Catalogue Search | MBRL
Are you sure you want to remove the book from the shelf?
{{itemTitle}}
2,018
result(s) for
"Brooks, Thomas"
Sort by:
Venice in the age of Canaletto
\"Canaletto's landscapes are arguably, even today, the most familiar artistic products of eighteenth-century Venice For those with the requisite means, no visit to the city would be considered complete without the purchase of at least one of the artist's views, which captured the city's topography and urban activity with apparent verisimilitude. ... View painting, not a favored genre during the preceding several centuries, gained considerable popularity in the 1700s. Its ascendency corresponded directly to increased foreign travel and in particular to the aristocratic Englishmen who, having embarked on the Grand Tour - an itinerary which necessarily included Venice - sought mementos of their travels. ... However, for all Canaletto's popularity and his ability to capture the fabric of Venice at its most appealing and evocative, his work is curiously devoid of the rich coloring, sensuality, and exuberance of most Venetian art of the period. To help elucidate the complicated forces that shaped Canaletto and the city of Venice during his age, this catalogue offers a range of essays.\"--preface.
BOOK
Generating correlated data for omics simulation
Simulation of realistic omics data is a key input for benchmarking studies that help users obtain optimal computational pipelines. Omics data involves large numbers of measured features on each sample and these measures are generally correlated with each other. However, simulation too often ignores these correlations, perhaps due to computational and statistical hurdles of doing so. To alleviate this, we describe three approaches for generating omics-scale data with correlated measures which mimic real datasets. These approaches are all based on a Gaussian copula approach with a covariance matrix that decomposes into a diagonal part and a low-rank part. This decomposition allows for extremely efficient simulation, overcoming a hurdle for adoption of past methods. We use these approaches to demonstrate the importance of including correlation in two benchmarking applications. First, we show that variance of results from the popular DESeq2 method increases when dependence is included. Second, we demonstrate that CYCLOPS, a method for inferring circadian time of collection from transcriptomics, improves in performance when given gene-gene dependencies in some circumstances. We provide an R package, dependentsimr, that has efficient implementations of these methods and can generate dependent data with arbitrary marginal distributions, including discrete (binary, ordered categorical, Poisson, negative binomial), continuous (normal), or with an empirical distribution.
Journal Article
Protected area targets post-2020
Outcome-based targets are needed to achieve biodiversity goals In 2010, Parties to the Convention on Biological Diversity (CBD) adopted the Strategic Plan for Biodiversity 2011–2020, and its 20 Aichi Biodiversity Targets, to catalyze national and international conservation efforts and reverse negative biodiversity trends. With the plan nearing an end, and attention turning toward a post-2020 biodiversity framework, it is timely to assess the strengths, weaknesses, and effectiveness of the Aichi Targets. Aichi Target 11, concerned with establishing effective and representative networks of protected areas (PAs) by 2020, has attracted considerable interest owing to widespread recognition of the pivotal role that appropriately situated and well-managed PAs have in conserving biodiversity ( 1 ). Substantial advances have been made toward the areal components of Aichi Target 11, with the PA estate increasing by 2.3% on land and 5.4% in the oceans since 2010 and now covering 15% of land and inland freshwater globally and 7% of the oceans ( 2 ). However, species' population abundance within and outside PAs continues to decline ( 1 ), the placement and resourcing of the majority of PAs has been poor ( 1 , 3 , 4 ), and more than half of PAs established before 1992 have suffered increasing human pressure ( 5 ). We discuss four problems with Aichi Target 11 that have contributed to its limited achievement and propose a formulation for a target for site-based conservation beyond 2020 aimed at overcoming them.
Journal Article
Harnessing online digital data in biodiversity monitoring
Online digital data from media platforms have the potential to complement biodiversity monitoring efforts. We propose a strategy for integrating these data into current biodiversity datasets in light of the Kunming-Montreal Global Biodiversity Framework.
Journal Article
Biodiversity: The ravages of guns, nets and bulldozers
The threats of old are still the dominant drivers of current species loss, indicates an analysis of IUCN Red List data by Sean Maxwell and colleagues.
Journal Article
3-manifolds with constant Ricci eigenvalues (λ,λ,0)
We consider complete Riemannian 3-manifolds whose Ricci tensors have constant eigenvalues
(
λ
,
λ
,
0
)
. When
π
1
is finitely generated, we classify the topology of such manifolds by showing that they have a free fundamental group if non-trivial and that every free group is obtained. We give a description up to isometry when the metric is locally irreducible or when it is analytic.
Journal Article
Scientific Foundations for an IUCN Red List of Ecosystems
An understanding of risks to biodiversity is needed for planning action to slow current rates of decline and secure ecosystem services for future human use. Although the IUCN Red List criteria provide an effective assessment protocol for species, a standard global assessment of risks to higher levels of biodiversity is currently limited. In 2008, IUCN initiated development of risk assessment criteria to support a global Red List of ecosystems. We present a new conceptual model for ecosystem risk assessment founded on a synthesis of relevant ecological theories. To support the model, we review key elements of ecosystem definition and introduce the concept of ecosystem collapse, an analogue of species extinction. The model identifies four distributional and functional symptoms of ecosystem risk as a basis for assessment criteria: A) rates of decline in ecosystem distribution; B) restricted distributions with continuing declines or threats; C) rates of environmental (abiotic) degradation; and D) rates of disruption to biotic processes. A fifth criterion, E) quantitative estimates of the risk of ecosystem collapse, enables integrated assessment of multiple processes and provides a conceptual anchor for the other criteria. We present the theoretical rationale for the construction and interpretation of each criterion. The assessment protocol and threat categories mirror those of the IUCN Red List of species. A trial of the protocol on terrestrial, subterranean, freshwater and marine ecosystems from around the world shows that its concepts are workable and its outcomes are robust, that required data are available, and that results are consistent with assessments carried out by local experts and authorities. The new protocol provides a consistent, practical and theoretically grounded framework for establishing a systematic Red List of the world's ecosystems. This will complement the Red List of species and strengthen global capacity to report on and monitor the status of biodiversity.
Journal Article
The benefits of contributing to the citizen science platform iNaturalist as an identifier
As the number of observations submitted to the citizen science platform iNaturalist continues to grow, it is increasingly important that these observations can be identified to the finest taxonomic level, maximizing their value for biodiversity research. Here, we explore the benefits of acting as an identifier on iNaturalist.
Journal Article
Comparative evaluation of full-length isoform quantification from RNA-Seq
Background
Full-length isoform quantification from RNA-Seq is a key goal in transcriptomics analyses and has been an area of active development since the beginning. The fundamental difficulty stems from the fact that RNA transcripts are long, while RNA-Seq reads are short.
Results
Here we use simulated benchmarking data that reflects many properties of real data, including polymorphisms, intron signal and non-uniform coverage, allowing for systematic comparative analyses of isoform quantification accuracy and its impact on differential expression analysis. Genome, transcriptome and pseudo alignment-based methods are included; and a simple approach is included as a baseline control.
Conclusions
Salmon, kallisto, RSEM, and Cufflinks exhibit the highest accuracy on idealized data, while on more realistic data they do not perform dramatically better than the simple approach. We determine the structural parameters with the greatest impact on quantification accuracy to be length and sequence compression complexity and not so much the number of isoforms. The effect of incomplete annotation on performance is also investigated. Overall, the tested methods show sufficient divergence from the truth to suggest that full-length isoform quantification and isoform level DE should still be employed selectively.
Journal Article