Searching for Nearest Strings with Neural-Like String Embedding

We analyze an approach to a similarity preserving coding of symbol sequences based on neural distributed representations and show that it can be viewed as a metric embedding process

Identifying Repeat Domains in Large Genomes

We present a graph-based method for the analysis of repeat families in a repeat library. We build a repeat domain graph that decomposes a repeat library into repeat domains, short subsequences shared by multiple repeat families, and reveals the mosaic structure of repeat families. Our method recovers documented mosaic repeat structures and suggests additional putative ones. Our method is useful for elucidating the evolutionary history of repeats and annotating de novo generated repeat libraries

Look at Me: Early Gaze Engagement Enhances Corticospinal Excitability During Action Observation

Direct gaze is a powerful social cue able to capture the onlooker's attention. Beside gaze, head and limb movements as well can provide relevant sources of information for social interaction. This study investigated the joint role of direct gaze and hand gestures on onlookers corticospinal excitability (CE). In two experiments we manipulated the temporal and spatial aspects of observed gaze and hand behavior to assess their role in affecting motor preparation. To do this, transcranial magnetic stimulation (TMS) on the primary motor cortex (M1) coupled with electromyography (EMG) recording was used in two experiments. In the crucial manipulation, we showed to participants four video clips of an actor who initially displayed eye contact while starting a social request gesture, and then completed the action while directing his gaze toward a salient object for the interaction. This way, the observed gaze potentially expressed the intention to interact. Eye tracking data confirmed that gaze manipulation was effective in drawing observers' attention to the actor's hand gesture. In the attempt to reveal possible time-locked modulations, we tracked CE at the onset and offset of the request gesture. Neurophysiological results showed an early CE modulation when the actor was about to start the request gesture looking straight to the participants, compared to when his gaze was averted from the gesture. This effect was time-locked to the kinematics of the actor's arm movement. Overall, data from the two experiments seem to indicate that the joint contribution of direct gaze and precocious kinematic information, gained while a request gesture is on the verge of beginning, increases the subjective experience of involvement and allows observers to prepare for an appropriate social interaction. On the contrary, the separation of gaze cues and body kinematics can have adverse effects on social motor preparation. CE is highly susceptible to biological cues, such as averted gaze, which is able to automatically capture and divert observer's attention. This point to the existence of heuristics based on early action and gaze cues that would allow observers to interact appropriately

Towards locality aware de novo dna assembly of short reads in colour space

This thesis presents a new approach towards de novo DNA assembly for short reads. Its two main contributions are a novel, robust filtering scheme for noisy reads that outperforms the (accuracy of the) widely used Sasson’s filter, and a novel assembly algorithm that, minimizing space and maximizing locality of accesses, runs faster than all state-of-the-art algorithms even when on substantially cheaper hardwar

Combining technologies to create bioactive hybrid scaffolds for bone tissue engineering

Combining technologies to engineer scaffolds that can offer physical and chemical cues to cells is an attractive approach in tissue engineering and regenerative medicine. In this study, we have fabricated polymer-ceramic hybrid scaffolds for bone regeneration by combining rapid prototyping (RP), electrospinning (ESP) and a biomimetic coating method in order to provide mechanical support and a physico-chemical environment mimicking both the organic and inorganic phases of bone extracellular matrix (ECM). Poly(ethylene oxide terephthalate)-poly(buthylene terephthalate) (PEOT/PBT) block copolymer was used to produce three dimensional scaffolds by combining 3D fiber (3DF) deposition, and ESP, and these constructs were then coated with a Ca-P layer in a simulated physiological solution. Scaffold morphology and composition were studied using scanning electron microscopy (SEM) coupled to energy dispersive X-ray analyzer (EDX) and Fourier Tranform Infrared Spectroscopy (FTIR). Bone marrow derived human mesenchymal stromal cells (hMSCs) were cultured on coated and uncoated 3DF and 3DF + ESP scaffolds for up to 21 d in basic and mineralization medium and cell attachment, proliferation, and expression of genes related to osteogenesis were assessed. Cells attached, proliferated and secreted ECM on all the scaffolds. There were no significant differences in metabolic activity among the different groups on days 7 and 21. Coated 3DF scaffolds showed a significantly higher DNA amount in basic medium at 21 d compared with the coated 3DF + ESP scaffolds, whereas in mineralization medium, the presence of coating in 3DF+ESP scaffolds led to a significant decrease in the amount of DNA. An effect of combining different scaffolding technologies and material types on expression of a number of osteogenic markers (cbfa1, BMP-2, OP, OC and ON) was observed, suggesting the potential use of this approach in bone tissue engineerin

Kermit : Guided Long Read Assembly using Coloured Overlap Graphs

Peer reviewe

Kermit: Guided Long Read Assembly using Coloured Overlap Graphs

With long reads getting even longer and cheaper, large scale sequencing projects can be accomplished without short reads at an affordable cost. Due to the high error rates and less mature tools, de novo assembly of long reads is still challenging and often results in a large collection of contigs. Dense linkage maps are collections of markers whose location on the genome is approximately known. Therefore they provide long range information that has the potential to greatly aid in de novo assembly. Previously linkage maps have been used to detect misassemblies and to manually order contigs. However, no fully automated tools exist to incorporate linkage maps in assembly but instead large amounts of manual labour is needed to order the contigs into chromosomes. We formulate the genome assembly problem in the presence of linkage maps and present the first method for guided genome assembly using linkage maps. Our method is based on an additional cleaning step added to the assembly. We show that it can simplify the underlying assembly graph, resulting in more contiguous assemblies and reducing the amount of misassemblies when compared to de novo assembly