Time to the MRCA of a sample in a Wright–Fisher model with variable population size

Determining the expected distribution of the time to the most recent common ancestor of a sample of individuals may deliver important information about the genetic markers and evolution of the population. In this paper, we introduce a new recursive algorithm to calculate the distribution of the time to the most recent common ancestor of the sample from a population evolved by any conditional multinomial sampling model. The most important advantage of our method is that it can be applied to a sample of any size drawn from a population regardless of its size growth pattern. We also present a very efficient method to implement and store the genealogy tree of the population evolved by the Galton–Watson process. In the final section we present results applied to a simulated population with a single bottleneck event and to real populations of known size histories.     

Critical test of bead–spring model to resolve the scaling laws of polymer melts: a molecular dynamics study

Abstract

To examine the intrinsic nature of the bead–spring Kremer–Grest (KG) model, long-time molecular dynamics simulations are performed. Certain scaling laws for representative polymer properties are compared with theoretical predictions. The results for static properties satisfy the expected static Gaussian nature, irrespective of the chain length. In contrast, the results for the dynamic properties of short chains show a clear discrepancy from theoretical predictions that assume ideal chain motion. This is clear evidence that the Gaussian nature of the dynamics of short chains is not necessarily established for the actual KG model, despite it being designed to have Gaussian characteristics by virtue of its stochastic equations of motion. This intrinsic nature of the KG model should be considered carefully when using this model for applications that involve relatively short chains.     

Egg size in relation to body size in rotifers: an indication of reproductive strategy?

Egg sizes and body sizes of 43 egg-bearing rotifer species of numerous, mostly tropical, general have been recorded. Larger absolute egg volumes have been found for larger rotifer species, but the increase was lower than expected in proportion to body size, i.e. the relative egg volume decreased with increasing body size. Obviously the relative investment per offspring is smaller in larger rotifer species.     

Fisheries-Led Development in the South Pacific: Charting a “Pacific Way” to a Sustainable Future

Considerable debate surrounds the appropriate mix of policies to drive fishing-led development among the developing nations in the South Pacific. Since the 1970s, South Pacific small island states have committed themselves to policies of tuna industry domestication, but serious doubts have emerged as to whether these can deliver improvements to the well-being of Pacific peoples. An alternative policy approach has been suggested by development economists that would see Pacific Island nations largely abandon direct involvement in the industry and return to collective efforts to secure reasonable access fees from distant water fishing nations that take the majority of the region's tuna catches. This article argues that one reason that this policy shift has not been taken is that tuna industry domestication policies remain bound up within the influential discourse of “resource nationalism.” It is contended that any movement toward a more environmentally and developmentally sustainable ocean fisheries policy will require close engagement and transformation of this sovereignty-focused narrative.     

Elasticity and geometry: a computational model of the Heineke–Mikulicz strictureplasty

Crohn’s disease is a challenging inflammatory process with a propensity for focal gastro-intestinal tract inflammation and stricture. Surgically, Crohn’s is often treated with resection. However, a subtype of diffuse disease with multiple strictures is treated by strictureplasty procedures in hope of avoiding short-gut syndrome. Prior work by Pocivavsek et al. defined the geometry of a Heineke–Mikulicz strictureplasty. Here, we bring this analysis one step closer to clinical and biological relevance by calculating the mechanical stresses and strains that the strictureplasty deformation generates on a model intestinal wall. The small bowel is simulated as a linearly elastic isotropic deformable cylindrical shell using finite element modeling. Data show a divergence in elastic response between the anti-mesenteric and mesenteric halves. The anti-mesenteric surface shows a bending dominated elastic response that correlates with the prior purely geometric analysis. However, the mesenteric half is not a neutral bystander during strictureplasty formation, as geometric arguments predict. Strong in-plane stretching strains develop in a rim around the image of the transverse closure, which may impact local perfusion and serve as sites of disease recurrence. Lastly, nearly all the deformation energy is stored in the central vertex stitch, placing this part at highest risk of dehiscence. This study enhances our understanding of mechanical response in complex nonlinear cylindrical geometries like the surgically manipulated intestinal tract. The developed framework serves as a platform for future addition of more complex clinically relevant parameters to our model, including real tissue properties, anisotropy, blood supply modeling, and patient deriver anatomic factors.     

Tentative identification of a vasopressin–neurophysin and an oxytocin–neurophysin in the rat

1. Rat neurohypophysial extracts have been examined by polyacrylamide-gel electrophoresis. 2. Three of the proteins were tentatively identified as neurophysins by their acidic nature and their disappearance after dehydration of the animals. 3. These proteins were radioactive 24h after intracisternal injection of [(35)S]cysteine. 4. Two of the proteins were present in much greater quantities than the third, and these two were present in the gland in the same ratio as the hormones vasopressin and oxytocin. 5. One of these proteins was absent from glands of rats homozygous for diabetes insipidus but present in heterozygous animals. 6. It is suggested that these two proteins are the vasopressin-neurophysin and oxytocin-neurophysin of the rat.     

Is the island biogeography model a poor predictor of biodiversity patterns in shallow lakes?

1. The classic island biogeography model (IBM) predicts highest species richness in large, connected habitats due to colonisation and reduced risk of extinction. Promoting large, connected habitats has subsequently become a common theme in conservation biology.
2. However, the IBM does not account for direct and indirect interactions among species. For example, planktivorous and benthivorous fish may reduce biodiversity in shallow lakes by inducing shifts to a turbid‐water lake state with low habitat complexity.
3. We assessed relationships between species richness, landscape features, fish biomass and lake state in 104 shallow lakes in Minnesota, U.S.A. First, we tested whether lake size and connectivity influenced species richness of fish and biomass of planktivores and benthivores (fish biomass). We subsequently tested whether fish biomass affected the probability that lakes were in turbid versus clear‐water states. Finally, we tested whether species richness of macrophytes and taxon richness of aquatic invertebrates showed stronger relationships with lake size and connectivity or with fish biomass and lake state.
4. Fish richness and biomass both increased with lake size and were higher in connected basins. Fish biomass, in turn, increased the probability that lakes would be turbid. In contrast, macrophyte and invertebrate richness were unrelated to lake size or connectivity. Instead, macrophyte richness was best predicted by lake state, while invertebrate richness was predicted by lake state and fish biomass. Richness of both macrophytes and invertebrates was higher in clear lakes, and invertebrate richness was inversely related to fish biomass.
5. Our results indicate the IBM poorly explains the diversity of macrophytes and invertebrates in shallow lakes, with diversity more strongly driven by biotic interactions and influences associated with fish. We suggest that ecological implications of increased connectivity and lake size should be considered in future conservation strategies for shallow lakes.

     

Scaling VOI size in 3D μCT studies of trabecular bone: a test of the over-sampling hypothesis

For comparative 3D microCT studies of trabecular bone, the use of a volume of interest (VOI) scaled to body size may avoid over-sampling the trabecular mass in smaller versus larger-bodied taxa and comparison of regions that are not functionally homologous (Fajardo and Müller: Am J Phys Anthropol 115 (2001) 327-336), though the influence on quantitative analyses using scaled versus nonscaled VOIs remains poorly characterized. We compare trabecular architectural properties reflecting mass, organization, and orientation from three volumes of interest (large, scaled, and small) obtained from the distal first metacarpal in a sample of Homo (n = 10) and Pan (n = 12). We test the null hypotheses that neither absolute VOI size, nor scaling of the VOI to metacarpal size as a proxy for body size, biases intraspecific analyses nor impacts the detection of interspecific differences. These hypotheses were only partially supported. While certain properties (e.g., bone volume fraction or trabecular thickness) were not affected by varying VOI size within taxa, others were significantly impacted (e.g., intersection surface, connectivity, and structure). In comparing large versus scaled VOIs, we found that the large VOI inflated the number and/or magnitude of significant differences between Homo and Pan. In summary, our results support the use of scaled VOIs in studies of trabecular architecture.     

Spatial synchronization of the θ and α band cortical electrical oscillations in the formation of a set to an angry face expression in 5- to 11-year-old children

The θ and α band EEG coherence during forming and testing sets to an emotionally negative facial expression (angry) was studied in five- to six-year-old (n = 18) and 10- to 11-year-old (n = 25) children. Younger children displayed lower coherence values, especially in the right hemisphere, than older ones. Differences in θ- and α band coherence in the cases of rigid and flexible sets to an angry face expression were also revealed. With relatively rigid forms of cognitive activity, the EEG coherence values were lower. A correlation between the electrophysiological and behavioral data was established. It supports the hypothesis that two functional brain integration systems, the corticohippocampal and the frontothalamic ones, play a role in the processes of facial expression recognition and provide cognition flexibility.     

Establishment of a pancreatic β cell proliferation model in vitro and a platform for diabetes drug screening

Diabetes, a disease resulting from loss of functional β cells, is globally an increasingly important condition. Based on the islet-differentiation ability of ductal epithelial cells and stimulating β cell proliferation ability of the Reg Iα gene, we aimed to establish an in vitro pancreatic β cell proliferation model for screening therapeutic drugs of diabetes in the future. Pancreatic ductal epithelial cells were isolated from male Wistar rats, and induced to differentiate into pancreatic β cells. Immunofluorescence staining assay, western blot, RT-PCR analysis, and dithizone staining were used to characterize the cells. Rat Reg Iα protein was transiently expressed in vitro by transfection of HEK 293 cells with the PCMV6-entry-REG Ia plasmid, and expression was verified by RT-PCR analysis, proliferation assay, and apoptosis assay. The pancreatic β cell proliferation model was further validated by a proliferation assay using differentiated pancreatic β cells treated with transfection supernatant. Finally, we have successfully established an in vitro pancreatic β cells proliferation model using transiently expressed rat Reg Iα protein and differentiated pancreatic β cells from pancreatic ductal epithelial cells. This model could be used as a platform to screen new drugs for islet neogenesis to cure diabetes, especially Chinese herbal drugs in the future.     

The effect of the entry and re-entry size in the aortic dissection: a two-way fluid–structure interaction simulation

Biomechanics and Modeling in Mechanobiology - Aortic dissection (AD) is one of the most catastrophic cardiovascular diseases. AD occurs when a layer inside the aorta is disrupted and gives rise to...     

Spatio-temporal pattern formation in Rosenzweig–MacArthur model: Effect of nonlocal interactions

Spatio-temporal pattern formation in reaction–diffusion models of interacting populations is an active area of research due to various ecological aspects. Instability of homogeneous steady-states can lead to various types of patterns, which can be classified as stationary, periodic, quasi-periodic, chaotic, etc. The reaction–diffusion model with Rosenzweig–MacArthur type reaction kinetics for prey–predator type interaction is unable to produce Turing patterns but some non-Turing patterns can be observed for it. This scenario changes if we incorporate non-local interactions in the model. The main objective of the present work is to reveal possible patterns generated by the reaction–diffusion model with Rosenzweig–MacArthur type prey–predator interaction and non-local consumption of resources by the prey species. We are interested in the existence of Turing patterns in this model and in the effect of the non-local interaction on the periodic travelling wave and spatio-temporal chaotic patterns. Global bifurcation diagrams are constructed to describe the transition from one pattern to another one.     

Evaluating DMS measurements and model results in the Northeast subarctic Pacific from 1996–2010

About a decade of dimethylsulphide (DMS) measurements in the North East Pacific are summarized and compared to model simulations. Bottle samples at various depths have been taken three times per year along Line P from the British Columbia coast to Ocean Station Papa (145°?W, 50°?N). Despite the long timeseries, DMS measurements are still sparse and the data show large variabilities in concentrations both spatially and temporally. DMS concentrations in late summer have been consistently high, while spring measurements at the offshore stations suggest a downward trend over the past years. Low values in spring, however, have also been recorded in the late 1990s, which might hint to interannual variability in the onset of the spring bloom and/or plankton assemblage rather than to a response to recent climate change. Some of the variability, both short-term and interannual, can be caused by regional or local preconditioning of the physical environment. The model simulations provide examples where periods of low winds, shallow mixed layers and sometimes high irradiance follow a mixing event and cause DMS peaks on various time scales as well as consistently elevated DMS concentrations for longer timeperiods. The model in its current configuration, which has been calibrated with measurements in the late 1990s/early 2000s, is not able to capture the low values in winter and spring observed in recent years. We suggest that this is due to missing or misrepresented links in the biogeochemical parameterizations of the model, e.g., an incomplete representation of variations in the phytoplankton assemblage. Including a seasonally varying S:N ratio to account for the absence of dinoflagellates in winter and spring significantly improves the simulation. Variability in DMS concentrations can also be induced by natural iron fertilization, which the model reproduces when timing is specified. For example, the model can reproduce the effects of natural volcanic Fe fertilization on surface water plankton dynamics and mixed layer DMS accumulation. The model also shows that the amplitude of the short term variability (days) increases when DMSP producing phytoplankton are less iron limited.     

The dynamics of the lynx–hare system: an application of the Lotka–Volterra model

The Lotka–Volterra model of predator–prey dynamics was used for approximation of the wellknown empirical time series on the lynx–hare system in Canada that was collected by the Hudson Bay Company in 1845–1935. The model was assumed to demonstrate satisfactory data approximation if the sets of deviations of the model and empirical data for both time series satisfied a number of statistical criteria (for the selected significance level). The frequency distributions of deviations between the theoretical (model) trajectories and empirical datasets were tested for symmetry (with respect to the Y-axis; the Kolmogorov–Smirnov and Lehmann–Rosenblatt tests) and the presence or absence of serial correlation (the Swed–Eisenhart and “jumps up–jumps down” tests). The numerical calculations show that the set of points of the space of model parameters, when the deviations satisfy the statistical criteria, is not empty and, consequently, the model is suitable for describing empirical data.     

Does prey size matter? Novel observations of feeding in the leatherback turtle (Dermochelys coriacea) allow a test of predator–prey size relationships

Optimal foraging models predict that large predators should concentrate on large prey in order to maximize their net gain of energy intake. Here, we show that the largest species of sea turtle, Dermochelys coriacea, does not strictly adhere to this general pattern. Field observations combined with a theoretical model suggest that a 300 kg leatherback turtle would meet its energetic requirements by feeding for 3-4 h a day on 4 g jellyfish, but only if prey were aggregated in high-density patches. Therefore, prey abundance rather than prey size may, in some cases, be the overriding parameter for foraging leatherbacks. This is a classic example where the presence of small prey in the diet of a large marine predator may reflect profitable foraging decisions if the relatively low energy intake per small individual prey is offset by high encounter rates and minimal capture and handling costs. This study provides, to our knowledge, the first quantitative estimates of intake rate for this species.     

Is the remodeling of the polyp prepattern in a hydrozoan planula a function of larval age or size and is it of “adaptive” significance?

Eggs of medusae develop into lecithotrophic planulae that undergo metamorphosis at different ages to form polyps. As planulae age they decrease in size as their yolk stores are utilized. The planulae of most Phialidium medusae develop into polyps where there is a decrease in the size of the holdfast region and a relative increase in the size of the hydranth region as they age. These changes occur independently of the decrease in planula size. In planulae with a decrease in the size of the holdfast region and an increase in the size of the hydranth-forming region there was a 50% decline in polyps that successfully stayed attached to the substrate after metamorphosis. These aged planulae produced an initial hydranth with the same number of tentacles as polyps from full-sized young planulae while young half-sized planulae produced hydranths where the tentacle number was smaller. The first phase of polyp colony growth with a small initial hydranth was slower than growth of a colony with a larger initial hydranth. Predation during this period led to more death in colonies with a small initial hydranth. The decline in successful attachment in aged planulae was not offset by the higher rate of growth and a smaller window of time where predation leads to death, suggesting that this age-related developmental change in planulae was not adaptive.