Template Matching on Vector Fields using Clifford Algebra

Due to the amount of flow simulation and measurement data, automatic detection, classification and visualization of features is necessary for an inspection. Therefore, many automated feature detection methods have been developed in recent years. However, one feature class is visualized afterwards in most cases, and many algorithms have problems in the presence of noise or superposition effects. In contrast, image processing and computer vision have robust methods for feature extraction and computation of derivatives of scalar fields. Furthermore, interpolation and other filter can be analyzed in detail. An application of these methods to vector fields would provide a solid theoretical basis for feature extraction. The authors suggest Clifford algebra as a mathematical framework for this task. Clifford algebra provides a unified notation for scalars and vectors as well as a multiplication of all basis elements. The Clifford product of two vectors provides the complete geometric information of the relative positions of these vectors. Integration of this product results in Clifford correlation and convolution which can be used for template matching on vector fields. Furthermore, for frequency analysis of vector fields and the behavior of vector-valued filters, a Clifford Fourier transform has been derived for 2 and 3 dimensions. Convolution and other theorems have been proved, and fast algorithms for the computation of the Clifford Fourier transform exist. Therefore the computation of Clifford convolution can be accelerated by computing it in Clifford Fourier domain. Clifford convolution and Fourier transform can be used for a thorough analysis and subsequent visualization of vector field

The Value of Comparative Animal Research : Krogh’s Principle Facilitates Scientific Discoveries

There are no conflicts of interest to declare. This paper developed from the 2016 Early Career Impact Award from the Federation of Associations in Behavioral & Brain Sciences to TJS. TJS has received funding from The Leverhulme Trust. FJPE is in receipt of funding from the BBSRC (BB/M001555/1). The National Institutes of Health has funded RDF (NS 034950, NS093277, NIMH 087930), AGO (HD079573, IOS-1354760) and AMK (HD081959). BAA is an Arnold O. Beckman postdoctoral fellow.Peer reviewedPostprin

TEMPLATE MATCHING ON VECTOR FIELDS USING CLIFFORD ALGEBRA

Due to the amount of flow simulation and measurement data, automatic detection, classification and visualization of features is necessary for an inspection. Therefore, many automated feature detection methods have been developed in recent years. However, only one feature class is visualized afterwards in most cases, and many algorithms have problems in the presence of noise or superposition effects. In contrast, image processing and computer vision have robust methods for feature extraction and computation of derivatives of scalar fields. Furthermore, interpolation and other filter can be analyzed in detail. An application of these methods to vector fields would provide a solid theoretical basis for feature extraction. The authors suggest Clifford algebra as a mathematical framework for this task. Clifford algebra provides a unified notation for scalars and vectors as well as a multiplication of all basis elements. The Clifford product of two vectors provides the complete geometric information of the relative positions of these vectors. Integration of this product results in Clifford correlation and convolution which can be used for template matching of vector fields. For frequency analysis of vector fields and the behavior of vector-valued filters, a Clifford Fourier transform has been derived for 2D and 3D. Convolution and other theorems have been proved, and fast algorithms for the computation of the Clifford Fourier transform exist. Therefore the computation of Clifford convolution can be accelerated by computing it in Clifford Fourier domain. Clifford convolution and Fourier transform can be used for a thorough analysis and subsequent visualization of flow fields

Hypothalamic ventricular ependymal thyroid hormone deiodinases are an important element of circannual timing in the siberian hamster (Phodopus sungorus)

Exposure to short days (SD) induces profound changes in the physiology and behaviour of Siberian hamsters, including gonadal regression and up to 30% loss in body weight. In a continuous SD environment after approximately 20 weeks, Siberian hamsters spontaneously revert to a long day (LD) phenotype, a phenomenon referred to as the photorefractory response. Previously we have identified a number of genes that are regulated by short photoperiod in the neuropil and ventricular ependymal (VE) cells of the hypothalamus, although their importance and contribution to photoperiod induced physiology is unclear. In this refractory model we hypothesised that the return to LD physiology involves reversal of SD expression levels of key hypothalamic genes to their LD values and thereby implicate genes required for LD physiology. Male Siberian hamsters were kept in either LD or SD for up to 39 weeks during which time SD hamster body weight decreased before increasing, after more than 20 weeks, back to LD values. Brain tissue was collected between 14 and 39 weeks for in situ hybridization to determine hypothalamic gene expression. In VE cells lining the third ventricle, expression of nestin, vimentin, Crbp1 and Gpr50 were down-regulated at 18 weeks in SD photoperiod, but expression was not restored to the LD level in photorefractory hamsters. Dio2, Mct8 and Tsh-r expression were altered by SD photoperiod and were fully restored, or even exceeded values found in LD hamsters in the refractory state. In hypothalamic nuclei, expression of Srif and Mc3r mRNAs was altered at 18 weeks in SD, but were similar to LD expression values in photorefractory hamsters. We conclude that in refractory hamsters not all VE cell functions are required to establish LD physiology. However, thyroid hormone signalling from ependymal cells and reversal of neuronal gene expression appear to be essential for the SD refractory response

The Familial Clustering of Age at Menarche in Extended Twin Families

The timing of puberty is complex, possibly involving many genetic factors that may interact with environmental influences. Familial resemblance for age at menarche was studied in a sample of 4,995 female twins, 1,296 sisters, 2,946 mothers and 635 female spouses of male twins. They had indicated their age at menarche as part of a larger longitudinal survey. We assessed assortative mating for age at menarche, gene–environment interaction effects and estimated the heritability of individual differences in pubertal timing. There was significant evidence of gene–environment interaction, accounting for 1.5% of the variance. There was no indication of consistent mate assortment on age at menarche. Individual differences in age at menarche are highly heritable, with additive genetic factors explaining at least 70% of the true variation. An additional 1.5% of the variation can be explained by a genotype–environment interaction effect where environmental factors are more important in individuals genetically predisposed for late menarche

Gerald Lincoln: a man for all seasons

Gerald Anthony Lincoln died after a short illness on 15 July 2020 at the age of 75 years. Gerald was Emeritus Professor of Biological Timing at Edinburgh University and a Fellow of the Royal Society of Edinburgh. He was an outstanding scientist and naturalist who was a seminal figure in developing our understanding of the neuroendocrine mechanisms underlying seasonal rhythmicity. This review considers his life and some of his major scientific contributions to our understanding of seasonality, photoperiodism and circannual rhythmicity. It is based on a presentation at the online 2nd annual seasonality symposium (2 October 2020) that was supported financially by the Journal of Neuroendocrinology

Genome sequencing and transcriptome analyses of the Siberian hamster hypothalamus identify mechanisms for seasonal energy balance

Synthesis of triiodothyronine (T3) in the hypothalamus induces marked seasonal neuromorphology changes across taxa. How species-specific responses to T3 signaling in the CNS drive annual changes in body weight and energy balance remains uncharacterized. These experiments sequenced and annotated the Siberian hamster (Phodopus sungorus) genome, a model organism for seasonal physiology research, to facilitate the dissection of T3-dependent molecular mechanisms that govern predictable, robust, and long-term changes in body weight. Examination of the Phodopus genome, in combination with transcriptome sequencing of the hamster diencephalon under winter and summer conditions, and in vivo-targeted expression analyses confirmed that proopiomelanocortin (pomc) is a primary genomic target for the long-term T3-dependent regulation of body weight. Further in silico analyses of pomc promoter sequences revealed that thyroid hormone receptor 1β-binding motif insertions have evolved in several genera of the Cricetidae family of rodents. Finally, experimental manipulation of food availability confirmed that hypothalamic pomc mRNA expression is dependent on longer-term photoperiod cues and is unresponsive to acute, short-term food availability. These observations suggest that species-specific responses to hypothalamic T3, driven in part by the receptor-binding motif insertions in some cricetid genomes, contribute critically to the long-term regulation of energy balance and the underlying physiological and behavioral adaptations associated with the seasonal organization of behavior. © 2019 National Academy of Sciences. All rights reserved

Genome sequencing and transcriptome analyses of the Siberian hamster hypothalamus identify mechanisms for seasonal energy balance

We thank the manuscript reviewers for constructive feedback; David G. Hazlerigg, Cristina Saenz de Miera, and Valerie Simonneaux for genome sequence contributions; Nicolas Scrutton and Lindsey Duguid for expert technical assistance; and Michael Jarsulic for technical assistance on the high-performance computing clusters. This project was supported by a project research grant from The British Society for Neuroendocrinology (to T.J.S.); Grants BB/M021629/1 and BB/M001555/1 (to F.J.P.E.) from the Biotechnology and Biological Sciences Research Council, and Grants UL1-TR000430 (to T.J.S. and B.J.P.) and R01-AI067406 (to B.J.P.) from the National Institutes of Health. T.J.S. is funded by The Leverhulme Trust. The Center for Research Informatics was supported by the Biological Sciences Division at the University of Chicago with additional support provided by the Institute for Translational Medicine/Clinical and Translational award (NIH 5UL1TR002389-02) and the University of Chicago Comprehensive Cancer Center Support Grant (NIH Grant P30CA014599). The bioinformatics analysis was performed on high-performance computing clusters at the Center for Research Informatics, Biological Sciences Division. P.B. was funded by the Scottish Government Rural and Environment Science and Analytical Services Division grant to the Rowett Institute.Peer reviewedPublisher PD

The ABCD of usability testing

We introduce a methodology for tracking and auditing feedback, errors and suggestions for software packages. This short paper describes how we innovate on the evaluation mechanism, introducing an (Antecedent, Barrier, Consequence and Development) ABCD form, embedded within an eParticipation platform to enable end users to easily report on any usability issues. This methodology will be utilised to improve the STEP cloud eParticipation platform (part of the current STEP Horizon2020 project http://step4youth.eu. The platform is currently being piloted in real life contexts, with the participation of public authorities that are integrating the eParticipation platform into their regular decision-making practices. The project is involving young people, through engagement and motivation strategies and giving them a voice in Environmental decision making at the local level. The pilot evaluation aims to demonstrate how open engagement needs to be embedded within public sector processes and the usability methodology reported here will help to identify the key barriers for wide scale deployment of the platform