Label-free cell segmentation of diverse lymphoid tissues in 2D and 3D

Unlocking and quantifying fundamental biological processes through tissue microscopy requires accurate, in situ segmentation of all cells imaged. Currently, achieving this is complex and requires exogenous fluorescent labels that occupy significant spectral bandwidth, increasing the duration and complexity of imaging experiments while limiting the number of channels remaining to address the study’s objectives. We demonstrate that the excitation light reflected during routine confocal microscopy contains sufficient information to achieve accurate, label-free cell segmentation in 2D and 3D. This is achieved using a simple convolutional neural network trained to predict the probability that reflected light pixels belong to either nucleus, cytoskeleton, or background classifications. We demonstrate the approach across diverse lymphoid tissues and provide video tutorials demonstrating deployment in Python and MATLAB or via standalone software for Windows

What do UK academics cite? An analysis of references cited in UK scholarly outputs

This study used a bibliometric method to find quantitative evidence of publication and citing patterns within UK academia. The publications of a random sample of UK research—active academics for each of the years 2003 and 2008—were collected and analysed to gather data regarding referencing practices, along with any identifiable trends between the 2 years. References were categorised by type of material to show the proportions of each type used. Comparisons between the 2 years showed that the use of journal articles had increased. There was also an increase in the average number of publications per author. A large number of authors had no publications in the target year

The origin of heterogeneous nanoparticle uptake by cells

Understanding nanoparticle uptake by biological cells is fundamentally important to wide-ranging fields from nanotoxicology to drug delivery. It is now accepted that the arrival of nanoparticles at the cell is an extremely complicated process, shaped by many factors including unique nanoparticle physico-chemical characteristics, protein-particle interactions and subsequent agglomeration, diffusion and sedimentation. Sequentially, the nanoparticle internalisation process itself is also complex, and controlled by multiple aspects of a cell’s state. Despite this multitude of factors, here we demonstrate that the statistical distribution of the nanoparticle dose per endosome is independent of the initial administered dose and exposure duration. Rather, it is the number of nanoparticle containing endosomes that are dependent on these initial dosing conditions. These observations explain the heterogeneity of nanoparticle delivery at the cellular level and allow the derivation of simple, yet powerful probabilistic distributions that accurately predict the nanoparticle dose delivered to individual cells across a population.J.W.W. would like to acknowledge Girton College and the Herchel Smith Fund of Cambridge for providing him with a post-doctoral Fellowship. The authors are grateful to J.J. Powell and S. H. Doak for their critical insights. This work was supported by the Engineering and Physical Sciences Research Council (EPSRC) (grant number EP/H008683/1). P.R. and H.D.S. would also like to acknowledge the support of the Biotechnology and Biological Sciences Research Council (BBSRC) under grants BB/N005163/1 and BB/P026818/1

Physical activity, motor competence and movement and gait quality: A principal component analysis

ObjectiveWhile novel analytical methods have been used to examine movement behaviours, to date, no studies have examined whether a frequency-based measure, such a spectral purity, is useful in explaining key facets of human movement. The aim of this study was to investigate movement and gait quality, physical activity and motor competence using principal component analysis.MethodsSixty-five children (38 boys, 4.3 ± 0.7y, 1.04 ± 0.05 m, 17.8 ± 3.2 kg, BMI; 16.2 ± 1.9 kg∙m2) took part in this study. Measures included accelerometer-derived physical activity and movement quality (spectral purity), motor competence (Movement Assessment Battery for Children 2nd edition; MABC2), height, weight and waist circumference. All data were subjected to a principal component analysis, and the internal consistency of resultant components were assessed using Cronbach's alpha.ResultsTwo principal components, with excellent internal consistency (Cronbach α >0.9) were found; the 1st principal component, termed “movement component”, contained spectral purity, traffic light MABC2 score, fine motor% and gross motor% (α = 0.93); the 2nd principal component, termed “anthropometric component”, contained weight, BMI, BMI% and body fat% (α = 0.91).ConclusionThe results of the present study demonstrate that accelerometric analyses can be used to assess motor competence in an automated manner, and that spectral purity is a meaningful, indicative, metric related to children's movement quality

Profiling Movement Quality Characteristics of Children (9-11y) During Recess

Introduction. Frequency spectrum characteristics derived from raw accelerometry, such as spectral purity, have the potential to reveal detailed information about children’s movement quality, but remain unexplored in children’s physical activity. The aim of this study was to investigate and profile children’s recess physical activity and movement quality using a novel analytical approach. Materials and Methods. A powered sample of twenty-four children (18 boys) (10.5±0.6y, 1.44±0.09m, 39.6±9.5kg, body mass index; 18.8±3.1 kg.m2) wore an ankle-mounted accelerometer during school recess, for one school-week. Hierarchical clustering, Spearman’s rho and the Mann-Whitney U test were used to assess relationships between characteristics, and to assess inter-day differences. Results. There were no significant inter-day differences found for overall activity (P>0.05), yet significant differences were found for spectral purity derived movement quality (P 0.05), sin embargo, se encontraron diferencias significativas para la calidad del movimiento derivado de la pureza espectral (P <0.001). La actividad global se agrupó jerárquicamente y se correlacionó positivamente con la pureza espectral (P <0,05). Discusión. Este es el primer estudio que informa la pureza espectral de la calidad del movimiento derivado de la actividad física de los niños, en un entorno no controlado y nuestros resultados destacan el potencial para la investigación futura

Water quality study of the Muchea livestock truck wash

Across Australia there is a lack of information on the quality of the water discharged from facilities that are used to wash livestock trucks. This water quality scoping study partially fills that information gap and provides a starting point for future planning, design and construction of livestock truck washes. The study was undertaken in 2011–12 at the Western Australian Muchea Livestock Centre, and aimed to gain insights into water quality associated with the truck wash facility at that site. These insights can help to inform the planning for further construction of truck wash facilities throughout the state, and whether disposing wastewater to Water Corporation’s sewerage system could be part of a new facility. We examined water quality at primary points of the wastewater treatment system to understand the impact of each part of the system and determine the most appropriate site for detailed temporal monitoring. This was followed by a two-day sampling program at one point in the treatment system. We concluded that the minimum infrastructure requirements to satisfy Water Corporation’s maximum allowable limits for disposal to the sewerage system include sieve bend screens (Hunter screens), an anaerobic or settling pond, and a holding pond to ensure sufficient safety margins if sewer disposal was ever delayed. We recommend that further consideration is given to estimating the capital and operational costs of a truck wash facility that meets these minimum requirements, compared to a closed system that retains all wastewater on-site, or other systems that recover nutrients from high-value products. We also recommend that a sampling program be conducted across all truck washes in WA to gain insight into possible geographical variations and the wider applicability of this study’s findings