gebhart/patrepeval huggingface dataset:
A connectivity based, table-driven decoder for convolutional codes (2002)

A connectivity based, table driven decoder for convolutional codes that is both fast and simple to implement has been devised. The decoding performance can be made to approach that of an optimal decoder.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Supplementary Data from Molecular Profiling of Cohorts of Tumor Samples to Guide Clinical Development of Pembrolizumab as Monotherapy (2023)

&lt;p&gt;Supplementary Tables S1, S2; Supplementary Figures S1, S2, S3, S4&lt;/p&gt;
Design and demonstration of high-Q photonic heterostructure nanocavities suitable for integration (2009)

We have investigated the localized design of heterostructure photonic crystal nanocavities in order to make them more suitable for integration. While retaining theoretical quality factors of more than ten million, the total length of the heterostructure nanocavity can be reduced to ~5 mum and the shifted air holes comprising the heterostructure can be restricted to the two rows nearest the nanocavity on each side. Though the area for the heterostructure nanocavity investigated thus far was larger than 10 x 10 microm(2) in the photonic crystal slab, heterostructure nanocavities of this new design have sizes of approximately 3 x 5 microm(2), thus allowing dense integration.
PPARG Regulates Gonadotropin-Releasing Hormone Signaling in LbetaT2 Cells In Vitro and Pituitary Gonadotroph Function In Vivo in Mice1 (2010)

Peroxisome proliferators-activated receptor gamma (PPARG) ligands improve insulin sensitivity in type 2 diabetes and polycystic ovarian syndrome (PCOS). Despite clinical studies showing normalization of pituitary responsiveness to gonadotropin-releasing hormone (GnRH) in patients with PCOS, the precise role of PPARG in regulating the hypothalamic-pituitary-gonadal axis remains unclear. In the present study, we tested the hypothesis that the PPARG agonist rosiglitazone has a direct effect on the pituitary. In mouse LbetaT2 immortalized gonadotrophs, rosiglitazone treatment inhibited GnRH stimulation of the stress kinases p38MAPK and MAPKs/JNKs, but did not alter activation of ERKs, both in the presence and absence of activin. Furthermore, p38MAPK signaling was critical for both Lhb and Fshb promoter activity, and rosiglitazone suppressed the GnRH-mediated induction of Lhb and Fshb mRNA. Depletion of PPARG using a lentivirally encoded short hairpin RNA abolishes the effect of rosiglitazone to suppress activation of JNKs and induction of the transcription factors EGR1 and FOS as well as the gonadotropin genes Lhb and Fshb. Lastly, we show conditional knockout of Pparg in pituitary gonadotrophs caused an increase in luteinizing hormone levels in female mice, a decrease in follicle-stimulating hormone in male mice, and a fertility defect characterized by reduced litter size. Taken together, our data support a direct role for PPARG in modulating pituitary function in vitro and in vivo.
Bimetallic platinum group metal-free catalysts for high power generating microbial fuel cells (2017)

M1-M2-N-C bimetallic catalysts with M1 as Fe and Co and M2 as Fe, Co, Ni and Mn were synthesized and investigated as cathode catalysts for oxygen reduction reaction (ORR). The catalysts were prepared by Sacrificial Support Method in which silica was the template and aminoantipyrine (AAPyr) was the organic precursor. The electro-catalytic properties of these catalysts were investigated by using rotating ring disk (RRDE) electrode setup in neutral electrolyte. Fe-Mn-AAPyr outperformed Fe-AAPyr that showed higher performances compared to Fe-Co-AAPyr and Fe-Ni-AAPyr in terms of half-wave potential. In parallel, Fe-Co-AAPyr, Co-Mn-AAPyr and Co-Ni-AAPyr outperformed Co-AAPyr. The presence of Co within the catalyst contributed to high peroxide production not desired for efficient ORR. The catalytic capability of the catalysts integrated in air-breathing cathode was also verified. It was found that Co-based catalysts showed an improvement in performance by the addition of second metal compared to simple Co- AAPyr. Fe-based bimetallic materials didn't show improvement compared to Fe-AAPyr with the exception of Fe-Mn-AAPyr catalyst that had the highest performance recorded in this study with maximum power density of 221.8 ± 6.6 μWcm<sup>-2</sup>. Activated carbon (AC) was used as control and had the lowest performances in RRDE and achieved only 95.6 ± 5.8 μWcm<sup>-2</sup> when tested in MFC.
TU‐A‐204B‐01: The CBCT Performance of a New Treatment Platform (2010)

Purpose : To characterize the CBCT performance of a new radiation therapy platform (Trilogy MX). Methods : An entirely new CBCT system has been developed for Trilogy MX. The new CBCT system differs from that of the On‐Board Imager® (OBI) in the use of a beam hardening filter, which reduces patient dose, and an improved reconstructor, which uses scatter correction algorithms to account for the x‐ray scatter caused by the cone‐beam geometry. Scans of Catphan® and electron density (Model 062A, CIRS) phantoms have been compared with OBI scans. Hounsfield unit (HU) accuracy was checked by changing the z scan length and the phantom diameters for pelvis (125kVp, 680mAs, 45cm dia.) acquisitions. The Catphan was imaged using doses ranging between 5–20mGy (CTDI w ). Projections acquired using clinical OBI units were also reconstructed for comparison using the new reconstructor. Results : The new CBCT system has higher dose efficiency and higher HU accuracy. When the volume length is reduced from 160mm to 90mm or when the phantom diameter is reduced from 330mm to 180mm, the HU values measured for the same inserts differ by −190 to +80HU for OBI scans and by –60 to +50HU for Trilogy MX scans (for electron densities between 0.2 and 1.2). The contrast detectability of the 1% contrast objects in the Catphan phantom improves from 9mm to 4mm diameter when using the same CTDI w dose as OBI. Clinical images exhibit much better uniformity, elimination of streaks and better definition of the skin surface. Conclusions : The new reconstruction algorithm makes substantial improvements in CBCT image quality, reduces patient dose and increases HU accuracy. The new system produces CBCT images, which are much better suited to image guidance and which may be suitable for other tasks such as adaptive RT planning.
Novel driver genes and genomic predictors of immune infiltrates in colorectal cancer. (2016)

557 Background: Despite progress that has been made in the molecular characterization of colorectal cancer (CRC), prior studies have had limited power to detect, as significantly mutated, less-frequently altered CRC genes. In addition, most large-scale sequencing studies have generally lacked clinicopathologic annotations to link genomic features with important CRC characteristics such as immune infiltration. Methods: We performed Whole-Exome Sequencing on 619 archival primary CRCs from two large prospective cohorts, the Nurses’ Health Study and the Health Professionals Follow-Up Study. We identified CRC driver genes using significance-calling algorithms and employed a novel computational pipeline to calculate tumor neoantigens (peptides resulting from somatic mutations and recognized by the immune system as foreign). The neoantigen load and altered genes/pathways were correlated to immunohistochemically determined immune infiltrates and survival data linked to these specimens. Results: We identified 90 significantly mutated genes in non-hypermutated CRC. These include previously underappreciated genes that participate in pathways such as WNT-signaling and RNA processing. Among all samples, the neoantigen load was associated with increased overall lymphocytic infiltration (P = 2.6e-11), tumor-infiltrating lymphocytes (TILs) (P = 2.0e-19), memory T-cells (P = 0.091) and CRC-specific survival (P = 0.025). Neoantigen load was also associated with higher TILs in microsatellite-stable tumors (P = 0.015). We found that HLA and Antigen Processing Machinery (APM) mutations have undergone positive selection in tumors with TILs. Conclusions: In the largest exome-sequencing study of CRC to date, we leveraged the increased number of samples and their associated clinicopathologic annotations to identify new driver genes and genomic predictors of immune infiltrates in this disease. Neoantigen load is prognostic in CRC and predictive of immune infiltration, even among microsatellite-stable tumors. We also find evidence of positive selection for HLA and APM mutations in immune-cell infiltrated tumors. These results have implications for patient selection in CRC immunotherapy trials.
Controlling Color Conversion Efficiency between Monolayer Tungsten Diselenide and Quantum Dots through Plasmonic Effect of Silver Nanodisks Metasurface (2019)

2019 International Conference on Solid State Devices and Materials ,Controlling Color Conversion Efficiency between Monolayer Tungsten Diselenide and Quantum Dots through Plasmonic Effect of Silver Nanodisks Metasurface
Growth of high quality N-polar AlN(0001¯) on Si(111) by plasma assisted molecular beam epitaxy (2009)

High quality N-polar AlN epilayers were grown and characterized on Si(111) substrates by plasma assisted molecular beam epitaxy as a first step toward growth of N-polar nitrides on Si(111). Polarity inversion to N-face by an optimized predeposition of Al adatoms on the reconstructed 7×7 Si(111) surface was investigated. Al adatoms can saturate the dangling bonds of Si atoms, resulting in growth of AlN in (0001¯) direction on subsequent exposure to N2 plasma. N-polarity was confirmed by observing strong 3×3 and 6×6 reflection high-energy electron diffraction reconstructions, convergent beam electron diffraction imaging and KOH etching studies. The structural properties were investigated by x-ray diffraction measurements, cross section and plan-view TEM studies.
Thiazolopyridine Ureas as Novel Antitubercular Agents Acting through Inhibition of DNA Gyrase B (2013)

A pharmacophore-based search led to the identification of thiazolopyridine ureas as a novel scaffold with antitubercular activity acting through inhibition of DNA Gyrase B (GyrB) ATPase. Evaluation of the binding mode of thiazolopyridines in a Mycobacterium tuberculosis (Mtb) GyrB homology model prompted exploration of the side chains at the thiazolopyridine ring C-5 position to access the ribose/solvent pocket. Potent compounds with GyrB IC50 ≤ 1 nM and Mtb MIC ≤ 0.1 μM were obtained with certain combinations of side chains at the C-5 position and heterocycles at the C-6 position of the thiazolopyridine core. Substitutions at C-5 also enabled optimization of the physicochemical properties. Representative compounds were cocrystallized with Streptococcus pneumoniae (Spn) ParE; these confirmed the binding modes predicted by the homology model. The target link to GyrB was confirmed by genetic mapping of the mutations conferring resistance to thiazolopyridine ureas. The compounds are bactericidal in vitro and efficacious in vivo in an acute murine model of tuberculosis.
Free fatty acids inhibit cytotoxic T lymphocyte-mediated lysis of allogeneic target cells. (1990)

Short term exposure of murine CTL clones to long chain cis unsaturated free fatty acid (FFA) inhibits alloantigen specific lysis of cognate target cells, whereas long-chain saturated FFA have no effect. Inhibition of lysis occurs when cis FFA is added before or within 10 min after CTL-target cell conjugate formation and thus appears to interfere with lethal hit delivery. Our previous studies have shown that similar treatment with cis FFA inhibits, in CTL, the Ag stimulated increase in intracellular calcium and degranulation, suggesting that inhibition of lysis probably results from perturbation of the CTL signaling pathway. However, inhibition of lysis is probably not due to the inhibition of the rise in intracellular calcium or degranulation, because lysis can occur under conditions in which FFA inhibit degranulation and because cis FFA inhibit calcium-independent killing. Inhibition of lysis is detectable at unbound FFA concentrations less than 1 microM and is generally complete at concentrations less than 5 microM. Although these levels of FFA are somewhat higher than reported for normal physiologic conditions, plasma FFA levels can be elevated into this range in states of stress and disease, suggesting that FFA modulation of the immune response has important physiologic consequences.
Impact of geometry-preserving encryption on rendering time (2014)

Collaborative creation workflows are calling for softer protection mechanisms than conventional encryption. Geometry-preserving encryption relates to protection techniques for 3D objects that alter the visual representation of the object after rendering but preserves some geometrical primitives, e.g. the bounding box. The advantage of this approach is the ability of legacy renderers to readily display composite scenes that contain both protected and unprotected objects. In this paper, we introduce a collection of geometry-preserving encryption algorithms, whose visual impact can be adjusted with a tuning parameter, and then report on the influence of the deformation on the actual rendering time of the object. Experimental results clearly highlight that special care needs to be taken in order to preserve interactivity, that is a de facto requirement for collaborative creation.
Si process compatible near-infrared photodetector using AU/SI nano-pillar array (2016)

We report on a near-infrared photodetector constructed on an n-typed Si wafer. Vertically oriented Au nano-pillars formed on the n-typed Si performed as optical antennas which absorb the infrared light effectively. Each nano-pillar had several hundred nm of diameter, 2.7-μm-height, and 1-μm-pitch. The nano-pillar exhibited low reflectance of 20% for the wavelength ranging from 1.25 μm (near-infrared) to 4μm (mid-infrared), indicating large absorbance. The absorbed energy is then transduced into photocurrent by the Schottky barrier diode formed on the Au/n-Si interface. The photocurrent sensitivity (responsivity) of the nano-pillar photodetector exhibited around 10-times increase compared with a control Schottky typed photodetector with a flat Au surface. The detectable wavelength limit was thus extended up to 1650 nm. Because this method is compatible with a Si fabrication process, it will serve as a fundamental way to construct a photodetector for multi-wavelength imaging.
Three-Dimensional Scattering Analysis of Lossy/Lossless Dielectrics Using Constrained Interpolation Profile Method (2009)

J. Chakarothai, Q. Chen, and K. Sawaya Department of Electrical and Communication Engineering, Tohoku University 6-6-05 Aoba, Aramaki Aza, Aoba-ku, Sendai, 980-8579, Japan E-mail: {jerd, chenq, sawaya}@ecei.tohoku.ac.jp Abstract—The constrained interpolation profile (CIP) method for three-dimensional scattering analysis of lossy and lossless dielectrics has been successfully developed. It is used to reduce the effect of averaging of the fields in the calculation of total scattered power. Validity of the method is demonstrated by calculated total scattering cross section (TSCS) of dielectric spheres comparing with the exact Mie’s result. Introduction The finite-difference time-domain (FDTD) method has been used extensively to calculate scattering and absorption from dielectrics in the past [1]. However, averaging have to be used in the calculation of radiated power because of the leapfrog arrangement of the field components. Recently, the CIP method have been developed for scattering problems [2]. Since the CIP method is considered to reduce the effect of averaging because all field components locate at the same place, it is applied to calculate the scattered power from dielectrics and its accuracy has been validated. Analysis model and results Fig. 1 shows an analysis model for the CIP method. A dielectric sphere was placed in the center of analysis region and an incident plane wave of a rectangular pulse with pulse width of 5Δ, whereΔ is cell size, was induced into the region from the left boundary. The TSCSs calculated on the surface encompassing the dielectric spheres of r = 2.0, σ = 0.01[S/m] and σ = 0.1[S/m] are shown in Fig. 2, in which the FDTD and Mie’s results are also plotted. The results show good agreement with the exact solutions of Mie, which demonstrates the validity of the method. Conclusions The CIP method for the 3D scattering of dielectrics has been successfully developed and its validity has been shown by the TSCS results in a wide range of frequency. References [1] A. Taflove and K. R. Umashankar, “Computation of the Electromagnetic Fields and Induced Temperatures within a Model of the Microwave-irradiated Human Eye,” IEEE Trans. Microwave Theory Tech., Vol.MTT-23, pp. 888-896, Nov. 1975. [2] J. Chakarothai, Q. Chen, and K. Sawaya, “Numerical Analysis of Electromagnetic Scattering Using Constrained Interpolation Profile Method,” ISAP’09, Bangkok, Thailand, Oct. 2009.
The time-reversal operator with virtual transducers: Application to far-field aberration correction (2008)

The decomposition of the time-reversal operator (DORT) is a detection and focusing technique using an array of transmit receive transducers. It can extract Green's functions of scatterers in a medium. A variant consists in transmitting focused beams (FDORT). It is shown here that the FDORT method can be interpreted as the decomposition of a time-reversal operator between an array of virtual transducers located at the transmit beams' foci and the physical array. The receive singular vectors correspond to scatterers' Green's functions expressed in the physical array while the transmit singular vectors correspond to Green's functions expressed in the virtual array. The position of the virtual array can be changed by varying the position of the foci, thus offering different points of view. Parameters and performance of some transmit schemes are discussed. Appropriately positioning the virtual transducers can simplify some problems. One application is measuring and correcting aberration in the case of a far-field phase screen model. Placing the virtual transducers near the phase screen transforms the problem in a simpler near-field phase screen problem.
Sub-100-nm gate length GaAs metal–semiconductor field-effect transistors and modulation-doped field-effect transistors fabricated by a combination of molecular-beam epitaxy and electron-beam lithography (1988)

GaAs metal–semiconductor field-effect transistors (MESFET’s) and modulation-doped field-effect transistors (MODFET’s) with recessed gates ≤100 nm long have been fabricated by incorporating a custom ultrahigh-resolution electron-beam lithography tool for gate fabrication with molecular-beam epitaxy grown wafers and a standard high-performance GaAs FET process. To the author’s knowledge, the MODFET’s have the smallest gate lengths reported to date. The electron-beam (e-beam) column was modified to hold 2- and 3-in. wafers within the final lens to maintain low aberration coefficients and facilitate device processing. 70-nm-thick polymethylmethacrylate (PMMA) was used for the gate definition. The gate recess was accomplished with a citric acid etch that did not attack the PMMA. Liftoff of e-beam evaporated TiAlAu completed the gate fabrication. DC IV characteristics were obtained for all the devices. The MODFET’s demonstrated dc transconductances as high as 400 S/m at 300 K. DC transconductances varied between 230 and 250 S/m for the MESFET’s. The MESFET’s have the desirable properties of low source resistance 0.3–0.5 Ω mm and low output conductance 8 S/m. It is shown that the drain–source saturation current for an arbitrary MESFET can be predicted to within±10% by an examination of the gate recess with a high-performance scanning electron microscope.
Water-Soluble Progesterone Analogues Are Effective, Injectable Treatments in Animal Models of Traumatic Brain Injury (2012)

After more than 30 years of research and 30 failed clinical trials with as many different treatments, progesterone is the first agent to demonstrate robust clinical efficacy as a treatment for traumatic brain injuries. It is currently being investigated in two, independent phase III clinical trials in hospital settings; however, it presents a formidable solubility challenge that has so far prevented the identification of a formulation that would be suitable for emergency field response use or battlefield situations. Accordingly, we have designed and tested a novel series of water-soluble analogues that address this critical need. We report here the synthesis of C-20 oxime conjugates of progesterone as therapeutic agents for traumatic brain injuries with comparable efficacy in animal models of traumatic brain injury and improved solubility and pharmacokinetic profiles. Pharmacodynamic analysis reveals that a nonprogesterone steroidal analogue may be primarily responsible for the observed activity.
VEGFR-3 mediated activation of lymphatic endothelium is crucial for tumor cell entry and spread via lymphatic vessels (2005)

2024 A number of signaling pathways regulate expression of and response to pro-angiogenic factors. Because the protein tyrosine kinase, Src has been implicated in both of these processes, we hypothesized that Src is a critical mediator of angiogenesis induced by colorectal carcinoma cells. To examine Src-mediated angiogenic properties, temperature-sensitive SV40 Tag immortalized endothelial cells from both the colon (CEC) and liver (HEC) were stimulated with conditioned media from HT29 human colorectal carcinoma cells previously treated with a selective Src kinase inhibitor, PP2, or DMSO control. Endothelial proliferation was determined by MTT; migration was determined by modified Boyden chamber assay. To asses the ability of Src to regulate growth factor-induced endothelial activation, the above assays were repeated in the presence of 1) 2% FBS, 2) EGF, 3) bFGF, 4) VEGF-A or 5) HGF either in the presence or absence of a selective Src inhibitor. For protein analysis, HEC pretreated with PP2 or DMSO were stimulated with EGF and lysed at various time points. Total and phosphorylated forms of Akt, Erk, and Src were assessed by western blotting and densitometry. Conditioned media from HT29 colorectal carcinoma cells induced a ∼2-fold increase in proliferation and migration in the CEC and >3-fold increase in proliferation and migration HEC respectively. The conditioned media from the Src-inhibited colorectal carcinoma cells failed to induce significant proliferation or migration in either cell line. Likewise, EGF, bFGF, VEGF, and HGF induced a 5.0-, 3.7-, 4.4-, and 3.9-fold increase in migration in HEC respectively and a 3.3-, 2.4-, 2.7- and 4.0-fold increase in migration in CEC respectively. In contrast, while EGF and bFGF caused ∼2-fold increase in proliferation in both HEC and CEC, VEGF failed to increase proliferation above control values. HGF induced a 1.5-fold increase in CEC proliferation, but failed to induce proliferation in HEC. Pretreatment with the selective Src inhibitor abrogated endothelial proliferation and migration induced by all factors. EGF treatment of HEC induced a 2-fold increase in Src kinase activity, a >5-fold increase in phosphorylated Erk and ∼3 fold increase in phosphorylated Akt, all of which were effectively blocked by Src inhibition. We therefore conclude that angiogenesis induced by colorectal carcinoma cells is regulated by Src kinase and that heterogeneous endothelial cells from distinct anatomic sites may be differentially activated by colorectal carcinoma cells.