gebhart/patrepeval huggingface dataset:
<i>FGFR3</i> Driven Metastatic Urothelial Carcinoma of the Urinary Bladder (mUCB): A Comprehensive Genomic Profiling Study. (2018)

4531 Background: Using comprehensive genomic profiling (CGP), we queried whether FGFR3-driven mUCB could be further defined by additional genomic alterations (GA) and biomarkers of response to immunotherapies. Methods: DNA from FFPE tissues of 1,576 mUCB underwent hybrid-capture based CGP to evaluate all classes of genomic alterations. Tumor mutational burden (TMB) was determined on 1.1 Mbp of sequenced DNA and microsatellite instability (MSI) was determined by principal components analysis of optimal homopolymer loci. Results: 385 (24%) of the 1,576 UCB featured GA affecting FGFR1-4. Of the FGFR3 GA identified in mUBC (FGFR3mut), 77% were SV, 2% were amplifications, 18% were fusions/rearrangements, and 4% had more than 1 GA type. When compared with a cohort of 1,275 FGFR3 WT mUCB, the GA/tumor and frequency of TERT GA were similar. GA in TP53 and RB1 were more common in FGFR3 WT than FGFRmut, whereas cell cycle GA (e.g., CDKN2A) were more common in FGFR3mut tumors. Genes associated with DNA repair were altered in both groups, with ARID1A GA more frequent in FGFR3 WT, KDM6A GA more frequent in FGFR3mut, and BRCA1/2 GA less frequent overall and similar in both groups. Targetable ERBB2 GA were significantly more common in FGFR3 WT cases. Targets in the MTOR pathway, including GA in PIK3CA and TSC1, were also more common in FGFR3mut mUBC. MSI-High status was extremely rare in both groups. The median TMB was higher in FGFR3 WT, and samples more often had TMB of ≥10 mut/Mb or ≥20 mut/Mb. Conclusions: CGP reveals both similarities and differences in the genomic landscapes of FGFR3mut and FGFR3 WT mUBC. In the 2% of mUBC with FGFR3 driver GA, other targetable GA affecting kinases or the MTOR pathway are present. As evidenced by TMB, the opportunity for immunotherapies remains significant. FGFR3 WT FGFR3mut Significance Cases 1,275 301 Median age (years) 67 67 NS Male/Female 75/25 72/28 NS GA/tumor 7.3 8.3 NS TERT 67% 73% NS TP53 64% 27% P < 0.0001 CDKN2A 30% 60% P < 0.0001 RB1 24% 3% P < 0.0001 ARID1A 24% 17% P = 0.001 KDM6A 20% 37% P < 0.0001 BRCA1 3% 1% NS BRCA2 3% 3% NS PIK3CA 20% 27% P = 0.001 ERBB2 18% 6% P < 0.0001 TSC1 6% 17% P < 0.0001 MSI < 1% 1% NS Median/Mean TMB (mut/Mb) 7.2/10.7 6.3/9.3 NS TMB > 10 mut/Mb 38% 28% P = 0.0008 TMB > 20 mut/Mb 13% 9% NS
H<sub>2</sub>hox: Dual-Channel Oxine-Derived Acyclic Chelating Ligand for <sup>68</sup>Ga Radiopharmaceuticals (2018)

An acyclic hexadentate oxine-derived chelating ligand, H<sub>2</sub>hox, was investigated as an alternative to current chelators for <sup>68</sup>Ga. The straightforward preparation of H<sub>2</sub>hox, involving only one or two steps, obviates the synthetic challenges associated with many reported <sup>68</sup>Ga chelators; it forms a Ga<sup>3+</sup> complex of great stability (log K = 34.4) with a remarkably high gallium scavenging ability (pGa<sup>3+</sup> = -log[Ga<sup>3+</sup><sub>free</sub>] = 28.3, ([Ga<sup>3+</sup>] = 1 μM; [L <sup>x-</sup>] = 10 μM; pH 7.4, and 25 °C)). Moreover, H<sub>2</sub>hox coordinates <sup>68</sup>Ga quantitatively in 5 min at room temperature in ligand concentrations as low as 1 × 10<sup>-7</sup> M, achieving an unprecedented high molar activity of 11 ± 1 mCi/nmol (407 ± 3.7 MBq/nmol) without purification, suggesting prospective kit-based convenience. [<sup>68</sup>Ga(hox)]<sup>+</sup> showed no decomposition in a plasma challenge. Good in vivo stability and fast renal and hepatic clearance of the [<sup>68</sup>Ga(hox)]<sup>+</sup> complex were demonstrated using dynamic positron emission tomography/computed tomography imaging. The intrinsic fluorescence of [Ga(hox)]<sup>+</sup> allowed for direct fluorescence imaging of cellular uptake and distribution, demonstrating the dual-channel detectability and intracellular stability of the metal complex.
Supplementary Figure Legends from Tumor Cell–Independent Estrogen Signaling Drives Disease Progression through Mobilization of Myeloid-Derived Suppressor Cells (2023)

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Fullerenes (2009)

This chapter contains sections titled: Introduction Chemistry Influenced by the Nontypical Structure: Modification of [60]Fullerene Physicochemical Properties and the Unusual Structure of Fullerenes Fullerene Aggregates Endohedral Fullerenes with Neutral Atoms and Molecules Hydrogenated Fullerenes Applications of Fullerenes References
Evaluation of Aerosol, Superfine Inkjet, and Photolithography Printing Techniques for Metallization of Application Specific Printed Electronic Circuits (2016)

Application specific printed electronic circuits (ASPECs) are the corresponding term with application-specified ICs for printed electronics. The same as any new technology, printed electronics is suffering from some restrictions in design and process technology aspects. An important stage in the ASPEC design is the final wiring of the organic thin-film transistor arrays or gate arrays to customize it to implement any specific target application that fits in their structure. In this paper, we evaluate two additive manufacturing technologies: aerosol jet using Optomec M3D and electrohydrodynamic printer using superfine inkjet. Both techniques are based on direct-writing of the pattern corresponding to any individual circuit being fabricated (digital printing) enabled by the mask-free noncontact deposition of materials. Finally, these structures will be compared with the corresponding photolithography mask technology. Some parameterized test vehicles, with different instantiations for the variation of line widths and separations, have been designed to be wired using the target technologies. These test vehicles have been fabricated at the Centre for Process Innovation by a five masks lithography and subtractive patterning technology. Results show that both direct printing technologies are feasible for the fabrication of the gate-array customization, thus allowing individual personalization of every circuit what can produce added value functionalities at low cost such as the equivalent effect of having an ROM memory which final contents could be customized at home by using low-cost digital printing technologies. Further interactions between transistor bulk and wiring technologies can improve the obtained performance in order to end up in an industrialized process.
Factors affecting stability of plasma brain-derived neurotrophic factor (2020)

Circulating concentrations of brain-derived neurotrophic factor (BDNF) have been linked to cancer, neuropsychiatric, diabetes, and gynecological disorders. However, factors influencing plasma storage and subsequent BDNF quantification are incompletely understood. Therefore, the anticoagulant used in plasma separator tubes, storage-time, storage-temperature, and repeated freeze-thaw cycles on circulating BDNF concentrations was evaluated. Peripheral blood samples were collected from healthy women (n = 14) and men (n = 10) recruited prospectively from McMaster University (August 2014). Blood was collected from the cubital vein into plasma separator tubes containing five different anticoagulant systems [K2EDTA, Li-Hep, Li-Hep (gel), Na-Hep, Na-Hep (glass)], and placed on ice for transport to the lab for centrifugation. Plasma samples (n = 16) collected in K2EDTA tubes from women recruited to a previous study (April 2011 to December 2012) were used to determine the effect of multiple freeze-thaw cycles. Plasma BDNF was quantified using a commercially available ELISA kit. Plasma concentrations of BDNF were significantly affected by the type of plasma separator tube, storage-time, and number of freeze-thaw cycles. Storage temperature (- 20 vs. - 80 °C) did not significantly affect the quantity of BDNF measured as mean BDNF concentrations generally fell within our calculated acceptable change limit up to 6 months in the freezer. Our results suggest that for quantification of circulating BDNF blood collected in K2EDTA tubes and plasma stored up to 6 months at either - 20 or - 80 °C produces reproducible results that fall within an acceptable range. However, plasma samples stored beyond 6 months and repeated freeze-thaw cycles should be avoided.
Noise characteristics in exchange-biased soft underlayers for perpendicular media (2001)

The characteristics of exchange-biased soft underlayers (SULs) were investigated using magnetic force microscopy and spin stand measurements with a single-pole (focused ion-beam trimmed gap) writer and magnetoresistive head. The SUL high-moment materials (FeCoB, FeAlN) were exchange biased by using IrMn. Spin stand data on perpendicular media (CoCrPtB) with an exchange-biased FeCoB SUL also showed a low integrated dc erase noise level, demonstrating its potential for use in double-layered perpendicular media.
Ease of Synthesis, Controllable Sizes, and In Vivo Large‐Animal‐Lymph Migration of Polymeric Nanoparticles (2010)

Flying south for the winter! Polymeric nanoparticles were synthesized using either a photoinduced or base-catalyzed free-radical polymerization method. The particles (Ø=50 nm), loaded with a dye (IR-786), were observed to migrate over 20 cm to the sentinel lymph node after injection in a live pig. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Determination of Flavopiridol (L 86 8275) in Rat Serum Using Ion-Pair Reversed-Phase High-Performance Liquid Chromatography (1997)

A specific, sensitive, and simple high-performance liquid chromatographic method has been developed for assaying flavopiridol in rat serum for preliminary bioavailability and pharmacokinetic studies. The drug and internal standard were extracted with dichloromethane from serum. After evaporating the solvent, the extract was reconstituted with mobile phase. Chromatography was performed on a 10-μ. Bondapak C18 column (30 cm × 3.9 mm ID), using methanol:water (50:50, v/v) containing 0.05 M ion-pairing reagent PIC B-6 as a mobile phase at a flow rate of 1.1 ml/min, with ultraviolet detection at 278 nm. The drug and internal standard were well resolved from other serum constituents. Due to high sensitivity and reproducibility the method can be adapted very well for assaying flavopiridol in higher animals.
The Putative PAX8/PPAR  Fusion Oncoprotein Exhibits Partial Tumor Suppressor Activity through Up-Regulation of Micro-RNA-122 and Dominant-Negative PPAR  Activity (2011)

In vitro studies have demonstrated that the PAX8/PPARγ fusion protein (PPFP), which occurs frequently in follicular thyroid carcinomas (FTC), exhibits oncogenic activity. However, paradoxically, a meta-analysis of extant tumor outcome studies indicates that 68% of FTC-expressing PPFP are minimally invasive compared to only 32% of those lacking PPFP (χ(2) = 6.86, P = 0.008), suggesting that PPFP favorably impacts FTC outcomes. In studies designed to distinguish benign thyroid neoplasms from thyroid carcinomas, the previously identified tumor suppressor miR-122, a major liver micro-RNA (miR) that is decreased in hepatocellular carcinoma, was increased 8.9-fold (P < 0.05) in all FTC versus normal, 9.2-fold in FTC versus FA (P < 0.05), and 16.8-fold (P < 0.001) in FTC + PPFP versus FTC - PPFP. Constitutive expression of PPFP in the FTC-derived cell line WRO (WRO-PPFP) caused a 5-fold increase of miR-122 expression (P < 0.05) and a striking 5.1-fold reduction (P < 0.0001) in tumor progression compared to WRO-vector cells in a mouse xenograft model. Constitutive expression of either miR-122 or a dominant-negative PPARγ mutant in WRO cells was less effective than PPFP at inhibiting xenograft tumor progression (1.8-fold [P < 0.001] and 1.7-fold [P < 0.03], respectively). PPFP-induced up-regulation of miR-122 expression was independent of its known dominant-negative PPARγ activity. Up-regulation of miR-122 negatively regulates ADAM-17, a known downstream target, in thyroid cells, suggesting an antiangiogenic mechanism in thyroid carcinoma. This latter inference is directly supported by reduced CD-31 expression in WRO xenografts expressing PPFP, miR-122, and DN-PPARγ. We conclude that, in addition to its apparent oncogenic potential in vitro, PPFP exhibits paradoxical tumor suppressor activity in vivo, mediated by multiple mechanisms including up-regulation of miR-122 and dominant-negative inhibition of PPARγ activity.
Preparation of Transparent YAG Ceramic and Its Application to Window Material of Infrared Spectrophotometer. (2000)

Transparent polycrystalline YAG(Y3Al5O12) ceramic, optical characteristics of which are comparable to those of a single crystalline YAG, was fabricated by a sintering method using >99.99mass% purity powders and its application to a window material of infrared spectrophotometer was investigated. Its average grain size and pore density were 50μm and about 1ppm, respectively. It showed high strength(modulus of rupture: 350MPa), high hardness(Vickers hardness [HV10]: 1280), low refractive index(1.8 at 590nm wavelength) and low thermal expansion coefficient(8×10-6K-1), and was very stable in various inorganic solvents, 10% HF solution, 1M HCl solution, 1M H2SO4 solution, 1M NaOH solution and 10% NH3 solution and organic solvents, methyl alcohol, acetone, toluene and dimethyl sulfoxide. The transmittance of 1 mm-thick YAG was about 85% for the wavelength of <6μm and decreased with increasing wavelength to reach almost 0% at 9μm. These results and some infrared spectral measurements indicate that the present YAG ceramic is a good window material in the range of 2.5 to 9μm.
Parallel Sparse Subspace Clustering via Joint Sample and Parameter Blockwise Partition (2017)

Sparse subspace clustering (SSC) is a classical method to cluster data with specific subspace structure for each group. It has many desirable theoretical properties and has been shown to be effective in various applications. However, under the condition of a large-scale dataset, learning the sparse sample affinity graph is computationally expensive. To tackle the computation time cost challenge, we develop a memory-efficient parallel framework for computing SSC via an alternating direction method of multiplier (ADMM) algorithm. The proposed framework partitions the data matrix into column blocks and then decomposes the original problem into parallel multivariate Lasso regression subproblems and samplewise operations. The proposed method allows us to allocate multiple cores/machines for the processing of individual column blocks. We propose a stochastic optimization algorithm to minimize the objective function. Experimental results on real-world datasets demonstrate that the proposed blockwise ADMM framework is substantially more efficient than its matrix counterpart used by SSC, without sacrificing performance in applications. Moreover, our approach is directly applicable to parallel neighborhood selection for Gaussian graphical models structure estimation.
Covering all clinically significant areas of the colon surface in virtual colonoscopy (2002)

We have developed a method that automatically displays, places in sized order and allows viewing of the areas of the colon surface not visualized during initial endoscopic navigational viewing. While complete surface visualization is possible, we demonstrate that all of these missed patches do not have to be reviewed to detect clinically significant colon polyps. CT scans are performed on 147 patients and volunteers after bowel preparation and colon distention with CO<SUB>2</SUB>. After automatic segmentation and electronic cleansing of the colon lumen, the medial axis (centerline) is extracted. Volume rendering fly-through along the centerline is performed and visualized surfaces are marked. To simulate optical colonoscopy, the virtual camera is passed in the antegrade direction. For virtual colonoscopy, the camera is passed both antegrade and retrograde, and the combined visible surface voxel count is recorded. After both fly-throughs, the total visualized surface is recorded and all 'patches' of connected surface area not yet seen are identified, measured, sorted by size, and counted. Clinically significant patches, defined as smallest diameter being &gt; 5mm, are sequentially visualized by stepping through the sorted list until reaching the patch diameter of 5 mm.. for each. By enabling endoscopic navigation in both antegrade and retrograde directions, virtual colonoscopy is able to evaluate behind haustral folds and around sharp bends, thereby visualizing significantly more surface area than optical colonoscopy. Furthermore, automatic marking of the visualized surface area and identifying and viewing unseen patches allows examination of all clinically significant surfaces of the colon.
Studies on tumor‐promoting activity of polyethylene: Inhibitory activity of metabolic cooperation on polyethylene surfaces is markedly decreased by surface modification with collagen but not with RGDS peptide (1997)

Tumor promotion activity of polyethylene (PE) was estimated in terms of the inhibitory potentials on the gap-junctional intercellular communication using the metabolic cooperation assay. The gap-junctional intercellular communication of test cells was inhibited on the PE film, but this inhibitory activity was markedly decreased when the surface of the PE film was immobilized with collagen. These results suggest that the in vivo tumor promotion activity of the untreated PE may be stronger than that of collagen-immobilized PE. On the other hand, surface modification with RGDS peptide, which is well knownn as the sequence of cell attachment domain in extracellular matrix proteins, did not reduce the promotion activity of PE film. In addition, neither modification with bovine serum albumin nor RGES peptide reduced the activity of PE film. These findings suggest that reduction of the inhibitory activity on gap-junctional intercellular communication of collagen immobilization is not simply due to improved cell adherence via the RGDS sequence but to some cell-cell recognition via collagen molecules essential for the gap-junctional intercellular communication. © 1997 John Wiley & Sons, Inc.
Two-dimensional phase unwrapping using a block least-squares method (1999)

We present a block least-squares (BLS) method for two-dimensional (2-D) phase unwrapping. The method works by tessellating the input image into small square blocks with only one phase wrap. These blocks are unwrapped using a simple procedure, and the unwrapped blocks are merged together using one of two proposed block merging algorithms. By specifying a suitable mask, the method can easily handle objects of any shape. This approach is compared with the Ghiglia-Romero method and the Marroquin-Rivera method. On synthetic images with different noise levels, the BLS method is shown to be superior, both with respect to the resulting gray values in the unwrapped image as well as visual inspection. The method is also shown to successfully unwrap synthetic and real images with shears, fiber-optic interferometry images, and medical magnetic resonance images. We believe the new method has the potential to improve the present quality of phase unwrapped images of several different image modalities.
High bandwidth data recording systems for pulsed power and laser produced plasma experiments (2006)

We present two high bandwidth data transmission and recording systems for the measurement of transient signals during pulsed power and laser produced plasmas. These systems use fiber optic cables to transmit analog data over long distances to high bandwidth digitizing oscilloscopes. One system is based on the direct modulation of a laser diode and has a bandwidth of 1.5GHz. The other system is based upon a Mach-Zehnder modulator and has a bandwidth of 12GHz, and is limited by the photoreceiver. The signals are recorded on commercial digitizing oscilloscopes that have approximately six effective bits. The transmission systems use many off-the-shelf components from the telecommunications industry and thus have a high reliability and a moderate cost. Investigation of the reduction in optical transmission of the fibers during exposure to high dose radiation will also be discussed.
A model-based analysis of phenytoin and carbamazepine toxicity treatment using binding-competition during hemodialysis (2020)

Hemodialysis (HD) has limited efficacy towards treatment of drug toxicity due to strong drug-protein binding. In this work, we propose to infuse a competitor drug into the extracorporeal circuit that increases the free fraction of a toxic drug and thereby increases its dialytic removal. We used a mechanistic model to assess the removal of phenytoin and carbamazepine during HD with or without binding-competition. We simulated dialytic removal of (1) phenytoin, initial concentration 70 mg/L, using 2000 mg aspirin, (2) carbamazepine, initial concentration 35 mg/L, using 800 mg ibuprofen, in a 70 kg patient. The competitor drug was infused at constant rate. For phenytoin (~ 13% free at t = 0), HD brings the patient to therapeutic concentration in 460 min while aspirin infusion reduces that time to 330 min. For carbamazepine (~ 27% free at t = 0), the ibuprofen infusion reduces the HD time to reach therapeutic concentration from 265 to 220 min. Competitor drugs with longer half-life further reduce the HD time. Binding-competition during HD is a potential treatment for drug toxicities for which current recommendations exclude HD due to strong drug-protein binding. We show clinically meaningful reductions in the treatment time necessary to achieve non-toxic concentrations in patients poisoned with these two prescription drugs.
Nonreciprocal Nongyrotropic Magnetless Metasurface (2017)

We introduce a nonreciprocal nongyrotropic magnetless metasurface. In contrast to previous nonreciprocal structures, this metasurface does not require a biasing magnet, and is therefore lightweight and amenable to integrated circuit fabrication. Moreover, it does not induce Faraday rotation, and hence does not alter the polarization of waves, which is a desirable feature in many nonreciprocal devices. The metasurface is designed according to a Surface-Circuit-Surface architecture and leverages the inherent unidirectionality of transistors for breaking time reversal symmetry. Interesting features include transmission gain as well as broad operating bandwidth and angular sector operation. It is finally shown that the metasurface is bianisotropic in nature, with nonreciprocity due to the electric-magnetic coupling parameters, and structurally equivalent to a moving uniaxial metasurface.