Genome sequencing reveals fine scale diversification and reticulation history during speciation in Sus

Background Elucidating the process of speciation requires an in-depth understanding of the evolutionary history of the species in question. Studies that rely upon a limited number of genetic loci do not always reveal actual evolutionary history, and often confuse inferences related to phylogeny and speciation. Whole-genome data, however, can overcome this issue by providing a nearly unbiased window into the patterns and processes of speciation. In order to reveal the complexity of the speciation process, we sequenced and analyzed the genomes of 10 wild pigs, representing morphologically or geographically well-defined species and subspecies of the genus Sus from insular and mainland Southeast Asia, and one African common warthog. Results Our data highlight the importance of past cyclical climatic fluctuations in facilitating the dispersal and isolation of populations, thus leading to the diversification of suids in one of the most species-rich regions of the world. Moreover, admixture analyses revealed extensive, intra- and inter-specific gene-flow that explains previous conflicting results obtained from a limited number of loci. We show that these multiple episodes of gene-flow resulted from both natural and human-mediated dispersal. Conclusions Our results demonstrate the importance of past climatic fluctuations and human mediated translocations in driving and complicating the process of speciation in island Southeast Asia. This case study demonstrates that genomics is a powerful tool to decipher the evolutionary history of a genus, and reveals the complexity of the process of speciation

Measuring Flexicurity: Precautionary Notes, a New Framework, and an Empirical Example

Recently, there has been an increase and abundance of literature measuring flexicurity across countries. However, there is yet to be any agreement on the definition of the key concepts of flexicurity as well as the framework in which to base one’s research. Due to this, the outcomes found in the existing studies are rather diverse, far from reaching a consensus, and can be misleading. This paper addresses the issues by first introducing a framework, namely, the various levels and stages of flexicurity, as well as introducing some key issues that should be addressed when doing flexicurity indicators research. In addition, an empirical example is given to show how the framework derived can be used to carry out flexicurity research, and to show how by not regarding these frameworks one can come to misleading outcomes

A monolithic integrated photonic microwave filter

[EN] Meeting the increasing demand for capacity in wireless networks requires the harnessing of higher regions in the radiofrequency spectrum, reducing cell size, as well as more compact, agile and power-efficient base stations that are capable of smoothly interfacing the radio and fibre segments. Fully functional microwave photonic chips are promising candidates in attempts to meet these goals. In recent years, many integrated microwave photonic chips have been reported in different technologies. To the best of our knowledge, none has monolithically integrated all the main active and passive optoelectronic components. Here, we report the first demonstration of a tunable microwave photonics filter that is monolithically integrated into an indium phosphide chip. The reconfigurable radiofrequency photonic filter includes all the necessary elements (for example, lasers, modulators and photodetectors), and its response can be tuned by means of control electric currents. This is an important step in demonstrating the feasibility of integrated and programmable microwave photonic processors.The authors acknowledge financial support from the Spanish Centro para el Desarrollo Tecnologico Industrial (CDTI) through the NEOTEC start-up programme, the European Commission through the 7th Research Framework Programme project, Photonic Advanced Research and Development for Integrated Generic Manufacturing (FP7-PARADIGM), the Generalitat Valenciana through the Programa para grupos de Investigacion de Excelencia (PROMETEO) project code 2013/012, the Spanish Ministerio de Economia y Comercio (MINECO) via project TEC2013-42332-P, PIF4ESP, and the Unwersitat Politecnica de Valencia (UPVOV) through projects 10-3E-492 and 08-3E-008 funded by the Fondos Europeos de Desarrollo Regional (FEDER). J.S. Fandino acknowledges financial support from Formacion de Profesorado Universitario (FPU) grant AP2010-1595.Sanchez Fandiño, JA.; Muñoz Muñoz, P.; Doménech Gómez, JD.; Capmany Francoy, J. (2017). A monolithic integrated photonic microwave filter. Nature Photonics. 11(2):124-129. https://doi.org/10.1038/NPHOTON.2016.233S124129112Novak, D. et al. Radio-over-fiber technologies for emerging wireless systems. IEEE J. Quantum Electron. 52, 1–11 (2016).Waterhouse, R. & Novak, D. Realizing 5G: microwave photonics for 5G mobile wireless systems. IEEE Microw. Mag. 16, 84–92 (2015).Won, R. Microwave photonics shines. Nat. Photon. 5, 736 (2011).Capmany, J. & Novak, D. Microwave photonics combines two worlds. Nat. Photon. 1, 319–330 (2007).Yao, J. Microwave photonics. J. Lightw. Technol. 27, 314–335 (2009).Andrews, J. G. et al. What will 5G be? IEEE J. Sel. Areas Commun. 32, 1065–1082 (2014).Gosh, A., et al. 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H. et al. Ultrabroad-bandwidth arbitrary radiofrequency waveform generation with a silicon photonic chip-based spectral shaper. Nat. Photon. 4, 117–122 (2010).Pagani, M. et al. Instantaneous frequency measurement system using four-wave mixing in an ultra-compact long silicon waveguide. In Proc. 41st European Conf. on Optical Communication (ECOC) 1–3 (IEEE, 2015).Khilo, A. et al. Photonic ADC: overcoming the bottleneck of electronic jitter. Opt. Express 20, 4454–4469 (2012).Wang, J. et al. Reconfigurable radio-frequency arbitrary waveforms synthesized in a silicon photonic chip. Nat. Commun. 6, 5957 (2015).Marpaung, D. et al. Si3N4 ring resonator-based microwave photonic notch filter with an ultrahigh peak rejection. Opt. Express 21, 23286–23294 (2013).Zhuang, L. et al. Ring resonator-based on-chip modulation transformer for high-performance phase-modulated microwave photonic links. Opt. Express 21, 25999–26013 (2013).Marpaung, D., Chevalier, L., Burla, M. & Roeloffzen, C. Impulse radio ultrawideband pulse shaper based on a programmable photonic chip frequency discriminator. Opt. Express 19, 24838–24848 (2011).Marpaung, D. On-chip photonic-assisted instantaneous microwave frequency measurement system. IEEE Photon. Technol. Lett. 25, 837–840 (2013).Burla, M. et al. On-chip CMOS compatible reconfigurable optical delay line with separate carrier tuning for microwave photonic signal processing. Opt. Express 19, 21475–21484 (2011).Tan, K. et al. Photonic-chip-based all-optical ultra-wideband pulse generation via XPM and birefringence in a chalcogenide waveguide. Opt. Express 21, 2003–2011 (2013).Pagani, M. et al. Tuneable wideband microwave photonic phase shifter using on-chip stimulated Brillouin scattering. Opt. Express 22, 28810–28818 (2014).Pérez, D., Gasulla, I. & Capmany, J. Software-defined reconfigurable microwave photonics processor. Opt. Express 23, 14640–14654 (2015).Capmany, J., Gasulla, I. & Pérez, D. 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Synchronization modulation increases transepithelial potentials in MDCK monolayers through Na/K pumps

Peer reviewedPublisher PD

UCP1 Induction during Recruitment of Brown Adipocytes in White Adipose Tissue Is Dependent on Cyclooxygenase Activity

Background The uncoupling protein 1 (UCP1) is a hallmark of brown adipocytes and pivotal for cold- and diet-induced thermogenesis. Methodology/Principal Findings Here we report that cyclooxygenase (COX) activity and prostaglandin E2 (PGE2) are crucially involved in induction of UCP1 expression in inguinal white adipocytes, but not in classic interscapular brown adipocytes. Cold-induced expression of UCP1 in inguinal white adipocytes was repressed in COX2 knockout (KO) mice and by administration of the COX inhibitor indomethacin in wild-type mice. Indomethacin repressed β-adrenergic induction of UCP1 expression in primary inguinal adipocytes. The use of PGE2 receptor antagonists implicated EP4 as a main PGE2 receptor, and injection of the stable PGE2 analog (EP3/4 agonist) 16,16 dm PGE2 induced UCP1 expression in inguinal white adipose tissue. Inhibition of COX activity attenuated diet-induced UCP1 expression and increased energy efficiency and adipose tissue mass in obesity-resistant mice kept at thermoneutrality. Conclusions/Significance Our findings provide evidence that induction of UCP1 expression in white adipose tissue, but not in classic interscapular brown adipose tissue is dependent on cyclooxygenase activity. Our results indicate that cyclooxygenase-dependent induction of UCP1 expression in white adipose tissues is important for diet-induced thermogenesis providing support for a surprising role of COX activity in the control of energy balance and obesity development

A regional Bayesian POT model for flood frequency analysis

Flood frequency analysis is usually based on the fitting of an extreme value distribution to the local streamflow series. However, when the local data series is short, frequency analysis results become unreliable. Regional frequency analysis is a convenient way to reduce the estimation uncertainty. In this work, we propose a regional Bayesian model for short record length sites. This model is less restrictive than the index flood model while preserving the formalism of "homogeneous regions". The performance of the proposed model is assessed on a set of gauging stations in France. The accuracy of quantile estimates as a function of the degree of homogeneity of the pooling group is also analysed. The results indicate that the regional Bayesian model outperforms the index flood model and local estimators. Furthermore, it seems that working with relatively large and homogeneous regions may lead to more accurate results than working with smaller and highly homogeneous regions

Somatic PIK3R1 Variation as a Cause of Vascular Malformations and Overgrowth

PurposeSomatic activating variants in the PI3K-AKT pathway cause vascular malformations with and without overgrowth. We previously reported an individual with capillary and lymphatic malformation harboring a pathogenic somatic variant in PIK3R1, which encodes three PI3K complex regulatory subunits. Here, we investigate PIK3R1 in a large cohort with vascular anomalies and identify an additional 16 individuals with somatic mosaic variants in PIK3R1.MethodsAffected tissue from individuals with vascular lesions and overgrowth recruited from a multisite collaborative network was studied. Next-generation sequencing targeting coding regions of cell-signaling and cancer-associated genes was performed followed by assessment of variant pathogenicity.ResultsThe phenotypic and variant spectrum associated with somatic variation in PIK3R1 is reported herein. Variants occurred in the inter-SH2 or N-terminal SH2 domains of all three PIK3R1 protein products. Phenotypic features overlapped those of the PIK3CA-related overgrowth spectrum (PROS). These overlapping features included mixed vascular malformations, sandal toe gap deformity with macrodactyly, lymphatic malformations, venous ectasias, and overgrowth of soft tissue or bone.ConclusionSomatic PIK3R1 variants sharing attributes with cancer-associated variants cause complex vascular malformations and overgrowth. The PIK3R1-associated phenotypic spectrum overlaps with PROS. These data extend understanding of the diverse phenotypic spectrum attributable to genetic variation in the PI3K-AKT pathway

Reaction rates and transport in neutron stars

Understanding signals from neutron stars requires knowledge about the transport inside the star. We review the transport properties and the underlying reaction rates of dense hadronic and quark matter in the crust and the core of neutron stars and point out open problems and future directions.Comment: 74 pages; commissioned for the book "Physics and Astrophysics of Neutron Stars", NewCompStar COST Action MP1304; version 3: minor changes, references updated, overview graphic added in the introduction, improvements in Sec IV.A.