A hybrid human and machine resource curation pipeline for the Neuroscience Information Framework

The breadth of information resources available to researchers on the Internet continues to expand, particularly in light of recently implemented data-sharing policies required by funding agencies. However, the nature of dense, multifaceted neuroscience data and the design of contemporary search engine systems makes efficient, reliable and relevant discovery of such information a significant challenge. This challenge is specifically pertinent for online databases, whose dynamic content is ‘hidden’ from search engines. The Neuroscience Information Framework (NIF; http://www.neuinfo.org) was funded by the NIH Blueprint for Neuroscience Research to address the problem of finding and utilizing neuroscience-relevant resources such as software tools, data sets, experimental animals and antibodies across the Internet. From the outset, NIF sought to provide an accounting of available resources, whereas developing technical solutions to finding, accessing and utilizing them. The curators therefore, are tasked with identifying and registering resources, examining data, writing configuration files to index and display data and keeping the contents current. In the initial phases of the project, all aspects of the registration and curation processes were manual. However, as the number of resources grew, manual curation became impractical. This report describes our experiences and successes with developing automated resource discovery and semiautomated type characterization with text-mining scripts that facilitate curation team efforts to discover, integrate and display new content. We also describe the DISCO framework, a suite of automated web services that significantly reduce manual curation efforts to periodically check for resource updates. Lastly, we discuss DOMEO, a semi-automated annotation tool that improves the discovery and curation of resources that are not necessarily website-based (i.e. reagents, software tools). Although the ultimate goal of automation was to reduce the workload of the curators, it has resulted in valuable analytic by-products that address accessibility, use and citation of resources that can now be shared with resource owners and the larger scientific community

Management of risk of breast carcinoma in postmenopausal women.

Breast carcinoma is the most frequent tumor in the female population. Many factors can influence the risk of breast cancer; some of them, such as old age and breast cancer 1/2 (BRCA1/BRCA2) gene mutations, are associated with a fourfold increase in risk. A previous diagnosis of atypical ductal or lobular hyperplasia or having a first-degree relative with a carcinoma are factors associated with a two- to fourfold increase in risk. A relative risk between 1 and 2 is associated with longer exposure to endogenous hormones as a result of early menarche, late menopause and obesity, or with recent and prolonged use of hormone replacement therapy (HRT) or with behavioural factors such as high alcohol and fat intake. Is it possible to modify breast cancer risk in postmenopausal women? Risk factors related to lifestyle can be changed, even if it is not clear whether modifying these behavioural factors during the postmenopausal period will influence the overall breast cancer risk. For instance, the influence of exogenous hormones throughout life (both oral contraceptives and HRT) should be evaluated according to the individual risk-benefit ratio. The problem is even more complex for women who carry genetic mutations and for those who have close relatives with breast cancer, who may be candidates for risk reduction strategies. Prophylactic bilateral mastectomy is still controversial, but is frequently offered to or requested by this group of women and may be indicated in BRCA1/BRCA2 carriers. Chemoprevention with tamoxifen and with the new selective estrogen receptor modulators, namely raloxifene, is very promising and deserves a thorough discussion for all high-risk women

Weekly paclitaxel as first-line chemotherapy in elderly advanced breast cancer patients: a phase II study of the Gruppo Italiano di Oncologia Geriatrica (GIOGer)

Background: First-line chemotherapy regimens suitable for elderly advanced breast cancer patients are still not defined. Patients and methods: Women with stage III or IV breast cancer aged >_70 years were enrolled in a phase II study aimed to evaluate both activity and toxicity of weekly paclitaxel. Among 46 planned patients, at least 18 responses and not more than seven unacceptable toxic events are required for a favourable conclusion. Paclitaxel 80 mg/m2 was administered weekly for 3 weeks every 28 days. Results: Unacceptable toxicity occurred in seven out of 46 patients evaluated for toxicity [15.2%; exact 95% confidence interval (CI) 7.6% to 28.2%] and was represented by one case of febrile neutropenia, one case of severe allergic reaction and five cases of cardiac toxicity. Among 41 patients evaluated for response, a complete response occurred in two (4.9%) patients and a partial response in 20 (48.8%), with an overall response rate of 53.7% (exact 95% CI 38.7% to 67.9%). The median progression-free survival was 9.7 months (95% CI 8.5\u201318.7) and median survival was 35.8 months (95% CI 19\u2013not defined). Conclusions: Weekly paclitaxel is highly active in elderly advanced breast cancer patients. Data on cardiovascular complications, however, indicate the need for a careful monitoring of cardiac function before and during chemotherap

Evaluating the structure and magnitude of the ash plume during the initial phase of the 2010 Eyjafjallajökull eruption using lidar observations and NAME simulations

The Eyjafjallajökull volcano in Iceland erupted explosively on 14 April 2010, emitting a plume of ash into the atmosphere. The ash was transported from Iceland toward Europe where mostly cloud-free skies allowed ground-based lidars at Chilbolton in England and Leipzig in Germany to estimate the mass concentration in the ash cloud as it passed overhead. The UK Met Office's Numerical Atmospheric-dispersion Modeling Environment (NAME) has been used to simulate the evolution of the ash cloud from the Eyjafjallajökull volcano during the initial phase of the ash emissions, 14–16 April 2010. NAME captures the timing and sloped structure of the ash layer observed over Leipzig, close to the central axis of the ash cloud. Relatively small errors in the ash cloud position, probably caused by the cumulative effect of errors in the driving meteorology en route, result in a timing error at distances far from the central axis of the ash cloud. Taking the timing error into account, NAME is able to capture the sloped ash layer over the UK. Comparison of the lidar observations and NAME simulations has allowed an estimation of the plume height time series to be made. It is necessary to include in the model input the large variations in plume height in order to accurately predict the ash cloud structure at long range. Quantitative comparison with the mass concentrations at Leipzig and Chilbolton suggest that around 3% of the total emitted mass is transported as far as these sites by small (<100 μm diameter) ash particles

Validation of Aura Microwave Limb Sounder O-3 and CO observations in the upper troposphere and lower stratosphere

International audienceGlobal satellite observations of ozone and carbon monoxide from the Microwave Limb Sounder (MLS) on the EOS Aura spacecraft are discussed with emphasis on those observations in the 215–100 hPa region (the upper troposphere and lower stratosphere). The precision, resolution and accuracy of the data produced by the MLS “version 2.2” processing algorithms are discussed and quantified. O3 accuracy is estimated at ~40 ppbv +5% (~20 ppbv +20% at 215 hPa) while the CO accuracy is estimated at ~30 ppbv +30% for pressures of 147 hPa and less. Comparisons with expectations and other observations show good agreements for the O3 product, generally consistent with the systematic errors quoted above. In the case of CO, a persistent factor of ~2 high bias is seen at 215 hPa. However, the morphology is shown to be realistic, consistent with raw MLS radiance data, and useful for scientific study. The MLS CO data at higher altitudes are shown to be consistent with other observations

Supressão de plantas daninhas por leguminosas anuais em sistema agroecológico na Pré-Amazônia.

Este trabalho teve por objetivos identificar e avaliar a agressividade potencial das plantas daninhas em um agrossistema com leguminosas herbáceas anuais como cobertura de solo. Foram plantadas, nas ruas de um sistema de aléias de sombreiro ( Clitoria fairchildiana) e no final do período agrícola, as leguminosas mucuna-preta, feijão-guandu, feijão-de-porco e calopogônio, em sistema de blocos ao acaso com cinco repetições. Para estudo da dinâmica da composição florística, avaliaram-se a freqüência, densidade, dominância, similaridade, diversidade de espécies e biomassa das plantas daninhas. Foram identificadas 42 espécies de plantas espontâneas, das quais as mais freqüentes e de maior densidade e dominância foram Leptochoa virgata, Panicumlaxum e Sidasp. Não foram detectadas diferenças significativas para densidade, número de espécies, diversidade e biomassa entre as plantas daninhas emergidas nos quatro tratamentos com leguminosas; nem destas em relação ao controle

Advances in understanding mineral dust and boundary layer processes over the Sahara from Fennec aircraft observations

International audienceThe Fennec climate program aims to improve understanding of the Saharan climate system through a synergy of observations and modelling. We present a description of the Fennec airborne observations during 2011 and 2012 over the remote Sahara (Mauritania and Mali) and the advances in the understanding of mineral dust and boundary layer processes they have provided. Aircraft instrumentation aboard the UK FAAM BAe146 and French SAFIRE Falcon 20 is described, with specific focus on instrumentation specially developed and relevant to Saharan meteorology and dust. Flight locations, aims and associated meteorology are described. Examples and applications of aircraft measurements from the Fennec flights are presented, highlighting new scientific results delivered using a synergy of different instruments and aircraft. These include: (1) the first airborne measurement of dust particles sized up to 300 microns and associated dust fluxes in the Saharan atmospheric boundary layer (SABL), (2) dust uplift from the breakdown of the nocturnal low-level jet before becoming visible in SEVIRI satellite imagery, (3) vertical profiles of the unique vertical structure of turbulent fluxes in the SABL, (4) in-situ observations of processes in SABL clouds showing dust acting as CCN and IN at −15 °C, (5) dual-aircraft observations of the SABL dynamics, thermodynamics and composition in the Saharan heat low region (SHL), (6) airborne observations of a dust storm associated with a cold-pool (haboob) issued from deep convection over the Atlas, (7) the first airborne chemical composition measurements of dust in the SHL region with differing composition, sources (determined using Lagrangian backward trajectory calculations) and absorption properties between 2011 and 2012, (8) coincident ozone and dust surface area measurements suggest coarser particles provide a route for ozone depletion, (9) discrepancies between airborne coarse mode size distributions and AERONET sunphotometer retrievals under light dust loadings. These results provide insights into boundary layer and dust processes in the SHL region – a region of substantial global climatic importance

Coarse-mode mineral dust size distributions, composition and optical properties from AER-D aircraft measurements over the tropical eastern Atlantic

Mineral dust is an important component of the climate system, affecting the radiation balance, cloud properties, biogeochemical cycles, regional circulation and precipitation, as well as having negative effects on aviation, solar energy generation and human health. Dust size and composition has an impact on all these processes. However, changes in dust size distribution and composition during transport, particularly for coarse particles, are poorly understood and poorly represented in climate models. Here we present new in situ airborne observations of dust in the Saharan Air Layer (SAL) and the marine boundary layer (MBL) at the beginning of its transatlantic transport pathway, from the AERosol Properties - Dust (AER-D) fieldwork in August 2015, within the peak season of North African dust export. This study focuses on coarse-mode dust properties, including size distribution, mass loading, shape, composition, refractive indices and optical properties. Size distributions from 0.1 to 100 µm diameter (d) are presented, fully incorporating the coarse and giant modes of dust. Within the MBL, mean effective diameter (deff) and volume median diameter (VMD) were 4.6 and 6.0 µm respectively, giant particles with a mode at 20-30 µm were observed, and composition was dominated by quartz and alumino-silicates at d > 1 µm. Within the SAL, particles larger than 20 µm diameter were always present up to 5 km altitude, in concentrations over 10−5 cm−3, constituting up to 40 % of total dust mass. Mean deff and VMD were 4.0 and 5.5 µm respectively. Larger particles were detected in the SAL than can be explained by sedimentation theory alone. Coarse-mode composition was dominated by quartz and alumino-silicates; the accumulation mode showed a strong contribution from sulfate-rich and sea salt particles. In the SAL, measured single scattering albedos (SSAs) at 550 nm representing d < 2.5 µm were 0.93 to 0.98 (mean 0.97). Optical properties calculated for the full size distribution (0.1 < d < 100 µm) resulted in lower SSAs of 0.91-0.98 (mean 0.95) and mass extinction coefficients of 0.27-0.35 m2 g−1 (mean 0.32 m2 g−1). Variability in SSA was mainly controlled by variability in dust composition (principally iron) rather than by variations in the size distribution, in contrast with previous observations over the Sahara where size is the dominant influence. It is important that models are able to capture the variability and evolution of both dust composition and size distribution with transport in order to accurately represent the impacts of dust on climate. These results provide a new SAL dust dataset, fully representing coarse and giant particles, to aid model validation and development