A semi-automatic workflow to process images from small mammal camera traps

Camera traps have become popular for monitoring biodiversity, but the huge amounts of image data that arise from camera trap monitoring represent a challenge and artificial intelligence is increasingly used to automatically classify large image data sets. However, it is still challenging to combine automatic classification with other steps and tools needed for efficient, quality-assured and adaptive processing of camera trap images in long-term monitoring programs. Here we propose a semi-automatic workflow to process images from small mammal cameras that combines all necessary steps from downloading camera trap images in the field to a quality checked data set ready to be used in ecological analyses. The workflow is implemented in R and includes (1) managing raw images, (2) automatic image classification, (3) quality check of automatic image labels, as well as the possibilities to (4) retrain the model with new images and to (5) manually review subsets of images to correct image labels. We illustrate the application of this workflow for the development of a new monitoring program of an Arctic small mammal community. We first trained a classification model for the specific small mammal community based on images from an initial set of camera traps. As the monitoring program evolved, the classification model was retrained with a small subset of images from new camera traps. This case study highlights the importance of model retraining in adaptive monitoring programs based on camera traps as this step in the workflow increases model performance and substantially decreases the total time needed for manually reviewing images and correcting image labels. We provide all R scripts to make the workflow accessible to other ecologists

First reported foodborne outbreak associated with microsporidia, Sweden, October 2009

Microsporidia are spore-forming intracellular parasites that infrequently cause disease in immunocompetent persons. This study describes the first report of a foodborne microsporidiosis outbreak which affected persons visiting a hotel in Sweden. Enterocytozoon bieneusi was identified in stool samples from 7/11 case-patients, all six sequenced samples were genotype C. To confirm that this was not a chance finding, 19 stool samples submitted by healthy persons from a comparable group who did not visit the hotel on that day were tested; all were negative for microsporidia. A retrospective cohort study identified 135 case-patients (attack rate 30%). The median incubation period was 9 days. Consumption of cheese sandwiches [relative risk (RR) 4·1, 95% confidence interval (CI) 1·4–12·2] and salad (RR 2·1, 95% CI 1·1–4) were associated with illness. Both items contained pre-washed, ready-to-eat cucumber slices. Microsporidia may be an under-reported cause of gastrointestinal outbreaks; we recommend that microsporidia be explored as potential causative agents in food- and waterborne outbreaks, especially when no other organisms are identified

A Dynamic Occupancy Model for Interacting Species with Two Spatial Scales

Occupancy models have been extended to account for either multiple spatial scales or species interactions in a dynamic setting. However, as interacting species (e.g., predators and prey) often operate at different spatial scales, including nested spatial structure might be especially relevant to models of interacting species. Here we bridge these two model frameworks by developing a multi-scale, two-species occupancy model. The model is dynamic, i.e. it estimates initial occupancy, colonization and extinction probabilities—including probabilities conditional to the other species’ presence. With a simulation study, we demonstrate that the model is able to estimate most parameters without marked bias under low, medium and high average occupancy probabilities, as well as low, medium and high detection probabilities, with only a small bias for some parameters in low-detection scenarios. We further evaluate the model’s ability to deal with sparse field data by applying it to a multi-scale camera trapping dataset on a mustelid-rodent predator–prey system. Most parameters are estimated with low uncertainty (i.e. narrow posterior distributions). More broadly, our model framework creates opportunities to explicitly account for the spatial structure found in many spatially nested study designs, and to study interacting species that have contrasting movement ranges with camera traps.Supplementary materials accompanying this paper appear online.publishedVersio

Long-term variations in Iceland–Scotland overflow strength during the Holocene

The overflow of deep water from the Nordic seas into the North Atlantic plays a critical role in global ocean circulation and climate. Approximately half of this overflow occurs via the Iceland–Scotland (I–S) overflow, yet the history of its strength throughout the Holocene (~ 0–11 700 yr ago, ka) is poorly constrained, with previous studies presenting apparently contradictory evidence regarding its long-term variability. Here, we provide a comprehensive reconstruction of I–S overflow strength throughout the Holocene using sediment grain size data from a depth transect of 13 cores from the Iceland Basin. Our data are consistent with the hypothesis that the main axis of the I–S overflow on the Iceland slope was shallower during the early Holocene, deepening to its present depth by ~ 7 ka. Our results also reveal weaker I–S overflow during the early and late Holocene, with maximum overflow strength occurring at ~ 7 ka, the time of a regional climate thermal maximum. Climate model simulations suggest a shoaling of deep convection in the Nordic seas during the early and late Holocene, consistent with our evidence for weaker I–S overflow during these intervals. Whereas the reduction in I–S overflow strength during the early Holocene likely resulted from melting remnant glacial ice sheets, the decline throughout the last 7000 yr was caused by an orbitally induced increase in the amount of Arctic sea ice entering the Nordic seas. Although the flux of Arctic sea ice to the Nordic seas is expected to decrease throughout the next century, model simulations predict that under high emissions scenarios, competing effects, such as warmer sea surface temperatures in the Nordic seas, will result in reduced deep convection, likely driving a weaker I–S overflow

Biometric Fish Classification of Temperate Species Using Convolutional Neural Network with Squeeze-and-Excitation

submittedVersio

Using machine learning to provide automatic image annotation for wildlife camera traps in the Arctic

Source at https://hdl.handle.net/10037/26504.The arctic tundra is considered the terrestrial biome expected to be most impacted by climate change, with temperatures projected to increase as much as 10 °C by the turn of the century. The Climate-ecological Observatory for Arctic Tundra (COAT) project monitors the climate and ecosystems using several sensor types. We report on results from projects that automate image annotations from two of the camera traps used by COAT: an artificial tunnel under the snow for capturing information about small mammals, and an open-air camera trap using bait that captures information of a range of larger sized birds and mammals. These traps currently produce over two million pictures per year. We have developed and trained several Convolutional Neural Network (CNN) models to automate annotation of images from these camera traps. Results show that we get a high accuracy: 97.84% for tunnel traps, and 94.1% for bait traps. This exceeds previous state of the art in animal identification on camera trap images, and is at a level where we can already relieve experts from manual annotation of images

Regional mechanical and biochemical properties of the porcine cortical meninges

peer-reviewedThe meninges are pivotal in protecting the brain against traumatic brain injury (TBI), an ongoing issue in most mainstream sports. Improved understanding of TBI biomechanics and pathophysiology is desirable to improve preventative measures, such as protective helmets, and advance our TBI diagnostic/prognostic capabilities. This study mechanically characterised the porcine meninges by performing uniaxial tensile testing on the dura mater (DM) tissue adjacent to the frontal, parietal, temporal, and occipital lobes of the cerebellum and superior sagittal sinus region of the DM. Mechanical characterisation revealed a significantly higher elastic modulus for the superior sagittal sinus region when compared to other regions in the DM. The superior sagittal sinus and parietal regions of the DM also displayed local mechanical anisotropy. Further, fatigue was noted in the DM following ten preconditioning cycles, which could have important implications in the context of repetitive TBI. To further understand differences in regional mechanical properties, regional variations in protein content (collagen I, collagen III, fibronectin and elastin) were examined by immunoblot analysis. The superior sagittal sinus was found to have significantly higher collagen I, elastin, and fibronectin content. The frontal region was also identified to have significantly higher collagen I and fibronectin content while the temporal region had increased elastin and fibronectin content. Regional differences in the mechanical and biochemical properties along with regional tissue thickness differences within the DM reveal that the tissue is a non-homogeneous structure. In particular, the potentially influential role of the superior sagittal sinus in TBI biomechanics warrants further investigation

Biologiske undersøkelser i 17 innsjøer i Sogn og Fjordane høsten 2000. Kalkingseffekter, vannkvalitet, fiskebestander, vegetasjon, bunndyr og dyreplankton

Årsliste 2001Biologiske undersøkelser er utført i 17 innsjøer i Sogn og Fjordane. Alle innsjøene med unntak av Kvangrøvatnet i Fjaler kommune er kalket eller påvirket av oppstrøms kalking. Undersøkelsene omfattet prøvefiske i 15 av innsjøene, og videre vannkjemisk prøvetaking, bunndyr og dyreplankton. I åtte av innsjøene ble det gjort kartlegging av vannvegetasjonen med spesiell vekt på krypsiv. Målsetningen med prosjektet var å vurdere kjemiske og biologisk effekter av kalkingen, og komme med forslag til eventuelle endringer i kalkingsstrategien. Vannkvaliteten, representert ved utløpsprøver, var relativt god i de undersøkte innsjøene. Ingen av innsjøene hadde pH under 5,5 - de fleste hadde pH 6,0 - 6,5. Samtlige innsjøer hadde ANC-verdier over 10 µekv/l. Konsentrasjonen av labilt aluminium varierte fra 1 - 15 µg/l. Det er viktig å merke seg at vannprøvene ble tatt i en periode på året hvor vannkvaliteten vanligvis er relativt god. Det ble fanget aure i samtlige av de prøvefiskede innsjøene - i Dingjevatnet og Brossvikvatnet i Gulen kommune ble det i tillegg fanget røye. Auretetthetene varierte en del, men var jevnt over gode. Kun seks av de undersøkte innsjøene hadde aurebestander med under middels tetthet: Atlevatnet, Fismavatnet, Krokevatnet, Kvangrøvatnet, Fagredalsvatnet og Bergsvatnet. På innløp Atlevatnet, innløp Fagredalsvatnet og utløpet av Bergsvatnet skilte fisken seg ut med forhøyede konsentrasjoner av gjellealuminium (snittverdier 131, 153 og 76 µg Al/g). For Torevatnet i Fjaler kommune og Skilbreida i Høyanger kommune anbefaler en å avslutte innsjøkalkingen, men fortsette med kalking av gytebekkene For de øvrige innsjøene anbefaler en at dagens kalkingsstrategi fortsetter.Fylkesmannen i Sogn og Fjordane, Miljøvernavdelinge

Asynchronous Antarctic and Greenland ice-volume contributions to the last interglacial sea-level highstand

The last interglacial (LIG; ~130 to ~118 thousand years ago, ka) was the last time global sea level rose well above the present level. Greenland Ice Sheet (GrIS) contributions were insufficient to explain the highstand, so that substantial Antarctic Ice Sheet (AIS) reduction is implied. However, the nature and drivers of GrIS and AIS reductions remain enigmatic, even though they may be critical for understanding future sea-level rise. Here we complement existing records with new data, and reveal that the LIG contained an AIS-derived highstand from ~129.5 to ~125 ka, a lowstand centred on 125–124 ka, and joint AIS + GrIS contributions from ~123.5 to ~118 ka. Moreover, a dual substructure within the first highstand suggests temporal variability in the AIS contributions. Implied rates of sea-level rise are high (up to several meters per century; m c−1), and lend credibility to high rates inferred by ice modelling under certain ice-shelf instability parameterisations.Universidade de VigoAustralian Research Council Laureate Fellowship | Ref. FL120100050RCN project THRESHOLDS | Ref. 2549

Revealing the last 13,500 years of environmental history from the multiproxy record of a mountain lake (Lago Enol, northern Iberian Peninsula)

This is the author's accepted manuscript. The final publication is available at Springer via http://dx.doi.org/10.1007/s10933-009-9387-7.We present the Holocene sequence from Lago Enol (43°16′N, 4°59′W, 1,070 m a.s.l.), Cantabrian Mountains, northern Spain. A multiproxy analysis provided comprehensive information about regional humidity and temperature changes. The analysis included sedimentological descriptions, physical properties, organic carbon and carbonate content, mineralogy and geochemical composition together with biological proxies including diatom and ostracod assemblages. A detailed pollen study enabled reconstruction of variations in vegetation cover, which were interpreted in the context of climate changes and human impact. Four distinct stages were recognized for the last 13,500 years: (1) a cold and dry episode that includes the Younger Dryas event (13,500–11,600 cal. year BP); (2) a humid and warmer period characterizing the onset of the Holocene (11,600–8,700 cal. year BP); (3) a tendency toward a drier climate during the middle Holocene (8,700–4,650 cal. year BP); and (4) a return to humid conditions following landscape modification by human activity (pastoral activities, deforestation) in the late Holocene (4,650–2,200 cal. year BP). Superimposed on relatively stable landscape conditions (e.g. maintenance of well established forests), the typical environmental variability of the southern European region is observed at this site.The Spanish Inter-Ministry Commission of Science and Technology (CICYT), the Spanish National Parks agency, the European Commission, the Spanish Ministry of Science, and the European Social Fund