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https://www.readbyqxmd.com/read/29325176/dynamic-motif-occupancy-dynamo-analysis-identifies-transcription-factors-and-their-binding-sites-driving-dynamic-biological-processes
#1
Zheng Kuang, Zhicheng Ji, Jef D Boeke, Hongkai Ji
Biological processes are usually associated with genome-wide remodeling of transcription driven by transcription factors (TFs). Identifying key TFs and their spatiotemporal binding patterns are indispensable to understanding how dynamic processes are programmed. However, most methods are designed to predict TF binding sites only. We present a computational method, dynamic motif occupancy analysis (DynaMO), to infer important TFs and their spatiotemporal binding activities in dynamic biological processes using chromatin profiling data from multiple biological conditions such as time-course histone modification ChIP-seq data...
January 9, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29325135/precipitation-is-not-limiting-for-xylem-formation-dynamics-and-vessel-development-in-european-beech-from-two-temperate-forest-sites
#2
Peter Prislan, Katarina Cufar, Martin De Luis, Jožica Gricar
We investigated the dynamics of xylem differentiation processes and vessel characteristics in Fagus sylvatica L. to evaluate the plasticity of xylem structures under different environmental conditions. In 2008-10, analyses were performed on microcores collected weekly from two temperate sites: Menina planina (1200 m above sea level (a.s.l.)) and Panska reka (400 m a.s.l.). The duration between the onset and end of major cell differentiation steps and vessel characteristics (i.e., density, VD; mean diameter, MVD; mean area, MVA; and theoretic conductivity area, TCA) were analysed in the first and last quarters of the xylem rings, also in respect of local weather conditions (precipitation, temperature)...
January 9, 2018: Tree Physiology
https://www.readbyqxmd.com/read/29323793/atmospheric-nitrogen-deposition-on-petals-enhances-seed-quality-of-the-forest-herb-anemone-nemorosa
#3
Pieter De Frenne, Haben Blondeel, Jörg Brunet, Maria Mercedes Caron, Olivier Chabrerie, Mathias Cougnon, Sara A O Cousins, Guillaume Decocq, Martin Diekmann, Bente J Graae, Mick E Hanley, Thilo Heinken, Martin Hermy, Annette Kolb, Jonathan Lenoir, Jaan Liira, Anna Orczewska, Anna Shevtsova, Thomas Vanneste, Kris Verheyen
Elevated atmospheric input of nitrogen (N) is currently affecting plant biodiversity and ecosystem functioning. The growth and survival of numerous plant species is known to respond strongly to N fertilization. Yet, few studies have assessed the effects of N deposition on seed quality and reproductive performance, which is an important life-history stage of plants. Here we address this knowledge gap by assessing the effects of atmospheric N deposition on seed quality of the ancient forest herb Anemone nemorosa using two complementary approaches...
January 11, 2018: Plant Biology
https://www.readbyqxmd.com/read/29322582/large-scale-disturbance-legacies-and-the-climate-sensitivity-of-primary-picea-abies-forests
#4
Jonathan S Schurman, Volodymyr Trotsiuk, Radek Bače, Vojtěch Čada, Shawn Fraver, Pavel Janda, Dominik Kulakowski, Jana Labusova, Martin Mikoláš, Thomas A Nagel, Rupert Seidl, Michal Synek, Kristýna Svobodová, Oleh Chaskovskyy, Marius Teodosiu, Miroslav Svoboda
Determining the drivers of shifting forest disturbance rates remains a pressing global change issue. Large-scale forest dynamics are commonly assumed to be climate driven, but appropriately scaled disturbance histories are rarely available to assess how disturbance legacies alter subsequent disturbance rates and the climate sensitivity of disturbance. We compiled multiple tree-ring based disturbance histories from primary Picea abies forest fragments distributed throughout five European landscapes spanning the Bohemian Forest and the Carpathian Mountains...
January 11, 2018: Global Change Biology
https://www.readbyqxmd.com/read/29322322/functional-traits-can-improve-our-understanding-of-niche-and-dispersal-based-processes
#5
Feng Jiang, Yanhan Xun, Huiying Cai, Guangze Jin
Ecologists often determine the relative importance of niche- and dispersal-based processes via variation partitioning based on species composition. Functional traits and their proxies of phylogeny are expected to increase the detection of niche-based processes and reduce the unexplained variation relative to species identity. We collected eight adult tree traits and phylogenetic data of 41 species and employed a phylogenetic fuzzy weighting method to address this issue in a 9-ha temperate forest dynamics plot...
January 10, 2018: Oecologia
https://www.readbyqxmd.com/read/29321886/gap-formation-and-dynamics-after-long-term-steady-state-in-an-old-growth-picea-abies-stand-in-norway-above-and-belowground-interactions
#6
Per Holm Nygaard, Line Tau Strand, Arne Oddvar Stuanes
Stand dynamics and the gap initiation prior to gap formation are not well-understood because of its long-term nature and the scarcity of late-successional stands. Reconstruction of such disturbance is normally based on historical records and dendroecological methods. We investigated gap initiation and formation at the fine-scale stand level in the old-growth reserve of Karlshaugen in Norway. Given its long-term conservation history, and thorough mapping in permanent marked plots with spatially referenced trees, it provides an opportunity to present stand development before, during, and after gap formation...
January 2018: Ecology and Evolution
https://www.readbyqxmd.com/read/29320467/accurate-natural-trail-detection-using-a-combination-of-a-deep-neural-network-and-dynamic-programming
#7
Shyam Prasad Adhikari, Changju Yang, Krzysztof Slot, Hyongsuk Kim
This paper presents a vision sensor-based solution to the challenging problem of detecting and following trails in highly unstructured natural environments like forests, rural areas and mountains, using a combination of a deep neural network and dynamic programming. The deep neural network (DNN) concept has recently emerged as a very effective tool for processing vision sensor signals. A patch-based DNN is trained with supervised data to classify fixed-size image patches into "trail" and "non-trail" categories, and reshaped to a fully convolutional architecture to produce trail segmentation map for arbitrary-sized input images...
January 10, 2018: Sensors
https://www.readbyqxmd.com/read/29317626/dynamic-metal-ligand-coordination-for-multicolour-and-water-jet-rewritable-paper
#8
Yun Ma, Pengfei She, Kenneth Yin Zhang, Huiran Yang, Yanyan Qin, Zihan Xu, Shujuan Liu, Qiang Zhao, Wei Huang
Rewritable paper has recently become prevalent in both academic research and marketplace due to the potential environmental advantages, including forest conservation, pollution reduction, energy saving and resource sustainability. However, its real-life applications are limited by a lack of effective strategy to realize multicolour and water-jet printing on rewritable paper with long legible image-lasting times. Herein, we report an effective strategy to construct rewritable paper based on colour or luminescence switching induced by dynamic metal-ligand coordination...
January 9, 2018: Nature Communications
https://www.readbyqxmd.com/read/29312587/tumour-microenvironmental-blood-flow-determines-a-metabolomic-signature-identifying-lysophospholipids-and-resolvin-d-as-biomarkers-in-endometrial-cancer-patients
#9
Núria Eritja, Mariona Jové, Kristine Eldevik Fasmer, Sònia Gatius, Manuel Portero-Otin, Jone Trovik, Camilla Krakstad, Joaquim Sol, Reinald Pamplona, Ingfrid S Haldorsen, Xavier Matias-Guiu
Purpose: We aimed to study the potential influence of tumour blood flow -obtained from dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI)- in the metabolomic profiles of endometrial tumours. Methods: Liquid chromatography coupled to mass spectrometry established the metabolomic profile of endometrial cancer lesions exhibiting high (n=12) or low (n=14) tumour blood flow at DCE-MRI. Univariate and multivariate statistics (ortho-PLS-DA, a random forest (RF) classifier and hierarchical clustering) and receiver operating characteristic (ROC) curves were used to establish a panel for potentially discriminating tumours with high versus low blood flow...
December 12, 2017: Oncotarget
https://www.readbyqxmd.com/read/29304165/genetic-diversity-genetic-structure-and-diet-of-ancient-and-contemporary-red-deer-cervus-elaphus-l-from-north-eastern-france
#10
Annik Schnitzler, José Granado, Olivier Putelat, Rose-Marie Arbogast, Dorothée Drucker, Anna Eberhard, Anja Schmutz, Yuri Klaefiger, Gérard Lang, Walter Salzburger, Joerg Schibler, Angela Schlumbaum, Hervé Bocherens
In north-eastern France, red deer (Cervus elaphus L.) populations were rebuilt from a few hundred individuals, which have subsisted in remote valleys of the Vosges mountains, and to a lesser extent from individuals escaped from private enclosures; at present times, this species occupies large areas, mainly in the Vosges Mountains. In this study, we examined the population dynamics of red deer in the Vosges Mountains using ancient and contemporary mitochondrial DNA (mtDNA) from 140 samples (23 ancient + 117 modern) spanning the last 7'000 years...
2018: PloS One
https://www.readbyqxmd.com/read/29299626/top-down-bottom-up-and-sideways-the-multilayered-complexities-of-multi-level-actors-shaping-forest-governance-and-redd-arrangements-in-madre-de-dios-peru
#11
Dawn Rodriguez-Ward, Anne M Larson, Harold Gordillo Ruesta
This study examines the role multilevel governance plays in the adoption of sustainable landscape management initiatives in emerging arrangements aimed at reducing emissions from deforestation and forest degradation (REDD+). It sheds light on the challenges these multiple layers of actors and interests encounter around such alternatives in a subnational jurisdiction. Through transcript analysis of 93 interviews with institutional actors in the region of Madre de Dios, Peru, particularly with regard to five sites of land-use change, we identified the multiple actors who are included and excluded in the decision-making process and uncovered their complex interactions in forest and landscape governance and REDD+ arrangements...
January 3, 2018: Environmental Management
https://www.readbyqxmd.com/read/29299291/regional-patterns-of-increasing-swiss-needle-cast-impacts-on-douglas-fir-growth-with-warming-temperatures
#12
E Henry Lee, Peter A Beedlow, Ronald S Waschmann, David T Tingey, Steven Cline, Michael Bollman, Charlotte Wickham, Cailie Carlile
The fungal pathogen, Phaeocryptopus gaeumannii, causing Swiss needle cast (SNC) occurs wherever Douglas-fir is found but disease damage is believed to be limited in the U.S. Pacific Northwest (PNW) to the Coast Range of Oregon and Washington (Hansen et al., Plant Disease, 2000, 84, 773; Rosso & Hansen, Phytopathology, 2003, 93, 790; Shaw, et al., Journal of Forestry, 2011, 109, 109). However, knowledge remains limited on the history and spatial distribution of SNC impacts in the PNW. We reconstructed the history of SNC impacts on mature Douglas-fir trees based on tree-ring width chronologies from western Oregon...
December 2017: Ecology and Evolution
https://www.readbyqxmd.com/read/29281752/associations-among-arbuscular-mycorrhizal-fungi-and-seedlings-are-predicted-to-change-with-tree-successional-status
#13
Bachelot Benedicte, María Uriarte, Robert Muscarella, Jimena Forero-Montaña, Jill Thompson, Krista McGuire, Jess Zimmerman, Nathan G Swenson, James S Clark
Arbuscular mycorrhizal (AM) fungi in the soil may influence tropical tree dynamics and forest succession. The mechanisms are poorly understood, because the functional characteristics and abundances of tree species and AM fungi are likely to be codependent. We used generalized joint attribute modeling to evaluate if AM fungi are associated with three forest community metrics for a sub-tropical montane forest in Puerto Rico. The metrics chosen to reflect changes during forest succession are: the abundance of seedlings of different successional status, the amount of foliar damage on seedlings of different successional status, and community-weighted mean functional trait values (adult specific leaf area (SLA), adult wood density, and seed mass)...
December 27, 2017: Ecology
https://www.readbyqxmd.com/read/29280282/integrating-community-assembly-and-biodiversity-to-better-understand-ecosystem-function-the-community-assembly-and-the-functioning-of-ecosystems-cafe-approach
#14
Katherine H Bannar-Martin, Colin T Kremer, Morgan Ernest, Mathew A Leibold, Harald Auge, Jonathan Chase, Steven A J Declerck, Nico Eisenhauer, Stanley Harpole, Helmut Hillebrand, Forest Isbell, Thomas Koffel, Stefano Larsen, Anita Narwani, Jana S Petermann, Christiane Roscher, Juliano Sarmento Cabral, Sarah R Supp
The research of a generation of ecologists was catalysed by the recognition that the number and identity of species in communities influences the functioning of ecosystems. The relationship between biodiversity and ecosystem functioning (BEF) is most often examined by controlling species richness and randomising community composition. In natural systems, biodiversity changes are often part of a bigger community assembly dynamic. Therefore, focusing on community assembly and the functioning of ecosystems (CAFE), by integrating both species richness and composition through species gains, losses and changes in abundance, will better reveal how community changes affect ecosystem function...
December 27, 2017: Ecology Letters
https://www.readbyqxmd.com/read/29279604/geographical-isolation-and-environmental-heterogeneity-contribute-to-the-spatial-genetic-patterns-of-quercus-kerrii-fagaceae
#15
Xiao-Long Jiang, Miao An, Si-Si Zheng, Min Deng, Zhi-Hao Su
Southwest China is one of the major global biodiversity hotspots. The Tanaka line, extending within southwestern China from its northwest to its southeast, is an important biogeographical boundary between the Sino-Japanese and Sino-Himalayan floristic regions. Understanding the evolutionary history of the regional keystone species would assist with both reconstructing historical vegetation dynamics and ongoing biodiversity management. In this research, we combined phylogeographic methodologies and species distribution models (SDMs) to investigate the spatial genetic patterns and distribution dynamics of Quercus kerrii, a dominant evergreen oak inhabiting southwest China lowland evergreen-broadleaved forests (EBLFs)...
December 27, 2017: Heredity
https://www.readbyqxmd.com/read/29278956/framework-for-infectious-disease-analysis-a-comprehensive-and-integrative-multi-modeling-approach-to-disease-prediction-and-management
#16
Madhav Erraguntla, Josef Zapletal, Mark Lawley
The impact of infectious disease on human populations is a function of many factors including environmental conditions, vector dynamics, transmission mechanics, social and cultural behaviors, and public policy. A comprehensive framework for disease management must fully connect the complete disease lifecycle, including emergence from reservoir populations, zoonotic vector transmission, and impact on human societies. The Framework for Infectious Disease Analysis is a software environment and conceptual architecture for data integration, situational awareness, visualization, prediction, and intervention assessment...
December 1, 2017: Health Informatics Journal
https://www.readbyqxmd.com/read/29275253/impact-of-land-use-changes-on-the-storage-of-soil-organic-carbon-in-active-and-recalcitrant-pools-in-a-humid-tropical-region-of-india
#17
Arun Jyoti Nath, Biplab Brahma, Gudeta W Sileshi, Ashesh Kumar Das
Quantifying soil organic carbon (SOC) dynamics is important in understanding changes in soil properties and carbon (C) fluxes. However, SOC measures all C fractions and it is not adequate to distinguish between the active C (AC) and recalcitrant or passive C (PC) fractions. It has been suggested that PC pools are the main drivers of long term soil C sink management. Therefore, the present study was undertaken with the objective of determining whether or not SOC fractions vary with land use changes under a humid tropical climate in the North East India...
December 20, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/29274288/biological-processes-dominate-seasonality-of-remotely-sensed-canopy-greenness-in-an-amazon-evergreen-forest
#18
Jin Wu, Hideki Kobayashi, Scott C Stark, Ran Meng, Kaiyu Guan, Ngoc Nguyen Tran, Sicong Gao, Wei Yang, Natalia Restrepo-Coupe, Tomoaki Miura, Raimundo Cosme Oliviera, Alistair Rogers, Dennis G Dye, Bruce W Nelson, Shawn P Serbin, Alfredo R Huete, Scott R Saleska
Satellite observations of Amazon forests show seasonal and interannual variations, but the underlying biological processes remain debated. Here we combined radiative transfer models (RTMs) with field observations of Amazon forest leaf and canopy characteristics to test three hypotheses for satellite-observed canopy reflectance seasonality: seasonal changes in leaf area index, in canopy-surface leafless crown fraction and/or in leaf demography. Canopy RTMs (PROSAIL and FLiES), driven by these three factors combined, simulated satellite-observed seasonal patterns well, explaining c...
December 23, 2017: New Phytologist
https://www.readbyqxmd.com/read/29261704/a-participatory-approach-to-elucidate-the-consequences-of-land-invasions-on-redd-initiatives-a-case-study-with-indigenous-communities-in-panama
#19
Gerardo Vergara-Asenjo, Javier Mateo-Vega, Alexis Alvarado, Catherine Potvin
Land tenure and tenure security are among the most important factors determining the viability and success of Reducing Emissions from Deforestation and Forest Degradation (REDD+) initiatives. The premise of the present paper is that territorial conflicts lead to forest loss and compromise the successful implementation of REDD+. Within this context, the main objectives of this paper are to (i) document, relying on participatory methods, the extent to which land conflicts drive deforestation and (ii) reflect on the legal context of REDD+ examining if, from an Indigenous perspective, it offers tools to resolve such conflicts...
2017: PloS One
https://www.readbyqxmd.com/read/29261481/genetic-structure-of-trypanosoma-congolense-forest-type-circulating-in-domestic-animals-and-tsetse-flies-in-the-south-west-region-of-cameroon
#20
Pythagore Soubgwi Fogue, Flobert Njiokou, Gustave Simo
Despite the economic impact of trypanosome infections, few investigations have been undertaken on the population genetics and transmission dynamics of animal trypanosomes. In this study, microsatellite markers were used to investigate the population genetics of Trypanosoma congolense "forest type", with the ultimate goal of understanding its transmission dynamics between tsetse flies and domestic animals. Blood samples were collected from pigs, sheep, goats and dogs in five villages in Fontem, South-West region of Cameroon...
2017: Parasite: Journal de la Société Française de Parasitologie
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