Finite mixture model: decompose a cytogram into "n" sub adjacent asymmetric Gaussian bells. A Mathematica 9 script.

The script works with Mathematica (version 9 or latest) however, the Laplacian filter and the finite mixture should be implement with any other mathematical software. The scripts includes different steps: 1) To import the original cytogram and convert it into a matrix f(x,y) of dimension "n x n" 2) To detect all potential pics in f(x,y) with the laplacian filter, 2, and create the list Ln that include the coordinate of each potential peak 3) To extract all i distinct proper subsets of Ln: P(Ln)={{ 1}1,{2}2,{3}3,{ 1, 2} 4……. {1, 2, 3,…, n}i} (where i=2n-1) 3) To run the finite mixture model for each subset 4) To select the bet model with the optimal number of peak according the Bayesian Information Criterion (BIC) descriptor.This script implements the Laplacian filter and the finite mixture approach to decompose a surface into an arbitrary number “n” of bi-dimensional asymmetric Gaussian probability distributions. Finite mixture are widely used in data mining or pattern recognition. Here, this tool in implemented to decompose an arbitrary surface f(x,y) with some peaks and shoulders. This approach can be useful to decompose any bidimensional data array. This document describes how to use this approach to deconvolve a cytogram

Use of metal oxide semiconductor sensors to measure methane in aquatic ecosystems in the presence of cross-interfering compounds

Monitoring dissolved methane in aquatic ecosystems contributes significantly to advancing our understanding of the carbon cycle in these habitats and capturing their impact on methane emissions. Low-cost metal oxide semiconductors (MOS) gas sensors are becoming an increasingly attractive tool to perform such measurements, especially at the air–water interface. However, the performance of MOS sensors in aquatic environmental sciences has come under scrutiny because of their cross-sensitivity to temperature, moisture, and sulfide interference. In this study, we evaluated the performance and limitations of a MOS methane sensor when measuring dissolved methane in waters. A MOS sensor was encapsulated in a hydrophobic extended polytetrafluoroethylene membrane to impede contact with water but allow gas perfusion. Therefore, the membrane enabled us to submerge the sensor in water and overcome cross-sensitivity to humidity. A simple portable, low-energy, flow-through cell system was assembled that included an encapsulated MOS sensor and a temperature sensor. Waters (with or without methane) were injected into the flow cell at a constant rate by a peristaltic pump. The signals from the two sensors were recorded continuously with a cost-efficient microcontroller. Tests specifically focused on the effect of water temperature and sulfide interference on sensor performance. Our experiments revealed that the lower limit of the sensor was in the range of 0.1–0.2 µmol¿L-1 and that it provided a stable response at water temperatures in the range of 18.5–28°C. Dissolved sulfide at a concentration of 0.4¿mmol¿L-1 or higher interfered with the sensor response, especially at low methane concentrations (0.5 µmol¿L-1 or lower). However, we show that if dissolved sulfide is monitored, its interference can be alleviated.Postprint (published version

Variability of DOC and nitrate responses to storms in a small Mediterranean forested catchment

International audienceSevere drought periods followed by intense rainfall often leads to major floods in Mediterranean catchments. The resulting hydrology is complex and the response of solutes in the streams is often unpredictable. This study aimed to identify the most relevant factors controlling the hydrological responses to storms of an intermittent Mediterranean stream and to link those factors with dissolved organic carbon (DOC) and nitrate during storm events. Measurements of climate, hydrology, DOC and nitrate concentrations during 26 storm events over three hydrological years were analysed. The contribution of the storm events to the total DOC and nitrate annual export was also calculated. Nitrate was mainly mobilised during high flow, while most of the DOC export occurred during baseflow. Solute concentrations peaked after drought periods and the solute export was maximal during the largest rainfalls (i.e. > 100 L m-2). One single large storm contributed some 22% of the total annual export of DOC, and about 80% of that of nitrate. Discharge was a good predictor of neither DOC nor nitrate responses, so variables other than discharge were considered. Factor Analysis was used to identify the main factors controlling the biogeochemical responses. Antecedent moisture conditions and the magnitude of the storm event were the most relevant factors and accounted for 63% of the total variance. Solute responses during high flow were highly variable. However, solute concentration changes showed a significant and moderate relationship with the factors controlling the hydrological responses (i.e. ? DOC v. the antecedent moisture conditions and ? NO3-N v. the magnitude of the storm event). Keywords: dissolved organic carbon, nitrate, Mediterranean, drought, Fuirosos catchment, storms</p

Pancreatic ductal adenocarcinoma can be detected by analysis of volatile organic compounds (VOCs) in alveolar air

Background: In the last decade many studies showed that the exhaled breath of subjects suffering from several pathological conditions has a peculiar volatile organic compound (VOC) profile. The objective of the present work was to analyse the VOCs in alveolar air to build a diagnostic tool able to identify the presence of pancreatic ductal adenocarcinoma in patients with histologically confirmed disease. Methods: The concentration of 92 compounds was measured in the end-tidal breath of 65 cases and 102 controls. VOCs were measured with an ion-molecule reaction mass spectrometry. To distinguish between subjects with pancreatic adenocarcinomas and controls, an iterated Least Absolute Shrinkage and Selection Operator multivariate Logistic Regression model was elaborated. Results: The final predictive model, based on 10 VOCs, significantly and independently associated with the outcome had a sensitivity and specificity of 100 and 84% respectively, and an area under the ROC curve of 0.99. For further validation, the model was run on 50 other subjects: 24 cases and 26 controls; 23 patients with histological diagnosis of pancreatic adenocarcinomas and 25 controls were correctly identified by the model. Conclusions: Pancreatic cancer is able to alter the concentration of some molecules in the blood and hence of VOCs in the alveolar air in equilibrium. The detection and statistical rendering of alveolar VOC composition can be useful for the clinical diagnostic approach of pancreatic neoplasms with excellent sensitivity and specificity

Stream hydrological fragmentation drives bacterioplankton community composition

In Mediterranean intermittent streams, the hydrological fragmentation in summer and the successive water flow reconvergence in autumn allow exploring how local processes shape the microbial community within the same habitat. The objectives of this study were to determine how bacterial community composition responded to hydrological fragmentation in summer, and to evaluate whether the seasonal shifts in community composition predominate over the effects of episodic habitat fragmentation. The bacterial community was assessed along the intermittent stream Fuirosos (Spain), at different levels of phylogenetic resolution by in situ hybridization, fingerprinting, and 16S rRNA gene sequencing. The hydrological fragmentation of the stream network strongly altered the biogeochemical conditions with the depletion of oxidized solutes and caused changes in dissolved organic carbon characteristics. In the isolated ponds, beta-Proteobacteria and Actinobacteria increased their abundance with a gradual reduction of the alpha-diversity as pond isolation time increased. Moreover, fingerprinting analysis clearly showed a shift in community composition between summer and autumn. In the context of a seasonal shift, the temporary stream fragmentation simultaneously reduced the microbial dispersion and affected local environmental conditions (shift in redox regime and quality of the dissolved organic matter) tightly shaping the bacterioplankton community composition

Effects of riparian vegetation removal on nutrient retention in a Mediterranean stream

We examined the effects of riparian vegetation removal on algal dynamics and stream nutrient retention efficiency by comparing NH4-N and PO4-P uptake lengths from a logged and an unlogged reach in Riera Major, a forested Mediterranean stream in northeastern Spain. From June to September 1995, we executed 6 short-term additions of N (as NH4Cl) and P (as Na2HPO4) in a 200-m section to measure nutrient uptake lengths. The study site included 2 clearly differentiated reaches in terms of canopy cover by riparian trees: the first 100 m were completely logged (i.e., the logged reach) and the remaining 100 m were left intact (i.e., the shaded reach). Trees were removed from the banks of the logged reach in the winter previous to our sampling. In the shaded reach, riparian vegetation was dominated by alders (Alnus glutinosa). The study was conducted during summer and fall months when differences in light availability between the 2 reaches were greatest because of forest canopy conditions. Algal biomass and % of stream surface covered by algae were higher in the logged than in the shaded reach, indicating that logging had a stimulatory effect on algae in the stream. Overall, nutrient retention efficiency was higher (i.e., shorter uptake lengths) in the logged than in the shaded reach, especially for PO4-P. Despite a greater increase in PO4-P retention efficiency relative to that of NH4-N following logging, retention efficiency for NH4-N was higher than for PO4-P in both study reaches. The PO4-P mass-transfer coefficient was correlated with primary production in both study reaches, indicating that algal activity plays an important role in controlling PO4-P dynamics in this stream. In contrast, the NH4-N mass-transfer coefficient showed a positive relation-ship only with % of algal coverage in the logged reach, and was not correlated with any algal-related parameter in the shaded reach. The lack of correlation with algal production suggests that mechanisms other than algal activity (i.e., microbial heterotrophic processes or abiotic mechanisms) may also influence NH4-N retention in this stream. Overall, this study shows that logging disturbances in small shaded streams may alter in-stream ecological features that lead to changes in stream nutrient retention efficiency. Moreover, it emphasizes that alteration of the tight linkage between the stream channel and the adjacent riparian zone may directly and indirectly impact biogeochemical processes with implications for stream ecosystem functioning

El Nino southern oscillation and seasonal drought drive riparian input dynamics in a Mediterranean stream

Inland waters substantially contribute to global carbon fluxes, and within them, low-order forested streams are important processors of allochthonous organic matter (OM) inputs. Leaf litter quantity and quality are expected to change in response to global change (e.g., climate change, land use change) but few long-term studies exist to better understand these shifts. The goal of this study was to assess the quantity and quality of OM sources to determine which global and local environmental factors control the dynamics of OM at the reach scale. The study was performed on a Mediterranean stream edged by a deciduous riparian forest over a 10-yr-time period. Riparian inputs, benthic and transported OM, and its carbon and nitrogen content were determined. The quantity of riparian inputs (912 +/- 56 g dry mass m(-2) yr(-1)) was comparable to temperate regions with deciduous riparian forests, but the Mediterranean climate determined the different dynamics of these inputs. El Nino Southern Oscillation was strongly related to the interannual variability in riparian inputs through changes in precipitation. The annual amount of inputs depended on previous cumulated nonflow periods, with successive nonflow periods causing a progressive decrease in riparian inputs. The distribution of inputs throughout the year followed either a unimodal or bimodal pattern according to the absence or presence of a nonflow period in summer. In addition, drought caused lower quality (higher carbon : nitrogen molar ratio) riparian inputs. Changes in the quantity and quality of OM were explained by both present and past local and global factors

Slow evolution toward "Super-Aggregation" of the oligomers formed through the swapping of RNase A N-Termini: a wish for amyloidosis?

Natively monomeric RNase A can oligomerize upon lyophilization from 40% acetic acid solutions or when it is heated at high concentrations in various solvents. In this way, it produces many dimeric or oligomeric conformers through the three-dimensional domain swapping (3D-DS) mechanism involving both RNase A N- or/and C-termini. Here, we found many of these oligomers evolving toward not negligible amounts of large derivatives after being stored for up to 15 months at 4 degrees C in phosphate buffer. We call these species super-aggregates (SAs). Notably, SAs do not originate from native RNase A monomer or from oligomers characterized by the exclusive presence of the C-terminus swapping of the enzyme subunits as well. Instead, the swapping of at least two subunits' N-termini is mandatory to produce them. Through immunoblotting, SAs are confirmed to derive from RNase A even if they retain only low ribonucleolytic activity. Then, their interaction registered with Thioflavin-T (ThT), in addition to TEM analyses, indicate SAs are large and circular but not "amyloid-like" derivatives. This confirms that RNase A acts as an "auto-chaperone", although it displays many amyloid-prone short segments, including the 16-22 loop included in its N-terminus. Therefore, we hypothesize the opening of RNase A N-terminus, and hence its oligomerization through 3D-DS, may represent a preliminary step favoring massive RNase A aggregation. Interestingly, this process is slow and requires low temperatures to limit the concomitant oligomers' dissociation to the native monomer. These data and the hypothesis proposed are discussed in the light of protein aggregation in general, and of possible future applications to contrast amyloidosis

Experimental evidence reveals impact of drought periods on dissolved organic matter quality and ecosystem metabolism in subalpine streams

Subalpine streams are predicted to experience lower summer discharge following climate change and water extractions. In this study, we aimed to understand how drought periods impact dissolved organic matter (DOM) processing and ecosystem metabolism of subalpine streams. We mimicked a gradient of drought conditions in stream‐side flumes and evaluated implications of drought on DOM composition, gross primary production, and ecosystem respiration. Our experiment demonstrated a production and release of DOM from biofilms and leaf litter decomposition at low discharges, increasing dissolved organic carbon concentrations in stream water by up to 50%. Absorbance and fluorescence properties suggested that the released DOM was labile for microbial degradation. Dissolved organic carbon mass balances revealed a high contribution of internal processes to the carbon budget during low flow conditions. The flumes with low discharge were transient sinks of atmospheric CO2 during the first 2 weeks of drought. After this autotrophic phase, the metabolic balance of these flumes turned heterotrophic, suggesting a nutrient limitation for primary production, while respiration remained high. Overall our experimental findings suggest that droughts in subalpine streams will enhance internal carbon cycling by transiently increasing primary production and more permanently respiration as the drought persists. We propose that the duration of a drought period combined with inorganic nutrient availability are key variables that determine if more carbon is respired in situ or exported downstream

Quality and reactivity of dissolved organic matter in a Mediterranean river across hydrological and spatial gradients.

Understanding DOM transport and reactivity in rivers is essential to having a complete picture of the global carbon cycle. In this study, we explore the effects of hydrological variability and downstream transport on dissolved organic matter (DOM) dynamics in a Mediterranean river. We sampled the main stem of the river Tordera from the source to the sea, over a range of fifteen hydrological conditions including extreme events (flood and drought). By exploring spatial and temporal gradients of DOM fluorescence properties, river hydrology was found to be a significant predictor of DOM spatial heterogeneity. An additional space-resolved mass balance analysis performed on four contrasting hydrological conditions revealed that this was due to a shift in the biogeochemical function of the river. Flood conditions caused a conservative transport of DOM, generating a homogeneous, humic-like spatial profile of DOM quality. Lower flows induced a non-conservative, reactive transport of DOM, which enhanced the spatial heterogeneity of DOM properties. Moreover, the downstream evolution of DOM chemostatic behaviour revealed that the role of hydrology in regulating DOM properties increased gradually downstream, indicating an organised inter-dependency between the spatial and the temporal dimensions. Overall, our findings reveal that riverine DOM dynamics is in constant change owing to varying hydrological conditions, and emphasize that in order to fully understand the role of rivers in the global carbon cycle, it is necessary to take into account the full range of hydrological variability, from floods to droughts