gebhart/patrepeval huggingface dataset:
Engineering High Assurance Distributed Cyber Physical Systems (2015)

Abstract : Distributed Adaptive Real-Time (DART) systems are interconnected and collaborating systems that continuously must satisfy guaranteed and highly critical requirements (e.g., collision avoidance), while at the same time adapt ing, smartly, to achieve best- effort and low-critical application requirements (e.g., protection coverage) when operating in dynamic and uncertain environments . This paper introduces our approach to engineering a DART system so that we achieve high assurance in its runtime behavior against a set of formally specified requirements. It describes our technique to : (i) ensure asymmetric timing protection between high-and low-critical threads (HCTs and LCTs) on each node in the DART system , and (ii) verify that the self- adaptation within, and coordination between, the nodes and their interaction with the physical environment do not violate high and low requirements. We present our ongoing research to integrate advances in model- based engineering with compositional analysis techniques to formally verify safety- critical properties demanded in safety- conscience domains such as aviation and automotive , and introduce our DART model problem that serves as an end- to-end demonstration of our integrated engineering approach.
Magnetic structure and multiferroic coupling in pyroxeneNaFeSi2O6 (2015)

By comprehensive neutron diffraction measurements we have studied the magnetic structure of aegirine $({\mathrm{NaFeSi}}_{2}{\mathrm{O}}_{6})$ in and above its multiferroic phase. Natural aegirine exhibits two magnetic transitions into incommensurate magnetic order with a propagation vector of ${\stackrel{P\vec}{k}}_{\mathrm{inc}}=(0,\ensuremath{\sim}0.78,0)$. Between 9 and 6 K, we find a transverse spin-density wave with moments pointing near the $c$ direction. Below 6 K, magnetic order becomes helical and spins rotate in the $ac$ plane. The same irreducible representation is involved in the two successive transitions. In addition, the ferroelectric polarization $\stackrel{P\vec}{P}$ appearing along the $b$ direction cannot be described by the most common multiferroic mechanism but follows $\stackrel{P\vec}{P}\ensuremath{\propto}{\stackrel{P\vec}{S}}_{i}\ifmmode\times\else\texttimes\fi{}{\stackrel{P\vec}{S}}_{j}$. Synthetic ${\mathrm{NaFeSi}}_{2}{\mathrm{O}}_{6}$ does not exhibit the pure incommensurate helical order but shows coexistence of this order with a commensurate magnetic structure. By applying moderate pressure to natural aegirine, we find that the incommensurate magnetic ordering partially transforms to the commensurate one, underlining the nearly degenerate character of the two types of order in ${\mathrm{NaFeSi}}_{2}{\mathrm{O}}_{6}$.
Induction of Anchorage-Independent Growth by Amphiregulin (1996)

We have previously shown that the epidermal growth factor receptor (EGFR) ligand, amphiregulin (AR) exhibits low potency as a result of its C-terminal truncation. This led us to investigate whether its inability to promote anchorage-independent growth (AIG) of normal cells arose because of its compromised interaction with EGFR. Wild type AR(1-84) was tested in AIG and mitogenesis assays using NRK-49F or NR6/HER fibroblasts. In contrast to NR6/HER cells, the response of NRK-49F fibroblasts to AR was much lower than expected. As the effect of AR was heparin-insensitive, contributions from heparan sulphate proteoglycan interactions could not explain the differing sensitivities of the cells. Comparison of the effects of AR on two additional cell lines indicated that low EGFR number correlated with AR insensitivity: this suggested that the low potency of AR precluded activation of sufficient receptors to elicit a response. Consistent with this proposal, a modified form of AR (AR[1-90(leu86)]) with enhanced potency was able to induce AIG of NRK-49F fibroblasts. Thus, the ability of AR to promote AIG is determined both by ligand potency and the EGFR complement of cells.
Structural basis of RNA cap modification by SARS-CoV-2 (2020)

The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), the causative agent of COVID-19 illness, has caused millions of infections worldwide. In SARS coronaviruses, the non-structural protein 16 (nsp16), in conjunction with nsp10, methylates the 5'-end of virally encoded mRNAs to mimic cellular mRNAs, thus protecting the virus from host innate immune restriction. We report here the high-resolution structure of a ternary complex of SARS-CoV-2 nsp16 and nsp10 in the presence of cognate RNA substrate analogue and methyl donor, S-adenosyl methionine (SAM). The nsp16/nsp10 heterodimer is captured in the act of 2'-O methylation of the ribose sugar of the first nucleotide of SARS-CoV-2 mRNA. We observe large conformational changes associated with substrate binding as the enzyme transitions from a binary to a ternary state. This induced fit model provides mechanistic insights into the 2'-O methylation of the viral mRNA cap. We also discover a distant (25 Å) ligand-binding site unique to SARS-CoV-2, which can alternatively be targeted, in addition to RNA cap and SAM pockets, for antiviral development.
The FERMI @ Elettra Technical Optimization Study: General Layoutand Parameters and Physics Studies of Longitudinal Space Charge, theSpreader, the Injector, and Preliminary FEL Performance (2005)

The FERMI {at} Elettra facility will make use of the existing GeV linac at Sincrotrone Elettra, which will become available for dedicated FEL applications following the completion of construction of a new injector booster complex for the storage ring. With a new rf photocathode injector, and some additional accelerating sections, this linac will be capable of providing high brightness bunches at 1.2 GeV and up to 50 Hz repetition rates.
On-board stereo sensor for intersection driving assistance architecture and specification (2009)

This paper presents the specifications and architecture for a stereovision sensor to be used in intersection assistance. The intersection problem imposes a wide field of view, reasonable accuracy for the typical intersection length, and fast response time. The image and 3D data provided by the low level routines are used to generate two kinds of environment descriptions - an unstructured description, composed of elevation maps, occupancy grids, and polylines delimiting obstacle areas and curbs, and a structured description, composed of lanes, cuboidal objects, and classified pedestrians. The descriptions can be further combined, and additional data sources can be used, in order to provide a complete and accurate description of the intersection.
77Se NMR studies of bis(alkylthio)selenides of biological thiols (1988)

Abstract To determine the feasibility of using 77 Se NMR spectroscopy to characterize bis(alkylthio)selenides formed by reaction of selenite with thiol groups of biological molecules, 77 Se NMR spectra have been measured for bis(alkylthio)selenides formed by reaction of selenite with cysteine, homocysteine, penicillamine, N ‐acetylpenicillamine, 2‐mercaptopropanoic acid, mercaptosuccinic acid, cysteamine and glutathione. The 77 Se chemical shift is extremely sensitive to the nature of the alkylthiol group, covering a range greater than 150 ppm for this series of thiols. The chemical shift is also sensitive to the stereochemistry of the alkylthiol group, and resolved resonances are observed for meso and D,L ‐stereoisomers, e.g. the meso and D,L ‐stereoisomers of bis(cysteine)selenide. 77 Se NMR spectra were also measured for mixed bis(alkylthio)selenides (RSSeSŔ) formed by reaction of selenite with two‐component mixtures of the various thiols. The effect of the two alkylthiol groups on the 77 Se chemical shift is additive, with 77 Se chemical shifts of the mixed bis(alkylthio)selenides located mid‐way between those of the two symmetric compounds. The 77 Se chemical shift is also sensitive to the protonation state of carboxylic acid and ammonium groups of the alkylthiol, and p K A values were determined from 77 Se chemical shift vs pH titration curves for selected symmetrical and mixed bis(alkylthio)selenides. The results demonstrate that 77 Se NMR is a sensitive method for the characterization and study of bis(alkylthio)selenides.
Colocalization of the α-subunit of gustducin with PYY and GLP-1 in L cells of human colon (2006)

In view of the importance of molecular sensing in the function of the gastrointestinal (GI) tract, we assessed whether signal transduction proteins that mediate taste signaling are expressed in cells of the human gut. Here, we demonstrated that the alpha-subunit of the taste-specific G protein gustducin (Galpha(gust)) is expressed prominently in cells of the human colon that also contain chromogranin A, an established marker of endocrine cells. Double-labeling immunofluorescence and staining of serial sections demonstrated that Galpha(gust) localized to enteroendocrine L cells that express peptide YY and glucagon-like peptide-1 in the human colonic mucosa. We also found expression of transcripts encoding human type 2 receptor (hT2R) family members, hT1R3, and Galpha(gust) in the human colon and in the human intestinal endocrine cell lines (HuTu-80 and NCI-H716 cells). Stimulation of HuTu-80 or NCI-H716 cells with the bitter-tasting compound phenylthiocarbamide, which binds hT2R38, induced a rapid increase in the intracellular Ca2+ concentration in these cells. The identification of Galpha(gust) and chemosensory receptors that perceive chemical components of ingested substances, including drugs and toxins, in open enteroendocrine L cells has important implications for understanding molecular sensing in the human GI tract and for developing novel therapeutic compounds that modify the function of these receptors in the gut.
Hemodynamic Monitoring of Spinal Cord with Diffuse Optical & Correlation Spectroscopies (2012)

We employ diffuse optics to measure spinal cord hemodynamics in response to pharmacologic and mechanical perturbations for the first time. Comparison of blood flow and blood pressure responses demonstrate robust spinal cord autoregulation.
Yield analysis and optimization of VLSI interconnects in multichip modules (2002)

A CAD approach integrating multidimensional correlated Monte-Carlo analysis and generalized l/sub 1/ optimization with lossy transmission line network simulations is presented. It is implemented in a CAD framework for statistical analysis and yield optimization of high-speed VLSI interconnects. Physical/geometrical based hierarchical Monte-Carlo analysis and yield optimization examples are presented.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Low-power state assignment targeting two- and multilevel logic implementations (1998)

The problem of minimizing power consumption during the state encoding of a finite-state machine is addressed. A new power cost model for state encoding is proposed, and encoding techniques that minimize this power cost for two- and multilevel logic implementations are described. These techniques are compared with those that minimize area or the switching activity at the present state bits. Experimental results show significant improvements.
Ship performance monitoring and analysis to improve fuel efficiency (2014)

A pilot project was launched to monitor vessel performance and to explore ways to reduce fuel consumption. A prototype Vessel Performance Monitoring and Analysis System (VPMAS) was used to collect information over a three week period. The project objective was to collect needed data, conduct preliminary analysis to establish trends, explore key performance indicators (KPI) to establish baseline, and explore data products for performance management. Performance management includes improving vessel performance and supporting efficient operation to reduce fuel consumption. For the pilot project, only a subset of vessel performance data was collected. Current key performance indicators (KPIs) include fuel consumption per trip, fuel consumption per distance travelled, fuel consumption per displacement distance and fuel consumption per payload distance. The dataset will expand in the future and will include the effect of environmental conditions. Preliminary analysis includes comparing the normal route for calm sea states and irregular routes taken probably to avoid heavy sea states; assessing the maneuvers in and out of harbors, computing key performance indicators, assessing the data trends and general statistics, and identifying data products to support performance management. Initial results show that automatic fuel measurement was in good agreement with manual tank sounding. A voyage on an irregular route consumed almost twice the amount of fuel consumed in a normal route. Fuel consumption would be reduced if constant speed is used in open water and if deviations from the desired routes could be minimized, for example, through optimized autopilot.
Dynamics of Particles and Rigid Bodies (2005)

This 2006 book is intended for undergraduate courses in dynamics. The work is a unique blend of conceptual, theoretical, and practical aspects of dynamics generally not found in dynamics books at the undergraduate level. In particular, in this book the concepts are developed in a highly rigorous manner and are applied to examples using a step-by-step approach that is completely consistent with the theory. In addition, for clarity, the notation used to develop the theory is identical to that used to solve example problems. The result of this approach is that a student is able to see clearly the connection between the theory and the application of theory to example problems. While the material is not new, instructors and their students will appreciate the highly pedagogical approach that aids in the mastery and retention of concepts. The approach used in this book teaches a student to develop a systematic approach to problem-solving.
Trapped-energy vibratory gyroscopes using a partially polarized piezoelectric ceramic plate (2001)

Most conventional piezoelectric vibratory gyroscopes have been constructed by using the bending vibrations as in a tuning-bar or a tuning-fork oscillator. However, this kind of vibratory gyroscope faces substantial practical problems because its vibration characteristics usually are easily influenced by the support or lead installation of the element. In contrast, if the trapped-energy vibrations are used because they have a high degree of concentration of the vibration energy and a nonvibrating region over a wide range, these problems would be solved at once, and highly precise and reliable piezoelectric vibratory gyroscopes could be implemented. In this paper, we propose a trapped-energy vibratory gyroscope with three electrodes, which uses the thickness-shear vibrations excited by a parallel electric field in a partially polarized piezoelectric ceramic plate, as the structure for this type of trapped-energy vibratory gyroscope and describe the principle of construction for the gyroscope. First, the energy trapping of thickness-shear vibrations in a partially polarized piezoelectric ceramic plate, which is the basic theory of the vibratory gyroscope, is theoretically analyzed and the mechanism and characteristics of energy trapping are clarified. Next, based on these results, the experimental results for the piezoelectric vibratory gyroscope using a partially polarized piezoelectric ceramic plate 1.5 mm thick are presented. © 2001 Scripta Technica, Electron Comm Jpn Pt 2, 84(3): 44–52, 2001
Preparation of SiO2‐Encapsulated BaTiO3 Nanoparticles with Tunable Shell Thickness by Reverse Microemulsion (2013)

A silica coating on hydrophobic BaTiO3 nanoparticles is created using a reverse microemulsion route. The process is sufficiently controllable to target a tunable silica shell thickness by choosing appropriate BaTiO3 concentrations. Increasing the concentration of BaTiO3 nanoparticles is found to be an effective approach to decrease silica thickness.
[Glass fiber polymerization--an effective method of increasing fracture resistance of the denture base (case reports)]. (2003)

Three cases are presented to demonstrate how the application of glass fibres could be integrated into the treatment plan of removable dentures. In Case one the lack of space excluded the use of chrome-cobalt framework, but glass fibre reinforcement for the implant prothesis, secured by ball attachments, ensured structural stability. In Case two in order to keep the upper canine, an overdenture was constructed, which incorporated glass fibres in its dental base to prevent fracture propagation there. In Case three where the transfer of an extremely great chewing load to the dental base caused repeated fractures, the complex treatment of second framed work, fibres reinforcement and reline gave a stable satisfactory result over a long-term monitoring period. It was concluded, as presented, that the application of glass fibre reinforcement polymerised in the denture base can ensure structural stability and prevent fracture.
HEPARANASE PRETREATMENT ATTENUATES ENDOTOXIN-INDUCED ACUTE LUNG INJURY IN RATS (2007)

A central event of systemic inflammation and septic organ injury is infiltration of tissues with polymorphonuclear neutrophils, likely modulated by the integrity of the extracellular matrix underlying the vascular endothelium. In the present study, the effect of matrix-modifying endoglycosidase (heparanase) on endotoxin (LPS)-induced inflammatory lung injury was investigated in rats. Animals were treated with heparanase or LPS or pretreated with heparanase before LPS injection, and acute lung injury was verified histologically and characterized by analysis of bronchoalveolar lavage fluids. Pretreatment with heparanase attenuated the mortality of animals and preserved the histological structure of the lungs. Furthermore, polymorphonuclear neutrophil accumulation and activation, analyzed by myeloperoxidase release and reactive oxygen species production associated with lung injury, were significantly reduced upon heparanase pretreatment. In addition, heparanase pretreatment elevated the IL-10 levels in the pulmonary compartment. Moreover, results from in vitro experiments have identified monocyte-derived IL-10 as an important mediator used by heparanase to suppress inflammatory reactions. The protective effect of heparanase may indicate a novel therapeutic strategy for sepsis.
Variable rates of evolution among Drosophila opsin genes. (1992)

DNA sequences and chromosomal locations of four Drosophila pseudoobscura opsin genes were compared with those from Drosophila melanogaster, to determine factors that influence the evolution of multigene families. Although the opsin proteins perform the same primary functions, the comparisons reveal a wide range of evolutionary rates. Amino acid identities for the opsins range from 90% for Rh2 to more than 95% for Rh1 and Rh4. Variation in the rate of synonymous site substitution is especially striking: the major opsin, encoded by the Rh1 locus, differs at only 26.1% of synonymous sites between D. pseudoobscura and D. melanogaster, while the other opsin loci differ by as much as 39.2% at synonymous sites. Rh3 and Rh4 have similar levels of synonymous nucleotide substitution but significantly different amounts of amino acid replacement. This decoupling of nucleotide substitution and amino acid replacement suggests that different selective pressures are acting on these similar genes. There is significant heterogeneity in base composition and codon usage bias among the opsin genes in both species, but there are no consistent relationships between these factors and the rate of evolution of the opsins. In addition to exhibiting variation in evolutionary rates, the opsin loci in these species reveal rearrangements of chromosome elements.
Deep Characterization of the Microbiomes of Calophya spp. (Hemiptera: Calophyidae) Gall-Inducing Psyllids Reveals the Absence of Plant Pathogenic Bacteria and Three Dominant Endosymbionts (2015)

Bacteria associated with sap-feeding insect herbivores include not only symbionts that may increase their hosts' fitness but also harmful plant pathogens. Calophya spp. gall-inducing psyllids (Hemiptera: Calophyidae) are being investigated for their potential as biological control agents of the noxious weed, Brazilian peppertree (Schinus terebinthifolia), in Florida. Although there are no examples of plant pathogen transmission by members of the family Calophyidae, several insects in the superfamily Psylloidea are known to transmit pathogenic bacteria in the genera Candidatus Liberibacter and Candidatus Phytoplasma. To determine whether Calophya spp. harbor potentially harmful plant pathogenic bacteria, we sequenced small subunit (SSU) ribosomal RNA (rRNA) gene amplicons generated from individuals from four Calophya spp. populations: All microbial SSU gene sequences fell into the bacterial domain, with 98-99% belonging to the Proteobacteria. The Calophya microbiomes contained a relatively simple community, with 49-79 operational taxonomic units (OTUs; 97%) detected, and only 5-8 OTUs with greater than 1% abundance. Candidatus Carsonella showed the highest relative abundance, with OTUs from this candidate genus representing between 51-65% of all recovered sequences. The next most abundant clade observed was an unclassified Enterobacteriacae group closely related to bacteria from the genera Buchnera and Blochmannia that ranged from 20-31% in relative abundance. Wolbachia populations were the third most abundant group and represented 7-27% of the diversity in microbial OTUs. No SSU rRNA gene sequences from putative pathogenic bacteria from the genera Ca. Liberibacter or Ca. Phytoplasma were detected in the microbiomes of the four Calophya populations. The probability that infected psyllids were present in our colonies, but were not sampled, was extremley low (1.39 x 10(-10)). As far as we are aware, our study is the first to characterize the microbiome of a candidate biological control agent, and coupled with previous work demonstrating a high degree of host specificity and absence of plant viruses, suggests that releasing Calophya spp. in United States poses minimal risk to non-target plants.
Analysis of electromagnetic bandgap structures embedded in printed circuit boards using the transmission line and periodic structure theory (2005)

The paper presents a new equivalent circuit model for electromagnetic bandgap structures embedded in a parallel-plate wave-guiding environment in a 2D fashion. The model, based on the transmission line theory and periodic structures, by employing a simple lumped-element substitute for the patch-via structure, presents a first order, but detailed, quantitative and qualitative analysis of the filtering properties of the metallo-dielectric electromagnetic bandgap structure. Comparison of results derived from this model and numerical modeling, shows that this model is able to describe the resonant properties of the structure as well as its pass-band and stop-band regions with enough accuracy to make it a useful tool as the first step in the design of the structures under consideration.
Hierarchical Evidence Set Modeling for Automated Fact Extraction and Verification (2020)

Automated fact extraction and verification is a challenging task that involves finding relevant evidence sentences from a reliable corpus to verify the truthfulness of a claim. Existing models either (i) concatenate all the evidence sentences, leading to the inclusion of redundant and noisy information; or (ii) process each claim-evidence sentence pair separately and aggregate all of them later, missing the early combination of related sentences for more accurate claim verification. Unlike the prior works, in this paper, we propose Hierarchical Evidence Set Modeling (HESM), a framework to extract evidence sets (each of which may contain multiple evidence sentences), and verify a claim to be supported, refuted or not enough info, by encoding and attending the claim and evidence sets at different levels of hierarchy. Our experimental results show that HESM outperforms 7 state-of-the-art methods for fact extraction and claim verification.