gebhart/patrepeval huggingface dataset:
Data and scripts for SCLC_CellMiner: Integrated Genomics and Therapeutics Predictors of Small Cell Lung Cancer Cell Lines based on their genomic signatures (2020)

This is the repository of data and scripts for the analysis of the CellminerCDB-SCLC manuscript and website (https://discover.nci.nih.gov/SclcCellMinerCDB/) CellMiner-SCLC (https://discover.nci.nih.gov/SclcCellMinerCDB) integrates 118 patient-derived cell lines with drug sensitivity and genomic datasets, including high resolution methylome and RNAseq data. CellMiner-SCLC provides a new resource for SCLC research for this “recalcitrant cancer”. Of fundamental importance, we demonstrate the reproducibility and stability of the cell line datasets from different institutions (CCLE, GDSC, CTRP, NCI and UTSW). We validate the classification based on four master transcription factors: NEUROD1, ASCL1, POU2F3 and YAP1 and show transcription networks connecting them with the MYC genes (MYC, MYCL1 and MYCN) and the NOTCH and HIPPO pathways. We find that the 4 subsets express specific surface markers for antibody-targeted therapies. The YAP1-driven (SCLC-Y) cell lines differ from the other subsets by expressing the NOTCH pathway, epithelial-mesenchymal-transition (EMT) and antigen-presenting machinery (APM) genes, and by responding to mTOR and AKT inhibitors, suggesting the potential of NOTCH modulators, YAP1 inhibitors and immune checkpoint inhibitors for SCLC-Y tumors.
Pattern of Failure in Bladder Cancer Patients Treated with Radical Cystectomy: Rationale for Adjuvant Radiotherapy (2010)

Thus far, the role of adjuvant radiotherapy (RT) after radical cystectomy (RC) in urinary bladder cancer patients has yet to be defined. The purpose of this study is to analyze patterns of failure, and suggest the rationale for RT. Between 1986 and 2005, a total of 259 patients treated with RC and pelvic lymph node dissection was enrolled. The age range was 27-82 yr (median, 62 yr). Node positivity increased according to tumor staging. Patients were divided into the following two groups based on pathologic analysis: organ-confined disease group (n=135) and extravesical/lymph node-positive disease group (n=80). Pelvic failures (PF) were observed in 8 (4.9%) in organ-confined disease group, and 21 (21.7%) in extravesical/lymph node-positive disease group. Five-year PF-free survival rates were 91.2% in organ-confined disease group and 68.0% in extravesical/lymph node-positive disease group. Five-year cancer-specific survival rates were 86.2% in organ-confined disease group and 53.9% in extravesical/lymph node-positive disease group. In conclusion, a relatively high PF rate was observed in extravesical lymph node-negative and lymph node-positive disease patients in this study. Adjuvant pelvic RT may be considered to reduce pelvic failures in extravesical lymph node-positive bladder cancer. Future prospective trials are required to test the clinical benefit of adjuvant RT.
Design of a K-Winners-Take-All Model With a Binary Spike Train (2018)

A continuous-time K -winners-take-all (KWTA) neural model that can identify the largest K of N inputs, where command signal is described. The model is given by a differential equation where the spike train is a sum of delta functions. A functional block-diagram of the model includes N feed-forward hard-limiting neurons and one feedback neuron, used to handle input dynamics. The existence and uniqueness of the model steady states are analyzed, the convergence analysis of the state variable trajectories to the KWTA operation is proven, the convergence time and number of spikes required are derived, as well as the processing of time-varying inputs and perturbations of the model nonlinearities are analyzed. The main advantage of the model is that it is not subject to the intrinsic convergence of speed limitations of comparable designs. The model also has an arbitrary finite resolution determined by a given parameter, low complexity, and initial condition independence. Applications of the model for parallel sorting and parallel rank-order filtering are presented. Theoretical results are derived and illustrated with computer-simulated examples that demonstrate the model's performance.
Memory-based hardware-accelerated system for high-speed human detection (2014)

The real-world applicability of modern computer vision and recognition applications is limited by its real-time performance. Hardware-based systems can provide fast solutions for real-time limited problems; however, hardware-friendly solutions usually lack the flexibility to handle highly complex tasks. On the other hand, software-based solutions are used to tackle complex tasks and allow for greater flexibility but lack the speeds which hardware systems can provide. Inspired by the function of the human memory, we propose a hardware-accelerated multi-prototype and nearest neighbor (NN) search-based learning and classification system, which overcomes these flexibility limitations. A major deficiency for NN-based implementations is the computational demand for the searching and clustering processes. An FPGA-implemented coprocessor architecture for the Euclidean distance search was designed to resolve this deficiency. We benchmarked the system on the complex application of human detection. The experimental results revealed that the system outperformed other implementations by significantly reducing training times and attained a per sample detection speed of 2.24 s.
Development and binding characteristics of phosphonate inhibitors of SplA protease from Staphylococcus aureus (2013)

Staphylococcus aureus is responsible for a variety of human infections, including life-threatening, systemic conditions. Secreted proteome, including a range of proteases, constitutes the major virulence factor of the bacterium. However, the functions of individual enzymes, in particular SplA protease, remain poorly characterized. Here, we report development of specific inhibitors of SplA protease. The design, synthesis, and activity of a series of α-aminoalkylphosphonate diaryl esters and their peptidyl derivatives are described. Potent inhibitors of SplA are reported, which may facilitate future investigation of physiological function of the protease. The binding modes of the high-affinity compounds Cbz-Phe(P) -(OC6 H4 -4-SO2 CH3 )2 and Suc-Val-Pro-Phe(P) -(OC6 H5 )2 are revealed by high-resolution crystal structures of complexes with the protease. Surprisingly, the binding mode of both compounds deviates from previously characterized canonical interaction of α-aminoalkylphosphonate peptidyl derivatives and family S1 serine proteases.
Increased group 2 innate lymphoid cells in peripheral blood of adults with mastocytosis (2020)

Our findings suggest a role for ILC2s and pathogenic ILC2-mast cell crosstalk in mastocytosis. We hypothesize that a high cutaneous D816V<sup>+</sup> mast cell burden alters the skin microenvironment to induce chronic local ILC2 activation and their dissemination into the circulation. Activated ILC2s could contribute to skin symptoms by producing inflammatory mediators and by further augmenting mast cell mediator release.
Novel Protein-Repellent and Antibacterial Resins and Cements to Inhibit Lesions and Protect Teeth (2019)

Orthodontic treatment is increasingly popular as people worldwide seek esthetics and better quality of life. In orthodontic treatment, complex appliances and retainers are placed in the patients’ mouths for at least one year, which often lead to biofilm plaque accumulation. This in turn increases the caries-inducing bacteria, decreases the pH of the retained plaque on an enamel surface, and causes white spot lesions (WSLs) in enamel. This article reviews the cutting-edge research on a new class of bioactive and therapeutic dental resins, cements, and adhesives that can inhibit biofilms and protect tooth structures. The novel approaches include the use of protein-repellent and anticaries polymeric dental cements containing 2-methacryloyloxyethyl phosphorylcholine (MPC) and dimethylaminododecyl methacrylate (DMAHDM); multifunctional resins that can inhibit enamel demineralization; protein-repellent and self-etching adhesives to greatly reduce oral biofilm growth; and novel polymethyl methacrylate resins to suppress oral biofilms and acid production. These new materials could reduce biofilm attachment, raise local biofilm pH, and facilitate the remineralization to protect the teeth. This novel class of dental resin with dual benefits of antibacterial and protein-repellent capabilities has the potential for a wide range of dental and biomedical applications to inhibit bacterial infection and protect the tissues.
ChemInform Abstract: Replacement of BF4‐ by PF6‐ Makes Selectfluor Greener. (2013)

Abstract Changing the counterion in Selectfluor® from tetrafluoroborate to hexafluorophosphate significantly reduces catalyst loading in amide oxidation reactions.
Robust and secure light-weight resource reservation for unicast IP traffic (2002)

A lightweight resource reservation protocol for unicast Internet traffic is described. The key feature of the protocol is that resources can be reserved on a per-connection basis without introducing connection states in the network. Issues addressed in the paper include robustness against lost signalling messages, route changes and robustness against theft-of-service attacks.
CCDC 875186: Experimental Crystal Structure Determination (2012)

An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
In-line high-speed all-fiber polarimeter with true real-time acquisition for sensor systems based on fast polarization rotation (2014)

We report on an all fiber polarimetric optical detector system suitable for sensor applications that rely on fast polarization measurements. Our device exhibits an RF bandwidth of 500 MHz and an optical calibration bandwidth of over 30nm in the S-C-L-bands (1460-1625 nm) and above, with minimal PMD, PDL, and return loss when used in-line. A set of automated self-calibration procedures ensure high accuracy without the need for external polarization optics or reference polarimeters. We integrated our polarimeter into an acquisition systems capable of measuring fast polarization rotation events over long period of time with 250 MS/s peak sampling rate.
Synthesis and Realizations of Miniaturized Fractal Microwave and RF Filters", Int. Workshop on Microwave Filters (2011)

International audience
A retrospective study of the influence of the vitreomacular interface on macular oedema secondary to retinal vein occlusion (2017)

We did not identify an association between VRI status and treatment outcomes with anti-VEGF agents for ME secondary to RVO.
ChemInform Abstract: Zeolites as Catalysts in Organic Reactions: Condensation of Aldehydes with Benzene Derivatives. (1991)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Fecal Microbiota Transplantation Decreases Amyloid Load and Improves Cognition in Alzheimer’s (2019)

Abstract The efficacy of fecal microbiota transplantation (FMT) in Alzheimer’s disease has yet to be investigated. Here, we show that FMT is capable of providing neuroprotective effects in two groups of treated 5xFAD Alzheimer’s mice, old transgenic (Tg) mice fed fecal slurry from healthy, wild-type donors of similar age (Old Tg-FO) and old mice fed fecal slurry from younger healthy, wild-type donors (Old Tg-FY). Improved spatial and recognition memory in Old Tg-FY and enhanced recognition memory in Old Tg-FO were observed when compared to Old Tg-Control mice given saline. Crucially, there was significant decreases in cortical Aβ loading in all treated mice, demonstrating the therapeutic effects of FMT in improving cognition and reducing amyloid pathology in AD brains. One Sentence Summary Fecal microbial transplants reduce amyloid pathology and improve cognition in Alzheimer’s mice.
SU‐F‐T‐178: Optimized Design of a Diamond Detector Specifically Dedicated to the Dose Distribution Measurements in Clinical Proton Pencil Beams (2016)

Purpose: In proton‐therapy, pencil beam scanning (PBS) dosimetry presents a real challenge due to the small size of the beam (about 3 to 8 mm in FWHM), the pulsed high dose rate (up to 100 Gy/s) and the proton energy variation (about 30 MeV to 250 MeV). In the framework of French INSERM DEDIPRO project, a specifically dedicated single crystal diamond dosimeter (SCDDo) was developed with the objective of obtaining accurate measurements of the dose distribution in PBS modality. Methods: Monte Carlo simulations with MCNPX were performed. A small proton beam of 5 mm in FWHM was simulated as well as diamond devices with various size, thickness and holder composition. The calculated doses‐to‐diamond were compared with the doses‐to‐water in order to reduce the perturbation effects. Monte‐Carlo simulations lead to an optimized SCDDo design for small proton beams dosimetry. Following the optimized design, SCDDos were mounted in water‐equivalent holders with electrical connection adapted to standard electrometer. First, SCDDos performances (stability, repeatability, signal‐to‐background ratio…) were evaluated with conventional photon beams. Then, characterizations (dose linearity, dose rate dependence…) with wide proton beams were performed at proton‐therapy center (IC‐CPO) from Curie Institute (France) with the passive proton delivery technique, in order to confirm dosimetric requirements. Finally, depth‐dose distributions were measured in a water tank, for native and modulated Bragg Peaks with the collimator of 12 cm, and compared to a commercial PPC05 parallel‐plate ionization chamber reference detector. Lateral‐dose profiles were also measured with the collimator of 5 mm, and compared to a commercial SFD diode. Results: The results show that SCDDo design does not disturb the dose distributions. Conclusion: The experimental dose distributions with the SCDDo are in good agreement with the commercial detectors and no energy dependence was observed with this device configuration.
CYP2C19 genotype-guided antiplatelet therapy in a patient with clopidogrel resistance. (2012)

We report a switch in antiplatelet medication based on platelet function and CYP2C19 genotype test results in a 74-year-old man with severe coronary arterial disease. Upon bare metal stent implantation at age 66, clopidogrel therapy (75 mg/ day) was initiated to supplement aspirin. Over the next eight years, the patient required multiple percutaneous coronary interventions for de novo coronary stenosis and in-stent restenosis. Platelet reactivity measured while on clopidogrel therapy was high, consistent with clopidogrel resistance. CYP2C19 genotype testing then revealed homozygosity for the *2 null allele. The *2/*2 designation indicates poor metabolizer status, indicating deficient capacity of the cytochrome p450 2C19 enzyme for activation of clopidogrel. A medication switch to prasugrel,which does not rely on activation by the 2C19 enzyme, reduced platelet reactivity by 86%. The patient has suffered no cardiovascular events in the 18 months since initiation of prasugrel therapy.
High temperature getter for compact HID lamps (2005)

In high intensity discharge (HID) lamps getters are generally used to remove gaseous impurities that otherwise may have negative effects on the lamp characteristics.Hydrogen, in particular, is a dangerous impurity because it can induce ignition problems and, in lamps with a quartz burner, it can diffuse from the outer bulb into the arc tube and cause early corrosion of the quartz.Recently a new getter, suitable to work in compact HID lamps operated at high temperatures, has been developed: this getter is an appropriate solution to sorb hydrogen at high working temperatures in lamps where the use of a conventional getter is inadequate because of its small capacity for gettering hydrogen, its relatively high hydrogen equilibrium pressure and problems associated with the evaporation of getter and container material.The newly developed getter, named high temperature getter (HTG), is based on a special alloy enclosed in a niobium container. The new alloy is very effective in sorbing hydrogen in the temperature region of 500–900°C.It has been proved that by introducing the HTG the processing of high-wattage compact HID lamps can be simplified and a better lamp performance can be obtained.
Multi-parametric photoacoustic microscopy with 1.2-MHz A-line rate (Conference Presentation) (2018)

In the current form of multi-parametric photoacoustic microscopy (PAM), imaging hemoglobin concentration and blood flow speed requires dense sampling. Moreover, large-scale recording beyond the focal zone of ultrasonic transducer requires time-consuming mechanical scan of the optical-acoustic dual foci. Thus, the image acquisition time of multi-parametric PAM has been severely limited by the laser repetition rate and the focal diameter of the transducer. Here, we report an ultrahigh-speed multi-parametric PAM with 1.2-MHz A-line rate for simultaneous real-time imaging of hemoglobin concentration, blood oxygenation, and blood flow in the mouse brain. Capitalizing on the pronounced stimulated Raman scattering in pure silica-core polarization-maintaining single-mode optical fibers, a dual-wavelength (532 and 558 nm) nanosecond laser with 1.2-MHz pulse repetition rate has been developed. Using a weakly focused ultrasonic transducer, we have achieved real-time acquisition of multi-parametric PAM images at a frame rate of 2.2 Hz over the 250-μm-diameter acoustic focal zone. By employing optical-mechanical hybrid scan, 25 dual-wavelength B-scans can be acquired simultaneously within one mechanical-scan trip, leading to a 25-fold improvement of imaging speed. As a result, the imaging frame rate is improved from 0.08 Hz in the conventional multi-parametric PAM to 2.2 Hz. The utility of this new PAM technology has been demonstrated in a mouse model of epilepsy by studying the dynamic neurovascular uncoupling during status epilepticus.
Inhibition of NO synthesis minimally affects the dynamic baroreflex regulation of sympathetic nerve activity (1997)

The purpose of this investigation was to examine the role of nitric oxide (NO) in the dynamic baroreflex regulation of cardiac sympathetic nerve activity. In anesthetized rabbits, we imposed random pressure perturbations on the isolated carotid sinuses before and after the intravenous administration of NG-monomethyl-L-arginine. We characterized the dynamic properties relating carotid sinus pressure input to sympathetic nerve activity by means of a transfer function analysis. NG-monomethyl-L-arginine decreased the corner frequency of the transfer function (0.100 +/- 0.054 vs. 0.074 +/- 0.035 Hz; P < 0.05), whereas other parameters such as the steady-state gain and transmission lag time remained unchanged. Although cursory examination of these findings would suggest a possible contribution of NO in the dynamic baroreflex regulation of sympathetic nerve activity, quantitative assessment of the transfer function reveals only a minimal effect on the baroreflex regulation of arterial pressure, particularly under closed-loop conditions. We conclude that NO noticeably affects the dynamic baroreflex regulation of sympathetic nerve activity. However, it may not significantly affect arterial pressure regulation through central modulation of the carotid sinus baroreflex.
ChemInform Abstract: Synthesis of Enantiomerically Pure 4‐Alkylsubstituted Tryptophan Derivatives by a Combination of Organometallic Reactions with Enantioselective Enzymatic Transformations. (1995)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Coherent Friendly Dispersion Map for Direct Detection Transmission Formats (2012)

A dispersion map that meets the conflicting needs of coherent and direct detection transmission is presented. Performance improvements over a conventional map are verified for coherent transmission by experiments and simulations.
Partial Activation of Natural Killer and γδ T Cells by Classical Swine Fever Viruses Is Associated with Type I Interferon Elicited from Plasmacytoid Dendritic Cells (2014)

Vaccination with live attenuated classical swine fever virus (CSFV) vaccines can rapidly confer protection in the absence of neutralizing antibodies. With an aim of providing information on the cellular mechanisms that may mediate this protection, we explored the interaction of porcine natural killer (NK) cells and γδ T cells with CSFV. Both NK and γδ T cells were refractory to infection with attenuated or virulent CSFV, and no stimulatory effects, as assessed by the expression of major histocompatibility complex (MHC) class II (MHC-II), perforin, and gamma interferon (IFN-γ), were observed when the cells were cultured in the presence of CSFV. Coculture with CSFV and myeloid dendritic cells (mDCs) or plasmacytoid dendritic cells (pDCs) showed that pDCs led to a partial activation of both NK and γδ T cells, with upregulation of MHC-II being observed. An analysis of cytokine expression by infected DC subsets suggested that this effect was due to IFN-α secreted by infected pDCs. These results were supported by ex vivo analyses of NK and γδ T cells in the tonsils and retropharyngeal lymph nodes from pigs that had been vaccinated with live attenuated CSFV and/or virulent CSFV. At 5 days postchallenge, there was evidence of significant upregulation of MHC-II but not perforin on NK and γδ T cells, which was observed only following a challenge of the unvaccinated pigs and correlated with increased CSFV replication and IFN-α expression in both the tonsils and serum. Together, these data suggest that it is unlikely that NK or γδ T cells contribute to the cellular effector mechanisms induced by live attenuated CSFV.
Impurity Doping Effect on Piezoelectricity and Strain Induced by Electric Field in Piezoelectric Ceramics (1996)

The effects of impurities on piezoelectric constant and the strain characteristics were investigated for ceramics with the composition of (Pb0.95Sr0.05)(Zr0.54Ti0.46)O3. The piezoelectric constant d31 of samples doped with Nb and W was larger than that of non-doped samples, and d31 of samples doped with Fe and Ni was smaller than that of non-doped samples. It was found that the actually found strain (δ) under high DC electric field was larger for donor doping and smaller for acceptor doping. In all samples, the δ values were larger than the calculated strain (δcal) obtained by multiplying d31 by DC electric field. This result suggested that the strain (δp) of domain orientation due to electric field exists. The δp values of samples doped with donor were larger than that of non-doped samples, and those of samples with acceptor were smaller than that of non-doped samples. We found that δp is related to the binding force of domain, and that the binding force of domain is dependent on the internal field of space charge produced by dopants.