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Landscape structure

P Ramilo, A P Martínez-Falcón, A García-López, H Brustel, E Galante, E Micó
Mediterranean oak forests of the Iberian Peninsula host a great diversity of saproxylic beetles. For centuries, humans have carried out traditional management practices in this area, at both habitat and tree level, causing changes in forest structure. The aim of this study was to evaluate the anthropic effect of these traditional practices on saproxylic beetle diversity by measuring a set of environmental variables related to forest structure at both plot and tree level. Fauna was collected using window traps over a period of 12 mo...
September 23, 2017: Environmental Entomology
Xianwen Meng, Qi Chen, Peijing Zhang, Ming Chen
Summary: Circular RNAs (circRNAs), a novel class of endogenous RNAs, are widespread in eukaryotic cells. Emerging roles in diverse biological processes suggest that circRNA is a promising key player in RNA world. Most circRNAs are generated through back-splicing of pre-mRNAs, forming a covalently closed loop structure with no 5' caps or 3' polyadenylated tails. In addition, most circRNAs were not associated with translating ribosomes, therefore, circRNAs were deemed to be noncoding. However, the latest research findings revealed that some circRNAs could generate proteins in vivo, which expands the landscape of transcriptome and proteome...
October 15, 2017: Bioinformatics
Shawn J Leroux, Eric Vander Wal, Yolanda F Wiersma, Louis Charron, Jonathan D Ebel, Nichola M Ellis, Christopher Hart, Emilie Kissler, Paul W Saunders, Lucie Moudrá, Amy L Tanner, Semra Yalcin
Human activities are altering the fundamental geography of biogeochemicals. Yet we lack an understanding of how the spatial patterns in organismal stoichiometry affect biogeochemical processes and the tools to predict the impacts of global changes on biogeochemical processes. In this contribution we develop stoichiometric distribution models (StDMs), which allow us to map spatial structure in resource elemental composition across a landscape and evaluate spatial responses of consumers. We parameterise StDMs for a consumer-resource (moose-white birch) system and demonstrate that we can develop predictive models of resource stoichiometry across a landscape and that such models could improve our predictions of consumer space use...
October 12, 2017: Ecology Letters
C R Hakkenberg, R K Peet, D L Urban, C Song
In light of the need to operationalize the mapping of forest composition at landscape scales, this study uses multi-scale nested vegetation sampling in conjunction with LiDAR-hyperspectral remotely-sensed data from the G-LiHT airborne sensor to map vascular plant compositional turnover in a compositionally- and structurally-complex North Carolina Piedmont forest. Reflecting a shift in emphasis from remotely sensing individual crowns to detecting aggregate optical-structural properties of forest stands, predictive maps reflect the composition of entire vascular plant communities - inclusive of those species smaller than the resolution of the remotely-sensed imagery, intertwined with proximate taxa, or otherwise obscured from optical sensors by dense upper canopies...
October 10, 2017: Ecological Applications: a Publication of the Ecological Society of America
Giovanni Strona, Werner Ulrich, Nicholas J Gotelli
Comparing the structure of presence/absence (i.e. binary) matrices with those of randomized counterparts is a common practice in ecology. However, differences in the randomization procedures (null models) can affect the results of the comparisons, leading matrix structural patterns to appear either 'random' or not. Subjectivity in the choice of one particular null model over another makes it often advisable to compare the results obtained using several different approaches. Yet, available algorithms to randomize binary matrices differ substantially in respect to the constraints they impose on the discrepancy between observed and randomized row and column marginal totals, which complicates the interpretation of contrasting patterns...
October 11, 2017: Ecology
Sanghamitra Pati, Rajeshwari Sinha, Meely Panda, Sandipana Pati, Anjali Sharma, Sanjay Zodpey
Today, health has transcended national boundaries and become more multifaceted. Global health has evolved as a new paradigm and is recently being identified as a thrust area now in India. Despite an existing need for a standardized global health curriculum, there is little information available on its education and curriculum in medical and health education space. In the Indian context, we are yet to have a fuller picture of the current status, including, content, structure, selection, teaching methods of global health, and how students are evaluated in India...
2017: Frontiers in Public Health
Ilya Potapov, Marko Järvenpää, Markku Åkerblom, Pasi Raumonen, Mikko Kaasalainen
Detailed and realistic tree form generators have numerous applications in ecology and forestry. For example, the varying morphology of trees contributes differently to formation of landscapes, natural habitats of species, and eco-physiological characteristics of the biosphere. Here, we present an algorithm for generating morphological tree "clones" based on the detailed reconstruction of the laser scanning data, statistical measure of similarity, and a plant growth model with simple stochastic rules. The algorithm is designed to produce tree forms, i...
October 1, 2017: GigaScience
Masahito Yoshihara, Ryoko Araki, Yasuji Kasama, Misato Sunayama, Masumi Abe, Kohji Nishida, Hideya Kawaji, Yoshihide Hayashizaki, Yasuhiro Murakawa
Induced pluripotent stem cells (iPSCs) are generated by direct reprogramming of somatic cells and hold great promise for novel therapies. However, several studies have reported genetic variations in iPSC genomes. Here, we investigated point mutations identified by whole-genome sequencing in mouse and human iPSCs in the context of epigenetic status. In contrast to disease-causing single-nucleotide polymorphisms, de novo point mutations introduced during reprogramming were underrepresented in protein-coding genes and in open chromatin regions, including transcription factor binding sites...
October 10, 2017: Cell Reports
Mark L Ioffe, Michael J Berry
Recent advances in experimental techniques have allowed the simultaneous recordings of populations of hundreds of neurons, fostering a debate about the nature of the collective structure of population neural activity. Much of this debate has focused on the empirical findings of a phase transition in the parameter space of maximum entropy models describing the measured neural probability distributions, interpreting this phase transition to indicate a critical tuning of the neural code. Here, we instead focus on the possibility that this is a first-order phase transition which provides evidence that the real neural population is in a 'structured', collective state...
October 11, 2017: PLoS Computational Biology
Christian Hanke, Holger Gohlke
Riboswitches are genetic regulatory elements mainly found in bacteria, which regulate gene expression based on the availability of a ligand. Purine-sensing riboswitches, including the guanine-sensing riboswitch (Gsw), possess tertiary interactions connecting the L2 and L3 loops. These interactions are important for ligand binding to the aptamer. However, atomic-level structural knowledge about the unbound state and how the tertiary interactions influence the conformational heterogeneity of the aptamer is still scarce...
October 11, 2017: Journal of Chemical Information and Modeling
Doris E Braun, Sreenivas R Lingireddy, Mark D Beidelschies, Rui Guo, Peter Müller, Sarah L Price, Susan M Reutzel-Edens
The solid form landscape of 5-HT2a antagonist 3-(4-(benzo[d]isoxazole-3-yl)piperazin-1-yl)-2,2-dimethylpropanoic acid hydrochloride (B5HCl) proved difficult to establish. Many crystalline materials were produced by solid form screening, but few forms readily grew high quality crystals to afford a clear picture or understanding of the solid form landscape. Careful control of crystallization conditions, a range of experimental methods, computational modeling of solvate structures, and crystal structure prediction were required to see potential arrangements of the salt in its crystal forms...
October 4, 2017: Crystal Growth & Design
Andrej Berg, Christine Peter, Karen Johnston
The structure and dynamics of water at gold surfaces is important for a variety of applications, including lab on a chip and electrowetting. Classical molecular dynamics (MD) simulations are frequently used to investigate systems with water-gold interfaces, such as biomacromolecules in gold nanoparticle dispersions, but the accuracy of the simulations depends on the suitability of the force field. Density functional theory (DFT) calculations of a water molecule on gold were used as a benchmark to assess force field accuracy...
October 9, 2017: Journal of Chemical Theory and Computation
Drew M Dolino, Sudeshna Chatterjee, David M MacLean, Charlotte Flatebo, Logan D C Bishop, Sana A Shaikh, Christy F Landes, Vasanthi Jayaraman
N-Methyl-D-aspartate (NMDA) receptors are the main calcium-permeable excitatory receptors in the mammalian central nervous system. The NMDA receptor gating is complex, exhibiting multiple closed, open, and desensitized states; however, central questions regarding the conformations and energetics of the transmembrane domains as they relate to the gating states are still unanswered. Here, using single-molecule Förster resonance energy transfer (smFRET), we map the energy landscape of the first transmembrane segment of the Rattus norvegicus NMDA receptor under resting and various liganded conditions...
October 9, 2017: Nature Chemical Biology
Andi Hermansyah, Erica Sainsbury, Ines Krass
The introduction of Universal Healthcare Coverage (JKN) in 2014 has changed the landscape of the Indonesian healthcare and affected the community pharmacy sector. This paper investigates perceptions of healthcare and pharmacy stakeholders about the impact of JKN on the practice of pharmacists and pharmacy in both public (Puskesmas) and private (Community or Retail pharmacy) settings. In-depth, semi-structured interviews were conducted from February to August 2016 involving 29 participants representing key stakeholders from different provinces in Indonesia...
October 9, 2017: Health & Social Care in the Community
Emlyn Resetarits, Sara Cathey, Mathew Leibold
Although the influence of regional processes on local patches is well studied, the influence of local patches and their spatial arrangement on regional processes is likely to be complex. One interesting idea is the keystone community concept (KCC); this posits that there may be some patches that have a disproportionately large effect on the metacommunity compared to other patches. We experimentally test the KCC by using replicate protist microcosm metacommunities with single-patch removals. Removing single patches had no effect on average community richness, evenness and biomass of our metacommunities, but did cause metacommunities to be assembled significantly less by local environmental conditions and more by spatial effects related to stochastic factors...
October 9, 2017: Ecology
Shilva Kayastha, Ryo Kunimoto, Dragos Horvath, Alexandre Varnek, Jürgen Bajorath
The analysis of structure-activity relationships (SARs) becomes rather challenging when large and heterogeneous compound data sets are studied. In such cases, many different compounds and their activities need to be compared, which quickly goes beyond the capacity of subjective assessments. For a comprehensive large-scale exploration of SARs, computational analysis and visualization methods are required. Herein, we introduce a two-layered SAR visualization scheme specifically designed for increasingly large compound data sets...
October 6, 2017: Journal of Computer-aided Molecular Design
Ute Rexroth, Joseph Kuhn
Steady changes in society present challenges to constructive cooperation between stakeholders in the diverse PH landscape of Germany through individualism, globalisation, medical progress, digitalisation, etc. Working group 8 therefore suggests that the PH community should build new internal structures, in order to be able to respond jointly to external challenges, facilitate networking amongst the actors and speak with one voice, when needed. The suggestion is to establish an office that has the task to organise further meetings, harmonize written joint statements and moderate the dialogue amongst peers...
October 6, 2017: Das Gesundheitswesen
Ajay Narendra, J Frances Kamhi, Yuri Ogawa
Visual navigation is a benchmark information processing task that can be used to identify the consequence of being active in dim-light environments. Visual navigational information that animals use during the day includes celestial cues such as the sun or the pattern of polarized skylight and terrestrial cues such as the entire panorama, canopy pattern, or significant salient features in the landscape. At night, some of these navigational cues are either unavailable or are significantly dimmer or less conspicuous than during the day...
August 8, 2017: Integrative and Comparative Biology
Louise C Bryan, Daniel R Weilandt, Andreas L Bachmann, Sinan Kilic, Carolin C Lechner, Pascal D Odermatt, Georg E Fantner, Sandrine Georgeon, Oliver Hantschel, Vassily Hatzimanikatis, Beat Fierz
Chromatin recruitment of effector proteins involved in gene regulation depends on multivalent interaction with histone post-translational modifications (PTMs) and structural features of the chromatin fiber. Due to the complex interactions involved, it is currently not understood how effectors dynamically sample the chromatin landscape. Here, we dissect the dynamic chromatin interactions of a family of multivalent effectors, heterochromatin protein 1 (HP1) proteins, using single-molecule fluorescence imaging and computational modeling...
August 3, 2017: Nucleic Acids Research
Shuai Wang, Xing-Quan Zhu, Xuepeng Cai
Gene duplication (GD), thought to facilitate evolutionary innovation and adaptation, has been studied in many phylogenetic lineages. However, it remains poorly investigated in trematodes, a medically important parasite group that has been evolutionarily specialized during long-term host-parasite interaction. In this study, we conducted a genome-wide study of GD modes and contributions in Schistosoma mansoni, a pathogen causing human schistosomiasis. We combined several lines of evidence provided by duplicate age distributions, genomic sequence similarity, depth-of-coverage and gene synteny to identify the dominant drivers that contribute to the origins of new genes in this parasite...
2017: Frontiers in Cellular and Infection Microbiology
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