gebhart/patrepeval huggingface dataset:
Why the –omic future of Apicomplexa should include gregarines (2020)

Abstract Gregarines, a polyphyletic group of apicomplexan parasites infecting mostly non‐vertebrates hosts, remains poorly known at taxonomic, phylogenetic and genomic levels. However, it represents an essential group for understanding evolutionary history and adaptive capacities of apicomplexan parasites to the remarkable diversity of their hosts. Because they have a mostly extracellular lifestyle, gregarines have developed other cellular developmental forms and host–parasite interactions, compared with their much better studied apicomplexan cousins, intracellular parasites of vertebrates (Hemosporidia, Coccidia, Cryptosporidia). This review highlights the promises offered by the molecular exploration of gregarines, that have been until now left on the side of the road of the comparative –omic exploration of apicomplexan parasites. Elucidating molecular bases for both their ultrastructural, functional and behavioural similarities and differences, compared with those of the typical apicomplexan models, is expected to provide entirely novel clues on the adaptive capacities developed by Apicomplexa over evolution. A challenge remains to identify which gregarines should be explored in priority, as recent metadata from open and host‐associated environments have confirmed how underestimated is our current view on true gregarine biodiversity. It is now time to turn to gregarines to widen the currently highly skewed view we have of adaptive mechanisms developed by Apicomplexa.
Reconfigurable directional couplers and junctions optically induced by nondiffracting Bessel beams (2005)

We put forward the concept of reconfigurable structures optically induced by mutually incoherent nondiffracting Bessel beams in Kerr-type nonlinear media. We address collinear couplers and X junctions and show how one can tune the switching properties of such structures by varying the intensity of the Bessel beams.
Epipolar Rectification for Autostereoscopic Camera Setup (2010)

International audience
The Neurobiology of Love. (2005)

Love is a complex neurobiological phenomenon, relying on trust, belief, pleasure and reward activities within the brain, i.e., limbic processes. These processes critically involve oxytocin, vasopressin, dopamine, and serotonergic signaling. Moreover, endorphin and endogenous morphinergic mechanisms, coupled to nitric oxide autoregulatory pathways, play a role. Naturally rewarding or pleasurable activities are necessary for survival and appetitive motivation, usually governing beneficial biological behaviors like eating, sex, and reproduction. Yet, a broad basis of common signaling and beneficial neurobiological features exists with connection to the love concept, thereby combining physiological aspects related to maternal, romantic or sexual love and attachment with other healthy activities or neurobiological states. Medical practice can make use of this concept, i.e., mind/body or integrative medicine. Thus, love, pleasure, and lust have a stress-reducing and health-promoting potential, since they carry the ability to heal or facilitate beneficial motivation and behavior. In addition, love and pleasure ensure the survival of individuals and their species. After all, love is a joyful and useful activity that encompasses wellness and feelings of well-being.
Carbon Tetrachloride Transformation on the Surface of Nanoscale Biogenic Magnetite Particles (2004)

Iron-reducing conditions in subsurface environments promote dechlorination reactions via both biotic and abiotic pathways, the latter often mediated via biologically activated minerals formed by dissimilatory iron-reducing bacteria (DIRB). Here we report the major products and pathways associated with the abiotic transformation of carbon tetrachloride (CT) by nanoscale biogenic magnetite/maghemite particles produced by the DIRB Geobacter metallireducens. Product formation and free radical/carbene trapping studies indicate that CT transformation occurs via three parallel pathways. The first pathway (hydrogenolysis) results in the formation of chloroform (45-50%) via a trichloromethyl free radical (*CCl3) and possibly a trichloromethyl carbanion (**CCl3-). The second and third pathways involve a dichlorocarbene intermediate (**CCl2), which either hydrolyzes to form CO (approximately 38%) (carbene hydrolysis), or undergoes further reduction to yield methane (8-10%) (carbene reduction). The mechanism of methane formation from **CCl2 is not known, but is speculated to involve a sequence of surface coordinated carbenoid and free radical complexes. The large fraction of relatively benign products formed by the carbene-mediated pathways suggests that magnetite/maghemite particles may have a beneficial application in the remediation of CT contaminated environments.
High-abstraction level complexity analysis and memory architecture simulations of multimedia algorithms (2005)

An appropriate complexity analysis stage is the first and fundamental step for any methodology aiming at the implementation of today's (complex) multimedia algorithms. Such a stage may have different final implementation goals such as defining a new architecture dedicated to the specific multimedia standard under study, or defining an optimal instruction set for a selected processor architecture, or to guide the software optimization process in terms of control-flow and data-flow optimization targeting a specific architecture. The complexity of nowadays multimedia standards, in terms of number of lines of codes and cross-relations among processing algorithms that are activated by specific input signals, goes far beyond what the designer can reasonably grasp from the "pencil and paper" analysis of the (software) specifications. Moreover, depending on the implementation goal different measures and metrics are required at different steps of the implementation methodology or design flow. The process of extracting the desired measures needs to be supported by appropriate automatic tools, since code rewriting, at each design stage, may result resource consuming and error prone. This paper reviews the state of the art of complexity analysis methodologies oriented to the design of multimedia systems and presents an integrated tool for automatic analysis capable of producing complexity results based on rich and customizable metrics. The tool is based on a C virtual machine that allows extracting from any C program execution the operations and data-flow information, according to the defined metrics. The tool capabilities include the simulation of virtual memory architectures. This paper shows some examples of complexity analysis results that can be yielded with the tool and presents how the tools can be used at different stages of implementation methodologies.
Computational Studies of Protons in Perovskite-Structured Oxides (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTComputational Studies of Protons in Perovskite-Structured OxidesM. Cherry, M. S. Islam, J. D. Gale, and C. R. A. CatlowCite this: J. Phys. Chem. 1995, 99, 40, 14614–14618Publication Date (Print):October 1, 1995Publication History Published online1 May 2002Published inissue 1 October 1995https://pubs.acs.org/doi/10.1021/j100040a007https://doi.org/10.1021/j100040a007research-articleACS PublicationsRequest reuse permissionsArticle Views671Altmetric-Citations78LEARN 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 options Get e-Alerts
Abstract WP101: Hypoxia Drives Anti-inflammatory Polarization of Microglia in Ischemic Stroke (2017)

Background: As the innate immune cell of the central nervous system (CNS), microglia are poised to be the first cellular responders to ischemic stroke. Microglia are capable of polarizing from a resting (M0) phenotype to a pro-inflammatory (M1) or anti-inflammatory (M2) phenotype depending on the signals these cells receive from the microenvironment. Typically cell damage through neurological injury results in a pro-inflammatory phenotype. Paradoxically, despite the cell death that occurs following ischemic stroke that presumably polarizes microglia to a pro-inflammatory phenotype, our lab and others have shown that microglia in mice are predominantly anti-inflammatory after ischemic stroke. Hypothesis: To possibly explain this anomaly, we hypothesized that hypoxia itself is a stimulus of anti-inflammatory microglia M2 polarization following ischemic stroke that overrides pro-inflammatory polarizing signals from cellular damage. Methods: We developed a novel method of culturing primary microglia from individual male and female neonatal mice. We then exposed isolated microglia to oxygen glucose deprivation (OGD, 95% nitrogen / 5% carbon dioxide) and examined the expression of M1 and M2 genes by quantitative PCR. Media was collected at 24hr and analyzed by lactate dehydrogenase (LDH) assay and ELISA. Results: We found that microglia are resistant to OGD-induced cytotoxicity, with LDH assay showing only 16% cell death after 8hr of OGD (p&lt;0.05). OGD induced a robust up-regulation of anti-inflammatory M2 genes (Interferon Regulatory Factor 4 (IRF4), 2.08±0.08-fold, p&lt;0.05; Vascular Endothelial Growth Factor (VEGF), 1.76±0.05-fold, p&lt;0.0001) immediately following OGD and also down-regulated expression of pro-inflammatory M1 genes (IRF5, 0.385±0.018-fold, p&lt;0.0001; Interleukin-1β (IL1B), 0.018±0.005-fold, p&lt;0.01; Tumor Necrosis Factor-α (TNFA), 0.345±0.024-fold, p&lt;0.0001) in both male and female microglia (n=7). ELISA of cell culture supernatant following OGD demonstrated that microglia secrete VEGF, suggesting OGD-treated microglia have anti-inflammatory functions. Conclusion: Collectively, our data suggest that hypoxia drives both male and female microglia to polarize to an anti-inflammatory M2 phenotype.
Aluminate-Based Nanostructured Luminescent Materials: Design of Processing and Functional Properties (2021)

Interest in luminescent materials has been continuously growing for several decades, looking for the development of new systems with optimized optical properties. Nowadays, research has been focused on the development of materials that satisfy specific market requirements in optoelectronics, radioelectronics, aerospace, bio-sensing, pigment applications, etc. Despite the fact that several efforts have made in the synthesis of organic luminescent materials, their poor stability under light exposure limits their use. Hence, luminescent materials based on inorganic phosphors are considered a mature topic. Within this subject, glass, glass-ceramics and ceramics have had great technological relevance, depending on the final applications. Supposing that luminescent materials are able to withstand high temperatures, have a high strength and, simultaneously, possess high stability, ceramics may be considered promising candidates to demonstrate required performance. In an ongoing effort to find a suitable synthesis method for their processing, some routes to develop nanostructured luminescent materials are addressed in this review paper. Several ceramic families that show luminescence have been intensively studied in the last few decades. Here, we demonstrate the synthesis of particles based on aluminate using the methods of sol-gel or molten salts and the production of thin films using screen printing assisted by a molten salt flux. The goal of this review is to identify potential methods to tailor the micro-nanostructure and to tune both the emission and excitation properties, focusing on emerging strategies that can be easily transferred to an industrial scale. Major challenges, opportunities, and directions of future research are specified.
Computation and Experimental Measurements of the Magnetic Fields between Filamentary Circular Coils (2015)

International audience
The Pseudomonas syringae type III effector AvrRpt2 functions downstream or independently of SA to promote virulence on Arabidopsis thaliana (2004)

Summary AvrRpt2, a Pseudomonas syringae type III effector protein, functions from inside plant cells to promote the virulence of P. syringae pv. tomato strain DC3000 ( Pst DC3000) on Arabidopsis thaliana plants lacking a functional copy of the corresponding RPS2 resistance gene. In this study, we extended our understanding of AvrRpt2 virulence activity by exploring the hypothesis that AvrRpt2 promotes Pst DC3000 virulence by suppressing plant defenses. When delivered by Pst DC3000, AvrRpt2 suppresses pathogen‐related ( PR ) gene expression during infection, suggesting that AvrRpt2 suppresses defenses mediated by salicylic acid (SA). However, AvrRpt2 promotes Pst DC3000 growth on transgenic plants expressing the SA‐degrading enzyme NahG, indicating that AvrRpt2 does not promote bacterial virulence by modulating SA levels during infection. AvrRpt2 general virulence activity does not depend on the RPM1 resistance gene, as mutations in RPM1 had no effect on AvrRpt2‐induced phenotypes. Transgenic plants expressing AvrRpt2 displayed enhanced susceptibility to Pst DC3000 strains defective in type III secretion, indicating that enhanced susceptibility of these plants is not because of suppression of defense responses elicited by other type III effectors. Additionally, avrRpt2 transgenic plants did not exhibit increased susceptibility to Peronospora parasitica and Erysiphe cichoracearum , suggesting that AvrRpt2 virulence activity is specific to P. syringae .
Pre-donation Assessment of Kidneys by Magnetic Resonance Angiography and Venography: Accuracy and Impact on Outcomes (2005)

Reports on the accuracy of magnetic resonance angiography (MRA) and magnetic resonance venography (MRV) in evaluating living donor renovasculature employ few patients or omit the consequences of inaccurate scans. We retrospectively compared intraoperative findings to MRA/MRV scans in 146 donor-recipient pairs. For detecting accessory arteries and early branching, MRA sensitivity was 57.6%, specificity 96.5%, false positive rate 3.5%, false negative rate 42.4%, positive predictive value 82.6%, negative predictive value 88.6% and overall accuracy 87.7%. By excluding clinically inconsequential accessory arteries, MRA sensitivity rose to 73.1%, specificity to 96.7% and overall accuracy to 92.5%. For MRVs, sensitivity was 56.2%, specificity 99%, false positive rate 1%, false negative rate 43.8%, positive predictive value 90%, negative predictive value 94.8% and accuracy 94.5%. Inaccurate scans were associated with prolonged donor and recipient operations and more frequently reconstructed arteries, but did not affect clinical outcomes. Because most missed accessory arteries are inconsequential, MRA is a useful, less invasive method for defining donor renovascular anatomy.
Co-designing a Lifestyle-Focused Text Message Intervention for Women After Breast Cancer Treatment: Mixed Methods Study (Preprint) (2021)

<sec> <title>BACKGROUND</title> Breast cancer is the most common cancer among women globally. Recovery from breast cancer treatment can be mentally and physically challenging. SMS text message programs offer a novel way to provide health information and support, but few programs are co-designed with consumer representatives. </sec> <sec> <title>OBJECTIVE</title> This study aims to report the procedures and outcomes of a co-design process of a lifestyle-focused SMS text message program to support women’s mental and physical health after breast cancer treatment. </sec> <sec> <title>METHODS</title> We followed an iterative mixed methods two-step process: (1) co-design workshop with consumers and health professionals and researchers to draft text messages and (2) evaluation of message content, which was scored (5-point Likert scale; 1=strongly disagree to 5=strongly agree) for ease of understanding, usefulness, and appropriateness, and readability (Flesch-Kincaid score). Additional free-text responses and semistructured interviews were coded into themes. Messages were edited or deleted based on the evaluations, with consumers’ evaluations prioritized. </sec> <sec> <title>RESULTS</title> In step 1, co-designed text messages (N=189) were semipersonalized, and the main content themes were (1) physical activity and healthy eating, (2) medications and side effects, (3) mental health, and (4) general breast cancer information. In step 2, consumers (n=14) and health professionals and researchers (n=14) provided 870 reviews of 189 messages and found that most messages were easy to understand (799/870, 91.8%), useful (746/870, 85.7%), and appropriate (732/870, 84.1%). However, consumers rated 50 messages differently from health professionals and researchers. On the basis of evaluations, 37.6% (71/189) of messages were deleted, 36.5% (69/189) were edited, and 12 new messages related to fatigue, self-care, and cognition were created. The final 130 text messages had a mean 7.12 (SD 2.8) Flesch-Kincaid grade level and 68.9 (SD 15.5) ease-of-reading score, which represents &lt;i&gt;standard&lt;/i&gt; reading ease. </sec> <sec> <title>CONCLUSIONS</title> Co-designing and evaluating a bank of evidence-based mental and physical health-themed text messages with breast cancer survivors, health professionals, and researchers was feasible and resulted in a bank of 130 text messages evaluated highly by participants. Some consumer evaluations differed from health professionals and researchers, supporting the importance of co-design. </sec>
4-phase sequences with near-optimum correlation properties (1992)

Two families of four-phase sequences are constructed using irreducible polynomials over Z/sub 4/. Family A has period L=2/sup r/-1. size L+2. and maximum nontrivial correlation magnitude C/sub max/<or=1+ square root (L+1), where r is a positive integer. Family B has period L=2(2/sup r/-1). size (L+2)/4. and C/sub max/ for complex-valued sequences. Of particular interest, family A has the same size and period as the family of binary Gold sequences. but its maximum nontrivial correlation is smaller by a factor of square root 2. Since the Gold family for r odd is optimal with respect to the Welch bound restricted to binary sequences, family A is thus superior to the best possible binary design of the same family size. Unlike the Gold design, families A and B are asymptotically optimal whether r is odd or even. Both families are suitable for achieving code-division multiple-access and are easily, implemented using shift registers. The exact distribution of correlation values is given for both families.<<ETX>>
Drought Severity-area-frequency Curves for NSW (2006)

The identification, monitoring and characterisation of drought are of importance in water resources management and planning in Australia. The predominance of agriculture and water-rich activities on the eastern seaboard of Australia and the susceptibility of these industries to drought events makes an understanding of the spatial and temporal characteristics of drought significant to long term water resources and agricultural planning. To assist in the quantification of the risk of the spatial extent of drought, the Standardised Precipitation Index (SPI) was used to characterise the frequency, severity and spatial extent of drought incidence in 30 meteorological districts of NSW, Australia for the period 1913-2002. Monthly district rainfall was aggregated on 1, 2, 3, 6, 9, 12 and 24 month time scales and characterised by SPIs for each phase. To assist in determining the spatial and temporal relationships of drought in NSW, drought severity-area-frequency curves were developed, enabling an assessment of the severity of drought throughout the state of NSW. Results obtained were contrasted with historical drought years to show the relationship between the severity and spatial extent of drought events as well as distinguishing short, medium and long term drought in NSW.
Laser microprobe and resonant laser ablation for depth profile measurements of hydrogen isotope atoms contained in graphite (2001)

We measured the depth profile of hydrogen atoms in graphite by laser microprobing combined with resonant laser ablation. Deuterium-implanted graphite was employed for the measurements. The sample was ablated by a tunable laser with a wavelength corresponding to the resonant wavelength of 1S-2S of deuterium with two-photon excitation. The ablated deuterium was ionized by a 2 + 1 resonant ionization process. The ions were analyzed by a time-of-flight mass spectrometer. The deuterium ions were detected clearly with the resonant ablation. The detection limit was estimated to be less than 10(16) atoms/cm(3) in our experiments. We determined the depth profile by considering the etching profile and the etching rate. The depth profile agreed well with Monte Carlo simulations to within a precision of 23 mum for the center position and 4-mum precision for distributions for three different implantation depths.
Precision Flash X-Ray Determination of Density Ratio in Gaseous Detonations (1958)

An x-ray densitometer has been used to measure the density ratio across a detonation wave in a number of different gaseous mixtures involving C2H2, C2N2, or H2 with O2 and Kr. In a 3-in. i.d. tube at an initial pressure of 60 cm the density ratios observed were between 1.64 and 1.67. Investigations of the influence on density ratio of tube diameter at constant initial pressure and of initial pressure at constant tube diameter both indicate an extrapolated infinite diameter density ratio of 1.70 for a 0.3 C2H2 + 0.3 O2 + 0.4 Kr mixture. This result is significantly lower than the ratio 1.79 which corresponds to the tangent point on the equilibrium Hugoniot from the initial state. At the present time these observations cannot adequately be explained by detonation theory.
T Cell Epitope Immunotherapy Induces a CD4+ T Cell Population with Regulatory Activity (2005)

This study provides evidence for the induction of a population of CD4(+) T cells with suppressor/regulatory activity following PIT. Furthermore, up-regulation of cell surface levels of CD5 may contribute to reduced reactivity to allergen.
Parallel gate-level circuit simulation on shared memory architectures (1995)

This paper presents the results of an experimental study to evaluate the effectiveness of parallel simulation in reducing the execution time of gate-level models of VLSI circuits. Specific contributions of this paper include (i) the design of a gate-level parallel simulator that can be executed, without any changes on both distributed memory and shared memory parallel architectures, (ii) demonstrated speedups with both conservative and optimistic simulation protocols (almost all previous studies on circuit simulation have failed to extract speedups with conservative protocols); in particular we showed that a speedup of about 3 was obtained on 8 processors of Sparc1000 for conservative algorithms and about 2 for optimistic algorithms for circuits in the ISCAS85 benchmark suite; and (iii) performance comparison between shared memory and distributed memory implementations of the simulator.