Postglacial expansion of the arctic keystone copepod calanus glacialis

Calanus glacialis, a major contributor to zooplankton biomass in the Arctic shelf seas, is a key link between primary production and higher trophic levels that may be sensitive to climate warming. The aim of this study was to explore genetic variation in contemporary populations of this species to infer possible changes during the Quaternary period, and to assess its population structure in both space and time. Calanus glacialis was sampled in the fjords of Spitsbergen (Hornsund and Kongsfjorden) in 2003, 2004, 2006, 2009 and 2012. The sequence of a mitochondrial marker, belonging to the ND5 gene, selected for the study was 1249 base pairs long and distinguished 75 unique haplotypes among 140 individuals that formed three main clades. There was no detectable pattern in the distribution of haplotypes by geographic distance or over time. Interestingly, a Bayesian skyline plot suggested that a 1000-fold increase in population size occurred approximately 10,000 years before present, suggesting a species expansion after the Last Glacial Maximum.GAME from the National Science Centre, the Polish Ministry of Science and Higher Education Iuventus Plus [IP2014 050573]; FCT-PT [CCMAR/Multi/04326/2013]; [2011/03/B/NZ8/02876

The Effect of Fractal Contact Lenses on Peripheral Refraction in Myopic Model Eyes

Purpose: To test multizone contact lenses in model eyes: Fractal Contact Lenses (FCLs), designed to induce myopic peripheral refractive error (PRE). Methods: Zemax ray-tracing software was employed to simulate myopic and accommodation-dependent model eyes fitted with FCLs. PRE, defined in terms of mean sphere M and 90–180 astigmatism J180, was computed at different peripheral positions, ranging from 0 to 35 in steps of 5, and for different pupil diameters (PDs). Simulated visual performance and changes in the PRE were also analyzed for contact lens decentration and model eye accommodation. For comparison purposes, the same simulations were performed with another commercially available contact lens designed for the same intended use: the Dual Focus (DF). Results: PRE was greater with FCL than with DF when both designs were tested for a 3.5 mm PD, and with and without decentration of the lenses. However, PRE depended on PD with both multizone lenses, with a remarkable reduction of the myopic relative effect for a PD of 5.5 mm. The myopic PRE with contact lenses decreased as the myopic refractive error increased, but this could be compensated by increasing the power of treatment zones. A peripheral myopic shift was also induced by the FCLs in the accommodated model eye. In regard to visual performance, a myopia under-correction with reference to the circle of least confusion was obtained in all cases for a 5.5 mm PD. The ghost images, generated by treatment zones of FCL, were dimmer than the ones produced with DF lens of the same power. Conclusions: FCLs produce a peripheral myopic defocus without compromising central vision in photopic conditions. FCLs have several design parameters that can be varied to obtain optimum results: lens diameter, number of zones, addition and asphericity; resulting in a very promising customized lens for the treatment of myopia progression.This research was supported by the Ministerio de Economia y Competitividad (grant FIS2011-23175), the Generalitat Valenciana (grant PROMETEO2009-077) and the Universitat Politecnica de Valencia (grant INNOVA SP20120569), Spain.Rodríguez Vallejo, M.; Benlloch Fornés, JI.; Pons Martí, A.; Monsoriu Serra, JA.; Furlan, WD. (2014). The Effect of Fractal Contact Lenses on Peripheral Refraction in Myopic Model Eyes. Current Eye Research. 39(12):1-10. https://doi.org/10.3109/02713683.2014.903498S110391

The mediating role of shared flow and perceived emotional synchrony on compassion for others in a mindful-dancing program

While there is a growing understanding of the relationship between mindfulness and compassion, this largely relates to the form of mindfulness employed in first-generation mindfulness-based interventions such as Mindfulness-Based Stress Reduction. Consequently, there is limited knowledge of the relationship between mindfulness and compassion in respect of the type of mindfulness employed in second-generation mindfulness-based interventions (SG-MBIs), including those that employ the principle of working harmoniously as a “secular sangha.” Understanding this relationship is important because research indicates that perceived emotional synchrony (PES) and shared flow—that often arise during participation in harmonized group contemplative activities—can enhance outcomes relating to compassion, subjective well-being, and group identity fusion. This pilot study analyzed the effects of participation in a mindful-dancing SG-MBI on compassion and investigated the mediating role of shared flow and PES. A total of 130 participants were enrolled into the study that followed a quasi-experimental design with an intervention and control group. Results confirmed the salutary effect of participating in a collective mindful-dancing program, and demonstrated that shared flow and PES fully meditated the effects of collective mindfulness on the kindness and common humanity dimensions of compassion. Further research is warranted to explore whether collective mindfulness approaches, such as mindful dancing, may be a means of enhancing compassion and subjective well-being outcomes due to the mediating role of PES and shared flow.N/

Genomic Characterization and High Prevalence of Bocaviruses in Swine

Using random PCR amplification followed by plasmid subcloning and DNA sequencing, we detected bocavirus related sequences in 9 out of 17 porcine stool samples. Using primer walking, we sequenced the nearly complete genomes of two highly divergent bocaviruses we provisionally named porcine bocavirus 1 isolate H18 (PBoV1-H18) and porcine bocavirus 2 isolate A6 (PBoV2-A6) which differed by 51.8% in their NS1 protein. Phylogenetic analysis indicated that PBoV1-H18 was very closely related to a ∼2 Kb central region of a porcine bocavirus-like virus (PBo-LikeV) from Sweden described in 2009. PBoV2-A6 was very closely related to the porcine bocavirus genomes PBoV-1 and PBoV2 from China described in 2010. Among 340 fecal samples collected from different age, asymptomatic swine in five Chinese provinces, the prevalence of PBoV1-H18 and PBoV2-A6 related viruses were 45–75% and 55–70% respectively, with 30–47% of pigs co-infected. PBoV1-A6 related strains were highly conserved, while PBoV2-H18 related strains were more diverse, grouping into two genotypes corresponding to the previously described PBoV1 and PBoV2. Together with the recently described partial bocavirus genomes labeled V6 and V7, a total of three major porcine bocavirus clades have therefore been described to date. Further studies will be required to elucidate the possible pathogenic impact of these diverse bocaviruses either alone or in combination with other porcine viruses

A community perspective on the concept of marine holobionts: Current status, challenges, and future directions

Host-microbe interactions play crucial roles in marine ecosystems. However, we still have very little understanding of the mechanisms that govern these relationships, the evolutionary processes that shape them, and their ecological consequences. The holobiont concept is a renewed paradigm in biology that can help to describe and understand these complex systems. It posits that a host and its associated microbiota with which it interacts, form a holobiont, and have to be studied together as a coherent biological and functional unit to understand its biology, ecology, and evolution. Here we discuss critical concepts and opportunities in marine holobiont research and identify key challenges in the field. We highlight the potential economic, sociological, and environmental impacts of the holobiont concept in marine biological, evolutionary, and environmental sciences. Given the connectivity and the unexplored biodiversity specific to marine ecosystems, a deeper understanding of such complex systems requires further technological and conceptual advances, e.g., the development of controlled experimental model systems for holobionts from all major lineages and the modeling of (info)chemical-mediated interactions between organisms. Here we propose that one significant challenge is to bridge cross-disciplinary research on tractable model systems in order to address key ecological and evolutionary questions. This first step is crucial to decipher the main drivers of the dynamics and evolution of holobionts and to account for the holobiont concept in applied areas, such as the conservation, management, and exploitation of marine ecosystems and resources, where practical solutions to predict and mitigate the impact of human activities are more important than ever

Quantitative image analysis for the characterization of microbial aggregates in biological wastewater treatment : a review

Quantitative image analysis techniques have gained an undeniable role in several fields of research during the last decade. In the field of biological wastewater treatment (WWT) processes, several computer applications have been developed for monitoring microbial entities, either as individual cells or in different types of aggregates. New descriptors have been defined that are more reliable, objective, and useful than the subjective and time-consuming parameters classically used to monitor biological WWT processes. Examples of this application include the objective prediction of filamentous bulking, known to be one of the most problematic phenomena occurring in activated sludge technology. It also demonstrated its usefulness in classifying protozoa and metazoa populations. In high-rate anaerobic processes, based on granular sludge, aggregation times and fragmentation phenomena could be detected during critical events, e.g., toxic and organic overloads. Currently, the major efforts and needs are in the development of quantitative image analysis techniques focusing on its application coupled with stained samples, either by classical or fluorescent-based techniques. The use of quantitative morphological parameters in process control and online applications is also being investigated. This work reviews the major advances of quantitative image analysis applied to biological WWT processes.The authors acknowledge the financial support to the project PTDC/EBB-EBI/103147/2008 and the grant SFRH/BPD/48962/2008 provided by Fundacao para a Ciencia e Tecnologia (Portugal)

A922 Sequential measurement of 1 hour creatinine clearance (1-CRCL) in critically ill patients at risk of acute kidney injury (AKI)

Meeting abstrac

Pan-cancer analysis of whole genomes

Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale(1-3). Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4-5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter(4); identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation(5,6); analyses timings and patterns of tumour evolution(7); describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity(8,9); and evaluates a range of more-specialized features of cancer genomes(8,10-18).Peer reviewe

Turbulent separated shear flow control by surface plasma actuator: experimental optimization by genetic algorithm approach

The final publication is available at Springer via http://dx.doi.org/10.1007/s00348-015-2107-3The potential benefits of active flow control are no more debated. Among many others applications, flow control provides an effective mean for manipulating turbulent separated flows. Here, a nonthermal surface plasma discharge (dielectric barrier discharge) is installed at the step corner of a backward-facing step (U0 = 15 m/s, Reh = 30,000, Re¿ = 1650). Wall pressure sensors are used to estimate the reattaching location downstream of the step (objective function #1) and also to measure the wall pressure fluctuation coefficients (objective function #2). An autonomous multi-variable optimization by genetic algorithm is implemented in an experiment for optimizing simultaneously the voltage amplitude, the burst frequency and the duty cycle of the high-voltage signal producing the surface plasma discharge. The single-objective optimization problems concern alternatively the minimization of the objective function #1 and the maximization of the objective function #2. The present paper demonstrates that when coupled with the plasma actuator and the wall pressure sensors, the genetic algorithm can find the optimum forcing conditions in only a few generations. At the end of the iterative search process, the minimum reattaching position is achieved by forcing the flow at the shear layer mode where a large spreading rate is obtained by increasing the periodicity of the vortex street and by enhancing the vortex pairing process. The objective function #2 is maximized for an actuation at half the shear layer mode. In this specific forcing mode, time-resolved PIV shows that the vortex pairing is reduced and that the strong fluctuations of the wall pressure coefficients result from the periodic passages of flow structures whose size corresponds to the height of the step model.Peer ReviewedPostprint (author's final draft

The impact of natural resource use on bird and reptile communities within multiple-use protected areas: evidence from sub-arid southern Madagascar

Multiple-use protected areas, in which sustainable levels of extractive livelihood activities are permitted, play an increasingly important role in the global protected area estate, and are expected to rise in prevalence. However, we know little about their effectiveness at conserving biodiversity. We surveyed bird and reptile communities in three areas across a forest disturbance gradient resulting from charcoal production and shifting cultivation within a multiple-use protected area in Madagascar’s sub-arid spiny forest. We scored individual species using a Conservation Value Index (CVI; a simple metric based on rarity, threat and distinctiveness), and estimated the total conservation value of each treatment by calculating the sum of frequency-weighted CVI scores across all present species. Bird and reptile community responses to forest disturbance were idiosyncratic. Bird richness was greatest in the moderate-disturbance treatment, but the low-disturbance treatment had the superior conservation value due to higher frequencies of locally-endemic species. Reptile richness was the same in low- and moderate-disturbance treatments, but the conservation value of the latter was greater. The high-disturbance areas had lowest richness and conservation value for both groups. For birds, increasing disturbance levels were accompanied by community turnover from high-value to low-value species, a pattern highlighted by CVI that is masked by assessing species richness alone. Although some endemic species appear to be resilient to degradation, multiple-use protected areas in Madagascar may lose biodiversity since most endemic species are forest-dependent. Stricter protected area models may be more appropriate in areas where much of the high-value biodiversity is sensitive to habitat degradation