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https://www.readbyqxmd.com/read/28319698/the-combined-effect-of-reduced-fossil-fuel-consumption-and-increasing-biomass-combustion-on-athens-air-quality-as-inferred-from-long-term-co-measurements
#1
Myrto Gratsea, Eleni Liakakou, Nikos Mihalopoulos, Anastasios Adamopoulos, Eirini Tsilibari, Evangelos Gerasopoulos
To evaluate the role of biomass burning emissions, and in particular of residential wood heating, as a result of the economic recession in Greece, carbon monoxide (CO) atmospheric concentrations from five (5) stations of the National Air Pollution Monitoring Network in Athens, spanning the period 2000-2015, in conjunction with black carbon (BC) concentrations from the NOA (National Observatory of Athens) station at Thissio were analysed. The contribution of the different sources to the diurnal cycle of these two pollutants is clear, resulting to a morning peak, mainly due to traffic, and a late evening peak attributed both to fossil fuel (traffic plus central heating) and biomass combustion...
March 14, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/28319121/growth-altering-microbial-interactions-are-responsive-to-chemical-context
#2
Angela Liu, Anne M Archer, Matthew B Biggs, Jason A Papin
Microbial interactions are ubiquitous in nature, and are equally as relevant to human wellbeing as the identities of the interacting microbes. However, microbial interactions are difficult to measure and characterize. Furthermore, there is growing evidence that they are not fixed, but dependent on environmental context. We present a novel workflow for inferring microbial interactions that integrates semi-automated image analysis with a colony stamping mechanism, with the overall effect of improving throughput and reproducibility of colony interaction assays...
2017: PloS One
https://www.readbyqxmd.com/read/28315039/ecology-and-feeding-habits-drive-infection-of-water-bugs-with-mycobacterium-ulcerans
#3
Solange Meyin A Ebong, Gabriel E García-Peña, Dominique Pluot-Sigwalt, Laurent Marsollier, Philippe Le Gall, Sara Eyangoh, Jean-François Guégan
Mycobacterium ulcerans (MU), the causative agent of Buruli ulcer, is present in a wide spectrum of environments, including terrestrial and aquatic ecosystems in tropical regions. The most promising studies on the epidemiological risk of this disease suggest that some ecological settings may favor infection of animals with MU including human. A species' needs and impacts on resources and the environment, i.e., its ecological niche, may influence its susceptibility to be infected by this microbial form. For example, some Naucoridae may dive in fresh waters to prey upon infected animals and thus may get infected with MU...
March 17, 2017: EcoHealth
https://www.readbyqxmd.com/read/28314784/integrative-cancer-pharmacogenomics-to-infer-large-scale-drug-taxonomy
#4
Nehme El-Hachem, Deena M A Gendoo, Laleh Soltan Ghoraie, Zhaleh Safikhani, Petr Smirnov, Christina Chung, Kenan Deng, Alisa Fang, Erin Birkwood, Chantal Ho, Ruth Isserlin, Gary Bader, Anna Goldenberg, Benjamin Haibe-Kains
Identification of drug targets and mechanism of action (MoA) for new and uncharacterized anticancer drugs is important for optimization of treatment efficacy. Current MoA prediction largely relies on prior information including side effects, therapeutic indication, and chemo-informatics. Such information is not transferable or applicable for newly identified, previously uncharacterized small molecules. Therefore, a shift in the paradigm of MoA predictions is necessary towards development of unbiased approaches that can elucidate drug relationships and efficiently classify new compounds with basic input data...
March 17, 2017: Cancer Research
https://www.readbyqxmd.com/read/28314238/paternity-testing-and-other-inference-about-relationships-from-dna-mixtures
#5
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
#6
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
#7
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
#8
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
#9
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
#10
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
https://www.readbyqxmd.com/read/28296635/dynamics-of-embryonic-stem-cell-differentiation-inferred-from-single-cell-transcriptomics-show-a-series-of-transitions-through-discrete-cell-states
#11
Sumin Jang, Sandeep Choubey, Leon Furchtgott, Ling-Nan Zou, Adele Doyle, Vilas Menon, Ethan B Loew, Anne-Rachel Krostag, Refugio A Martinez, Linda Madisen, Boaz P Levi, Sharad Ramanathan
The complexity of gene regulatory networks that lead multipotent cells to acquire different cell fates makes a quantitative understanding of differentiation challenging. Using a statistical framework to analyze single-cell transcriptomics data, we infer the gene expression dynamics of early mouse embryonic stem (mES) cell differentiation, uncovering discrete transitions across nine cell states. We validate the predicted transitions across discrete states using flow cytometry. Moreover, using live-cell microscopy, we show that individual cells undergo abrupt transitions from a naïve to primed pluripotent state...
March 15, 2017: ELife
https://www.readbyqxmd.com/read/28294630/peak-integrating-curated-and-noisy-prior-knowledge-in-gene-regulatory-network-inference
#12
Doaa Altarawy, Fatma-Elzahraa Eid, Lenwood S Heath
With abundance of biological data, computational prediction of gene regulatory networks (GRNs) from gene expression data has become more feasible. Although incorporating other prior knowledge (PK), along with gene expression data, greatly improves prediction accuracy, the overall accuracy is still low. PK in GRN inference can be categorized into noisy and curated. In noisy PK, relations between genes do not necessarily correspond to regulatory relations and are thus considered inaccurate by inference algorithms such as transcription factor binding and protein-protein interactions...
March 15, 2017: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/28294287/learning-gene-regulatory-networks-from-next-generation-sequencing-data
#13
Bochao Jia, Suwa Xu, Guanghua Xiao, Vishal Lamba, Faming Liang
In recent years, next generation sequencing (NGS) has gradually replaced microarray as the major platform in measuring gene expressions. Compared to microarray, NGS has many advantages, such as less noise and higher throughput. However, the discreteness of NGS data also challenges the existing statistical methodology. In particular, there still lacks an appropriate statistical method for reconstructing gene regulatory networks using NGS data in the literature. The existing local Poisson graphical model method is not consistent and can only infer certain local structures of the network...
March 10, 2017: Biometrics
https://www.readbyqxmd.com/read/28292731/pathway-cross-talk-network-analysis-identifies-critical-pathways-in-neonatal-sepsis
#14
Yu-Xiu Meng, Quan-Hong Liu, Deng-Hong Chen, Ying Meng
BACKGROUND: Despite advances in neonatal care, sepsis remains a major cause of morbidity and mortality in neonates worldwide. Pathway cross-talk analysis might contribute to the inference of the driving forces in bacterial sepsis and facilitate a better understanding of underlying pathogenesis of neonatal sepsis. OBJECTIVE: This study aimed to explore the critical pathways associated with the progression of neonatal sepsis by the pathway cross-talk analysis. METHODS: By integrating neonatal transcriptome data with known pathway data and protein-protein interaction data, we systematically uncovered the disease pathway cross-talks and constructed a disease pathway cross-talk network for neonatal sepsis...
February 27, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28292312/comprehensive-discovery-of-subsample-gene-expression-components-by-information-explanation-therapeutic-implications-in-cancer
#15
Shirley Pepke, Greg Ver Steeg
BACKGROUND: De novo inference of clinically relevant gene function relationships from tumor RNA-seq remains a challenging task. Current methods typically either partition patient samples into a few subtypes or rely upon analysis of pairwise gene correlations that will miss some groups in noisy data. Leveraging higher dimensional information can be expected to increase the power to discern targetable pathways, but this is commonly thought to be an intractable computational problem. METHODS: In this work we adapt a recently developed machine learning algorithm for sensitive detection of complex gene relationships...
March 15, 2017: BMC Medical Genomics
https://www.readbyqxmd.com/read/28290051/construction-of-a-comprehensive-protein-protein-interaction-map-for-vitiligo-disease-to-identify-key-regulatory-elements-a-systemic-approach
#16
Anvita Gupta Malhotra, Mohit Jha, Sudha Singh, Khushhali M Pandey
Vitiligo is an idiopathic disorder characterized by depigmented patches on the skin due to progressive loss of melanocytes. Several genetic, immunological, and pathophysiological investigations have established vitiligo as a polygenetic disorder with multifactorial etiology. However, no definite model explaining the interplay between these causative factors has been established hitherto. Therefore, we studied the disorder at the system level to identify the key proteins involved by exploring their molecular connectivity in terms of topological parameters...
March 13, 2017: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/28289601/3d-scattering-transforms-for-disease-classification-in-neuroimaging
#17
Tameem Adel, Taco Cohen, Matthan Caan, Max Welling
Classifying neurodegenerative brain diseases in MRI aims at correctly assigning discrete labels to MRI scans. Such labels usually refer to a diagnostic decision a learner infers based on what it has learned from a training sample of MRI scans. Classification from MRI voxels separately typically does not provide independent evidence towards or against a class; the information relevant for classification is only present in the form of complicated multivariate patterns (or "features"). Deep learning solves this problem by learning a sequence of non-linear transformations that result in feature representations that are better suited to classification...
2017: NeuroImage: Clinical
https://www.readbyqxmd.com/read/28288905/bioinformatic-approaches-to-interrogating-vitamin-d-receptor-signaling
#18
Moray J Campbell
Bioinformatics applies unbiased approaches to develop statistically-robust insight into health and disease. At the global, or "20,000 foot" view bioinformatic analyses of vitamin D receptor (NR1I1/VDR) signaling can measure where the VDR gene or protein exerts a genome-wide significant impact on biology; VDR is significantly implicated in bone biology and immune systems, but not in cancer. With a more VDR-centric, or "2000 foot" view, bioinformatic approaches can interrogate events downstream of VDR activity...
March 10, 2017: Molecular and Cellular Endocrinology
https://www.readbyqxmd.com/read/28288164/bayesian-model-of-signal-rewiring-reveals-mechanisms-of-gene-dysregulation-in-acquired-drug-resistance-in-breast-cancer
#19
A K M Azad, Alfons Lawen, Jonathan M Keith
Small molecule inhibitors, such as lapatinib, are effective against breast cancer in clinical trials, but tumor cells ultimately acquire resistance to the drug. Maintaining sensitization to drug action is essential for durable growth inhibition. Recently, adaptive reprogramming of signaling circuitry has been identified as a major cause of acquired resistance. We developed a computational framework using a Bayesian statistical approach to model signal rewiring in acquired resistance. We used the p1-model to infer potential aberrant gene-pairs with differential posterior probabilities of appearing in resistant-vs-parental networks...
2017: PloS One
https://www.readbyqxmd.com/read/28287569/self-assembling-morphologies-obtained-from-helical-polycarbodiimide-copolymers-and-their-triazole-derivatives
#20
Oleg V Kulikov, Dumindika A Siriwardane, Gregory T McCandless, Samsuddin F Mahmood, Bruce M Novak
A facile method for the preparation of polycarbodiimide-based secondary structures (e.g., nano-rings, "craters," fibers, looped fibers, fibrous networks, ribbons, worm-like aggregates, toroidal structures, and spherical particles) is described. These aggregates are morphologically influenced by extensive hydrophobic side chain-side chain interactions of the singular polycarbodiimide strands, as inferred by atomic force microscopy (AFM) and scanning electron microscopy (SEM) techniques. Polycarbodiimide-g-polystyrene copolymers (PS-PCDs) were prepared by a combination of synthetic methods, including coordination-insertion polymerization, copper(I)-catalyzed azide alkyne cycloaddition (CuAAC) "click" chemistry, and atom transfer radical polymerization (ATRP)...
February 7, 2017: Journal of Visualized Experiments: JoVE
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