Methods for cleaning the BOLD fMRI signal

Available online 9 December 2016 http://www.sciencedirect.com/science/article/pii/S1053811916307418?via%3Dihubhttp://www.sciencedirect.com/science/article/pii/S1053811916307418?via%3DihubBlood oxygen-level-dependent functional magnetic resonance imaging (BOLD fMRI) has rapidly become a popular technique for the investigation of brain function in healthy individuals, patients as well as in animal studies. However, the BOLD signal arises from a complex mixture of neuronal, metabolic and vascular processes, being therefore an indirect measure of neuronal activity, which is further severely corrupted by multiple non-neuronal fluctuations of instrumental, physiological or subject-specific origin. This review aims to provide a comprehensive summary of existing methods for cleaning the BOLD fMRI signal. The description is given from a methodological point of view, focusing on the operation of the different techniques in addition to pointing out the advantages and limitations in their application. Since motion-related and physiological noise fluctuations are two of the main noise components of the signal, techniques targeting their removal are primarily addressed, including both data-driven approaches and using external recordings. Data-driven approaches, which are less specific in the assumed model and can simultaneously reduce multiple noise fluctuations, are mainly based on data decomposition techniques such as principal and independent component analysis. Importantly, the usefulness of strategies that benefit from the information available in the phase component of the signal, or in multiple signal echoes is also highlighted. The use of global signal regression for denoising is also addressed. Finally, practical recommendations regarding the optimization of the preprocessing pipeline for the purpose of denoising and future venues of research are indicated. Through the review, we summarize the importance of signal denoising as an essential step in the analysis pipeline of task-based and resting state fMRI studies.This work was supported by the Spanish Ministry of Economy and Competitiveness [Grant PSI 2013–42343 Neuroimagen Multimodal], the Severo Ochoa Programme for Centres/Units of Excellence in R & D [SEV-2015-490], and the research and writing of the paper were supported by the NIMH and NINDS Intramural Research Programs (ZICMH002888) of the NIH/HHS

Effect of prewhitening in resting-state functional near-infrared spectroscopy data

Published: 24 October 2018Near-infrared spectroscopy (NIRS) offers the potential to characterize resting-state functional connectivity (RSFC) in populations that are not easily assessed otherwise, such as young infants. In addition to the advantages of NIRS, one should also consider that the RS-NIRS signal requires specific data preprocessing and analysis. In particular, the RS-NIRS signal shows a colored frequency spectrum, which can be observed as temporal autocorrelation, thereby introducing spurious correlations. To address this issue, prewhitening of the RS-NIRS signal has been recently proposed as a necessary step to remove the signal temporal autocorrelation and therefore reduce false-discovery rates. However, the impact of this step on the analysis of experimental RS-NIRS data has not been thoroughly assessed prior to the present study. Here, the results of a standard preprocessing pipeline in a RS-NIRS dataset acquired in infants are compared with the results after incorporating two different prewhitening algorithms. Our results with a standard preprocessing replicated previous studies. Prewhitening altered RSFC patterns and disrupted the antiphase relationship between oxyhemoglobin and deoxyhemoglobin. We conclude that a better understanding of the effect of prewhitening on RS-NIRS data is still needed before directly considering its incorporation to the standard preprocessing pipeline.This research was possible due to the support of the Basque Government predoctoral grant PRE_2016_2_0188 to Borja Blanco, as well as the support of the Spanish Ministry of Economy and Competitiveness through the project PSI 2014-54512-P, Juan de la Cierva Fellowship (IJCI-2014-20821) and the “Severo Ochoa” Programme for Centres/Units of Excellence in R & D (SEV-2015-490)

Linking spatial patterns of soil redistribution traced with 137Cs and soil nutrients in a Mediterranean mountain agroecosystem (NE Spain)

1 Pag.This study aims to address soil movement and soil nutrient dynamics closely related to the status of soil degradation. A rain-fed cereal field (1.6 ha) representative of Mediterranean mountain agricultural landscapes (42 25’41”N 1 13’8”W) was selected to examine the effects of soil redistribution processes on the spatial variability of soil organic carbon (SOC) and nitrogen (SON) and their relationships with soil properties and topographic characteristics.Peer reviewe

Spatial patterns and stability of topsoil water content in a rainfed fallow cereal field and Calcisol-type soil

26 Pags.- 7 Fgis.- 4 Tabls. The definitive version is available at: http://www.sciencedirect.com/science/journal/03783774Topsoil water content (TSWC) is a key factor for crop establishment and subsequent production, runoff generation, soil detachment, and other soil processes. TSWC is one of the most variable soil properties due to the complexity of water fluxes in the unsaturated zone. The studies about TSWC in cultivated Calcisols are limited and almost inexistent under fallow treatment in rainfed cereal fields. We hypothesize that certain wetness characteristics (patterns, ranges and changes) of a soil portion remain over time. This study seeks to identify the spatial patterns of TSWC and their temporal stability in a Mediterranean fallow rainfed cereal field (1.6 ha, partial stubble retention, no weed growth allowed) and Haplic Calcisol-type soil. During 15 months (December 2009 to February 2011) and 25 field surveys measurements were made at 156 points (three values per point) by using a frequency-domain probe. Values of TSWC varied significantly and four humidity periods were identified using antecedent rainfall and evapotranspiration values: wet (November–February, 27.1 vol.% on average), spring (March–June, 18.8 vol.%), dry (July–September, 12.1 vol.%) and wetting-up (October, 18.8 vol.%). The relative differences within the field decreased under wet conditions and were higher in the dry surveys. The combined analysis of the standard deviation of the relative differences (SDRD) and the maps of TSWC showed that the spatial patterns of both the water content and the value changes were not stable at short-term. However, eight water content zones were defined at long-term supporting the initial hypothesis: wettest (23.8 vol.%), driest (16.8 vol.%), stable (SDRD 0.247) and moist and dry. Satisfactory correlations were obtained with two topographic factors (average slope of the contributing area and convexity) and four soil properties (rock, silt, carbonates and the water content at field capacity) and correlations improved in the wet period related to the dry period. A different time response of the TSWC values appeared in the wet (between 2 and 3 days) and dry (6 and 7 days) periods related to the antecedent rainfall and evapotranspiration. The different water content zones presented different values of the soil and topographic factors that explain the different temporal stability of the relative differences in TSWC.This research was funded by the project “Erosion and redistribution of soils and nutrients in Mediterranean agroecosystems: radioisotopic tracers of sources and sinks and modelling of scenarios (EROMED) (CGL2011-25486/BTE)” of the Spanish Ministry of Economy and Competitiveness.Peer reviewe

Neural correlates of phonological, orthographic and semantic reading processing in dyslexia

Developmental dyslexia is one of the most prevalent learning disabilities, thought to be associated with dysfunction in the neural systems underlying typical reading acquisition. Neuroimaging research has shown that readers with dyslexia exhibit regional hypoactivation in left hemisphere reading nodes, relative to control counterparts. This evidence, however, comes from studies that have focused only on isolated aspects of reading. The present study aims to characterize left hemisphere regional hypoactivation in readers with dyslexia for the main processes involved in successful reading: phonological, orthographic and semantic. Forty-one participants performed a demanding reading task during MRI scanning. Results showed that readers with dyslexia exhibited hypoactivation associated with phonological processing in parietal regions; with orthographic processing in parietal regions, Broca's area, ventral occipitotemporal cortex and thalamus; and with semantic processing in angular gyrus and hippocampus. Stronger functional connectivity was observed for readers with dyslexia than for control readers 1) between the thalamus and the inferior parietal cortex/ventral occipitotemporal cortex during pseudoword reading; and, 2) between the hippocampus and the pars opercularis during word reading. These findings constitute the strongest evidence to date for the interplay between regional hypoactivation and functional connectivity in the main processes supporting reading in dyslexia. Keywords: Dyslexia, Reading, Hypoactivation, Functional connectivity, Thalamus, Hippocampu

Modelling the effect of land management changes on soil organic carbon stocks in a mediterranean cultivated field

28 Pags.- 5 Tabls.- 4 Figs. The definitive version is available at: http://onlinelibrary.wiley.com/journal/10.1002/(ISSN)1099-145XLand management in agricultural lands has important effects on soil organic carbon (SOC) dynamics. These effects are particularly relevant in the Mediterranean region, where soils are fragile and prone to erosion. Increasing interest of modelling to simulate SOC dynamics and the significance of soil erosion on SOC redistribution have been linked to the development of some recent models. In this study, the SPEROS-C model was implemented in a 1.6-ha cereal field for a 150-year period covering 100 years of minimum tillage by animal traction, 35 years of conventional tillage followed by 15 years of reduced tillage by chisel to evaluate the effects of changes in land management on SOC stocks and lateral carbon fluxes in a Mediterranean agroecosystem. The spatial patterns of measured and simulated SOC stocks were in good agreement, and their spatial variability appeared to be closely linked to soil redistribution. Changes in the magnitude of lateral SOC fluxes differed between land management showing that during the conventional tillage period the carbon losses is slightly higher (0.06 g C m−2 yr−1) compared to the period of reduced till using chisel (0.04 g C m−2 yr−1). Although the results showed that the SPEROS-C model is a potential tool to evaluate erosion induced carbon fluxes and assess the relative contribution of different land management on SOC stocks in Mediterranean agroecosystems, the model was not able to fully represent the observed SOC stocks. Further research (e.g. input parameters) and model development will be needed to achieve more accurate results.This work was funded by the CICYT project (CGL2014-52986-R).Peer reviewe

Soil organic matter patterns in relation to soil redistribution in a cultivated field

copia .pdf del póster original de los autores. 4 Figs.- 1 Tabl.Objective: to examine the effect of soil redistribution processes on the distribution of soil organic matter using 137Cs to identify eroded and depositional areas in a Mediterranean cultivated field.This work was funded by the CICYT project EROMED (CGL2011–25486).Peer reviewe