The exploration of brain networks with resting-state fMRI (rs-fMRI) combined with graph theoretical approaches has become popular, with the perspective of finding network graph metrics as biomarkers ...in the context of clinical studies. A preliminary requirement for such findings is to assess the reliability of the graph based connectivity metrics. In previous test-retest (TRT) studies, this reliability has been explored using intraclass correlation coefficient (ICC) with heterogeneous results. But the issue of sample size has not been addressed. Using the large TRT rs-fMRI dataset from the Human Connectome Project (HCP), we computed ICCs and their corresponding p-values (applying permutation and bootstrap techniques) and varied the number of subjects (from 20 to 100), the scan duration (from 400 to 1200 time points), the cost and the graph metrics, using the Anatomic-Automatic Labelling (AAL) parcellation scheme. We quantified the reliability of the graph metrics computed both at global and regional level depending, at optimal cost, on two key parameters, the sample size and the number of time points or scan duration. In the cost range between 20% to 35%, most of the global graph metrics are reliable with 40 subjects or more with long scan duration (14min 24s). In large samples (for instance, 100 subjects), most global and regional graph metrics are reliable for a minimum scan duration of 7min 14s. Finally, for 40 subjects and long scan duration (14min 24s), the reliable regions are located in the main areas of the default mode network (DMN), the motor and the visual networks.
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•ICCs should be associated with p-values to measure graph metrics reliability.•Sample size and scan duration are key parameters to obtain reliable graph metrics.•The number of regions with reliable global efficiency increased with the sample size.•In large samples (n=100), nearly all global and regional metrics are reliable.•In small samples (around 40 subjects), we found reliable regions in motor, visual networks and DMN.
Epithelial cells experience constant mechanical forces, including fluid shear stress (FSS) on their apical surface. These forces alter both structure and function. While precise recapitulation of the ...complex mechanobiology of organs remains challenging, better understanding of the effect of mechanical stimuli is necessary towards the development of biorelevant in vitro models. This is especially relevant to organs-on-chip models which allow for fine control of the culture environment. In this study, the effects of the FSS on Caco-2 cell monolayers were systematically determined using a microfluidic device based on Hele-Shaw geometry. This approach allowed for a physiologically relevant range of FSS (from ∼0 to 0.03 dyn/cm2) to be applied to the cells within a single device. Exposure to microfluidic FSS induced significant phenotypical and functional changes in Caco-2 cell monolayers as compared to cells grown in static conditions. The application of FSS significantly altered the production of mucus, expression of tight junctions, vacuolization, organization of cytoskeleton, formation of microvilli, mitochondrial activity and expression of cytochrome P450. In the context of the intestinal epithelium, this detailed understanding of the effects of the FSS will enable the realization of in vitro organs-on-chip models with well-defined and tailored characteristics to a specific purpose, including for drug and nanoparticle absorption studies. The Hele-Shaw approach used in this study could be readily applied to other cell types and adapted for a wide range of physiologically relevant FSS.
Abiotic release of nitrous acid (HONO) in equilibrium with soil nitrite (NO 2 - ) was suggested as an important contributor to the missing source of atmospheric HONO and hydroxyl radicals (OH). The ...role of total soil-derived HONO in the biogeochemical and atmospheric nitrogen cycles, however, has remained unknown. In laboratory experiments, we found that for nonacidic soils from arid and arable areas, reactive nitrogen emitted as HONO is comparable with emissions of nitric oxide (NO). We show that ammonia-oxidizing bacteria can directly release HONO in quantities larger than expected from the acid-base and Henry's law equilibria of the aqueous phase in soil. This component of the nitrogen cycle constitutes an additional loss term for fixed nitrogen in soils and a source for reactive nitrogen in the atmosphere.
Atmospheric nitrogen depends on land surface exchanges of nitrogen compounds. In Sub Saharan Africa, deposition and emission fluxes of nitrogen compounds are poorly quantified, and are likely to ...increase in the near future due to land use change and anthropogenic pressure. This work proposes an estimate of atmospheric N compounds budget in West and Central Africa, along an ecosystem transect, from dry savanna to wet savanna and forest, for years 2000−2007. The budget may be considered as a one point in time budget, to be included in long term studies as one of the first reference point for Sub Saharan Africa. Gaseous dry deposition fluxes are estimated by considering N compounds concentrations measured in the frame of the IDAF network (IGAC DEBITS AFrica) at the monthly scale and modeling of deposition velocities at the IDAF sites, taking into account the bi directional exchange of ammonia. Particulate dry deposition fluxes are calculated using the same inferential method. Wet deposition fluxes are calculated from measurements of ammonium and nitrate chemical content in precipitations at the IDAF sites combined with the annual rainfall amount. In terms of emission, biogenic NO emissions are simulated at each IDAF site with a surface model coupled to an emission module elaborated from an artificial neural network equation. Ammonia emissions from volatilization are calculated from literature data on livestock quantity in each country and N content in manure. NOx and NH3 emission from biomass burning and domestic fires are estimated from satellite data and emission factors. The total budget shows that emission sources of nitrogen compounds are in equilibrium with deposition fluxes in dry and wet savannas, with respectively 7.40 ( 1.90) deposited and 9.01 ( 3.44) kgN ha−1 yr−1 emitted in dry savanna, 8.38 ( 2.04) kgN ha−1 yr−1 deposited and 9.60 ( 0.69) kgN ha−1 yr−1 emitted in wet savanna. In forested ecosystems, the total budget is dominated by wet plus dry deposition processes (14.75 2.36 kgN ha−1 yr−1), compared to emissions processes (8.54 0.50 kgN ha−1 yr−1).
This work is part of the IDAF program (IGAC-DEBITS-AFRICA) and is based on the long-term monitoring of gas concentrations (1998–2007) established at seven remote sites representative of major African ...ecosystems. Dry deposition fluxes were estimated by the inferential method using on the one hand surface measurements of gas concentrations (NO2, HNO3, NH3, SO2 and O3) and on the other hand modeled exchange rates. Dry deposition velocities (Vd) were calculated using the big-leaf model of Zhang et al. (2003b). The bidirectional approach is used for NH3 surface–atmosphere exchange (Zhang et al., 2010). Surface and meteorological conditions specific to IDAF sites have been used in the models of deposition. The seasonal and annual mean variations of gaseous dry deposition fluxes (NO2, HNO3, NH3, O3 and SO2) are analyzed. Along the latitudinal transect of ecosystems, the annual mean dry deposition fluxes of nitrogen compounds range from −0.4 to −0.8 kg N ha−1 yr−1 for NO2, from −0.7 to −1.0 kg N ha−1 yr−1 for HNO3 and from −0.7 to −8.3 kg N ha−1 yr−1 for NH3 over the study period (1998–2007). The total nitrogen dry deposition flux (NO2+HNO3+NH3) is more important in forests (−10 kg N ha−1 yr−1) than in wet and dry savannas (−1.6 to −3.9 kg N ha−1 yr−1). The annual mean dry deposition fluxes of ozone range between −11 and −19 kg ha−1 yr−1 in dry and wet savannas, and −11 and −13 kg ha−1 yr−1 in forests. Lowest O3 dry deposition fluxes in forests are correlated to low measured O3 concentrations, lower by a factor of 2–3, compared to other ecosystems. Along the ecosystem transect, the annual mean of SO2 dry deposition fluxes presents low values and a small variability (−0.5 to −1 kg S ha−1 yr−1). No specific trend in the interannual variability of these gaseous dry deposition fluxes is observed over the study period.
In the present study, we measured independently CH4 ebullition and diffusion in the footprint of an eddy covariance system (EC) measuring CH4 emissions in the Nam Theun 2 Reservoir, a recently ...impounded (2008) subtropical hydroelectric reservoir located in the Lao People's Democratic Republic (PDR), Southeast Asia. The EC fluxes were very consistent with the sum of the two terms measured independently (diffusive fluxes + ebullition = EC fluxes), indicating that the EC system picked up both diffusive fluxes and ebullition from the reservoir. We showed a diurnal bimodal pattern of CH4 emissions anti-correlated with atmospheric pressure. During daytime, a large atmospheric pressure drop triggers CH4 ebullition (up to 100 mmol m-2 d-1 ), whereas at night, a more moderate peak of CH4 emissions was recorded. As a consequence, fluxes during daytime were twice as high as during nighttime. Additionally, more than 4800 discrete measurements of CH4 ebullition were performed at a weekly/fortnightly frequency, covering water depths ranging from 0.4 to 16 m and various types of flooded ecosystems. Methane ebullition varies significantly seasonally and depends mostly on water level change during the warm dry season, whereas no relationship was observed during the cold dry season. On average, ebullition was 8.5 ± 10.5 mmol m-2 d-1 and ranged from 0 to 201.7 mmol m-2 d-1 . An artificial neural network (ANN) model could explain up to 46% of seasonal variability of ebullition by considering total static pressure (the sum of hydrostatic and atmospheric pressure), variations in the total static pressure, and bottom temperature as controlling factors. This model allowed extrapolation of CH4 ebullition on the reservoir scale and performance of gap filling over four years. Our results clearly showed a very high seasonality: 50% of the yearly CH4 ebullition occurs within four months of the warm dry season. Overall, ebullition contributed 60-80% of total emissions from the surface of the reservoir (disregarding downstream emissions), suggesting that ebullition is a major pathway in young hydroelectric reservoirs in the tropics.
In the framework of the IDAF (IGAC/DEBITS/AFrica) international program, this study aims to study the chemical composition of precipitation and associated wet deposition at the rural site of Djougou ...in Benin, representative of a West and Central African wet savanna. Five hundred and thirty rainfall samples were collected at Djougou, Benin, from July 2005 to December 2009 to provide a unique database. The chemical composition of precipitation was analyzed for inorganic (Ca2+, Mg2+, Na+, NH4+, K+, NO3−, Cl−, SO42−) and organic (HCOO−, CH3COO−, C2H5COO−, C2O42−) ions, using ion chromatography. The 530 collected rain events represent a total of 5706.1 mm of rainfall compared to the measured pluviometry 6138.9 mm, indicating that the collection efficiency is about 93%. The order of total annual loading rates for soluble cations is NH4+ > Ca2+ > Mg2+ > K+. For soluble anions the order of loading is carbonates > HCOO− > NO3− > CH3COO− > SO42− > Cl− > C2O42− > C2H5COO−. In the wet savanna of Djougou, 86% of the measured pH values range between 4.7 and 5.7 with a median pH of 5.19, corresponding to a VWM (Volume Weighed Mean) H+ concentration of 6.46 μeq·L−1. This acidity results from a mixture of mineral and organic acids. The annual sea salt contribution was computed for K+, Mg2+, Ca2+ and SO42− and represents 4.2% of K+, 41% of Mg2+, 1.3% of Ca2+, and 7.4% of SO42−. These results show that K+, Ca2+, SO42−, and Mg2+ were mainly of non-marine origin. The marine contribution is estimated at 9%. The results of the chemical composition of rainwater of Djougou indicates that, except for the carbonates, ammonium has the highest VWM concentration (14.3 μeq·L−1) and nitrate concentration is 8.2 μeq·L−1. The distribution of monthly VWM concentration for all ions is computed and shows the highest values during the dry season, comparing to the wet season. Identified nitrogenous compound sources (NOx and NH3) are domestic animals, natural emissions from savanna soils, biomass burning and biofuel combustions. The second highest contribution is the calcium ion (13.3 μeq·L−1), characteristic of dust aerosols from terrigenous sources, Calcium contributes up to 46% of the precipitation chemistry in Djougou. Finally, these results are compared to those obtained for other selected African sites representative of other main natural ecosystems: dry savanna and forest. The study of the African ecosystem transect indicates a pH gradient with more acidic pH in the forested ecosystem. Nitrogenous contribution to the chemical composition of rain in Lamto, wet savanna, (24%) is equivalent to the one estimated in Djougou (24%). The last contribution concerns organic acidity, which represents 7% of total ionic content of precipitation at Djougou. The relative particulate contribution PC and the relative gaseous contribution GC are calculated using the mean chemical composition measured in Djougou for the studied period. The comparison with other African sites gives 40% and 43% PC in wet savannas of Lamto (Côte d’Ivoire) and Djougou (Benin) respectively, 20% PC in the equatorial forest of Zoetele (Cameroon) and 80% PC in dry savanna of Banizoumbou (Niger). The results shown here indicate the existence of a North-South gradients of organic, marine, terrigenous and nitrogenous contributions along the transect in West and Central Africa.
•We provide a background study of the rain chemistry of a rural wet savanna site.•The frequency distribution of pH of rainwater at Djougou (Benin) is computed.•We estimate the nitrogenous compound emitted monthly by different sources.•We compute the distribution of monthly means of the wet deposition of major ions.•We estimate the sources contributions to the rain chemical content in West Africa.
The Gourma site in Mali is one of the three instrumented meso-scale sites deployed in West-Africa as part of the African Monsoon Multi-disciplinary Analysis (AMMA) project. Located both in the ...Sahelian zone
sensu stricto, and in the Saharo–Sahelian transition zone, the Gourma meso-scale window is the northernmost site of the AMMA-CATCH observatory reached by the West African Monsoon.
The experimental strategy includes deployment of a variety of instruments, from local to meso-scale, dedicated to monitoring and documentation of the major variables characterizing the climate forcing, and the spatio-temporal variability of surface processes and state variables such as vegetation mass, leaf area index (LAI), soil moisture and surface fluxes. This paper describes the Gourma site, its associated instrumental network and the research activities that have been carried out since 1984. In the AMMA project, emphasis is put on the relations between climate, vegetation and surface fluxes. However, the Gourma site is also important for development and validation of satellite products, mainly due to the existence of large and relatively homogeneous surfaces. The social dimension of the water resource uses and governance is also briefly analyzed, relying on field enquiry and interviews.
The climate of the Gourma region is semi-arid, daytime air temperatures are always high and annual rainfall amounts exhibit strong inter-annual and seasonal variations. Measurements sites organized along a north–south transect reveal sharp gradients in surface albedo, net radiation, vegetation production, and distribution of plant functional types. However, at any point along the gradient, surface energy budget, soil moisture and vegetation growth contrast between two main types of soil surfaces and hydrologic systems. On the one hand, sandy soils with high water infiltration rates and limited run-off support almost continuous herbaceous vegetation with scattered woody plants. On the other hand, water infiltration is poor on shallow soils, and vegetation is sparse and discontinuous, with more concentrated run-off that ends in pools or low lands within structured endorheic watersheds.
Land surface in the Gourma is characterized by rapid response to climate variability, strong intra-seasonal, seasonal and inter-annual variations in vegetation growth, soil moisture and energy balance. Despite the multi-decadal drought, which still persists, ponds and lakes have increased, the grass cover has largely recovered, and there are signs of increased tree cover at least in the low lands.
Cells regulate the biophysical properties of their membranes by coordinated synthesis of different classes of lipids. Here, we identified a highly dynamic feedback mechanism by which the budding ...yeast Saccharomyces cerevisiae can regulate phospholipid biosynthesis. Phosphatidic acid on the endoplasmic reticulum directly bound to the soluble transcriptional repressor Opi1p to maintain it as inactive outside the nucleus. After the addition of the lipid precursor inositol, this phosphatidic acid was rapidly consumed, releasing Opi1p from the endoplasmic reticulum and allowing its nuclear translocation and repression of target genes. Thus, phosphatidic acid appears to be both an essential ubiquitous metabolic intermediate and a signaling lipid.
Background
Patients with Crohn's disease (CD) in remission are exposed to chronic psychological distress, due to the constant risk of relapse. This permanent situation of anticipation and uncertainty ...can lead to anxiety, which may, in turn, trigger relapse. We aimed to investigate the effects of uncertainty on behavioral and brain responses to anticipation of visceral discomfort in quiescent CD patients.
Methods
Barostat‐controlled rectal distensions were preceded by cued uncertain or certain anticipation in nine CD patients and nine matched healthy volunteers. Brain responses obtained before distension across the different anticipation conditions in regions of interest (ROI) involved in (anticipation of) pain were measured using functional magnetic resonance imaging and compared between CD and controls. The association between anxiety‐related psychological variables and cerebral anticipatory activity was tested.
Key Results
During uncertainty, CD patients had significantly stronger activations than controls in the cingulate cortex, insula, amygdala, and thalamus with trends in the hippocampus, prefrontal, and secondary somatosensory cortex. In patients, brain responses to uncertainty in the majority of ROI correlated positively with gastrointestinal symptom‐specific anxiety, trait‐anxiety, and intolerance of uncertainty.
Conclusions & Inferences
In a context of uncertainty regarding occurrence of uncomfortable visceral sensations, CD is associated with excessive reactivity in brain regions known to be involved in sensory, cognitive and emotional aspects of pain processing and modulation, and threat appraisal. Our findings contribute to a better understanding of the role of emotional and cognitive processes in CD. This may, in turn, lead to the development of new (psycho)therapeutic approaches for management of symptoms and related anxiety.
During uncertainty regarding the occurrence of visceral discomfort, CD patients have significantly stronger activations than controls in brain regions implicated in sensory, cognitive and emotional aspects of pain and threat appraisal, and in autonomic responses. These brain responses to uncertainty correlate positively with gastrointestinal symptom‐specific anxiety, trait‐anxiety, and intolerance of uncertainty.
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