SlamTracker Accuracy under Static and Controlled Movement Conditions

Accelerometry is the de facto standard in objective physical activity monitoring. However traditional accelerometer units undergo proprietary pre-processing, resulting in the ‘black-box’ phenomenon, where researchers are unaware of the processes and filters used on their data. Raw accelerometers where all frequencies related to human movement are included in the signal, would facilitate novel analyses, such as frequency domain analysis and pattern recognition. The aim of this study was to quantify the mean, standard deviation and variance of the SlamTracker raw accelerometer at a range of speeds. Four tri-axial accelerometers underwent a one minute static condition test nine movement condition tests. Accelerometers were assessed for mean, standard deviation, sample variance and coefficient of variation throughout in all axes for all experimental conditions. The sample variance was <0.001g across all speeds and axes during the movement condition tests. In conclusion, the SlamTracker is shown to be an accurate and reliable device for measuring the raw accelerations of moveme

Implementation of the LANS-alpha turbulence model in a primitive equation ocean model

This paper presents the first numerical implementation and tests of the Lagrangian-averaged Navier-Stokes-alpha (LANS-alpha) turbulence model in a primitive equation ocean model. The ocean model in which we work is the Los Alamos Parallel Ocean Program (POP); we refer to POP and our implementation of LANS-alpha as POP-alpha. Two versions of POP-alpha are presented: the full POP-alpha algorithm is derived from the LANS-alpha primitive equations, but requires a nested iteration that makes it too slow for practical simulations; a reduced POP-alpha algorithm is proposed, which lacks the nested iteration and is two to three times faster than the full algorithm. The reduced algorithm does not follow from a formal derivation of the LANS-alpha model equations. Despite this, simulations of the reduced algorithm are nearly identical to the full algorithm, as judged by globally averaged temperature and kinetic energy, and snapshots of temperature and velocity fields. Both POP-alpha algorithms can run stably with longer timesteps than standard POP. Comparison of implementations of full and reduced POP-alpha algorithms are made within an idealized test problem that captures some aspects of the Antarctic Circumpolar Current, a problem in which baroclinic instability is prominent. Both POP-alpha algorithms produce statistics that resemble higher-resolution simulations of standard POP. A linear stability analysis shows that both the full and reduced POP-alpha algorithms benefit from the way the LANS-alpha equations take into account the effects of the small scales on the large. Both algorithms (1) are stable; (2) make the Rossby Radius effectively larger; and (3) slow down Rossby and gravity waves.Comment: Submitted to J. Computational Physics March 21, 200

Prying into the intimate secrets of animal lives; software beyond hardware for comprehensive annotation in ‘Daily Diary’ tags

BACKGROUND: Smart tags attached to freely-roaming animals recording multiple parameters at infra-second rates are becoming commonplace, and are transforming our understanding of the way wild animals behave. Interpretation of such data is complex and currently limits the ability of biologists to realise the value of their recorded information.DESCRIPTION: This work presents Framework4, an all-encompassing software suite which operates on smart sensor data to determine the 4 key elements considered pivotal for movement analysis from such tags (Endangered Species Res 4: 123-37, 2008). These are; animal trajectory, behaviour, energy expenditure and quantification of the environment in which the animal moves. The program transforms smart sensor data into dead-reckoned movements, template-matched behaviours, dynamic body acceleration-derived energetics and position-linked environmental data before outputting it all into a single file. Biologists are thus left with a single data set where animal actions and environmental conditions can be linked across time and space.CONCLUSIONS: Framework4 is a user-friendly software that assists biologists in elucidating 4 key aspects of wild animal ecology using data derived from tags with multiple sensors recording at high rates. Its use should enhance the ability of biologists to derive meaningful data rapidly from complex data.</p

A new direction for differentiating animal activity based on measuring angular velocity about the yaw axis

The use of animal-attached data loggers to quantify animal movement has increased in popularity and application in recent years. High-resolution tri-axial acceleration and magnetometry measurements have been fundamental in elucidating fine-scale animal movements, providing information on posture, traveling speed, energy expenditure, and associated behavioral patterns. Heading is a key variable obtained from the tandem use of magnetometers and accelerometers, although few field investigations have explored fine-scale changes in heading to elucidate differences in animal activity (beyond the notable exceptions of dead-reckoning). This paper provides an overview of the value and use of animal heading and a prime derivative, angular velocity about the yaw axis, as an important element for assessing activity extent with potential to allude to behaviors, using “free-ranging” Loggerhead turtles (Caretta caretta) as a model species. We also demonstrate the value of yaw rotation for assessing activity extent, which varies over the time scales considered and show that various scales of body rotation, particularly rate of change of yaw, can help resolve differences between fine-scale behavior-specific movements. For example, oscillating yaw movements about a central point of the body's arc implies bouts of foraging, while unusual circling behavior, indicative of conspecific interactions, could be identified from complete revolutions of the longitudinal axis. We believe this approach should help identification of behaviors and “space-state” approaches to enhance our interpretation of behavior-based movements, particularly in scenarios where acceleration metrics have limited value, such as for slow-moving animals

A transfer function approach to measuring cell inheritance

<p>Abstract</p> <p>Background</p> <p>The inheritance of cellular material between parent and daughter cells during mitosis is highly influential in defining the properties of the cell and therefore the population lineage. This is of particular relevance when studying cell population evolution to assess the impact of a disease or the perturbation due to a drug treatment. The usual technique to investigate inheritance is to use time-lapse microscopy with an appropriate biological marker, however, this is time consuming and the number of inheritance events captured are too low to be statistically meaningful.</p> <p>Results</p> <p>Here we demonstrate the use of a high throughput fluorescence measurement technique e.g. flow cytometry, to measure the fluorescence from quantum dot markers which can be used to target particular cellular sites. By relating, the fluorescence intensity measured between two time intervals to a transfer function we are able to deconvolve the inheritance of cellular material during mitosis. To demonstrate our methodology we use CdTe/ZnS quantum dots to measure the ratio of endosomes inherited by the two daughter cells during mitosis in the U2-OS, human osteoscarcoma cell line. The ratio determined is in excellent agreement with results obtained previously using a more complex and computational intensive bespoke stochastic model.</p> <p>Conclusions</p> <p>The use of a transfer function approach allows us to utilise high throughput measurement of large cell populations to derive statistically relevant measurements of the inheritance of cellular material. This approach can be used to measure the inheritance of organelles, proteins etc. and also particles introduced to cells for drug delivery.</p

A Kinematic Analysis of Fundamental Movement Skills

Abstract Fundamental movement skills are considered the basic building blocks for movement and provide the foundation for specialized and sport-specific movement skills required for participation in a variety of physical activities. However, kinematic analyses of fundamental movement has not been performed. The aims of this study were to, (1) characterise the relationship between facets of fundamental movement and, (2) characterise the relationship between overall integrated acceleration and three-dimensional kinematic variables whilst performing fundamental movement skills. Eleven participants (10±0.8y, 1.41±0.07m, 33.4±8.6kg, body mass index; 16.4±3.1 kg·m2) took part in this study, had anthropometric variables recorded and performed a series of fundamental movement tasks, whilst wearing a tri-axial accelerometer and were recorded using a three-dimensional motion capture system. Maximum shoulder external rotation (°) and maximum shoulder internal rotation velocity (°.s−1) (r=0.86, p&lt;0.001), mediolateral centre of mass range (cm) and centre of mass coefficient of variation (%) (r=0.83, p&lt;0.001), maximum stride angle (°) in the jog and walk (r=0.74, p=0.01) and maximum sprint stride angle and maximum shoulder internal rotation velocity (°.s−1) (r=0.67, p&lt;0.02) were significantly correlated. Maximum sprint stride angle (hip: r=0.96, p&lt;0.001, ankle: r=0.97, p&lt;0.001) and maximum internal rotation velocity (ankle: r=0.6, p=0.05) were significantly correlated to overall integrated acceleration. Overall integrated acceleration was comparable between participants (CV: 10.5), whereas three-dimensional variables varied by up to 65%. Although overall integrated acceleration was comparable between participants, three-dimensional variables were much more varied. Indicating that although overall activity may be correspondent, the characteristics of a child’s movement may be highly varied.</jats:p

Testing angular velocity as a new metric for metabolic demands of slow-moving marine fauna: a case study with Giant spider conchs Lambis truncata

BackgroundQuantifying metabolic rate in free-living animals is invaluable in understanding the costs of behaviour and movement for individuals and communities. Dynamic body acceleration (DBA) metrics, such as vectoral DBA (VeDBA), are commonly used as proxies for the energy expenditure of movement but are of limited applicability for slow-moving species. It has recently been suggested that metrics based on angular velocity might be better suited to characterise their energetics. We investigated whether a novel metric—the ‘Rate of change of Rotational Movement (RocRM)’, calculated from the vectoral sum of change in the pitch, roll and yaw/heading axes over a given length of time, is a suitable proxy for energy expenditure.ResultsWe found that RocRM can be used as an alternative energy expenditure proxy in a slow-moving benthic invertebrate. Eleven Giant spider conchs Lambis truncata (collected in the Red Sea) were instrumented with multiple channel (Daily Diary) tags and kept in sealed chambers for 5 h while their oxygen consumption, V̇O2, was measured. We found RocRM to be positively correlated with V̇O2, this relationship being affected by the time-step (i.e. the range of the calculated differential) of the RocRM. Time steps of 1, 5, 10 and 60 s yielded an explained variability of between 15 and 31%. The relationship between V̇O2 and VeDBA was not statistically significant, suggesting RocRM to provide more accurate estimations of metabolic rates in L. truncata.ConclusionsRocRM proved to be a statistically significant predictor of V̇O2 where VeDBA did not, validating the approach of using angular-based metrics over dynamic movement-based ones for slower moving animals. Further work is required to validate the use of RocRM for other species, particularly in animals with minimally dynamic movement, to better understand energetic costs of whole ecosystems. Unexplained variability in the models might be a consequence of the methodology used, but also likely a result of conch activity that does not manifest in movement of the shell. Additionally, density plots of mean RocRM at each time-step suggest differences in movement scales, which may collectively be useful as a species fingerprint of movement going forward

Activity of loggerhead turtles during the U-shaped dive: insights using angular velocity metrics

Understanding the behavioural ecology of endangered taxa can inform conservation strategies. The activity budgets of the loggerhead turtle Caretta caretta are still poorly understood because many tracking methods show only horizontal displacement and ignore dives and associated behaviours. However, time-depth recorders have enabled researchers to identify flat, U-shaped dives (or type 1a dives) and these are conventionally labelled as resting dives on the seabed because they involve no vertical displacement of the animal. Video- and acceleration-based studies have demonstrated this is not always true. Focusing on sea turtles nesting on the Cabo Verde archipelago, we describe a new metric derived from magnetometer data, absolute angular velocity, that integrates indices of angular rotation in the horizontal plane to infer activity. Using this metric, we evaluated the variation in putative resting behaviours during the bottom phase of type 1a dives for 5 individuals over 13 to 17 d at sea during a single inter-nesting interval (over 75 turtle d in total). We defined absolute resting within the bottom phase of type 1a dives as periods with no discernible acceleration or angular movement. Whilst absolute resting constituted a significant proportion of each turtle’s time budget for this 1a dive type, turtles allocated 16−38% of their bottom time to activity, with many dives being episodic, comprised of intermittent bouts of rest and rotational activity. This implies that previously considered resting behaviours are complex and need to be accounted for in energy budgets, particularly since energy budgets may impact conservation strategies. © The authors 2021. Open Access under Creative Commons by Attribution Licence. Use, distribution and reproduction are unrestricted. Authors and original publication must be credite

A transcriptomic analysis of Echinococcus granulosus larval stages:implications for parasite biology and host adaptation

The cestode Echinococcus granulosus--the agent of cystic echinococcosis, a zoonosis affecting humans and domestic animals worldwide--is an excellent model for the study of host-parasite cross-talk that interfaces with two mammalian hosts. To develop the molecular analysis of these interactions, we carried out an EST survey of E. granulosus larval stages. We report the salient features of this study with a focus on genes reflecting physiological adaptations of different parasite stages.We generated ~10,000 ESTs from two sets of full-length enriched libraries (derived from oligo-capped and trans-spliced cDNAs) prepared with three parasite materials: hydatid cyst wall, larval worms (protoscoleces), and pepsin/H(+)-activated protoscoleces. The ESTs were clustered into 2700 distinct gene products. In the context of the biology of E. granulosus, our analyses reveal: (i) a diverse group of abundant long non-protein coding transcripts showing homology to a middle repetitive element (EgBRep) that could either be active molecular species or represent precursors of small RNAs (like piRNAs); (ii) an up-regulation of fermentative pathways in the tissue of the cyst wall; (iii) highly expressed thiol- and selenol-dependent antioxidant enzyme targets of thioredoxin glutathione reductase, the functional hub of redox metabolism in parasitic flatworms; (iv) candidate apomucins for the external layer of the tissue-dwelling hydatid cyst, a mucin-rich structure that is critical for survival in the intermediate host; (v) a set of tetraspanins, a protein family that appears to have expanded in the cestode lineage; and (vi) a set of platyhelminth-specific gene products that may offer targets for novel pan-platyhelminth drug development.This survey has greatly increased the quality and the quantity of the molecular information on E. granulosus and constitutes a valuable resource for gene prediction on the parasite genome and for further genomic and proteomic analyses focused on cestodes and platyhelminths

Metagenomic analysis of viruses associated with maize lethal necrosis in Kenya

Background: Maize lethal necrosis is caused by a synergistic co-infection of Maize chlorotic mottle virus (MCMV) and a specific member of the Potyviridae, such as Sugarcane mosaic virus (SCMV), Wheat streak mosaic virus (WSMV) or Johnson grass mosaic virus (JGMV). Typical maize lethal necrosis symptoms include severe yellowing and leaf drying from the edges. In Kenya, we detected plants showing typical and atypical symptoms. Both groups of plants often tested negative for SCMV by ELISA. Methods: We used next-generation sequencing to identify viruses associated to maize lethal necrosis in Kenya through a metagenomics analysis. Symptomatic and asymptomatic leaf samples were collected from maize and sorghum representing sixteen counties. Results: Complete and partial genomes were assembled for MCMV, SCMV, Maize streak virus (MSV) and Maize yellow dwarf virus-RMV (MYDV-RMV). These four viruses (MCMV, SCMV, MSV and MYDV-RMV) were found together in 30 of 68 samples. A geographic analysis showed that these viruses are widely distributed in Kenya. Phylogenetic analyses of nucleotide sequences showed that MCMV, MYDV-RMV and MSV are similar to isolates from East Africa and other parts of the world. Single nucleotide polymorphism, nucleotide and polyprotein sequence alignments identified three genetically distinct groups of SCMV in Kenya. Variation mapped to sequences at the border of NIb and the coat protein. Partial genome sequences were obtained for other four potyviruses and one polerovirus. Conclusion: Our results uncover the complexity of the maize lethal necrosis epidemic in Kenya. MCMV, SCMV, MSV and MYDV-RMV are widely distributed and infect both maize and sorghum. SCMV population in Kenya is diverse and consists of numerous strains that are genetically different to isolates from other parts of the world. Several potyviruses, and possibly poleroviruses, are also involved