Structural and evolutionary relationships among protein tyrosine phosphatase domains

With the current access to the whole genomes of various organisms and the completion of the first draft of the human genome, there is a strong need for a structure-function classification of protein families as an initial step in moving from DNA databases to a comprehensive understanding of human biology. As a result of the explosion in nucleic acid sequence information and the concurrent development of methods for high-throughput functional characterization of gene products, the genomic revolution also promises to provide a new paradigm for drug discovery, enabling the identification of molecular drug targets in a significant number of human diseases. This molecular view of diseases has contributed to the importance of combining primary sequence data with three-dimensional structure and has increased the awareness of computational homology modeling and its potential to elucidate protein function. In particular, when important proteins or novel therapeutic targets are identified—like the family of protein tyrosine phosphatases (PTPs) (reviewed in reference 53)—a structure-function classification of such protein families becomes an invaluable framework for further advances in biomedical science. Here, we present a comparative analysis of the structural relationships among vertebrate PTP domains and provide a comprehensive resource for sequence analysis of phosphotyrosine-specific PTPs

Bathypelagic particle flux signatures from a suboxic eddy in the oligotrophic tropical North Atlantic: production, sedimentation and preservation

Particle fluxes at the Cape Verde Ocean Observatory (CVOO) in the eastern tropical North Atlantic for the period December 2009 until May 2011 are discussed based on bathypelagic sediment trap time-series data collected at 1290 and 3439 m water depth. The typically oligotrophic particle flux pattern with weak seasonality is modified by the appearance of a highly productive and low oxygen (minimum concentration below 2 µmol kg−1 at 40 m depth) anticyclonic modewater eddy (ACME) in winter 2010. The eddy passage was accompanied by unusually high mass fluxes of up to 151 mg m−2 d−1, lasting from December 2009 to May 2010. Distinct biogenic silica (BSi) and organic carbon flux peaks of ∼ 15 and 13.3 mg m−2 d−1, respectively, were observed in February–March 2010 when the eddy approached the CVOO. The flux of the lithogenic component, mostly mineral dust, was well correlated with that of organic carbon, in particular in the deep trap samples, suggesting a tight coupling. The lithogenic ballasting obviously resulted in high particle settling rates and, thus, a fast transfer of epi-/meso-pelagic signatures to the bathypelagic traps. We suspect that the two- to three-fold increase in particle fluxes with depth as well as the tight coupling of mineral dust and organic carbon in the deep trap samples might be explained by particle focusing processes within the deeper part of the eddy. Molar C : N ratios of organic matter during the ACME passage were around 18 and 25 for the upper and lower trap samples, respectively. This suggests that some productivity under nutrient (nitrate) limitation occurred in the euphotic zone of the eddy in the beginning of 2010 or that a local nitrogen recycling took place. The δ15N record showed a decrease from 5.21 to 3.11 ‰ from January to March 2010, while the organic carbon and nitrogen fluxes increased. The causes of enhanced sedimentation from the eddy in February/March 2010 remain elusive, but nutrient depletion and/or an increased availability of dust as a ballast mineral for organic-rich aggregates might have contributed. Rapid remineralisation of sinking organic-rich particles could have contributed to oxygen depletion at shallow depth. Although the eddy formed in the West African coastal area in summer 2009, no indications of coastal flux signatures (e.g. from diatoms) were found in the sediment trap samples, confirming the assumption that the suboxia developed within the eddy en route. However, we could not detect biomarkers indicative of the presence of anammox (anaerobic ammonia oxidation) bacteria or green sulfur bacteria thriving in photic zone suboxia/hypoxia, i.e. ladderane fatty acids and isorenieratene derivatives, respectively. This could indicate that suboxic conditions in the eddy had recently developed and/or the respective bacterial stocks had not yet reached detection thresholds. Another explanation is that the fast-sinking organic-rich particles produced in the surface layer did not interact with bacteria from the suboxic zone below. Carbonate fluxes dropped from ∼ 52 to 21.4 mg m−2 d−1 from January to February 2010, respectively, mainly due to reduced contribution of shallow-dwelling planktonic foraminifera and pteropods. The deep-dwelling foraminifera Globorotalia menardii, however, showed a major flux peak in February 2010, most probably due to the suboxia/hypoxia. The low oxygen conditions forced at least some zooplankton to reduce diel vertical migration. Reduced “flux feeding” by zooplankton in the epipelagic could have contributed to the enhanced fluxes of organic materials to the bathypelagic traps during the eddy passage. Further studies are required on eddy-induced particle production and preservation processes and particle focusin

Child-computer interaction, ubiquitous technologies, and big data

In this forum we celebrate research that helps to successfully bring the benefits of computing technologies to children, older adults, people with disabilities, and other populations that are often ignored in the design of mass-marketed products. The children’s technology landscape is changing quickly. The ubiquity of interactive technologies means children can access them just about anytime, anywhere. At the same time, these technologies constantly collect data from and about children, bringing them into the age of big data, voluntarily or not. These developments have the potential to significantly change children’s relationship to technology and the long-term impact of technology use. To discuss these changes, the child-computer-interaction community held a special interest group (SIG) meeting during the CHI 2018 conference

An AeroCom initial assessment – optical properties in aerosol component modules of global models

The AeroCom exercise diagnoses multi-component aerosol modules in global modeling. In an initial assessment simulated global distributions for mass and mid-visible aerosol optical thickness (aot) were compared among 20 different modules. Model diversity was also explored in the context of previous comparisons. For the component combined aot general agreement has improved for the annual global mean. At 0.11 to 0.14, simulated aot values are at the lower end of global averages suggested by remote sensing from ground (AERONET ca. 0.135) and space (satellite composite ca. 0.15). More detailed comparisons, however, reveal that larger differences in regional distribution and significant differences in compositional mixture remain. Of particular concern are large model diversities for contributions by dust and carbonaceous aerosol, because they lead to significant uncertainty in aerosol absorption (aab). Since aot and aab, both, influence the aerosol impact on the radiative energy-balance, the aerosol (direct) forcing uncertainty in modeling is larger than differences in aot might suggest. New diagnostic approaches are proposed to trace model differences in terms of aerosol processing and transport: These include the prescription of common input (e.g. amount, size and injection of aerosol component emissions) and the use of observational capabilities from ground (e.g. measurements networks) or space (e.g. correlations between aerosol and clouds)

The impact of dietary diversity and seasonality in food availability on the quantile distribution of birth size among pregnant women in rural Malawi – a cross-sectional study

Background: Dietary diversity scores can be used as a proxy for dietary intakes and for assessment of nutrient adequacy. Studies from low-resource settings have found maternal dietary diversity scores to be associated with neonatal birth size. We here investigated the relationship between the dietary diversity score among pregnant mothers and birth size of their offspring across quantiles of the birth size variables; birth weight, length, abdominal circumference, and head circumference. We also investigated if seasonality affects birth size across different quantiles. Methods: Dietary intake and anthropometric data were collected from 190 pregnant women and their neonates in rural Malawi through two agricultural seasons. Dietary data was collected using 24-hour recall interviews and was categorized into the 10-food group dietary diversity score proposed for women by the Food and Agriculture Organization. Neonatal anthropometrics were collected upon delivery at health facilities. Quantile regression analyses were used to investigate associations between dietary diversity scores and birth size, as well as between seasonality and birth size. Results: We found that neonatal abdominal circumference was 0.9 cm larger during the post-harvest season compared to the pre-harvest season among neonates in the 25th quantile. Birth weight was 281.4 g higher for those born during the post-harvest season in the 90th quantile. For a one-unit increase in maternal dietary diversity score, birth weight increased by 56.7 g among those in the 25th quantile and neonatal head circumference increased by 0.2 cm for those in the 70th quantile. However, these findings did not remain significant when considering the cluster effect of the neonatal anthropometric data. Conclusions: Our findings indicate that the relationship between seasonality and birth size differs across the distribution of birth size. Investigating the effect of seasonality across the distribution of birth size could be important to identify vulnerable subgroups and develop better, targeted interventions to improve maternal and child nutrition and health

Rapid Adjustments Cause Weak Surface Temperature Response to Increased Black Carbon Concentrations

We investigate the climate response to increased concentrations of black carbon (BC), as part of the Precipitation Driver Response Model Intercomparison Project (PDRMIP). A tenfold increase in BC is simulated by nine global coupled‐climate models, producing a model median effective radiative forcing of 0.82 (ranging from 0.41 to 2.91) W m⁻², and a warming of 0.67 (0.16 to 1.66) K globally and 1.24 (0.26 to 4.31) K in the Arctic. A strong positive instantaneous radiative forcing (median of 2.10 W m⁻² based on five of the models) is countered by negative rapid adjustments (−0.64 W m⁻² for the same five models), which dampen the total surface temperature signal. Unlike other drivers of climate change, the response of temperature and cloud profiles to the BC forcing is dominated by rapid adjustments. Low‐level cloud amounts increase for all models, while higher‐level clouds are diminished. The rapid temperature response is particularly strong above 400 hPa, where increased atmospheric stabilization and reduced cloud cover contrast the response pattern of the other drivers. In conclusion, we find that this substantial increase in BC concentrations does have considerable impacts on important aspects of the climate system. However, some of these effects tend to offset one another, leaving a relatively small median global warming of 0.47 K per W m⁻²—about 20% lower than the response to a doubling of CO₂. Translating the tenfold increase in BC to the present‐day impact of anthropogenic BC (given the emissions used in this work) would leave a warming of merely 0.07 K

Analysis and quantification of the diversities of aerosol life cycles within AeroCom

Simulation results of global aerosol models have been assembled in the framework of the AeroCom intercomparison exercise. In this paper, we analyze the life cycles of dust, sea salt, sulfate, black carbon and particulate organic matter as simulated by sixteen global aerosol models. The diversities among the models for the sources and sinks, burdens, particle sizes, water uptakes, and spatial dispersals have been established. These diversities have large consequences for the calculated radiative forcing and the aerosol concentrations at the surface. The AeroCom all-models-average emissions are dominated by the mass of sea salt (SS), followed by dust (DU), sulfate (SO_4), particulate organic matter (POM), and finally black carbon (BC). Interactive parameterizations of the emissions and contrasting particles sizes of SS and DU lead generally to higher diversities of these species, and for total aerosol. The lower diversity of the emissions of the fine aerosols, BC, POM, and SO_4, is due to the use of similar emission inventories, and does therefore not necessarily indicate a better understanding of their sources. The diversity of SO_4-sources is mainly caused by the disagreement on depositional loss of precursor gases and on chemical production. The diversities of the emissions are passed on to the burdens, but the latter are also strongly affected by the model-specific treatments of transport and aerosol processes. The burdens of dry masses decrease from largest to smallest: DU, SS, SO_4, POM, and BC. The all-models-average residence time is shortest for SS with about half a day, followed by S_O4 and DU with four days, and POM and BC with six and seven days, respectively. The wet deposition rate is controlled by the solubility and increases from DU, BC, POM to SO_4 and SS. It is the dominant sink for SO_4, BC, and POM, and contributes about one third to the total removal rate coefficients of SS and DU species. For SS and DU we find high diversities for the removal rate coefficients and deposition pathways. Models do neither agree on the split between wet and dry deposition, nor on that between sedimentation and turbulent dry Deposition. We diagnose an extremely high diversity for the uptake of ambient water vapor that influences the particle size and thus the sink rate coefficients. Furthermore, we find little agreement among the model results for the partitioning of wet removal into scavenging by convective and stratiform rain. Large differences exist for aerosol dispersal both in the vertical and in the horizontal direction. In some models, a minimum of total aerosol concentration is simulated at the surface. Aerosol dispersal is most pronounced for SO4 and BC and lowest for SS. Diversities are higher for meridional than for vertical dispersal, they are similar for a given species and highest for SS and DU. For these two components we do not find a correlation between vertical and meridional aerosol dispersal. In addition the degree of dispersals of SS and DU is not related to their residence times. SO_4, BC, and POM, however, show increased meridional dispersal in models with larger vertical dispersal, and dispersal is larger for longer simulated residence times

The effect of harmonized emissions on aerosol properties in global models – an AeroCom experiment

The effects of unified aerosol sources on global aerosol fields simulated by different models are examined in this paper. We compare results from two AeroCom experiments, one with different (ExpA) and one with unified emissions, injection heights, and particle sizes at the source (ExpB). Surprisingly, harmonization of aerosol sources has only a small impact on the simulated diversity for aerosol burden, and consequently optical properties, as the results are largely controlled by model-specific transport, removal, chemistry (leading to the formation of secondary aerosols) and parameterizations of aerosol microphysics (e.g. the split between deposition pathways) and to a lesser extent on the spatial and temporal distributions of the (precursor) emissions. The burdens of black carbon and especially sea salt become more coherent in ExpB only, because the large ExpA diversity for these two species was caused by few outliers. The experiment also indicated that despite prescribing emission fluxes and size distributions, ambiguities in the implementation in individual models can lead to substantial differences. These results indicate the need for a better understanding of aerosol life cycles at process level (including spatial dispersal and interaction with meteorological parameters) in order to obtain more reliable results from global aerosol simulations. This is particularly important as such model results are used to assess the consequences of specific air pollution abatement strategies

A PDRMIP multi-model study on the impacts of regional aerosol forcings on global and regional precipitation

Atmospheric aerosols such as sulfate and black carbon (BC) generate inhomogeneous radiative forcing and can affect precipitation in distinct ways compared to greenhouse gases (GHGs). Their regional effects on the atmospheric energy budget and circulation can be important for understanding and predicting global and regional precipitation changes, which act on top of the background GHG-induced hydrological changes. Under the framework of the Precipitation Driver Response Model Inter-comparison Project (PDRMIP), multiple models were used for the first time to simulate the influence of regional (Asian and European) sulfate and BC forcing on global and regional precipitation. The results show that, as in the case of global aerosol forcing, the global fast precipitation response to regional aerosol forcing scales with global atmospheric absorption, and the slow precipitation response scales with global surface temperature response. Asian sulphate aerosols appear to be a stronger driver of global temperature and precipitation change compared to European aerosols, but when the responses are normalised by unit radiative forcing or by aerosol burden change, the picture reverses, with European aerosols being more efficient in driving global change. The global apparent hydrological sensitivities of these regional forcing experiments are again consistent with those for corresponding global aerosol forcings found in the literature. However, the regional responses and regional apparent hydrological sensitivities do not align with the corresponding global values. Through a holistic approach involving analysis of the energy budget combined with exploring changes in atmospheric dynamics, we provide a framework for explaining the global and regional precipitation responses to regional aerosol forcing