gebhart/patrepeval huggingface dataset:
Critical Role of Type 1 Cytokines in Controlling Initial Infection withBurkholderia mallei (2006)

Burkholderia mallei is a gram-negative bacterium which causes the potentially fatal disease glanders in humans; however, there is little information concerning cell-mediated immunity to this pathogen. The role of gamma interferon (IFN-gamma) during B. mallei infection was investigated using a disease model in which infected BALB/c mice normally die between 40 and 60 days postinfection. IFN-gamma knockout mice infected with B. mallei died within 2 to 3 days after infection, and there was uncontrolled bacterial replication in several organs, demonstrating the essential role of IFN-gamma in the innate immune response to this pathogen. Increased levels of IFN-gamma, interleukin-6 (IL-6), and monocyte chemoattractant protein 1 were detected in the sera of immunocompetent mice in response to infection, and splenic mRNA expression of IFN-gamma, IL-6, IL-12p35, and IL-27 was elevated 24 h postinfection. The effects of IL-18, IL-27, and IL-12 on stimulation of the rapid IFN-gamma production were investigated in vitro by analyzing IFN-gamma production in the presence of heat-killed B. mallei. IL-12 was essential for IFN-gamma production in vitro; IL-18 was also involved in induction of IFN-gamma, but IL-27 was not required for IFN-gamma production in response to heat-killed B. mallei. The main cellular sources of IFN-gamma were identified in vitro as NK cells, CD8+ T cells, and TCRgammadelta T cells. Our data show that B. mallei is susceptible to cell-mediated immune responses which promote expression of type 1 cytokines. This suggests that development of effective vaccines against glanders should target the production of IFN-gamma.
(1H-Benzotriazol-1-yloxy)tris(dimethylamino)phosphonium Hexafluorophosphate- and (1H-Benzotriazol-1-yloxy)tripyrrolidinophosphonium Hexafluorophosphate-Mediated Activation of Monophosphonate Esters: Synthesis of Mixed Phosphonate Diesters, the Reactivity of the Benzotriazolyl Phosphonic Esters vs the Reactivity of the Benzotriazolyl Carboxylic Esters (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXT(1H-Benzotriazol-1-yloxy)tris(dimethylamino)phosphonium Hexafluorophosphate- and (1H-Benzotriazol-1-yloxy)tripyrrolidinophosphonium Hexafluorophosphate-Mediated Activation of Monophosphonate Esters: Synthesis of Mixed Phosphonate Diesters, the Reactivity of the Benzotriazolyl Phosphonic Esters vs the Reactivity of the Benzotriazolyl Carboxylic EstersJean-Marc Campagne, Jacques Coste, and Patrick JouinCite this: J. Org. Chem. 1995, 60, 16, 5214–5223Publication Date (Print):August 1, 1995Publication History Published online1 May 2002Published inissue 1 August 1995https://pubs.acs.org/doi/10.1021/jo00121a045https://doi.org/10.1021/jo00121a045research-articleACS PublicationsRequest reuse permissionsArticle Views1134Altmetric-Citations59LEARN 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
Analyzing CUDA workloads using a detailed GPU simulator (2009)

Modern Graphic Processing Units (GPUs) provide sufficiently flexible programming models that understanding their performance can provide insight in designing tomorrow's manycore processors, whether those are GPUs or otherwise. The combination of multiple, multithreaded, SIMD cores makes studying these GPUs useful in understanding tradeoffs among memory, data, and thread level parallelism. While modern GPUs offer orders of magnitude more raw computing power than contemporary CPUs, many important applications, even those with abundant data level parallelism, do not achieve peak performance. This paper characterizes several non-graphics applications written in NVIDIA's CUDA programming model by running them on a novel detailed microarchitecture performance simulator that runs NVIDIA's parallel thread execution (PTX) virtual instruction set. For this study, we selected twelve non-trivial CUDA applications demonstrating varying levels of performance improvement on GPU hardware (versus a CPU-only sequential version of the application). We study the performance of these applications on our GPU performance simulator with configurations comparable to contemporary high-end graphics cards. We characterize the performance impact of several microarchitecture design choices including choice of interconnect topology, use of caches, design of memory controller, parallel workload distribution mechanisms, and memory request coalescing hardware. Two observations we make are (1) that for the applications we study, performance is more sensitive to interconnect bisection bandwidth rather than latency, and (2) that, for some applications, running fewer threads concurrently than on-chip resources might otherwise allow can improve performance by reducing contention in the memory system.
Chronic obstructive pulmonary disease (2019)

Chronic obstructive pulmonary disease (COPD) is a major cause of death and disability worldwide. Recognition that the burden of this disorder will continue to increase over the next 20 years despite medical intervention has stimulated new research into the underlying mechanisms, leading to a rational basis for evaluation of existing therapies, and has suggested novel treatment approaches. Tobacco exposure remains the main but not exclusive cause of COPD. Whether the lung is injured by changes in the balance of proteases and antiproteases, tissue damage by oxidative stress, or a combination of the two is still not known. The genetic basis of susceptibility to COPD is now being studied as is the role of computed tomography in the identification of structural damage in individuals with less symptomatic disease. Clinical diagnosis still relies heavily on an appropriate history confirmed by abnormal spirometry. Smoking cessation is possible in a substantial proportion of individuals with symptoms but is most effective if withdrawal is supported by pharmacological treatment. Treatment with long-acting inhaled bronchodilators and, in more severe disease, inhaled corticosteroids reduces symptoms and exacerbation frequency and improves health status. Rehabilitation can be even more effective, at least for a year after the treatment. Recent guidelines have made practical suggestions about how to optimise these treatments and when to consider addition of oxygen, surgery, and non-invasive ventilation. Regular review of this guidance is important if future management advances are to be implemented effectively.
Targeted treatment of cancer with radiofrequency electromagnetic fields amplitude-modulated at tumor-specific frequencies (2013)

In the past century, there have been many attempts to treat cancer with low levels of electric and magnetic fields. We have developed noninvasive biofeedback examination devices and techniques and discovered that patients with the same tumor type exhibit biofeedback responses to the same, precise frequencies. Intrabuccal administration of 27.12 MHz radiofrequency (RF) electromagnetic fields (EMF), which are amplitude-modulated at tumor-specific frequencies, results in long-term objective responses in patients with cancer and is not associated with any significant adverse effects. Intrabuccal administration allows for therapeutic delivery of very low and safe levels of EMF throughout the body as exemplified by responses observed in the femur, liver, adrenal glands, and lungs. In vitro studies have demonstrated that tumor-specific frequencies identified in patients with various forms of cancer are capable of blocking the growth of tumor cells in a tissue- and tumor-specific fashion. Current experimental evidence suggests that tumor-specific modulation frequencies regulate the expression of genes involved in migration and invasion and disrupt the mitotic spindle. This novel targeted treatment approach is emerging as an appealing therapeutic option for patients with advanced cancer given its excellent tolerability. Dissection of the molecular mechanisms accounting for the anti-cancer effects of tumor-specific modulation frequencies is likely to lead to the discovery of novel pathways in cancer.
Biosynthesis of Branched-Chain Amino Acids in Yeast: Regulation of Synthesis of the Enzymes of Isoleucine and Valine Biosynthesis (1969)

Regulation of the levels of the five enzymes required for the biosynthesis of isoleucine and valine was studied in a Saccharomyces sp. When a mixture of isoleucine, valine, and leucine was added to the medium, the enzymes in the wild-type strain were repressed from about 30% (transaminase B) to about 90% (acetohydroxy acid synthetase) relative to the level in minimal medium-grown cells. Repression was also observed when threonine replaced isoleucine in the mixture but not when it replaced the other two amino acids. Significant derepression relative to the level in minimal-grown cells was not obtained by growing suitably blocked auxotrophs on medium containing limiting amounts of valine, isoleucine, or leucine.
Video Segmentation by Tracking Many Figure-Ground Segments (2013)

We propose an unsupervised video segmentation approach by simultaneously tracking multiple holistic figure-ground segments. Segment tracks are initialized from a pool of segment proposals generated from a figure-ground segmentation algorithm. Then, online non-local appearance models are trained incrementally for each track using a multi-output regularized least squares formulation. By using the same set of training examples for all segment tracks, a computational trick allows us to track hundreds of segment tracks efficiently, as well as perform optimal online updates in closed-form. Besides, a new composite statistical inference approach is proposed for refining the obtained segment tracks, which breaks down the initial segment proposals and recombines for better ones by utilizing high-order statistic estimates from the appearance model and enforcing temporal consistency. For evaluating the algorithm, a dataset, SegTrack v2, is collected with about 1,000 frames with pixel-level annotations. The proposed framework outperforms state-of-the-art approaches in the dataset, showing its efficiency and robustness to challenges in different video sequences.
A novel cache design for vector processing (1992)

This paper introduces an innovative cache design for vector computers, called prime-mapped cache. By utilizing the special properties of a Mersenne prime, the new design does not increase the critical path length of a processor, nor does it increase the cache access time as compared to a direct-mapped cache. The prime-mapped cache minimizes cache miss ratio caused by line interferences that have been shown to be critical for numerical applications by previous investigators. We show that significant performance gains are possible by adding the proposed cache memory into an existing vector computer provided that application programs can be blocked. The performance gain will increase with the increase of the speed gap between processors and memories. We develop an analytical performance model based on a generic vector computation model to study the performance of the design. Our preliminary performance analysis on various vector access patterns shows that the prime-mapped cache can provide as much as a factor of 2 to 3 performance improvement over the conventional direct-mapped cache in the vector processing environment. Moreover, the additional hardware cost introduced by the new mapping scheme is negligible.
Epilepsy and the older person (1995)

Epilepsy is twice as common in elderly people than in the population as a whole. But would you know what to do if one of your patients had a seizure? Epilepsy nurse specialist Carina Mack provides an invaluable update
A Fast Mask Projection Stereolithography Process for Fabricating Digital Models in Minutes (2012)

The purpose of this paper is to present a direct digital manufacturing (DDM) process that is an order of magnitude faster than other DDM processes that are currently available. The developed process is based on a mask-image-projection-based stereolithography (MIP-SL) process, in which a digital micromirror device (DMD) controls projection light to selectively cure liquid photopolymer resin. In order to achieve high-speed fabrication, we investigate the bottom-up projection system in the MIP-SL process. A two-way linear motion approach has been developed for the quick spreading of liquid resin into uniform thin layers. The system design and related settings for achieving a fabrication speed of a few seconds per layer are presented. Additionally, the hardware, software, and material setups for fabricating three-dimensional (3D) digital models are presented. Experimental studies using the developed testbed have been performed to verify the effectiveness and efficiency of the presented fast MIP-SL process. The test results illustrate that the newly developed process can build a moderately sized part within minutes instead of hours that are typically required.
Design of flash-based DBMS (2007)

The popularity of high-density flash memory as data storage media has increased steadily for a wide spectrum of computing devices such as PDA's, MP3 players, mobile phones and digital cameras. More recently, computer manufacturers started launching new lines of mobile or portable computers that did away with magnetic disk drives altogether, replacing them with tens of gigabytes of NAND flash memory. Like EEPROM and magnetic disk drives, flash memory is non-volatile and retains its contents even when the power is turned off. As its capacity increases and price drops, flash memory will compete more successfully with lower-end, lower-capacity disk drives. It is thus not inconceivable to consider running a full database system on the flash-only computing platforms or running an embedded database system on the lightweight computing devices. In this paper, we present a new design called in-page logging (IPL) for flash memory based database servers. This new design overcomes the limitations of flash memory such as high write latency, and exploits unique characteristics of flash memory to achieve the best attainable performance for flash-based database servers. We show empirically that the IPL approach can yield considerable performance benefit over traditional design for disk-based database servers. We also show that the basic design of IPL can be elegantly extended to support transactional database recovery.
Pleiotropic changes resulting from depletion of Era, an essential GTP‐binding protein in Escherichia coli (1991)

Phenotypic analysis of a temperature-sensitive era mutant strain indicates that Escherichia coli cells depleted of Era undergo many physiological changes. At 43 degrees C, a completely non-permissive temperature, growth is arrested because of loss of the gene and depletion of the Era protein. Depletion of Era at 43 degrees C results in depressed synthesis of heat-shock proteins DnaK, GroEL/ES, D33.4 and C62.5, lack of thermal induction of ppGpp pool levels, and increased capacity for carbon source metabolism through the citric acid cycle. Thus, in addition to inhibition of cell growth and viability, loss of Era function results in pleiotropic changes including abnormal adaptation to thermal stress.
Safety and immunogenicity of intramuscular and intravaginal delivery of HIV‐1 DNA constructs to infant chimpanzees (1997)

Any global strategy for controlling the human immunodeficiency virus (HIV) epidemic is likely to rely heavily on immunization of infants and children. Given the well-documented differences in children's responses to traditional vaccines, we initiated this study to extend our findings on DNA vaccination of adult chimpanzees to immunologically immature infant chimpanzees. Our findings were consistent with our previous work in adults as we observed that the DNA vaccines used here were both well tolerated and immunogenic within weeks of the initial vaccination.
Spatial Impulse Response Rendering I: Analysis and Synthesis (2005)

Spatial impulse response rendering (SIRR) is a recent technique for the reproduction of room acoustics with a multichannel loudspeaker system. SIRR analyzes the time-dependent direction of arrival and diffuseness of measured room responses within frequency bands. Based on the analysis data, a multichannel response suitable for reproduction with any chosen surround loudspeaker setup is synthesized. When loaded to a convolving reverberator, the synthesized responses create a very natural perception of space corresponding to the measured room. A technical description of the analysis-synthesis method is provided. Results of formal subjective evaluation and further analysis of SIRR are presented in a companion paper to be published in JAES in 2006 Jan./Feb.
The Lit Sphere: A Model for Capturing NPR Shading from Art (2001)

While traditional graphics techniques provide for the realistic display of three-dimensional objects, these methods often lack the flexibility to emulate expressive effects found in the works of artists such as Michelangelo and Cezanne. We introduce a technique for capturing custom artistic shading models from sampled art work. Our goal is to allow users to easily generate shading models which give the impression of light, depth, and material properties as accomplished by artists. Our system provides real-time feedback to immediately illustrate aesthetic choices in shading model design, and to assist the user in the exploration of novel viewpoints. We describe rendering algorithms which are easily incorporated into existing shaders, making non-photorealistic rendering of materials such as skin, metal, or even painted objects fast and simple. The flexibility of these methods for generating shading models enables users to portray a large range of materials as well as to capture the look and feel of a work of art. (Color images can be found at http://www.cs.utah.edu/npr/papers/LitSphere_HTML.)
Metal-directed self-assembly of two- and three-dimensional synthetic receptors (1998)

This article reviews recent progress in the study of the transition-metal mediated self-assembly of two- and three-dimensional synthetic receptors. Whereas macrocyclization under kinetic control is undoubtedly an unfavorable process, the self-assembly strategy offers quite efficient methods for constructing macrocycles under thermodynamic control. In particular, cis-protected Pd(II) and Pt(II) blocks are quite effective in obtaining the cyclic framework from simple molecules. Examples disclosed in this article are spontaneously assembled in quantitative yields by just mixing component molecules. This approach is successfully applied to the construction of cage compounds. The self-assembly of nanosized macrocycles and cages is also discussed.
Hodgkin's Lymphoma Cell Lines Express a Fusion Protein Encoded by Intergenically Spliced mRNA for the Multilectin Receptor DEC-205 (CD205) and a Novel C-type Lectin Receptor DCL-1 (2003)

Classic Hodgkin's lymphoma (HL) tissue contains a small population of morphologically distinct malignant cells called Hodgkin and Reed-Sternberg (HRS) cells, associated with the development of HL. Using 3'-rapid amplification of cDNA ends (RACE) we identified an alternative mRNA for the DEC-205 multilectin receptor in the HRS cell line L428. Sequence analysis revealed that the mRNA encodes a fusion protein between DEC-205 and a novel C-type lectin DCL-1. Although the 7.5-kb DEC-205 and 4.2-kb DCL-1 mRNA were expressed independently in myeloid and B lymphoid cell lines, the DEC-205/DCL-1 fusion mRNA (9.5 kb) predominated in the HRS cell lines (L428, KM-H2, and HDLM-2). The DEC-205 and DCL-1 genes comprising 35 and 6 exons, respectively, are juxtaposed on chromosome band 2q24 and separated by only 5.4 kb. We determined the DCL-1 transcription initiation site within the intervening sequence by 5'-RACE, confirming that DCL-1 is an independent gene. Two DEC-205/DCL-1 fusion mRNA variants may result from cotranscription of DEC-205 and DCL-1, followed by splicing DEC-205 exon 35 or 34-35 along with DCL-1 exon 1. The resulting reading frames encode the DEC-205 ectodomain plus the DCL-1 ectodomain, the transmembrane, and the cytoplasmic domain. Using DCL-1 cytoplasmic domain-specific polyclonal and DEC-205 monoclonal antibodies for immunoprecipitation/Western blot analysis, we showed that the fusion mRNA is translated into a DEC-205/DCL-1 fusion protein, expressed in the HRS cell lines. These results imply an unusual transcriptional control mechanism in HRS cells, which cotranscribe an mRNA containing DEC-205 and DCL-1 prior to generating the intergenically spliced mRNA to produce a DEC-205/DCL-1 fusion protein.
DIX Domains of Dvl and Axin Are Necessary for Protein Interactions and Their Ability To Regulate β-Catenin Stability (1999)

The N-terminal region of Dvl-1 (a mammalian Dishevelled homolog) shares 37% identity with the C-terminal region of Axin, and this related region is named the DIX domain. The functions of the DIX domains of Dvl-1 and Axin were investigated. By yeast two-hybrid screening, the DIX domain of Dvl-1 was found to interact with Dvl-3, a second mammalian Dishevelled relative. The DIX domains of Dvl-1 and Dvl-3 directly bound one another. Furthermore, Dvl-1 formed a homo-oligomer. Axin also formed a homo-oligomer, and its DIX domain was necessary. The N-terminal region of Dvl-1, including its DIX domain, bound to Axin directly. Dvl-1 inhibited Axin-promoted glycogen synthase kinase 3beta-dependent phosphorylation of beta-catenin, and the DIX domain of Dvl-1 was required for this inhibitory activity. Expression of Dvl-1 in L cells induced the nuclear accumulation of beta-catenin, and deletion of the DIX domain abolished this activity. Although expression of Axin in SW480 cells caused the degradation of beta-catenin and reduced the cell growth rate, expression of an Axin mutant that lacks the DIX domain did not affect the level of beta-catenin or the growth rate. These results indicate that the DIX domains of Dvl-1 and Axin are important for protein-protein interactions and that they are necessary for the ability of Dvl-1 and Axin to regulate the stability of beta-catenin.
Lack of Effect of Coumarin in Women with Lymphedema after Treatment for Breast Cancer (1999)

Coumarin is not effective therapy for women who have lymphedema of the arm after treatment for breast cancer.