gebhart/patrepeval huggingface dataset:
Optimized Deep Learning Framework for Water Distribution Data-Driven Modeling (2017)

Deep Learning (DL), unlike conventional Artificial Neural network (ANN), is capable of self-learning data features layer by layer in unsupervised manner and creating a data-driven model with the given dataset. DL has been widely applied to big data analytics, graphics object detection, classification, voice recognition and many other problems. This paper presents an integrated data-driven modelling framework that couples DL with the well-developed evolutionary optimization tool in a scalable and heterogeneous high performance computing paradigm. The integrated framework enables modellers to effectively and efficiently construct a model with a given dataset. It is demonstrated that the framework has wide applicability including but not limited to the simulation, optimization and operation decision of water distribution systems. The paper elaborates the development of the deep learning framework with potential applications of facilitating the data fusion, system simulation and predictive analysis, anomaly detection from the time series data (pressures, flows and consumptions etc.), water usage prediction, construction of a meta-model as a surrogate to the physics-based models (hydraulic and water quality) for water distribution management.
Standardization of acellular pertussis vaccine by assay of serum neutralizing antibodies to pertussis toxin (antitoxin): analogy with diphtheria toxoid. (1998)

Immunity conferred by vaccination with cellular pertussis vaccines and pertussis wanes so that adults are now the main reservoir of B. pertussis. Similar to diphtheria toxoid, acellular pertussis vaccines are suitable for vaccination of adults and it is probable that addition of pertussis toxoid to DT will be recommended for this age group. If this can be achieved, it is easy to predict that pertussis will be eliminated and the possibility of eradicating B. pertussis will become feasible. We propose that, despite the relative inaccuracy of correlating levels of antitoxin with individual immunity, a standardized assay and reference antiserum for pertussis toxoid will control acellular pertussis vaccines as was achieved with diphtheria toxoid.
A Regression-Based Analysis of Ribosome-Profiling Data Reveals a Conserved Complexity to Mammalian Translation (2015)

A fundamental goal of genomics is to identify the complete set of expressed proteins. Automated annotation strategies rely on assumptions about protein-coding sequences (CDSs), e.g., they are conserved, do not overlap, and exceed a minimum length. However, an increasing number of newly discovered proteins violate these rules. Here we present an experimental and analytical framework, based on ribosome profiling and linear regression, for systematic identification and quantification of translation. Application of this approach to lipopolysaccharide-stimulated mouse dendritic cells and HCMV-infected human fibroblasts identifies thousands of novel CDSs, including micropeptides and variants of known proteins, that bear the hallmarks of canonical translation and exhibit translation levels and dynamics comparable to that of annotated CDSs. Remarkably, many translation events are identified in both mouse and human cells even when the peptide sequence is not conserved. Our work thus reveals an unexpected complexity to mammalian translation suited to provide both conserved regulatory or protein-based functions.
25-kW Three-Phase Unity Power Factor Buck–Boost Rectifier With Wide Input and Output Range for Pulse Load Applications (2008)

Pulse loads, like solid-state pulse modulators, generate short pulses with a high peak power that exceeds the average power by 100-1000 times depending on the pulse repetition rate. There, the peak power usually is drawn from an energy buffer such as a capacitor bank. The pulse discharges the energy buffer, and it is fully recharged in the time between the pulses by a power supply, which is usually connected to the mains. Due to the worldwide variation in mains voltages and the desired ability to adapt to the capacitor voltage of the modulator, the power supply has to support a wide input and output voltage range. Additionally, the supply should draw a sinusoidal current from the mains while providing energy to the pulse modulator due to electromagnetic interference regulations. Therefore, a general control concept for pulse load applications, which guarantees continuous power consumption from the mains and power factor correction, is described in this paper. Furthermore, measurements of the control principle, which is independent from the converter topology, are presented for a three-phase buck-boost rectifier.
Expression levels of thyroglobulin processing proteases are reduced upon trace amine-associated receptor 1 deficiency in mice (2016)

Searchable abstracts of presentations at key conferences in endocrinology ISSN 1470-3947 (print) | ISSN 1479-6848 (online)
Spectral analysis of the DNA targeting bisalkylaminoanthraquinone DRAQ5 in intact living cells (2006)

The study provides new clues to modes of DNA binding of the modified anthraquinone molecule in vivo, and its AT base-pair selectivity. The combination of low quantum yield but high DNA affinity explains the favorable signal-to-noise profile of DRAQ5-nuclear fluorescence. The robust nature of cell cycle reporting using DRAQ5, even when restricted spectral windows are selected, facilitates the analysis of encroaching spectral emissions from other fluorescent reporters, including GFP-tagged proteins.
Presence of 2,4-D-catabolizing Bacteria in a Japanese Arable Soil that Belong to BANA (Bradyrhizobium-Agromonas-Nitrobacter-Afipia) Cluster in .ALPHA.-Proteobacteria. (2000)

We isolated the 2, 4-D-catabolizing bacterial strain RD5-C2 from Japanese upland soil that had no history of 2, 4-D exposure.RD5-C2 could use 2, 4-D as the sole carbon and energy sources for their growth.Phylogenetic analyses based on 16S rDNA sequencing revealed that RD5-C2 was a member of the BANA(Bradyrhizobium-Agromonas-Nitrobacter-Afipia)cluster in the α subdivision of the class Proteobacteria.The gene sequence of RD5-C2 most closely matched that of Bradyrhizobium sp.and also closely related to those of 2, 4-D-catabolizing α-Proteobacteria previously isolated from pristine environments of Hawaii, northern Canada and central Chile.This is the first instance that 2, 4-D-catabolizing bacteria in that phylogenetic group was isolated from an arable soil environment.
GaAs nanowire Schottky barrier photovoltaics utilizing Au–Ga alloy catalytic tips (2012)

Single GaAs nanowire photovoltaic devices were fabricated utilizing rectifying junctions in the Au–Ga catalytic tip/nanowire contact interface. Current-voltage measurements were performed under simulated Air Mass 1.5 global illumination with the best performance delivering an overall energy conversion efficiency of ∼2.8% for a nanowire of 70 nm in diameter. As compared with metal contacts directly deposited on top of the nanowire, this nanoscale contact is found to alleviate the well-known Fermi-level pinning to achieve effective formation of Schottky barrier responsible for the superior photovoltaic response. All these illustrate the potency of these versatile nanoscale contact configurations for future technological device applications.
Combination of whole cell pertussis vaccine and the pneumococcal surface protein A (PspA) antigen: proposal of a combined vaccine against pertussis and pneumococcal diseases (2010)

Background: Streptococcus pneumoniae (pneumococcus) is one of the major agents of respiratory acute diseases, accounting for 1 million deaths per year around the world. In developing countries, pneumococcal diseases kill 800,000 children annually. PspA is a surface pneumococcal antigen, shown to elicit protection against animal models of pneumococcal infections, in different vaccine formulations. The whole cell pertussis vaccine (WCP) is widely used in developing countries and its first dose is indicated to be given at 2 months of age. As an inactivated bacteria-based vaccine, it has the potential to exert adjuvant activity upon co-administration with other antigens. Methods: Here, we analyzed the adjuvant activity of WCP in combination with PspA and tested the efficacy of WCP-PspA nasal vaccination against a pneumococcal challenge in mice. Results: Nasal immunization of Balb/C mice with WCP-PspA elicited higher amounts of anti- PspA IgG and sIgA than the immunization with PspA alone. Mice immunized with the combination were 100% protected after a respiratory lethal challenge, whereas immunization with PspA alone produced around 60% protection. In time course experiments of challenged mice, IL-6, TNF and IFN-g cytokine signaling was observed in vaccinated animals, with a peak 12 h after challenge followed by a quick reduction in secretion, indicating controlled inflammatory responses. In contrast, cytokine secretion in control mice remained high long after challenge, showing that these animals are unable to control the inflammatory response elicited by pneumococcal infection. Pneumococci loads increase in the lungs of control animals and reach the bloodstream 30 h after infection, leading to death at 72 h after infection. On the other hand, vaccinated mice displayed steadily pneumococcal numbers in the lungs in the first hours and a marked decrease 72 h after challenge. In this group, pneumococci did not reach the bloodstream. Sera collected from WCP-PspA immunized mice displayed increased capacity of induction of complement deposition on bacteria surface, indicating a potential role of antibodies in the protection observed. Moreover, sera from WCP-PspA immunized mice protected naïve mice in passive immunization experiments. Conclusion: These results open the possibility for the combination of WCP vaccines with PspA, taking advantage of the adjuvant activity of WCP. Supported by: FAPESP, CNPq, Fundação Butantan. Abstracts for SupplementInternational Journal of Infectious DiseasesVol. 14Preview Full-Text PDF Open Archive
Quantification moléculaire par spectrométrie de masse à base de NEMS : modélisation et inversion du problème. (2011)

National audience
1147: Favorable Long-Term Outcomes in Patients with Seminal Vesicle Invasion or Lymph Node Invasion at Radical Prostatectomy (2007)

You have accessJournal of UrologyModerated Poster 34, Monday, May 21, 2007, 3:30 - 5:30 pm1 Apr 20071147: Favorable Long-Term Outcomes in Patients with Seminal Vesicle Invasion or Lymph Node Invasion at Radical Prostatectomy Andrea Gallina, Jochen Walz, Miriam Traumann, Georg C. Hutterer, Thorsten Schlomm, Marco Roscigno, James A. Eastham, Peter T. Scardino, Eric A. Klein, Alwyn M. Reuther, Francesco Montorsi, Markus Graefen, Hartwig Huland, Fred Saad, and Pierre I. Karakiewicz Andrea GallinaAndrea Gallina More articles by this author , Jochen WalzJochen Walz More articles by this author , Miriam TraumannMiriam Traumann More articles by this author , Georg C. HuttererGeorg C. Hutterer More articles by this author , Thorsten SchlommThorsten Schlomm More articles by this author , Marco RoscignoMarco Roscigno More articles by this author , James A. EasthamJames A. Eastham More articles by this author , Peter T. ScardinoPeter T. Scardino More articles by this author , Eric A. KleinEric A. Klein More articles by this author , Alwyn M. ReutherAlwyn M. Reuther More articles by this author , Francesco MontorsiFrancesco Montorsi More articles by this author , Markus GraefenMarkus Graefen More articles by this author , Hartwig HulandHartwig Huland More articles by this author , Fred SaadFred Saad More articles by this author , and Pierre I. KarakiewiczPierre I. Karakiewicz More articles by this author View All Author Informationhttps://doi.org/10.1016/S0022-5347(18)31361-2AboutPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookLinked InTwitterEmail "1147: Favorable Long-Term Outcomes in Patients with Seminal Vesicle Invasion or Lymph Node Invasion at Radical Prostatectomy." The Journal of Urology, 177(4S), pp. 378–379 © 2016 by American Urological AssociationFiguresReferencesRelatedDetails Volume 177Issue 4SApril 2007Page: 378-379 Advertisement Copyright & Permissions© 2016 by American Urological AssociationMetricsAuthor Information Andrea Gallina More articles by this author Jochen Walz More articles by this author Miriam Traumann More articles by this author Georg C. Hutterer More articles by this author Thorsten Schlomm More articles by this author Marco Roscigno More articles by this author James A. Eastham More articles by this author Peter T. Scardino More articles by this author Eric A. Klein More articles by this author Alwyn M. Reuther More articles by this author Francesco Montorsi More articles by this author Markus Graefen More articles by this author Hartwig Huland More articles by this author Fred Saad More articles by this author Pierre I. Karakiewicz More articles by this author Expand All Advertisement PDF DownloadLoading ...
Conception et Mise en Oeuvre d’un Emulateur de Chaînes de Conversion avec Lissage : Applications aux Houlogénérateurs Directs (2016)

International audience
Precise RF Phase Measurement by Optical Sideband Generation Using Mach–Zehnder Modulators (2023)

A novel radio frequency (RF) phase measurement method that uses optical modulation was proposed. The mathematical model of Mach–Zehnder modulator (MZM) characterization was reviewed. By measuring the output sideband power of the optical modulator, the phase difference of the electric signals fed to the modulator was experimentally measured, and picosecond-level accuracies were achieved. This technique is expected to be useful for radio-over-fiber-based antenna array systems.
Abstract 1763: Frequency of homologous recombination repair defects across breast cancer subtypes. (2013)

Abstract Introduction: Defects in homologous recombination (HR) repair have potential therapeutic relevance, and current clinical studies are focused on examining the efficacy of agents that exploit HR deficiency in triple negative breast cancer. A homologous recombination deficiency (HRD) score based on whole genome tumor LOH profiles has been developed that is highly correlated with defects in BRCA1/2, and other HR pathway genes, in ovarian cancer(1), and which predicts response to platinum-based neoadjuvant therapy in triple negative breast cancer(2). This study examines the frequency of BRCA1/2 defects and elevated HRD score across breast cancer subtypes as defined by IHC hormone receptor status. Methods: A targeted custom hybridization panel was developed targeting BRCA1, BRCA2, and 50,000 selected SNPs across the entire human genome. This panel, in combination with sequencing on the Illumina HiSeq, was used to analyze approximately 50 randomly ascertained tumors from each of 4 breast cancer subtypes (triple negative, ER+/Her2-, ER-/Her2+, ER+/Her2+) for BRCA1/2 somatic and germline mutations, and SNP allele frequencies. HRD scores were calculated using LOH profiles reconstructed from the SNP analysis. A BRCA1 promoter methylation assay was also performed on all samples. Results: BRCA1/2 somatic and germline mutations were detected in all breast cancer subtypes. BRCA1/2 mutations were observed most frequently in triple negative and ER+/Her2+ tumors. BRCA1 promoter methylation was confined almost exclusively to triple negative tumors. Association between elevated HRD score and BRCA defects was observed regardless of tumor type, and BRCA1/2 intact tumors with elevated HRD scores were observed in all breast cancer subtypes. Conclusions: Elevated HRD score is significantly associated with BRCA1/2 defects in breast cancer. BRCA1/2 defects and elevated HRD scores were observed in all subtypes of breast cancer, suggesting the presence of HR defects in genes other than BRCA1/2 are present in all breast cancer subtypes. HRD score could potentially be used to facilitate the expansion of platinum or PARP inhibitor therapy beyond triple negative breast cancer into other subtypes. Citation Format: Kirsten M. Timms, Victor Abkevich, Chris Neff, Brian Morris, Jennifer Potter, Thanh V. Tran, Jian Chen, Zaina Sangale, Eliso Tikishvili, Andrey Zharkikh, Michael Perry, Alexander Gutin, Jerry Lanchbury. Frequency of homologous recombination repair defects across breast cancer subtypes. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 1763. doi:10.1158/1538-7445.AM2013-1763
Dual-Polarized Phased Array With End-Fire Radiation for 5G Handset Applications (2019)

This communication proposes a dual-polarized end-fire phased array for 5G handset devices at 28 GHz. The proposed four-element array has low profile of 1.1 mm, small clearance of 2.7 mm, and symmetric patterns in the vertical plane. The array element is fed by substrate-integrated waveguide (SIW), which works as a waveguide (WG) antenna with vertically polarized radiation pattern. Two transition plates are introduced to improve the impedance matching of the WG antenna. The horizontal polarization is generated by exciting one of the transition plates as an antenna. The other transition plate is modified as a group of triangle strips to minimize its reflection to the horizontal radiation patterns. A −10 dB frequency bandwidth of 5.3% and a −6 dB bandwidth of 25% are achieved, overlapping between the vertical and horizontal polarization. The array scanning angle is from −54° to 44° at 29 GHz for both polarization. Within the scanning range, the end-fire gain varies from 7.48 to 8.14 dBi for the horizontal polarization, whereas from 4.49 to 8.05 dBi for the vertical polarization. Good agreements between simulations and measurements are well achieved and shown in this communication.
Transcriptional silencing of the p73 gene in acute lymphoblastic leukemia and Burkitt's lymphoma is associated with 5' CpG island methylation. (1999)

The p73 gene is located on 1p36.2-3, a region that is frequently deleted in human cancer. Because p73 encodes for a protein that is both structurally and functionally homologous to the p53 protein, p73 has been postulated to be a candidate tumor suppressor gene. To date, however, mutations of p73 have not been found. To study methylation of the p73 5'CpG island, a human bacterial artificial chromosome clone containing exon 1 and the 5' region of p73 was isolated. There was no evidence for p73 exon 1 methylation in normal tissues. In contrast, p73 was aberrantly methylated in approximately 30% of primary acute lymphoblastic leukemias (ALLs) and Burkitt's lymphomas. There was no evidence for methylation in any other types of hematological malignancies or solid tumors examined. In both leukemia cell lines and primary ALLs, methylation was associated with transcriptional loss of p73 by reverse transcription-PCR. We used single-strand conformational polymorphisms to screen for point mutations in a series of primary ALLs and found no mutations leading to a change in protein structure. Our results show that methylation of p73 is a frequent event in specific types of hematological malignancies and suggest that epigenetic silencing of p73 could have important consequences for cell-cycle regulation.
Mycobacterium tuberculosisprotein tyrosine phosphatase (PtpA) excludes host vacuolar-H+–ATPase to inhibit phagosome acidification (2011)

Mycobacterium tuberculosis (Mtb) pathogenicity depends on its ability to inhibit phagosome acidification and maturation processes after engulfment by macrophages. Here, we show that the secreted Mtb protein tyrosine phosphatase (PtpA) binds to subunit H of the macrophage vacuolar-H(+)-ATPase (V-ATPase) machinery, a multisubunit protein complex in the phagosome membrane that drives luminal acidification. Furthermore, we show that the macrophage class C vacuolar protein sorting complex, a key regulator of endosomal membrane fusion, associates with V-ATPase in phagosome maturation, suggesting a unique role for V-ATPase in coordinating phagosome-lysosome fusion. PtpA interaction with host V-ATPase is required for the previously reported dephosphorylation of VPS33B and subsequent exclusion of V-ATPase from the phagosome during Mtb infection. These findings show that inhibition of phagosome acidification in the mycobacterial phagosome is directly attributed to PtpA, a key protein needed for Mtb survival and pathogenicity within host macrophages.
Memory based computing (2011)

Conventional Field Programmable Gate Array (FPGA) architectures leverage on the purely spatial computing model where a design is realized in the form of a small multiple-input single-output lookup tables (LUTs) connected through programmable interconnect switches. However, such a model incorporates an elaborate programmable interconnect network which becomes a major performance bottleneck and leads to poor scalability across process technology nodes. In this paper we evaluate an alternative two-dimensional static random access memory (SRAM) array based reconfigurable computing fabric, referred to as "Memory Based Computing" (MBC) that departs from a purely spatial architecture by advocating multi-cycle evaluation at each computational element. Within a computational element, it uses a dense two-dimensional SRAM array to map large multi-input multi-output functions as LUT and evaluate them in time-multiplexed topological fashion. Multi-cycle execution at each computing node is accomplished using a local interconnect architecture. The proposed framework substantially reduces the requirement for global interconnects by folding computational resources onto a single computational element. We explore the design space for MBC to optimize the major design parameters and compare the performance, power dissipation and energy-delay product for benchmark applications between MBC and conventional SRAM-based FPGA. Simulation results show that compared to a clustered FPGA model, the proposed framework achieves 57% improvement in performance, 30% improvement in Energy Delay Product (EDP) and 10% improvement in technological scalability of performance for standard benchmark circuits. Finally, we validate the functionality of MBC framework and timing of different operations by mapping several small applications on a Cyclone III FPGA platform from Altera.
ASYMMETRIC SYNTHESIS OF CARBOCYCLIC PYRIMIDINE NUCLEOSIDES VIA π-ALLYLPALLADIUM COMPLEX (2001)

Racemic and enantiomerically pure carbocyclic pyrimidine nucleosides were synthesized efficiently by a convergent approach using Trost nucleophilic addition of π-allylpalladium complexes.
Supplementary Tables S1-S3 from Systematic siRNA Screen Unmasks NSCLC Growth Dependence by Palmitoyltransferase DHHC5 (2023)

&lt;p&gt;Tables S1-S3 Table S1. Non-small cell lung cancer cell lines used in the current study. Table S2. Clinicopathological characteristics for 194 primary patient samples (NSCLC). Table S3. siRNA used in screen (purchased from Qiagen) in 53 NSCLC lines and 5 HEBCs.&lt;/p&gt;
Impact of nitridation on the reliability of 4H-SiC(1120) MOS devices (2022)

Abstract The leakage current and flat-band voltage ( V FB ) instability of NO-nitrided SiC(11 <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" overflow="scroll"> <mml:mover accent="true"> <mml:mn>2</mml:mn> <mml:mo>¯</mml:mo> </mml:mover> </mml:math> 0) (a-face) MOS devices were systematically investigated. Although NO nitridation is effective in improving the interface properties, we found that it reduces the onset field of Fowler–Nordheim current by about 1 MV cm −1 , leading to pronounced leakage current. Synchrotron radiation X-ray photoelectron spectroscopy revealed that the nitridation reduces the conduction band offset at the SiO 2 /SiC interface, corroborating the above finding. Furthermore, systematical positive and negative bias stress tests clearly indicated the enhancement of V FB instability of nitrided a-face MOS devices against electron and hole injection.