gebhart/patrepeval huggingface dataset:
Exosomes from HIV-1-infected Cells Stimulate Production of Pro-inflammatory Cytokines through Trans-activating Response (TAR) RNA (2015)

HIV-1 infection results in a chronic illness because long-term highly active antiretroviral therapy can lower viral titers to an undetectable level. However, discontinuation of therapy rapidly increases virus burden. Moreover, patients under highly active antiretroviral therapy frequently develop various metabolic disorders, neurocognitive abnormalities, and cardiovascular diseases. We have previously shown that exosomes containing trans-activating response (TAR) element RNA enhance susceptibility of undifferentiated naive cells to HIV-1 infection. This study indicates that exosomes from HIV-1-infected primary cells are highly abundant with TAR RNA as detected by RT-real time PCR. Interestingly, up to a million copies of TAR RNA/μl were also detected in the serum from HIV-1-infected humanized mice suggesting that TAR RNA may be stable in vivo. Incubation of exosomes from HIV-1-infected cells with primary macrophages resulted in a dramatic increase of proinflammatory cytokines, IL-6 and TNF-β, indicating that exosomes containing TAR RNA could play a direct role in control of cytokine gene expression. The intact TAR molecule was able to bind to PKR and TLR3 effectively, whereas the 5' and 3' stems (TAR microRNAs) bound best to TLR7 and -8 and none to PKR. Binding of TAR to PKR did not result in its phosphorylation, and therefore, TAR may be a dominant negative decoy molecule in cells. The TLR binding through either TAR RNA or TAR microRNA potentially can activate the NF-κB pathway and regulate cytokine expression. Collectively, these results imply that exosomes containing TAR RNA could directly affect the proinflammatory cytokine gene expression and may explain a possible mechanism of inflammation observed in HIV-1-infected patients under cART.
Surface chemistry of Ru: relevance to optics lifetime in EUVL (2007)

Ruthenium capping layers ~2 nm thick are used to protect and extend the lifetimes of Si/Mo multilayer mirrors used in extreme ultraviolet lithography (EUVL) applications. In the present work, we use ultrahigh vacuum surface science methods to address two aspects of Ru surface chemistry: (a) use of atomic hydrogen to remove oxygen from O-covered Ru, and (b) the effects of a model background hydrocarbon gas (methyl methacrylate, MMA) on the accumulation of carbon on a Ru(10 1010) single crystal surface. Atomic H is very effective in removing O from Ru even at 300K; the interpretation is that H reacts directly with adsorbed O to make OH, and a subsequent H atom reacts with OH to make H<sub>2</sub>O, which desorbs at 300K. MMA adsorbs strongly on Ru in the first monolayer and dissociates upon heating; H2 and CO desorption products are seen upon heating from 300 to 600K, while a fractional monolayer of C remains on the surface. Physisorbed multilayers of MMA form at temperatures below ~170K. Thermal desorption of MMA dosed onto O-covered Ru shows that MMA reacts and completely removes an adsorbed O monolayer upon heating. Electron bombardment of MMA/Ru causes polymerization and also can induce accumulation of carbon - all depends on electron fluence, partial pressure of MMA, and substrate temperature.
Lymphocyte proteins in Huntington's disease: quantitative analysis by use of two-dimensional electrophoresis and computerized densitometry. (1982)

We used quantitative two-dimensional electrophoresis to study lymphocyte proteins in Hungtington's disease. Three hundred and six polypeptides from 14C-labeled, phytohemagglutinin-stimulated lymphocytes were measured for variation in relative spot density and 186 for variation in spot position by use of a computer program requiring operator interaction. Each polypeptide was measured in a total of 30 electrophoretograms from 28 individuals, including 13 with Huntington's disease, 2 at risk for it, and 13 controls. The study included two sets of identical twins and, as neurological controls, individuals with neurofibromatosis, Alzheimer's disease, or Shy-Drager syndrome. Seven protein polymorphisms were identified among the 186 most dense polypeptides of each gel, corresponding to a minimum average heterozygosity of 1.4%. Stringent criteria were used to define polymorphic proteins, including observation of at least one individual with each of two homozygous phenotypes and one with the heterozygous phenotype, demonstration of the expected gene dosage relationship by quantitative densitometry, consistency with genetic relationships, and reproducibility. One polymorphic protein showed three electrophoretically variant alleles. Our identification of seven polymorphisms among the 186 proteins measured on a single electrophoretogram illustrates the potential of this technique for performing linkage analysis in diseases of genetic origin. However, we observed no quantitative or positional protein variations that were characteristic of (i.e. specific for) Huntington's disease.
A Quantitative Structure−Property Relationship Study of the Glass Transition Temperature of OLED Materials (2003)

Organic light-emitting-diodes (OLED) materials possess great potential applications. Stability and efficiency are the two major factors to be improved toward commercialization, especially the thermal stability, because in the working device, the organic molecular materials can have high temperature. One of the most important factors, which influences the stability, is the glass transition temperature (T(g)). We employed a QSPR (quantitative structure-properties relationship) approach to establish a theoretical model to predict the glass transition temperatures of organic molecular materials. A six-parameter correlation with the squared correlation coefficient R(2) = 0.9270 and the average absolute error 8.5 K was developed for a diverse set of 73 OLED materials. All descriptors were derived solely from the chemical structures of the organic compounds. A satisfactory average absolute error of 17.9 K for a test set of 15 OLED materials makes the model very useful for the prediction of the unknown OLED materials.
A role for inositol hexakisphosphate in the maintenance of basal resistance to plant pathogens (2008)

Phytic acid (myo-inositol hexakisphosphate, InsP6) is an important phosphate store and signal molecule in plants. However, low-phytate plants are being developed to minimize the negative health effects of dietary InsP6 and pollution caused by undigested InsP6 in animal waste. InsP6 levels were diminished in transgenic potato plants constitutively expressing an antisense gene sequence for myo-inositol 3-phosphate synthase (IPS, catalysing the first step in InsP6 biosynthesis) or Escherichia coli polyphosphate kinase. These plants were less resistant to the avirulent pathogen potato virus Y and the virulent pathogen tobacco mosaic virus (TMV). In Arabidopsis thaliana, mutation of the gene for the enzyme catalysing the final step of InsP6 biosynthesis (InsP5 2-kinase) also diminished InsP6 levels and enhanced susceptibility to TMV and to virulent and avirulent strains of the bacterial pathogen Pseudomonas syringae. Arabidopsis thaliana has three IPS genes (AtIPS1-3). Mutant atips2 plants were depleted in InsP6 and were hypersusceptible to TMV, turnip mosaic virus, cucumber mosaic virus and cauliflower mosaic virus as well as to the fungus Botrytis cinerea and to P. syringae. Mutant atips2 and atipk1 plants were as hypersusceptible to infection as plants unable to accumulate salicylic acid (SA) but their increased susceptibility was not due to reduced levels of SA. In contrast, mutant atips1 plants, which were also depleted in InsP6, were not compromised in resistance to pathogens, suggesting that a specific pool of InsP6 regulates defence against phytopathogens.
Effects of a Sublethal and Transient Stress of the Endoplasmic Reticulum on the Mitochondrial Population (2015)

Endoplasmic reticulum (ER) and mitochondria are not discrete intracellular organelles but establish close physical and functional interactions involved in several biological processes including mitochondrial bioenergetics, calcium homeostasis, lipid synthesis, and the regulation of apoptotic cell death pathways. As many cell types might face a transient and sublethal ER stress during their lifetime, it is thus likely that the adaptive UPR response might affect the mitochondrial population. The aim of this work was to study the putative effects of a non-lethal and transient endoplasmic reticulum stress on the mitochondrial population in HepG2 cells. The results show that thapsigargin and brefeldin A, used to induce a transient and sublethal ER stress, rapidly lead to the fragmentation of the mitochondrial network associated with a decrease in mitochondrial membrane potential, O2 (•-) production and less efficient respiration. These changes in mitochondrial function are transient and preceded by the phosphorylation of JNK. Inhibition of JNK activation by SP600125 prevents the decrease in O2 (•-) production and the mitochondrial network fragmentation observed in cells exposed to the ER stress but has no impact on the reduction of the mitochondrial membrane potential. In conclusion, our data show that a non-lethal and transient ER stress triggers a rapid activation of JNK without inducing apoptosis, leading to the fragmentation of the mitochondrial network and a reduction of O2 (•-) production. J. Cell. Physiol. 231: 1913-1931, 2016. © 2015 Wiley Periodicals, Inc.
Stemness, fusion and renewal of hematopoietic and embryonic stem cells (2003)

Development of replacement cell therapies awaits the identification of factors that regulate nuclear reprogramming and the mechanisms that control stem cell renewal and differentiation. Once such factors and signals will begin to be elucidated, new technologies will have to be envisaged where uniform differentiation of adult or embryonic stem cells along one differentiation pathway can be induced. Controlled differentiation of stem cells will require the engineering of niches and extracellular signal combinations that would amplify a particular signaling network and allow uniform and selective differentiation. Three recent advances in stem cell research open the possibility to approach engineering studies for cell replacement therapies. Fusion events between stem cells and adult cells or between adult and embryonic stem cells have been shown to result in altered fates and nuclear reprogramming of cell hybrids. Hematopoietic stem cells were shown to require Wnt signaling in order to renew. The purification of Wnt proteins would allow their use as exogenous purified cytokines in attempts to amplify stem cells before bone marrow transplantation. The homeodomain protein Nanog has been shown to be crucial for the embryonic stem cell renewal and pluripotency. However, the cardinal question of how stemness is preserved in the early embryo and adult stem cells remains opened.
Enhancement of Microwave Absorption Characteristics in Aligned M-type Barium Ferrite Ba1-xLaxZnxFe12-x-y(Me0.5Mn0.5)yO19 (x=0.0-0.5, Me: Sn,Zr, y=1.0-3.0) by Metal Substitution. (2003)

Microwave radiation in the GHz band is increasingly being used in many various communication devices. However, this has brought about the problems of electromagnetic interference (EMI). Now M-type Ba ferrite is expected to be used as a powerful countermeasure to EMI. Our recent works have shown that M-type Ba ferrite is promising material for microwave absorber in the GHz range. The electromagnetic resonance absorption properties depend on the complex permeability μ=μ'-jμ", particularly the imaginary part μ"=Ms/2HAα(Ms: saturation magnetization, HA: anisotropy field, a: extinction coefficient). We investigated the effects of substitution composition (x) of Me for Ba (Me: La) and substitution composition (y) of Me ion (Me: Zn, Zr, Sn) for Fe3+ on the electromagnetic absorption properties of the Ba1-xLaxZnxFe12-x-y(Me0.5Mn0.5)yO19 compound. The c-axis aligned samples were formed into toroidal shapes. The magnetic properties (Ms, HA) and the resonance absorption properties (μr', μr" etc) were measured using a VSM and a network analyzer. The aligned Zr-substituted samples (x=0.0, y=1.4) showed values of HA =0.21 MAm-1, and μ'= 7.5 and μ" =7.1 that were higher than those of (TiMn) substituted samples. The matching thickness dm decreased to 0.8 mm at the matching frequency of 7.6 GHz. In the sample of x=0.0 and y=1.5, μ'=7.7 and μ" = 6.7 were obtained, and the matching thickness dm was 0.98 mm at 5.95 GHz. Also, Sn-substituted samples showed high m' and m" values of 6.3 and 6.3, respectively, and dm of 1.02mm. It is therefore concluded that Sn or Zr substitution is effective in enhancing the electromagnetic wave absorption characteristics of M-type Ba ferrite absorber.
PGTOOL: an automatic interactive program generation tool for testing new-generation memory devices (2003)

PGTOOL generates pattern and timing source files for device testing on the 1937 memory test system. Using macro files that describe the main sequence and testing specifications for patterns and timing, PGTOOL communicates this information in pictures, making programming faster, easier, and less prone to errors. The program combines automatic code generation with a graphics interface, resulting in higher-quality test programs, generated up to 87% faster than those created by conventional methods.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Microarray Innovations Technology and Experimentation (2009)

Introduction to Gene Expression Profiling with DNA Microarray Technology, M.D. Kane Introduction to Large-Scale Gene Expression Data Analysis, A. Lourdusamy, M. Ubaldi, L. Soverchia, G. Hardiman, and Roberto Ciccocioppo The Statistical Design and Analysis of Gene Expression Data, S. Jain Laboratory Automation for Microarray Experimentation, D. Gurevitch How to Evaluate a Microarray Scanner, Y. Zong, S. Zhang, Y. Wang, and Y. Shi The Role of Substrates in Microarray Experimentation and How to Choose the Correct Coating for Microarraying, R. Dietrich, D. Haines, R. Redkar, and A. Rees Towards Highly Efficient Automated Hybridizations, K. Pappaert, J. Vanderhoeven, G. Desmet, and P. Van Hummelen Characterization of Microarray Hybridization Stoichiometry, R.J.D. Rouse and G. Hardiman Data Normalization Selection, P. Stafford Methods for Assessing Microarray Performance, S.G. Oeser, S.C. Baker, E.Chudin, K.Kuhn, and T.K. McDaniel Comparison of Different Normalization Methods for Applied Biosystems Expression Array System, C. Barbacioru, Y. Wang, R. Canales, Y. Sun, D. Keys, F. Chan, K. Hunkapiller, K. Poulter, and R.R. Samaha A Systematic Comparison of Gene Expression Measurements Across Different Hybridization-Based Technologies, W.P. Kuo, F. Liu, T.-K. Jensen, S.L. Benson, C.L. Cepko, E. Hovig, and L. Ohno-Machado DNA Methylation Arrays: Methods and Analysis, N.P. Thorne, J.C. Marioni, V. Rakyan, A.E.K. Ibrahim, C. Massie, C. Curtis, J.D. Brenton, A. Murrell, and S. Tavare Electronic Microarrays: Progress toward DNA Diagnostics, H. Reese, D. Smolko, P. Swanson, and D. Hodko New Applications for Microarrays, M. Andersen, S. Warrick, and C. Adams Development of an Oligonucleotide Microarray for Mutational Analysis Using Single or Multiple Sample Hybridization, I.-J. Kim, H.C. Kang, and J.-G. Park Development of an Integrated Molecular Diagnostic Test to Identify Respiratory Viruses, F. Raymond, W.-K. Wu, and J. Corbeil Microarrays in Neuroscience, M. Ubaldi, W. Sommer, L.Soverchia, A. Lourdusamy, B. Ruggeri, R. Ciccocioppo, and G. Hardiman Optimization of Protein Array Fabrication for Establishing High Throughput Ultra-Sensitive Microarray Assays for Cancer Research, G. Hardiman, C.R. Bhasker, and R.J.D. Rouse Index
A Two-year Common Foundation Course for the BE Degree (1990)

The Bachelor of Engineering program at the University of Tasmania provides a two-year common foundation course for all engineering students. This paper outlines the history of the Tasmanian BE program and the reasons for this unusual degree of commonality. Some recent developments in the foundation program and the current structure of first and second year courses are discussed in detail. A notable feature of these courses is the use of shared teaching between Engineering and Science departments within individual subjects.
Levels of plasma neurofilament light chain and cognitive function in patients with Alzheimer or Parkinson disease (2018)

Plasma neurofilament light (NFL) has been proposed as a blood-based biomarker for neurodegeneration in Alzheimer's disease (AD) and parkinsonian disorders. However, the relationship between plasma NFL and cognitive decline in dementia due to Parkinson's disease (PD) remains to be elucidated. In this research, 119 AD, 56 mild cognitive impairment (MCI), 26 non-demented PD (PDND), and 23 Parkinson's disease dementia (PDD) patients, as well as 59 cognitively healthy controls (HC) were recruited. Each subject underwent a battery of neuropsychological testing. Plasma NFL levels were measured in duplicate using an NF-Light assay and transferred onto the Simoa platform with a home-brew kit. Plasma NFL was significantly increased in the AD group, compared with the control, MCI, PDND, and PDD groups. Plasma NFL was significantly higher in the PDD group, compared with the PDND group. High plasma NFL correlated with poor cognition in AD and PD, but not with motor symptoms in PD. Plasma NFL may represent a biomarker of cognitive decline in AD and PD, with more specificity for AD.
A Magnetically Tuned Quadrature Oscillator (2007)

Continuous frequency tuning by control of the magnetic field of a transformer - capacitor tank, in a selective oscillator, is explored in this work. A quadrature generator is built connecting two identical transformer - capacitor oscillator cells in a feedback loop. The topology itself assures the currents in the transformer windings are aligned in phase, while their relative amplitude determines, via magnetic coupling, oscillators' tank reactance, i.e., oscillation frequency. This paper introduces the idea, analyzes oscillation amplitude, frequency tuning band, phase noise, and phase accuracy, and discusses design and experiments. Prototypes, realized in 65 nm CMOS, employing MOS varactors to further extend operation bandwidth, show the following performances: 3.2 GHz and 7.3 GHz minimum and maximum oscillation frequency, respectively. Phase noise figure of merit of 176.5 dB at 3.2 GHz and 170.5 dB at 6.4 GHz is observed, with 24 mW maximum power consumption and 1.5 maximum deviation from quadrature.
Why do certain ants thrive in the urban environment (2005)

In recent years very large marine protected areas (VLMPAs) have become the dominant form of spatial protection in the marine environment. Whilst seen as a holistic and geopolitically achievable approach to conservation, there is currently a mismatch between the size of VLMPAs, and the data available to underpin their establishment and inform on their management. Habitat mapping has increasingly been adopted as a means of addressing paucity in biological data, through use of environmental proxies to estimate species and community distribution. Small-scale studies have demonstrated environmental-biological links in marine systems. Such links, however, are rarely demonstrated across larger spatial scales in the benthic environment. As such, the utility of habitat mapping as an effective approach to the ecosystem-based management of VLMPAs remains, thus far, largely undetermined. The aim of this study was to assess the ecological relevance of broadscale landscape mapping. Specifically we test the relationship between broad-scale marine landscapes and the structure of their benthic faunal communities. We focussed our work at the sub-Antarctic island of South Georgia, site of one of the largest MPAs in the world. We demonstrate a statistically significant relationship between environmentally derived landscape mapping clusters, and the composition of presence-only species data from the region. To demonstrate this relationship required specific re-sampling of historical species occurrence data to balance biological rarity, biological cosmopolitism, range-restricted sampling and fine-scale heterogeneity between sampling stations. The relationship reveals a distinct biological signature in the faunal composition of individual landscapes, attributing ecological relevance to South Georgia's environmentally derived marine landscape map. We argue therefore, that landscape mapping represents an effective framework for ensuring representative protection of habitats in management plans. Such scientific underpinning of marine spatial planning is critical in balancing the needs of multiple stakeholders whilst maximising conservation payoff.
Personality trait structure as a human universal. (1997)

Patterns of covariation among personality traits in English-speaking populations can be summarized by the five-factor model (FFM). To assess the cross-cultural generalizability of the FFM, data from studies using 6 translations of the Revised NEO Personality Inventory (P.T. Costa & R. R. McCrae, 1992) were compared with the American factor structure. German, Portuguese, Hebrew, Chinese, Korean, and Japanese samples (N = 7,134) showed similar structures after varimax rotation of 5 factors. When targeted rotations were used, the American factor structure was closely reproduced, even at the level of secondary loadings. Because the samples studied represented highly diverse cultures with languages from 5 distinct language families, these data strongly suggest that personality trait structure is universal.
A framework-based approach for automated testing of CNC firmware (2014)

The product- and technology-specific nature of embedded software components often results in a high overhead for the setup and automation of testing procedures. This paper presents the adaptation of the generic, modular Eclipse Test and Performance Tools Platform Project (TPTP) framework for managing and running automated tests and creating test reports for firmware releases of a computerized numerical control (CNC) device product. TPTP, built upon the development and user interface context of the Eclipse platform, is extended by product-specific plugins and TPTP module extensions. The actual test execution is performed remotely on CNC devices, controlled and evaluated by the testing framework. CNC firmware releases, configuration setups and the test results become manageable as TPTP resources. To facilitate modelling of test oracles and complex algorithms for CNC track evaluation, dynamic MATLAB code execution in the course of test procedures is supported.