gebhart/patrepeval huggingface dataset:
Multi-Structural Games and Number of Quantifiers (2025)

We study multi-structural games, played on two sets $\mathcal{A}$ and $\mathcal{B}$ of structures. These games generalize Ehrenfeucht-Fra\&amp;quot;{i}ss\'{e} games. Whereas Ehrenfeucht-Fra\&amp;quot;{i}ss\'{e} games capture the quantifier rank of a first-order sentence, multi-structural games capture the number of quantifiers, in the sense that Spoiler wins the $r$-round game if and only if there is a first-order sentence $\phi$ with at most $r$ quantifiers, where every structure in $\mathcal{A}$ satisfies $\phi$ and no structure in $\mathcal{B}$ satisfies $\phi$. We use these games to give a complete characterization of the number of quantifiers required to distinguish linear orders of different sizes, and develop machinery for analyzing structures beyond linear orders.
The C-terminal region of α-crystallin: involvement in protection against heat-induced denaturation (1993)

Recent studies have demonstrated that the alpha-crystallins can protect other proteins against heat-induced denaturation and aggregation. To determine the possible involvement of the C-terminal region in this activity, the alpha-crystallins were subjected to limited tryptic digestion, and the amount of cleavage from the N-terminal and C-terminal regions of the alpha-A and alpha-B crystallin chains was assessed using antisera specific for these regions. Limited tryptic digestion resulted in cleavage only from the C-terminal region of alpha-A crystallin. This trypsin-treated alpha-A crystallin preparation showed a decreased ability to protect proteins from heat-induced aggregation using an in vitro assay. Together, these results demonstrate that the C-terminal region of alpha-A crystallin is important for its ability to protect against heat-induced aggregation, which is consistent with the hypothesis that post-translational changes that are known to occur at the C-terminal region may have significant effects on the ability of alpha-A crystallin to protect against protein denaturation in vivo.
Assessing the role of alkane hydroxylase genotypes in environmental samples by competitive PCR (2005)

The study illustrates the distribution of two different alkB genotypes in two types of ecosystems, and highlights their respective roles in the environment.
Adiabatic Resonant Microrings (ARMs) with Directly Integrated Thermal Microphotonics (2009)

A new class of microphotonic-resonators, Adiabatic Resonant Microrings (ARMs), is introduced. The ARM resonator geometry enables heater elements to be formed within the resonator, simultaneously enabling record low-power (4.4μW/GHz) and record high-speed (1μs) thermal tuning.
Detailed seismic lithofluid distribution using Bayesian stochastic inversion for a thinly bedded reservoir: A case study over Huntington UK Central North Sea (2017)

A geostatistical inversion scheme was designed and performed for reservoir characterization of the UK Central North Sea (CNS) Huntington Oil field, with the goal of increasing the resolution of the seismic inversion and derived attributes, and to provide statistical measures of the uncertainties involved in the seismic facies prediction. The aim of the study was to fully understand lithology and pore-fluid rock properties in the Forties sandstone reservoir, Late Paleocene Sele Formation fan system of the UK CNS. In the Forties, multiple sand beds are separated by thin layers of silt and shale. Reprocessed prestack seismic volumes and considerable well-log data were input to an advanced stochastic simultaneous inversion method. This method combines the strengths of geostatistical inversion with sequential Gaussian simulation and Bayesian inversion. The approach allowed the inversion to be built on a fine-scale stratigraphic grid at a reservoir scale rather than at a seismic scale, and it enabled a detailed description of facies distribution and associated uncertainty. A sufficiently large number of stochastic solutions (100 realizations) enabled probabilistic models of lithofluid distribution to be generated. Facies geobody connectivity can also be derived, but this was not part of this work. As a consequence of our study, a sidetrack water injector well location was evaluated, and a potential undrilled hydrocarbon accumulation was identified, which could extend the field life of the Huntington asset.
Compositions, devices and methods for SERS and LSPR (2023)

The present invention relates to compositions, devices and methods for detecting microorganisms (e.g., anthrax). In particular, the present invention provides portable, surface-enhanced Raman biosensors, and associated substrates, and methods of using the same, for use in rapidly detecting and identifying microorganisms (e.g., anthrax).
Structural changes at the myrtenol backbone reverse its positive allosteric potential into inhibitory GABA A receptor modulation (2018)

GABAA receptors are ligand-gated anion channels that form pentameric arrangements of various subunits. Positive allosteric modulators of GABAA receptors have been reported as being isolated either from plants or synthesized analogs of known GABAA receptor targeting drugs. Recently, we identified monoterpenes, e.g. myrtenol as a positive allosteric modulator at α1β2 GABAA receptors. Here, along with pharmacophore-based virtual screening studies, we demonstrate that scaffold modifications of myrtenol resulted in the loss of modulatory activity. Two independent approaches, fluorescence-based compound analysis and electrophysiological recordings in whole-cell configurations were used for analysis of transfected cells. C-atoms 1 and 2 of the myrtenol backbone were identified as crucial to preserve positive allosteric potential. A modification at C-atom 2 and lack of the hydroxyl group at C-atom 1 exhibited significantly reduced GABAergic currents at α1β2, α1β2γ, α2β3, α2β3γ and α4β3δ receptors. This effect was independent of the γ2 subunit. A sub-screen with side chain length and volume differences at the C-atom 1 identified two compounds that inhibited GABAergic responses but without receptor subtype specificity. Our combined approach of pharmacophore-based virtual screening and functional readouts reveals that side chain modifications of the bridged six-membered ring structure of myrtenol are crucial for its modulatory potential at GABAA receptors.
FEM Simulation Of Charging Effect During SEM Metrology (2018)

International audience
Identification, Selection and Immune Assessment of Liver Stage CD8 T Cell Epitopes From Plasmodium falciparum (2021)

Immunization with radiation-attenuated sporozoites (RAS) has been shown to protect against malaria infection, primarily through CD8 T cell responses, but protection is limited based on parasite strain. Therefore, while CD8 T cells are an ideal effector population target for liver stage malaria vaccine development strategies, such strategies must incorporate conserved epitopes that cover a large range of class I human leukocyte antigen (HLA) supertypes to elicit cross-strain immunity across the target population. This approach requires identifying and characterizing a wide range of CD8 T cell epitopes for incorporation into a vaccine such that coverage across a large range of class I HLA alleles is attained. Accordingly, we devised an experimental framework to identify CD8 T cell epitopes from novel and minimally characterized antigens found at the pre-erythrocytic stage of parasite development. Through in silico analysis we selected conserved <i>P. falciparum</i> proteins, using <i>P. vivax</i> orthologues to establish stringent conservation parameters, predicted to have a high number of T cell epitopes across a set of six class I HLA alleles representative of major supertypes. Using the decision framework, five proteins were selected based on the density and number of predicted epitopes. Selected epitopes were synthesized as peptides and evaluated for binding to the class I HLA alleles <i>in vitro</i> to verify in silico binding predictions, and subsequently for stimulation of human T cells using the Modular IMmune In-vitro Construct (MIMIC<sup>®</sup>) technology to verify immunogenicity. By combining the in silico tools with the <i>ex vivo</i> high throughput MIMIC platform, we identified 15 novel CD8 T cell epitopes capable of stimulating an immune response in alleles across the class I HLA panel. We recommend these epitopes should be evaluated in appropriate <i>in vivo</i> humanized immune system models to determine their protective efficacy for potential inclusion in future vaccines.
The erccdashboard: an R Package for Analysis of External Spike-in RNA Controls in Gene Expression Experiments (2014)

External RNA spike-in control ratio abundance mixtures enable assessment of technical performance of a gene expression experiment and comparison of performance between gene expression experiments. We've developed an R package, the “erccdashboard”, to analyze ratio abundance mixtures of the External RNA Control Consortium (ERCC) controls for the purpose of gene expression experiment method validation. For RNA-Seq, analysis of sequence reads with existing QC metrics provides an assessment of sequencing and mapped read quality, the analysis of ERCC control ratio mixtures is intended to provide QC metrics that are relevant for gene expression analysis methods including transcript quantification and differential expression testing. The erccdashboard package addresses this critical analysis need with QC metrics for gene expression experiments including dynamic range, biases and variability in ratio measurements, diagnostic performance (discrimination of true positive and true negative controls), and empirical determination of the limit of detection of ratios. Using the erccdashboard package quantitative differences between these ratio measurement performance metrics were shown for experiments within the same laboratory, between different laboratories, and for different gene expression measurement technologies (sequencing platforms and microarrays). The ERCC control ratio measurements also provide a quantification of biases that may be addressed with normalization approaches, such as differences in mRNA fraction of total RNA for a pair of gene expression experiment samples and batch effects. The erccdashboard R software package is freely available and may be adopted as part of the QC process for any gene expression measurement analysis pipeline.
Investigation on Weld Pool Dynamics in Laser Welding of AISI 304 Stainless Steel With an Interface Gap Via a Three-Dimensional Dynamic Model and Experiments (2017)

This paper reports on numerical and experimental investigations involving examination of the effects of an interfacial gap in the range of 0–0.3 mm on keyhole and molten pool dynamics. A numerical model was developed to investigate the three-dimensional transient dynamics of the keyhole in lap welding processes with an interface gap. The model was able to reliably predict the weld profile. In addition, the modeling results provided detailed information regarding the interaction between the molten pool and the solid/liquid boundary that led to the extended weld width. Experimentally, AISI 304 stainless steel was joined in a lap welding configuration using an IPG YLR-1000 fiber laser. The tensile shear and T-peel testing of the lap joints showed that adding an adequate amount of interface gap improves weld strength.
Analysis of video content using statistical spatio-temporal models (2005)

In this thesis we develop statistical spatio-temporal modeling framework for the automatic understanding and structuring of the content of videos. The framework is applied to echocardiogram videos, which are one of the widely used modalities of diagnostic imaging. A digital library of the structured echocardiogram videos is created. The contents of the structured echocardiogram videos are summarized and augmented by contextual information. The innovative claims of this research are the following: (1) Developed an approach for multi-class object recognition under ambiguity resulting from model and data distortion factors. The novelty of the approach is the fact that it uses the collection of the generative models of the different object classes to project objects into an anchor space, which essentially fuses the assessments of the object by all models. Discriminative methods are then used to classify the object in the anchor space. The approach is shown to be effective in disambiguating the confusion in object classification. (2) A novel framework for modeling the multi-phase activity pattern of objects represented by the collection of their parts is proposed. In this framework the idea of pictorial structure, which is a method for modeling the appearance of the individual parts and their spatial relationships to the other parts in the representation of the object, is extended to the time domain. Inferencing and learning methods are provided for the model. The proposed framework is shown to be effective in the experiments. (3) A framework for categorizing different activity patterns of an object is proposed. The novelty of the approach is that only a statistical spatio-temporal model for the normal activity of the object is learned from training exemplars and all other forms of the activity of the object are assessed with respect to this model. Fisher score mapping is employed to obtain the assessments of each activity pattern with respect to the model of the normal activity. The work presented in this thesis is the first work on automatic understanding and structuring of the content of the echocardiogram videos.
ChemInform Abstract: Diastereoselective Synthesis of the Key Lactone Intermediate (VI) for the Preparation of Hydroxyethylene Dipeptide Isosteres. (1994)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Simulation of Aircraft Wake Vortex Using Pressure-Based Unified Numerical Approach for Incompressible and Compressible Flows (2004)

A wake vortex simulation using CFD methodology based on a new pressure-based unified approach is presented. A numerical method is developed to attain calculation for both in incompressible and compressible flows regime with a low numerical diffusive property and for high prediction accuracy of pressure gradient. This scheme is constructed by splitting the full Navier-Stokes equation into an advection role by velocity and a propagation role by acoustic wave. In the advection phase, concept of the advective upwind splitting method (AUSM) is adapted to non-conservative advection equations. For the acoustic phase, SMAC-like Poisson's equation is derived to reduce a numerical error. Newly developed scheme shows good agreement except strong shock capturing capability for validation problems including incompressible, compressible and vortical flow calculations. Finally, wake vortex simulation for NACA0012 rectangular wing is investigated. The computation results show availability of new approach for wake vortex flow predictions.
Abstract CN01-02: Glycoproteomic discovery of liver cancer biomarkers: Be careful how you use it! (2011)

Abstract This presentation will describe the discovery and use of the new serum biomarkers of HCC, called GP73 and its fucosylated glycoforms, identified, in part, by comparative glycoproteomics. We will also provide an explanation as to why fucosylated glycoforms are elevated in people with HCC. There are now more than 25 publications reporting that these markers are elevated in the serum of people with HCC, but there are also several papers suggesting they are no better in distinguishing between people with HCC and liver cirrhosis than are other markers such as AFP. We will also provide a theory, supported with data, as to why these differences in observations have occurred. Briefly, the etiology of the HCC, the specific linkage of the glycoform on the putative cancer biomarker as well as the ability of the cancer cells to re-fucosylate the circulating biomarkers, all play roles in how the markers are sorted and the extent to which they can be used as risk and diagnostic markers of cancer. Failure to take these variables into consideration can result in their underperformance as biomarkers of disease. Citation Information: Cancer Prev Res 2011;4(10 Suppl):CN01-02.
Effect of Substituents on Molecular Geometry and Self-Aggregation in the Crystal Structures of Ethylenediamine-N,N,N‘,N‘-tetraamides (2007)

The derivatives of ethylenediamine-N,N,N‘,N‘-tetraamides were prepared, and their crystal structures were analyzed in order to understand the variations in their molecular and supramolecular geometries with respect to the substituents. The crystal structures of these compounds indicated that these moieties can exhibit four types of molecular geometries. These geometries contain a minimum of two intramolecular N−H···N hydrogen bonds between the amine N-atom and N−H group of the amide. The p-bromophenyl, p-chlorophenyl, 3-pyridyl, and 4-pyridyl derivatives exhibit H-shape geometry, p-iodophenyl, p-toloyl, and 4-pyridyl derivatives exhibit similar geometrical shape, the 4-pyridyl derivative exhibited the geometry of the Greek character π, and the benzyl derivative exhibited the geometry of a swastika. Among the halogen derivatives, the iodo derivative was found to behave differently from bromo and chloro derivatives. The amide-to-amide hydrogen bonds between the iodo-substituted molecules were sacrificed in favor of inclusion of DMF.
Allele-specific RNA interference prevents neuropathy in Charcot-Marie-Tooth disease type 2D mouse models (2019)

Gene therapy approaches are being deployed to treat recessive genetic disorders by restoring the expression of mutated genes. However, the feasibility of these approaches for dominantly inherited diseases - where treatment may require reduction in the expression of a toxic mutant protein resulting from a gain-of-function allele - is unclear. Here we show the efficacy of allele-specific RNAi as a potential therapy for Charcot-Marie-Tooth disease type 2D (CMT2D), caused by dominant mutations in glycyl-tRNA synthetase (GARS). A de novo mutation in GARS was identified in a patient with a severe peripheral neuropathy, and a mouse model precisely recreating the mutation was produced. These mice developed a neuropathy by 3-4 weeks of age, validating the pathogenicity of the mutation. RNAi sequences targeting mutant GARS mRNA, but not wild-type, were optimized and then packaged into AAV9 for in vivo delivery. This almost completely prevented the neuropathy in mice treated at birth. Delaying treatment until after disease onset showed modest benefit, though this effect decreased the longer treatment was delayed. These outcomes were reproduced in a second mouse model of CMT2D using a vector specifically targeting that allele. The effects were dose dependent, and persisted for at least 1 year. Our findings demonstrate the feasibility of AAV9-mediated allele-specific knockdown and provide proof of concept for gene therapy approaches for dominant neuromuscular diseases.
DIIM: a foundation for translating loosely-specified queries into executable plans in large-scale information systems (2002)

Challenging issues for processing queries specified over large-scale information spaces (e.g. digital libraries or the World Wide Web) include the diversity of the information sources (ISs) in terms of their structures, query interfaces, as well as the dynamics of ISs continuously being added, removed or upgraded. Typically user queries are loosely specified expressing what the user wants but not how and from where the information is to be retrieved. In this paper we give an innovative solution for semantical query planning in such environments. The key idea underlying our solution is the notion of connected query rules defined to be precisely specified, executable queries that are semantically equivalent to a user query. For query planning in such a large-scale space, we introduce DIIM-the Dynamic Information Integration Model which supports the description of not only content but also capabilities of ISs, e.g., query templates of and interrelationships between ISs. This then lays the foundation for the translation algorithm that based on the connected query rule principle maps a loosely-specified query into the set of semantically equivalent queries.
LARAC-SN and Mole in the Hole: Enabling Routing through Service Function Chains (2018)

With the emergence of Software-Defined Networking (SDN) and Network Function Virtualization (NFV), the problem of centralized routing through intermediate specified nodes (for which several candidates can be defined) has become an important issue. Indeed, an SDN controller routing flows through Service Function Chains (SFCs) has to efficiently solve this problem to achieve the online provisioning of routing requests and the online placement of Virtual Network Functions (VNFs). In this paper, we propose two algorithms for solving this problem. First, we propose LARAC for specified nodes (LARAC-SN), a fast and close to optimal algorithm for finding the constrained shortest path (CSP) visiting an ordered set of specified nodes. Second, we propose Mole in the Hole (MITH), a graph transformation algorithm which can force any state-of-the-art routing algorithm to visit an ordered set of specified nodes. While LARAC-SN is bounded to the specific CSP problem and can only handle one candidate per specified node, MITH can be used for any routing problem and can deal with several candidates per specified node. Through evaluations, we show that LARAC-SN is fast and close to optimal (its optimality gap stays lower than 1.62% in average) and that MITH has the potential of reaching optimality for any problem, but at the cost of a higher runtime.
Polar Correction: new overlay control method for higher-order intra-field error dependent on the wafer coordinates (2009)

A new overlay control method called "Polar Correction" has been developed. In the 3x nm half-pitch generation and beyond, even in the case of using a high-end optical exposure system such as immersion lithography with NA 1.3 over, the overlay accuracy becomes the most critical issue, and the accuracy below 10nm is indispensable [1]. In view of the severe overlay accuracy required, the shot-to-shot intra-field overlay control cannot be disregarded in this generation. In particular, the shot-to-shot intra-field overlay error caused by the influence of evaporation heat has been added in the immersion exposure system. However, it is impossible to correct the shot-to-shot intra-field overlay error by the conventional overlay control method. Therefore, we have developed the new overlay control method called Polar Correction for higher-order intra-field error dependent on the wafer coordinates. In this paper, we explain our new overlay control method for higher-order intra-field error, and show the simulation data and the experimental data. We believe that Polar Correction corresponds to the generation below 10nm overlay accuracy.