Patterns of nucleotides that flank substitutions in human orthologous genes

<p>Abstract</p> <p>Background</p> <p>Sequence context is an important aspect of base mutagenesis, and three-base periodicity is an intrinsic property of coding sequences. However, how three-base periodicity is influenced in the vicinity of substitutions is still unclear. The effect of context on mutagenesis should be revealed in the usage of nucleotides that flank substitutions. Relative entropy (also known as Kullback-Leibler divergence) is useful for finding unusual patterns in biological sequences.</p> <p>Results</p> <p>Using relative entropy, we visualized the periodic patterns in the context of substitutions in human orthologous genes. Neighbouring patterns differed both among substitution categories and within a category that occurred at three codon positions. Transition tended to occur in periodic sequences relative to transversion. Periodic signals were stronger in a set of flanking sequences of substitutions that occurred at the third-codon positions than in those that occurred at the first- or second-codon positions. To determine how the three-base periodicity was affected near the substitution sites, we fitted a sine model to the values of the relative entropy. A sine of period equal to 3 is a good approximation for the three-base periodicity at sites not in close vicinity to some substitutions. These periods were interrupted near the substitution site and then reappeared away from substitutions. A comparative analysis between the native and codon-shuffled datasets suggested that the codon usage frequency was not the sole origin of the three-base periodicity, implying that the native order of codons also played an important role in this periodicity. Synonymous codon shuffling revealed that synonymous codon usage bias was one of the factors responsible for the observed three-base periodicity.</p> <p>Conclusions</p> <p>Our results offer an efficient way to illustrate unusual periodic patterns in the context of substitutions and provide further insight into the origin of three-base periodicity. This periodicity is a result of the native codon order in the reading frame. The length of the period equal to 3 is caused by the usage bias of nucleotides in synonymous codons. The periodic features in nucleotides surrounding substitutions aid in further understanding genetic variation and nucleotide mutagenesis.</p

Neuromorphic event-based slip detection and suppression in robotic grasping and manipulation

Slip detection is essential for robots to make robust grasping and fine manipulation. In this paper, a novel dynamic vision-based finger system for slip detection and suppression is proposed. We also present a baseline and feature based approach to detect object slips under illumination and vibration uncertainty. A threshold method is devised to autonomously sample noise in real-time to improve slip detection. Moreover, a fuzzy based suppression strategy using incipient slip feedback is proposed for regulating the grip force. A comprehensive experimental study of our proposed approaches under uncertainty and system for high-performance precision manipulation are presented. We also propose a slip metric to evaluate such performance quantitatively. Results indicate that the system can effectively detect incipient slip events at a sampling rate of 2kHz ($\Delta t = 500\mu s$) and suppress them before a gross slip occurs. The event-based approach holds promises to high precision manipulation task requirement in industrial manufacturing and household services.Comment: 18 pages, 14 figure

Privacy-Preserving Predictive Modeling: Harmonization of Contextual Embeddings From Different Sources

Background: Data sharing has been a big challenge in biomedical informatics because of privacy concerns. Contextual embedding models have demonstrated a very strong representative capability to describe medical concepts (and their context), and they have shown promise as an alternative way to support deep-learning applications without the need to disclose original data. However, contextual embedding models acquired from individual hospitals cannot be directly combined because their embedding spaces are different, and naive pooling renders combined embeddings useless. Objective: The aim of this study was to present a novel approach to address these issues and to promote sharing representation without sharing data. Without sacrificing privacy, we also aimed to build a global model from representations learned from local private data and synchronize information from multiple sources. Methods: We propose a methodology that harmonizes different local contextual embeddings into a global model. We used Word2Vec to generate contextual embeddings from each source and Procrustes to fuse different vector models into one common space by using a list of corresponding pairs as anchor points. We performed prediction analysis with harmonized embeddings. Results: We used sequential medical events extracted from the Medical Information Mart for Intensive Care III database to evaluate the proposed methodology in predicting the next likely diagnosis of a new patient using either structured data or unstructured data. Under different experimental scenarios, we confirmed that the global model built from harmonized local models achieves a more accurate prediction than local models and global models built from naive pooling. Conclusions: Such aggregation of local models using our unique harmonization can serve as the proxy for a global model, combining information from a wide range of institutions and information sources. It allows information unique to a certain hospital to become available to other sites, increasing the fluidity of information flow in health care

Impacts of mutation effects and population size on mutation rate in asexual populations: a simulation study

<p>Abstract</p> <p>Background</p> <p>In any natural population, mutation is the primary source of genetic variation required for evolutionary novelty and adaptation. Nevertheless, most mutations, especially those with phenotypic effects, are harmful and are consequently removed by natural selection. For this reason, under natural selection, an organism will evolve to a lower mutation rate. Overall, the action of natural selection on mutation rate is related to population size and mutation effects. Although theoretical work has intensively investigated the relationship between natural selection and mutation rate, most of these studies have focused on individual competition within a population, rather than on competition among populations. The aim of the present study was to use computer simulations to investigate how natural selection adjusts mutation rate among asexually reproducing subpopulations with different mutation rates.</p> <p>Results</p> <p>The competition results for the different subpopulations showed that a population could evolve to an "optimum" mutation rate during long-term evolution, and that this rate was modulated by both population size and mutation effects. A larger population could evolve to a higher optimum mutation rate than could a smaller population. The optimum mutation rate depended on both the fraction and the effects of beneficial mutations, rather than on the effects of deleterious ones. The optimum mutation rate increased with either the fraction or the effects of beneficial mutations. When strongly favored mutations appeared, the optimum mutation rate was elevated to a much higher level. The competition time among the subpopulations also substantially shortened.</p> <p>Conclusions</p> <p>Competition at the population level revealed that the evolution of the mutation rate in asexual populations was determined by both population size and mutation effects. The most striking finding was that beneficial mutations, rather than deleterious mutations, were the leading force that modulated the optimum mutation rate. The initial configuration of the population appeared to have no effect on these conclusions, confirming the robustness of the simulation method developed in the present study. These findings might further explain the lower mutation rates observed in most asexual organisms, as well as the higher mutation rates in some viruses.</p

Capital social, brechas digitales y transmisión intergeneracional del capital cultural en comunidades urbanas estadounidenses desfavorecidas: un estudio exploratorio

Advancing the classic network model of cultural capital, this study draws on social capital theories and digital divide and inclusion literature to examine the implications of social capital and digital connections for parents’ cultural capital in marginalized urban communities in two aspects: parents’ cultural knowledge and intergenerational cultural participation. Drawing on a household survey of an extremely disadvantaged population living in public housing communities in a major American city, results show that parents with greater social capital command greater cultural knowledge, which in turn can increase their intergenerational cultural participation. Parents’ social capital, however, has no direct impacts on intergenerational cultural participation. By contrast, the findings suggested that internet access alone is not enough for digital inclusion to increase cultural capital.Este estudio busca contribuir al modelo de red clásico del capital cultural, basándose en las teorías del capital social y la literatura sobre brecha digital e inclusión. Pretende examinar la influencia del capital social y las conexiones digitales en el capital cultural de los padres de comunidades urbanas marginadas en dos aspectos: el conocimiento cultural de estos y la participación cultural intergeneracional. A partir de una encuesta a hogares de una población de extremadamente desfavorecida, que vive en comunidades de viviendas públicas de una gran ciudad estadounidense, los resultados muestran que los padres con mayor capital social poseen mayor conocimiento cultural, que puede aumentar su participación cultural intergeneracional. Sin embargo, el capital social de estos no tiene efectos directos en la participación cultural intergeneracional. En cambio, los resultados sugieren que el acceso a Internet por sí solo no es suficiente para que la inclusión digital en las comunidades desfavorecidas aumente el capital cultural

Neuromorphic vision based contact-level classification in robotic grasping applications

In recent years, robotic sorting is widely used in the industry, which is driven by necessity and opportunity. In this paper, a novel neuromorphic vision-based tactile sensing approach for robotic sorting application is proposed. This approach has low latency and low power consumption when compared to conventional vision-based tactile sensing techniques. Two Machine Learning (ML) methods, namely, Support Vector Machine (SVM) and Dynamic Time Warping-K Nearest Neighbor (DTW-KNN), are developed to classify material hardness, object size, and grasping force. An Event-Based Object Grasping (EBOG) experimental setup is developed to acquire datasets, where 243 experiments are produced to train the proposed classifiers. Based on predictions of the classifiers, objects can be automatically sorted. If the prediction accuracy is below a certain threshold, the gripper re-adjusts and re-grasps until reaching a proper grasp. The proposed ML method achieves good prediction accuracy, which shows the effectiveness and the applicability of the proposed approach. The experimental results show that the developed SVM model outperforms the DTW-KNN model in term of accuracy and efficiency for real time contact-level classification