gebhart/patrepeval huggingface dataset:
Three Vector Generation of Crystal Space Groups in Geometric Algebra (2006)

Abstract: This paper focuses on the symmetries of crystal space lattices. All two dimensional (2D) and three dimensional (3D) point groups of 2D and 3D crystal cells are exclusively described by vectors (two in 2D, three in 3D for one particular cell) taken from the physical cells. Geometric multiplication of these vectors completely generates all symmetries, including reflections, rotations, inversions, rotary-reflections and rotary-inversions. We then extend this treatment to 3D space groups by including translations, glide reflections and screw rotations. We focus on the monoclinic case as an example. A software demonstration shows the spacegroup visualizer.
Data Race Detection for Interrupt-Driven Programs via Bounded Model Checking (2013)

In Cyber-Physical Systems with interrupt mechanism, interrupts may cause unexpected interleaving executions and even wrong execution results. A kind of frequently occurred errors are caused by data race. We present an approach under the framework of bounded model checking (BMC) to detect data race for interrupt driven programs. The key idea is to automatically serialize a concurrent interrupt driven program as a non-deterministic sequential program, whose possible execution set includes all the possible executions of the interrupt driven program. Moreover, our approach checks data race in the sequential program and collects all the path condition of the data race location. On this basis, we leverage bounded model checking to convert all the path conditions into SMT formulae. Furthermore, our analysis uses a decision procedure to determine whether the formula is satisfiable, from which the analysis eliminates false alarms which can't occur in real concurrent executions. A prototype based on CBMC is implemented and preliminary experimental results are encouraging.
Cyclic AMP responsiveness of human gonadotropin-alpha gene transcription is directed by a repeated 18-base pair enhancer. Alpha-promoter receptivity to the enhancer confers cell-preferential expression. (1987)

The human chorionic gonadotropin-alpha (CG-alpha) gene is transcriptionally activated by cAMP. Sequencing the CG-alpha 5'-flanking region identified two copies of a palindrome, 5'-TGACGTCA-3', homologous to sequences in other cAMP-responsive genes. The two palindromes are contained within two identical 18-base pair (bp) sequences arranged as adjacent direct repeats. One or two synthetic copies of the 18-bp sequences were inserted into plasmids containing either the CG-alpha promoter or the SV40 promoter directing transcription of the chloramphenicol acetyltransferase gene. The 36-bp (double) element markedly enhanced chloramphenicol acetyltransferase activity in placental choriocarcinoma (JEG-3) cells when inserted in either orientation both 5' to the cap site or 3' of the coding sequence, thus defining it as an enhancer. Moreover, 8-br-cAMP stimulated the enhancer activity 30-40-fold. A single 18-bp element also stimulated chloramphenicol acetyltransferase activity, although 5-fold less than the double element, but still imparted a 35-fold transcriptional cAMP responsivity. The enhancer activates its homologous promoter much more efficiently than the SV40 promoter in JEG-3 cells. The alpha-promoter is not nearly as receptive to activation by the enhancer in baby hamster kidney fibroblasts, whereas the more modest enhancement of the SV40 promoter is less cell-specific. These studies suggest that the interaction of a 36-bp enhancer-like element with the homologous promoter represents part of the mechanism of cell-specific expression of the CG-alpha gene and that the enhancer is co-localized with a highly effective cAMP-response element.
Atom modulus quantization for matching pursuit video coding (2003)

We provide an analytical study of the selection and modulus quantization of matching pursuits (MP) coefficients. We demonstrate that an optimal rate-distortion trade-off is achieved by selecting the atoms up to a dead-zone threshold, and by defining the modulus quantizer in terms of that threshold. In doing so, we take into account quantization error re-injection resulting from inserting the modulus quantizer inside the MP atom computation loop. In-loop quantization affects the stepsize of the uniform quantizer, and results in a non-uniform optimal entropy constrained quantizer. Improvements larger than one dB are obtained for video coding.
ASSEMBLY OF FUNCTIONAL ALGINATE GEL MODULE (2017)

This paper reports a method of alginate hydrogel module assembly for heterogeneous 3D structure. This assembly was done by connecting alginate gel modules with ‘cationic nanoparticle’ (CNP) solution. The adhesion is caused by the interaction between CNP and the anionic surface of alginate gel modules. We showed that our method can connect alginate gel modules without external stimuli or maleffect to alginate gel modules with human malignant epithelial cells (HeLa). Alginate gel plates were connected with CNPs and its connection was confirmed to be kept under a mechanical stress. As a demonstration, we achieved to make a bundle of microfiber containing HeLa cells. We believe that our method provides a suitable method for fabrication of artificial tissue structures in the field of tissue engineering.
Single cell multiomic analysis of T cell exhaustion in vitro (2019)

Abstract A key step in the clinical production of CAR-T cells is the expansion of engineered T cells. To generate enough cells for a therapeutic product, cells must be chronically stimulated, which raises the risk of inducing T-cell exhaustion and reducing therapeutic efficacy. As protocols for T-cell expansion are being developed to optimize CAR T cell yield, function and persistence, fundamental questions about the impact of in vitro manipulation on T-cell identity are important to answer. Namely: 1) what types of cells are generated during chronic stimulation? 2) how many unique cell states can be defined during chronic stimulation? We sought to answer these fundamental questions by performing single-cell multiomic analysis to simultaneously measure expression of 39 proteins and 399 genes in human T cells expanded in vitro . This approach allowed us to study – with unprecedented depth - how T cells change over the course of chronic stimulation. Comprehensive immunophenotypic and transcriptomic analysis at day 0 enabled a refined characterization of T-cell maturational states (from naïve to TEMRA cells) and the identification of a donor-specific subset of terminally differentiated T-cells that would have been otherwise overlooked using canonical cell classification schema. As expected, T-cell activation induced downregulation of naïve-associated markers and upregulation of effector molecules, proliferation regulators, co-inhibitory and co-stimulatory receptors. Our deep kinetic analysis further revealed clusters of proteins and genes identifying unique states of activation defined by markers temporarily expressed upon 3 days of stimulation (PD-1, CD69, LTA) , markers constitutively expressed throughout chronic activation (CD25, GITR, LGALS1 ), and markers uniquely up-regulated upon 14 days of stimulation (CD39, ENTPD1, TNFDF10 ). Notably, different ratios of cells expressing activation or exhaustion markers were measured at each time point. These data indicate high heterogeneity and plasticity of chronically stimulated T cells in response to different kinetics of activation. In this study, we demonstrate the power of a single-cell multiomic approach to comprehensively characterize T cells and to precisely monitor changes in differentiation, activation and exhaustion signatures in response to different activation protocols.
Hereditary malignant melanoma is not linked to the hla complex on chromosome 6 (1985)

Detailed HLA typing was performed in 11 families with hereditary cutaneous malignant melanoma (CMM) and dysplastic nevi to determine if the melanoma susceptibility locus was genetically linked to the major histocompatibility complex. Previously published data from 19 other families were re-analyzed in the same manner. When data from all 30 families were pooled and CMM was defined as the disease trait, the hypothesis of linkage was rejected for all values of recombination (theta) less than 40%. Data on family members' status regarding dysplastic nevi (DN), a well-characterized precursor of hereditary CMM, were available for our 11 families and 7 previously-reported families. Linkage analysis between the combined CMM/DN trait and HLA provided strong evidence against this hypothesis. Significant heterogeneity was observed when various sub-groups of families were compared; these data suggested that preferential reporting of positive linkage findings and misclassification of study subjects' CMM susceptibility status may have contributed to previous beliefs that the hereditary melanoma gene was linked to HLA. When our data are combined with previously-published information, we conclude that there is strong evidence against linkage of a CMM/DN gene with the major histocompatibility complex.
Primary Care: delivering the future? (1997)

Primary Care: Delivering the Future, published in December 1996, was the latest in the recent avalanche of White Papers addressing the need to place more emphasis and resources within the community health arena. Sceptics in the profession may suggest, with some justice, that the timing appears to coincide quite neatly with mounting pre-election fever. However, whilst this may be a factor in the timing, the content should not be overlooked for the positive steps it is proposing.
Strength Pareto Evolutionary algorithm for sizing a set of SiC converter connected to AC machines winding by short planar cable (2015)

This paper deals with a set of ultra fast converter connected to the winding of AC machine by a short planar cable. The main feature of this study is to design a set of bus bar, a planar cable to mitigate surges produced at each switching commutation of the SiC Transistor, without consequently modifying its rise time. This calculation is obtained by the principle of genetic algorithm based on Strength Pareto Evolutionary Algorithm (SPEA), with as extra constraint a limited volume of the overall size of the system. Simulations analysis and experimental tests are carried out and compared, they underline the main benefits of the developed method.
The future of NMR-based metabolomics (2016)

The two leading analytical approaches to metabolomics are mass spectrometry (MS) and nuclear magnetic resonance (NMR) spectroscopy. Although currently overshadowed by MS in terms of numbers of compounds resolved, NMR spectroscopy offers advantages both on its own and coupled with MS. NMR data are highly reproducible and quantitative over a wide dynamic range and are unmatched for determining structures of unknowns. NMR is adept at tracing metabolic pathways and fluxes using isotope labels. Moreover, NMR is non-destructive and can be utilized in vivo. NMR results have a proven track record of translating in vitro findings to in vivo clinical applications.
Boosting Search Engines with Interactive Agents (2021)

This paper presents first successful steps in designing search agents that learn meta-strategies for iterative query refinement in information-seeking tasks. Our approach uses machine reading to guide the selection of refinement terms from aggregated search results. Agents are then empowered with simple but effective search operators to exert fine-grained and transparent control over queries and search results. We develop a novel way of generating synthetic search sessions, which leverages the power of transformer-based language models through (self-)supervised learning. We also present a reinforcement learning agent with dynamically constrained actions that learns interactive search strategies from scratch. Our search agents obtain retrieval and answer quality performance comparable to recent neural methods, using only a traditional term-based BM25 ranking function and interpretable discrete reranking and filtering actions.
Extensive Analyses of Superconducting Cables 3D Geometry With Advanced Tomographic Examinations (2021)

In the framework of activities embedding magnet design and associated R&D activities and relying on Cable in Conduit Conductors (CICC) technology, the singularity of the concept can rise some challenges versus their modelling in operation. Indeed, CICC includes thousands of superconducting strands, twisted together under a multi-staged scheme that also includes deformation by cabling and compaction during manufacture. This causes the accurate predictability of strands position in CICC extremely difficult, while it can be a key element for modelling their performances in operation. As a matter of fact the coupling losses rely on the CICC capability to establish inter-strand shielding currents, driven by the inter-strand contacts mapping which are only accessible in prediction via accurate 3D strand trajectories geometry. Same applies for prediction of CICC mechanical properties (deformation of Nb3Sn strands) and hydraulic properties (helium coolant force-flowed between the strands), making those investigations of high added-value. In this context, INFLPR installed a new set-up dedicated to micro-tomography to examine CICCs with high resolution, and get an overall overall 3D overview regarding picture of the strands location. CEA and INFLPR further developed a post-processing method to reconstruct the strands trajectories with high accuracy. The measurement and data analysis workflow was applied to two CEA middle-size CICCs with variable void fraction from which contact statistics were issued. The obtained database was exploited to reconstruct equivalent 3D resistive network. Above applications using CICC topology database are discussed, compared to experimental AC losses database issued by CEA and interpreted considering the CEA model COLISEUM. The outcomes are discussed and subsequent guidelines for future work presented.
Implementation of the Prometheus Taxonomic Model: a comparison of database models and query languages and an introduction to the Prometheus ObjectOriented Model (2002)

Abstract Types of databases commonly used for handling taxonomic data are compared. It is shown that none of the existing types of databases fully support the requirements of taxonomic data. The results of this comparison provide a rationale for the design and implementation of a new database system based on an Extended Object­Oriented model. The new model, the Prometheus Object­Oriented Model (POOM) and its query language Prometheus Object­Oriented Language (POOL) , are discussed in relation to the requirements of taxonomic data and the Prometheus Taxonomic Data Model. POOM provides the ability to represent the semantics of relationships between data. This allows us to build the type of graph structures that are found in taxonomic hierarchies. In addition, the system can query and manipulate these graphs ( POOL ). These features have been used to improve the original Prometheus Taxonomic Data Model . These improvements and the advantages they offer are described and discussed.
SARS coronavirus: a new challenge for prevention and therapy (2003)

A new and deadly clinical syndrome now called severe acute respiratory syndrome (SARS) was brought to the attention of the WHO by Dr. Carlo Urbani and his colleagues in a Vietnamese hospital in February 2003 (1). The WHO, the medical staffs in hospitals where the disease had appeared, and local and regional governments, together with a dozen cooperating laboratories across the globe, immediately responded. They provided a provisional case definition to identify the extent and geographic distribution of the outbreak (2), laboratory investigations to identify the infectious agent, and travel advisories and quarantines to limit the spread of the disease (3, 4). This extraordinary and effective collaboration limited the potentially explosive spread of the outbreak, while initial case reports with clinical and epidemiological information were quickly posted on the Internet to help physicians identify additional cases of the new syndrome (2, 4–9). The press and scientific journals played valuable roles in rapidly distributing accurate information about SARS to the frightened public and making key scientific publications about SARS available via the Internet before they could appear in print. A stroke of good fortune in this crisis was the discovery that a novel virus could be readily isolated from patients’ lungs and sputum and cultivated in a monkey kidney cell line (8, 10, 11). Laboratory investigations using electron microscopy, virus-discovery microarrays containing conserved nucleotide sequences characteristic of many virus families, randomly primed RT-PCR, and serological tests quickly identified the virus as a new coronavirus (8, 10, 11). Inoculation of monkeys with the SARS-associated coronavirus (SARS-CoV) caused interstitial pneumonia resembling SARS, and the virus was isolated from the nose and throat (12). No viral or bacterial copathogen was needed to induce the disease. These experiments fulfilled Koch’s postulates and proved that SARS-CoV is the cause of SARS.
Synthesis of 4,5-Dianilinophthalimide and Related Analogues for Potential Treatment of Alzheimer's Disease via Palladium-Catalyzed Amination (2005)

DAPH (4,5-dianilinophthalimide) has previously been shown to reverse the formation of neurotoxic fibrils associated with Alzheimer's disease. We have developed a synthetic route to DAPH and structurally related analogues that employs palladium-catalyzed amination as the key bond-forming step. The requisite substrates are easily obtained, and their coupling with substituted anilines proceeds in generally high yields. Thus, a variety of DAPH analogues can be quickly accessed in a modular fashion. In addition, the route described herein should also be amenable to the incorporation of other classes of nucleophiles into the molecular framework.
Ceramic transactions: Bioceramics - materials and applications II. Volume 63 (1996)

Several secondary structures, such as π-helix and left-handed helix, have been frequently identified at protein ligand-binding sites. A secondary structure is considered to be constrained to a specific region of dihedral angles. However, a comprehensive analysis of the correlation between main chain dihedral angles and ligand-binding sites has not been performed. We undertook an extensive analysis of the relationship between dihedral angles in proteins and their distance to ligand-binding sites, frequency of occurrence, molecular potential energy, amino acid composition, van der Waals contacts, and hydrogen bonds with ligands. The results showed that the values of dihedral angles have a strong preference for ligand-binding sites at certain regions in the Ramachandran plot. We discovered that amino acids preceding the ligand-prefer ϕ/ψ box residues are exposed more to solvents, whereas amino acids following ligand-prefer ϕ/ψ box residues form more hydrogen bonds and van der Waals contacts with ligands. Our method exhibited a similar performance compared with the program Ligsite-csc for both ligand-bound structures and ligand-free structures when just one ligand-binding site was predicted. These results should be useful for the prediction of protein ligand-binding sites and for analysing the relationship between structure and function.
Effects of controlling the interface trap densities in InGaZnO thin-film transistors on their threshold voltage shifts (2014)

In this paper, the threshold voltage stability characteristics of indium-gallium-zinc-oxide (IGZO) thin-film transistors (TFT) are discussed. The IGZO TFTs were found to induce a parallel threshold voltage (V th ) shift with changing field effect mobility (μ FE ) or a sub-threshold gate voltage swing (SS) due to various thermal annealing conditions. The IGZO TFT that was post-annealed in an O2 ambient was found to be more stable for use in oxide-based TFT devices and to have better performance characteristics, such as the on/off current ratio (I on/off ), SS, and V th , than other TFTs did. The mechanism for improving the V th stability in the post-annealed IGZO TFT is a decrease in the number of trap sites for the electrons and the weak oxygen bonding in the IGZO thin films. The device’s performance could be significantly affected by adjusting the annealing conditions. This mechanism is closely related to that of modulation annealing, where the number of localized trapped carriers and defect centers at the interface or in the channel layer are reduced.
Accordable repetition rate hybrid-type mode-locked fiber laser (2011)

We have observed and demonstrated the linear and non linear parameters dependent optimum power and repetition rates of a hybrid - type actively and passively mode locked laser pulses in an erbium doped fiber laser of the figure of eight geometry by using a nonlinear amplifying loop mirror (NALM) totally made up of microstructured optical fiber MOF as a saturable absorber and a nonlinear optical loop (NOL) incorporating an electro-optic modulator as an active mode locker. An accordable repetition rate fiber laser was obtained. The repetition rate and power of generated pulses depend on the NALM gain and the electro-optic modulator.
Synthesis and in Vitro Multidrug Resistance Modulating Activity of a Series of Dihydrobenzopyrans and Tetrahydroquinolines (1999)

A series of dihydrobenzopyrans and tetrahydroquinolines was synthesized and pharmacologically tested for their ability to inhibit P-glycoprotein mediated daunomycin efflux in multidrug resistant CCRF-CEM vcr1000 cells. Several compounds exhibit activities in the range of the reference compounds verapamil and propafenone. Preliminary structure-activity relationship studies propose the importance of high molar refractivity values of the compounds and the presence of an additional basic nitrogen atom.
Classification of SOx Scrubber for Ships (2011)

Wärtsilä is one of the biggest ship propulsion solution producers in the world. New IMO regulations concerning air emissions have tighten also the limits for sulphur emissions. For this reason Wärtsilä has begun to manufacture SOX Scrub-bers, which can be installed both new build vessels and retro-fitted in existing vessel regardless of engine brand.&#13;\n&#13;\nClassifications are procedures, where classification society ensures compliance of the ship and its main components with class rules and grants certifications based on fulfilled standards. There are several marine classification societies. The pur-pose of this work is to present tests to be done and analyse classification regula-tions especially for Germanischer Lloyd, involved with installation of SOx scrubber. The empirical part of this work includes analysis of first commercial installa-tion of SOX Scrubber in Containership VII.&#13;\n&#13;\nThe results of this study will be applied in future SOX scrubber installation projects.