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Computer models of wildfires are an important tool for fire managers and scientists. However, fuel inputs to wildfire models can be difficult to represent with sufficient detail in a computationally efficient manner. Recent advances in fuel mapping with airborne and terrestrial laser scanning (LIDAR) techniques present new opportunities to capture variation in fuels within a tree canopy and on a landscape. In this paper, we develop a technique for building 3D representations of vegetation from point clouds created by Terrestrial Laser Scans (TLS). Our voxel based approach is capable of representing heterogeneous crown fuels as collections of fuel cells in modern 3D Computational Fluid Dynamics wildfire models such as FDS, QUIC-Fire, or FIRETEC. We evaluated the effectiveness of our technique at different fuel cell resolutions by using the DAKOTA optimization toolkit to compare simulated fire behavior in FDS with observed burn data collected during a series of experiments at the Missoula Fire Sciences Laboratory. The difference between simulated and observed fire behavior was quantified by taking the Root Mean Square Error between the observed and simulated mass curves over time. Our primary finding was that the point cloud derived fuel cells accurately describe observed fire behavior when evaluated over fuel moisture content and dry foliage mass. We also found that the global minimum RMSE persists across fuel cells at each resolution. However, the RMSE gradient increases with fuel cell size. This result implies that while both low and high resolution fuel cells are capable of accurately representing complex fuel distributions in 3D fire models, low resolution fuel cells are more sensitive to changes in fuel moisture content and dry foliage mass. The results of this paper offer fire managers and scientists responsible for simulating fire behavior guidelines for how best to translate LIDAR data to 3D fire models, and what fuel cell resolution can best capture accurate fire behavior. With these best practices in mind, fire managers will be able to generate improved fire behavior predictions for prescribed burns, forest thinning plans, and suppression activities.

We investigate changing precipitation patterns in the Kangerlussuaq region of west central Greenland during the Holocene thermal maximum, using a new chronology of ice sheet terminus position through the Holocene and a novel inverse modeling approach based on the unscented transform (UT). The UT is applied to estimate changes in annual precipitation in order to reduce the misfit between modeled and observed terminus positions. We demonstrate the effectiveness of the UT for time-dependent data assimilation, highlighting its low computational cost and trivial parallel implementation. Our results indicate that Holocene warming coincided with elevated precipitation, without which modeled retreat in the Kangerlussuaq region is more rapid than suggested by observations. Less conclusive is if high temperatures during the HTM were specifically associated with a transient increase in precipitation, as the results depend on the assumed temperature history. The importance of precipitation in controlling ice sheet extent during the Holocene underscores the importance of Arctic sea ice loss and changing precipitation patterns on the future stability of the GrIS.

This paper gives sharp linear bounds on the genus of a normal surface in a triangulated compact, orientable 3--manifold in terms of the quadrilaterals in its cell decomposition---different bounds arise from varying hypotheses on the surface or triangulation. Two applications of these bounds are given. First, the minimal triangulations of the product of a closed surface and the closed interval are determined. Second, an alternative approach to the realisation problem using normal surface theory is shown to be less powerful than its dual method using subcomplexes of polytopes., 38 pages, 25 figures

We show that the bridge distance of a knot determines a lower bound on the genera of essential surfaces and Heegaard surfaces in the manifolds that result from non-trivial Dehn surgeries on the knot. In particular, knots with high bridge distance do not admit non-trivial non-hyperbolic surgeries or non-trivial cosmetic surgeries. We further show that if a knot has bridge distance at least 3 then its bridge number is bounded above by a function of Seifert genus, or indeed by the genus of (almost) any essential surface or Heegaard surface in the surgered manifold.

Background FSTL1 (follistatin-like protein 1) is an emerging cardiokine/myokine that is upregulated in heart failure (HF) and is found to be cardioprotective in animal models of cardiac injury. We tested the hypothesis that circulating FSTL1 can affect cardiac function and metabolism under baseline physiological conditions and in HF. Methods and Results FSTL1 was acutely (10 minutes) or chronically (2 weeks) infused to attain clinically relevant blood levels in conscious dogs with cardiac tachypacing-induced HF. Dogs with no cardiac pacing and FSTL1 infusion served as control. 3 H-oleate and 14 C-glucose were infused to track the metabolic fate of free fatty acids and glucose. Cardiac uptake of lactate and ketone bodies and systemic respiratory quotient were also measured. HF caused a shift from prevalent cardiac and systemic fat to carbohydrate oxidation. Although acute FSTL1 administration caused minimal hemodynamic changes at baseline, in HF dogs it enhanced cardiac oxygen consumption and transiently reversed the changes in free fatty acid and glucose oxidation and systemic respiratory quotient. In HF, chronic FSTL1 infusion stably normalized cardiac free fatty acid, glucose, ketone body consumption, and systemic respiratory quotient, while moderately improving diastolic and contractile function. Consistently, FSTL1 prevented the downregulation of medium-chain acyl-CoA dehydrogenase—a representative enzyme of the free fatty acid oxidation pathway. Complementary in vitro experiments in primary cardiac and skeletal muscle myocytes showed that FSTL1 stimulated oxygen consumption through AMPK (AMP-activated kinase) activation. Conclusions These findings support a novel function for FSTL1 and provide the first direct evidence that a circulating cardiokine/myokine can alter myocardial and systemic energy substrate metabolism, in vivo.

We use some notions from computability in an uncountable setting to describe a difference between the “Zilber field” of size ℵ 1 and the “Zilber cover” of size ℵ 1 .

We show that a pseudo-Anosov map on a boundary component of an irreducible 3-manifold has a power that partially extends to the interior if and only if its (un)stable lamination is a projective limit of meridians. The proof is through 3-dimensional hyperbolic geometry, and involves an investigation of algebraic limits of convex cocompact compression bodies., 29 pages

For a Heegaard surface F in a closed orientable 3-manifold M, H(M,F) = Diff(M)/Diff(M,F) is the space of Heegaard surfaces equivalent to the Heegaard splitting (M,F). Its path components are the isotopy classes of Heegaard splittings equivalent to (M,F). We describe H(M,F) in terms of Diff(M) and the Goeritz group of (M,F). In particular, for hyperbolic M each path component is a classifying space for the Goeritz group, and when the (Hempel) distance of (M,F) is greater than 3, each path component of H(M,F) is contractible. For splittings of genus 0 or 1, we determine the complete homotopy type (modulo the Smale Conjecture for M in the cases when it is not known)., Comment: Minor rewriting as suggested by referee, no change in mathematical content. To appear in J. Reine Angew. Math

A clustering algorithm partitions a set of data points into smaller sets (clusters) such that each subset is more tightly packed than the whole. Many approaches to clustering translate the vector data into a graph with edges reflecting a distance or similarity metric on the points, then look for highly connected subgraphs. We introduce such an algorithm based on ideas borrowed from the topological notion of thin position for knots and 3-dimensional manifolds., Comment: 12 pages, 2 figures

In this paper, we give an example of a complete computable infinitary theory T with countable models \({\mathcal{M}}\) and \({\mathcal{N}}\) , where \({\mathcal{N}}\) is a proper computable infinitary extension of \({\mathcal{M}}\) and T has no uncountable model. In fact, \({\mathcal{M}}\) and \({\mathcal{N}}\) are (up to isomorphism) the only models of T. Moreover, for all computable ordinals α, the computable \({\Sigma_\alpha}\) part of T is hyperarithmetical. It follows from a theorem of Gregory (JSL 38:460–470, 1972; Not Am Math Soc 17:967–968, 1970) that if T is a Π11 set of computable infinitary sentences and T has a pair of models \({\mathcal{M}}\) and \({\mathcal{N}}\) , where \({\mathcal{N}}\) is a proper computable infinitary extension of \({\mathcal{M}}\) , then T would have an uncountable model.

Stochastic walk-on-spheres (WOS) algorithms for solving the linearized Poisson-Boltzmann equation (LPBE) provide several attractive features not available in traditional deterministic solvers: Gaussian error bars can be computed easily, the algorithm is readily parallelized and requires minimal memory and multiple solvent environments can be accounted for by reweighting trajectories. However, previously-reported computational times of these Monte Carlo methods were not competitive with existing deterministic numerical methods. The present paper demonstrates a series of numerical optimizations that collectively make the computational time of these Monte Carlo LPBE solvers competitive with deterministic methods. The optimization techniques used are to ensure that each atom’s contribution to the variance of the electrostatic solvation free energy is the same, to optimize the bias-generating parameters in the algorithm and to use an epsilon-approximate rather than exact nearest-neighbor search when determining the size of the next step in the Brownian motion when outside the molecule.

Rationale:Various types of viable stem cells have been reported to result in modest improvement in cardiac function after acute myocardial infarction. The mechanisms for improvement from different stem cell populations remain unknown. Objective:To determine whether irradiated (nonviable) embryonic stem cells (iESCs) improve postischemic cardiac function without adverse consequences. Methods and Results:After coronary artery ligation-induced cardiac infarction, either conditioned media or male murine or male human iESCs were injected into the penumbra of ischemic myocardial tissue of female mice or female rhesus macaque monkeys, respectively. Murine and human iESCs, despite irradiation doses that prevented proliferation and induced cell death, significantly improved cardiac function and decreased infarct size compared with untreated or media-treated controls. Fluorescent in situ hybridization of the Y chromosome revealed disappearance of iESCs within the myocardium, whereas 5-bromo-2′-deoxyuridine assays r...

The mapping class group of a Heegaard splitting is the group of connected components in the set of automorphisms of the ambient manifold that map the Heegaard surface onto itself. For the genus-three Heegaard splitting of the 3-torus, we find an eight element generating set for this group. Six of these generators induce generating elements of the mapping class group of the 3-torus and the remaining two are isotopy trivial in the 3-torus.

Many well-preserved bones of medium-sized goose have been recovered from the Zeto Point archaeological site (ADK-011) on Adak Island in the central Aleutians, Alaska, that date to ca. 170–415 years before present based on conventional radiometric dates of the deposits. This prehistoric sample includes remains of adults and unfledged goslings that defied confident identification based on osteological criteria. While the presence of newborns indicates that Adak was a breeding ground, which species was doing the nesting remained uncertain. Of the five species of medium-sized goose (order Anseriformes, family Anatidae) known or presumed to visit Adak Island, three are rarely sighted. The only common visitor is the Emperor Goose ( Chen canagica (Sevastianov, 1802)). The Aleutian Cackling Goose ( Branta hutchinsii leucopareia (Brandt, 1836)) breeds elsewhere in the Aleutians but does not currently breed on Adak Island and there are no records of it nesting there in the past. Here DNA sequences from portions of the cytochrome b (cytb) gene and the control region (CR) of the mitochondrial genome were recovered from 28 of 29 Adak prehistoric goose remains. All adult specimens identified to species were either C. canagica or B. h. leuopareia, but all specifically identified juvenile specimens were B. h. leuopareia. The results demonstrate that Adak Island was a breeding ground of the Aleutian Cackling Goose prior to European contact.

This study was designed to address issues regarding sample size and marker location that have arisen from the discovery of SNPs in the genomes of poorly characterized primate species and the application of these markers to the study of primate population genetics. We predict the effect of discovery sample size on the probability of discovering both rare and common SNPs and then compare this prediction with the proportion of common and rare SNPs discovered when different numbers of individuals are sequenced. Second, we examine the effect of genomic region on estimates of common population genetic data, comparing markers from both coding and non-coding regions of the rhesus macaque genome and the population genetic data calculated from these markers, to measure the degree and direction of bias introduced by SNPs located in coding versus non-coding regions of the genome. We found that both discovery sample size and genomic region surveyed affect SNP marker attributes and population genetic estimates, even when these are calculated from an expanded data set containing more individuals than the original discovery data set. Although none of the SNP detection methods or genomic regions tested in this study was completely uninformative, these results show that each has a different kind of genetic variation that is suitable for different purposes, and each introduces specific types of bias. Given that each SNP marker has an individual evolutionary history, we calculated that the most complete and unbiased representation of the genetic diversity present in the individual can be obtained by incorporating at least 10 individuals into the discovery sample set, to ensure the discovery of both common and rare polymorphisms.

In the curve complex for a surface, a handlebody set is the set of loops that bound properly embedded disks in a given handlebody bounded by the surface. A boundary set is the set of non-separating loops in the curve complex that bound two-sided, properly embedded surfaces. For a Heegaard splitting, the distance between the boundary sets of the handlebodies is zero if and only if the ambient manifold contains a non-separating, two sided incompressible surface. We show that the boundary set is 2-dense in the curve complex, i.e. every vertex is within two edges of a point in the boundary set., 6 pages

We define integral measures of complexity for Heegaard splittings based on the graph dual to the curve complex and on the pants complex defined by Hatcher and Thurston. As the Heegaard splitting is stabilized, the sequence of complexities turns out to converge to a non-trivial limit depending only on the manifold. We then use a similar method to compare different manifolds, defining a distance which converges under stabilization to an integer related to Dehn surgeries between the two manifolds., This is the version published by Algebraic & Geometric Topology on 11 July 2006

A finite element model for ice sheets has been modified to include an accounting of basal melt water. The calculated amount of basal water is used to find the velocity of ice sliding over the bed. The interplay of the basal water and sliding velocity is investigated by a series of modeling experiments. Simulations of the interception, growth, and de-glaciation of the Northern Hemisphere are considered. The simulations are driven with a climate controlled by the GRIP ice core data. The experiments contrast a number of different mechanisms for relating the amount of basal water and the sliding velocity. The mechanisms range from no sliding whatsoever, to a scheme in which the sliding velocity is proportional to the amount of basal water. The modeled results demonstrate that choice of sliding mechanism has a dramatic effect on the glaciation cycle. Furthermore, modeling results indicate that the sliding velocity must be related to the basal water depth to correctly simulate a complete glacial cycle. The relation is important to inception and all other phases of a glacial cycle. The volume of the ice at the last glacial maximum can be compared to the estimated sea level rise to further constrain the new modeling approaches.

We show that every knot is one crossing change away from a knot of arbitrarily high bridge number and arbitrarily high bridge distance., Comment: Accepted by American Mathematical Monthly. New version incorporates referee comments

We show that the Kakimizu complex of minimal genus Seifert surfaces for a knot in the 3-sphere is quasi-isometric to a Euclidean integer lattice $\mathbb Z^n$ for some $n \geq 0$., Comment: 12 pages. Improvements to the exposition made in version 2

In this paper, we characterize all links in the 3-sphere with bridge number at least three that have a bridge sphere of distance two. We show that a link L has a bridge sphere of distance at most two then it falls into at least one of three categories: (1) The exterior of L contains an essential meridional sphere. (2) L can be decomposed as a tangle product of a Montesinos tangle with an essential tangle in a way that respects the bridge surface and either the Montesinos tangle is rational or the essential tangle contains an incompressible, boundary-incompressible annulus. (3) L is obtained by banding from another link L' that has a bridge sphere of the same Euler characteristic as the bridge sphere for L but of distance 0 or 1., 27 pages, 13 figures

To gain a better understanding of North American population history, complete mitochondrial genomes (mitogenomes) were generated from four ancient and three living individuals of the northern Northwest Coast of North America, specifically the north coast of British Columbia, Canada, current home to the indigenous Tsimshian, Haida, and Nisga’a. The mitogenomes of all individuals were previously unknown and assigned to new sub-haplogroup designations D4h3a7, A2ag and A2ah. The analysis of mitogenomes allows for more detailed analyses of presumed ancestor–descendant relationships than sequencing only the HVSI region of the mitochondrial genome, a more traditional approach in local population studies. The results of this study provide contrasting examples of the evolution of Native American mitogenomes. Those belonging to sub-haplogroups A2ag and A2ah exhibit temporal continuity in this region for 5000 years up until the present day. Of possible associative significance is that archaeologically identified house structures in this region maintain similar characteristics for this same period of time, demonstrating cultural continuity in residence patterns. The individual dated to 6000 years before present (BP) exhibited a mitogenome belonging to sub-haplogroup D4h3a. This sub-haplogroup was earlier identified in the same general area at 10300 years BP on Prince of Wales Island, Alaska, and may have gone extinct, as it has not been observed in any living individuals of the Northwest Coast. The presented case studies demonstrate the different evolutionary paths of mitogenomes over time on the Northwest Coast.

We calculate the bridge distance for $m$-bridge knots/links in the $3$-sphere with sufficiently complicated $2m$-plat projections. In particular we show that if the underlying braid of the plat has $n - 1$ rows of twists and all its exponents have absolute value greater than or equal to three then the distance of the bridge sphere is exactly $\lceil n/(2(m - 2)) \rceil$, where $\lceil x \rceil$ is the smallest integer greater than or equal to $x$. As a corollary, we conclude that if such a diagram has more than $4m(m-2)$ rows then the bridge sphere defining the plat projection is the unique minimal bridge sphere for the knot., Comment: 21 pages 13 figures

The development of DNA markers is becoming increasingly useful in the field of primatology for studies on paternity, population history, and biomedical research. In this study, we determine the efficacy of using cross-species amplification to identify single nucleotide polymorphisms (SNPs) in closely related species. The DNA of 93 individuals representing seven Old World Monkey species was analyzed to identify SNPs using cross-species amplification and genotyping. The loci genotyped were 653 SNPs identified and validated in rhesus macaques. Of the 653 loci analyzed, 27% were estimated to be polymorphic in the samples studied. SNPs identified at the same locus among different species (coincident SNPs) were found in six of the seven species studied with longtail macaques exhibiting the highest number of coincident SNPs (84). The distribution of coincident SNPs among species is not biased based on proximity to genes in the samples studied. In addition, the frequency of coincident SNPs is not consistent with expectations based on their phylogenetic relationships. This study demonstrates that cross-species amplification and genotyping using the Illumina Golden Gate Array is a useful method to identify a large number of SNPs in closely related species, although issues with ascertainment bias may limit the type of studies where this method can be applied.

We define a combinatorial structure on 3-manifolds that combines the model manifolds constructed in Minsky's proof of the ending lamination conjecture with the layered triangulations defined by Jaco and Rubinstein., 12 pages

Results from the Heinrich Event INtercOmparison (HEINO) topic of the Ice-Sheet Model Intercomparison Project (ISMIP) are presented. ISMIP HEINO was designed to explore internal large-scale ice-sheet instabilities in different contemporary ice-sheet models. These instabilities are of interest because they are a possible cause of Heinrich events. A simplified geometry experiment reproduces the main characteristics of the Laurentide ice sheet, including the sedimented region over Hudson Bay and Hudson Strait. The model experiments include a standard run plus seven variations. Nine dynamic/thermodynamic ice-sheet models were investigated; one of these models contains a combination of the shallow-shelf (SSA) and shallow-ice approximation (SIA), while the remaining eight models are of SIA type only. Seven models, including the SIA-SSA model, exhibit oscillatory surges with a period of ?1000 years for a broad range of parameters, while two models remain in a permanent state of streaming for most parameter settings. In a number of models, the oscillations disappear for high surface temperatures, strong snowfall and small sediment sliding parameters. In turn, low surface temperatures and low snowfall are favourable for the ice-surge cycles. We conclude that further improvement of ice-sheet models is crucial for adequate, robust simulations of cyclic large-scale instabilities.

We show that sub-surfaces of a Heegaard surface for which the relative Hempel distance of the splitting is sufficiently high have to appear in any Heegaard surface of genus bounded by half that distance., Comment: 23 pages and 5 figures

We show that if the Hempel distance of a Heegaard splitting is larger than three then the mapping class group of the Heegaard splitting is isomorphic to a subgroup of the mapping class group of the ambient 3-manifold. This implies that given two handlebody sets in the curve complex for a surface that are distance at least four apart, the group of automorphisms of the curve complex that preserve both handlebody sets is finite., 9 pages, 1 figure

The topological index of a surface was previously introduced by the first author as the topological analogue of the index of an unstable minimal surface. Here we show that surfaces of arbitrarily high topological index exist., 8 pages, 1 figure

Mitochondrial DNA analysis of 31 unrelated Shuswap speakers from a previously poorly sampled region of North America revealed two individuals with haplogroups rarely found in the Americas, C4c and C1d. Comparison of the complete genomes of the two individuals with others found in the literature confirms that C4c is a founding haplotype and gives insight into the evolution of the C1d haplotype. This study demonstrates the importance of collecting and analyzing data from Native North Americans when addressing hypotheses about the peopling of the Americas.

We show that if $K$ is a knot in $S^3$ and $\Sigma$ is a bridge sphere for $K$ with high distance and $2n$ punctures, the number of perturbations of $K$ required to interchange the two balls bounded by $\Sigma$ via an isotopy is $n$. We also construct a knot with two different bridge spheres with $2n$ and $2n-1$ bridges respectively for which any common perturbation has at least $3n-1$ bridges. We generalize both of these results to bridge surfaces for knots in any 3-manifold., Comment: 20 pages, 7 figures