Character-based DNA barcoding allows discrimination of genera, species and populations in Odonata

© 2007 The Author et al. This is an open-access article distributed under the terms of the Creative Commons 2.5 Attribution License. The definitive version was published in Proceedings of The Royal Society B 275 (2008): 237-247, doi:10.1098/rspb.2007.1290.DNA barcoding has become a promising means for identifying organisms of all life stages. Currently, phenetic approaches and tree-building methods have been used to define species boundaries and discover 'cryptic species'. However, a universal threshold of genetic distance values to distinguish taxonomic groups cannot be determined. As an alternative, DNA barcoding approaches can be 'character based', whereby species are identified through the presence or absence of discrete nucleotide substitutions (character states) within a DNA sequence. We demonstrate the potential of character-based DNA barcodes by analysing 833 odonate specimens from 103 localities belonging to 64 species. A total of 54 species and 22 genera could be discriminated reliably through unique combinations of character states within only one mitochondrial gene region (NADH dehydrogenase 1). Character-based DNA barcodes were further successfully established at a population level discriminating seven population-specific entities out of a total of 19 populations belonging to three species. Thus, for the first time, DNA barcodes have been found to identify entities below the species level that may constitute separate conservation units or even species units. Our findings suggest that character-based DNA barcoding can be a rapid and reliable means for (i) the assignment of unknown specimens to a taxonomic group, (ii) the exploration of diagnosability of conservation units, and (iii) complementing taxonomic identification systems.The work was supported by the Federal Government Research Program (BMBF) BIOTA South Africa (S08) and the German Science Foundation (DFG) Special Priority Program 'Deep Metazoan Phylogeny' SP1174 (DFG HA 1947/5-1 and 5-2); grants given to the last author

Low-Complexity 3D-DWT video encoder applicable to IPTV

3D-DWT encoders are good candidates for applications like professional video editing, IPTV video surveillance, live event IPTV broadcast, multispectral satellite imaging, HQ video delivery, etc., where a frame must be reconstructed as fast as possible. However, the main drawback of the algorithms that compute the 3D-DWT is the huge memory requirement in practical implementations. In this paper, and in order to considerably reduce the memory requirements of this kind of video encoders, we present a new 3D-DWT video encoder based on (a) the use of a novel frame-based 3D-DWT transform that avoids video sequence partitioning in Groups Of Pictures (GOP) and (b) a very fast run-length encoder. Furthermore, an exhaustive evaluation of the proposed encoder (3D-RLW) has been performed, analyzing the sensibility of the ¿lters employed in the 3D-DWT transform and comparing the evaluation results with other video encoders in terms of R/D, coding/decoding delay and memory consumptionThanks to Spanish Ministry of Education and Science under grants DPI2007-66796-C03-03 for funding.López ., O.; Piñol ., P.; Martinez Rach, MO.; Perez Malumbres, MJ.; Oliver Gil, JS. (2011). Low-Complexity 3D-DWT video encoder applicable to IPTV. Signal Processing: Image Communication. 26(7):358-369. https://doi.org/10.1016/j.image.2011.01.008S35836926

Rate-control algorithms for non-embedded wavelet-based image coding

During the last decade, there has been an increasing interest in the design of very fast wavelet image encoders focused on specific applications like interactive real-time image and video systems, running on power-constrained devices such as digital cameras, mobile phones where coding delay and/or available computing resources (working memory and power processing) are critical for proper operation. In order to reduce complexity, most of these fast wavelet image encoders are non-(SNR)-embedded and as a consequence, precise rate control is not supported. In this work, we propose some simple rate control algorithms for these kind of encoders and we analyze their impact to determine if, despite their inclusion, the global encoder is still competitive with respect to popular embedded encoders like SPIHT and JPEG2000. In this study we focus on the non-embedded LTW encoder, showing that the increase in complexity due to the rate control algorithm inclusion, maintains LTW competitive with respect to SPIHT and JPEG2000 in terms of R/D performance, coding delay and memory consumption. © Springer Science+Business Media, LLC 2011This work was funded by Spanish Ministry of education and Science under grant DPI2007-66796-C03-03.Lopez Granado, OM.; Onofre Martinez-Rach, M.; Pinol Peral, P.; Oliver Gil, JS.; Perez Malumbres, MJ. (2012). Rate-control algorithms for non-embedded wavelet-based image coding. Journal of Signal Processing Systems. 68(2):203-216. https://doi.org/10.1007/s11265-011-0598-6S203216682Antonini, M., Barlaud, M., Mathieu, P., & Daubechies, I. (1992). Image coding using wavelet transform. IEEE Transaction on Image Processing, 1(2), 205–220.Cho, Y., & Pearlman, W.A. (2007). Hierarchical dynamic range coding of wavelet subbands for fast and efficient image compression. IEEE Transactions on Image Processing, 16, 2005–2015.Chrysafis, C., Said, A., Drukarev, A., Islam, A., & Pearlman, W. (2000). SBHP—A low complexity wavelet coder. In IEEE international conference on acoustics, speech and signal processing.CIPR: http://www.cipr.rpi.edu/resource/stills/kodak.html . Center for Image Processing Research.Davis, P. J. (1975) Interpolation and approximation. Dover Publications.Grottke, S., Richter, T., & Seiler, R. (2006). Apriori rate allocation in wavelet-based image compression. In Second international conference on automated production of cross media content for multi-channel distribution, 2006. AXMEDIS ’06 (pp. 329–336). doi: 10.1109/AXMEDIS.2006.12 .Guo, J., Mitra, S., Nutter, B., & Karp, T. (2006). Backward coding of wavelet trees with fine-grained bitrate control. Journal of Computers, 1(4), 1–7. doi: 10.4304/jcp.1.4.1-7 .ISO/IEC 10918-1/ITU-T Recommendation T.81 (1992). Digital compression and coding of continuous-tone still image.ISO/IEC 15444-1 (2000). JPEG2000 image coding system.Kakadu, S. (2006). http://www.kakadusoftware.com .Kasner, J., Marcellin, M., & Hunt, B. (1999). Universal trellis coded quantization. IEEE Transactions on Image Processing, 8(12), 1677–1687. doi: 10.1109/83.806615 .Lancaster, P. (1986). Curve and surface fitting: An introduction. Academic Press.Oliver, J., & Malumbres, M. (2001). A new fast lower-tree wavelet image encoder. In Proceedings of international conference on image processing, 2001 (Vol. 3, pp. 780–783). doi: 10.1109/ICIP.2001.958236 .Oliver, J., & Malumbres, M. P. (2006). Low-complexity multiresolution image compression using wavelet lower trees. IEEE Transactions on Circuits and Systems for Video Technology, 16(11), 1437–1444.Pearlman, W. A. (2001). Trends of tree-based, set partitioning compression techniques in still and moving image systems. In Picture coding symposium.Said, A., & Pearlman, A. (1996). A new, fast and efficient image codec based on set partitioning in hierarchical trees. IEEE Transactions on Circuits, Systems and Video Technology, 6(3), 243–250.Table Curve 3D 3.0 (1998). http://www.systat.com. Systat Software Inc.Wu, X. (2001). The transform and data compression handbook, chap. Compression of wavelet transform coefficients, (pp. 347–378). CRC Press.Zhidkov, N., & Kobelkov, G. (1987). Numerical methods. Moscow: Nauka

Using linear and natural cubic splines, SITAR, and latent trajectory models to characterise nonlinear longitudinal growth trajectories in cohort studies

BACKGROUND: Longitudinal data analysis can improve our understanding of the influences on health trajectories across the life-course. There are a variety of statistical models which can be used, and their fitting and interpretation can be complex, particularly where there is a nonlinear trajectory. Our aim was to provide an accessible guide along with applied examples to using four sophisticated modelling procedures for describing nonlinear growth trajectories. METHODS: This expository paper provides an illustrative guide to summarising nonlinear growth trajectories for repeatedly measured continuous outcomes using (i) linear spline and (ii) natural cubic spline linear mixed-effects (LME) models, (iii) Super Imposition by Translation and Rotation (SITAR) nonlinear mixed effects models, and (iv) latent trajectory models. The underlying model for each approach, their similarities and differences, and their advantages and disadvantages are described. Their application and correct interpretation of their results is illustrated by analysing repeated bone mass measures to characterise bone growth patterns and their sex differences in three cohort studies from the UK, USA, and Canada comprising 8500 individuals and 37,000 measurements from ages 5–40 years. Recommendations for choosing a modelling approach are provided along with a discussion and signposting on further modelling extensions for analysing trajectory exposures and outcomes, and multiple cohorts. RESULTS: Linear and natural cubic spline LME models and SITAR provided similar summary of the mean bone growth trajectory and growth velocity, and the sex differences in growth patterns. Growth velocity (in grams/year) peaked during adolescence, and peaked earlier in females than males e.g., mean age at peak bone mineral content accrual from multicohort SITAR models was 12.2 years in females and 13.9 years in males. Latent trajectory models (with trajectory shapes estimated using a natural cubic spline) identified up to four subgroups of individuals with distinct trajectories throughout adolescence. CONCLUSIONS: LME models with linear and natural cubic splines, SITAR, and latent trajectory models are useful for describing nonlinear growth trajectories, and these methods can be adapted for other complex traits. Choice of method depends on the research aims, complexity of the trajectory, and available data. Scripts and synthetic datasets are provided for readers to replicate trajectory modelling and visualisation using the R statistical computing software. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12874-022-01542-8

The Global Genome Biodiversity Network (GGBN) Data Standard specification

© The Author(s) 2016. Published by Oxford University Press. Page 1 of 11 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. The article attached is the publisher's pdf

Electrophysiological Evidence of Atypical Spatial Attention in Those with a High Level of Self-reported Autistic Traits

Selective attention is atypical in individuals with autism spectrum conditions. Evidence suggests this is also the case for those with high levels of autistic traits. Here we investigated the neural basis of spatial attention in those with high and low levels of self-reported autistic traits via analysis of ERP deflections associated with covert attention, target selection and distractor suppression (the N2pc, NT and PD). Larger N2pc and smaller PD amplitude was observed in those with high levels of autistic traits. These data provide neural evidence for differences in spatial attention, specifically, reduced distractor suppression in those with high levels of autistic traits, and may provide insight into the experience of perceptual overload often reported by individuals on the autism spectrum

Microbial production of long-chain n-alkanes: Implication for interpreting sedimentary leaf wax signals

Relative distributions as well as compound-specific carbon and hydrogen isotope ratios of long-chain C-25 to C-33 n-alkanes in sediments provide important paleoclimate and paleoenvironmental information. These compounds in aquatic sediments are generally attributed to leaf waxes produced by higher plants. However, whether microbes, such as fungi and bacteria, can make a significant contribution to sedimentary long-chain n-alkanes is uncertain, with only scattered reports in the early 1960s to 1970s that microbes can produce long-chain n-alkanes. Given the rapidly expanding importance of leaf waxes in paleoclimate and paleoenvironmental studies, the impact of microbial contribution to long-chain n-alkanes in sediments must be fully addressed. In this study, we performed laboratory incubation of peat-land soils under both anaerobic and aerobic conditions in the absence of light with deuterium-enriched water over 1.5 years and analyzed compound-specific hydrogen isotopic ratios of n-alkanes. Under aerobic conditions, we find n-alkanes of different chain length display variable degrees of hydrogen isotopic enrichments, with short-chain (C-18-C-21) n-alkanes showing the greatest enrichment, followed by long-chain "leaf wax" (C-27-C-31) n-alkanes, and minimal or no enrichment for mid-chain (C-22-C-25) n-alkanes. In contrast, only the shorter chain (C-18 and C-19) n-alkanes display appreciable isotopic enrichment under anaerobic conditions. The degrees of isotopic enrichment for individual n-alkanes allow for a quantitative assessment of microbial contributions to n-alkanes. Overall our results show the microbial contribution to long-chain n-alkanes can reach up to 0.1% per year in aerobic conditions. For shorter chain n-alkanes, up to 2.5% per year could be produced by microbes in aerobic and anaerobic conditions respectively. Our results indicate that prolonged exposure to aerobic conditions can lead to substantial accumulation of microbially derived long-chain n-alkanes in sediments while original n-alkanes of leaf wax origin are degraded; hence caution must be exercised when interpreting sedimentary records of long-chain n-alkanes, including chain length distributions and isotopic ratios. (c) 2017 Elsevier Ltd. All rights reserved

Portable single-beam cesium zero-field magnetometer for magnetocardiography

Optically pumped magnetometers (OPMs) are becoming common in the realm of biomagnetic measurements. We discuss the development of a prototype zero-field cesium portable OPM and its miniaturized components. Zero-field sensors operate in a very low static magnetic field environment and exploit physical effects in this regime. OPMs of this type are extremely sensitive to small magnetic fields, but they bring specific challenges to component design, material choice, and current routing. The miniaturized cesium atomic vapor cell within this sensor has been produced through integrated microfabrication techniques. The cell must be heated to 120°C for effective sensing, while the sensor external faces must be skin safe ≤40 ° C making it suitable for use in biomagnetic measurements. We demonstrate a heating system that results in a stable outer package temperature of 36°C after 1.5 h of 120°C cell heating. This relatively cool package temperature enables safe operation on human subjects which is particularly important in the use of multi-sensor arrays. Biplanar printed circuit board coils are presented that produce a reliable homogeneous field along three axes, compensating residual fields and occupying only a small volume within the sensor. The performance of the prototype portable sensor is characterized through a measured sensitivity of 90 fT / Hz in the 5 to 20 Hz frequency band and demonstrated through the measurement of a cardiac magnetic signal

Portable single-beam cesium zero-field magnetometer for magnetocardiography

Optically pumped magnetometers (OPMs) are becoming common in the realm of biomagnetic measurements. We discuss the development of a prototype zero-field cesium portable OPM and its miniaturized components. Zero-field sensors operate in a very low static magnetic field environment and exploit physical effects in this regime. OPMs of this type are extremely sensitive to small magnetic fields, but they bring specific challenges to component design, material choice, and current routing. The miniaturized cesium atomic vapor cell within this sensor has been produced through integrated microfabrication techniques. The cell must be heated to 120°C for effective sensing, while the sensor external faces must be skin safe ≤40°C making it suitable for use in biomagnetic measurements. We demonstrate a heating system that results in a stable outer package temperature of 36°C after 1.5 h of 120°C cell heating. This relatively cool package temperature enables safe operation on human subjects which is particularly important in the use of multi-sensor arrays. Biplanar printed circuit board coils are presented that produce a reliable homogeneous field along three axes, compensating residual fields and occupying only a small volume within the sensor. The performance of the prototype portable sensor is characterized through a measured sensitivity of 90 fT / Hz in the 5 to 20 Hz frequency band and demonstrated through the measurement of a cardiac magnetic signal