gebhart/patrepeval huggingface dataset:
Software for embedded systems: serializing compilers and their applications (2007)

In order to cope with the complexity of systems, engineers are turning to software. In part, well established programming models, highly evolved tool chains, ease of software reuse, availability of open-source software, and expeditious nature of the design-compile-execute paradigm make developing a new feature in software more favorable. It is assumed that, in coming years, more than 70% of product features are going to be supported by software. 
In particular, the concurrent programming paradigm is an ideal model of computation for design of embedded systems, which often encompass inherent concurrency. The support for concurrent programming is usually provided by a real-time operating system (RTOS). Usually, an RTOS is a generic framework which can be used across a large number of processors and applications. An RTOS provides coarse grained timing support, and is loosely coupled to the running tasks. As a result, an RTOS is seldom optimized for any particular application. 
Despite of all the recent enhancements to compiler technology, current compilers have a limited understanding of tasks. While traditional compilers are efficient in using platform specific resources, and in generating an optimized instruction sequence (by extracting instruction-level parallelism), they are unable to detect parallelism at the task level. Parallelism detection is usually restricted to basic block structures, or slightly higher level constructs such as loops. 
In this thesis, we propose an alternative to an RTOS based on the idea of serializing compilers. A serializing compiler is an automated software synthesis methodology that can transform a multitasking application into an equivalent and optimized monolithic sequential code, to be compiled with the embedded processor's native optimizing compiler. The serializing compiler can analyze the tasks at compile time and generate a fine-tuned, application specific infrastructure to support multitasking, resulting in a more efficient executable than one that is intended to run on top of a generic RTOS. By having control over the application execution and context switches, the serializing compiler enables the fine grain control of task timing while enhancing overall performance. Our serializing compiler technology strengthens existing compilers, making them timing and task-aware. 
The Phantom compiler, our implementation of a serializing compiler, provides a fully automated mechanism to synthesize a single threaded, ANSI C/C++ program from a multithreaded C/C++ (extended with POSIX) program. The Phantom generated code is highly tuned for the input application. With a serializing compiler such as the Phantom compiler, it is possible to generate a multitasking infrastructure that is small in size, very efficient when context-switching, and customized for each specific application.
A Decision Theoretic Framework for Ranking using Implicit Feedback (2008)

Social ties forged in online spaces provide the basis for performing relevant self-management work that can improve an individual's illness experience, tackling aspects of self-management that are particularly difficult to meet offline. Membership in online groups can provide those living with a long-term condition with ready access to a self-management support illness workforce and illness and emotional support. The substitutability of offline illness work may be particularly important to those whose access to support offline is either limited or absent. Furthermore, such resources require little negotiation online because information and support is seemingly gifted to the community by its members.
Simultaneous sources in marine acquisition: experiences to date (2013)

A modified inversion approach is presented for the effective separation of sources in marine simultaneous shooting acquisition. The method aims to distribute all energy in the simultaneous shot records by reconstructing the individual shot records at their respective locations. The method is applied to a simulated simultaneous long offset data set, where two sources are used to acquire long offsets with conventional cables. In the second example, the performance is investigated on a data set from Western Australia, where two sources where located within close proximity, with only a small cross line distance between them. Results demonstrate that the individual sources can be separated satisfactory for both simultaneous source configurations.
Light-weight low-frequency loudspeaker (2002)

In an aerospace application, we require a very low-mass sound generator with good performance at low audio frequencies (i.e., 30–400 Hz). A number of device configurations have been explored using various actuation technologies. Two particularly interesting devices have been developed, both using ‘‘Thunder’’ transducers (Face Intl. Corp.) as the actuation component. One of these devices has the advantage of high sound output but a complex phase spectrum, while the other has somewhat lower output but a highly uniform phase. The former is particularly novel in that the actuator is coupled to a flat, compliant diaphragm supported on the edges by an inflatable tube. This results in a radiating surface with very high modal complexity. Sound pressure levels measured in the far field (25 cm) using only 200-V peak drive (one-third or its rating) were nominally 74 6 dB over the band from 38 to 330 Hz. The second device essentially operates as a stiff low-mass piston, and is more suitable for our particular application, which is exploring the use of active controlled surface covers for reducing sound levels in payload fairing regions. [Work supported by NRL/ONR Smart Blanket program.]
Therapeutic efficacy of a respiratory syncytial virus fusion inhibitor (2017)

Respiratory syncytial virus is a major cause of acute lower respiratory tract infection in young children, immunocompromised adults, and the elderly. Intervention with small-molecule antivirals specific for respiratory syncytial virus presents an important therapeutic opportunity, but no such compounds are approved today. Here we report the structure of JNJ-53718678 bound to respiratory syncytial virus fusion (F) protein in its prefusion conformation, and we show that the potent nanomolar activity of JNJ-53718678, as well as the preliminary structure-activity relationship and the pharmaceutical optimization strategy of the series, are consistent with the binding mode of JNJ-53718678 and other respiratory syncytial virus fusion inhibitors. Oral treatment of neonatal lambs with JNJ-53718678, or with an equally active close analog, efficiently inhibits established acute lower respiratory tract infection in the animals, even when treatment is delayed until external signs of respiratory syncytial virus illness have become visible. Together, these data suggest that JNJ-53718678 is a promising candidate for further development as a potential therapeutic in patients at risk to develop respiratory syncytial virus acute lower respiratory tract infection.Respiratory syncytial virus causes lung infections in children, immunocompromised adults, and in the elderly. Here the authors show that a chemical inhibitor to a viral fusion protein is effective in reducing viral titre and ameliorating infection in rodents and neonatal lambs.
Near memory data structure rearrangement (2015)

As CPU core counts continue to increase, the gap between compute power and available memory bandwidth has widened. A larger and deeper cache hierarchy benefits locality-friendly computation, but offers limited improvement to irregular, data intensive applications. In this work we explore a novel approach to accelerating these applications through in-memory data restructuring. Unlike other proposed processing-in-memory architectures, the rearrangement hardware performs data reduction, not compute offload. Using a custom FPGA emulator, we quantitatively evaluate performance and energy benefits of near-memory hardware structures that dynamically restructure in-memory data to cache-friendly layout, minimizing wasted memory bandwidth. Our results on representative irregular benchmarks using the Micron Hybrid Memory Cube memory model show speedup, bandwidth savings, and energy reduction. We present an API for the near-memory accelerator and describe the interaction between the CPU and the rearrangement hardware with application examples. The merits of an SRAM vs. a DRAM scratchpad buffer for rearranged data are explored.
Interactive Similarity Search for Video Browsing and Retrieval (2000)

We present an interactive system that allows a user to locate regions of video that are similar to a video query. Thus segments of video can be found by simply providing an example of the video of interest. The user selects a video segment for the query from either a static frame-based interface or a video player. A statistical model of the query is calculated on-the-fly, and is used to find similar regions of video. The similarity measure is based on a Gaussian model of reduced frame image transform coefficients. Similarity in a single video is displayed in the Metadata Media Player. The player can be used to navigate through the video by jumping between regions of similarity. Similarity can be rapidly calculated for multiple video files as well. These results are displayed in MBase, a Web-based video browser that allows similarity in multiple video files to be visualized simultaneously.
Requirements for Scalable DNS-Based Service Discovery (DNS-SD) / Multicast DNS (mDNS) Extensions (2015)

DNS-based Service Discovery (DNS-SD) over Multicast DNS (mDNS) is
widely used today for discovery and resolution of services and names
on a local link, but there are use cases to extend DNS-SD/mDNS to
enable service discovery beyond the local link. This document provides
a problem statement and a list of requirements for scalable DNS-SD.
Improvements in biomaterial matrices for neural precursor cell transplantation (2014)

Progress is being made in developing neuroprotective strategies for traumatic brain injuries; however, there will never be a therapy that will fully preserve neurons that are injured from moderate to severe head injuries. Therefore, to restore neurological function, regenerative strategies will be required. Given the limited regenerative capacity of the resident neural precursors of the CNS, many investigators have evaluated the regenerative potential of transplanted precursors. Unfortunately, these precursors do not thrive when engrafted without a biomaterial scaffold. In this article we review the types of natural and synthetic materials that are being used in brain tissue engineering applications for traumatic brain injury and stroke. We also analyze modifications of the scaffolds including immobilizing drugs, growth factors and extracellular matrix molecules to improve CNS regeneration and functional recovery. We conclude with a discussion of some of the challenges that remain to be solved towards repairing and regenerating the brain.
Filament-based stimulated Raman spectroscopy (2010)

A new multiplexed stimulated Raman spectroscopic technique encompassing a single-shot spectral measurement range of over 3900 cm<sup>-1</sup> is presented. Impulsive excitation of all Raman active vibrational modes present in a medium is achieved by self-compression of a laser pulse undergoing filamentation in air, creating coherent vibrational wave-packets. These wave-packets create a macroscopic polarization of the medium that imparts sidebands on a delayed narrowband probe pulse. The background-free measurement of impulsively excited Raman modes in gas-phase N<sub>2</sub>, O<sub>2</sub>, H<sub>2</sub>, CO<sub>2</sub>, toluene, ammonia, and chloroform with a spectral resolution of 25 cm<sup>-1</sup> is presented.
Smart Geo-fencing with Location Sensitive Product Affinity (2017)

Geo-fencing is a location based service that allows sending of messages to users who enter/exit a specified geographical area, known as a geo-fence. Today, it has become one of the popular location based mobile marketing strategies. However, the process of designing geo-fences is presently manual, i.e. a retailer must specify the location and the radius of area around it to setup the geo-fences. Moreover, this process does not consider the user's preference towards the targeted product/service and thus, can compromise his/her experience of the app that sends these communications. We attempt to solve this problem by presenting a novel end-to-end system for automated design of affinity based smart geo-fences. Affinity towards a product/service refers to the user's interest in a product/service. Our unique formulation to estimate affinity, using historical app usage data, is sensitive to a user's location and thus, the affinity is termed as location sensitive product affinity (LSPA). The geo-fence logic tries to capture contiguous groups of locations where the affinity high. Experiments on real world e-commerce dataset reveals that geo-fences designed by our approach performs significantly better at accurately targeting the users who are interested in a product. We thus show that, using historical app usage data, geo-fences can be designed in an automated manner and can help enterprises target interested users with better accuracy as compared to the present industry practices.
Validation of a humanized anti-EGFR variant III chimeric antigen receptor for a Phase I trial of CART-EGFRvIII in glioblastoma (2015)

Chimeric antigen receptors (CARs) are synthetic molecules designed to re-direct T cells to specific antigens; CAR-modified T cells can mediate long-term durable remissions in B cell malignancies, but expanding this platform to solid tumors requires the discovery of novel surface targets with limited expression in normal tissues. The variant III mutation of the epidermal growth factor receptor (EGFR variant III) results from an in-frame deletion of a portion of the extracellular domain. In glioblastoma, the EGFRvIII mutation is oncogenic, portends a poor prognosis, and is thought to be enriched in glioblastoma stem cells. However, because the neoepitope of EGFR variant III is based on a small peptide sequence, an antibody or single-chain variable fragment (scFv) directed to this epitope must be rigorously tested to confirm lack of cross-reactivity to the ubiquitously expressed wild-type EGFR. We chose a vector backbone encoding a second generation CAR based on efficacy of a murine scFv-based CAR in a xenograft model of glioblastoma. Next, we generated a panel of humanized scFv’s and tested their specificity and function as soluble proteins and in the form of CAR-transduced T cells; a low affinity scFv was chosen based on its specificity for EGFR variant III over wild type EGFR. The lead candidate scFv was tested in vitro for its ability to direct CAR-transduced T cells to specifically lyse, proliferate, and secrete cytokines in response to antigen-bearing targets. We further evaluated the specificity of the lead candidate CAR in vitro against EGFR expressing keratinocytes and in vivo in immunodeficient mice grafted with normal human skin; a cetuximab-based CAR served as a positive control. EGFRvIII-directed CAR-T cells were also able to control tumor growth in xenogeneic subcutaneous and orthotopic models of human EGFR variant III+ glioblastoma. We have designed a phase I clinical study of CAR T cells transduced with humanized scFv directed to EGFR variant III in patients with either residual or recurrent glioblastoma (NCT02209376).
Ginsenoside Rg1 Improves Male Copulatory Behavior Via Nitric Oxide/Cyclic Guanosine Monophosphate Pathway (2009)

Ginsenoside Rg1 improved copulatory behavior of male mice and this may attribute to its actions at both testosterone level and signal transduction pathway in corpus cavernosum. NO/cGMP pathway appeared to play a key role in mediating the effect of Rg1 on male sexual function. These experimental data provide evidence that Rg1 could be a promising new drug for erectile dysfunction and low libido.
Changes in Microstructure and Soft Magnetic Properties of an Fe<SUB>86</SUB>Zr<SUB>7</SUB>B<SUB>6</SUB>Cu<SUB>1</SUB> Amorphous Alloy upon Crystallization (1991)

In order to clarify the dominant factors for excellent soft magnetic properties of nanocrystalline bcc Fe–Zr–B alloys, we examined the change in the microstructure, soft magnetic properties and magnetostriction (λs) of an Fe86Zr7B6Cu1 amorphous alloy upon crystallization. The amorphous phase changed to a mostly single bcc phase with a grain size of about 10 nm by annealing for 3.6 ks at temperatures between 773 and 923 K. The phase transition causes a marked reduction of λs from 16.6×10−6 to an extremely low value of 10−7. The permeability (μe) also increased significantly by the transition to the nanocrystalline bcc phase and reached a maximum value of 48000 at Ta=873 K at which the λs approaches zero value. Thus, the excellent soft magnetic properties seem to result from the simultaneous satisfaction of small λs and nanocrystalline bcc structure. Consequently, it appears important for the achievement of the good soft magnetic properties that the nanocrystalline structure remains almost unchanged up to the high temperature range where the nearly zero λs value is obtained. Based on the data for the temperature dependence of magnetization and μe, it is presumed that the high thermal stability of the nanocrystalline bcc phase is due to the presence of an amorphous thin layer with higher Zr and B contents along the grain boundary of the bcc phase.
Comparison of three pattern recognition methods using broadband sonar echoes (1984)

Three target recognition methods were tested using broadband ultrasonic echoes from nine cylinders differing in material, size, and internal structure. Echoes were obtained from targets ensonified with simulated dolphin echolocation pulses, and were processed by the human auditory system, by the constant-Q filter-bank model of Chestnut et al. [J. Acoust. Soc. Am. 66, 140–147 (1979)], and by a time-domain feature model derived from descriptions of features used by humans. Humans appear to discriminate between these targets by using features related by differences in time separation and differences in relative amplitudes of each echo highlights. The filter-bank model uses a nearest-neighbor algorithm, described by Chestnut, to evaluate frequency-dependent reflection characteristics, and the time-domain model calculates distances between test and reference feature lists, where features contain time separation and amplitude information of the highlights. All systems peformed above 90% correct under ideal conditions. The filter model was adversely affected by slight changes in the configuration of the echo collection system which had no effect on the other models. Data comparing performance of the three recognition methods in noise will be discussed.
<i>In vitro</i> PHOTODYNAMIC INACTIVATION OF <i>Herpes simplex</i> VIRUS WITH SAPPHYRINS: 22 π‐ELECTRON PORPHYRIN‐LIKE MACROCYCLES (1991)

The photodynamic inactivation of HSV-1, a virus having a membranous envelope, with both a decaalkyl sapphyrin and its dicarboxy-substituted analog was studied. The decaalkyl sapphyrin was as efficient in the inactivation of HSV-1 on a per macrocycle basis as DHE, whereas the efficiency of the dicarboxy-substituted sapphyrin was approximately two orders of magnitude less. Fluorescence studies of sapphyrin's binding to liposomes and VSV suggested that the decaalkylsapphyrin bound monomerically to cholesterol-rich regions of the viral envelope, whereas its charged analog localized in a more polar environment.
Use and interpretation of microbiological assaysin periodontal diseases (1986)

This report summarizes the rationale and illustrates the use of microbiological assays for specific microorganisms such as Actinobacillus (Haemophilus) actinomycetemcomitans in periodontal diseases. Data on the prevalence and monitoring of A. actinomycetemcomitans in patients with localized juvenile periodontitis (LJP) are presented. A. actinomycetemcomitans was found in 57 of 60 LJP patients for a prevalence of 95%. Two of the three patients not demonstrating the organism had serum antibodies to A. actinomycetemcomitans suggesting that they were once infected. Large numbers of A. actinomycetemcomitans were found in two‐thirds or more of the periodontally involved sites in the LJP patients. Microbiologic and clinical data illustrates the critical need for complete eradication of this organism in order to ensure successful therapy. The general use of microbiological tests for specific microorganisms in individual periodontitis patients can be applied to: (a) determine the causative agent, (b) assess disease activity for treatment planning, (c) monitor the effects of treatment, and (d) decide on recall intervals. Bacterial culture of the subgingival flora and determination of antibiotic susceptibility is likely to be useful in patients in whom therapy has not been successful. Rapid assays are also useful in examining subjects in epidemiologic studies to determine the prevalence of pathogens in various populations, in longitudinal studies to assess the importance of various microorganisms in the etiology of periodontal disease, and to identify persons at‐risk for either the initial episode of periodontal disease or for recurrent disease. The data presented here and the review of the relevant literature strongly support the use of microbiological assays for specific microorganisms as adjuncts in the diagnosis and management of periodontal disease. It is clear that meticulous, long‐term supragingival plaque control and root planing to achieve smooth surfaces of the roots is very important for the management of most forms of periodontal disease, however, identification and monitoring of specific microorganisms represents a new approach to the management of periodontal disease and provides a rationale for treatment of the specific infections of the periodontium. Although all of the specific periodontal pathogens have not been defined, a sufficient number of important pathogens are known and testing for these organisms is, therefore, indicated. Furthermore, technologies have developed to the point where rapid microbiological tests are feasible and practical. Future developments will likely provide more efficient and improved tests. In conclusion, the rationale for assessment of several important periodontal pathogens and the present level of technology making such assessment feasible, strongly support the use of microbiologic assays as adjuncts in the clinical management of various forms of periodontal disease.
Low bit rate colour fractal video (2002)

We report real time fractal coding of 168 by 144 pixel YUV colour images using a standard 33 MHz i486 computer. The Bath fractal transform (BFT) has nearly symmetrical coding and decoding cost. When applied to square image blocks of 144 pixels, the BFT codes in 560 /spl mu/sec and decodes in 450 /spl mu/sec. The biquadratic BFT compresses individual luminance blocks typically to 0.4 bpp. Our rate buffering system manages the video bit rate and can achieve any desired overall compression. Only the blocks most in error are transmitted, and the Y, U, and V components are treated separately. The overall compression at 64 Kbps is to 0.11 bpp average with a full colour moving head sequence, equivalent to 220:1 with a 24 bpp original.