Influence of thresholding in mass and entropy dimension of 3-D soil images

With the advent of modern non-destructive tomography techniques, there have been many attempts to analyze 3-D pore space features mainly concentrating on soil structure. This analysis opens a challenging opportunity to develop techniques for quantifying and describe pore space properties, one of them being fractal analysis. Undisturbed soil samples were collected from four horizons of Brazilian soil and 3-D images at 45μm resolution. Four different threshold criteria were used to transform computed tomography (CT) grey-scale imagery into binary imagery (pore/solid) to estimate their mass fractal dimension (Dm) and entropy dimension (D1). Each threshold criteria had a direct influence on the porosity obtained, varying from 8 to 24% in one of the samples, and on the fractal dimensions. Linear scaling was observed over all the cube sizes, however depending on the range of cube sizes used in the analysis, Dm could vary from 3.00 to 2.20, realizing that the threshold influenced mainly the scaling in the smallest cubes (length of size from 1 to 16 voxels). Dm and D1 showed a logarithmic relation with the apparent porosity in the image, however, the increase of both values respect to porosity defined a characteristic feature for each horizon that can be related to soil texture and depth

Natural products triptolide, celastrol, and withaferin A inhibit the chaperone activity of peroxiredoxin I

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How do nutrient conditions and species identity influence the impact of mesograzers in eelgrass-epiphyte systems?

Coastal eutrophication is thought to cause excessive growth of epiphytes in eelgrass beds, threatening the health and survival of these ecologically and economically valuable ecosystems worldwide. Mesograzers, small crustacean and gastropod grazers, have the potential to prevent seagrass loss by grazing preferentially and efficiently on epiphytes. We tested the impact of three mesograzers on epiphyte biomass and eelgrass productivity under threefold enriched nutrient concentrations in experimental indoor mesocosm systems under summer conditions. We compared the results with earlier identical experiments that were performed under ambient nutrient supply. The isopod Idotea baltica, the periwinkle Littorina littorea, and the small gastropod Rissoa membranacea significantly reduced epiphyte load under high nutrient supply with Rissoa being the most efficient grazer, but only high densities of Littorina and Rissoa had a significant positive effect on eelgrass productivity. Although all mesograzers increased epiphyte ingestion with higher nutrient load, most likely as a functional response to the quantitatively and qualitatively better food supply, the promotion of eelgrass growth by Idotea and Rissoa was diminished compared to the study performed under ambient nutrient supply. Littorina maintained the level of its positive impact on eelgrass productivity regardless of nutrient concentrations

Wanted dead or alive : high diversity of macroinvertebrates associated with living and ’dead’ Posidonia oceanica matte

The Mediterranean endemic seagrass Posidonia oceanica forms beds characterised by a dense leaf canopy and a thick root-rhizome ‘matte’. Death of P. oceanica shoots leads to exposure of the underlying matte, which can persist for many years, and is termed ‘dead’ matte. Traditionally, dead matte has been regarded as a degraded habitat. To test whether this assumption was true, the motile macroinvertebrates of adjacent living (with shoots) and dead (without shoots) matte of P. oceanica were sampled in four different plots located at the same depth (5–6 m) in Mellieha Bay, Malta (central Mediterranean). The total number of species and abundance were significantly higher (ANOVA; P<0.05 and P<0.01, respectively) in the dead matte than in living P. oceanica matte, despite the presence of the foliar canopy in the latter. Multivariate analysis (MDS) clearly showed two main groups of assemblages, corresponding to the two matte types. The amphipods Leptocheirus guttatus and Maera grossimana, and the polychaete Nereis rava contributed most to the dissimilarity between the two different matte types. Several unique properties of the dead matte contributing to the unexpected higher number of species and abundance of motile macroinvertebrates associated with this habitat are discussed. The findings have important implications for the conservation of bare P. oceanica matte, which has been generally viewed as a habitat of low ecological value.peer-reviewe

Current challenges in software solutions for mass spectrometry-based quantitative proteomics

This work was in part supported by the PRIME-XS project, grant agreement number 262067, funded by the European Union seventh Framework Programme; The Netherlands Proteomics Centre, embedded in The Netherlands Genomics Initiative; The Netherlands Bioinformatics Centre; and the Centre for Biomedical Genetics (to S.C., B.B. and A.J.R.H); by NIH grants NCRR RR001614 and RR019934 (to the UCSF Mass Spectrometry Facility, director: A.L. Burlingame, P.B.); and by grants from the MRC, CR-UK, BBSRC and Barts and the London Charity (to P.C.

Movement disorder and neuronal migration disorder due to ARFGEF2 mutation

We report a child with a severe choreadystonic movement disorder, bilateral periventricular nodular heterotopia (BPNH), and secondary microcephaly based on compound heterozygosity for two new ARFGEF2 mutations (c.2031_2038dup and c.3798_3802del), changing the limited knowledge about the phenotype. The brain MRI shows bilateral hyperintensity of the putamen, BPNH, and generalized atrophy. Loss of ARFGEF2 function affects vesicle trafficking, proliferation/apoptosis, and neurotransmitter receptor function. This can explain BPNH and microcephaly. We hypothesize that the movement disorder and the preferential damage to the basal ganglia, specifically to the putamen, may be caused by an increased sensitivity to degeneration, a dynamic dysfunction due to neurotransmitter receptor mislocalization or a combination of both

Microwave studies of the fractional Josephson effect in HgTe-based Josephson junctions

The rise of topological phases of matter is strongly connected to their potential to host Majorana bound states, a powerful ingredient in the search for a robust, topologically protected, quantum information processing. In order to produce such states, a method of choice is to induce superconductivity in topological insulators. The engineering of the interplay between superconductivity and the electronic properties of a topological insulator is a challenging task and it is consequently very important to understand the physics of simple superconducting devices such as Josephson junctions, in which new topological properties are expected to emerge. In this article, we review recent experiments investigating topological superconductivity in topological insulators, using microwave excitation and detection techniques. More precisely, we have fabricated and studied topological Josephson junctions made of HgTe weak links in contact with two Al or Nb contacts. In such devices, we have observed two signatures of the fractional Josephson effect, which is expected to emerge from topologically-protected gapless Andreev bound states. We first recall the theoretical background on topological Josephson junctions, then move to the experimental observations. Then, we assess the topological origin of the observed features and conclude with an outlook towards more advanced microwave spectroscopy experiments, currently under development.Comment: Lectures given at the San Sebastian Topological Matter School 2017, published in "Topological Matter. Springer Series in Solid-State Sciences, vol 190. Springer

Oyster Reefs as Natural Breakwaters Mitigate Shoreline Loss and Facilitate Fisheries

Shorelines at the interface of marine, estuarine and terrestrial biomes are among the most degraded and threatened habitats in the coastal zone because of their sensitivity to sea level rise, storms and increased human utilization. Previous efforts to protect shorelines have largely involved constructing bulkheads and seawalls which can detrimentally affect nearshore habitats. Recently, efforts have shifted towards “living shoreline” approaches that include biogenic breakwater reefs. Our study experimentally tested the efficacy of breakwater reefs constructed of oyster shell for protecting eroding coastal shorelines and their effect on nearshore fish and shellfish communities. Along two different stretches of eroding shoreline, we created replicated pairs of subtidal breakwater reefs and established unaltered reference areas as controls. At both sites we measured shoreline and bathymetric change and quantified oyster recruitment, fish and mobile macro-invertebrate abundances. Breakwater reef treatments mitigated shoreline retreat by more than 40% at one site, but overall vegetation retreat and erosion rates were high across all treatments and at both sites. Oyster settlement and subsequent survival were observed at both sites, with mean adult densities reaching more than eighty oysters m−2 at one site. We found the corridor between intertidal marsh and oyster reef breakwaters supported higher abundances and different communities of fishes than control plots without oyster reef habitat. Among the fishes and mobile invertebrates that appeared to be strongly enhanced were several economically-important species. Blue crabs (Callinectes sapidus) were the most clearly enhanced (+297%) by the presence of breakwater reefs, while red drum (Sciaenops ocellatus) (+108%), spotted seatrout (Cynoscion nebulosus) (+88%) and flounder (Paralichthys sp.) (+79%) also benefited. Although the vertical relief of the breakwater reefs was reduced over the course of our study and this compromised the shoreline protection capacity, the observed habitat value demonstrates ecological justification for future, more robust shoreline protection projects

A Primary Prevention Clinical Risk Score Model for Patients With Brugada Syndrome (BRUGADA-RISK)

OBJECTIVES: The goal of this study was to develop a risk score model for patients with Brugada syndrome (BrS). BACKGROUND: Risk stratification in BrS is a significant challenge due to the low event rates and conflicting evidence. METHODS: A multicenter international cohort of patients with BrS and no previous cardiac arrest was used to evaluate the role of 16 proposed clinical or electrocardiogram (ECG) markers in predicting ventricular arrhythmias (VAs)/sudden cardiac death (SCD) during follow-up. Predictive markers were incorporated into a risk score model, and this model was validated by using out-of-sample cross-validation. RESULTS: A total of 1,110 patients with BrS from 16 centers in 8 countries were included (mean age 51.8 ± 13.6 years; 71.8% male). Median follow-up was 5.33 years; 114 patients had VA/SCD (10.3%) with an annual event rate of 1.5%. Of the 16 proposed risk factors, probable arrhythmia-related syncope (hazard ratio [HR]: 3.71; p < 0.001), spontaneous type 1 ECG (HR: 3.80; p < 0.001), early repolarization (HR: 3.42; p < 0.001), and a type 1 Brugada ECG pattern in peripheral leads (HR: 2.33; p < 0.001) were associated with a higher risk of VA/SCD. A risk score model incorporating these factors revealed a sensitivity of 71.2% (95% confidence interval: 61.5% to 84.6%) and a specificity of 80.2% (95% confidence interval: 75.7% to 82.3%) in predicting VA/SCD at 5 years. Calibration plots showed a mean prediction error of 1.2%. The model was effectively validated by using out-of-sample cross-validation according to country. CONCLUSIONS: This multicenter study identified 4 risk factors for VA/SCD in a primary prevention BrS population. A risk score model was generated to quantify risk of VA/SCD in BrS and inform implantable cardioverter-defibrillator prescription

Response of Coastal Fishes to the Gulf of Mexico Oil Disaster

The ecosystem-level impacts of the Deepwater Horizon disaster have been largely unpredictable due to the unique setting and magnitude of this spill. We used a five-year (2006–2010) data set within the oil-affected region to explore acute consequences for early-stage survival of fish species inhabiting seagrass nursery habitat. Although many of these species spawned during spring-summer, and produced larvae vulnerable to oil-polluted water, overall and species-by-species catch rates were high in 2010 after the spill (1,989±220 fishes km-towed−1 [μ ± 1SE]) relative to the previous four years (1,080±43 fishes km-towed−1). Also, several exploited species were characterized by notably higher juvenile catch rates during 2010 following large-scale fisheries closures in the northern Gulf, although overall statistical results for the effects of fishery closures on assemblage-wide CPUE data were ambiguous. We conclude that immediate, catastrophic losses of 2010 cohorts were largely avoided, and that no shifts in species composition occurred following the spill. The potential long-term impacts facing fishes as a result of chronic exposure and delayed, indirect effects now require attention