A fluorescence assay for monitoring and analyzing fusion biological membrane vesicles in vitro

A new technique has been developed to study fusion of biological membrane vesicles. Bovine chromaffin granule ghosts (CGG) were loaded with fluorescein isothiocyanate-dextran (FITC-dextran) at self-quenching concentrations. Loaded ghosts were then made to fuse with empty CGG. Fusion was induced by synexin, a protein previously proposed to be involved in exocytosis. The fusion process was monitored by measuring the dequenching of the fluorescence. Dequenching occurred as FITC-dextran was diluted into the increased volume due to fusion with empty ghosts. Spurious signals from leakage or breakage of vesicles were removed by including a specific anti-fluorescein antibody in the reaction medium. This new technique may prove to be of more general use for studying membrane fusion processes in other systems.     

A review of big data analysis methods for baleen whale passive acoustic monitoring

Many organizations collect large passive acoustic monitoring (PAM) data sets that need to be efficiently and reliably analyzed. To determine appropriate methods for effective analysis of big PAM data sets, we undertook a literature review of baleen whale PAM analysis methods. Methodologies from 166 studies (published between 2000–2019) were summarized, and a detailed review was performed on the 94 studies that recorded more than 1,000 hr of acoustic data (“big data”). Analysis techniques for extracting baleen whale information from PAM data sets varied depending on the research observed. A spectrum of methodologies was used and ranged from manual analysis of all acoustic data by human experts to completely automated techniques with no manual validation. Based on this assessment, recommendations are provided to encourage robust research methods that are comparable across studies and sectors, achievable across research groups, and consistent with previous work. These include using automated techniques when possible to increase efficiency and repeatability, supplementing automation with manual review to calculate automated detector performance, and increasing consistency in terminology and presentation of results. This work can be used to facilitate discussion for minimum standards and best practices to be implemented in the field of marine mammal PAM.     

基于文献计量的中国自然保护地监测研究

建立自然保护地是迄今为止世界上公认的最有效的保护自然生态系统、维护生物多样性的理想模式,对其进行监测是保护管理工作的重要一环。为了把握我国自然保护地的监测研究现状与发展趋势,基于CNKI和万方数据库检索并筛选出自然保护地监测文献698篇,基于文献计量法,对自然保护地的监测研究趋势、监测指标、监测方法和所属行政区域四个方面进行了分析。结果发现,我国自然保护地监测研究发文量在历经30多年的萌芽期与缓慢增长期后,当前正处于跳跃式增长期。其中,自然保护区的监测发文量最高,占比达67%;在监测内容方面,关注度由高到低依次为:生物多样性>生态环境>人类活动>生态安全,其中,涉及鸟类监测的文献数量最多,占比20.75%。目前,人工实地调查方法仍然是主要的监测研究方法,但随着红外相机、卫星遥感和自动监测系统的发展,其占比已降到60%;在所属行政区域方面,各区不平衡现象十分显著,发文量在6—48篇不等。因此,今后科研监测应兼顾不同自然保护地类型,尽可能采用新的科技手段开展监测,并对两栖爬行类、鱼类、无脊椎动物以及人类活动和生态安全方面给予更高的关注度,最后本文还提出了相应的监测管理建议...     

基于音节聚类分析的被动声学监测技术及其在鸟类监测中的应用

被动声学监测通过分析鸟鸣声信息来实现物种识别,为鸟类多样性监测提供了一种切实可行的技术方案。由于鸟种的鸣声复杂多变,如何通过声纹快速准确辨别物种,分析鸟类丰度,降低对人工操作的需求等技术难题,成为基于声纹的鸟类多样性监测所面临的挑战。本文提出了基于音节聚类的鸟类鸣声监测框架:首先通过音高、频率平坦度等音频特征在声纹数据中提取音节,然后通过无监督表征学习与狄利克雷过程(Dirichlet process)混合模型对音节进行深度无监督聚类训练,完成音节聚类和自动音节种类推断。分析结果表明,本文提出的基于音节聚类的鸟类鸣声监测框架在处理开源数据集白腰文鸟(Lonchura striata)的曲目时可获得接近90%的聚类准确率。在此基础上,本研究对2022年4-5月在广州市白云山公园固定监测点所录制的10种鸟类鸣声进行了无监督的音节聚类分析,验证了本文所提出的基于音节聚类的鸟类鸣声监测框架的有效性:本技术不仅可以支持快速鸟类物种识别,还可以统计和分析不同物种鸟鸣在时间、频度、数量上的变化。这些结果表明,基于音节聚类的鸟类鸣声监测框架可以显著降低对人工标注训练数据的要求,克服传统鸟鸣物种识别框架...     

被动声学监测技术在西黑冠长臂猿监测中的应用

近年来, 被动声学监测技术被广泛应用于陆生哺乳动物的监测, 它能以较低的价格和非侵入的方式在特定区域进行野生动物无人值守监测, 面临的主要问题是需要人工收回数据和后期数据分析整理较为困难。本研究设计了一套被动声学监测系统用于西黑冠长臂猿(Nomascus concolor)监测, 监测系统在野外由太阳能供电, 使用自研的指向性拾音器阵列采集鸣声数据, 并通过无线网桥实时传输数据至管护局办公楼的服务器进行存储, 通过后台的鸣声数据管理系统辅助研究人员识别鸣声和辨认鸣声来源方向, 简化数据采集和处理流程。该系统在哀牢山国家级自然保护区枇杷箐科研监听点对两个西黑冠长臂猿群体进行了351天的连续监测, 特点为: 系统运行长期稳定, 数据通过无线方式传输便捷高效且不受季节天气影响。指向性拾音器阵列能有效分辨长臂猿鸣声来源方向, 弥补了传统监测设备难以分辨鸣声方向的缺陷。该系统与现有人工监测方法相比在数据采集的持续性、连续性、完整度以及鸣声数据处理智能化和监测成本方面均具有一定优势, 符合西黑冠长臂猿持续长期监测需求, 未来可作为西黑冠长臂猿自动化监测的解决方案进行推广应用。     

Method for passive acoustic monitoring of bird communities using UMAP and a deep neural network

An effective practice for monitoring bird communities is the recognition and identification of their acoustic signals, whether simple, complex, fixed or variable. A method for the passive monitoring of diversity, activity and acoustic phenology of structural species of a bird community in an annual cycle is presented. The method includes the semi-automatic elaboration of a dataset of 22 vocal and instrumental forms of 16 species. To analyze bioacoustic richness, the UMAP algorithm was run on two parallel feature extraction channels. A convolutional neural network was trained using STFT-Mel spectrograms to perform the task of automatic identification of bird species. The predictive performance was evaluated by obtaining a minimum average precision of 0.79, a maximum equal to 1.0 and a mAP equal to 0.97. The model was applied to a huge set of passive recordings made in a network of urban wetlands for one year. The acoustic activity results were synchronized with climatological temperature data and sunlight hours. The results confirm that the proposed method allows for monitoring a taxonomically diverse group of birds that nourish the annual soundscape of an ecosystem, as well as detecting the presence of cryptic species that often go unnoticed.     

被动声学监测技术在陆生哺乳动物研究中的应用、进展和展望

被动声学监测(passive acoustic monitoring,PAM)技术指将自动录音机安装在自然环境中收集野生动物及其所在环境的声音信号的监测方法。20世纪90年代以来,PAM技术陆续被应用于翼手目和灵长目等陆生哺乳动物的监测和研究,探究了陆生哺乳动物行为学、生态学和保护生物学等方面的科学问题。然而,当前缺乏对这些研究的系统性总结和展望。本文从活动规律和时间分配、栖息地利用、物种分布、种群大小与密度、生物多样性、人为干扰的影响等领域综述了PAM技术在陆生哺乳动物中的研究进展,并列举了相关应用实例。总体上,PAM技术涉及到生物学、生态学、声学、计算机科学等多学科的交叉融合,其应用受限于声学数据的储存和管理、物种或个体自动化识别以及声学指数评估的普适性,设备价格也相对昂贵,这些可能是导致该技术在我国陆生哺乳动物监测和研究方面的应用还相对滞后于其他国家的原因。最后,本文对未来研究方向进行了展望,并建议尽快建立和完善我国陆生哺乳动物PAM网络和数据共享平台、组织开展面对面访问调查或生物多样性保护相关的知识竞赛等公民科学项目、向更多科研机构或保护区推广PAM技术的应用,使该技术成为陆生...     

A survey on methods for modeling and analyzing integrated biological networks

Understanding how cellular systems build up integrated responses to their dynamically changing environment is one of the open questions in Systems Biology. Despite their intertwinement, signaling networks, gene regulation and metabolism have been frequently modeled independently in the context of well-defined subsystems. For this purpose, several mathematical formalisms have been developed according to the features of each particular network under study. Nonetheless, a deeper understanding of cellular behavior requires the integration of these various systems into a model capable of capturing how they operate as an ensemble. With the recent advances in the "omics" technologies, more data is becoming available and, thus, recent efforts have been driven toward this integrated modeling approach. We herein review and discuss methodological frameworks currently available for modeling and analyzing integrated biological networks, in particular metabolic, gene regulatory and signaling networks. These include network-based methods and Chemical Organization Theory, Flux-Balance Analysis and its extensions, logical discrete modeling, Petri Nets, traditional kinetic modeling, Hybrid Systems and stochastic models. Comparisons are also established regarding data requirements, scalability with network size and computational burden. The methods are illustrated with successful case studies in large-scale genome models and in particular subsystems of various organisms.     

Development of a flatbed passive integrated transponder antenna grid for continuous monitoring of fishes in natural streams

This paper describes a flatbed antenna grid designed for continuous remote monitoring of fish tagged with 23 mm passive integrated transponder (PIT) tags in a natural stream with extensive spatial coverage. A range of applications of the system is presented.     

A computer-assisted technique for long-term gastric pH monitoring

A computer-assisted technique for prolonged gastric pH monitoring has been developed using a personal computer. Segments of signal from several studies performed in controls and on patients with duodenal ulcers were chosen for comparison between manual and digital pH readings; no significant difference was detected. In clinical practice this system might provide an additional tool in the diagnostic and therapeutic treatment of peptic ulcer disease.     

A process-orientated design and performance assessment methodology for passive mine water treatment systems

The aim of this paper is the development of a methodology for assessing the iron removal efficiency of passive mine water treatment settling lagoons and reed beds. Previous work in the design and sizing of coal mine drainage lagoons and wetlands has focussed on the use of standard hydraulic residence times or using the 10 g m⁻² d⁻¹ metric, these criteria have been applied without regard to the fundamental physical and chemical processes controlling iron removal in the system, namely the pH dependent rates of Fe(II) oxidation and physical settling of the particulate Fe(III). In this study field water quality data have been collected from lagoons and reed beds. These data are examined alongside data from the UK Coal Authority database and combined with simple mathematical formulations to provide a framework through which to understand passive treatment schemes from a process-orientated perspective. It is demonstrated that for the sites studied reed beds are more efficient for iron removal. This paper recommends that judgements of iron removal performance should be based on a derived treatment efficiency index (?) and that the modelling approach espoused in this paper should be used when designing passive mine water treatment schemes.     

The sound of the illegal: Applying bioacoustics for long-term monitoring of illegal cattle in protected areas

Passive acoustic monitoring coupled with automated signal recognition software has been widely used in recent years as an effective and affordable tool for wildlife monitoring and to combat illegal activities within protected areas. Here, we evaluate this technique to monitor the patterns of illegal cattle occurrence in the Brazilian Pantanal over a complete annual cycle. We aim to provide one of the first assessments of the performance of automated signal recognition software to detect ungulates. Cattle occurrences reached their maximum during the end of the dry season when lowland areas provide excellent pastures for cattle. In contrast, cattle occurrences were very low during the rainy season when the study area was seasonally inundated. Automated software was an efficient tool that was able to detect approximately three-quarters of cow calls within the recordings. Passive acoustic monitoring can be used to direct patrols to areas where illegal activities, such as cattle and poaching or logging, have been confirmed, which could be a method that would be especially well suited for remote areas, such as tropical forests. Future studies should evaluate whether there is a relationship between cattle grazing intensity and its associated impacts on wildlife and flora. Rapid advances in automated recognition and the recent development of low-cost recorders foresee a new era of acoustic ecology for improved conservation in the short term.     

加拿大自然保护区规划的启迪

为了更好地国际接轨,搞好自然保护区的管理工作,我们需要学习其他国家的先进经验,本文重点介绍加拿大自然保护区规划方面的典型经验,包括系统规划,综合管理规划,资源管理规划,服务规划,行动规划,以及各种规划之间的关系,并提出了对我们的启迪与可借鉴之处。     

A review of detection range testing in aquatic passive acoustic telemetry studies

Passive acoustic telemetry provides an important tool to study the spatial ecology and behaviour of organisms in marine and freshwater systems, but understanding the detection range of acoustic receivers is critical for interpreting acoustic data and establishing receiver spacing to maximize study efficiency. This study presents a comprehensive review of how acoustic detection range has been considered and assessed to date, summarizes important variables to monitor when determining the detection range of a receiver array, and provides recommendations to account for detection range during experimental design, analysis and data interpretation. A total of 378 passive acoustic telemetry studies (1986–2012) were scored against a set of pre-defined criteria to provide a standardized assessment of how well detection range was accounted for, from a maximum possible score of 45. Scores ranged from 0 to 39 (11.1 ± 0.4; mean ± 1 SE). Over the past decade mean scores have been consistently between 6.7 and 12.9 which indicates that detection range has not been adequately considered in most contemporary acoustic telemetry studies. Given the highly variable nature of detection range over space and time, it is necessary to create a culture of detection range testing among the scientific community. For robust telemetry studies it is recommended that consideration of detection range should be given a greater focus within study design, execution and data analysis. To aid array design in new systems, short-term detection range tests should be conducted in the most representative area of the study system prior to deployment. As well, fixed distance sentinel tags should ideally be deployed at a representative receiver site within the array to provide a continuous assessment of detection range and influential environmental parameters should be monitored to facilitate modeling of detection range variability over time. When warranted, data analysis should incorporate modeled variation in detection ranges.