Shotgun Mitogenomics Provides a Reference Phylogenetic Framework and Timescale for Living Xenarthrans

Xenarthra (armadillos, sloths, and anteaters) constitutes one of the four major clades of placental mammals. Despite their phylogenetic distinctiveness in mammals, a reference phylogeny is still lacking for the 31 described species. Here we used Illumina shotgun sequencing to assemble 33 new complete mitochondrial genomes, establishing Xenarthra as the first major placental clade to be fully sequenced at the species level for mitogenomes. The resulting data set allowed the reconstruction of a robust phylogenetic framework and timescale that are consistent with previous studies conducted at the genus level using nuclear genes. Incorporating the full species diversity of extant xenarthrans points to a number of inconsistencies in xenarthran systematics and species definition. We propose to split armadillos in two distinct families Dasypodidae (dasypodines) and Chlamyphoridae (euphractines, chlamyphorines, and tolypeutines) to better reflect their ancient divergence, estimated around 42 million years ago. Species delimitation within long-nosed armadillos (genus Dasypus) appeared more complex than anticipated, with the discovery of a divergent lineage in French Guiana. Diversification analyses showed Xenarthra to be an ancient clade with a constant diversification rate through time with a species turnover driven by high but constant extinction. We also detected a significant negative correlation between speciation rate and past temperature fluctuations with an increase in speciation rate corresponding to the general cooling observed during the last 15 million years. Biogeographic reconstructions identified the tropical rainforest biome of Amazonia and the Guianan shield as the cradle of xenarthran evolutionary history with subsequent dispersions into more open and dry habitats.Fil: Gibb, Gillian C.. Universite de Montpellier; Francia. Massey Universit; Nueva ZelandaFil: Condamine, Fabien L.. University of Gothenburg; Suecia. Universite de Montpellier; Francia. University of Alberta; CanadáFil: Kuch, Melanie. McMaster University; CanadáFil: Enk, Jacob. McMaster University; CanadáFil: Moraes Barros, Nadia. Universidade Do Porto; Portugal. Universidade de Sao Paulo; BrasilFil: Superina, Mariella. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza. Instituto de Medicina y Biología Experimental de Cuyo; ArgentinaFil: Poinar, Hendrik N.. McMaster University; CanadáFil: Delsuc, Frederic. Universite de Montpellier; Franci

Experimental Transmission of African Swine Fever (ASF) Low Virulent Isolate NH/P68 by Surviving Pigs

African swine fever (ASF) has persisted in Eastern Europe since 2007, and two endemic zones have been identified in the central and southern parts of the Russian Federation. Moderate- to low-virulent ASF virus isolates are known to circulate in endemic ASF-affected regions. To improve our knowledge of virus transmission in animals recovered from ASF virus infection, an experimental in vivo study was carried out. Four domestic pigs were inoculated with the NH/P68 ASF virus, previously characterized to develop a chronic form of ASF. Two additional in-contact pigs were introduced at 72 days post-inoculation (dpi) in the same box for virus exposure. The inoculated pigs developed a mild form of the disease, and the virus was isolated from tissues in the inoculated pigs up to 99 dpi (pigs were euthanized at 36, 65, 99 and 134 dpi). In-contact pigs showed mild or no clinical signs, but did become seropositive, and a transient viraemia was detected at 28 days post-exposure (dpe), thereby confirming late virus transmission from the inoculated pigs. Virus transmission to in-contact pigs occurred at four weeks post-exposure, over three months after the primary infection. These results highlight the potential role of survivor pigs in disease maintenance and dissemination in areas where moderate- to low-virulent viruses may be circulating undetected. This study will help design better and more effective control programmes to fight against this disease.EU project, ASFORCE Targeted Research Effort on African Swine Fever (KBBE.2012.1.3-02, 311931) and the European Union Reference laboratory for ASF (grant no UE- LR PPA/03).Peer Reviewe

Dynamics of the terrestrial biosphere, climate and atmospheric CO₂ concentration during interglacials: a comparison between Eemian and Holocene

A complex earth system model (atmosphere and ocean general circulation models, ocean biogeochemistry and terrestrial biosphere) was used to perform transient simulations of two interglacial sections (Eemian, 128&ndash;113 ky B.P., and Holocene, 9 ky B.P.&ndash;present). The changes in terrestrial carbon storage during these interglacials were studied with respect to changes in the earth&apos;s orbit. The effects of different climate factors on changes in carbon storage were studied in offline experiments in which the vegetation model was forced only with temperature, hydrological parameters, radiation, or CO₂ concentration from the transient runs. <br><br> The largest anomalies in terrestrial carbon storage were caused by temperature changes. However, the increase in storage due to forest expansion and increased photosynthesis in the high latitudes was nearly balanced by the decrease due to increased respiration. Large positive effects on carbon storage were caused by an enhanced monsoon circulation in the subtropics between 128 and 121 ky B.P. and between 9 and 6 ky B.P., and by increases in incoming radiation during summer for 45&deg; to 70&deg; N compared to a control simulation with present-day insolation. <br><br> Compared to this control simulation, the net effect of these changes was a positive carbon storage anomaly in the terrestrial biosphere of about 200 Pg C for 125 ky B.P. and 7 ky B.P., and a negative anomaly around 150 Pg C for 116 ky B.P. Although the net increases for Eemian and Holocene were rather similar, the magnitudes of the processes causing these effects were different. The decrease in terrestrial carbon storage during the experiments was the main driver of an increase in atmospheric CO₂ concentration during both the Eemian and the Holocene

Concurrent Segmentation and Localization for Tracking of Surgical Instruments

Real-time instrument tracking is a crucial requirement for various computer-assisted interventions. In order to overcome problems such as specular reflections and motion blur, we propose a novel method that takes advantage of the interdependency between localization and segmentation of the surgical tool. In particular, we reformulate the 2D instrument pose estimation as heatmap regression and thereby enable a concurrent, robust and near real-time regression of both tasks via deep learning. As demonstrated by our experimental results, this modeling leads to a significantly improved performance than directly regressing the tool position and allows our method to outperform the state of the art on a Retinal Microsurgery benchmark and the MICCAI EndoVis Challenge 2015.Comment: I. Laina and N. Rieke contributed equally to this work. Accepted to MICCAI 201

She Works - She Writes (performance) and Research and Collaboration (artists talk)

‘She Works - She Writes’ is a work that simultaneously incorporates the narrative documentation of a live action as an integral element of its performance. It analyses the processes and methods of the body as archival record and interpretative account and explores the dialogue between the body politic, as the objectifiable property of performance, and its socialisation as documentary artifact. Effectively, it examines the ways in which the live can be denied being made static through documentation. In expanding and exploring the role of the documenter and their methods of communication in this way, a sense of narrative, of interpretation, is engaged. The document tells a story - it describes an actuality. Yet is it possible to take the document as a true account of the event being transcribed? This dilemma is explored in this work as the documenter will act as the communicator of a ‘hidden’ performance, a performance that only they can see. Beyond hearing the sounds of the ‘hidden’ performer, the audiences understanding of the work will be wholly reliant on the process of textual documentation. The documenter is effectively the sole observer of the methods and processes informing their narration, and they are relied upon to communicate the truth. Like looking through a lens that has been set up for someone else and responds to their viewpoint only, they are positioned to respond to the process of documentation and to analyse their relationship to it. The performer’s body will be denied politicization here, as its objectification will be denied. Instead the documenter, the usually veiled interpreter of the live experience, will trade places with the performer. In this way they will become the body of objectification by communicating the archival legacy of the live event. ‘She Works - She Writes’ is a development from ‘Live / Archive’ which was made and performed as part of a residency in Spring 2012 at Grace Exhibition Space, New York. The performance and accompanying talk titled 'Research and Collaboration', which discusses and details the varying approaches in our work, were scheduled by invitation from Miami International Festival

Functional morphology of the forelimb of Early Miocene caviomorph rodents from Patagonia

Caviomorph rodents (New World Hystricognathi) are represented in the Santa Cruz Formation of Patagonia (Early Miocene, Santacrucian) by four superfamilies. From this unit, excellent cranial and associated postcranial remains of Neoreomys, Eocardia, Schistomys (Cavioidea), Perimys (Chinchilloidea) and Steiromys (Erethizontoidea) are known. To interpret their use of substrate, a comparative description of limb bones (scapula, humerus, radius and ulna) of the five genera was performed within a taxonomic and ecologically diverse sample of extant rodents. Using palaeobiological inferences based on the habits and functional morphology of members of the extant sample, hypotheses were generated for the use of substrate by the Santacrucian taxa. Neoreomys would have had a marked flexo-extension capacity of the humerus and a moderate flexion of the manus. This genus and Eocardia would have had a complete and stabilized forearm extension, with wide stride and moderate extension of the forearm for the latter. Schistomys presents features similar to Eocardia. Perimys would have had strong external rotation of the humerus, moderate flexion of the manus and moderate, complete and stabilized extension of the forearm. Steiromys would have had good pronation/supination capacity, strong internal rotation of the humerus and flexion of the forearm and manus. Neoreomys would have been ambulatory and an occasional runner. Eocardia and Schistomys would have been good runners. Perimys would have been a digger and Steiromys a climber. This morphological disparity reflects a high ecological diversity, compatible with differential use of space during the Santacrucian.Fil: Muñoz, Nahuel Antu. Universidad Nacional de La Plata. Facultad de Ciencias Naturales y Museo. División Paleontología Vertebrados; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata; ArgentinaFil: Toledo, Néstor. Universidad Nacional de La Plata. Facultad de Ciencias Naturales y Museo. División Paleontología Vertebrados; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata; ArgentinaFil: Candela, Adriana Magdalena. Universidad Nacional de La Plata. Facultad de Ciencias Naturales y Museo. División Paleontología Vertebrados; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata; ArgentinaFil: Vizcaíno, Sergio Fabián. Universidad Nacional de La Plata. Facultad de Ciencias Naturales y Museo. División Paleontología Vertebrados; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata; Argentin

Hydrogen and vacancy clustering in zirconium

The effect of solute hydrogen on the stability of vacancy clusters in hexagonal closed packed zirconium is investigated with an ab initio approach, including contributions of H vibrations. Atomistic simulations within the density functional theory evidence a strong binding of H to small vacancy clusters. The hydrogen effect on large vacancy loops is modeled through its interaction with the stacking faults. A thermodynamic modeling of H segregation on the various faults, relying on ab initio binding energies, shows that these faults are enriched in H, leading to a decrease of the stacking fault energies. This is consistent with the trapping of H by vacancy loops observed experimentally. The stronger trapping, and thus the stronger stabilization, is obtained for vacancy loops lying in the basal planes, i.e. the loops responsible for the breakaway growth observed under high irradiation dose.Comment: submitte

Assessment of the risk of African swine fever introduction into Finland using NORA : a rapid tool for semiquantitative assessment of the risk

The NORA rapid risk assessment tool was developed for situations where there is a change in the disease status of easily transmissible animal diseases in neighbouring countries or in countries with significant interactions with Finland. The goal was to develop a tool that is quick to use and will provide consistent results to support risk management decisions. The model contains 63 questions that define the potential for entry and exposure by nine different pathways. The magnitude of the consequences is defined by 23 statements. The weight of different pathways is defined according to the properties of the assessed disease. The model was built as an Excel spreadsheet and is intended for use by animal health control administrators. As an outcome, the model gives the possible pathways of disease entry into the country, an overall approximation for the probability of entry and the subsequent exposure, an overall estimate for the consequences and a combined overall risk estimate (probability multiplied by magnitude of consequences). Model validity was assessed by expert panels. Outside Africa, African swine fever is currently established in Russia and Sardinia. In addition, there have been cases in both wild boar and domestic pigs in Latvia, Lithuania, Poland and Estonia. Finland has frequent contacts with Russia and Estonia, especially through passengers. The risk of African swine fever (ASF) introduction into Finland was tested with NORA for the situation in December 2015, when ASF was endemic in many parts of Russia, Africa and Sardinia and was present in Baltic countries and in Poland. African swine fever was assessed to have a high probability of entry into Finland, with high consequences and therefore a high overall risk