gebhart/patrepeval huggingface dataset:
Walk-Assist Robot: A Novel Approach to Gain Selection of a Braking Controller Using Differential Flatness (2013)

With increasing populations of the elderly in our society, robot technology will play an important role in providing functional mobility to humans. From the perspective of human safety, it is desirable that controllers for walk-assist robots be dissipative, i.e., the energy is supplied from the human to the walker, while the controller modulates this energy. The simplest form of a dissipating controller is a brake, where resistive torques are applied to the wheels proportional to their speeds. The fundamental question that we ask in this brief is how to modulate these proportional gains over time for the two wheels so that the walker can perform point-to-point motions. The unique contribution of this brief is a novel way in which the theory of differential flatness is used to plan the trajectory of these braking gains. Since the user input forces are not known a priori , the trajectory of the braking gain is computed iteratively during the motion. Simulation and experimental results show that the walk-assist robot, along with the structure of this proposed control scheme, can guide the user to reach the goal.
A novel susceptibility locus in MST1 and gene‐gene interaction network for Crohn's disease in the Chinese population (2018)

The incidence of Crohn's disease is increasing in many Asian countries, but considerable differences in genetic susceptibility have been reported between Western and Asian populations. This study aimed to fine-map 23 previously reported Crohn's disease genes and identify their interactions in the Chinese population by Illumina-based targeted capture sequencing. Our results showed that the genetic polymorphism A>G at rs144982232 in MST1 showed the most significant association (P = 1.78 × 10<sup>-5</sup> ; odds ratio = 4.87). JAK2 rs1159782 (T>C) was also strongly associated with Crohn's disease (P = 2.34 × 10<sup>-4</sup> ; odds ratio = 3.72). Gene-gene interaction analysis revealed significant interactions between MST1 and other susceptibility genes, including NOD2, MUC19 and ATG16L1 in contributing to Crohn's disease risk. Main genetic associations and gene-gene interactions were verified using ImmunoChip data set. In conclusion, a novel susceptibility locus in MST1 was identified. Our analysis suggests that MST1 might interact with key susceptibility genes involved in autophagy and bacterial recognition. These findings provide insight into the genetic architecture of Crohn's disease in Chinese and may partially explain the disparity of genetic signals in Crohn's disease susceptibility across different ethnic populations by highlighting the contribution of gene-gene interactions.
On the radial component of the electric field for a monopole phased array antenna focused in the near zone (1992)

The near-zone radial and principal spherical components of the electric field for a linear phased array antenna that is focused at one to two aperture diameters in the near zone are investigated. The phased array antenna, consisting of thin monopole elements, is analyzed by using the method of moments. A theoretical formulation is described and computer simulation results are presented. The results show that the radial component is negligible in the focused near-field region, which allows the principal component to be accurately computed from knowledge of only the tangential electric field on the focal plane. near-field focusing, method of moments, antenna testing. radial electric field component, focal plane, monopole phased array, near-field radiation pattern.
Dynamic modelling of a short-stop fixed bed reactor for the gas phase polymerisation of olefins (2012)

International audience
LGLC Tunable Laser for Small-Form-Factor Transceiver: High Optical Power and High SMSR With Low Power Consumption (2013)

A lateral-grating-assisted lateral co-directional coupler (LGLC) type tunable laser with high optical power and low power consumption is proposed. An approach to reduce the injection current in the gain section, by means of a new laser design, provide the power consumption of the LGLC laser from 0.25 to 0.13 W. The LGLC tunable laser with new design achieved good laser characteristics, and side-mode suppression ratio of over 40-dB in the 45-nm wavelength range.
Integrated clinical and omics approach to rare diseases: novel genes and oligogenic inheritance in holoprosencephaly (2018)

Holoprosencephaly is a pathology of forebrain development characterized by high phenotypic heterogeneity. The disease presents with various clinical manifestations at the cerebral or facial levels. Several genes have been implicated in holoprosencephaly but its genetic basis remains unclear: different transmission patterns have been described including autosomal dominant, recessive and digenic inheritance. Conventional molecular testing approaches result in a very low diagnostic yield and most cases remain unsolved. In our study, we address the possibility that genetically unsolved cases of holoprosencephaly present an oligogenic origin and result from combined inherited mutations in several genes. Twenty-six unrelated families, for whom no genetic cause of holoprosencephaly could be identified in clinical settings [whole exome sequencing and comparative genomic hybridization (CGH)-array analyses], were reanalysed under the hypothesis of oligogenic inheritance. Standard variant analysis was improved with a gene prioritization strategy based on clinical ontologies and gene co-expression networks. Clinical phenotyping and exploration of cross-species similarities were further performed on a family-by-family basis. Statistical validation was performed on 248 ancestrally similar control trios provided by the Genome of the Netherlands project and on 574 ancestrally matched controls provided by the French Exome Project. Variants of clinical interest were identified in 180 genes significantly associated with key pathways of forebrain development including sonic hedgehog (SHH) and primary cilia. Oligogenic events were observed in 10 families and involved both known and novel holoprosencephaly genes including recurrently mutated FAT1, NDST1, COL2A1 and SCUBE2. The incidence of oligogenic combinations was significantly higher in holoprosencephaly patients compared to two control populations (P < 10-9). We also show that depending on the affected genes, patients present with particular clinical features. This study reports novel disease genes and supports oligogenicity as clinically relevant model in holoprosencephaly. It also highlights key roles of SHH signalling and primary cilia in forebrain development. We hypothesize that distinction between different clinical manifestations of holoprosencephaly lies in the degree of overall functional impact on SHH signalling. Finally, we underline that integrating clinical phenotyping in genetic studies is a powerful tool to specify the clinical relevance of certain mutations.
Exact Analysis of Intrinsic Qualitative Features of Phosphorelays using\n Mathematical Models (2011)

Phosphorelays are a class of signaling mechanisms used by cells to respond to\nchanges in their environment. Phosphorelays (of which two-component systems\nconstitute a special case) are particularly abundant in prokaryotes and have\nbeen shown to be involved in many fundamental processes such as stress\nresponse, osmotic regulation, virulence, and chemotaxis. We develop a general\nmodel of phosphorelays extending existing models of phosphorelays and\ntwo-component systems. We analyze the model analytically under the assumption\nof mass-action kinetics and prove that a phosphorelay has a unique stable\nsteady-state. Furthermore, we derive explicit functions relating stimulus to\nthe response in any layer of a phosphorelay and show that a limited degree of\nultrasensitivity (the ability to respond to changes in stimulus in a\nswitch-like manner) in the bottom layer of a phosphorelay is an intrinsic\nfeature which does not depend on any reaction rates or substrate amounts. On\nthe other hand, we show how adjusting reaction rates and substrate amounts may\nlead to higher degrees of ultrasensitivity in intermediate layers. The explicit\nformulas also enable us to prove how the response changes with alterations in\nstimulus, kinetic parameters, and substrate amounts. Aside from providing\nbiological insight, the formulas may also be used to avoid time-consuming\nsimulations in numerical analyses and simulations.\n
Distance-Correlation based Gene Set Analysis in Longitudinal Studies (2016)

Longitudinal gene expression profiles of patients are collected in some clinical studies to monitor disease progression and understand disease etiology. The identification of gene sets that have coordinated changes with relevant clinical outcomes over time from these data could provide significant insights into the molecular basis of disease progression and hence may lead to better treatments. In this article, we propose a Distance-Correlation based Gene Set Analysis (dcGSA) method for longitudinal gene expression data. dcGSA is a non-parametric approach, statistically robust, and can capture both linear and nonlinear relationships between gene sets and clinical outcomes. In addition, dcGSA is able to identify related gene sets in cases where the effects of gene sets on clinical outcomes differ across patients due to the patient heterogeneity, alleviate the confounding effects of some unobserved covariates, and allow the assessment of associations between gene sets and multiple related outcomes simultaneously. Through extensive simulation studies, we demonstrate that dcGSA is more powerful of detecting relevant genes than other commonly used gene set analysis methods. When dcGSA is applied to multiple real datasets of different characteristics, we are able to identify more disease related gene sets than other methods.
Synthesis and UV−Visible-Light Photoactivity of Noble-Metal−SrTiO3 Composites (2006)

The photocatalytic activity of strontium titanate (SrTiO3) perovskite films has been examined and compared with that of commercially available titania (TiO2, Degussa P25) in the degradation of a model pollutant, Victoria Blue dye. The effects of pH, synthesis temperature, and Sr/Ti ratio in the synthesis of the perovskite were examined. SrTiO3 was prepared using Ag, Pt, or Au and characterized using optical and surface analysis methods. We found no clear evidence of substitution of the noble metal into the SrTiO3 lattice, and most metal existed as zerovalent metal deposits. Addition of Ag to SrTiO3 showed the most promising catalytic activity toward dye degradation. Degradation of the dye under UV−visible light was also observed to be enhanced only for Ag−SrTiO3.
Frontispiece: Interplay of Polarity and Confinement in Asymmetric Catalysis with Chiral Rh Diene Complexes in Microemulsions (2021)

The influence of anionic and cationic co-surfactants in nonionic microemulsions on the performance of chiral Rh-norbornadiene complexes with different counterions in the 1,2-addition of phenylboronic acids to N-tosylimines is described. Catalytic studies revealed the unique role of the counterion and the type of co-surfactant. NMR experiments and the calculated intrinsic binding orbitals suggest that the anion exchange with co-surfactant accelerates the formation of the catalytically active Rh-OH complex, thus increasing the yield and affecting the enantioselectivity. For more information, see the Full Paper by M. Kirchhof, K. Abitaev and co-workers on page 16853 ff.
Dynamic structure of motor cortical neuron coactivity carries behaviorally relevant information (2022)

Skillful, voluntary movements are underpinned by computations performed by networks of interconnected neurons in the primary motor cortex (M1). Computations are reflected by patterns of coactivity between neurons. Using pairwise spike time statistics, coactivity can be summarized as a <i>functional network</i> (<i>FN</i>). Here, we show that the structure of FNs constructed from an instructed-delay reach task in nonhuman primates is behaviorally specific: Low-dimensional embedding and graph alignment scores show that FNs constructed from closer target reach directions are also closer in network space. Using short intervals across a trial, we constructed <i>temporal FNs</i> and found that temporal FNs traverse a low-dimensional subspace in a reach-specific trajectory. Alignment scores show that FNs become separable and correspondingly decodable shortly after the <i>Instruction</i> cue. Finally, we observe that reciprocal connections in FNs transiently decrease following the <i>Instruction</i> cue, consistent with the hypothesis that information external to the recorded population temporarily alters the structure of the network at this moment.
A software project dynamics model for process cost, schedule and risk assessment (1994)

A dynamic model of an inspection-based software lifecycle process has been developed to support quantitative evaluation of the process. In conjunction with a knowledge-based method that has been developed for cost estimation and project risk assessment, these modeling techniques can support project planning and management, and aid in process improvement.
The model serves to examine the effects of inspection practices on cost, schedule and quality throughout the lifecycle. It uses system dynamics to model the interrelated flows of tasks, errors and personnel throughout different development phases and is calibrated to industrial data. It extends previous software project dynamics research by examining an inspection-based process with an original model, integrating it with the knowledge-based method for risk assessment and cost estimation, and using an alternative modeling platform.
While specific enough to investigate inspection practices, it is sufficiently general to incorporate changes for other phenomena. It demonstrates the effects of performing inspections, the effectiveness of varied inspection policies, and the effects of other managerial policies such as manpower allocation. The dynamic effects are tracked throughout the time history of a project to show resource usage, task completions and defect trends per phase. Cumulative metrics and development tradeoffs for decision making are also presented.
The knowledge-based method has been implemented on multiple platforms. As an extension to COCOMO, it aids in project planning by identifying, categorizing, quantifying and prioritizing project risks. It also detects cost estimate input anomalies and provides risk control advice in addition to conventional cost and schedule calculation. It extends previous work by focusing on risk assessment, incorporating substantially more rules, going beyond standard COCOMO, performing quantitative validation, and providing a user-friendly interface. The method is being used and enhanced in industrial environments as part of an integrated capability to assist in system acquisition, project planning and risk management.
Several types of validation tests are performed against industrial data, existing theory and other prediction models, and practitioners are used to evaluate the model. The results indicate a valid model that can be used for process evaluation and project planning, and serve as a framework for incorporating other dynamic process factors.
Coded modulation DPSK on fading channels (2003)

Coded modulation for differentially encoded PSK with non-coherent reception on flat fading channels is considered. We derive theoretical limits on the performance and show how to design multilevel coding schemes and bit-interleaved coded modulation. Since Gray labeling is not possible for multiple symbol differential detection and PSK constellations, bit-interleaved coded modulation exhibits severe degradation compared to the multilevel coding approach. By means of simulations, where turbo codes are used as component codes, the theoretical considerations are confirmed and we show how close theoretical limits of differentially encoded PSK transmission over flat fading channels can be approached by applying properly designed coded modulation schemes.
Correction: Epitope Mapping of Antibodies Suggests the Novel Membrane Topology of B-Cell Receptor Associated Protein 31 on the Cell Surface of Embryonic Stem Cells: The Novel Membrane Topology of BAP31 (2017)

[This corrects the article DOI: 10.1371/journal.pone.0130670.].
Hepatocyte growth factor is a coupling factor for osteoclasts and osteoblasts in vitro. (1996)

Hepatocyte growth factor (HGF), also known as scatter factor, is a powerful motogen, mitogen, and morphogen produced by cells of mesodermal origin, acting on epithelial and endothelial cells. Its receptor is the tyrosine kinase encoded by the c-MET protooncogene. We show that the HGF receptor is expressed by human primary osteoclasts, by osteoclast-like cell lines, and by osteoblasts. In both cell lineages, HGF stimulation triggers the receptor kinase activity and autophosphorylation. In osteoclasts, HGF receptor activation is followed by increase in intracellular Ca2+ concentration and by activation of the pp60c-Src kinase. HGF induces changes in osteoclast shape and stimulates chemotactic migration and DNA replication. Osteoblasts respond to HGF by entering the cell cycle, as indicated by stimulation of DNA synthesis. Interestingly, osteoclasts were found to synthesize and secrete biologically active HGF. These data strongly suggest the possibility of an autocrine regulation of the osteoclast by HGF and a paracrine regulation of the osteoblast by the HGF produced by the osteoclast.
Error Crrection for Read-hot Data in 3D-TLC NAND Flash by Read-disturb Modeled Artificial Neural Network Coupled LDPC ECC (2019)

Read-disturb Modeled Artificial Neural Network Coupled LDPC ECC (RDNN-LDPC) is proposed to correct errors of read-hot data for 3D-TLC NAND flash. Conventional ANN-LDPC is optimized to correct errors of read-cold data. However, ANN-LDPC does not correct errors of read-hot data. To correct errors of read-hot data, this paper analyzes how input parameter and model change. As a result, measured results of proposed RDNN-LDPC extend acceptable read cycle of 3D-TLC NAND flash by 10-times.
A Weighted Least-Squares Approach to Parameter Estimation Problems Based on Binary Measurements (2009)

We present a new approach to parameter estimation problems based on binary measurements, motivated by the need to add integrated low-cost self-test features to microfabricated devices. This approach is based on the use of original weighted least-squares criteria: as opposed to other existing methods, it requires no dithering signal and it does not rely on an approximation of the quantizer. In this technical note, we focus on a simple choice for the weights and establish some asymptotical properties of the corresponding criterion. To achieve this, the assumption that the quantizer's input is Gaussian and centered is made. In this context, we prove that the proposed criterion is locally convex and that it is possible to use a simple gradient descent to find a consistent estimate of the unknown system parameters, regardless of the presence of measurement noise at the quantizer's input.
Surface Interactome in Streptococcus pyogenes (2011)

Very few studies have so far been dedicated to the systematic analysis of protein interactions occurring between surface and/or secreted proteins in bacteria. Such interactions are expected to play pivotal biological roles that deserve investigation. Taking advantage of the availability of a detailed map of surface and secreted proteins in Streptococcus pyogenes (group A Streptococcus (GAS)), we used protein array technology to define the "surface interactome" in this important human pathogen. Eighty-three proteins were spotted on glass slides in high density format, and each of the spotted proteins was probed for its capacity to interact with any of the immobilized proteins. A total of 146 interactions were identified, 25 of which classified as "reciprocal," namely, interactions that occur irrespective of which of the two partners was immobilized on the chip or in solution. Several of these interactions were validated by surface plasmon resonance and supported by confocal microscopy analysis of whole bacterial cells. By this approach, a number of interesting interactions have been discovered, including those occurring between OppA, DppA, PrsA, and TlpA, proteins known to be involved in protein folding and transport. These proteins, all localizing at the septum, might be part, together with HtrA, of the recently described ExPortal complex of GAS. Furthermore, SpeI was found to strongly interact with the metal transporters AdcA and Lmb. Because SpeI strictly requires zinc to exert its function, this finding provides evidence on how this superantigen, a major player in GAS pathogenesis, can acquire the metal in the host environment, where it is largely sequestered by carrier proteins. We believe that the approach proposed herein can lead to a deeper knowledge of the mechanisms underlying bacterial invasion, colonization, and pathogenesis.
Development of Anilino-Maytansinoid ADCs that Efficiently Release Cytotoxic Metabolites in Cancer Cells and Induce High Levels of Bystander Killing (2015)

Antibody anilino maytansinoid conjugates (AaMCs) have been prepared in which a maytansinoid bearing an aniline group was linked through the aniline amine to a dipeptide, which in turn was covalently attached to a desired monoclonal antibody. Several such conjugates were prepared utilizing different dipeptides in the linkage including Gly-Gly, l-Val-l-Cit, and all four stereoisomers of the Ala-Ala dipeptide. The properties of AaMCs could be altered by the choice of dipeptide in the linker. Each of the AaMCs, except the AaMC bearing a d-Ala-d-Ala peptide linker, displayed more bystander killing in vitro than maytansinoid ADCs that utilize disulfide linkers. In mouse models, the anti-CanAg AaMC bearing a d-Ala-l-Ala dipeptide in the linker was shown to be more efficacious against heterogeneous HT-29 xenografts than maytansinoid ADCs that utilize disulfide linkers, while both types of the conjugates displayed similar tolerabilities.
Tagging chromatin with retrotransposons: target specificity of the Saccharomyces Ty5 retrotransposon changes with the chromosomal localization of Sir3p and Sir4p (1999)

Retrotransposon and retroviral insertions are not randomly distributed on chromosomes, suggesting that retroelements actively select integration sites. This is the case for the yeast Ty5 retrotransposons, which preferentially integrate into domains of silent chromatin at the HM loci and telomeres. Here we demonstrate that loss of Sir3p or Sir4p-components of silent chromatin-causes a greater than ninefold decrease in Ty5 targeting to the HM loci and largely randomizes chromosomal integration patterns. Strains with a deletion of SIR4 also display an approximately 10-fold increase in cDNA recombination, which is due both to the expression a- and alpha-mating-type information and the loss of Sir4p. It is known that in old yeast cells or in strains carrying the sir4-42 allele, the Sir complex relocalizes to the rDNA. About 26% of Ty5 insertions occur within the rDNA in sir4-42 strains compared with 3% in wild type. Ty5, therefore, is sensitive to changes in chromatin, indicating that retrotransposons may be useful for dissecting chromatin dynamics that occur during developmental programs such as aging.