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https://www.readbyqxmd.com/read/28921541/automatic-labeling-of-mr-brain-images-through-extensible-learning-and-atlas-forests
#1
Lijun Xu, Hong Liu, Enmin Song, Meng Yan, Renchao Jin, Chih-Cheng Hung
PURPOSE: Multi-atlas-based method is extensively used in MR brain images segmentation because of its simplicity and robustness. This method provides excellent accuracy while time-consuming and limited in terms of obtaining information about new atlases. In this study, an automatic labeling of MR brain images through extensible learning and atlas forest is presented to address these limitations. METHODS: We propose an extensible learning model which allows the multi-atlas-based framework capable of managing the datasets with numerous atlases or dynamic atlas datasets and simultaneously ensure the accuracy of automatic labeling...
September 18, 2017: Medical Physics
https://www.readbyqxmd.com/read/28904787/spatiotemporal-variability-of-soil-respiration-in-a-seasonal-tropical-forest
#2
Vanessa E Rubio, Matteo Detto
We monitored soil CO 2 effluxes for over 3 years in a seasonally wet tropical forest in Central Panama using automated and manual measurements from 2013 to 2016. The measurements displayed a high degree of spatial and temporal variability. Temporal variability could be largely explained by surface soil water dynamics over a broad range of temporal scales. Soil moisture was responsible for seasonal cycles, diurnal cycles, intraseasonal variability such as rain-induced pulses following dry spells, as well as suppression during near saturated conditions, and ultimately, interannual variability...
September 2017: Ecology and Evolution
https://www.readbyqxmd.com/read/28904759/different-facets-of-tree-sapling-diversity-influence-browsing-intensity-by-deer-dependent-on-spatial-scale
#3
Bettina Ohse, Carolin Seele, Frédéric Holzwarth, Christian Wirth
Browsing of tree saplings by deer hampers forest regeneration in mixed forests across Europe and North America. It is well known that tree species are differentially affected by deer browsing, but little is known about how different facets of diversity, such as species richness, identity, and composition, affect browsing intensity at different spatial scales. Using forest inventory data from the Hainich National Park, a mixed deciduous forest in central Germany, we applied a hierarchical approach to model the browsing probability of patches (regional scale) as well as the species-specific proportion of saplings browsed within patches (patch scale)...
September 2017: Ecology and Evolution
https://www.readbyqxmd.com/read/28902466/learning-based-deformable-registration-for-infant-mri-by-integrating-random-forest-with-auto-context-model
#4
Lifang Wei, Xiaohuan Cao, Zhensong Wang, Yaozong Gao, Shunbo Hu, Li Wang, Guorong Wu, Dinggang Shen
PURPOSE: Accurately analyzing the rapid structural evolution of human brain in the first year of life is a key step in early brain development studies, which requires accurate deformable image registration. However, due to 1) dynamic appearance and 2) large anatomical changes, very few methods in the literature can work well for the registration of two infant brain MR images acquired at two arbitrary development phases, such as birth and one-year-old. METHODS: To address these challenging issues, we propose a learning-based registration method, which can handle the anatomical structures and the appearance changes between the two infant brain MR images with possible time gap...
September 13, 2017: Medical Physics
https://www.readbyqxmd.com/read/28898262/climate-and-air-pollution-impacts-on-habitat-suitability-of-austrian-forest-ecosystems
#5
Thomas Dirnböck, Ika Djukic, Barbara Kitzler, Johannes Kobler, Janet P Mol-Dijkstra, Max Posch, Gert Jan Reinds, Angela Schlutow, Franz Starlinger, Wieger G W Wamelink
Climate change and excess deposition of airborne nitrogen (N) are among the main stressors to floristic biodiversity. One particular concern is the deterioration of valuable habitats such as those protected under the European Habitat Directive. In future, climate-driven shifts (and losses) in the species potential distribution, but also N driven nutrient enrichment may threaten these habitats. We applied a dynamic geochemical soil model (VSD+) together with a novel niche-based plant response model (PROPS) to 5 forest habitat types (18 forest sites) protected under the EU Directive in Austria...
2017: PloS One
https://www.readbyqxmd.com/read/28894648/impact-of-litter-quantity-on-the-soil-bacteria-community-during-the-decomposition-of-quercus-wutaishanica-litter
#6
Quanchao Zeng, Yang Liu, Shaoshan An
The forest ecosystem is the main component of terrestrial ecosystems. The global climate and the functions and processes of soil microbes in the ecosystem are all influenced by litter decomposition. The effects of litter decomposition on the abundance of soil microorganisms remain unknown. Here, we analyzed soil bacterial communities during the litter decomposition process in an incubation experiment under treatment with different litter quantities based on annual litterfall data (normal quantity, 200 g/(m(2)/yr); double quantity, 400 g/(m(2)/yr) and control, no litter)...
2017: PeerJ
https://www.readbyqxmd.com/read/28894646/canopy-soil-bacterial-communities-altered-by-severing-host-tree-limbs
#7
Cody R Dangerfield, Nalini M Nadkarni, William J Brazelton
Trees of temperate rainforests host a large biomass of epiphytic plants, which are associated with soils formed in the forest canopy. Falling of epiphytic material results in the transfer of carbon and nutrients from the canopy to the forest floor. This study provides the first characterization of bacterial communities in canopy soils enabled by high-depth environmental sequencing of 16S rRNA genes. Canopy soil included many of the same major taxonomic groups of Bacteria that are also found in ground soil, but canopy bacterial communities were lower in diversity and contained different operational taxonomic units...
2017: PeerJ
https://www.readbyqxmd.com/read/28894167/carbon-sequestration-potential-and-physicochemical-properties-differ-between-wildfire-charcoals-and-slow-pyrolysis-biochars
#8
Cristina Santín, Stefan H Doerr, Agustin Merino, Thomas D Bucheli, Rob Bryant, Philippa Ascough, Xiaodong Gao, Caroline A Masiello
Pyrogenic carbon (PyC), produced naturally (wildfire charcoal) and anthropogenically (biochar), is extensively studied due to its importance in several disciplines, including global climate dynamics, agronomy and paleosciences. Charcoal and biochar are commonly used as analogues for each other to infer respective carbon sequestration potentials, production conditions, and environmental roles and fates. The direct comparability of corresponding natural and anthropogenic PyC, however, has never been tested. Here we compared key physicochemical properties (elemental composition, δ(13)C and PAHs signatures, chemical recalcitrance, density and porosity) and carbon sequestration potentials of PyC materials formed from two identical feedstocks (pine forest floor and wood) under wildfire charring- and slow-pyrolysis conditions...
September 11, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28894004/waiting-can-be-an-optimal-conservation-strategy-even-in-a-crisis-discipline
#9
Gwenllian D Iacona, Hugh P Possingham, Michael Bode
Biodiversity conservation projects confront immediate and escalating threats with limited funding. Conservation theory suggests that the best response to the species extinction crisis is to spend money as soon as it becomes available, and this is often an explicit constraint placed on funding. We use a general dynamic model of a conservation landscape to show that this decision to "front-load" project spending can be suboptimal if a delay allows managers to use resources more strategically. Our model demonstrates the existence of temporal efficiencies in conservation management, which parallel the spatial efficiencies identified by systematic conservation planning...
September 11, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28892848/source-dynamics-of-radiocesium-contaminated-particulate-matter-deposited-in-an-agricultural-water-reservoir-after-the-fukushima-nuclear-accident
#10
Sylvain Huon, Seiji Hayashi, J Patrick Laceby, Hideki Tsuji, Yuichi Onda, Olivier Evrard
The Fukushima nuclear accident in Japan resulted in the deposition of radiocesium over forested and rural landscapes northwest of the power plant. Although there have been several investigations into the dynamics of contaminated river sediment, less attention has been paid to the sources of deposited particulate matter in dams and reservoirs. In the Fukushima Prefecture, there are 10 significant dams and over a 1000 reservoirs for both agricultural and surface water management. These reservoirs may have trapped a significant volume of radiocesium-contaminated sediment...
September 6, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/28892301/deep-nirs-amplicon-sequencing-of-san-francisco-bay-sediments-enables-prediction-of-geography-and-environmental-conditions-from-denitrifying-community-composition
#11
Jessica A Lee, Christopher A Francis
Denitrification is a dominant nitrogen loss process in the sediments of San Francisco Bay. In this study, we sought to understand the ecology of denitrifying bacteria by using next-generation sequencing (NGS) to survey the diversity of a denitrification functional gene, nirS (encoding cytchrome-cd1 nitrite reductase), along the salinity gradient of San Francisco Bay over the course of a year. We compared our dataset to a library of nirS sequences obtained previously from the same samples by standard PCR cloning and Sanger sequencing, and showed that both methods similarly demonstrated geography, salinity, and, to a lesser extent, nitrogen, to be strong determinants of community composition...
September 11, 2017: Environmental Microbiology
https://www.readbyqxmd.com/read/28892277/ungulates-increase-forest-plant-species-richness-to-the-benefit-of-non-forest-specialists
#12
Vincent Boulanger, Jean-Luc Dupouey, Frédéric Archaux, Vincent Badeau, Christophe Baltzinger, Richard Chevalier, Emmanuel Corcket, Yann Dumas, Françoise Forgeard, Anders Mårell, Pierre Montpied, Yoan Paillet, Jean-François Picard, Sonia Saïd, Erwin Ulrich
Large wild ungulates are a major biotic factor shaping plant communities. They influence species abundance and occurrence directly by herbivory and plant dispersal, or indirectly by modifying plant-plant interactions and through soil disturbance. In forest ecosystems, researchers' attention has been mainly focused on deer overabundance. Far less is known about the effects on understory plant dynamics and diversity of wild ungulates where their abundance is maintained at lower levels to mitigate impacts on tree regeneration...
September 11, 2017: Global Change Biology
https://www.readbyqxmd.com/read/28892141/novel-insights-on-population-and-range-edge-dynamics-using-an-unparalleled-spatiotemporal-record-of-species-invasion
#13
Kristine Grayson, Derek M Johnson
Quantifying the complex spatial dynamics taking place at range edges is critical for understanding future distributions of species, yet very few systems have sufficient data or the spatial resolution to empirically test these dynamics. This paper reviews how data from a large-scale pest management program have provided important contributions to the fields of population dynamics and invasion biology. The invasion of gypsy moth (Lymantria dispar) is well-documented from its introduction near Boston, Massachusetts USA in 1869 to its current extent of over 900,000 km(2) in Eastern North America...
September 11, 2017: Journal of Animal Ecology
https://www.readbyqxmd.com/read/28885556/combining-multi-source-remotely-sensed-data-and-a-process-based-model-for-forest-aboveground-biomass-updating
#14
Xiaoman Lu, Guang Zheng, Colton Miller, Ernesto Alvarado
Monitoring and understanding the spatio-temporal variations of forest aboveground biomass (AGB) is a key basis to quantitatively assess the carbon sequestration capacity of a forest ecosystem. To map and update forest AGB in the Greater Khingan Mountains (GKM) of China, this work proposes a physical-based approach. Based on the baseline forest AGB from Landsat Enhanced Thematic Mapper Plus (ETM+) images in 2008, we dynamically updated the annual forest AGB from 2009 to 2012 by adding the annual AGB increment (ABI) obtained from the simulated daily and annual net primary productivity (NPP) using the Boreal Ecosystem Productivity Simulator (BEPS) model...
September 8, 2017: Sensors
https://www.readbyqxmd.com/read/28883445/plant-litter-dynamics-in-the-forest-stream-interface-precipitation-is-a-major-control-across-tropical-biomes
#15
Alan M Tonin, José F Gonçalves, Paulino Bambi, Sheyla R M Couceiro, Lorrane A M Feitoza, Lucas E Fontana, Neusa Hamada, Luiz U Hepp, Vânia G Lezan-Kowalczuk, Gustavo F M Leite, Aurea L Lemes-Silva, Leonardo K Lisboa, Rafael C Loureiro, Renato T Martins, Adriana O Medeiros, Paula B Morais, Yara Moretto, Patrícia C A Oliveria, Evelyn B Pereira, Lidiane P Ferreira, Javier Pérez, Mauricio M Petrucio, Deusiano F Reis, Renan S Rezende, Nadia Roque, Luiz E P Santos, Ana E Siegloch, Gabriela Tonello, Luz Boyero
Riparian plant litter is a major energy source for forested streams across the world and its decomposition has repercussions on nutrient cycling, food webs and ecosystem functioning. However, we know little about plant litter dynamics in tropical streams, even though the tropics occupy 40% of the Earth's land surface. Here we investigated spatial and temporal (along a year cycle) patterns of litter inputs and storage in multiple streams of three tropical biomes in Brazil (Atlantic forest, Amazon forest and Cerrado savanna), predicting major differences among biomes in relation to temperature and precipitation regimes...
September 7, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28877258/an-empirical-hierarchical-typology-of-tree-species-assemblages-for-assessing-forest-dynamics-under-global-change-scenarios
#16
Jennifer K Costanza, John W Coulston, David N Wear
The composition of tree species occurring in a forest is important and can be affected by global change drivers such as climate change. To inform assessment and projection of global change impacts at broad extents, we used hierarchical cluster analysis and over 120,000 recent forest inventory plots to empirically define forest tree assemblages across the U.S., and identified the indicator and dominant species associated with each. Cluster typologies in two levels of a hierarchy of forest assemblages, with 29 and 147 groups respectively, were supported by diagnostic criteria...
2017: PloS One
https://www.readbyqxmd.com/read/28876416/considerations-of-potential-vectors-and-animal-reservoirs-in-an-emerging-cutaneous-leishmaniasis-area-in-s%C3%A3-o-domingos-ranch-paran%C3%A3-state-in-southearn-brazil
#17
Norberto Assis Membrive, Flora Hisatugo, Thaís Gomes Verzignassi Silveira, Jorge Juarez Vieira Teixeira, Kárin Rosi Reinhold-Castro, Ueslei Teodoro
The aim of this study was to better understand the dynamics of Leishmania sand flies and reservoirs in São Domingos ranch, Arapongas municipality, Paraná State, an anthropic environment in an endemic area of cutaneous leishmaniasis (CL). Sand flies were collected in wild animal burrows, residences and in the forest, with Falcão light trap (FA), Shannon trap (SH) and quadrangular pyramidal trap (QP). The search for Leishmania was made on sand flies, biological samples of wild rodents and dogs using PCR and culture; while parasite direct search (DS) was carried out on animal skin lesions; infection of gold hamsters; and indirect immunofluorescence (IIF) test in dog blood samples...
September 4, 2017: Revista do Instituto de Medicina Tropical de São Paulo
https://www.readbyqxmd.com/read/28876195/bifiguratus-adelaidae-gen-et-sp-nov-a-new-member-of-mucoromycotina-in-endophytic-and-soil-dwelling-habitats
#18
Terry J Torres-Cruz, Terri L Billingsley Tobias, Maryam Almatruk, Cedar N Hesse, Cheryl R Kuske, Alessandro Desirò, Gian Maria Niccolò Benucci, Gregory Bonito, Jason E Stajich, Christopher Dunlap, A Elizabeth Arnold, Andrea Porras-Alfaro
Illumina amplicon sequencing of soil in a temperate pine forest in the southeastern United States detected an abundant, nitrogen (N)-responsive fungal genotype of unknown phylogenetic affiliation. Two isolates with ribosomal sequences consistent with that genotype were subsequently obtained. Examination of records in GenBank revealed that a genetically similar fungus had been isolated previously as an endophyte of moss in a pine forest in the southwestern United States. The three isolates were characterized using morphological, genomic, and multilocus molecular data (18S, internal transcribed spacer [ITS], and 28S rRNA sequences)...
May 2017: Mycologia
https://www.readbyqxmd.com/read/28873090/deficiencies-in-natura-2000-for-protecting-recovering-large-carnivores-a-spotlight-on-the-wolf-canis-lupus-in-poland
#19
Tom A Diserens, Tomasz Borowik, Sabina Nowak, Maciej Szewczyk, Natalia Niedźwiecka, Robert W Mysłajek
If protected areas are to remain relevant in our dynamic world they must be adapted to changes in species ranges. In the EU one of the most notable such changes is the recent recovery of large carnivores, which are protected by Natura 2000 at the national and population levels. However, the Natura 2000 network was designed prior to their recent recovery, which raises the question whether the network is sufficient to protect the contemporary ranges of large carnivores. To investigate this question we evaluated Natura 2000 coverage of the three wolf Canis lupus populations in Poland...
2017: PloS One
https://www.readbyqxmd.com/read/28869190/year-to-year-variation-in-the-density-of-ixodes-ricinus-ticks-and-the-prevalence-of-the-rodent-associated-human-pathogens-borrelia-afzelii-and-b-miyamotoi-in-different-forest-types
#20
Sanne C Ruyts, Wesley Tack, Evy Ampoorter, Elena C Coipan, Erik Matthysen, Dieter Heylen, Hein Sprong, Kris Verheyen
The human pathogens Borrelia afzelii, which causes Lyme borreliosis and B. miyamotoi, which causes relapsing fever, both circulate between Ixodes ricinus ticks and rodents. The spatiotemporal dynamics in the prevalence of these pathogens have not yet been fully elucidated, but probably depend on the spatiotemporal population dynamics of small rodents. We aimed to evaluate the effect of different forest types on the density of infected nymphs in different years and to obtain more knowledge about the spatial and temporal patterns of ticks and tick-borne pathogens...
August 26, 2017: Ticks and Tick-borne Diseases
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