Perturbation approaches for integral projection models

Perturbation analysis of population models is fundamental to elucidating mechanisms of population dynamics and examining scenarios of change. The use of integral projection models (IPMs) has increased in the last decade, and while many of the tools and approaches developed for matrix models remain relevant, the nature of IPMs expands the framework of perturbation analysis, with different approaches often requiring important considerations. This article provides a review of – and practical guide to – different perturbation approaches for IPMs, formalizes methodologies for perturbing IPM size transition probabilities, and highlights areas where researchers should be particularly careful and critical when conducting and interpreting perturbation analysis. I use a simulated dataset to compare five hierarchical perturbation approaches for IPMs found within 63 published studies, and apply a combination of approaches to the example of an invasive perennial plant. Other perturbation approaches for IPMs are also highlighted. Most perturbation analyses for IPMs to date have focused on the response of the asymptotic population growth rate (λ) to changes in elements of the discretized projection kernel and/or the growth– survival and reproduction– recruitment sub‐kernels. Perturbations to vital rate functions and regression predictions underlying these kernels provide mechanistic insight, but are less common and can require important considerations regarding the perturbation of size transitions separate from survival and the nature of the state variable (used to represent size). The second most common approach is more specific to IPMs and examines the influence of vital rate regression parameters, each of which can have broad influence on the population growth rate. Researchers using IPMs have many perturbation options available and should carefully consider which approach or combination of approaches is most applicable and interpretable for their specific questions.     

The Influence of Physical Habitat,Pyrethroids, and Metals on Benthic Community Condition in an Urban and Residential Stream in California

This study was designed to characterize benthic communities and physical habitat in both an urban (Kirker Creek) and residential (Pleasant Grove Creek) stream in California in late spring of 2006 and 2007. Concurrent water quality evaluations, physical sediment parameters, pyrethroids, bulk metals, and SEM/AVS ratios were also measured during both years of this study. The relationship of various benthic metrics to physical habitat metrics, pyrethroids, and metals was evaluated for each stream using stepwise multiple linear regressions with both years combined for each stream, as well as both years and both streams combined, to increase the statistical power for determining significant relationships. Physical habitat was determined to be poor in each stream during both years of sampling. More than 100 benthic taxa were reported annually for both streams based on 2006 and 2007 sampling. A significant result from the stepwise regression analysis combining data for 2 years across both streams is that when habitat metrics and to a lesser degree metals are considered in the statistical models pyrethroids do not display any significant relationships to the benthic metrics. In summary, it is apparent from this analysis that the health of benthic communities in both streams is primarily affected by habitat metrics.     

FogBank: a single cell segmentation across multiple cell lines and image modalities

Background

Many cell lines currently used in medical research, such as cancer cells or stem cells, grow in confluent sheets or colonies. The biology of individual cells provide valuable information, thus the separation of touching cells in these microscopy images is critical for counting, identification and measurement of individual cells. Over-segmentation of single cells continues to be a major problem for methods based on morphological watershed due to the high level of noise in microscopy cell images. There is a need for a new segmentation method that is robust over a wide variety of biological images and can accurately separate individual cells even in challenging datasets such as confluent sheets or colonies.

Results

We present a new automated segmentation method called FogBank that accurately separates cells when confluent and touching each other. This technique is successfully applied to phase contrast, bright field, fluorescence microscopy and binary images. The method is based on morphological watershed principles with two new features to improve accuracy and minimize over-segmentation.First, FogBank uses histogram binning to quantize pixel intensities which minimizes the image noise that causes over-segmentation. Second, FogBank uses a geodesic distance mask derived from raw images to detect the shapes of individual cells, in contrast to the more linear cell edges that other watershed-like algorithms produce.We evaluated the segmentation accuracy against manually segmented datasets using two metrics. FogBank achieved segmentation accuracy on the order of 0.75 (1 being a perfect match). We compared our method with other available segmentation techniques in term of achieved performance over the reference data sets. FogBank outperformed all related algorithms. The accuracy has also been visually verified on data sets with 14 cell lines across 3 imaging modalities leading to 876 segmentation evaluation images.

Conclusions

FogBank produces single cell segmentation from confluent cell sheets with high accuracy. It can be applied to microscopy images of multiple cell lines and a variety of imaging modalities. The code for the segmentation method is available as open-source and includes a Graphical User Interface for user friendly execution.

Electronic supplementary material

The online version of this article (doi:10.1186/s12859-014-0431-x) contains supplementary material, which is available to authorized users.     

Contrasting genetic trajectories of endangered and expanding red fox populations in the western U.S

As anthropogenic disturbances continue to drive habitat loss and range contractions, the maintenance of evolutionary processes will increasingly require targeting measures to the population level, even for common and widespread species. Doing so requires detailed knowledge of population genetic structure, both to identify populations of conservation need and value, as well as to evaluate suitability of potential donor populations. We conducted a range-wide analysis of the genetic structure of red foxes in the contiguous western U.S., including a federally endangered distinct population segment of the Sierra Nevada subspecies, with the objectives of contextualizing field observations of relative scarcity in the Pacific mountains and increasing abundance in the cold desert basins of the Intermountain West. Using 31 autosomal microsatellites, along with mitochondrial and Y-chromosome markers, we found that populations of the Pacific mountains were isolated from one another and genetically depauperate (e.g., estimated Ne range = 3–9). In contrast, red foxes in the Intermountain regions showed relatively high connectivity and genetic diversity. Although most Intermountain red foxes carried indigenous western matrilines (78%) and patrilines (85%), the presence of nonindigenous haplotypes at lower elevations indicated admixture with fur-farm foxes and possibly expanding midcontinent populations as well. Our findings suggest that some Pacific mountain populations could likely benefit from increased connectivity (i.e., genetic rescue) but that nonnative admixture makes expanding populations in the Intermountain basins a non-ideal source. However, our results also suggest contact between Pacific mountain and Intermountain basin populations is likely to increase regardless, warranting consideration of risks and benefits of proactive measures to mitigate against unwanted effects of Intermountain gene flow.Subject terms: Conservation biology, Population genetics     

A comparison of treatment modes in the management of myofascial pain dysfunction syndrome

This research compares different treatment regimes for the management of chronic facial pain associated with the masticatory musculature. Twenty-one females meeting specific criteria were randomly assigned to one of three treatment conditions: a dental splint and physiotherapy program; a relaxation program utilizing progressive muscle relaxation, biofeedback, and stress management techniques; or a minimal treatment program involving transcutaneous electrical nerve stimulation. Improvement was assessed through a dental examination, self-monitoring of pain, and an assessment of EMG activity during resting and task conditions. Significant changes were obtained in response to all treatment programs. The treatment programs differed only in the relative pattern of treatment effects obtained from the self-report monitoring of pain. The data are consistent with the concept of MPD as a psychological response to stress which maintains chronic pain through increased muscle tension in the jaw.This article is based on a thesis submitted in partial fulfillment of the requirement for a master's degree from the University of British Columbia by the second author. This research was facilitated by National Health and Welfare Grant NAHS 30-9625 and provincial government Youth Employment Program project #1225-01 made to Drs. Crockett and Alden, respectively. The authors would like to thank J. Dory, D.D.S., M.Sc. and B. Lundgren, B.P.T. for their help in completing this project. The authors also would like to thank S. Edwards and J. Snyder for their assistance in the preparation of this paper.     

Some observations on the primitive and definitive erythrocytes of the developing chick

Summary The cytological changes in the primitive and definitive erythrocytes of the incubating chick have been followed. Observations have been made on the nucleoli, vital granules, mitochondria,Golgi apparatus, reticulum ofSinigaglia and the reticulation patterns of the basophilic substance. The cells of the primitive and definitive lines are ordinarily readily distinguished from one another. Data are included on the rate of disappearance of the primitive cells from the circulation. They may persist as long as two weeks after hatching. Giant primitive erythrocytes are common during the first week of incubation. The cells have one, two three or four nuclei. The nuclearplasma relationship is maintained somewhere near a constant. These atypical cells are due to aberrations in mitosis. Data on the percentage of mitosis in both types of erythrocytes are also included. The initial activity of the spleen and bone-marrow is reflected in the blood stream. There is a distinct rise in the proportion of young definitive erythrocytes. An attempt is made to correlate the findings ofHall (1934) on the changing affinity of the hemoglobin for oxygen with the changing blood picture. The primitive line does not persist long enough to account for the phenomenon. It is suggested, however, that the hemoglobin of the erythrocytes produced by the yolk sac may differ from that of the cells produced by the spleen and bone-marrow. With Plates I–III.     

BOOK REVIEWS

Book reviewed in this article:
CENTRAL AND SOUTH AMERICA: Preliminary Report on the Smithsonian Institution-Harvard University Archaeological Expedition to Northwestern Honduras, 1936 . W illiam D uncan S trong , A lfred K idder II and A. J. D rexel P aul , J r .
CENTRAL AND SOUTH AMERICA: An Archaeological Reconnaissance of Northwestern Honduras: A Report of the Work of the Tulane University-Danish National Museum Expedition to Central America 1935 . J ens Y de .     

Biochemical characterization and electron-transfer reactions of sym1, a Rhodobacter capsulatus reaction center symmetry mutant which affects the initial electron donor.

A 51 bp section of the Rhodobacter capsulatus photosynthetic reaction center M subunit gene (nucleotides M562-M612 of the pufM structural sequence) encoding amino acids M187-M203 was replaced by the homologous region of the L subunit gene. This resulted in the symmetrization of much of the amino acid environment of the reaction center initial electron donor, P. This is the first in a series of large-scale symmetry mutations and is referred to as sym1. The sym1 mutant was able to grow photosynthetically, indicating that reaction center function was largely intact. Isolated reaction centers showed an approximately 10-nm blue shift in the QY band of P. The standard free energy change between P* and P+BphA- determined from analysis of the long-lived fluorescence from quinone-reduced reaction centers decreased from about -120 meV in the wild-type to about -75 meV in the sym1 mutant. A 65-70% quantum yield of electron transfer from P* to P+QA- was observed, most of the yield loss occurring between P* and P+BphA-. The decay of the stimulated emission from P* was about 3-fold slower in this mutant than in the wild-type. Time-resolved spectral analysis of the charge-separated intermediates formed in sym1 reaction centers indicated that the major product was P+BphA-. A model-dependent analysis of the observed rates and electron-transfer yields gave the following microscopic rate constants for sym1 reaction centers (wild-type values under the same conditions are given in parentheses): [formula: see text] Analysis of the sym1 mutant, mutants near P made by other groups, and interspecies variation of amino acids in the vicinity of P suggests that the protein asymmetry in the environment of the initial electron donor is important for optimizing the rate and yield of electron transfer, but is not strictly required for overall reaction center function.