Permutation of Two-Term Local Quadrat Variance Analysis: General Concepts for Interpretation of Peaks

Many ecological studies use Two-Term Local Quadrat Variance Analysis (TTLQV) and its derivatives for spatial pattern analysis. Currently, rules for determining variance peak significance are arbitrary. Variance peaks found at block size 1 and at \u3e 50 % of the transect length are the only peaks whose use is explicitly prohibited. Although the use of variance peaks found at block sizes \u3e 10 % of the transect length have also been warned against, many researchers interpret them regardless. We show in this paper that variance peaks derived from TTLQV are subject to additional ‘rules of thumb’. Through the use of randomization and permutation analyses on real and simulated data of species abundance in contiguous plots along a single transect, we show that variance peaks found at block sizes 1, 2 and 3 occur frequently by chance and thus likely do not indicate biologically meaningful patterns. The use of multiple replicate transects decreases the probability of Type II error

Cohesin cleavage by separase is enhanced by a substrate motif distinct from the cleavage site.

Chromosome segregation begins when the cysteine protease, separase, cleaves the Scc1 subunit of cohesin at the metaphase-to-anaphase transition. Separase is inhibited prior to metaphase by the tightly bound securin protein, which contains a pseudosubstrate motif that blocks the separase active site. To investigate separase substrate specificity and regulation, here we develop a system for producing recombinant, securin-free human separase. Using this enzyme, we identify an LPE motif on the Scc1 substrate that is distinct from the cleavage site and is required for rapid and specific substrate cleavage. Securin also contains a conserved LPE motif, and we provide evidence that this sequence blocks separase engagement of the Scc1 LPE motif. Our results suggest that rapid cohesin cleavage by separase requires a substrate docking interaction outside the active site. This interaction is blocked by securin, providing a second mechanism by which securin inhibits cohesin cleavage

Impact of Ground Water Depletion on the Mesquite Community at Edwards Air Force Base, Western Mojave Desert, California

Edwards Air Force Base (EAFB) provides a habitat refugium for mesquite woodlands in the western Mojave Desert of the Antelope Valley. Although many mesquite communities in the arid southwest are considered invasive as they reduce the extent of grazing lands, the community at EAFB is composed primarily of large, widely spaced trees that provide food and shelter for local wildlife species and recreational opportunities for base personnel. Unfortunately, the range of these mesquite trees appears to be contracting as mature and old individuals dominate the community. Although anecdotal evidence suggests that the fall in the local groundwater table is responsible for the decline of the mesquite community at EAFB, no research has been carried out to confirm this. Our results corroborate the hypothesis that the groundwater table at EAFB has declined in the second half of the 20th century and that the area of the mesquite community is diminishing. Although the mesquite community expanded vigorously from 1956 to 1968, it contracted considerably from 1984 to 2000. The evidence for this observed decline is reinforced by the results of the age-class analysis as the community in 2003 is made up largely of mature, old, dying and dead trees. Few saplings (older than 2 years) and no new seedlings (1–2 years) are present in the study sites, suggesting that the mesquite community may not be able to replenish itself

New Salamanders (Caudata: Plethodontidae) From Guatemala, with Miscellaneous Notes on Known Species

New salamanders in the genera Bolitoglossa and Dendrotriton are described from the highlands of Guatemala. These species are distinguished from their congeners by morphology and molecular differences, including elements of color pattern. These new species of salamanders were collected over the last 30 years, and for many of them the localities of some of these new species are now badly degradedhttp://deepblue.lib.umich.edu/bitstream/2027.42/111063/1/MP200.pd

Squidpops: A Simple Tool to Crowdsource a Global Map of Marine Predation Intensity

We present a simple, standardized assay, the squidpop, for measuring the relative feeding intensity of generalist predators in aquatic systems. The assay consists of a 1.3-cm diameter disk of dried squid mantle tethered to a rod, which is either inserted in the sediment in soft-bottom habitats or secured to existing structure. Each replicate squidpop is scored as present or absent after 1 and 24 hours, and the data for analysis are proportions of replicate units consumed at each time. Tests in several habitats of the temperate southeastern USA (Virginia and North Carolina) and tropical Central America (Belize) confirmed the assay’s utility for measuring variation in predation intensity among habitats, among seasons, and along environmental gradients. In Belize, predation intensity varied strongly among habitats, with reef\u3eseagrass = mangrove\u3eunvegetated bare sand. Quantitative visual surveys confirmed that assayed feeding intensity increased with abundance and species richness of fishes across sites, with fish abundance and richness explaining up to 45% and 70% of the variation in bait loss respectively. In the southeastern USA, predation intensity varied seasonally,being highest during summer and declining in late autumn. Deployments in marsh habitats generally revealed a decline in mean predation intensity from fully marine to tidal freshwater sites. The simplicity, economy, and standardization of the squidpop assay should facilitate engagement of scientists and citizens alike, with the goal of constructing high-resolution maps of how top-down control varies through space and time in aquatic ecosystems, and addressing a broad array of long-standing hypotheses in macro- and community ecolog

Clustering in surgical trials : database of intracluster correlations

PMID: 22217216 [PubMed - indexed for MEDLINE] PMCID: PMC3311136 Free PMC ArticlePeer reviewedPublisher PD

A 3-D in vitro co-culture model of mammary gland involution.

Involution is a process whereby the mammary gland undergoes extensive tissue remodelling involving exquisitely coordinated cell death, extracellular matrix degradation and adipose tissue regeneration following the weaning of offspring. These processes are mediated in part through Jak/Stat signalling pathways, which can be deregulated in breast cancer. Synthetic in vitro analogues of the breast could become important tools for studying tumorigenic processes, or as personalized drug discovery platforms and predictors of therapeutic response. Ideally, such models should support 3D neo-tissue formation, so as to recapitulate physiological organ function, and be compatible with high-throughput screening methodologies. We have combined cell lines of epithelial, stromal and immunological origin within engineered porous collagen/hyaluronic acid matrices, demonstrating 3D-specific molecular signatures. Furthermore seeded cells form mammary-like branched tissues, with lobuloalveolar structures that undergo inducible involution phenotypes reminiscent of the native gland under hormonal/cytokine regulation. We confirm that autophagy is mediated within differentiated mammary epithelial cells in a Stat-dependent manner at early time points following the removal of a prolactin stimulus (H/WD). In addition, epithelial cells express markers of an M2 macrophage lineage under H/WD, a process that is attenuated with the introduction of the monocyte/macrophage cell line RAW 264.7. Thus, such 3D models are suitable platforms for studying cell-cell interactions and cell death mechanisms in relation to cancer.This is the accepted manuscript. The final version is available from RSC at http://pubs.rsc.org/en/content/articlehtml/2014/ib/c3ib40257f

Rapid Oscillations in Cataclysmic Variables. XVI. DW Cancri

We report photometry and spectroscopy of the novalike variable DW Cancri. The spectra show the usual broad H and He emission lines, with an excitation and continuum slope characteristic of a moderately high accretion rate. A radial-velocity search yields strong detections at two periods, 86.1015(3) min and 38.58377(6) min. We interpret these as respectively the orbital period P_orb of the binary, and the spin period P_spin of a magnetic white dwarf. The light curve also shows the spin period, plus an additional strong signal at 69.9133(10) min, which coincides with the difference frequency 1/P_spin-1/P_orb. These periods are stable over the 1 year baseline of measurement. This triply-periodic structure mimics the behavior of several well-credentialed members of the "DQ Herculis" (intermediate polar) class of cataclysmic variables. DQ Her membership is also suggested by the mysteriously strong sideband signal (at nu_spin-nu_orb), attesting to a strong pulsed flux at X-ray/EUV/UV wavelengths. DW Cnc is a new member of this class, and would be an excellent target for extended observation at these wavelengths.Comment: PDF, 28 pages, 6 tables, 9 figures; accepted, in press, to appear June 2004, PASP; more info at http://cba.phys.columbia.edu

Maximizing geographical efficiency : An analysis of the configuration of Colorado’s trauma system

ACKNOWLEDGEMENT The data used for this study were supplied by the Health Facilities and Emergency Medical Services Division of the Colorado Department of Public Health and Environment, which specifically disclaims responsibility for any analyses, interpretations, or conclusions it has not provided. The data used for this study were supplied by the Health Facilities and Emergency Medical Services Division of the Colorado Department of Public Health and Environment, which specifically disclaims responsibility for any analyses, interpretations, or conclusions it has not provided.Peer reviewedPostprin