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network inference

Malgorzata A Gazda, Pedro Andrade, Sandra Afonso, Jolita Dilyte, John P Archer, Ricardo J Lopes, Rui Faria, Miguel Carneiro
Racing pigeons have been selectively bred to find their way home quickly over what are often extremely long distances. This breed is of substantial commercial value and is also an excellent avian model to gain empirical insights into the evolution of traits associated with flying performance and spatial orientation. Here, we investigate the molecular basis of the superior athletic and navigational capabilities of racing pigeons using whole-genome and RNA sequencing data. We inferred multiple signatures of positive selection distributed across the genome of racing pigeons...
March 13, 2018: Molecular Biology and Evolution
Marinho A Lopes, Mark P Richardson, Eugenio Abela, Christian Rummel, Kaspar Schindler, Marc Goodfellow, John R Terry
Recent studies have shown that mathematical models can be used to analyze brain networks by quantifying how likely they are to generate seizures. In particular, we have introduced the quantity termed brain network ictogenicity (BNI), which was demonstrated to have the capability of differentiating between functional connectivity (FC) of healthy individuals and those with epilepsy. Furthermore, BNI has also been used to quantify and predict the outcome of epilepsy surgery based on FC extracted from pre-operative ictal intracranial electroencephalography (iEEG)...
2018: Frontiers in Neurology
Wouter Saelens, Robrecht Cannoodt, Yvan Saeys
A critical step in the analysis of large genome-wide gene expression datasets is the use of module detection methods to group genes into co-expression modules. Because of limitations of classical clustering methods, numerous alternative module detection methods have been proposed, which improve upon clustering by handling co-expression in only a subset of samples, modelling the regulatory network, and/or allowing overlap between modules. In this study we use known regulatory networks to do a comprehensive and robust evaluation of these different methods...
March 15, 2018: Nature Communications
Junling Long, H S Ku, Xian Wu, Xiu Gu, Russell E Lake, Mustafa Bal, Yu-Xi Liu, David P Pappas
Quantum networks will enable extraordinary capabilities for communicating and processing quantum information. These networks require a reliable means of storage, retrieval, and manipulation of quantum states at the network nodes. A node receives one or more coherent inputs and sends a conditional output to the next cascaded node in the network through a quantum channel. Here, we demonstrate this basic functionality by using the quantum interference mechanism of electromagnetically induced transparency in a transmon qubit coupled to a superconducting resonator...
February 23, 2018: Physical Review Letters
Kathleen S Rockland
Recent commentaries on the role of the thalamus consider a wide sphere of influence beyond sensory-motor transformation, to include task-relevant cognitive processes. In this short review, I reconsider known anatomic features of corticothalamic connectivity, primarily for macaque monkey, and discuss these as part of an intricate network architecture consistent with multiple connectional re-combinations and a diversity of functional tasks. Drawing mainly on results from single axon analysis for the two broad classes of corticothalamic (CT) connections, I review the strikingly complementary spatial parameters of their extrinsic CT arbors in relation to intrinsic cortical collaterals...
March 14, 2018: European Journal of Neuroscience
Balasundaram Kadirvelu, Yoshikatsu Hayashi, Slawomir J Nasuto
A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has not been fixed in the paper.
March 14, 2018: Scientific Reports
Darren A Cusanovich, James P Reddington, David A Garfield, Riza M Daza, Delasa Aghamirzaie, Raquel Marco-Ferreres, Hannah A Pliner, Lena Christiansen, Xiaojie Qiu, Frank J Steemers, Cole Trapnell, Jay Shendure, Eileen E M Furlong
Understanding how gene regulatory networks control the progressive restriction of cell fates is a long-standing challenge. Recent advances in measuring gene expression in single cells are providing new insights into lineage commitment. However, the regulatory events underlying these changes remain unclear. Here we investigate the dynamics of chromatin regulatory landscapes during embryogenesis at single-cell resolution. Using single-cell combinatorial indexing assay for transposase accessible chromatin with sequencing (sci-ATAC-seq), we profiled chromatin accessibility in over 20,000 single nuclei from fixed Drosophila melanogaster embryos spanning three landmark embryonic stages: 2-4 h after egg laying (predominantly stage 5 blastoderm nuclei), when each embryo comprises around 6,000 multipotent cells; 6-8 h after egg laying (predominantly stage 10-11), to capture a midpoint in embryonic development when major lineages in the mesoderm and ectoderm are specified; and 10-12 h after egg laying (predominantly stage 13), when each of the embryo's more than 20,000 cells are undergoing terminal differentiation...
March 14, 2018: Nature
Ilia Korvigo, Andrey Afanasyev, Nikolay Romashchenko, Mikhail Skoblov
Many automatic classifiers were introduced to aid inference of phenotypical effects of uncategorised nsSNVs (nonsynonymous Single Nucleotide Variations) in theoretical and medical applications. Lately, several meta-estimators have been proposed that combine different predictors, such as PolyPhen and SIFT, to integrate more information in a single score. Although many advances have been made in feature design and machine learning algorithms used, the shortage of high-quality reference data along with the bias towards intensively studied in vitro models call for improved generalisation ability in order to further increase classification accuracy and handle records with insufficient data...
2018: PloS One
Taryn Klarner, E Paul Zehr
Evidence first described in reduced animal models over 100 years ago led to deductions about the control of locomotion through spinal locomotor central pattern generating (CPG) networks. These discoveries in nature were contemporaneous with another form of deductive reasoning found in popular culture-that of Arthur Conan Doyle's detective "Sherlock Holmes". Since the invasive methods used in reduced non-human animal preparations are not amenable to study in humans, we are left instead with deducing from other measures and observations...
March 14, 2018: Journal of Neurophysiology
Kumar Parijat Tripathi, Marina Piccirillo, Mario Rosario Guarracino
BACKGROUND: The endomembrane system, known as secretory pathway, is responsible for the synthesis and transport of protein molecules in cells. Therefore, genes involved in the secretory pathway are essential for the cellular development and function. Recent scientific investigations show that ER and Golgi apparatus may provide a convenient drug target for cancer therapy. On the other hand, it is known that abundantly expressed genes in different cellular organelles share interconnected pathways and co-regulate each other activities...
March 8, 2018: BMC Bioinformatics
Tom Dudding, Mattias Johansson, Steven J Thomas, Paul Brennan, Richard M Martin, Nicholas J Timpson
Circulating 25-hydroxyvitamin D (25OHD) is an appealing potential intervention for cancer risk and has been associated with oral and oropharyngeal cancer risk but evidence is inconsistent. The availability of genetic variants, uncorrelated with known confounders, but predictive of 25OHD and genetic data in a large oral and oropharyngeal cancer collaboration aids causal inference when assessing this association. 5,133 oral and oropharyngeal cancer cases and 5,984 controls with genetic data were included in the study...
March 14, 2018: International Journal of Cancer. Journal International du Cancer
Guangyong Zheng, Tao Huang
In post-genomic era, an important task is to explore the function of individual biological molecules (i.e., gene, noncoding RNA, protein, metabolite) and their organization in living cells. For this end, gene regulatory networks (GRNs) are constructed to show relationship between biological molecules, in which the vertices of network denote biological molecules and the edges of network present connection between nodes (Strogatz, Nature 410:268-276, 2001; Bray, Science 301:1864-1865, 2003). Biologists can understand not only the function of biological molecules but also the organization of components of living cells through interpreting the GRNs, since a gene regulatory network is a comprehensively physiological map of living cells and reflects influence of genetic and epigenetic factors (Strogatz, Nature 410:268-276, 2001; Bray, Science 301:1864-1865, 2003)...
2018: Methods in Molecular Biology
J M Colston, A M S Ahmed, S B Soofi, E Svensen, R Haque, J Shrestha, R Nshama, Z Bhutta, I F N Lima, A Samie, L Bodhidatta, A A M Lima, P Bessong, M Paredes Olortegui, A Turab, V R Mohan, L H Moulton, E N Naumova, G Kang, M N Kosek
Improving understanding of the pathogen-specific seasonality of enteric infections is critical to informing policy on the timing of preventive measures and to forecast trends in the burden of diarrhoeal disease. Data obtained from active surveillance of cohorts can capture the underlying infection status as transmission occurs in the community. The purpose of this study was to characterise rotavirus seasonality in eight different locations while adjusting for age, calendar time and within-subject clustering of episodes by applying an adapted Serfling model approach to data from a multi-site cohort study...
March 14, 2018: Epidemiology and Infection
Cora L Bernard, Margaret L Brandeau
Structural assumptions in infectious disease models, such as the choice of network or compartmental model type or the inclusion of different types of heterogeneity across individuals, might affect model predictions as much as or more than the choice of input parameters. We explore the potential implications of structural assumptions on HIV model predictions and policy conclusions. We illustrate the value of inference robustness assessment through a case study of the effects of a hypothetical HIV vaccine in multiple population subgroups over eight related transmission models, which we sequentially modify to vary over two dimensions: parameter complexity (e...
November 2017: Infectious Disease Modelling
Heng Yao, Xiaoxuan Wang, Pengcheng Chen, Ling Hai, Kang Jin, Lixia Yao, Chuanzao Mao, Xin Chen
An advanced functional understanding of omics data is important for elucidating the design logic of physiological processes in plants and effectively controlling desired traits in plants. We present the latest version of the predicted Arabidopsis interactome resource (PAIR) and of the gene set linkage analysis (GSLA) tool, which enable the interpretation of an observed transcriptomic change (differentially expressed genes, DEGs) in Arabidopsis with respect to its functional impact for biological processes. PAIR v5...
March 12, 2018: Plant Physiology
Petra Bilić, Nicolas Guillemin, Alan Kovačević, Blanka Beer Ljubić, Ines Jović, Asier Galan, Peter David Eckersall, Richard Burchmore, Vladimir Mrljak
Idiopathic dilated cardiomyopathy (iDCM) is a primary myocardial disorder with an unknown aetiology, characterized by reduced contractility and ventricular dilation of the left or both ventricles. Naturally occurring canine iDCM was used herein to identify serum proteomic signature of the disease compared to the healthy state, providing an insight into underlying mechanisms and revealing proteins with biomarker potential. To achieve this, we used high-throughput label-based quantitative LC-MS/MS proteomics approach and bioinformatics analysis of the in silico inferred interactome protein network created from the initial list of differential proteins...
March 9, 2018: Journal of Proteomics
Christopher S Parker, Jonathan D Clayden, M Jorge Cardoso, Roman Rodionov, John S Duncan, Catherine Scott, Beate Diehl, Sebastien Ourselin
Patients with medically-refractory focal epilepsy may be candidates for neurosurgery and some may require placement of intracranial EEG electrodes to localise seizure onset. Assessing cerebral responses to single pulse electrical stimulation (SPES) may give diagnostically useful data. SPES produces cortico-cortical evoked potentials (CCEPs), which infer effective brain connectivity. Diffusion-weighted images and tractography may be used to estimate structural brain connectivity. This combination provides the opportunity to observe seizure onset and its propagation throughout the brain, spreading contiguously along the cortex explored with electrodes, or non-contiguously...
2018: NeuroImage: Clinical
Eugenio Parente, Teresa Zotta, Karoline Faust, Francesca De Filippis, Danilo Ercolini
The structure of microbial association networks was investigated for seventeen studies on food bacterial communities using the CoNet app. The results were compared with those for host and environmental microbiomes. Microbial association networks of food bacterial communities shared several properties with those of host microbiomes, although they were less complex and lacked a scale-free, small world structure that is characteristic of environmental microbial communities. This may depend on both the initial contamination pattern, whose main source is the raw material microbiome, and on the copiotrophic nature of food environments, with lack of well defined, specific niches...
August 2018: Food Microbiology
Lucas M B Yoshihara, Elizabeth P G Arêas
The coacervation of carboxymethylcellulose (CMC) and hen egg white lysozyme (HEWL) was investigated. The work focused on the effects of pH, ionic strength, I, temperature, T, and mass fraction of the macromolecular components on the coacervation process by spectrophotometry, and on characteristics of the resulting coacervate phase by rheology in the linear and non-linear regimes. Coacervation was found to be highest at HEWL mass fraction ≈0.25 with very slight dependence on pH in the range from 5 to 9. The process was favored at I < 0...
March 2, 2018: Biophysical Chemistry
Michael Habeck, Thach Nguyen
Biological macromolecules often undergo large conformational rearrangements during a functional cycle. To simulate these structural transitions with full atomic detail typically demands extensive computational resources. Moreover, it is unclear how to incorporate, in a principled way, additional experimental information that could guide the structural transition. This article develops a probabilistic model for conformational transitions in biomolecules. The model can be viewed as a network of anharmonic springs that break, if the experimental data support the rupture of bonds...
March 9, 2018: Proteins
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