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https://www.readbyqxmd.com/read/28448931/tree-growth-climate-relationships-in-a-forest-plot-network-on-mediterranean-mountains
#1
Nikolaos M Fyllas, Anastasia Christopoulou, Alexandros Galanidis, Chrysanthi Z Michelaki, Panayiotis G Dimitrakopoulos, Peter Z Fulé, Margarita Arianoutsou
In this study we analysed a novel tree-growth dataset, inferred from annual ring-width measurements, of 7 forest tree species from 12 mountain regions in Greece, in order to identify tree growth - climate relationships. The tree species of interest were: Abies cephalonica, Abies borisii-regis, Picea abies, Pinus nigra, Pinus sylvestris, Fagus sylvatica and Quercus frainetto growing across a gradient of climate conditions with mean annual temperature ranging from 5.7 to 12.6°C and total annual precipitation from 500 to 950mm...
April 24, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/28448927/time-varying-sensitivity-analysis-of-hydrologic-and-sediment-parameters-at-multiple-timescales-implications-for-conservation-practices
#2
Hui Xie, Zhenyao Shen, Lei Chen, Jiali Qiu, Jianwei Dong
Environmental models can be used to better understand the hydrologic and sediment behavior in a watershed system. However, different processes may dominate at different time periods and timescales, which highly complicate the model interpretation. The related parameter uncertainty may be significant and needs to be addressed to avoid bias in the watershed management. In this study, we used the time-varying and multi-timescale (TVMT) method to characterize the temporal dynamics of parameter sensitivity at different timescales in hydrologic and sediment modeling...
April 24, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/28448508/a-longitudinal-cline-characterizes-the-genetic-structure-of-human-populations-in-the-tibetan-plateau
#3
Choongwon Jeong, Benjamin M Peter, Buddha Basnyat, Maniraj Neupane, Cynthia M Beall, Geoff Childs, Sienna R Craig, John Novembre, Anna Di Rienzo
Indigenous populations of the Tibetan plateau have attracted much attention for their good performance at extreme high altitude. Most genetic studies of Tibetan adaptations have used genetic variation data at the genome scale, while genetic inferences about their demography and population structure are largely based on uniparental markers. To provide genome-wide information on population structure, we analyzed new and published data of 338 individuals from indigenous populations across the plateau in conjunction with worldwide genetic variation data...
2017: PloS One
https://www.readbyqxmd.com/read/28446158/parameter-inference-for-stochastic-single-cell-dynamics-from-lineage-tree-data
#4
Irena Kuzmanovska, Andreas Milias-Argeitis, Jan Mikelson, Christoph Zechner, Mustafa Khammash
BACKGROUND: With the advance of experimental techniques such as time-lapse fluorescence microscopy, the availability of single-cell trajectory data has vastly increased, and so has the demand for computational methods suitable for parameter inference with this type of data. Most of currently available methods treat single-cell trajectories independently, ignoring the mother-daughter relationships and the information provided by the population structure. However, this information is essential if a process of interest happens at cell division, or if it evolves slowly compared to the duration of the cell cycle...
April 26, 2017: BMC Systems Biology
https://www.readbyqxmd.com/read/28445751/curcumin-dictates-divergent-fates-for-the-central-salt-bridges-in-amyloid-%C3%AE-40-and-amyloid-%C3%AE-42
#5
Bappaditya Chandra, Venus Singh Mithu, Debanjan Bhowmik, Anand Kant Das, Bankanidhi Sahoo, Sudipta Maiti, Perunthiruthy K Madhu
There are three specific regions in the Amyloid beta (Aβ) peptide sequence where variations cause enhanced toxicity in Alzheimer's disease: the N-terminus, the central salt bridge, and the C-terminus. Here, we investigate if there is a close conformational connection between these three regions, which may suggest a concerted mechanism of toxicity. We measure the effects of Zn(2+) and curcumin on Aβ40, and compare these with their previously reported effects on Aβ42. Aβ42 and Aβ40 differ only near the C-terminus, where curcumin interacts, while Zn(2+) interacts near the N-terminus...
April 25, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28445722/genomic-analyses-reveal-the-influence-of-geographic-origin-migration-and-hybridization-on-modern-dog-breed-development
#6
Heidi G Parker, Dayna L Dreger, Maud Rimbault, Brian W Davis, Alexandra B Mullen, Gretchen Carpintero-Ramirez, Elaine A Ostrander
There are nearly 400 modern domestic dog breeds with a unique histories and genetic profiles. To track the genetic signatures of breed development, we have assembled the most diverse dataset of dog breeds, reflecting their extensive phenotypic variation and heritage. Combining genetic distance, migration, and genome-wide haplotype sharing analyses, we uncover geographic patterns of development and independent origins of common traits. Our analyses reveal the hybrid history of breeds and elucidate the effects of immigration, revealing for the first time a suggestion of New World dog within some modern breeds...
April 25, 2017: Cell Reports
https://www.readbyqxmd.com/read/28445658/a-time-and-a-place-for-everything-phylogenetic-history-and-geography-as-joint-predictors-of-oak-plastome-phylogeny
#7
Kasey Khanh Pham, Andrew L Hipp, Paul S Manos, Richard C Cronn
Due to high rates of introgressive hybridization, the plastid genome is poorly suited to fine-scale DNA barcoding and phylogenetic studies of the oak genus (Quercus, Fagaceae). At the tips of the oak plastome phylogeny, recent gene migration and reticulation generally cause topology to reflect geographic structure, while deeper branches reflect lineage divergence. In this study, we quantify the simple and partial effects of geographic proximity and nucleome-inferred phylogenetic history on oak plastome phylogeny at different evolutionary scales...
April 26, 2017: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/28445232/organised-chaos-in-late-specialisation-team-sports-weekly-training-loads-of-elite-adolescent-rugby-union-players
#8
Padraic J Phibbs, Ben Jones, Gregory Roe, Dale Read, Joshua Darrall-Jones, Jonathon Weakley, Andrew Rock, Kevin Till
The aim of this study was to quantify the mean weekly training load (TL) of elite adolescent rugby union players participating in multiple teams, and examine the differences between playing positions. Twenty elite male adolescent rugby union players (17.4 ± 0.7 years) were recruited from a regional academy and categorised by playing position; forwards (n=10) and backs (n=10). Global positioning system and accelerometer microtechnology was used to quantify external TL, and session-rating of perceived exertion (sRPE) was used to quantify internal TL during all sessions throughout a 10-week in-season period...
April 18, 2017: Journal of Strength and Conditioning Research
https://www.readbyqxmd.com/read/28442597/the-emergence-evolution-and-diversification-of-the-mir390-tas3-arf-pathway-in-land-plants
#9
Rui Xia, Jing Xu, Blake C Meyers
In plants, miR390 directs the production of tasiRNAs from TRANS-ACTING SIRNA 3 (TAS3) transcripts to regulate AUXIN RESPONSIVE FACTOR (ARF) genes, critical for auxin signaling; these tasiRNAs are known as tasiARFs. To understand the evolution of this miR390-TAS3-ARF pathway, we characterized homologs of these three genes from thousands of plant species, from bryophytes to angiosperms. We found the lower-stem region of MIR390 genes, critical for accurate DCL1 (DICER-LIKE 1) processing, is conserved in sequence in seed plants...
April 24, 2017: Plant Cell
https://www.readbyqxmd.com/read/28441519/grounding-principles-for-inferring-agency-two-cultural-perspectives
#10
Bethany L Ojalehto, Douglas L Medin, Salino G García
The present research investigates cultural variation in grounding principles for inferring agency in order to address an important theoretical debate: does cultural diversity in agency concepts reflect an animistic overextension of (universal) folkpsychology, as many have argued, or an alternative theory of folkcommunication based on relational principles? In two experiments, mind perception measures were adapted to assess beliefs concerning the agency of non-animal kinds (plants, abiotic kinds, complex artifacts) among Indigenous Ngöbe adults in Panama and US college students...
April 22, 2017: Cognitive Psychology
https://www.readbyqxmd.com/read/28441061/precisely-where-are-we-going-charting-the-new-terrain-of-precision-prevention
#11
Karen M Meagher, Michelle L McGowan, Richard A Settersten, Jennifer R Fishman, Eric T Juengst
In addition to genetic data, precision medicine research gathers information about three factors that modulate gene expression: lifestyles, environments, and communities. The relevant research tools-epidemiology, environmental assessment, and socioeconomic analysis-are those of public health sciences rather than molecular biology. Because these methods are designed to support inferences and interventions addressing population health, the aspirations of this research are expanding from individualized treatment toward precision prevention in public health...
April 24, 2017: Annual Review of Genomics and Human Genetics
https://www.readbyqxmd.com/read/28439002/reading-a-400-000-year-record-of-earthquake-frequency-for-an-intraplate-fault
#12
Randolph T Williams, Laurel B Goodwin, Warren D Sharp, Peter S Mozley
Our understanding of the frequency of large earthquakes at timescales longer than instrumental and historical records is based mostly on paleoseismic studies of fast-moving plate-boundary faults. Similar study of intraplate faults has been limited until now, because intraplate earthquake recurrence intervals are generally long (10s to 100s of thousands of years) relative to conventional paleoseismic records determined by trenching. Long-term variations in the earthquake recurrence intervals of intraplate faults therefore are poorly understood...
April 24, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28434666/heavy-metal-distribution-and-contamination-status-in-the-sedimentary-environment-of-cochin-estuary
#13
P M Salas, C H Sujatha, C S Ratheesh Kumar, Eldhose Cheriyan
Heavy metals (Fe, Mn, Cr, Zn, Ni, Pb, Cu, Co and Cd) in the surface sediments of Cochin estuary, Southwest coast of India were analyzed to understand the spatio-temporal variation and contamination status via six sampling campaigns. Pollution indices like enrichment factor, geoaccumulation index and pollution load index inferred that the sediments of the northern arm of the estuary exhibited severe trace metal accumulation. Numerical sediment quality guidelines were applied to assess adverse biological effects of the trace metals, suggesting that occasional biological effect may occur due to Cr, Cu, Ni and Pb...
April 20, 2017: Marine Pollution Bulletin
https://www.readbyqxmd.com/read/28431121/starbeast2-brings-faster-species-tree-inference-and-accurate-estimates-of-substitution-rates
#14
Huw A Ogilvie, Remco R Bouckaert, Alexei J Drummond
Fully Bayesian multispecies coalescent (MSC) methods like *BEAST estimate species trees from multiple sequence alignments. Today thousands of genes can be sequenced for a given study, but using that many genes with *BEAST is intractably slow. An alternative is to use heuristic methods which compromise accuracy or completeness in return for speed. A common heuristic is concatenation, which assumes that the evolutionary history of each gene tree is identical to the species tree. This is an inconsistent estimator of species tree topology, a worse estimator of divergence times, and induces spurious substitution rate variation when incomplete lineage sorting is present...
April 14, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28428849/species-distribution-models-predict-temporal-but-not-spatial-variation-in-forest-growth
#15
Ernst van der Maaten, Andreas Hamann, Marieke van der Maaten-Theunissen, Aldo Bergsma, Geerten Hengeveld, Ron van Lammeren, Frits Mohren, Gert-Jan Nabuurs, Renske Terhürne, Frank Sterck
Bioclimate envelope models have been widely used to illustrate the discrepancy between current species distributions and their potential habitat under climate change. However, the realism and correct interpretation of such projections has been the subject of considerable discussion. Here, we investigate whether climate suitability predictions correlate to tree growth, measured in permanent inventory plots and inferred from tree-ring records. We use the ensemble classifier RandomForest and species occurrence data from ~200,000 inventory plots to build species distribution models for four important European forestry species: Norway spruce, Scots pine, European beech, and pedunculate oak...
April 2017: Ecology and Evolution
https://www.readbyqxmd.com/read/28426211/dry-particulate-nitrate-deposition-in-china
#16
Lei Liu, Xiuying Zhang, Yan Zhang, Wen Xu, Xuejun Liu, Xiaomin Zhang, Junlan Feng, Xinrui Chen, Yuehan Zhang, Xuehe Lu, Shanqian Wang, Wuting Zhang, Limin Zhao
A limited number of ground measurements of dry particulate nitrate deposition (NO3(-)) makes it difficult and challenging to fully know the status of the spatial and temporal variations of dry NO3(-) depositions over China. This study tries to expand the ground measurements of NO3(-) concentrations at monitoring sites to a national scale, based on the Ozone Monitoring Instrument (OMI) NO2 columns, NO2 profiles from an atmospheric chemistry transport model (Model for Ozone and Related chemical Tracers, version 4, MOZART-4) and monitor-based sources, and then estimates the NO3(-) depositions on a regional scale based on an inferred model...
April 28, 2017: Environmental Science & Technology
https://www.readbyqxmd.com/read/28424728/landscape-population-genomics-of-forsythia-forsythia-suspensa-reveal-that-ecological-habitats-determine-the-adaptive-evolution-of-species
#17
Jie Yang, Cai-Yun Miao, Run-Li Mao, Yong Li
Understanding the genetic mechanisms of adaptation to environmental variables is a key concern in molecular ecology and evolutionary biology. Determining the adaptive evolutionary direction and evaluating the adaptation status of species can improve our understanding of these mechanisms. In this study, we sampled 20 populations of Forsythia suspensa to infer the relationship between environmental variables and adaptive genetic variations. Population structure analysis revealed that four genetic groups of F...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28424454/inference-of-the-infection-status-of-individuals-using-longitudinal-testing-data-from-cryptic-populations-towards-a-probabilistic-approach-to-diagnosis
#18
Svetlana N Buzdugan, Timothée Vergne, Vladimir Grosbois, Richard J Delahay, Julian A Drewe
Effective control of many diseases requires the accurate detection of infected individuals. Confidently ascertaining whether an individual is infected can be challenging when diagnostic tests are imperfect and when some individuals go for long periods of time without being observed or sampled. Here, we use a multi-event capture-recapture approach to model imperfect observations of true epidemiological states. We describe a method for interpreting potentially disparate results from individuals sampled multiple times over an extended period, using empirical data from a wild badger population naturally infected with Mycobacterium bovis as an example...
April 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28421622/bayesian-inference-on-mixed-effects-location-scale-models-with-skew-t-distribution-and-mismeasured-covariates-for-longitudinal-data
#19
Tao Lu
In AIDS studies, heterogeneous between and within subject variations are often observed on longitudinal endpoints. To accommodate heteroscedasticity in the longitudinal data, statistical methods have been developed to model the mean and variance jointly. Most of these methods assume (conditional) normal distributions for random errors, which is not realistic in practice. In this article, we propose a Bayesian mixed-effects location scale model with skew-t distribution and mismeasured covariates for heterogeneous longitudinal data with skewness...
April 18, 2017: Statistics in Medicine
https://www.readbyqxmd.com/read/28419235/a-bayesian-group-sparse-multi-task-regression-model-for-imaging-genetics
#20
Keelin Greenlaw, Elena Szefer, Jinko Graham, Mary Lesperance, Farouk S Nathoo
Motivation: Recent advances in technology for brain imaging and high-throughput genotyping have motivated studies examining the influence of genetic variation on brain structure. Wang et al. (Bioinformatics, 2012) have developed an approach for the analysis of imaging genomic studies using penalized multi-task regression with regularization based on a novel group l2,1-norm penalty which encourages structured sparsity at both the gene level and SNP level. While incorporating a number of useful features, the proposed method only furnishes a point estimate of the regression coefficients; techniques for conducting statistical inference are not provided...
April 13, 2017: Bioinformatics
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