gebhart/patrepeval huggingface dataset:
Expression of an <i>Escherichia coli</i> antigenic fusion protein comprising the heat labile toxin B subunit and the heat stable toxin, and its assembly as a functional oligomer in transplastomic tobacco plants (2008)

Summary Enterotoxigenic Escherichia coli (ETEC) strains are important pathogens in developing countries. Some vaccine formulations containing the heat labile toxin B subunit (LTB) have been used in clinical trials; however, the induction of neutralizing antibodies against the heat‐stable toxin (ST), a poor immunogenic peptide, is necessary, as most ETEC strains can produce both toxins. In this study, a plant optimized synthetic gene encoding for the LTB‐ST fusion protein has been introduced into plastids of tobacco leaf tissues, using biolistic microprojectile bombardment, in an effort to develop a single plant‐based candidate vaccine against both toxins. Transplastomic tobacco plants carrying the LTB‐ST transgene have been recovered. Transgene insertion into the plastid was confirmed by both PCR and Southern blot analysis. GM1‐ELISA revealed that the LTB‐ST fusion protein retained its oligomeric structure, and displayed antigenic determinants for both LTB and ST. Western blot analysis, using LTB antisera, confirmed the presence of a 17‐KDa protein in transplastomic lines, with the correct antigenicity of the fusion protein. Expression levels of this fusion protein in different lines reached up to 2.3% total soluble protein. Oral immunization of mice with freeze‐dried transplastomic tobacco leaves led to the induction of both serum and mucosal LTB‐ST specific antibodies. Following cholera toxin challenge, a decrease of intestinal fluid accumulation was observed in mice immunized with LTB‐ST‐containing tobacco. These findings suggest that tobacco plants expressing LTB‐ST could serve as a plant‐based candidate vaccine model providing broad‐spectrum protection against ETEC‐induced diarrhoeal disease.
Huntingtin Is Present in the Nucleus, Interacts with the Transcriptional Corepressor C-terminal Binding Protein, and Represses Transcription (2002)

Huntingtin is a protein of unknown function that contains a polyglutamine tract, which is expanded in patients with Huntington's disease (HD). We investigated the localization and a potential function for huntingtin in the nucleus. In human fibroblasts from normal and HD patients, huntingtin localized diffusely in the nucleus and in subnuclear compartments identified as speckles, promyelocytic leukemia protein bodies, and nucleoli. Huntingtin-positive nuclear bodies redistributed after treatment with sodium butyrate. By Western blot, purified nuclei had low levels of full-length huntingtin compared with the cytoplasm but contained high levels of N- and C-terminal huntingtin fragments, which tightly bound the nuclear matrix. Full-length huntingtin co-immunoprecipitated with the transcriptional corepressor C-terminal binding protein, and polyglutamine expansion in huntingtin reduced this interaction. Full-length wild-type and mutant huntingtin repressed transcription when targeted to DNA. Truncated N-terminal mutant huntingtin repressed transcription, whereas the corresponding wild-type fragment did not repress transcription. We speculate that wild-type huntingtin may function in the nucleus in the assembly of nuclear matrix-bound protein complexes involved with transcriptional repression and RNA processing. Proteolysis of mutant huntingtin may alter nuclear functions by disrupting protein complexes and inappropriately repressing transcription in HD.
Selected Five-Color Operation Of A CO2 Laser (1981)

A simple CO2 laser can be caused to exhibit a specific sequence of five rotational lines or "colors" with cavity length tuning. The sequence, useful in multicolor interferometric distance measurement, is predicted to appear only near certain discrete laser cavity lengths. Three different length breadboard lasers are described in which a desired sequence is found.
A Self-Organizing Wireless Sensor Network and Distributed Computing Engine for Commodity and Future Palmtop Computers (2015)

The embedded class processors found in commodity palmtop computers continue to become increasingly capable while retaining an energy-efficient footprint. Palmtop computers themselves, including smartphones and tablets, provide a small form factor system integrating wireless communication and non-volatile storage with these energy-efficient processors. Also, various wireless connectivity functions on mobile devices provide new opportunities in designing more flexible, smarter wireless sensor networks (WSNs), and utilizing the computation power in a way we could never imagine before. In this dissertation, I present a WSN concept for current and future generation tablet devices. My contributions include developments at the system level, architecture level, and collaborative design between different layers of the system. At the system level, I developed Ocelot, a grid-like computing environment for palmtop computers in place of traditional workstation or server class machines to compute highly parallel light to medium-weight tasks in an energy efficient manner. Additionally, I developed Lynx, a self-organizing wireless sensor network, which is a further step taken in exploiting the potential of palmtop computers. At the architecture level, to increase the storage capacity of future palmtop computers, I explore the use of a new storage class magnetic memory, Racetrack Memory (RM), throughout the memory hierarchy. Thus, I developed FusedCache, a naturally inclusive, dual-level private cache design for RM that provides fast uniform access at one level, and non-uniform access at the next, which allows RM to be effective as close to the processor as an L1 cache. For higher levels of the memory hierarchy such as the last level cache, I propose a Multilane Racetrack Cache (MRC), an RM last level cache design utilizing lightweight compression combined with independent shifting. MRCs allow cache lines mapped to the same Racetrack structure to be accessed in parallel when compressed, mitigating potential shifting stalls in an RM cache. Finally, leveraging the lightweight compression from MRC and the need for efficient communication in Lynx, I present a cross-level design combining memory-level lightweight compression with network-level packet transfer, together with a technique called Source-Aware Layout Reorganization (SALR) to increase the compressibility of sensor data.
A 10-bit 220-MSample/s CMOS sample-and-hold circuit (2002)

A fully differential sample-and-hold (S/H) circuit using double-sampling is presented. Compared to a conventional S/H configuration with a similar opamp the double-sampling gives a factor of two increase in the sampling rate while maintaining comparable power consumption. The circuit is designed in 0.5 /spl mu/m CMOS technology. Measurements show 10 bit operation up to the Nyquist frequency at the sampling rate of 220 MS/s with 25 mW at 3 V power dissipation.
Studies on Synthesizing Magnesium Aspartate as A Feed Additive (2005)

The series experiments were carried to develop the optimal technology of synthesizing magnesium aspartate with material of L-aspartate acid and magnesian oxide as materials. The results show that the optimal technology conditions are: the action temperature is 80 ℃,the quality ratio of H_2O/LAA is 3∶1 and mol ratio of LAA/MgO is 1.2∶1. The conditions for crystal are 30 r/min of stiring and 10 ℃ per hour of temperature drop graduation, with output of over 85%.
Nontypeable <i>Haemophilus influenzae</i> in the Lower Respiratory Tract of Patients with Chronic Bronchitis (2001)

The frequency of colonization and intracellular localization of nontypeable Haemophilus influenzae (NTHi) in the lower respiratory tract was determined in healthy adults and in clinically stable and acutely ill chronic bronchitis (CB) patients. NTHi was recovered from bronchial wash or bronchial brush specimens in 6 of 23 (26%) stable CB patients and in 1 of 15 (7%) CB patients with a respiratory exacerbation. No NTHi (0 of 26) was recovered from lower tract specimens of healthy adults undergoing anesthesia for elective surgery. Molecular typing of NTHi strains revealed that five of nine patients with stable CB had different strains in upper respiratory tract and bronchial wash/brush specimens collected simultaneously. Four stable patients with CB had different strains recovered on repeat bronchoscopy. These results demonstrate the frequent colonization of the lower airways of stable CB patients with multiple strains of NTHi. Bronchial biopsies also were examined for intracellular NTHi by in situ hybridization and immunofluorescence microscopy. Intracellular NTHi were found in 0 of 7 healthy adults, 8 of 24 patients with clinically stable CB, and 13 of 15 acutely ill CB patients. This observation suggests a role for intracellular infection by NTHi in the pathogenesis of exacerbations of CB.
Model checking fault tolerant systems (2002)

Abstract This paper proposes a modelling approach suitable for formalizing fault tolerant systems, taking into account different fault scenarios. Verification of the properties of such systems is then performed using model checking. A general framework for the formal specification and verification of fault tolerant systems is defined starting from these principles, and experience with its application to two case studies is then presented. Copyright © 2002 John Wiley & Sons, Ltd.
Experimental Results on the Cross-Coupled Phase-Locked Loop Interference Canceller with Closed Loop Amplitude Control (1986)

Experimental results demonstrating practical performance capabilities and limitations on the cross-coupled phase-locked loop (CCPLL) interference canceller with closed loop amplitude control are presented. Hardware was designed and constructed to demonstrate its potential in suppressing CW, AM. FM. AM/FM and pulsed RF interference. Practical rules of design are also advanced. In addition to the experimental study. computer aided analysis of the defining set of coupled nonlinear differential equations was also conducted to derive "stability regions" which reveal the range of loop parameters over which successful cancellation of the interferer and demodulation of the desired signal can be assured.
Multiple alignment of protein sequences with repeats and rearrangements (2006)

Multiple sequence alignments are the usual starting point for analyses of protein structure and evolution. For proteins with repeated, shuffled and missing domains, however, traditional multiple sequence alignment algorithms fail to provide an accurate view of homology between related proteins, because they either assume that the input sequences are globally alignable or require locally alignable regions to appear in the same order in all sequences. In this paper, we present ProDA, a novel system for automated detection and alignment of homologous regions in collections of proteins with arbitrary domain architectures. Given an input set of unaligned sequences, ProDA identifies all homologous regions appearing in one or more sequences, and returns a collection of local multiple alignments for these regions. On a subset of the BAliBASE benchmarking suite containing curated alignments of proteins with complicated domain architectures, ProDA performs well in detecting conserved domain boundaries and clustering domain segments, achieving the highest accuracy to date for this task. We conclude that ProDA is a practical tool for automated alignment of protein sequences with repeats and rearrangements in their domain architecture.
Groups and crowd simulation (2005)

A crowd is not only a group of many individuals: crowd modeling involves problems arising only when we focus on crowds. For instance, collision avoidance among a large number of individuals in the same area requires different resolving strategies in comparison with the methods used to avoid collisions between just two individuals. Also, motion planning for a group walking together requires more information than needed to implement individual motion planning. This Chapter presents the related works on the subject of groups and crowd simulation as well as discusses the requirements to model behaviors of groups and crowds of virtual actors; current applications, recently applied approaches and challenges of crowd simulations are described.
A digital signal processing approach to interpolation (1973)

In many digital signal precessing systems, e.g., vacoders, modulation systems, and digital waveform coding systems, it is necessary to alter the sampling rate of a digital signal Thus it is of considerable interest to examine the problem of interpolation of bandlimited signals from the viewpoint of digital signal processing. A frequency dmnain interpretation of the interpolation process, through which it is clear that interpolation is fundamentally a linear filtering process, is presented, An examination of the relative merits of finite duration impulse response (FIR) and infinite duration impulse response (IIR) digital filters as interpolation filters indicates that FIR filters are generally to be preferred for interpolation. It is shown that linear interpolation and classical polynomial interpolation correspond to the use of the FIR interpolation filter. The use of classical interpolation methods in signal processing applications is illustrated by a discussion of FIR interpolation filters derived from the Lagrange interpolation formula. The limitations of these filters lead us to a consideration of optimum FIR filters for interpolation that can be designed using linear programming techniques. Examples are presented to illustrate the significant improvements that are obtained using the optimum filters.
Structural Basis of Ligand Discrimination by Two Related RNA Aptamers Resolved by NMR Spectroscopy (1996)

In a previous study, an RNA aptamer for the specific recognition of arginine was evolved from a parent sequence that bound citrulline specifically. The two RNAs differ at only 3 positions out of 44. The solution structures of the two aptamers complexed to their cognate amino acids have now been determined by two-dimensional nuclear magnetic resonance spectroscopy. Both aptamers contain two asymmetrical internal loops that are not well ordered in the free RNA but that fold into a compact structure upon ligand binding. Those nucleotides common to both RNAs include a conserved cluster of purine residues, three of which form an uneven plane containing a G:G pair, and two other residues nearly perpendicular to that surface. Two of the three variant nucleotides are stacked on the cluster of purines and form a triple contact to the amino acid side chain, whereas the edge of the third variant nucleotide is capping the binding pocket.
Adaptive Routing and Traffic Control in Damaged Circuit Switched Networks (1987)

This paper presents a local traffic control, the failure detection algorithm, which is designed to duplicate the performance of a no-calls-to-dead-nodes traffic control on a damaged circuit switched network. Results of simulations run on a discrete event simulator show that, under the conditions tested, the local control gives better network performance than no-learning and approaches the performance of a no-calls-to-dead-notes algorithm which uses perfect knowledge of damaged network topology. Under conditions of heavy congestion, the local traffic control works better than global adaptive routing. An important advantage of the local algorithm is that it is simpler and more economical to implement than algorithms which depend on global network knowledge.
<title>Intersatellite-laser-ranging experiment for global-change sensing and 21st century satellite control</title> (1995)

The optimal integration of precise multiple-antenna GPS receivers, advanced cryogenic inertial measurement units (IMU's), and ultra-stable frequency laser ranging devices on two low altitude, copolar orbiting spacecraft forms the basis of a multifaceted/interdisciplinary proposal. Scientific objectives are to (1) sense geodynamic gravitation changes and (2) substantially improve a variety of temporal geophysical models. Such models will make the Air Force Satellite Control Network's orbit determination process more accurate and affordable. The use of differential GPS (DGPS) observations, as external updates in an elaborate Kalman filter optimally integrating the three data types, puts a bound on the low frequency IMU and laser error buildups. In the filter the DGPS, IMU, and laser data streams aid each other to obtain the experiment's two navigation goals: determining the satellites' positions and orientations to centimeter and arc second accuracies. If each satellite also possesses stereo optical (3D) and multispectral sensors, global 3D Earth background image files could be built in both the visible and IR regimes.
Tenomodulin is Associated with Obesity and Diabetes Risk: The Finnish Diabetes Prevention Study (2007)

We recently showed that long-term weight reduction changes the gene expression profile of adipose tissue in overweight individuals with impaired glucose tolerance (IGT). One of the responding genes was X-chromosomal tenomodulin (TNMD), a putative angiogenesis inhibitor. Our aim was to study the associations of individual single nucleotide polymorphisms and haplotypes with adiposity, glucose metabolism, and the risk of type 2 diabetes (T2D). Seven single nucleotide polymorphisms from two different haploblocks were genotyped from 507 participants of the Finnish Diabetes Prevention Study (DPS). Sex-specific genotype effects were observed. Three markers of haploblock 1 were associated with features of adiposity in women (rs5966709, rs4828037) and men (rs11798018). Markers rs2073163 and rs1155794 from haploblock 2 were associated with 2-hour plasma glucose levels in men during the 3-year follow-up. The same two markers together with rs2073162 associated with the conversion of IGT to T2D in men. The risk of developing T2D was approximately 2-fold in individuals with genotypes associated with higher 2-hour plasma glucose levels; the hazard ratios were 2.192 (p = 0.025) for rs2073162-A, 2.191 (p = 0.027) for rs2073163-C, and 1.998 (p = 0.054) for rs1155974-T. These results suggest that TNMD polymorphisms are associated with adiposity and also with glucose metabolism and conversion from IGT to T2D in men.
Peroxidase Activity in Seeds of Soybean Varieties<sup>1</sup> (1968)

Varieties of soybean ( Glycine max (L.) Merr.) were separated into two main groups on the basis of high or low peroxidase activity in the seed coat. Differences in peroxidase activity were detected following electrophoresis of extracts on polyacrylamide gel and by quantitative determinations. Seed‐coat extracts from the high level group exhibited more than 78 tunes the peroxidase activity of seed‐coat extracts of the low level group. A survey of peroxidase activity of soybean varieties was carried out by using a specially developed spot test. Pedigree relationships among the varieties indicated that high and low activity is highly heritable and that it is not a case of ‘extra‐nuclear’ maternal inheritance. Disc electrophoresis using suitable amounts of seedcoat extracts resulted in a major band of isoperoxidase which was common to both groups. Two minor bands of isoperoxidase were also identified in all high‐level varieties and in two of the five low‐level varieties tested. Between the two groups, isoperoxidases appeared to be qualitatively identical but quantitatively different.
Extremely high gain 0.15 μm gate-length InAlAs/InGaAs/InP HEMTs (1991)

High electron mobility transistors (HEMTs) based on the InAlAs/InGaAs heterojunction grown lattice matched to InP were fabricated with 0.15 μm T-shaped gates. The use of an undoped InGaAs cap layer in the epitaxial structure leads to excellent gate characteristics and very high transistor gain. At 95 GHz, a maximum available gain of 13.6 dB was measured. A maximum frequency of oscillation fmax of 455 GHz was obtained by extrapolating from 95 GHz at –6 dB/octave. This is the best reported gain performance for any transistor.
Effect of poly(ethylene glycol) graft polymerization of poly(methyl methacrylate) on cell adhesion (2001)

Surface modification of PMMA using PEG grafting reduced cell adhesion. This may decrease the incidence of retroprosthetic membrane formation after keratoprosthesis surgery.
Time-Triggered Ethernet and IEEE 1588 Clock Synchronization (2007)

The time-triggered Ethernet unifies real-time and non-real-time traffic into a single communication architecture. We have built a prototype implementation of an FPGA TT-Ethernet switch and an FPGA TT Ethernet communication controller supporting a network bandwidth of 100 Mbit/sec. Time-Triggered Ethernet introduces two message classes, i) the standard event-triggered Ethernet messages, denoted as ET messages, and ii) the time-triggered Ethernet messages, denoted as TT messages. All TT messages are transmitted periodically and are scheduled a priori in a way that there are no conflicts on the network. The network handles these messages according to the cut-through paradigm. Computer nodes containing TT Ethernet communication controllers establish and maintain global time base. However nodes containing standard Ethernet controllers can be connected to a TT Ethernet system and can send ET messages without affecting the temporal properties of the TT messages. The global time format of the TT Ethernet deploys the UTC time format which is compatible with the time format of the IEEE 1588 standard. In these work we present how we deploy the IEEE 1588 in order to synchronize the TT Ethernet controllers which require a tight synchronization among them. Additionally the IEEE 1588 clock synchronization based protocol will be implemented at standard Ethernet controllers such that they can be establish and maintain a global time base.
Motion Compensation Using Polyline Based Block Partition (2009)

The tree structure based block partition in H.264 has been shown to be more efficient than simple uniform block partition. However, tree based partition still does not code efficiently enough with video information, as it is unable to capture the geometric structure of 2D data. Concerned with this problem, this paper proposes a new motion compensation technique using polyline based block partition. A polyline, composed of two line segments, is used to approximate the curve contour of moving objects. By using polyline based partition, the accuracy of motion compensation can be improved and the prediction error can be reduced. Curvature analysis of object contour within macroblocks verified the validity of the proposed method. Experimental results show that the proposed method improves the coding efficiency by 0.2-0.3 dB in PSNR, when compared to H.264/AVC.