Virtually every coastal country in the world is affected by harmful algal blooms (HABs, commonly called “red tides”). These phenomena are caused by blooms of microscopic algae. Some of these algae ...are toxic, and can lead to illness and death in humans, fish, seabirds, marine mammals, and other oceanic life, typically as a result of the transfer of toxins through the food web. Sometimes the direct release of toxic compounds can be lethal to marine animals. Non-toxic HABs cause damage to ecosystems, fisheries resources, and recreational facilities, often due to the sheer biomass of the accumulated algae. The term “HAB” also applies to non-toxic blooms of macroalgae (seaweeds), which can cause major ecological impacts such as the displacement of indigenous species, habitat alteration and oxygen depletion in bottom waters.
Globally, the nature of the HAB problem has changed considerably over the last several decades. The number of toxic blooms, the resulting economic losses, the types of resources affected, and the number of toxins and toxic species have all increased dramatically. Some of this expansion has been attributed to storms, currents and other natural phenomena, but human activities are also frequently implicated. Humans have contributed by transporting toxic species in ballast water, and by adding massive and increasing quantities of industrial, agricultural and sewage effluents to coastal waters. In many urbanized coastal regions, these inputs have altered the size and composition of the nutrient pool which has, in turn, created a more favorable nutrient environment for certain HAB species. The steady expansion in the use of fertilizers for agricultural production represents a large and worrisome source of nutrients in coastal waters that promote some HABs.
The diversity in HAB species and their impacts presents a significant challenge to those responsible for the management of coastal resources. Furthermore, HABs are complex oceanographic phenomena that require multidisciplinary study ranging from molecular and cell biology to large-scale field surveys, numerical modelling, and remote sensing from space. Our understanding of these phenomena is increasing dramatically, and with this understanding comes technologies and management tools that can reduce HAB incidence and impact. Here I summarize the global HAB problem, its trends and causes, and new technologies and approaches to monitoring, control and management, highlighting molecular probes for cell detection, rapid and sensitive toxin assays, remote sensing detection and tracking of blooms, bloom control and mitigation strategies, and the use of large-scale physical/biological models to analyze past blooms and forecast future ones.
The public health, tourism, fisheries, and ecosystem impacts from harmful algal blooms (HABs) have all increased over the past few decades. This has led to heightened scientific and regulatory ...attention, and the development of many new technologies and approaches for research and management. This, in turn, is leading to significant paradigm shifts with regard to, e.g., our interpretation of the phytoplankton species concept (strain variation), the dogma of their apparent cosmopolitanism, the role of bacteria and zooplankton grazing in HABs, and our approaches to investigating the ecological and genetic basis for the production of toxins and allelochemicals. Increasingly, eutrophication and climate change are viewed and managed as multifactorial environmental stressors that will further challenge managers of coastal resources and those responsible for protecting human health. Here we review HAB science with an eye toward new concepts and approaches, emphasizing, where possible, the unexpected yet promising new directions that research has taken in this diverse field.
Faster permutation inference in brain imaging Winkler, Anderson M.; Ridgway, Gerard R.; Douaud, Gwenaëlle ...
NeuroImage (Orlando, Fla.),
11/2016, Letnik:
141
Journal Article, Web Resource
Recenzirano
Odprti dostop
Permutation tests are increasingly being used as a reliable method for inference in neuroimaging analysis. However, they are computationally intensive. For small, non-imaging datasets, recomputing a ...model thousands of times is seldom a problem, but for large, complex models this can be prohibitively slow, even with the availability of inexpensive computing power. Here we exploit properties of statistics used with the general linear model (GLM) and their distributions to obtain accelerations irrespective of generic software or hardware improvements. We compare the following approaches: (i) performing a small number of permutations; (ii) estimating the p-value as a parameter of a negative binomial distribution; (iii) fitting a generalised Pareto distribution to the tail of the permutation distribution; (iv) computing p-values based on the expected moments of the permutation distribution, approximated from a gamma distribution; (v) direct fitting of a gamma distribution to the empirical permutation distribution; and (vi) permuting a reduced number of voxels, with completion of the remainder using low rank matrix theory. Using synthetic data we assessed the different methods in terms of their error rates, power, agreement with a reference result, and the risk of taking a different decision regarding the rejection of the null hypotheses (known as the resampling risk). We also conducted a re-analysis of a voxel-based morphometry study as a real-data example. All methods yielded exact error rates. Likewise, power was similar across methods. Resampling risk was higher for methods (i), (iii) and (v). For comparable resampling risks, the method in which no permutations are done (iv) was the absolute fastest. All methods produced visually similar maps for the real data, with stronger effects being detected in the family-wise error rate corrected maps by (iii) and (v), and generally similar to the results seen in the reference set. Overall, for uncorrected p-values, method (iv) was found the best as long as symmetric errors can be assumed. In all other settings, including for familywise error corrected p-values, we recommend the tail approximation (iii). The methods considered are freely available in the tool PALM — Permutation Analysis of Linear Models.
•Permutation methods can be accelerated through additional statistical approaches.•Six approaches are described and assessed.•Methods can be 100 times faster than in the non-accelerated case.•Recommendations are provided for various common scenarios.
Hear ye, hear ye … submissions now being accepted for a new Adaptations series aimed at sharing insights gained from the widespread educational transitions currently taking place.
Pursuit of the triple bottom line of economic, community and ecological sustainability has increased the complexity of fishery management; fisheries assessments require new types of data and analysis ...to guide science-based policy in addition to traditional biological information and modeling. We introduce the Fishery Performance Indicators (FPIs), a broadly applicable and flexible tool for assessing performance in individual fisheries, and for establishing cross-sectional links between enabling conditions, management strategies and triple bottom line outcomes. Conceptually separating measures of performance, the FPIs use 68 individual outcome metrics--coded on a 1 to 5 scale based on expert assessment to facilitate application to data poor fisheries and sectors--that can be partitioned into sector-based or triple-bottom-line sustainability-based interpretative indicators. Variation among outcomes is explained with 54 similarly structured metrics of inputs, management approaches and enabling conditions. Using 61 initial fishery case studies drawn from industrial and developing countries around the world, we demonstrate the inferential importance of tracking economic and community outcomes, in addition to resource status.
Alzheimer's disease is an irreversible, progressive brain disorder that accounts for about 50-75% of all cases of dementia.1 Alzheimer's disease is characterised by the presence of amyloid plaques ...(amyloid β) and neurofibrillary (tau) tangles, plus the loss of connections between neurons in the brain. The damage to the brain induced by abnormal deposits of amyloid β and tau tangles is believed to start a decade or more before a decline in cognitive function is apparent.1,2
Summary Background Artemisinin resistance in Plasmodium falciparum lengthens parasite clearance half-life during artemisinin monotherapy or artemisinin-based combination therapy. Absence of in-vitro ...and ex-vivo correlates of artemisinin resistance hinders study of this phenotype. We aimed to assess whether an in-vitro ring-stage survival assay (RSA) can identify culture-adapted P falciparum isolates from patients with slow-clearing or fast-clearing infections, to investigate the stage-dependent susceptibility of parasites to dihydroartemisinin in the in-vitro RSA, and to assess whether an ex-vivo RSA can identify artemisinin-resistant P falciparum infections. Methods We culture-adapted parasites from patients with long and short parasite clearance half-lives from a study done in Pursat, Cambodia, in 2010 (registered with ClinicalTrials.gov , number NCT00341003 ) and used novel in-vitro survival assays to explore the stage-dependent susceptibility of slow-clearing and fast-clearing parasites to dihydroartemisinin. In 2012, we implemented the RSA in prospective parasite clearance studies in Pursat, Preah Vihear, and Ratanakiri, Cambodia ( NCT01736319 ), to measure the ex-vivo responses of parasites from patients with malaria. Continuous variables were compared with the Mann-Whitney U test. Correlations were analysed with the Spearman correlation test. Findings In-vitro survival rates of culture-adapted parasites from 13 slow-clearing and 13 fast-clearing infections differed significantly when assays were done on 0–3 h ring-stage parasites (10·88% vs 0·23%; p=0·007). Ex-vivo survival rates significantly correlated with in-vivo parasite clearance half-lives (n=30, r =0·74, 95% CI 0·50–0·87; p<0·0001). Interpretation The in-vitro RSA of 0–3 h ring-stage parasites provides a platform for the molecular characterisation of artemisinin resistance. The ex-vivo RSA can be easily implemented where surveillance for artemisinin resistance is needed. Funding Institut Pasteur du Cambodge and the Intramural Research Program, NIAID, NIH.
•Values reported for indolic metabolites of tryptophan were compiled and compared.•Consistencies and discrepancies in reported values were discussed.•The progress in analytical and chromatographic ...methodologies used was reviewed.•Areas in need of greater attention were noted.
Concentrations reported for indolic microbial metabolites of tryptophan in human and rodent brain, cerebrospinal fluid, plasma, saliva and feces were compiled and discussed. A systematic review of the literature was accomplished by key word searches of Pubmed, Google Scholar and the Human Metabolome Data Base (HMDB), and by searching bibliographies of identified publications including prior reviews. The review was prompted by the increasing appreciation of the physiological importance of the indolic compounds in human health and disease. The compounds included were indoleacetic acid (IAA), indole propionic acid (IPA), indoleacrylic acid (IACR), indolelactic acid (ILA) indolepyruvic acid (IPY), indoleacetaldehyde (IAALD), indolealdehyde (IALD), tryptamine (TAM), indole (IND) and skatole (SKT). The undertaking aimed to vet and compare existing reports, to resolve apparent discrepancies, to draw biological inferences from the consideration of multiple analytes across sample types, to survey the analytical methodologies used, and to point out areas in need of greater attention.
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