gebhart/patrepeval huggingface dataset:
A framework for realistic virtual clinical trials in photon counting computed tomography (2019)

Although photon counting systems have shown strong clinical potential, this technology has not yet been fully evaluated or optimized for specific clinical applications. The purpose of this study was to develop a framework for realistic virtual clinical trials (VCTs) in photon counting CT (PCCT) imaging. We developed a photon counting CT simulator based on the geometry and physics of an existing research prototype scanner. The developed simulator models primary, scatter, and noise signals, detector responses, vendor-specific bowtie filters and X-ray spectra, axial/helical trajectories, vendor-specific acquisition modes, and multiple energy thresholds per detector pixel. The simulation procedure is accelerated by parallel processing using multiple GPUs. The generated projection images can be reconstructed using generic reconstruction algorithms as well as a commercial reconstruction software (ReconCT Siemens). A computational model of a physical Mercury phantom was imaged at multiple energy thresholds (25 and 75 keV) and dose levels (36, 72, 144, and 216 mAs). Noise magnitude was measured in the simulated images and compared against noise measurements in a real scan acquired with a research prototype photon counting scanner (Siemens Healthcare). The results showed that our simulator was capable of synthesizing realistic photon counting CT data. The simulator can be combined with realistic 4D high-resolution XCAT phantoms with intra-organ heterogeneities to conduct VCTs for specific clinical applications. This framework can greatly facilitate the evaluation, optimization, and eventual clinical use of PCCT.
Nanoparticle Shape Anisotropy Dictates the Collective Behavior of Surface-Bound Ligands* (2020)

This chapter reports on the modification of the properties of surface-confined ligands in nanoparticle systems through the introduction of shape anisotropy. Specifically, triangular gold nanoprisms, densely functionalized with oligonucleotide ligands, hybridize to complementary particles with an affinity that is several million times higher than that of spherical nanoparticle conjugates functionalized with the same amount of DNA. It is well established that the size of a nano-object significantly affects its physical properties. However, recent interest has centered around the concept of nanoparticle shape and the properties that arise from geometric anisotropy. In addition, DNA-functionalized gold nanoparticles (DNA-AuNPs) have been shown to exhibit unique properties that can be directly linked to a dense surface coverage of oligonucleotides. These include sharp melting transitions when hybridized to complementary particles, elevated binding constants for the capture of free DNA, and the ability to naturally transfect cells.
Genes Required for Bacillus anthracis Secondary Cell Wall Polysaccharide Synthesis (2016)

The secondary cell wall polysaccharide (SCWP) is essential for Bacillus anthracis growth, cell shape, and division. SCWP is comprised of trisaccharide repeats (→4)-β-ManNAc-(1→4)-β-GlcNAc-(1→6)-α-GlcNAc-(1→) with α-Gal and β-Gal substitutions; however, the genetic determinants and enzymes for SCWP synthesis are not known. Here, we identify WpaA and WpaB and report that depletion of these factors affects vegetative growth, cell shape, and S-layer assembly. We hypothesize that WpaA and WpaB are involved in the assembly of SCWP prior to transfer of this polymer onto peptidoglycan.
Predicting Salmonella Populations from Biological, Chemical, and Physical Indicators in Florida Surface Waters (2013)

Coliforms, Escherichia coli, and various physicochemical water characteristics have been suggested as indicators of microbial water quality or index organisms for pathogen populations. The relationship between the presence and/or concentration of Salmonella and biological, physical, or chemical indicators in Central Florida surface water samples over 12 consecutive months was explored. Samples were taken monthly for 12 months from 18 locations throughout Central Florida (n = 202). Air and water temperature, pH, oxidation-reduction potential (ORP), turbidity, and conductivity were measured. Weather data were obtained from nearby weather stations. Aerobic plate counts and most probable numbers (MPN) for Salmonella, E. coli, and coliforms were performed. Weak linear relationships existed between biological indicators (E. coli/coliforms) and Salmonella levels (R(2) < 0.1) and between physicochemical indicators and Salmonella levels (R(2) < 0.1). The average rainfall (previous day, week, and month) before sampling did not correlate well with bacterial levels. Logistic regression analysis showed that E. coli concentration can predict the probability of enumerating selected Salmonella levels. The lack of good correlations between biological indicators and Salmonella levels and between physicochemical indicators and Salmonella levels shows that the relationship between pathogens and indicators is complex. However, Escherichia coli provides a reasonable way to predict Salmonella levels in Central Florida surface water through logistic regression.
Phorbol ester-mediated inhibition of growth and regulation of proto-oncogene expression in the human T cell leukemia line JURKAT. (1991)

The expression and function of several proto-oncogenes were examined in a human acute T cell leukemia line, JURKAT, during phorbol ester-induced terminal differentiation. Treating JURKAT cells with the phorbol ester tetradecanoyl phorbol acetate (TPA) inhibited their proliferation and induced expression of the gene for the interleukin 2 receptor alpha chain (IL2R-alpha), consistent with previous reports. In unstimulated proliferating JURKAT cells, high levels of C-MYC, N-RAS, and BCL2 mRNAs were found that diminished rapidly following TPA-induced cessation of growth. In contrast, accumulation of mRNAs for the C-FOS, C-JUN, and EGR-1 genes increased markedly in TPA-treated cells and preceded the induction of IL2R-alpha mRNA. Expression of C-MYB, C-RAF-1, C-LCK, C-FYN, and C-FGR proto-oncogenes was relatively unchanged. To explore directly the function of two of these protooncogenes in regulating the growth of JURKAT T cells, we stably transferred C-MYC and BCL2 expression plasmids into these cells. Despite sustained expression of C-MYC, BCL2, or the combination of these protooncogenes, TPA continued to inhibit JURKAT cell growth and to induce IL2R expression. Thus, although C-MYC and BCL2 proto-oncogene expression correlated with proliferation in TPA-treated JURKAT cells, continuous over-expression of even the combination of these oncogenes was insufficient for abrogating the effects of TPA in these leukemic T cells. Because human lymphoid malignancies frequently contain chromosomal translocations that deregulate the expression of C-MYC and BCL2, our findings could have relevance for attempts to induce terminal differentiation of leukemic cells by in vitro exposure of patients' bone marrow cells to phorbol esters.
Selective Conversion of Lignin-Derivable 4-Alkylguaiacols to 4-Alkylcyclohexanols over Noble and Non-Noble-Metal Catalysts (2016)

Recent lignin-first catalytic lignocellulosic biorefineries produce large quantities of two potential platform chemicals, 4-n-propylguaiacol (PG) and 4-n-propylsyringol. Because conversion into 4-n-propylcyclohexanol (PCol), a precursor for novel polymer building blocks, presents a promising valorization route, reductive demethoxylation of PG was examined here in the liquid-phase over three commercial hydrogenation catalysts, viz. 5 wt % Ru/C, 5 wt % Pd/C and 65 wt % Ni/SiO2–Al2O3, at elevated temperatures ranging from 200 to 300 °C under hydrogen atmosphere. Kinetic profiles suggest two parallel conversion pathways: Pathway I involves PG hydrogenation to 4-n-propyl-2-methoxycyclohexanol (PMCol), followed by its demethoxylation to PCol, whereas Pathway II constitutes PG hydrodemethoxylation to 4-n-propylphenol (PPh), followed by its hydrogenation into PCol. The slowest step in the catalytic formation of PCol is the reductive methoxy removal from PMCol. Moreover, under the applied reaction conditions, PCol may react further into hydrocarbons. The following criteria are therefore essential to reach a high PCol yield: (i) catalytic pathway II is preferred as this route does not involve stable intermediates; (ii) reactivity of PMCol should be higher than that of PCol, and (iii) the overall carbon balance should be high. Both the catalyst type and the reaction conditions have a substantial impact on the PCol yield. Only the commercial Ni catalyst meets the three criteria, provided the reaction is performed at 250 °C in hexadecane. Additional advantages of this solvent choice are a high boiling point (low operational pressure in closed reactor systems), high solubility of PG and derived products, high thermal, reductive stability, and easy derivability from fatty biomass feedstock. This Ni catalyst also showed an excellent stability in recycling runs and is capable of converting highly concentrated (up to 20 wt %) PG in hexadecane. Ru and Pd on carbon showed a low PCol yield, as they are not conform the three criteria. Low hydrogen pressure favors Pathway II, resulting in a very high PCol yield of 85% at 10 bar. Catalytic conversion of guaiacol, 4-methyl- and 4-ethylguaiacol in comparable circumstances showed similarly high yields of the corresponding cyclohexanols.
GS0329 Strain Measurement Properties by Small Type of Digital Output Sensor using Oscillator Circuit (2016)

The strain measurement system using CMOS inverter oscillator circuits can be omit an amplifier because a counting device measures frequency changes of circuit voltage output caused by resistance changes of a strain gauge, then the miniaturization of this system become possible comparatively easily. In this study, the authors manufactured a new small type of digital output strain sensor using CMOS inverter oscillator circuits. This digital output strain sensor was applied to the strain measurement on static tensile tests of specimens and its measurement accuracy was examined. The test results showed that the same level of accuracy as conventional sensor has been achieved by this digital output strain sensor.
Nanoscale Polymer Electrolytes:  Ultrathin Electrodeposited Poly(Phenylene Oxide) with Solid-State Ionic Conductivity (2004)

Incorporating ions within electrodeposited polymer dielectric films creates ultrathin solid electrolytes on a length scale (<50 nm) that bridges molecular electronics and conventional electrochemical devices. Electrooxidation of phenol in basic acetonitrile generates electrodeposited nanoscale (21 ± 2 nm), pinhole-free poly(phenylene oxide), PPO, films on indium−tin-oxide substrates. Solid-state electrical measurements using top electrode contacts (vapor-deposited Au, liquid Hg, or liquid Ga−In eutectic) confirm that these PPO films are electronically insulating (7 ± 2 × 10-12 S cm-1) with a high dielectric strength (1.7 ± 0.1 × 106 V cm-1). The insulating film is converted to an ultrathin solid polymer electrolyte by soaking in a solution of LiClO4−propylene carbonate and then heating under vacuum to remove solvent. Atomic force microscopy establishes that the salt-impregnated film is thicker (43 ± 10 nm) than the as-prepared PPO film. The X-ray photoelectron spectroscopic measurements suggest minimal retention of solvent in the film. Electrochemical impedance measurements demonstrate that the incorporated ions are mobile in the solid state with an ionic conductivity of 7 ± 4 × 10-10 S cm-1. Such ultrathin solid polymer electrolytes should enable progress toward nanoscopic solid-state ionic devices and power sources.
A medication adherence monitoring system for pill bottles based on a wearable inertial sensor (2014)

This paper presents a medication adherence monitoring system for pill bottles based on a wearable inertial sensor. Signal templates corresponding to the two actions of twist-cap and hand-to-mouth are created using a camera-assisted training phase. The act of pill intake is then identified by performing a moving window dynamic time warping in real-time between signal templates and the signals acquired by the wearable inertial sensor. The outcomes of the experimentations carried out indicate that the developed medical adherence monitoring system identifies the act of pill intake with a high degree of accuracy.
Antisense MBD2 gene therapy inhibits tumorigenesis (2002)

These results support the hypothesis that one or both of the functions described for MBD2 are critical in tumorigenesis and that MBD2 is a potential anticancer target.
Supercritical fluid extraction of mastic gum (Pistacia lentiscus var. chia) and phytochemical characterization of the generated extracts (2016)

The European Medicines Agency (EMA) recently issued an assessment report concerning the role of Chios mastic gum (the resin of Pistacia lentiscus L. var. chia) against mild dyspeptic disorders and the symptomatic treatment of minor inflammations. Mastiha has been proven to be effective against several gastrointestinal disorders, most of the times connected to the bacterium Helicobacter pylori [1]. Mastic is a complex chemical mixture, consisting of the polymer (beta-myrcene), the essential oil and the triterpenic fraction [2]. There are indications that the activity of mastic against H. pylori is localized to the total mastic extract without the polymer, i.e. the triterpenic fraction[3]. In the present study Supercritical fluid extraction technology was used for the development of an environmentally friendly and stepwise methodology, resulting in the extraction and enrichment of the valuable constituents of the resin. Application of several experimental conditions yielded to a volatile and a bioactive triterpenic fraction, while the polymer was finally isolated. The volatile fraction, analyzed by GC-MS, was found of improved composition and of higher resemblance to mastic resin in comparison to the essential oil obtained by distillation. The triterpenic fraction was separated to the acidic and the neutral part. The GC-MS analysis of the neutral part proved that triterpenes were the major constituents (mainly noroleanenone and noroleanenol derivatives, dammarane and oleanenone derivatives, beta-amyrin, beta-amyrone and oleanonic aldehyde). For the analysis of the acidic fraction a new LC-HRMS/MS methodology was developed for the first time on an Orbitrap platform. The extract was found to contain a large number of triterpenic acids. The major ones were identified as isomasticadienoic, masticadienoic, oleanonic and moronic, while the structures of minor triterpenic acids, like masticadienolic and isomasticadienolic were also identified.
Biodirected epitaxial nanodeposition of polymers on oriented macromolecular templates (2002)

Biodirected epitaxial nanodeposition of polymers was achieved on a template with an oriented molecular surface. Acetobacter xylinum synthesized a ribbon of cellulose I microfibrils onto a fixed, nematic ordered substrate of glucan chains with unique surface characteristics. The substrate directed the orientation of the motion due to the inverse force of the secretion during biosynthesis, and the microfibrils were aligned along the orientation of the molecular template. Using real-time video analysis, the patterns and rates of deposition were elucidated. Field emission scanning electron microscopy revealed that a strong molecular interaction allowed for the deposition of nascent biosynthesized 3.5-nm cellulose microfibrils with inter-microfibrillar spacings of 7-8 nm on the surface of the template. The cellulose was deposited parallel to the molecular orientation of the template. Directed cellulose synthesis and ordered movement of cells were observed only by using a nematic ordered substrate made from cellulose, and not from ordered crystalline cellulose substrates or ordered cellulose-related synthetic polymers such as polyvinyl alcohol. This unique relationship between directed biosynthesis and the ordered fabrication from the nano to the micro scales could lead to new methodologies for the design of functional materials with desired nanostructures.
Dynamic hit logic with embedded 8Kb SRAM in 45nm SOI for the zEnterprise&#x2122; processor (2011)

With the push to ever higher core frequencies, more logic functions are making their way onto critical path SRAMs in the L1 cache look up structure. Described in this paper is a 14 bit dynamic hit logic scheme with an embedded 8K bit SRAM in IBM's 45nm SOI. The hit logic uses a "search-for-a-hit" scheme (i.e., XOR's followed by AND functions, pre-charged to a miss) to provide optimal performance, timing, and power. A custom microcode programmable Array-Built -In-Self-Test (ABIST) engine tests both the SRAM and hit logic function jointly, resulting in comprehensive "at-speed" test coverage to guarantee circuit functionality and timing margins. The SRAM is organized as a 64x15bx8W (way, or set) array and uses a 6T SRAM cell (1Read/1Write, 0.462μm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> ) in a "domino" hierarchal dual read bitline approach.
Generation of femtosecond high-power optical pulses from a hybrid mode-locked semiconductor laser (1991)

Compact and efficient sources of high repetition rate, high peak power optical pulses are needed to replace the standard ultrashort optical pulse generation schemes because of their relatively large size and poor wall plug efficiency. In this paper, we present a hybrid mode-locked semiconductor laser system that is capable of producing optical pulses of 207 fsec in duration with peak powers in excess of 150 W. To the best of our knowledge, these optical pulses are both the shortest and most intense ever produced from an all-semiconductor laser diode system. The optical pulses were generated by forming a hybrid mode-locked external cavity semiconductor laser, which incorporates a GaAs/AlGaAs semiconductor traveling wave amplifier as the gain medium, a multiple quantum well (MQW) saturable absorber, and a four-prism sequence to compensate for group velocity dispersion.
Trends in packaging of high power semiconductor laser bars (1997)

Several different approaches to packaging high power diode laser bars for pumping solid state lasers or for direct diode laser applications are examined. The benefit and utility of each package is strongly dependent upon the fundamental optoelectronic properties of the individual diode laser bars. Factors which influence these properties are outlined and comparisons of packaging approaches for these materials are made.
Ultrasound and optical tissue-mimicking phantom for bi-modality imaging of prostate cancer diagnosis (2009)

International audience
Transformation of Alkyl N-(Vinyloxy)benzimidates to Alkyloxazoles. Mechanism and Extension (1994)

Abstract Transformation of alkyl N-(vinyloxy)benzimidates to alkyloxazoles proceeds through the intermediates: a charge-separated 1,2-oxazetidine derivative and then 1-hydroxy-2-[[methylthio(phenyl)methylene]imino]maleic acid diester, while their photochemical transformation takes place via a concerted [1,3] sigmatropic shift. As the extension of this reaction, the preparation of the precursor proposed for virginiamycin M2 synthesis and the reaction of N-analogs of alkyl N-(vinyloxy)benzimidates are described.
Endomyocardial biopsy-integrating electrode at the bioptome tip (2015)

Background: The addition of electroanatomic mapping to a standard echo-guided endomyocardial biopsy could identify areas of abnormal pathology and increase the diagnostic yield of the procedure. Methods and results: In this demonstration of a novel technique, a 45-year-old woman with clinical suspicion for cardiac sarcoidosis underwent right ventricular bipolar electroanatomical mapping with identification of areas of signal fractionation and low voltage. A bioptome, configured to record an electrogram from the tip, was then visualized on the three-dimensional electroanatomic mapping (3DEAM) system, and directed to these areas. The biopsy was assisted by the use of a steerable introducer sheath, and by recording unipolar and extended bipolar signals from the bioptome tip. A prominent change in the signal was detected by the electrode at the bioptome tip when the jaws closed on the endomyocardial tissue. Patient tolerated the procedure without complications, and the biopsied samples were appropriate for pathological analysis. Conclusions: Using existing technology, the 3DEAM, which integrates unipolar and bipolar signal from the bioptome tip, is feasible, and can be safely added to a standard echocardiographically guided endomyocardial biopsy. Future studies should investigate whether such a technique could increase the safety and diagnostic yield of endomyocardial biopsies in patients with suspected cardiomyopathies.
Pharmacogenetic Content of Commercial Genome-Wide Genotyping Arrays (2018)

The combination of the Affymetrix precision medicine array and PharmacoScan arrays provided both genome-wide and pharmacogene coverage, which is crucial in the discovering of new variants responsible for drug adverse effects. These results will help in the design of pharmacogenomic studies and will enable a critical review of results from past studies.
Near-field mapping of infrared optical antennas (2008)

The near-field distribution of linear optical antennas is measured with phase-contrast scattering-type near-field microscopy (s-SNOM). A distinct scaling behavior with antenna length is observed for different structures with and without gap. © 2008 Optical Society of America.
A comparison of perpendicular and longitudinal recording (1988)

Based on the projected error rate, an optimistic figure of merit is established which applies to general pulse shapes. This figure of merit is used to compare the performance of thin-film longitudinal and double-layer perpendicular recording systems. Although the precise comparison depends on the details of the dominant noise mechanism, there does not appear to be a significant advantage to double-layer perpendicular recording for rigid disk products.
ChemInform Abstract: AZAMORPHINAN UND VERWANDTE VERBINDUNGEN 3. MITT. SYNTH. VON 3‐HYDROXY‐N‐SUBSTITUIERTEN‐9‐AZAMORPHINANEN (1971)

Abstract Aufgrund der z.Tl. guten Morphin‐ähnlichen Wirkung verschiedener bekannter Azamorphinane werden weitere Vertreter dieser Substanzklasse hergestellt.
Avoiding common security flaws in composed service-oriented systems (2012)

Network-centric information systems are increasingly called upon to support complex tasks and missions that serve multiple communities of interest. As a result, existing capabilities are exposed as services in a service-oriented system, and newer capabilities are derived by discovering and composing available services. While service-orientation enables and facilitates such composition-based system construction, the evolving nature and variety of standards and the varying level of compliance of otherwise feature-rich vendor products has made achieving acceptable level of security and resilience in such systems a daunting and error-prone task. This paper presents a number of factors that contribute to the security of composed service-oriented systems, and outlines ways to avoid common pitfalls and mistakes that stem from these factors and weaken the resiliency and survivability of the composed system.
Conjugate Reduction of α,β‐Unsaturated Carbonyl Compounds Catalyzed by a Copper Carbene Complex. (2003)

Abstract For Abstract see ChemInform Abstract in Full Text.