gebhart/patrepeval huggingface dataset:
Single event induced charge transport modeling of GaAs MESFETs (1993)

Two-dimensional computer simulations of charge collection phenomena in GaAs MESFETs have been performed for alpha and laser ionization. In both cases, more charge is collected than is created by the ionizing event. The simulations indicate that a bipolar transport mechanism (t<60 ps) and a channel modulation mechanism (t>40 ps) are responsible for this enhanced charge collection. The first mechanism is a bipolar type effect that injects charge into the bulk of the device and is collected at the drain due to the electric field. The second is a back channel turn-on mechanism that is associated with a positive hole density located beneath the channel and exists on a much longer time scale. These results show that electrons supplied by the source implant are responsible for charge collected at the drain in excess of any collected deposited charge.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
An analytic solution for energy deposition in model spherical tumours undergoing ultrasound-hyperthermia treatments (1994)

In this paper, we develop a method to predict the energy deposition in tumours undergoing ultrasound-hyperthermia treatments. Energy depositions are calculated using an exact, analytic solution to the problem of ultrasound scattering from a spherical tumour. The biological tissues are modelled as solid, lossy elastic media so that (i) transverse-wave modes, in addition to longitudinal-wave modes, are considered, and (ii) mode coupling is fully accounted for during the scattering. The model tumour is of arbitrary size and no restrictions are placed on its material parameters relative to the surrounding tissue. Simpler analytic results are given for tumours that differ in densities and rigidities only slightly from the surrounding tissue. We briefly discuss how the above analysis could be extended to more complex systems, i.e., irregularly shaped tumours.
High Temperatures Cause Male Sterility in Rice Plants with Transcriptional Alterations During Pollen Development (2009)

Plant male reproductive development is highly organized and sensitive to various environmental stressors, including high temperature. We have established an experimental procedure to evaluate high temperature injury in japonica rice plants. High temperature treatment (39 degrees C/30 degrees C) starting at the microspore stage repeatedly reduced spikelet fertility in our system. Morphological observations revealed that pollen viability in plants exposed to high temperatures was lower than that in control plants. Most pollen grains in high temperature-treated plants displayed a normal round shape and stained reddish purple with Alexander's reagent; however, the pollen grains were very poorly attached and displayed limited germination on the stigma. To investigate gene regulatory mechanisms in the anther in high temperature environments, DNA microarray analysis was performed by comparing non-treated samples with samples treated with 2-4 d of high heat. Genes responsive to high temperatures were identified from clustering of microarray data. Among these, at least 13 were designated as high temperature-repressed genes in the anther. Expression analyses revealed that these genes were expressed specifically in the immature anther mainly in the tapetum at the microspore stage and down-regulated after 1 d of high temperature. The expression levels of Osc6, OsRAFTIN and TDR, which are tapetum-specific genes, were unaffected by high temperatures. These results suggest that not all tapetal genes are inhibited by increased temperatures and the tapetum itself is not degraded in such an environment. However, high temperatures may disrupt some of the tapetum functions required for pollen adhesion and germination on the stigma.
<i>In silico</i> design of a T-cell epitope vaccine candidate for parasitic helminth infection (2019)

Abstract Trichuris trichiura is a parasite that infects 500 million people worldwide, leading to colitis, growth retardation and Trichuris dysentery syndrome. There are no licensed vaccines available to prevent Trichuris infection and current treatments are of limited efficacy. Trichuris infections are linked to poverty, reducing children’s educational performance and the economic productivity of adults. We employed a systematic, multi-stage process to identify a candidate vaccine against trichuriasis based on the incorporation of selected T cell epitopes into virus-like particles. We conducted a systematic review to identify the most appropriate in silico prediction tools to predict histocompatibility complex class II (MHC-II) molecule T-cell epitopes. These tools were used to identify candidate MHC-II epitopes from predicted ORFs in the Trichuris genome, selected using inclusion and exclusion criteria. Selected epitopes were incorporated into Hepatitis B core antigen virus-like particles (VLPs). A combined VLP vaccine containing four Trichuris MHC-II T-cell epitopes stimulated dendritic cells and macrophages to produce pro-inflammatory and anti-inflammatory cytokines. The VLPs were internalized and co-localized in the antigen presenting cell lysosomes. Upon challenge infection, mice vaccinated with the VLPs+T-cell epitopes showed a significantly reduced worm burden, and mounted Trichuris -specific IgM and IgG2c antibody responses. The protection of mice by VLPs+T-cell epitopes was characterised by the production of mesenteric lymph node (MLN)-derived Th2 cytokines and goblet cell hyperplasia. Collectively our data establishes that a combination of in silico genome-based CD4+ T cell epitope prediction, combined with VLP delivery, offers a promising pipeline for the development of an effective, safe and affordable helminth vaccine. Author Summary The soil transmitted helminth Trichuris trichiura is a major parasite in developing countries; development of a comprehensive vaccine has been elusive. Here we used a systematic approach based on in silico identification of MHC-II T cell epitopes from genome sequences, their incorporation into a virus-like particle (VLP), characterization of the assemblies and testing in an in vivo murine infection model. Animals vaccinated with a preparation of four different VLP-antigen fusions showed significant reductions in intestinal worm burdens and associated antibody responses consistent with protection. The results suggest that a pipeline based on in silico prediction of potent MHC-II T cell epitopes, followed by incorporation into VLPs, could be a strategy which enables rapid translation into a vaccine against Trichuris trichiura .
Inhibitory Effect of Rapamycin on Corneal Neovascularization In Vitro and In Vivo (2005)

Rapamycin strongly inhibited HUVEC migration at doses that did not cause cytotoxicity and apoptosis in this in vitro model. Rapamycin also suppressed corneal neovascularization, possibly by inhibiting proinflammatory cytokines, as shown by the in vivo study. Therefore, rapamycin may be useful as an angiogenic regulator in the treatment of corneal diseases that manifest with neovascularization.
On the Mechanism of Action of Aminopterin. (1950)

Rat liver slices form from synthetic folic acid (PGA) a factor (CF) utilized for growth by Leuconostoc citrovorum; this conversion is inhibited by aminopterin. In rats given PGA, a similar inhibition of the synthesis of CF is shown by a marked decrease in the urinary excretion of CF following the administration of aminopterin. The antagonist not only prevents the metabolic alteration of PGA but also competes with the product (CF) derived from PGA. The lethal action in rats of aminopterin, 25 μg daily, is not prevented by PGA, but the daily administration of 250,000 units of CF completely counteracts the toxic effects of the antagonist. That CF is a biologically active derivative of PGA is shown by the fact that rats in which growth is arrested by PGA-deficiency, and which due to aminopterin are refractory to PGA, grow remarkably when given concentrates of the citrovorum factor.
Investigation of mode activity in NBI-heated experiments of Wendelstein 7-X (2020)

The 2018 operation phase (OP 1.2b) of the stellarator Wendelstein 7-X (W7-X) included, for the first time, neutral beam injection (NBI) to heat the plasma. Since the injection geometry at W7-X is not parallel, this generates both passing and trapped fast particles. During longer phases of NBI injection, with the primary purpose to study the heating efficiency of this system, Alfvén eigenmodes (AEs) were observed by a number of diagnostics, including the phase contrast imaging (PCI) system, the magnetic pick-up coils (Mirnov coils), and the soft x-ray multi-camera tomography system (XMCTS). Alfvén eigenmodes are of great interest for future fusion reactors as it has been shown that the resonant interaction of fast ions with self-excited AEs can lead to enhanced transport of fast ions and potentially to energy losses. This is especially true for so-called gap-modes, Alfvén eigenmodes with frequencies in gaps of the continuous spectrum, since they lack continuum damping. These modes are commonly known to be excited by fast ions, but other destabilizing mechanisms, e.g. the electron-pressure gradient are also possible. In this article we present a first analysis of the experimentally observed frequencies from the theoretical side. The calculation of shear Alfvén wave continua for selected cases and the assignment of observed frequencies to the gaps of the continuous spectra are presented. Using the ideal-MHD code CKA (Könies A. 2007 10th IAEA TM on Energetic Particles in Magnetic Confinement System), we find gap modes that match the experimental measurements in terms of the observed frequencies. We emphasize the crucial roles played by the coupling of sound and Alfvén waves as well as of the Doppler shift arising as a consequence of the radial electric field in W7-X. We employ the perturbative gyrokinetic code CKA-EUTERPE (Feh´er 2013 Simulation of the interaction between Alfv´en waves and fast particles), using a slowing-down distribution function for the fast ions as calculated by the Monte-Carlo particle following code ASCOT (Hirvijoki et al 2014 Comput. Phys. Commun. 185 1310–21) to assess the fast-ion drive. Here we find that the fast-ion drive is insufficient to overcome the background-plasma damping. The fact that unstable modes were observed experimentally may point to problems with the modelling or indicate the existence of other destabilizing mechanisms, e.g. associated with the electron-pressure gradient (Windisch et al 2017 Plasma Phys. Control. Fusion 59 105002) that sensitively depend on the profiles of the background plasma.
Retinex preprocessing of uncalibrated images for color-based image retrieval (2003)

The <i>Journal of Electronic Imaging</i> (JEI), copublished bimonthly with the Society for Imaging Science and Technology, publishes peer-reviewed papers that cover research and applications in all areas of electronic imaging science and technology.
Hydrogen Evolution Reaction Kinetics on Electrodeposited Pt-M (M = Ir, Ru, Rh, and Ni) Cathodes for Ammonia Electrolysis (2013)

Metallic and bimetallic electrocatalysts of the type PtxM1-x (where M = Ru, Rh, Ir, Ni) electrodeposited on carbon fiber paper were evaluated as electrocatalysts for the hydrogen evolution reaction (HER) in an ammonia electrolytic cell. The addition of 1 M ammonia resulted in an increase in the HER overpotential for all electrocatalysts except Rh. The bimetallic electrocatalysts offer higher HER activity compared to metallic ones with the trend Pt-Ir > Pt-Rh > Pt-Ru > Pt-Ni. The enhanced activity of the bimetals is attributed to the synergistic activity. Ammonia adsorption is specific to the more electropositive alloying material, leaving the Pt sites active for hydrogen underpotential deposition and HER. Increasing the loading by a factor of two resulted in a decrease in the pore size thereby leading to a poor three-phase electrocatalyst, which in-turn causes a decrease in the HER electrocatalytic activity in the presence and absence of 1 M ammonia. Maximum electrocatalytic activity was achieved with a Pt-Ir electrocatalyst with a loading (Me / [Me + Pt]) of 13%, a Pt content of 68% and an intercrystallite distance of 7.2 nm.
Role of Inorganic Pyrophosphatase in the Mechanism of Action of Parathyroid Hormone and Calcitonin (1971)

The role of inorganic pyrophosphatase in the mechanism of action of parathyroid hormone and calcitonin was studied by measuiing the enzyme activity of the tibia of rats following the administration of PTH and/or calcitonin. Calcitonin caused a significant and rapid increase in the pyrophosphatase activity of the tibia which preceded the development of significant hypocalcemia. PTH, on the other hand, significantly decreased the enzyme activity of the tibia in thyroparathyroidectomized rats. These results suggest that the alteration of pyrophosphatase activity is directly involved in the mechanism of action of calcitonin and PTH. In view of the fact that pyrophosphate plays a key role in the regulation of bone formation through the inhibition of calcification, as has been suggested by Fleisch et al., its removal by pyrophosphatase would facilitate bone mineralization. (Endocrinology89: 852,1971)
TH‐C‐351‐01: Design of the Washington University Small Animal Conformal Micro Irradiator (2008)

Purpose: To design a conformal small animal micro radiation therapy (microRT) instrument, consisting of a cone beam microCT subsystem for submillimeter low dose structural imaging and image guided radiotherapy and an orthovoltage conformal micro irradiator with high radiation dose rate for high throughput conformal irradiation. Method and Materials: The microCT subsystem is based on an 80kVp micro‐focus x‐ray source with 75×75 um 2 focal spot and a flat panel amorphous silicon detector with 1024×1024 pixels. The microRT subsystem design utilizes a 320kVp orthovoltage source with dual focus spots (0.4×0.4 mm 2 at 800W and 1×1 mm 2 at 1800 W). The orthovoltage beam is collimated using two orthogonal jaws and exchangeable apertures. The resolution of the cone‐beam micro CT and the therapy beam spatial precision was determined using a numerical model. The microCT radiation dose, the orthovoltage source spectral output, and dose rate were evaluated using a mouse digital phantom (MOBY) and a pencil beam algorithm. Results: microCT reconstructed tomographic data with a resolution of 125 μm is achievable using 128 projections and a maximum radiation dose of 2cGy. Automatic animal positioning and handling is performed within a precision of 100 μm. The treatment beam can be aimed at different latitude and longitude angles in steps of 2 arc min. and translated at 50μm steps (x,y,z). The beam cross section can be modulated with submillimeter precision using steps of 50μm. A radiation dose rate of 40 Gy/min is delivered when the system is operated at an average half‐value layer of 4.6 mm Cu and a maximum beam penumbra of 0.35 mm. Conclusion: We designed and numerically evaluated the performance of a microRT system integrated with a microCT for conformal radiotherapy of murine animal models. This work supported in part by NIH grant CA108677.
Detection and Online Classification of the Near-infrared Spectroscopy Fast Optical Signal for Brain-computer Interfaces (2016)

Near-infrared spectroscopy (NIRS) can detect a fast optical signal (FOS), corresponding to optical property changes in neuronal tissue during neuronal activation. The FOS has high temporal and spatial resolution, but has a low signal-to-noise ratio. The FOS has yet to be automatically classi- fied, hence its value as a BCI control signal remains unknown. During offline and online sessions, participants performed a visual oddball task. In offline sessions, the FOS was validated with elec- troencephalography (EEG) measurements of event-related potential (ERPs). Spectral relationships between FOS and ERP oddball responses were found in upper delta and theta bands using coherence and Granger causality metrics. A temporal FOS-ERP correlation was also found 200 ms after oddball presentation. Offline and online FOS classification of oddballs versus frequent responses was achieved with average balanced accuracies of 62 Âą 5% and 63 Âą 6%, respectively. FOS classification results were above chance but did not reach the threshold (>70%) for effective BCI communication.
Crystal and Molecular Structures of Asymmetric <i>cis</i>- and <i>trans</i>-Platinum(II/IV) Compounds and Their Reactions with DNA Fragments (1997)

The asymmetrically substituted platinum(II) complexes cis-Pt(NH3)(c-C6H11NH2)Cl2 and trans-Pt(NH3)(c-C6H11NH2)Cl2 have been synthesized and their crystal structures have been determined. Crystals of cis-Pt(NH3)(c-C6H11NH2)Cl2 (1) are orthorhombic, space group Pbca (no. 61) with a = 10.1994(12), b = 10.494(2), c = 18.826(2) Å, Z = 8. The structure refinement converged to R1 = 0.0518 and wR2 = 0.1143. Crystals of trans-Pt(NH3)(c-C6H11NH2)Cl2 (2) are monoclinic, space group P21/c (no. 14) with a = 12.141(3), b = 6.0965(9), c = 19.864(3) Å, β = 118.71(2)°, Z = 4. The structure refinement converged to R1 = 0.0711 and wR2 = 0.1846. In addition, the Pt(IV) analogues with axial hydroxide ligands have been synthesized. Also the corresponding bis(carboxylato)platinum(IV) compound of formula trans,cis,cis-Pt(NH3)(c-C6H11NH2)Cl2(OOCCH3)2 has been obtained by conversion of the hydroxide with acetic anhydride. Reactions of these platinum complexes with 9-methylhypoxanthine and guanosine-5‘-monophosphate (5‘-GMP) have been studied in significant detail. The course of the reactions was followed by NMR spectroscopy, and 1H and 195Pt techniques were used to identify the formation of the products. It was found that the Pt(II) compounds easily react with the bases at the N7 position, whereas the Pt(IV) compounds react very slowly (for trans,cis,cis-Pt(NH3)(c-C6H11NH2)Cl2(OOCCH3)2) or not at all (for trans,trans,trans-Pt(NH3)(c-C6H11NH2)Cl2(OH)2). Only in the presence of glutathione does a reaction of the latter with 5‘-GMP takes place. In this case a major product was found to be the reduced trans-Pt(II) complex with one molecule of 5‘-GMP and one molecule of S-bonded glutathione.
Bilayer Designed Hydrocarbon Membranes for All-Climate Vanadium Flow Batteries To Shield Catholyte Degradation and Mitigate Electrolyte Crossover (2019)

The use of low-cost hydrocarbon membranes in vanadium flow batteries (VFBs) still remains a great challenge because of the strong oxidation of VO<sub>2</sub><sup>+</sup> catholyte and rapid capacity fading. Here, we report a bilayer design strategy using an antioxidant and dense cross-linked sulfonated polyimide (cSPI) layer as a protective layer for a sulfonated poly(ether ether ketone) (SPEEK) membrane to shield catholyte degradation and mitigate electrolyte crossover. A scalable process is developed to fabricate an integrated bilayer SPEEK/cSPI membrane without delamination by spraying a SPEEK transition layer between the two polymers. The tightly bridged cSPI layer not only protects the SPEEK membrane from degradation but also enhances its mechanical strength, puncture resistance, and proton/vanadium-ion selectivity. When assembled in a VFB, the bilayer SPEEK/cSPI membrane demonstrates excellent rate performance under current densities of 40-200 mA cm<sup>-2</sup>, high adaptability at a wide temperature range of -15 to 60 °C, very slow capacity decay rate of 0.054% per cycle at 160 mA cm<sup>-2</sup>, and a maximum power density of 480 mW cm<sup>-2</sup>. These merits make the bilayer SPEEK/cSPI membrane a promising candidate for the next-generation VFB to achieve low-cost, high-rate, and all-climate energy storage.
Steroid Treatment for Experimental Autoimmune Myasthenia Gravis (1980)

Short-term, high-dose steroids (prednisolone sodium succinate) were given to female Lewis rats in the chronic stage of experimental autoimmune myasthenia gravis (EAMG). Abnormally low amplitude miniature endplate potentials (MEPPs) persisted, and were even slightly lower than those seen in saline-treated animals with chronic EAMG. The MEPPs were also studied in normal female Lewis rats treated with short-term, high-dose steroids, and no significant change was noted when compared with normal controls. Previous investigators have reported normalization of the abnormally low amplitude MEPPs within 24 hours of high-dose steroid treatment. Our different results might be explained by our higher dose of receptor, addition of pertussis to the inoculum, and study of a different muscle. A survey of endplate ultrastructure revealed some definite postsynaptic membrane abnormalities in both steroid-treated and saline-treated rats with EAMG, but clear distinction among the groups studied was not possible by direct visualization.
Increased hepatic CD36 expression with age is associated with enhanced susceptibility to nonalcoholic fatty liver disease (2014)

CD36 has been associated with obesity and diabetes in human liver diseases, however, its role in age-associated nonalcoholic fatty liver disease (NAFLD) is unknown. Therefore, liver biopsies were collected from individuals with histologically normal livers (n=30), and from patients diagnosed with simple steatosis (NAS; n=26). Patients were divided into two groups according to age and liver biopsy samples were immunostained for CD36. NAFLD parameters were examined in young (12-week) and middle-aged (52-week) C57BL/6J mice, some fed with chow-diet and some fed with low-fat (LFD; 10% kcal fat) or high-fat diet (HFD; 60% kcal fat) for 12-weeks. CD36 expression was positively associated with age in individuals with normal livers but not in NAS patients. However, CD36 was predominantly located at the plasma membrane of hepatocytes in aged NAS patients as compared to young. In chow-fed mice, aging, despite an increase in hepatic CD36 expression, was not associated with the development of NAFLD. However, middle-aged mice did exhibit the development of HFD-induced NAFLD, mediated by an increase of CD36 on the membrane. Enhanced CD36-mediated hepatic fat uptake may contribute to an accelerated progression of NAFLD in mice and humans. Therapies to prevent the increase in CD36 expression and/or CD36 from anchoring at the membrane may prevent the development of NAFLD.
Myeloid-derived suppressor cells are increased and correlated with type 2 immune responses, malnutrition, inflammation, and poor prognosis in patients with breast cancer (2017)

Myeloid-derived suppressor cells (MDSCs) have been identified in the majority of patients and experimental mice with tumors by their suppression of T cell activation. MDSCs have also been reported to be associated with chronic inflammation. In advanced cancer, the T helper (Th) cell balance tends to shift from Th1 to Th2 predominance, and immune function, including cell-mediated immunity, is impaired by cytokines produced by Th2 cells. The present study examined the correlations between MDSC levels and inflammation, immune suppression, malnutrition, and poor prognosis in 155 patients with breast cancer. The levels of MDSCs in preoperative patients and in patients with recurrent breast cancer were significantly higher compared with postoperative patients, patients with recurrent breast cancer who received chemotherapy and healthy volunteers. The MDSC levels of preoperative patients were significantly positively correlated with interleukin (IL)-6 production by peripheral blood mononuclear cells (PBMCs), the neutrophil/lymphocyte ratio and C-reactive protein, and were negatively correlated with the production of interferon-γ and IL-12, serum concentration of rapid turnover protein, and the stimulation index. These patients were divided into two groups based on the levels of MDSCs. In preoperative patients with MDSC levels >1.0% of total PBMCs, the overall survival of patients with stage IV disease was significantly shorter compared with other disease stages, and was also significantly shorter compared with patients with MDSC levels <1.0% of total PBMCs. Thus, the MDSC levels of preoperative patients may function as a good prognostic indicator, particularly in patients with advanced breast cancer.