Early redox activities modulate Xenopus tail regeneration.

Redox state sustained by reactive oxygen species (ROS) is crucial for regeneration; however, the interplay between oxygen (O2), ROS and hypoxia-inducible factors (HIF) remains elusive. Here we observe, using an optic-based probe (optrode), an elevated and steady O2 influx immediately upon amputation. The spatiotemporal O2 influx profile correlates with the regeneration of Xenopus laevis tadpole tails. Inhibition of ROS production but not ROS scavenging decreases O2 influx. Inhibition of HIF-1α impairs regeneration and stabilization of HIF-1α induces regeneration in the refractory period. In the regeneration bud, hypoxia correlates with O2 influx, ROS production, and HIF-1α stabilization that modulate regeneration. Further analyses reveal that heat shock protein 90 is a putative downstream target of HIF-1α while electric current reversal is a de facto downstream target of HIF-1α. Collectively, the results show a mechanism for regeneration via the orchestration of O2 influx, ROS production, and HIF-1α stabilization

Packing Squares into a Disk with Optimal Worst-Case Density

We provide a tight result for a fundamental problem arising from packing squares into a circular container: The critical density of packing squares into a disk is ? = 8/(5?)? 0.509. This implies that any set of (not necessarily equal) squares of total area A ? 8/5 can always be packed into a disk with radius 1; in contrast, for any ? > 0 there are sets of squares of total area 8/5+? that cannot be packed, even if squares may be rotated. This settles the last (and arguably, most elusive) case of packing circular or square objects into a circular or square container: The critical densities for squares in a square (1/2), circles in a square (?/(3+2?2) ? 0.539) and circles in a circle (1/2) have already been established, making use of recursive subdivisions of a square container into pieces bounded by straight lines, or the ability to use recursive arguments based on similarity of objects and container; neither of these approaches can be applied when packing squares into a circular container. Our proof uses a careful manual analysis, complemented by a computer-assisted part that is based on interval arithmetic. Beyond the basic mathematical importance, our result is also useful as a blackbox lemma for the analysis of recursive packing algorithms. At the same time, our approach showcases the power of a general framework for computer-assisted proofs, based on interval arithmetic

Distributed Variance Reduction with Optimal Communication

We consider the problem of distributed variance reduction: $n$ machines each receive probabilistic estimates of an unknown true vector $\Delta$, and must cooperate to find a common estimate of $\Delta$ with lower variance, while minimizing communication. Variance reduction is closely related to the well-studied problem of distributed mean estimation, and is a key procedure in instances of distributed optimization, such as data-parallel stochastic gradient descent. Previous work typically assumes an upper bound on the norm of the input vectors, and achieves an output variance bound in terms of this norm. However, in real applications, the input vectors can be concentrated around the true vector $\Delta$, but $\Delta$ itself may have large norm. In this case, output variance bounds in terms of input norm perform poorly, and may even increase variance. In this paper, we show that output variance need not depend on input norm. We provide a method of quantization which allows variance reduction to be performed with solution quality dependent only on input variance, not on input norm, and show an analogous result for mean estimation. This method is effective over a wide range of communication regimes, from sublinear to superlinear in the dimension. We also provide lower bounds showing that in many cases the communication to output variance trade-off is asymptotically optimal. Further, we show experimentally that our method yields improvements for common optimization tasks, when compared to prior approaches to distributed mean estimation.Comment: 28 pages, 14 figure

Phylogenetics and evolution of nematode-trapping fungi (Orbiliales) estimated from nuclear and protein coding genes

The systematic classification of nematode-trapping fungi is redefined based on phylogenies inferred from sequence analyses of 28S rDNA, 5.8S rDNA and ß-tubulin genes. Molecular data were analyzed with maximum parsimony, maximum likelihood and Bayesian analysis. An emended generic concept of nematode-trapping fungi is provided. Arthrobotrys is characterized by adhesive networks, Dactylellina by adhesive knobs, and Drechslerella by constricting-rings. Phylogenetic placement of taxa characterized by stalked adhesive knobs and non-constricting rings also is confirmed in Dactylellina. Species that produce unstalked adhesive knobs that grow out to form loops are transferred from Gamsylella to Dactylellina, and those that produce unstalked adhesive knobs that grow out to form networks are transferred from Gamsylella to Arthrobotrys. Gamsylella as currently circumscribed cannot be treated as a valid genus. A hypothesis for the evolution of trapping-devices is presented based on multiple gene data and morphological studies. Predatory and nonpredatory fungi appear to have been derived from nonpredatory members of Orbilia. The adhesive knob is considered to be the ancestral type of trapping device from which constricting rings and networks were derived via two pathways. In the first pathway adhesive knobs retained their adhesive material forming simple two-dimension networks, eventually forming complex three-dimension networks. In the second pathway adhesive knobs lost their adhesive materials, with their ends meeting to form nonconstricting rings and they in turn formed constricting rings with three inflated-cells.published_or_final_versio

The family Pleosporaceae: intergeneric relationships and phylogenetic perspectives based on sequence analyses of partial 28S rDNA

The Pleosporaceae is an important loculoascomycete family. There has been disagreement, however, regarding the taxonomic placement of many genera within this family. This study investigates phylogenetic relationships among the genera Cochliobolus, Kirschsteiniothelia, Leptosphaerulina, Macroventuria, Pleospora, Pyrenophora, and Wettsteinina. Partial 28S rDNA sequences from taxa within these genera were analyzed with maximum parsimony, likelihood and Bayesian methods. Cochliobolus can be segregated broadly into two groups as previously proposed. Pleospora is polyphyletic in its current sense. Taxa with Stemphylium anamorphs are closely related to Cochliobolus and fit within the Pleosporaceae, whereas the affinities of Pleospora herbarum and P. ambigua are still ambiguous. Pyrenophora constitutes a monophyletic group within the Pleosporaceae, whereas Leptosphaerulina and Macroventuria appear to share phylogenetic affinities with the Leptosphaeriaceae and Phaeosphaeriaceae. Phylogenies indicate that Wettsteinina should be excluded from the Pleosporaceae. Similar findings are reported for Kirschsteiniothelia, which is probably polyphyletic. Anamorphic characters appear to be significant (especially in Cochliobolus) while ascospore morphologies, such as shape and color and substrate occurrence are poor indicators of phylogenetic relationships among these loculoascomycetes.published_or_final_versio

Biomechanical, ultrastructural, and electrophysiological characterization of the non-human primate experimental glaucoma model.

Laser-induced experimental glaucoma (ExGl) in non-human primates (NHPs) is a common animal model for ocular drug development. While many features of human hypertensive glaucoma are replicated in this model, structural and functional changes in the unlasered portions of trabecular meshwork (TM) of laser-treated primate eyes are understudied. We studied NHPs with ExGl of several years duration. As expected, ExGl eyes exhibited selective reductions of the retinal nerve fiber layer that correlate with electrophysiologic measures documenting a link between morphologic and elctrophysiologic endpoints. Softening of unlasered TM in ExGl eyes compared to untreated controls was observed. The degree of TM softening was consistent, regardless of pre-mortem clinical findings including severity of IOP elevation, retinal nerve fiber layer thinning, or electrodiagnostic findings. Importantly, this softening is contrary to TM stiffening reported in glaucomatous human eyes. Furthermore, microscopic analysis of unlasered TM from eyes with ExGl demonstrated TM thinning with collapse of Schlemm's canal; and proteomic analysis confirmed downregulation of metabolic and structural proteins. These data demonstrate unexpected and compensatory changes involving the TM in the NHP model of ExGl. The data suggest that compensatory mechanisms exist in normal animals and respond to elevated IOP through softening of the meshwork to increase outflow

Multiple Sublineages of Influenza A Virus (H5N1), Vietnam, 2005−2007

Clade 2.3.4 viruses that are dominant in southern China have now spread to northern Vietnam

Analysis of Swine Movements in a Province in Northern Vietnam and Application in the Design of Surveillance Strategies for Infectious Diseases

While swine production is rapidly growing in South-East Asia, the structure of the swine industry and the dynamic of pig movements have not been well-studied. However, this knowledge is a prerequisite for understanding the dynamic of disease transmission in swine populations and designing cost-effective surveillance strategies for infectious diseases. In this study, we assessed the farming and trading practices in the Vietnamese swine familial farming sector, which accounts for most pigs in Vietnam, and for which disease surveillance is a major challenge. Farmers from two communes of a Red River Delta Province (northern Vietnam) were interviewed, along with traders involved in pig transactions. Major differences in the trade structure were observed between the two communes. One commune had mainly transversal trades, that is between farms of equivalent sizes, whereas the other had pyramidal trades, that is from larger to smaller farms. Companies and large familial farrow-to-finish farms were likely to act as major sources of disease spread through pig sales, demonstrating their importance for disease control. Familial fattening farms with high pig purchases were at greater risk of disease introduction and should be targeted for disease detection as part of a risk-based surveillance. In contrast, many other familial farms were isolated or weakly connected to the swine trade network limiting their relevance for surveillance activities. However, some of these farms used boar hiring for breeding, increasing the risk of disease spread. Most familial farms were slaughtering pigs at the farm or in small local slaughterhouses, making the surveillance at the slaughterhouse inefficient. In terms of spatial distribution of the trades, the results suggested that northern provinces were highly connected and showed some connection with central and southern provinces. These results are useful to develop risk-based surveillance protocols for disease detection in the swine familial sector and to make recommendations for disease control. (Résumé d'auteur

The recent establishment of North American H10 lineage influenza viruses in Australian wild waterfowl and the evolution of Australian avian influenza viruses

Influenza A H10N7 virus with a hemagglutinin gene of North American origin was detected in Australian chickens and poultry abattoir workers in New South Wales, Australia, in 2010 and in chickens in Queensland, Australia, on a mixed chicken and domestic duck farm in 2012. We investigated their genomic origins by sequencing full and partial genomes of H10 viruses isolated from wild aquatic birds and poultry in Australia and analyzed them with all available avian influenza virus sequences from Oceania and representative viruses from North America and Eurasia. Our analysis showed that the H10N7 viruses isolated from poultry were similar to those that have been circulating since 2009 in Australian aquatic birds and that their initial transmission into Australia occurred during 2007 and 2008. The H10 viruses that appear to have developed endemicity in Australian wild aquatic birds were derived from several viruses circulating in waterfowl along various flyways. Their hemagglutinin gene was derived from aquatic birds in the western states of the United States, whereas the neuraminidase was closely related to that from viruses previously detected in waterfowl in Japan. The remaining genes were derived from Eurasian avian influenza virus lineages. Our analysis of virological data spanning 40 years in Oceania indicates that the long-term evolutionary dynamics of avian influenza viruses in Australia may be determined by climatic changes. The introduction and long-term persistence of avian influenza virus lineages were observed during periods with increased rainfall, whereas bottlenecks and extinction were observed during phases of widespread decreases in rainfall. These results extend our understanding of factors affecting the dynamics of avian influenza and provide important considerations for surveillance and disease control strategies. © 2013, American Society for Microbiology

The Origins of Ethno/National Separatist Terrorism: A Cross-National Analysis of the Background Conditions of Terrorist Campaigns

This study measures the influence that multiple social, political, and economic conditions have on the development of ethno/national separatist terrorist organizations. It begins by analyzing the nationalist theories of primordialism, modernism, and ethnosymbolism, and the terrorist theories of strategic logic and psychology. The nationalist theories consider cultural symbols a powerful component behind nationalist movements and populations with significant symbolic attachments especially prone to react aggressively against perceived threats to those symbols. Proponents of strategic logic and psychological theory also view terrorism as reactive but deviate on whether this response is conceived rationally. Examining the origins of Basque and Catalan terrorism and Roma passivity in Spain assists in identifying background conditions that are evaluated using a logit regression model. The logit model assesses two-hundred ninety-seven minority populations in one-hundred twenty-six states, primarily between 1945 and 2003. The results show cultural identity and sensitivity, violent encounters, political freedom, social unrest, underrepresentation, disproportionate economic privation, and stagnant educational systems and other factors of civil development correlating significantly with the formation of ethno/national separatist terrorist organizations. These findings imply an ability to detect populations and environments with increased potential for producing ethno/national separatist terrorism, and that by addressing those conditions facilitating its development, it may be possible to reduce the probability of additional campaigns developing