A metadata reporting framework (FRAMES) for synthesis of ecohydrological observations

Metadata describe the ancillary information needed for data preservation and independent interpretation, comparison across heterogeneous datasets, and quality assessment and quality control (QA/QC). Environmental observations are vastly diverse in type and structure, can be taken across a wide range of spatiotemporal scales in a variety of measurement settings and approaches, and saved in multiple formats. Thus, well-organized, consistent metadata are required to produce usable data products from diverse environmental observations collected across field sites. However, existing metadata reporting protocols do not support the complex data synthesis and model-data integration needs of interdisciplinary earth system research. We developed a metadata reporting framework (FRAMES) to enable management and synthesis of observational data that are essential in advancing a predictive understanding of earth systems. FRAMES utilizes best practices for data and metadata organization enabling consistent data reporting and compatibility with a variety of standardized data protocols. We used an iterative scientist-centered design process to develop FRAMES, resulting in a data reporting format that incorporates existing field practices to maximize data-entry efficiency. Thus, FRAMES has a modular organization that streamlines metadata reporting and can be expanded to incorporate additional data types. With FRAMES\u27s multi-scale measurement position hierarchy, data can be reported at observed spatial resolutions and then easily aggregated and linked across measurement types to support model-data integration. FRAMES is in early use by both data originators (persons generating data) and consumers (persons using data and metadata). In this paper, we describe FRAMES, identify lessons learned, and discuss areas of future development

The Extreme Hosts of Extreme Supernovae

We use GALEX ultraviolet (UV) and optical integrated photometry of the hosts of seventeen luminous supernovae (LSNe, having peak M_V < -21) and compare them to a sample of 26,000 galaxies from a cross-match between the SDSS DR4 spectral catalog and GALEX interim release 1.1. We place the LSNe hosts on the galaxy NUV-r versus M_r color magnitude diagram (CMD) with the larger sample to illustrate how extreme they are. The LSN hosts appear to favor low-density regions of the galaxy CMD falling on the blue edge of the blue cloud toward the low luminosity end. From the UV-optical photometry, we estimate the star formation history of the LSN hosts. The hosts have moderately low star formation rates (SFRs) and low stellar masses (M_*) resulting in high specific star formation rates (sSFR). Compared with the larger sample, the LSN hosts occupy low-density regions of a diagram plotting sSFR versus M_* in the area having higher sSFR and lower M_*. This preference for low M_*, high sSFR hosts implies the LSNe are produced by an effect having to do with their local environment. The correlation of mass with metallicity suggests that perhaps wind-driven mass loss is the factor that prevents LSNe from arising in higher-mass, higher-metallicity hosts. The massive progenitors of the LSNe (>100 M_sun), by appearing in low-SFR hosts, are potential tests for theories of the initial mass function that limit the maximum mass of a star based on the SFR.Comment: 8 pages, 3 figures, 2 tables, accepted to ApJ, amended references and updated SN designation

Toward identifying reproducible brain signatures of obsessive-compulsive profiles: rationale and methods for a new global initiative

Background Obsessive-compulsive disorder (OCD) has a lifetime prevalence of 2–3% and is a leading cause of global disability. Brain circuit abnormalities in individuals with OCD have been identified, but important knowledge gaps remain. The goal of the new global initiative described in this paper is to identify robust and reproducible brain signatures of measurable behaviors and clinical symptoms that are common in individuals with OCD. A global approach was chosen to accelerate discovery, to increase rigor and transparency, and to ensure generalizability of results. Methods We will study 250 medication-free adults with OCD, 100 unaffected adult siblings of individuals with OCD, and 250 healthy control subjects at five expert research sites across five countries (Brazil, India, Netherlands, South Africa, and the U.S.). All participants will receive clinical evaluation, neurocognitive assessment, and magnetic resonance imaging (MRI). The imaging will examine multiple brain circuits hypothesized to underlie OCD behaviors, focusing on morphometry (T1-weighted MRI), structural connectivity (Diffusion Tensor Imaging), and functional connectivity (resting-state fMRI). In addition to analyzing each imaging modality separately, we will also use multi-modal fusion with machine learning statistical methods in an attempt to derive imaging signatures that distinguish individuals with OCD from unaffected siblings and healthy controls (Aim #1). Then we will examine how these imaging signatures link to behavioral performance on neurocognitive tasks that probe these same circuits as well as to clinical profiles (Aim #2). Finally, we will explore how specific environmental features (childhood trauma, socioeconomic status, and religiosity) moderate these brain-behavior associations. Discussion Using harmonized methods for data collection and analysis, we will conduct the largest neurocognitive and multimodal-imaging study in medication-free subjects with OCD to date. By recruiting a large, ethno-culturally diverse sample, we will test whether there are robust biosignatures of core OCD features that transcend countries and cultures. If so, future studies can use these brain signatures to reveal trans-diagnostic disease dimensions, chart when these signatures arise during development, and identify treatments that target these circuit abnormalities directly. The long-term goal of this research is to change not only how we conceptualize OCD but also how we diagnose and treat it

The FLUXNET2015 dataset and the ONEFlux processing pipeline for eddy covariance data

The FLUXNET2015 dataset provides ecosystem-scale data on CO2, water, and energy exchange between the biosphere and the atmosphere, and other meteorological and biological measurements, from 212 sites around the globe (over 1500 site-years, up to and including year 2014). These sites, independently managed and operated, voluntarily contributed their data to create global datasets. Data were quality controlled and processed using uniform methods, to improve consistency and intercomparability across sites. The dataset is already being used in a number of applications, including ecophysiology studies, remote sensing studies, and development of ecosystem and Earth system models. FLUXNET2015 includes derived-data products, such as gap-filled time series, ecosystem respiration and photosynthetic uptake estimates, estimation of uncertainties, and metadata about the measurements, presented for the first time in this paper. In addition, 206 of these sites are for the first time distributed under a Creative Commons (CC-BY 4.0) license. This paper details this enhanced dataset and the processing methods, now made available as open-source codes, making the dataset more accessible, transparent, and reproducible.Peer reviewe

Toward identifying reproducible brain signatures of obsessive-compulsive profiles: rationale and methods for a new global initiative

Background Obsessive-compulsive disorder (OCD) has a lifetime prevalence of 2–3% and is a leading cause of global disability. Brain circuit abnormalities in individuals with OCD have been identified, but important knowledge gaps remain. The goal of the new global initiative described in this paper is to identify robust and reproducible brain signatures of measurable behaviors and clinical symptoms that are common in individuals with OCD. A global approach was chosen to accelerate discovery, to increase rigor and transparency, and to ensure generalizability of results. Methods We will study 250 medication-free adults with OCD, 100 unaffected adult siblings of individuals with OCD, and 250 healthy control subjects at five expert research sites across five countries (Brazil, India, Netherlands, South Africa, and the U.S.). All participants will receive clinical evaluation, neurocognitive assessment, and magnetic resonance imaging (MRI). The imaging will examine multiple brain circuits hypothesized to underlie OCD behaviors, focusing on morphometry (T1-weighted MRI), structural connectivity (Diffusion Tensor Imaging), and functional connectivity (resting-state fMRI). In addition to analyzing each imaging modality separately, we will also use multi-modal fusion with machine learning statistical methods in an attempt to derive imaging signatures that distinguish individuals with OCD from unaffected siblings and healthy controls (Aim #1). Then we will examine how these imaging signatures link to behavioral performance on neurocognitive tasks that probe these same circuits as well as to clinical profiles (Aim #2). Finally, we will explore how specific environmental features (childhood trauma, socioeconomic status, and religiosity) moderate these brain-behavior associations. Discussion Using harmonized methods for data collection and analysis, we will conduct the largest neurocognitive and multimodal-imaging study in medication-free subjects with OCD to date. By recruiting a large, ethno-culturally diverse sample, we will test whether there are robust biosignatures of core OCD features that transcend countries and cultures. If so, future studies can use these brain signatures to reveal trans-diagnostic disease dimensions, chart when these signatures arise during development, and identify treatments that target these circuit abnormalities directly. The long-term goal of this research is to change not only how we conceptualize OCD but also how we diagnose and treat it

The dark side of the tradition: The polluting effect of Epiphany folk fires in the eastern Po Valley (Italy)

In the Veneto Region (Po Valley, Northeastern Italy) on the eve of Epiphany, an important religious celebration, during the night between January 5th and 6th thousands of folk fires traditionally burn wooden material. The object of this study is to characterize the 2013 episode, bymonitoring the effects on the air quality in the region's lowlands. The daily concentrations ofPM2.5 and PM10 exceeded 250 and 300 μg m−3, respectively and the PM10 hourly values were above 600 μg m−3 in many sites. The levels of total carbon, major inorganic ions, polycyclic aromatic hydrocarbons and biomass burning tracers (levoglucosan and K+)weremeasured in 84 samples of PM10 and 38 of PM2.5 collected at 32 sites between January 4th and 7th. Total carbon ranged from 11 μg m−3 before the pollution episode to 131 μg m−3 a day afterwards, K+ from 0.6 to 5.1 μg m−3, benzo(a)pyrene from 2 to 23 ng m−3, and levoglucosan from 0.5 to 8.3 μg m−3. The dispersion of the particulate matter was traced by analyzing the levels of PM10 and PM2.5 in 133 and 51 sites, respectively, in the Veneto and neighboring regions. In addition to biomass burning the formation of secondary inorganic aerosol was revealed to be a key factor on a multivariate statistical data processing. By providing direct information on the effects of an intense and widespread biomass burning episode in the Po Valley, this study also enables some general considerations on biomass burning practices

Estimation of local and external contributions of biomass burning to PM2.5 in an industrial zone included in a large urban settlement

A total of 85 PM2.5 samples were collected at a site located in a large industrial zone (Porto Marghera, Venice, Italy) during a 1-year-long sampling campaign. Samples were analyzed to determine water-soluble inorganic ions, elemental and organic carbon, and levoglucosan, and results were processed to investigate the seasonal patterns, the relationship between the analyzed species, and the most probable sources by using a set of tools, including (i) conditional probability function (CPF), (ii) conditional bivariate probability function (CBPF), (iii) concentration weighted trajectory (CWT), and (iv) potential source contribution function (PSCF) analyses. Furthermore, the importance of biomass combustions to PM2.5 was also estimated. Average PM2.5 concentrations ranged between 54 and 16 μg m−3 in the cold and warm period, respectively. The mean value of total ions was 11 μg m−3 (range 1–46 μg m−3): The most abundant ion was nitrate with a share of 44 % followed by sulfate (29 %), ammonium (14 %), potassium (4 %), and chloride (4 %). Levoglucosan accounted for 1.2 % of the PM2.5 mass, and its concentration ranged from few ng m−3 in warm periods to 2.66 μg m−3 during winter. Average concentrations of levoglucosan during the cold period were higher than those found in other European urban sites. This result may indicate a great influence of biomass combustions on particulate matter pollution. Elemental and organic carbon (EC, OC) showed similar behavior, with the highest contributions during cold periods and lower during summer. The ratios between biomass burning indicators (K+, Cl−, NO3−, SO42−, levoglucosan, EC, and OC) were used as proxy for the biomass burning estimation, and the contribution to the OC and PM2.5 was also calculated by using the levoglucosan (LG)/OC and LG/PM2.5 ratios and was estimated to be 29 and 18 %, respectively

Phanton developing and caractherizing for radiotherapy using conventional magnetic resonance imaging and magnetization transfer contrast

A dosimetria 3D utilizando gel à base de monômeros é uma importante ferramenta utilizada em casos de Radioterapia, em que há necessidade de uma alta resolução da distribuição espacial de dose. Neste trabalho, desenvolvemos um gel à base de monômeros do acido metacrilico, denominado MAGIC®, com a finalidade de avaliar a distribuição espacial de dose em simulações de tratamento de radioterapia, utilizando duas técnicas de imagens por ressonância magnética, Magnetic Resonance Imaging (MRI): a relaxometria (RT) e a transferência de magnetização (Magnetization Transfer, MT). Para tal, o trabalho foi desenvolvido em três etapas. Na primeira, desenvolvemos fantomas para serem irradiados com radiação ? e x, sobre os quais imagens de ressonância foram obtidas e analisadas. Desenvolvemos também um software, escrito em Matlab®, para analisar as imagens e traçar curvas de isodose dos fantomas irradiados. Em seguida, aperfeiçoamos o preparo, a composição, e as maneiras de adquirir e processar as imagens do gel irradiado. Nessa etapa incorporamos o formaldeido ao gel MAGIC, aumentando sua sensibilidade em 15%. Por fim, simulamos cinco configurações de tratamento de radioterapia e avaliamos as isodoses adquiridas, comparando-as com aquelas obtidas pelo software de planejamento radioterápico virtual, TPS®. As avaliações feitas com a técnica de relaxometria corresponderam às nossas expectativas. Com ela foi possível caracterizar o gel MAGIC, com alguns testes dosimétricos, bem como avaliar as 5 simulações de tratamentos radioterápicos propostas. O gel se mostrou linear até 20 Gy, mas não apresentou níveis aceitáveis de reprodutibilidade, necessitando de uma curva de calibração em cada teste. O gel possui número atômico efetivo próximo ao da água não necessitando de fatores de correções. Na maioria dos casos simulados, as isodoses das simulações feitas com o gel MAGIC reproduziram as simulações virtuais. Infelizmente, não obtivemos, por enquanto, o mesmo sucesso com a avaliação por MT. As imagens de MT não se mostraram confiáveis e por esse motivo as simulações com o gel só foram feitas com a técnica de RT.The 3D monomeric gel dosimetry is an important tool in radiation therapy cases which needs high spatial dose resolution. In this work we developed a methacrilic acid monomeric gel called MAGIC® to evaluate spatial dose distributions in simulations of radiation therapy treatments. We used two Magnetic Resonance Imaging (MRI) techniques, the relaxometry (RT) and the magnetization transfer (MT). The work was developed in three stages. First of all, the phantoms were created to be irradiated using and x radiations, the MRI were acquired and analyzed. We also developed a software, programmed in Matlab®, to analyze the images and to draw isodoses curves of irradiated phantoms. Following it, we improved the way the gel was prepared and its composition, as well the image acquisition and processing. In this part we added formaldehyde to the gel, improving its sensibility in 15%. Finally, we simulated 5 different radiation therapy treatments and compared the isodoses measured with the isodoses of the radiation therapy treatment planning software (TPS®). The results of the RT technique corresponded to our expectations. Using the RT we characterized the gel with dosimetric tests and evaluated five different radiation therapy treatments. The gel showed a linear relation with the dose until 20 Gy, but the results of the tests were not reproducibles, because of that we made a calibration curve for each test. The effective atomic number of the gel is close to the water, so it was not necessary any correction. In most of the simulated cases, the isodoses measured with the gel reproduced the virtual simulations. Unfortunately, until now, we didn\' t have the same success using the MT technique. The MT images were not reliable and because of that the simulations were only made with the RT technique

Searching for epileptiform region in patients with temporal lobe epilepsy: alternative methods based on fMRI and EEG-fMRI

A epilepsia do lobo temporal (ELT) é a forma mais comum de epilepsia e a mais resistente ao tratamento medicamentoso. Existem diversos tipos de drogas anti-epilépticas usadas no controle das crises. Entretanto, em alguns casos, esse tipo de tratamento não é eficaz e a cirurgia para remoção da zona epileptogênica (ZE) pode ser uma alternativa recomendada. A ZE é definida como aquela onde as crises são originadas. Trata-se de um conceito teórico e, atualmente, não existem técnicas capazes de delimitá-la precisamente. Na prática, exames de EEG, vídeo-EEG, MEG, SPECT, PET e diversas técnicas de MRI, em especial as funcionais, têm sido usados para mapear zonas relacionadas à ZE. Contudo, em alguns casos, os resultados permanecem não convergentes e a determinação da ZE inconclusiva. Desse modo, é evidente a importância do surgimento de novas metodologias para auxiliar a localização da ZE. Assim, pois, o objetivo deste trabalho foi desenvolver dois métodos para a avaliação da ZE, ambos baseados na imagem funcional por ressonância magnética. No primeiro, investigamos possíveis alterações da resposta hemodinâmica (HRF) quando da modulação da pressão parcial de CO2. Para tanto, fizemos um estudo sobre 22 pacientes com ELT e 10 voluntários assintomáticos modulando a pressão parcial de CO2 sanguíneo cerebral por um protocolo de manobra de pausa respiratória e outro de inalação passiva de CO2/ar. Os resultados mostram que o tempo de onset da HRF tende a ser maior e a amplitude da HRF tende a ser menor em áreas do lobo temporal de pacientes com ELT quando comparados com os dados de voluntários assintomáticos. Além disso, os resultados mostram mapas de onset individuais coincidentes com exames de SPECT ictal. O segundo estudo foi baseado em medidas de EEG-fMRI simultâneo. Neste, avaliamos a relação entres as potências dos ritmos cerebrais alfa e teta (EEG) e o contraste BOLD (fMRI) de 41 pacientes com ELT e 7 voluntários assintomáticos em estado de repouso. A análise da banda alfa mostrou correlações negativas nos lobos occipital, parietal e frontal tanto nos voluntários quanto nos pacientes com ELT. As correlações positivas nos voluntários foram dispersas e variáveis em ambos hemisférios cerebrais. Por outro lado, encontramos forte correlação positiva no tálamo e ínsula dos pacientes com ELT. Na análise da banda teta observamos correlações positivas bilaterais nos giros pré e pós central de voluntários. Ainda, foram observados clusters no cíngulo anterior, tálamo, ínsula, putamen, em regiões parietais superior, frontais e giros temporais. Também, utilizamos um cálculo de índice de lateralização (IL) no lobo temporal em confrontos entre pacientes com ELT à direita, pacientes com ELT à esquerda e voluntários assintomáticos. Verificamos que os ILs, utilizando os clusters obtidos nas análises em teta, foram coincidentes com o diagnóstico clínico prévio da localização da ZE em todas as análises dos grupos de pacientes com ELT à direita, e na maioria do grupo de pacientes com ELT à esquerda. De forma geral, verificamos que o método de hipercapnia se mostrou ferramenta interessante na localização da ZE comprovada pelos coincidentes achados pela avaliação de SPECT. Inferimos que o maior tempo de onset e menor amplitude da HRF observadas nos pacientes em relação a voluntários possam estar relacionados a um stress vascular devido à recorrência de crises. Já o método de ritmicidade alfa e teta proposto parece promissor para ser usado na determinação da lateralização da ZE em pacientes com ELT.Temporal lobe epilepsy (TLE) is the most common and resistant form of epilepsy to anti-epileptic drug. There are several types of anti-epileptic drugs used in seizure control. However, in some cases drug treatment is not effective and surgery to remove the epileptogenic zone (EZ) is a recommended alternative. EZ is a theoretical concept and there are many techniques that have been applied to enclose it precisely. In practice, EEG, video-EEG, MEG, SPECT, PET and various MRI techniques, especially functional MRI (fMRI), have been used to map areas related to EZ. However, in some cases, the results remain non-convergent and the EZ, undefined. Therefore, the use of new methodologies to assist the location of EZ have been proposed. Herein, our goal was to develop two methods for assessing the EZ. The first one was designed to access changes in the hemodynamic response (HRF) of the EZ in response to hypercapnia. 22 patients with TLE and 10 normal volunteers were evaluated by modulating the partial pressure of CO2 during the acquisition of fMRI in a breathing holding and a passive inhalation CO2/air protocols. The results show increased onset times and decreased amplitude of the HRF in the temporal lobe of TLE patients compared with asymptomatic volunteers. Moreover, most patients had onset maps coincident with ictal SPECT localizations. The second proposed study was based on simultaneous EEG-fMRI acquisitions. The relationship between powers of alpha and theta bands (EEG) and BOLD contrast (fMRI) was investigated in 41 TLE patients and 7 healthy controls. Alpha band results show a consistent negative correlation in the occipital, parietal and frontal lobes both in controls and TLE patients. In addition, controls show disperse positive correlations in both hemispheres. On the other hand, TLE patients presented strong positive correlations in the thalamus and insula. Theta band analysis, in controls, primarily show positive correlations in bilateral pre-and post-central gyri. In patients, robust positive correlations were observed in the anterior cingulate gyrus, thalamus, insula, putamen, superior parietal, frontal and temporal gyri. Moreover, the lateralization index (LI) indicates a coincidence between the side of the EZ evaluated by clinical diagnosis and clusters detected in the theta band. In conclusion, the hipercapnia study showed to be an interesting tool in locating EZ and the results are similar to SPECT findings. The longer onset and lower amplitude of the HRF observed in patients may be related to a vascular stress due to the recurrence of seizures. Furthermore, alpha and theta rhythms may be a promising tool to be used in determining the lateralization of EZ in patients with TLE