An evaluation of the analysis system of video transects used to sample subtidal epibiota

Two popular methods of benthic cover estimation (the point intercept technique with two sets of position points, and digital interactive color segmentation) were compared with an alternative method of digital cover estimation using Bezier curves as a tool for outlining the objects on an images and AutoCAD® software for the final evaluation of abundance. The comparison was done using still video images obtained from two 10-m transects on subtidal rocks off the Rimsky-Korsakov islands in the Sea of Japan (Russia). Ten rectangular sectors (1×0.4 m each) selected randomly within both video transects were analyzed. One-way ANOVA for repeated measurements was used to test the differences between methods. The point intercept technique differed significantly from both methods of digital estimation and had an essential positive bias. The Tukey multiple comparison test revealed the differences among digital estimation methods in the species, which have the complicated color with many contrast spots. The proposed approach using Bezier curves has an advantage over the interactive color segmentation if the objects under selection are lit at different levels or have a contrast coloration or are hidden by canopy organisms. Besides, estimation of cover in the field of AutoCAD® software is more precise and takes less time than that obtained using a scaled grid, available for automatically segmented species. The results showed that digital cover estimation using Bezier curves and AutoCAD® software is a convenient method for analyzing benthic samples at large spatial scales.     

Differential introgression across newt hybrid zones: Evidence from replicated transects

Genomic heterogeneity of divergence between hybridizing species may reflect heterogeneity of introgression, but also processes unrelated to hybridization. Heterogeneous introgression and its repeatability can be directly tested in natural hybrid zones by examining multiple transects. Here, we studied hybrid zones between the European newts Lissotriton montandoni and two lineages of Lissotriton vulgaris, with replicate transects within each zone. Over 1,000 nuclear genes located on a linkage map and mitochondrial DNA were investigated using geographical and genomic clines. Overall, the five transects were all similar, showing hallmarks of strong reproductive isolation: bimodal distribution of genotypes in central populations and narrow allele frequency clines. However, the extent of introgression differed between the zones, possibly as a consequence of their different ages, as suggested by the analysis of heterozygosity runs in diagnostic markers. In three transects genomic signatures of small‐scale (~2 km) zone movements were detected. We found limited overlap of cline outliers between transects, and only weak evidence of stronger differentiation of introgression between zones than between transects within zones. Introgression was heterogeneous across linkage groups, with patterns of heterogeneity similar between transects and zones. Predefined candidates for increased or reduced introgression exhibited only a subtle tendency in the expected direction, suggesting that interspecific differentiation is not a reliable indicator for the strength of introgression. These hierarchically sampled hybrid zones of apparently different ages show how introgression unfolds with time and offer an excellent opportunity to dissect the dynamics of hybridization and architecture of reproductive isolation at advanced stages of speciation.     

A simple pressure filtration apparatus for field use

A simple apparatus for pressure-filtering water samples in the field is described. It is used in conjunction with the low pressure outlet of a standard regulator attached to an aqualung. The apparatus is useful in situations where electricity to run electric vacuum pumps is not available and is superior to conventional hand vacuum pumps.     

An evaluation of artificial substrates for sampling macrobenthos in reservoirs

Artificial substrates were compared with a Ponar grab for sampling benthic macroinvertebrates in Lake Anna, Louisa Co., Virginia. The objective was t0 find which technique was best for assessment 0f thermal effluent effects using the following criteria: 1) provide reliable data on density and composition 0f the macrobenthos with a reasonable number 0f replicates; 2) collect the most taxa; and, 3) require the least amount 0f time. Leaves, 3M Corporation's #200 conservation web, and limestone rocks were compared. Each material was tested separately in chicken wire baskets placed 0n the bottom at several depths. Three replicates of each type were retrieved monthly from each depth using SCUBA and cloth flour sacks and compared with grab samples taken from the same depths. Lesser amounts of these materials were tested separately in smaller plastic containers. All large artificial substrate samplers collected significantly more individuals (P = 0.05) and taxa than the Ponar grab. Small web and leaf samplers best met all three 0f the established criteria. The SCUBA system developed in the study is a fast and reliable sampling method.     

Land surface phenology and temperature variation in the International Geosphere–Biosphere Program high-latitude transects

The International Geosphere–Biosphere Program has delineated five study areas that form a northern high‐latitude network for the analyses of vegetation and carbon dynamics. We examined the magnitude and significance of changes in the land surface phenologies of ecoregions within these transects using the NASA Pathfinder Advanced Very High‐Resolution Radiometer Land dataset. We applied the seasonal Mann–Kendall (SMK) trend test, a robust and nonparametric approach, to determine the significance of trends in the normalized difference vegetation index (NDVI) over the five transects. The SMK trend test provides an important alternative over the frequently used but unreliable trend analysis based on linear regression. In addition, we modeled the land surface phenology using quadratic or nonlinear spherical models to relate the NDVI data to accumulated growing degree‐days (base 0°C). Nonlinear spherical models parsimoniously describe the green‐up dynamics in taiga and tundra ecoregions. Models for each ecoregion within each transect were fitted separately for two time periods (1985–1988 and 1995–1999) and their parameter coefficient estimates were compared. In 10 of 24 ecoregions that comprise 72% of the land area in the transects, the date of the peak NDVI value was significantly earlier (range 2–18 days) in the second study period than in the first study period. This progression was more pronounced in North America than in Siberia (weighted average of 9.3 vs. 6.3 days earlier). Understanding of what constitutes significant change in land surface phenology amidst background variation is a critical component of global change science. A diversity of datasets, techniques, and study areas has led to a range of conclusions about boreal phenology. We discuss statistical pitfalls in standard analyses and offer a framework to conduct statistically reliable change assessments of land surface phenologies.     

Techniques for assessing the abundance of Brown Hares Lepus europaeus

Over the last few decades, there have been significant declines in Brown Hare Lepus europaeus numbers throughout Europe, leading to concern for their status in many countries. In Britain, there were no quantified data on the extent of this decline, on current population levels, or any baseline against which to monitor future population changes. The need for a quantified national hare survey led to this evaluation of the techniques available to assess hare numbers. Published information on counting hares is reviewed, and various techniques compared by applying them to a number of sites in southern England. Three basic approaches are available: counts of inactive hares, counts of active hares and indirect methods. Counts of inactive hares include total clearance, wide belt and line transect counts. Total clearance counts give an absolute figure, but are labour intensive and can only be applied to restricted areas. Wide-belt assessments are difficult to apply in certain habitats and even in open areas tend to produce a substantial over-estimate. Line transect counts are easy to undertake and are not labour intensive but should only be applied to large areas, or data from several small areas combined. Counts based on active hares are more problematical, because it is difficult to determine what proportion of the population is inactive at any one time. Spotlight counts based on variable circular plots are the most accurate but difficult to apply widely, and twilight counts are very subjective in their interpretation, especially when surveying small areas or areas with a large proportion of concealing habitats. Of the indirect methods, dung pellet counts can be valuable in specific areas but are difficult to apply across a range of habitats. We concluded that, of the various techniques considered, line transect counts have the greatest potential for a national survey, but need to be stratified so that enough transects are undertaken within each habitat stratum to obtain a reliable mean population estimate for each stratum.     

Terrestrial transects for global change research

The International Geosphere-Biosphere Program has proposed a set of large-scale terrestrial transects to study the effects of changes in climate, land use, and atmospheric composition (global change) on biogeochemistry, surface-atmosphere exchange, and vegetation dynamics of terrestrial ecosystems. The transects ( 1000 km) will be located along existing environmental and land use intensity gradients that span transitions between biomes in regions likely to be widely affected by forcing from components of global change or where the impacts of global change are likely to feed back to affect atmospheric, climatic, or hydrologic systems. Experimental studies on the transects will examine short-term changes in ecosystem function and biosphere-atmosphere interaction in response to variation in primary controlling variables. A hierarchy of modeling approaches will develop predictions of long-term changes in biome boundaries and vegetation distribution. The proposed initial set of IGBP terrestrial transects are located in four key regions: (1) humid tropical forests undergoing land use change, (2) high latitudes including the transition from boreal forest to tundra, (3) semi-arid tropical regions including transitions from dry forest to shrublands and savannas, and (4) mid latitude semi-arid regions encompassing transitions from shrubland or grassland to forests. We discuss here the rationale and general research design of transect studies proposed for each of these priority regions.GCTE Focus 1 Office     

An artificial muscle actuator for biomimetic underwater propulsors

In this paper, we introduce the analytical framework of the modeling dynamic characteristics of a soft artificial muscle actuator for aquatic propulsor applications. The artificial muscle used for this underwater application is an ionic polymer-metal composite (IPMC) which can generate bending motion in aquatic environments. The inputs of the model are the voltages applied to multiple IPMCs, and the output can be either the shape of the actuators or the thrust force generated from the interaction between dynamic actuator motions and surrounding water. In order to determine the relationship between the input voltages and the bending moments, the simplified RC model is used, and the mechanical beam theory is used for the bending motion of IPMC actuators. Also, the hydrodynamic forces exerted on an actuator as it moves relative to the surrounding medium or water are added to the equations of motion to study the effect of actuator bending on the thrust force generation. The proposed method can be used for modeling the general bending type artificial muscle actuator in a single or segmented form operating in the water. The segmented design has more flexibility in controlling the shape of the actuator when compared with the single form, especially in generating undulatory waves. Considering an inherent nature of large deformations in the IPMC actuator, a large deflection beam model has been developed and integrated with the electrical RC model and hydrodynamic forces to develop the state space model of the actuator system. The model was validated against existing experimental data.     

Using remote underwater video to estimate freshwater fish species richness

Species richness records from replicated deployments of baited remote underwater video stations (BRUVS) and unbaited remote underwater video stations (UBRUVS) in shallow (<1 m) and deep (>1 m) water were compared with those obtained from using fyke nets, gillnets and beach seines. Maximum species richness (14 species) was achieved through a combination of conventional netting and camera‐based techniques. Chanos chanos was the only species not recorded on camera, whereas Lutjanus argentimaculatus, Selenotoca multifasciata and Gerres filamentosus were recorded on camera in all three waterholes but were not detected by netting. BRUVSs and UBRUVSs provided versatile techniques that were effective at a range of depths and microhabitats. It is concluded that cameras warrant application in aquatic areas of high conservation value with high visibility. Non‐extractive video methods are particularly desirable where threatened species are a focus of monitoring or might be encountered as by‐catch in net meshes.     

An automated apparatus for the real-time monitoring of bioluminescence in plants

We developed an automated, high-throughput, bioluminescence-monitoring apparatus that can monitor 1920 individual plant seedlings under uniform light conditions. The apparatus is composed of five units: (i) a plate platform that can hold 20 96-well microplates under uniform light conditions, (ii) a scintillation counter, (iii) a robot that conveys plates between the plate platform and a scintillation counter, (iv) a sequence controller, and (v) an external computer that collects and analyzes bioluminescence data automatically. The apparatus gave reproducible and reliable results for both bioluminescence photon counts and period length of bioluminescence rhythms; neither was affected by the well position in a plate or the plate position on the platform. The apparatus is a powerful tool for both large-scale detailed analysis of gene expression and large-scale screening of mutants.     

一种构建基因组文库的改进方法

构建基因组文库是一项非常基础和重要的工作。但利用传统方法构建基因组文库存在操作步骤繁琐、背景高等问题。为了解决这些问题,对传统构建文库的方法进行了改进。由于Ear I位点经酶切后突出3个可变碱基,经过设计可使酶切后的两个粘端无法匹配,从而防止载体环化,所以用两个Ear I位点作为克隆位点。基因片段是通过用Sau3AI部分酶切基因组总DNA,并在部分酶切片段的3`凹端补一个碱基G获得,因此片段无法串连或环化。本实验构建了基于上述改进的ARS探针载体pHBM803/Trp,并分别用改进方法和传统方法构建水稻基因组文库进行比较。实验结果表明,经过上述两点改进可使文库质量大大提高。     

An inflatable minirhizotron system for stony soils

Commonly used minirhizotron methodologies imply the introduction of rigid frames into the soil. This can be a problem if the hole presents an irregular surface, because the presence of gaps can modify the normal behaviour of roots growing along the soil-tube interface. Some authors have developed inflatable adaptations of the technique, but some of these still need the introduction of a rigid frame and others have the often added problem of the wall opaqueness. An inflatable adaptation of the minirhizotron technique has been developed to be used in stony soils. These kind of soils, common in many forests, as in mediterranean forested areas, would present too irregular surface holes to place rigid frames inside. The adaptation proposed allows the use of minirhizotrons in stony soils, with the added advantage of not having anything between the endoscope and the roots when recordings are made, which highly improves the image quality.     

An image enhancement approach for coral reef fish detection in underwater videos

Coral reefs are rich in fisheries and aquatic resources, and the study and monitoring of coral reef ecosystems are of great economic value and practical significance. Due to complex backgrounds and low-quality videos, it is challenging to identify coral reef fish. This study proposed an image enhancement approach for fish detection in complex underwater environments. The method first uses a Siamese network to obtain a saliency map and then multiplies this saliency map by the input image to construct an image enhancement module. Applying this module to the existing mainstream one-stage and two-stage target detection frameworks can significantly improve their detection accuracy. Good detection performance was achieved in a variety of scenarios, such as those with luminosity variations, aquatic plant movements, blurred images, large targets and multiple targets, demonstrating the robustness of the algorithm. The best performance was achieved on the LCF-15 dataset when combining the proposed method with the cascade region-based convolutional neural network (Cascade-RCNN). The average precision at an intersection-over-union (IoU) threshold of 0.5 (AP₅₀) was 0.843, and the F1 score was 0.817, exceeding the best reported results on this dataset. This study provides an automated video analysis tool for marine-related researchers and technical support for downstream applications.     

Prevalence and effects of Argemone Mexicana (Papaveraceae) on biodiversity in Ethiopia

The prevalence and potentials of Argemone mexicana on biodiversity was assessed at Farta, Gondar and Bahir Dar zuria districts. The study areas were stratified into 100 m by 5 m as roadside, fallow land and farmland transect belts. Its effects as poultry feed component were studied on three poultry breeds. Body weights, abnormalities in appetite, egg production and health were recorded. The results indicated that the mean prevalence of Argemone per transect belt in roadside land (17.41 ± 5.9) was higher than that of fallow land (3.35 ± 0.8) and farmland (2.65 ± 0.8) at Farta district. The number and distribution of native plant species under the shed of A. mexicana in roadside, fallow land and farmland per transect belts were 1.15 ± 1.6, 2.25 ± 1.8 and 1.15 ± 0.5, respectively. The number and distribution of Argemone plants in the roadside land per transect increased by 163.4%, 158.5% and 151.9% from 2006 to 2010 in above respective districts. The mean losses in appetite, body weight and egg production were higher in exotic and cross bred than in indigenous chicken ecotypes. Therefore, A. mexicana had negative impacts on biodiversity, native plant species and when used as animal feed components.