基于核密度估计的动物生境适宜度制图方法

生境适宜度制图能提供动物适宜生境的空间分布信息,对野生动物种群管理、保护地规划等非常重要。生境适宜度制图的关键是构建生境适宜度模型(habitat suitability model, HSM),只基于动物出现位置数据构建HSM的方法在实践中得到了非常广泛的应用。然而现有的只基于动物出现位置数据构建HSM的方法还不能很好地直接表达动物生境适宜度和环境因子之间具有生态学意义的数量关系,因此也就不能很好地体现环境因子对动物生境利用的生态学作用。 本文提出了一种基于核密度估计构建HSM的方法,在地理信息系统技术支持下,通过运用核密度估计从代表性的动物出现位置数据中估计出动物出现对各个环境因子的概率密度函数来直接表达生境适宜度与各个环境因子之间的数量关系,以体现环境因子对动物生境利用的生态学作用,在此基础上对生境适宜度与各个环境因子之间的数量关系进行综合构建了具有明确生态学意义的HSM用于动物生境适宜度制图。以美国Voyageures国家公园的白尾鹿(Odocoileus virginianus)生境适宜度制图为例,基于365个出现位置点位数据并结合积雪深度、地表覆被类型、森林边界长度和坡度等环境因子数据,开展了该方法的案例研究。通过交叉验证计算连续Boyce指数对制图结果进行评价,结果表明：基于核密度估计方法构建的HSM预测能力强,所得出的生境适宜度图经10次交叉验证,连续Boyce指数平均值为0.75,标准差为0.11,达到了较高精度。此外,由于基于核密度估计的方法能以“生境适宜度和环境因子之间具有生态学意义的数量关系”的形式来直接体现环境因子对动物生境利用的生态学作用,就模型的可解释性而言,该方法要优于现有的其他构建HSM的方法。     

基于核密度估算的路网格局与景观破碎化分析

道路网络的发展是导致区域景观破碎化程度加剧的重要因素,如何定量表征道路网络特征及其破碎化效应是道路生态学的一个关键科学问题。本研究以珠江三角洲核心区为案例,采用核密度估算(KDE)结合道路密度指数方法,探讨了区域路网格局及其对景观破碎化的影响。结果表明:KDE法能有效识别和提取高密度路网热点区域;道路密度指数分析显示,道路密度与景观破碎化之间存在较强的相关性;道路密度与KDE法结合能突破传统基于行政边界计算道路密度的局限,为研究路网特征及其景观破碎化程度提供了一个很好的量化工具。     

Smooth statistical torsion angle potential derived from a large conformational database via adaptive kernel density estimation improves the quality of NMR protein structures

Statistical potentials that embody torsion angle probability densities in databases of high‐quality X‐ray protein structures supplement the incomplete structural information of experimental nuclear magnetic resonance (NMR) datasets. By biasing the conformational search during the course of structure calculation toward highly populated regions in the database, the resulting protein structures display better validation criteria and accuracy. Here, a new statistical torsion angle potential is developed using adaptive kernel density estimation to extract probability densities from a large database of more than 10⁶ quality‐filtered amino acid residues. Incorporated into the Xplor‐NIH software package, the new implementation clearly outperforms an older potential, widely used in NMR structure elucidation, in that it exhibits simultaneously smoother and sharper energy surfaces, and results in protein structures with improved conformation, nonbonded atomic interactions, and accuracy.     

基于空间结构调查的林分密度估计

利用林分空间结构抽样调查技术,采用测量抽样点到其第k株最近相邻木的距离(距离法)进行密度估计,分别选取k=4和k=6两种距离调查方法进行分析,并对Prodan、Persson、Thompson 3种不同密度估计方法的预估能力进行检验.结果表明：不同预估方法的预估能力受林木水平分布格局影响.Prodan法在均匀分布的林分中有较强的预估能力,随着分布格局聚集性增加会产生越来越大的偏差;Persson计算法在均匀及随机分布的林分中产生正偏差,但随着分布格局聚集性增加产生的相对误差接近0,预估能力增强;Thompson计算法对随机或接近随机分布的林分有较强的预估能力,而在均匀分布和聚集分布的格局中分别产生正偏差和负偏差.抽样点为49个时,选择6株木与4株木预估能力无显著差异,因此,密度估计可与选取4株相邻木的空间结构参数调查整合在一起.     

A transformation‐based approach to Gaussian mixture density estimation for bounded data

Finite mixture of Gaussian distributions provide a flexible semiparametric methodology for density estimation when the continuous variables under investigation have no boundaries. However, in practical applications, variables may be partially bounded (e.g., taking nonnegative values) or completely bounded (e.g., taking values in the unit interval). In this case, the standard Gaussian finite mixture model assigns nonzero densities to any possible values, even to those outside the ranges where the variables are defined, hence resulting in potentially severe bias. In this paper, we propose a transformation‐based approach for Gaussian mixture modeling in case of bounded variables. The basic idea is to carry out density estimation not on the original data but on appropriately transformed data. Then, the density for the original data can be obtained by a change of variables. Both the transformation parameters and the parameters of the Gaussian mixture are jointly estimated by the expectation‐maximization (EM) algorithm. The methodology for partially and completely bounded data is illustrated using both simulated data and real data applications.     

A likelihood approach to estimating animal density from binary acoustic transects

We propose an approximate maximum likelihood method for estimating animal density and abundance from binary passive acoustic transects, when both the probability of detection and the range of detection are unknown. The transect survey is purposely designed so that successive data points are dependent, and this dependence is exploited to simultaneously estimate density, range of detection, and probability of detection. The data are assumed to follow a homogeneous Poisson process in space, and a second-order Markov approximation to the likelihood is used. Simulations show that this method has small bias under the assumptions used to derive the likelihood, although it performs better when the probability of detection is close to 1. The effects of violations of these assumptions are also investigated, and the approach is found to be sensitive to spatial trends in density and clustering. The method is illustrated using real acoustic data from a survey of sperm and humpback whales.     

Motor unit number estimation as a complementary test to routine electromyography in the diagnosis of amyotrophic lateral sclerosis

Electromyographic (EMG) abnormalities that reveal denervation and reinnervation caused by lower motor neuron degeneration do not reflect the number of motor units that determines muscle strength. Consequently, motor unit activity potential (MUAP) parameters do not reflect muscle dysfunction.The aim of the study was to compare the value of motor unit number estimation (MUNE) and MUAP parameters as indicators of clinical muscle dysfunction in patients with amyotrophic lateral sclerosis (ALS), and to analyze the role of MUNE as a supplement to the EMG criteria for the diagnosis of ALS.In 25 patients with ALS, MUNE by the multipoint incremental method in the abductor digiti minimi (ADM) and quantitative EMG in the first dorsal interosseous (FDI) were obtained. The Medical Research Council (MRC) scale was used to evaluate clinical muscle dysfunction. A strong correlation between the number of motor units evaluated by MUNE and ADM clinical function by the MRC scale was found (P < 0.001). An increased value of surface-detected single motor action potential was associated with a decreased MRC score for ADM (P < 0.1). No relation was found between MUAP parameters in FDI and MRC scores. Our data support the value of the MUNE method for the detection of motor unit loss in ALS, and it could be postulated that MUNE studies may be considered complementary tests for ALS in a future revision of ALS criteria.     

The response of lions and spotted hyaenas to sound playbacks as a technique for estimating population size

Overall, 217 lions (>1 year) Panthera leo (Linnaeus) and 2069 spotted hyaenas (>8 mo) Crocuta crocuta (Erxleben) responded to broadcast vocalizations, call‐ins, during six surveys in the Masai Mara National Reserve, Kenya.
Carnivore response varied seasonally and was significantly higher and more uniform when migratory prey were absent. Variation in wildebeest abundance, by affecting food availability, was the only significant predictor of response. Variability in response with overall prey abundance was higher for lions than hyaenas. Lion response occurred within a radius of 2·5 km, was independent of age and sex but dropped virtually to zero whenever lions possessed a carcass at the time of broadcasting.
An independent total census recorded 547 lions (all ages) in the Reserve, 9·96% of which were nomads. This proportion increased by 7·94% following the influx of migrants and raised lion (>1 year) density from 0·292 to 0·320 lions/km². The call‐in estimate of 0·294±0·009 (95% c.l.) lions/km² practically equalled the total count. The high precision and low bias (−0·224%) of this estimate imply that call‐in surveys are reliable and may be employed to effectively monitor carnivore populations in the long term. Under simple random sampling, covering about 20% of an area would seem adequate to produce reliable density estimates.     

High density lipoprotein binding protein of eel (Anguilla japonica) liver with specificity of binding to apoAI as a ligand

High-density lipoprotein (HDL) binding protein (HBP) was isolated from the microsomal fraction of eel liver homogenate by affinity chromatography with a HDL-column. After SDS-PAGE and blotting, HBP on the PVDF membrane was detected by FITC-labeled HDL and apolipoprotein AI (apoAI) as a ligand. HBP in the microsomal fraction was most abundant among microsomal, mitochondrial and cytosolic fractions. The HBP isolated by a HDL-column consisted of at least three proteins with low molecular weights of 18.5, 14.5 and 13.5 kDa; the main component was 14.5 kDa. These proteins are not products of protease digestion, as the procedure was carried out in the presence of protease inhibitors including (p-aminophenyl) methansulfonyl fluoride, 4-(2-aminoethyl)-benzenesulfonyl fluoride, pepstatin A, E-64, bestatin, leupeptin, aprotinin and EDTA. The HBP specifically bound to FITC-apoAI and faintly bound or did not bind to FITC-apoAII. Furthermore, binding of HDL labeled with lipophilic fluorescence to isolated eel hepatocytes was inhibited by the antibody to apoAI, but not inhibited by the antibody to apolipoprotein AII (apoAII). These results strongly suggest that the HBP isolated from the microsomal fraction is present on the plasma membrane of eel liver and plays important roles for the lipid transport through the interaction with HDL.     

Percent ash‐free dry weight as a robust method to estimate energy density across taxa

Determining how energy flows through ecosystems reveals underlying ecological patterns that drive processes such as growth and food web dynamics. Models that assess the transfer of energy from producers to consumers require information on the energy content or energy density (ED) of prey species. ED is most accurately measured through bomb calorimetry, but this method suffers from limitations of cost, time, and sample requirements that often make it unrealistic for many studies. Percent dry weight (DW) is typically used as a proxy for ED, but this measure includes an indigestible portion (e.g., bones, shell, salt) that can vary widely among organisms. Further, several distinct models exist for various taxonomic groups, yet none can accurately estimate invertebrate, vertebrate and plant ED with a single equation. Here, we present a novel method to estimate the ED of organisms using percent ash‐free dry weight (AFDW). Using data obtained from 11 studies diverse in geographic, temporal and taxonomic scope, AFDW, DW as well as percent protein and percent lipid were compared as predictors of ED. Linear models were produced on a logarithmic scale, including dummy variables for broad taxonomic groups. AFDW was the superior predictor of ED compared to DW, percent protein content and percent lipid content. Model selection revealed that using correction factors (dummy variables) for aquatic animals (AA) and terrestrial invertebrates (TI) produced the best‐supported model—log₁₀(ED) = 1.07*log₁₀(AFDW) ? 0.80 (R² = 0.978, p < .00001)—with an intercept adjustment of 0.09 and 0.04 for AA and TI, respectively. All models including AFDW as a predictor had high predictive power (R² > 0.97), suggesting that AFDW can be used with high degrees of certainty to predict the ED of taxonomically diverse organisms. Our AFDW model will allow ED to be determined with minimal cost and time requirements and excludes ash‐weight from estimates of digestible mass. Its ease of use will allow for ED to be more readily and accurately determined for diverse taxa across different ecosystems.     

Characterization and feasibility of a miniaturized stirred tank bioreactor to perform E. coli high cell density fed-batch fermentations

The use of small scale bioreactors that are mechanically and functionally similar to large scale reactors is highly desirable to accelerate bioprocess development because they enable well-defined scale translations. In this study, a 25-mL miniaturized stirred tank bioreactor (MSBR) has been characterized in terms of its power input, hydrodynamics, and volumetric oxygen transfer coefficient (k(L)a) to assess its potential to grow high cell density (HCD) cultures using adequate scale-down criteria. Engineering characterization results show scale down, based on matched specific power input (P(G)/V), is feasible from a 20-L pilot scale stirred tank bioreactor. Results from fed-batch fermentations performed using Fab' producing E. coli W3110 at matched (P(G)/V) in the MSBR and 20-L STR demonstrated that the MSBR can accurately scale down the 20-L fermentation performance in terms of growth and Fab' production. Successful implementation of a fed-batch strategy in the MSBR resulted in maximum optical density of ca. 114 and total Fab' concentration of 940 μg/mL compared with ca. 118 and 990 μg/mL in 20-L STR. Furthermore, the use of the MSBR in conjunction with primary recovery scale-down tools to assess the harvest material of both reactors showed comparable shear sensitivity and centrifugation performance. The conjoint use of the MSBR with ultra scale-down (USD) centrifugation mimics can provide a cost-efficient manner in which to design and develop bioprocesses that account for good upstream performance as well as their manufacturability downstream.     

Evaluating the usefulness of hemispherical photographs as a means to estimate photosynthetic photon flux density during a growing season in the understorey of Nothofagus pumilio forests

Abstract

Old-growth Nothofagus pumilio forests in Chile are managed employing a shelterwood system. A wide range of canopy openings can be found in old-growth and managed forests. Plant survival and growth in the understorey are influenced by the light available. There are limitations (practical and economic) to monitoring the light in the understorey. The aim of this study was to assess the options to estimate the forest understorey photosynthetic photon flux density (PPFD) measured during the growing season (GS) using canopy openness (CO) estimated by means of hemispherical photographs (HP). PPFD was measured using 31 sensors (Li-190SA quantum sensor) over the course of three GSs (October to March). The sensors were installed in an old-growth stand and another subjected to a regeneration felling under a shelterwood system. One HP was taken above each sensor (during the final GS) and the CO estimated. A comparison of the three seasons revealed that the sum of the PPFD during the GSs did not differ significantly. The CO could be used to effectively predict the sum of the PPFD during a GS (R ² = 0.959). These results demonstrate the usefulness of HPs as a means to estimate the sum of the PPFD during a GS.