Nanoinformatics: developing new computing applications for nanomedicine

Nanoinformatics has recently emerged to address the need of computing applications at the nano level. In this regard, the authors have participated in various initiatives to identify its concepts, foundations and challenges. While nanomaterials open up the possibility for developing new devices in many industrial and scientific areas, they also offer breakthrough perspectives for the prevention, diagnosis and treatment of diseases. In this paper, we analyze the different aspects of nanoinformatics and suggest five research topics to help catalyze new research and development in the area, particularly focused on nanomedicine. We also encompass the use of informatics to further the biological and clinical applications of basic research in nanoscience and nanotechnology, and the related concept of an extended ?nanotype? to coalesce information related to nanoparticles. We suggest how nanoinformatics could accelerate developments in nanomedicine, similarly to what happened with the Human Genome and other -omics projects, on issues like exchanging modeling and simulation methods and tools, linking toxicity information to clinical and personal databases or developing new approaches for scientific ontologies, among many others

Estimating magnetic filling factors from simultaneous spectroscopy and photometry : disentangling spots, plage, and network

A.C.C. acknowledges support from the Science and Technology Facilities Council (STFC) consolidated grant number ST/R000824/1.State-of-the-art radial velocity (RV) exoplanet searches are limited by the effects of stellar magnetic activity. Magnetically active spots, plage, and network regions each have different impacts on the observed spectral lines and therefore on the apparent stellar RV. Differentiating the relative coverage, or filling factors, of these active regions is thus necessary to differentiate between activity-driven RV signatures and Doppler shifts due to planetary orbits. In this work, we develop a technique to estimate feature-specific magnetic filling factors on stellar targets using only spectroscopic and photometric observations. We demonstrate linear and neural network implementations of our technique using observations from the solar telescope at HARPS-N, the HK Project at the Mt. Wilson Observatory, and the Total Irradiance Monitor onboard SORCE. We then compare the results of each technique to direct observations by the Solar Dynamics Observatory. Both implementations yield filling factor estimates that are highly correlated with the observed values. Modeling the solar RVs using these filling factors reproduces the expected contributions of the suppression of convective blueshift and rotational imbalance due to brightness inhomogeneities. Both implementations of this technique reduce the overall activity-driven rms RVs from 1.64 to 1.02 m s(-1), corresponding to a 1.28 m s(-1) reduction in the rms variation. The technique provides an additional 0.41 m s(-1) reduction in the rms variation compared to traditional activity indicators.PostprintPeer reviewe

The striking geographical pattern of gastric cancer mortality in Spain: environmental hypotheses revisited

<p>Abstract</p> <p>Background</p> <p>Gastric cancer is decreasing in most countries. While socioeconomic development is the main factor to which this decline has been attributed, enormous differences among countries and within regions are still observed, with the main contributing factors remaining elusive. This study describes the geographic distribution of gastric cancer mortality at a municipal level in Spain, from 1994-2003.</p> <p>Methods</p> <p>Smoothed relative risks of stomach cancer mortality were obtained, using the Besag-York-Molliè autoregressive spatial model. Maps depicting relative risk (RR) estimates and posterior probabilities of RR being greater than 1 were plotted.</p> <p>Results</p> <p>From 1994-2003, 62184 gastric cancer deaths were registered in Spain (7 percent of all deaths due to malignant tumors). The geographic pattern was similar for both sexes. RRs displayed a south-north and coast-inland gradient, with lower risks being observed in Andalusia, the Mediterranean coastline, the Balearic and Canary Islands and the Cantabrian seaboard. The highest risk was concentrated along the west coast of Galicia, broad areas of the Castile & Leon Autonomous community, the province of Cáceres in Extremadura, Lleida and other areas of Catalonia.</p> <p>Conclusion</p> <p>In Spain, risk of gastric cancer mortality displays a striking geographic distribution. With some differences, this persistent and unique pattern is similar across the sexes, suggesting the implication of environmental exposures from sources, such as diet or ground water, which could affect both sexes and delimited geographic areas. Also, the higher sex-ratios found in some areas with high risk of smoking-related cancer mortality in males support the role of tobacco in gastric cancer etiology.</p

Methods to estimate aboveground wood productivity from long-term forest inventory plots

Forest inventory plots are widely used to estimate biomass carbon storage and its change over time. While there has been much debate and exploration of the analytical methods for calculating biomass, the methods used to determine rates of wood production have not been evaluated to the same degree. This affects assessment of ecosystem fluxes and may have wider implications if inventory data are used to parameterise biospheric models, or scaled to large areas in assessments of carbon sequestration. Here we use a dataset of 35 long-term Amazonian forest inventory plots to test different methods of calculating wood production rates. These address potential biases associated with three issues that routinely impact the interpretation of tree measurement data: (1) changes in the point of measurement (POM) of stem diameter as trees grow over time; (2) unequal length of time between censuses; and (3) the treatment of trees that pass the minimum diameter threshold (“recruits”). We derive corrections that control for changing POM height, that account for the unobserved growth of trees that die within census intervals, and that explore different assumptions regarding the growth of recruits during the previous census interval. For our dataset we find that annual aboveground coarse wood production (AGWP; in Mg ha−1 year−1 of dry matter) is underestimated on average by 9.2% if corrections are not made to control for changes in POM height. Failure to control for the length of sampling intervals results in a mean underestimation of 2.7% in annual AGWP in our plots for a mean interval length of 3.6 years. Different methods for treating recruits result in mean differences of up to 8.1% in AGWP. In general, the greater the length of time a plot is sampled for and the greater the time elapsed between censuses, the greater the tendency to underestimate wood production. We recommend that POM changes, census interval length, and the contribution of recruits should all be accounted for when estimating productivity rates, and suggest methods for doing this.European UnionUK Natural Environment Research CouncilGordon and Betty Moore FoundationCASE sponsorship from UNEP-WCMCRoyal Society University Research FellowshipERC Advanced Grant “Tropical Forests in the Changing Earth System”Royal Society Wolfson Research Merit Awar

How society’s negative view of videogames can discourage brands from sponsoring eSports

The purpose of this research was to identify the main motives that contribute to society’s negative view of videogames and that present a risk to the eSports sponsors’ image. To achieve this, an exploratory, qualitative, and integrative literature review was conducted. According to the theoretical data, there are four main reasons why society has a negative perception of videogames. It is commonly believed that: (1) gaming is an unproductive activity, (2) violent videogames incite aggressive behaviors, (3) videogames lead to gaming-addiction, and (4) eSports lead to eSports-related gambling addiction. However, while the literature presents convincing evidence that gaming can create addiction and that eSports can promote gambling addiction, there is no conclusive evidence to assume that violent videogames lead to aggressiveness and there is evidence showing that playing videogames can be a productive activity. Nevertheless, these four beliefs are a threat to the eSports sponsors’ image and may lead them to cancel their existing sponsorships or lead other brands to not want to sponsor eSports to prevent being associated with these negative notions. This research will help expand the minor literature on eSports sponsorships and advance the knowledge of why some eSports sponsorships are terminated and why some brands may be reluctant to sponsor eSports.info:eu-repo/semantics/publishedVersio

Residual effects of natural Zn chelates on navy bean response, Zn leaching and soil status

greenhouse experiment was conducted on weakly acidic and calcareous soils to evaluate the aging and residual effects of three natural organic Zn chelates [Zn-ethylenediaminedisuccinate (Zn-EDDS), Zn-polyhydroxyphenylcarboxylate and Zn-aminelignosulfonate] each administered in a single application to a first navy bean (Phaseolus vulgaris L.) crop at several different Zn application rates. In a second navy bean crop, we determined the following parameters: the extent of Zn leaching, the amount of available Zn remaining in soils, the amount of easily leachable Zn, the size of Zn fractions in soils, the pH and redox potential, the dry matter yield, and the soluble and total Zn concentrations in plants. The residual effect after 2 years of Zn fertilization mainly depended on the aging effect of Zn chelates and losses due to Zn leaching. The data relating to the evolution from the first to the second crop showed that the aging effect was noticeable in the calcareous soil. In the latter soil, the Zn-S,S-EDDS treatments showed greater decreases in the Zn uptake by plants than the other Zn treatments and the greatest Zn uptake by plants occurred when Zn was applied as Zn-aminelignosulfonate (10 mg Zn kg−1 rate, 6.85 mg Zn per lysimeter; 5 mg Zn kg−1 rate, 3.36 mg Zn per lysimeter). In contrast, in the calcareous soil, the maximum amount of Zn uptake, for the three chelates was 0.82 mg Zn per lysimeter. Consequently, a further application of Zn would be needed to prevent Zn deficiencies in the plants of a subsequent crop. The behaviour of the pH and Eh parameters in the soils and leachates did not depend on the natural Zn sources applied. In this study, the easily leachable Zn estimated by BaCl2 extraction was not adequate to predict Zn leaching from the soils in subsequent crops

A dual function of SnRK2 kinases in the regulation of SnRK1 and plant growth

[EN] Adverse environmental conditions trigger responses in plants that promote stress tolerance and survival at the expense of growth(1). However, little is known of how stress signalling pathways interact with each other and with growth regulatory components to balance growth and stress responses. Here, we show that plant growth is largely regulated by the interplay between the evolutionarily conserved energy-sensing SNF1-related protein kinase 1 (SnRK1) protein kinase and the abscisic acid (ABA) phytohormone pathway. While SnRK2 kinases are main drivers of ABA-triggered stress responses, we uncover an unexpected growth-promoting function of these kinases in the absence of ABA as repressors of SnRK1. Sequestration of SnRK1 by SnRK2-containing complexes inhibits SnRK1 signalling, thereby allowing target of rapamycin (TOR) activity and growth under optimal conditions. On the other hand, these complexes are essential for releasing and activating SnRK1 in response to ABA, leading to the inhibition of TOR and growth under stress. This dual regulation of SnRK1 by SnRK2 kinases couples growth control with environmental factors typical for the terrestrial habitat and is likely to have been critical for the water-to-land transition of plants.We thank J.-K. Zhu for the snrk2 mutants, M. Bennett for the SnRK2.2-GFP line, C. Koncz for the SnRK1-GFP line, X. Li for the SnRK2.3-FLAG OE line, J. Schroeder for the GFP-His-FLAG and SnRK2.6-His-FLAG OE lines, C. Mackintosh for the TPS5 antibody and the Nottingham Arabidopsis stock centre for T-DNA mutant seeds. The IGC Plant Facility (Vera Nunes) is thanked for excellent plant care. This work was supported by Fundacao para a Ciencia e a Tecnologia through the R&D Units UIDB/04551/2020 (GREEN-IT-Bioresources for Sustainability) and UID/MAR/04292/2019, FCT project nos. PTDC/BIA-PLA/7143/2014, LISBOA-01-0145-FEDER-028128 and PTDC/BIA-BID/32347/2017, and FCT fellowships/contract nos. SFRH/BD/122736/2016 (M.A.), SFRH/BPD/109336/2015 (A.C.), PD/BD/150239/2019 (D.R.B.), and IF/00804/2013 (E.B.G.). Work in P.L.R.'s laboratory was funded by MCIU grant no. BIO2017-82503-R. C.M. thanks the LabEx Paris Saclay Plant Sciences-SPS (ANR-10-LABX-040-SPS) for support. B.B.P. was funded by Programa VALi+d GVA APOSTD/2017/039. This project has received funding from the European Union Horizon 2020 research and innovation programme (grant agreement no. 867426-ABA-GrowthBalance-H2020-WF-2018-2020/H2020-WF-01-2018, awarded to B.B.P.). This work is dedicated to the memory of our beloved friend and colleague Americo Rodrigues.Belda-Palazón, B.; Adamo, M.; Valerio, C.; Ferreira, LJ.; Confraria, A.; Reis-Barata, D.; Rodrigues, A.... (2020). A dual function of SnRK2 kinases in the regulation of SnRK1 and plant growth. 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SnRK1A-interacting negative regulators modulate the nutrient starvation signaling sensor SnRK1 in source-sink communication in cereal seedlings under abiotic stress. Plant Cell 26, 808–27 (2014).Lu, C. A. et al. The SnRK1A protein kinase plays a key role in sugar signaling during germination and seedling growth of rice. Plant Cell 19, 2484–2499 (2007).Radchuk, R. et al. Sucrose non-fermenting kinase 1 (SnRK1) coordinates metabolic and hormonal signals during pea cotyledon growth and differentiation. Plant J. 61, 324–338 (2010).Radchuk, R., Radchuk, V., Weschke, W., Borisjuk, L. & Weber, H. Repressing the expression of the SUCROSE NONFERMENTING-1-RELATED PROTEIN KINASE gene in pea embryo causes pleiotropic defects of maturation similar to an abscisic acid-insensitive phenotype. Plant Physiol. 140, 263–278 (2006).Tsai, A. Y. & Gazzarrini, S. AKIN10 and FUSCA3 interact to control lateral organ development and phase transitions in Arabidopsis. Plant J. 69, 809–821 (2012).Tsai, A. 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The Arabidopsis TOR kinase specifically regulates the expression of nuclear genes coding for plastidic ribosomal proteins and the phosphorylation of the cytosolic ribosomal protein S6. Front. Plant Sci. 7, 1611 (2016).Wang, P. et al. Reciprocal regulation of the TOR kinase and ABA receptor balances plant growth and stress response. Mol. Cell 69, 100–112 e106 (2018).Van Leene, J. et al. Capturing the phosphorylation and protein interaction landscape of the plant TOR kinase. Nat. Plants 5, 316–327 (2019).Dietrich, D. et al. Root hydrotropism is controlled via a cortex-specific growth mechanism. Nat. Plants 3, 17057 (2017).Wu, Q. et al. Ubiquitin ligases RGLG1 and RGLG5 regulate abscisic acid signaling by controlling the turnover of phosphatase PP2CA. Plant Cell 28, 2178–2196 (2016).Belin, C. et al. Identification of features regulating OST1 kinase activity and OST1 function in guard cells. Plant Physiol. 141, 1316–1327 (2006).Fujii, H. & Zhu, J. K. Arabidopsis mutant deficient in 3 abscisic acid-activated protein kinases reveals critical roles in growth, reproduction, and stress. Proc. Natl Acad. Sci. USA 106, 8380–8385 (2009).Fujita, Y. et al. Three SnRK2 protein kinases are the main positive regulators of abscisic acid signaling in response to water stress in Arabidopsis. Plant Cell Physiol. 50, 2123–2132 (2009).Nakashima, K. et al. Three Arabidopsis SnRK2 protein kinases, SRK2D/SnRK2.2, SRK2E/SnRK2.6/OST1 and SRK2I/SnRK2.3, involved in ABA signaling are essential for the control of seed development and dormancy. Plant Cell Physiol. 50, 1345–1363 (2009).Fujii, H. et al. In vitro reconstitution of an abscisic acid signalling pathway. Nature 462, 660–664 (2009).Shen, W., Reyes, M. I. & Hanley-Bowdoin, L. Arabidopsis protein kinases GRIK1 and GRIK2 specifically activate SnRK1 by phosphorylating its activation loop. Plant Physiol. 150, 996–1005 (2009).Cheng, C. et al. SCFAtPP2-B11 modulates ABA signaling by facilitating SnRK2.3 degradation in Arabidopsis thaliana. PLoS Genet. 13, e1006947 (2017).Harthill, J. E. et al. Phosphorylation and 14-3-3 binding of Arabidopsis trehalose-phosphate synthase 5 in response to 2-deoxyglucose. Plant J. 47, 211–223 (2006).Song, Y. et al. Identification of novel interactors and potential phosphorylation substrates of GsSnRK1 from wild soybean (Glycine soja). Plant Cell Environ. 42, 145–157 (2018).Wang, X., Du, Y. & Yu, D. Trehalose phosphate synthase 5-dependent trehalose metabolism modulates basal defense responses in Arabidopsis thaliana. J. Integr. Plant Biol. 61, 509–527 (2019).Broeckx, T., Hulsmans, S. & Rolland, F. The plant energy sensor: evolutionary conservation and divergence of SnRK1 structure, regulation, and function. J. Exp. Bot. 67, 6215–6252 (2016).Wang, Y. et al. 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Elevated visual dependency in young adults after chemotherapy in childhood

Chemotherapy in childhood can result in long-term neurophysiological side-effects, which could extend to visual processing, specifically the degree to which a person relies on vision to determine vertical and horizontal (visual dependency). We investigated whether adults treated with chemotherapy in childhood experience elevated visual dependency compared to controls and whether any difference is associated with the age at which subjects were treated. Visual dependency was measured in 23 subjects (mean age 25.3 years) treated in childhood with chemotherapy (CTS) for malignant, solid, non-CNS tumors. We also stratified CTS into two groups: those treated before 12 years of age and those treated from 12 years of age and older. Results were compared to 25 healthy, age-matched controls. The subjective visual horizontal (SVH) and vertical (SVV) orientations was recorded by having subjects position an illuminated rod to their perceived horizontal and vertical with and without a surrounding frame tilted clockwise and counter-clockwise 20° from vertical. There was no significant difference in rod accuracy between any CTS groups and controls without a frame. However, when assessing visual dependency using a frame, CTS in general (p = 0.006) and especially CTS treated before 12 years of age (p = 0.001) tilted the rod significantly further in the direction of the frame compared to controls. Our findings suggest that chemotherapy treatment before 12 years of age is associated with elevated visual dependency compared to controls, implying a visual bias during spatial activities. Clinicians should be aware of symptoms such as visual vertigo in adults treated with chemotherapy in childhood

TRY plant trait database - enhanced coverage and open access

Plant traits-the morphological, anatomical, physiological, biochemical and phenological characteristics of plants-determine how plants respond to environmental factors, affect other trophic levels, and influence ecosystem properties and their benefits and detriments to people. Plant trait data thus represent the basis for a vast area of research spanning from evolutionary biology, community and functional ecology, to biodiversity conservation, ecosystem and landscape management, restoration, biogeography and earth system modelling. Since its foundation in 2007, the TRY database of plant traits has grown continuously. It now provides unprecedented data coverage under an open access data policy and is the main plant trait database used by the research community worldwide. Increasingly, the TRY database also supports new frontiers of trait-based plant research, including the identification of data gaps and the subsequent mobilization or measurement of new data. To support this development, in this article we evaluate the extent of the trait data compiled in TRY and analyse emerging patterns of data coverage and representativeness. Best species coverage is achieved for categorical traits-almost complete coverage for 'plant growth form'. However, most traits relevant for ecology and vegetation modelling are characterized by continuous intraspecific variation and trait-environmental relationships. These traits have to be measured on individual plants in their respective environment. Despite unprecedented data coverage, we observe a humbling lack of completeness and representativeness of these continuous traits in many aspects. We, therefore, conclude that reducing data gaps and biases in the TRY database remains a key challenge and requires a coordinated approach to data mobilization and trait measurements. This can only be achieved in collaboration with other initiatives

Frequency of nut consumption and mortality risk in the PREDIMED nutrition intervention trial

BackgroundProspective studies in non-Mediterranean populations have consistently related increasing nut consumption to lower coronary heart disease mortality. A small protective effect on all-cause and cancer mortality has also been suggested. To examine the association between frequency of nut consumption and mortality in individuals at high cardiovascular risk from Spain, a Mediterranean country with a relatively high average nut intake per person.MethodsWe evaluated 7,216 men and women aged 55 to 80 years randomized to 1 of 3 interventions (Mediterranean diets supplemented with nuts or olive oil and control diet) in the PREDIMED (‘PREvención con DIeta MEDiterránea’) study. Nut consumption was assessed at baseline and mortality was ascertained by medical records and linkage to the National Death Index. Multivariable-adjusted Cox regression and multivariable analyses with generalized estimating equation models were used to assess the association between yearly repeated measurements of nut consumption and mortality.ResultsDuring a median follow-up of 4.8 years, 323 total deaths, 81 cardiovascular deaths and 130 cancer deaths occurred. Nut consumption was associated with a significantly reduced risk of all-cause mortality (P for trend 3 servings/week (32% of the cohort) had a 39% lower mortality risk (hazard ratio (HR) 0.61; 95% CI 0.45 to 0.83). A similar protective effect against cardiovascular and cancer mortality was observed. Participants allocated to the Mediterranean diet with nuts group who consumed nuts >3 servings/week at baseline had the lowest total mortality risk (HR 0.37; 95% CI 0.22 to 0.66).ConclusionsIncreased frequency of nut consumption was associated with a significantly reduced risk of mortality in a Mediterranean population at high cardiovascular risk.Please see related commentary: http://www.biomedcentral.com/1741-7015/11/165.Trial registrationClinicaltrials.gov. International Standard Randomized Controlled Trial Number (ISRCTN): 35739639. Registration date: 5 October 2005