Spectro-ViT: A Vision Transformer Model for GABA-edited MRS Reconstruction Using Spectrograms

Purpose: To investigate the use of a Vision Transformer (ViT) to reconstruct/denoise GABA-edited magnetic resonance spectroscopy (MRS) from a quarter of the typically acquired number of transients using spectrograms. Theory and Methods: A quarter of the typically acquired number of transients collected in GABA-edited MRS scans are pre-processed and converted to a spectrogram image representation using the Short-Time Fourier Transform (STFT). The image representation of the data allows the adaptation of a pre-trained ViT for reconstructing GABA-edited MRS spectra (Spectro-ViT). The Spectro-ViT is fine-tuned and then tested using \textit{in vivo} GABA-edited MRS data. The Spectro-ViT performance is compared against other models in the literature using spectral quality metrics and estimated metabolite concentration values. Results: The Spectro-ViT model significantly outperformed all other models in four out of five quantitative metrics (mean squared error, shape score, GABA+/water fit error, and full width at half maximum). The metabolite concentrations estimated (GABA+/water, GABA+/Cr, and Glx/water) were consistent with the metabolite concentrations estimated using typical GABA-edited MRS scans reconstructed with the full amount of typically collected transients. Conclusion: The proposed Spectro-ViT model achieved state-of-the-art results in reconstructing GABA-edited MRS, and the results indicate these scans could be up to four times faster

Chronic effects of fire suppressors on the reproduction of the copepod Nitocra sp.

Fire suppressors are widely used in firefighting and their chemical composition may present a mixture of perfluorochlorinated surfactants (PFCs), including the perfluorooctane sulfonate (PFOS) which has been internationally banned due to its classification as a persistent organic pollutant (POP). PFCs have been found in environmental matrices and soft tissues of organisms, but the potential effect of such compounds on marine organisms has been overlooked. Here, it was evaluated whether the chronic exposures (i.e., seven days) to the fire suppressors Ageofoam, Cold Fire, Kidde and Argus could affect the reproduction of the copepod Nitocra sp. The tested concentrations consisted of those recommended on the products’ manuals and those ranging between 0.0001% and 1%. For each compound, the effective concentrations to 50% exposed organisms (EC50) and the lowest observed effect concentrations (LOEC) were estimated. All the fire suppressors exhibited high toxicity, causing fecundity reduction. At the recommended dilutions, 100% lethality occurred for all compounds. The EC50 values ranged from 0.00817% - Ageofoam - to 0.03081% - Argus. The LOECs ranged from 0.001% - Ageofoam - to 0.1% - Argus and Kidde; and were much lower than the concentrations recommended for commercial use. The fire suppressors showed high toxicity to the copepod, reducing the reproduction rates, even in very low concentrations, suggesting that the release of such substances in the estuary caused severe effects to the environment. This assessment provides subsides to the environmental regulation of fire suppressors in Brazil, because these compounds do not have national regulations for their use and disposal

OCORRÊNCIA DE Vouacapoua americana Aubl. e Virola surinamensis Warb. EM ÁREAS IMPACTADAS PELA UHE BELO MONTE

OCCURRENCE OF Vouacapoua americana Aubl. and Virola surinamensis Warb. IN AREAS IMPACTED BY UHE BELO MONTEPRESENCIA DE Vouacapoua americana Aubl. y Virola surinamensis Warb. EN ZONAS IMPACTADAS POR UHE BELO MONTERESUMOO georreferenciamento de espécies ameaçadas é de grande importância na determinação de planos de conservação mais efetivos e a definição de áreas prioritárias. Objetivo desse trabalho foi georreferenciar áreas de ocorrência e distribuição geográfica de matrizes de Vouacapoua americana e Virola surinamensis localizadas em áreas impactadas pela UHE Belo Monte. Foram coletadas coordenadas das áreas de ocorrência e distribuição de matrizes de acapu em áreas impactadas por Belo Monte, a partir de duas fontes: (1) Relatórios de Inventários Florestais (matrizes suprimidas e não suprimidas) e (2) Coletas realizadas em campo. Foi contabilizado o número de matrizes obtidas no relatório e em campo. Com base nas coordenadas, foram produzidos mapas georreferenciados da área de ocorrência e distribuição geográfica das duas espécies. Para acapu, foram obtidas 75 coordenadas, 22 coletadas em campo e 53 retiradas dos Relatórios (25 matrizes suprimidas e 28 não suprimidas). Observou-se a ocorrência de acapu de maneira distribuída na área do estudo, e sua ocorrência na região do estudo deve-se às condições ambientais favoráveis para seu biociclo. Notou-se a distribuição de matrizes em aglomerados, com aproximadamente 4 matrizes por aglomerado. Para Virola surinamensis, a distribuição geográfica segue um padrão de distribuição em aglomerados. Foram obtidos 2 aglomerados nos dados atuais com área ocupacional total de 3,52 ha com 14 matrizes e 3 aglomerados com os dados de 2011, apresentando a área de 1010,46 ha com 40 indivíduos. Por serem ameaçadas de extinção, é necessário o uso de geotecnologias para subsidiar políticas públicas de conservação da biodiversidade.Palavras-chave: Floresta Amazônica; Espécie Florestal; Impactos Ambientais; Geoprocessamento.ABSTRACTGeoreferencing of threatened species is of great importance in determining more effective conservation plans and defining priority areas. The objective of this work was to georeference areas of occurrence and geographic distribution of Vouacapoua americana and Virola surinamensis matrices located in areas impacted by the Belo Monte HPP. Coordinates were collected from the areas of occurrence and distribution of acapu matrices in areas impacted by Belo Monte, from two sources: (1) Forest Inventory Reports (suppressed and non-suppressed matrices) and (2) Field surveys. The number of matrices obtained in the report and in the field was counted. Based on the coordinates, georeferenced maps of the area of occurrence and geographical distribution of the two species were produced. For acapu, 75 coordinates were obtained, 22 collected in the field and 53 taken from the Reports (25 suppressed and 28 non-suppressed matrices). It was observed the occurrence of acapu in a distributed way in the study area, its occurrence in the study region due to the favorable environmental conditions for its biocycle. Matrix distribution in clusters was noted, with approximately 4 matrices per cluster. For Virola surinamensis, geographic distribution follows a pattern of distribution in clusters. We obtained 2 clusters in the current data with total occupational area of 3.52 ha with 14 matrices and 3 clusters with the 2011 data, presenting the area of 1010.46 ha with 40 individuals. Because they are threatened with extinction, the use of geotechnologies is necessary to support public policies for biodiversity conservation.Keywords: Amazon Rainforest; Forest Species; Environmental Impacts; Geoprocessing.RESUMENLa georreferenciación de especies amenazadas es de gran importancia para determinar planes de conservación más efectivos y definir áreas prioritarias. El objetivo de este trabajo fue georreferenciar áreas de ocurrencia y distribución geográfica de matrices de Vouacapoua americana y Virola surinamensis ubicadas en áreas afectadas por la HPP de Belo Monte. Se recopilaron coordenadas de las áreas de ocurrencia y distribución de matrices de acapu en áreas afectadas por Belo Monte, de dos fuentes: (1) Informes de inventario forestal (matrices suprimidas y no suprimidas) y (2) Encuestas de campo. Se contó el número de matrices obtenidas en el informe y en el campo. Con base en las coordenadas, se produjeron mapas georreferenciados del área de ocurrencia y distribución geográfica de las dos especies. Para acapu, se obtuvieron 75 coordenadas, 22 recogidas en el campo y 53 tomadas de los Informes (25 matrices suprimidas y 28 no suprimidas). Se observó la ocurrencia de acapu de manera distribuida en el área de estudio, su ocurrencia en la región de estudio debido a las condiciones ambientales favorables para su biociclo. Se observó la distribución de matrices en grupos, con aproximadamente 4 matrices por grupo. Para Virola surinamensis, la distribución geográfica sigue un patrón de distribución en grupos. Obtuvimos 2 grupos en los datos actuales con un área ocupacional total de 3.52 ha con 14 matrices y 3 grupos con los datos de 2011, presentando el área de 1010.46 ha con 40 individuos. Debido a que están en peligro de extinción, el uso de geotecnologías es necesario para apoyar las políticas públicas para la conservación de la biodiversidad.Palabras clave: Selva Amazónica; Especies Forestales; Impactos Ambientales; Geoprocesamiento

Prime Focus Spectrograph - Subaru's future -

The Prime Focus Spectrograph (PFS) of the Subaru Measurement of Images and Redshifts (SuMIRe) project has been endorsed by Japanese community as one of the main future instruments of the Subaru 8.2-meter telescope at Mauna Kea, Hawaii. This optical/near-infrared multi-fiber spectrograph targets cosmology with galaxy surveys, Galactic archaeology, and studies of galaxy/AGN evolution. Taking advantage of Subaru's wide field of view, which is further extended with the recently completed Wide Field Corrector, PFS will enable us to carry out multi-fiber spectroscopy of 2400 targets within 1.3 degree diameter. A microlens is attached at each fiber entrance for F-ratio transformation into a larger one so that difficulties of spectrograph design are eased. Fibers are accurately placed onto target positions by positioners, each of which consists of two stages of piezo-electric rotary motors, through iterations by using back-illuminated fiber position measurements with a wide-field metrology camera. Fibers then carry light to a set of four identical fast-Schmidt spectrographs with three color arms each: the wavelength ranges from 0.38 {\mu}m to 1.3 {\mu}m will be simultaneously observed with an average resolving power of 3000. Before and during the era of extremely large telescopes, PFS will provide the unique capability of obtaining spectra of 2400 cosmological/astrophysical targets simultaneously with an 8-10 meter class telescope. The PFS collaboration, led by IPMU, consists of USP/LNA in Brazil, Caltech/JPL, Princeton, & JHU in USA, LAM in France, ASIAA in Taiwan, and NAOJ/Subaru.Comment: 13 pages, 11 figures, submitted to "Ground-based and Airborne Instrumentation for Astronomy IV, Ian S. McLean, Suzanne K. Ramsay, Hideki Takami, Editors, Proc. SPIE 8446 (2012)

Advancing GABA-edited MRS Research through a Reconstruction Challenge

Purpose To create a benchmark for the comparison of machine learning-based Gamma-Aminobutyric Acid (GABA)-edited Magnetic Resonance Spectroscopy (MRS) reconstruction models using one quarter of the transients typically acquired during a complete scan.Methods The Edited-MRS reconstruction challenge had three tracks with the purpose of evaluating machine learning models trained to reconstruct simulated (Track 1), homogeneous in vivo (Track 2), and heterogeneous in vivo (Track 3) GABA-edited MRS data. Four quantitative metrics were used to evaluate the results: mean squared error (MSE), signal-to-noise ratio (SNR), linewidth, and a shape score metric that we proposed. Challenge participants were given three months to create, train and submit their models. Challenge organizers provided open access to a baseline U-NET model for initial comparison, as well as simulated data, in vivo data, and tutorials and guides for adding synthetic noise to the simulations.Results The most successful approach for Track 1 simulated data was a covariance matrix convolutional neural network model, while for Track 2 and Track 3 in vivo data, a vision transformer model operating on a spectrogram representation of the data achieved the most success. Deep learning (DL) based reconstructions with reduced transients achieved equivalent or better SNR, linewidth and fit error as conventional reconstructions with the full amount of transients. However, some DL models also showed the ability to optimize the linewidth and SNR values without actually improving overall spectral quality, pointing to the need for more robust metrics.Conclusion The edited-MRS reconstruction challenge showed that the top performing DL based edited-MRS reconstruction pipelines can obtain with a reduced number of transients equivalent metrics to conventional reconstruction pipelines using the full amount of transients. The proposed metric shape score was positively correlated with challenge track outcome indicating that it is well-suited to evaluate spectral quality.Competing Interest StatementThe authors have declared no competing interest

Prime Focus Spectrograph (PFS) for the Subaru Telescope: Overview, recent progress, and future perspectives

PFS (Prime Focus Spectrograph), a next generation facility instrument on the 8.2-meter Subaru Telescope, is a very wide-field, massively multiplexed, optical and near-infrared spectrograph. Exploiting the Subaru prime focus, 2394 reconfigurable fibers will be distributed over the 1.3 deg field of view. The spectrograph has been designed with 3 arms of blue, red, and near-infrared cameras to simultaneously observe spectra from 380nm to 1260nm in one exposure at a resolution of ~1.6-2.7A. An international collaboration is developing this instrument under the initiative of Kavli IPMU. The project is now going into the construction phase aiming at undertaking system integration in 2017-2018 and subsequently carrying out engineering operations in 2018-2019. This article gives an overview of the instrument, current project status and future paths forward.Comment: 17 pages, 10 figures. Proceeding of SPIE Astronomical Telescopes and Instrumentation 201

An Overview of the 2014 ALMA Long Baseline Campaign

A major goal of the Atacama Large Millimeter/submillimeter Array (ALMA) is to make accurate images with resolutions of tens of milliarcseconds, which at submillimeter (submm) wavelengths requires baselines up to ~15 km. To develop and test this capability, a Long Baseline Campaign (LBC) was carried out from September to late November 2014, culminating in end-to-end observations, calibrations, and imaging of selected Science Verification (SV) targets. This paper presents an overview of the campaign and its main results, including an investigation of the short-term coherence properties and systematic phase errors over the long baselines at the ALMA site, a summary of the SV targets and observations, and recommendations for science observing strategies at long baselines. Deep ALMA images of the quasar 3C138 at 97 and 241 GHz are also compared to VLA 43 GHz results, demonstrating an agreement at a level of a few percent. As a result of the extensive program of LBC testing, the highly successful SV imaging at long baselines achieved angular resolutions as fine as 19 mas at ~350 GHz. Observing with ALMA on baselines of up to 15 km is now possible, and opens up new parameter space for submm astronomy.Comment: 11 pages, 7 figures, 2 tables; accepted for publication in the Astrophysical Journal Letters; this version with small changes to affiliation

Measurements of Higgs boson production and couplings in diboson final states with the ATLAS detector at the LHC

Measurements are presented of production properties and couplings of the recently discovered Higgs boson using the decays into boson pairs, H →γ γ, H → Z Z∗ →4l and H →W W∗ →lνlν. The results are based on the complete pp collision data sample recorded by the ATLAS experiment at the CERN Large Hadron Collider at centre-of-mass energies of √s = 7 TeV and √s = 8 TeV, corresponding to an integrated luminosity of about 25 fb−1. Evidence for Higgs boson production through vector-boson fusion is reported. Results of combined fits probing Higgs boson couplings to fermions and bosons, as well as anomalous contributions to loop-induced production and decay modes, are presented. All measurements are consistent with expectations for the Standard Model Higgs boson

Standalone vertex finding in the ATLAS muon spectrometer

A dedicated reconstruction algorithm to find decay vertices in the ATLAS muon spectrometer is presented. The algorithm searches the region just upstream of or inside the muon spectrometer volume for multi-particle vertices that originate from the decay of particles with long decay paths. The performance of the algorithm is evaluated using both a sample of simulated Higgs boson events, in which the Higgs boson decays to long-lived neutral particles that in turn decay to bbar b final states, and pp collision data at √s = 7 TeV collected with the ATLAS detector at the LHC during 2011

Search for displaced vertices arising from decays of new heavy particles in 7 TeV pp collisions at ATLAS

We present the results of a search for new, heavy particles that decay at a significant distance from their production point into a final state containing charged hadrons in association with a high-momentum muon. The search is conducted in a pp-collision data sample with a center-of-mass energy of 7 TeV and an integrated luminosity of 33 pb^-1 collected in 2010 by the ATLAS detector operating at the Large Hadron Collider. Production of such particles is expected in various scenarios of physics beyond the standard model. We observe no signal and place limits on the production cross-section of supersymmetric particles in an R-parity-violating scenario as a function of the neutralino lifetime. Limits are presented for different squark and neutralino masses, enabling extension of the limits to a variety of other models.Comment: 8 pages plus author list (20 pages total), 8 figures, 1 table, final version to appear in Physics Letters