Machine learned daily life history classification using low frequency tracking data and automated modelling pipelines: application to North American waterfowl

Background: Identifying animal behaviors, life history states, and movement patterns is a prerequisite for many animal behavior analyses and effective management of wildlife and habitats. Most approaches classify short-term movement patterns with high frequency location or accelerometry data. However, patterns reflecting life history across longer time scales can have greater relevance to species biology or management needs, especially when available in near real-time. Given limitations in collecting and using such data to accurately classify complex behaviors in the long-term, we used hourly GPS data from 5 waterfowl species to produce daily activity classifications with machine-learned models using “automated modelling pipelines”. Methods: Automated pipelines are computer-generated code that complete many tasks including feature engineering, multi-framework model development, training, validation, and hyperparameter tuning to produce daily classifications from eight activity patterns reflecting waterfowl life history or movement states. We developed several input features for modeling grouped into three broad categories, hereafter “feature sets”: GPS locations, habitat information, and movement history. Each feature set used different data sources or data collected across different time intervals to develop the “features” (independent variables) used in models. Results: Automated modelling pipelines rapidly developed easily reproducible data preprocessing and analysis steps, identification and optimization of the best performing model and provided outputs for interpreting feature importance. Unequal expression of life history states caused unbalanced classes, so we evaluated feature set importance using a weighted F1-score to balance model recall and precision among individual classes. Although the best model using the least restrictive feature set (only 24 hourly relocations in a day) produced effective classifications (weighted F1 = 0.887), models using all feature sets performed substantially better (weighted F1 = 0.95), particularly for rarer but demographically more impactful life history states (i.e., nesting). Conclusions: Automated pipelines generated models producing highly accurate classifications of complex daily activity patterns using relatively low frequency GPS and incorporating more classes than previous GPS studies. Near real-time classification is possible which is ideal for time-sensitive needs such as identifying reproduction. Including habitat and longer sequences of spatial information produced more accurate classifications but incurred slight delays in processing

Informing wetland management with waterfowl movement and sanctuary use responses to human-induced disturbance

Long-term environmental management to prevent waterfowl population declines is informed by ecology, movement behavior and habitat use patterns. Extrinsic factors, such as human-induced disturbance, can cause behavioral changes which may influence movement and resource needs, driving variation that affects management efficacy. To better understand the relationship between human-based disturbance and animal movement and habitat use, and their potential effects on management, we GPS tracked 15 dabbling ducks in California over ~4-weeks before, during and after the start of a recreational hunting season in October/November 2018. We recorded locations at 2-min intervals across three separate 24-h tracking phases: Phase 1) two weeks before the start of the hunting season (control (undisturbed) movement); Phase 2) the hunting season opening weekend; and Phase 3) a hunting weekend two weeks after opening weekend. We used GLMM models to analyze variation in movement and habitat use under hunting pressure compared with ‘normal’ observed patterns prior to commencement of hunting. We also compared responses to differing levels of disturbance related to the time of day (high - shooting/~daytime); moderate - non-lethal (~crepuscular); and low - night). During opening weekend flight (% time and distance) more than doubled during moderate and low disturbance and increased by ~50% during high disturbance compared with the pre-season weekend. Sanctuary use tripled during moderate and low disturbance and increased ~50% during high disturbance. Two weeks later flight decreased in all disturbance levels but was only less than the pre-season levels during high disturbance. In contrast, sanctuary use only decreased at night, although not to pre-season levels, while daytime doubled from ~45% to \u3e80%. Birds adjust rapidly to disturbance and our results have implications for energetics models that estimate population food requirements. Management would benefit from reassessing the juxtaposition of essential sanctuary and feeding habitats to optimize wetland management for waterfowl

Good prospects: high-resolution telemetry data suggests novel brood site selection behaviour in waterfowl

Breeding success should increase with prior knowledge of the surrounding environment, which is dependent upon an animal\u27s ability to evaluate habitat. Prospecting for nesting locations and migratory stopover sites are well-established behaviours among bird species. We assessed whether three species of California dabbling ducks – mallards, Anas platyrhynchos, gadwall, Mareca strepera, and cinnamon teal, Spatula cyanoptera – in Suisun Marsh, California, U.S.A., a brackish marsh, prospect for suitable wetlands in the week prior to brooding. K-means cluster analyses grouped 29 mallard and gadwall hens into three groups. One group (N = 13) demonstrated evidence of brood site prospecting, with the fewest and latest prebrooding wetland visits. Of these hens, seven visited their future brood pond an average of 1.14 times and only shortly before brooding (1.29 days), obtaining current information on habitat suitability. For the remaining six hens, we did not detect a brooding wetland visit, possibly due to data limitations or because these hens acquired sufficient familiarity with the wetland habitat during nest breaks in adjacent wetlands, obviating the need to prospect the specific brood pond. The second identified group of hens (N = 11) visited the brooding wetland most frequently (on 4.55 days), further in advance (5.27 days), with the fewest unique wetland visits and the earliest brooding date (26 May). The final group of hens (N = 5) were the latest to brood (21 June) and visited the most wetlands, possibly due to less water or more broods present across the landscape. Brood ponds were always farther from the nest than the nearest ponds, indicating that habitat suitability or presence of conspecifics is more important to brood site selection. Prospecting provides hens with knowledge about current habitat conditions and allows them to ‘crowdsource’ public information regarding use of that habitat by other brooding hens. Prospecting may, therefore, benefit ducks inhabiting ephemeral habitats like those within Suisun Marsh, where brood habitat is limited and water cover changes rapidly during the breeding season

Pathways for avian influenza virus spread: GPS reveals wild waterfowl in commercial livestock facilities and connectivity with the natural wetland landscape

Zoonotic diseases are of considerable concern to the human population and viruses such as avian influenza (AIV) threaten food security, wildlife conservation and human health. Wild waterfowl and the natural wetlands they use are known AIV reservoirs, with birds capable of virus transmission to domestic poultry populations. While infection risk models have linked migration routes and AIV outbreaks, there is a limited understanding of wild waterfowl presence on commercial livestock facilities, and movement patterns linked to natural wetlands. We documented 11 wild waterfowl (three Anatidae species) in or near eight commercial livestock facilities in Washington and California with GPS telemetry data. Wild ducks used dairy and beef cattle feed lots and facility retention ponds during both day and night suggesting use for roosting and foraging. Two individuals (single locations) were observed inside poultry facility boundaries while using nearby wetlands. Ducks demonstrated high site fidelity, returning to the same areas of habitats (at livestock facilities and nearby wetlands), across months or years, showed strong connectivity with surrounding wetlands, and arrived from wetlands up to 1251 km away in the week prior. Telemetry data provides substantial advantages over observational data, allowing assessment of individual movement behaviour and wetland connectivity that has significant implications for outbreak management. Telemetry improves our understanding of risk factors for waterfowl–livestock virus transmission and helps identify factors associated with coincident space use at the wild waterfowl–domestic livestock interface. Our research suggests that even relatively small or isolated natural and artificial water or food sources in/near facilities increases the likelihood of attracting waterfowl, which has important consequences for managers attempting to minimize or prevent AIV outbreaks. Use and interpretation of telemetry data, especially in near-real-time, could provide key information for reducing virus transmission risk between waterfowl and livestock, improving protective barriers between wild and domestic species, and abating outbreaks

Computerized analysis of coronary artery disease: Performance evaluation of segmentation and tracking of coronary arteries in CT angiograms

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/134780/1/mp0294.pd

Characteristics of large Martian dust devils using Mars Odyssey Thermal Emission Imaging System visual and infrared images

A search for Martian dust devils has been carried out, using Mars Odyssey Thermal Emission Imaging System (THEMIS) visible-wavelength images. Simultaneous THEMIS thermal infrared wavelength images were then processed and analyzed to investigate the thermal properties of the dust devils observed; 3079 images were checked, concentrating on northern spring, summer, and autumn (LS from 0° to 270°, 20°S to 50°N). Mars Express High Resolution Stereo Camera, Mars Global Surveyor Mars Orbiter Camera, and other THEMIS visible images were used for comparison to potentially rule out any ambiguous geological features. Eight clear examples of dust devils have been found in five separate images, with a comparable number of unconfirmed possible devils. The rarity of dust devils observed is believed to result from a combination of the difficulty in identifying dust devils in medium resolution THEMIS data and the fact that the Mars Odyssey orbit flyover local time is later in the afternoon than would be optimum for dust devil searching. The temporal distribution of dust devil activity appears to be weighted more toward later afternoon, compared to Earth, but this may be a sampling effect due to size variation with time of sol, greater coverage later in the sol, or the small-number statistics. The thermal infrared images indicate that the lofted dust in the column is cooler than the surrounding surface and must be equilibrating with the atmosphere in the dust devil. This energy transfer is estimated to be about 10% of the heat flux energy that is available to drive the systems. The ground shadowed by the dust column also appears colder than the surroundings, because of reduced solar illumination. From the visible-wavelength images, the shadows of the dust columns were used to estimate the column opacity, which in turn gave estimates of the dust loadings, which ranged from 1.9 × 10?5 to 1.5 × 10?4 kg m?3, similar to lander-based observations. No thermal or visible trails are associated with the dust devils, indicating that the surface equilibrates quickly after the devil has passed and that track counting as a dust devil survey technique must underestimate dust devil populations and consequently dust loading calculations, confirming previous work

The effect of long-term homocysteine-lowering on carotid intima-media thickness and flow-mediated vasodilation in stroke patients: a randomized controlled trial and meta-analysis

<p>Abstract</p> <p>Background</p> <p>Experimental and epidemiological evidence suggests that homocysteine (tHcy) may be a causal risk factor for atherosclerosis. B-vitamin supplements reduce tHcy and improve endothelial function in short term trials, but the long-term effects of the treatment on vascular structure and function are unknown.</p> <p>Methods</p> <p>We conducted a sub-study of VITATOPS, a randomised, double-blind, placebo-controlled intervention trial designed to test the efficacy of long term B-vitamin supplementation (folic acid 2 mg, vitamin B₆25 mg and vitamin B₁₂0.5 mg) in the prevention of vascular events in patients with a history of stroke. We measured carotid intima-medial thickness (CIMT) and flow-mediated dilation (FMD) at least two years after randomisation in 162 VITATOPS participants. We also conducted a systematic review and meta-analysis of studies designed to test the effect of B-vitamin treatment on CIMT and FMD.</p> <p>Results</p> <p>After a mean treatment period of 3.9 ± 0.9 years, the vitamin-treated group had a significantly lower mean plasma homocysteine concentration than the placebo-treated group (7.9 μmol/L, 95% CI 7.5 to 8.4 versus 11.8 μmol/L, 95% CI 10.9 to 12.8, p < 0.001). Post-treatment CIMT (0.84 ± 0.17 mm vitamins versus 0.83 ± 0.18 mm placebo, p = 0.74) and FMD (median of 4.0%, IQR 0.9 to 7.2 vitamins versus 3.0%, IQR 0.6 to 6.6 placebo, p = 0.48) did not differ significantly between groups. A meta-analysis of published randomised data, including those from the current study, suggested that B-vitamin supplements should reduce CIMT (-0.10 mm, 95% CI -0.20 to -0.01 mm) and increase FMD (1.4%, 95% CI 0.7 to 2.1%). However, the improvement in endothelial function associated with homocysteine-lowering treatment was significant in short-term studies but not in longer trials.</p> <p>Conclusion</p> <p>Although short-term treatment with B-vitamins is associated with increased FMD, long-term homocysteine-lowering did not significantly improve FMD or CIMT in people with a history of stroke.</p> <p>Trial Registration</p> <p>Clinical Trial Registration URL: <url>http://www.actr.org.au/</url></p> <p>Trial Registration number: 12605000005651</p

Adhesions Assemble!—Autoinhibition as a Major Regulatory Mechanism of Integrin-Mediated Adhesion

The advent of cell-cell and cell-extracellular adhesion enabled cells to interact in a coherent manner, forming larger structures and giving rise to the development of tissues, organs and complex multicellular life forms. The development of such organisms required tight regulation of dynamic adhesive structures by signaling pathways that coordinate cell attachment. Integrin-mediated adhesion to the extracellular matrix provides cells with support, survival signals and context-dependent cues that enable cells to run different cellular programs. One mysterious aspect of the process is how hundreds of proteins assemble seemingly spontaneously onto the activated integrin. An emerging concept is that adhesion assembly is regulated by autoinhibition of key proteins, a highly dynamic event that is modulated by a variety of signaling events. By enabling precise control of the activation state of proteins, autoinhibition enables localization of inactive proteins and the formation of pre-complexes. In response to the correct signals, these proteins become active and interact with other proteins, ultimately leading to development of cell-matrix junctions. Autoinhibition of key components of such adhesion complexes—including core components integrin, talin, vinculin, and FAK and important peripheral regulators such as RIAM, Src, and DLC1—leads to a view that the majority of proteins involved in complex assembly might be regulated by intramolecular interactions. Autoinhibition is relieved via multiple different signals including post-translation modification and proteolysis. More recently, mechanical forces have been shown to stabilize and increase the lifetimes of active conformations, identifying autoinhibition as a means of encoding mechanosensitivity. The complexity and scope for nuanced adhesion dynamics facilitated via autoinhibition provides numerous points of regulation. In this review, we discuss what is known about this mode of regulation and how it leads to rapid and tightly controlled assembly and disassembly of cell-matrix adhesion