Miracle-dz/UniFAR-FTUs huggingface dataset:
The complete mitochondrial genome sequence of the little egret (Egretta garzetta)

Many phylogenetic questions in the Ciconiiformes remain unresolved and complete mitogenome data are urgently needed for further molecular investigation. In this work, we determined the complete mitogenome sequence of the little egret (Egretta garzetta). The genome was 17,361 bp in length and the gene organization was typical of other avian mtDNA. In protein-coding genes (PCGs), a C insertion was found in ND3, and COIII and ND4 terminated with incomplete stop codons (T). tRNA-Val and tRNA-Ser (AGY) were unable to fold into canonical cloverleaf secondary structures because they had lost the DHU arms. Long repetitive sequences consisting of five types of tandem repeats were found at the 3′ end of Domain III in the control region. A phylogenetic analysis of 11 species of Ciconiiformes was done using complete mitogenome data and 12 PCGs. The tree topologies obtained with these two strategies were identical, which strongly confirmed the monophyly of Ardeidae, Threskiorothidae and Ciconiidae. The phylogenetic analysis also revealed that Egretta was more closely related to Ardea than to Nycticorax in the Ardeidae, and Platalea was more closely related to Threskiornis than to Nipponia in the Threskiornithidae. These findings contribute to our understanding of the phylogenetic relationships of Ciconiiformes based on complete mitogenome data.
Serial hook-ups: a comparative usability study of secure device pairing methods

Secure Device Pairing is the bootstrapping of secure communication between two previously unassociated devices over a wireless channel. The human-imperceptible nature of wireless communication, lack of any prior security context, and absence of a common trust infrastructure open the door for Man-in-the-Middle (aka Evil Twin) attacks. A number of methods have been proposed to mitigate these attacks, each requiring user assistance in authenticating information exchanged over the wireless channel via some human-perceptible auxiliary channels, e.g., visual, acoustic or tactile. In this paper, we present results of the first comprehensive and comparative study of eleven notable secure device pairing methods. Usability measures include: task performance times, ratings on System Usability Scale (SUS), task completion rates, and perceived security. Study subjects were controlled for age, gender and prior experience with device pairing. We present overall results and identify problematic methods for certain classes of users as well as methods best-suited for various device configurations.
An efficient hybrid clustering approach of microarray gene expression data

Today, DNA microarray technology is the most widely employed functional genomics approach in the bioinformatics domain. Disclosing the patterns masked in gene expression data provides an opportunity for an enhanced comprehension of functional genomics. But, the large number of genes and the intricate biological networks has greatly increased the challenges of comprehending and interpreting the resulting mass of data, which often contains millions of measurements. So, clustering techniques are used to tackle this challenge. Several clustering techniques have been developed and used in the analysis of microarray data. But, such techniques are not much efficient in analyzing the gene expression data. In this paper, we propose a novel efficient hybrid clustering approach based on quad tree data structure. In the hierarchical clustering process, the creation of the closest pair data structure in each level is an important time factor that provides the processing time of clustering. Here, a quad tree based data structure is used for identifying the closest pair elements. Thus, the proposed approach reduces the processing time successfully and offers a better analysis of gene expression data.
RXTE and BeppoSAX Observations of MCG –5-23-16: Reflection from Distant Cold Material

We examine the spectral variability of the Seyfert 1.9 galaxy MCG -5-23-16 by using the Rossi X-Ray Timing Explorer (RXTE) and BeppoSAX observations spanning 2 years from 1996 April to 1998 April. During the first year the X-ray source brightens by a factor of ~25% on timescales of days to months. During this time, the reprocessed continuum emission seen with RXTE does not respond measurably to the continuum increase. However, by the end of the second year during the BeppoSAX epoch the X-ray source has faded again. This time, the reprocessed emission has also faded, indicating that the reprocessed flux has responded to the continuum. If these effects are caused by time delays due to the distance between the X-ray source and the reprocessing region, we derive a light crossing time between ~1 lt-day and ~1.5 lt-yr. This corresponds to a distance of 0.001 to 0.55 pc, which implies that the reprocessed emission originates between 3 × 1015 and 1.6 × 1018 cm from the X-ray source. In other words, the reprocessing in MCG -5-23-16 is not dominated by the inner regions of a standard accretion disk.
Distributed complex event processing with query rewriting

The nature of data in enterprises and on the Internet is changing. Data used to be stored in a database first and queried later. Today timely processing of new data, represented as events, is increasingly valuable. In many domains, complex event processing (CEP) systems detect patterns of events for decision making. Examples include processing of environmental sensor data, trades in financial markets and RSS web feeds. Unlike conventional database systems, most current CEP systems pay little attention to query optimisation. They do not rewrite queries to more efficient representations or make decisions about operator distribution, limiting their overall scalability. This paper describes the NEXT CEP system that was especially designed for query rewriting and distribution. Event patterns are specified in a high-level query language and, before being translated into event automata, are rewritten in a more efficient form. Automata are then distributed across a cluster of machines for detection scalability. We present algorithms for query rewriting and distributed placement. Our experiments on the Emulab test-bed show a significant improvement in system scalability due to rewriting and distribution.
CONTINUOUS-TIME DYNKIN GAMES WITH MIXED STRATEGIES

Let (X,Y, Z) be a triple of payoff processes defining a Dynkin game R̃(σ, τ) = E [ Xσ1{τ>σ} + Yτ1{τ<σ} + Zτ1{τ=σ} ] , where σ and τ are stopping times valued in [0, T ]. In the case Z = Y , it is well known that the condition X ≤ Y is needed in order to establish the existence of value for the game, i.e., infτ supσ R̃(σ, τ) = supσ infτ R̃(σ, τ). In order to remove the condition X ≤ Y , we introduce an extension of the Dynkin game by allowing for an extended set of strategies, namely, the set of mixed strategies. The main result of the paper is that the extended Dynkin game has a value when Z ≤ Y , and the processes X and Y are restricted to be semimartingales continuous at the terminal time T .
The emerging role of FTY720 (Fingolimod) in cancer treatment

FTY720 (Fingolimod) is a clinically approved immunomodulating therapy for multiple sclerosis that sequesters T-cells to lymph nodes through functional antagonism of sphingosine-1-phosphate 1 receptor. FTY720 also demonstrates a proven efficacy in multiple in vitro and in vivo cancer models, suggesting a potential therapeutic role in cancer patients. A potential anticancer mechanism of FTY720 is through the inhibition of sphingosine kinase 1, a proto-oncogene with in vitro and clinical cancer association. In addition, FTY720's anticancer properties may be attributable to actions on several other molecular targets. This study focuses on reviewing the emerging evidence regarding the anticancer properties and molecular targets of FTY720. While the clinical transition of FTY720 is currently limited by its immune suppression effects, studies aiming at FTY720 delivery and release together with identifying its key synergetic combinations and relevant patient subsets may lead to its rapid introduction into the clinic.
Patients Infected with CRF07_BC Have Significantly Lower Viral Loads than Patients with HIV-1 Subtype B: Mechanism and Impact on Disease Progression

Background:The circulating recombinant form (CRF) 07_BC is the most prevalent HIV-1 strain among injection drug users in Taiwan. It contains a 7 amino-acid deletion (7d) in its p6gag. The objectives of this study were to conduct a cohort study to compare viral load and CD4 cell count changes between patients infected with subtype B and CRF07_BC and to elucidate its mechanism. Methods:Twenty-one patients infected with CRF07_BC and 59 patients with subtype B were selected from a cohort of 667 HIV-1/AIDS patients whom have been followed up for more than 3 years. Generalized estimated equation was used for statistical analysis. The replicative kinetics, tropism and cytopathic effects were determined. HIV-1 NL4-3 which containing a 7 amino-acid deletion in p6gag (7d virus) was generated and its virological properties were compared with the wild-type. Results:Patients infected with CRF07_BC had significantly lower viral load than patients with subtype B. CRF07_BC isolates had lower replicative capacity than subtype B isolates although they were all CCR5 tropic. 7d virus had significantly lower gag processing efficiency and slower viral life cycle. Electronic microscopy showed 7d virus had poorer viral maturation processes: more viruses attached to the cell membrane and less mature virions. The interaction between p6gag and Alix protein was less efficient in cells infected with 7d virus. Conclusions:Patients infected with CRF07_BC had significantly slower disease progression. The differences of virological characteristics between CRF07_BC and subtype B were due to its 7 amino-acid deletion in p6gag.
STIMulating a new treatment for sepsis.

During sepsis, acute lung injury (ALI) results from activation of innate immune cells and endothelial cells by endotoxins, leading to systemic inflammation through proinflammatory cytokine overproduction, oxidative stress, and intracellular Ca2+ overload. Despite considerable investigation, the underlying molecular mechanism(s) leading to LPS-induced ALI remain elusive. To determine whether stromal interaction molecule 1-dependent (STIM1-dependent) signaling drives endothelial dysfunction in response to LPS, we investigated oxidative and STIM1 signaling of EC-specific Stim1-knockout mice. Here we report that LPS-mediated Ca2+ oscillations are ablated in ECs deficient in Nox2, Stim1, and type II inositol triphosphate receptor (Itpr2). LPS-induced nuclear factor of activated T cells (NFAT) nuclear accumulation was abrogated by either antioxidant supplementation or Ca2+ chelation. Moreover, ECs lacking either Nox2 or Stim1 failed to trigger store-operated Ca2+ entry (SOCe) and NFAT nuclear accumulation. LPS-induced vascular permeability changes were reduced in EC-specific Stim1-/- mice, despite elevation of systemic cytokine levels. Additionally, inhibition of STIM1 signaling prevented receptor-interacting protein 3-dependent (RIP3-dependent) EC death. Remarkably, BTP2, a small-molecule calcium release-activated calcium (CRAC) channel blocker administered after insult, halted LPS-induced vascular leakage and pulmonary edema. These results indicate that ROS-driven Ca2+ signaling promotes vascular barrier dysfunction and that the SOCe machinery may provide crucial therapeutic targets to limit sepsis-induced ALI.
Assigning energy costs to activities in children: a review and synthesis.

PURPOSE Compendia of energy costs are often used to assign energy expenditures (EE) to self-reported and observed activity. As there is a lack of data on the energy cost of children's everyday activities, adult values are often used as surrogates. However, the best way to adjust adult values for use with children remains unclear. Various strategies have been used to estimate rates of EE in children. METHODS To evaluate these existing methods for assigning EE to children, a literature search reviewed all English-language studies that measured energy costs in healthy 6.0-17.9 yr olds using criterion EE measures. Data were combined using the Monte Carlo simulation procedure, with walking and running forming separate data sets. RESULTS The resultant data set (excluding walking and running) contained 5592 data points encompassing 51 activities. Analyses revealed using adults METs, combined with child resting metabolic rates, as the best existing technique to assign EE to children when measured values are not available. Prediction equations for the energy cost of walking and running were calculated using multiple regression. CONCLUSION This study has provided a literature base and analytical support for a compendium of energy costs for use with children with energy costs expressed as METs.
La teoría del consumo y de los ciclos en Thorstein Veblen

Thorstein Veblen (1857-1929) fue uno de los fundadores de la economia institucional norteamericana. Este articulo presenta su teoria del consumo basada en los habitos expuesta en la Teoria de la clase ociosa, y su teoria de los ciclos economicos y las crisis expuesta en la Teoria de la empresa de negocios. Para situarlas en contexto se esboza una sintesis de su pensamiento y de sus criticas a la economia ortodoxa.
How university athletic program success associates with university prestige via the halo effect for different types of universities

Title of Document: HOW UNIVERSITY ATHLETIC PROGRAM SUCCESS ASSOCIATES WITH UNIVERSITY PRESTIGE VIA THE HALO EFFECT FOR DIFFERENT TYPES OF UNIVERSITIES. Westleigh Alan Quattrone, Master of Arts, 2008 Directed By: Professor Jeffrey Lucas, Sociology Department Athletic program success may be a way for universities to achieve prestigious status. The halo effect may allow perceptions of athletic programs to be extended to other aspects of the university. This process was hypothesized not only to occur, but to occur to a differing extent across university types. I predicted that universities that are new, secular, public, outside of the Northeastern United States, and that do not have name designations would show the greatest gains in prestige upon achieving high athletic success. Regression analyses tested the relationship between expert ratings of universities and athletic success rates of major football and basketball sports programs. Results indicated a positive association between athletic success rates and university prestige. This process did not significantly vary by university types. Results also showed expert ratings of universities highly correlated with those of non-experts, indicating that expert assessment is a good proxy for typical prestige perceptions. HOW UNIVERSITY ATHLETIC PROGRAM SUCCESS ASSOCIATES WITH UNIVERSITY PRESTIGE VIA THE HALO EFFECT FOR DIFFERENT TYPES OF UNIVERSITIES.
Investigation of Deep Belief Networks in modeling Sequential Data

This project is an investigation of the Conditional Restricted Boltzmann Machine (CRBM) in modeling sequential data. The main goal is to examine which parameters of the model and which aspects of the data are crucial to the overall performance of the learned model and draw general conclusions concerning its generic capabilites. In order to do so, we first conduct an exploratory analysis, during which we examine the importance of different parameters of the model using a training set that consists of handwriten character sequences. Then we conduct a comparative analysis, during which we examine the results of 2-level CRBMs in conjunction with ones obtained by multivariate Autoregressive models (mAR). For the comparative analysis we use results from models trained on both, the character sequences dataset, and a dataset comprising human motion sequences, for which the model was initially proposed. Our results show that the 2-level CRBM fails to adequately generate synthetic characters and it is outperformed by the mAR model on the specific dataset. On the other hand, the mAR model is clearly outperformed on the motion dataset, where the 2-level CRBM exhibits exceptionally good generic capabilities. The conducted analysis indicates that the incapability of the 2-level Conditional Restricted Boltzmann Machine to generate realistic synthetic characters can be partially accredited to the training procedure currently used.
An HSUS Report: The Welfare of Animals in the Aquaculture Industry

In the United States, approximately 1.3 billion fish are raised in off-shore and land-based aquaculture systems each year for food, making them the second-most commonly farmed animal domestically, following broiler chickens. The majority of farmed fish are subject to overcrowded and restrictive conditions, which, if unchecked, can quickly deteriorate water quality, cause severe stress, and result in increased mortality. Aquaculture practices and production—including handling, grading, transport, genetic manipulation, aggression from conspecifics, predation, physiological stress, and inhumane slaughter—compromise the welfare of these animals.
Violence Attribution Errors Among Low-Risk and High-Risk Offenders

Juvenile offenders have numerous factors that contribute to their delinquency, including family dysfunction, drug and alcohol abuse, negative peer influences, and social cognitive development. One area of social cognitive development linked to deviant behavior is attributional biases. Based on the prior research of Daley and Onwuegbuzie (2004), the purpose of the present concurrent mixed methods study was to explore the differences in the frequency of violence attribution errors among juvenile delinquents; the extent that peer-victimization, self-esteem, and demographic variables predict violence attribution errors among juveniles; and the differences in the types of violence attribution errors between incarcerated (high-risk) and probation (low-risk) juvenile delinquents. The results indicated juvenile offenders made violence attribution errors more than 50% of the time when evaluating the behavior of others, suggesting that the lowrisk offenders are at major risk of committing high-risk offenses in the future. The results of the multiple regression analysis indicated that 5 variables (i.e., attitude towards the violent acts of others, verbal victimization, attacks on property, social relationships, and morals) statistically predicted the number of violence attribution errors a youth made (F [21, 88] = 2.28,p = .004). Further, with regard to the typology of reasons for violence attributions, the same 7 emergent themes were extracted for all 3 offender samples: self-control, violation of rights, provocation, irresponsibility, poor judgment, fate, and conflict resolution. Findings are discussed relative to the literature on attributional bias and offender behavior. CHAPTER
Robust anticipatory stigmergic collision avoidance in multi-agent systems

Anticipatory Stigmergic Collision Avoidance (ASCA) is a reciprocal collision avoidance model in which agents interact by indicating intended future paths to other agents in their local environment. Other agents can then incorporate that information to guide their path planning decisions. Additionally, constraints such as restricted movements and noise are incorporated. Our evaluation shows that ASCA is consistently more robust than Reciprocal Velocity Obstacles in noisy environments in which ransmitted information can be lost or degraded.
MASK+: Data-driven regions selection for acoustic fingerprinting

Acoustic fingerprinting is the process to deterministically obtain a compact representation of an audio segment, used to compare multiple audio files or to efficiently search for a file within a big database. Recently, we proposed a novel fingerprint named MASK (Masked Audio Spectral Keypoints) that encodes the relationship between pairs of spectral regions around a single spectral energy peak into a binary representation. In the original proposal the configuration of location and size of the regions pairs was determined manually to optimally encode how energy flows around the spectral peak. Such manual selection has always been considered as a weakness in the process as it might not be adapted to the actual data being represented. In this paper we address this problem by proposing a unsupervised, data-driven method based on mutual information theory to automatically define an optimal MASK fingerprint structure. Audio retrieval experiments optimizing for data distorted with additive Gaussian white noise show that the proposed method is much more robust than the original MASK and a well known acoustic fingerprint.
Modulating drug release profiles by lipid semi solid matrix formulations for BCS class II drug – an in vitro and an in vivo study

Abstract The main objective of the study was to alter the dissolution profile of a practically insoluble Biopharmaceutics Classification System class II drug, aceclofenac, by formulating into lipid semisolid matrix (SSM) formulations using liquid filling technology in hard gelatin capsules, for both immediate and sustained release. SSM formulations of aceclofenac were prepared by melt fusion technique, using Gelucires (44/14, 50/13, 33/01 and 43/01), polyethylene glycols (4000 and 6000) and Poloxamer 188 at different levels. Role of additives like docusate sodium, Tween 80, Aerosil 200 and polyvinylpyrrolidone K-30 in enhancement of drug release was investigated. The optimized immediate and sustained SSM capsules were characterized in terms of assay, in vitro drug release, moisture uptake and differential scanning calorimetry. More than 80% of the drug was released within 15 min in various dissolution media studied, from Gelucire 44/14-based immediate release formulations. Incorporation of docusate sodium and Tween 80 provided further enhancement in drug dissolution when compared to plain drug and marketed tablet. SSM formulations based on Gelucire blends of 50/13 and 43/01 and 44/14 and 43/01 sustained the release of the drug for a period of 24 h following zero-order kinetics. The in vivo study of the optimized immediate release and sustained release formulations revealed significant enhancement in anti inflammatory activity (p < 0.01) in rats. From these findings, liquid fill technique in hard gelatin capsules using Gelucire and their blends might be an efficacious approach for designing immediate or sustained drug release profiles for poorly soluble drugs like aceclofenac.
Automatic Mapping of the Lava Flows at Piton de la Fournaise Volcano, by Combining Thermal Data in Near and Visible Infrared

Z. Servadio1,2, N. Villeneuve1 and P. Bachelery3,4 1Laboratoire Geosciences Reunion, Universite de la Reunion, Institut de Physique du Globe de Paris, CNRS, UMR 7154, Geologie des Systemes Volcaniques, Saint Denis 2Institut de Recherche pour le Developpement, US 140, BP172, 97492 Sainte-Clotilde Cedex 3Clermont Universite, Universite Blaise Pascal, Laboratoire Magmas et Volcans, CNRS, UMR 6524, Observatoire de Physique du Globe de Clermont-Ferrand, BP 10448, F-63000 Clermont-Ferrand 4IRD, R 163, LMV, F-63038 Clermont-Ferrand France
gCLUTO – An Interactive Clustering, Visualization, and Analysis System

Clustering algorithms are exploratory data analysis tools that have proved to be essential for gaining valuable insights on various aspects and relationships of the underlying systems. In this paper we present gCLUTO, a stand-alone clustering software package which serves as an easy-to-use platform that combines clustering algorithms along with a number of analysis, reporting, and visualization tools to aid in interactive exploration and clustering-driven analysis of large datasets. gCLUTO provides a wide-range of algorithms that operate either directly on the original feature-based representation of the objects or on the object-to-object similarity graphs and are capable of analyzing different types of datasets and finding clusters with different characteristics. In addition, gCLUTO implements a project-oriented work-flow that eases the process of data analysis.