Miracle-dz/UniFAR-FTUs huggingface dataset:
TEMPORAL AND SPATIAL TURBULENT SPECTRA OF MHD PLASMA AND AN OBSERVATION OF VARIANCE ANISOTROPY

The nature of magnetohydrodynamic (MHD) turbulence is analyzed through both temporal and spatial magnetic fluctuation spectra. A magnetically turbulent plasma is produced in the MHD wind tunnel configuration of the Swarthmore Spheromak Experiment. The power of magnetic fluctuations is projected into directions perpendicular and parallel to a local mean field; the ratio of these quantities shows the presence of variance anisotropy which varies as a function of frequency. Comparisons among magnetic, velocity, and density spectra are also made, demonstrating that the energy of the turbulence observed is primarily seeded by magnetic fields created during plasma production. Direct spatial spectra are constructed using multi-channel diagnostics and are used to compare to frequency spectra converted to spatial scales using the Taylor hypothesis. Evidence for the observation of dissipation due to ion inertial length scale physics is also discussed, as well as the role laboratory experiments can play in understanding turbulence typically studied in space settings such as the solar wind. Finally, all turbulence results are shown to compare fairly well to a Hall–MHD simulation of the experiment.
Effects of Coated Compound Proteases on Apparent Total Tract Digestibility of Nutrients and Apparent Ileal Digestibility of Amino Acids for Pigs

Two experiments were conducted to evaluate effects of coated compound proteases (CC protease) on apparent total tract digestibility (ATTD) of nitrogen (N) and energy, and apparent ileal digestibility (AID) of amino acids (AA) and nutrients in diets for pigs. In Exp. 1, 12 crossbred barrows (initial body weight: 20.14±1.71 kg) were housed in individual metabolism crates and allotted into 2 treatments with 6 piglets per treatment according to weight in a randomized complete block design. The 2 diets were corn-soybean meal basal diets with (0.2 g/kg) or without CC protease supplementation. The CC protease supplementation increased (p<0.05) the digestible and metabolizable N and energy values and the digestibility and retention rate of N in the diet. The ATTD of energy and nutrients had been improved (p<0.05) in the diet supplemented with CC protease. In Exp. 2, 12 crossbred barrows (initial body weight: 20.79±1.94 kg), fitted with T-cannulas at the distal ileum, were blocked by body weight into 2 groups with 6 pigs each. The diets were the same as those in Exp. 1. The CC protease increased (p<0.05) the AID of crude protein and some essential AA including arginine, isoleucine and leucine. The AID and ATTD of energy and nutrients had been improved (p<0.05) by supplemental CC protease, but the hindgut digestibility of nutrients was unaffected. Overall, the CC protease improved the ATTD of N and energy and AID of some indispensible AA and nutrients in the corn-soybean meal diet for pigs. Therefore, the CC protease supplement could improve the utilization of protein in the corn-soybean meal diet and thus contribute to lower N excretion to the environment.
Opposing Effects of CD70 Costimulation during Acute and Chronic Lymphocytic Choriomeningitis Virus Infection of Mice

ABSTRACT T cell costimulation is important for T cell activation. The CD27/CD70 pathway contributes to effector and memory T cell development and is involved in T cell and B cell activation. CD27/CD70 is known for having opposing roles during different models of antigenic challenges. During primary T cell responses to influenza virus infection or during tumor challenges, CD27/CD70 costimulation has a positive role on T cell responses. However, during some chronic infections, constitutive triggering of this signaling pathway has a negative role on T cell responses. It is currently unclear what specific characteristic of an antigen determines the outcome of CD27/CD70 costimulation. We investigated the effect of a transient CD70 blockade during an acute or a chronic lymphocytic choriomeningitis virus (LCMV) infection in mice. Blockade of this pathway during acute LCMV infection (Armstrong strain) resulted in delayed T cell responses and decreased CD127 (interleukin-7 receptor α [IL-7Rα] chain) conversion. Upregulation of CD127 is an important event in T cell differentiation that heralds the passage of an effector T cell to a long-lived memory T cell. In contrast to the reduced CD8 T cell responses after CD70 blockade during acute infection, CD70 blockade during chronic LCMV infection resulted in increased CD8 T cell responses. Our data show the dual roles of this costimulatory pathway in acute versus persistent antigen challenge. Our findings suggest that antigen persistence may determine the effect of CD27/CD70 signaling on CD8 T cell responses. Tailored triggering or blockade of this costimulatory pathway may be important in vaccination regimens against acute or chronic pathogens.
Status of serum VEGF and ICAM-1 and its association with external limiting membrane and inner segment-outer segment junction disruption in type 2 diabetes mellitus

Purpose To correlate the serum levels of vascular endothelial growth factor (VEGF) and intercellular adhesion molecule-1 (ICAM-1) with the severity of retinopathy and disruption of the external limiting membrane (ELM) and inner segment-outer segment (IS-OS) junction in type 2 diabetes mellitus (DM). Methods Study subjects included patients with type 2 DM [diabetes mellitus with no retinopathy (No DR; n=19); non-proliferative diabetic retinopathy (NPDR; n=19); proliferative diabetic retinopathy (PDR; n=20)] and healthy controls (n=19) between the ages of 40 and 65 years. Disruption of the ELM and the IS-OS junction was graded by spectral domain optical coherence tomography as follows: grade 0—no disruption of ELM and IS-OS junction; grade 1—ELM disrupted, inner segment-outer segment (IS-OS) junction intact; grade 2—both ELM and IS-OS junction disrupted. The serum levels of VEGF and ICAM-1were analyzed using the standard protocol. Results A significant difference was found between the serum levels of VEGF and ICAM-1 and the various study groups (p<0.001). A positive correlation was found between the grade of disruption and the levels of VEGF (r=0.45, p<0.0001) and ICAM-1 (r=0.40, p=0.0003). A significant positive correlation was found between logMAR visual acuity and grade of disruption (r=0.85, p<0.0001). Conclusions An increase in serum VEGF and ICAM-1 levels is associated with an increase in the severity of diabetic retinopathy and the grade of ELM and IS-OS junction disruption.
Synergistic Antimicrobial Activity of Camellia sinensis and Juglans regia against Multidrug-Resistant Bacteria

Synergistic combinations of antimicrobial agents with different mechanisms of action have been introduced as more successful strategies to combat infections involving multidrug resistant (MDR) bacteria. In this study, we investigated synergistic antimicrobial activity of Camellia sinensis and Juglans regia which are commonly used plants with different antimicrobial agents. Antimicrobial susceptibility of 350 Gram-positive and Gram-negative strains belonging to 10 different bacterial species, was tested against Camellia sinensis and Juglans regia extracts. Minimum inhibitory concentrations (MICs) were determined by agar dilution and microbroth dilution assays. Plant extracts were tested for synergistic antimicrobial activity with different antimicrobial agents by checkerboard titration, Etest/agar incorporation assays, and time kill kinetics. Extract treated and untreated bacteria were subjected to transmission electron microscopy to see the effect on bacterial cell morphology. Camellia sinensis extract showed higher antibacterial activity against MDR S. Typhi, alone and in combination with nalidixic acid, than to susceptible isolates. ” We further explore anti-staphylococcal activity of Juglans regia that lead to the changes in bacterial cell morphology indicating the cell wall of Gram-positive bacteria as possible target of action. The synergistic combination of Juglans regia and oxacillin reverted oxacillin resistance of methicillin resistant Staphylococcus aureus (MRSA) strains in vitro. This study provides novel information about antimicrobial and synergistic activity of Camellia sinensis and Juglans regia against MDR pathogens
Identification of Asymmetric Prediction Intervals Through Causal Forces

When causal forces are specified, the expected direction of the trend can be compared with the trend based on extrapolation. Series in which the expected trend conflicts with the extrapolated trend are called contrary series. We hypothesized that contrary series would have asymmetric forecast errors, with larger errors in the direction of the expected trend. Using annual series that contained minimal information about causality, we examined 671 contrary forecasts. As expected, most (81%) of the errors were in the direction of the causal forces. Also as expected, the asymmetries were more likely for longer forecast horizons; for six-year-ahead forecasts, 89% of the forecasts were in the expected direction. The asymmetries were often substantial. Contrary series should be flagged and treated separately when prediction intervals are estimated, perhaps by shifting the interval in the direction of the causal forces.
Parsimony Score of Phylogenetic Networks: Hardness Results and a Linear-Time Heuristic

Phylogenies-the evolutionary histories of groups of organisms-play a major role in representing the interrelationships among biological entities. Many methods for reconstructing and studying such phylogenies have been proposed, almost all of which assume that the underlying history of a given set of species can be represented by a binary tree. Although many biological processes can be effectively modeled and summarized in this fashion, others cannot: recombination, hybrid speciation, and horizontal gene transfer result in networks of relationships rather than trees of relationships. In previous works, we formulated a maximum parsimony (MP) criterion for reconstructing and evaluating phylogenetic networks, and demonstrated its quality on biological as well as synthetic data sets. In this paper, we provide further theoretical results as well as a very fast heuristic algorithm for the MP criterion of phylogenetic networks. In particular, we provide a novel combinatorial definition of phylogenetic networks in terms of ldquoforbidden cycles,rdquo and provide detailed hardness and hardness of approximation proofs for the "smallrdquo MP problem. We demonstrate the performance of our heuristic in terms of time and accuracy on both biological and synthetic data sets. Finally, we explain the difference between our model and a similar one formulated by Nguyen et al., and describe the implications of this difference on the hardness and approximation results.
Urinary Prostaglandin E2 Metabolite and Risk for Colorectal Adenoma

COX-2 is upregulated in most colorectal cancers. Most of the COX-2 tumor–inducing effects are believed to be mediated through overproduction of prostaglandin E2 (PGE2), which can be measured using a urinary metabolite of PGE2, PGE-M. Urinary PGE-M was assessed in a case–control study of colorectal adenoma. Included in the analysis were 224 cases with at least one advanced adenoma, 152 cases with multiple small tubular adenomas, 300 cases with only a single small tubular adenoma, and 364 polyp-free controls. There were no statistical differences in PGE-M levels between controls and cases with a single small tubular adenoma. However, cases with either an advanced adenoma or multiple small tubular adenomas had more than 25% higher levels of PGE-M than controls. Participants with the highest quartile level of PGE-M were approximately 2.5-fold more likely to have advanced or multiple small tubular adenoma in comparison with those with the lowest level of PGE-M [OR = 2.53; 95% confidence interval (CI), 1.54–4.14; Ptrend < 0.001]. The association was strongest among women. PGE-M level was associated with increased risk for multiple or advanced adenoma but not single small adenoma. Our study suggests that PGE-M may be a useful risk marker for assessing the risk of harboring clinically more important versus less important colorectal neoplasia. Cancer Prev Res; 5(2); 336–42. ©2011 AACR.
Heading Toward a Society of Networks

In the essay, it is first argued that Western societies are moving towards a society of networks, i.e. a society, in which the formal, vertically integrated organization that has dominated the 20th century is replaced or at least complemented by consciously created and goal directed networks of three and more organizations (whole networks). To substantiate this proposition we describe and analyze the development of organizational forms and the subsequent scientific efforts to grasp these developments theoretically and methodologically in the last 200-300 years. Second, the current state of network theory is briefly evaluated with regard to whole networks. In a third part, future research avenues concerning the development of theories that explain the coming into being, functioning, structure, governance and dissolution of whole networks (network theories) are discussed.
Meaning-making after partner suicide: A narrative exploration using the meaning of loss codebook

ABSTRACT This study explored meaning-making in the narratives of survivors of partner suicide. The 117 posts of 50 users of a public online grief support forum were analyzed using the Meaning of Loss Codebook (MLC; Gillies, Neimeyer, & Milman, 2014). There was evidence of substantial psychological distress and an ongoing struggle to make meaning of the death, in addition to focusing on memories, longing for the deceased, and efforts to actively cope with the loss. Given the importance of meaning-making in the adjustment to loss, and through the application of the MLC, these findings deepen the understanding of this component of grief.
Akt is transferred to the nucleus of cells treated with apoptin, and it participates in apoptin‐induced cell death

Abstract. Objectives: The phosphatidylinositol 3‐kinase (PI3‐K)/Akt pathway is well known for the regulation of cell survival, proliferation, and some metabolic routes. Meterials and Methods: In this study, we document a novel role for the PI3‐K/Akt pathway during cell death induced by apoptin, a tumour‐selective inducer of apoptosis. Results: We show for the first time that apoptin interacts with the p85 regulatory subunit, leading to constitutive activation of PI3‐K. The inhibition of PI3‐K activation either by chemical inhibitors or by genetic approaches severely impairs cell death induced by apoptin. Downstream of PI3‐K, Akt is activated and translocated to the nucleus together with apoptin. Direct interaction between apoptin and Akt is documented. Co‐expression of nuclear Akt significantly potentiates cell death induced by apoptin. Thus, apoptin‐facilitated nuclear Akt, in contrast to when in its cytoplasmic pool, appears to be a positive regulator, rather than repressor of apoptosis. Conclusions: Our observations indicate that PI3‐K/Akt pathways have a dual role in both survival and cell death processes depending on the stimulus. Nuclear Akt acts as apoptosis stimulator rather than as a repressor, as it likely gains access to a new set of substrates in the nucleus. The implicated link between survival and cell death pathways during apoptosis opens new pharmacological opportunities to modulate apoptosis in cancer, for example through the manipulation of Akt's cellular localization.
THE DIMENSIONALITY OF GENETIC VARIATION FOR WING SHAPE IN DROSOPHILA MELANOGASTER

Abstract Absolute constraints are limitations on genetic variation that preclude evolutionary change in some aspect of the phenotype. Absolute constraints may reflect complete absence of variation, lack of genetic variation that extends the range of phenotypes beyond some limit, or lack of additive genetic variation. This last type of absolute constraint is bidirectional, because the mean cannot evolve to be larger or smaller. Most traits do possess genetic variation, so bidirectional absolute constraints are most likely to be detected in a multivariate context, where they would reflect combinations of traits, or dimensions in phenotype space that cannot evolve. A bidirectional absolute constraint will cause the additive genetic covariance matrix (G) to have a rank less than the number of traits studied. In this study, we estimate the rank of the G-matrix for 20 aspects of wing shape in Drosophila melanogaster. Our best estimates of matrix rank are 20 in both sexes. Lower 95% confidence intervals of rank are 17 for females and 18 for males. We therefore find little evidence of bidirectional absolute constraints. We discuss the importance of this result for resolving the relative roles of selection and drift processes versus constraints in the evolution of wing shape in Drosophila.
Supplementary Meta-Learning: Towards a Dynamic Model for Deep Neural Networks

Data diversity in terms of types, styles, as well as radiometric, exposure and texture conditions widely exists in training and test data of vision applications. However, learning in traditional neural networks (NNs) only tries to find a model with fixed parameters that optimize the average behavior over all inputs, without using data-specific properties. In this paper, we develop a meta-level NN (MLNN) model that learns meta-knowledge on data-specific properties of images during learning and that dynamically adapts its weights during application according to the properties of the images input. MLNN consists of two parts: the dynamic supplementary NN (SNN) that learns meta-information on each type of inputs, and the fixed base-level NN (BLNN) that incorporates the meta-information from SNN into its weights at run time to realize the generalization for each type of inputs. We verify our approach using over ten network architectures under various application scenarios and loss functions. In low-level vision applications on image super-resolution and demising, MLNN has 0.1~0.3 dB improvements on PSNR, whereas for high-level image classification, MLNN has accuracy improvement of 0.4~0.6% for Cifar10 and 1.2~2.1% for ImageNet when compared to convolutional NNs (CNNs). Improvements are more pronounced as the scale or diversity of data is increased.
Population Genomics of the Foothill Yellow-Legged Frog (Rana boylii) and RADseq Parameter Choice for Large-Genome Organisms

Genomic data are useful for attaining high resolution in population genetic studies and have become increasingly available for answering questions in biological conservation. We analyzed RADseq data for the protected foothill yellow-legged frog (Rana boylii) throughout its native range in California and Oregon, including many of the same localities included in an earlier study based on mitochondrial DNA. We recovered five primary clades that correspond to geographic regions within California and Oregon, with better resolution and more spatially consistent patterns than the previous study, confirming the increased resolving power of genomic approaches compared to single-locus analyses. Bayesian clustering, PCA and population differentiation with admixture analyses all indicated that approximately half the range of R. boylii consists of a single, relatively uniform population, while regions in the Sierra Nevada and Central Coast Range of California are deeply differentiated genetically. Additionally, a major methodological challenge for large genome organisms, including many amphibians, is deciding on sequence similarity clustering thresholds for population genetic analyses using RADseq data, and we develop a novel set of metrics that allow researchers to set a sequence similarity threshold that maximizes the separation of paralogous regions while minimizing the oversplitting of naturally occurring allelic variation within loci.
XenoSearch: distributed resource discovery in the XenoServer open platform

We describe the XenoSearch system for performing expressive resource discovery searches in a distributed environment. We represent server meta-data, such as their locations and facilities, as points in a multi-dimensional space and then express queries as predicates over these points. Each XenoSearch node holds a portion of this space and the key goal of XenoSearch is to direct queries to those nodes containing the meta-data of matching XenoServers. Communication between these XenoSearch nodes is based on the self-organizing Pastry peer-to-peer routing substrate. Our initial performance evaluation on a wide-area prototype shows that queries are only a factor of 3 to 5 times longer than basic Pastry routing, while supporting multi-dimensional searches of arbitrary shapes.
Geometry, Topology and Physics I

1 Topology 1 1.1 Definitions . 2 1.2 Homotopy . 5 1.3 Manifolds . 8 1.4 Surfaces . 9 1.5 Homology . 13 1.6 Intersection numbers and the mapping class group . 15
Idea Evaluation Mechanisms for Collective Intelligence in Open Innovation Communities: Do Traders Outperform Raters?

The increasing popularity of open innovation approaches has led to the rise of various open innovation communities on the Internet which might contain several thousand user-generated ideas. However, a company’s absorptive capacity is limited regarding such an amount of ideas so that there is a strong need for mechanisms supporting the evaluation of these ideas. In this paper, we focus on the evaluation of such mechanisms for collective idea evaluation. Applying a multi-method approach, we compare six different configurations of a prediction market with a multi-criteria rating scale that performed best in previous research. We combine a web-based experiment with 448 participants, data from a participant survey, and an independent expert jury. Based on cognitive load theory, we explain why a multi-criteria rating scale outperforms prediction markets in terms of evaluation accuracy and evaluation satisfaction. This study contributes to theory building in the emerging field of collective intelligence.
Secure Computation on Floating Point Numbers

Secure computation undeniably received a lot of attention in the recent years, with the shift toward cloud computing offering a new incentive for secure computation and outsourcing. Surprisingly little attention, however, has been paid to computation with non-integer data types. To narrow this gap, in this work we develop efficient solutions for computation with real numbers in floating point representation, as well as more complex operations such as square root, logarithm, and exponentiation. Our techniques are information-theoretically secure, do not use expensive cryptographic techniques, and can be applied to a variety of settings. Our experimental results also show that the techniques exhibit rather fast performance and in some cases outperform operations on integers.