A new procedure to analyze RNA non-branching structures

RNA structure prediction and structural motifs analysis are challenging tasks in the investigation of RNA function. We propose a novel procedure to detect structural motifs shared between two RNAs (a reference and a target). In particular, we developed two core modules: (i) nbRSSP_extractor, to assign a unique structure to the reference RNA encoded by a set of non-branching structures; (ii) SSD_finder, to detect structural motifs that the target RNA shares with the reference, by means of a new score function that rewards the relative distance of the target non-branching structures compared to the reference ones. We integrated these algorithms with already existing software to reach a coherent pipeline able to perform the following two main tasks: prediction of RNA structures (integration of RNALfold and nbRSSP_extractor) and search for chains of matches (integration of Structator and SSD_finder)

Antecedent of Innovation and Marketing Performance In Batik Industry

Batik is one of the important industries and the pride of Indonesia. Batik is a world cultural heritage which is originally Indonesia. In batik industry, innovation is one of the important factors that will improve marketing performance. This study wanted to test some of the main drivers of innovation and marketing performance on Batik SMEs. The purpose of this study is (1) Testing the influence of social capital on innovation and marketing performance; (2) Testing the effect of entrepreneurial orientation on innovation and marketing performance; and (3) Testing the influence of co-creation on innovation and marketing performance. The research sample consisted of 161 batik businesses in the city of Sragen and Purwodadi. Data were analyzed using SEM PLS and processed using WarpPls with version 5. The results of this study indicate that only some of the hypotheses are accepted, such as (1) entrepreneurial orientation is able to significantly improve innovation, (2) co-creation is able to significantly increase innovation, (3) market capability is able to significantly improve innovation, and (4) market capability is able to significantly improve marketing performance Keywords: Entrepreneurial Orientation, Social Capital, Market Capabilities, Co-Creation, Innovation, Marketing Performanc

Impact of observational incompleteness on the structural properties of protein interaction networks

The observed structure of protein interaction networks is corrupted by many false positive/negative links. This observational incompleteness is abstracted as random link removal and a specific, experimentally motivated (spoke) link rearrangement. Their impact on the structural properties of gene-duplication-and-mutation network models is studied. For the degree distribution a curve collapse is found, showing no sensitive dependence on the link removal/rearrangement strengths and disallowing a quantitative extraction of model parameters. The spoke link rearrangement process moves other structural observables, like degree correlations, cluster coefficient and motif frequencies, closer to their counterparts extracted from the yeast data. This underlines the importance to take a precise modeling of the observational incompleteness into account when network structure models are to be quantitatively compared to data.Comment: 17 pages, 7 figures, accepted by Physica

Disruption to control network function correlates with altered dynamic connectivity in the wider autism spectrum.

Autism is a common developmental condition with a wide, variable range of co-occurring neuropsychiatric symptoms. Contrasting with most extant studies, we explored whole-brain functional organization at multiple levels simultaneously in a large subject group reflecting autism's clinical diversity, and present the first network-based analysis of transient brain states, or dynamic connectivity, in autism. Disruption to inter-network and inter-system connectivity, rather than within individual networks, predominated. We identified coupling disruption in the anterior-posterior default mode axis, and among specific control networks specialized for task start cues and the maintenance of domain-independent task positive status, specifically between the right fronto-parietal and cingulo-opercular networks and default mode network subsystems. These appear to propagate downstream in autism, with significantly dampened subject oscillations between brain states, and dynamic connectivity configuration differences. Our account proposes specific motifs that may provide candidates for neuroimaging biomarkers within heterogeneous clinical populations in this diverse condition

STDP-driven networks and the \emph{C. elegans} neuronal network

We study the dynamics of the structure of a formal neural network wherein the strengths of the synapses are governed by spike-timing-dependent plasticity (STDP). For properly chosen input signals, there exists a steady state with a residual network. We compare the motif profile of such a network with that of a real neural network of \emph{C. elegans} and identify robust qualitative similarities. In particular, our extensive numerical simulations show that this STDP-driven resulting network is robust under variations of the model parameters.Comment: 16 pages, 14 figure