gebhart/patrepeval huggingface dataset:
Interrelations entre les différents indices d'adiposité et le tissu adipeux viscéral à la suite d'un programme de modification des habitudes alimentaires et d'activité physique chez des hommes dyslipidémiques avec obésité abdominale (2012)

L'obésité est un fléau mondial. Il est démontré que le tissu adipeux abdominal viscéral (TAV) est plus néfaste à la santé que l'accumulation de tissu adipeux abdominal sous-cutané (TASC). Les recherches étudiant la réponse des différents compartiments adipeux à la suite d'une modification des habitudes de vie chez l'homme sédentaire sont presque inexistantes. Le présent ouvrage a pour objectif d'étudier les interrelations entre différents indices du tissu adipeux à la suite de l'amélioration des habitudes de vie pendant une année chez des hommes présentant une obésité abdominale. En réponse à l'intervention, contrairement à la mesure du tour de taille, la mesure des plis cutanés prédisait faiblement les variations dans la réponse du TAV ainsi que du TASC. Par conséquence, la pertinence clinique de la mesure des plis adipeux est donc remise en question. Notre étude ne suggère pas que le TASC profond et le TAV auraient le même comportement à la suite d'une perte de poids induite par un programme d'amélioration des habitudes de vie.
Examination of Energy and Group Velocities in Positive and Negative Index Chiral Materials With and Without Dispersion (2007)

Concepts of energy and group velocities, Poynting and propagation vectors are examined for both positive and negative index materials. Known definitions for these entities are explored in terms of the interplay of chirality and dispersion. It is shown that in isotropic materials, energy and group velocities are identical, and negative index may be realized via topological chirality and dispersion.
CMOS Conductometric System for Growth Monitoring and Sensing of Bacteria (2010)

We present the design and implementation of a prototype complementary metal-oxide semiconductor (CMOS) conductometric integrated circuit (IC) for colony growth monitoring and specific sensing of Escherichia coli (E. coli) bacteria. The detection of E. coli is done by employing T4 bacteriophages as receptor organisms. The conductometric system operates by measuring the resistance of the test sample between the electrodes of a two-electrode electrochemical system (reference electrode and working electrode). The CMOS IC is fabricated in a TSMC 0.35-μm process and uses a current-to-frequency (I to F) conversion circuit to convert the test sample resistance into a digital output modulated in frequency. Pulsewidth control (one-shot circuit) is implemented on-chip to control the pulsewidth of the output digital signal. The novelty in the current work lies in the ability of the CMOS sensor system to monitor very low initial concentrations of bacteria (4×10(2) to 4×10(4) colony forming unit (CFU)/mL). The CMOS system is also used to record the interaction between E. coli and its specific receptor T4 bacteriophage. The prototype CMOS IC consumes an average power of 1.85 mW with a 3.3-V dc power supply.
Nano-design of quantum dot-based photocatalysts for hydrogen generation using advanced surface molecular chemistry (2014)

Efficient photocatalytic hydrogen generation in a suspension system requires a sophisticated nano-device that combines a photon absorber with effective redox catalysts. This study demonstrates an innovative molecular linking strategy for fabricating photocatalytic materials that allow effective charge separation of excited carriers, followed by efficient hydrogen evolution. The method for the sequential replacement of ligands with appropriate molecules developed in this study tethers both quantum dots (QDs), as photosensitizers, and metal nanoparticles, as hydrogen evolution catalysts, to TiO2 surfaces in a controlled manner at the nano-level. Combining hydrophobic and hydrophilic interactions on the surface, CdSe-ZnS core-shell QDs and an Au-Pt alloy were attached to TiO2 without overlapping during the synthesis. The resultant nano-photocatalysts achieved substantially high-performance visible-light-driven photocatalysis for hydrogen evolution. All syntheses were conducted at room temperature and in ambient air, providing a promising route for fabricating visible-light-responsive photocatalysts.
AIMS (2002)

As individuals and organizations increasingly rely on services provided by complex computing systems for their everyday tasks, system dependability becomes a main concern. The dependability of a system is commonly defined as the property of it such that reliance can justifiably be placed on the service it delivers [1] and includes, as special cases, attributes such as reliability, availability, safety, and security. In addition, dependable systems must also be robust when facing the "messiness" of the real world, delivering correct service across a wide range of operational conditions and failing gracefully outside that range [15, 16].
Multivalent Antimicrobial Peptides from a Reactive Polymer Scaffold (2006)

We report an application of the principle of multivalency to create new antimicrobial agents using the reactive polymaleic anhydride (PMA) chain to link antimicrobial tetrapeptides to afford multivalent variants containing approximately 40 monomer units. Relative to the free peptides, the product shows a 10-fold improvement in IC(50) without provoking more severe hemolysis of red blood cells. Thus, multivalency or polyvalency may offer a route to enhance the activity of antimicrobial peptides.
Heparin-Induced Thrombocytopenia in Intensive Care Patients (2008)

Heparin-induced thrombocytopenia (HIT) is a serious, prothrombotic, immune-mediated complication of heparin therapy that can cause limb- and life-threatening thromboembolic events. Prompt diagnosis and therapeutic dose anticoagulation by an alternative anticoagulant are crucial to improve clinical outcome. In critically ill patients, the diagnosis of HIT is difficult due to the high incidence of thrombocytopenia, often caused by reasons other than HIT, and the high incidence of clinically irrelevant, non-platelet-activating anti-PF4-heparin antibodies. Also, treatment of HIT is problematic in these patients. No antidote is available for any of the alternative anticoagulants, and their half-lives are often prolonged in the presence of renal or hepatic insufficiency. This increases the risk of bleeding complications and mandates careful balancing of both risks, thrombosis and bleeding. Therefore, accurate diagnosis of HIT and individual choice of alternative anticoagulant are important for the adequate management of critically ill HIT patients.
Energy-based attack detection in networked control systems (2014)

The increased prevalence of attacks on Cyber-Physical Systems(CPS) as well as the safety-critical nature of these systems, has resulted in increased concerns regarding the security of CPS. In an effort towards the security of CPS, we consider the detection of attacks based on the fundamental notion of a system's energy. We propose a discrete-time Energy-Based Attack Detection mechanism for networked cyber-physical systems that are dissipative or passive in nature. We present analytical results to show that the detection mechanism is effective in detecting a class of attack models in networked control systems (NCS). Finally, using simulations we illustrate the effectiveness of the proposed approach in detecting attacks.
Transaction-level models for AMBA bus architecture using SystemC 2.0 (2005)

The concept of a SOC platform architecture introduces the concept of a communication infrastructure. In the transaction-level a finite set of architecture components (memories, arithmetic units, address generators, caches, etc) communicate among each other over shared resources (buses). Until recently, modeling architectures required pin-level hardware descriptions, typically coded in RTL. Great effort is required to design and verify the models, and simulation at this level of detail is tediously slow. Transaction level modeling is the solution. Transaction level models (TLMs) effectively create an executable platform model that simulates orders of magnitude faster than a RTL model. In this paper, we present a SystemC 2.0 TLM of the AMBA architecture developed by ARM, oriented to SOC platform architectures.
Identifying driver networks in cancer (2011)

Pathway analysis can be a critical step in evaluating cancer genomic data sets, and translating genomic data into biological and clinical insights. Several key aspects of pathway analysis in cancer genomics are explored, including two novel algorithmic frameworks for identifying frequently altered subnetworks in cancer, the application of pathway analysis to the Homologous Recombination (HR) pathway in the TCGA serous ovarian project, and the development of two open-access infrastructure tools for pathway analysis. Both algorithmic approaches analyze integrated genomic profiling data in the context of large interaction networks in order to identify subnetworks of frequently altered and highly connected genes. These subnetworks represent candidate driver networks which substantively contribute to tumorigenesis. Key elements in the approaches include the integrated analysis of sequence mutations and DNA copy number alterations, and the identification and statistical assessment of targeted network modules. 
Pathway analysis of the Homologous Recombination (HR) pathway in serous ovarian cancer identified several novel aspects of cancer biology, including mutual exclusivity between BRCA mutation events and BRCA1 epigenetic silencing events, and depletion of CCNE1 amplification events in BRCA altered cases. Both of these observations also provide new insight into the longterm survival of patients with BRCA1, BRCA2 and CCNE1 alterations. Additionally, extended pathway analysis identified potential HR genomic defects in 51% of cases, providing a rationale for genomic profiling of HR defects in clinical trials of PARP inhibitors. 
The two pathway infrastructure projects are open-access and now freely available to the scientific community. The first, Pathway Commons ( http://www,pathwaycommons.org), is an open-access resource for biological pathway data, which integrates data from nine public databases and contains over 1,400 pathways and 687,000 interactions. The second, the cBio Cancer Genomics Portal (http://cbioportal.org ), provides integrated visualization, download and analysis of all public TCGA data sets. These two tools make pathway and cancer genomic data sets and analysis tools more easily and readily available to the entire biomedical community, helping to translate cancer genomic data into biological insights and clinical applications.
Position control using off-line model predictive control in piecewise affine system experimental verification (2008)

This paper presents an experimental verification of off-line model predictive control for switched systems. The method is based on hybrid dynamical system theory. The system is modeled as a piecewise affine system so that an explicit solution can be obtained by means of a multi-parametric quadratic programming in which not only constraints but also tracking performance are incorporated explicitly, where the parameters are the components of the state vector. The multi-parametric quadratic programming is a promising method for implementation as the computational amount is less than that of conventional online model predictive control. To illustrate the effectiveness of the proposed method, some simulation and experimental results are shown.
Supplementary Figure 8 from Identification and Characterization of NVP-BKM120, an Orally Available Pan-Class I PI3-Kinase Inhibitor (2023)

&lt;p&gt;PDF file - 727K&lt;/p&gt;
Establishment and Validation of Computational Model for MT1-MMP Dependent ECM Degradation and Intervention Strategies (2012)

MT1-MMP is a potent invasion-promoting membrane protease employed by aggressive cancer cells. MT1-MMP localizes preferentially at membrane protrusions called invadopodia where it plays a central role in degradation of the surrounding extracellular matrix (ECM). Previous reports suggested a role for a continuous supply of MT1-MMP in ECM degradation. However, the turnover rate of MT1-MMP and the extent to which the turnover contributes to the ECM degradation at invadopodia have not been clarified. To approach this problem, we first performed FRAP (Fluorescence Recovery after Photobleaching) experiments with fluorescence-tagged MT1-MMP focusing on a single invadopodium and found very rapid recovery in FRAP signals, approximated by double-exponential plots with time constants of 26 s and 259 s. The recovery depended primarily on vesicle transport, but negligibly on lateral diffusion. Next we constructed a computational model employing the observed kinetics of the FRAP experiments. The simulations successfully reproduced our FRAP experiments. Next we inhibited the vesicle transport both experimentally, and in simulation. Addition of drugs inhibiting vesicle transport blocked ECM degradation experimentally, and the simulation showed no appreciable ECM degradation under conditions inhibiting vesicle transport. In addition, the degree of the reduction in ECM degradation depended on the degree of the reduction in the MT1-MMP turnover. Thus, our experiments and simulations have established the role of the rapid turnover of MT1-MMP in ECM degradation at invadopodia. Furthermore, our simulations suggested synergetic contributions of proteolytic activity and the MT1-MMP turnover to ECM degradation because there was a nonlinear and marked reduction in ECM degradation if both factors were reduced simultaneously. Thus our computational model provides a new in silico tool to design and evaluate intervention strategies in cancer cell invasion.
Germline RAD51B variants confer susceptibility to breast and ovarian cancers deficient in homologous recombination (2021)

Pathogenic germline mutations in the RAD51 paralog genes RAD51C and RAD51D, are known to confer susceptibility to ovarian and triple-negative breast cancer. Here, we investigated whether germline loss-of-function variants affecting another RAD51 paralog gene, RAD51B, are also associated with breast and ovarian cancer. Among 3422 consecutively accrued breast and ovarian cancer patients consented to tumor/germline sequencing, the observed carrier frequency of loss-of-function germline RAD51B variants was significantly higher than control cases from the gnomAD population database (0.26% vs 0.09%), with an odds ratio of 2.69 (95% CI: 1.4-5.3). Furthermore, we demonstrate that tumors harboring biallelic RAD51B alteration are deficient in homologous recombination DNA repair deficiency (HRD), as evidenced by analysis of sequencing data and in vitro functional assays. Our findings suggest that RAD51B should be considered as an addition to clinical germline testing panels for breast and ovarian cancer susceptibility.
Implementation of hearing aid signal processing algorithms on the TI DHP-100 platform (2004)

While the traditional deployment platform for digital hearing aids has been custom ICs, recent advances in the power efficiency of digital signal processors (DSPs) have generated interest in their use. A primary motivation for this interest is the increased algorithmic flexibility that a DSP provides over a fixed-function IC. The C54xx family of DSPs from Texas Instruments is among the leaders in power efficiency, and TI provides a development platform (the DHP-100) aimed at exploring the hearing aid design space. Here, we report on our experience porting hearing aid signal processing algorithms (J.L. Goldstein, August 2001) to the DHP-100 and report on the resulting performance, both for real-time response and power consumption.
Real-time, reconfigurable, handheld molecular chemical imaging sensing for standoff detection of threats (2019)

As the nature of explosive, chemical and narcotic threats become more pervasive and lethal to innocent bystanders and unsuspecting military and law enforcement authorities, there is a growing demand for rapid and effective detection of materials in real-time with a high degree of autonomy at safe distances. In an effort to address this need, ChemImage has been developing novel, adaptable, short-wave infrared (SWIR) molecular chemical imaging systems for real-time analysis of complex environments, including for detection of hazardous materials (e.g., explosives, chemical warfare agents, drugs of abuse). At the heart of these systems is the Conformal Filter (CF), which is a liquid crystal (LC)-based tunable filter that transmits multi-band waveforms. Building on concepts of multivariate optical computing, the CF is tuned electro-optically and dynamically to mimic the functionality of a discriminant vector for classification. The resulting integrated detector response approximates the detection response of conventional hyperspectral imaging with only two discrete measurements instead of hundreds to thousands. Real-time detection is achieved by operating two CFs in tandem within a dual polarization (DP) system, which exploits the polarization sensitivity of the LC filters and allows for simultaneous acquisition of the compressed hyperspectral imagery. This paper will discuss the development, characterization, and test results of a prototype, handheld CF sensor, with a focus on its application to explosives, chemical and narcotic threat detection.
Development of a Dosimeter System for Unsymmetrical Dimethylhydrazine, Monomethylhydrazine and Hydrazine (1994)

A dosimeter for real-time, colorimetric detection of current and proposed threshold limit value (TLV) levels of hydrazine, monomethylhydrazine (MMH) and unsymmetrical dimethylhydrazine (UDMH)in air has been developed. The dosimeter consists of a replaceable dosimeter card and a reusable, polypropylene badge housing containing a clear, LTV adsorbent shield. The replaceable dosimeter card has two reaction sites, each containing one of two chemistries on a paper substrate. One chemistry uses 2,4-dinitrobenzaldehyde which is an excellent derivatization agent for UDMH, though less effective for hydrazine and MMH. Through a condensation reaction, 2,4-dinitrobenzaldehyde reacts with UDMH to form a colored product that absorbs in the visible region. The hydrazone formed in the reaction is yellow to golden yellow. The intensity of the color is proportional to the dose. When coated on porous filter paper and exposed passively to UDMH, the detection limit is &lt;20 ppb-hrs. Actively drawing UDMH vapors through the paper gives a detection limit of &lt;50 ppb-L. The second reaction utilized in the dosimeter system involves 3-methoxy-4hydroxbenzaldehyde (vanillin) for the detection of hydrazine and MMH (U.S. patent 4,900,681). In the reaction between vanillin and hydrazine or MMH, a yellow hydrazone is formed. When coated on porous filter paper and exposed to MMH or hydrazine, the detection limit is 7 ppb-hours. Neither chemistry is hindered by a sensitivity to relative humidity changes. Badges remain sensitive to hydrazines vapors for at least one year when stored in a freezer. Interferences with the chemistries are limited to tobacco smoke and sunlight for the vanillin and 2,4- dinitrobenzaldehyde chemistries, respectively.
Longterm follow up of transjugular intrahepatic portosystemic stent shunt (TIPSS) for the treatment of portal hypertension: results in 130 patients. (1996)

TIPSS is an effective treatment for variceal bleeding, resistant ascites, and portal hypertensive gastropathy. Rebleeding is invariably associated with shunt dysfunction, the frequency of which increases with time, therefore regular and longterm shunt surveillance is required.
Transcriptional Regulation of Angiogenesis (2007)

Until recently, the transcription factors necessary for regulating vascular development were largely unknown. This is in sharp contrast with other developmental processes, such as hematopoiesis and myogenesis, in which several cell- or tissue-specific transcription factors have been identified. Vascular development requires the differentiation of endothelial cells from pluripotent stem cells. Progress in identifying the molecular mechanisms underlying vascular development has lagged considerably, in large part the model systems for studying vascular blood vessel development are more limited. The identification of several vascular-specific genes involved in vasculogenesis and the genomic regulatory regions required for directing their expression over the past decade has facilitated the identification of the transcriptional mechanisms required for vascular-specific gene expression. Targeted disruption of additional transcription factors that have been associated with vascular defects led to the elucidation of a role for these factors in vascular development. Angiogenesis, the development of additional blood vessels from a primary vascular network, may recapitulate many of the molecular events occurring during vascular development.
Stress Characteristics of Multilayered Polysilicon Film for the Fabrication of Microresonators (1999)

Micro-polysilicon actuators, which are widely used in the field of microelectromechanical system (MEMS) technology, were fabricated using a novel stacking method. Polysilicon film was deposited to have a symmetrical layer structure using a low-pressure chemical vapor deposition (LPCVD) system. We have also measured the physical characteristics using micromachined test patterns to verify the minimal stress and stress gradient in the polysilicon layers, according to the film stacking, doping, and thermal treatment methods. Finally, the fabricated planar polysilicon resonators, symmetrically stacked to 6.5 µm thickness, showed Q of 1270 and oscillation amplitude of 5 µm under 1000 mTorr. The developed micro-polysilicon resonator can be utilized in the fabrication of both microgyroscopes and accelerometer sensors.
Single‐parent expression drives dynamic gene expression complementation in maize hybrids (2020)

Single-parent expression (SPE) is defined as gene expression in only one of the two parents. SPE can arise from differential expression between parental alleles, termed non-presence/absence (non-PAV) SPE, or from the physical absence of a gene in one parent, termed PAV SPE. We used transcriptome data of diverse Zea mays (maize) inbreds and hybrids, including 401 samples from five different tissues, to test for differences between these types of SPE genes. Although commonly observed, SPE is highly genotype and tissue specific. A positive correlation was observed between the genetic distance of the two inbred parents and the number of SPE genes identified. Regulatory analysis showed that PAV SPE and non-PAV SPE genes are mainly regulated by cis effects, with a small fraction under trans regulation. Polymorphic transposable element insertions in promoter sequences contributed to the high level of cis regulation for PAV SPE and non-PAV SPE genes. PAV SPE genes were more frequently expressed in hybrids than non-PAV SPE genes. The expression of parentally silent alleles in hybrids of non-PAV SPE genes was relatively rare but occurred in most hybrids. Non-PAV SPE genes with expression of the silent allele in hybrids are more likely to exhibit above high parent expression level than hybrids that do not express the silent allele, leading to non-additive expression. This study provides a comprehensive understanding of the nature of non-PAV SPE and PAV SPE genes and their roles in gene expression complementation in maize hybrids.