Miracle-dz/UniFAR-FTUs huggingface dataset:
The origin of the supersoft X-ray-optical/UV flux anticorrelation in the symbiotic binary AG Draconis

Context. AG Draconis produces a strong supersoft X-ray emission. The X-ray and optical/UV fluxes are in strict anticorrelation throughout the active and quiescent phases. Aims. We identify the source of the X-ray emission and reveal the nature of the observed flux anticorrelation. Methods. We used X-ray and UV observations with XMM-Newton, far-UV spectroscopy from FUSE, low- and high-resolution IUE spectra, and optical/near-IR spectroscopic and/or photometric observations. We modeled the spectral energy distribution and broad wings of the O vi λ1032 ,λ 1038 and He ii λ1640 lines by the electron-scattering during the maximum of the 2003 burst, and the subsequent transition and quiescent phase. Results. The X-ray-near-IR energy distribution at different levels of the star’s brightness confirmed the observed flux anticorrelation quantitatively and showed that the optical bursts are associated to an increase in the nebular component of radiation. The profile-fitting analysis revealed a significant increase in the mean particle density around the hot star from ∼2.6 × 10 10 cm −3 during quiescent phase to ∼1.1 × 10 12 cm −3 during the burst. Conclusions. The supersoft X-ray emission is produced by the white dwarf photosphere. The X-ray and far-UV fluxes make it possible to determine its temperature unambiguously. The supersoft X-ray-optical/UV flux anticorrelation is caused by the variable wind from the hot star. The enhanced hot star wind gives rise to the optical bursts by reprocessing high-energy photons from the Lyman continuum to the optical/UV.
Modeling complex cellular networks - robust switching in the cell cycle ensures a piecewise linear reduction of the regulatory network

Cellular networks are inherently complex due to their large number of genes and proteins interacting through non-linear feedback loops. The identification of cellular networks from large-scale parallel measurements from the activity of genes and proteins is a tremendous challenge in the postgenomic era, i. e. after the sequencing of the genome. Traditionally, this system identification problem has been viewed as a huge parameter estimation problem of an unknown non-linear system. Here we develop an approach where we approximate the complex system equations with a piecewise linear system, using a computational model of the cell cycle as a proof of principle. The modular and sparse structure of the cellular network makes it possible, to divide the model into subsystems, each having only a small number of inputs and outputs. As a rule, the subsystems operate as switches with or without delay. Since the cell cycle, as most biological systems, is robust against perturbations, the subsystems can be replaced by step functions and the main dynamical behaviour of the full complex cellular network can therefore be captured by the piecewise linear system. If other cellular networks are robust, sparse and modular, our approach of targeting a reduced system description instead of the full complex system, set the stage for not only a thorough characterization of the system dynamics but most importantly, it reduces the complexity of the parameter estimation problem.
A Time-Based Low Voltage Body Temperature Monitoring Unit

A neonatal temperature monitoring system operating in sub threshold regime that utilizes time mode signal processing is presented. Resistance deviations in a thermistor due to temperature variations are converted to delay variations that are subsequently quantized by a Delay measurement unit (DMU). The DMU does away with the need for any analog circuitry and is synthesizable entirely from digital logic. An FPGA implementation of the system demonstrates the viability of employing time mode signal processing, and measured results show that temperature resolution better than 0.1 oC can be achieved using this approach.
VLA Observations of H2O Masers in the Class 0 Protostar S106 FIR: Evidence for a 10 AU Scale Accelerating Jetlike Flow

We conducted VLA observations at 0. ″06 resolution of the 22 GHz water masers toward the Class 0 source S106 FIR (d = 600 pc; 15′′ west of S106 IRS 4) on two epochs separated by ~3 months. Two compact clusters of the maser spots were found in the center of the submillimeter core of S106 FIR. The separation of the clusters was ~80 mas (48 AU) along P.A. = 70°, and the size of each cluster was ~20 mas × 10 mas. The western cluster, which had three maser components, was 8.0 km s-1 blueshifted, and the eastern cluster, which had a single component, was 7.0 km s-1 redshifted with respect to the ambient cloud velocity. Each component was composed of a few spatially localized maser spots and was aligned on a line connecting the clusters. We found relative proper motions of the components with ≈30 mas yr-1 (18 AU yr-1) along the line. In addition, a series of single-dish observations shows that the maser components drifted with radial accelerations of ~1 km s-1 yr-1. These facts indicate that the masers could be excited by a 10 AU scale jetlike accelerating flow ejected from an assumed protostar located between the two clusters. The outflow size traced by the masers was 50 AU × 5 AU after correction for an inclination angle of 10°, which was derived from the relative proper motions and radial velocities of the maser components. The three-dimensional outflow velocity ranged from 40 to 70 km s-1 assuming symmetric proper motions for the blue and red components. Since no distinct CO molecular outflows have been detected so far, we suggest that S106 FIR is an extremely young protostar observed just after the onset of outflowing activity.
The Self of Sundanese Ethnic: Interdependent Construal and Religious Self

This paper aims to introduce the religious self-viewed from the Indonesian context. Indonesia is a large country with diverse ethnic groups and the study seeks to investigate the self in relation to ethnicity. Specifically, the study examines the Sundanese ethnic group that has relatively few sub-groups compared with others found on the archipelago. The study undertakes a conceptual analysis to illustrate the religious self. In this regard, the social and cultural factors are examined to enable a proper account of the religious self, particularly in Indonesia. Relevant empirical evidence is presented to support and explain the religious self-concept. The study further presents a comparative analysis with previous self-concept studies. Finally, the paper concludes with a discussion on the direction of future research on the religious self.
On the controllability of nearest neighbor interconnections

In this paper we derive necessary and sufficient conditions for a group of systems interconnected via nearest neighbor rules, to be controllable by one of them acting as a leader. It is indicated that connectivity seems to have an adverse effect on controllability, and it is formally shown why a path is controllable while a complete graph is not. The dependence of the graph controllability property on the size of the graph and its connectivity is investigated in simulation. Results suggest analytical means of selecting the right leader and/or the appropriate topology to be able to control an interconnected system with nearest neighbor interaction rules.
Developmental expression of dnaA is required for sporulation and timing of fruiting body formation in Myxococcus xanthus

Inhibition of DNA replication within the first 6 h of development results in a block in the developmental programme in the social soil bacterium Myxococcus xanthus. We have interpreted these data to imply that M. xanthus requires a new round of DNA replication early in the developmental programme. To further understand the role of DNA replication during development in M. xanthus we focused on the regulation of dnaA which encodes the initiator protein of DNA replication. In this work, we demonstrate that immediately upon nutrient deprivation dnaA (MXAN1001) transcript levels decrease to 10–15% of vegetative levels and then transiently increase between 4 and 6 h post initiation. This expression is dependent on several early developmental regulators, including relA (MXAN3204), sigD (MXAN2957) and sdeK (MXAN1014). It is also dependent upon an 85 bp region located just upstream to the dnaA promoter. Our data suggest that while developmental dnaA expression is not essential for development, its expression allows for the proper timing and maximum efficiency of the sporulation process. In addition, we speculate that developmental control of dnaA expression may provide a mechanism for predetermination of cell fate during the differentiation process.
Comparative proteomic analysis using samples obtained with laser microdissection and saturation dye labelling

Comparative proteomic methods are rapidly being applied to many different biological systems including complex tissues. One pitfall of these methods is that in some cases, such as oncology and neuroscience, tissue complexity requires isolation of specific cell types and sample is limited. Laser microdissection (LMD) is commonly used for obtaining such samples for proteomic studies. We have combined LMD with sensitive thiol‐reactive saturation dye labelling of protein samples and 2‐D DIGE to identify protein changes in a test system, the isolated CA1 pyramidal neurone layer of a transgenic (Tg) rat carrying a human amyloid precursor protein transgene. Saturation dye labelling proved to be extremely sensitive with a spot map of over 5,000 proteins being readily produced from 5 μg total protein, with over 100 proteins being significantly altered at p < 0.0005. Of the proteins identified, all showed coherent changes associated with transgene expression. It was, however, difficult to identify significantly different proteins using PMF and MALDI‐TOF on gels containing less than 500 μg total protein. The use of saturation dye labelling of limiting samples will therefore require the use of highly sensitive MS techniques to identify the significantly altered proteins isolated using methods such as LMD.
Ribozyme-mediated revision of RNA and DNA.

The splicing activity of Group I and Group II introns can be harnessed as a molecular tool that may potentially revise any gene of interest. Although hurdles remain, progress has been made in the development of these ribozymes for therapeutic application. While gene therapy is showing promise in the treatment of some diseases, many genes are regulated in ways that are not easily recapitulated by adding back a functional copy of the gene. Therefore, as an alternative to the traditional approach, it may be possible to correct the genetic information directly in the genome or in the messages transcribed from mutant genes. In this way, genetic information is left intact so that the cell may properly regulate the expression and processing of genetic information. Several classes of catalytic RNAs, or ribozymes, have the capacity to revise genetic information. Group I and Group II ribozymes are derived from naturally occurring Group I and Group II introns, respectively (1). These introns are found in the genes of a variety of lower eukaryotes and prokaryotes. They differ fundamentally from spliceosomal introns since Group I and Group II introns self-splice from the precursor RNA independent of the spliceosome. The intron adopts the catalytic structure that is capable of cleaving RNA splice sites and ligating the flanking exons together. In addition to self-splicing from RNA precursors, some Group II introns are able to reverse-splice into DNA. The splicing activity of these introns can be harnessed as a molecular tool that may potentially revise any gene of interest. The therapeutic revision of RNA by ribozymes is mechanistically different from that of DNA. To revise RNA sequences, a Group I intron from Tetrahymena thermophila has been adapted for trans-splicing (2). Trans-splicing ribozymes splice therapeutic RNA sequences onto a target transcript in a process called ribozyme-mediated RNA repair. Considerable progress has been made in the development of trans-splicing ribozymes for therapeutic applications such as treating sickle cell disease and cancer. The spliceosome has also been shown to trans-splice RNA transcripts (3). Spliceosomal-mediated RNA trans-splicing (SMaRT) is discussed by Mariano Garcia-Blanco (4) in this Perspective series. To modify genomic DNA, a Group II ribozyme has recently been developed that reverse-splices into target genes of interest (5, 6). If applicable to mammalian cell genomes, this exciting technology may allow the therapeutic insertion of genetic information into a specific target locus. In this Perspective series article, we report on the progress made in development of Group I and Group II ribozymes as tools to revise RNA and DNA. We will also discuss the hurdles that must be overcome to make clinical use of these molecular therapeutics.
Compressed temporal synchronization with opportunistic signals

In this paper we propose a temporal synchronization method using opportunistic signals for wireless networks. Instead of broadcasting a dedicated broadband signal throughout the network for synchronization, high-bandwidth opportunistic signals already existing in the environment can be used. To avoid the necessity that all the nodes in the network are able to decode the opportunistic reference signal, a central node should receive the reference signal and then sends it again to all other nodes. Using ideas from the compressed sensing (CS) area, the high-bandwidth reference signal to be transmitted can be compressed efficiently before being sent to the other nodes, while still achieving an accurate correlation function compared to the low bandwidth reference signal scenario. In this way, only a low-bandwidth signal needs to be transmitted. Numerical results demonstrate that the proposed compressed technique achieves a similar performance at a much lower cost compared to using the high-bandwidth opportunistic signal directly.
Vascular cell adhesion molecule 1 expression by biliary epithelium promotes persistence of inflammation by inhibiting effector T‐cell apoptosis

Chronic hepatitis occurs when effector lymphocytes are recruited to the liver from blood and retained in tissue to interact with target cells, such as hepatocytes or bile ducts (BDs). Vascular cell adhesion molecule 1 (VCAM‐1; CD106), a member of the immunoglobulin superfamily, supports leukocyte adhesion by binding α4β1 integrins and is critical for the recruitment of monocytes and lymphocytes during inflammation. We detected VCAM‐1 on cholangiocytes in chronic liver disease (CLD) and hypothesized that biliary expression of VCAM‐1 contributes to the persistence of liver inflammation. Hence, in this study, we examined whether cholangiocyte expression of VCAM‐1 promotes the survival of intrahepatic α4β1 expressing effector T cells. We examined interactions between primary human cholangiocytes and isolated intrahepatic T cells ex vivo and in vivo using the Ova‐bil antigen‐driven murine model of biliary inflammation. VCAM‐1 was detected on BDs in CLDs (primary biliary cirrhosis, primary sclerosing cholangitis, alcoholic liver disease, and chronic hepatitis C), and human cholangiocytes expressed VCAM‐1 in response to tumor necrosis factor alpha alone or in combination with CD40L or interleukin‐17. Liver‐derived T cells adhered to cholangiocytes in vitro by α4β1, which resulted in signaling through nuclear factor kappa B p65, protein kinase B1, and p38 mitogen‐activated protein kinase phosphorylation. This led to increased mitochondrial B‐cell lymphoma 2 accumulation and decreased activation of caspase 3, causing increased cell survival. We confirmed our findings in a murine model of hepatobiliary inflammation where inhibition of VCAM‐1 decreased liver inflammation by reducing lymphocyte recruitment and increasing CD8 and T helper 17 CD4 T‐cell survival. Conclusions: VCAM‐1 expression by cholangiocytes contributes to persistent inflammation by conferring a survival signal to α4β1 expressing proinflammatory T lymphocytes in CLD. (Hepatology 2014;59:1932–1943)
Sparql Rules! Sparql Rules!

As the data and ontology layers of the Semantic Web stack have achieved a certain level of maturity in standard recommendations such as RDF and OWL, the current focus lies on two related aspects. On the one hand, the deﬁnition of a suitable query language for RDF, SPARQL, seems to be close to candidate recommendation status within the W3C. The establishment of the rules layer on top of the existing stack on the other hand marks the next step to be taken, where especially languages with their roots in Logic Programming and Deductive Databases are receiving considerable attention. The purpose of this paper is threefold. First, we discuss the formal semantics of SPARQL extending recent results in several ways. Second, we provide translations from SPARQL to Datalog with stratiﬁed negation as failure. Third, we propose some useful and easy to implement extensions of SPARQL, based on this translation. As it turns out, the combination serves for direct implementations of SPARQL on top of existing rules engines as well as a basis for more general rules and query languages on top of RDF. A prototype implementation is available for evaluation of our approach.
The Cambridge Handbook of Australian Criminology

1. Introduction Peter Grabosky and Adam Graycar 2. Trends in Australian crime and criminal justice Peter Grabosky and Adam Graycar 3. The criminal justice system - overview and data Australian Bureau of Statistics 4. The policing complex Tim Prenzler and Rick Sarre 5. Courts, criminal law and procedure Gregor Urbas and Simon Bronitt 6. Correctional systems John Dawes and Adam Grant 7. Illicit drugs and crime Toni Makkai 8. White collar crime Russell Smith 9. Homicide Jenny Mouzos 10. Gender, race, class and crime in Australia Emma Ogilvie and Mark Lynch 11. Juvenile justice Ian O'Connor and Margaret Cameron 12. Crime and older people Marianne James and Adam Graycar 13. Crime and indigenous people Rod Broadhurst 14. Victims Anna Grant, Fiona David and Bree Cook 15. Restorative justice and conferencing Kathleen Daly and Hennessey Hayes 16. Crime prevention in Australia Margaret Cameron and Gloria Laycock.
Analysis of pulsed magnetic field - biologic tissue interaction with alteration of extracellular area characteristics

The paper is dealing with an analysis of behavior of biologic tissue in interaction with a pulsed magnetic field (a magnetic field commonly used within investigations and treatments, but which can also occur by accident in electric equipments requiring continuous alteration of running energy parameters). In this interaction, the essential feature pointed out in the paper is that of a major influence of extracellular environment of biologic tissue. The analysis is being performed within the theory of electric circuits by using the electric model of cell membrane. As far the extracellular environment is concerned, it was modelled both as conductive and semiconductive environment to visualize the importance of its characteristics on membrane cell polarization and depolarization phenomena. The analysis has been performed using PSIM software environment by reducing the biologic tissue to the size of two cells and the extracellular environment between them, for this purpose.
Putting Priors in Mixture Density Mercer Kernels

This paper presents a new methodology for automatic knowledge driven data mining based on the theory of Mercer Kernels, which are highly nonlinear symmetric positive definite mappings from the original image space to a very high, possibly infinite dimensional feature space. We describe a new method called Mixture Density Mercer Kernels to learn kernel function directly from data, rather than using predefined kernels. These data adaptive kernels can en- code prior knowledge in the kernel using a Bayesian formulation, thus allowing for physical information to be encoded in the model. We compare the results with existing algorithms on data from the Sloan Digital Sky Survey (SDSS). The code for these experiments has been generated with the AUTOBAYES tool, which automatically generates efficient and documented C/C++ code from abstract statistical model specifications. The core of the system is a schema library which contains template for learning and knowledge discovery algorithms like different versions of EM, or numeric optimization methods like conjugate gradient methods. The template instantiation is supported by symbolic- algebraic computations, which allows AUTOBAYES to find closed-form solutions and, where possible, to integrate them into the code. The results show that the Mixture Density Mercer-Kernel described here outperforms tree-based classification in distinguishing high-redshift galaxies from low- redshift galaxies by approximately 16% on test data, bagged trees by approximately 7%, and bagged trees built on a much larger sample of data by approximately 2%.
Differential Evolution with Novel Mutation and Adaptive Crossover Strategies for Solving Large Scale Global Optimization Problems

This paper presents Differential Evolution algorithm for solving high-dimensional optimization problems over continuous space. The proposed algorithm, namely, ANDE, introduces a new triangular mutation rule based on the convex combination vector of the triplet defined by the three randomly chosen vectors and the difference vectors between the best, better, and the worst individuals among the three randomly selected vectors. The mutation rule is combined with the basic mutation strategy DE/rand/1/bin, where the new triangular mutation rule is applied with the probability of 2/3 since it has both exploration ability and exploitation tendency. Furthermore, we propose a novel self-adaptive scheme for gradual change of the values of the crossover rate that can excellently benefit from the past experience of the individuals in the search space during evolution process which in turn can considerably balance the common trade-off between the population diversity and convergence speed. The proposed algorithm has been evaluated on the 20 standard high-dimensional benchmark numerical optimization problems for the IEEE CEC-2010 Special Session and Competition on Large Scale Global Optimization. The comparison results between ANDE and its versions and the other seven state-of-the-art evolutionary algorithms that were all tested on this test suite indicate that the proposed algorithm and its two versions are highly competitive algorithms for solving large scale global optimization problems.
Subfamily of Olfactory Receptors Characterized by Unique Structural Features and Expression Patterns

Abstract: The complex chemospecificity of the olfactory system is probably due to the large family of short‐looped, heptahelical receptor proteins expressed in neurons widely distributed throughout one of the several zones within the nasal neuroepithelium. In this study, a subfamily of olfactory receptors has been identified that is characterized by distinct structural features as well as a unique expression pattern. Members of this receptor family are found in mammals, such as rodents and opossum, but not in lower vertebrates. All identified subtypes comprise an extended third extracellular loop that exhibits amphiphilic properties and contains numerous charged amino acids in conserved positions. Olfactory sensory neurons expressing these receptor types are segregated in small clusters on the tip of central turbinates, thus representing a novel pattern of expression for olfactory receptors. In mouse, genes encoding the new subfamily of receptors were found to be harbored within a small contiguous segment of genomic DNA. Based on species specificity as well as the unique structural properties and expression pattern, it is conceivable that the novel receptor subfamily may serve a special function in the olfactory system of mammals.