gebhart/patrepeval huggingface dataset:
Inferring epidemiologic dynamics from viral evolution: 2014–2015 Eurasian/North American highly pathogenic avian influenza viruses exceed transmission threshold, R0 = 1, in wild birds and poultry in North America (2017)

Highly pathogenic avian influenza virus (HPAIV) is a multihost pathogen with lineages that pose health risks for domestic birds, wild birds, and humans. One mechanism of intercontinental HPAIV spread is through wild bird reservoirs, and wild birds were the likely sources of a Eurasian (EA) lineage HPAIV into North America in 2014. The introduction resulted in several reassortment events with North American (NA) lineage low-pathogenic avian influenza viruses and the reassortant EA/NA H5N2 went on to cause one of the largest HPAIV poultry outbreaks in North America. We evaluated three hypotheses about novel HPAIV introduced into wild and domestic bird hosts: (i) transmission of novel HPAIVs in wild birds was restricted by mechanisms associated with highly pathogenic phenotypes; (ii) the HPAIV poultry outbreak was not self-sustaining and required viral input from wild birds; and (iii) reassortment of the EA H5N8 generated reassortant EA/NA AIVs with a fitness advantage over fully Eurasian lineages in North American wild birds. We used a time-rooted phylodynamic model that explicitly incorporated viral population dynamics with evolutionary dynamics to estimate the basic reproductive number (<i>R</i><sub>0</sub>) and viral migration among host types in domestic and wild birds, as well as between the EA H5N8 and EA/NA H5N2 in wild birds. We did not find evidence to support hypothesis (i) or (ii) as our estimates of the transmission parameters suggested that the HPAIV outbreak met or exceeded the threshold for persistence in wild birds (<i>R</i><sub>0</sub> > 1) and poultry (<i>R</i><sub>0</sub> ≈ 1) with minimal estimated transmission among host types. There was also no evidence to support hypothesis (iii) because <i>R</i><sub>0</sub> values were similar among EA H5N8 and EA/NA H5N2 in wild birds. Our results suggest that this novel HPAIV and reassortments did not encounter any transmission barriers sufficient to prevent persistence when introduced to wild or domestic birds.
Inflammation, Stem Cells, and the Aging Hypothalamus (2017)

The aging hypothalamus has been hypothesized to play a key role in vertebrate aging. Increased inflammation in microglial cells during aging reduces the number of neural stem cells (NSCs) in the mediobasal region of the hypothalamus. Ectopic brain-specific expression of SIRT1 and localized hypothalamic expression of a dominantly acting nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) inhibitor to microglia or to NSCs extend life span in mice. NSCs in the hypothalamus secrete miRNA-containing exosomes and gonadotropin-releasing hormone (GnRH) that oppose aging-associated neurological and skeletomuscular dysfunction. These results suggest that stem cells are not mere repositories of future differentiated cells, but can also be active physiological effectors. Development of drugs that attenuate microglial inflammation and/or promoted maintenance of NSC viability may have significant utility for extending health and life span.
JP-CoMP with antenna selection for multi-carrier C-RAN with finite backhaul capacity (2017)

We consider a multi-carrier joint processing (JP) coordinated multi-point (CoMP) cellular system wherein the beamformers are designed by a centralized controller (CC). Those are subsequently fed back to the respective base stations (BSs) via finite capacity backhaul link. Hence, we design transmit beamformers at the CC that associate users to BSs depending on their backhaul capacity and users channel state to address this problem. Upon identifying the active links, user multiplexing and scheduling over spatial and frequency dimensions are performed in conjunction with the beamformer design for all BSs subject to the objective of minimizing the number of backlogged packets at the CC. Since the beamformers are notified to the respective BSs along with the data, the backhaul utilization must include the overhead incurred by the quantized beamformers, which has higher precision as it is used by all data symbols transmitted over a coherence block. In this paper, we assume fixed quantization levels for each complex entry in the beamformers. Therefore, we select a subset of entries for each beamformer to reduce the overhead incurred by the active antennas, which when removed has the minimal impact on the user rate. With the above mentioned constraints and requirements, the beamformer design becomes a nonconvex combinatorial problem. Therefore, we provide a solution for the proposed formulation by employing successive convex approximation technique to handle the nonconvexity and the combinatorial search involving binary variables are replaced by a linear bounds along with a sparsity inducing term in the objective. The proposed method is useful only when the backhaul usage due to the beamformers is significantly larger when compared to the overhead incurred by the active users data. Numerical results are provided to illustrate the performance.
Fate and metabolism of isopropylphenyl diphenyl phosphate in freshwater sediments (1984)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTFate and metabolism of isopropylphenyl diphenyl phosphate in freshwater sedimentsMichael A. Heitkamp, James N. Huckins, Jimmie D. Petty, and James L. JohnsonCite this: Environ. Sci. Technol. 1984, 18, 6, 434–439Publication Date (Print):June 1, 1984Publication History Published online1 May 2002Published inissue 1 June 1984https://pubs.acs.org/doi/10.1021/es00124a008https://doi.org/10.1021/es00124a008research-articleACS PublicationsRequest reuse permissionsArticle Views151Altmetric-Citations18LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Computationally Assisted Assignment of Kahalalide Y Configuration Using an NMR-Constrained Conformational Search (2013)

Assignment of the absolute configuration of cyclic peptides frequently yields challenges, leaving one or more stereogenic centers unassigned due to small quantities of sample and the limited utility of Marfey's or other methods for assigning amino or hydroxy acids. Here, we report isolation of kahalalide Y (1) from Bryopsis pennata for the first time; in addition, the application of a combination of molecular modeling and NOE distance constraint calculations was utilized to determine the conformation of 1 and the absolute configuration of the final stereogenic center of 1. Using the Schrödinger suite, the structure of 1 was sketched in Maestro and minimized using the OPLS2005 force field in Macromodel. A conformational search was performed separately for structures having an R or S configuration at C-3 of the beta-hydroxy fatty acid subunit that completes the cyclic scaffold of 1, after which multiple minimizations for all generated conformers were carried out. The lowest energy conformers of R and S stereoisomers were then subjected to B3LYP geometry optimizations including solvent effects. The S stereoisomer was shown to be in excellent agreement with the NOE-derived distance constraints and hydrogen-bonding stability studies.
Temperature and Heater Responses during Transition between Radiant and Incubator Thermal Environment in Newborn Preterm Lambs (2001)

These data suggest the Versalet provides similar thermal stability to traditional devices, with fewer adverse events associated with the lack of physical movement between warming configurations. The impact of this device on the care of the preterm neonate will be evaluated in a clinical trial.
Yersinia enterocolitica biotype 1 in South Africa. (1979)

Two clinical isolates of Yersinia enterocolitica biotype 1, positive for indole and lecithinase production, xylose and salicin fermentation, and aesculin hydrolysis, are reported. One strain, serotype 0 6, was recovered from a healthy food handler, while the other, serotype 0 5, was associated with a diarrhoeal illness in a 1-year-old child. This is the first report of either of these serotypes from human material in South Africa.
DNA immunization combined with scFv phage display identifies antagonistic GCGR specific antibodies and reveals new epitopes on the small extracellular loops (2016)

The identification of functional monoclonal antibodies directed against G-protein coupled receptors (GPCRs) is challenging because of the membrane-embedded topology of these molecules. Here, we report the successful combination of llama DNA immunization with scFv-phage display and selections using virus-like particles (VLP) and the recombinant extracellular domain of the GPCR glucagon receptor (GCGR), resulting in glucagon receptor-specific antagonistic antibodies. By immunizing outbred llamas with plasmid DNA containing the human GCGR gene, we sought to provoke their immune system, which generated a high IgG1 response. Phage selections on VLPs allowed the identification of mAbs against the extracellular loop regions (ECL) of GCGR, in addition to multiple VH families interacting with the extracellular domain (ECD) of GCGR. Identifying mAbs binding to the ECL regions of GCGR is challenging because the large ECD covers the small ECLs in the energetically most favorable 'closed conformation' of GCGR. Comparison of Fab with scFv-phage display demonstrated that the multivalent nature of scFv display is essential for the identification of GCGR specific clones by selections on VLPs because of avid interaction. Ten different VH families that bound 5 different epitopes on the ECD of GCGR were derived from only 2 DNA-immunized llamas. Seven VH families demonstrated interference with glucagon-mediated cAMP increase. This combination of technologies proved applicable in identifying multiple functional binders in the class B GPCR context, suggesting it is a robust approach for tackling difficult membrane proteins.
What is the outcome of treatment for osteolysis? (2008)

Periprosthetic osteolysis secondary to wear-induced particle generation is a common long-term complication of hip and knee replacement and frequently results in the need for revision surgery. Management of significant bone defects remains a surgical challenge. Surgical intervention must address the wear particle generator (usually, but not always, the bearing surface), the osteolytic defects, and implant-related issues, primarily fixation and alignment. Indications for surgical intervention in the absence of loosening and pain are not well established. In general, patient age and activity level, the location and size of the osteolytic defect, and the clinical record of the implant system will dictate treatment choices.
Miniaturized low profile dual-band antenna enabled by a novel two-layered metasurface loaded with CSRRs and rectangular patches (2016)

In this paper a novel two-layered metasurface (MS) based antenna is proposed and simulated results are presented. Using the proposed MS as an artificial ground plane for a monopole antenna, the integrated antenna realizes both size miniaturization and dual-band functionality. The footprint of the proposed integrated antenna is only 0. 06λq with two operation bands around 4.1 and 5.1 GHz.
SIDE-LOOKING RADAR MOSAICKING EXPERIMENT (1976)

A block of 24 overlapping synthetic aperture side-looking radar images flown over a well mapped area of about 90,000 sq km provided an opportunity to evaluate the mapping accuracy achieved in current radar mosaicking projects. The maps of scale 1:24,000 that are available in the imaged area permitted the study of the geometric errors of the radar mosaics and of individual radar strips. An estimate was obtained for the effect of the distribution and density of ground control points and for the accuracy of different mosaicking methods that are currently employed with synthetic aperture radar images. It is shown that a successful radar mosaicking process requires the elimination of image errors of up to several kilometers. These errors are introduced as a result of the limited precision of the inertial aircraft navigation. An example of a radar mapping effort in which the navigation errors could be eliminated is presented. The resulting radar mosaics have residual RMS mapping errors of planimetry of about plus or minus 150 m.
A volatile-by-default JVM for server applications (2017)

A *memory consistency model* (or simply *memory model*) defines the possible values that a shared-memory read may return in a multithreaded programming language. Choosing a memory model involves an inherent performance-programmability tradeoff. The Java language has adopted a *relaxed* (or *weak*) memory model that is designed to admit most traditional compiler optimizations and obviate the need for hardware fences on most shared-memory accesses. The downside, however, is that programmers are exposed to a complex and unintuitive semantics and must carefully declare certain variables as `volatile` in order to enforce program orderings that are necessary for proper behavior. This paper proposes a simpler and stronger memory model for Java through a conceptually small change: *every* variable has `volatile` semantics by default, but the language allows a programmer to tag certain variables, methods, or classes as `relaxed` and provides the current Java semantics for these portions of code. This *volatile-by-default* semantics provides *sequential consistency* (SC) for all programs by default. At the same time, expert programmers retain the freedom to build performance-critical libraries that violate the SC semantics. At the outset, it is unclear if the `volatile`-by-default semantics is practical for Java, given the cost of memory fences on today's hardware platforms. The core contribution of this paper is to demonstrate, through comprehensive empirical evaluation, that the `volatile`-by-default semantics is arguably acceptable for a predominant use case for Java today -- server-side applications running on Intel x86 architectures. We present VBD-HotSpot, a modification to Oracle's widely used HotSpot JVM that implements the `volatile`-by-default semantics for x86. To our knowledge VBD-HotSpot is the first implementation of SC for Java in the context of a modern JVM. VBD-HotSpot incurs an average overhead versus the baseline HotSpot JVM of 28% for the Da Capo benchmarks, which is significant though perhaps less than commonly assumed. Further, VBD-HotSpot incurs average overheads of 12% and 19% respectively on standard benchmark suites for big-data analytics and machine learning in the widely used Spark framework.
Automated Control of Injection Times for Unattended Acquisition of Multiplexed Individual Ion Mass Spectra (2022)

Charge detection mass spectrometry (CDMS) provides mass domain spectra of large and highly heterogeneous analytes. Over the past few years, we have multiplexed CDMS on Orbitrap instruments, an approach termed Individual Ion Mass Spectrometry (I<sup>2</sup>MS). Until now, I<sup>2</sup>MS required manual adjustment of injection times to collect spectra in the individual ion regime. To increase sample adaptability, enable online separations, and reduce the barrier for entry, we report an automated method for adjusting ion injection times in I<sup>2</sup>MS for image current detectors like the Orbitrap. Automatic Ion Control (AIC) utilizes the density of signals in the <i>m</i>/<i>z</i> domain to adjust an ensemble of ions down to the individual ion regime in real-time. The AIC technique was applied to both denatured and native proteins yielding high quality data without human intervention directly in the mass domain.
Additional file 1: of Characterization of the human T cell response to in vitro CD27 costimulation with varlilumab (2015)

Multiplexed biomarker analysis showing modulation of Th1/Th2 cytokines, chemokines and growth factors post varlilumab stimulation.
Learning Gaze Transitions from Depth to Improve Video Saliency Estimation (2017)

In this paper we introduce a novel Depth-Aware Video Saliency approach to predict human focus of attention when viewing videos that contain a depth map (RGBD) on a 2D screen. Saliency estimation in this scenario is highly important since in the near future 3D video content will be easily acquired yet hard to display. Despite considerable progress in 3D display technologies, most are still expensive and require special glasses for viewing, so RGBD content is primarily viewed on 2D screens, removing the depth channel from the final viewing experience. We train a generative convolutional neural network that predicts the 2D viewing saliency map for a given frame using the RGBD pixel values and previous fixation estimates in the video. To evaluate the performance of our approach, we present a new comprehensive database of 2D viewing eye-fixation ground-truth for RGBD videos. Our experiments indicate that it is beneficial to integrate depth into video saliency estimates for content that is viewed on a 2D display. We demonstrate that our approach outperforms state-of-the-art methods for video saliency, achieving 15% relative improvement.
Lithium Vanadium Oxide (Li1.1V3O8) Coated with Amorphous Lithium Phosphorous Oxynitride (LiPON): Role of Material Morphology and Interfacial Structure on Resulting Electrochemistry (2017)

In the present work, lithium vanadium oxide (Li<sub>1.1</sub>V<sub>3</sub>O<sub>8</sub>) particles synthesized at two different temperatures were coated with an amorphous lithium phosphorous oxynitride (LiPON) film for the first time, and the effects of the LiPON coating on the electrochemistry of the Li<sub>1.1</sub>V<sub>3</sub>O<sub>8</sub> materials with different morphologies were systematically investigated by comparing uncoated Li<sub>1.1</sub>V<sub>3</sub>O<sub>8</sub> and Li<sub>1.1</sub>V<sub>3</sub>O<sub>8</sub> coated with LiPON of various thicknesses. Galvanostatic discharge-charge cycling revealed increased functional capacity for the LiPON-coated materials. Post-cycling electrochemical impedance spectroscopy showed that LiPON-coated Li<sub>1.1</sub>V<sub>3</sub>O<sub>8</sub> materials developed less interfacial resistance with extended cycling, rationalized by vanadium migration into the LiPON coating seen by electron energy loss spectra. Post-mortem quantitative analysis of the anodes revealed more severe vanadium dissolution for the more irregularly shaped Li<sub>1.1</sub>V<sub>3</sub>O<sub>8</sub> materials with less LiPON coverage. Thus, this study highlights the specific benefits and limitations of LiPON coatings for stabilizing a moderate voltage Li<sub>1.1</sub>V<sub>3</sub>O<sub>8</sub> cathode material under extended cycling in liquid electrolyte, and describes a generally applicable approach for comprehensive characterization of a composite electroactive material which can be used to understand interfacial transport properties in other functional systems.
Computing Machinery and Intelligence (2004)

This chapter contains sections titled: The Imitation Game, Critique of the New Problem, The Machines Concerned in the Game, Digital Computers, Universality of Digital Computers, Contrary Views on the Main Question, Learning Machines
Synthesis of cervical tissue second harmonic generation images using Markov random field modeling (2011)

This paper presents a statistical image modeling approach based on Markov random field to synthesize cervical tissue second harmonic generation (SHG) images. Binary images representing fiber and pore areas of the cervix tissue are first obtained from SHG images using an image processing pipeline consisting of noise removal, contrast enhancement and optimal thresholding. These binary images are modeled using a Markov random field whose parameters are estimated via the least squares method. The parameters are then used to synthesize fiber and pore areas of cervical tissue in the form of binary images. The effectiveness of the synthesis is demonstrated by reporting the classification outcome for two classes of cervical SHG images collected from mice at two different stages of normal pregnancy. The developed synthesis allows generation of realistic fiber and pore area binary images for cervical tissue studies.
A Distributed Filtering Architecture for Multimedia Sensors (2004)

The use of high bit-rate multimedia sensors in networked applications poses a number of scalability challenges. In this paper, we present how IRISNET, a software infrastructure for authoring wide-area sensor-enriched services, supports scalable data collection from such sensors by greatly reducing the bandwidth demands. The architecture makes a number of novel contributions. First, it enables the use of application-specific filtering of sensor feeds near their sources and provides interfaces that simplify the programming and manipulation of these widely distributed filters. Second, its sensor feed processing API, when used by multiple different services running on the same machine, automatically and transparently detects repeated computations among the services and eliminates as much of the redundancy as possible within the soft real-time constraints of the services. Third, IRISNET distinguishes between the trusted and untrusted services, and provides mechanisms to hide sensitive sensor data from the untrusted services. Using implementations of a number of real world sensor-enriched services on IRISNET, we present an evaluation of the benefits of our distributed filtering architecture. Our evaluation shows that our design can: 1) reduce the bandwidth demands of many applications to a few hundred bytes per second on each sensor, 2) support a large number of services on each sensor through the use of redundant computation elimination, and 3) address privacy/security concerns with little additional overhead. 1