The K-Server Dual and Loose Competitiveness for Paging

This paper has two results. The first is based on the surprising observation that the well-known ``least-recently-used'' paging algorithm and the ``balance'' algorithm for weighted caching are linear-programming primal-dual algorithms. This observation leads to a strategy (called ``Greedy-Dual'') that generalizes them both and has an optimal performance guarantee for weighted caching. For the second result, the paper presents empirical studies of paging algorithms, documenting that in practice, on ``typical'' cache sizes and sequences, the performance of paging strategies are much better than their worst-case analyses in the standard model suggest. The paper then presents theoretical results that support and explain this. For example: on any input sequence, with almost all cache sizes, either the performance guarantee of least-recently-used is O(log k) or the fault rate (in an absolute sense) is insignificant. Both of these results are strengthened and generalized in``On-line File Caching'' (1998).Comment: conference version: "On-Line Caching as Cache Size Varies", SODA (1991

A spatial assessment of Brassica napus gene flow potential to wild and weedy relatives in the fynbos biome

The original publication is available at http://www.scielo.org.za/Gene flow between related plant species, and between transgenic and non-transgenic crop varieties, may be considered a form of biological invasion. Brassica napus (oilseed rape or canola) and its relatives are well known for intra- and inter-specific gene flow, hybridisation and weediness. Gene flow associated with B. napus poses a potential ecological risk in the Fynbos Biome of South Africa, because of the existence of both naturalised (alien, weedy) and native relatives in this region. This risk is particularly pertinent given the proposed use of B. napus for biofuel and the potential future introduction of herbicide-tolerant transgenic B. napus. Here we quantify the presence and co-occurrence of S. napus and its wild and weedy relatives in the Fynbos Biome, as a first step in the ecological risk assessment for this crop. Several alien and at least one native relative of B. napus were found to be prevalent in the region, and to be spatially congruent with B. napus fields. The first requirement for potential gene flow to occur has thus been met. In addition, a number of these species have elsewhere been found to be reproductively compatible with S. napus. Further assessment of the potential ecological risks associated with B. napus in South Africa is constrained by uncertainties in the phylogeny of the Brassicaceae, difficulties with morphology-based identification, and poor knowledge of the biology of several of the species involved, particularly under South African conditions.Publishers' versio

Saproxylic beetle diversity in a managed boreal forest : importance of stand characteristics and forestry conservation measures

CITATION: McGeoch, M. A., et al. 2007. Saproxylic beetle diversity in a managed boreal forest: importance of stand characteristics and forestry conservation measures. Diversity and Distributions, 13(4): 418-429. doi:10.1111/j.1472-4642.2007.00350.xThe original publication is available at https://onlinelibrary.wiley.com/journal/14724642Saproxylic beetles constitute a significant proportion of boreal forest biodiversity. However, the long history of timber production in Fennoscandia has significantly reduced the availability of dead wood and is considered a threat to the conservation of saproxylic beetle assemblages. Therefore, since the mid-1990s dead wood retention in harvested stands has formed an integral part of silvicultural practices. However, the contribution of this biodiversity-orientated management approach to conserving saproxylic beetle assemblages in boreal forest landscapes that include production forestry remains largely untested. We examined differences in resident saproxylic beetle assemblages among stands under different management in a boreal forest landscape in Central Sweden, and in particular stands managed according to new conservation-orientated practices. We also investigated the relationship between beetle diversity and forest stand characteristics. Bark of coarse woody debris (CWD) was sieved for beetles in old managed stands, unmanaged nature reserves, and set-aside areas, and clear-cut stands harvested according to certification guidelines [new forestry (NF) clear-cuts]. All stand types contributed significantly to the total diversity of beetles found. While stand size, position, and distance to nearest reserve were unimportant, both the quality and the quantity of CWD in stands contributed significantly to explaining beetle abundance and species richness. This extends the previous findings for red-listed invertebrates, and shows that heterogeneous substrate quality and a range of management practices are necessary to maintain saproxylic beetle diversity in boreal forest landscapes that include production forestry. The unique abiotic conditions in combination with the abundant and varied CWD associated with NF clear-cuts form an important component of forest stand heterogeneity for saproxylic beetles. It is thus essential that sufficient, diverse, CWD is retained in managed boreal landscapes to ensure the conservation of boreal saproxylic beetle assemblages.Centre of Excellence for Invasion Biolog

Mechanistic reconciliation of community and invasion ecology

Community and invasion ecology have mostly grown independently. There is substantial overlap in the processes captured by different models in the two fields, and various frameworks have been developed to reduce this redundancy and synthesize information content. Despite broad recognition that community and invasion ecology are interconnected, a process-based framework synthesizing models across these two fields is lacking. Here we review 65 representative community and invasion models and propose a common framework articulated around six processes (dispersal, drift, abiotic interactions, within-guild interactions, cross-guild interactions, and genetic changes). The framework is designed to synthesize the content of the two fields, provide a general perspective on their development, and enable their comparison. The application of this framework and of a novel method based on network theory reveals some lack of coherence between the two fields, despite some historical similarities. Community ecology models are characterized by combinations of multiple processes, likely reflecting the search for an overarching theory to explain community assembly and structure, drawing predominantly on interaction processes, but also accounting largely for the other processes. In contrast, most models in invasion ecology invoke fewer processes and focus more on interactions between introduced species and their novel biotic and abiotic environment. The historical dominance of interaction processes and their independent developments in the two fields is also reflected in the lower level of coherence for models involving interactions, compared to models involving dispersal, drift, and genetic changes. It appears that community ecology, with a longer history than invasion ecology, has transitioned from the search for single explanations for patterns observed in nature to investigate how processes may interact mechanistically, thereby generating and testing hypotheses. Our framework paves the way for a similar transition in invasion ecology, to better capture the dynamics of multiple alien species introduced in complex communities. Reciprocally, applying insights from invasion to community ecology will help us understand and predict the future of ecological communities in the Anthropocene, in which human activities are weakening species' natural boundaries. Ultimately, the successful integration of the two fields could advance a predictive ecology that is urgently required in a rapidly changing world

Comparison of Langevin and Markov channel noise models for neuronal signal generation

The stochastic opening and closing of voltage-gated ion channels produces noise in neurons. The effect of this noise on the neuronal performance has been modelled using either approximate or Langevin model, based on stochastic differential equations or an exact model, based on a Markov process model of channel gating. Yet whether the Langevin model accurately reproduces the channel noise produced by the Markov model remains unclear. Here we present a comparison between Langevin and Markov models of channel noise in neurons using single compartment Hodgkin-Huxley models containing either $Na^{+}$ and $K^{+}$, or only $K^{+}$ voltage-gated ion channels. The performance of the Langevin and Markov models was quantified over a range of stimulus statistics, membrane areas and channel numbers. We find that in comparison to the Markov model, the Langevin model underestimates the noise contributed by voltage-gated ion channels, overestimating information rates for both spiking and non-spiking membranes. Even with increasing numbers of channels the difference between the two models persists. This suggests that the Langevin model may not be suitable for accurately simulating channel noise in neurons, even in simulations with large numbers of ion channels

A Genome-Wide Comparative Evolutionary Analysis of Herpes Simplex Virus Type 1 and Varicella Zoster Virus

Herpes simplex virus type 1 (HSV-1) and varicella zoster virus (VZV) are closely related viruses causing lifelong infections. They are typically associated with mucocutaneous or skin lesions, but may also cause severe neurological or ophthalmic diseases, possibly due to viral- and/or host-genetic factors. Although these viruses are well characterized, genome-wide evolutionary studies have hitherto only been presented for VZV. Here, we present a genome-wide study on HSV-1. We also compared the evolutionary characteristics of HSV-1 with those for VZV. We demonstrate that, in contrast to VZV for which only a few ancient recombination events have been suggested, all HSV-1 genomes contain mosaic patterns of segments with different evolutionary origins. Thus, recombination seems to occur extremely frequent for HSV-1. We conclude by proposing a timescale for HSV-1 evolution, and by discussing putative underlying mechanisms for why these otherwise biologically similar viruses have such striking evolutionary differences

Risk Prediction Models for Colorectal Cancer Incorporating Common Genetic Variants: A Systematic Review.

Colorectal cancer screening reduces colorectal cancer incidence and mortality. Risk models based on phenotypic variables have relatively good discrimination in external validation and may improve efficiency of screening. Models incorporating genetic variables may perform better. In this review, we updated our previous review by searching Medline and EMBASE from the end date of that review (January 2014) to February 2019 to identify models incorporating at least one SNP and applicable to asymptomatic individuals in the general population. We identified 23 new models, giving a total of 29. Of those in which the SNP selection was on the basis of published genome-wide association studies, in external or split-sample validation the AUROC was 0.56 to 0.57 for models that included SNPs alone, 0.61 to 0.63 for SNPs in combination with other risk factors, and 0.56 to 0.70 when age was included. Calibration was only reported for four. The addition of SNPs to other risk factors increases discrimination by 0.01 to 0.06. Public health modeling studies suggest that, if determined by risk models, the range of starting ages for screening would be several years greater than using family history alone. Further validation and calibration studies are needed alongside modeling studies to assess the population-level impact of introducing genetic risk-based screening programs

Garden varieties: how attractive are recommended garden plants to butterflies?

One way the public can engage in insect conservation is through wildlife gardening, including the growing of insect-friendly flowers as sources of nectar. However, plant varieties differ in the types of insects they attract. To determine which garden plants attracted which butterflies, we counted butterflies nectaring on 11 varieties of summer-flowering garden plants in a rural garden in East Sussex, UK. These plants were all from a list of 100 varieties considered attractive to British butterflies, and included the five varieties specifically listed by the UK charity Butterfly Conservation as best for summer nectar. A total of 2659 flower visits from 14 butterfly and one moth species were observed. We performed a principal components analysis which showed contrasting patterns between the species attracted to Origanum vulgare and Buddleia davidii. The “butterfly bush” Buddleia attracted many nymphalines, such as the peacock, Inachis io, but very few satyrines such as the gatekeeper, Pyronia tithonus, which mostly visited Origanum. Eupatorium cannibinum had the highest Simpson’s Diversity score of 0.75, while Buddleia and Origanum were lower, scoring 0.66 and 0.50 respectively. No one plant was good at attracting all observed butterfly species, as each attracted only a subset of the butterfly community. We conclude that to create a butterfly-friendly garden, a variety of plant species are required as nectar sources for butterflies. Furthermore, garden plant recommendations can probably benefit from being more precise as to the species of butterfly they attract

Mechanistic reconciliation of community and invasion ecology

CITATION: Latombe, G., et al. 2021. Mechanistic reconciliation of community and invasion ecology. Ecosphere, 12(2):e03359, doi:10.1002/ecs2.3359.The original publication is available at https://esajournals.onlinelibrary.wiley.comCommunity and invasion ecology have mostly grown independently. There is substantial overlap in the processes captured by different models in the two fields, and various frameworks have been developed to reduce this redundancy and synthesize information content. Despite broad recognition that community and invasion ecology are interconnected, a process‐based framework synthesizing models across these two fields is lacking. Here we review 65 representative community and invasion models and propose a common framework articulated around six processes (dispersal, drift, abiotic interactions, within‐guild interactions, cross‐guild interactions, and genetic changes). The framework is designed to synthesize the content of the two fields, provide a general perspective on their development, and enable their comparison. The application of this framework and of a novel method based on network theory reveals some lack of coherence between the two fields, despite some historical similarities. Community ecology models are characterized by combinations of multiple processes, likely reflecting the search for an overarching theory to explain community assembly and structure, drawing predominantly on interaction processes, but also accounting largely for the other processes. In contrast, most models in invasion ecology invoke fewer processes and focus more on interactions between introduced species and their novel biotic and abiotic environment. The historical dominance of interaction processes and their independent developments in the two fields is also reflected in the lower level of coherence for models involving interactions, compared to models involving dispersal, drift, and genetic changes. It appears that community ecology, with a longer history than invasion ecology, has transitioned from the search for single explanations for patterns observed in nature to investigate how processes may interact mechanistically, thereby generating and testing hypotheses. Our framework paves the way for a similar transition in invasion ecology, to better capture the dynamics of multiple alien species introduced in complex communities. Reciprocally, applying insights from invasion to community ecology will help us understand and predict the future of ecological communities in the Anthropocene, in which human activities are weakening species’ natural boundaries. Ultimately, the successful integration of the two fields could advance a predictive ecology that is urgently required in a rapidly changing world.https://esajournals.onlinelibrary.wiley.com/doi/full/10.1002/ecs2.3359Publisher's versio

Cryotomography of budding influenza a virus reveals filaments with diverse morphologies that mostly do not bear a genome at their distal end

Influenza viruses exhibit striking variations in particle morphology between strains. Clinical isolates of influenza A virus have been shown to produce long filamentous particles while laboratory-adapted strains are predominantly spherical. However, the role of the filamentous phenotype in the influenza virus infectious cycle remains undetermined. We used cryo-electron tomography to conduct the first three-dimensional study of filamentous virus ultrastructure in particles budding from infected cells. Filaments were often longer than 10 microns and sometimes had bulbous heads at their leading ends, some of which contained tubules we attribute to M1 while none had recognisable ribonucleoprotein (RNP) and hence genome segments. Long filaments that did not have bulbs were infrequently seen to bear an ordered complement of RNPs at their distal ends. Imaging of purified virus also revealed diverse filament morphologies; short rods (bacilliform virions) and longer filaments. Bacilliform virions contained an ordered complement of RNPs while longer filamentous particles were narrower and mostly appeared to lack this feature, but often contained fibrillar material along their entire length. The important ultrastructural differences between these diverse classes of particles raise the possibility of distinct morphogenetic pathways and functions during the infectious process