Karyotype instability in the ponerine ant genus Diacamma

The queenless ponerine ant Diacamma ceylonense and a population of Diacamma from the Nilgiri hills which we refer to as `nilgiri', exhibit interesting similarities as well as dissimilarities. Molecular phylogenetic study of these morphologically almost similar taxa has shown that D ceylonense is closely related to `nilgiri' and indicates that `nilgiri' is a recent diversion in the Diacamma phylogenetic tree. However, there is a striking behavioural difference in the way reproductive monopoly is maintained by the respective gamergates (mated egg laying workers), and there is evidence that they are genetically differentiated, suggesting a lack of gene flow To develop a better understanding of the mechanism involved in speciation of Diacamma, we have analysed karyotypes of D. ceylonense and `nilgiri' In both, we found surprising inter-individual and intra-individual karyotypic mosaicism. The observed numerical variability, both at intra-individual and inter-individual levels, does not appear to have hampered the sustainability of the chromosomal diversity in each population under study Since the related D. indicum, displays no such intra-individual or inter-Individual variability whatsoever under identical experimental conditions, these results are unlikely to he artifacts. Although no known mechanisms can account for the observed karyotypic variability of this nature, we believe that the present findings on the ants under study would provide opportunities for exciting new discoveries concerning the origin, maintenance and significance of intra-individual and inter-individual karyotypic mosaicism.

Large scale features and assessment of spatial scale correspondence between TMPA and IMD rainfall datasets over Indian landmass

Daily rainfall datasets of 10 years (1998-2007) of Tropical Rainfall Measuring Mission (TRMM) Multi-satellite Precipitation Analysis (TMPA) version 6 and India Meteorological Department (IMD) gridded rain gauge have been compared over the Indian landmass, both in large and small spatial scales. On the larger spatial scale, the pattern correlation between the two datasets on daily scales during individual years of the study period is ranging from 0.4 to 0.7. The correlation improved significantly (similar to 0.9) when the study was confined to specific wet and dry spells each of about 5-8 days. Wavelet analysis of intraseasonal oscillations (ISO) of the southwest monsoon rainfall show the percentage contribution of the major two modes (30-50 days and 10-20 days), to be ranging respectively between similar to 30-40% and 5-10% for the various years. Analysis of inter-annual variability shows the satellite data to be underestimating seasonal rainfall by similar to 110 mm during southwest monsoon and overestimating by similar to 150 mm during northeast monsoon season. At high spatio-temporal scales, viz., 1 degrees x1 degrees grid, TMPA data do not correspond to ground truth. We have proposed here a new analysis procedure to assess the minimum spatial scale at which the two datasets are compatible with each other. This has been done by studying the contribution to total seasonal rainfall from different rainfall rate windows (at 1 mm intervals) on different spatial scales (at daily time scale). The compatibility spatial scale is seen to be beyond 5 degrees x5 degrees average spatial scale over the Indian landmass. This will help to decide the usability of TMPA products, if averaged at appropriate spatial scales, for specific process studies, e.g., cloud scale, meso scale or synoptic scale.

Enhancing reproducibility of ultrasonic measurements by new users

Perception of operator influences ultrasound image acquisition and processing. Lower costs are attracting new users to medical ultrasound. Anticipating an increase in this trend, we conducted a study to quantify the variability in ultrasonic measurements made by novice users and identify methods to reduce it. We designed a protocol with four presets and trained four new users to scan and manually measure the head circumference of a fetal phantom with an ultrasound scanner. In the first phase, the users followed this protocol in seven distinct sessions. They then received feedback on the quality of the scans from an expert. In the second phase, two of the users repeated the entire protocol aided by visual cues provided to them during scanning. We performed off-line measurements on all the images using a fully automated algorithm capable of measuring the head circumference from fetal phantom images. The ground truth (198.1 +/- 1.6 mm) was based on sixteen scans and measurements made by an expert. Our analysis shows that: (1) the inter-observer variability of manual measurements was 5.5 mm, whereas the inter-observer variability of automated measurements was only 0.6 mm in the first phase (2) consistency of image appearance improved and mean manual measurements was 4-5 mm closer to the ground truth in the second phase (3) automated measurements were more precise, accurate and less sensitive to different presets compared to manual measurements in both phases. Our results show that visual aids and automation can bring more reproducibility to ultrasonic measurements made by new users.

Long-Term Environmental Correlates of Invasion by Lantana camara (Verbenaceae) in a Seasonally Dry Tropical Forest

Invasive species, local plant communities and invaded ecosystems change over space and time. Quantifying this change may lead to a better understanding of the ecology and the effective management of invasive species. We used data on density of the highly invasive shrub Lantana camara (lantana) for the period 1990-2008 from a 50 ha permanent plot in a seasonally dry tropical forest of Mudumalai in southern India. We used a cumulative link mixed-effects regression approach to model the transition of lantana from one qualitative density state to another as a function of biotic factors such as indicators of competition from local species (lantana itself, perennial grasses, invasive Chromolaena odorata, the native shrub Helicteres isora and basal area of native trees) and abiotic factors such as fire frequency, inter-annual variability of rainfall and relative soil moisture. The density of lantana increased substantially during the study period. Lantana density was negatively associated with the density of H. isora, positively associated with basal area of native trees, but not affected by the presence of grasses or other invasive species. In the absence of fire, lantana density increased with increasing rainfall. When fires occurred, transitions to higher densities occurred at low rainfall values. In drier regions, lantana changed from low to high density as rainfall increased while in wetter regions of the plot, lantana persisted in the dense category irrespective of rainfall. Lantana seems to effectively utilize resources distributed in space and time to its advantage, thus outcompeting local species and maintaining a population that is not yet self-limiting. High-risk areas and years could potentially be identified based on inferences from this study for facilitating management of lantana in tropical dry forests.

And yet it shrinks: A novel method for correcting bias in forest tree growth estimates caused by water-induced fluctuations

Accuracy in tree woody growth estimates is important to global carbon budget estimation and climate-change science. Tree growth in permanent sampling plots (PSPs) is commonly estimated by measuring stem diameter changes, but this method is susceptible to bias resulting from water-induced reversible stem shrinkage. In the absence of bias correction, temporal variability in growth is likely to be overestimated and incorrectly attributed to fluctuations in resource availability, especially in forests with high seasonal and inter-annual variability in water. We propose and test a novel approach for estimating and correcting this bias at the community level. In a 50-ha PSP from a seasonally dry tropical forest in southern India, where tape measurements have been taken every four years from 1988 to 2012, for nine trees we estimated bias due to reversible stem shrinkage as the difference between woody growth measured using tree rings and that estimated from tape. We tested if the bias estimated from these trees could be used as a proxy to correct bias in tape-based growth estimates at the PSP scale. We observed significant shrinkage-related bias in the growth estimates of the nine trees in some censuses. This bias was strongly linearly related to tape-based growth estimates at the level of the PSP, and could be used as a proxy. After bias was corrected, the temporal variance in growth rates of the PSP decreased, while the effect of exceptionally dry or wet periods was retained, indicating that at least a part of the temporal variability arose from reversible shrinkage-related bias. We also suggest that the efficacy of the bias correction could be improved by measuring the proxy on trees that belong to different size classes and census timing, but not necessarily to different species. Our approach allows for reanalysis - and possible reinterpretation of temporal trends in tree growth, above ground biomass change, or carbon fluxes in forests, and their relationships with resource availability in the context of climate change. (C) 2014 Elsevier B.V. All rights reserved.

Impact of compost, vermicompost and biochar on soil fertility, maize yield and soil erosion in Northern Vietnam: A three year mesocosm experiment

Compost, vermicompost and biochar amendments are thought to improve soil quality and plant yield. However, little is known about their long-term impact on crop yield and the environment in tropical agro-ecosystems. In this study we investigated the effect of organic amendments (buffalo manure, compost and verrnicompost) and biochar (applied alone or with vermicompost) on plant yield, soil fertility, soil erosion and water dynamics in a degraded Acrisol in Vietnam. Maize growth and yield, as well as weed growth, were examined for three years in terrestrial mesocosms under natural rainfall. Maize yield and growth showed high inter-annual variability depending on the organic amendment. Vermicompost improved maize growth and yield but its effect was rather small and was only significant when water availability was limited (year 2). This suggests that vermicompost could be a promising substrate for improving the resistance of agrosystems to water stress. When the vermicompost biochar mixture was applied, further growth and yield improvements were recorded in some cases. When applied alone, biochar had a positive influence on maize yield and growth, thus confirming its interest for improving long-term soil productivity. All organic amendments reduced water runoff, soil detachment and NH4+ and NO3- transfer to water. These effects were more significant with vermicompost than with buffalo manure and compost, highlighting that the beneficial influence of vermicompost is not limited to its influence on plant yield. In addition, this study showed for the first time that the combination of vermicompost and biochar may not only improve plant productivity but also reduce the negative impact of agriculture on water quality. (C) 2015 Elsevier B.V. All rights reserved.

Measures of turbidity in coastal waters, Coconut Island, Oahu, Hawaii, August 31 - September 2, 2005: workshop proceedings

A three day workshop on turbidity measurements was held at the Hawaii Institute of Marine Biology from August 3 1 to September 2, 2005. The workshop was attended by 30 participants from industry, coastal management agencies, and academic institutions. All groups recognized common issues regarding the definition of turbidity, limitations of consistent calibration, and the large variety of instrumentation that nominally measure "turbidity." The major recommendations, in order of importance for the coastal monitoring community are listed below: 1. The community of users in coastal ecosystems should tighten instrument design configurations to minimize inter-instrument variability, choosing a set of specifications that are best suited for coastal waters. The IS0 7027 design standard is not tight enough. Advice on these design criteria should be solicited through the ASTM as well as Federal and State regulatory agencies representing the majority of turbidity sensor end users. Parties interested in making turbidity measurements in coastal waters should develop design specifications for these water types rather than relying on design standards made for the analysis of drinking water. 2. The coastal observing groups should assemble a community database relating output of specific sensors to different environmental parameters, so that the entire community of users can benefit from shared information. This would include an unbiased, parallel study of different turbidity sensors, employing a variety of designs and configuration in the broadest range of coastal environments. 3. Turbidity should be used as a measure of relative change in water quality rather than an absolute measure of water quality. Thus, this is a recommendation for managers to develop their own local calibrations. See next recommendation. 4. If the end user specifically wants to use a turbidity sensor to measure a specific water quality parameter such as suspended particle concentration, then direct measurement of that water quality parameter is necessary to correlate with 'turbidity1 for a particular environment. These correlations, however, will be specific to the environment in which they are measured. This works because there are many environments in which water composition is relatively stable but varies in magnitude or concentration. (pdf contains 22 pages)

Avaliação dos efeitos da disponibilidade de luz sobre o crescimento e competição entre cepas de Planktothrix agardhii e Microcystis aeruginosa

As cianobactérias Microcystis aeruginosa e Planktothrix agardhii são espécies formadoras de florações comuns em ecossistemas aquáticos eutrofizados. Nestes ambientes, a disponibilidade de luz é um dos fatores determinantes para o desenvolvimento e estruturação da comunidade fitoplanctônica. O presente estudo teve como objetivo investigar o efeito da luz na fisiologia de cepas de cianobactérias (M. aeruginosa e P. agardhii), avaliando o crescimento, a variabilidade inter e intra-específica e a competição por luz. Para tanto foram realizados cultivos estanques em diferentes intensidades luminosas (10, 40, 60, 100 e 500 mol m-2 s-1) e calculadas as taxas de crescimento e os rendimentos máximos das culturas. O requerimento mínimo de luz de cada cepa foi determinado em experimentos com monoculturas em sistemas de cultivo contínuo (quimiostatos) sob condições de limitação de luz. A competição por luz foi avaliada através de experimentos com biculturas em quimiostatos. Foi observada variabilidade intra e inter-específica das cepas, nas diferentes intensidades luminosas testadas. Em 500 μmol m-2 s-1, as cepas de M. aeruginosa obtiveram maior biomassa do que P. agardhii, corroborando a maior sensibilidade de P. agardhii luz. Embora com rendimento máximo menor, P. agardhii cresceu em intensidades luminosas consideradas elevadas para a espécie, 100 e 500 μmol m-2 s-1. Estes resultados evidenciam a capacidade de P. agardhii ocorrer em ambientes com grandes amplitudes de luminosidade. Na intensidade de 10 μmol m-2 s-1, M. aeruginosa e P. agardhii apresentaram crescimento semelhante, demonstrando a habilidade das duas espécies em crescer com pouca luz. Nas monoculturas em quimiostato, sob condições de limitação de luz, as cepas de M. aeruginosa atingiram maior biomassa durante o equilíbrio (steady-state) do que P. agadhii, refletindo uma capacidade suporte mais elevada, enquanto que os valores de requerimento mínimo de luz foram semelhantes entre as duas espécies. Ao competirem, M. aeruginosa superou P. agardhii imediatamente após o início do experimento. Esse rápido crescimento resultou na dominância de M. aeruginosa em todos os pares de cepas testados e, em dois casos, ocorreu exclusão competitiva de P. agardhii. Quando não ocorreu exclusão, P. agardhii conseguiu manter-se no sistema com uma baixa biomassa (ca.15%). Estes resultados ajudam a entender a co-ocorrência destas espécies no ambiente e a dominância de M. aeruginosa mesmo em condições de baixa luminosidade.

Estimating overall fish bycatch in U.S. commercial fisheries

Bycatch, or the unintended capture of fish, marine mammals, sea turtles, and seabirds by fishing gear, occurs to some degree in most fisheries. The recently released National Marine Fisheries Service’s (NMFS) U.S. National Bycatch Report provides information on bycatch in U.S. commercial fisheries by fishery and species. The report also provides national statistics in the form of national bycatch ratio and a national bycatch estimate. We describe the methods used to develop these statistics and compare them to similar studies. We conclude that the national bycatch ratio and national bycatch estimates developed by NMFS represent the best available information on bycatch in U.S. fisheries. However, given changes in bycatch management over time, as well as inter-annual variability in bycatch levels and a high percentage of fisheries for which data on bycatch are not currently available, we recommend that NMFS continue to support bycatch data collection and reporting efforts to improve the quality and quantity of bycatch data and estimates available to fisheries managers and scientists over time. This will enable NMFS to meet its requirements for bycatch reporting under the Magnuson-Stevens Act (MSA), as well as requirements for bycatch minimization under the MSA, Marine Mammal Protection Act, and Endangered Species Act.

A stochastic model of temporal variations in monthly temperature, precipitation, snowfall, and resulting snowpack

We report a Monte Carlo representation of the long-term inter-annual variability of monthly snowfall on a detailed (1 km) grid of points throughout the southwest. An extension of the local climate model of the southwestern United States (Stamm and Craig 1992) provides spatially based estimates of mean and variance of monthly temperature and precipitation. The mean is the expected value from a canonical regression using independent variables that represent controls on climate in this area, including orography. Variance is computed as the standard error of the prediction and provides site-specific measures of (1) natural sources of variation and (2) errors due to limitations of the data and poor distribution of climate stations. Simulation of monthly temperature and precipitation over a sequence of years is achieved by drawing from a bivariate normal distribution. The conditional expectation of precipitation. given temperature in each month, is the basis of a numerical integration of the normal probability distribution of log precipitation below a threshold temperature (3°C) to determine snowfall as a percent of total precipitation. Snowfall predictions are tested at stations for which long-term records are available. At Donner Memorial State Park (elevation 1811 meters) a 34-year simulation - matching the length of instrumental record - is within 15 percent of observed for mean annual snowfall. We also compute resulting snowpack using a variation of the model of Martinec et al. (1983). This allows additional tests by examining spatial patterns of predicted snowfall and snowpack and their hydrologic implications.

A high-resolution atlas and statistical model of the human heart from multislice CT

Atlases and statistical models play important roles in the personalization and simulation of cardiac physiology. For the study of the heart, however, the construction of comprehensive atlases and spatio-temporal models is faced with a number of challenges, in particular the need to handle large and highly variable image datasets, the multi-region nature of the heart, and the presence of complex as well as small cardiovascular structures. In this paper, we present a detailed atlas and spatio-temporal statistical model of the human heart based on a large population of 3D+time multi-slice computed tomography sequences, and the framework for its construction. It uses spatial normalization based on nonrigid image registration to synthesize a population mean image and establish the spatial relationships between the mean and the subjects in the population. Temporal image registration is then applied to resolve each subject-specific cardiac motion and the resulting transformations are used to warp a surface mesh representation of the atlas to fit the images of the remaining cardiac phases in each subject. Subsequently, we demonstrate the construction of a spatio-temporal statistical model of shape such that the inter-subject and dynamic sources of variation are suitably separated. The framework is applied to a 3D+time data set of 138 subjects. The data is drawn from a variety of pathologies, which benefits its generalization to new subjects and physiological studies. The obtained level of detail and the extendability of the atlas present an advantage over most cardiac models published previously. © 1982-2012 IEEE.

太阳辐射对热层和电离层变化性的影响

Solar ultraviolet (UV) radiation at wavelengths less than 400 nm is an important source of energy for aeronomic processes throughout the solar system. Solar UV photons are absorbed in planetary atmospheres, as well as throughout the heliosphere, via photodissociation of molecules, photoionization of molecules and atoms, and photoexcitation toexcitation including resonance scattering. In this paper, the solar irradiances data measured by TIMED SEE, as well as the solar proxies such as F10.7 and Mg II, thermosphere neutral density of CHAMP measurements and topside ionospheric plasmas densities from DMSP, are used to analyze solar irradiance effects on the variabilities of the thermosphere and the ionosphere. First, thermosphere densities near 410 km altitude are analyzed for solar irradiance variability effects during the period 2002-2004. Correlations between the densities and the solar irradiances for different spectral lines and wavelength ranges reveal significantly different characteristics. The density correlates remarkably well with all the selected solar irradiances except the lower chromospheric O I (130.4 nm) emission. Among the chosen solar proxies, the Mg II core-to-wing ratio index, EUV (30-120 nm) and F10.7 show the highest correlations with the density for short-term (< ~27 days) variations. For both long- (> ~27 days) and short-term variations, linear correlation coefficients exhibit a decreasing trend from low latitudes towards high latitudes. The density variability can be effectively modeled (capturing 71% of the variance) using multiple solar irradiance indices, including F10.7, SEUV (the EUV 30-120 nm index), and SFUV (the FUV 120-193 nm index), in which a lag time of 1 day was used for both F10.7 and SEUV, and 5 days for SFUV. In our regression formulation SEUV has the largest contribution to the density variation (40%), with the F10.7 having the next largest contribution (32%) and SFUV accounting for the rest (28%). Furthermore, a pronounced period of about 27.2 days (mean period of the Sun's rotation) is present in both density and solar irradiance data of 2003 and 2004, and a pronounced period of about 54.4 days (doubled period of the solar rotation) is also revealed in 2004. However, soft X-ray and FUV irradiances did not present a pronounced 54.4 day period in 2004, in spite of their high correlation with the densities. The Ap index also shows 54-day periodicities in 2004, and magnetic activity, together with solar irradiance, affects the 54-day variation in density significantly. In addition, NRLMSISE00, DTM-2000 and JB2006 model predictions are compared with density measurements from CHAMP to assess their accuracy, and the results show that these models underestimate the response of the thermosphere to variations induced by solar rotation. Next, the equatorial topside ionospheric plasmas densities Ni are analyzed for solar irradiance variability effects during the period 2002-2005. Linear correlations between Ni and the solar irradiances for different wavelength ranges reveal significantly different characteristics. XUV (0-35 nm) and EUV (115-130 nm) show higher correlation with Ni for the long-term variations, whereas EUV (35-115 nm) show higher correlation for the short-term variations. Moreover, partial correlation analysis shows that the long-term variations of Ni are affected by both XUV (0-35 nm) and EUV (35-115 nm), whereas XUV (0-35 nm) play a more important role; the short-term variations of Ni are mostly affected by EUV (35-115 nm). Furthermore, a pronounced period of about 27 days is present in both Ni and solar irradiance data of 2003 and 2004, and a pronounced period of about 54 days is also revealed in 2004. Finally, prompted by previous studies that have suggested solar EUV radiation as a means of driving the semiannual variation, we investigate the intra-annual variation in thermosphere neutral density near 400 km during 2002-2005. The intra-annual variation, commonly referred to as the ‘semiannual variation’, is characterized by significant latitude structure, hemispheric asymmetries, and inter-annual variability. The magnitude of the maximum yearly difference, from the yearly minimum to the yearly maximum, varies by as much as 60% from year to year, and the phases of the minima and maxima also change by 20-40 days from year to year. Each annual harmonic of the intra-annual variation, namely, annual, semiannual, ter-annual and quatra-annual, exhibits a decreasing trend from 2002 through 2005 that is correlated with the decline in solar activity. In addition, some variations in these harmonics are correlated with geomagnetic activity, as represented by the daily mean value of Kp. Recent empirical models of the thermosphere are found to be deficient in capturing most of the latitude dependencies discovered in our data. In addition, the solar flux and geomagnetic activity proxies that we have employed do not capture some latitude and inter-annual variations detected in our data. It is possible that these variations are partly due to other effects, such as seasonal-latitudinal variations in turbopause altitude (and hence O/N2 composition) and ionosphere coupling processes that remain to be discovered in the context of influencing the intra-annual variations depicted here. Our results provide a new dataset to challenge and validate thermosphere-ionosphere general circulation models that seek to delineate the thermosphere intra-annual variation and to understand the various competing mechanisms that may contribute to its existence and variability. We furthermore suggest that the term “intra-annual” variation be adopted to describe the variability in thermosphere and ionosphere parameters that is well-captured through a superposition of annual, semiannual, ter-annual, and quatra-annual harmonic terms, and that “semiannual’ be used strictly in reference to a pure 6-monthly sinusoidal variation. Moreover, we propose the term “intra-seasonal” to refer to those shorter-term variations that arise as residuals from the above Fourier representation.

Host genetics and HIV-1: the final phase?

This is a crucial transition time for human genetics in general, and for HIV host genetics in particular. After years of equivocal results from candidate gene analyses, several genome-wide association studies have been published that looked at plasma viral load or disease progression. Results from other studies that used various large-scale approaches (siRNA screens, transcriptome or proteome analysis, comparative genomics) have also shed new light on retroviral pathogenesis. However, most of the inter-individual variability in response to HIV-1 infection remains to be explained: genome resequencing and systems biology approaches are now required to progress toward a better understanding of the complex interactions between HIV-1 and its human host.

How should sparse marine in situ measurements be compared to a continuous model: an example

This work demonstrates an example of the importance of an adequate method to sub-sample model results when comparing with in situ measurements. A test of model skill was performed by employing a point-to-point method to compare a multi-decadal hindcast against a sparse, unevenly distributed historic in situ dataset. The point-to-point method masked out all hindcast cells that did not have a corresponding in situ measurement in order to match each in situ measurement against its most similar cell from the model. The application of the point-to-point method showed that the model was successful at reproducing the inter-annual variability of the in situ datasets. Furthermore, this success was not immediately apparent when the measurements were aggregated to regional averages. Time series, data density and target diagrams were employed to illustrate the impact of switching from the regional average method to the point-to-point method. The comparison based on regional averages gave significantly different and sometimes contradicting results that could lead to erroneous conclusions on the model performance. Furthermore, the point-to-point technique is a more correct method to exploit sparse uneven in situ data while compensating for the variability of its sampling. We therefore recommend that researchers take into account for the limitations of the in situ datasets and process the model to resemble the data as much as possible.

Impact of climate change on Antarctic krill

Antarctic krill Euphausia superba (hereafter ‘krill’) occur in regions undergoing rapid environmental change, particularly loss of winter sea ice. During recent years, harvesting of krill has increased, possibly enhancing stress on krill and Antarctic ecosystems. Here we review the overall impact of climate change on krill and Antarctic ecosystems, discuss implications for an ecosystem-based fisheries management approach and identify critical knowledge gaps. Sea ice decline, ocean warming and other environmental stressors act in concert to modify the abundance, distribution and life cycle of krill. Although some of these changes can have positive effects on krill, their cumulative impact is most likely negative. Recruitment, driven largely by the winter survival of larval krill, is probably the population parameter most susceptible to climate change. Predicting changes to krill populations is urgent, because they will seriously impact Antarctic ecosystems. Such predictions, however, are complicated by an intense inter-annual variability in recruitment success and krill abundance. To improve the responsiveness of the ecosystem-based management approach adopted by the Commission for the Conservation of Antarctic Marine Living Resources (CCAMLR), critical knowledge gaps need to be filled. In addition to a better understanding of the factors influencing recruitment, management will require a better understanding of the resilience and the genetic plasticity of krill life stages, and a quantitative understanding of under-ice and benthic habitat use. Current precautionary management measures of CCAMLR should be maintained until a better understanding of these processes has been achieved.