014)

Combining computer-assisted drug design and synthetic efforts, we generated compounds with potent and balanced activities toward both D3 dopamine receptor and fatty acid amide hydrolase (FAAH) enzyme. By concurrently modulating these targets, our compounds hold great potential toward exerting a disease-modifying effect on nicotine addiction and other forms of compulsive behavior.
Dehydration of green peas. (1970)

Investigations were carried out in an attempt to standardize on a method of preparation for dehydrated green peas of acceptable quality from sweet wrinkled varieties without recourse to mechanical slitting. These can be considered under 2 headings: (i) experiments involving the pre-treatment of the peas with solutions of different salts; (ii) experiments involving variations in blanching conditions. Among the salts used in (i) were sodium citrate, sodium oxalate, sodium pyrophosphate, sodium orthosphates (mono, di- and tri-basic) and sodium hexametaphosphate, and of these sodium citrate and sodium di- and tri-phosphates caused softening of the pea skin without adversely affecting flavour. The soaking had to be carried out for fairly extended periods (12-16 h) which might not be feasible under factory conditions. In (ii) freshly shelled peas were subjected to: water blanching; atmospheric steam blanching; steam blanching under pressure; and combinations of 2 different blanching procedures. It was found that preliminary blanching of the peas in water containing 0.1% NaHCO3, 0.1% MgO and 0.4% potassium metabisulphite for a short period softened the skin of the peas sufficiently for checking (introduction of minor cracks in the skin) to take place during subsequent steam blanching at 0.5 kg/cm-2 pressure and programmed dehydration using a fairly high dry bulb tem. initially.
COMBINED MAGNETIC AND PULSED LASER FIELDS PRODUCE SYNERGISTIC ACCELERATION OF CELLULAR ELECTRON TRANSFER (2009)

We have studied the acceleration of cellular electron transfer by the combined magnetic and pulsed laser field at high peak power, but very low average intensity. To monitor the acceleration of electron transfer, the reduction of 2,2,6,6-tetramethyl piperidine-N-oxyl (TEMPO) was followed using the EPR technique. It was shown that the electromagnetic field alone, or the magnetic field alone, produced no reduction of the TEMPO EPR signal. Only a combination between a laser of very low average intensity, but high peak power and a low-intensity magnetic field, reduced the TEMPO signal. The experiment was performed in a medium containing 107 Escherichia coli (E. coli) bacteria per cc. It was verified that at high average intensity the obtained reduction of the TEMPO by electromagnetic radiation was unaffected by the addition of a magnetic field. A possible mechanism underlying the photo-magnetic synergy is proposed.
Dominant wave frequency and amplitude estimation for adaptive control of wave energy converters (2017)

Adaptive control is of great interest for wave energy converters (WEC) due to the inherent time-varying nature of sea conditions. Robust and accurate estimation algorithms are required to improve the knowledge of the current sea state on a wave-to-wave basis in order to ensure power harvesting as close as possible to optimal behavior. In this paper, we present a simple but innovative approach for estimating the wave force dominant frequency and wave force dominant amplitude based on the unscented Kalman filter. The main benefits of the proposed method are illustrated by a numerical example concerning a small-scale wave energy converter prototype, with data coming from experimental recordings obtained in a test basin with irregular waves.
Analysis of Energy Consumption and Energy-saving of Residential Buildings Based on LM-BP Algorithm (2013)

In order to improve the accuracy of statistics and analysis of building energy consumption and energy saving, the paper chose Hebei residential building as the object, analyzing their energy consumption and energy saving by means of LM-BP algorithm. The LM-BP algorithm could establish the response relationship between input and output, and the fitting effect is directly related to the precision of the model. So the practical physical phenomena must be quantified and normalized by the impact factors, which combines local convergence of Gauss-Newton Method with global characteristics of Gradient Descent Method to achieve the analysis of buildings energy consumption data. Through simulation, the algorithm can achieve the effect of heating, ventilation, orientation and building shape on residential building energy consumption, so as to promote the energy saving analysis.
Plowing Friction in Dry and Lubricated Metal Sliding (1986)

Experimental evidence for plowing under dry and lubricated sliding conditions is presented and analytical expressions for the coefficient of friction due to plowing are obtained. The theoretical friction coefficient was found to be a function of the sharpness of the hard asperities, the interfacial “friction” conditions and the shape of the plastic zone. The agreement between theoretical and experimental friction coefficients from lubricated sliding and cutting experiments was remarkably good. The discrepancy between theory and experiment in the case of dry sliding between like metals was shown to be due to plastic deformation of the asperities. Consequently, a different model for plowing was proposed for the case of dry sliding between like metals which produced estimates for the coefficient of friction in fair agreement with the experimental results.
Solution of Simultaneous Linear Equations using a Magnetic-Tape Store (1960)

This paper discusses the special problems involved in solving a set of simultaneous linear equations when magnetic tape is being used for auxiliary storage. An account is given of a sub-routine written to carry out this process on EDSAC 2. A description of EDSAC 2 and its auxiliary magnetic-tape equipment is given as an Appendix.
Dual-beam interferometry for ocean surface current vector mapping (2001)

The recent use of along-track interferometry (ATI) in synthetic aperture radar (SAR) has shown promise for synoptic measurement of ocean surface currents. ATI-SARs have been used to estimate wave fields, currents, and current features. This paper describes and analyzes a dual-beam along-track interferometer to provide spatially resolved vector surface velocity estimates with a single pass of an aircraft. The design employs a pair of interferometer beams, one squinted forward and one squinted aft. Each interferometric phase is sensitive to the component of surface Doppler velocity in the direction of the beam. Therefore, a proper combination of these measurements provides a vector surface velocity estimate in one pass of the aircraft. The authors find that precise measurements dictate widely spaced beams and that the spatial resolution for the squinted SAR is essentially identical to the sidelooking case. Practical instrument design issues are discussed, and an airborne system currently in development is described. Through computer simulation, they observe the azimuthal displacement of interferometric phases by moving surfaces identical to those of conventional SAR and find that such displacement can bias the estimated surface velocity.
Functional analysis of spontaneous movements in preterm infants (1994)

Spontaneous movements of premature infants between 25 and 34 weeks conceptional age were observed for 1 hr on two or three occasions. Subjects had low-risk prognoses and were clinically stable at the time of testing. Behavioral acts were scored using a 0/1 time sampling technique in 60 continuous, 1-min time blocks. Temporal associations between individual movements were found using chi-square analyses. Some associated behaviors contained combinations consistent with neonatal action patterns, for example, single and bilateral leg kicking, head turning, and mouthing. Features of state organization were also evident in that general motor activity (GM), which has been used as a marker of active sleep (AS) in neonates, was found to cluster temporally with startle, facial, and head movements but not eye movements. Behavioral quiescence (> or = 5 s) was dissociated from AS-related behaviors (GM, facial, head, and eye movements). Combinations of state-segregated behaviors were more likely to exhibit co-occurrence within 1-min intervals in infants 30 weeks conceptional age and older.
Laser plasma interaction at an early stage of laser ablation (1999)

Laser scattering and its interaction with plasma during KrF excimer laser ablation of silicon are investigated by ultrafast phototube detection. There are two peaks in an optical signal with the first peak attributed to laser scattering and the second one to plasma generation. For laser fluence above 5.8 J/cm2, the second peak rises earlier to overlap with the first one. The optical signal is fitted by a pulse distribution for the scattered laser light and a drifted Maxwell–Boltzmann distribution with a center-of-mass velocity for the plasma. Peak amplitude and its arrival time, full width at half maximum (FWHM), starting time, and termination time of the profiles are studied for different laser fluences and detection angles. Laser pulse is scattered from both the substrate and the plasma with the latter part as a dominant factor during the laser ablation. Peak amplitude of the scattered laser signal increases but its FWHM decreases with the laser fluence. Angular distribution of the peak amplitude can be fitted with cosn θ(n=4) while the detection angle has no obvious influence on the FWHM. In addition, FWHM and peak amplitude of plasma signal increase with the laser fluence. However, starting time and peak arrival time of plasma signal reduce with the laser fluence. The time interval between plasma starting and scattered laser pulse termination is proposed as a quantitative parameter to characterize laser plasma interaction. Threshold fluence for the interaction is estimated to be 3.5 J/cm2. For laser fluence above 12.6 J/cm2, the plasma and scattered laser pulse distributions tend to saturate.
An Industrial Robotics Application with Cloud Computing and High-Speed Networking (2017)

This paper describes an industrial cloud robotics distributed application that was executed across a high-speed wide-area network. The application was implemented using ROS libraries and packages. The purpose of the application is to enable an industrial robot to perform surface blending. A Kinect sensor, a surface blending tool and a laser scanner are mounted on the robot arm. The arm is moved under software control to scan a work bench on which metal parts of variable size can be laid out at any orientation. The collected point cloud data is processed by a segmentation algorithm to find the surface boundaries. A Cartesian path planning algorithm is executed to determine paths for the robot arm to execute the blending action and a laser scan on a selected surface. A new ROS package was implemented to collect CPU, memory and bandwidth usage for each significant ROS node in this distributed application. To emulate a scenario in which computing resources at a remote datacenter can be used for the segmentation and path planning algorithms in conjunction with the robots located on a factory floor, a software-defined network testbed called GENI was used to distribute compute-heavy ROS nodes. Measurements show that with TCP tuning, and high-speed end-to-end paths, the total execution time in the Cloud scenario can be reasonably close to a local scenario in which computing is collocated with the robot.
Anodal transcranial direct current stimulation boosts synaptic plasticity and memory in mice via epigenetic regulation of Bdnf expression (2016)

The effects of transcranial direct current stimulation (tDCS) on brain functions and the underlying molecular mechanisms are yet largely unknown. Here we report that mice subjected to 20-min anodal tDCS exhibited one-week lasting increases in hippocampal LTP, learning and memory. These effects were associated with enhanced: i) acetylation of brain-derived neurotrophic factor (Bdnf) promoter I; ii) expression of Bdnf exons I and IX; iii) Bdnf protein levels. The hippocampi of stimulated mice also exhibited enhanced CREB phosphorylation, pCREB binding to Bdnf promoter I and recruitment of CBP on the same regulatory sequence. Inhibition of acetylation and blockade of TrkB receptors hindered tDCS effects at molecular, electrophysiological and behavioral levels. Collectively, our findings suggest that anodal tDCS increases hippocampal LTP and memory via chromatin remodeling of Bdnf regulatory sequences leading to increased expression of this gene, and support the therapeutic potential of tDCS for brain diseases associated with impaired neuroplasticity.
Comparison of Two Preoperative Skin Antiseptic Preparations and Resultant Surgical Incise Drape Adhesion to Skin in Healthy Volunteers (2012)

The data suggest that the type of skin preparation affects drape adhesion. For surgical procedures in which incise drapes are used, choosing a skin preparation that enhances drape adhesion may minimize drape lifting and the potential for wound contamination.
Decoherence, Continuous Observation, and Quantum Computing: A Cavity QED Model (1995)

We use the theory of continuous measurement to analyze the effects of decoherence on a realistic model of a quantum computer based on cavity QED. We show how decoherence affects the computation, and methods to prevent it.
Underwater shear-stress sensor (2003)

This paper reports the development of a micromachined, vacuum-cavity insulated, thermal shear-stress sensor for underwater applications. We focus on two major challenges for underwater shear-stress sensors: the waterproof coating and pressure sensitivity. It is found that thin-film CVD Parylene is a good waterproof material and sensors coated with 2 /spl mu/m Parylene N can survive in water for at least one month at 55/spl deg/C. It is also found that reducing the size and increasing the thickness of the sensor diaphragm are effective in minimizing the pressure sensitivity.
Mapping the Interaction Between Murine IgA and Murine Secretory Component Carrying Epitope Substitutions Reveals a Role of Domains II and III in Covalent Binding to IgA (1999)

We have identified sites for epitope insertion in the murine secretory component (SC) by replacing individual surface-exposed loops in domains I, II, and III with the FLAG sequence (Crottet, P., Peitsch, M. C., Servis, C., and Corthésy, B. (1999) J. Biol. Chem. 274, 31445-31455). We had previously shown that epitope-carrying SC reassociated with dimeric IgA (IgA(d)) can serve as a mucosal delivery vehicle. When analyzing the capacity of SC mutants to associate with IgA(d), we found that all domain II and III mutants bound specifically with immobilized IgA(d), and their affinity for IgA(d) was comparable to that of the wild type protein (IC(50) approximately 1 nM). We conclude that domains II and III in SC are permissive to local mutation and represent convenient sites to antigenize the SC molecule. No mutant bound to monomeric IgA. SC mutants exposing the FLAG at their surface maintained this property once bound to IgA(d), thereby defining regions not required for high affinity binding to IgA(d). Association of IgA(d) with SC mutants carrying a buried FLAG did not expose de novo the epitope, consistent with limited, local changes in the SC structure upon binding. Only wild type and two mutant SCs bound covalently to IgA(d), thus implicating domains II and III in the correct positioning of the reactive cysteine in SC. This establishes that the integrity of murine SC domains II and III is not essential to preserve specific IgA(d) binding but is necessary for covalency to take place. Finally, SC mutants existing in the monomeric and dimeric forms exhibited the same IgA(d) binding capacity as monomeric wild type SC known to bind with a 1:1 stoichiometry.