Search results for "Computation"
showing 10 items of 7362 documents
unitas: the universal tool for annotation of small RNAs
2017
AbstractBackgroundNext generation sequencing is a key technique in small RNA biology research that has led to the discovery of functionally different classes of small non-coding RNAs in the past years. However, reliable annotation of the extensive amounts of small non-coding RNA data produced by high-throughput sequencing is time-consuming and requires robust bioinformatics expertise. Moreover, existing tools have a number of shortcomings including a lack of sensitivity under certain conditions, limited number of supported species or detectable sub-classes of small RNAs.ResultsHere we introduce unitas, an out-of-the-box ready software for complete annotation of small RNA sequence datasets, …
Identification and Characterization of Stress-Responsive TAS3-Derived TasiRNAs in Melon
2019
Small interfering RNAs (siRNA) are key regulators of gene expression that play essential roles in diverse biological processes. Trans-acting siRNAs (tasiRNAs) are a class of plant-endogenous siRNAs that lead the cleavage of non-identical transcripts. TasiRNAs are usually involved in fine-tuning development. However, increasing evidence supports that tasiRNAs may be involved in stress response. Melon is a crop of great economic importance extensively cultivated in semiarid regions frequently exposed to changing environmental conditions that limit its productivity. However, knowledge of the precise role of siRNAs in general, and of tasiRNAs in particular, in regulating the response to adverse…
Tackling the Limitations of Copolymeric Small Interfering RNA Delivery Agents by a Combined Experimental–Computational Approach
2019
Despite the first successful applications of nonviral delivery vectors for small interfering RNA in the treatment of illnesses, such as the respiratory syncytial virus infection, the preparation of a clinically suitable, safe, and efficient delivery system still remains a challenge. In this study, we tackle the drawbacks of the existing systems by a combined experimental-computational in-depth investigation of the influence of the polymer architecture over the binding and transfection efficiency. For that purpose, a library of diblock copolymers with a molar mass of 30 kDa and a narrow dispersity (Đ1.12) was synthesized. We studied in detail the impact of an altered block size and/or compos…
GSWABE: faster GPU-accelerated sequence alignment with optimal alignment retrieval for short DNA sequences
2014
In this paper, we present GSWABE, a graphics processing unit GPU-accelerated pairwise sequence alignment algorithm for a collection of short DNA sequences. This algorithm supports all-to-all pairwise global, semi-global and local alignment, and retrieves optimal alignments on Compute Unified Device Architecture CUDA-enabled GPUs. All of the three alignment types are based on dynamic programming and share almost the same computational pattern. Thus, we have investigated a general tile-based approach to facilitating fast alignment by deeply exploring the powerful compute capability of CUDA-enabled GPUs. The performance of GSWABE has been evaluated on a Kepler-based Tesla K40 GPU using a varie…
A distributed-memory MPI parallelization scheme for multi-domain incompressible SPH
2022
A parallel scheme for a multi-domain truly incompressible smoothed particle hydrodynamics (SPH) approach is presented. The proposed method is developed for distributed-memory architectures through the Message Passing Interface (MPI) paradigm as communication between partitions. The proposal aims to overcome one of the main drawbacks of the SPH method, which is the high computational cost with respect to mesh-based methods, by coupling a multi-resolution approach with parallel computing techniques. The multi-domain approach aims to employ different resolutions by subdividing the computational domain into non-overlapping blocks separated by block interfaces. The particles belonging to differe…
Penalty Function Methods for the Numerical Solution of Nonlinear Obstacle Problems with Finite Elements
2008
A class of penalty function methods for the solution of nonlinear variational inequalities with obstacles ⩽ 0 fur alle v ⩾ ψ in the Sobolev space W1, p (ω) is studied. The (nonlinear) penalty equations are solved by finite element techniques; the order of convergence of this procedure which depends on the regularity of the solution as well as on the finite elements used is investigated. Eine Klasse von Penalty-Methoden zur Losung nichtlinearer Variationsungleichungen mit Hindernisnebenbedingungen ⩽ 0 fur alle v ⩾ ψ im Sobolev Raum W1, p (ω) wird untersucht. Die (nichtlinearen) Penalty-Gleichungen werden mit Hilfe der Finite Elemente Methode gelost; die Konvergenzordnung dieses Verfahrens, w…
See how it feels to move: Relationships between movement characteristics and perception of emotions in dance
2020
Music makes humans move in ways found to relate to, for instance, musical characteristics, personality, or emotional content of the music. In this study, we investigated associations between embodiments of musical emotions and the perception thereof. After collecting motion capture data of dancers moving to emotionally distinct musical stimuli, silent stick-figure animations were rated by a set of observers regarding perceived discrete emotions, while 10 movement features were computationally extracted from the motion capture data. Results indicate kinematic profiles—emotion-specific sets of movement characteristics—that furthermore conform with dimensional models of valence and arousal, su…
Reservoir computing model of prefrontal cortex creates novel combinations of previous navigation sequences from hippocampal place-cell replay with sp…
2019
As rats learn to search for multiple sources of food or water in a complex environment, they generate increasingly efficient trajectories between reward sites. Such spatial navigation capacity involves the replay of hippocampal place-cells during awake states, generating small sequences of spatially related place-cell activity that we call “snippets”. These snippets occur primarily during sharp-wave-ripples (SWRs). Here we focus on the role of such replay events, as the animal is learning a traveling salesperson task (TSP) across multiple trials. We hypothesize that snippet replay generates synthetic data that can substantially expand and restructure the experience available and make learni…
Multilayer Network Model of Movie Script
2018
Network models have been increasingly used in the past years to support summarization and analysis of narratives, such as famous TV series, books and news. Inspired by social network analysis, most of these models focus on the characters at play. The network model well captures all characters interactions, giving a broad picture of the narration's content. A few works went beyond by introducing additional semantic elements, always captured in a single layer network. In contrast, we introduce in this work a multilayer network model to capture more elements of the narration of a movie from its script: people, locations, and other semantic elements. This model enables new measures and insights…
AMUSED: An Annotation Framework of Multi-modal Social Media Data
2020
In this paper, we present a semi-automated framework called AMUSED for gathering multi-modal annotated data from the multiple social media platforms. The framework is designed to mitigate the issues of collecting and annotating social media data by cohesively combining machine and human in the data collection process. From a given list of the articles from professional news media or blog, AMUSED detects links to the social media posts from news articles and then downloads contents of the same post from the respective social media platform to gather details about that specific post. The framework is capable of fetching the annotated data from multiple platforms like Twitter, YouTube, Reddit.…