gebhart/patrepeval huggingface dataset:
Effects of Sensor Position Errors on Farfield/Nearfield Wideband Beamformers for Microphone Arrays (2015)

It is well known that the presence of sensor position errors may lead to failure of farfield/nearfield wideband beamformers for microphone arrays. Therefore, many efforts have been made to design wideband beamformers for microphone arrays robust against sensor position errors in recent years. This paper presents the findings obtained on the study and analysis of the effects of sensor position errors to the performance of farfield/nearfield wideband beamformers for microphone arrays. Several useful properties have been derived through the conduct of a comprehensive statistical analysis, including the bias and variance analysis of array response, to provide in-depth insights into the robustness characteristics of farfield and nearfield wideband beamformers in the presence of sensor position errors. The analysis does not assume any specific array geometry and is thus applicable to arrays with arbitrary geometries. Numerical examples obtained via Monte Carlo simulations are presented to verify the proposed theoretical analysis. This paper is helpful to better understand the effects of sensor position errors on wideband beamformers and useful in microphone array design.
Studies of coupled metallic magnetic thin-film trilayers (1998)

Results are reported of a detailed study of static and dynamic responses in symmetric systems consisting of two ferromagnetic films separated by a nonferromagnetic spacer layer. A comparison is made with experimental results for two systems grown by sputter deposition in an UHV chamber, namely, NiFe/Cu/NiFe and Fe/Cr/Fe. First, we present model calculations where the coupling between the magnetic films through magnetic dipolar, bilinear, and biquadratic exchange interactions are fully taken into account, together with surface, in-plane uniaxial, and cubic anisotropies. An analytical expression is given that can readily be used to consistently interpret magnetoresistance, magneto-optical Kerr effect, ferromagnetic resonance, and Brillouin light scattering (BLS) data in such trilayers. Application of the results to BLS data in Ni81Fe19(d)/Cu(25 Å)Ni81Fe19(d), with d=200 and 300 Å, shows that it is essential to treat the dipolar interaction adequately in moderately thick systems. The results are also applied to interpret very interesting data in Fe(40 Å)/Cr(s)/Fe(40 Å), with 5 Å&amp;lt;s&amp;lt;35 Å, investigated by the four techniques mentioned above, at room temperature. It is shown that consistent values for all magnetic parameters can be extracted from the data with a theory that treats both static and dynamic responses on equal footing.
Potential distribution in three-dimensional periodic myocardium. II. Application to extracellular stimulation (1990)

Modeling potential distribution in the myocardium treated as a periodic structure implies that activation from high-current stimulation with extracellular electrodes is caused by the spatially oscillating components of the transmembrane potential. This hypothesis is tested by comparing the results of the model with experimental data. The conductivity, fiber orientation, the extent of the region, the location of the pacing site, and the stimulus strength determined from experiments are components of the model used to predict the distributions of potential, potential gradient, and the transmembrane potential throughout the region. Next, assuming that a specific value of the transmembrane potential is necessary and sufficient to activate fully repolarized myocardium, the model provides an analytical relation between large-scale field parameters, such as gradient and current density, and small-scale parameters, such as transmembrane potential. This relation is used to express the stimulation threshold in terms of gradient or current density components and to explain its dependence upon fiber orientation. The concept of stimulation threshold is generalized to three dimensions, and an excitability surface is constructed, which for cardiac muscle is approximately conical in shape. The numerical values of transmembrane potential and stimulation thresholds calculated using asymptotic analysis are in agreement with the results of animal experiments, confirming the validity of this approach to study the electrophysiology of periodic cardiac muscle.
High-Density Vertical Bloch Line Data Storage Chips for Small Satellite Applications (1994)

Vertical Bloch Line storage is an emerging technology which has the potential for offering a number of desired data storage attributes in a single chip for space and commercial applications.
Twist on Protein Microarrays: Layering Wax-Patterned Nitrocellulose to Create Customizable and Separable Arrays of Multiplexed Affinity Columns (2014)

We developed the simple and inexpensive FoRe microarray to simultaneously test several 1 μL samples for multiple proteins. By combining forward and reverse phase microarrays into an innovative three-dimensional format, the FoRe array exploits the advantages and eliminates several drawbacks of the traditional approaches (i.e., large sample volumes, protein loss, and cross-reactivity between detection antibodies). Samples are pipetted into an array of separable, multiplexed affinity columns. Several nitrocellulose membranes, each functionalized with a different capture antibody, are stacked to create a customizable affinity column. The nitrocellulose is patterned with wax to form 25 isolated microspots on each layer, allowing us to analyze multiple samples in parallel. After running the immunoassay, the stacks are quickly disassembled, revealing 2D microarrays of different fractions from multiple samples. By combining the stack-and-separate technique with wax patterning, we keep the arrays low cost and easily tailored to a variety of applications. We successfully performed 3D multiplexing using a model system with mouse and rabbit IgG. Binding proved to be independent of the position in the stack, and the limit of detection for a mouse IgG sandwich assay was 7.3 pM in BSA and 15 pM in human plasma. The FoRe microarray makes it possible to identify protein expression patterns across several minute volume samples; for example, it could be used to analyze cell lysate in drug response studies or pricks of blood from small animal studies.
TSG-6 Potentiates the Antitissue Kallikrein Activity of Inter–α-inhibitor through Bikunin Release (2006)

TSG-6 (the protein product of TNF-stimulated gene-6), an inflammation-associated protein, forms covalent complexes with heavy chains (HCs) from inter-alpha-inhibitor and pre-alpha-inhibitor and associates noncovalently with their common bikunin chain, potentiating the antiplasmin activity of this serine protease inhibitor. We show that TSG-6 and TSG-6.HC complexes are present in bronchoalveolar lavage fluid from patients with asthma and increase after allergen challenge. Immunodetection demonstrated elevated TSG-6 in the airway tissue and secretions of smokers. Experiments conducted in vitro with purified components revealed that bikunin.HC complexes (byproducts of TSG-6.HC formation) release bikunin. Immunoprecipitation revealed that bikunin accounts for a significant proportion of tissue kallikrein inhibition in bronchoalveolar lavage after allergen challenge but not in baseline conditions, confirming that bikunin in its free state, but not when associated with HCs, is a relevant protease inhibitor in airway secretions. In primary cultures of differentiated human airway epithelial and submucosal gland cells, TSG-6 is induced by TNF-alpha and IL-1beta, which suggests that these cells are responsible for TSG-6 release in vivo. Bikunin and HC3 (i.e., pre-alpha-inhibitor) were also induced by TNF-alpha in primary cultures. Our results suggest that TSG-6 may play an important protective role in bronchial epithelium by increasing the antiprotease screen on the airway lumen.
Optical vortices in fiber (2013)

Abstract Optical vortex beams, possessing spatial polarization or phase singularities, have intriguing properties such as the ability to yield super‐resolved spots under focussing, and the ability to carry orbital angular momentum that can impart torque to objects. In this review, we discuss the means by which optical fibers, hitherto considered unsuitable for stably supporting optical vortices, may be used to generate and propagate such exotic beams. We discuss the multitude of applications in which a new class of fibers that stably supports vortices may be used, and review recent experiments and demonstration conducted with such fibers.
Simulated-annealing studies of structural trends in carbon clusters (1993)

The structural properties of carbon clusters (${\mathrm{C}}_{\mathit{n}}$, n=2--60) are studied using tight-binding molecular-dynamics simulations. The low-energy ground-state configurations of the clusters are obtained by annealing and compressing n carbon atoms (n=2--60) from the gas phase at high temperatures (\ensuremath{\ge}6000 K). We observed a transition from one-dimensional linear and cyclic structures to two-dimensional cage structures as the number of atoms in the cluster increases beyond n=20.
Differentially Private Distributed Data Summarization under Covariate\n Shift (2019)

We envision AI marketplaces to be platforms where consumers, with very less\ndata for a target task, can obtain a relevant model by accessing many private\ndata sources with vast number of data samples. One of the key challenges is to\nconstruct a training dataset that matches a target task without compromising on\nprivacy of the data sources. To this end, we consider the following distributed\ndata summarizataion problem. Given K private source datasets denoted by\n$[D_i]_{i\\in [K]}$ and a small target validation set $D_v$, which may involve a\nconsiderable covariate shift with respect to the sources, compute a summary\ndataset $D_s\\subseteq \\bigcup_{i\\in [K]} D_i$ such that its statistical\ndistance from the validation dataset $D_v$ is minimized. We use the popular\nMaximum Mean Discrepancy as the measure of statistical distance. The\nnon-private problem has received considerable attention in prior art, for\nexample in prototype selection (Kim et al., NIPS 2016). Our work is the first\nto obtain strong differential privacy guarantees while ensuring the quality\nguarantees of the non-private version. We study this problem in a Parsimonious\nCurator Privacy Model, where a trusted curator coordinates the summarization\nprocess while minimizing the amount of private information accessed. Our\ncentral result is a novel protocol that (a) ensures the curator accesses at\nmost $O(K^{\\frac{1}{3}}|D_s| + |D_v|)$ points (b) has formal privacy guarantees\non the leakage of information between the data owners and (c) closely matches\nthe best known non-private greedy algorithm. Our protocol uses two hash\nfunctions, one inspired by the Rahimi-Recht random features method and the\nsecond leverages state of the art differential privacy mechanisms. We introduce\na novel "noiseless" differentially private auctioning protocol for winner\nnotification and demonstrate the efficacy of our protocol using real-world\ndatasets.\n
Abandonment and its impact on P2P VoD streaming (2013)

Peer-to-Peer (P2P) systems have evolved from being used for file sharing to delivering streaming video on demand (VoD). The policies adopted in P2P VoD, however, have not taken user viewing behavior - that users abandon videos - into account. We show that abandonment can result in increased interruptions and wasted resources. As a result, we reconsider the set of policies to use in the presence of abandonment. Our goal is to balance the conflicting needs of delivering videos without interruptions while minimizing wastage. We find that an Earliest-First chunk selection policy in conjunction with the Earliest-Deadline peer selection policy allows us to achieve high download rates. We take advantage of abandonment by converting peers to “partial seeds”; this increases capacity. We minimize wastage by using a playback lookahead window. We use analysis and simulation experiments using real-world traces to show the effectiveness of our approach.
Effects of Pulsed Electric Field Treatment on Compression Properties and Solutes Diffusion Behaviors of Jerusalem artichoke (2019)

<i>Jerusalem artichoke</i> is widely used as raw material for industrial production of inulin. Pressing (compression) and diffusion are two effective technologies for bio-compounds' recovery from plants. In this work, pulsed electric field (PEF) treatment at 400, 600, and 800 V/cm during 100 ms was applied to facilitate juice and solutes recovery from <i>Jerusalem artichoke</i>. The application of PEF led to electroporation of cell membranes and enhanced the tissue compression/juice expression and solutes diffusion. The consolidation coefficient (calculated by application of semi-empirical model) of PEF treated sample at 800 V/cm was 6.50 × 10<sup>-7</sup> m²/s, which is significantly higher than that of untreated sample (5.02 × 10<sup>-9</sup> m²/s) and close to that of freeze-thawed sample. Diffusion experiments with PEF treated samples were carried out at 25, 50, and 75 °C. A PEF treatment of <i>Jerusalem artichoke</i> at 800 V/cm led to a similar diffusion behavior at 25 °C, compared to diffusion behavior obtained from untreated sample at 75 °C.
Abstract 5567: A scalable and integrated computational and experimental workflow to identify new driver genes in cancer genome data (2017)

Abstract High throughput sequencing has revolutionized the study of the cancer genome, enabling numerous discoveries in basic and clinical research. However, considerable sample sizes are required to find cancer driver genes with intermediate and low mutation frequencies, and for a large proportion of patients the molecular cause (e.g. driver gene(s)) of disease is unknown. Here, we describe an integrated computational and experimental workflow that combines cancer genome data, molecular network information, multiplexed in vivo tumorigenesis assays, and reanalysis of driver-gene-negative cancer patients to predict and validate new driver genes. We develop a statistic, network mutation burden, that combines molecular network information with data from 4,742 cancer genomes to accurately classify known driver genes across 21 tumor types and predict 62 driver gene candidates.Of these, 35 gene candidates were tested in multiplexed in vivo tumorigenesis cell assays using sensitized immortalized human embryonic kidney (HA1E-M) and immortalized human lung epithelial (SALE-Y) cell lines.Tumor formation in vivo was observed for 11 genes (2 in HA1E-M, 3 in SALE-Y, 6 in both). By reanalyzing 242 lung adenocarcinoma patients with an unknown molecular cause of disease we show that two of these candidates, TFDP2 and AKT2, are significantly amplified in multiple samples.Overall, we describe a scalable combined computational and experimental framework to predict and validate driver genes across many tumor types. Our proof-of-concept approach should become increasingly useful as the number of cancer genomes continues to grow. Citation Format: Heiko Horn, Michael S. Lawrence, Candace R. Chouinard, Yashaswi Shrestha, Jessica Xin Hu, Elizabeth Worstell, Emily Shea, Nina Ilic, Eejung Kim, Atanas Kamburov, Alireza Kashani, William C. Hahn, Joshua D. Campbell, Jesse S. Boehm, Gad Getz, Kasper Lage. A scalable and integrated computational and experimental workflow to identify new driver genes in cancer genome data [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 5567. doi:10.1158/1538-7445.AM2017-5567
Simeprevir for the treatment of hepatitis C virus infection (2014)

Simeprevir (TMC435, Olysio™), a second-generation hepatitis C virus (HCV) protease inhibitor, has been recently approved for the treatment of genotype 1 chronic hepatitis C in combination with pegylated interferon and ribavirin. This molecule has very different characteristics from first-generation protease inhibitors. Results from trials show that simeprevir is highly effective and safe, with few adverse events. We discuss the specific features of this new treatment option for HCV infection, in terms of in vitro data, pharmacological data, and clinical trials. We also discuss the impact of Q80K polymorphism at baseline. Studies evaluating interferon-free regimens with simeprevir are ongoing. Future combinations of two or more direct-acting antiviral agents, targeting different viral enzymes and with synergistic antiviral effects, will be approved, allowing treatment of pan-genotypic HCV with optimized sustained virologic responses. Simeprevir will undoubtedly be part of future treatment strategies.
A virtual world for network management (2002)

Existing network management systems typically use a combination of textual displays and 2-D directed graph representations of network topology. A network management system is being designed that uses a virtual world presented through a 3-D stereo display and manipulated with a 3-D mouse. The goal is to allow the user to better understand and control the structure and behavior of a large, complex network. In the current prototype, the user interacts with a 3-D representation of a network whose topology and behavior are specified by a separate network emulator. The user can choose from among a set of different views of the network. For example, one view shows a selected virtual path as a series of logical links contained within a physical path. The system will serve as a testbed for the knowledge-based design of network visualizations.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
PTH Therapy Reverses Radiation Induced Non Union and Normalizes Radiomorphometrics in a Murine Mandibular Model of Distraction Osteogenesis (2011)

Sarhaddi, D. BA; Gallagher, K.K. MD; Deshpande, S.S.; Tchanque-Fossuo, C.N. MS, MD; Donneys, A. MS, MD; Nelson, N.S.; Sun, H. PhD; Krebsbach, P.H. DDS, PhD; Chepeha, D.B. MD; Buchman, S.R. MD
Junge Patientin mit Diabetes mellitus, kleinknotiger Leberzirrhose, hoher Transferrin-Sättigung und negativem HFE-Test (2005)

If liver cirrhosis is present in hemochromatosis, the overall risk of developing heptatocellular carcinoma is 20 times higher than in the normal population. Therefore it is suggested to perform an ultrasound examination of the liver and an AFP-test every 6 months, whereas an MRI-scan should be performed once a year, as a basis for further treatment options.
The deubiquitinating enzymes USP4 and USP17 target hyaluronan synthase 2 and differentially affect its function (2017)

The levels of hyaluronan, a ubiquitous glycosaminoglycan prominent in the extracellular matrix, is balanced through the actions of hyaluronan-synthesizing enzymes (HAS1, 2 and 3) and degrading hyaluronidases (Hyal 1, 2, 3 and PH20). Hyaluronan accumulates in rapidly remodeling tissues, such as breast cancer, due to deregulated expression of the HAS2 gene and/or alterations of HAS2 activity. The activity of HAS2 is regulated by post-translational modifications, including ubiquitination. In order to identify deubiquitinating enzymes (DUBs) that are involved in de-ubiquitination of HAS2, a complementary (cDNA) library of 69 Flag-HA-tagged human DUBs cloned into retroviral vectors was screened in human embryonic kidney (HEK) 293T cells for their ability to de-ubiquitinate myc-tagged HAS2. Several DUBs were found to decrease the ubiquitination of 6myc-HAS2, among which, the most effective were USP17 and USP4. USP17 efficiently removed polyubiquitination, whereas USP4 preferentially removed monoubiquitination of 6myc-HAS2. Co-immunoprecipitation studies revealed interactions between HAS2 and USP17, as well as between HAS2 and USP4, in membrane preparations of HEK293T cells. USP17 significantly stabilized 6myc-HAS2 protein levels, whereas USP4 did not. The silencing of USP17 led to decreased hyaluronan production, whereas the suppression of USP4 increased hyaluronan synthesis. Importantly, high levels of USP17 and HAS2 were detected in a panel of cancer cell lines compared to normal cells, and immunohistochemical stainings revealed higher expression of USP17 and HAS2 in tissues of lung cancer patients compared to normal tissue. In conclusion, USP17 and USP4 differently affect HAS2 ubiquitination, and the stability and function of HAS2.
A Standardized DNA Variant Scoring System for Pathogenicity Assessments in Mendelian Disorders (2015)

We developed a rules-based scoring system to classify DNA variants into five categories including pathogenic, likely pathogenic, variant of uncertain significance (VUS), likely benign, and benign. Over 16,500 pathogenicity assessments on 11,894 variants from 338 genes were analyzed for pathogenicity based on prediction tools, population frequency, co-occurrence, segregation, and functional studies collected from internal and external sources. Scores were calculated by trained scientists using a quantitative framework that assigned differential weighting to these five types of data. We performed descriptive and comparative statistics on the dataset and tested interobserver concordance among the trained scientists. Private variants defined as variants found within single families (n = 5,182), were either VUS (80.5%; n = 4,169) or likely pathogenic (19.5%; n = 1,013). The remaining variants (n = 6,712) were VUS (38.4%; n = 2,577) or likely benign/benign (34.7%; n = 2,327) or likely pathogenic/pathogenic (26.9%, n = 1,808). Exact agreement between the trained scientists on the final variant score was 98.5% [95% confidence interval (CI) (98.0, 98.9)] with an interobserver consistency of 97% [95% CI (91.5, 99.4)]. Variant scores were stable and showed increasing odds of being in agreement with new data when re-evaluated periodically. This carefully curated, standardized variant pathogenicity scoring system provides reliable pathogenicity scores for DNA variants encountered in a clinical laboratory setting.
HPM Sources: The DoD Perspective (2009)

This chapter contains sections titled: Introduction Role of the DoD in Basic Research DoD Needs History Advances in HPM Development Enabling Technologies Summary Acknowledgments This chapter contains sections titled: References 
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360° deterministic magnetization rotation in a three-ellipse magnetoelectric heterostructure (2018)

A magnetic dipole-coupled magnetoelectric heterostructure comprised of three closely spaced ellipse shapes was designed and shown to be capable of achieving deterministic in-plane magnetization rotation. The design approach used a combination of conventional micromagnetic simulations to obtain preliminary configurations followed by simulations using a fully strain-coupled, time domain micromagnetic code for a detailed assessment of performance. The conventional micromagnetic code has short run times and was used to refine the ellipse shape and orientation, but it does not accurately capture the effects of the strain gradients present in the piezoelectric and magnetostrictive layers that contribute to magnetization reorientation. The fully coupled code was used to assess the effects of strain and magnetic field gradients on precessional switching in the side ellipses and on the resulting dipole-field driven magnetization reorientation in the center ellipse. The work led to a geometry with a CoFeB ellipse (125 nm × 95 nm × 4 nm) positioned between two smaller CoFeB ellipses (75 nm × 50 nm × 4 nm) on a 500 nm PZT-5H film substrate clamped at its bottom surface. The smaller ellipses were oriented at 45° and positioned at 70° and 250° about the central ellipse due to the film deposition on a thick substrate. A 7.3 V pulse applied to the PZT for 0.22 ns produced 180° switching of the magnetization in the outer ellipses that then drove switching in the center ellipse through dipole-dipole coupling. Full 360° deterministic rotation was achieved with a second pulse. The temporal response of the resulting design is discussed.