Front propagation and arrival times in networks with application to neurodegenerative diseases

Many physical, epidemiological, or physiological dynamical processes on networks support front-like propagation, where an initial localized perturbation grows and systematically invades all nodes in the network. A key question is then to extract estimates for the dynamics. In particular, if a single node is seeded at a small concentration, when will other nodes reach the same initial concentration? Here, motivated by the study of toxic protein propagation in neurodegenerative diseases, we present and compare three different estimates for the arrival time in order of increasing analytical complexity: the linear arrival time, obtained by linearizing the underlying system; the Lambert time, obtained by considering the interaction of two nodes; and the nonlinear arrival time, obtained by asymptotic techniques. We use the classic Fisher-Kolmogorov-Petrovsky-Piskunov equation as a paradigm for the dynamics and show that each method provides different insight and time estimates. Further, we show that the nonlinear asymptotic method also gives an approximate solution valid in the entire domain and the correct ordering of arrival regions over large regions of parameters and initial conditions.

Simultaneous inference of parental admixture proportions and admixture times from unphased local ancestry calls

Population genetic analyses of local ancestry tracts routinely assume that the ancestral admixture process is identical for both parents of an individual, an assumption that may be invalid when considering recent admixture. Here we present Parental Admixture Proportion Inference (PAPI), a Bayesian tool for inferring the admixture proportions and admixture times for each parent of a single admixed individual. PAPI analyzes unphased local ancestry tracts and has two components models: a binomial model that exploits the informativeness of homozygous ancestry regions to infer parental admixture proportions, and a hidden Markov model (HMM) that infers admixture times from tract lengths. Crucially, the HMM employs an approximation to the pedigree crossover dynamics that accounts for unobserved within-ancestry recombination, enabling inference of parental admixture times. We compared the accuracy of PAPI's admixture proportion estimates with those of ANCESTOR in simulated admixed individuals and found that PAPI outperforms ANCESTOR by an average of 46% in a representative set of simulation scenarios, with PAPI's estimates deviating from the ground truth by 0.047 on average. Moreover, PAPI's admixture time estimates were strongly correlated with the ground truth in these simulations (R = 0.76), but have an average downward bias of 1.01 generations that is partly attributable to inaccuracies in local ancestry inference. As an illustration of its utility, we ran PAPI on real African Americans from the PAGE study (N = 5,786) and found strong evidence of assortative mating by ancestry proportion: couples' ancestry proportions are closer to each other than expected by chance (P<10-6), and are highly correlated (R = 0.87). We anticipate that PAPI will be useful in studying the population dynamics of admixture and will also be of interest to individuals seeking to learn about their personal genealogies.

Stationary solutions in thermodynamics of stochastically forced fluids

We study the full Navier–Stokes–Fourier system governing the motion of a general viscous, heat-conducting, and compressible fluid subject to stochastic perturbation. The system is supplemented with non-homogeneous Neumann boundary conditions for the temperature and hence energetically open. We show that, in contrast with the energetically closed system, there exists a stationary solution. Our approach is based on new global-in-time estimates which rely on the non-homogeneous boundary conditions combined with estimates for the pressure.

Design Methodology for Grout Curtains Under Dams Founded on Rock

Grout curtains are commonly constructed under dams to reduce the seepage through the rock foundation. In the design of grout curtains, empirical methods have mainly been used since the introduction of dam foundation grouting. Although empirical methods have been used with success in several projects, they have their limitations, such as poor control of the grout spread, only an indirect consideration of the threat of internal erosion of fracture infillings in the grouted zones, and the risk of hydraulic jacking. This paper presents a theory-based design methodology for grout curtains under dams founded on rock. In the design methodology, the grout curtain is designed as a structural component of the dam. The risk of erosion of fracture infilling material is explicitly accounted for along with the reduction of the hydraulic conductivity of the rock mass, and an optimization of the total uplift force. By applying the proposed design methodology, engineers can create a design better adapted to the prevailing geological and hydrogeological conditions in the rock mass, resulting in more durable grout curtains. The proposed methodology also enables cost and time estimates to be calculated for the grout curtain’s construction. Applying the principles of the observational method during the grouting execution also allows the design to be modified via predefined measures if the initial design is found to be unsuitable.

Ancient genomes from the last three millennia support multiple human dispersals into Wallacea

Previous research indicates that the human genetic diversity found in Wallacea - islands in present-day Eastern Indonesia and Timor-Leste that were never part of the Sunda or Sahul continental shelves - has been shaped by complex interactions between migrating Austronesian farmers and indigenous hunter-gatherer communities. Here, we provide new insights into this region's demographic history based on genome-wide data from 16 ancient individuals (2600-250 yrs BP) from islands of the North Moluccas, Sulawesi, and East Nusa Tenggara. While the ancestry of individuals from the northern islands fit earlier views of contact between groups related to the Austronesian expansion and the first colonization of Sahul, the ancestry of individuals from the southern islands revealed additional contributions from Mainland Southeast Asia, which seems to predate the Austronesian admixture in the region. Admixture time estimates for the oldest individuals of Wallacea are closer to archaeological estimates for the Austronesian arrival into the region than are admixture time estimates for present-day groups. The decreasing trend in admixture times exhibited by younger individuals supports a scenario of multiple or continuous admixture involving Papuan- and Asian-related groups. Our results clarify previously debated times of admixture and suggest that the Neolithic dispersals into Island Southeast Asia are associated with the spread of multiple genetic ancestries.

Highly refractory dunite formation at Gibbs Island and Bruce Bank, and its role in the evolution of the circum-Antarctic continent

ABSTRACT The continental margin is of profound importance as it records continental growth by accretion of orogenic magmas and following continental rifting. A high degree of mantle melting due to hydrous fluid input is expected to simultaneously stimulate continental growth and lower the intrinsic density of the mantle than more fertile mantle, which in turn isolates the continental lithosphere from the convective mantle. The mantle peridotites from Gibbs Island (South Shetland Islands) and Bruce Bank in the Drake Passage provide us an insight into the tectonic history in the circum-Antarctic region. To elucidate the continental growth of Antarctica, we present geochemical data of eight dunites from Gibbs Island and one dunite from Bruce Bank, including Re–Os isotope and highly siderophile element compositions. The dunites are severely affected by serpentinization as evidenced by antigorite + brucite or lizardite (loss on ignition = LOI ranging from 3 to 34 wt.%) but contain primary euhedral to subhedral chromites with or without spherical inclusions. The chromites rarely form lens-shaped aggregates. A dunite from Gibbs Island contains fresh olivine grains filling a fracture in the chromite with low LOI (3 wt.%), indicating a deserpentinization origin from a precursor serpentinized dunite. The dunites show highly depleted bulk-rock major element compositions (Mg/Si = 1.4–1.6 and Al/Si = 0.004–0.01 for Gibbs Island dunites, Mg/Si = 0.66 and Al/Si = 0.008 for Bruce Bank dunite), overlapping a compositional field defined by forearc peridotites. The positive correlation in Re/Ir–LOI space corroborates Re input during the later serpentinization process. The 187Os/188Os ratios of the dunites range from 0.11907 to 0.14493. Phanerozoic Re-depletion (melt depletion) ages of ca. 535–129 Ma are recorded in the Gibbs Island dunites, except for one with a Mesoproterozoic Re-depletion age of ca. 1.2 Ga. Since there exists serpentinization-related perturbation of Re, the ages provide minimum time estimates for melt depletion events. The early Paleozoic melt depletion is inferred to have occurred at a very early stage of Antarctic Peninsula formation in response to plate convergence along the margin of Gondwana, whereas the Mesoproterozoic Re-depletion age reflects convecting mantle heterogeneity unrelated to any nearby crust-forming events. The petrographic characteristics of the chromites and highly depleted nature of the dunites are attributed to melt–peridotite reaction in a subduction zone setting. A feasible interpretation for the dunite formation is that the mantle had experienced two stages of melting with the final stage occurring along the Gondwana continental margin in the subduction zone setting. Resultant highly refractory lithospheric mantle was later displaced and dispersed during the Gondwana breakup. Widespread existence of the dunite may be attributed to multi-stage melt depletion along the continental margin.

Zircon (U-Th)/(He-Pb) double-dating constraints on the interplay between thrust deformation and foreland basin architecture, Sevier foreland basin, Utah

The Cretaceous Cordilleran foreland basin strata exposed in the Book Cliffs of eastern Utah and western Colorado have motivated important concepts linking thrust belt deformation and foreland basin evolution largely on the basis of sequence stratigraphy, stratal architecture, and sediment provenance evolution. However, these methods and approaches generally cannot provide critical insights into the temporal or causal linkages between foreland basin architecture and thrust belt deformation. This is in part due to discrepancies in age resolution and lack of evidence with which to directly couple sediment supply and basin-fill evolution to thrust belt unroofing. New detrital zircon (DZ) geothermochronometric data from Upper Cretaceous proximal to distal foreland basin strata in the Book Cliffs provide new quantitative insights into sediment origin and dispersal in relation to thrust belt deformation and exhu­mation. Detailed DZ U-Pb and (U-Th)/He double dating reveals that the Book Cliffs foredeep detritus was mainly delivered by transverse routing systems from two major sources: (1) Neoproterozoic and Lower Paleozoic strata from the central Utah Sevier thrust belt, and (2) Permian–Jurassic and synorogenic Cretaceous strata recycled from the frontal part of the thrust belt. A dramatic increase in Sierran magmatic arc and Yavapai-Mazatzal DZ U-Pb ages, as well as Paleozoic DZ He ages, in the deeper marine portions of the foreland basin points to axial fluvial and littoral sediment input from the Sierran magmatic arc and Mogollon highland sources. Both transverse and axial transport sys­tems acted contemporaneously during eastward propagation of the Late Cretaceous thrust belt. DZ He depositional lag time estimates reveal three distinct exhumation pulses in the Sevier thrust belt in the Cenomanian and Campanian. The exhumation pulses correlate with shifts in sediment prove­nance, dispersal style, and progradation rates in the foreland basin. These new data support conceptual models that temporally and causally link accelerated exhumation and unroofing in the thrust belt to increases in sediment supply and rapid clastic progradation in the foreland basin.

Taxonomy, Phylogeny, Molecular Dating and Ancestral State Reconstruction of Xylariomycetidae (Sordariomycetes)

Xylariomycetidae ( Ascomycota ) is a highly diversified group with variable stromatic characters. Our research focused on inconspicuous stromatic xylarialean taxa from China, Italy, Russia, Thailand and the United Kingdom. Detailed morphological descriptions, illustrations and combined ITS-LSU- rpb 2- tub 2- tef 1 phylogenies revealed 38 taxa from our collections belonging to Amphisphaeriales and Xylariales . A new family ( Appendicosporaceae ), five new genera ( Magnostiolata , Melanostictus , Neoamphisphaeria , Nigropunctata and Paravamsapriya ), 27 new species ( Acrocordiella photiniicola , Allocryptovalsa sichuanensis , Amphisphaeria parvispora , Anthostomella lamiacearum , Apiospora guiyangensis , Ap. sichuanensis , Biscogniauxia magna , Eutypa camelliae , Helicogermslita clypeata , Hypocopra zeae , Magnostiolata mucida , Melanostictus longiostiolatus , Me. thailandicus , Nemania longipedicellata , Ne. delonicis , Ne. paraphysata , Ne. thailandensis , Neoamphisphaeria hyalinospora , Neoanthostomella bambusicola , Nigropunctata bambusicola , Ni. nigrocircularis , Ni. thailandica , Occultitheca rosae , Paravamsapriya ostiolata , Peroneutypa leucaenae , Seiridium italicum and Vamsapriya mucosa ) and seven new host/geographical records are introduced and reported. Divergence time estimates indicate that Delonicicolales diverged from Amphisphaeriales + Xylariales at 161 (123–197) MYA. Amphisphaeriales and Xylariales diverged 154 (117–190) MYA with a crown age of 127 (92–165) MYA and 147 (111–184) MYA, respectively. Appendicosporaceae ( Amphisphaeriales ) has a stem age of 89 (65–117) MYA. Ancestral character state reconstruction indicates that astromatic, clypeate ascomata with aseptate, hyaline ascospores that lack germ slits may probably be ancestral Xylariomycetidae having plant-fungal endophytic associations. The Amphisphaeriales remained mostly astromatic with common septate, hyaline ascospores. Stromatic variations may have developed mostly during the Cretaceous period. Brown ascospores are common in Xylariales , but they first appeared in Amphisphaeriaceae , Melogrammataceae and Sporocadaceae during the early Cretaceous. The ascospore germ slits appeared only in Xylariales during the Cretaceous after the divergence of Lopadostomataceae . Hyaline, filiform and apiospores may have appeared as separate lineages providing the basis to Xylariaceae , which may have diverged independently. The future classification of polyphyletic xylarialean taxa will not be based on stromatic variations, but the type of ring, the colour of the ascospores, and the presence or absence of the type of germ slit.