gebhart/patrepeval huggingface dataset:
Abstract 3646: Highly sensitive and cost-effective detection of somatic cancer variants using single-molecule, real-time sequencing (2016)

Abstract Next-Generation Sequencing (NGS) technologies allow for molecular profiling of cancer samples with high sensitivity and speed at reduced cost. For efficient profiling of cancer samples, it is important that the NGS methods used are not only robust but also capable of accurately detecting low-frequency somatic mutations. Single Molecule, Real-Time (SMRT®) Sequencing offers several advantages, including the ability to sequence single molecules with very high accuracy (&amp;gt;QV40) using the circular consensus sequencing (CCS) approach. The availability of genetically defined, human genomic reference standards provides an industry standard for the development and quality control of molecular assays for studying cancer variants. Here we characterize SMRT Sequencing for the detection of low-frequency somatic variants using the Quantitative Multiplex DNA Reference Standards from Horizon Diagnostics, combined with amplification of the variants using the Multiplicom Tumor Hotspot MASTR Plus assay. First, we sequenced a reference standard containing precise allelic frequencies from 1% to 24.5% for major oncology targets verified using digital PCR. This reference material recapitulates the complexity of tumor composition and serves as a well-characterized control. The control sample was amplified using the Multiplicom Tumor Hotspot MASTR Plus assay that targets 252 amplicons (121-254 bp) from 26 relevant cancer genes, which includes all 11 variants in the control sample. We also sequenced a second sample containing a series of mixes, each with known mutations, at levels below 10% and down to 0.01%. PCR-amplified targets were sequenced and analyzed using SMRT Sequencing to identify the variants and determine the observed frequency. The random error profile and high-accuracy CCS reads make it possible to accurately detect low-frequency somatic variants. Citation Format: Steve Kujawa, Anand Sethuraman, Kevin Eng, Primo Baybayan, Lien Heyrman, Jurgen Del Favero. Highly sensitive and cost-effective detection of somatic cancer variants using single-molecule, real-time sequencing. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 3646.
Space-Frequency Bit-Interleaved Coded Modulation for MIMO-OFDM (2006)

This paper presents the design of a novel space- frequency bit-interleaver for MIMO-OFDM systems. The pro- posed space-frequency interleaver (SFI) interleaves convolution- ally coded bits across transmit antennas and frequency tones. Performance is analyzed for a simplified channel model and is demonstrated for a modeled IEEE 802.16e OFDM PHY layer using ITU channel models. The proposed space-frequency interleaver outperforms a frequency only interleaver by 2-10 dB for 1000 byte packets.
Message-efficient dissemination for loop-free centralized routing (2008)

With steady improvement in the reliability and performance of communication devices, routing instabilities now contribute to many of the remaining service degradations and interruptions in modern networks. This has led to a renewed interest in centralized routing systems that, compared to distributed routing, can provide greater control over routing decisions and better visibility of the results. One benefit of centralized control is the opportunity to readily eliminate transient routing loops, which arise frequently after network changes because of inconsistent routing states across devices. Translating this conceptual simplicity into a solution with tolerable message complexity is non-trivial. Addressing this issue is the focus of this paper. We identify when and why avoiding transient loops might require a significant number of messages in a centralized routing system, and demonstrate that this is the case under many common failure scenarios. We also establish that minimizing the number of required messages is NP-hard, and propose a greedy heuristic that we show to perform well under many conditions. The paper's results can facilitate the deployment and evaluation of centralized architectures by leveraging their strengths without incurring unacceptable overhead.
An isoxazole route to unsaturated α-alkoxycarbonyl-β-diketones (1993)

Cycloaddition of diethylphosphonomethyl nitrile oxide to the enamine from ethyl acetoacetate produces 4-ethoxycarbonyl-3-diethoxyphosphonylmethyl-5-methylisoxazole; condensation of the phosphonate with aldehydes and ketones gives 3-alkenylisoxazoles that are cleaved by hexacarbonylmolybdenum to afford unsaturated α-alkoxycarbonyl-β-diketones.
(Invited) Wafer Bonding Technology in Nitride Semiconductors for Applications in Energy and Communications (2010)

Wafer bonding is an enabling technology for the fabrication of advanced electronic devices based on the integration of high-quality heterogeneous materials. This paper summarizes our work on wafer-level bonding of nitride semiconductors and its application to electronic devices. Our bonding technology uses a thin silicon dioxide (SiO2) or Benzocyclobutene (BCB) interlayer to enhance the bonding, and it has been applied to the fabrication of three different kinds of devices: hybrid chips where Si (100) MOSFETs are integrated with GaN transistors in close proximity; N-face GaN transistors on Ga-face grown material for high frequency applications; and high power GaN power switches with record breakdown characteristics.
Paired exome analysis of Barrett's esophagus and adenocarcinoma (2015)

Barrett's esophagus is thought to progress to esophageal adenocarcinoma (EAC) through a stepwise progression with loss of CDKN2A followed by TP53 inactivation and aneuploidy. Here we present whole-exome sequencing from 25 pairs of EAC and Barrett's esophagus and from 5 patients whose Barrett's esophagus and tumor were extensively sampled. Our analysis showed that oncogene amplification typically occurred as a late event and that TP53 mutations often occurred early in Barrett's esophagus progression, including in non-dysplastic epithelium. Reanalysis of additional EAC exome data showed that the majority (62.5%) of EACs emerged following genome doubling and that tumors with genomic doubling had different patterns of genomic alterations, with more frequent oncogenic amplification and less frequent inactivation of tumor suppressors, including CDKN2A. These data suggest that many EACs emerge not through the gradual accumulation of tumor-suppressor alterations but rather through a more direct path whereby a TP53-mutant cell undergoes genome doubling, followed by the acquisition of oncogenic amplifications.
Investigation of wave propagation phenomena in microfabricated arrays of nonlinearly coupled oscillators (2015)

We demonstrate a MEMS platform for the investigation of energy propagation behavior in an array of nonlinearly coupled oscillators. The long-term objective is to experimentally demonstrate behaviors that have, until recently, only been theorized to occur in oscillator networks, such as passively reconfiguring bandgaps, energy localization, and chimera states. An improved fundamental understanding and of these phenomena could offer new capabilities for the prevention of catastrophic failures from shock loads, passive amplitude and frequency filters, and energy conversion systems. Here, we detail the design and fabrication of a coupled oscillator testbed, and then demonstrate transverse wave propagation along 1-D magnetically coupled oscillator arrays. Ongoing experiments seek to realize more complicated energy transfer behavior via design variations on this testbed.
Covariances of zero crossings in Gaussian processes (2010)

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Modal Analysis of Silicon Photonic Wire and TM-pass Nanowaveguide Polarizer (2008)

Modal analysis of silicon photonic wire is presented based on the full-vectorial eigenmode solution. Numerical results indicate that for different height and width of silicon photonic wire, there are five regions corresponding to different modal characteristics, namely, multimode region, singlemode region, single TE polarization region, single TM polarization region and cutoff region. Simple expressions are correspondingly proposed for the singlemode, single polarization mode and cut off conditions. With this modal analysis, a TM-pass nanowaveguide polarizer based on a tapered silicon nanowaveguide structure is proposed and demonstrated numerically.
Studies of Steel Microstructure by Acoustical Methods (1979)

We are using measurements of acoustic velocity and attenuation for nondestructive characterization of the microstructure of materials. variation of the acoustic velocity in Jominy endquench specimens was found to correlate very well with Rockwell C hardness scans, indicating a potentially practical method for measuring the hardening response of heat treated steel. Attenuation measurements have also been performed by using broadband acoustic pulses corrected for transducer response, liquid buffer/solid specimen reflections, and diffraction effects. Higher attenuation was observed for pearlitic than for martensitic microstructures. The spatial
Fiber Optic Sensing Technologies for Battery Management Systems and Energy Storage Applications (2021)

Applications of fiber optic sensors to battery monitoring have been increasing due to the growing need of enhanced battery management systems with accurate state estimations. The goal of this review is to discuss the advancements enabling the practical implementation of battery internal parameter measurements including local temperature, strain, pressure, and refractive index for general operation, as well as the external measurements such as temperature gradients and vent gas sensing for thermal runaway imminent detection. A reasonable matching is discussed between fiber optic sensors of different range capabilities with battery systems of three levels of scales, namely electric vehicle and heavy-duty electric truck battery packs, and grid-scale battery systems. The advantages of fiber optic sensors over electrical sensors are discussed, while electrochemical stability issues of fiber-implanted batteries are critically assessed. This review also includes the estimated sensing system costs for typical fiber optic sensors and identifies the high interrogation cost as one of the limitations in their practical deployment into batteries. Finally, future perspectives are considered in the implementation of fiber optics into high-value battery applications such as grid-scale energy storage fault detection and prediction systems.
Fast Neural Models for Symbolic Regression at Scale (2020)

Deep learning owes much of its success to the astonishing expressiveness of neural networks. However, this comes at the cost of complex, black-boxed models that extrapolate poorly beyond the domain of the training dataset, conflicting with goals of finding analytic expressions to describe science, engineering and real world data. Under the hypothesis that the hierarchical modularity of such laws can be captured by training a neural network, we introduce OccamNet, a neural network model that finds interpretable, compact, and sparse solutions for fitting data, a la Occam's razor. Our model defines a probability distribution over a non-differentiable function space. We introduce a two-step optimization method that samples functions and updates the weights with backpropagation based on cross-entropy matching in an evolutionary strategy: we train by biasing the probability mass toward better fitting solutions. OccamNet is able to fit a variety of symbolic laws including simple analytic functions, recursive programs, implicit functions, simple image classification, and can outperform noticeably state-of-the-art symbolic regression methods on real world regression datasets. Our method requires minimal memory footprint, does not require AI accelerators for efficient training, fits complicated functions in minutes of training on a single CPU, and demonstrates significant performance gains when scaled on a GPU. Our implementation, demonstrations and instructions for reproducing the experiments are available at this https URL.
Effect of Crystal Imperfections on Reactivity and Photoreactivity of TiO2(Rutile) with Oxygen, Water, and Bacteria (2011)

The present work considers the effect of crystal imperfections (point defects) on several properties of TiO2 (rutile), such as semiconducting properties and segregation-induced surface properties as well as crystalline structure-related quantities, such as lattice parameter and electronic structure. This work considers the defect disorder of rutile and its solid solutions in terms of both intrinsic and extrinsic defects. The collected empirical data and the related theoretical models indicate that the development of oxide semiconductors with enhanced performance as photocatalysts and photoelectrodes requires recognition of the profound influence of crystal imperfections (point defects) on reactivity and photoreactivity. The effect of defect disorder on the performance of rutile is discussed in terms of its photocatalytic properties in solar water disinfection. The chemistry of the photocatalytic system, consisting of the semiconducting photocatalyst immersed in water involving bacteria, is considered in terms of (i) the reactivity at the oxide/H2O interface leading to the formation of active radical species, (ii) the transport of these species toward bacteria, and (iii) the reactivity of the species with bacteria. It has been documented that changes in defect disorder result in substantial variations of these properties within the stability range of the single phase of rutile. It is shown that defect chemistry may be used as a framework in the modification of semiconducting properties as well as the reactivity and photoreactivity of TiO2 with oxygen, water, and bacteria. The well-defined standard in the studies of TiO2-based materials is proposed.
Climbing favours the tripod gait over alternative faster insect gaits (2017)

To escape danger or catch prey, running vertebrates rely on dynamic gaits with minimal ground contact. By contrast, most insects use a tripod gait that maintains at least three legs on the ground at any given time. One prevailing hypothesis for this difference in fast locomotor strategies is that tripod locomotion allows insects to rapidly navigate three-dimensional terrain. To test this, we computationally discovered fast locomotor gaits for a model based on Drosophila melanogaster. Indeed, the tripod gait emerges to the exclusion of many other possible gaits when optimizing fast upward climbing with leg adhesion. By contrast, novel two-legged bipod gaits are fastest on flat terrain without adhesion in the model and in a hexapod robot. Intriguingly, when adhesive leg structures in real Drosophila are covered, animals exhibit atypical bipod-like leg coordination. We propose that the requirement to climb vertical terrain may drive the prevalence of the tripod gait over faster alternative gaits with minimal ground contact.
A Hybrid Variance Reduction Method Based on Gaussian Process for Core Simulation (2011)

Variance reduction techniques is usually employed to accelerate the convergence of Monte Carlo (MC) simulation. Hybrid deterministic-MC methods [1, 2, 3] have been recently developed to achieve the goal of global variance reduction. Hybrid methods employ deterministic models (both forward and adjoint) to bias source particles and assign appropriate importance map to MC models. If done properly, hybrid methods have been shown to accelerate the convergence of MC simulation that is obtaining acceptable reduction in the statistical uncertainties for the responses of interest with less computational overhead. Under the assumption that the statistical uncertainties resulting from the radiation transport may be treated as a Gaussian Process (GP) [4], a new hybrid approach for global variance reduction was presented in an earlier publication [5]. The principle behind this approach is recalled here along with a comparison to FW-CADIS method [6, 7], which is currently implemented in the SCALE package [8]. Unlike previous work, in which the covariance matrix describing the Gaussian process was calculated using analog MC calculation, this summary estimates the covariance matrix using a deterministic model. In previous work, MC model was used as a proof of principle, but in realistic calculations, the covariance matrix must be estimated inexpensively, hence the need to approximate it using a deterministic model. The construction of the covariance matrix as needed by the GP method is implemented in the MAVRIC sequence of SCALE to facilitate the comparison of the GP and the FW-CADIS approaches. Building on the work presented before which focused on simplified BWR assembly models [5], we apply the GP approach to a higher dimensional problem representing a prototypical PWR core model.
Modeling Li-ion Battery First Venting Events Before Thermal Runaway (2021)

Li-ion battery failure and thermal runaway usually follow gas venting events, which can be categorized into the first venting and thermal runaway venting. Since first venting events occur prior to thermal runaway, identifying the first venting event is essential for early detection of a battery failure. This study presents a model for CO2 gas generation at elevated temperature, which can be used to predict the occurrence of venting based on the buildup of cell internal pressure. The model considers the pressure of the generated gas and electrolyte vapor saturation pressure. To validate the model, an external short circuit (ESC) experiment is conducted for a nickel manganese cobalt (NMC) pouch cell that led to cell venting without thermal runaway. The model’s output can be used in conjunction with CO2 sensors and electro-mechanical cell measurements to detect first venting events, and hopefully estimate the probability of an upcoming thermal runaway based on the amount of CO2 released.
Bounding the efforts on congestion optimization for physical synthesis (2003)

In this era of Deep Sub-Micron (DSM) technologies, interconnects are becoming increasingly important as their effects strongly impact the integrated circuit (IC) functionality and performance. Moreover, logic block size is no longer determined exclusively by total cell area, and is often limited by wiring resources, yet synthesis optimization objectives are focused on minimizing the number and size of library cells. Methodologies that incorporate congestion within the logic synthesis have been proposed in the past. However, in [15] and [16] it was demonstrated that predicting the true congestion prior to layout is not possible, since different layout regions can have very different routing demands, and the effectiveness of any congestion minimization approach can only be evaluated after routing is completed within the assigned die size. In these works, congestion minimization efforts at the synthesis level are controlled by means of a global weighting factor in the technology mapping cost function. Nevertheless, due to the lack of accurate congestion models, during logic synthesis it is not possible to estimate a priori which values of the congestion minimization factor will yield a congestion-free synthesized netlist. In this paper, we derive practical bounds, which limit the search space for an optimal congestion minimization factor that produces a routable netlist within fixed floorplan constraints. Although we believe that a top-down single-pass congestion-aware logic synthesis is not going to work in general, the bounds obtained in this work can be used in a practical and robust congestion minimization methodology, which can be implemented into any commercial design flow.
Dielectric media based on isolated metallic nanostructures (2005)

We study the dielectric properties of nanocomposites in the 0–1.5-GHz frequency regime. These composites consist of electrically insulated metallic nanoparticles and carbon nanotubes, the elongated nanostructures in this study, uniformly dispersed in a dielectric matrix. We find that the properties of these composites depend crucially on the shape and monodispersity of the nanoparticles. While at high concentrations the spherical nanoparticles cause only slight modification of the dielectric function of the composite with respect to the matrix, the elongated nanoparticles produce composites with an enhanced real part of the dielectric function and low imaginary part. Our theory, which is in excellent agreement with these results, suggests specific ways to further improve the dielectric properties of the composites.
Transcatheter Mitral Annuloplasty (2021)

Mitral ring annuloplasty is an essential component of successful surgical mitral valve repair. Left atrial and left ventricular enlargements are common sequelae of chronic uncorrected mitral regurgitation (MR), and subsequent mitral annular dilatation contributes to MR progression. The Millipede semirigid complete annular reshaping ring is the first complete transcatheter transfemoral annuloplasty ring to be used successfully for the treatment of MR. The initial Phase 1 of the first-in-human experience involved implantation of the Millipede surgical device with median sternotomy, standard bicaval cannulation, and cardiopulmonary bypass. The Millipede ring is the first complete semirigid annuloplasty ring to be delivered by a percutaneous, transfemoral, and transseptal route. Further, device, delivery system, and intraprocedural imaging improvements are ongoing and the device will be further evaluated in ongoing clinical trials.
High moment FeRhN/NiFe laminated thin films for write head applications (2002)

FeRhN(∼50 nm)/NiFe(∼5 nm) laminated thin films were deposited by dc magnetron sputtering. Upon optimizing the sputtering conditions, FeRhN/NiFe laminated thin films showed good soft magnetic properties, and a well defined uniaxial anisotropy: Bs∼20.3 kG, Hc&amp;lt;1.0 Oe, Hk∼5 Oe. It was shown that a NiFe underlayer improved the soft magnetic properties of a FeRhN layer more effectively than a NiFe top layer. The data obtained by x-ray diffraction study showed that the FeRhN film with a NiFe underlayer had a much stronger (110) texture, as compared to single layer FeRhN film. Columnar grain structure with size of about 10 nm was observed in FeRhN films by high resolution transmission electron microscope. It is believed that the modification of FeRhN microstructure by NiFe underlayer plays a more important role in improving the soft magnetic properties than the exchange coupling between the FeRhN and NiFe layers.