gebhart/patrepeval huggingface dataset:
Identification of regulatory genes through global gene expression analysis of a Helicobacter pylori co-culture system (2019)

Abstract Helicobacter pylori is a gram-negative bacterium that establishes life-long infections by inducing immunoregulatory responses. We have developed a novel ex vivo H. pylori co-culture system to identify new regulatory genes based on expression kinetics overlapping with that of genes with known regulatory functions. Using this novel experimental platform, in combination with global transcriptomic analysis, we have identified five lead candidates, validated them using mouse models of H. pylori infection and in vitro co-cultures under pro-inflammatory conditions. Plexin domain containing 2 (Plxdc2) was selected as the top lead immunoregulatory target. Gene silencing and ligand-induced activation studies confirmed its predicted regulatory function. Our integrated bioinformatics analyses and experimental validation platform has enabled the discovery of new immunoregulatory genes. This pipeline can be used for the identification of genes with therapeutic applications for treating infectious, inflammatory, and autoimmune diseases.
Multiplexed fibre Bragg grating sensors for in-core thermometry in nuclear reactors (2000)

In-core temperature measurement is a critical issue for the safe operation of nuclear reactors. Classical thermocouples require shielded connections and are known to drift under high neutron fluence. As an alternative, we propose to take advantage of the multiplexing capabilities of Fibre Bragg Grating (FBG) temperature sensors to perform the in-core temperature measurements. We first report on our irradiation experiments on multiplexed FBGs, written in different fibres, employed to measure the in-pile temperature of an air-cooled graphite-moderated nuclear reactor. For some FBGs the difference between the measurements and the readings of calibrated backup thermocouples was within the measurement uncertainty. In the worst case, the difference saturated after 30 hours of reactor operation at about 5°C. Afterwards, we irradiated multiplexed FBG sensors in our material testing nuclear reactor, evidencing the possibility to use FBG sensing technology for in-core monitoring of nuclear reactors with specific care and in well-specified conditions.
Reg IV can serve for early diagnosis and therapy (2007)

Commentary to:Dysregulation of Reg Gene Expression Occurs Early in Gastrointestinal Tumorigenesis and Regulates Anti-Apoptotic GenesKumar S. Bishnupuri, Qizhi Luo, Joshua R. Korzenik, Jeffrey O. Henderson, Courtney W. Houchen, Shrikant Anant and Brian K. DieckgraefeVolume: 5 | Issue: 12
Smooth soft mel-spectrographic masks based on blind sparse source separation (2007)

Abstract This paper investigates the use of DUET, a recently proposedblind source separation method, as front-end for missing dataspeech recognition. Based on the attenuation and delay estima-tion in stereo signals soft time-frequency masks are designedto extract a target speaker from a mixture containing multiplespeech sources. A postprocessing step is introduced in order toremove isolated mask points that can cause insertion errors inthe speech decoder. The results for connected digit experimentsin a multi-speaker environment demonstrate that the proposedsoft masks closely match the performance of the oracle maskdesigned with a priori knowledge of the source spectra. Index Terms : speech recognition, missing data, attenuationand delay estimation 1. Introduction The concept of time-frequency (TF) masking has recently at-tracted some interest in the ﬁeld of blind signal separation (BSS)[1, 2]. Demixing via TF-masks has the potential to separatemixtures with more sources than sensors as it does not rely onmatrix inversion. Instead the TF-plane is partitioned into dis-joint regions each assigned to a particular source. The sourcesare then recovered by converting each region back into the timedomain. It seems promising to use BSS systems as front-endsfor automatic speech recognition (ASR). In [3] we have pro-posed such a combination using a BSS technique called DUETand a missing data (MD) speech recognizer. The proposedsystem uses DUET to estimate TF-masks in the sparse Short-Time-Fourier-Transform (STFT) domain before converting thehigh STFT frequency resolution to a perceptual mel-frequencyscale suitable for ASR. In this way we can avoid source re-construction and directly exploit the spectrographic masks forMD-ASR. This paper extends our previous work in two regards.Firstly, we replace binary masks with soft masks which havebeen proven to be beneﬁcial for both speech recognition andspeech enhancement. Several studies [2, 4] have reported thatbinary TF-masking can lead to audible unnatural sound arti-facts that can be avoided to some degree by soft masks. Theadvantages of soft masks in MD-ASR are even more evidentas marginalization approaches based on soft decisions consis-tently outperformed hard masks [5]. Secondly, we show thata simple mask postprocessing can lead to substantial recogni-tion improvements. A two-dimensional (2-D) median ﬁlter wasapplied to reduce the inﬂuence of outliers visible as scattered
Large-Scale Proteomics and Phosphoproteomics of Urinary Exosomes (2008)

Normal human urine contains large numbers of exosomes, which are 40- to 100-nm vesicles that originate as the internal vesicles in multivesicular bodies from every renal epithelial cell type facing the urinary space. Here, we used LC-MS/MS to profile the proteome of human urinary exosomes. Overall, the analysis identified 1132 proteins unambiguously, including 177 that are represented on the Online Mendelian Inheritance in Man database of disease-related genes, suggesting that exosome analysis is a potential approach to discover urinary biomarkers. We extended the proteomic analysis to phosphoproteomic profiling using neutral loss scanning, and this yielded multiple novel phosphorylation sites, including serine-811 in the thiazide-sensitive Na-Cl co-transporter, NCC. To demonstrate the potential use of exosome analysis to identify a genetic renal disease, we carried out immunoblotting of exosomes from urine samples of patients with a clinical diagnosis of Bartter syndrome type I, showing an absence of the sodium-potassium-chloride co-transporter 2, NKCC2. The proteomic data are publicly accessible at http://dir.nhlbi.nih.gov/papers/lkem/exosome/.
Updates on retinal imaging technology for screening and diagnosis (2017)

Summary There has been a revolution in retinal imaging, allowing better screening, diagnosis, risk stratification and management of diabetic retinopathy ( DR ), age‐related macular degeneration ( AMD ), and retinal vascular disorders. In terms of DR screening, current imaging techniques employ fundus photography and skilled readers for DR assessment. There has been development of automated retinal image analysis software such as deep learning techniques using artificial intelligence. Current screening programs also do not effectively screen for diabetic macular edema ( DME ). Optical coherence tomography ( OCT ) can potentially provide cost‐effective solutions for improving DME detection. New screening techniques to image the peripheral retina such as ultra‐widefield imaging offers further potential. For diagnosis and risk stratification, spectral domain OCT ( SD ‐ OCT ) and swept source OCT ( SW ‐ OCT ) are increasing used to diagnosis AMD , DME , and other conditions. Traditionally, FFA is used to evaluate AMD and DR . OCT angiography ( OCT ‐A) technology is a major advance that offers the opportunity to non‐invasively visualize different retinal capillary layers without injection of dye. OCT ‐A is primed to replace FFA for most clinical scenarios.
Mosaic Transparent Armor System Final Report CRADA No. TC02162.0 (2017)

This was a collaborative effort between Lawrence Livermore National Security, LLC as manager and operator of Lawrence Livermore National Laboratory (LLNL) and The Protective Group, Inc. (TPG) to improve the performance of the mosaic transparent armor system (MTAS) for transparent armor applications, military and civilian. LLNL was to provide the unique MTAS technology and designs to TPG for innovative construction and ballistic testing of improvements needed for current and near future application of the armor windows on vehicles and aircraft. The goal of the project was to advance the technology of MTAS to the point that these mosaic transparent windows would be introduced and commercially manufactured for military vehicles and aircraft.
Surface morphology and transport properties of Cr nanoparticles in single electron tunneling regime (2011)

We have carried out an investigation of surface structures of Cr nanoparticles grown on a MgO layer for studying single electron tunneling (SET). Reflection high-energy electron diffraction pattern changes from spotty to streak with decreasing Cr nominal thickness, while Cr forms nano size particles with the size of around 3.5 nm in diameter for all the samples. The double tunnel junctions for the Cr nominal thickness of 0.1 nm show clear Coulomb blockade with the threshold voltage of 50 mV, indicating that this Cr nanoparticle satisfies the condition for the appearance of SET. The relatively large volume of the Cr nanoparticles may be related with the fact that tunnel magnetoresistance due to spin accumulation in Cr nanoparticles is small.
Effects of race and periodontal status on antibody reactive with Actinobacillus actinomycetemcomitans strain Y4 (1988)

Higher levels of serum antibody reactive with Actinobacillus actinomycetemcomitans strain Y4 (AAY4) have been demonstrated in localized juvenile periodontitis than in other forms of periodontal diseases. However, in studies which reported the racial distribution of the clinical groups, a predominantly black juvenile periodontitis population has been compared with a non‐periodontitis control population that was predominantly white. The purpose of this study was to determine the effect of race (black or white) on antibody reactivity to AAY4 for subjects with clinical diagnoses of adult periodontitis (AP), non‐periodontitis (NP), juvenile periodontitis (JP) and severe generalized periodontitis in young adults (SP). A radioimmunoassay (RIA) was utilized to detect and quantitate antibody to AAY4. Within clinical groups of NP, JP and SP a higher prevalence of seropositive black subjects than white subjects was found. The association between a high prevalence of positive antibody responses to AAY4 in JP subjects compared to NP subjects still exists, but was reduced compared to previous reports. White non‐periodontitis subjects, used as control subjects in previous reports, were found to have a significantly lower frequency of seropositivity to AAY4 than black non‐periodontitis subjects. This relationship held whether the periodontatly healthy subject was ascertained from a family with a JP or SP family member or was ascertained solely on the basis of a diagnosis of non‐periodontitis. The difference in the prevalence of seropositivity to AAY4 between JP and SP subjects was entirely due to the racial composition of the two groups, as nearly half the SP subjects were white compared with only 15% of the JP subjects. Thus, antibody reactivity to AAY4 was found to be related to both clinical diagnosis and race.
Notch effects on room temperature tensile and bend properties of Ni3Al and Ni3Al+B (1989)

The notched mechanical properties of Ni3Al and Ni3Al+B prepared by powder metallurgy techniques have been determined in both tension and bending at room temperature. Tensile tests performed using double-notched specimens containing relatively blunt notches produced intergranular fracture in both Ni3Al and Ni3Al+B, with evidence of fracture initiating in an intergranular manner ahead of the blunt notch in both cases. Estimates of notched fracture toughness from bend tests and of local grain boundary fracture stress from the notched tensile tests suggest an increase in these values with boron addition.
-Interfacial LayerFormation byCycle-by-Cycle Deposition andAnnealing - (2007)

FUSI-NiSi gateelectrodes wereformed at500'C.After Wehavesuccessfully fabricated a0.5nmFUSI-NiSi/FGA at400'CinH2ambient, thegate-first MOSFET HfO2/HfSiOx/ Sigatestack structure withthegate-first fabrication process wasfinished. process. TheHfSiOx interfacial layer wasformed bythe cycle-by-cycle deposition and annealing process, Results andDiscussion followed bythein-situ layer-by-layer deposition and Figure3 showscapacitance versus gatevoltage annealing forHfO2growth. Thegate leakage current of- (Cg-Vg) characteristics ofgatestacks withCC-ILof4 10A/cmatVfb -1.0Vandtheeffective electron mobilitycycles forthegate-first andthegate-last processed of120cm2/Vsat0.8MV/cm wereobtained for pMOS.No capacitance reduction isobserved after n-MOSFETwithEOT=0.49nm. gate-first process withthehightemperature annealing compared withthegate-last process. Figure 4showsthe
A 15Gb&#x002F;s AC-Coupled VCSEL Driver with Waveform Shaping in 65nm CMOS (2015)

A Vertical Cavity Surface Emitting Laser (VCSEL) driver in 65nm CMOS selectively-enables parallel low-power CMOS drivers to shape the output current waveforms and compensate VCSEL nonlinearities. The CMOS waveform-shaping drivers are AC-coupled allowing them to operate from a 1-V supply to save power, while parallel low-frequency paths provide programmable DC biasing from a 3-V supply. The measured VCSEL driver is able to achieve 15Gb/s with up to 5.1dBm OMA at a total power dissipation of 60mW, or 2.1dBm OMA at 28mW corresponding to 1.9pJ/bit. The driver occupies 250 × 160μm including the on-die AC-coupling.
3D Occlusion Inference from Silhouette Cues (2007)

We consider the problem of detecting and accounting for the presence of occluders in a 3D scene based on silhouette cues in video streams obtained from multiple, calibrated views. While well studied and robust in controlled environments, silhouette-based reconstruction of dynamic objects fails in general environments where uncontrolled occlusions are commonplace, due to inherent silhouette corruption by occluders. We show that occluders in the interaction space of dynamic objects can be detected and their 3D shape fully recovered as a byproduct of shape-from-silhouette analysis. We provide a Bayesian sensor fusion formulation to process all occlusion cues occurring in a multi-view sequence. Results show that the shape of static occluders can be robustly recovered from pure dynamic object motion, and that this information can be used for online self-correction and consolidation of dynamic object shape reconstruction.
Supplementary Table S5 from Discovery of Candidate DNA Methylation Cancer Driver Genes (2023)

&lt;p&gt;MethSig DNAme drivers enriched pathways.&lt;/p&gt;
Monitoring Controlled Release of Payload from Gold Nanocages Using Surface Enhanced Raman Scattering (2013)

Novel organic and inorganic nanostructures for localized and externally triggered delivery of therapeutic agents at a target site have received immense attention over the past decade owing to their enormous potential in treating complex diseases such as cancer. Gold nanocages, a novel class of hollow plasmonic nanostructures, have been recently demonstrated to serve as carriers for the delivery of payload with external trigger such as light or ultrasound. In this article, we demonstrate that surface enhanced Raman spectroscopy (SERS) can be employed to noninvasively monitor the release of payload from these hollow plasmonic nanostructures. The large enhancement of electromagnetic (EM) field at the interior surface of these nanostructures enables us to monitor the controlled release of Raman-active cargo from nanocages. Considering that SERS can be excited and collected in near-infrared (NIR) therapeutic window, this technique can serve as a powerful tool to monitor the drug release in vivo, providing additional control over externally triggered drug administration.
Lyotropic Liquid Crystalline Properties of Poly(N,N‘-di-n-hexylguanidine) (2004)

ADVERTISEMENT RETURN TO ISSUEPREVNoteNEXTLyotropic Liquid Crystalline Properties of Poly(N,N'-di-n-hexylguanidine)Jeonghan Kim, Bruce M. Novak, and Alan John WaddonView Author Information Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695 Department of Polymer Science & Engineering, University of Massachusetts, Amherst, Massachusetts 01003 Cite this: Macromolecules 2004, 37, 4, 1660–1662Publication Date (Web):January 30, 2004Publication History Received5 August 2003Revised29 December 2003Published online30 January 2004Published inissue 1 February 2004https://doi.org/10.1021/ma035135eCopyright © 2004 American Chemical SocietyRIGHTS & PERMISSIONSArticle Views289Altmetric-Citations28LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit Read OnlinePDF (104 KB) Get e-AlertsSUBJECTS:Liquid crystals,Mesostructures,Physical and chemical processes,Polymer solutions,Polymers Get e-Alerts
Interpenetrating Polymer Networks for High‐Performance Electroelastomer Artificial Muscles (2006)

New interpenetrating elastomeric networks have been prepared in which the high tension in the first network is balanced by the compression of the second network. The composite films exhibit high electrically induced strain without need for any external mechanical prestraining. Strains of up to 233% in terms of area expansion have been obtained at an electrical field of 300 MV m–1. These new electroelastomers may have applications as actuators (see figure) and artificial muscles.
All-optical multiwavelength switching for hybrid WDM/TDM demultiplexing and signal processing (2003)

Summary form only given. Hybrid approaches to optical communications and signal processing systems have previously been proposed that exploit the parallelism of wavelength division multiplexing (WDM) and the speed of time division multiplexing (TDM). In this paper, we demonstrate an all-optical switch capable of simultaneously switching multiple wavelength channels with high-speed capability using a semiconductor optical amplifier (SOA) asymmetrically placed inside a loop mirror.
The Electrical and Mechanical Characterization of Metal-Reinforced Bi-2223/Ag Conductors for High Field Insert Coil (2009)

In this study, we investigated in field properties of high- <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">Tc</i> superconductor (HTS) tapes electrically as well as mechanically. Metallic reinforced Bi-2223/Ag superconductor tapes were used in this work. The critical current ( <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">Ic</i> ), which is highly dependent on the magnetic field, was measured using fields applied parallel and perpendicular to the tape surface. The conductor was exposed to fields of up to 28 T at 4.2 K. In order to confirm the performance of tapes in practical NMR operation, <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">Ic</i> was also measured around 2 K. The conductor was wound on a large diameter bobbin and mechanical properties were then measured as the coil current was increased. Finally, we verified the conductor properties from coil <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">Ic</i> and maximum stress/strain of it.
Study of EMC for Cu bonding wire application (2010)

The influence of EMC (Epoxy Molding Compound) and reliability with fine Cu wire was studied. It is found that the failure mode was corrosion at the intermetallic layer of the wire bonding part by failure analysis after HAST (Highly Accelerated Temperature & Humidity Stress Test). Al elution and Cl ion was observed at the intermetallic layer. EMC with lower Cl ion content and Al inhibitor of corrosion shows better HAST property. The selection of flame retardant for green EMC is important because some retardant has a negative impact on HAST performance.
Automatic construction of structural models for unconstrained handwritten characters (2002)

The clues for discontinuous structural transformation in handwriting lie in deformation around singular points and stroke connections of handwriting. For designing an algorithm for automatic construction of structural models incorporating discontinuous transformations, we analyze systematically how global structures and features are changed by stroke connections. Based on the set of systematic laws of shape transformations, we design an algorithm for finding component correspondence between a pair of deformed patterns, and present an algorithm for automatic construction of structural models for unconstrained handwritten characters along with some examples. The proposed algorithm can generalize unconstrained handwritten characters into a small number of classes, and one class can represent various deformed patterns.
RNF43 is frequently mutated in colorectal and endometrial cancers (2014)

We report somatic mutations of RNF43 in over 18% of colorectal adenocarcinomas and endometrial carcinomas. RNF43 encodes an E3 ubiquitin ligase that negatively regulates Wnt signaling. Truncating mutations of RNF43 are more prevalent in microsatellite-unstable tumors and show mutual exclusivity with inactivating APC mutations in colorectal adenocarcinomas. These results indicate that RNF43 is one of the most commonly mutated genes in colorectal and endometrial cancers.
Electrical Properties of Metal-Oxide-Containing SiO2 Films Formed by Organosiloxane Sol–Gel Precursor (2010)

High-quality SiO 2 film formation is important for many applications, such as large-scale integration (LSI) circuit and micro-electro-mechanical system (MEMS) industries. We evaluated the structural and electrical insulation properties of SiO 2 films using an organosiloxane-based silica sol–gel precursor derived from a mixture of tetraethoxysilane (TEOS) and methyltrimethoxysilane (MTMS) by changing the molar ratio of TEOS/MTMS. This sol–gel precursor was converted not only to a low-dielectric-constant film with a relative dielectric constant of 2.8 but also to a dense SiO 2 film by optimizing baking conditions. The dense SiO 2 film from this sol–gel precursor has excellent dielectric characteristics of low leakage current density and high breakdown voltage, whose values are comparable to those of thermal oxide SiO 2 films. Furthermore, the breakdown field intensity of these films was improved by adding a small amount of metal oxides, such as TiO 2 , HfO 2 , and ZrO 2 . A maximum breakdown field intensity of 15 MV/cm can be achieved in the case of 10% TiO 2 addition.