Deep learning for supervised classification of temporal data in ecology

Temporal data is ubiquitous in ecology and ecologists often face the challenge of accurately differentiating these data into predefined classes, such as biological entities or ecological states. The usual approach consists of transforming the time series into user-defined features and then using these features as predictors in conventional statistical or machine learning models. Here we suggest the use of deep learning models as an alternative to this approach. Recent deep learning techniques can perform the classification directly from the time series, eliminating subjective and resource-consuming data transformation steps, and potentially improving classification results. We describe some of the deep learning architectures relevant for time series classification and show how these architectures and their hyper-parameters can be tested and used for the classification problems at hand. We illustrate the approach using three case studies from distinct ecological subdisciplines: i) insect species identification from wingbeat spectrograms; ii) species distribution modelling from climate time series and iii) the classification of phenological phases from continuous meteorological data. The deep learning approach delivered ecologically sensible and accurate classifications demonstrating its potential for wide applicability across subfields of ecology.info:eu-repo/semantics/publishedVersio

Experimental Demonstration of an Allee Effect in Microbial Populations

Microbial populations can be dispersal limited. However, microorganisms that successfully disperse into physiologically ideal environments are not guaranteed to establish. This observation contradicts the Baas-Becking tenet: ‘Everything is everywhere, but the environment selects’. Allee effects, which manifest in the relationship between initial population density and probability of establishment, could explain this observation. Here, we experimentally demonstrate that small populations of Vibrio fischeri are subject to an intrinsic demographic Allee effect. Populations subjected to predationby the bacterivore Cafeteria roenbergensis display both intrinsic and extrinsic demographic Allee effects. The estimated critical threshold required to escape positive densitydependence is around 5, 20 or 90 cells ml-1 under conditions of high carbon resources, low carbon resources or low carbon resources with predation, respectively. Thiswork builds on the foundations ofmodern microbial ecology, demonstrating that mechanisms controlling macroorganisms apply to microorganisms, and provides a statistical method to detect Allee effects in data

Rapid Targeted Gene Disruption in Bacillus Anthracis

Anthrax is a zoonotic disease recognized to affect herbivores since Biblical times and has the widest range of susceptible host species of any known pathogen. The ease with which the bacterium can be weaponized and its recent deliberate use as an agent of terror, have highlighted the importance of gaining a deeper understanding and effective countermeasures for this important pathogen. High quality sequence data has opened the possibility of systematic dissection of how genes distributed on both the bacterial chromosome and associated plasmids have made it such a successful pathogen. However, low transformation efficiency and relatively few genetic tools for chromosomal manipulation have hampered full interrogation of its genome. Results: Group II introns have been developed into an efficient tool for site-specific gene inactivation in several organisms. We have adapted group II intron targeting technology for application in Bacillus anthracis and generated vectors that permit gene inactivation through group II intron insertion. The vectors developed permit screening for the desired insertion through PCR or direct selection of intron insertions using a selection scheme that activates a kanamycin resistance marker upon successful intron insertion. Conclusions: The design and vector construction described here provides a useful tool for high throughput experimental interrogation of the Bacillus anthracis genome and will benefit efforts to develop improved vaccines and therapeutics.Chem-Bio Diagnostics program from the Department of Defense Chemical and Biological Defense program through the Defense Threat Reduction Agency (DTRA) B102387MNIH GM037949Welch Foundation F-1607Cellular and Molecular Biolog

The association between care co-ordination and emergency department use in older managed care enrollees

OBJECTIVE: To investigate the association between care co-ordination and use of the Emergency Department (ED) in older managed care enrollees. DESIGN: Nested case-control with 103 cases (used the ED) and 194 controls (did not use the ED). PATIENTS AND METHODS: Older patients with multiple chronic illnesses enrolled in a care management programme of a large group-model health maintenance organisation with more than 50,000 members over the age of 64. Better care co-ordination was defined as timely follow-up after a change in treatment; fewer decision-makers involved with the care plan; and a higher patient-perceived rating of overall care co-ordination. Logistic regression was used to assess the relationship between ED use (the outcome variable) and measures of care co-ordination (the predictor variables). RESULTS: Self-reported care co-ordination was not significantly different between cases and controls for any of the four classifications of inappropriate ED use. Similarly, no differences were found in the number of different physicians or medication prescribers involved in the patients' care. Four-week follow-up after potentially high-risk events for subsequent ED use, including changes in chronic disease medications, missed encounters, and same day encounters, did not differ between subjects with inappropriate ED use and controls. CONCLUSION: Existing measures of care co-ordination were not associated with inappropriate ED use in this study of older adults with complex care needs. The absence of an association may, in part, be attributable to the paucity of validated measures to assess care co-ordination, as well as the methodological complexity inherent in studying this topic. Future research should focus on the development of new measures and on approaches that better isolate the role of care co-ordination from other potential variables that influence utilisation

Chandra Smells a RRAT: X-ray Detection of a Rotating Radio Transient

"Rotating RAdio Transients" (RRATs) are a newly discovered astronomical phenomenon, characterised by occasional brief radio bursts, with average intervals between bursts ranging from minutes to hours. The burst spacings allow identification of periodicities, which fall in the range 0.4 to 7 seconds. The RRATs thus seem to be rotating neutron stars, albeit with properties very different from the rest of the population. We here present the serendipitous detection with the Chandra X-ray Observatory of a bright point-like X-ray source coincident with one of the RRATs. We discuss the temporal and spectral properties of this X-ray emission, consider counterparts in other wavebands, and interpret these results in the context of possible explanations for the RRAT population.Comment: 5 pages, 2 b/w figures, 1 color figure. To appear in the proceedings of "Isolated Neutron Stars", Astrophysics & Space Science, in pres

Superheating fields of superconductors: Asymptotic analysis and numerical results

The superheated Meissner state in type-I superconductors is studied both analytically and numerically within the framework of Ginzburg-Landau theory. Using the method of matched asymptotic expansions we have developed a systematic expansion for the solutions of the Ginzburg-Landau equations in the limit of small $\kappa$, and have determined the maximum superheating field $H_{\rm sh}$ for the existence of the metastable, superheated Meissner state as an expansion in powers of $\kappa^{1/2}$. Our numerical solutions of these equations agree quite well with the asymptotic solutions for $\kappa<0.5$. The same asymptotic methods are also used to study the stability of the solutions, as well as a modified version of the Ginzburg-Landau equations which incorporates nonlocal electrodynamics. Finally, we compare our numerical results for the superheating field for large-$\kappa$ against recent asymptotic results for large-$\kappa$, and again find a close agreement. Our results demonstrate the efficacy of the method of matched asymptotic expansions for dealing with problems in inhomogeneous superconductivity involving boundary layers.Comment: 14 pages, 8 uuencoded figures, Revtex 3.