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https://www.readbyqxmd.com/read/28343362/climate-controls-over-ecosystem-metabolism-insights-from-a-fifteen-year-inductive-artificial-neural-network-synthesis-for-a-subalpine-forest
#1
REVIEW
Loren P Albert, Trevor F Keenan, Sean P Burns, Travis E Huxman, Russell K Monson
Eddy covariance (EC) datasets have provided insight into climate determinants of net ecosystem productivity (NEP) and evapotranspiration (ET) in natural ecosystems for decades, but most EC studies were published in serial fashion such that one study's result became the following study's hypothesis. This approach reflects the hypothetico-deductive process by focusing on previously derived hypotheses. A synthesis of this type of sequential inference reiterates subjective biases and may amplify past assumptions about the role, and relative importance, of controls over ecosystem metabolism...
March 25, 2017: Oecologia
https://www.readbyqxmd.com/read/28343000/evidence-for-similar-patterns-of-neural-activity-elicted-by-picture-and-word-based-representations-of-natural-scenes
#2
Manoj Kumar, Kara D Federmeier, Li Fei-Fei, Diane M Beck
A long-standing core question in cognitive science is whether different modalities and representation types (pictures, words, sounds, etc.) access a common store of semantic information. Although different input types have been shown to activate a shared network of brain regions, this does not necessitate that there is a common representation, as the neurons in these regions could still differentially process the different modalities. However, multi-voxel pattern analysis can be used to assess whether, e.g...
March 22, 2017: NeuroImage
https://www.readbyqxmd.com/read/28338930/expath-tool-a-system-for-comprehensively-analyzing-regulatory-pathways-and-coexpression-networks-from-high-throughput-transcriptome-data
#3
Han-Qin Zheng, Nai-Yun Wu, Chi-Nga Chow, Kuan-Chieh Tseng, Chia-Hung Chien, Yu-Cheng Hung, Guan-Zhen Li, Wen-Chi Chang
Next generation sequencing (NGS) has become the mainstream approach for monitoring gene expression levels in parallel with various experimental treatments. Unfortunately, there is no systematical webserver to comprehensively perform further analysis based on the huge amount of preliminary data that is obtained after finishing the process of gene annotation. Therefore, a user-friendly and effective system is required to mine important genes and regulatory pathways under specific conditions from high-throughput transcriptome data...
March 13, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/28337675/an-ontology-based-search-engine-for-digital-reconstructions-of-neuronal-morphology
#4
Sridevi Polavaram, Giorgio A Ascoli
Neuronal morphology is extremely diverse across and within animal species, developmental stages, brain regions, and cell types. This diversity is functionally important because neuronal structure strongly affects synaptic integration, spiking dynamics, and network connectivity. Digital reconstructions of axonal and dendritic arbors are thus essential to quantify and model information processing in the nervous system. NeuroMorpho.Org is an established repository containing tens of thousands of digitally reconstructed neurons shared by several hundred laboratories worldwide...
March 23, 2017: Brain Informatics
https://www.readbyqxmd.com/read/28334998/spatiotemporal-mapping-of-epileptic-spikes-using-simultaneous-eeg-functional-mri
#5
Jennifer M Walz, Mangor Pedersen, Amir Omidvarnia, Mira Semmelroch, Graeme D Jackson
Epileptic spikes occur on the sub-second timescale and are known to involve not only epileptic foci but also large-scale distributed brain networks. There is likely to be a sequence of neural activity in multiple brain regions that occurs within the duration of a single spike, but standard electroencephalography-functional magnetic resonance imaging analyses, which use only the timing of the spikes to model the functional magnetic resonance imaging data, cannot determine the sequence of these activations. Our aim in this study is to temporally resolve these spatial activations to observe the spatiotemporal dynamics of the spike-related neural activity at a sub-second timescale...
February 20, 2017: Brain: a Journal of Neurology
https://www.readbyqxmd.com/read/28334943/effects-of-prefrontal-cortex-damage-on-emotion-understanding-eeg-and-behavioural-evidence
#6
Anat Perry, Samantha N Saunders, Jennifer Stiso, Callum Dewar, Jamie Lubell, Torstein R Meling, Anne-Kristin Solbakk, Tor Endestad, Robert T Knight
Humans are highly social beings that interact with each other on a daily basis. In these complex interactions, we get along by being able to identify others' actions and infer their intentions, thoughts and feelings. One of the major theories accounting for this critical ability assumes that the understanding of social signals is based on a primordial tendency to simulate observed actions by activating a mirror neuron system. If mirror neuron regions are important for action and emotion recognition, damage to regions in this network should lead to deficits in these domains...
February 22, 2017: Brain: a Journal of Neurology
https://www.readbyqxmd.com/read/28334268/an-algorithmic-perspective-of-de-novo-cis-regulatory-motif-finding-based-on-chip-seq-data
#7
Bingqiang Liu, Jinyu Yang, Yang Li, Adam McDermaid, Qin Ma
Transcription factors are proteins that bind to specific DNA sequences and play important roles in controlling the expression levels of their target genes. Hence, prediction of transcription factor binding sites (TFBSs) provides a solid foundation for inferring gene regulatory mechanisms and building regulatory networks for a genome. Chromatin immunoprecipitation sequencing (ChIP-seq) technology can generate large-scale experimental data for such protein-DNA interactions, providing an unprecedented opportunity to identify TFBSs (a...
March 8, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28333591/evidence-accumulation-and-change-rate-inference-in-dynamic-environments
#8
Adrian E Radillo, Alan Veliz-Cuba, Krešimir Josić, Zachary P Kilpatrick
In a constantly changing world, animals must account for environmental volatility when making decisions. To appropriately discount older, irrelevant information, they need to learn the rate at which the environment changes. We develop an ideal observer model capable of inferring the present state of the environment along with its rate of change. Key to this computation is an update of the posterior probability of all possible change point counts. This computation can be challenging, as the number of possibilities grows rapidly with time...
March 23, 2017: Neural Computation
https://www.readbyqxmd.com/read/28328516/anrad-a-neuromorphic-anomaly-detection-framework-for-massive-concurrent-data-streams
#9
Qiuwen Chen, Ryan Luley, Qing Wu, Morgan Bishop, Richard W Linderman, Qinru Qiu
The evolution of high performance computing technologies has enabled the large-scale implementation of neuromorphic models and pushed the research in computational intelligence into a new era. Among the machine learning applications, unsupervised detection of anomalous streams is especially challenging due to the requirements of detection accuracy and real-time performance. Designing a computing framework that harnesses the growing computing power of the multicore systems while maintaining high sensitivity and specificity to the anomalies is an urgent research topic...
March 17, 2017: IEEE Transactions on Neural Networks and Learning Systems
https://www.readbyqxmd.com/read/28328514/dynamic-uncertain-causality-graph-for-knowledge-representation-and-reasoning-utilization-of-statistical-data-and-domain-knowledge-in-complex-cases
#10
Qin Zhang, Quanying Yao
The dynamic uncertain causality graph (DUCG) is a newly presented framework for uncertain causality representation and probabilistic reasoning. It has been successfully applied to online fault diagnoses of large, complex industrial systems, and decease diagnoses. This paper extends the DUCG to model more complex cases than what could be previously modeled, e.g., the case in which statistical data are in different groups with or without overlap, and some domain knowledge and actions (new variables with uncertain causalities) are introduced...
March 17, 2017: IEEE Transactions on Neural Networks and Learning Systems
https://www.readbyqxmd.com/read/28327936/guidock-vnc-using-a-graphical-desktop-sharing-system-to-provide-a-browser-based-interface-for-containerized-software
#11
Varun Mittal, Ling-Hong Hung, Jayant Keswani, Daniel Kristiyanto, Sung Bong Lee, Ka Yee Yeung
Background: Software container technology such as Docker can be used to package and distribute bioinformatics workflows consisting of multiple software implementations and dependencies. However, Docker is a command line based tool and many bioinformatics pipelines consist of components that require a graphical user interface. Findings: We present a container tool called GUIdock-VNC that uses a graphical desktop sharing system to provide a browser-based interface for containerized software...
February 24, 2017: GigaScience
https://www.readbyqxmd.com/read/28326099/disease-risk-assessment-using-a-voronoi-based-network-analysis-of-genes-and-variants-scores
#12
Lin Chen, Gouri Mukerjee, Ruslan Dorfman, Seyed M Moghadas
Much effort has been devoted to assess disease risk based on large-scale protein-protein network and genotype-phenotype associations. However, the challenge of risk prediction for complex diseases remains unaddressed. Here, we propose a framework to quantify the risk based on a Voronoi tessellation network analysis, taking into account the disease association scores of both genes and variants. By integrating ClinVar, SNPnexus, and DISEASES databases, we introduce a gene-variant map that is based on the pairwise disease-associated gene-variant scores...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28325918/robust-analysis-of-fluxes-in-genome-scale-metabolic-pathways
#13
Michael MacGillivray, Amy Ko, Emily Gruber, Miranda Sawyer, Eivind Almaas, Allen Holder
Constraint-based optimization, such as flux balance analysis (FBA), has become a standard systems-biology computational method to study cellular metabolisms that are assumed to be in a steady state of optimal growth. The methods are based on optimization while assuming (i) equilibrium of a linear system of ordinary differential equations, and (ii) deterministic data. However, the steady-state assumption is biologically imperfect, and several key stoichiometric coefficients are experimentally inferred from situations of inherent variation...
March 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28325438/fetal-ecg-extraction-via-type-2-adaptive-neuro-fuzzy-inference-systems
#14
Hajar Ahmadieh, Babak Mohammadzadeh Asl
BACKGROUND AND OBJECTIVE: We proposed a noninvasive method for separating the fetal ECG (FECG) from maternal ECG (MECG) by using Type-2 adaptive neuro-fuzzy inference systems. METHODS: The method can extract FECG components from abdominal signal by using one abdominal channel, including maternal and fetal cardiac signals and other environmental noise signals, and one chest channel. The proposed algorithm detects the nonlinear dynamics of the mother's body. So, the components of the MECG are estimated from the abdominal signal...
April 2017: Computer Methods and Programs in Biomedicine
https://www.readbyqxmd.com/read/28314238/paternity-testing-and-other-inference-about-relationships-from-dna-mixtures
#15
Peter J Green, Julia Mortera
We present methods for inference about relationships between contributors to a DNA mixture and other individuals of known genotype: a basic example would be testing whether a contributor to a mixture is the father of a child of known genotype. The evidence for such a relationship is evaluated as the likelihood ratio for the specified relationship versus the alternative that there is no relationship. We analyse real casework examples from a criminal case and a disputed paternity case; in both examples part of the evidence was from a DNA mixture...
February 16, 2017: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/28306748/does-landscape-connectivity-shape-local-and-global-social-network-structure-in-white-tailed-deer
#16
Erin L Koen, Marie I Tosa, Clayton K Nielsen, Eric M Schauber
Intraspecific social behavior can be influenced by both intrinsic and extrinsic factors. While much research has focused on how characteristics of individuals influence their roles in social networks, we were interested in the role that landscape structure plays in animal sociality at both individual (local) and population (global) levels. We used female white-tailed deer (Odocoileus virginianus) in Illinois, USA, to investigate the potential effect of landscape on social network structure by weighting the edges of seasonal social networks with association rate (based on proximity inferred from GPS collar data)...
2017: PloS One
https://www.readbyqxmd.com/read/28301504/identification-of-marginal-causal-relationships-in-gene-networks-from-observational-and-interventional-expression-data
#17
Gilles Monneret, Florence Jaffrézic, Andrea Rau, Tatiana Zerjal, Grégory Nuel
Causal network inference is an important methodological challenge in biology as well as other areas of application. Although several causal network inference methods have been proposed in recent years, they are typically applicable for only a small number of genes, due to the large number of parameters to be estimated and the limited number of biological replicates available. In this work, we consider the specific case of transcriptomic studies made up of both observational and interventional data in which a single gene of biological interest is knocked out...
2017: PloS One
https://www.readbyqxmd.com/read/28301472/independent-introductions-and-admixtures-have-contributed-to-adaptation-of-european-maize-and-its-american-counterparts
#18
Jean-Tristan Brandenburg, Tristan Mary-Huard, Guillem Rigaill, Sarah J Hearne, Hélène Corti, Johann Joets, Clémentine Vitte, Alain Charcosset, Stéphane D Nicolas, Maud I Tenaillon
Through the local selection of landraces, humans have guided the adaptation of crops to a vast range of climatic and ecological conditions. This is particularly true of maize, which was domesticated in a restricted area of Mexico but now displays one of the broadest cultivated ranges worldwide. Here, we sequenced 67 genomes with an average sequencing depth of 18x to document routes of introduction, admixture and selective history of European maize and its American counterparts. To avoid the confounding effects of recent breeding, we targeted germplasm (lines) directly derived from landraces...
March 16, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28298703/a-tutorial-on-the-free-energy-framework-for-modelling-perception-and-learning
#19
Rafal Bogacz
This paper provides an easy to follow tutorial on the free-energy framework for modelling perception developed by Friston, which extends the predictive coding model of Rao and Ballard. These models assume that the sensory cortex infers the most likely values of attributes or features of sensory stimuli from the noisy inputs encoding the stimuli. Remarkably, these models describe how this inference could be implemented in a network of very simple computational elements, suggesting that this inference could be performed by biological networks of neurons...
February 2017: Journal of Mathematical Psychology
https://www.readbyqxmd.com/read/28298218/systematic-identification-of-an-integrative-network-module-during-senescence-from-time-series-gene-expression
#20
Chihyun Park, So Jeong Yun, Sung Jin Ryu, Soyoung Lee, Young-Sam Lee, Youngmi Yoon, Sang Chul Park
BACKGROUND: Cellular senescence irreversibly arrests growth of human diploid cells. In addition, recent studies have indicated that senescence is a multi-step evolving process related to important complex biological processes. Most studies analyzed only the genes and their functions representing each senescence phase without considering gene-level interactions and continuously perturbed genes. It is necessary to reveal the genotypic mechanism inferred by affected genes and their interaction underlying the senescence process...
March 15, 2017: BMC Systems Biology
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