Generic acquisition protocol for quantitative MRI of the spinal cord

Quantitative spinal cord (SC) magnetic resonance imaging (MRI) presents many challenges, including a lack of standardized imaging protocols. Here we present a prospectively harmonized quantitative MRI protocol, which we refer to as the spine generic protocol, for users of 3T MRI systems from the three main manufacturers: GE, Philips and Siemens. The protocol provides guidance for assessing SC macrostructural and microstructural integrity: T1-weighted and T2-weighted imaging for SC cross-sectional area computation, multi-echo gradient echo for gray matter cross-sectional area, and magnetization transfer and diffusion weighted imaging for assessing white matter microstructure. In a companion paper from the same authors, the spine generic protocol was used to acquire data across 42 centers in 260 healthy subjects. The key details of the spine generic protocol are also available in an open-access document that can be found at https://github.com/spine-generic/protocols. The protocol will serve as a starting point for researchers and clinicians implementing new SC imaging initiatives so that, in the future, inclusion of the SC in neuroimaging protocols will be more common. The protocol could be implemented by any trained MR technician or by a researcher/clinician familiar with MRI acquisition

Influenza A H5N1 Immigration Is Filtered Out at Some International Borders

Geographic spread of highly pathogenic influenza A H5N1, the bird flu strain, appears a necessary condition for accelerating the evolution of a related human-to-human infection. As H5N1 spreads the virus diversifies in response to the variety of socioecological environments encountered, increasing the chance a human infection emerges. Genetic phylogenies have for the most part provided only qualitative evidence that localities differ in H5N1 diversity. For the first time H5N1 variation is quantified across geographic space.We constructed a statistical phylogeography of 481 H5N1 hemagglutinin genetic sequences from samples collected across 28 Eurasian and African localities through 2006. The MigraPhyla protocol showed southern China was a source of multiple H5N1 strains. Nested clade analysis indicated H5N1 was widely dispersed across southern China by both limited dispersal and long distance colonization. The UniFrac metric, a measure of shared phylogenetic history, grouped H5N1 from Indonesia, Japan, Thailand and Vietnam with those from southeastern Chinese provinces engaged in intensive international trade. Finally, H5N1's accumulative phylogenetic diversity was greatest in southern China and declined beyond. The gradient was interrupted by areas of greater and lesser phylogenetic dispersion, indicating H5N1 migration was restricted at some geopolitical borders. Thailand and Vietnam, just south of China, showed significant phylogenetic clustering, suggesting newly invasive H5N1 strains have been repeatedly filtered out at their northern borders even as both countries suffered recurring outbreaks of endemic strains. In contrast, Japan, while successful in controlling outbreaks, has been subjected to multiple introductions of the virus.The analysis demonstrates phylogenies can provide local health officials with more than hypotheses about relatedness. Pathogen dispersal, the functional relationships among disease ecologies across localities, and the efficacy of control efforts can also be inferred, all from viral genetic sequences alone

Lawson criterion for ignition exceeded in an inertial fusion experiment

For more than half a century, researchers around the world have been engaged in attempts to achieve fusion ignition as a proof of principle of various fusion concepts. Following the Lawson criterion, an ignited plasma is one where the fusion heating power is high enough to overcome all the physical processes that cool the fusion plasma, creating a positive thermodynamic feedback loop with rapidly increasing temperature. In inertially confined fusion, ignition is a state where the fusion plasma can begin "burn propagation" into surrounding cold fuel, enabling the possibility of high energy gain. While "scientific breakeven" (i.e., unity target gain) has not yet been achieved (here target gain is 0.72, 1.37 MJ of fusion for 1.92 MJ of laser energy), this Letter reports the first controlled fusion experiment, using laser indirect drive, on the National Ignition Facility to produce capsule gain (here 5.8) and reach ignition by nine different formulations of the Lawson criterion

Genetic consequences of multigenerational and landscape colonisation bottlenecks for a neotropical forest pioneer tree, Vochysia ferruginea

Deforestation and abandonment of neotropical agricultural land has led to rapid exploitation by pioneer species. As recolonised populations may be founded by a limited number of individuals, there is significant potential for genetic bottlenecks. Previous studies of pioneer tree dynamics have failed to consider population density interactions (by sampling populations with different densities)and the multigenerational consequences of recolonisation. In this paper we examine the genetic outcomes of a clearance / recolonisation regime for a Costa Rican long-lived pioneer species, Vochysia ferruginea, at a series of sites with different densities and across multi-generational cohorts (old growth forest,secondary forest and seedlings) using variation for amplified fragment length polymorphism (AFLPs) and single sequence repeats (SSRs, microsatellites). A clearance/recolonisation phase was found to significantly increase fine-scale genetic structuring (average intensity of spatial genetic structure, Sp [SSR] = 0.0358) compared to old growth forest (Sp = 0.0126), and significantly reduces genetic diversity (Shannon’s index [AFLP] = 0.202 and 0.271–0.355 for other forest histories following density correction), which compounds over generations (e.g. at Tirimbina: old growth forest, allelic richness, RT [SSR] = 8.86; secondary forest RT = 7.95; seedlings RT = 4.76). Spatial structuring of closely related individuals suggests that V. ferruginea colonises sites via early invaders, which establish patches with half sib relationship. The variability observed between cohorts for genetic differentiation and inbreeding coefficients suggests that the presence of remnant trees can have an important impact on the genetic make up of recolonised populations. One main concern from these results is that if secondary forest blocks harbour reduced genetic diversity and persist in the landscape, then species like V. ferruginea may be forced into a downward spiral of diversity loss if old growth remnants, which harbour higher diversity, are cleared and secondary blocks are used as reforestation sources