A model for querying semistructured data through the exploitation of regular sub-structures

Much research has been undertaken in order to speed up the processing of semistructured data in general and XML in particular. Many approaches for storage, compression, indexing and querying exist, e.g. [1, 2]. We do not present yet another such algorithm but a unifying model in which these algorithm can be understood. The key idea behind this research is the assumption, that most practical queries are based on a particular pattern of data that can be deduced from the query and which can then be captured using a regular structure amendable to efficient processing techniques

Preliminary studies on the use of the Cascade Rolling Circle Amplification technique for Plum pox virus detection

Isothermal techniques for the amplification of nucleic acids have emerged in the last years. In contrast to the Polymerase chain reaction (PCR), the most prevalent method to amplify DNA in vitro, the reactions can be run at constant temperatures. Specificity and sensitivity are at least as high as that obtained by using PCR and the methods are less time consuming. Therefore, the isothermal amplification of nucleic acids provides a powerful tool for the detection of Plum pox virus (PPV), the causal agent of the Sharka disease. The cascade rolling circle amplification (CRCA), first described by Thomas et al. (1999), is based on the rolling circle mechanism that many viruses use to replicate their genome multiplicatively. Circular Probes, also called Padlock probes (PLP), which arise from the ligation of the terminal region of DNA probes upon side by side hybridization to the target serve as template (Nilsson et al. 1994).For detecting PPV by CRCA, RNA was extracted and reverse transcribed to cDNA using a PPV specific primer. Several PLPs with varying lengths and sequences complementary region to the cDNA were designed and tested. Furthermore, different pairs of primers for the subsequent amplification were developed. For specific ligation Ampligase and T4 DNA Ligase were tested. In CRCA, two polymerases with strong strand displacement activity were compared: Phi29 DNA Polymerase and Bst DNA Polymerase. These enzymes differ in their optimal reaction temperature.Ligation as well as amplification do occur, but there is high background amplification also in negative and no template controls. Discrimination was possible after a restriction digestion is carried out. As proven by sequencing of reaction products non-specific signals were a result of primer polymerization. Current work focuses on the reduction of the background amplification and improvement of the sensitivity. Keywords: Cascade Rolling Circle Amplification, CRCA, isothermal amplification of DNA, Plum pox virus, PP

"I Am a Total...Loser" - The Role of Interpretation Biases in Youth Depression

Negative interpretation biases have been found to characterize adults with depression and to be involved in the development and maintenance of the disorder. However, less is known about their role in youth depression. The present study investigated i) whether negative interpretation biases characterize children and adolescents with depression and ii) to what extent these biases are more pronounced in currently depressed youth compared to youth at risk for depression (as some negative interpretation biases have been found already in high-risk youth before disorder onset). After a negative mood induction interpretation biases were assessed with two experimental tasks: Ambiguous Scenarios Task (AST) and Scrambled Sentences Task (SST) in three groups of 9-14-year-olds: children and adolescents with a diagnosis of major depression (n = 32), children and adolescents with a high risk for depression (children of depressed parents; n = 48), as well as low-risk children and adolescents (n = 42). Depressed youth exhibited substantially more negative interpretation biases than both high-risk and low-risk groups (as assessed with both tasks), while the high-risk group showed more negative interpretation biases than the low-risk group only as assessed via the SST. The results indicate that the negative interpretation biases that are to some extent already present in high-risk populations before disorder onset are strongly amplified in currently depressed youth. The different findings for the two tasks suggest that more implicit interpretation biases (assessed with the SST) might represent cognitive vulnerabilities for depression whereas more explicit interpretation biases (assessed with the AST) may arise as a consequence of depressive symptomatology

Structural Organization of the Presynaptic Density at Identified Synapses in the Locust Central Nervous System

In a synaptic active zone, vesicles aggregate around a densely staining structure called the presynaptic density. We focus on its three-dimensional architecture and a major molecular component in the locust. We used electron tomography to study the presynaptic density in synapses made in the brain by identified second-order neuron of the ocelli. Here, vesicles close to the active zone are organized in two rows on either side of the presynaptic density, a level of organization not previously reported in insect central synapses. The row of vesicles that is closest to the density's base includes vesicles docked with the presynaptic membrane and thus presumably ready for release, whereas the outer row of vesicles does not include any that are docked. We show that a locust ortholog of the Drosophila protein Bruchpilot is localized to the presynaptic density, both in the ocellar pathway and compound eye visual neurons. An antibody recognizing the C-terminus of the Bruchpilot ortholog selectively labels filamentous extensions of the presynaptic density that reach out toward vesicles. Previous studies on Bruchpilot have focused on its role in neuromuscular junctions in Drosophila, and our study shows it is also a major functional component of presynaptic densities in the central nervous system of an evolutionarily distant insect. Our study thus reveals Bruchpilot executes similar functions in synapses that can sustain transmission of small graded potentials as well as those relaying large, spike-evoked signals. J. Comp. Neurol. 520:384–400, 2012. © 2011 Wiley Periodicals, Inc

An Eye-Tracking Study of Attention Biases in Children at High Familial Risk for Depression and Their Parents with Depression

Attention biases (AB) are a core component of cognitive models of depression yet it is unclear what role they play in the transgenerational transmission of depression. 44 children (9-14 years) with a high familial risk of depression (HR) were compared on multiple measures of AB with 36 children with a low familial risk of depression (LR). Their parents: 44 adults with a history of depression (HD) and 36 adults with no history of psychiatric disorder (ND) were also compared. There was no evidence of group differences in AB; neither between the HR and LR children, nor between HD and ND parents. There was no evidence of a correlation between parent and child AB. The internal consistency of the tasks varied greatly. The Dot-Probe Task showed unacceptable reliability whereas the behavioral index of the Visual-Search Task and an eye-tracking index of the Passive-Viewing Task showed better reliability. There was little correlation between the AB tasks and the tasks showed minimal convergence with symptoms of depression or anxiety. The null-findings of the current study contradict our expectations and much of the previous literature. They may be due to the poor psychometric properties associated with some of the AB indices, the unreliability of AB in general, or the relatively modest sample size. The poor reliability of the tasks in our sample suggest caution should be taken when interpreting the positive findings of previous studies which have used similar methods and populations

Overcritical states of a superconductor strip in a magnetic environment

A current-carrying superconducting strip partly penetrated by magnetic flux and surrounded by a bulk magnet of high permeability is considered. Two types of samples are studied: those with critical current controlled by an edge barrier dominating over the pinning, and those with high pinning-mediated critical current masking the edge barrier.It is shown for both cases that the current distribution in a central flux-free part of the strip is strongly affected by the actual shape of the magnetic surroundings. Explicit analytical solutions for the sheet current and self-field distributions are obtained which show that, depending on the geometry, the effect may suppress the total loss-free transport current of the strip or enhance it by orders of magnitude. The effect depends strongly on the shape of the magnet and its distance to the superconductor but only weakly on the magnetic permeability.Comment: 20 pages, 20 figure

Electron Tomography of Fusiform Vesicles and Their Organization in Urothelial Cells

The formation of fusiform vesicles (FVs) is one of the most distinctive features in the urothelium of the urinary bladder. FVs represent compartments for intracellular transport of urothelial plaques, which modulate the surface area of the superficial urothelial (umbrella) cells during the distension-contraction cycle. We have analysed the three-dimensional (3D) structure of FVs and their organization in umbrella cells of mouse urinary bladders. Compared to chemical fixation, high pressure freezing gave a new insight into the ultrastructure of urothelial cells. Electron tomography on serial sections revealed that mature FVs had a shape of flattened discs, with a diameter of up to 1.2 µm. The lumen between the two opposing asymmetrically thickened membranes was very narrow, ranging from 5 nm to 10 nm. Freeze-fracturing and immunolabelling confirmed that FVs contain two opposing urothelial plaques connected by a hinge region that made an omega shaped curvature. In the central cytoplasm, 4–15 FVs were often organized into stacks. In the subapical cytoplasm, FVs were mainly organized as individual vesicles. Distension-contraction cycles did not affect the shape of mature FVs; however, their orientation changed from parallel in distended to perpendicular in contracted bladder with respect to the apical plasma membrane. In the intermediate cells, shorter and more dilated immature FVs were present. The salient outcome from this research is the first comprehensive, high resolution 3D view of the ultrastructure of FVs and how they are organized differently depending on their location in the cytoplasm of umbrella cells. The shape of mature FVs and their organization into tightly packed stacks makes them a perfect storage compartment, which transports large amounts of urothelial plaques while occupying a small volume of umbrella cell cytoplasm