gebhart/patrepeval huggingface dataset:
D-101 CryoEM Studies of HIV-1 Envelope Glycoprotein (2014)

HIV-1 is an enveloped retrovirus that is the causative agent of AIDS. To date there is no effective vaccine that prevents acquisition of the virus, and therefore represents a significant burden on worldwide health. Structures of the HIV-1 envelope glycoprotein (Env) trimer in complex with neutralizing antibodies are a key component of ongoing rational vaccine design efforts aimed at creating stable immunogens that mimic Env. Thus, we have created a cryoEM pipeline to solve a number of such structures that are actively being used to design new immunogens for testing in animals. I will describe the types of information generated by cryoEM and the methods used to solve a diversity of structures that are representative of Env across multiple clades. By understanding the molecular determinants of trimer formation and quaternary epitope presentation across different Env sequences we can start to build a consensus for the creation of new and exciting immunogens.
Automated Assessment of the Optic Nerve Head on Stereo Disc Photographs (2008)

The automated ONH analysis method provides an objective and quantitative ONH evaluation using widely available stereo disc photographs.
A New Model to Obtain Representative Field Relative Permeability for Reservoirs Produced under Solution Gas Drive (2003)

Abstract The relative permeability curves (Kr) control the production and are of primary importance for any type of recovery process. In the case of production by displacement (waterflood or gasflood) the Kr curves obtained in laboratory can be used in numerical simulators to predict hydrocarbon recovery (after upscaling to account for heterogeneity). In the case of reservoirs produced under solution gas drive (depressurized field, foamy oils), the experiments conducted in laboratory depend on the depletion rate and cannot be used directly for reservoir simulations. We have developed a novel approach for calculating representative field-relative permeabilities. This new method is based on a physical model, which takes into account the various mechanisms of the process: bubble nucleation (preexisting bubbles model), phase transfer (volumic transfer function), gas displacement (bubbles flow). In our model, we have identified a very few number of "invariant" parameters that are not sensitive to depletion rate and are specific of the rock-fluids system (mainly the preexisting bubble size distribution and a factor between gas velocity and oil velocity in the dispersed phase regime). These invariant parameters are determined by history matching of one experiment at a given depletion rate. The calibrated model is then used to generate synthetic data at any depletion rate, and especially at very low depletion rates representative of the reservoir conditions. Relative permeability are derived from these "numerical" experiments in the same way as real experiments. The calculated Kr are finally introduced in commercial reservoir simulators. We have tested our model by using several series of published experiments with light and heavy oils. After adjusting the invariant parameters on one or two experiments, we are able to predict other experiments performed at different depletion rates with a very good accuracy. Finally, we present an example of determination of relative permeabilities at reservoir depletion rates.
delta 6 Hexadecenoic acid is synthesized by the activity of a soluble delta 6 palmitoyl-acyl carrier protein desaturase in Thunbergia alata endosperm. (1994)

delta 6 Hexadecenoic acid (16:1 delta 6) composes more than 80% of the seed oil of Thunbergia alata. Studies were conducted to determine the biosynthetic origin of the double bond of this unusual fatty acid. Assays of fractions of developing T. alata seed endosperm with [1-14C]palmitoyl (16:0)-acyl carrier protein (ACP) revealed the presence of a soluble delta 6 desaturase activity. This activity was greatest when 16:0-ACP was provided as a substrate, whereas no desaturation of the coenzyme A ester of this fatty acid was detected. In addition, delta 6 16:0-ACP desaturase activity in T. alata endosperm extracts was dependent on the presence of ferredoxin and molecular oxygen and was stimulated by catalase. To further characterize this enzyme, a cDNA encoding a diverged acyl-ACP desaturase was isolated from a T. alata endosperm cDNA library using polymerase chain reaction with degenerate oligonucleotides corresponding to conserved amino acid sequences in delta 9 stearoyl (18:0)- and delta 4 16:0-ACP desaturases. The primary structure of the mature peptide encoded by this cDNA shares 66% identity with the mature castor delta 9 18:0-ACP desaturase and 57% identity with the mature coriander delta 4 16:0-ACP desaturase. Extracts of Escherichia coli that express the T. alata cDNA catalyzed the delta 6 desaturation of 16:0-ACP. These results demonstrate that 16:1 delta 6 in T. alata endosperm is formed by the activity of a soluble delta 6 16:0-ACP desaturase that is structurally related to the delta 9 18:0- and delta 4 16:0-ACP desaturases. Implications of this work to an understanding of active site structures of acyl-ACP desaturases are discussed.
Spoken Web Search (2011)

paper, we describe the Spoken Web Search Task, which was held as part of the 2011 MediaEval campaign. The purpose of this task was to perform audio search in several languages, with very little resources being available in each language. The data was taken from audio content that was created in live settings and was submitted to the spoken web over a mobile connection.
Applications of the long-range alpha detector for site-characterization technology (1994)

Traditional alpha-particle detectors are limited by relatively poor sensitivity, small size, and difficulty of operation. These factors result in laborious effort and imprecise results. In addition, it is difficult for these detectors to monitor the inside of pipes and large areas having nonuniform surfaces. To be effective, traditional monitors require the probe to be held less than 1 cm from the surface while scanning with a slow, steady, and continuous motion. Long-range alpha detector (LRAD) technology overcomes the limitations imposed by the short range of alpha particles and provides a detailed analysis of alpha contamination in a cost-effective manner. Using a combination of LRAD airflow and electrostatic methods, we have developed several monitors for the detection of alpha contamination on hands and arms, in surface soil, and for radon gas.
Computational intelligence and neuromorphic computing potential for cybersecurity applications (2013)

In today’s highly mobile, networked, and interconnected internet world, the flow and volume of information is overwhelming and continuously increasing. Therefore, it is believed that the next frontier in technological evolution and development will rely in our ability to develop intelligent systems that can help us process, analyze, and make-sense of information autonomously just as a well-trained and educated human expert. In computational intelligence, neuromorphic computing promises to allow for the development of computing systems able to imitate natural neurobiological processes and form the foundation for intelligent system architectures.
Continuous-wave photoacoustic microscopy (2007)

We have built a photoacoustic microscope (PAM) using an amplitude-modulated continuous-wave (CW) laser source, which is an inexpensive 120-mW laser diode. By using a bowl-shaped piezoelectric transducer, whose numerical aperture is 0.85 and resonance frequency is 2.45 MHz, we have experimentally demonstrated a lateral resolution of 600 &mgr;m, an axial resolution of 700 &mgr;m, and a signal-to-noise ratio (SNR) as high as 43 dB. Although the SNR in the CW PAM system is an order of magnitude worse than that of the pulsed-laser-based PAM system, CW PAM shows potential for biomedical applications as it uses durable and inexpensive semiconductor lasers, which will significantly reduce operation costs of the PAM systems.
Separation of fetal and maternal ECG complexes from a mixed signal using an algorithm based on linear regression (1995)

Fetal scalp ECG and Doppler ultrasound are the two methods universally used to derive the fetal heart rate (FHR) for cardiotocography. Other fetal signal sources have not been used successfully because of the complexity of the signal and the need for an additional maternal ECG input. In this paper, we present an algorithm for separating the fetal and maternal ECG signals obtained from intrauterine electrodes during labour. The algorithm detects all occurrences of ECG complexes and uses linear regression functions to compare each complex with a set templates. Sets of templates are identified as either maternal or fetal in origin and two signals are output for heart rate measurement. The outputs are also processed to eliminate artefacts that may occur when the maternal and fetal complexes are coincident. The algorithm processes 10 seconds of data at a time (in about 200 ms on a standard PC) while a further 10 s of data is being acquired. It has the advantage that no extra input is required, such as maternal ECG obtained from chest leads, and only assumes that two different populations of complexes of two different shapes are present in the input signal. The algorithm could also be used for the separation of fetal and maternal signals obtained from abdominal electrodes.
ralGDS family members interact with the effector loop of ras p21. (1994)

Using a yeast two-hybrid system, we identified a novel protein which interacts with ras p21. This protein shares 69% amino acid homology with ral guanine nucleotide dissociation stimulator (ralGDS), a GDP/GTP exchange protein for ral p24. We designated this protein RGL, for ralGDS-like. Using the yeast two-hybrid system, we found that an effector loop mutant of ras p21 was defective in interacting with the ras p21-interacting domain of RGL, suggesting that this domain binds to ras p21 through the effector loop of ras p21. Since ralGDS contained a region highly homologous with the ras p21-interacting domain of RGL, we examined whether ralGDS could interact with ras p21. In the yeast two-hybrid system, ralGDS failed to interact with an effector loop mutant of ras p21. In insect cells, ralGDS made a complex with v-ras p21 but not with a dominant negative mutant of ras p21. ralGDS interacted with the GTP-bound form of ras p21 but not with the GDP-bound form in vitro. ralGDS inhibited both the GTPase-activating activity of the neurofibromatosis gene product (NF1) for ras p21 and the interaction of Raf with ras p21 in vitro. These results demonstrate that ralGDS specifically interacts with the active form of ras p21 and that ralGDS can compete with NF1 and Raf for binding to the effector loop of ras p21. Therefore, ralGDS family members may be effector proteins of ras p21 or may inhibit interactions between ras p21 and its effectors.
Gate-Level Information Flow Tracking for Security Lattices (2014)

High-assurance systems found in safety-critical infrastructures are facing steadily increasing cyber threats. These critical systems require rigorous guarantees in information flow security to prevent confidential information from leaking to an unclassified domain and the root of trust from being violated by an untrusted party. To enforce bit-tight information flow control, gate-level information flow tracking (GLIFT) has recently been proposed to precisely measure and manage all digital information flows in the underlying hardware, including implicit flows through hardware-specific timing channels. However, existing work in this realm either restricts to two-level security labels or essentially targets two-input primitive gates and several simple multilevel security lattices. This article provides a general way to expand the GLIFT method for multilevel security. Specifically, it formalizes tracking logic for an arbitrary Boolean gate under finite security lattices, presents a precise tracking logic generation method for eliminating false positives in GLIFT logic created in a constructive manner, and illustrates application scenarios of GLIFT for enforcing multilevel information flow security. Experimental results show various trade-offs in precision and performance of GLIFT logic created using different methods. It also reveals the area and performance overheads that should be expected when expanding GLIFT for multilevel security.
The Influence of Ovine MHC Class II<i>DRB1</i>Alleles on Immune Response in Bovine Leukemia Virus Infection (2003)

We have reported previously that the alleles of the ovine leukocyte antigen (OLA)-DRB1 gene that encode the Arg-Lys (RK) motif and the Ser-Arg (SR) motif at positions beta70/71 of the OLA-DRbeta1 domain are associated with resistance and susceptibility, respectively, to development of bovine leukemia virus (BLV)-induced ovine lymphoma. Here, to investigate the different immune response in sheep that carried alleles associated with resistance and susceptible for 30 weeks after infection with BLV, we selected sheep that had the RK/RK or SR/SR genotype among the 52 sheep analyzed by polymerase chain reaction-restriction fragment length polymorphism and DNA sequencing of PCR product for the OLA-DRB1 exon 2 and infected them with BLV. Although the number of BLV-infected cells and virus titer had been maintaining low levels throughout the experimental period, the sheep with the RK/RK genotype could induce expansion of CD5- B-cells and rapid production of neutralizing antibody in the early phase of infection. The level of incorporation of [3H]thymidine by peripheral blood mononuclear cells from the sheep with RK/RK genotype gave a strong response to BLV virion antigen and synthetic antigenic peptides that corresponded to T-helper epitope of the BLV envelope glycoprotein gp51. In contrast, the sheep with SR/SR genotype showed a strong response to BLV virion antigen and synthetic antigenic peptides that corresponded to T-cytotoxic and B-cell epitopes. In such cases, the animals with the RK/RK strongly expressed IFN-gamma, the animals with SR/SR genotype strongly expressed IL-2. To determine the proliferating cells, we tried a blocking assay with monoclonal antibodies such as anti-CD4, -CD8 and -DR molecule. We found that these proliferating cells were MHC-restricted CD4+ T-cells.
Automated Slice-Based Artery Identification in Various Field-of-View CTA Scans (2015)

Automated identification of main arteries in Computed Tomography Angiography (CTA) scans plays a key role in the initialization of vessel tracking algorithms. Automated vessel tracking tools support physicians in vessel analysis and make their workflow time-efficient. We present a fully-automated framework for identification of five main arteries of three different body regions in various field-of-view CTA scans. Our method detects the two common iliac arteries, the aorta and the two common carotid arteries and delivers seed positions in them. After the field-of-view of a CTA scan is identified, artery candidate positions are regressed slice-wise and the best candidates are selected by Naive Bayes classification. Final artery seed positions are detected by picking the most optimal path over the artery classification results from slice to slice. Our method was evaluated on 20 CTA scans with various field-of-views. The high detection performance on different arteries shows its generality and future applicability for automated vessel analysis systems.
<title>Low-cost passive fiber optic gyroscope</title> (1992)

This paper presents a passive fiber optic gyroscope without nonreciprocal phase modulation. A fused fiber 3 X 3 directional coupler provides a constant phase shift, thus enabling the detection of rotation rate at the quadrature point. Bias and scale factor errors due to indeterministically changing birefringent coupling centers in the non-polarization preserving monomode fiber coil are eliminated by using a contrast insensitive signal recovery scheme. A simple temperature compensation procedure has been implemented in the gyro software which yields a bias stability < 0.04 deg/sec and scale factor errors < 0.5% in the whole temperature range between -40$DEGC and +70 degree(s)C.
Rapid Synthesis of Polyanhydrides by Microwave Polymerization (2003)

Abstract Summary: Polyanhydrides were synthesized from aliphatic and aromatic diacids using microwave radiation without vacuum at significantly reduced reaction times when compared to conventional melt polycondensation. Reaction conditions, such as duration of polymerization, equivalents of acetic anhydride, and choice of starting species, were studied. In addition, copolymers were synthesized and monomer sequence lengths were calculated using dyad conditional probabilities. The results are in good agreement with monomer sequence lengths from conventional copolymerization. Comparison of the monomer sequence lengths in poly(CPH‐ co ‐SA) synthesized both conventionally and by microwave heating. magnified image Comparison of the monomer sequence lengths in poly(CPH‐ co ‐SA) synthesized both conventionally and by microwave heating.
Abstract 16547: Thrombin-Thrombomodulin Fusion Proteins as New Anticoagulants (2016)

Introduction: Thrombin is a trypsin-like protease that plays opposing functional roles in blood coagulation due to the interaction with numerous macromolecular substrates, receptors and inhibitors. The specific binding of fibrinogen and PAR-1 to the exosite-1 leads to the conversion of fibrinogen to fibrin, platelet activation and clot formation. Binding of the cofactor thrombomodulin to the same exosite-1 hinders docking of the procoagulant substrates and accelerates the activation of protein C by 1500-fold thereby enabling the most powerful enzymatic anticoagulant system that exists in vivo . Down-regulation and washout of thrombomodulin from the endothelium have been documented in pathological conditions such as atherosclerotic lesions, sepsis and disseminated intravascular coagulation leading to impaired activation of protein C and thrombosis. Hypothesis: A solution to this problem would be the administration of a thrombomodulin-independent protein C activator. Results: In this study we report the design, expression and functional characterization of a new family of fusion proteins that specifically activate protein C without the need of endogenous thrombomodulin. In our molecules, the enzyme thrombin is genetically fused via artificial linkers to the soluble extracellular portion of the cofactor thrombomodulin. A total of 6 fusion proteins were expressed in mammalian cells at high yield and high purify. As expected, their anticoagulant profile varies with the length of the artificial linker. An optimal anticoagulant activity is achieved with a linker composed of 31 and 41 amino acids. Specifically, the activity of the L31 and L41 fusion proteins towards procoagulant substrates such as fibrinogen and PAR-1 was reduced >100-fold while protein C activation was minimally affected (2-fold) compared to the endogenous complex. Conclusions: Similar values of specificity for protein C activation constitute evidence of productive docking between the subunits of thrombin and thrombomodulin in vitro . However, the partial blockade of the procoagulant substrate suggests that further optimization of length, composition and localization of the linker and/or of the protein partners is necessary to achieve an exquisite anticoagulant profile.
High-capacity packet-switched optical ring network (2002)

We propose a novel architecture with MAC and admission control protocols for a high-capacity packet-switched optical ring network. In this network the link capacity significantly exceeds the node bit rate. Nodes transmit and receive packets on multiple wavelengths in parallel by using novel optical techniques. Network control is simple since the load is balanced over wavelengths at the physical layer. The MAC protocol is based on credits, and the derived admission control protocol has similar complexity as in a single channel network. Consequently, the network can follow fast traffic changes which are typical in data networks.
Rhodamine-based compounds as fluorogenic substrates for serine proteinases (1983)

A new fluorogenic substrate for serine proteinases, bis(N-benzyloxycarbonyl-L-argininamido)Rhodamine [(Cbz-Arg-NH)2-Rhodamine], was synthesized, purified and chemically and enzymically characterized. This compound, which employs Rhodamine as a fluorophoric leaving group, is the first in a series of substrates designed to measure the amidase activity of proteinases. Cleavage of one of the amide bonds of (Cbz-Arg-NH)2-Rhodamine by a trypsin-like serine proteinase converts the non-fluorescent bisamide substrate into a highly fluorescent monoamide product. Significant differences in the electronic absorption and fluorescence emission spectra and quantum yields of bis-, mono- and un-substituted Rhodamine are reported. Macroscopic kinetic constants for the interaction of (Cbz-Arg-NH)2-Rhodamine with bovine trypsin, human and dog plasmin and human thrombin were determined. Compared with the corresponding 7-amino-4-methylcoumarin-based analogue, (Cbz-Arg-NH)2-Rhodamine exhibits an increase in sensitivity with these enzymes of 50--300-fold. The physical basis for this increase in sensitivity is discussed.
Development of a PCR-Based Line Probe Assay for Identification of Fungal Pathogens (2000)

We report on a reverse-hybridization line probe assay (LiPA) which when combined with PCR amplification detects and identifies clinically significant fungal pathogens including Candida, Aspergillus, and Cryptococcus species. DNA probes have been designed from the internal transcribed-spacer (ITS) regions of Candida albicans, Candida parapsilosis, Candida glabrata, Candida tropicalis, Candida krusei, Candida dubliniensis, Cryptococcus neoformans, Aspergillus fumigatus, Aspergillus versicolor, Aspergillus nidulans and Aspergillus flavus. The probes were incorporated into a LiPA for detection of biotinylated ITS PCR products, and the specificity of the probes was evaluated. We established LiPA detection limits for ITS 1 and for full ITS amplicons for genomic DNA from C. albicans, A. fumigatus, and C. neoformans. Further evaluation of the LiPA was carried out on clinical fungal isolates. One hundred twenty-seven isolates consisting of dimorphic yeasts and dermatophytic and filamentous fungi were tested by the LiPA, which correctly identified 77 dimorphic yeasts and 23 of the filamentous isolates; the remaining 27 isolates represented species of fungi for which probes were not included in the LiPA. The fungal-PCR-LiPA technology was applied to blood samples inoculated with Candida cells which were pretreated by minibead beating to mechanically disrupt the cells, with the DNA extracted by either a previously described guanidium thiocyanate-silica method or the commercially available QIAmp tissue kit. PCR amplification of the extracted DNA and subsequent DNA probe hybridization in the LiPA assay yielded detection limits of 2 to 10 cells/ml. An internal standard control was included in the PCR amplification to monitor for PCR inhibition. This fungal PCR-LiPA assay is robust and sensitive and can easily be integrated into a clinical-testing laboratory with the potential for same-day diagnosis of fungal infection.