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https://www.readbyqxmd.com/read/27912731/predicting-the-recurrence-of-noncoding-regulatory-mutations-in-cancer
#1
Woojin Yang, Hyoeun Bang, Kiwon Jang, Min Kyung Sung, Jung Kyoon Choi
BACKGROUND: One of the greatest challenges in cancer genomics is to distinguish driver mutations from passenger mutations. Whereas recurrence is a hallmark of driver mutations, it is difficult to observe recurring noncoding mutations owing to a limited amount of whole-genome sequenced samples. Hence, it is required to develop a method to predict potentially recurrent mutations. RESULTS: In this work, we developed a random forest classifier that predicts regulatory mutations that may recur based on the features of the mutations repeatedly appearing in a given cohort...
December 3, 2016: BMC Bioinformatics
https://www.readbyqxmd.com/read/27903706/phase-amplitude-coupling-and-long-range-phase-synchronization-reveal-frontotemporal-interactions-during-visual-working-memory
#2
Jonathan Daume, Thomas Gruber, Andreas K Engel, Uwe Friese
: It has been suggested that cross-frequency phase-amplitude coupling (PAC) particularly in temporal brain structures serves as a neural mechanism for coordinated working memory storage. In this magnetoencephalography study, we show that during visual working memory maintenance, temporal cortex regions, which exhibit enhanced PAC, interact with prefrontal cortex via enhanced low-frequency phase synchronization. Healthy human participants were engaged in a visual delayed-matching-to-sample task with pictures of natural objects...
November 30, 2016: Journal of Neuroscience: the Official Journal of the Society for Neuroscience
https://www.readbyqxmd.com/read/27903261/discrete-phenotypes-are-not-underpinned-by-genome-wide-genetic-differentiation-in-the-squat-lobster-munida-gregaria-crustacea-decapoda-munididae-a-multi-marker-study-covering-the-patagonian-shelf
#3
Chen Wang, Shobhit Agrawal, Jürgen Laudien, Vreni Häussermann, Christoph Held
BACKGROUND: DNA barcoding has demonstrated that many discrete phenotypes are in fact genetically distinct (pseudo)cryptic species. Genetically identical, isogenic individuals, however, can also express similarly different phenotypes in response to a trigger condition, e.g. in the environment. This alternative explanation to cryptic speciation often remains untested because it requires considerable effort to reject the hypothesis that the observed underlying genetic homogeneity of the different phenotypes may be trivially caused by too slowly evolving molecular markers...
December 1, 2016: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/27895562/brain-computation-is-organized-via-power-of-two-based-permutation-logic
#4
Kun Xie, Grace E Fox, Jun Liu, Cheng Lyu, Jason C Lee, Hui Kuang, Stephanie Jacobs, Meng Li, Tianming Liu, Sen Song, Joe Z Tsien
There is considerable scientific interest in understanding how cell assemblies-the long-presumed computational motif-are organized so that the brain can generate intelligent cognition and flexible behavior. The Theory of Connectivity proposes that the origin of intelligence is rooted in a power-of-two-based permutation logic (N = 2 (i) -1), producing specific-to-general cell-assembly architecture capable of generating specific perceptions and memories, as well as generalized knowledge and flexible actions. We show that this power-of-two-based permutation logic is widely used in cortical and subcortical circuits across animal species and is conserved for the processing of a variety of cognitive modalities including appetitive, emotional and social information...
2016: Frontiers in Systems Neuroscience
https://www.readbyqxmd.com/read/27887859/olanzapine-modulation-of-long-and-short-range-functional-connectivity-in-the-resting-brain-in-a-sample-of-patients-with-schizophrenia
#5
Wenbin Guo, Feng Liu, Jindong Chen, Renrong Wu, Lehua Li, Zhikun Zhang, Jingping Zhao
Treatment effects of antipsychotic drugs on cerebral function are seldom examined. Exploring functional connectivity (FC) in drug-free schizophrenia patients before and after antipsychotic treatment can improve the understanding of antipsychotic drug mechanisms. A total of 17 drug-free patients with recurrent schizophrenia and 24 healthy controls underwent resting-state functional magnetic resonance imaging scans. Long- and short-range FC strengths (FCS) were calculated for each participant. Compared with the controls, the patients at baseline exhibited increased long-range positive FCS (lpFCS) in the bilateral inferior parietal lobule (IPL) and decreased lpFCS in the brain regions of the default-mode network (DMN) regions and sensorimotor circuits of the brain...
November 22, 2016: European Neuropsychopharmacology: the Journal of the European College of Neuropsychopharmacology
https://www.readbyqxmd.com/read/27886204/characterization-of-structural-connectivity-of-the-default-mode-network-in-dogs-using-diffusion-tensor-imaging
#6
Jennifer L Robinson, Madhura Baxi, Jeffrey S Katz, Paul Waggoner, Ronald Beyers, Edward Morrison, Nouha Salibi, Thomas S Denney, Vitaly Vodyanoy, Gopikrishna Deshpande
Diffusion tensor imaging (DTI) provides us an insight into the micro-architecture of white-matter tracts in the brain. This method has proved promising in understanding and investigating the neuronal tracts and structural connectivity between the brain regions in primates as well as rodents. The close evolutionary relationship between canines and humans may have spawned a unique bond in regard to social cognition rendering them useful as an animal model in translational research. In this study, we acquired diffusion data from anaesthetized dogs and created a DTI-based atlas for a canine model which could be used to investigate various white matter diseases...
November 25, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27886166/generation-of-single-photons-with-highly-tunable-wave-shape-from-a-cold-atomic-ensemble
#7
Pau Farrera, Georg Heinze, Boris Albrecht, Melvyn Ho, Matías Chávez, Colin Teo, Nicolas Sangouard, Hugues de Riedmatten
The generation of ultra-narrowband, pure and storable single photons with widely tunable wave shape is an enabling step toward hybrid quantum networks requiring interconnection of remote disparate quantum systems. It allows interaction of quantum light with several material systems, including photonic quantum memories, single trapped ions and opto-mechanical systems. Previous approaches have offered a limited tuning range of the photon duration of at most one order of magnitude. Here we report on a heralded single photon source with controllable emission time based on a cold atomic ensemble, which can generate photons with temporal durations varying over three orders of magnitude up to 10 μs without a significant change of the readout efficiency...
November 25, 2016: Nature Communications
https://www.readbyqxmd.com/read/27881803/inferring-animal-social-networks-and-leadership-applications-for-passive-monitoring-arrays
#8
David M P Jacoby, Yannis P Papastamatiou, Robin Freeman
Analyses of animal social networks have frequently benefited from techniques derived from other disciplines. Recently, machine learning algorithms have been adopted to infer social associations from time-series data gathered using remote, telemetry systems situated at provisioning sites. We adapt and modify existing inference methods to reveal the underlying social structure of wide-ranging marine predators moving through spatial arrays of passive acoustic receivers. From six months of tracking data for grey reef sharks (Carcharhinus amblyrhynchos) at Palmyra atoll in the Pacific Ocean, we demonstrate that some individuals emerge as leaders within the population and that this behavioural coordination is predicted by both sex and the duration of co-occurrences between conspecifics...
November 2016: Journal of the Royal Society, Interface
https://www.readbyqxmd.com/read/27881755/unravelling-darwin-s-entangled-bank-architecture-and-robustness-of-mutualistic-networks-with-multiple-interaction-types
#9
Wesley Dáttilo, Nubia Lara-Rodríguez, Pedro Jordano, Paulo R Guimarães, John N Thompson, Robert J Marquis, Lucas P Medeiros, Raul Ortiz-Pulido, Maria A Marcos-García, Victor Rico-Gray
Trying to unravel Darwin's entangled bank further, we describe the architecture of a network involving multiple forms of mutualism (pollination by animals, seed dispersal by birds and plant protection by ants) and evaluate whether this multi-network shows evidence of a structure that promotes robustness. We found that species differed strongly in their contributions to the organization of the multi-interaction network, and that only a few species contributed to the structuring of these patterns. Moreover, we observed that the multi-interaction networks did not enhance community robustness compared with each of the three independent mutualistic networks when analysed across a range of simulated scenarios of species extinction...
November 30, 2016: Proceedings. Biological Sciences
https://www.readbyqxmd.com/read/27880846/potential-impacts-of-climate-change-on-native-plant-distributions-in-the-falkland-islands
#10
Rebecca Upson, Jennifer J Williams, Tim P Wilkinson, Colin P Clubbe, Ilya M D Maclean, Jim H McAdam, Justin F Moat
The Falkland Islands are predicted to experience up to 2.2°C rise in mean annual temperature over the coming century, greater than four times the rate over the last century. Our study investigates likely vulnerabilities of a suite of range-restricted species whose distributions are associated with archipelago-wide climatic variation. We used present day climate maps calibrated using local weather data, 2020-2080 climate predictions from regional climate models, non-climate variables derived from a digital terrain model and a comprehensive database on local plant distributions...
2016: PloS One
https://www.readbyqxmd.com/read/27876855/navigation-by-anomalous-random-walks-on-complex-networks
#11
Tongfeng Weng, Jie Zhang, Moein Khajehnejad, Michael Small, Rui Zheng, Pan Hui
Anomalous random walks having long-range jumps are a critical branch of dynamical processes on networks, which can model a number of search and transport processes. However, traditional measurements based on mean first passage time are not useful as they fail to characterize the cost associated with each jump. Here we introduce a new concept of mean first traverse distance (MFTD) to characterize anomalous random walks that represents the expected traverse distance taken by walkers searching from source node to target node, and we provide a procedure for calculating the MFTD between two nodes...
November 23, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27876079/copenhagen-infant-mental-health-project-study-protocol-for-a-randomized-controlled-trial-comparing-circle-of-security-parenting-and-care-as-usual-as-interventions-targeting-infant-mental-health-risks
#12
Mette Skovgaard Væver, Johanne Smith-Nielsen, Theis Lange
BACKGROUND: Infant mental health is a significant public health issue as early adversity and exposure to early childhood stress are significant risk factors that may have detrimental long-term developmental consequences for the affected children. Negative outcomes are seen on a range of areas such as physical and mental health, educational and labor market success, social network and establishing of family. Secure attachment is associated with optimal outcomes in all developmental domains in childhood, and both insecure and disorganized attachment are associated with a range of later problems and psychopathologies...
November 22, 2016: BMC Psychology
https://www.readbyqxmd.com/read/27875020/linking-otolith-microchemistry-and-dendritic-isoscapes-to-map-heterogeneous-production-of-fish-across-river-basins
#13
Sean R Brennan, Daniel E Schindler
Production patterns of highly mobile species, such as anadromous fish, often exhibit high spatial and temporal heterogeneity across landscapes. Such variability is often asynchronous in time among habitats, which stabilizes production at aggregate scales of complexity. Reconstructing production patterns explicitly in space and time across multiple scales, however, remains difficult but is important for prioritizing habitat conservation. This is especially true for fishes inhabiting river basins due to long-range dispersal, high mortality at early life stages, complex population structure and elusive life history variation...
November 22, 2016: Ecological Applications: a Publication of the Ecological Society of America
https://www.readbyqxmd.com/read/27874019/long-range-synchrony-and-emergence-of-neural-reentry
#14
Hanna Keren, Shimon Marom
Neural synchronization across long distances is a functionally important phenomenon in health and disease. In order to access the basis of different modes of long-range synchrony, we monitor spiking activities over centimetre scale in cortical networks and show that the mode of synchrony depends upon a length scale, λ, which is the minimal path that activity should propagate through to find its point of origin ready for reactivation. When λ is larger than the physical dimension of the network, distant neuronal populations operate synchronously, giving rise to irregularly occurring network-wide events that last hundreds of milliseconds to several seconds...
November 22, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27871920/integrating-long-acting-reversible-contraception-larc-services-into-new-york-city-school-based-health-centers-sbhcs-quality-improvement-to-ensure-provision-of-youth-friendly-services
#15
Manaswi Sangraula, Samantha Garbers, Janet Garth, Emily Birchfield Shakibnia, Sarah Timmons, Melanie A Gold
STUDY OBJECTIVE: Adolescents face barriers to accessing youth-friendly family planning services, specifically long-acting reversible contraception (LARC). School-Based Health Centers (SBHCs) can provide youth-friendly care. A quality improvement (QI) project was undertaken to assess quality of care before, during and after LARC services at three SBHCs, and to identify specific strategies for improving these LARC services. METHODS: We interviewed 18 female adolescents who received LARC services...
November 18, 2016: Journal of Pediatric and Adolescent Gynecology
https://www.readbyqxmd.com/read/27871677/impetus-interactive-multiphysics-environment-for-unified-simulations
#16
Vi Q Ha, George Lykotrafitis
We introduce IMPETUS - Interactive MultiPhysics Environment for Unified Simulations, an object oriented, easy-to-use, high performance, C++ program for three-dimensional simulations of complex physical systems that can benefit a large variety of research areas, especially in cell mechanics. The program implements cross-communication between locally interacting particles and continuum models residing in the same physical space while a network facilitates long-range particle interactions. Message Passing Interface is used for inter-processor communication for all simulations...
October 31, 2016: Journal of Biomechanics
https://www.readbyqxmd.com/read/27867785/lightning-mapping-array-flash-detection-performance-with-variable-receiver-thresholds
#17
Vanna C Chmielewski, Eric C Bruning
This study characterizes Lightning Mapping Array performance for networks that participated in the Deep Convective Clouds and Chemistry field program using new Monte Carlo and curvature matrix model simulations. These open-source simulation tools are readily adapted to real-time operations or detailed studies of performance. Each simulation accounted for receiver threshold and location, as well as a reference distribution of source powers and flash sizes based on thunderstorm observations and the mechanics of station triggering...
July 27, 2016: Journal of Geophysical Research. Atmospheres: JGR
https://www.readbyqxmd.com/read/27866925/extracorporeal-membrane-oxygenation-support-and-post-heart-transplant-outcomes-among-united-states-adults
#18
Sandip Zalawadiya, Marat Fudim, Geetha Bhat, William Cotts, JoAnn Lindenfeld
BACKGROUND: Patients supported with extracorporeal membrane oxygenation (ECMO) are given priority listing status for heart transplant (HT). Data on post-HT outcomes for adults with ECMO support at the time of HT are limited. METHODS: We analyzed data from the United Network for Organ Registry (UNOS) registry for 157 ECMO-supported adults (age ≥ 18 years) undergoing HT after January 1, 2000. Data at the time of HT were examined for their association with post-transplant mortality using multivariable Cox proportional hazard analyses...
October 15, 2016: Journal of Heart and Lung Transplantation
https://www.readbyqxmd.com/read/27862302/scoping-review-shows-wide-variation-in-the-definitions-of-bronchopulmonary-dysplasia-in-preterm-infants-and-calls-for-a-consensus
#19
REVIEW
Delaney Hines, Neena Modi, Shoo K Lee, Tetsuya Isayama, Gunnar Sjörs, Luigi Gagliardi, Liisa Lehtonen, Maximo Vento, Satoshi Kusuda, Dirk Bassler, Rintaro Mori, Brian Reichman, Stellan Håkansson, Brian A Darlow, Mark Adams, Franca Rusconi, Laura San Feliciano, Kei Lui, Naho Morisaki, Natasha Musrap, Prakesh S Shah
: The use of different definitions for bronchopulmonary dysplasia (BPD) has been an on-going challenge. We searched papers published in English from 2010 and 2015 reporting BPD as an outcome, together with studies that compared BPD definitions between 1978 and 2015. We found that the incidence of BPD ranged from 6% to 57%, depending on the definition chosen, and that studies that investigated correlations with long-term pulmonary and, or, neurosensory outcomes reported moderate to low predictive values regardless of the BPD criteria...
November 12, 2016: Acta Paediatrica
https://www.readbyqxmd.com/read/27861906/all-optical-functional-synaptic-connectivity-mapping-in-acute-brain-slices-using-campari
#20
Timothy A Zolnik, Fern Sha, Friedrich Johenning, Eric R Schreiter, Loren L Looger, Matthew E Larkum, Robert N S Sachdev
The calcium-modulated photoactivatable ratiometric integrator CaMPARI (Fosque et al., 2015) facilitates the study of neural circuits by permanently marking cells active during user-specified temporal windows. Permanent marking enables measurement of signals from large swathes of tissue and easy correlation of activity with other structural or functional labels. One potential application of CaMPARI is labeling neurons postsynaptic to specific populations targeted for optogenetic stimulation, giving rise to all-optical functional connectivity mapping...
November 11, 2016: Journal of Physiology
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