River otter and mink occupancy dynamics in riparian systems

Semi-aquatic mammals are dependent upon streams and riparian areas, which are a product of the landscapes they drain. Both local stream morphology and surrounding land use are likely to have important influences on current occupancy of semi-aquatic mammals and potentially affect future geographic distributions. We identified aspects of the riparian system and stream structure at multiple scales that relate to the presence of river otter (Lontra canadensis) and mink (Neovison vison) to better understand how changing landscapes affect occupancy dynamics of these semi-aquatic mammals and to facilitate future monitoring and management. We estimated multi-season occupancy using 103 sites sampled over 6 seasonal sampling periods in southern Illinois, USA (44,526 km²) during 2012–2014. We hypothesized river otter and mink occupancy were related to multiple aspects of landscape and local habitat attributes including land cover, water availability, human disturbance, and stream characteristics. Occupancy of river otter was predicted by large stream size, less developed area near the stream site, and proximity to areas with reintroduced or remnant populations of river otter. Mink were more likely to occupy sites with small streams and decreased water availability near the site. However, top models for both species had low weights and high uncertainty for multiple variables. Habitat-based models may not be the best predictors of occupancy for these carnivores because they are more likely to respond to prey diversity or availability, but landscape changes that decrease natural water availability and increase human disturbance to the stream at the local scale are likely to negatively affect river otter. © 2019 The Authors. The Journal of Wildlife Management published by Wiley Periodicals, Inc. on behalf of The Wildlife Society.     

Nestboxes and immigration drive the growth of an urban Peregrine Falcon Falco peregrinus population

Drivers of wildlife population dynamics are generally numerous and interacting. Some of these drivers may impact demographic processes that are difficult to estimate, such as immigration into the focal population. Populations may furthermore be small and subject to demographic stochasticity. All of these factors contribute to blur the causal relationship between past management action and current population trends. The urban Peregrine Falcon Falco peregrinus population in Cape Town, South Africa, increased from three pairs in 1997 to 18 pairs in 2010. Nestboxes were installed over this period to manage the interface between new urban pairs of Falcons and the human users of colonized buildings, and incidentally to improve breeding success. We used integrated population models (IPMs) formally to combine information from a capture–mark–recapture study, monitoring of reproductive success and counts of population size. As all local demographic processes were directly observed, the IPM approach also allowed us to estimate immigration by difference. The provision of nestboxes, as a possible stimulant of population growth, improved breeding success and accounted for an estimated 3–26% of the population increase. The most important driver of growth, however, was immigration. Despite low sample sizes, the IPM approach allowed us to obtain relatively precise estimates of the population‐level impact of nestbox deployment. The goal of conservation interventions is often to increase population size, so the effectiveness of such interventions should ideally be assessed at the population level. IPMs are powerful tools in this context for combining demographic information that may be limited due to small population size or practical constraints on monitoring. Our study quantitatively documented both the immigration process that led to growth of a small population and the effect of a management action that helped the process.     

Seasonality of Rotifers and Temperature in Lough Neagh,N. Ireland

Long runs of seasonal rotifer population data allow analysis of seasonal occurrence using mathematical tools. The application of Fourier analysis to a 15 year dataset describes seasonality in simple mathematical terms. This facilitates comparison of population expression with potential population driving variables and provides a basic modelling tool. Results show that annual patterns of occurrence and density have linkages with annual maximum and minimum environmental temperature, although the exact relationships are not clear.     

Advancing Science for Water Resources Management

Despite the major advances in science to underpin water resources and river management that have taken place over the past two decades, a need remains to establish a unifying framework that will lead to new, appropriate tools for water resources management. In Europe, this need has been highlighted by the promotion of the Water Framework Directive. From a scientific perspective, key questions focus on the ecological significance of flow variability over a range of timescales and the linkage between flow variability, habitat variability and biological population responses, and the biological interactions among these populations. Creation of scientifically sound tools requires development of knowledge at the level of first principles to realize sustainable developments within the context of adaptive management. Similitude analyses provide a mechanism for upscaling from fine ‘research’ scales to the coarser scales of water resource managers. Lack of appropriate data is the major obstacle to the development of these tools, especially those concerned with large rivers.     

OLS Client and OLS Dialog: Open Source Tools to Annotate Public Omics Datasets

The availability of user‐friendly software to annotate biological datasets and experimental details is becoming essential in data management practices, both in local storage systems and in public databases. The Ontology Lookup Service (OLS, http://www.ebi.ac.uk/ols ) is a popular centralized service to query, browse and navigate biomedical ontologies and controlled vocabularies. Recently, the OLS framework has been completely redeveloped (version 3.0), including enhancements in the data model, like the added support for Web Ontology Language based ontologies, among many other improvements. However, the new OLS is not backwards compatible and new software tools are needed to enable access to this widely used framework now that the previous version is no longer available. We here present the OLS Client as a free, open‐source Java library to retrieve information from the new version of the OLS. It enables rapid tool creation by providing a robust, pluggable programming interface and common data model to programmatically access the OLS. The library has already been integrated and is routinely used by several bioinformatics resources and related data annotation tools. Secondly, we also introduce an updated version of the OLS Dialog (version 2.0), a Java graphical user interface that can be easily plugged into Java desktop applications to access the OLS. The software and related documentation are freely available at https://github.com/PRIDE-Utilities/ols-client and https://github.com/PRIDE-Toolsuite/ols-dialog .     

A database of computational models of a half-center oscillator for analyzing how neuronal parameters influence network activity

A half-center oscillator (HCO) is a common circuit building block of central pattern generator networks that produce rhythmic motor patterns in animals. Here we constructed an efficient relational database table with the resulting characteristics of the Hill et al.’s (J Comput Neurosci 10:281–302, 2001) HCO simple conductance-based model. The model consists of two reciprocally inhibitory neurons and replicates the electrical activity of the oscillator interneurons of the leech heartbeat central pattern generator under a variety of experimental conditions. Our long-range goal is to understand how this basic circuit building block produces functional activity under a variety of parameter regimes and how different parameter regimes influence stability and modulatability. By using the latest developments in computer technology, we simulated and stored large amounts of data (on the order of terabytes). We systematically explored the parameter space of the HCO and corresponding isolated neuron models using a brute-force approach. We varied a set of selected parameters (maximal conductance of intrinsic and synaptic currents) in all combinations, resulting in about 10 million simulations. We classified these HCO and isolated neuron model simulations by their activity characteristics into identifiable groups and quantified their prevalence. By querying the database, we compared the activity characteristics of the identified groups of our simulated HCO models with those of our simulated isolated neuron models and found that regularly bursting neurons compose only a small minority of functional HCO models; the vast majority was composed of spiking neurons.     

适于癌基因表达数据集的新特征提取标准NFEC及其分类新算法研究

癌基因表达数据集具有小样本、高维数之特点,一般的机器学习机难以对其有效分类。因此,通常需要采用某些特征提取度量标准来进行降维处理。可是常用的一些特征提取度量标准亦会导致分类效果欠佳之问题。依据微分容量控制学习机DCCM,提出了一个新的特征提取度量标准NFEC,然后依据NFEC和DCCM,提出了适于癌基因表达数据集的特征提取算法DCCFE。实验表明,新的度量NFEC和新的特征提取算法DCCFE较之现有方法对癌基因表达数据集分类时更为有效。本文的工作意义在于:(1)提出了一个新的更有意义的特征提取度量标准;(2)DCCM可以采用比核函数更为一般的一阶可微函数,因而提出的新的特征提取算法更具普遍应用意义。     

DichroWeb,a website for calculating protein secondary structure from circular dichroism spectroscopic data

Circular dichroism (CD) spectroscopy is a widely‐used method for characterizing the secondary structures of proteins. The well‐established and highly used analysis website, DichroWeb (located at: http://dichroweb.cryst.bbk.ac.uk/html/home.shtml) enables the facile quantitative determination of helix, sheet, and other secondary structure contents of proteins based on their CD spectra. DichroWeb includes a range of reference datasets and algorithms, plus graphical and quantitative methods for determining the quality of the analyses produced. This article describes the current website content, usage and accessibility, as well as the many upgraded features now present in this highly popular tool that was originally created nearly two decades ago.     

Gene-Expression Omnibus integration and clustering tools in SeqExpress

SeqExpress, a gene-expression analysis suite, has been extended to offer a number of cluster generation, refinement and visualization techniques. The cluster generation methods have been specialized to deal with aspects of the sparseness and extreme values that occur within microarray data. The results of such cluster analysis can then be refined using either: a functional enrichment based procedure, which examines each cluster to see if it possesses an unusually high or low concentration of ontology terms; or by using Expectation-Maximization to find a mixture of model based distributions within the datasets. Visualizations are provided both to explore and compare the results of the cluster generation algorithms. In addition, a tool has been developed which integrates SeqExpress with the Gene-Expression Omnibus repository. The tool provides seamless access to the large number of experimental results in the repository, so that they can be visualized and analysed locally using SeqExpress. AVAILABILITY: SeqExpress is available as a 6 MB download from http://www.seqexpress.com and runs under Windows. A server-based version is available and is required for the GEO integration. SeqExpress is not affiliated with any academic institution, funding body or commercial organization and is free to use by all.