gebhart/patrepeval huggingface dataset:
Accelerating Large-Scale Graph Analytics with FPGA and HMC (2017)

Graph analytics that explores the relationship among interconnected entities is becoming increasingly important due to its broad applicability from machine learning to social science. However, one major challenge for graph processing systems is the irregular data access pattern of graph computation which can significantly degrade the performance. The algorithms, software, and hardware that have been tailored for mainstream parallel applications are, as a result, generally not effective for massive-scale sparse graphs from the real world due to their complexity and irregularity. To address the performance issues in large-scale graph analytics, we combine the emerging Hybrid Memory Cube (HMC) with a modern FPGA in order to achieve exceptional random access performance without any loss of flexibility or efficiency in computation. In particular, we develop collaborative software/hardware techniques to perform a level-synchronized breadth first search (BFS) on the FPGA-HMC platform. From the software perspective, we develop an architecture-aware graph clustering algorithm that fully exploits the platform's capability to improve data locality and memory access efficiency. For each input graph, this algorithm provides an efficient data layout that allows the FPGA to coalesce memory requests into the largest possible HMC payload requests so that the number of memory requests, which is the primary factor in runtime, can be minimized. From the hardware perspective, we further improve the FPGA-HMC graph processor architecture by adding a merging unit. The merging unit takes the best advantage of the increased data locality resulting from graph clustering. We evaluated the performance of our BFS implementation using the AC-510 development kit from Micron over a set of benchmarks from a wide range of applications. We observed that the combination of the clustering algorithm and the merging hardware achieved 2.8 × average performance improvement compared to the latest FPGA-HMC based graph processing system.
Volume warping for adaptive isosurface extraction (2002)

Polygonal approximations of isosurfaces extracted from uniformly sampled volumes are increasing in size due to the availability of higher resolution imaging techniques. The large number of I primitives represented hinders the interactive exploration of the dataset. Though many solutions have been proposed to this problem, many require the creation of isosurfaces at multiple resolutions or the use of additional data structures, often hierarchical, to represent the volume. We propose a technique for adaptive isosurface extraction that is easy to implement and allows the user to decide the degree of adaptivity as well as the choice of isosurface extraction algorithm. Our method optimizes the extraction of the isosurface by warping the volume. In a warped volume, areas of importance (e.g. containing significant details) are inflated while unimportant ones are contracted. Once the volume is warped, any extraction algorithm can be applied. The extracted mesh is subsequently unwarped such that the warped areas are rescaled to their initial proportions. The resulting isosurface is represented by a mesh that is more densely sampled in regions decided as important.
Spider Codes: Practical erasure codes for distributed storage systems (2016)

Distributed storage systems use erasure codes to reliably store data with a small storage overhead. To further improve system performance, some novel erasure codes introduce new features such as the regenerating property or symbol locality, enabling these codes to have optimal repair times and optimal degraded read performance. Unfortunately, the introduction of these new features often exacerbates the performance of other system metrics such as encoding throughput, data reliability, and storage overhead, among others. In this paper we describe the intricate relationships between erasure code properties and system-level performance metrics, showing the different tradeoffs distributed storage designers need to face. We also present Spider Codes, a new erasure code achieving a practical trade-off between the different system-level performance metrics.
Effects of pre‐eclampsia and fetal growth restriction on C‐type natriuretic peptide (2015)

CNP secretion during gestation is responsive to vascular stress. Plasma NTproCNP measurements may have clinical application in late pregnancy in defining the different phenotypes associated with pre-eclampsia.
Estimation of changes in instantaneous aortic blood flow by the analysis of arterial blood pressure (2012)

The purpose of this study was to introduce and validate a new algorithm to estimate instantaneous aortic blood flow (ABF) by mathematical analysis of arterial blood pressure (ABP) waveforms. The algorithm is based on an autoregressive with exogenous input (ARX) model. We applied this algorithm to diastolic ABP waveforms to estimate the autoregressive model coefficients by requiring the estimated diastolic flow to be zero. The algorithm incorporating the coefficients was then applied to the entire ABP signal to estimate ABF. The algorithm was applied to six Yorkshire swine data sets over a wide range of physiological conditions for validation. Quantitative measures of waveform shape (standard deviation, skewness, and kurtosis), as well as stroke volume and cardiac output from the estimated ABF, were computed. Values of these measures were compared with those obtained from ABF waveforms recorded using a Transonic aortic flow probe placed around the aortic root. The estimation errors were compared with those obtained using a windkessel model. The ARX model algorithm achieved significantly lower errors in the waveform measures, stroke volume, and cardiac output than those obtained using the windkessel model (P < 0.05).
Tinnitus treatment with customized sounds. (2008)

Recent studies have indicated that the pathophysiological basis for tinnitus may be abnormal activity in the auditory areas of the brain rather than aberrant activity in the periphery. Tinnitus-related activity leads to changes in tonotopic representation in auditory cortex. However, such reorganization can be reversed through training-induced changes in the response pattern of cortical neurons. We address this problem by using customized sounds that reproduce the subjective experience to reduce overactive auditory circuits. The results of two preliminary studies indicate that customized sound therapy (CST*) aimed at this central dysfunction reduces tinnitus quickly and safely. Participants described immediate relief, showed changes on the Tinnitus Handicap Questionnaire, and reported changes in hearing threshold within 3 weeks. We also saw changes in the intensity dependence of the auditory N100 in tinnitus patients, supporting the idea that tinnitus reflects a reorganization of tonotopic maps in the auditory cortex. The main correlate of this reorganization was the enhanced contrast between responses to the perceived tinnitus pitch and tones approximately one octave lower. After 3 weeks of CST, the intensity dependence to the tinnitus pitch decreased, making these responses more similar to those from normal subjects responding to tones in the same frequency.
High strength reversible adhesive closures (2017)

ABSTRACT Closures such as buttons, clasps, zippers, and hook‐and‐loops find widespread use in daily life, and all work by mechanical interlocking. However, these traditional closures are often rigid, lose performance with age, and can produce a harsh sound during use. Here high strength (>50 N cm −2 ), reusable, and nearly silent closure devices are fabricated based on recently developed fibril‐less gecko‐inspired adhesives. Guided by a reversible adhesion scaling law, the closure force capacity is tuned by modifying the closure materials and geometry. A simple analytical model is presented which accurately predicts system performance, based on the reversible adhesion scaling parameter. The force capacity of these adhesive closures is measured and compared to commercially‐available hook‐and‐loop closures, and it is found that the adhesive closures sustain forces that are 4.4 times greater for comparable geometry. The sound of release is also quantified and shown to be minimal for adhesive closures. This work provides motivation to develop new high strength, reusable closures for commercial and industrial applications. © 2017 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2017 , 55 , 1783–1790
Injectable and tunable poly(ethylene glycol) analogue hydrogels based on poly(oligoethylene glycol methacrylate) (2014)

Injectable PEG-analogue hydrogels based on poly(oligoethylene glycol methacrylate) have been developed based on complementary hydrazide and aldehyde reactive linear polymer precursors. These hydrogels display the desired biological properties of PEG, form covalent networks in situ following injection, and are easily modulated for improved control over their functionality and physiochemical properties.
Thin multiplication region InAlAs homojunction avalanche photodiodes (1998)

Low excess noise in avalanche photodetectors (APDs) is desired for improved sensitivity and high-frequency performance. Gain and noise characteristics are measured for InAlAs p-i-n homojunction APDs that were grown with varying i-region widths on InP by molecular beam epitaxy. The effective ionization ratio k (β/α) determined by noise measurements shows a dependence on multiplication region width, reducing from 0.31 to 0.18 for multiplication region thicknesses of 1600–200 nm. This trend follows previously shown results in AlGaAs-based APDs, which exhibit reduced excess noise due to nonlocal multiplication effects. These results show that this effect is a characteristic of thin avalanche regions and is not a material-specific phenomenon.
Au-Free Epitaxial Growth of InAs Nanowires (2006)

III-V nanowires have been fabricated by metal-organic vapor-phase epitaxy without using Au or other metal particles as a catalyst. Instead, prior to growth, a thin SiOx layer is deposited on the substrates. Wires form on various III-V substrates as well as on Si. They are nontapered in thickness and exhibit a hexagonal cross-section. From high-resolution X-ray diffraction, the epitaxial relation between wires and substrates is demonstrated and their crystal structure is determined.
A V-Band MMIC SPDT passive HEMT switch using impedance transformation networks (2001)

A V-Band MMIC single pole double throw (SPDT) switch using GaAs PHEMT process is designed, fabricated and tested. In contrast to the conventional resonant-type switch design method, this passive FET switch circuit utilizes impedance transformation to compensate the drain-source capacitance effect for the off-state in millimeter-wave frequency range. This SPDT switch has a measured isolation better than 30 dB for the off-state and 4 dB insertion loss for the on-state from 53 GHz to 61 GHz. The isolation performance of this design approach outmatches previously published FET switches in this frequency range.
Dispersion analysis of resonance cone behaviour in magnetically anisotropic transmission-line metamaterials (2004)

We apply a periodic dispersion analysis to the study of two-dimensional, anisotropic transmission-line (TL) metamaterials that, although electrically isotropic, possess magnetic anisotropy in the effective medium limit. It is shown that these structures can be designed to exhibit hyperbolic dispersion surfaces in phase space, and resonance cones, akin to those observed by K.G. Balmain et al., in real space. Full-wave simulations demonstrate that these resonance cones can be made to refract negatively at, and to focus through, an interface between two anisotropic TL metamaterials whose axes are mutually transposed by 90 degrees.
In vivo detection of normal and pathologic bowel electrical activity using a SQUID magnetometer (2002)

The Superconducting QUantum Interference Device (SQUID) magnetometer can non-invasively detect the magnetic fields created by the Basic Electrical Rhythm (BER) of the Gastrointestinal Tract (GIT). Using anesthetized adult male New Zealand rabbits the authors recorded signals from two isolated bowel segments at the same time, before and after ischemia was induced in either one or both bowel segments. The dominant frequency peaks for each period of recording were determined using autoregressive (AR) spectral analysis. There was a significant fall in the BER frequency in the ischemic segment from 11.8/spl plusmn/0.9 to 7.8/spl plusmn/0.6 cycles per minute (cpm), while there was no change in the normal bowel. It was possible for two observers (LAB, WOR) who were blinded to the preparation, to identify which bowel segment was ischemic. The results of this experiment demonstrate the ability of the SQUID magnetometer to noninvasively detect and differentiate signals from normal and ischemic bowel sources.
Glial Cell Line–Derived Neurotrophic Factor Enhances Human Islet Posttransplantation Survival (2011)

Our study shows that GDNF has beneficial effects on human islet survival and could be used to improve islet posttransplantation survival.
A Chemically Cross-Linked Knottin Dimer Binds Integrins with Picomolar Affinity and Inhibits Tumor Cell Migration and Proliferation (2014)

Molecules that target and inhibit αvβ3, αvβ5, and α5β1 integrins have generated great interest because of the role of these receptors in mediating angiogenesis and metastasis. Attempts to increase the binding affinity and hence the efficacy of integrin inhibitors by dimerization have been marginally effective. In the present work, we achieved this goal by using oxime-based chemical conjugation to synthesize dimers of integrin-binding cystine knot (knottin) miniproteins with low-picomolar binding affinity to tumor cells. A non-natural amino acid containing an aminooxy side chain was introduced at different locations within a knottin monomer and reacted with dialdehyde-containing cross-linkers of different lengths to create knottin dimers with varying molecular topologies. Dimers cross-linked through an aminooxy functional group located near the middle of the protein exhibited higher apparent binding affinity to integrin-expressing tumor cells compared with dimers cross-linked through an aminooxy group near the C-terminus. In contrast, the cross-linker length had no effect on the integrin binding affinity. A chemical-based dimerization strategy was critical, as knottin dimers created through genetic fusion to a bivalent antibody domain exhibited only modest improvement (less than 5-fold) in tumor cell binding relative to the knottin monomer. The best oxime-conjugated knottin dimer achieved an unprecedented 150-fold increase in apparent binding affinity over the knottin monomer. Also, this dimer bound 3650-fold stronger and inhibited tumor cell migration and proliferation compared with cilengitide, an integrin-targeting peptidomimetic that performed poorly in recent clinical trials, suggesting promise for further therapeutic development.
Microwave Balloon Angioplasty (1989)

Preliminary experiments on the induction of 1ocalized myocardial tissuie modification by microwave energy, without causing any cardiac arrhythmias, were the first step in the development of both microwave ablation and an innovative procedure called microwave balloon angioplasty (MBA). MBA combines the traditional angioplasty technique with microwave energy to open narrowed arteries and reduce the occurence of restenosis. Microwave balloon angioplasty was used in anesthetized rabbits to induce tissue modification in the intima, media and adventitia. Resu1ts of initial in-vitro and in-vivo experiments are presented, and the potential advantages of adding microwave heating to balloon angioplasty are discussed.
Isotope separation by selective dissociative electron attachment. Final technical report (1978)

A description of work performed on isotopically selective, photo-enhanced production of SF/sup -//sub 5/ from SF/sub 6/ is included. The primary task under the present contract was the construction of a second-generation experimental apparatus for the study of the simultaneous interaction of electrons, photons, and molecules. The collinear electron and laser beam arrangement employed previously has been retained, but a new electron gun design has been adopted which avoids the troublesome interaction of the laser beam with the electron gun filament. The system has been designed for maximum compatibility with aggressive gases such as UF/sub 6/. Details of the design and construction of this system are given. Proposals for future work include work on SF/sub 6/ and UF/sub 6/.
44-Gb/s/λ Upstream OFDMA-PON Transmission with Polarization-Insensitive Source-Free ONUs (2010)

For the first time, we demonstrate colorless 44-Gb/s/λ, upstream OFDMA-PON transmission with polarization-insensitive, source-free ONUs. Superior performance is reported over 20 km SSMF plus 1:32 split, featuring OLT-side coherent detection and no ONU-side temperature control.
Development of a Human Immunodeficiency Virus Type 1-Based Lentiviral Vector That Allows Efficient Transduction of both Human and Rhesus Blood Cells (2009)

Human immunodeficiency virus type 1 (HIV-1) vectors transduce rhesus blood cells poorly due to a species-specific block by TRIM5alpha and APOBEC3G, which target HIV-1 capsid and viral infectivity factor (Vif), respectively. We sought to develop a lentiviral vector capable of transducing both human and rhesus blood cells by combining components of both HIV-1 and simian immunodeficiency virus (SIV), including SIV capsid (sCA) and SIV Vif. A chimeric HIV-1 vector including sCA (chiHIV) was superior to the conventional SIV in transducing a human blood cell line and superior to the conventional HIV-1 vector in transducing a rhesus blood cell line. Among human CD34(+) hematopoietic stem cells (HSCs), the chiHIV and HIV-1 vectors showed similar transduction efficiencies; in rhesus CD34(+) HSCs, the chiHIV vector yielded superior transduction rates. In in vivo competitive repopulation experiments with two rhesus macaques, the chiHIV vector demonstrated superior marking levels over the conventional HIV-1 vector in all blood lineages (first rhesus, 15 to 30% versus 1 to 5%; second rhesus, 7 to 15% versus 0.5 to 2%, respectively) 3 to 7 months postinfusion. In summary, we have developed an HIV-1-based lentiviral vector system that should allow comprehensive preclinical testing of HIV-1-based therapeutic vectors in the rhesus macaque model with eventual clinical application.
Clinical activity and safety of pegylated human IL-10 (AM0010) in combination with anti-PD1. (2016)

3018 Background: IL-10 has anti-inflammatory properties but stimulates the cytotoxicity and proliferation of CD8 T cells. The observation that T cell receptor mediated activation induces the expression of IL-10 receptors and PD1 on CD8 T cells, provides the mechanistic rationale for combining AM0010 and anti-PD1 in the clinic. Tolerability and anti-tumor activity of AM0010 alone was established in the ongoing phase 1 study. Objective responses were observed in pts with uveal melanoma, cutaneous T cell lymphoma and in 4 of 15 pts with RCC. Methods: Pts with advanced melanoma, RCC or NSCLC were treated with AM0010 (daily SC) and Pembrolizumab (q3wk IV). Tumor responses were monitored following irRC. Immune responses were measured by analysis of serum cytokines, activation of blood derived T cells, peripheral T cell clonality and immunohistochemistry of tumor infiltrating CD8 T cells. Results: In 19 pts, AM0010 10 mg/kg (n=13) or 20 mg/kg (n=6) in combination with anti-PD1 (2mg/kg) was well tolerated (observation period 10-15 months). All TrAEs were transient and DLTs or TrAEs leading to study discontinuation were not observed. There was no colitis, pneumonitis, or endocrine disruptions. G3/4 TrAEs were observed in 7 of 19 pts and included pruritus (1), anemia (3), thrombocytopenia (3) and malaise (1). Objective responses (PR/CR) were observed in 4 of 8 RCC pts, 2 of 5 NSCLC pts and 2 of 6 melanoma pts. 2 additional melanoma pts had tumor increase followed by decrease (pseudoprogression). AM0010 / anti-PD1 increased Th1 cytokines (IL-18, IFNg, IL-7) and the number and proliferation of PD1+ activated CD8 T cells while decreasing the proliferation of FoxP3+ Tregs and TGFb in the blood. AM0010 / anti-PD1 induced de-novo oligoclonal expansion of T cell clones in the blood without affecting total lymphocyte counts. AM0010 / anti-PD1 increased the number of tumor infiltrating Granzyme+ PD1+ CD8+ T cells in tumor biopsies of treated patients. Conclusions: AM0010 in combination with anti-PD1 is well-tolerated. The clinical activity and the observed CD8 T cell activation encourages the continued exploration of AM0010 in combination with anti-PD1. Clinical trial information: NCT02009449.Best Response SD PR CR CBR (SD, PR, CR: > 24 weeks) RCC (n=8) 4 3 1 5 NSCLC (n=5) 3 2 - 4 Melanoma (n=6) 2 2 - 2 (NR)
A closed form solution to the microphone position self-calibration problem (2012)

This paper presents a novel algorithm for the automatic 3D localization of a set of microphones in an unknown environment. Given the times of arrival at each microphone of a set of sound events, the approach simultaneously estimates the 3D positions of the sensors and the sources that have generated the events. The only assumption made is that the emission time of the sound events must be known in order to measure the time of flight for each event. A closed form solution is also proposed whenever a sound event coincides with a microphone position. Simulated and real experiments show the validity of the approach for different setups of sensors and number of events.
A fault-tolerant forwarding strategy for interest-based information centric networks (2015)

We show that the forwarding strategies in the named data networking (NDN) architecture and the original content centric networking (CCN) architecture cannot ensure that Interests return the requested data objects when routing-table loops exist in a stable or dynamic network. We also show that no correct Interest forwarding strategy that allows Interest aggregation can be designed solely on the basis of identifying Interests uniquely in order to detect Interest loops. We introduce SIFAH (Strategy for Interest Forwarding and Aggregation with Hop-Counts). SIFAH prevents or detects Interest loops when Interests are aggregated or forwarded over one or multiple paths. As a result, it is far more efficient than the forwarding strategy in NDN and the original CCN proposal. SIFAH operates by having forwarding information bases (FIB) store the next hops and number of hops to named content prefixes, and by using Interests that state the names of requested content and hop counts that reflect the information in their FIBs.
Inhibitory effect of indole analogs against Paenibacillus larvae, the causal agent of American foulbrood disease (2017)

Paenibacillus larvae, a Gram-positive bacterium, causes American foulbrood (AFB) in honey bee larvae (Apis mellifera Linnaeus [Hymenoptera: Apidae]). P. larvae spores exit dormancy in the gut of bee larvae, the germinated cells proliferate, and ultimately bacteremia kills the host. Hence, spore germination is a required step for establishing AFB disease. We previously found that P. larvae spores germinate in response to l-tyrosine plus uric acid in vitro. Additionally, we determined that indole and phenol blocked spore germination. In this work, we evaluated the antagonistic effect of 35 indole and phenol analogs and identified strong inhibitors of P. larvae spore germination in vitro. We further tested the most promising candidate, 5-chloroindole, and found that it significantly reduced bacterial proliferation. Finally, feeding artificial worker jelly containing anti-germination compounds to AFB-exposed larvae significantly decreased AFB infection in laboratory-reared honey bee larvae. Together, these results suggest that inhibitors of P. larvae spore germination could provide another method to control AFB.