gebhart/patrepeval huggingface dataset:
Abstract 397: Whole genome copy number variation analysis using a SNP-focused targeted sequencing panel for tumor analysis (2017)

Abstract Accurate genome-wide copy number variation (CNV) analysis is critical for disease and cancer research. Current approaches for CNV analysis include fluorescence in situ hybridization (FISH), array comparative genomic hybridization (array CGH), and SNP arrays. Unfortunately, these methods are not sensitive enough for real world cancer samples because of tumor ploidy, purity and heterogeneity. NGS-based targeted sequencing is increasingly being used for CNV analysis due to throughput, coverage, cost, and sample input requirements. For CNV analysis, detection power is improved by combining both read depth and SNP allele frequency analysis, particularly for copy-neutral events such as loss of heterozygosity. A custom xGen Lockdown CNV backbone panel was developed for broad, uniform genome coverage and to enrich for population-based SNPs. We demonstrate use of the panel as an addition to the xGen Exome Research Panel and a custom cancer focused panel. Downstream analysis incorporates both read depth and observed minor allele frequencies to determine CNVs with enhanced sensitivity. To increase the resolution for large-scale alterations of chromosome 7, a hot-spot for disease-associated CNVs, probe density was increased 6 fold. A known standard, NA12878, was used to validate the panel’s ability to detect heterozygous SNPs with high confidence. In addition, mixtures of cancer cell lines from the Cancer Cell Line Encyclopedia (CCLE) were tested with varying levels of background copy-neutral genomic DNA. The sensitivity and specificity of the panel to detect CNV and LOH events with was assessed using deep exome and Affymetrix SNP array data. The ability to detect copy number alterations with high resolution and accuracy would be a valuable resource for disease and cancer research. Citation Format: Jiashi Wang, Kristina Giorda, Zhongwu Lai, Daniel Stetson, Mirna Jarosz. Whole genome copy number variation analysis using a SNP-focused targeted sequencing panel for tumor analysis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 397. doi:10.1158/1538-7445.AM2017-397
Comparison of arterial spin labeling and first‐pass dynamic contrast‐enhanced MR imaging in the assessment of pulmonary perfusion in humans: The inflow spin‐tracer saturation effect (2004)

The flow-sensitive alternating inversion recovery (FAIR) and the first-pass dynamic contrast-enhanced MR imaging (CE-MRI) techniques have both been shown to be effective in the assessment of human pulmonary perfusion. However, no comprehensive comparison of the measurements by these two methods has been reported. In this study, healthy adults were recruited, with FAIR and CE-MRI performed for an estimation of the relative pulmonary blood flow (rPBF). Regions of interest were encircled from the right and left lungs, with right-to-left rPBF ratios calculated. Results indicated that, on posterior coronal slices, the rPBF ratios obtained with the FAIR technique agreed well with CE-MRI measurements (mean difference = -0.02, intraclass correlation coefficient RI = 0.78, 95% confidence interval = [0.67, 0.86]). On middle coronal slices, however, FAIR showed a substantially lower rPBF by up to 43% in the right lung compared with CE-MRI (mean difference = -0.38, RI = 0.34, 95% confidence interval = [-0.09, 0.68]). The location-dependent discrepancy between measurements by FAIR and CE-MRI methods is attributed to tracer saturation effects of arterial inflow when the middle coronal slice contains the in-plane-oriented right pulmonary artery, whereas the left lung rPBF is less affected due to oblique orientation of the left pulmonary artery. Intrasequence comparison on additional subjects using FAIR at different slice orientations supported the above hypothesis. It is concluded that FAIR imaging for pulmonary perfusion in the coronal plane provides equivalent rPBF information with CE-MRI only in the absence of tracer saturation effects; hence, FAIR should be carefully exercised to avoid misleading interpretations.
Provisions: Privacy-preserving proofs of solvency for Bitcoin exchanges. (2015)

Bitcoin exchanges function like banks, securely holding their cus-tomers ’ bitcoins on their behalf. Several exchanges have suffered catastrophic losses with customers permanently losing their sav-ings. A proof of solvency demonstrates that the exchange controls sufficient reserves to settle each customer’s account. We introduce Provisions, a privacy-preserving proof of solvency whereby an ex-change does not have to disclose its Bitcoin addresses; total hold-ings or liabilities; or any information about its customers. We also propose an extension which prevents exchanges from colluding to cover for each other’s losses. We have implemented Provisions and it offers practical computation times and proof sizes even for a large Bitcoin exchange with millions of customers.
Energy Profiles for Organic Reactions in Solution (1988)

This chapter contains sections titled: Introduction Methodology Computed Potentials of Mean Force Concluding Remarks
A novel mouse model for segmental orthotopic colon cancer (2005)

Spontaneous colon tumor mouse strains offer numerous advantages in modeling disease. However, the wide temporal window in which lesions form and the stochastic nature of lesion location require larger cohorts for assessment of disease modulation. Reliable, reproducible and inexpensive mouse models of early-stage and invasive cancer would add to existing transgenic models. We show a new method for the creation of orthotopic murine tumors centered in the mucosal and submucosal layers anywhere in the colon, allowing creation of lesions of known age, location and extent. The system overcomes the disadvantages of heterotopic implantation and allows evaluation of lesions distally in the colon as well as proximally, thereby providing an additional method to study the effects of regionality. Invasion, host vascularization and application to disparate cell lines are demonstrated. Noninvasive imaging with magnetic resonance and colonoscopy, allowed in part by the tumor location, show potential applications of this approach.
Current initiation in low-density foam z-pinch plasmas (1997)

Low density agar and aerogel foams were tested as z-pinch loads on the Saturn accelerator to study current flow initiation. In these first experiments, we studied the initial plasma conditions by measuring the visible emission at early times with a framing camera and a streaked one-dimensional imaging system. Later, near the stagnation when the plasma is hotter, x-ray imaging and spectral diagnostics were used to characterize the plasma. Filamentation and arcing at the current contacts were observed. Bright implosion features were also observed. Increasing the early time conductivity, by coating the target with a high-z layer and by providing a low-current prepulse, is the most important factor in obtaining good coupling to the machine. None of the pinches were uniform along the z axis. The prime causes of these problems are believed to be the electrode contacts and the current return configuration. Solutions are discussed.
Restoration of myocellular copper-trafficking proteins and mitochondrial copper enzymes repairs cardiac function in rats with diabetes-evoked heart failure (2019)

Abstract Diabetes impairs systemic copper regulation, and acts as a major independent risk factor for heart failure (HF) wherein mitochondrial dysfunction is a key pathogenic process. Here we asked whether diabetes might alter mitochondrial structure/function and thus impair cardiac performance by damaging myocellular pathways that mediate cell-copper homeostasis. We measured activity of major mitochondria-resident copper-enzymes cytochrome c oxidase (mt-Cco) and superoxide dismutase 1 (mt-Sod1); expression of three main mitochondrial copper-chaperones [Cco copper chaperone 17 (Cox17), Cox11, and mitochondria-resident copper chaperone for Sod1 (mt-Ccs)]; of copper-dependent Cco-assembly protein Sco1; and regulation of mitochondrial biogenesis, in left-ventricular (LV) tissue from groups of non-diabetic-control, untreated-diabetic, and divalent-copper-selective chelator-treated diabetic rats. Diabetes impaired LV pump function; ∼halved LV-copper levels; substantively decreased myocellular expression of copper chaperones, and enzymatic activity of mt-Cco and mt-Sod1. Divalent-copper chelation with triethylenetetramine improved cardiac pump function, restored levels of myocardial copper, the copper chaperones, and Sco1; and enzymatic activity of mt-Cco and mt-Sod1. Copper chelation also restored expression of the key mitochondrial biogenesis regulator, peroxisome-proliferator-activated receptor gamma co-activator-1α (Pgc-1α). This study shows for the first time that altered myocardial copper-trafficking is a key pathogenic process in diabetes-evoked HF. We also describe a novel therapeutic effect of divalent-copper-selective chelation, namely restoration of myocellular copper trafficking, which is thus revealed as a potentially tractable target for novel pharmacological intervention to improve cardiac function.
Implementation of different 2D finite element modelling approaches in axial flux permanent magnet disc machines (2017)

Three‐dimensional (3D) finite element (FE) modelling of axial flux permanent magnet (AFPM) motors is one of the time‐consuming tasks which must be completed before manufacturing the prototype motor. A simple, fast, accurate, and effective numerical modelling approach for such 3D problems would be particularly useful for researchers. This study presents simple and effective 2D FE modelling approaches for AFPM motors with good accuracy with less computational effort. The modelling approaches are based on a number of 2D models or planes with inner rotor, outer rotor, or linear motor topologies. All the 2D planes with either topology are superposed together to represent the real AFPM machine. These approaches are examined in detail with various types of experimentally verified AFPM motors. Results obtained from the proposed modelling approaches are verified with 3D FE analyses and experimental data. The results indicate that the proposed 2D modelling approaches can significantly reduce the computation time with good accuracy as opposed to conventional 3D FE modelling of AFPM motors.
Conductive CM and DM Noise Analysis of Power Electronic Converters in Electric and Hybrid Electric Vehicles (2007)

In developing a complex power electronic system, proper modeling at prototype sample level can save the time and cost to develop final product. Hybrid Electric Vehicle (HEV) is equipped with several high powered electric devices such as DC/DC converters and DC/AC inverters. Considering that there are many restrictions in mounting and wiring the electric power system in engine room, analysis and modeling of Electromagnetic Interference (EMI) coupling path is crucial in designing optimal electric power system satisfying various EMC regulations. In this paper, conductive common mode (CM) and differential mode (DM) equivalent models for those electric power converters used in HEV were developed and evaluated through the simulation both in time domain and frequency domain using FFT. It is confirmed that the suggested model followed the actual circuit in the point of conducted CM and DM EMI view.
Strengthening Software Self-Checksumming via Self-Modifying Code (2006)

Recent research has proposed self-checksumming as a method by which a program can detect any possibly malicious modification to its code. Wurster et al. developed an attack against such programs that renders code modifications undetectable to any self-checksumming routine. The attack replicated pages of program text and altered values in hardware data structures so that data reads and instruction fetches retrieved values from different memory pages. A cornerstone of their attack was its applicability to a variety of commodity hardware: they could alter memory accesses using only a malicious operating system. In this paper, we show that their page-replication attack can be detected by self-checksumming programs with self-modifying code. Our detection is efficient, adding less than 1 microsecond to each checksum computation in our experiments on three processor families, and is robust up to attacks using either costly interpretive emulation or specialized hardware
Fire behavior of simulated low voltage intumescent cables with and without electric current (2017)

Many circumstances can lead to an electrical fire. It is then helpful to reproduce those circumstances in laboratory conditions to duplicate fire scenarios in order to increase knowledge and to develop safer and flame-retarded materials and electrical systems. Our approach was to develop specific bench scale tests. The mass loss cone calorimeter coupled with Fourier transform infrared was used to mimic a fire scenario on simulated low voltage cable (flame-retarded polymer molded around copper wire) and to characterize the gas phase. The electric current creates an additional heating condition (Joule effect) which can modify the decomposition of the flammable material (e.g. the cable jacket made in thermoplastic), and so its fire behavior in case of fire. It is the reason why we performed the experiments mimicking different fire scenarios with and without electric current. Specific test was also developed to investigate the flame spread and the delamination of the polymer around the wire. The bench scale tests presented in this article were applied on intumescent polymers (ethylene-vinyl acetate containing commercial intumescent additive). The results were discussed with a special emphasis on the influence of electric current on the fire behavior.
Randomly Distributed Conjugated Polymer Repeat Units for High-Efficiency Photovoltaic Materials with Enhanced Solubility and Processability (2018)

Three structurally disordered terpolymer derivatives of PffBT4T-2OD (PCE11), prepared by replacing a varied amount of bithiophene linkers with single thiophenes, were found to exhibit reduced aggregation in solution with increasing thiophene content, while important redox and optoelectronic properties remained similar to those of PffBT4T-2OD. Solar cells based on random terpolymer-PC<sub>71</sub>BM blends exhibited average power conversion efficiencies of over 9.5% when processed with preheated substrates, with fill factors above 70%, exceeding those from PffBT4T-2OD. Thanks to increased solubility, random terpolymer devices were able to be fabricated on room-temperature substrates, reaching virtually identical performance among all three polymers despite remarkable thicknesses of ∼400 nm. Thus, we show that the random terpolymer approach is successful in improving processability while maintaining device performance.
FY10 Engineering Innovations, Research and Technology Report (2011)

This report summarizes key research, development, and technology advancements in Lawrence Livermore National Laboratory's Engineering Directorate for FY2010. These efforts exemplify Engineering's nearly 60-year history of developing and applying the technology innovations needed for the Laboratory's national security missions, and embody Engineering's mission to ''Enable program success today and ensure the Laboratory's vitality tomorrow.'' Leading off the report is a section featuring compelling engineering innovations. These innovations range from advanced hydrogen storage that enables clean vehicles, to new nuclear material detection technologies, to a landmine detection system using ultra-wideband ground-penetrating radar. Many have been recognized with R&D Magazine's prestigious R&D 100 Award; all are examples of the forward-looking application of innovative engineering to pressing national problems and challenging customer requirements. Engineering's capability development strategy includes both fundamental research and technology development. Engineering research creates the competencies of the future where discovery-class groundwork is required. Our technology development (or reduction to practice) efforts enable many of the research breakthroughs across the Laboratory to translate from the world of basic research to the national security missions of the Laboratory. This portfolio approach produces new and advanced technological capabilities, and is a unique component of the value proposition of the Lawrence Livermore Laboratory. The balance of the report highlights this work in research and technology, organized into thematic technical areas: Computational Engineering; Micro/Nano-Devices and Structures; Measurement Technologies; Engineering Systems for Knowledge Discovery; and Energy Manipulation. Our investments in these areas serve not only known programmatic requirements of today and tomorrow, but also anticipate the breakthrough engineering innovations that will be needed in the future.
Cavitation effects during lithotripsy. Part I. Results of in vitro experiments. (1990)

Cavitation effects and microbubble formation are due to the rarefactive (negative pressure) component of shock waves. The in vitro application of shock waves generated by a commercial lithotriptor to an anthropomorphic phantom showed that stone fragmentation occurred more completely in fluid media that support cavitation than in a solid agar-graphite gel. Various fluids (saline, iodinated contrast material, bile) supported different degrees of cavitation. Bile exhibited cavitation at low energy and gave rise to intense microbubble formation at 19 kV. Cavitation increased dramatically with an increase in the rate of generation from 1.0 to 1.8 shock waves per second. The authors conclude that during biliary lithotripsy the environment of a stone will influence the extent of cavitation and fragmentation.
Retraction: “A novel investigation on carbon nanotube/ZnO, Ag/ZnO and Ag/carbon nanotube/ZnO nanowires junctions for harvesting piezoelectric potential on textile” [J. Appl. Phys. 116, 034505 (2014)] (2022)

A novel investigation on carbon nanotube/ZnO, Ag/ZnO and Ag/carbon nanotube
Structural deformation of the preterm trachea during acute distention and collapse. (1991)

The compliant airways of the premature neonate undergo episodic distention and collapse in response to changes in transmural pressure such as occur during spontaneous breathing, mechanical ventilation, and various therapeutic maneuvers. To identify and quantitate the effects of distending and collapsing transmural pressures on the structure of immature airways, tracheal segments from fetal rabbits, fixed at 0, +30, and -30 cm H2O transmural pressure, were examined using histologic and morphometric techniques. In comparison to control sections fixed at 0 cm H2O transmural pressure, application of distending pressures led to evagination of the posterior tracheal wall and significantly increased (P less than 0.05) cross-sectional area, antero-posterior diameter, circumference and muscle length, and decreased muscle thickness. Collapsed tracheal segments (-30 cm H2O) demonstrated invagination of the posterior wall and significantly (P less than 0.05) lower cross-sectional area, and antero-posterior diameter compared to the control segments; all the other parameters remained relatively unchanged. These data demonstrate extreme changes in tracheal geometry in response to the acute application of transmural pressure. From a methodological perspective, these observations suggest that fixation pressures may present significant artifact in histological analyses. Functionally, the noted deformation may lead to alterations in anatomic dead space and airway resistance, and mechanical function of the airways; all of which may compromise respiratory status in ventilated premature infant.
Generation of O−2 and tyrosine cation‐mediated chemiluminescence during the fertilization of sea urchin eggs (1989)

Sea urchin eggs emit light in the visible region during their fertilization. Judging from the chemiluminescence spectra, one of the excited species generated is considered to have originated from a tyrosine cation radical-mediated reaction. Chemiluminescence probes such as luminol or a cypridina luciferin analog (See text) are useful for detecting the ovoperoxidase +H2O2 reaction associated with membrane hardening and O2- generation, respectively, during fertilization of sea urchin eggs.
Generative models of the human connectome (2015)

The human connectome represents a network map of the brain's wiring diagram and the pattern into which its connections are organized is thought to play an important role in cognitive function. The generative rules that shape the topology of the human connectome remain incompletely understood. Earlier work in model organisms has suggested that wiring rules based on geometric relationships (distance) can account for many but likely not all topological features. Here we systematically explore a family of generative models of the human connectome that yield synthetic networks designed according to different wiring rules combining geometric and a broad range of topological factors. We find that a combination of geometric constraints with a homophilic attachment mechanism can create synthetic networks that closely match many topological characteristics of individual human connectomes, including features that were not included in the optimization of the generative model itself. We use these models to investigate a lifespan dataset and show that, with age, the model parameters undergo progressive changes, suggesting a rebalancing of the generative factors underlying the connectome across the lifespan.
Data from ALK1-Fc Inhibits Multiple Mediators of Angiogenesis and Suppresses Tumor Growth (2023)

&lt;div&gt;Abstract&lt;p&gt;Activin receptor–like kinase-1 (ALK1) is a type I, endothelial cell–specific member of the transforming growth factor-β superfamily of receptors known to play an essential role in modulating angiogenesis and vessel maintenance. In the present study, we sought to examine the angiogenic and tumorigenic effects mediated upon the inhibition of ALK1 signaling using a soluble chimeric protein (ALK1-Fc). Of 29 transforming growth factor-β–related ligands screened by surface plasmon resonance, only bone morphogenetic protein (BMP9) and BMP10 displayed high-affinity binding to ALK1-Fc. In cell-based assays, ALK1-Fc inhibited BMP9-mediated Id-1 expression in human umbilical vein endothelial cells and inhibited cord formation by these cells on a Matrigel substrate. In a chick chorioallantoic membrane assay, ALK1-Fc reduced vascular endothelial growth factor–, fibroblast growth factor–, and BMP10-mediated vessel formation. The growth of B16 melanoma explants was also inhibited significantly by ALK1-Fc in this assay. Finally, ALK1-Fc treatment reduced tumor burden in mice receiving orthotopic grafts of MCF7 mammary adenocarcinoma cells. These data show the efficacy of chimeric ALK1-Fc proteins in mitigating vessel formation and support the view that ALK1-Fc is a powerful antiangiogenic agent capable of blocking vascularization. Mol Cancer Ther; 9(2); 379–&lt;/p&gt;&lt;/div&gt;