A thorough and quantified method for classifying seabird diving behaviour

Time-depth recorders are commonly deployed on diving animals to obtain information on their aquatic behaviour. The recorded data provide a 2D profile of diving activity. As analyses of diving behaviour from such profiles have become more complex, these analyses have often suffered from a lack of consistency and rigour. There is a growing need for a simple, comparative method to classify diving behaviour thoroughly and quantitatively. Here, a new approach to the classification of the dive profiles of penguins is described, which probably has applicability for many other diving predators as well. This simple approach uses a small, coherent set of criteria to classify behaviours in a detailed and quantified manner, and with relative objectivity. Classification of diving behaviour is possible from the temporal scale of a wiggle within a dive to the scale of a bout of dives. The new method will make comparisons between species easier and clearer because these comparisons will be undertaken within a consistent, more objective framework.     

Anti-parasite treatment removes negative effects of environmental pollutants on reproduction in an Arctic seabird

Recent studies have shown that the detrimental effects of anthropogenic pollutants may be worse if organisms are exposed to natural stress. In this study, we examined whether negative effects of organochlorines (OCs) could be influenced by parasites. In two breeding seasons, we administered an anti-helminthic drug to groups of breeding glaucous gulls (Larus hyperboreus), whereas control groups were placebo treated. In all birds, blood residues of the most important OCs in the study population (hexachlorobenzene, oxychlordane, p,p'-dichlorodiphenyldichloroethylene and polychlorinated biphenyl), were measured. The relationships between OCs and fitness components (i.e. nesting success and return rate between breeding seasons) were then compared between the birds receiving anti-parasite treatment and the controls. Among untreated males, higher blood residues of OCs were associated with lowered nesting success, while in males receiving anti-parasite treatment, there was no detrimental effect of OCs on fitness. Return rate was not affected by treatment or OCs. Our findings suggest that parasites may be an important factor in triggering reproductive effects of such pollutants, and that relatively low levels of OCs may have serious reproductive consequences in natural populations when stress from other sources is high.     

A reliable method for assessing rotational power

Rotational core training is said to be beneficial for rotational power athletes. Currently, there has been no method proposed for the reliable assessment of rotational power. Therefore, our purpose was to determine the test-retest reliability of kinetic and kinematic rotational characteristics of a pulley system when performing a rotational exercise of the axial skeleton in the transverse plane to find out if this would be a reliable tool for evaluating rotational power. Healthy, college-aged men (n = 8) and women (n = 15) reported for 3 testing sessions. The participants were seated on a box, and they held the handle with both arms extended in front of their body, starting their motion with their torso rotated toward the machine. All the participants rotated their torso forcefully until they reached 180° of rotation, and they then slowly returned to the starting position, 3 times per trial, with 3 loads: 9% body weight (BW), 12% BW, and 15% BW. The repetition with the greatest power for each trial for each load was analyzed. The mean peak power repetition (watts) for all the subjects was 20.09 ± 7.16 (9% BW), 26.17 ± 8.6 (12% BW), and 30.74 ± 11.022 (15% BW) in the first training session and 22.3 ± 8.087 (9% BW), 28.7 ± 11.295 (12% BW), and 33.52 ± 12.965 (15% BW) in the second training session with intraclass correlation coefficients of 0.97 (9%BW), 0.94 (12%BW), and 0.95 (15%BW). When the participants were separated by sex, there were no significant differences between groups. Based on these results, it was found that a pulley system and an external dynamometer can be used together as a reliable research tool to assess rotational power.     

A framework for assessing the vulnerability of species to climate change: a case study of the Australian elapid snakes

Frameworks that provide a system for assessing species according to their vulnerability to climate change can offer considerable guidance to conservation managers who need to allocate limited resources among a large number of taxa. To date, climate change vulnerability assessments have largely been based on projected changes in range size derived from the output of species distribution models (SDMs). A criticism of risk assessments based solely on these models is that information on species ecological and life history traits is lacking. Accordingly, we developed a points-based framework for assessing species vulnerability to climate change that considered species traits together with the projections of SDMs. Applying this method to the Australian elapid snakes (family Elapidae), we determined which species may be particularly susceptible in the future and assessed broad-scale biogeographic patterns in species vulnerability. By offering a more comprehensive and rigorous method for assessing vulnerability than those based solely on SDMs, this framework provides greater justification for resource allocation, and can help guide decisions regarding the most appropriate adaptation strategies.     

A field cage method for assessing resistance to turnip root fly in brassicas

A field cage method was evaluated as an alternative to field trials for identifying sources of resistance to turnip root fly in brassicas. This involved the controlled release of adult flies and the use of egg traps to quantify egg-laying on potted plants. Overall levels of resistance to Delia floralis, and its components, were assessed for 15 swede genotypes. Significant levels of antixenosis and antibiosis type resistance were identified in several cultivars and breeding lines. There was a close agreement between the field cage results and those from previous field trials, using comparable susceptible and resistance control cultivars. Compared with field selection, the field cage method reduced by c. 40% the time required to quantify resistance and each of its components.     

A cost-effective method to quantify biological surface sediment reworking

We propose a simple and inexpensive method to determine the rate and pattern of surface sediment reworking by benthic organisms. Unlike many existing methods commonly used in bioturbation studies, which usually require sediment sampling, our approach is fully non-destructive and is well suited for investigating non-cohesive fine sediments in streams and rivers. Optical tracer (e.g. luminophores or coloured sand) disappearance or appearance is assessed through time based on optical quantification of surfaces occupied by tracers. Data are used to calculate surface sediment reworking (SSR) coefficients depicting bioturbation intensities. Using this method, we evaluated reworking activity of stream organisms (three benthic invertebrates and a fish) in laboratory microcosms mimicking pool habitats or directly in the field within arenas set in depositional zones. Our method was sensitive enough to measure SSR as low as 0.2 cm² day^?1, such as triggered by intermediate density (774 m^?2) of Gammarus fossarum (Amphipoda) in microcosms. In contrast, complex invertebrate community in the field and a fish (Barbatula barabatula) in laboratory microcosms were found to yield to excessively high SSR (>60 cm² day^?1). Lastly, we suggest that images acquired during experiments can be used for qualitative evaluation of species-specific effects on sediment distribution.     

Identifying and modelling environmental indicators for assessing population vulnerability to conflict using ground and satellite data

Conflicts may be directly responsible for the modification of features in the landscape by causing damage to built-up areas or to the environment. Landscape features may also be indirectly affected by conflict as the result of changes in the way of life of inhabitants and their use of natural resource. Conflict-induced changes in landuse features may thus be associated with changes in population vulnerability. This study focuses on the environmental indicators for population vulnerability, an important parameter contributing to risk assessment during and after conflict.These environmental indicators are first identified using field data and are then derived from satellite data. The satellite-derived indicators are used as model input to create a risk map for two areas in Northern Iraq that were targeted during the Anfal Campaigns in 1987 and 1988: Jafati Valley and the southern region of Dahuk. The satellite-driven model is further applied to three dates for the same study areas: 1987, 1989 and 2000–2001. The output describes the risk level within the region for each of the dates studied, and the changes which occurred in Northern Iraq as the result of the Anfal Campaigns.Results show that spatial-based hazard risk assessment is possible using environmental indicators derived from Earth Observation data. For conflict-driven changes in the Jafati Valley study area, there is an apparent change in human activity, manifested as a conversion from agricultural land to grassland, the harvesting of rural mountainous woodland and the net disappearance of built-up areas. For this study area affected by conflict, 86% of the regions where these land cover changes occur were labelled as being at risk according to the model output. In the second study area, 63% of the changes in land cover occur in the regions labelled as being most vulnerable. Further research on this second study site shows that the area was affected by climatic and economic factors rather than conflict.     

Iowa anatomical position system. A method of assessing posture

A computerized method for assessing standing posture was described and evaluated. As experimentally determined, the precision of the method was to the nearest millimeter. The accuracy (measurement error) of the system was 1.0% for the X direction, 3% for the Y direction, and 2.6% for the Z direction. Using 32 subjects the intraday and interday reliability was good. The validity of the method was satisfactory for acquiring measurements of the spinal column.     

A method for assessing the statistical significance of RNA folding

We have developed a statistical method that is designed for analyzing potential RNA folded substructures. The statistical significance of RNA folding is assessed by the segment score. The segment score is defined as the difference between the lowest free energy calculated for the real biological sequence and the mean of the lowest free energies from random permutations of the real segment sequence, divided by the standard deviation of the random sample. This procedure was applied to the well-studied Escherichia coli 16S rRNA and potato spindle tuber viroid (PSTV) RNA. The results showed that the predictions of the locally significant secondary structures in these two molecules are in accord with the universally conserved local secondary structure elements (Gutell, Weiser & Noller, 1985, Prog. Nucl. Acid Res. molec. Biol. 32, 155-216; Riesner & Gross, 1985, A. Rev. Biochem. 54, 531-564). In addition, a statistical analysis indicated that the lowest free energies of a random sample set follow an approximately normal distribution. A reasonable size for the random sample set was determined statistically. Moreover, the statistical evaluation has been carried out using three different sets of energy rules--two sets (Salser, 1977, Cold Spring Harb. Symp. Quant Biol. 42, 985-1002; Freier, Kierzek, Jaeger, Sugimoto, Caruthers, Neilson & Turner, 1986, Proc. natn. Acad. Sci. U.S.A. 83, 9373-9377) take into account stacking energies and are based on experimental data and their computational extension (Salser, 1977)--the third set is a simplistic "unitary matrix" approach, where any base-pair is given a weight of "minus one" and an unpaired based is "zero". The Freier energy rules usually yield the strongest indication of significant folding region. However, the results derived from paired comparisons test don't provide sufficient evidence for concluding that a different set of energy rules is effective in changing the segment score level for local stem-loop structures in the 16S rRNA.     

A new method of assessing anxiety-phobic states in rats]

A new multiparameter method for evaluating anxiety-phobic states in rats is elaborated. The method is based on the ranged scale consisting of parameters which characterize the species-specific rat response to the series of ethologically adequate test-stimuli inducing manifestation of the anxiety-phobic states. The method makes it possible to evaluate individual anxiety-phobic level in rats, to form experimental groups with rats of known individual anxiety-phobic level, to conduct repeated observations in the same animals. The method is easy to perform in laboratory and makes it possible to get the results quickly.     

A method for assessing factors influencing'false check'formation in fish scales

Scales are widely used to determine both the growth rates and the age of fish. Their use in this method of scale reading is however complicated by the occurrence of false checks. It has been difficult to investigate the particular environmental factors that normally cause these interruptions in growth because it usually takes many weeks before a check can be detected and the growing scale is a complex system. A technique has therefore been devised in which a scale is isolated from the fish and used to measure its metabolism of radioactive glycine. This gives a measure of protein synthesis which correlates well with the normal growth of the scale and of the whole fish. It is, however, a measurement of the'instantaneous growth rate'of the fish instead of one compounded over a long period of time and it thus opens up the possibility of investigating specific environmental factors that might cause changes in growth. The effects of handling, low oxygen levels, starvation, light and temperature changes have been studied by this technique. It has been shown that handling has the most marked effect but that oxygen levels and starvation also have direct effects that could induce false checks.     

A simple method for assessing muscle function in common marmosets

A novel method of assessing muscle function in the common marmoset was developed as part of a multidisciplinary long-term study. The method involved home cage presentation of a weight-pulling task. Over a 4-5 month period, 38 of 42 animals were successfully trained to displace weights of up to 920 g (mean 612+/-20 g). Performance, following initial training, was stable and independent of gender or body weight.     

蛋白质二级结构预测方法的评价

目前评价蛋白质二级结构预测方法主要考虑预测准确率,并没有充分考虑方法自身参数对方法的影响。本文提出一种新型评价方法,将内在评价与外在评价相结合评价预测方法的优劣。以基于混合并行遗传算法的蛋白质二级结构预测方法为例,通过内在评价,合理选取内在参数——切片长度和组内类别数,有效提高预测准确率,同时,通过外在评价,与其他基于随机算法的蛋白质二级结构预测算法比较和与CASP所提供的结论比较,说明了方法的有效性与正确性,以此验证内在评价和外在评价的客观性、公正性和全面性。     

A simple method for assessing sample sizes in microarray experiments

Background  

In this short article, we discuss a simple method for assessing sample size requirements in microarray experiments.