gebhart/patrepeval huggingface dataset:
Target Identification Using Drug Affinity Responsive Target Stability (DARTS) (2011)

Drug Affinity Responsive Target Stability is a general methodology for identifying and studying protein-ligand interactions. The technique is based on the principle that when a small molecule compound binds to a protein, the interaction stabilizes the target protein's structure such that it becomes protease resistant. DARTS is particularly useful for the initial identification of the protein targets of small molecules, but can also be used to validate potential protein-ligand interactions predicted or identified by other means and to estimate the affinity of interactions. The approach is simple and advantageous because it can be performed using crude cell lysates and other complex protein mixtures (without requiring purified proteins), and uses native, unmodified small molecules. The protocols provided in this article describe the general approach for performing DARTS experiments, which can be easily modified and scaled to fit the criteria and purpose of any individual project.
2-D Phase Demodulation for Deformable Fingerprint Registration (2018)

Fingerprint matching with elastic distortion is very challenging to deal with, and severe fingerprint distortion usually leads to false non-matches. This paper proposes a phase-based registration algorithm which can effectively eliminate the distortion between fingerprints and therefore is beneficial to the subsequent fingerprint matching. The key of the proposed algorithm is to reconstruct the distortion field through unwrapping phase difference between two fingerprints. Experiments on FVC2004, Tsinghua distorted fingerprint database, and NIST SD27 demonstrate that our algorithm outperforms other fingerprint registration methods and significantly improves matching accuracy.
A Feasibility Study of Collaborative Stream Routing in Peer-to-Peer Multiparty Video Conferencing (2011)

Video transmission in multiparty video conferencing is challenging due to the demanding bandwidth usage and stringent latency requirement. In this paper, we systematically analyze the problem of collaborative stream routing using one-hop forwarding assistance in a bandwidth constraint environment. We model the problem as a multi-source degree-constrained multicast tree construction problem, and investigate heuristic algorithms to construct bandwidth-feasible shared multicast trees. The contribution of this work is primarily two-fold: (1) we study the solution space of finding a feasible bandwidth configuration for stream routing in a peer-to-peer (P2P) setting, and propose two heuristic algorithms that can quickly produce a bandwidth-feasible solution, making them suitable for large-scale conference sessions, (2) we conduct an empirical study using a realistic dataset and show the effectiveness of our heuristic algorithms. Various QoS metrics are taken into account to evaluate the performance of our algorithms. Finally, we discuss open issues for further exploration. The feasibility study presented in this paper will shed light on the design and implementation of practical P2P multiparty video conferencing applications.
Highly Enantio- and Diastereoselective One-Pot Synthesis of Acyclic Epoxy Alcohols with Three Contiguous Stereocenters. (2005)

For Abstract see ChemInform Abstract in Full Text.
Design and Fabrication of Multimode Optical Switches. (1982)

Abstract : A new optical switching component for multimode fiber-optic networks has been developed. This voltage-controlled switch is an 8-port device coupled by GRINrod lenses to four input fibers and to four output fibers (graded index, 50 micron core diameter). The device switches light from any input fiber to any output fiber in a simultaneous 4-fold input/output pairing, and there are 24 such states in this nonblocking matrix switch. Switching is accomplished via controlled reflection from two 6 micron layers of nematic liquid crystal. This switch is the first multimode, electro-optic, fiber-optic matrix. Construction is simple and compact; only four glass prisms and two liquid layers are used in the switch. The matrix architecture is based on a new dual-switching-array concept, a two stage interconnection that provides very low levels of optical crosstalk; more than 53 dB below the optical input level. The 5-ms on/off response time is faster than that of electro-mechanical matrices, although the 40 Vrms addressing voltage is higher. The optical insertion loss had a minimum value of 6dB and an average value of 15 dB. The latter is due to misalignment of fibers during attachment to the switch, which can be remedied. Because the present switch does not use moving parts, it is quite reliable. (Author)
Multi-Step Prediction of Occupancy Grid Maps with Recurrent Neural\n Networks (2018)

We investigate the multi-step prediction of the drivable space, represented\nby Occupancy Grid Maps (OGMs), for autonomous vehicles. Our motivation is that\naccurate multi-step prediction of the drivable space can efficiently improve\npath planning and navigation resulting in safe, comfortable and optimum paths\nin autonomous driving. We train a variety of Recurrent Neural Network (RNN)\nbased architectures on the OGM sequences from the KITTI dataset. The results\ndemonstrate significant improvement of the prediction accuracy using our\nproposed difference learning method, incorporating motion related features,\nover the state of the art. We remove the egomotion from the OGM sequences by\ntransforming them into a common frame. Although in the transformed sequences\nthe KITTI dataset is heavily biased toward static objects, by learning the\ndifference between subsequent OGMs, our proposed method provides accurate\nprediction over both the static and moving objects.\n
Molecular Characterization of the Cotton <i>GhTUB1</i> Gene That Is Preferentially Expressed in Fiber (2002)

Each fiber of cotton (Gossypium hirsutum) is a single epidermal cell that rapidly elongates to 2.5 to 3.0 cm from the ovule surface within about 16 d after anthesis. A large number of genes are required for fiber differentiation and development, but so far, little is known about how these genes control and regulate the process of fiber development. To investigate gene expression patterns in fiber, a cDNA, GhTUB1, encoding beta-tubulin was isolated from a cotton fiber cDNA library. The analyses of RNA northern-blot hybridization and reverse transcriptase-polymerase chain reaction demonstrated that GhTUB1 transcripts preferentially accumulated at high levels in fiber, at low levels in ovules at the early stage of cotton boll development, and at very low levels in other tissues of cotton. The corresponding GhTUB1 gene including the promoter region was isolated by screening a cotton genomic DNA library. To demonstrate the specificity of the GhTUB1 promoter, the 5'-flanking region including the promoter and 5'-untranslated region was fused with the beta-glucuronidase reporter gene. The expression of the reporter chimera was examined in a large number of transgenic cotton plants. Histochemical assays demonstrated that GhTUB1::beta-glucuronidase fusion genes were expressed preferentially at high levels in fiber and primary root tip of 1- to 3-d-old seedlings and at low levels in other tissues such as ovule, pollen, seedling cotyledon, and root basal portion. The results suggested that the GhTUB1 gene may play a distinct and required role in fiber development. In addition, the GhTUB1 promoter may have great potential for cotton improvement by genetic engineering.
Protection of Nonself Surfaces from Complement Attack by Factor H-Binding Peptides: Implications for Therapeutic Medicine (2011)

Exposure of nonself surfaces such as those of biomaterials or transplanted cells and organs to host blood frequently triggers innate immune responses, thereby affecting both their functionality and tolerability. Activation of the alternative pathway of complement plays a decisive role in this unfavorable reaction. Whereas previous studies demonstrated that immobilization of physiological regulators of complement activation (RCA) can attenuate this foreign body-induced activation, simple and efficient approaches for coating artificial surfaces with intact RCA are still missing. The conjugation of small molecular entities that capture RCA with high affinity is an intriguing alternative, as this creates a surface with autoregulatory activity upon exposure to blood. We therefore screened two variable cysteine-constrained phage-displayed peptide libraries for factor H-binding peptides. We discovered three peptide classes that differed with respect to their main target binding areas. Peptides binding to the broad middle region of factor H (domains 5-18) were of particular interest, as they do not interfere with either regulatory or binding activities. One peptide in this group (5C6) was further characterized and showed high factor H-capturing activity while retaining its functional integrity. Most importantly, when 5C6 was coated to a model polystyrene surface and exposed to human lepirudin-anticoagulated plasma, the bound peptide captured factor H and substantially inhibited complement activation by the alternative pathway. Our study therefore provides a promising and novel approach to produce therapeutic materials with enhanced biocompatibility.
ChemInform Abstract: Biologically Useful Chelators That Take Up Ca2+ Upon Illumination. (1990)

Abstract Two approaches are explored toward the goal of synthesizing physiologically useful Ca2+‐selective chelators, whose Ca 2+ affinities increase markedly upon photolysis.
Beam-Steering Subsystem For Laser Communication (1995)

Proposed free-space laser communication system contains fewer optical and mechanical components. Involves novel fast beam-steering subsystem stabilizing only angle between transmitting and receiving beams instead of stabilizing both transmitting and receiving lines of sight individually. Received and transmitted beams of light both imaged onto CCD array at focal plane. Relative angular positions of beams computed from centroids of their images.
Reducing Power and Cycle Requirement for Fast Fourier Transform of Electrocardiogram Signals Through Low Level Arithmetic Optimizations for Cardiac Implantable Devices (2016)

The Fast Fourier Transform or FFT remains to be the de facto standard in almost all disciplines for computing discrete Fourier transform. In embedded biomedical applications, efficient signal processing algorithms such as FFT for spectrum analysis are indispensable. The FFT is an O(Nlog<sub>2</sub>N) algorithm which requires complex multiplication and addition using floating point numbers. On extremely power constrained embedded systems such as cardiac pacemakers, floating point operations are very cycle intensive and costly in terms of power. This work aims to exploit the repetitive nature of the Electrocardiogram (ECG) to reduce the number of total arithmetic operations required to execute a 128 point FFT routine. Using the simple concept of lookup tables, the proposed algorithm is able to improve both the performance and energy footprint for computing the FFT of the ECG data. An increase of 9.22% in computational speed and an improvement of 10.1% in battery life on a 32 bit embedded platform for a standard split-radix-2 FFT routine is achieved. The concept is tested using actual ECG data collected from PhysioNet.
Remote-Field Eddy Current Inspection Tool for Small-Diameter Unpiggable Pipelines (2008)

Inspection of natural gas pipelines is necessary to ensure their integrity. Considerable pipeline mileage exists where the lines, particularly those in the smaller-diameter range, have internal restrictions and/or low pressure/flow rates. Conventional magnetic flux leakage (MFL) inspection pigs cannot be used because the product flow and pressure is not sufficient to propel the pig, and the large MFL magnets cannot readily move through restricted areas. To overcome these problems, an untethered, self-powered tool was developed that can adjust to inspect different pipe sizes and can retract to pass through obstructions such as elbows and tees. Southwest Research Institute developed a remote-field eddy current (RFEC) inspection system for detecting and characterizing pipe wall loss, and this system was integrated with Explorer II, a robotic transport device developed by Carnegie Mellon. The resulting tool has the capability to inspect 6- to 8-inch-diameter pipelines containing tight bends and tees, and can be launched, operated, and retrieved with the pipeline in service. This paper describes the RFEC inspection technology, the RFEC system modules developed for Explorer II, and preliminary test results.
Three- and four-satellite continuous-coverage constellations (1984)

This paper addresses the problem of obtaining continuous satellite line-of-sight coverage of every point in either the northern hemisphere or on the entire Earth's surface with the minimum number of satellites. Geometric theorems and corollaries relating to coverage are presented. A three-satellite elliptic-orbit constellation covering the entire northern hemisphere is described. Also, a four-satellite constellation giving continuous global coverage is defined. An extensive search has uncovered no other three-satellite continuous hemispheric or four-satellite continuous global coverage constellations.
Erratum: Preparation and characterization of multiwalled carbon nanotube dispersions in polypropylene: Melt mixing versus solid‐state shear pulverization (2010)

A correction is required to the paper “Preparation and Characterization of Multiwalled Carbon Nanotube Dispersions in Polypropylene: Melt Mixing Versus Solid-State Shear Pulverization” published in the Journal of Polymer Science Part B: Polymer Physics, Volume 47 (2009), pages 1426–1436, DOI: 10.1002/polb.21744. Figure 5(b) should be replaced with the following figure: In the published work, the legends on Figure 5(b) were labeled wrong.
Testing high speed VLSI devices using slower testers (2003)

The speed of new VLSI designs is rapidly increasing. Assuring the performance of the circuit requires that the circuit be tested at its intended operating speed. The high cost of high speed testers makes it impossible for the testers to follow the designs in terms of speed increase. This gap between the speed of the new circuits and the speed of the testers is not likely to disappear. In this paper, we focus on at-speed strategies for testing high speed designs on slower testers. Conventional at-speed testing strategies assume that the primary inputs/outputs can be applied/observed at the circuit rated speed. This requires a high speed tester. Our assumption is that a fast clock matching the speed of the designs is available. We describe two classes of at-speed strategies that can be used on a low speed tester. The first class consists of testing schemes for which the test generation procedure is independent of the speed of the tester. These methods apply multiple input patterns in one tester cycle and the test application time for them can be long. The strategies in the second class of at-speed testing schemes integrate the tester's speed limitations with the test generation process. Due to constraints placed at the test generation process, these schemes might result in a reduced fault coverage. To increase the fault coverage and reduce the test application time, the slow-fast-slow and at-speed strategies can be combined for testing high speed designs on slower testers. We present preliminary experimental results for at-speed schemes for slow testers for transition faults.
A comparison of the sensitivity of wound‐infecting species of bacteria to the antibacterial activity of manuka honey and other honey (1992)

Both honey and sugar are used with good effect as dressings for wounds and ulcers. The good control of infection is attributed to the high osmolarity, but honey can have additional antibacterial activity because of its content of hydrogen peroxide and unidentified substances from certain floral sources. Manuka honey is known to have a high level of the latter. Seven major wound-infecting species of bacteria were studied to compare their sensitivity to the non-peroxide antibacterial activity of manuka honey and to a honey in which the antibacterial activity was primarily due to hydrogen peroxide. Honeys with activity in the middle of the normal range were used. A comparison of the median response of the various species of bacteria showed no significant difference between the two types of activity overall, but marked differences between the two types of activity in the rank order of sensitivity of the seven bacterial species. The non-peroxide antibacterial activity of manuka honey at a honey concentration of 1.8% (v/v) completely inhibited the growth of Staphylococcus aureus during incubation for 8 h. The growth of all seven species was completely inhibited by both types of honey at concentrations below 11% (v/v).
Homogeneous Bimetallic Hydroformylation Catalysis (1992)

Homobimetallic rhodium complexes based on the electron-rich binucleating linear tetratertiary phosphine ligand (Et2CH2CH2)(Ph)-PCH2P(Ph)(CHC2PEt2) (eLTTP) are surprisingly active and selective hydroformylation catalysts. This behavior is remarkable because monometallic rhodium catalysts based on electron-rich chelating phosphine ligands are extremely poor hydroformylation catalysts. The proposed key rate-enhancing step in the bimetallic Rh2(eLTTP) catalyst system is an intramolecular hydride transfer that facilitates the elimination of the aldehyde product. This proposal has been tested by preparing model binucleating tetraphosphine ligands of the general type Et2PCH2CH2P(Ph)Y(Ph)PCH2CH2PEt2 (Y is p-xylene or propylene) to space the two metal centers apart and limit the extent of bimetallic cooperativity. These spaced bimetallic complexes, as well as related monometallic model complexes, are very poor hydroformylation catalysts. This evidence clearly points to the most dramatic example of homobimetallic cooperativity ever seen for a major catalytic process.
Quantum Hashing for Multimedia (2009)

In this paper, a novel multimedia identification system based on quantum hashing is considered. Many traditional systems are based on binary hash which is obtained by encoding intermediate hash extracted from multimedia content. In the system considered, the intermediate hash values extracted from a query are encoded into quantum hash values by incorporating uncertainty in the binary hash values. For this, the intermediate hash difference between the query and its true-underlying content is considered as a random process. Then, the uncertainty is represented by the probability density estimate of the intermediate hash difference. The quantum hashing system is evaluated using both audio and video databases, and with marginal increment in computational cost, the quantum hashing system is shown to be more robust against various distortions than the binary hashing system using the same intermediate hash values.
Towards the InfiniBand SR-IOV vSwitch Architecture (2015)

To meet the demands of the Exascale era and facilitate Big Data analytics in the cloud while maintaining flexibility, cloud providers will have to offer efficient virtualized High Performance Computing clusters in a pay-as-you-go model. As a consequence, high performance network interconnect solutions, like InfiniBand (IB), will be beneficial. Currently, the only way to provide IB connectivity on Virtual Machines (VMs) is by utilizing direct device assignment. At the same time to be scalable, Single-Root I/O Virtualization (SR-IOV) is used. However, the current SR-IOV model employed by IB adapters is a Shared Port implementation with limited flexibility, as it does not allow transparent virtualization and live-migration of VMs. In this paper, we explore an alternative SR-IOV model for IB, the virtual switch (vSwitch), and propose and analyze two vSwitch implementations with different scalability characteristics. Furthermore, as network reconfiguration time is critical to make live-migration a practical option, we accompany our proposed architecture with a scalable and topology agnostic dynamic reconfiguration method, implemented and tested using OpenSM. Our results show that we are able to significantly reduce the reconfiguration time as route recalculations are no longer needed, and in large IB subnets, for certain scenarios, the number of reconfiguration subnet management packets (SMPs) sent is reduced from several hundred thousand down to a single one.
Canine brucellosis: newer knowledge. (1976)

Canine brucellosis is a worldwide disease of dogs characterized prinicpally by abortions in females and epididymitis and infertility in males. It originally was observed in the USA, but recently it has been discovered in Japan, Mexico, Peru, Germany and, possibly, in Brazil. It affects dogs of all breeds and has been diagnosed in breeding kennels and in stray dogs. Several human cases have occurred, with 6 being accidental infections by laboratory personnel. B. canis, like B. ovis, is naturally mucoid, lacking "S" antigens. Serological tests therefore are not appropriate to classification. On the basis of manometric technics, B. canis is similar to B. suis; nevertheless the host range excludes swine. Agreement on its taxonomic status is not universal, although it has been provisionally accepted by the Subcommittee on Taxonomy of Brucella as a new species. A brief review of salient characteristics of B. canis was presented, however the principal discussion focused on recently observed aspects of the immunopathogenesis of male infertility and reported the development of a rapid slide agglutination test, using as antigen a concentrated and stained (Rose Bengal dye) suspension of B. ovis.
Therapeutic Anti-Methamphetamine Antibody Fragment-Nanoparticle Conjugates: Synthesis and <i>in Vitro</i> Characterization (2012)

Treatments specific to the medical problems caused by methamphetamine (METH) abuse are greatly needed. Toward this goal, we are developing new multivalent anti-METH antibody fragment-nanoparticle conjugates with customizable pharmacokinetic properties. We have designed a novel anti-METH single chain antibody fragment with an engineered terminal cysteine (scFv6H4Cys). Generation 3 (G3) polyamidoamine dendrimer nanoparticles were chosen for conjugation due to their monodisperse properties and multiple amine functional groups. ScFv6H4Cys was conjugated to G3 dendrimers via a heterobifunctional PEG cross-linker that is reactive to a free amine on one end and a thiol group on the other. PEG modified dendrimers were synthesized by reacting the PEG cross-linker with dendrimers in a stoichiometric ratio of 11:1, which were further reacted with 3-fold molar excess of anti-METH scFv6H4Cys. This reaction resulted in a heterogeneous mix of G3-PEG-scFv6H4Cys conjugates (dendribodies) with three to six scFv6H4Cys conjugated to each dendrimer. The dendribodies were separated from the unreacted PEG modified dendrimers and scFv6H4Cys using affinity chromatography. A detailed in vitro characterization of the PEG modified dendrimers and the dendribodies was performed to determine size, purity, and METH binding function. The dendribodies were found to have affinity for METH identical to that of the unconjugated scFv6H4Cys in saturation binding assays, whereas the PEG modified dendrimers had no affinity for METH. These data suggest that an anti-METH scFv can be successfully conjugated to a PEG modified dendrimer nanoparticle with no adverse effects on METH binding properties. This study is a critical step toward preclinical characterization and development of a novel nanomedicine for the treatment of METH abuse.