Please find below, some of the more interesting examples of ggtern being used within peer-reviewed publication. Also included below is a non-exhaustive list of other publications, books and references where ggtern has been used or mentioned.

rouger2016effects_scaled2

Rouger et. al. [1]
kalenitchenko2016ecological_scaled2

Kalenitchenko et. al. [2]
witte2015high_scaled2

Witte et. al. [3]
wenger2016loss_scaled2

Wenger et. al. [4]
ho2016resilience_scaled2

Ho et. al. [5]
bustos2015effects_scaled2

Bustos et. al. [6]

References

[7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 16, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 5, 58, 59, 1, 60, 61, 62, 63, 64, 65, 66, 67, 2, 4, 3, 6, 68, 69, 70, 71, 72, 73]
[1] [doi] R. Rouger, K. Reichel, F. Malrieu, J. Masson, and S. Stoeckel, “Effects of Complex Life Cycles on Genetic Diversity: Cyclical Parthenogenesis,” Heredity, 2016.
[Bibtex]
@Article{rouger2016effects,
author = {Rouger, R and Reichel, K and Malrieu, F and Masson, JP and Stoeckel, S},
title = {Effects of Complex Life Cycles on Genetic Diversity: Cyclical Parthenogenesis},
journal = {Heredity},
year = {2016},
doi = {10.1038/hdy.2016.52},
abstract = {Neutral patterns of population genetic diversity in species with complex life cycles are difficult to anticipate. Cyclical parthenogenesis (CP), in which organisms undergo several rounds of clonal reproduction followed by a sexual event, is one such life cycle. Many species, including crop pests (aphids), human parasites (trematodes) or models used in evolutionary science (Daphnia), are cyclical parthenogens. It is therefore crucial to understand the impact of such a life cycle on neutral genetic diversity. In this paper, we describe distributions of genetic diversity under conditions of CP with various clonal phase lengths. Using a Markov chain model of CP for a single locus and individual-based simulations for two loci, our analysis first demonstrates that strong departures from full sexuality are observed after only a few generations of clonality. The convergence towards predictions made under conditions of full clonality during the clonal phase depends on the balance between mutations and genetic drift. Second, the sexual event of CP usually resets the genetic diversity at a single locus towards predictions made under full sexuality. However, this single recombination event is insufficient to reshuffle gametic phases towards full-sexuality predictions. Finally, for similar levels of clonality, CP and acyclic partial clonality (wherein a fixed proportion of individuals are clonally produced within each generation) differentially affect the distribution of genetic diversity. Overall, this work provides solid predictions of neutral genetic diversity that may serve as a null model in detecting the action of common evolutionary or demographic processes in cyclical parthenogens (for example, selection or bottlenecks).},
file = {rouger2016effects.pdf:Users/nick/Copy/UNSW/PhD/References/Referenced/rouger2016effects.pdf:PDF},
owner = {nick},
publisher = {Nature Publishing Group},
timestamp = {20160726},
}
[2] [doi] D. Kalenitchenko, M. Dupraz, N. Le Bris, C. Petetin, C. Rose, N. J. West, and P. E. Galand, “Ecological Succession Leads to Chemosynthesis in Mats Colonizing Wood in Sea Water,” The ISME Journal, 2016.
[Bibtex]
@Article{kalenitchenko2016ecological,
author = {Kalenitchenko, Dimitri and Dupraz, Marl{\`e}ne and Le Bris, Nadine and Petetin, Carole and Rose, Christophe and West, Nyree J and Galand, Pierre E},
title = {Ecological Succession Leads to Chemosynthesis in Mats Colonizing Wood in Sea Water},
journal = {The ISME Journal},
year = {2016},
doi = {10.1038/ismej.2016.12},
abstract = {Chemosynthetic mats involved in cycling sulfur compounds are often found in hydrothermal vents, cold seeps and whale falls. However, there are only few records of wood fall mats, even though the presence of hydrogen sulfide at the wood surface should create a perfect niche for sulfide-oxidizing bacteria. Here we report the growth of microbial mats on wood incubated under conditions that simulate the Mediterranean deep-sea temperature and darkness. We used amplicon and metagenomic sequencing combined with fluorescence in situ hybridization to test whether a microbial succession occurs during mat formation and whether the wood fall mats present chemosynthetic features. We show that the wood surface was first colonized by sulfide-oxidizing bacteria belonging to the Arcobacter genus after only 30 days of immersion. Subsequently, the number of sulfate reducers increased and the dominant Arcobacter phylotype changed. The ecological succession was reflected by a change in the metabolic potential of the community from chemolithoheterotrophs to potential chemolithoautotrophs. Our work provides clear evidence for the chemosynthetic nature of wood fall ecosystems and demonstrates the utility to develop experimental incubation in the laboratory to study deep-sea chemosynthetic mats.},
file = {kalenitchenko2016ecological.pdf:Users/nick/Copy/UNSW/PhD/References/Referenced/kalenitchenko2016ecological.pdf:PDF},
owner = {nick},
publisher = {Nature Publishing Group},
review = {Uses ggtern},
timestamp = {20160227},
}
[3] [doi] S. Witte, A. Bradley, A. J. Enright, and S. A. Muljo, “High-Density P300 Enhancers Control Cell State Transitions,” BMC Genomics, vol. 16, iss. 1, p. 903, 2015.
[Bibtex]
@Article{witte2015high,
author = {Witte, Steven and Bradley, Allan and Enright, Anton J and Muljo, Stefan A},
title = {High-Density P300 Enhancers Control Cell State Transitions},
journal = {BMC Genomics},
year = {2015},
volume = {16},
number = {1},
pages = {903},
doi = {10.1186/s12864-015-1905-6},
file = {witte2015high.pdf:Users/nick/Copy/UNSW/PhD/References/Referenced/witte2015high.pdf:PDF},
owner = {nick},
publisher = {BioMed Central Ltd},
timestamp = {20151110},
}
[4] [doi] Y. Wenger, W. Buzgariu, and B. Galliot, “Loss of Neurogenesis in Hydra Leads to Compensatory Regulation of Neurogenic and Neurotransmission Genes in Epithelial Cells,” Phil. Trans. R. Soc. B, vol. 371, iss. 1685, p. 20150040, 2016.
[Bibtex]
@Article{wenger2016loss,
Title = {Loss of Neurogenesis in Hydra Leads to Compensatory Regulation of Neurogenic and Neurotransmission Genes in Epithelial Cells},
Author = {Wenger, Yvan and Buzgariu, W and Galliot, Brigitte},
Journal = {Phil. Trans. R. Soc. B},
Year = {2016},
Number = {1685},
Pages = {20150040},
Volume = {371},
Abstract = {Hydra continuously differentiates a sophisticated nervous system made of mechanosensory cells (nematocytes) and sensory-motor and ganglionic neurons from interstitial stem cells. However, this dynamic adult neurogenesis is dispensable for morphogenesis. Indeed animals depleted of their interstitial stem cells and interstitial progenitors lose their active behaviours but maintain their developmental fitness, and regenerate and bud when force-fed. To characterize the impact of the loss of neurogenesis in Hydra, we first performed transcriptomic profiling at five positions along the body axis. We found neurogenic genes predominantly expressed along the central body column, which contains stem cells and progenitors, and neurotransmission genes predominantly expressed at the extremities, where the nervous system is dense. Next, we performed transcriptomics on animals depleted of their interstitial cells by hydroxyurea, colchicine or heat-shock treatment. By crossing these results with cell-type-specific transcriptomics, we identified epithelial genes up-regulated upon loss of neurogenesis: transcription factors (Dlx, Dlx1, DMBX1/Manacle, Ets1, Gli3, KLF11, LMX1A, ZNF436, Shox1), epitheliopeptides (Arminins, PW peptide), neurosignalling components (CAMK1D, DDCl2, Inx1), ligand-ion channel receptors (CHRNA1, NaC7), G-Protein Coupled Receptors and FMRFRL. Hence epitheliomuscular cells seemingly enhance their sensing ability when neurogenesis is compromised. This unsuspected plasticity might reflect the extended multifunctionality of epithelial-like cells in early eumetazoan evolution.},
Doi = {10.1098/rstb.2015.0040},
File = {wenger2016loss.pdf:Users/nick/Copy/UNSW/PhD/References/Referenced/wenger2016loss.pdf:PDF},
Owner = {nick},
Publisher = {The Royal Society},
Timestamp = {20151201}
}
[5] [doi] A. Ho, C. Lüke, A. Reim, and P. Frenzel, “Resilience of (Seed Bank) Aerobic Methanotrophs and Methanotrophic Activity to Desiccation and Heat Stress,” Soil Biology and Biochemistry, vol. 101, pp. 130-138, 2016.
[Bibtex]
@Article{ho2016resilience,
author = {Ho, Adrian and L{\"u}ke, Claudia and Reim, Andreas and Frenzel, Peter},
title = {Resilience of (Seed Bank) Aerobic Methanotrophs and Methanotrophic Activity to Desiccation and Heat Stress},
journal = {Soil Biology and Biochemistry},
year = {2016},
volume = {101},
pages = {130--138},
doi = {10.1016/j.soilbio.2016.07.015},
abstract = {In seasonally changing environments, aerobic methanotrophs are exposed to elevated temperatures and drought. Prior exposure to adverse conditions (site history) may leave an imprint on the methanotrophic community composition in the form of a seed bank. While the significance of a microbial seed bank is established, the potential of this seemingly preserved community following emergence from inactive states and its sensitivity to adverse conditions are still lacking. We used a paddy soil representing an environment experiencing recurring desiccation and heat stress as per agricultural practice, and two lake sediments with sporadic/limited or no exposure to desiccation and heat stress as model systems. In a microcosm study, we induced drought combined with a heat treatment by air-drying the samples at ambient (25 °C) and elevated (75 °C) temperatures, designated as mild and severe stress, respectively. Fresh soil/sediment were used as reference. Upon rewetting, we followed the recovery of the methane uptake rate, and the population dynamics was monitored using qPCR assays and a diagnostic microarray analysis. Remarkably, methane uptake rates were not adversely affected even after severe stress, and activity recovered to levels comparable to the fresh soil/sediment incubations after 40 days. In particular, the alphaproteobacterial methanotrophs (Methylosinus-Methylocystis group) exponentially increased in population size upon rewetting. Interestingly, the qPCR and microarray analyses revealed that some gammaproteobacterial methanotrophs (e.g. Methylocaldum- and Methylosarcina-related methanotrophs) increased in relative abundance after the desiccation and heat stress, indicating the unexpected resistance of this subgroup to the stress treatment. Although the initial and recovering communities were significantly different, population abundance recovered over time. The shift in the trajectory of the recovering communities suggests that repeated exposure to adverse factors will change the seed bank's composition. Overall, the indigenous (seed bank) methanotroph populations showed remarkable recovery from the induced stress.},
file = {ho2016resilience.pdf:Users/nick/Copy/UNSW/PhD/References/Referenced/ho2016resilience.pdf:PDF},
owner = {nick},
publisher = {Elsevier},
timestamp = {20160730},
}
[6] [doi] C. Bustos-Segura, C. Külheim, and W. Foley, “Effects of Terpene Chemotypes of Melaleuca Alternifolia on Two Specialist Leaf Beetles and Susceptibility to Myrtle Rust,” Journal of Chemical Ecology, pp. 1-11, 2015.
[Bibtex]
@Article{bustos2015effects,
author = {Bustos-Segura, Carlos and K{\"u}lheim, Carsten and Foley, William},
title = {Effects of Terpene Chemotypes of Melaleuca Alternifolia on Two Specialist Leaf Beetles and Susceptibility to Myrtle Rust},
journal = {Journal of Chemical Ecology},
year = {2015},
month = {9},
pages = {1--11},
doi = {10.1007/s10886-015-0628-0},
abstract = {Plant chemical polymorphisms, or plant chemotypes, are characterized by intraspecific discrete differences of plant secondary metabolites in the same plant tissue. Chemotypes that differ in foliar terpene composition are found commonly in Myrtaceae. In this study, we focused on terpene chemotypes of medicinal tea tree, Melalecua alternifolia, to explore whether this variation affects two specialist herbivores Paropsisterna tigrina and Faex sp. (Coleoptera: Chrysomelidae), and if this could explain the maintenance of this variation. We tested whether insect performance, oviposition preference, and plant damage were associated with different chemotypes. We found that larval growth rate of Faex sp. was higher in chemotypes with high concentrations of 1,8-cineole, and that oviposition preference depended on the chemotype of the larval diet. Although performance traits and preference for oviposition of P. tigrina did not vary among chemotypes, adults inflicted less damage on plants with a high concentration of terpinolene. Additionally, we tested whether different chemotypes showed different levels of susceptibility by myrtle rust (Puccinia psidii). We found that plants with a high concentration of 1,8-cineole were more likely to be infected under controlled conditions. Although there is evidence that terpene chemotypes are a mediator of the interaction with natural enemies, the most detrimental pest of this plant, P. tigrina, does not seem to be affected by variation in plant terpenes.},
file = {bustos2015effects.pdf:Users/nick/Copy/UNSW/PhD/References/Referenced/bustos2015effects.pdf:PDF},
owner = {nick},
publisher = {Springer-Verlag},
timestamp = {20150925},
}
[7] [doi] A. Markert, K. Bohne, M. Facklam, and G. Wessolek, “Pedotransfer Functions of Soil Thermal Conductivity for the Textural Classes Sand, Silt, and Loam,” Soil Science Society of America Journal, 2017.
[Bibtex]
@Article{markert2017pedotransfer,
author = {Markert, A and Bohne, K and Facklam, M and Wessolek, G},
title = {Pedotransfer Functions of Soil Thermal Conductivity for the Textural Classes Sand, Silt, and Loam},
journal = {Soil Science Society of America Journal},
year = {2017},
doi = {10.2136/sssaj2017.02.0062},
abstract = {Data of soil thermal conductivity (λ) covering the whole range of soil water content (θ) are needed in many environmental disciplines. However, laboratory measurements of λ(θ) are time consuming and costly. Therefore the use of pedotransfer functions is promising. In this study, we describe the procedure of deriving such λ(θ) pedotransfer functions for the FAO texture groups (TG) of Sand, Silt and Loam. First, high-resolution λ(θ) measurements from saturation to dryness of 43 soils were conducted by two laboratory methods: the evaporation approach and single-point measurements of λ at distinct water contents. Measurements were obtained for a set of sandy, silty, loamy, and clayey soils, and for two urban soils and two peat soils. The slope and magnitude of the λ(θ) curves show typical dependencies on bulk density (ρb) and soil texture. In a second step, the λ(θ) data were used to evaluate the λ(θ) model as suggested by Lu et al. (2014). Fitting this model to the complete data set yielded a poor agreement with RMSE = 0.53 W m-1 K-1. However, satisfying results were obtained by dividing the data into TGs Sand, Silt and Loam resulting in RMSEs of 0.18, 0.11 and 0.24 W m-1 K-1, respectively. Estimated λ values at low soil moisture (wilting point) were hardly different among texture classes, but λ differences become highly relevant when soil moisture increased to field capacity. The derived pedotransfer functions are an easy-to-use approach providing reliable λ(θ) curves for sandy, silty and loamy soils, when only basic soil information (texture and bulk density) are available.},
file = {markert2017pedotransfer.pdf:Referenced/markert2017pedotransfer.pdf:PDF},
owner = {nick},
publisher = {The Soil Science Society of America, Inc.},
timestamp = {20171108},
}
[8] [doi] S. D. Jurburg, T. Natal-da-Luz, J. Raimundo, P. V. Morais, J. P. Sousa, J. D. van Elsas, and J. F. Salles, “Bacterial Communities in Soil Become Sensitive to Drought Under Intensive Grazing,” Science of The Total Environment, 2017.
[Bibtex]
@Article{jurburg2017bacterial,
author = {Jurburg, Stephanie D and Natal-da-Luz, Tiago and Raimundo, Jo{\~a}o and Morais, Paula V and Sousa, Jos{\'e} Paulo and van Elsas, Jan Dirk and Salles, Joana Falcao},
title = {Bacterial Communities in Soil Become Sensitive to Drought Under Intensive Grazing},
journal = {Science of The Total Environment},
year = {2017},
doi = {10.1016/j.scitotenv.2017.10.012},
abstract = {Increasing climatic and anthropogenic pressures on soil ecosystems are expected to create a global patchwork of disturbance scenarios. Some regions will be strongly impacted by climate change, others by agricultural intensification, and others by both. Soil microbial communities are integral components of terrestrial ecosystems, but their responses to multiple perturbations are poorly understood. Here, we exposed soils from sustainably- or intensively-managed grasslands in an agro-silvo-pastoral oak woodland to month-long intensified drought and flood simulation treatments in a controlled mesocosm setting. We monitored the response of the bacterial communities at the end of one month as well as during the following month of recovery. The communities in sustainably-managed plots under all precipitation regimes were richer and more diverse than those in intensively-managed plots, and contained a lower proportion of rapidly-growing taxa. Soils from both land managements exhibited changes in bacterial community composition in response to flooding, but only intensively-managed soils were affected by drought. The ecologies of bacteria favored by both drought and flood point to both opportunism and stress tolerance as key traits shaping the community following disturbance. Finally, the response of several taxa (i.e. Chloracidobacteria RB41, Janthinobacterium sp.) to precipitation depended on land management, suggesting that the community itself affected individual disturbance responses. Our findings provide an in-depth view of the complexity of soil bacterial community responses to climatic and anthropogenic pressures in time, and highlight the potential of these stressors to have multiplicative effects on the soil biota.},
file = {jurburg2017bacterial.pdf:Referenced/jurburg2017bacterial.pdf:PDF},
owner = {nick},
publisher = {Elsevier},
timestamp = {20171025},
}
[9] R. Mart{‘i}nez-Santos, E. Mart{‘i}nez-Gutiérrez, and M. Mujika-Garc{‘i}a, “Lógica Temporal del Tiro Libre en ACB,” Revista de psicolog\’\ia del deporte, vol. 26, iss. 3, pp. 101-107, 2017.
[Bibtex]
@Article{martinez2017logica,
author = {Mart{\'\i}nez-Santos, Ra{\'u}l and Mart{\'\i}nez-Guti{\'e}rrez, Endika and Mujika-Garc{\'\i}a, Mikel},
title = {L{\'o}gica Temporal del Tiro Libre en ACB},
journal = {Revista de psicolog{\'\i}a del deporte},
year = {2017},
volume = {26},
number = {3},
pages = {0101--107},
file = {martinez2017logica.pdf:Referenced/martinez2017logica.pdf:PDF},
owner = {nick},
timestamp = {20171023},
}
[10] J. D. Silverman and R. K. Silverman, “The Bayesian Sorting Hat: A Decision-Theoretic Approach to Size-Constrained Clustering,” arXiv preprint arXiv:1710.06047, 2017.
[Bibtex]
@Article{silverman2017bayesian,
author = {Silverman, Justin D and Silverman, Rachel K},
title = {The Bayesian Sorting Hat: A Decision-Theoretic Approach to Size-Constrained Clustering},
journal = {arXiv preprint arXiv:1710.06047},
year = {2017},
file = {silverman2017bayesian.pdf:Referenced/silverman2017bayesian.pdf:PDF},
owner = {nick},
timestamp = {20171023},
}
[11] [doi] T. R. Barnum, D. E. Weller, and M. Williams, “Urbanization Reduces and Homogenizes Trait Diversity in Stream Macroinvertebrate Communities,” Ecological Applications, 2017.
[Bibtex]
@Article{barnum2017urbanization,
author = {Barnum, Thomas R and Weller, Donald E and Williams, Meghan},
title = {Urbanization Reduces and Homogenizes Trait Diversity in Stream Macroinvertebrate Communities},
journal = {Ecological Applications},
year = {2017},
doi = {10.1002/eap.1619},
abstract = {More than half the world's population lives in urban areas, so quantifying the effects of urbanization on ecological communities is important for understanding whether anthropogenic stressors homogenize communities across environmental and climatic gradients. We examined the relationship of impervious surface coverage (a marker of urbanization) and the structure of stream macroinvertebrate communities across the state of Maryland and within each of Maryland's three ecoregions: Coastal Plain, Piedmont, and Appalachian, which differ in stream geomorphology and community composition. We considered three levels of trait organization: individual traits, unique combinations of traits, and community metrics (functional richness, functional evenness, and functional divergence) and three levels of impervious surface coverage (low (<2.5%), medium (2.5% to 10%), and high (>10%). The prevalence of an individual trait modality differed very little between low impervious surface and high impervious surface sites. The arrangement of trait combinations in community trait space for each ecoregion differed when impervious surface coverage was low, but the arrangement became more similar among ecoregions as impervious surface coverage increased. Furthermore, trait combinations that occurred only at low or medium impervious surface coverage were clustered in a subset of the community trait space, indicating impervious surface affected the presence of only a subset of trait combinations. Functional richness declined with increasing impervious surface, providing evidence for environmental filtering. Community metrics that include abundance were also sensitive to increasing impervious surface coverage–functional divergence decreased while functional evenness increased. These changes demonstrate that increasing impervious surface coverage homogenizes the trait diversity of macroinvertebrate communities in streams, despite differences in initial community composition and stream geomorphology among ecoregions. Community metrics were also more sensitive to changes in the abundance rather than the gain or loss of trait combinations, showing the potential for trait-based approaches to serve as early warning indicators of environmental stress for monitoring and biological assessment programs.},
file = {barnum2017urbanization.pdf:Referenced/barnum2017urbanization.pdf:PDF},
owner = {nick},
publisher = {Wiley Online Library},
timestamp = {20171023},
}
[12] [doi] A. N. Barbeira, S. P. Dickinson, J. M. Torres, R. Bonazzola, J. Zheng, E. S. Torstenson, H. E. Wheeler, K. P. Shah, T. Edwards, T. Garcia, and others, “Exploring the Phenotypic Consequences of Tissue Specific Gene Expression Variation Inferred from GWAS Summary Statistics,” bioRxiv, p. 45260, 2017.
[Bibtex]
@Article{barbeira2017exploring,
author = {Barbeira, Alvaro N and Dickinson, Scott P and Torres, Jason M and Bonazzola, Rodrigo and Zheng, Jiamao and Torstenson, Eric S and Wheeler, Heather E and Shah, Kaanan P and Edwards, Todd and Garcia, Tzintzuni and others},
title = {Exploring the Phenotypic Consequences of Tissue Specific Gene Expression Variation Inferred from GWAS Summary Statistics},
journal = {bioRxiv},
year = {2017},
pages = {045260},
doi = {10.1101/045260},
file = {barbeira2017exploring.pdf:Referenced/barbeira2017exploring.pdf:PDF},
owner = {nick},
publisher = {Cold Spring Harbor Laboratory},
timestamp = {20171023},
}
[13] R. J. Wilson, D. C. Speirs, A. Sabatino, and M. R. Heath, “A Synthetic Map of the Northwest European Shelf Sedimentary Environment for Applications in Marine Science.”
[Bibtex]
@Article{wilson2017synthetic,
author = {Wilson, Robert J and Speirs, Douglas C and Sabatino, Alessandro and Heath, Michael R},
title = {A Synthetic Map of the Northwest European Shelf Sedimentary Environment for Applications in Marine Science},
file = {wilson2017synthetic.pdf:Referenced/wilson2017synthetic.pdf:PDF},
owner = {nick},
timestamp = {20171023},
}
[14] A. Pinder, M. Lyons, M. Collins, L. Lewis, K. Quinlan, R. Shiel, R. Coppen, and F. Thompson, “Wetland Biodiversity Patterning Along the Middle to Upper Fortescue Valley (Pilbara: Western Australia) to Inform Conservation Planning,” , 2017.
[Bibtex]
@Article{pinder2017wetland,
author = {Pinder, Adrian and Lyons, Michael and Collins, Margaret and Lewis, Loretta and Quinlan, Kirsty and Shiel, Russell and Coppen, Rebecca and Thompson, Faye},
title = {Wetland Biodiversity Patterning Along the Middle to Upper Fortescue Valley (Pilbara: Western Australia) to Inform Conservation Planning},
year = {2017},
file = {pinder2017wetland.pdf:Referenced/pinder2017wetland.pdf:PDF},
owner = {nick},
timestamp = {20171023},
}
[15] [doi] L. W. Bielczynski, M. K. {Ł}{k{a}}cki, I. Hoefnagels, A. Gambin, and R. Croce, “Leaf and plant age affects photosynthetic performance and photoprotective capacity,” Plant Physiology, p. pp–00904, 2017.
[Bibtex]
@Article{bielczynski2017leaf,
author = {Bielczynski, Ludwik Wiktor and {\L}{\k{a}}cki, Mateusz Krzysztof and Hoefnagels, Iris and Gambin, Anna and Croce, Roberta},
title = {Leaf and plant age affects photosynthetic performance and photoprotective capacity},
journal = {Plant Physiology},
year = {2017},
pages = {pp--00904},
doi = {10.1104/pp.17.00904},
abstract = {In this work, we studied the changes in high light tolerance and photosynthetic activity in leaves of the Arabidopsis thaliana rosette throughout the vegetative stage of growth. We implemented an image analysis workflow to analyze the capacity of both the whole plant and individual leaves to cope with excess excitation energy by following the changes in the absorbed light energy partitioning. The data show that leaf and plant age are both important factors influencing the fate of excitation energy. During the dark-to-light transition, the age of the plant affects mostly steady state levels of photochemical and non-photochemical quenching (NPQ), leading to an increased photosynthetic performance of its leaves. The age of the leaf affects the induction kinetics of NPQ. These observations were confirmed using model selection procedures. We further investigate how different leaves on a rosette acclimate to high light and show that younger leaves are less prone to photoinhibition than older leaves. Our results stress that both plant and leaf age should be taken into consideration during the quantification of photosynthetic and photoprotective traits to produce repeatable and reliable results.},
file = {bielczynski2017leaf.pdf:Referenced/bielczynski2017leaf.pdf:PDF},
owner = {nick},
publisher = {Am Soc Plant Biol},
timestamp = {20171020},
}
[16] [doi] M. Azevedo, J. R. Parizek, H. N. Webb, K. N. Dennis, M. T. Dorsey, N. C. Fenton, C. M. Hall, and G. H. Girty, “Recognizing Non-Steady-State Weathering Conditions In Ancient Submarine Fan Systems: Correcting For K-Metasomatism Reveals A Late Cretaceous Non-Steady-State Weathering Regime, Point Loma Formation, Southwestern California, USA,” Journal of Sedimentary Research, vol. 87, iss. 7, pp. 707-721, 2017.
[Bibtex]
@Article{azevedo2017recognizing,
author = {Azevedo, Marcelo and Parizek, Jason R and Webb, Heather N and Dennis, Kristen N and Dorsey, Matthew T and Fenton, Nicole C and Hall, Craig M and Girty, Gary H},
title = {Recognizing Non-Steady-State Weathering Conditions In Ancient Submarine Fan Systems: Correcting For K-Metasomatism Reveals A Late Cretaceous Non-Steady-State Weathering Regime, Point Loma Formation, Southwestern California, USA},
journal = {Journal of Sedimentary Research},
year = {2017},
volume = {87},
number = {7},
pages = {707--721},
doi = {10.2110/jsr.2017.41},
abstract = {During steady-state weathering, the rate of removal of the exposed weathering zone is balanced by the rate of generation of mineralogically identical material through chemical weathering. As steady-state conditions prevail, the mineralogical and chemical composition of sediments derived from the weathering profile should be invariant over time. In A-CN-K space, a steady-state weathering condition is characterized by tightly grouped compositions, with dispersion between sands and muds a consequence of sorting during fluvial transportation. The purpose of this study was to assess whether such a condition was present during the development of the Upper Cretaceous Point Loma Formation.
Published paleotectonic reconstructions portray the upper Campanian–lower Maastrichtian(?) Point Loma Formation as being deposited in a forearc basin developed westward of a continental-margin magmatic arc. In such accounts, during the subduction of an oceanic plateau (or aseismic ridge) or during constant-dip subduction, rocks in the magmatic arc were uplifted and the volcanic cover nearly stripped clean, exposing its plutonic roots. Published detrital-zircon data derived from samples of the Point Loma Formation indicate that exposed igneous rocks in the source area were mainly from 135 Ma to 100 Ma plutons located in the western zone of the Peninsular Ranges batholith. New point-count, XRD, and chemical data show that detritus in mudstones and some fine-grained feldspathic sandstones of the Point Loma Formation following deposition and shallow burial were subjected to a K-metasomatic event. After correcting for introduction of K+, and consideration of the effects of hydraulic sorting, resulting mudstone and fine-grained sandstone data plot in A-CN-K space in overlapping fields, whereas samples of coarse-grained sandstone lie between rays extending through the most and least weathered mudstones. Hence, detritus in the Point Loma Formation was derived mainly from regolith during non-steady-state weathering conditions.},
file = {azevedo2017recognizing.html:Referenced/azevedo2017recognizing.html:URL},
owner = {nick},
publisher = {SEPM},
timestamp = {20170724},
}
[17] M. Cruz, “Field Mapping Investigation and Geochemical Analysis of Volcanic Units within the Dinner Creek Tuff Eruptive Center, Malheur County, Eastern Oregon,” PhD Thesis, 2017.
[Bibtex]
@PhdThesis{cruz2017field,
author = {Cruz, Matthew},
title = {Field Mapping Investigation and Geochemical Analysis of Volcanic Units within the Dinner Creek Tuff Eruptive Center, Malheur County, Eastern Oregon},
year = {2017},
file = {cruz2017field.pdf:Referenced/cruz2017field.pdf:PDF},
owner = {nick},
timestamp = {20171005},
}
[18] [doi] E. Eronen-Rasimus, A. Luhtanen, J. Rintala, B. Delille, G. Dieckmann, A. Karkman, and J. Tison, “An active bacterial community linked to high chl-a concentrations in Antarctic winter-pack ice and evidence for the development of an anaerobic sea-ice bacterial community.,” The ISME journal, iss. 11, p. 2345-–2355, 2017.
[Bibtex]
@Article{eronen2017active,
author = {Eronen-Rasimus, Eeva and Luhtanen, Anne-Mari and Rintala, Janne-Markus and Delille, Bruno and Dieckmann, Gerhard and Karkman, Antti and Tison, Jean-Louis},
title = {An active bacterial community linked to high chl-a concentrations in Antarctic winter-pack ice and evidence for the development of an anaerobic sea-ice bacterial community.},
journal = {The ISME journal},
year = {2017},
number = {11},
pages = {2345-–2355},
doi = {10.1038/ismej.2017.96},
abstract = {Antarctic sea-ice bacterial community composition and dynamics in various developmental stages were investigated during the austral winter in 2013. Thick snow cover likely insulated the ice, leading to high (<4 μg l–1) chlorophyll-a (chl-a) concentrations and consequent bacterial production. Typical sea-ice bacterial genera, for example, Octadecabacter, Polaribacter and Glaciecola, often abundant in spring and summer during the sea-ice algal bloom, predominated in the communities. The variability in bacterial community composition in the different ice types was mainly explained by the chl-a concentrations, suggesting that as in spring and summer sea ice, the sea-ice bacteria and algae may also be coupled during the Antarctic winter. Coupling between the bacterial community and sea-ice algae was further supported by significant correlations between bacterial abundance and production with chl-a. In addition, sulphate-reducing bacteria (for example, Desulforhopalus) together with odour of H2S were observed in thick, apparently anoxic ice, suggesting that the development of the anaerobic bacterial community may occur in sea ice under suitable conditions. In all, the results show that bacterial community in Antarctic sea ice can stay active throughout the winter period and thus possible future warming of sea ice and consequent increase in bacterial production may lead to changes in bacteria-mediated processes in the Antarctic sea-ice zone.},
file = {eronen2017active.pdf:Referenced/eronen2017active.pdf:PDF},
owner = {nick},
timestamp = {20171003},
}
[19] R. E. Hughes, “Agricultural Development and Dietary Change in Switzerland from the Hallstatt (800 BCE) to the Rise of the Carolingian Dynasty (754 CE),” PhD Thesis, 2016.
[Bibtex]
@PhdThesis{hughes2016agricultural,
author = {Hughes, Ryan E},
title = {Agricultural Development and Dietary Change in Switzerland from the Hallstatt (800 BCE) to the Rise of the Carolingian Dynasty (754 CE)},
year = {2016},
file = {hughes2016agricultural.pdf:Referenced/hughes2016agricultural.pdf:PDF},
owner = {nick},
school = {State University of New York at Buffalo},
timestamp = {20170925},
}
[20] A. M. Merritt, “Lessons from the Past: The Endangered California Ridgway’s Rail (Rallus obsoletus obsoletus) as an Indicator for Underlying Changes to the San Francisco Bay Estuary,” PhD Thesis, 2016.
[Bibtex]
@PhdThesis{merritt2016lessons,
author = {Merritt, Angela Marie},
title = {Lessons from the Past: The Endangered California Ridgway's Rail (Rallus obsoletus obsoletus) as an Indicator for Underlying Changes to the San Francisco Bay Estuary},
year = {2016},
file = {merritt2016lessons.pdf:Referenced/merritt2016lessons.pdf:PDF},
owner = {nick},
school = {University of California, Davis},
timestamp = {20170925},
}
[21] E. Llop Vallverdú, “Càlcul de la mida mostral a estudis metagenòmics.”
[Bibtex]
@Article{llop2017calcul,
author = {Llop Vallverd{\'u}, Esteve},
title = {C{\`a}lcul de la mida mostral a estudis metagen{\`o}mics},
file = {llop2017calcul.pdf:Referenced/llop2017calcul.pdf:PDF},
owner = {nick},
publisher = {Universitat Oberta de Catalunya},
timestamp = {20170920},
}
[22] КИРИЛЛ. АЛЕКСАНДРОВИЧ. КОРЗНИКОВ, “Сосудистые растения спонтанно зарастающих участков разработки россыпного месторождения золота (р. Лангери, центральный Сахалин),” Вестник Томского государственного университета. Биология, iss. 4 (36), 2016.
[Bibtex]
@Article{корзников2016сосудистые,
author = {КОРЗНИКОВ, КИРИЛЛ АЛЕКСАНДРОВИЧ},
title = {Сосудистые растения спонтанно зарастающих участков разработки россыпного месторождения золота (р. Лангери, центральный Сахалин)},
journal = {Вестник Томского государственного университета. Биология},
year = {2016},
number = {4 (36)},
file = {корзников2016сосудистые.pdf:Referenced/корзников2016сосудистые.pdf:PDF},
owner = {nick},
publisher = {Федеральное государственное бюджетное образовательное учреждение высшего профессионального образования {\guillemotleft}Национальный исследовательский Томский государственный университет{\guillemotright}},
timestamp = {20170920},
}
[23] [doi] C. G. Eger, D. G. Chandler, and C. T. Driscoll, “Hydrologic processes that govern stormwater infrastructure behavior,” Hydrological Processes.
[Bibtex]
@Article{eger2017hydrologic,
author = {Eger, Caitlin G and Chandler, David G and Driscoll, Charles T},
title = {Hydrologic processes that govern stormwater infrastructure behavior},
journal = {Hydrological Processes},
doi = {10.1002/hyp.11353},
abstract = {Using water budget data from published literature, we demonstrate how hydrologic processes govern the function of various stormwater infrastructure technologies. Hydrologic observations are displayed on a Water Budget Triangle, a ternary plot tool developed to visualize simplified water budgets, enabling side-by-side comparison of green and grey approaches to stormwater management. The tool indicates ranges of hydrologic function for green roofs, constructed wetlands, cisterns, bioretention and other stormwater control management structures. Water budgets are plotted for several example systems to provide insight on structural and environmental design factors, and seasonal variation in hydrologic processes of stormwater management systems. Previously published water budgets and models are used to suggest appropriate operational standards for several green and grey stormwater control structures and compare between conventional and low-impact development approaches. We compare models, characterize and quantify water budgets and expected ranges for green and grey infrastructure systems, and demonstrate how the Water Budget Triangle tool may help users to develop a data-driven approach for understanding design and retrofit of green stormwater infrastructure.},
file = {eger2017hydrologic.pdf:Referenced/eger2017hydrologic.pdf:PDF},
owner = {nick},
publisher = {Wiley Online Library},
timestamp = {20170919},
}
[24] [doi] A. Boyé, P. Legendre, J. Grall, and O. Gauthier, “Constancy despite variability: Local and regional macrofaunal diversity in intertidal seagrass beds,” Journal of Sea Research, 2017.
[Bibtex]
@Article{boye2017constancy,
author = {Boy{\'e}, Aur{\'e}lien and Legendre, Pierre and Grall, Jacques and Gauthier, Olivier},
title = {Constancy despite variability: Local and regional macrofaunal diversity in intertidal seagrass beds},
journal = {Journal of Sea Research},
year = {2017},
doi = {10.1016/j.seares.2017.06.004},
file = {boye2017constancy.pdf:Referenced/boye2017constancy.pdf:PDF},
owner = {nick},
publisher = {Elsevier},
timestamp = {20170914},
}
[25] [doi] W. Dai, W. Yu, J. Zhang, J. Zhu, Z. Tao, and J. Xiong, “The gut eukaryotic microbiota influences the growth performance among cohabitating shrimp,” Applied Microbiology and Biotechnology, vol. 101, iss. 16, pp. 6447-6457, 2017.
[Bibtex]
@Article{dai2017gut,
author = {Dai, Wenfang and Yu, Weina and Zhang, Jinjie and Zhu, Jinyong and Tao, Zhen and Xiong, Jinbo},
title = {The gut eukaryotic microbiota influences the growth performance among cohabitating shrimp},
journal = {Applied Microbiology and Biotechnology},
year = {2017},
volume = {101},
number = {16},
pages = {6447--6457},
doi = {10.1007/s00253-017-8388-0},
abstract = {Increasing evidence has revealed a close interplay between the gut bacterial communities and host growth performance. However, until recently, studies generally ignored the contribution of eukaryotes, endobiotic organisms. To fill this gap, we used Illumina sequencing technology on eukaryotic 18S rRNA gene to compare the structures of gut eukaryotic communities among cohabitating retarded, overgrown, and normal shrimp obtained from identically managed ponds. Results showed that a significant difference between gut eukaryotic communities differed significantly between water and intestine and among three shrimp categories. Structural equation modeling revealed that changes in the gut eukaryotic community were positively related to digestive enzyme activities, which in turn influenced shrimp growth performance (λ = 0.97, P < 0.001). Overgrown shrimp exhibited a more complex and cooperative gut eukaryotic interspecies interaction than retarded and normal shrimp, which may facilitate their nutrient acquisition efficiency. Notably, the distribution of dominant eukaryotic genera and shifts in keystone species were closely concordant with shrimp growth performance. In summary, this study provides an integrated overview on direct roles of gut eukaryotic communities in shrimp growth performance instead of well-studied bacterial assembly.},
file = {dai2017gut.pdf:Referenced/dai2017gut.pdf:PDF},
owner = {nick},
publisher = {Springer},
timestamp = {20170829},
}
[26] [doi] C. Liu, Q. Meng, Y. Chen, M. Xu, M. Shen, R. Gao, and S. Gan, “Role of Age-Related Shifts in Rumen Bacteria and Methanogens in Methane Production in Cattle,” Frontiers in Microbiology, vol. 8, p. 1563, 2017.
[Bibtex]
@Article{liu2017role,
author = {Liu, Chong and Meng, Qinghui and Chen, Yongxing and Xu, Mengsi and Shen, Min and Gao, Rui and Gan, Shangquan},
title = {Role of Age-Related Shifts in Rumen Bacteria and Methanogens in Methane Production in Cattle},
journal = {Frontiers in Microbiology},
year = {2017},
volume = {8},
pages = {1563},
doi = {10.3389/fmicb.2017.01563},
abstract = {Rumen microbiota are essential for maintaining digestive and metabolic functions, producing methane as a byproduct. Dairy heifers produce large amounts of methane based on fermentation of digested organic matter, with adverse consequences for feed efficiency and the environment. It is therefore important to understand the influence of host age on the relationship between microbiota and methane production. This study explored the age effect on the relationship between microbial communities and enteric methane production in dairy cows and heifers using high-throughput sequencing. Methane production and volatile fatty acid concentrations were age-related. Heifers (9–10 months) had lower methane production but higher methane production per dry matter intake (DMI). The acetate:propionate ratio decreased significantly with increasing age. Age-related microbiota changes in the rumen were reflected by a significant shift in bacterial taxa, but relatively stable archaeal taxa. Prevotella, Ruminococcus, Flavonifractor, Succinivibrio, and Methanobrevibacter were affected by age. This study revealed different associations between predominant bacterial phylotypes and Methanobrevibacter with increasing age. Prevotella was strongly correlated with Methanobrevibacter in heifers; howerver, in older cows (96–120 months) this association was replaced by a correlation between Succinivibrio and Methanobrevibacter. This shift may account for the age-related difference in rumen fermentation and methane production per DMI.},
file = {liu2017role.pdf:Referenced/liu2017role.pdf:PDF},
owner = {nick},
publisher = {Frontiers},
timestamp = {20170829},
}
[27] [doi] R. Trancoso, J. R. Larsen, T. R. McVicar, S. R. Phinn, and C. A. McAlpine, “CO2-vegetation feedbacks and other climate changes implicated in reducing base flow,” Geophysical Research Letters, vol. 44, iss. 5, pp. 2310-2318, 2017.
[Bibtex]
@Article{trancoso2017co2,
author = {Trancoso, Ralph and Larsen, Joshua R and McVicar, Tim R and Phinn, Stuart R and McAlpine, Clive A},
title = {CO2-vegetation feedbacks and other climate changes implicated in reducing base flow},
journal = {Geophysical Research Letters},
year = {2017},
volume = {44},
number = {5},
pages = {2310--2318},
doi = {10.1002/2017GL072759},
abstract = {Changes in the hydrological cycle have a significant impact in water limited environments. Globally, some of these regions are experiencing declining precipitation yet are simultaneously becoming greener, partly due to vegetation feedbacks associated with increasing atmospheric CO2 concentrations. Reduced precipitation together with increasing rates of actual evapotranspiration diminishes streamflow, especially base flow, a critical freshwater dry-season resource. Here we assess recent changes in base flow in Australia from 1981–2013 and 1950–2013 and separate the contribution of precipitation, potential evapotranspiration, and other factors on base flow trends. Our findings reveal that these other factors influencing the base flow trends are best explained by an increase in photosynthetic activity. These results provide the first robust observational evidence that increasing atmospheric CO2 and its associated vegetation feedbacks are reducing base flow in addition to other climatic impacts. These findings have broad implications for water resource management, especially in the world's water limited regions.},
file = {trancoso2017co2.pdf:Referenced/trancoso2017co2.pdf:PDF},
owner = {nick},
publisher = {Wiley Online Library},
timestamp = {20170824},
}
[28] [doi] F. Ordines, M. Ramón, J. Rivera, C. Rodr{‘i}guez-Prieto, T. M. Farriols, B. Guijarro, C. Pasqual, and E. Massut{‘i}, “Why Long Term Trawled Red Algae Beds Off Balearic Islands (Western Mediterranean) Still Persist?,” Regional Studies in Marine Science, 2017.
[Bibtex]
@Article{ordines2017long,
author = {Ordines, Francesc and Ram{\'o}n, Montserrat and Rivera, Jes{\'u}s and Rodr{\'\i}guez-Prieto, Conxi and Farriols, M Teresa and Guijarro, Beatriz and Pasqual, Catalina and Massut{\'\i}, Enric},
title = {Why Long Term Trawled Red Algae Beds Off Balearic Islands (Western Mediterranean) Still Persist?},
journal = {Regional Studies in Marine Science},
year = {2017},
doi = {10.1016/j.rsma.2017.07.005},
abstract = {The bottom morphology, the surface sediments and the epibenthic community of two adjacent areas within the fishing ground traditionally known as Pesquera Rica (Balearic Islands) were characterized using multibeam echosounder, van Veen dredge and beam trawl. Red algae beds predominate in both areas, but one has been exploited by trawling since at least 90 years ago, whereas the presence of natural barriers prevents this fishing activity in the other one. Comparisons between the two areas showed a biomass reduction of 46.8 and 39.3% of dominant red algae taxonomic groups Peyssonneliaceae and Corallinophycidae, respectively, in the trawled area (TA). Similarly, both mean abundance and biomass of most groups of fauna were higher in the not trawled area (NTA). N90 biodiversity index showed higher mean values of algae species in NTA than in TA (7.0 and 4.9, respectively), whereas no differences were detected neither for sessile nor for mobile fauna. SIMPER analysis showed that large species of both sessile and mobile epibenthic fauna (e.g. the ascidia Polycarpa mamillaris and the echinoderm Spatangus purpureus, respectively) presented higher abundance and contribution to within area similarity in NTA than in TA. In coincidence, these are the most abundant epibenthic species in the commercial hauls from the Pesquera Rica. The relatively low fishing effort and the gears used, addressed to avoid large catches of algae allowing longer hauls, may explain the subsistence of red algae beds in the Balearic Islands trawl fishing grounds. However, the detrimental effects shown here claim for urgent management measures aiming to preserve these beds.},
file = {ordines2017long.pdf:Referenced/ordines2017long.pdf:PDF},
owner = {nick},
publisher = {Elsevier},
timestamp = {20170801},
}
[29] C. Gonson, “Intégration Des Usages récréatifs et de la Biodiversité Marine Pour la Gestion et L’évaluation Des Espaces côtiers. Application Aux Aires Marines Protégées de Nouvelle-Calédonie à Partir de Suivis de la Fréquentation et la Biodiversité et d’un Modèle d’aide à la Gestion,” PhD Thesis, 2017.
[Bibtex]
@PhdThesis{gonson2017integration,
author = {Gonson, Charles},
title = {Int{\'e}gration Des Usages r{\'e}cr{\'e}atifs et de la Biodiversit{\'e} Marine Pour la Gestion et L'{\'e}valuation Des Espaces c{\^o}tiers. Application Aux Aires Marines Prot{\'e}g{\'e}es de Nouvelle-Cal{\'e}donie {\`a} Partir de Suivis de la Fr{\'e}quentation et la Biodiversit{\'e} et d'un Mod{\`e}le d'aide {\`a} la Gestion},
year = {2017},
file = {gonson2017integration.pdf:Referenced/gonson2017integration.pdf:PDF},
owner = {nick},
school = {Universit{\'e} Pierre et Marie Curie},
timestamp = {20170724},
}
[30] [doi] C. Vélez-Agudelo, M. Espinosa, R. Fayó, and F. Isla, “Modern Diatoms From a Temperate River in South America: the Colorado River (North Patagonia, Argentina),” Diatom Research, pp. 1-20, 2017.
[Bibtex]
@Article{velez2017modern,
author = {V{\'e}lez-Agudelo, Camilo and Espinosa, Marcela and Fay{\'o}, Rocio and Isla, Federico},
title = {Modern Diatoms From a Temperate River in South America: the Colorado River (North Patagonia, Argentina)},
journal = {Diatom Research},
year = {2017},
pages = {1--20},
doi = {10.1080/0269249X.2017.1321046},
abstract = {Diatom assemblage composition and distribution from surface sediment samples of the Colorado River, Patagonia were analysed in relation to environmental variables using multivariate techniques. The aim of this study was to determine the ecological preferences of the taxa and provide analogues for paleoenvironmental reconstructions in estuarine and fluvial environments of southern South America. Cluster analysis identified two main diatom assemblages, one grouping sites with a marine influence, and another group influenced by typical riverine conditions. Canonical correspondence analysis indicated that major ion concentrations contribute significantly to explain the variation in the composition of diatom assemblages. A total of 208 taxa belonging to 56 genera were recorded. In estuarine sites, the assemblages were characterized by marine-brackish tychoplankton, such as Cymatosira belgica, Rhaphoneis amphiceros, Delphineis minutissima, Paralia sulcata and Paralia sulcata var. coronota. Diatom communities in riverine sites were dominated by freshwater taxa such as Staurosira venter, Pseudostaurosira brevistriata, Punctastriata glubokoensis and Punctastriata lancettula. Two Punctastriata species that were difficult to distinguish with LM were examined in detail with SEM, and the value of detailed LM and SEM analysis for distinguishing Punctastriata spp. and other small fragilarioids is discussed. Based on their autoecological affinities, it is likely that the dominance of small fragilarioids is related to the increase in ionic concentration in the basin, as a consequence of both precipitation decrease, and an increase in urban, industrial and agricultural activities. The construction of a flood-control structure in the northern branch of the delta modified the diatom community so that marine taxa were replaced by brackish-freshwater taxa in response to changes in salinity, substrata and water depth.},
file = {velez2017modern.pdf:Referenced/velez2017modern.pdf:PDF},
owner = {nick},
publisher = {Taylor \& Francis},
timestamp = {20170724},
}
[31] [doi] E. K. Mitter, R. J. de Freitas, and J. J. Germida, “Bacterial Root Microbiome of Plants Growing in Oil Sands Reclamation Covers,” Frontiers in microbiology, vol. 8, 2017.
[Bibtex]
@Article{mitter2017bacterial,
author = {Mitter, Eduardo K and de Freitas, J Renato and Germida, James J},
title = {Bacterial Root Microbiome of Plants Growing in Oil Sands Reclamation Covers},
journal = {Frontiers in microbiology},
year = {2017},
volume = {8},
doi = {10.3389/fmicb.2017.00849},
abstract = {Oil sands mining in northern Alberta impacts a large footprint, but the industry is committed to reclaim all disturbed land to an ecologically healthy state in response to environmental regulations. However, these newly reconstructed landscapes may be limited by several factors that include low soil nutrient levels and reduced microbial activity. Rhizosphere microorganisms colonize plant roots providing hosts with nutrients, stimulating growth, suppressing disease and increasing tolerance to abiotic stress. High-throughput sequencing techniques can be used to provide a detailed characterization of microbial community structure. This study used 16S rRNA amplicon sequencing to characterize the bacterial root microbiome associated with annual barley (Hordeum vulgare) and sweet clover (Melilotus albus) growing in an oil sands reclamation area. Our results indicate that Proteobacteria dominated the endosphere, whereas other phyla such as Acidobacteria and Gemmatimonadetes were restricted to the rhizosphere, suggesting that plants have the ability to select for certain soil bacterial consortia. The bacterial community in the endosphere compartments were less rich and diverse compared to the rhizosphere. Furthermore, it was apparent that sweet clover plants were more selective, as the community exhibited a lower richness and diversity compared to barley. Members of the family Rhizobiaceae, such as Sinorhizobium and Rhizobium were mainly associated with clover, whereas Acholeplasma (wall-less bacteria transmitted by insects) was unique to barley. Genera from the Enterobacteriaceae family, such as Yersinia and Lentzea were also mostly detected in barley, while other genera such Pseudomonas and Pantoea were able to successfully colonize both plants. Endophytic bacterial profiles varied within the same plant species at different sampling locations; however, these differences were driven by factors other than slope positions or cover management. Our results suggest that bacterial endophytic communities of plants growing in land reclamation systems are a subset of the rhizosphere community and selection is driven by plant factors.},
file = {mitter2017bacterial.pdf:Referenced/mitter2017bacterial.pdf:PDF},
owner = {nick},
publisher = {Frontiers Media SA},
timestamp = {20170724},
}
[32] [doi] L. T. Lancaster, R. Y. Dudaniec, B. Hansson, and E. I. Svensson, “Do Group Dynamics Affect Colour Morph Clines During a Range Shift?,” Journal of evolutionary biology, vol. 30, iss. 4, pp. 728-737, 2017.
[Bibtex]
@Article{lancaster2017group,
author = {Lancaster, Lesley T and Dudaniec, Rachael Y and Hansson, Bengt and Svensson, Erik I},
title = {Do Group Dynamics Affect Colour Morph Clines During a Range Shift?},
journal = {Journal of evolutionary biology},
year = {2017},
volume = {30},
number = {4},
pages = {728--737},
doi = {10.5061/dryad.g8h4s},
abstract = {Species exhibiting colour polymorphism are thought to have an ecological advantage at the landscape scale, because spatial segregation of alternatively adapted ecotypes into diverse habitats can increase the species' niche breadth and thus confer greater geographic range size. However, morph frequencies are also influenced by intrapopulational processes such as frequency- or density-dependent social interactions. To identify how social feedback may affect clinal variation in morph frequencies, we investigated reciprocal interactions between morph-specific thermal tolerance, local climatic conditions and social environments, in the context of a colour-morph frequency cline associated with a recent range expansion in blue-tailed damselflies (Ischnura elegans) in Sweden. Cold tolerances of gynochromes (female-like female morph) were positively correlated with local gynochrome frequencies, suggesting a positive frequency-dependent fitness benefit. In contrast, androchrome (male-mimic female morph) cold tolerances were improved following recent exposure to cold weather, suggesting a beneficial environmental acclimation effect. Thus, according to an environment-matching hypothesis for clinal variation, androchrome frequencies should therefore increase towards the (cooler) range limit. In contrast to this prediction, gynochrome frequencies increased at the expanding range limit, consistent with a positive frequency-dependent social feedback that is beneficial when invading novel climates. Our results suggest that when phenotypes or fitnesses are affected by interactions with conspecifics, beneficial social effects on environmental tolerances may (i) facilitate range shifts, and (ii) reverse or counteract typical patterns of intraspecific interactions and environment-matching clines observed in stable populations observed over broader geographic scales.},
file = {lancaster2017group.pdf:Referenced/lancaster2017group.pdf:PDF},
owner = {nick},
publisher = {Wiley Online Library},
timestamp = {20170724},
}
[33] [doi] J. Ragusa, P. Kindler, B. Segvic, and L. M. Ospina-Ostios, “Provenance Analysis of the Voirons Flysch (Gurnigel Nappe, Haute-Savoie, France): Stratigraphic and Palaeogeographic Implications,” International Journal of Earth Sciences, pp. 1-33, 2017.
[Bibtex]
@Article{ragusa2017provenance,
author = {Ragusa, J{\'e}r{\'e}my and Kindler, Pascal and Segvic, Branimir and Ospina-Ostios, Lina Maria},
title = {Provenance Analysis of the Voirons Flysch (Gurnigel Nappe, Haute-Savoie, France): Stratigraphic and Palaeogeographic Implications},
journal = {International Journal of Earth Sciences},
year = {2017},
pages = {1--33},
doi = {10.1007/s00531-017-1474-9},
abstract = {The Chablais Prealps (Haute-Savoie, France) represent a well-preserved accretionary wedge of the Western Alpine Tethys. They comprise a stack of sedimentary nappes related to palaeogeographic realms ranging from the Ultrahelvetic to the Southern Penninic. The provenance analysis is based on the Gazzi-Dickinson method and on QEMSCAN® for heavy-minerals. The Quartzose petrofacies is the most important of the two sources, and supplied three of the four formations of the Voirons Flysch. It is similar to the sources that fed the other flyschs from the Gurnigel nappe. It is characterised by a mature, quartz-rich assemblage and a heavy-mineral population dominated by apatite and the zircon–tourmaline–rutile mineral group. These observations suggest a Clastic wedge provenance. The Feldspathic petrofacies is derived from a feldspar-rich source associated with metamorphic clasts and a heavy-mineral population dominated by garnet. This provenance characterises only one formation of the Voirons Flysch, and is related to the axial belt provenance. This provenance analysis shows that the Middle Eocene to Early Oligocene Voirons Flysch was fed by two sources, in contrast to the other flyschs of the Gurnigel nappe, and further suggests that this flysch was not deposited in the Piemont Ocean but in the Valais domain. Based on the results and comparative provenance analysis with the other flyschs of the Gurnigel nappe, we propose a generic feeding model which involves the Sesia–Dent Blanche nappe, the sedimentary nappes incorporated in the accretionary prism, and probably the Briançonnais basement.},
file = {ragusa2017provenance.pdf:Referenced/ragusa2017provenance.pdf:PDF},
owner = {nick},
publisher = {Springer},
timestamp = {20170724},
}
[34] [doi] A. Gayle and M. Shimaoka, “Public Response to Scientific Misconduct: Assessing Changes in Public Sentiment Toward the Stimulus-Triggered Acquisition of Pluripotency (STAP) Cell Case via Twitter,” JMIR Public Health and Surveillance, vol. 3, iss. 2, 2017.
[Bibtex]
@Article{gayle2017public,
author = {Gayle, Alberto and Shimaoka, Motomu},
title = {Public Response to Scientific Misconduct: Assessing Changes in Public Sentiment Toward the Stimulus-Triggered Acquisition of Pluripotency (STAP) Cell Case via Twitter},
journal = {JMIR Public Health and Surveillance},
year = {2017},
volume = {3},
number = {2},
doi = {10.2196/publichealth.5980},
abstract = {Background
In this age of social media, any news—good or bad—has the potential to spread in unpredictable ways. Changes in public sentiment have the potential to either drive or limit investment in publicly funded activities, such as scientific research. As a result, understanding the ways in which reported cases of scientific misconduct shape public sentiment is becoming increasingly essential—for researchers and institutions, as well as for policy makers and funders. In this study, we thus set out to assess and define the patterns according to which public sentiment may change in response to reported cases of scientific misconduct. This study focuses on the public response to the events involved in a recent case of major scientific misconduct that occurred in 2014 in Japan—stimulus-triggered acquisition of pluripotency (STAP) cell case.
Objectives
The aims of this study were to determine (1) the patterns according to which public sentiment changes in response to scientific misconduct; (2) whether such measures vary significantly, coincident with major timeline events; and (3) whether the changes observed mirror the response patterns reported in the literature with respect to other classes of events, such as entertainment news and disaster reports.
Methods
The recent STAP cell scandal is used as a test case. Changes in the volume and polarity of discussion were assessed using a sampling of case-related Twitter data, published between January 28, 2014 and March 15, 2015. Rapidminer was used for text processing and the popular bag-of-words algorithm, SentiWordNet, was used in Rapidminer to calculate sentiment for each sample Tweet. Relative volume and sentiment was then assessed overall, month-to-month, and with respect to individual entities.
Results
Despite the ostensibly negative subject, average sentiment over the observed period tended to be neutral (−0.04); however, a notable downward trend (y=−0.01 x +0.09; R ²=.45) was observed month-to-month. Notably polarized tweets accounted for less than one-third of sampled discussion: 17.49% (1656/9467) negative and 12.59% positive (1192/9467). Significant polarization was found in only 4 out of the 15 months covered, with significant variation month-to-month (P<.001). Significant increases in polarization tended to coincide with increased discussion volume surrounding major events (P<.001).
Conclusions
These results suggest that public opinion toward scientific research may be subject to the same sensationalist dynamics driving public opinion in other, consumer-oriented topics. The patterns in public response observed here, with respect to the STAP cell case, were found to be consistent with those observed in the literature with respect to other classes of news-worthy events on Twitter. Discussion was found to become strongly polarized only during times of increased public attention, and such increases tended to be driven primarily by negative reporting and reactionary commentary.
Keywords: scientific misconduct, retraction of publication as a topic, mass media, social media, public opinion, public policy, data mining, publication, stem cells, Japan},
file = {gayle2017public.pdf:Referenced/gayle2017public.pdf:PDF},
owner = {nick},
publisher = {JMIR Publications Inc.},
timestamp = {20170724},
}
[35] J. Fogarty and G. Parameswaran, “Alcohol Sin Taxes,” UWA Agricultural and Resource Economics, University of Western Australia2017-15-05 2017.
[Bibtex]
@TechReport{fogarty2017alcohol,
author = {James Fogarty and Giri Parameswaran},
title = {Alcohol Sin Taxes},
institution = {UWA Agricultural and Resource Economics, University of Western Australia},
year = {2017},
date = {2017-15-05},
abstract = {The externality costs generated by excessive alcohol consumption warrant the imposition of alcohol speci c excise taxes. For all U.S. States, average alcohol taxes are signicantly below estimates of average externality costs, suggesting the current excise tax regime is ineciently low relative to the Pigovian benchmark. However, with heterogeneous consumption patterns, this benchmark may be sub-optimal if it fails to consider the welfare losses imposed on non-abusers. Here, using a model calibrated at the State level, we show that once these welfare losses are considered, current U.S. wine and spirit taxes are too high, while beer taxes, on average, are about right.},
file = {fogarty2017alcohol.pdf:Referenced/fogarty2017alcohol.pdf:PDF},
owner = {nick},
timestamp = {20170724},
}
[36] [doi] S. van Donk, K. C. Camphuysen, J. Shamoun-Baranes, and J. van der Meer, “The Most Common Diet Results in Low Reproduction in a Generalist Seabird,” Ecology and Evolution, 2017.
[Bibtex]
@Article{van2017most,
author = {van Donk, Susanne and Camphuysen, Kees CJ and Shamoun-Baranes, Judy and van der Meer, Jaap},
title = {The Most Common Diet Results in Low Reproduction in a Generalist Seabird},
journal = {Ecology and Evolution},
year = {2017},
doi = {10.1002/ece3.3018},
abstract = {Dietary specialization has been described across a wide range of taxa in the animal kingdom. Fitness consequences are, however, not well documented. We examined the reproductive consequences of different dietary specializations in the herring gull Larus argentatus, an omnivorous seabird, using an extensive dataset which includes breeding and dietary data of 10 successive years. We hypothesized that pairs that focused on prey of higher energetic value would yield higher fledging rates. An alternative hypothesis is that pairs that relied on more resources simultaneously would reproduce better. The novelty of this study is that we used continuous measurements representing dietary composition and degree of specialization rather than restricting our analysis to predefined categories. By relating these two continuous measurements for diet to several proxies for reproductive success, we show clear consequences of dietary choice. Most pairs concentrated on bivalves, a prey type not particularly rich in energy. Pairs feeding on energy-rich prey (e.g., “domestic refuse and fishery discards”) during chick rearing were found to have a higher reproductive success, supporting the first hypothesis. Pairs that used more resources did not clearly have a higher reproductive success. The majority of the pairs did not switch to energy-rich prey during chick rearing, despite low breeding outcome. We discuss how trade-offs between factors such as resource availability, predictability, and the time and energy needed to obtain certain prey species may influence resource selection.},
file = {van2017most.pdf:Referenced/van2017most.pdf:PDF},
owner = {nick},
publisher = {Wiley Online Library},
timestamp = {20170724},
}
[37] [doi] C. Gonson, D. Pelletier, F. Alban, C. Giraud-Carrier, and J. Ferraris, “Influence of Settings Management and Protection Status on Recreational Uses and Pressures in Marine Protected Areas,” Journal of Environmental Management, vol. 200, pp. 170-185, 2017.
[Bibtex]
@Article{gonson2017influence,
author = {Gonson, Charles and Pelletier, Dominique and Alban, Frederique and Giraud-Carrier, Charlotte and Ferraris, Jocelyne},
title = {Influence of Settings Management and Protection Status on Recreational Uses and Pressures in Marine Protected Areas},
journal = {Journal of Environmental Management},
year = {2017},
volume = {200},
pages = {170--185},
doi = {10.1016/j.jenvman.2017.05.051},
abstract = {Coastal populations and tourism are growing worldwide. Consequently outdoor recreational activity is increasing and diversifying. While Marine Protected Areas (MPAs) are valuable for mitigating anthropogenic impacts, recreational uses are rarely monitored and studied, resulting in a lack of knowledge on users' practices, motivation and impacts. Based on boat counts and interview data collected in New Caledonia, we i) explored factors affecting user practices and motivations, ii) constructed fine-scale pressure indices covering activities and associated behaviors, and iii) assessed the relationships between user practices and site selection. User practices were found to depend on protection status, boat type and user characteristics. Pressure indices were higher within no-take MPAs, except for fishing. We found significant relationships between user practices and settings characteristics. In the context of increasing recreational uses, these results highlight options for managing such uses through settings management without jeopardizing the social acceptance of MPAs or the attainment of conservation goals.},
file = {gonson2017influence.pdf:Referenced/gonson2017influence.pdf:PDF},
owner = {nick},
publisher = {Elsevier},
timestamp = {20170724},
}
[38] J. Carrasco, S. Garc{‘i}a, M. del Mar Rueda, and F. Herrera, “rNPBST: An R Package Covering Non-parametric and Bayesian Statistical Tests,” in International Conference on Hybrid Artificial Intelligence Systems, 2017, pp. 281-292.
[Bibtex]
@InProceedings{carrasco2017rnpbst,
author = {Carrasco, Jacinto and Garc{\'\i}a, Salvador and del Mar Rueda, Mar{\'\i}a and Herrera, Francisco},
title = {rNPBST: An R Package Covering Non-parametric and Bayesian Statistical Tests},
booktitle = {International Conference on Hybrid Artificial Intelligence Systems},
year = {2017},
organization = {Springer},
pages = {281--292},
abstract = {Statistical tests has arisen as a reliable procedure for the validation of results in many kind of problems. In particular, due to their robustness and applicability, non-parametric tests are a common and useful tool in the process of design and evaluation of a machine learning algorithm or in the context of an optimization problem. New trends in the field of statistical comparison applied to the field of algorithms’ performance comparison indicate that Bayesian tests, which provides a distribution over the parameter of interest, are a promising approach.
In this contribution rNPBST (R Non-Parametric and Bayesian Statistical tests), an R package that contains a set of non-parametric and Bayesian tests for different purposes as randomness tests, goodness of fit tests or two-sample and multiple-sample analysis is presented. This package constitutes also a solution which integrates many of non-parametric and Bayesian tests in a single repository.},
owner = {nick},
timestamp = {20170724},
}
[39] [doi] D. M. Chu, J. Ma, A. L. Prince, K. M. Antony, M. D. Seferovic, and K. M. Aagaard, “Maturation of the Infant Microbiome Community Structure and Function Across Multiple Body Sites and in Relation to Mode of Delivery,” Nature Medicine, 2017.
[Bibtex]
@Article{chu2017maturation,
author = {Chu, Derrick M and Ma, Jun and Prince, Amanda L and Antony, Kathleen M and Seferovic, Maxim D and Aagaard, Kjersti M},
title = {Maturation of the Infant Microbiome Community Structure and Function Across Multiple Body Sites and in Relation to Mode of Delivery},
journal = {Nature Medicine},
year = {2017},
doi = {10.1038/nm.4272},
abstract = {Human microbial communities are characterized by their taxonomic, metagenomic and metabolic diversity, which varies by distinct body sites and influences human physiology. However, when and how microbial communities within each body niche acquire unique taxonomical and functional signatures in early life remains underexplored. We thus sought to determine the taxonomic composition and potential metabolic function of the neonatal and early infant microbiota across multiple body sites and assess the effect of the mode of delivery and its potential confounders or modifiers. A cohort of pregnant women in their early third trimester (n = 81) were prospectively enrolled for longitudinal sampling through 6 weeks after delivery, and a second matched cross-sectional cohort (n = 81) was additionally recruited for sampling once at the time of delivery. Samples across multiple body sites, including stool, oral gingiva, nares, skin and vagina were collected for each maternal–infant dyad. Whole-genome shotgun sequencing and sequencing analysis of the gene encoding the 16S rRNA were performed to interrogate the composition and function of the neonatal and maternal microbiota. We found that the neonatal microbiota and its associated functional pathways were relatively homogeneous across all body sites at delivery, with the notable exception of the neonatal meconium. However, by 6 weeks after delivery, the infant microbiota structure and function had substantially expanded and diversified, with the body site serving as the primary determinant of the composition of the bacterial community and its functional capacity. Although minor variations in the neonatal (immediately at birth) microbiota community structure were associated with the cesarean mode of delivery in some body sites (oral gingiva, nares and skin; R2 = 0.038), this was not true for neonatal stool (meconium; Mann–Whitney P > 0.05), and there was no observable difference in community function regardless of delivery mode. For infants at 6 weeks of age, the microbiota structure and function had expanded and diversified with demonstrable body site specificity (P < 0.001, R2 = 0.189) but without discernable differences in community structure or function between infants delivered vaginally or by cesarean surgery (P = 0.057, R2 = 0.007). We conclude that within the first 6 weeks of life, the infant microbiota undergoes substantial reorganization, which is primarily driven by body site and not by mode of delivery.},
file = {chu2017maturation.pdf:Referenced/chu2017maturation.pdf:PDF},
owner = {nick},
publisher = {Nature Research},
timestamp = {20170128},
}
[40] [doi] F. J. Valverde-Albacete and C. Peláez-Moreno, “The Evaluation of Data Sources Using Multivariate Entropy Tools,” Expert Systems with Applications, 2017.
[Bibtex]
@Article{valverde2017evaluation,
author = {Valverde-Albacete, Francisco J and Pel{\'a}ez-Moreno, Carmen},
title = {The Evaluation of Data Sources Using Multivariate Entropy Tools},
journal = {Expert Systems with Applications},
year = {2017},
doi = {10.1016/j.eswa.2017.02.010},
abstract = {We introduce from first principles an analysis of the information content of multivariate distributions as information sources. Specifically, we generalize a balance equation and a visualization device, the Entropy Triangle, for multivariate distributions and find notable differences with similar analyses done on joint distributions as models of information channels.
As an example application, we extend a framework for the analysis of classifiers to also encompass the analysis of data sets. With such tools we analyze a handful of UCI machine learning task to start addressing the question of how well do datasets convey the information they are supposed to capture about the phenomena they stand for.},
file = {valverde2017evaluation.pdf:Referenced/valverde2017evaluation.pdf:PDF},
owner = {nick},
publisher = {Elsevier},
timestamp = {20170212},
}
[41] [doi] I. Galván-Femen{‘i}a, J. Graffelman, and C. Barceló-i-Vidal, “Graphics for Relatedness Research,” Molecular Ecology Resources, 2017.
[Bibtex]
@Article{galvan2017graphics,
author = {Galv{\'a}n-Femen{\'\i}a, Iv{\'a}n and Graffelman, Jan and Barcel{\'o}-i-Vidal, Carles},
title = {Graphics for Relatedness Research},
journal = {Molecular Ecology Resources},
year = {2017},
doi = {10.1111/1755-0998.12674},
abstract = {Studies of relatedness have been crucial in molecular ecology over the last decades. Good evidence of this is the fact that studies of population structure, evolution of social behaviours, genetic diversity and quantitative genetics all involve relatedness research. The main aim of this article was to review the most common graphical methods used in allele sharing studies for detecting and identifying family relationships. Both IBS- and IBD-based allele sharing studies are considered. Furthermore, we propose two additional graphical methods from the field of compositional data analysis: the ternary diagram and scatterplots of isometric log-ratios of IBS and IBD probabilities. We illustrate all graphical tools with genetic data from the HGDP-CEPH diversity panel, using mainly 377 microsatellites genotyped for 25 individuals from the Maya population of this panel. We enhance all graphics with convex hulls obtained by simulation and use these to confirm the documented relationships. The proposed compositional graphics are shown to be useful in relatedness research, as they also single out the most prominent related pairs. The ternary diagram is advocated for its ability to display all three allele sharing probabilities simultaneously. The log-ratio plots are advocated as an attempt to overcome the problems with the Euclidean distance interpretation in the classical graphics.},
file = {galvan2017graphics.pdf:Referenced/galvan2017graphics.pdf:PDF},
owner = {nick},
publisher = {Wiley Online Library},
timestamp = {20170409},
}
[42] [doi] J. Yravedra, F. Diez-Mart{‘i}n, C. P. Egeland, M. Á. Maté-González, J. F. Palomeque-González, M. C. Arriaza, J. Aramendi, E. Garc{‘i}a Vargas, V. Estaca-Gómez, P. Sánchez, and others, “FLK West (Lower Bed II, Olduvai Gorge, Tanzania): A New eEarly Acheulean Site With Evidence for Human Exploitation of Fauna,” Boreas, 2017.
[Bibtex]
@Article{yravedra2017flk,
author = {Yravedra, Jos{\'e} and Diez-Mart{\'\i}n, Fernando and Egeland, Charles P and Mat{\'e}-Gonz{\'a}lez, Miguel {\'A}ngel and Palomeque-Gonz{\'a}lez, Juan Francisco and Arriaza, Mari Carmen and Aramendi, Julia and Garc{\'\i}a Vargas, Elena and Estaca-G{\'o}mez, Ver{\'o}nica and S{\'a}nchez, Policarpo and others},
title = {FLK West (Lower Bed II, Olduvai Gorge, Tanzania): A New eEarly Acheulean Site With Evidence for Human Exploitation of Fauna},
journal = {Boreas},
year = {2017},
doi = {10.1111/bor.12243},
file = {yravedra2017flk.pdf:Referenced/yravedra2017flk.pdf:PDF},
owner = {nick},
publisher = {Wiley Online Library},
timestamp = {20170409},
}
[43] [doi] J. Qian, Q. Ding, A. Guo, D. Zhang, and K. Wang, “Alteration in Successional Trajectories of Bacterioplankton Communities in Response to Co-Exposure of Cadmium and Phenanthrene in Coastal Water Microcosms,” Environmental Pollution, 2016.
[Bibtex]
@Article{qian2016alteration,
author = {Qian, Jie and Ding, Qifang and Guo, Annan and Zhang, Demin and Wang, Kai},
title = {Alteration in Successional Trajectories of Bacterioplankton Communities in Response to Co-Exposure of Cadmium and Phenanthrene in Coastal Water Microcosms},
journal = {Environmental Pollution},
year = {2016},
doi = {10.1016/j.envpol.2016.12.020},
file = {qian2016alteration.pdf:Users/nick/Copy/UNSW/PhD/References/Referenced/qian2016alteration.pdf:PDF},
owner = {nick},
publisher = {Elsevier},
timestamp = {20161220},
}
[44] [doi] I. Galván-Femen{‘i}a, J. Graffelman, and C. Barceló-i-Vidal, “A Compositional Approach to Allele Sharing Analysis,” Compositional Data Analysis, p. 63, 2016.
[Bibtex]
@Article{galvan2016compositional,
author = {Galv{\'a}n-Femen{\'\i}a, I and Graffelman, J and Barcel{\'o}-i-Vidal, C},
title = {A Compositional Approach to Allele Sharing Analysis},
journal = {Compositional Data Analysis},
year = {2016},
pages = {63},
doi = {10.1007/978-3-319-44811-4_5},
abstract = {Relatedness is of great interest in population-based genetic association studies. These studies search for genetic factors related to disease. Many statistical methods used in population-based genetic association studies (such as standard regression models, t-tests, and logistic regression) assume that the observations (individuals) are independent. These techniques can fail if independence is not satisfied. Allele sharing is a powerful data analysis technique for analyzing the degree of dependence in diploid species. Two individuals can share 0, 1, or 2 alleles for any genetic marker. This sharing may be assessed for alleles identical by state (IBS) or identical by descent (IBD). Starting from IBS alleles, it is possible to detect the type of relationship of a pair of individuals by using graphical methods. Typical allele sharing analysis consists of plotting the fraction of loci sharing 2 IBS alleles versus the fraction of sharing 0 IBS alleles. Compositional data analysis can be applied to allele sharing analysis because the proportions of sharing 0, 1 or 2 IBS alleles (denoted by p0p0 , p1p1 , and p2p2 ) form a 3-part-composition. This chapter provides a graphical method to detect family relationships by plotting the isometric log-ratio transformation of p0p0 , p1p1 , and p2p2 . On the other hand, the probabilities of sharing 0, 1, or 2 IBD alleles (denoted by k0,k1,k2k0,k1,k2 ), which are termed Cotterman’s coefficients, depend on the relatedness: monozygotic twins, full-siblings, parent-offspring, avuncular, first cousins, etc. It is possible to infer the type of family relationship of a pair of individuals by using maximum likelihood methods. As a result, the estimated vector kk^=(k̂ 0,k̂ 1,k̂ 2)kk^=(k^0,k^1,k^2) for each pair of individuals forms a 3-part-composition and can be plotted in a ternary diagram to identify the degree of relatedness. An R package has been developed for the study of genetic relatedness based on genetic markers such as microsatellites and single nucleotide polymorphisms from human populations, and is used for the computations and graphics of this contri},
owner = {nick},
publisher = {Springer},
timestamp = {20161124},
}
[45] [doi] J. Silterra, M. A. Gillette, M. Lanaspa, K. G. Pellé, C. Valim, R. Ahmad, S. Acácio, K. D. Almendinger, Y. Tan, L. Madrid, and others, “Transcriptional Categorization of the Etiology of Pneumonia Syndrome in Pediatric Patients in Malaria Endemic Areas,” Journal of Infectious Diseases, p. jiw531, 2016.
[Bibtex]
@Article{silterra2016transcriptional,
author = {Silterra, Jacob and Gillette, Michael A and Lanaspa, Miguel and Pell{\'e}, Karell G and Valim, Clarissa and Ahmad, Rushdy and Ac{\'a}cio, Sozinho and Almendinger, Katherine D and Tan, Yan and Madrid, Lola and others},
title = {Transcriptional Categorization of the Etiology of Pneumonia Syndrome in Pediatric Patients in Malaria Endemic Areas},
journal = {Journal of Infectious Diseases},
year = {2016},
pages = {jiw531},
doi = {10.1093/infdis/jiw531},
abstract = {Background. Pediatric acute respiratory distress in tropical settings is very common. Bacterial pneumonia is a major contributor to morbidity and mortality and requires adequate diagnosis for correct treatment. A rapid test that could identify bacterial (vs. other) infections would have great clinical utility.
Methods and Findings. We performed RNA-Seq and analyzed the transcriptomes of 68 pediatric patients with well-characterized clinical phenotype to identify transcriptional features associated with each disease class. We refined the features to predictive models (support vector machine, elastic net) and validated those models on an independent test set of 37 patients (80 – 85% accuracy).
Conclusions. We have identified sets of genes that are differentially expressed in pediatric patients with pneumonia syndrome attributable to different infections and requiring different therapeutic interventions. This study demonstrates that human transcription signatures in infected patients recapitulate the underlying biology and provide models for predicting a bacterial diagnosis to inform treatment},
file = {silterra2016transcriptional.pdf:Referenced/silterra2016transcriptional.pdf:PDF},
owner = {nick},
publisher = {Oxford University Press},
timestamp = {20161115},
}
[46] [doi] T. Nguyen Van, A. Ozaki, H. Nguyen Tho, A. Nguyen Duc, Y. Tran Thi, and K. Kurosawa, “Arsenic and Heavy Metal Contamination in Soils Under Different Land Use in an Estuary in Northern Vietnam,” International Journal of Environmental Research and Public Health, vol. 13, iss. 11, p. 1091, 2016.
[Bibtex]
@Article{nguyen2016arsenic,
author = {Nguyen Van, Thinh and Ozaki, Akinori and Nguyen Tho, Hoang and Nguyen Duc, Anh and Tran Thi, Yen and Kurosawa, Kiyoshi},
title = {Arsenic and Heavy Metal Contamination in Soils Under Different Land Use in an Estuary in Northern Vietnam},
journal = {International Journal of Environmental Research and Public Health},
year = {2016},
volume = {13},
number = {11},
pages = {1091},
doi = {10.3390/ijerph13111091},
abstract = {Heavy metal contamination of soil and sediment in estuaries warrants study because a healthy estuarine environment, including healthy soil, is important in order to achieve ecological balance and good aquaculture production. The Ba Lat estuary of the Red River is the largest estuary in northern Vietnam and is employed in various land uses. However, the heavy metal contamination of its soil has not yet been reported. The following research was conducted to clarify contamination levels, supply sources, and the effect of land use on heavy metal concentrations in the estuary. Soil samples were collected from the top soil layer of the estuary, and their arsenic (As), chromium (Cr), cadmium (Cd), copper (Cu), lead (Pb), and zinc (Zn) concentrations were analyzed, as were other soil properties. Most soils in the estuary were loam, silt loam, or sandy loam. The pH was neutral, and the cation exchange capacity ranged from 3.8 to 20 cmol·kg−1. Manganese and iron concentrations averaged 811 µg·g−1 and 1.79%, respectively. The magnitude of the soil heavy metal concentrations decreased in the order of Zn > Pb > Cr > Cu > As > Cd. The concentrations were higher in the riverbed and mangrove forest than in other land-use areas. Except for As, the mean heavy metal concentrations were lower than the permissible levels for agricultural soils in Vietnam. The principal component analyses suggested that soil As, Pb, Zn, Cd, and Cu were of anthropogenic origin, whereas Cr was of non-anthropogenic origin. The spatial distribution of concentration with land use indicated that mangrove forests play an important role in preventing the spread of heavy metals to other land uses and in maintaining the estuarine environment.},
file = {nguyen2016arsenic.pdf:Users/nick/Copy/UNSW/PhD/References/Referenced/nguyen2016arsenic.pdf:PDF},
owner = {nick},
publisher = {Multidisciplinary Digital Publishing Institute},
timestamp = {20161113},
}
[47] [doi] T. Maš{‘i}nová, B. D. Bahnmann, T. Větrovsk{`y}, M. Tomšovsk{`y}, K. Merunková, and P. Baldrian, “Drivers of Yeast Community Composition in the Litter and Soil of a Temperate Forest,” FEMS Microbiology Ecology, p. fiw223, 2016.
[Bibtex]
@Article{mavsinova2016drivers,
author = {Ma{\v{s}}{\'\i}nov{\'a}, Tereza and Bahnmann, Barbara Doreen and V{\v{e}}trovsk{\`y}, Tom{\'a}{\v{s}} and Tom{\v{s}}ovsk{\`y}, Michal and Merunkov{\'a}, Kristina and Baldrian, Petr},
title = {Drivers of Yeast Community Composition in the Litter and Soil of a Temperate Forest},
journal = {FEMS Microbiology Ecology},
year = {2016},
pages = {fiw223},
doi = {10.1093/femsec/fiw223},
file = {mavsinova2016drivers.pdf:Users/nick/Copy/UNSW/PhD/References/Referenced/mavsinova2016drivers.pdf:PDF},
owner = {nick},
publisher = {The Oxford University Press},
timestamp = {20161102},
}
[48] [doi] J. Schmidt, F. E. Fassnacht, A. Lausch, and S. Schmidtlein, “Assessing the Functional Signature of Heathland Landscapes via Hyperspectral Remote Sensing,” Ecological Indicators, vol. 73, pp. 505-512, 2017.
[Bibtex]
@Article{schmidt2017assessing,
author = {Schmidt, Johannes and Fassnacht, Fabian Ewald and Lausch, Angela and Schmidtlein, Sebastian},
title = {Assessing the Functional Signature of Heathland Landscapes via Hyperspectral Remote Sensing},
journal = {Ecological Indicators},
year = {2017},
volume = {73},
pages = {505--512},
doi = {10.1016/j.ecolind.2016.10.017},
file = {schmidt2017assessing.pdf:Referenced/schmidt2017assessing.pdf:PDF},
owner = {nick},
publisher = {Elsevier},
timestamp = {20161029},
}
[49] M. Leblanc, “Relations Entre les Caractéristiques Pédologiques et les Pratiques de Fertilisation et de Conservation Des Sols,” PhD Thesis, 2016.
[Bibtex]
@PhdThesis{leblanc2016relations,
author = {Leblanc, Micha{\"e}l},
title = {Relations Entre les Caract{\'e}ristiques P{\'e}dologiques et les Pratiques de Fertilisation et de Conservation Des Sols},
year = {2016},
file = {leblanc2016relations.pdf:Users/nick/Copy/UNSW/PhD/References/Referenced/leblanc2016relations.pdf:PDF},
owner = {nick},
school = {Universit{\'e} Laval},
timestamp = {20161016},
}
[50] [doi] J. A. Doering, S. Tang, H. Peng, B. K. Eisner, J. Sun, J. P. Giesy, S. Wiseman, and M. Hecker, “High Conservation in Transcriptomic and Proteomic Response of White Sturgeon to Equipotent Concentrations of 2,3,7,8-TCDD, PCB 77, and Benzo [a] Pyrene,” Environmental science & technology, vol. 50, iss. 9, pp. 4826-4835, 2016.
[Bibtex]
@Article{doering2016high,
author = {Doering, Jon A and Tang, Song and Peng, Hui and Eisner, Bryanna K and Sun, Jianxian and Giesy, John P and Wiseman, Steve and Hecker, Markus},
title = {High Conservation in Transcriptomic and Proteomic Response of White Sturgeon to Equipotent Concentrations of 2,3,7,8-TCDD, PCB 77, and Benzo [a] Pyrene},
journal = {Environmental science \& technology},
year = {2016},
volume = {50},
number = {9},
pages = {4826--4835},
doi = {10.1021/acs.est.6b00490},
file = {doering2016high.pdf:Users/nick/Copy/UNSW/PhD/References/Referenced/doering2016high.pdf:PDF},
owner = {nick},
publisher = {ACS Publications},
timestamp = {20161016},
}
[51] [doi] D. Orton, J. Gaastra, and M. Vander Linden, “Between the Danube and the Deep Blue Sea: Zooarchaeological Meta-Analysis Reveals Variability in the Spread and Development of Neolithic Farming across the Western Balkans,” Open Quaternary, vol. 2, 2016.
[Bibtex]
@Article{orton2016between,
Title = {Between the Danube and the Deep Blue Sea: Zooarchaeological Meta-Analysis Reveals Variability in the Spread and Development of Neolithic Farming across the Western Balkans},
Author = {Orton, David and Gaastra, Jane and Vander Linden, Marc},
Journal = {Open Quaternary},
Year = {2016},
Volume = {2},
Doi = {10.5334/oq.28},
File = {orton2016between.pdf:Users/nick/Copy/UNSW/PhD/References/Referenced/orton2016between.pdf:PDF},
Owner = {nick},
Publisher = {Ubiquity Press},
Timestamp = {20160921}
}
[52] [doi] R. E. Jelley, M. Herbst-Johnstone, S. Klaere, L. I. Pilkington, C. Grose, D. Martin, D. Barker, and B. Fedrizzi, “Optimization of Ecofriendly Extraction of Bioactive Monomeric Phenolics and Useful Flavor Precursors from Grape Waste,” , 2016.
[Bibtex]
@Article{jelley2016optimization,
Title = {Optimization of Ecofriendly Extraction of Bioactive Monomeric Phenolics and Useful Flavor Precursors from Grape Waste},
Author = {Jelley, Rebecca E and Herbst-Johnstone, Mandy and Klaere, Steffen and Pilkington, Lisa I and Grose, Claire and Martin, Damian and Barker, David and Fedrizzi, Bruno},
Year = {2016},
Abstract = {Grape marc, also known as grape pomace, is an underutilized biowaste composed predominantly of grape skin and seeds that is produced as a byproduct of winemaking on the million-tonne scale annually. The most important high-value current use of grape marc is in the production of oenological tannins, widely used additives in the food and beverage industry. More commonly, grape marc is simply either disposed of or used as feed or fertilizer. With recent evidence showing that extracts enriched in grape tannins contain significant amounts of the thiol precursors Cys-3SH and GSH-3SH and the possibility that these could influence food and beverage aroma, it was decided to investigate grape pomace extraction procedures in order to try to define extraction protocols that could maximize the recovery of these compounds from grape marc. Should such an extraction protocol be shown to be commercially viable, this could lead to further utilization of material that would otherwise be disposed of. Two thiol precursors and eight monomeric phenolics (quercetin 3-O-glucoside, quercetin, resveratrol, grape reaction product, trans-caftaric acid, catechin, epicatechin, and gallic acid) were identified and simultaneously extracted from Sauvignon Blanc grape marc using solid–liquid extractions. The optimal solvent ratio of acetone:water:EtOH was explored for each compound. Ten ternary diagrams were constructed, showing the effectiveness of extraction across 66 different solvent combinations using the aforementioned solvents. Effective extraction of thiol precursors was dependent on a high water content which is an advantage from an economic and environmental perspective, while for the most abundant phenolic, quercetin 3-O-glucoside, optimal extraction levels (1017 mg per kg of grape marc) were achieved using a 40:50:10 solvent mixture. In addition, this manuscript details the first extraction of thiol precursors from grape pomace which adds a significant potential commercial value to this underutilized byproduct.},
Doi = {10.1021/acssuschemeng.6b01551},
File = {jelley2016optimization.pdf:Users/nick/Copy/UNSW/PhD/References/Referenced/jelley2016optimization.pdf:PDF},
Owner = {nick},
Publisher = {ACS Publications},
Timestamp = {20160823}
}
[53] [doi] M. Melwani Daswani, S. Schwenzer, M. Reed, I. Wright, and M. Grady, “Alteration Minerals, Fluids and Gases on Early Mars: Predictions From 1D flow Geochemical Modelling of Mineral Assemblages in Meteorite ALH 84001,” Meteoritics & Planetary Science, vol. 10, 2016.
[Bibtex]
@Article{melwani2016alteration,
author = {Melwani Daswani, M and Schwenzer, SP and Reed, MH and Wright, IP and Grady, MG},
title = {Alteration Minerals, Fluids and Gases on Early Mars: Predictions From 1D flow Geochemical Modelling of Mineral Assemblages in Meteorite ALH 84001},
journal = {Meteoritics \& Planetary Science},
year = {2016},
volume = {10},
doi = {10.1111/maps.12713},
abstract = {Clay minerals, although ubiquitous on the ancient terrains of Mars, have not been observed in Martian meteorite Allan Hills (ALH) 84001, which is an orthopyroxenite sample of the early Martian crust with a secondary carbonate assemblage. We used a low-temperature (20 °C) one-dimensional (1-D) transport thermochemical model to investigate the possible aqueous alteration processes that produced the carbonate assemblage of ALH 84001 while avoiding the coprecipitation of clay minerals. We found that the carbonate in ALH 84001 could have been produced in a process, whereby a low-temperature (~20 °C) fluid, initially equilibrated with the early Martian atmosphere, moved through surficial clay mineral and silica-rich layers, percolated through the parent rock of the meteorite, and precipitated carbonates (thereby decreasing the partial pressure of CO2) as it evaporated. This finding requires that before encountering the unweathered orthopyroxenite host of ALH 84001, the fluid permeated rock that became weathered during the process. We were able to predict the composition of the clay minerals formed during weathering, which included the dioctahedral smectite nontronite, kaolinite, and chlorite, all of which have been previously detected on Mars. We also calculated host rock replacement in local equilibrium conditions by the hydrated silicate talc, which is typically considered to be a higher temperature hydrothermal phase on Earth, but may have been a common constituent in the formation of Martian soils through pervasive aqueous alteration. Finally, goethite and magnetite were also found to precipitate in the secondary alteration assemblage, the latter associated with the generation of H2. Apparently, despite the limited water–rock interaction that must have led to the formation of the carbonates ~ 3.9 Ga ago, in the vicinity of the ALH 84001 source rocks, clay formation would have been widespread.},
file = {melwani2016alteration.pdf:Users/nick/Copy/UNSW/PhD/References/Referenced/melwani2016alteration.pdf:PDF},
owner = {nick},
timestamp = {20160817},
}
[54] M. Friendly and D. Meyer, Discrete Data Analysis with R: Visualization and Modeling Techniques for Categorical and Count Data, CRC Press, 2015, vol. 120.
[Bibtex]
@Book{friendly2015discrete,
Title = {Discrete Data Analysis with R: Visualization and Modeling Techniques for Categorical and Count Data},
Author = {Friendly, Michael and Meyer, David},
Publisher = {CRC Press},
Year = {2015},
Volume = {120},
Owner = {nick},
Timestamp = {20160812}
}
[55] H. Wickham, “Toolbox,” in ggplot2, Springer, 2016, pp. 33-74.
[Bibtex]
@InCollection{wickham2016toolbox,
Title = {Toolbox},
Author = {Wickham, Hadley},
Booktitle = {ggplot2},
Publisher = {Springer},
Year = {2016},
Pages = {33--74},
Owner = {nick},
Timestamp = {20160812}
}
[56] P. F. Alves, “Uma Analise Empirica do Mercado de Revenda de Carros Usando Raspagem de Dados da Internet,” PhD Thesis, 2016.
[Bibtex]
@PhdThesis{alves2016analise,
author = {Alves, Patrick Franco},
title = {Uma Analise Empirica do Mercado de Revenda de Carros Usando Raspagem de Dados da Internet},
year = {2016},
file = {alves2016analise.pdf:Referenced/alves2016analise.pdf:PDF},
owner = {nick},
timestamp = {20160811},
}
[57] J. Fuerst and E. O. Kirkegaard, “Admixture in the Americas: Regional and National Differences,” Mankind Quarterly, vol. 56, pp. 255-373, 2016.
[Bibtex]
@Article{fuerst2016admixture,
author = {Fuerst, John and Kirkegaard, Emil OW},
title = {Admixture in the Americas: Regional and National Differences},
journal = {Mankind Quarterly},
year = {2016},
volume = {56},
pages = {255--373},
file = {fuerst2016admixture.pdf:Users/nick/Copy/UNSW/PhD/References/Referenced/fuerst2016admixture.pdf:PDF},
owner = {nick},
timestamp = {20160811},
}
[58] G. A. Cosultchi, “Las Causas y Efectos del Reclutamiento en la Dinamica de Poblaciones de Cactaceas Columnares,” PhD Thesis, 2016.
[Bibtex]
@PhdThesis{cosultchi2016las,
author = {Gabriel Arroyo Cosultchi},
title = {Las Causas y Efectos del Reclutamiento en la Dinamica de Poblaciones de Cactaceas Columnares},
year = {2016},
file = {cosultchi2016las.pdf:Users/nick/Copy/UNSW/PhD/References/Referenced/cosultchi2016las.pdf:PDF},
owner = {nick},
school = {Universidad Autonoma Metropolitana},
timestamp = {20160729},
}
[59] H. Sadiq, “A Topic Model-Based Approach to Inferring Episodic Directional Selection in Protein-Coding Sequences,” PhD Thesis, 2015.
[Bibtex]
@PhdThesis{sadiq2015topic,
Title = {A Topic Model-Based Approach to Inferring Episodic Directional Selection in Protein-Coding Sequences},
Author = {Sadiq, Hassan},
School = {University of Cape Town, South Africa},
Year = {2015},
File = {sadiq2015topic.pdf:Users/nick/Copy/UNSW/PhD/References/Referenced/sadiq2015topic.pdf:PDF},
Owner = {nick},
Timestamp = {20160727}
}
[60] [doi] S. Babicki, D. Arndt, A. Marcu, Y. Liang, J. R. Grant, A. Maciejewski, and D. S. Wishart, “Heatmapper: Web-Enabled Heat Mapping for All,” Nucleic acids research, p. gkw419, 2016.
[Bibtex]
@Article{babicki2016heatmapper,
author = {Babicki, Sasha and Arndt, David and Marcu, Ana and Liang, Yongjie and Grant, Jason R and Maciejewski, Adam and Wishart, David S},
title = {Heatmapper: Web-Enabled Heat Mapping for All},
journal = {Nucleic acids research},
year = {2016},
pages = {gkw419},
doi = {10.1093/nar/gkw419},
owner = {nick},
publisher = {Oxford Univ Press},
timestamp = {20160724},
}
[61] A. Bustard, “Fingerprinting and Tracing the Signature of Basement-Hosted Unconformity-Type Uranium Alteration Through Thick Quaternary Tills: An Example From The Thelon Basin, Nunavut,” Master Thesis, 2016.
[Bibtex]
@MastersThesis{bustard2016fingerprinting,
author = {Bustard, Aaron},
title = {Fingerprinting and Tracing the Signature of Basement-Hosted Unconformity-Type Uranium Alteration Through Thick Quaternary Tills: An Example From The Thelon Basin, Nunavut},
year = {2016},
file = {bustard2016fingerprinting.pdf:Users/nick/Copy/UNSW/PhD/References/Referenced/bustard2016fingerprinting.pdf:PDF},
owner = {nick},
publisher = {University of Waterloo},
timestamp = {20160724},
}
[62] [doi] F. A. Comin, J. M. Sánchez-Pérez, C. Español, F. Carranza, S. Sauvage, I. Antiguedad, A. Zabaleta, M. Martinez-Santos, M. Gerino, J. M. Yao, and others, “Floodplain Capacity to Depollute Water in Relation to the Structure of Biological Communities,” Ecological Engineering, 2016.
[Bibtex]
@Article{comin2016floodplain,
author = {Comin, Francisco A and S{\'a}nchez-P{\'e}rez, Jos{\'e} M and Espa{\~n}ol, Cecilia and Carranza, Fabi{\'a}n and Sauvage, Sabine and Antiguedad, I{\~n}aki and Zabaleta, Ane and Martinez-Santos, Miren and Gerino, Magali and Yao, Jing M and others},
title = {Floodplain Capacity to Depollute Water in Relation to the Structure of Biological Communities},
journal = {Ecological Engineering},
year = {2016},
doi = {10.1016/j.ecoleng.2016.06.007},
file = {comin2016floodplain.pdf:Users/nick/Copy/UNSW/PhD/References/Referenced/comin2016floodplain.pdf:PDF},
owner = {nick},
publisher = {Elsevier},
review = {Uses ggtern},
timestamp = {20160724},
}
[63] [doi] Y. Zhi, T. Guo, J. Shi, L. Zeng, and L. Wu, “Expressing Lead Isotopic Compositions by Fractional Abundances for Environmental Source Apportionment,” Environmental Pollution, 2016.
[Bibtex]
@Article{zhi2016expressing,
author = {Zhi, Yuyou and Guo, Tiantian and Shi, Jiachun and Zeng, Lingzao and Wu, Laosheng},
title = {Expressing Lead Isotopic Compositions by Fractional Abundances for Environmental Source Apportionment},
journal = {Environmental Pollution},
year = {2016},
doi = {10.1016/j.envpol.2016.07.024},
file = {zhi2016expressing.pdf:Users/nick/Copy/UNSW/PhD/References/Referenced/zhi2016expressing.pdf:PDF},
owner = {nick},
publisher = {Elsevier},
review = {uses ggtern},
timestamp = {20160723},
}
[64] [doi] L. Graves, “Boundaries Not Drawn: Mapping the Institutional Roots of the Global Fact-Checking Movement,” Journalism Studies, pp. 1-19, 2016.
[Bibtex]
@Article{graves2016boundaries,
author = {Graves, Lucas},
title = {Boundaries Not Drawn: Mapping the Institutional Roots of the Global Fact-Checking Movement},
journal = {Journalism Studies},
year = {2016},
pages = {1--19},
doi = {10.1080/1461670X.2016.1196602},
abstract = {The last five years have seen a global surge in political fact-checking, reporting that specializes in debunking political misinformation. A growing occupational movement, originating in the United States but increasingly international in scope, has sought to legitimize fact-checking as unbiased journalism, to establish common standards and practices, and to secure reliable funding for this emerging genre. As a genuinely transnational professional movement which includes practitioners from multiple journalistic cultures as well as other fields, fact-checking offers a new site to consider whether and how professional journalism is meaningfully becoming globalized. This paper models a novel approach to mapping a diverse organizational landscape in terms of institutional ties to the fields of journalism, academia, and politics. Drawing on fieldwork from two international gatherings of fact-checkers, I array fact-checking outlets on a ternary graph and review their competing understandings of the mission, the target, and the practices of fact-checking. I highlight areas of convergence as well as divergence in this organizational milieu, focusing particular attention on boundaries not drawn—the willingness of professional journalists in this global movement to share jurisdictional authority with non-journalists. I conclude with suggestions for a comparative research agenda focused on this emergent area of practice.},
file = {graves2016boundaries.pdf:Users/nick/Copy/UNSW/PhD/References/Referenced/graves2016boundaries.pdf:PDF},
owner = {nick},
publisher = {Taylor \& Francis},
review = {Uses ggtern},
timestamp = {20160629},
}
[65] [doi] C. M. Balogh, S. C. Barrett, and R. Ree, “Stochastic Processes During Invasion: The Influence of Population Size on Style-Morph Frequency Variation in Lythrum Salicaria (Purple Loosestrife),” International Journal of Plant Sciences, vol. 177, iss. 5, 2016.
[Bibtex]
@Article{balogh2016stochastic,
author = {Balogh, Christopher M and Barrett, Spencer CH and Ree, Richard},
title = {Stochastic Processes During Invasion: The Influence of Population Size on Style-Morph Frequency Variation in Lythrum Salicaria (Purple Loosestrife)},
journal = {International Journal of Plant Sciences},
year = {2016},
volume = {177},
number = {5},
pages = {000--000},
doi = {10.1086/686023},
abstract = {Premise of research. During biological invasion, the genetic diversity of populations may be reduced by founder events and genetic drift. The floral polymorphism tristyly provides an exceptional opportunity to investigate the influence of stochastic forces on the maintenance of genetic polymorphism, because small population size leads to a characteristic signature of morph loss from populations. Here, we investigate the relations between population size and morph-frequency variation in invasive populations of tristylous Lythrum salicaria in Ontario, Canada. We also compare our results to a similar survey conducted 25 years ago in the same region.
Methodology. We surveyed the size and morph ratios of 114 L. salicaria populations in 2013. We calculated the relations between population size and style morph absence, population size and style morph evenness, and the number of populations lacking particular style morphs. For comparison of the patterns of morph-frequency variation between surveys, we used a sample of populations (1988/1989: 51 populations; 2013: 101 populations) with similar size distributions.
Pivotal results. Our survey confirmed that smaller populations were more likely to lack a style morph than larger populations and that morph ratios were less even in smaller populations. In dimorphic populations, the short-styled morph (S-morph) was absent most often, and the long-styled morph (L-morph) was least often missing, a pattern consistent with the stochastic theory of asymmetrical morph loss for tristylous species. There were no significant differences between the 1988/1989 and 2013 surveys in the frequency of populations missing style morphs or the relations between population size and style morph evenness.
Conclusions. Despite an increase in abundance of L. salicaria in Ontario during the past 25 years, genetic drift and founder events still play a dominant role in governing patterns of morph-frequency variation.},
file = {balogh2016stochastic.pdf:Users/nick/Copy/UNSW/PhD/References/Referenced/balogh2016stochastic.pdf:PDF},
owner = {nick},
publisher = {University of Chicago Press Chicago, IL},
review = {Uses ggtern},
timestamp = {20160510},
}
[66] [doi] F. J. Valverde-Albacete and C. Peláez-Moreno, “The Multivariate Entropy Triangle and Applications,” in Hybrid Artificial Intelligent Systems, Springer-Verlag, 2016, pp. 647-658.
[Bibtex]
@InCollection{valverde2016multivariate,
Title = {The Multivariate Entropy Triangle and Applications},
Author = {Valverde-Albacete, Francisco Jos{\'e} and Pel{\'a}ez-Moreno, Carmen},
Booktitle = {Hybrid Artificial Intelligent Systems},
Publisher = {Springer-Verlag},
Year = {2016},
Pages = {647--658},
Doi = {10.1007/978-3-319-32034-2_54},
File = {valverde2016multivariate.pdf:Users/nick/Copy/UNSW/PhD/References/Referenced/valverde2016multivariate.pdf:PDF},
Owner = {nick},
Timestamp = {20160419}
}
[67] [doi] M. A. Leblanc, É. Parent, and L. E. Parent, “Lime Requirement Using Mehlich-III Extraction and Infrared-Inferred Cation Exchange Capacity,” Soil Science Society of America Journal, 2016.
[Bibtex]
@Article{leblanc2016lime,
Title = {Lime Requirement Using Mehlich-III Extraction and Infrared-Inferred Cation Exchange Capacity},
Author = {Leblanc, Micha{\"e}l A and Parent, {\'E}lizabeth and Parent, L{\'e}on E},
Journal = {Soil Science Society of America Journal},
Year = {2016},
Abstract = {Lime requirement (LR) to reach and maintain target soil pH levels could be determined using environmentally friendly methods to avoid buffer solutions containing toxic chemicals. Infrared (IR) spectroscopy can predict soil properties related to soil pH buffering capacity, potentially supporting LR models. The aim of this study was to develop IR-based LR models across a wide range of soils in Québec, Canada. The estimated exchangeable acidity (EEA) index was computed from the cation exchange capacity determined by the NH4OAc (pH 7.0) method (CEC-NH4OAc) minus the sum of Mehlich-III extractable non-acidic cations. The performance was high for IR-inferred CEC-NH4OAc predicted from mid-infrared (MIR) and near-infrared (NIR) spectra or computed from quantified organic C and NIR- and MIR-predicted clay content (0.82 ≤ R2 ≤ 0.91 in validation). The performance in cross-validation of EEA using quantified CEC-NH4OAc (0.81 ≤ R2 ≤ 0.89) was higher than Shoemaker–McLean–Pratt (SMP) buffer (0.15 ≤ R2 ≤ 0.77) for target pHH2O values between 5.5 and 6.5, and similar for a target pHH2O of 7.0. To support LR determination of cropping systems such as potato (Solanum tuberosum L.) that requires low pH (<6.5) or to maintain adequate pH levels at low LRs (<1.5 g CaCO3 kg−1), the EEA index using CEC-NH4OAc inferred within ±2.3 cmolc kg−1 was found to be more accurate than the SMP buffer. Direct prediction of the EEA-derived LR using NIR and MIR spectroscopy showed low performance (validation R2 ≤ 0.48) compared with EEA computed from IR-inferred CEC-NH4OAc. The IR spectroscopy can improve routine LR determination at low cost.},
Doi = {10.2136/sssaj2015.07.0282},
Owner = {nick},
Publisher = {The Soil Science Society of America, Inc.},
Timestamp = {20160403}
}
[68] [doi] L. Milani, F. Ghiselli, A. Pecci, M. G. Maurizii, and M. Passamonti, “The Expression of a Novel Mitochondrially-Encoded Gene in Gonadic Precursors May Drive Paternal Inheritance of Mitochondria,” PloS one, vol. 10, iss. 9, p. e0137468, 2015.
[Bibtex]
@Article{milani2015expression,
Title = {The Expression of a Novel Mitochondrially-Encoded Gene in Gonadic Precursors May Drive Paternal Inheritance of Mitochondria},
Author = {Milani, Liliana and Ghiselli, Fabrizio and Pecci, Andrea and Maurizii, Maria Gabriella and Passamonti, Marco},
Journal = {PloS one},
Year = {2015},
Number = {9},
Pages = {e0137468},
Volume = {10},
Doi = {10.1371/journal.pone.0137468},
File = {milani2015expression.pdf:Users/nick/Copy/UNSW/PhD/References/Referenced/milani2015expression.pdf:PDF},
Owner = {nick},
Publisher = {Public Library of Science},
Review = {Uses ggtern},
Timestamp = {20150910}
}
[69] [doi] M. P. Bhatt, N. Takeuchi, and M. F. Acevedo, “Chemistry of Supraglacial Ponds in the Debris-Covered Area of Lirung Glacier in Central Nepal Himalayas,” Aquatic Geochemistry, pp. 1-30, 2015.
[Bibtex]
@Article{bhatt2015chemistry,
Title = {Chemistry of Supraglacial Ponds in the Debris-Covered Area of Lirung Glacier in Central Nepal Himalayas},
Author = {Bhatt, Maya P and Takeuchi, Nozomu and Acevedo, Miguel F},
Journal = {Aquatic Geochemistry},
Year = {2015},
Pages = {1--30},
Doi = {10.1007/s10498-015-9276-9},
File = {bhatt2015chemistry.pdf:Users/nick/Copy/UNSW/PhD/References/Referenced/bhatt2015chemistry.pdf:PDF},
Owner = {nick},
Publisher = {Springer-Verlag},
Review = {Uses ggtern},
Timestamp = {20150909}
}
[70] T. P. Campbell, “Tree Islands of Fertility Structure Bacterial Community Assembly and Functional Genes Contributing to Ecosystem Processes,” PhD Thesis, 2015.
[Bibtex]
@PhdThesis{campbell2015tree,
Title = {Tree Islands of Fertility Structure Bacterial Community Assembly and Functional Genes Contributing to Ecosystem Processes},
Author = {Campbell, Tayte Paul},
School = {Brigham Young University},
Year = {2015},
Owner = {nick},
Publisher = {Brigham Young University},
Review = {Uses ggtern},
Timestamp = {20150827}
}
[71] Y. Lu, “Microbial Ecology of Fermentative Microbes in Anaerobic Granules,” PhD Thesis, 2014.
[Bibtex]
@PhdThesis{lu2014microbial,
Title = {Microbial Ecology of Fermentative Microbes in Anaerobic Granules},
Author = {Lu, Yang},
Year = {2014},
File = {lu2014microbial.pdf:Users/nick/Copy/UNSW/PhD/References/Referenced/lu2014microbial.pdf:PDF},
Owner = {nick},
Timestamp = {20160810}
}
[72] [doi] E. A. Alcid and T. Tsukiyama, “ATP-Dependent Chromatin Remodeling Shapes the Long Noncoding RNA Landscape,” Genes & development, vol. 28, iss. 21, pp. 2348-2360, 2014.
[Bibtex]
@Article{alcid2014atp,
author = {Alcid, Eric A and Tsukiyama, Toshio},
title = {ATP-Dependent Chromatin Remodeling Shapes the Long Noncoding RNA Landscape},
journal = {Genes \& development},
year = {2014},
volume = {28},
number = {21},
pages = {2348--2360},
doi = {10.1101/gad.250902.114},
file = {alcid2014atp.pdf:Users/nick/Copy/UNSW/PhD/References/Referenced/alcid2014atp.pdf:PDF},
owner = {nick},
publisher = {Cold Spring Harbor Lab},
review = {Uses ggtern},
timestamp = {20150803},
}
[73] [doi] S. Pfenninger and J. Keirstead, “Renewables, Nuclear, or Fossil Fuels? Scenarios for Great Britain’s Power System Considering Costs, Emissions and Energy Security,” Applied Energy, vol. 152, pp. 83-93, 2015.
[Bibtex]
@Article{pfenninger2015renewables,
Title = {Renewables, Nuclear, or Fossil Fuels? Scenarios for Great Britain's Power System Considering Costs, Emissions and Energy Security},
Author = {Pfenninger, Stefan and Keirstead, James},
Journal = {Applied Energy},
Year = {2015},
Pages = {83--93},
Volume = {152},
Doi = {10.1016/j.apenergy.2015.04.102},
File = {pfenninger2015renewables.pdf:Users/nick/Copy/UNSW/PhD/References/Referenced/pfenninger2015renewables.pdf:PDF},
Owner = {nick},
Publisher = {Elsevier},
Review = {Uses ggtern},
Timestamp = {20150803}
}