gebhart/patrepeval huggingface dataset:
Abstract PR01: Global chromatin profiling identifies NSD2 mutations in pediatric acute lymphoblastic leukemia (2013)

Abstract Epigenetic dysregulation is an emerging hallmark of cancers, and the identification of recurrent somatic mutations in chromatin modifying enzymes implies a causal role for altered chromatin states in tumorigenesis. While the genomic characterization of cancers is well advanced, our current understanding of cancer epigenomes is limited. Here, we developed a high-information-content mass spectrometry approach to profile global histone modifications in human cancer cells. When applied to 115 cell lines of the Cancer Cell Line Encyclopedia, this approach identified distinct molecular chromatin signatures (MCS) that provided novel insights into their epigenetic states. One MCS cluster, characterized by high H3K27 trimethylation, strongly correlated with EZH2 gain-of-function mutations, whereas another MCS cluster provided functional epigenetic correlates of EZH2 loss-of-function mutations. A third MCS cluster was characterized by increased H3K36 dimethylation and contained several cell lines harboring NSD2 translocations. Analysis of genomic correlates of the remaining cell lines within this third cluster identified a novel NSD2 E1099K variant in acute lymphoblastic leukemia (ALL) lines. Ectopic expression of the NSD2 E1099K variant induced a MCS profile characteristic of NSD2 hyperactivation and promoted transformation. Moreover, NSD2 knockdown selectively inhibited the proliferation of cell lines harboring NSD2 mutations. Massively parallel sequencing analysis of over 1000 pediatric cancer genomes identified the same NSD2 E1099K mutation in 14% of t(12;21)[ETV6-RUNX1]-containing ALLs. Together, these findings identify NSD2 as a potential therapeutic target for pediatric ALL and provide a general framework for the functional annotation of cancer epigenomes. Citation Format: Jacob Jaffe, Yan Wang, HoMan Chan, Jinghui Zhang, Roberts Huether, Gregory Kryukov, Jordan Taylor, Min Hu, Nathan Englund, Feng Yan, Zhaofu Wang, Lei Wei, Lei Wei, Jing Ma, John Easton, William R. Sellers, Nicholas Keen, Jun Liu, Jun Liu, Charles Mullighan, Steven Carr, James Downing, Levi Garraway, Frank Stegmeier. Global chromatin profiling identifies NSD2 mutations in pediatric acute lymphoblastic leukemia. [abstract]. In: Proceedings of the AACR Special Conference on Chromatin and Epigenetics in Cancer; Jun 19-22, 2013; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2013;73(13 Suppl):Abstract nr PR01.
Minimal-invasive Computer-assistierte fluoroskopische Navigation der Kyphoplastie (2005)

In challenging cases of deteriorated anatomy and difficult radiomorphologic orientation, especially of the lower thoracic spine, the CAOS-procedure succeeds in finding the optimal pedicular approach to the vertebral body, helps to avoid collateral damage and minimises the overall risk of the procedure. High accuracy and reduced radiation exposure justify the clinical use of fluoroscopic navigation for transpedicular instrumentation.
A novel approach to the nonlinear H<sub>&#x0221E;</sub> regulator problem (2007)

This paper presents a theoretical approach to the nonlinear H <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">∞</sub> regulator problem. From a fixed point theoretic point of view, it is shown that the nonlinear H <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">∞</sub> state feedback law is characterized as a fixed point of a mapping and its suboptimal solution can be obtained using standard optimization techniques. A simple numerical example is included to verify that the resulting feedback law actually enhances the robustness of a system.
Design and testing of an intervertebral disc prosthesis (2002)

The primary rationale for an intervertebral disc prosthesis is to restore normal anatomical relationships while duplicating the normal lumbar spine biomechanics, thereby allowing for normal and uniform stress transfer to adjacent motion segments. The design and test requirements for such a prosthesis are summarised.
Priced based operation in an auction market structure (1996)

Open transmission access is a new legal requirement within the electric power industry. Interchange will require evaluation of the existing conditions to determine if the product can be delivered at the time required and at the level awarded through the bidding or negotiation process. This paper seeks to identify the likely deregulation details for a full market implementation when native load is considered equal to any other third party load (comparability). This paper seeks to identify the technical issues, such as standards and algorithms, necessary for changing the national infrastructure from a vertically integrated industry to a horizontally integrated industry.
Comparison of the Performance of Drag Reducing Agent Between 2.5 cP Oil and 6.0 cP Oil in Multiphase Flow in Horizontal Pipes (2001)

Abstract Experimental studies have been performed in a 10 cm diameter, 36 m long, multiphase flow loop to examine the effect of drag reducing agents using 6 cP oil. Studies were performed for superficial liquid velocities of 0.5, 1.0 and 1.5 m/s and superficial gas velocities between 2 and 12 m/s. Carbon dioxide was used as the gas phase. The drag reducing agent (DRA) concentrations were 20 and 50 ppm. The system was maintained at a pressure of 0.13 MPa and a temperature of 25 °C. The comparison of the conditioning of flow with DRA between 2.5 cP oil and 6 cP oil is presented. The results show that pressure drop in both 2.5 cP oil and 6 cP oil was reduced significantly in multiphase flow with addition of DRA. A DRA concentration of 50 ppm was more effective than 20 ppm DRA for all cases. As the oil viscosity was increased from 2.5 cP to 6 cP oil, the transition to annular flow was observed to occur at lower superficial gas velocities. For slug flow and lower superficial gas velocities, the effectiveness in 2.5 cP oil was much higher than that in 6 cP oil with addition of DRA. However, for higher superficial gas velocities, the effectiveness in both oils was similar. For annular flow, the effectiveness in 2.5 cP oil was higher than in 6 cP oil with 50 ppm DRA. At low superficial gas velocities, DRA in 2.5 cP oil was more effective in reducing the slug frequency. This led to a higher average pressure drop reduction in 2.5 cP oil. However, at higher superficial gas velocities, the slug frequency decreased in both oils almost the same magnitude.
Electron beam characterization techniques for the study of wear in sliding contacts (2015)

In this study different methods for studying phenomena of adhesive wear in sliding electrical contacts using electron beam characterization methods within a dual beam workstation are presented. The interface between the substrate and transferred material is complex exhibiting small grain size as well as mechanical deformation. For this purpose, a dual beam workstation is used in order to perform high resolution imaging, structural investigation by electron backscatter diffraction as well as FIB cross sectioning. Only a combination of different imaging techniques with different contrast mechanisms can provide a full understanding of the wear mechanism. During wear a prow is formed on the slider. The structure implies a multi-generation history. The deformation texture resembles a simple shear texture, which is in agreement with the presumed deformation mode. The study mainly gives a guideline for future work in the field of wear in sliding contacts.
Electrically Switchable Diffraction Grating Using a Hybrid Liquid Crystal and Carbon Nanotube‐Based Nanophotonic Device (2013)

A hybrid liquid crystal and carbon nanotube‐based device which shows the capacity to perform as a switchable diffraction grating is demonstrated. A liquid crystal layer was sandwiched between two electrodes (patterned into gratings). The bottom electrode consists of a two dimensional square array of carbon nanotubes, while the top electrode comprises an ITO‐based in‐plane switching electrode on glass. The carbon nanotubes, due to their high aspect ratios, produce defects within the liquid crystal layer, producing a two dimensional grating. The device displays distinct voltage‐dependent diffraction patterns due to the two different electrodes. The diffraction patterns are studied both computationally and experimentally, with good agreement between the results obtained. Both the diffraction pattern and efficiency from the device could be switched by varying the applied voltage across the liquid crystal layer.
Biodegradable Fluorescent Nanoparticles for Endoscopic Detection of Colorectal Carcinogenesis (2019)

Early and comprehensive endoscopic detection of colonic dysplasia - the most clinically significant precursor lesion to colorectal adenocarcinoma - provides an opportunity for timely, minimally-invasive intervention to prevent malignant transformation. Here, the development and evaluation of biodegradable near-infrared fluorescent silica nanoparticles (FSN) is described that have the potential to improve adenoma detection during fluorescence-assisted white-light colonoscopic surveillance in rodent and human-scale models of colorectal carcinogenesis. FSNs are biodegradable (t<sub>1/2</sub> of 2.7 weeks), well-tolerated, and enable detection and delineation of adenomas as small as 0.5 mm<sup>2</sup> with high tumor-to-background ratios. Furthermore, in the human-scale, <i>APC</i> <sup><i>1311/+</i></sup> porcine model, the clinical feasibility and benefit of using FSN-guided detection of colorectal adenomas using video-rate fluorescence-assisted white-light endoscopy is demonstrated. Since nanoparticles of similar size (<i>e.g</i>., 100-150-nm) or composition (<i>i.e</i>., silica, silica/gold hybrid) have already been successfully translated to the clinic, and, clinical fluorescent/white light endoscopy systems are becoming more readily available, there is a viable path towards clinical translation of the proposed strategy for early colorectal cancer detection and prevention in high-risk patients.
False estimates of stimulated Raman pumping efficiency caused by the optical Stark effect (2011)

One technique for measuring the fraction of molecules pumped to the excited state in stimulated Raman pumping (SRP) is to record the depletion of molecules in the lower state by resonance enhanced multiphoton ionization (REMPI). The presence of electric fields on the order of 10(7) V/cm arising from the pulsed SRP laser beams is sufficient to shift the line position of the REMPI transition to such an extent that the estimate of the pumping efficiency is overestimated unless this shift is accounted for.
Publisher's Note: Measurement of theWboson polarization in top decay at CDF ats=1∶8  TeV[Phys. Rev. D71, 031101 (2005)] (2005)

Received 25 February 2005DOI:https://doi.org/10.1103/PhysRevD.71.059901©2005 American Physical Society
End-to-End Visual Domain Adaptation Network for Cross-Domain 3D CPS Data Retrieval (2019)

3D CPS (Cyber Physical System) data has been widely generated and utilized for multiple applications, e.g. autonomous driving, unmanned aerial vehicle and so on. For large-scale 3D CPS data analysis, 3D object retrieval plays a significant role for urban perception. In this paper, we propose an end-to-end domain adaptation framework for cross-domain 3D objects retrieval (C3DOR-Net), which learns a joint embedding space for 3D objects from different domains in an end-to-end manner. Specifically, we focus on the unsupervised case when 3D objects in the target domain are unlabeled. To better encode a 3D object, the proposed method learns multi-view visual features in a data-driven manner for 3D object representation. Then, the domain adaptation strategy is implemented to benefit both domain alignment and final classification. Specifically, an center-based discriminative feature learning method enables the domain invariant features with better intra-class compactness and inter-class separability. C3DOR-Net can achieve remarkable retrieval performances by maximizing the inter-class divergence and minimizing the intra-class divergence. We evaluate our method on two cross-domain protocols: 1) CAD-to-CAD object retrieval on two popular 3D datasets (NTU and PSB) in three designed cross-domain scenarios; 2) SHREC’19 monocular image based 3D object retrieval. Experimental results demonstrate that our method can significantly boost the cross-domain retrieval performances.
Impact of the Ga flux incidence angle on the growth kinetics of self-assisted GaAs nanowires on Si(111) (2019)

In this work we show that the incidence angle of group-III element fluxes plays a significant role in the diffusion-controlled growth of III-V nanowires (NWs) by molecular beam epitaxy (MBE). We present a thorough experimental study on the self-assisted growth of GaAs NWs by using a MBE reactor equipped with two Ga cells located at different incidence angles with respect to the surface normal of the substrate, so as to ascertain the impact of such a parameter on the NW growth kinetics. The as-obtained results show a dramatic influence of the Ga flux incidence angle on the NW length and diameter, as well as on the shape and size of the Ga droplets acting as catalysts. In order to interpret the results we developed a semi-empirical analytical model inspired by those already developed for MBE-grown Au-catalyzed GaAs NWs. Numerical simulations performed with the model allow us to reproduce thoroughly the experimental results (in terms of NW length and diameter and of droplet size and wetting angle), putting in evidence that under formally the same experimental conditions the incidence angle of the Ga flux is a key parameter which can drastically affect the growth kinetics of the NWs grown by MBE.
Low-cost and fine-pitch micro-ball mounting technology for WLCSP (2012)

Ball mount technology uses performed solder spheres dropping through a metal template onto wafer at once. This technology is directly producing bumps on wafer with high throughput and consistent bump results. Ball mounting process without using electroplating decreases cost and chemical pollution. This technique is applicable for many applications but several issues associated with this technology that limits its widespread use in high volume and high yield applications. These limitations include: (1) a practical lower limit to the size of sphere that can be dropped, and (2) the stencil between the performed solder spheres and the wafer can fail, causing a release of all the spheres into the tool (often referred to as bursts or escapes), and the yields are statistically low. To meet high I/O density IC request, the trend of wafer level chip scale package (WLCSP) I/O pad distributed design is toward to reduce the I/O pitch and increase the I/O density, and therefore impact solder ball size application of ball mount process, WLCSP micro-ball mount technology is requested. In this study, a low-cost and fine-pitch micro-ball mounting technology is developed. Emphasis is placed on determining the most important factors such as accurate dropping parameters, stencil quality and reflow conditions for microball mounting design, materials, and process. Three different ball sizes are considered: 70μm, 100μm, and 250μm. Their corresponding pitches are 130μm, 180μm, and 400μm. WLCSP micro balls with diameter = 70μm and pitch = 130μm on 300mm wafers (with ~2KK I/Os) have been successful produced. The yield is more than 99.99% without any missing micro ball and bridging.
The preclinical characterization of [18F]hGTS13 for imaging of xC- transporter activity (2018)

607 Objectives: We set out to explore [18F]hGTS13 as a novel radiopharmaceutical to measure xC- transporter activity by positron emission tomography (PET) imaging. The xC- transporter is an emerging oncologic target, mediating oxidative stress and providing a growth advantage for a variety of tumors. This study was performed to evaluate the tumor uptake and biodistribution of [18F]hGTS13 compared to [18]FSPG, a previously described xC- transporter substrate. Methods: Synthesis of [18F]hGTS13 was adopted from US2015/0011773. The cellular uptake of [18F]hGTS13 was first evaluated in H460 and A549 lung carcinoma cell lines. Competition studies were performed using known substrates or inhibitors of the xC- transporter, L-cystine, L-glutamate, (S)-4-carboxyphenyglycine (CPG). To further confirm the specificity of [18F]hGTS13 for the xC- transporter, small inhibitory RNA (siRNA) methodology was used to reduce transporter expression in A549 cells. Human peripheral blood mononuclear cells (PBMCs) were derived from freshly obtained buffy coat fractions and T cells isolated using the Naive Pan T cell Isolation Kit. T cells were activated with the T cell activation/expansion kit (Miltenyi Biotec) and radiotracer uptake was performed 48 hours after activation. H460 tumor bearing rats were investigated with [18F]FSPG and [18F]hGTS13 PET/CT imaging. Results: Cell assays with [18F]hGTS13 revealed rapid and extensive uptake in both A549 and H460 human lung carcinoma cells. Uptake values at 60 mins were 21.6 ± 3.6 and 32.1 ± 0.8 %uptake/mg protein in A549 and H460 cells respectively. Transient reduction of xC- transporter expression in A549 cells resulted in a significant reduction in [18F]hGTS13 uptake (p
3D Point Cloud Analysis and Classification in Large-Scale Scene Based on Deep Learning (2019)

We present a deep learning framework for efficient large-scale 3D point cloud analysis and classification using the designed feature description matrix (FDM). As the 3D points are unordered in the large-scale scene, and no topology structure can be employed directly for classification and recognition, it is difficult to apply deep neural network directly on 3D point clouds as points cannot be arranged in a fixed order as 2D image pixels. We design a new pipeline for 3D data processing by combining the traditional features extraction method and deep learning method. Our FDM encapsulates the 3D features of the point and can be used as the input of the deep neural network for training and testing. The experiments demonstrate that our method can acquire higher classification accuracy compared with our previous work and other state-of-art works.
Computationally Optimized Irradiation Chamber Design for Production of 135 Xe in the Washington State University TRIGA Reactor (2023)

This work summarizes the radiation transport–based design for a new D2O-moderated ex-core irradiation facility in the Washington State University (WSU) TRIGA reactor for optimization of 135Xe sources used for calibration and quality control testing of Xe gas detection equipment in support of the Comprehensive Test Ban Treaty (CTBT). Three-dimensional (3-D) particle transport analysis characterizing the WSU reactor core using MCNP6.2 (3-D Monte Carlo) and PENTRAN (3-D deterministic parallel SN) form the basis for the computational optimization. Excellent agreement between MCNP6.2 and PENTRAN predictions is observed. A fundamental fuel bundle depletion analysis is applied to enable a more accurate prediction of neutron flux and neutron spectrum distribution, which drives production rates of 135Xe and 133Xe. The results of various model simulations were used to inform recommendations for the final irradiation chamber design, which has been optimized for safe placement in the reactor tank prior to startup and will allow for insertion and rotation of xenon “bean” samples using existing WSU irradiation equipment, while remaining within operational parameters. The irradiation chamber is expected to produce samples that will remain viable for use in CTBT standards applications for durations 70% to 80% longer than samples produced using current procedures. Thus, this design is expected to improve CTBT-related calibrations and performance testing and to support the continued stability of the CTBT monitoring network.
Unravelling the structure and function of human hair (2013)

Human hair is transformed into functional nano-dimensional material using a benign choline chloride–urea ionic liquid composite as a deep eutectic melt. The hair and isolated central fibres after treatment with the ionic liquid composite have the ability to immobilise microalgal cells for wastewater treatment and the cuticle cells are effective as templates in coating a sparingly soluble drug molecule which is slowly released at physiological pH. Thus, instead of human hair being a waste, it can be converted to end products with potentially high-end value, with reduced negative impact on the environmental.
Hydrogen sulfide significantly mitigates cellular injury in intestinal ischemia (2008)

Singh, Sunil P. BA; Rafii, Daniel C. BA; Lyden, David C. MD, PhD; Spector, Jason A. MD Author Information
A Parameter for IL-10 and TGF-ß Mediated Regulation of HIV-1 Specific T Cell Activation Provides Novel Information and Relates to Progression Markers (2014)

HIV replication is only partially controlled by HIV-specific activated effector T cells in chronic HIV infection and strategies are warranted to improve their efficacy. Chronic T cell activation is generally accompanied by regulation of antigen-specific T cell responses which may impair an effective control of chronic infections. The impact of HIV-induced T cell regulation on individual patients' disease progression is largely unknown, since classical T cell activation assays reflect net activation with regulation as unknown contributing factor. We here explore a quantitative parameter for antigen-induced cytokine-mediated regulation (R(AC) of HIV-specific effector T cell activation by functional antibody-blockade of IL-10 and transforming growth factor-β. HIV Env- and Gag-specific T cell activation and R(AC) were estimated in peripheral blood mononuclear cells from 30 treatment-naïve asymptomatic HIV-infected progressors (CD4 count 472/µl, HIV RNA 37500 copies/ml) stimulated with overlapping peptide panels for 6 days. R(AC) was estimated from differences in T cell activation between normal and blocked cultures, and related to annual CD4 loss, immune activation (CD38) and microbial translocation (plasma lipopolysaccharides). R(AC) was heterogeneously distributed between individual patients and the two HIV antigens. Notably, RAC did not correlate to corresponding classical activation. Env R(AC) correlated with CD38 and CD4 loss rates (r> = 0.37, p = <0.046) whereas classical Gag activation tended to correlate with HIV RNA (r = -0.35, p = 0.06). 14 patients (47%) with low R(AC)'s to both Env and Gag had higher CD8 counts (p = 0.014) and trends towards lower annual CD4 loss (p = 0.056) and later start with antiretroviral treatment (p = 0.07) than the others. In contrast, patients with high RAC to both Env and Gag (n = 8) had higher annual CD4 loss (p = 0.034) and lower CD8 counts (p = 0.014). R(AC) to Env and Gag was not predicted by classical activation parameters and may thus provide additional information on HIV-specific immunity. R(AC) and other assessments of regulation deserve further in-depth exploration.
Adaptive Dual Maximum Power Point Tracking Algorithm for PV DC-DC Conversion Stage (2018)

This paper proposes an adaptive dual maximum power point tracking (DMPPT) algorithm to maximize the energy harvested from a photovoltaic (PV) source. The proposed method tracks the maximum power from the PV source and the maximum efficiency of the DC-DC converter by perturbing both the PV voltage and the DC-DC converter switching frequency, and then observing the output power of the converter. The proposed method is very fast since it uses adaptive variable step sizes through the search loop. The proposed method employs various termination techniques that avoids, to a great extent, false termination of the search algorithm when local maximum points are detected. Moreover, the proposed method guarantees convergence and is very simple to implement. Derivation of the proposed technique followed by experimental verification are presented.