gebhart/patrepeval huggingface dataset:
Extraction of Airways From CT (EXACT'09) (2012)

This paper describes a framework for establishing a reference airway tree segmentation, which was used to quantitatively evaluate fifteen different airway tree extraction algorithms in a standardized manner. Because of the sheer difficulty involved in manually constructing a complete reference standard from scratch, we propose to construct the reference using results from all algorithms that are to be evaluated. We start by subdividing each segmented airway tree into its individual branch segments. Each branch segment is then visually scored by trained observers to determine whether or not it is a correctly segmented part of the airway tree. Finally, the reference airway trees are constructed by taking the union of all correctly extracted branch segments. Fifteen airway tree extraction algorithms from different research groups are evaluated on a diverse set of twenty chest computed tomography (CT) scans of subjects ranging from healthy volunteers to patients with severe pathologies, scanned at different sites, with different CT scanner brands, models, and scanning protocols. Three performance measures covering different aspects of segmentation quality were computed for all participating algorithms. Results from the evaluation showed that no single algorithm could extract more than an average of 74% of the total length of all branches in the reference standard, indicating substantial differences between the algorithms. A fusion scheme that obtained superior results is presented, demonstrating that there is complementary information provided by the different algorithms and there is still room for further improvements in airway segmentation algorithms.
Biosynthesis of benastatin A. (1992)

The biosynthesis of benastatin A, produced by Streptomyces sp. MI384-DF12, has been studied by feeding experiments with 14C- and 13C-labeled compounds followed by measurement of radioactivity and 13C NMR analysis. The results indicate that benastatin A is derived from two methionine units and fourteen acetate units, condensed in the "head-to-tail" fashion of typical polyketide biosynthesis.
Heat shock protein 90-targeted photodynamic therapy enables treatment of subcutaneous and visceral tumors (2020)

Photodynamic therapy (PDT) ablates malignancies by applying focused near-infrared (nIR) light onto a lesion of interest after systemic administration of a photosensitizer (PS); however, the accumulation of existing PS is not tumor-exclusive. We developed a tumor-localizing strategy for PDT, exploiting the high expression of heat shock protein 90 (Hsp90) in cancer cells to retain high concentrations of PS by tethering a small molecule Hsp90 inhibitor to a PS (verteporfin, VP) to create an Hsp90-targeted PS (HS201). HS201 accumulates to a greater extent than VP in breast cancer cells both in vitro and in vivo, resulting in increased treatment efficacy of HS201-PDT in various human breast cancer xenografts regardless of molecular and clinical subtypes. The therapeutic index achieved with Hsp90-targeted PDT would permit treatment not only of localized tumors, but also more diffusely infiltrating processes such as inflammatory breast cancer.
Occupational hand eczema among nursing staffs inKorea:Self‐reported hand eczema and contact sensitization of hospital nursing staffs (2013)

Occupational hand eczema is frequent in hospital workers, especially in nurses. A comprehensive understanding regarding hand eczema is essential for establishing proper prevention and treatment strategies. The purpose of this study was to identify the risk factors for hand eczema in hospital nursing staffs. A self-administered questionnaire study was performed on hospital nursing staffs at a single general hospital in Korea. In addition, 70 patients with hand eczema underwent patch testing. Five hundred and twenty-five of 700 invited nurses completed the study (response rate, 75.0%). The overall frequency of symptom-based hand eczema was 75.6%, and self-reported hand eczema was 31.0%. Risk factors for hand eczema were young age, history of atopic dermatitis, frequent hand washing (>20 times/day) and long duration of glove wearing (>5 min). Hand eczema was less frequent among frequent hand moisturizer users (>3-4 times/day). Positive patch test reactions were observed in 61.4%. Frequent allergens were nickel sulfate (35.7%), cobalt chloride (28.6%) and thiomersal (21.4%). Among various antibiotics, ciprofloxacin (11.4%), trimethoprim/sulfamethoxazole (11.4%) and gentamicin (7.1%) were revealed as common allergens, in order of frequency. Hand eczema is quite common among hospital nursing staffs. Proper preventive programs and educations are demanded.
Sol–gel processes at the droplet interface: hydrous zirconia and hafnia nanocapsules by interfacial inorganic polycondensation (2012)

We report a simple method to prepare nanocapsules of hydrous zirconia and hafnia by interfacial precipitation in water-in-oil miniemulsions. We show that the sol–gel precipitation of transition metal hydroxides, exemplified for the cases of zirconium and hafnium, can be driven to the droplet interface by addition of an organic base. The prompt addition of triethylamine generates hydroxide ions at the interface, which initiate a polycondensation of the metal hydroxo species. Electron and X-ray diffractions indicate that the resulting materials are amorphous, but can be transformed to monoclinic ZrO2 or HfO2 upon thermolytic treatment. Mixed oxides of Hf and Zr with different compositions (HfxZr1−xO2) can also be formed by using the desired ratios of precursors. Furthermore, the ability of the hollow particles to encapsulate efficiently hydrophilic materials without leakage has been proven with the example of a water-soluble dye (fluorescein isothiocyanate).
Pretreatment with a soluble activin type IIB receptor/Fc fusion protein improves hypoxia-induced muscle dysfunction (2009)

Hypoxia, or reduced oxygen, occurs in a variety of clinical and environmental situations. Hypoxic exposure is associated with decreased muscle mass and a concomitant reduction in exercise capacity, although the exact mechanisms are not completely understood. The activin type IIB receptor (ActRIIB) is a receptor for transforming growth factor-beta (TGFbeta) superfamily members that are involved in the negative regulation of lean tissue mass. Given that hypoxia has negative effects on muscle mass and function and that modulation of the ActRIIB has been shown to increase muscle mass, we tested the hypothesis that pharmacological targeting of the ActRIIB for 2 wk would attenuate the loss of muscle mass and function in mice after exposure to normobaric hypoxia. ActRIIB modulation was achieved using a soluble activin receptor/Fc fusion protein (sActRIIB) in mice housed in a hypoxic chamber for 1 or 2 wk. Hypoxia induced a reduction in body weight in PBS- and sActRIIB-treated mice, although sActRIIB-treated mice remained larger throughout the hypoxic exposure. The absolute forces generated by extensor digitorum longus muscles were also significantly greater in sActRIIB- than PBS-treated mice and were more resistant to eccentric contraction-induced force drop after eccentric lengthening contractions. In summary, sActRIIB pretreatment attenuated hypoxia-induced muscle dysfunction. These data suggest that targeting the ActRIIB is an effective strategy to counter hypoxia-induced muscle dysfunction and to preacclimatize to hypoxia in clinical or high-altitude settings.
Comparison of High- and Low-Pressure Electric Supercharging of a HDD Engine: Steady State and Dynamic Air-Path Considerations (2016)

&lt;div class="section abstract"&gt;&lt;div class="htmlview paragraph"&gt;This paper numerically investigates the performance implications of the use of an electric supercharger in a heavy-duty DD13 diesel engine. Two electric supercharger configurations are examined. The first is a high-pressure (HP) configuration where the supercharger is placed after the turbocharger compressor, while the second is a low-pressure (LP) one, where the supercharger is placed before the turbocharger compressor. At steady state, high engine speed operation, the airflows of the HP and LP implementations can vary by as much as 20%. For transient operation under the Federal Test Procedure (FTP) heavy duty diesel (HDD) engine transient drive cycle, supercharging is required only at very low engine speeds to improve airflow and torque. Under the low speed transient conditions, both the LP and HP configurations show similar increases in torque response so that there are 44 fewer engine cycles at the smoke-limit relative to the baseline turbocharged engine. When the requested engine torque rise rate is increased from the FTP ramps to steps, the benefit of supercharging is extended to also include mid-range engine speeds, with over ∼ 70% fewer cycles at the smoke-limit line. In addition, the results show an improvement in the overall fuel economy of the supercharged engine during low engine speed transients compared to the baseline turbocharged engine. The study highlights the importance of supercharger by-pass valve control, where the transient response of the valve should be twice as fast as the electric supercharger drive motor for accurate and minimal supercharger power consumption during transient maneuvers. Finally, an engine re-calibration with increased exhaust gas recirculation at low engine speeds/loads, resulted 4.6% fuel economy improvements at that low speed/load region while the supercharger enabled fast air-flow increase during aggressive tip-ins.&lt;/div&gt;&lt;/div&gt;
Properties of Parallel Tetramolecular G-Quadruplex Carrying N-Acetylgalactosamine as Potential Enhancer for Oligonucleotide Delivery to Hepatocytes (2022)

The development of oligonucleotide conjugates for in vivo targeting is one of the most exciting areas for oligonucleotide therapeutics. A major breakthrough in this field was the development of multifunctional GalNAc-oligonucleotides with high affinity to asialoglycoprotein receptors (ASGPR) that directed therapeutic oligonucleotides to hepatocytes. In the present study, we explore the use of G-rich sequences functionalized with one unit of GalNAc at the 3'-end for the formation of tetrameric GalNAc nanostructures upon formation of a parallel G-quadruplex. These compounds are expected to facilitate the synthetic protocols by providing the multifunctionality needed for the binding to ASGPR. To this end, several G-rich oligonucleotides carrying a TGGGGGGT sequence at the 3'-end functionalized with one molecule of <i>N</i>-acetylgalactosamine (GalNAc) were synthesized together with appropriate control sequences. The formation of a self-assembled parallel G-quadruplex was confirmed through various biophysical techniques such as circular dichroism, nuclear magnetic resonance, polyacrylamide electrophoresis and denaturation curves. Binding experiments to ASGPR show that the size and the relative position of the therapeutic cargo are critical for the binding of these nanostructures. The biological properties of the resulting parallel G-quadruplex were evaluated demonstrating the absence of the toxicity in cell lines. The internalization preferences of GalNAc-quadruplexes to hepatic cells were also demonstrated as well as the enhancement of the luciferase inhibition using the luciferase assay in HepG2 cell lines versus HeLa cells. All together, we demonstrate that tetramerization of G-rich oligonucleotide is a novel and simple route to obtain the beneficial effects of multivalent <i>N</i>-acetylgalactosamine functionalization.
Computation of deflection defocusing in CRT electron beams with three dimensional nonlinear analysis of magnetic fields (2003)

An analysis is made of the CRT deflection fields using a finite element method (FEM), by both ignoring and considering the nonlinearity in the yoke materials. The results of the linear and nonlinear analyses are compared with the measured values of the fields when the fields are strong enough to deflect the beams to the screen periphery. These computations show that the linear analysis results deviate considerably from the measurements, especially near the yoke. However, the nonlinear analysis results agree well with the measurements. In addition, the paraxial ray theory is applied to calculate the deflection defocusing of CRT beams. The present paraxial ray theory can be used only when either magnetic or electric field exists: the space charge effect of the electron beam is neglected in the analyses. However, the thermal spread of the beam, electron lens aberrations, and the aberrations in deflection fields are all considered.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Modires: a programmable single component for spread spectrum receiver (2002)

LETI, a laboratory of the French Atomic Energy Commission, has built several direct sequence spread spectrum systems using SAW devices, the binary data rate of these systems goes from 256 kbit/s up to 8 Mbits/s and the frequency range is large (from 900 MHz up to 60 GHz). Taking into account its knowledge of this particular field of radio communications in multipath environments, LETI has designed a powerful programmable single chip that is able to perform as the matched filter of a direct spread spectrum receiver, the delay line of a differential demodulator, the demodulation, the data generation and the clock recovery.
The first case of detection of Listeria monocytogenes sequence types ST7, ST20, ST425 in wastewater during an investigation of water bodies in the Vologda region (2022)

Introduction. Listeria monocytogenes is an important human pathogen causing various forms of listeriosis, including foodborne infections, meningitis, neonatal sepsis, and abortion. Listeria are common all over the world.The purpose of the study was to conduct microbiological monitoring of L. monocytogenes in water reservoirs near livestock premises in the Vologda district of the Vologda region.Materials and methods. Bacterial cultures were isolated using two methods, titration and filtration, followed by analysis using methods of conventional bacteriology, serotyping, and species identification by instrumental procedures such as whole genome sequencing, and bioinformatic analysis.Results. Three isolates of L. monocytogenes and one isolate of Listeria innocua were isolated from 12 analyzed water samples (wastewater — 6, river water — 4, and storm water — 2 samples). whole genome sequencing of three L. monocytogenes strains attributed them to the evolutionary line II, and to three sequence types and two serogroups ST425(1/2a-3a), ST20(1/2a-3a), ST7 (4a-4c). The strains are shown to belong to multiple drug resistant ones conferring resistance to three functional groups of antibacterials such as tetracyclines, macrolides, and sulfonamides. Antibiotic resistance genes (fox, psp-like, lin,norB,sul), virulence Islands LIPI-1 and LIPI-2, and virulence genes inlABCJ, oatA, ami, gtcA, vip, and lisK in genomes of the strain were identified. Stress tolerance Island SSI-1 was identified in one strain.Conclusions. The data obtained indicate contamination of water sources near the livestock premises with L. monocytogenes strains possessing high pathogenic potentiality for outbreaks of listeriosis in humans. This shows the necessity of careful monitoring of water sources for the presence of the causative agent of listeriosis as well as the implementing of anti-epidemic measures.
Compact and Low-Loss 8×8 Silicon Photonic Switch Module for Transponder Aggregators in CDC-ROADM Application (2015)

We present 8×8 silicon photonic switch modules with newly designed spot size converters on a silicon chip. Averaged module excess loss as low as 7.2 dB on all 64 paths is achieved along with 0.15-ms switching.
Plasmodium berghei EXP-1 interacts with host Apolipoprotein H during Plasmodium liver-stage development (2017)

The first, obligatory replication phase of malaria parasite infections is characterized by rapid expansion and differentiation of single parasites in liver cells, resulting in the formation and release of thousands of invasive merozoites into the bloodstream. Hepatic <i>Plasmodium</i> development occurs inside a specialized membranous compartment termed the parasitophorous vacuole (PV). Here, we show that, during the parasite's hepatic replication, the C-terminal region of the parasitic PV membrane protein exported protein 1 (EXP-1) binds to host Apolipoprotein H (ApoH) and that this molecular interaction plays a pivotal role for successful <i>Plasmodium</i> liver-stage development. Expression of a truncated EXP-1 protein, missing the specific ApoH interaction site, or down-regulation of ApoH expression in either hepatic cells or mouse livers by RNA interference resulted in impaired intrahepatic development. Furthermore, infection of mice with sporozoites expressing a truncated version of EXP-1 resulted in both a significant reduction of liver burden and delayed blood-stage patency, leading to a disease outcome different from that generally induced by infection with wild-type parasites. This study identifies a host-parasite protein interaction during the hepatic stage of infection by <i>Plasmodium</i> parasites. The identification of such vital interactions may hold potential toward the development of novel malaria prevention strategies.
Numerical Investigation of a Transonic Centrifugal Compressor (2006)

A three-dimensional Navier-Stokes solver is used to investigate the flow field of a high pressure ratio centrifugal compressor for turbocharger applications. Such a compressor consists of a double-splitter impeller followed by a vane diffuser. The inlet flow to the open shrouded impeller is transonic, thus giving rise to interactions between shock waves and boundary layers and between shock waves and tip leakage vortices. These interactions generate complex flow structures which are convected and distorted through the impeller blades. Detailed Laser Doppler Velocimetry (LDV) flow measurements are available at various cross sections inside the impeller blades highlighting the presence of low velocity flow regions near the shroud. Particular attention is focused on understanding the physical mechanisms which govern the flow phenomena in the near shroud region. To this end numerical investigations are performed using different tip clearance modelizations and various turbulence models, and their impact on the computed flow field is discussed.
TAF1 Differentially Enhances Androgen Receptor Transcriptional Activity via Its N-Terminal Kinase and Ubiquitin-Activating and -Conjugating Domains (2010)

Aberrant expression of androgen receptor (AR) coregulators has been linked to progression of prostate cancers to castration resistance. Using the repressed transactivator yeast two-hybrid system, we found that TATA binding protein-associated factor 1 (TAF1) interacted with the AR. In tissue microarrays, TAF1 was shown to steadily increase with duration of neoadjuvant androgen withdrawal and with progression to castration resistance. Glutathione S-transferase pulldown assays established that TAF1 bound through its acetylation and ubiquitin-activating/conjugating domains (E1/E2) directly to the AR N terminus. Coimmunoprecipitation and ChIP assays revealed colocalization of TAF1 and AR on the prostate-specific antigen promoter/enhancer in prostate cancer cells. With respect to modulation of AR activity, overexpression of TAF1 enhanced AR activity severalfold, whereas small interfering RNA knockdown of TAF1 significantly decreased AR transactivation. Although full-length TAF1 showed enhancement of both AR and some generic gene transcriptional activity, selective AR coactivator activity by TAF1 was demonstrated in transactivation experiments using cloned N-terminal kinase and E1/E2 functional domains. In keeping with AR coactivation by the ubiquitin-activating and -conjugating domain, TAF1 was found to greatly increase the cellular amount of polyubiquitinated AR. In conclusion, our results indicate that increased TAF1 expression is associated with progression of human prostate cancers to the lethal castration-resistant state. Because TAF1 is a coactivator of AR that binds and enhances AR transcriptional activity, its overexpression could be part of a compensatory mechanism adapted by cancer cells to overcome reduced levels of circulating androgens.
A continuous-time &#x03A3;&#x0394; modulator with a Gm-C input stage, 120-dB CMRR and &#x2212;87 dB THD (2011)

This paper describes a precision continuous-time ΣΔ modulator for sensor applications. To achieve high input impedance, it uses a G <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">m</sub> -C integrator as its input stage. The non-linearity of this stage is cancelled by a replica transconductor in the modulator's feedback path, which is driven by a low-pass filtered version of the modulator's single-bit output. Since the filter adds extra delay, this path is bypassed at high frequencies to preserve modulator stability. The modulator was implemented in a 0.7-μm CMOS process and achieves 79-dB SNR/SNDR and 82-dB DR over a 100-Hz signal bandwidth. It also achieves 32-μV offset, 120-dB CMRR, 120-dB PSRR, and -87 dB THD.
PRAME peptide‐specific CD8+ T cells represent the predominant response against leukemia‐associated antigens in healthy individuals (2018)

Antigen-specific T cells isolated from healthy individuals (HIs) have shown great therapeutic potential upon adoptive transfer for the treatment of viremia in immunosuppressed patients. The lack of comprehensive data on the prevalence and characteristics of leukemia-associated antigen (LAA)-specific T cells in HIs still limits such an approach for tumor therapy. Therefore, we have investigated T-cell responses against prominent candidates comprising Wilms' tumor protein 1 (WT1), preferentially expressed antigen in melanoma (PRAME), Survivin, NY-ESO, and p53 by screening PBMCs from HIs using intracellular IFN-γ staining following provocation with LAA peptide mixes. Here, we found predominantly poly-functional effector/effector memory CCR7<sup>-</sup> /CD45RA<sup>+/-</sup> /CD8<sup>+</sup> LAA peptide-specific T cells with varying CD95 expression in 34 of 100 tested HIs, whereas CD4<sup>+</sup> T cells responses were restricted to 5. Most frequent LAA peptide-specific T cell responses were directed against WT1 and PRAME peptides with a prevalence of 20 and 17%, respectively, showing the highest magnitude (0.16% ± 0.22% (mean ± SD)) for PRAME peptides. Cytotoxicity of PRAME peptide-specific T cells was demonstrated by specific killing of PRAME peptide-pulsed T2 cells. Furthermore, the proliferative capacity of PRAME peptide-specific T cells was confined to HIs responsive toward PRAME peptide challenge corroborating the accuracy of the screening results. In conclusion, we identified PRAME as a promising target antigen for adoptive leukemia therapy.