Validation of the TracmorD Triaxial Accelerometer to Assess Physical Activity in Preschool Children

Objectives: To assess validity evidence of Tracmor_D to determine energy used for physical activity in 3‐4‐year‐old children. Design and Methods: Participants were randomly selected from GECKO Drenthe cohort (n = 30, age 3.4 ± 0.3 years). Total energy expenditure (TEE) was measured using the doubly labeled water method. Sleeping metabolic rate (SMR) was measured by indirect calorimetry (Deltatrac). TEE and SMR were used to calculate physical activity level (PAL) and activity energy expenditure (AEE). Physical activity was monitored using a DirectLife triaxial accelerometer, Tracmor_D with activity counts per minute (ACM) and activity counts per day (ACD) as outcome measures. Results: The best predictor for PAL was ACM with gender and weight, the best predictor for AEE was ACM alone (backward regression, R² = 0.50, P = 0.010 and R² = 0.31, P = 0.011, respectively). With ACD, the prediction model for PAL included ACD, height, gender, and sleep duration (R² = 0.48, P = 0.033), the prediction model for AEE included ACD, gender and sleep duration (R² = 0.39, P = 0.042). The accelerometer was worn for 5 days, but 3 days did not give a different estimated PAL. Conclusion: Tracmor_D provides moderate‐to‐strong validity evidence that supports its use to evaluate energy used for physical activity in 3‐4‐year‐old children.     

Taxonomic challenges in freshwater fishes: a mismatch between morphology and DNA barcoding in fish of the north‐eastern part of the Congo basin

This study evaluates the utility of DNA barcoding to traditional morphology‐based species identifications for the fish fauna of the north‐eastern Congo basin. We compared DNA sequences (COI) of 821 samples from 206 morphologically identified species. Best match, best close match and all species barcoding analyses resulted in a rather low identification success of 87.5%, 84.5% and 64.1%, respectively. The ratio ‘nearest‐neighbour distance/maximum intraspecific divergence’ was lower than 1 for 26.1% of the samples, indicating possible taxonomic problems. In ten genera, belonging to six families, the number of species inferred from mtDNA data exceeded the number of species identified using morphological features; and in four cases indications of possible synonymy were detected. Finally, the DNA barcodes confirmed previously known identification problems within certain genera of the Clariidae, Cyprinidae and Mormyridae. Our results underscore the large number of taxonomic problems lingering in the taxonomy of the fish fauna of the Congo basin and illustrate why DNA barcodes will contribute to future efforts to compile a reliable taxonomic inventory of the Congo basin fish fauna. Therefore, the obtained barcodes were deposited in the reference barcode library of the Barcode of Life Initiative.     

Short-Term Effect of Pollen and Spore Exposure on Allergy Morbidity in the Brussels-Capital Region

Belgium is among the European countries that are the most affected by allergic rhinitis. Pollen grains and fungal spores represent important triggers of symptoms. However, few studies have investigated their real link with disease morbidity over several years. Based on aeroallergen counts and health insurance datasets, the relationship between daily changes in pollen, fungal spore concentrations and daily changes in reimbursable systemic antihistamine sales has been investigated between 2005 and 2011 in the Brussels-Capital Region. A Generalized Linear Model was used and adjusted for air pollution, meteorological conditions, flu, seasonal component and day of the week. We observed an augmentation in drug sales despite no significant increase in allergen levels in the long term. The relative risk of buying allergy medications associated with an interquartile augmentation in pollen distributions increased significantly for Poaceae, Betula, Carpinus, Fraxinus and Quercus. Poaceae affected the widest age group and led to the highest increase of risk which reached 1.13 (95% CI [1.11–1.14]) among the 19- to 39-year-old men. Betula showed the second most consistent relationship across age groups. Clear identification of the provoking agents may improve disease management by customizing prevention programmes. This work also opens several research perspectives related to impact of climate modification or subpopulation sensitivity.     

A method for three-dimensional quantification of vascular smooth muscle orientation: application in viable murine carotid arteries

When studying in vivo arterial mechanical behaviour using constitutive models, smooth muscle cells (SMCs) should be considered, while they play an important role in regulating arterial vessel tone. Current constitutive models assume a strictly circumferential SMC orientation, without any dispersion. We hypothesised that SMC orientation would show considerable dispersion in three dimensions and that helical dispersion would be greater than transversal dispersion. To test these hypotheses, we developed a method to quantify the 3D orientation of arterial SMCs. Fluorescently labelled SMC nuclei of left and right carotid arteries of ten mice were imaged using two-photon laser scanning microscopy. Arteries were imaged at a range of luminal pressures. 3D image processing was used to identify individual nuclei and their orientations. SMCs showed to be arranged in two distinct layers. Orientations were quantified by fitting a Bingham distribution to the observed orientations. As hypothesised, orientation dispersion was much larger helically than transversally. With increasing luminal pressure, transversal dispersion decreased significantly, whereas helical dispersion remained unaltered. Additionally, SMC orientations showed a statistically significant (\(p < 0.05\)) mean right-handed helix angle in both left and right arteries and in both layers, which is a relevant finding from a developmental biology perspective. In conclusion, vascular SMC orientation (1) can be quantified in 3D; (2) shows considerable dispersion, predominantly in the helical direction; and (3) has a distinct right-handed helical component in both left and right carotid arteries. The obtained quantitative distribution data are instrumental for constitutive modelling of the artery wall and illustrate the merit of our method.     

How Do General Practitioners Conceptualise Advance Care Planning in Their Practice? A Qualitative Study

ObjectivesTo explore how GPs conceptualise advance care planning (ACP), based on their experiences with ACP in their practice.MethodsFive focus groups were held with 36 GPs. Discussions were analysed using a constant comparative method.ResultsFour overarching themes in the conceptualisations of ACP were discerned: (1) the organisation of professional care required to meet patients’ needs, (2) the process of preparing for death and discussing palliative care options, (3) the discussion of care goals and treatment decisions, (4) the completion of advance directives. Within these themes, ACP was both conceptualised in terms of content of ACP and/or in terms of tasks for the GP. A specific task that was mentioned throughout the discussion of the four different themes was (5) the task of actively initiating ACP by the GP versus passively waiting for patients’ initiation.ConclusionsThis study illustrates that GPs have varying conceptualisations of ACP, of which some are more limited to specific aspects of ACP. A shared conceptualisation and agreement on the purpose and goals of ACP is needed to ensure successful implementation, as well as a systematic integration of ACP in routine practice that could lead to a better uptake of all the important elements of ACP.     

Boundaries of the wolf and the wild: a conceptual examination of the relationship between rewilding and animal reintroduction

Animal reintroduction and rewilding are two widely appealing and frequently connected forms of ecological restoration. However, the critical assumption that animal reintroduction automatically helps to restore formerly wild places is under‐theorized. To fill this void, we identified three common rewilding elements from the literature—ecological functioning, wilderness experience, and natural autonomy—and screened these against a hypothetical wolf reintroduction to Scotland. Each of the rewilding elements was likely to be positively impacted by a wolf reintroduction. Yet, there is a key conceptual difficulty in that the different rewilding elements do not necessarily enforce each other, and at times may even collide. Thus, a reintroduced species like the wolf may obfuscate the clear‐cut, purified nature category to which rewilding often aspires. As a way forward, we suggest that there is merit in actively engaging with the tensions created by rewilding and reintroductions. A reconceptualisation of the nature–culture spectrum as consisting of multiple layers (e.g. ecological functioning, wilderness experience, and natural autonomy) may help to interpret ecological restoration as a tentative, deliberative, and gradual enterprise. This bears some resemblance to the notion of approaching a landscape like a ‘palimpsest’ (i.e. a text built up of different layers written on top of each other), which may support the reconciliation of conflicting views without necessarily making those disappear. When viewed as feeding into a multilayered nature–culture spectrum, animal reintroduction and rewilding can be promoted as inspiring and essentially non‐controlling forms of ecological restoration and human interaction with nature.     

GPU accelerated sequence alignment with traceback for GATK HaplotypeCaller

Background

Pairwise sequence alignment is widely used in many biological tools and applications. Existing GPU accelerated implementations mainly focus on calculating optimal alignment score and omit identifying the optimal alignment itself. In GATK HaplotypeCaller (HC), the semi-global pairwise sequence alignment with traceback has so far been difficult to accelerate effectively on GPUs.

Results

We first analyze the characteristics of the semi-global alignment with traceback in GATK HC and then propose a new algorithm that allows for retrieving the optimal alignment efficiently on GPUs. For the first stage, we choose intra-task parallelization model to calculate the position of the optimal alignment score and the backtracking matrix. Moreover, in the first stage, our GPU implementation also records the length of consecutive matches/mismatches in addition to lengths of consecutive insertions and deletions as in the CPU-based implementation. This helps efficiently retrieve the backtracking matrix to obtain the optimal alignment in the second stage.

Conclusions

Experimental results show that our alignment kernel with traceback is up to 80x and 14.14x faster than its CPU counterpart with synthetic datasets and real datasets, respectively. When integrated into GATK HC (alongside a GPU accelerated pair-HMMs forward kernel), the overall acceleration is 2.3x faster than the baseline GATK HC implementation, and 1.34x faster than the GATK HC implementation with the integrated GPU-based pair-HMMs forward algorithm. Although the methods proposed in this paper is to improve the performance of GATK HC, they can also be used in other pairwise alignments and applications.