Real-time, multi-spectral motion artefact correction and compensation for laser speckle contrast imaging.

Laser speckle contrast imaging (LSCI) is so sensitive to motion that it can measure the movement of red blood cells. However, this extreme sensitivity to motion is also its pitfall as the clinical translation of LSCI is slowed down due to the inability to deal with motion artefacts. In this paper we study the effectiveness of a real-time, multi-spectral motion artefact correction and compensation by subduing an in vitro flow phantom and ex vivo porcine kidney to computer-controlled motion artefacts. On the in vitro flow phantom, the optical flow showed a good correlation with the total movement. This model results in a better signal-to-noise ratios for multiple imaging distances and the overestimation of perfusion was reduced. In the ex vivo kidney model, the perfusion overestimation was also reduced and we were still able to distinguish between ischemia and non-ischemia in the stabilized data whereas this was not possible in the non-stabilized data. This leads to a notably better perfusion estimation that could open the door to a multitude of new clinical applications for LSCI.

Phylogeny and classification of Odonata using targeted genomics.

Dragonflies and damselflies are a charismatic, medium-sized insect order (~6300 species) with a unique potential to approach comparative research questions. Their taxonomy and many ecological traits for a large fraction of extant species are relatively well understood. However, until now, the lack of a large-scale phylogeny based on high throughput data with the potential to connect both perspectives has precluded comparative evolutionary questions for these insects. Here, we provide an ordinal hypothesis of classification based on anchored hybrid enrichment using a total of 136 species representing 46 of the 48 families or incertae sedis, and a total of 478 target loci. Our analyses recovered the monophyly for all three suborders: Anisoptera, Anisozygoptera and Zygoptera. Although the backbone of the topology was reinforced and showed the highest support values to date, our genomic data was unable to stronglyresolve portions of the topology. In addition, a quartet sampling approach highlights the potential evolutionary scenarios that may have shaped evolutionary phylogeny (e.g., incomplete lineage sorting and introgression) of this taxon. Finally, in light of our phylogenomic reconstruction and previous morphological and molecular information we proposed an updated odonate classification and define five new families (Amanipodagrionidae fam. nov., Mesagrionidae fam. nov., Mesopodagrionidae fam. nov., Priscagrionidae fam. nov., Protolestidae fam. nov.) and reinstate another two (Rhipidolestidae stat. res., Tatocnemididae stat. res.). Additionally, we feature the problematic taxonomic groupings for examination in future studies to improve our current phylogenetic hypothesis.

A strategy for the next decade to address data deficiency in neglected biodiversity.

Measuring progress toward international biodiversity targets requires robust information on the conservation status of species, which the International Union for Conservation of Nature (IUCN) Red List of Threatened Species provides. However, data and capacity are lacking for most hyperdiverse groups, such as invertebrates, plants, and fungi, particularly in megadiverse or high-endemism regions. Conservation policies and biodiversity strategies aimed at halting biodiversity loss by 2020 need to be adapted to tackle these information shortfalls after 2020. We devised an 8-point strategy to close existing data gaps by reviving explorative field research on the distribution, abundance, and ecology of species; linking taxonomic research more closely with conservation; improving global biodiversity databases by making the submission of spatially explicit data mandatory for scientific publications; developing a global spatial database on threats to biodiversity to facilitate IUCN Red List assessments; automating preassessments by integrating distribution data and spatial threat data; building capacity in taxonomy, ecology, and biodiversity monitoring in countries with high species richness or endemism; creating species monitoring programs for lesser-known taxa; and developing sufficient funding mechanisms to reduce reliance on voluntary efforts. Implementing these strategies in the post-2020 biodiversity framework will help to overcome the lack of capacity and data regarding the conservation status of biodiversity. This will require a collaborative effort among scientists, policy makers, and conservation practitioners.

Una Estrategia para la Siguiente Década para Enfrentar la Deficiencia de Datos de la Biodiversidad Ignorada Resumen La medida del avance hacia los objetivos internacionales para la biodiversidad requiere información sólida sobre el estado de conservación de las especies, la cual proporciona la Lista Roja de Especies Amenazadas de la Unión Internacional para la Conservación de la Naturaleza (UICN). Sin embargo, los grupos más hiperdiversos, como los invertebrados, las plantas y los hongos, carecen de datos y capacidad, particularmente en regiones megadiversas o de endemismo alto. Las políticas de conservación y las estrategias de biodiversidad dirigidas hacia el cese de la pérdida de biodiversidad para el 2020 necesitan ser adaptadas para solucionar estas insuficiencias de información para después del año 2020. Diseñamos una estrategia de ocho puntos para cerrar las brechas existentes en los datos mediante la reactivación de la investigación exploratoria en el campo sobre la distribución, abundancia y ecología de las especies; la vinculación más cercana entre la investigación taxonómica y la conservación; la mejora a las bases de datos mundiales sobre biodiversidad mediante la presentación obligatoria de datos espacialmente explícitos para las publicaciones científicas; el desarrollo de una base mundial de datos espaciales sobre las amenazas para la biodiversidad para facilitar las valoraciones de la Lista Roja de la UICN; la automatización de las preevaluaciones mediante la integración de datos de distribución y datos de amenazas espaciales; el desarrollo de la capacidad en la taxonomía, la ecología y el monitoreo de la biodiversidad en países con una gran riqueza de especies o endemismos; la creación de programas de monitoreo de especies para los taxones menos conocidos; el desarrollo de suficientes mecanismos de financiamiento para reducir la dependencia de los esfuerzos voluntarios. La implementación de estas estrategias en el marco de trabajo para la biodiversidad posterior al 2020 ayudará a superar la falta de capacidad y datos con respecto al estado de conservación de la biodiversidad. Lo anterior requerirá de un esfuerzo colaborativo entre científicos, formuladores de políticas y practicantes de la conservación.

Application of laser speckle contrast imaging in laparoscopic surgery.

Anastomotic leakage is a worldwide problem in gastrointestinal surgery which seems to be related to the state of microcirculation. Laser speckle contrast imaging (LSCI) could give surgeons insight in the state of microcirculation to attune the site of anastomosis. This work studies the feasibility of LSCI as a tool for this purpose. An experimental setup was developed using a commercially available laparoscopic video system. Laser speckle contrast imaging is capable of detecting ischemic areas on the large intestine. Further research and development are required before adaptation of this technique in the operating room.

DNA barcode reference libraries for the monitoring of aquatic biota in Europe: Gap-analysis and recommendations for future work.

Effective identification of species using short DNA fragments (DNA barcoding and DNA metabarcoding) requires reliable sequence reference libraries of known taxa. Both taxonomically comprehensive coverage and content quality are important for sufficient accuracy. For aquatic ecosystems in Europe, reliable barcode reference libraries are particularly important if molecular identification tools are to be implemented in biomonitoring and reports in the context of the EU Water Framework Directive (WFD) and the Marine Strategy Framework Directive (MSFD). We analysed gaps in the two most important reference databases, Barcode of Life Data Systems (BOLD) and NCBI GenBank, with a focus on the taxa most frequently used in WFD and MSFD. Our analyses show that coverage varies strongly among taxonomic groups, and among geographic regions. In general, groups that were actively targeted in barcode projects (e.g. fish, true bugs, caddisflies and vascular plants) are well represented in the barcode libraries, while others have fewer records (e.g. marine molluscs, ascidians, and freshwater diatoms). We also found that species monitored in several countries often are represented by barcodes in reference libraries, while species monitored in a single country frequently lack sequence records. A large proportion of species (up to 50%) in several taxonomic groups are only represented by private data in BOLD. Our results have implications for the future strategy to fill existing gaps in barcode libraries, especially if DNA metabarcoding is to be used in the monitoring of European aquatic biota under the WFD and MSFD. For example, missing species relevant to monitoring in multiple countries should be prioritized for future collaborative programs. We also discuss why a strategy for quality control and quality assurance of barcode reference libraries is needed and recommend future steps to ensure full utilisation of metabarcoding in aquatic biomonitoring.

Six, not two, species of Acisoma pintail dragonfly (Odonata: Libellulidae).

The dragonfly genus Acisoma is revised based on adult male morphology and COI sequence data. Six species are recognised, including the new species A. attenboroughi sp. nov. Diagnoses and a key to males of all species and illustrations of all relevant characters are provided. A. inflatum, A. variegatum and A. trifidum are confined to continental Africa, while A. panorpoides is restricted to Asia. A. ascalaphoides is known only from threatened littoral forest fragments on the east coast of Madagascar, while A. attenboroughi is widespread across the island. The new species honours Sir David Attenborough on his 90th birthday.

Redescription of the larva of Gynacantha cylindrata Karsch (Insecta: Odonata: Aeshnidae).

The ultimate stadium larva of Gynacantha cylindrata Karsch, 1891 is described and illustrated based on fifteen male and female exuviae from Bundibugyo, Uganda. The larva resembles those of the few described African species of the genus but shows a denser coverage of spine-like setae on body surface and abundance of hair-like setae on mouthparts. The female gonapophyses appear to be the longest described in the genus up to now and similar to those of G. villosa, a species included in the same group of African species.

Comparison of Inoculation with the InoqulA and WASP Automated Systems with Manual Inoculation.

The quality of sample inoculation is critical for achieving an optimal yield of discrete colonies in both monomicrobial and polymicrobial samples to perform identification and antibiotic susceptibility testing. Consequently, we compared the performance between the InoqulA (BD Kiestra), the WASP (Copan), and manual inoculation methods. Defined mono- and polymicrobial samples of 4 bacterial species and cloudy urine specimens were inoculated on chromogenic agar by the InoqulA, the WASP, and manual methods. Images taken with ImagA (BD Kiestra) were analyzed with the VisionLab version 3.43 image analysis software to assess the quality of growth and to prevent subjective interpretation of the data. A 3- to 10-fold higher yield of discrete colonies was observed following automated inoculation with both the InoqulA and WASP systems than that with manual inoculation. The difference in performance between automated and manual inoculation was mainly observed at concentrations of >10(6) bacteria/ml. Inoculation with the InoqulA system allowed us to obtain significantly more discrete colonies than the WASP system at concentrations of >10(7) bacteria/ml. However, the level of difference observed was bacterial species dependent. Discrete colonies of bacteria present in 100- to 1,000-fold lower concentrations than the most concentrated populations in defined polymicrobial samples were not reproducibly recovered, even with the automated systems. The analysis of cloudy urine specimens showed that InoqulA inoculation provided a statistically significantly higher number of discrete colonies than that with WASP and manual inoculation. Consequently, the automated InoqulA inoculation greatly decreased the requirement for bacterial subculture and thus resulted in a significant reduction in the time to results, laboratory workload, and laboratory costs.

Quantification of the effect of oil layer thickness on entrainment of surface oil.

This study quantifies the effect of oil layer thickness on entrainment and dispersion of oil into seawater, using a plunging jet with a camera system. In contrast to what is generally assumed, we revealed that for the low viscosity "surrogate MC252 oil" we used, entrainment rate is directly proportional to layer thickness. Furthermore, the volume of stably suspended small oil droplets increases with energy input (plunge height) and is mostly proportional to layer thickness. Oil pre-treated with dispersants (dispersant-oil ratio ranges from 1:50 to 1:300) is greatly entrained in such large amounts of small droplets that quantification was impossible with the camera system. Very low interfacial tension causes entrainment by even minor secondary surface disturbances. Our results indicate that the effect of oil layer thickness should be included in oil entrainment and dispersion modelling.

Mitragomphus ganzanus Needham, 1944, a geographically misplaced dragonfly, is a junior synonym of Gomphidia kirschii Selys, 1878 (Odonata: Gomphidae).

Based on comparison of specimens and descriptions, Mitragomphus ganzanus Needham, 1944, described from Braganza [Bragança], Pará State, Brazil, and known only from the holotype, is found to be a junior synonym of Gomphidia kirschii Selys, 1878, a species from the Philippines. The monotypic genus Mitragomphus Needham, 1944, is synonymized with the genus Gomphidia Selys, 1854. 

Freshwater biodiversity and aquatic insect diversification.

Inland waters cover less than 1% of Earth's surface but harbor more than 6% of all insect species: Nearly 100,000 species from 12 orders spend one or more life stages in freshwater. Little is known about how this remarkable diversity arose, although allopatric speciation and ecological adaptation are thought to be primary mechanisms. Freshwater habitats are highly susceptible to environmental change and exhibit marked ecological gradients. Standing waters appear to harbor more dispersive species than running waters, but there is little understanding of how this fundamental ecological difference has affected diversification. In contrast to the lack of evolutionary studies, the ecology and habitat preferences of aquatic insects have been intensively studied, in part because of their widespread use as bioindicators. The combination of phylogenetics with the extensive ecological data provides a promising avenue for future research, making aquatic insects highly suitable models for the study of ecological diversification.

System integration and radiation pattern measurements of a phased array antenna employing an integrated photonic beamformer for radio astronomy applications.

In this paper we describe the system integration and the experimental demonstration of a photonically beamformed four-element receiving array antenna for radio astronomy applications. To our knowledge, the work described here is the first demonstration of the squint-free, continuously tunable beamsteering capability offered by an integrated photonic beamformer based on optical ring resonator true-time-delay units, with measured radiation patterns. The integrated beamformer is realized in a low loss, complementary metal-oxide-semiconductor (CMOS) compatible optical waveguide technology. The measurements show a wideband, continuous beamsteering operation over a steering angle of 23.5 degrees and an instantaneous bandwidth of 500 MHz limited only by the measurement setup.

Backbone and side chain NMR assignments for the intrinsically disordered cytoplasmic domain of human neuroligin-3.

Neuroligins act as heterophilic adhesion molecules at neuronal synapses. Their cytoplasmic domains interact with synaptic scaffolding proteins, and have been shown to be intrinsically disordered. Here we report the backbone and side chain (1)H, (13)C and (15)N resonance assignments for the cytoplasmic domain of human neuroligin 3.