gebhart/patrepeval huggingface dataset:
SCF (2012)

Heterogeneous computing systems comprised of accelerators such as FPGAs, GPUs, and manycore processors coupled with standard microprocessors are becoming an increasingly popular solution for future computing systems due to their higher performance and energy efficiency. Although programming languages and tools are evolving to simplify device-level design, programming such systems is still difficult and time-consuming largely due to system-wide challenges involving communication between heterogeneous devices, which currently require ad hoc solutions. Most communication frameworks and APIs which have dominated parallel application development for decades were developed for homogeneous systems, and hence cannot be directly employed for hybrid systems. To solve this problem, this article presents the System Coordination Framework (SCF), which employs message passing to transparently enable communication between tasks described using different programming tools (and languages), and running on heterogeneous processing devices of systems from domains ranging from embedded systems to High-Performance Computing (HPC) systems. By hiding low-level architectural details of the underlying communication from an application designer, SCF can improve application development productivity, provide higher levels of application portability, and offer rapid design-space exploration of different task/device mappings. In addition, SCF enables custom communication synthesis that exploits mechanisms specific to different devices and platforms, which can provide performance improvements over generic solutions employed previously. Our results indicate a performance improvement of 28× and 682× by employing FPGA devices for two applications presented in this article, while simultaneously improving the developer productivity by approximately 2.5 to 5 times by using SCF.
The NADPH oxidase Nox2 regulates VEGFR1/CSF‐1R‐mediated microglial chemotaxis and promotes early postnatal infiltration of phagocytes in the subventricular zone of the mouse cerebral cortex (2013)

The phagocyte NADPH oxidase Nox2 generates superoxide ions implicated in the elimination of microorganisms and the redox control of inflammatory signaling. However, the role of Nox2 in phagocyte functions unrelated to immunity or pathologies is unknown. During development, oriented cell migrations insure the timely recruitment and function of phagocytes in developing tissues. Here, we have addressed the role of Nox2 in the directional migration of microglial cells during development. We show that microglial Nox2 regulates the chemotaxis of purified microglia mediated by the colony stimulating factor-1 receptor (CSF-1R) and the vascular endothelial growth factor receptor-1 (VEGFR1). Stimulation of these receptors triggers activation of Nox2 at the leading edge of polarized cells. In the early postnatal stages of mouse brain development, Nox2 is activated in macrophages / microglial cells in the lateral ventricle or the adjacent subventricular zone (SVZ). Fluorescent microglia injected into the lateral ventricle infiltrate the dorso-caudal SVZ through a mechanism that is blocked by pretreatment of the injected cells with an irreversible Nox inhibitor. Infiltration of endogenous microglia into the caudal SVZ of the cerebral cortex is prevented by (1) Nox2 gene deficiency, (2) treatment with a Nox2 inhibitor (apocynin), and (3) invalidation of the VEGFR1 kinase. We conclude that phagocytes move out of the lateral ventricle soon after birth and infiltrate the cortical SVZ through a mechanism requiring microglial Nox2 and VEGFR1 activation. Nox2 therefore modulates the migration of microglia and their development.
A review of interventional clinical trials (CTs) in renal cell carcinoma (RCC): A status report from the ClinicalTrials.gov website. (2014)

e15542 Background: Therapy (Tx) and CTs in RCC have rapidly evolved with the introduction of targeted therapy (TT) and more recently novel immunotherapy (IT). The objective of this study was to assess the current landscape of CTs in RCC to identify areas of strength and opportunities for improvement. Methods: ClinicalTrials.gov was queried on September 24, 2013 using pre-specified search criteria. Only open, RCC-dedicated, interventional CTs in adult patients (pts) were included. Descriptive statistics and Fisher’s exact tests were used to compare features of CTs. Results: Of the 169 CTs analyzed, 42 were phase I or I/II (25%), 67 phase II (40%), 15 phase III (9%), and 45 other (26%). Overall, 27% were randomized and 65% were single-arm. Most CTs were at least partially based in the U.S. (68%) and 16% were industry sponsored. The majority of CTs allowed any histology (60%), but 31% were for clear cell RCC only and 9% were for strictly non-clear cell RCC. Studies of pts with advanced disease (AD) comprised 67% of the CTs, 15% were surgery CTs, 11% were studying pts in a neo-adjuvant or adjuvant setting and 7% were other. Of the CTs evaluating pts with metastatic disease, 30% were for 1st line Tx, 40% for 2nd line or beyond and 30% for any line Tx. TT was the most commonly studied systemic Tx, with 57% of all CTs including at least one TT. IT was tested alone or in combination in 8%. The primary endpoint of feasibility or biomarker analysis, progression free survival (PFS), or overall survival (OS) was noted in 28%/52%/2% of TT CTs and 43%/36%/14% of IT CTs (P=0.037). Biomarkers were assessed in 45% of CTs overall and were more frequently examined in TT and IT CTs (54% and 64%) than in surgery and other CTs (22% and 28%) (P=0.002). Sponsorship differed by Tx type (P=0.003), with IT CTs most commonly sponsored by industry (36%), and academic sponsorship more common for TT (46%), surgery (89%) and other (63%) CTs. Conclusions: CTs in RCC are largely non-randomized, single arm, with minimal focus on non-clear cell RCC and evaluating primarily pts with AD. TT is the predominant systemic Tx being tested. Significant differences were noted in the primary endpoint, sponsorship and biomarker assessment between Tx types.
OpenCL and parallel primitives for digital TV applications (2010)

Open Computing Language® (OpenCL®), which is created to support parallel programming of heterogeneous multicore-processor systems, has a very large potential for high-performance computing and consumer electronics since it provides application programming interfaces (APIs) to help make a portable code that runs across multiple devices. OpenCL is still under development, and it is not clear whether OpenCL has any advantages over other frameworks aside from portability. The purpose of our project was to define evaluation criteria, empirically evaluate OpenCL as a programming framework using evaluation criteria (e.g., performance, productivity, and portability criteria), define and implement parallel primitives in OpenCL, and demonstrate how the use of the implemented parallel primitives can have benefits for our target applications. Parallel primitive library APIs are defined to implement parallel algorithms in OpenCL, and a set of data- and task-parallel primitives is implemented and incorporated in the target applications. Multicore central processing units, the Cell Broadband Engine® (Cell/B.E.®), and graphics processing units are used as target platforms, and digital TV applications are used to evaluate usefulness of OpenCL. Preliminary results show that parallel primitives can be one of the ways to improve application performance and programmer productivity with respect to OpenCL while still maintaining software portability.
Multiple New Paralytic Shellfish Toxin Vectors in Offshore North Sea Benthos, a Deep Secret Exposed (2020)

In early 2018, a large easterly storm hit the East Anglian coast of the UK, colloquially known as the 'Beast from the East', which also resulted in mass strandings of benthic organisms. There were subsequent instances of dogs consuming such organisms, leading to illness and, in some cases, fatalities. Epidemiological investigations identified paralytic shellfish toxins (PSTs) as the cause, with toxins present in a range of species and concentrations exceeding 14,000 µg STX eq./kg in the sunstar <i>Crossaster papposus</i>. This study sought to better elucidate the geographic spread of any toxicity and identify any key organisms of concern. During the summers of 2018 and 2019, various species of benthic invertebrates were collected from demersal trawl surveys conducted across a variety of locations in the North Sea. An analysis of the benthic epifauna using two independent PST testing methods identified a 'hot spot' of toxic organisms in the Southern Bight, with a mean toxicity of 449 µg STX eq./kg. PSTs were quantified in sea chervil (<i>Alcyonidium diaphanum</i>), the first known detection in the phylum bryozoan, as well as eleven other new vectors (>50 µg STX eq./kg), namely the opisthobranch <i>Scaphander lignarius</i>, the starfish <i>Anseropoda placenta, Asterias rubens, Luidia ciliaris</i>, <i>Astropecten irregularis</i> and <i>Stichastrella rosea</i>, the brittlestar <i>Ophiura ophiura</i>, the crustaceans <i>Atelecyclus rotundatus</i> and <i>Munida rugosa</i>, the sea mouse <i>Aphrodita aculeata</i>, and the sea urchin <i>Psammechinus miliaris</i>. The two species that showed consistently high PST concentrations were <i>C. papposus</i> and <i>A. diaphanum</i>. Two toxic profiles were identified, with one dominated by dcSTX (decarbamoylsaxitoxin) associated with the majority of samples across the whole sampling region. The second profile occurred only in North-Eastern England and consisted of mostly STX (Saxitoxin) and GTX2 (gonyautoxin 2). Consequently, this study highlights widespread and variable levels of PSTs in the marine benthos, together with the first evidence for toxicity in a large number of new species. These findings highlight impacts to 'One Health', with the unexpected sources of toxins potentially creating risks to animal, human and environmental health, with further work required to assess the severity and geographical/temporal extent of these impacts.
Simultaneous measurements and flow visualization in a plane mixing layer (1982)

Wind tunnel experiments performed to determine the flow characteristics of a plane mixing layer are described. Two parallel streams of air moving at different velocities were separated by a splitter plate prior to their mixing in the test section. Gaseous NH/sub 3/ and gaseous HCl were introduced near the splitter plate to produce an ammonium chloride aerosol which made flow visualization possible. Flow visualization records (movies) and velocity measurements, using laser-doppler-velocimeters tracking silicone oil particles in the flow, were made simultaneously and synchronized using a chopped beam of a He-Ne laser which left a signature on the move film and provided a signal for flow rate data acquisition. Analysis of these synchronized data verified the existence of large, essentially two-dimensional coherent structures in the plane mixing layer. Also, other features exhibited by the flow-fields of these coherent structures, such as vorticity distribution, potential fluctuations in ambient fluid caused by passage of large structures and velocity fluctuations within the coherent structures themselves can be studied using this experimental technique. (LCL)
The WHOI micromodem-2: A scalable system for acoustic communications and networking (2010)

A successor to the WHOI Micromodem-1 underwater acoustic modem has recently been developed. The Micromodem-2 has the same compact form-factor as the Micromodem-1 and will support all of the existing applications for the Micromodem-1, as well as interoperate with the Micromodem-1. Existing acoustic communications protocols using phase-shift keying (PSK) as well as frequency-hopping frequency-shift keying (FH-FSK) are supported, as are navigation features including narrow-band and broadband long-baseline (LBL) navigation. The Micromodem-2 is significantly more capable than the Micromodem-1 in computational ability and memory, bandwidth, non-volatile data storage, user expansion interfaces, and real-time clock precision. The expanded capabilities will allow new communications algorithms, modulation, errorcorrection methods, navigation features, and networking capabilities to be implemented. The improvements in processing capability and acoustic interfaces on the Micromodem-2 allow it to operate at acoustic frequencies from approximately 1kHz to 100kHz. The significant increases in available non-volatile storage enable the Micromodem-2 to capture data in-situ for diagnostic and research purposes. The Micro mo dem-2's firmware architecture is similar to the Micromodem-1's firmware architecture, using a real-time operating system based on modular signal processing blocks. It has been improved to increase modularity and facilitate future portability, and it offers significant improvements in timing for use with navigation and networking applications.
Restricted Likelihood Ratio Testing for Zero Variance Components in Linear Mixed Models (2008)

The goal of our article is to provide a transparent, robust, and computationally feasible statistical platform for restricted likelihood ratio testing (RLRT) for zero variance components in linear mixed models. This problem is nonstandard because under the null hypothesis the parameter is on the boundary of the parameter space. Our proposed approach is different from the asymptotic results of Stram and Lee who assumed that the outcome vector can be partitioned into many independent subvectors. Thus, our methodology applies to a wider class of mixed models, which includes models with a moderate number of clusters or nonparametric smoothing components. We propose two approximations to the finite sample null distribution of the RLRT statistic. Both approximations converge weakly to the asymptotic distribution obtained by Stram and Lee when their assumptions hold. When their assumptions do not hold, we show in extensive simulation studies that both approximations outperform the Stram and Lee approximation and the parametric bootstrap. We also identify and address numerical problems associated with standard mixed model software. Our methods are motivated by and applied to a large longitudinal study on air pollution health effects in a highly susceptible cohort. Relevant software is posted as an online supplement.
Image-based evaluation of contraction–relaxation kinetics of human-induced pluripotent stem cell-derived cardiomyocytes: Correlation and complementarity with extracellular electrophysiology (2014)

In this study, we used high-speed video microscopy with motion vector analysis to investigate the contractile characteristics of hiPS-CM monolayer, in addition to further characterizing the motion with extracellular field potential (FP), traction force and the Ca(2+) transient. Results of our traction force microscopy demonstrated that the force development of hiPS-CMs correlated well with the cellular deformation detected by the video microscopy with motion vector analysis. In the presence of verapamil and isoproterenol, contractile motion of hiPS-CMs showed alteration in accordance with the changes in fluorescence peak of the Ca(2+) transient, i.e., upstroke, decay, amplitude and full-width at half-maximum. Simultaneously recorded hiPS-CM motion and FP showed that there was a linear correlation between changes in the motion and field potential duration in response to verapamil (30-150nM), isoproterenol (0.1-10μM) and E-4031 (10-50nM). In addition, tetrodotoxin (3-30μM)-induced delay of sodium current was corresponded with the delay of the contraction onset of hiPS-CMs. These results indicate that the electrophysiological and functional behaviors of hiPS-CMs are quantitatively reflected in the contractile motion detected by this image-based technique. In the presence of 100nM E-4031, the occurrence of early after-depolarization-like negative deflection in FP was also detected in the hiPS-CM motion as a characteristic two-step relaxation pattern. These findings offer insights into the interpretation of the motion kinetics of the hiPS-CMs, and are relevant for understanding electrical and mechanical relationship in hiPS-CMs.
Statistical morphological disambiguation for agglutinative languages (2000)

In this paper, we present statistical models for morphological disambiguation in Turkish. Turkish presents an interesting problem for statistical models since the potential tag set size is very large because of the productive derivational morphology. We propose to handle this by breaking up the morhosyntactic tags into inflectional groups, each of which contains the inflectional features for each (intermediate) derived form. Our statistical models score the probability of each morhosyntactic tag by considering statistics over the individual inflection groups in a trigram model. Among the three models that we have developed and tested, the simplest model ignoring the local morphotactics within words performs the best. Our best trigram model performs with 93.95% accuracy on our test data getting all the morhosyntactic and semantic features correct. If we are just interested in syntactically relevant features and ignore a very small set of semantic features, then the accuracy increases to 95.07%.
Abstract 2028: PDE3A modulation for cancer therapy (2017)

Abstract In a differential cytotoxicity screen, we identified a novel small molecule modulator of phosphodiesterase 3A (PDE3A) that kills cancer cells expressing elevated levels of PDE3A and SLFN12 (de Waal, Nat Chem Biol, 2016). Treatment with this cell-selective cytotoxic small molecule, DNMDP, induces complex formation between PDE3A and SLFN12, resulting in apoptosis. Inhibition of PDE3A enzymatic activity is not sufficient for cancer cell killing, and expression of both PDE3A and SLFN12 are required. Although the mechanism of signaling to the apoptosis machinery remains unclear, we examined more closely the role of the PDE3A-SLFN12 complex in cancer cell killing mediated by DNMDP. We found that cancer cell lines made resistant to DNMDP by persistent exposure downregulated SLFN12 expression and that re-expression of SLFN12 was sufficient to restore sensitivity. Furthermore, ectopic expression of PDE3A and SLFN12 are sufficient to sensitize cancer cells to DNMDP. These data underscore the tight correlation of PDE3A-SLFN12 complex formation and cancer cell killing mediated by DNMDP. Citation Format: Xiaoyun Wu, Timothy Lewis, Luc de Waal, Galen Gao, Jian Zhang, Monica Schenone, Colin Garvie, Brett Diamond, Selena Lorrey, Andrew Cherniack, Steven Corsello, Alex Burgin, Todd Golub, Stuart Schreiber, Matthew Meyerson, Heidi Greulich. PDE3A modulation for cancer therapy [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 2028. doi:10.1158/1538-7445.AM2017-2028
Cancellation of associated frequency dithering in a single-frequency compound-ring erbium-doped fiber laser (1996)

The stabilizing mechanism of a single-frequency compound-ring erbium-doped fiber laser is greatly improved by canceling the associated frequency dithering. This is achieved by exploiting the filter feature of an optical fiber compound-ring resonator to produce a net resultant intensity modulation. The theory of this cancellation method, derived from the phase resonant condition of the compound-ring resonator, shows that a full cancellation of the frequency dithering can be attained when two antiphase dithers are applied. Experimentally, the frequency jitter of the laser is greatly suppressed and the linewidth is less than 5 kHz.
Genomic Sequence Comparisons, 1987-2003 Final Report (2004)

This project was to develop new DNA sequencing and RNA and protein quantitation methods and related genome annotation tools. The project began in 1987 with the development of multiplex sequencing (published in Science in 1988), and one of the first automated sequencing methods. This lead to the first commercial genome sequence in 1994 and to the establishment of the main commercial participants (GTC then Agencourt) in the public DOE/NIH genome project. In collaboration with GTC we contributed to one of the first complete DOE genome sequences, in 1997, that of Methanobacterium thermoautotropicum, a species of great relevance to energy-rich gas production.
Modeling urban peer-to-peer channel characteristics for the 700 MHz and 4.9 GHz public safety bands (2012)

We report on models developed for peer-to-peer (ground-based) wireless channels for an urban environment in the 700 MHz and 4.9 GHz bands, both allocated for public safety and “emergency responder” applications. Results are based upon measurements taken in downtown Denver, CO for link distances up to approximately 100 m. Heretofore, measurement-based models for an urban environment in these bands and for low antenna heights have not been developed. Our measurements employed a vector network analyzer, from which log-distance models for path loss and dispersive channel models have been extracted. Our dispersive channel models employ a statistical algorithm for the number of multipath components, previously used only in indoor settings. The channel models should be useful for public safety communication system designers.
Instrument design and characterization of the Millimeter Bolometer Array Camera on the Atacama Cosmology Telescope (2008)

The Millimeter Bolometer Array Camera (MBAC) was commissioned in the fall of 2007 on the new 6-meter&#13;\nAtacama Cosmology Telescope (ACT). The MBAC on the ACT will map the temperature anisotropies of the&#13;\nCosmic Microwave Background (CMB) with arc-minute resolution. For this ̄rst observing season, the MBAC&#13;\ncontained a di®raction-limited, 32 by 32 element, focal plane array of Transition Edge Sensor (TES) bolometers&#13;\nfor observations at 145 GHz. This array was coupled to the telescope with a series of cold, refractive, reimaging&#13;\noptics. To meet the performance speci ̄cations, the MBAC employs four stages of cooling using closed-cycle&#13;\n3He/4He sorption fridge systems in combination with pulse tube coolers. In this paper we present the design of&#13;\nthe instrument and discuss its performance during the ̄rst observing season. Finally, we report on the status&#13;\nof the MBAC for the 2008 observing season, when the instrument will be upgraded to a total of three separate&#13;\n1024-element arrays at 145 GHz, 220 GHz and 280 GHz.
X-ray photoelectron spectroscopy study of fluorine-treated YBa2Cu3O7−δ crystals (1990)

An x-ray photoelectron-spectroscopy study of flux-grown YBa2Cu3O7−δ crystals left in moist atmospheric conditions has shown some aspects of the degradation process. Besides peaks which correspond to YO and BaO bonding in the superconducting phase, higher binding-energy components can be attributed to BaCO3, YOH, and/or YCO3 bonding. An x-ray photoreduction of the copper species is observed in the ultrahigh vacuum. Fluorine-gas treatments carried out at low temperature drastically modify the surface properties of the crystals. The peaks attributed to MO bonding (M=Y, Ba, or Cu) disappear and are substituted by MF bonding with a subsequent increase in Eb. In the F 1s region, the peak corresponding to those bondings is observed around Eb ≂684.5 eV, a value which is in agreement with those claimed for the corresponding inorganic fluorides. The signature of those surface fluorides remains, even when the samples are left for long periods in moist air. Within the F 1s envelope, chemisorbed fluoro species with Eb ≂686.5 eV are observed, especially when the fluorination process is performed at room temperature. These species are eliminated by vacuum annealing at 350 °C. In specific conditions, a high-binding-energy contribution arises (Eb ≂689 eV) which can be ascribed to the formation of surface ‘‘carbon fluoride.’’