195 research outputs found
Atlas of Ocean Wealth
The Atlas of Ocean Wealth is the largest collection to date of information about the economic, social and cultural values of coastal and marine habitats from all over the world. It is a synthesis of innovative science, led by The Nature Conservancy (TNC), with many partners around the world. Through these efforts, they've gathered vast new datasets from both traditional and less likely sources.The work includes more than 35 novel and critically important maps that show how nature's value to people varies widely from place to place. They also illustrate nature's potential. These maps show that one can accurately quantify the value of marine resources. Further, by enumerating such values, one can encourage their protection or enhancement for the benefit of people all around the world. In summary, it clearly articulates not just that we need nature, but how much we need it, and where
Ecology Of River Otters (Lutra Canadensis) In Marine Coastal Environments
Thesis (M.S.) University of Alaska Fairbanks, 198
Hidden variables unseen by Random Forests
Random Forests are widely claimed to capture interactions well. However, some
simple examples suggest that they perform poorly in the presence of certain
pure interactions that the conventional CART criterion struggles to capture
during tree construction. We argue that alternative partitioning schemes can
enhance identification of these interactions. Furthermore, we extend recent
theory of Random Forests based on the notion of impurity decrease by
considering probabilistic impurity decrease conditions. Within this framework,
consistency of a new algorithm coined 'Random Split Random Forest' tailored to
address function classes involving pure interactions is established. In a
simulation study, we validate that the modifications considered enhance the
model's fitting ability in scenarios where pure interactions play a crucial
role
Bat exploitation of Sitka Spruce plantations: Impacts of management on bats and nocturnal invertebrates
Plantations are widespread throughout temperate regions, and the area of plantation land cover is
predicted to get larger in the future. Interest in ensuring sustainable plantation management is also
growing, as it is increasingly recognised that productive areas should play a role in biodiversity
conservation. Plantation landscapes can comprise the majority of forested cover in some countries,
but taxon-specific guidance can be lacking, due to plantations often being under surveyed.
Therefore, despite substantial incentives existing to ensure that plantations meet various ecological
criteria, plantation managers lack the information necessary to implement effective management
plans. Many bat species have undergone widespread declines in recent decades, attributed to
habitat loss and fragmentation, particularly of forested habitat. In many temperate countries,
historical deforestation has resulted in very low native tree cover, and subsequently, considerable
replanting with non-native commercial coniferous plantations has taken place. Species specific
habitat surveys have often demonstrated avoidance of conifer plantations by bats, which has been
attributed to a lack of roosts and low invertebrate prey abundance. Furthermore, widespread
lepidopteran declines have been partly attributed to afforestation with non-native conifer, but moth
associations with commercial coniferous plantations are usually only studied for pest species.
Bats present a particular challenge in plantation landscapes; tree cover is important to many species
to a greater or lesser extent, and in the United Kingdom, destruction of a roost site is illegal,
regardless of whether it was deliberate or accidental. However, the extent to which bats associate
with non-native commercial plantations is relatively unexplored. This is the first study to explicitly
test bat associations with Picea sitchensis plantations (using acoustic detectors, trapping and radio
tracking), and shows that, contrary to expectations, they may be an important habitat for breeding
populations of Pipistrellus spp., particularly P. pygmaeus. High levels of activity were recorded for
both P. pygmaeus and P. pipistrellus, despite little difference in dipteran abundance between
different stand types, both species preferentially foraged in felled or less dense stands. This suggests
that bats preferentially forage in areas with less acoustic and physical clutter, which will increase
foraging efficiency. The impacts of felling in non-native commercial coniferous plantations on
foraging activity was tested, for the first time, using a Before – After – Control – Impact experimental
design. Bat activity (specifically P. pipistrellus and Nyctalus) increased after felling, particularly in
smaller stands. In contrast felling had significant, negative impacts on moth abundance, species
richness and diversity, and these effects remain after constraining for functional trait similarity.
Reductions in richness and diversity in response to felling were similarly large for both rare and
abundant species. Therefore, while bats may benefit from clear fell practices, albeit as long as the
size of patches is small, moth populations could benefit from a shift towards other forestry methods,
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such as continuous cover forestry. These results also have implications for the recent, but increasing
practice of siting wind turbines in commercial coniferous plantations, as pre-installation preparation
involves clearing small patches of forest which may attract foraging bats; post felling monitoring
should be carried out to examine potential impacts on bat populations.
The presence of broadleaf trees in and around plantations significantly increased moth richness,
mostly through increased occurrence of rare species. Broadleaf woodlands (defined as land spanning
more than 0.5 ha, with trees higher than 5m and a combined cover of shrubs, bushes and trees
above 10%), also had higher functional redundancy than plantation sites. For a diverse moth
population to persist in plantation landscapes, preserving remnant patches of broadleaf trees is
essential. There was little difference in bat activity between broadleaf woodlands and plantation
sites. However, bat abundance, particularly that of reproductively active females, was greater in
broadleaf sites compared to plantations. This was particularly true for Myotis and Nyctalus spp., very
few of which were trapped in commercial plantations. Therefore, although reproductively active
female Myotis bats are present in the surrounding landscape, they do not appear to associate with
plantations themselves. This may reflect a lack of roost availability; both P. pygmaeus and P.
pipistrellus preferentially form large maternity colonies in buildings, but for Myotis and Nyctalus spp.
which roost switch regularly and often use trees, it is unlikely many suitable roosts exist within the
plantations themselves.
Many substantial P. pygmaeus maternity colonies were identified in and around Galloway forest,
with some holding more than 500 individuals. All maternity colonies were in buildings, and most
inhabited (and one uninhabited) buildings within the plantation contained a roost. Although females
occasionally used old or dead deciduous trees as temporary roosts, there was no evidence of
roosting in crop trees such as P. sitchensis. During this study, the Forestry Commission installed 36
bat boxes; within 6 months over 90% had been used, with a number of harems found inside. This
fast uptake compared with bat use of boxes in other locations reflects the paucity of appropriate
structures for either roost or harem use in commercial plantations.
Twelve bats were captured while foraging, tagged with small radio transmitters, and followed for
between 2 and 6 nights during 2014 and 2015. All but one tagged female preferentially foraged
within the plantation, with individuals selecting equally riparian habitats and felled stands. Tagged
females which roosted furthest from the plantation had the largest home ranges; one individual flew
nearly 40km each night to reach foraging areas distant from her roost, suggesting that the food
availability within the plantation was sufficient to render such a long journey energetically viable.
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These results have important implications for bat populations in and around commercial coniferous
plantations. Far from being avoided by bats, plantation landscapes may constitute an important
habitat type for both P. pygmaeus and P. pipistrellus, likely due to the high abundance of
nematoceran diptera in plantation woodlands. Furthermore, plantation forests support a similar
richness of moth species to urban and agricultural woodlands, including a number of declining
species of special conservation concern. A list of management recommendations to benefit both bat
and moth populations in commercial plantations is presented at the end of this thesis
Learning to live with novelty: Implications of exotic earthworms and their interactions with seeds, mulch, and wood ash for ecological restoration
A major challenge in restoration ecology is the biological invasion of ‘exotic’ species, some of which may spread widely and have undesirable impacts as ‘invasive’ species. Ongoing debates and changing perspectives suggest we may be overlooking opportunities to consider exotic species more broadly, not only as adversaries but also as potential null players or even allies in restoration. This may be exemplified by the invasion of exotic earthworms in North America, a long-term and widespread invasion of ecologically-influential organisms without practical ways to control it. The purpose of this dissertation is to consider the integration of exotic earthworms into restoration by exploring how they interact with three restoration interventions: seeds, mulch, and wood ash. I used laboratory microcosms and field-based experiments with a focus on the ecosystem engineering nightcrawler earthworm (Lumbricus terrestris L.). Overall, earthworms had effects that might be contextually beneficial or detrimental to ecological restoration: earthworms selectively consumed and buried seeds which could reduce recruitment from seed mixes or contribute to seed bank formation (Chapter 2); earthworms collected and buried mulch which exposed the soil underneath but could help mix organic matter into degraded soils (Chapter 3); and earthworms responded behaviourally and in population density to different wood ashes and helped mix surface-applied wood ash into the soil (Chapter 4). I propose that by recognizing exotic earthworms as a novel and increasingly common ecosystem feature in North America and by learning how to mitigate their undesirable impacts and take advantage of their benefits, we could more efficiently and effectively restore these changing ecosystems. This dissertation contributes to our expanding knowledge of earthworm ecology, facilitates increased integration of earthworm interactions into restoration, and offers insights into the broader implications of biological invasion for conservation. Studying the case of exotic earthworms in North America raises important questions about why we restore and conserve, the value of case-by-case management of invasions based on impact, the importance of considering the longer-term outcomes of invasion and naturalization, and – in some cases – the merit in learning to live with novelty
Practical book on medical biology
BIOLOGY MEDICALPRACTICAL BOOKБИОЛОГИЯБИОЛОГИЯ МЕДИЦИНСКАЯПРАКТИЧЕСКИЕ ПОСОБИЯIn the practical book the main divisions and aims of biology are described
Resource allocation for acorn production: A comparison across species pairs of oaks with contrasting acorn production patterns and water use strategies
Mast seeding, or masting, is a phenomenon where inter-annual seed production by individuals is synchronized across a population of plants. Masting is hypothesized to confer a selective advantage to plants by increasing rates of pollination or by decreasing rates of seed predation. Masting can also play a crucial role in ecosystem functioning as fluctuations in annual seed crops correspond with fluctuations in seed predator populations, which in turn have consequences that ripple throughout food webs. The mechanism(s) that causes masting is unresolved, but the high variability in seed production of masting plants is hypothesized to be caused, in part, by resource limitation. One hypothesized mechanism for masting that has gained support in recent years is known as the resource budget model (RBM). The RBM hypothesizes that plants store up resources across years until a threshold is reached, after which they flower and set seed, which depletes resources. It is still unknown how common the RBM is in masting species, and it is unknown whether the RBM describes a pattern of resource allocation that is distinctive of masting species, or if non-masting plants exhibit similar patterns. In this dissertation, we seek to resolve some of this uncertainty by comparing patterns of resource allocation and seed production among four species of California oak trees and shrubs. In Chapter 1, we test predictions of the RBM in two shrub species, one masting and one non-masting, in the Klamath Mountains of northern California. In chapter 2, we explore the carbon demands for acorn development of the masting species used in Chapter 1, in order to learn more about whether carbohydrates are limiting for seed production in this species. In Chapter 3, we use two masting tree species in central coastal California with contrasting water use strategies to test for resource limitation to flowering and seed production, and to compare which nutrients are the most important for each species. Overall, we found evidence for resource-limited reproduction in all three masting species. Furthermore, differences in patterns of seed production and in species traits matter for how resources are used for seed production.
Advisor: Johannes M. H. Knop
Novelty, distillation, and federation in machine learning for medical imaging
The practical application of deep learning methods in the medical domain
has many challenges. Pathologies are diverse and very few examples may
be available for rare cases. Where data is collected it may lie in multiple
institutions and cannot be pooled for practical and ethical reasons. Deep
learning is powerful for image segmentation problems but ultimately its output
must be interpretable at the patient level. Although clearly not an exhaustive
list, these are the three problems tackled in this thesis.
To address the rarity of pathology I investigate novelty detection algorithms
to find outliers from normal anatomy. The problem is structured as first finding
a low-dimension embedding and then detecting outliers in that embedding
space. I evaluate for speed and accuracy several unsupervised embedding and
outlier detection methods. Data consist of Magnetic Resonance Imaging (MRI)
for interstitial lung disease for which healthy and pathological patches are
available; only the healthy patches are used in model training.
I then explore the clinical interpretability of a model output. I take related
work by the Canon team — a model providing voxel-level detection of acute
ischemic stroke signs — and deliver the Alberta Stroke Programme Early CT
Score (ASPECTS, a measure of stroke severity). The data are acute head
computed tomography volumes of suspected stroke patients. I convert from
the voxel level to the brain region level and then to the patient level through a
series of rules. Due to the real world clinical complexity of the problem, there
are at each level — voxel, region and patient — multiple sources of “truth”; I
evaluate my results appropriately against these truths.
Finally, federated learning is used to train a model on data that are divided
between multiple institutions. I introduce a novel evolution of this algorithm
— dubbed “soft federated learning” — that avoids the central coordinating
authority, and takes into account domain shift (covariate shift) and dataset
size. I first demonstrate the key properties of these two algorithms on a series
of MNIST (handwritten digits) toy problems. Then I apply the methods to the
BraTS medical dataset, which contains MRI brain glioma scans from multiple
institutions, to compare these algorithms in a realistic setting
Computer-aided image quality assessment in automated 3D breast ultrasound images
Automated 3D breast ultrasound (ABUS) is a valuable, non-ionising adjunct to X-ray mammography for breast cancer screening and diagnosis for women with dense breasts. High image quality is an important prerequisite for diagnosis and has to be guaranteed at the time of acquisition. The high throughput of images in a screening scenario demands for automated solutions. In this work, an automated image quality assessment system rating ABUS scans at the time of acquisition was designed and implemented. Quality assessment of present diagnostic ultrasound images has rarely been performed demanding thorough analysis of potential image quality aspects in ABUS. Therefore, a reader study was initiated, making two clinicians rate the quality of clinical ABUS images. The frequency of specific quality aspects was evaluated revealing that incorrect positioning and insufficiently applied contact fluid caused the most relevant image quality issues. The relative position of the nipple in the image, the acoustic shadow caused by the nipple as well as the shape of the breast contour reflect patient positioning and ultrasound transducer handling. Morphological and histogram-based features utilized for machine learning to reproduce the manual classification as provided by the clinicians. At 97 % specificity, the automatic classification achieved sensitivities of 59 %, 45 %, and 46 % for the three aforementioned aspects, respectively. The nipple is an important landmark in breast imaging, which is generally---but not always correctly---pinpointed by the technicians. An existing nipple detection algorithm was extended by probabilistic atlases and exploited for automatic detection of incorrectly annotated nipple marks. The nipple detection rate was increased from 82 % to 85 % and the classification achieved 90 % sensitivity at 89 % specificity. A lack of contact fluid between transducer and skin can induce reverberation patterns and acoustic shadows, which can possibly obscure lesions. Parameter maps were computed in order to localize these artefact regions and yielded a detection rate of 83 % at 2.6 false positives per image. Parts of the presented work were integrated to clinical workflow making up a novel image quality assessment system that supported technicians in their daily routine by detecting images of insufficient quality and indicating potential improvements for a repeated scan while the patient was still in the examination room. First evaluations showed that the proposed method sensitises technicians for the radiologists' demands on diagnostically valuable images
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