gebhart/patrepeval huggingface dataset:
Establishment of an accurate and fast detection method using molecular beacons in loop-mediated isothermal amplification assay (2017)

This study established a constant-temperature fluorescence quantitative detection method, combining loop-mediated isothermal amplification (LAMP) with molecular beacons. The advantages of LAMP are its convenience and efficiency, as it does not require a thermocycler and results are easily visualized by the naked eye. However, a major disadvantage of current LAMP techniques is the use of indirect evaluation methods (e.g., electrophoresis, SYBR Green I dye, precipitation, hydroxynaphthol blue dye, the turbidimetric method, calcein/Mn<sup>2+</sup> dye, and the composite probe method), which cannot distinguish between the desired products and products of nonspecific amplification, thereby leading to false positives. Use of molecular beacons avoids this problem because molecular beacons produce fluorescence signals only when binding to target DNA, thus acting as a direct indicator of amplification products. Our analyses determined the optimal conditions for molecular beacons as an evaluation tool in LAMP: beacon length of 25-45 bp, beacon concentration of 0.6-1 pmol/μL, and reaction temperature of 60-65 °C. In conclusion, we validated a novel molecular beacon loop-mediated isothermal amplification method (MB-LAMP), realizing the direct detection of LAMP product.
Regulation of telomerase activity and anti‐apoptotic function by protein–protein interaction and phosphorylation (2003)

The enzyme telomerase is necessary for the synthesis and maintenance of telomere length. The catalytic subunit, telomerase reverse transcriptase (TERT), is regulated by interaction with the 90 kDa heat shock protein (HSP90) and by Akt-dependent phosphorylation. Here, we demonstrate that HSP90 and Akt physically interact with TERT. Treatment of cells with novobiocin, which blocks C-terminal interaction of HSP90, disrupted HSP90 binding to Akt, induced Akt dephosphorylation and significantly reduced telomerase activity. The reduction of TERT activity by novobiocin was associated with an increase in apoptosis. Likewise, the induction of Akt dephosphorylation by protein phosphatase 2A (PP2A) reduced telomerase activity. HSP90 is known to prevent PP2A-mediated dephosphorylation of Akt. To investigate whether the effect of novobiocin is due to the reduction of Akt or TERT phosphorylation, we overexpressed a phospho-mimetic, active Akt (T308D/S473D). Akt (T308D/S473D) prevented novobiocin-induced reduction of telomerase activity and the stimulation of apoptosis. Moreover, overexpression of a dominant negative PP2A construct (PP2A(L199P)) as well as incubation with the PP2A inhibitor okadaic acid blocked the inhibition of telomerase activity by novobiocin. These data suggest that the association between HSP90, Akt and TERT in concert with the phosphorylation of TERT is necessary for maintaining telomerase activity and inhibition of apoptosis.
Advancements in Complementary Carbon Nanotube Field-Effect Transistors (2004)

High performance p- and n-type single-walled carbon nanotube (SWNT) field-effect transistors (FETs) are obtained by using high and low work function metals, Pd and Al as source/drain (S/D) electrodes respectively. Ohmic contacts made to chemically intrinsic SWNTs, with no or small Schottky barriers (SB), afford high ON-state currents up to 20 uA per tube. The lack of significant Fermi-level pinning at the nanotube-metal interfaces allows for fine-tuning of the barrier heights for p-and n-channel conductions by changing the contact metals. The air-stable p- and n-FETs thus obtained can be used for complementary nanoelectronics, as demonstrated with the fabrication of an inverter. Other important issues regarding nanotube FETs including hysteresis, OFF-state leak currents, choice of nanotube diameter, and threshold voltage control are discussed.
A 256-Mb Double-Data-Rate SDRAM with a 10-mW Analog DLL Circuit (2000)

The developed 256-Mb double-data-rate (DDR) SDRAM employs a one-cycle stage-selection analog DLL (delayed-locked loop) circuit-running at IO mW with a 20-ps jitter and a 65- cycles lock-in - and a fully differential clocking system to provide 2~ 0.33-ns clock-to-data-output delay, 0.06-ns setup time and 0.26-ns hold time with respect to the data strobe. This performance represents the possibility of over 250-MHz (500 Mb/s/pin) operation. An even/odd-shared redundancy circuit for a 2-b prefetch reduces the number of fuses by 33%.
Screening Common Bean for Resistance to Four <i>Sclerotinia sclerotiorum</i> Isolates Collected in Northern Spain (2010)

White mold, caused by the fungus Sclerotinia sclerotiorum, is a serious disease in common bean (Phaseolus vulgaris) causing significant yield loss. Few cultivars with high levels of physiological resistance to white mold have been described in common bean. The objectives of this study were to (i) determine variation in aggressiveness for the local S. sclerotiorum isolates and (ii) identify sources of resistance against local isolates using the greenhouse straw test. The evaluated materials included 199 accessions of a core collection established from the main bean gene bank in Spain and 29 known cultivars or lines, 5 of them described as resistant sources to white mold: G122, PC50, A195, Cornell 606, and MO162. Significant differences for aggressiveness among the four S. sclerotiorum isolates were detected. Generally, isolates 1 and 3 were more aggressive than isolates 2 and 4. In all, 19 genotypes exhibited a level of resistance equal to or significantly better than G122: 11 accessions from the core collection and 8 cultivars or lines from known materials, including the lines A195 and Cornell 606. To confirm resistance, 19 selected genotypes were tested using a more severe straw test with reactions evaluated 21 days after inoculation. Fifteen genotypes exhibited significantly less susceptibility than G122: eight accessions from the core collection and the known cultivars or lines AB136, Kaboon, BRB57, BRB130, Don Timoteo, and A195. The logical next step will be to evaluate the best genotypes for field reaction to white mold and conduct inheritance studies.
Accurate Titration of Infectious AAV Particles Requires Measurement of Biologically Active Vector Genomes and Suitable Controls (2018)

Although the clinical use of recombinant adeno-associated virus (rAAV) vectors is constantly increasing, the development of suitable quality control methods is still needed for accurate vector characterization. Among the quality criteria, the titration of infectious particles is critical to determine vector efficacy. Different methods have been developed for the measurement of rAAV infectivity <i>in vitro</i>, based on detection of vector genome replication in <i>trans</i>-complementing cells infected with adenovirus, detection of transgene expression in permissive cells, or simply detection of intracellular vector genomes following the infection of indicator cells. In the present study, we have compared these methods for the titration of infectious rAAV8 vector particles, and, to assess their ability to discriminate infectious and non-infectious rAAV serotype 8 particles, we have generated a VP1-defective AAV8-GFP vector. Since VP1 is required to enter the cell nucleus, the lack of VP1 should drastically reduce the infectivity of rAAV particles. The AAV8 reference standard material was used as a positive control. Our results demonstrated that methods based on measurement of rAAV biological activity (i.e., vector genome replication or transgene expression) were able to accurately discriminate infectious versus non-infectious particles, whereas methods simply measuring intracellular vector genomes were not. Several cell fractionation protocols were tested in an attempt to specifically measure vector genomes that had reached the nucleus, but genomes from wild-type and VP1-defective AAV8 particles were equally detected in the nuclear fraction by qPCR. These data highlight the importance of using suitable controls, including a negative control, for the development of biological assays such as infectious unit titration.
An End-to-End Dynamic Trust Framework for Service-Oriented Architecture (2017)

Service-oriented architecture (SOA) is an architectural paradigm that advocates composition of loosely-coupled services in order to construct more complex applications. The agility and complexity of modern web services on one hand and the arbitrary interconnections among them on the other hand, make it difficult to maintain a sustainable trustworthiness in long-running SOA-based applications. Moreover, the chain of participating services in a specific SOA invocation may not be visible to the service consumers, which leads to a lack of accountability. To address these challenges in SOA, we propose the following contributions. First, we design a new dynamic and flexible trust model based on graph abstraction that uses multiple trust strategies to calculate trust across SOA. This trust model keeps track of three trust metrics: individual service trust, session trust, and composite trust. We further design a trust engine component that implements the proposed trust model and that continuously maintains the quantitative end-to-end trust based on processing actual execution of services. Second, to prove the practicality and usefulness of the proposed framework, we have implemented an adaptive and secure service composition engine (ASSC) which takes advantage of an efficient algorithm to generate service compositions with near-optimal trustworthiness under predefined QoS constraints. Finally, we have developed a tool that is able to automatically deploy SOA testbeds from arbitrary directed acyclic graphs (created in the GUI). This tool enables the researcher to study the dynamics of new trust algorithms and strategies under different scenarios (e.g., arbitrary SOA topologies and attacks). We have extensively studied the effectiveness and performance of the proposed solutions using testbeds in the Amazon EC2 cloud.
Car park reservation system (2012)

Nominated as OAPS (Outstanding Academic Papers by Students) paper by Department in 2012-13.
Extraction of species-specific glycan substructures. (2004)

Glycans, which are carbohydrate sugar chains attached to some lipids or proteins, have a huge variety of structures and play a key role in cell communication, protein interaction and immunity. The availability of a number of glycan structures stored in the KEGG/GLYCAN database makes it possible for us to conduct a large-scale comparative research of glycans. In this paper, we present a novel approach to compare glycan structures and extract characteristic glycan substructures of certain organisms. In the algorithm we developed a new similarity measure of glycan structures taking into account of several biological aspects of glycan synthesis and glycosyltransferases, and we confirmed the validity of our similarity measure by conducting experiments on its ability to classify glycans between organisms in the framework of a support vector machine. Finally, our method successfully extracted a set of candidates of substructrues which are characteristic to human, rat, mouse, bovine, pig, chicken, yeast, wheat and sycamore, respectively. We confirmed that the characteristic substructures extracted by our method correspond to the substructures which are known as the species-specific sugar chain of gamma-glutamyltranspeptidases in the kidney.
RObust Header Compression (ROHC): Framework and four profiles: RTP, UDP, ESP, and uncompressed (2001)

Existing header compression schemes do not work well when used over
links with significant error rates and long round-trip times. For many
bandwidth limited links where header compression is essential, such
characteristics are common. A highly robust and efficient header
compression scheme for RTP/UDP/IP, UDP/IP and ESP/IP headers is
specified in this document. This is done in a framework designed to be
extensible. For example, a scheme for compressing TCP/IP headers will
be simple to add, and is in development. Headers specific to Mobile
IPv4 are not subject to special treatment, but are expected to be
compressed sufficiently well by the provided methods for compression
of sequences of extension headers and tunneling headers. For the most
part, the same will apply to work in progress on Mobile IPv6, but
future work might be required to handle some extension headers, when a
standards track Mobile IPv6 has been completed. Revision history
(remove before publishing) -08: Incorporate changes from second,
abbreviated WG last call; ready for submission to an IESG last-call.
-07: Incorporate changes from WG last call -06: Final changes for WG
last call -05: Editorial changes -04: Complete 5.5 and 5.8. Remove
section 7 (no longer needed) and renumber. Restructure section 5 to
clearly separate the profiles. -03: Redo packet formats to allow new
ROHC framework. Fill in gaps. -02: Major changes after 48th IETF -01:
Minor editorial changes for 48th IETF -00: Document created from ROHC
submissions
Explainable Neural Networks based on Additive Index Models (2018)

Machine Learning algorithms are increasingly being used in recent years due to their flexibility in model fitting and increased predictive performance. However, the complexity of the models makes them hard for the data analyst to interpret the results and explain them without additional tools. This has led to much research in developing various approaches to understand the model behavior. In this paper, we present the Explainable Neural Network (xNN), a structured neural network designed especially to learn interpretable features. Unlike fully connected neural networks, the features engineered by the xNN can be extracted from the network in a relatively straightforward manner and the results displayed. With appropriate regularization, the xNN provides a parsimonious explanation of the relationship between the features and the output. We illustrate this interpretable feature--engineering property on simulated examples.
Investigating semantic similarity measuresacross the Gene Ontology: the relationship betweensequence and annotation (2003)

Software available from http://www.russet.org.uk.
Castable Polyurethane Elastomers (2015)

This second edition of a bestseller is a practical guide to the production of castable polyurethane articles. The book shows the progression from raw materials to prepolymer production, including the chemistry and functionality of the processes. It provides a comprehensive look at various problem-solving and processing techniques, examining the selection of different systems on both the micro and macro levels. Reorganized for better flow, this edition describes new processing methods, expands coverage of health and safety aspects, and brings all standards up to date.
Stereo-Based Visual Odometry for Autonomous Robot Navigation (2016)

Mobile robots should possess accurate self-localization capabilities in order to be successfully deployed in their environment. A solution to this challenge may be derived from visual odometry (VO), which is responsible for estimating the robot's pose by analysing a sequence of images. The present paper proposes an accurate, computationally-efficient VO algorithm relying solely on stereo vision images as inputs. The contribution of this work is twofold. Firstly, it suggests a non-iterative outlier detection technique capable of efficiently discarding the outliers of matched features. Secondly, it introduces a hierarchical motion estimation approach that produces refinements to the global position and orientation for each successive step. Moreover, for each subordinate module of the proposed VO algorithm, custom non-iterative solutions have been adopted. The accuracy of the proposed system has been evaluated and compared with competent VO methods along DGPS-assessed benchmark routes. Experimental results of relevance to rough terrain routes, including both simulated and real outdoors data, exhibit remarkable accuracy, with positioning errors lower than 2%.
Conjugative plasmids and the degradation of arylsulfonates in Comamonas testosteroni (1997)

Comamonas testosteroni T-2 degrades p-toluenesulfonate (TSA) via p-sulfobenzoate (PSB) and protocatechuate and degrades toluenecarboxylate via terephthalate (TER) and protocatechuate. The appropriate genes are expressed in at least five regulatory units, some of which are also found in C. testosteroni PSB-4 (F. Junker, R. Kiewitz, and A. M. Cook, J. Bacteriol. 179:919-927, 1997). C. testosteroni T-2 was found to contain two plasmids, pTSA (85 kbp) and pT2T (50 kbp); a TSA- mutant (strain TER-1) contained only plasmid pT2T. C. testosteroni PSB-4, which does not degrade TSA, contained one plasmid, pPSB (85 kbp). The type strain contained no plasmids. Conjugation experiments showed that plasmid pTSA (possibly in conjunction with pT2T) was conjugative, and the single copy of the TSA operon (tsaMBCD) with its putative regulator gene (tsaR) in strain T-2 was found on plasmid pTSA, which also carried the PSB genes (psbAC) and presumably transport for both substrates. Plasmid pTSA was assigned to the IncP1 beta group and was found to carry two copies of insertion element IS1071. Plasmid pPSB (of strain PSB-4), which could be maintained in strains with plasmid pTSA or pT2T, was also conjugative and was found to carry the PSB genes as well as to contain two copies of IS1071. In attempted conjugations with the type strain, no plasmid was recovered, but the PSB+ transconjugant carried two copies of IS1071 in the chromosome. We presume the PSB genes to be located in a composite transposon. The genes encoding the putative TER operon and degradation of protocatechuate, with the meta cleavage pathway, were attributed a chromosomal location in strains T-2 and PSB-4.
<title>NVEOD FLIR92 thermal imaging systems performance model</title> (1992)

The Night Vision and Electro-Optics Directorate's FLIR92 model predicts minimum resolvable temperature difference (MRTD) and minimum detectable temperature difference (MDTD) for scanning and staring infrared sensors. FLIR92 retains unchanged for two- dimensional MRTD, and incorporates sampling effects and three-dimensional noise more thoroughly than the simple approximations used in the FLIR90 model. The FLIR92 MRTD predictions are shown to be valid for representative scanning and staring systems.
Forty Years of Steam Injection in California - The Evolution of Heat Management (2003)

Steam injection EOR began in California forty years ago, and has been highly successful. As a consequence, California's thermal recovery operations represent a leading source of EOR production in the world.The understanding of most early thermal recovery operators was limited to the concept of
The effects of walking with pedometers on quality of life and various symptoms and issues relating to aging (2008)

AIMS: This study is aimed to elucidate the effect of aerobic walking using watch-type pedometers with or without a heart rate checker, which may support to keep moderate exercise intensity.METHODS: Thirty one healthy subjects (mean age, 59.1 ± 5.0, 17 men and 14 women) were divided into 2 groups: the study group of 15 subjects (8 men and 7 women) using a pedometer with a heart rate checker and the control group of 16 subjects (9 men and 7 women) using a common pedometer checking heart rates by themselves. All participants tried aerobic walking exercises alone for 8 weeks, 5 days a week, for 45 minutes a day with an instructed exercise intensity 40 to 60%. The subjects underwent height, weight, body fat percentage, blood pressure, and hematological and blood chemistry tests before and after the study. In addition, all participants completed an aging and QOL questionnaire before and after the study.RESULTS: A decrease of systolic blood pressure (before-study value 140.2 ± 23.2 mmHg) by 3.7% and an increase of estrogen levels (by 37%) in women were observed in both groups. In a comparative study of the 2 groups, the study group showed significant improvements in “lethargy”, “tinnitus”, “early satiety”, “constipation” and “arthralgia” as physical symptoms and in “difficulty in falling asleep” and “pessimism” as mental symptoms.CONCLUSIONS: Aerobic walking with a heart rate checker may help to maintain the exercise intensity within the range of 40% to 60% of maximum, thus resulted more desirable data than walking with self heart rate checking at one’s own pace.
The C-17: Modern Airlift Technology (1991)

<div class="htmlview paragraph">Three SAE technical papers in recent years have addressed the C-17 program: “C-17 Technical Description” by Robert van't Riet, presented 8 March 1989, and “C-17 Flight Control System” by Alex Brown, and “Meeting the C-17 Reverse Thrust Requirements” by Frank Junkermann, both presented 3 October 1988. This paper provides an update of these previous presentations by members of the McDonnell Douglas C-17 team. The paper discusses technology adapted from commercial aircraft for military airlift; the military requirement to move large cargo items long distances and land on short runways, which drove C-17 design; and significant design alternatives and the solutions selected.</div>
Acoustic wave propagation in one-dimensional phononic crystals containing Helmholtz resonators (2008)

One-dimensional acoustic waveguide containing subwavelength-sized Helmholtz resonators is known to exhibit novel physical phenomena. However, no systematic theoretical study on this system has been carried out so far except on a few limited cases. We present a thorough theoretical calculation on the acoustic wave propagation in phononic crystals containing Helmholtz resonators without any geometrical size restrictions. The band structures, transmission spectra, and defect states are studied for diverse geometries using the interface response theory. It is shown that the acoustic band structure of the model is fundamentally different from the conventional acoustic–elastic cases and richer due to the coexistence of the resonant and the Bragg gaps. It is also shown that the presence of a defect resonator in the system can give rise to a localized mode inside the resonance gaps. The results clearly show that the presence of the Helmholtz resonators singly or periodically can play a prominent role in designing any acoustic band gap materials.
Autoantibodies against exocrine pancreas in Crohn's disease are directed against two antigens: The glycoproteins CUZD1 and GP2 (2012)

The concordant reactivities of the different platforms can be regarded as a proof for the authenticity of the two identified autoantigens.
Semiquantitative Proteomic Analysis of Rat Forebrain Postsynaptic Density Fractions by Mass Spectrometry (2004)

The postsynaptic density (PSD) of central excitatory synapses plays a key role in postsynaptic signal transduction and contains a high concentration of glutamate receptors and associated scaffold and signaling proteins. We report here a comprehensive analysis of purified PSD fractions by liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS). We identified 374 different proteins that copurified with the PSD structure and discovered thirteen phosphorylated sites from eight proteins. These proteins were classified into numerous functional groups, implying that the signaling pathways in the PSD are complex and diverse. Furthermore, using quantitative mass spectrometry, we measured the molar concentration and relative stoichiometries of a number of glutamate receptor subunits and scaffold proteins in the postsynaptic density. Thus this proteomic study reveals crucial information about molecular abundance as well as molecular diversity in the PSD, and provides a basis for further studies on the molecular mechanisms of synaptic function and plasticity.