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https://www.readbyqxmd.com/read/28632944/deconstructing-the-landscape-of-fear-in-stable-multi-species-societies
#1
A E Martínez, E Parra, L F Collado, V T Vredenburg
Animal distributions are influenced by variation in predation risk in space, which has been described as the "landscape of fear." Many studies suggest animals also reduce predation risk by eavesdropping on heterospecific alarm calls, allowing them to occupy otherwise risky habitats. One unexplored area of study is understanding how different species' alarms vary in quality, and how this variation is distributed in the landscape. We tested this phenomenon in a unique system of avian mixed species flocks in Amazonian rainforests: flock mates (eavesdropping species) strongly associate with alarm-calling antshrikes (genus Thamnomanes), which act as sentinel species...
June 20, 2017: Ecology
https://www.readbyqxmd.com/read/28602945/the-energy-landscape-underpinning-module-dynamics-in-the-human-brain-connectome
#2
Arian Ashourvan, Shi Gu, Marcelo G Mattar, Jean M Vettel, Danielle S Bassett
Human brain dynamics can be viewed through the lens of statistical mechanics, where neurophysiological activity evolves around and between local attractors representing mental states. Many physically-inspired models of these dynamics define brain states based on instantaneous measurements of regional activity. Yet, recent work in network neuroscience has provided evidence that the brain might also be well-characterized by time-varying states composed of locally coherent activity or functional modules. We study this network-based notion of brain state to understand how functional modules dynamically interact with one another to perform cognitive functions...
June 7, 2017: NeuroImage
https://www.readbyqxmd.com/read/28595327/parallel-evolution-of-metazoan-mitochondrial-proteins
#3
Galya V Klink, Georgii A Bazykin
Amino acid propensities at amino acid sites change with time due to epistatic interactions or changing environment, affecting the probabilities of fixation of different amino acids. Such changes should lead to an increased rate of homoplasies (reversals, parallelisms, and convergences) at closely related species. Here, we reconstruct the phylogeny of twelve mitochondrial proteins from several thousand metazoan species, and measure the phylogenetic distances between branches at which either the same allele originated repeatedly due to homoplasies, or different alleles originated due to divergent substitutions...
May 1, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28593198/biphasic-metabolism-and-host-interaction-of-a-chlamydial-symbiont
#4
Lena König, Alexander Siegl, Thomas Penz, Susanne Haider, Cecilia Wentrup, Julia Polzin, Evelyne Mann, Stephan Schmitz-Esser, Daryl Domman, Matthias Horn
Chlamydiae are obligate intracellular bacteria comprising well-known human pathogens and ubiquitous symbionts of protists, which are characterized by a unique developmental cycle. Here we comprehensively analyzed gene expression dynamics of Protochlamydia amoebophila during infection of its Acanthamoeba host by RNA sequencing. This revealed a highly dynamic transcriptional landscape, where major transcriptional shifts are conserved among chlamydial symbionts and pathogens. Our data served to propose a time-resolved model for type III protein secretion during the developmental cycle, and we provide evidence for a biphasic metabolism of P...
May 2017: MSystems
https://www.readbyqxmd.com/read/28587188/a-review-of-activity-trackers-for-senior-citizens-research-perspectives-commercial-landscape-and-the-role-of-the-insurance-industry
#5
REVIEW
Salvatore Tedesco, John Barton, Brendan O'Flynn
The objective assessment of physical activity levels through wearable inertial-based motion detectors for the automatic, continuous and long-term monitoring of people in free-living environments is a well-known research area in the literature. However, their application to older adults can present particular constraints. This paper reviews the adoption of wearable devices in senior citizens by describing various researches for monitoring physical activity indicators, such as energy expenditure, posture transitions, activity classification, fall detection and prediction, gait and balance analysis, also by adopting consumer-grade fitness trackers with the associated limitations regarding acceptability...
June 3, 2017: Sensors
https://www.readbyqxmd.com/read/28585537/single-mutation-fitness-landscapes-for-an-enzyme-on-multiple-substrates-reveal-specificity-is-globally-encoded
#6
Emily E Wrenbeck, Laura R Azouz, Timothy A Whitehead
Our lack of total understanding of the intricacies of how enzymes behave has constrained our ability to robustly engineer substrate specificity. Furthermore, the mechanisms of natural evolution leading to improved or novel substrate specificities are not wholly defined. Here we generate near-comprehensive single-mutation fitness landscapes comprising >96.3% of all possible single nonsynonymous mutations for hydrolysis activity of an amidase expressed in E. coli with three different substrates. For all three selections, we find that the distribution of beneficial mutations can be described as exponential, supporting a current hypothesis for adaptive molecular evolution...
June 6, 2017: Nature Communications
https://www.readbyqxmd.com/read/28568112/factors-associated-with-early-extubation-after-superior-cavopulmonary-connection-analysis-from-single-ventricle-reconstruction-trial
#7
D Zakaria, M Rettiganti, J M Gossett, P Gupta
BACKGROUND: To evaluate the landscape of early extubation, and identify factors associated with early extubation (≤ 24 h) after superior cavopulmonary connection (stage 2 operation) among children with single ventricle anatomy. METHODS: Patients undergoing stage 2 operation after Norwood operation from the Pediatric Heart Network Single Ventricle Reconstruction (SVR) trial public-use dataset were included. Elastic net regularized logistic regression models were fitted to evaluate the factors associated with early extubation after stage 2 operation...
June 1, 2017: Acta Anaesthesiologica Scandinavica
https://www.readbyqxmd.com/read/28566553/systematic-analysis-of-ca-2-homoeostasis-in-saccharomyces-cerevisiae-based-on-chemical-genetic-interaction-profiles
#8
Farzan Ghanegolmohammadi, Mitsumori Yoshida, Shinsuke Ohnuki, Yuko Sukegawa, Hiroki Okada, Keisuke Obara, Akio Kihara, Kuninori Suzuki, Tetsuya Kojima, Nozomu Yachie, Dai Hirata, Yoshikazu Ohya
We investigated the global landscape of Ca(2+) homeostasis in the budding yeast based on high-dimensional chemical-genetic interaction profiles. The morphological responses of 62 Ca(2+)-sensitive (cls) mutants were quantitatively analyzed with the image processing program CalMorph following exposure to a high concentration of Ca(2+) After a generalized linear model was applied, an analysis of covariance model was used to detect significant Ca(2+)-cls interactions. We found that high-dimensional, morphological Ca(2+)-cls interactions were mixed with positive (86%) and negative (14%) chemical-genetic interactions, while one-dimensional fitness Ca(2+)-cls interactions were all negative in principle...
May 31, 2017: Molecular Biology of the Cell
https://www.readbyqxmd.com/read/28554561/environmental-heterogeneity-and-the-evolution-of-plant-virus-interactions-viruses-in-wild-pepper-populations
#9
REVIEW
Aurora Fraile, Michael J McLeish, Israel Pagán, Pablo González-Jara, Daniel Piñero, Fernando García-Arenal
Understanding host-pathogen interactions requires analyses to address the multiplicity of scales in heterogeneous landscapes. Anthropogenic influence on plant communities, especially cultivation, is a major cause of environmental heterogeneity. We have approached the analysis of how environmental heterogeneity determines plant-virus interactions by studying virus infection in a wild plant currently undergoing incipient domestication, the wild pepper or chiltepin, across its geographical range in Mexico. We have shown previously that anthropogenic disturbance is associated with higher infection and disease risk, and with disrupted patterns of host and virus genetic spatial structure...
May 26, 2017: Virus Research
https://www.readbyqxmd.com/read/28553715/novel-approach-for-characterizing-ph-dependent-uptake-of-ionizable-chemicals-in-aquatic-organisms
#10
Maja V Karlsson, Laura J Carter, Annika Agatz, Alistair B A Boxall
Here, we present and evaluate a combined experimental and modeling approach for characterizing the uptake of ionizable chemicals from water and sediments into aquatic organisms under different pH conditions. We illustrate and evaluate the approach for two pharmaceuticals (diclofenac and fluoxetine) and one personal care product ingredient (triclosan) for the oligochaete Lumbriculus variegatus. Initially, experimental data on the uptake of the three chemicals at two pH values were fitted using a toxicokinetic model to derive uptake and depuration constants for the neutral and ionized species of each molecule...
June 8, 2017: Environmental Science & Technology
https://www.readbyqxmd.com/read/28544059/objective-assessment-of-the-evolutionary-action-equation-for-the-fitness-effect-of-missense-mutations-across-cagi-blinded-contests
#11
Panagiotis Katsonis, Olivier Lichtarge
A major challenge in genome interpretation is to estimate the fitness effect of coding variants of unknown significance (VUS). Labor, limited understanding of protein functions, and lack of assays generally limit direct experimental assessment of VUS, and make robust and accurate computational approaches a necessity. Often, however, algorithms that predict mutational effect disagree among themselves and with experimental data, slowing their adoption for clinical diagnostics. To objectively assess such methods, the Critical Assessment of Genome Interpretation (CAGI) community organizes contests to predict unpublished experimental data, available only to CAGI assessors...
May 23, 2017: Human Mutation
https://www.readbyqxmd.com/read/28540440/from-product-to-place-spatializing-governance-in-a-commodified-landscape
#12
Cora van Oosten, Moira Moeliono, Freerk Wiersum
This article analyzes the potential for landscape governance in large-scale commodity landscapes in Indonesia. It conceptualizes landscape governance as the spatialization of governance, which entails the interplay between natural-spatial conditions of place, public-private actor constellations, and policy responses. The article presents the case of a commodified oil palm landscape in West Kalimantan, where a potentially new type of landscape governance is emerging out of the experimental activities of an ecologically responsible commercial enterprise...
May 24, 2017: Environmental Management
https://www.readbyqxmd.com/read/28539069/real-world-challenges-for-hepatitis-c-virus-medications-a-critical-overview
#13
Imran Shahid, Waleed Hassan AlMalki, Sajida Hassan, Muhammad Hassan Hafeez
From 2010, the landscape of hepatitis C therapeutics has been changed rapidly, and today we are standing at a cusp of a pharmacological revolution where highly effective and interferon (IFN)-free direct acting antivirals (DAAs) are already on the market. Such treatment paradigms attain 90-95% sustained virologic response (SVR; undetectable viral load at week 12 or 24 at the end of therapy) rates in treated individuals compared to 50-70% with treatment completion of dual-therapy-pegylated interferon (PEG-IFN) and ribavirin (RBV)...
May 25, 2017: Critical Reviews in Microbiology
https://www.readbyqxmd.com/read/28535588/pedogenic-knowledge-aided-modelling-of-soil-inorganic-carbon-stocks-in-an-alpine-environment
#14
Ren-Min Yang, Fan Yang, Fei Yang, Lai-Ming Huang, Feng Liu, Jin-Ling Yang, Yu-Guo Zhao, De-Cheng Li, Gan-Lin Zhang
Accurate estimation of soil carbon is essential for accounting carbon cycling on the background of global environment change. However, previous studies made little contribution to the patterns and stocks of soil inorganic carbon (SIC) in large scales. In this study, we defined the structure of the soil depth function to fit vertical distribution of SIC based on pedogenic knowledge across various landscapes. Soil depth functions were constructed from a dataset of 99 soil profiles in the alpine area of the northeastern Tibetan Plateau...
December 1, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/28530655/a-quantitative-and-multiplexed-approach-to-uncover-the-fitness-landscape-of-tumor-suppression-in-vivo
#15
Zoë N Rogers, Christopher D McFarland, Ian P Winters, Santiago Naranjo, Chen-Hua Chuang, Dmitri Petrov, Monte M Winslow
Cancer growth is a multistage, stochastic evolutionary process. While cancer genome sequencing has been instrumental in identifying the genomic alterations that occur in human tumors, the consequences of these alterations on tumor growth remain largely unexplored. Conventional genetically engineered mouse models enable the study of tumor growth in vivo, but they are neither readily scalable nor sufficiently quantitative to unravel the magnitude and mode of action of many tumor-suppressor genes. Here, we present a method that integrates tumor barcoding with ultradeep barcode sequencing (Tuba-seq) to interrogate tumor-suppressor function in mouse models of human cancer...
May 22, 2017: Nature Methods
https://www.readbyqxmd.com/read/28522360/sex-with-no-regrets-how-sexual-reproduction-uses-a-no-regret-learning-algorithm-for-evolutionary-advantage
#16
Omer Edhan, Ziv Hellman, Dana Sherill-Rofe
The question of 'why sex' has long been a puzzle. The randomness of recombination, which potentially produces low fitness progeny, contradicts notions of fitness landscape hill climbing. We use the concept of evolution as an algorithm for learning unpredictable environments to provide a possible answer. While sex and asex both implement similar machine learning no-regret algorithms in the context of random samples that are small relative to a vast genotype space, the algorithm of sex constitutes a more efficient goal-directed walk through this space...
May 16, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28507232/energy-landscape-analysis-of-neuroimaging-data
#17
Takahiro Ezaki, Takamitsu Watanabe, Masayuki Ohzeki, Naoki Masuda
Computational neuroscience models have been used for understanding neural dynamics in the brain and how they may be altered when physiological or other conditions change. We review and develop a data-driven approach to neuroimaging data called the energy landscape analysis. The methods are rooted in statistical physics theory, in particular the Ising model, also known as the (pairwise) maximum entropy model and Boltzmann machine. The methods have been applied to fitting electrophysiological data in neuroscience for a decade, but their use in neuroimaging data is still in its infancy...
June 28, 2017: Philosophical Transactions. Series A, Mathematical, Physical, and Engineering Sciences
https://www.readbyqxmd.com/read/28493816/sample-types-applied-for-molecular-diagnosis-of-therapeutic-management-of-advanced-non-small-cell-lung-cancer-in-the-precision-medicine
#18
Yanxi Han, Jinming Li
In this era of precision medicine, molecular biology is becoming increasingly significant for the diagnosis and therapeutic management of non-small cell lung cancer. The specimen as the primary element of the whole testing flow is particularly important for maintaining the accuracy of gene alteration testing. Presently, the main sample types applied in routine diagnosis are tissue and cytology biopsies. Liquid biopsies are considered as the most promising alternatives when tissue and cytology samples are not available...
May 11, 2017: Clinical Chemistry and Laboratory Medicine: CCLM
https://www.readbyqxmd.com/read/28486496/phenotypic-heterogeneity-promotes-adaptive-evolution
#19
Zoltán Bódi, Zoltán Farkas, Dmitry Nevozhay, Dorottya Kalapis, Viktória Lázár, Bálint Csörgő, Ákos Nyerges, Béla Szamecz, Gergely Fekete, Balázs Papp, Hugo Araújo, José L Oliveira, Gabriela Moura, Manuel A S Santos, Tamás Székely, Gábor Balázsi, Csaba Pál
Genetically identical cells frequently display substantial heterogeneity in gene expression, cellular morphology and physiology. It has been suggested that by rapidly generating a subpopulation with novel phenotypic traits, phenotypic heterogeneity (or plasticity) accelerates the rate of adaptive evolution in populations facing extreme environmental challenges. This issue is important as cell-to-cell phenotypic heterogeneity may initiate key steps in microbial evolution of drug resistance and cancer progression...
May 2017: PLoS Biology
https://www.readbyqxmd.com/read/28484629/multiple-phase-transitions-in-an-agent-based-evolutionary-model-with-neutral-fitness
#20
Dawn M King, Adam D Scott, Sonya Bahar
Null models are crucial for understanding evolutionary processes such as speciation and adaptive radiation. We analyse an agent-based null model, considering a case without selection-neutral evolution-in which organisms are defined only by phenotype. Universal dynamics has previously been demonstrated in a related model on a neutral fitness landscape, showing that this system belongs to the directed percolation (DP) universality class. The traditional null condition of neutral fitness (where fitness is defined as the number of offspring each organism produces) is extended here to include equal probability of death among organisms...
April 2017: Royal Society Open Science
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