High fidelity imaging and high performance computing in nonlinear EIT

We show that nonlinear EIT provides images with well defined characteristics when smoothness of the image is used as a constraint in the reconstruction process. We use the gradient of the logarithm of resistivity as an effective measure of image smoothness, which has the advantage that resistivity and conductivity are treated with equal weight. We suggest that a measure of the fidelity of the image to the object requires the explicit definition and application of such a constraint. The algorithm is applied to the simulation of intra-ventricular haemorrhaging (IVH) in a simple head model. The results indicate that a 5% increase in the blood content of the ventricles would be easily detectable with the noise performance of contemporary instrumentation. The possible implementation of the algorithm in real time via high performance computing is discussed

Fas Signalling Promotes Intercellular Communication in T Cells

Cell-to-cell communication is a fundamental process for development and maintenance of multicellular organisms. Diverse mechanisms for the exchange of molecular information between cells have been documented, such as the exchange of membrane fragments (trogocytosis), formation of tunneling nanotubes (TNTs) and release of microvesicles (MVs). In this study we assign to Fas signalling a pivotal role for intercellular communication in CD4+ T cells. Binding of membrane-bound FasL to Fas expressing target cells triggers a well-characterized pro-apoptotic signalling cascade. However, our results, pairing up flow cytometric studies with confocal microscopy data, highlight a new social dimension for Fas/FasL interactions between CD4+ T cells. Indeed, FasL enhances the formation of cell conjugates (8 fold of increase) in an early time-frame of stimulation (30 min), and this phenomenon appears to be a crucial step to prime intercellular communication. Our findings show that this communication mainly proceeds along a cytosolic material exchange (ratio of exchange >10, calculated as ratio of stimulated cells signal divided by that recorded in control cells) via TNTs and MVs release. In particular, inhibition of TNTs genesis by pharmacological agents (Latruculin A and Nocodazole) markedly reduced this exchange (inhibition percentage: >40% and >50% respectively), suggesting a key role for TNTs in CD4+ T cells communication. Although MVs are present in supernatants from PHA-activated T cells, Fas treatment also leads to a significant increase in the amount of released MVs. In fact, the co-culture performed between MVs and untreated cells highlights a higher presence of MVs in the medium (1.4 fold of increase) and a significant MVs uptake (6 fold of increase) by untreated T lymphocytes. We conclude that Fas signalling induces intercellular communication in CD4+ T cells by different mechanisms that seem to start concomitantly with the main pathway (programmed cell death) promoted by FasL

Sampling, separation, and quantification of N-acyl homoserine lactones from marine intertidal sediments

N-acyl homoserine lactones (AHLs) are molecules produced by many Gram-negative bacteria as mediators of cell-cell signaling in a mechanism known as quorum sensing (QS). QS is widespread in marine bacteria regulating diverse processes, such as virulence or excretion of polymers that mediate biofilm formation. Associated eukaryotes, such as microalgae, respond to these cues as well, leading to an intricate signaling network. To date, only very few studies attempted to measure AHL concentrations in phototrophic microbial communities, which are hot spots for bacteria-bacteria as well as microalgae-bacteria interactions. AHL quantification in environmental samples is challenging and requires a robust and reproducible sampling strategy. However, knowing about AHL concentrations opens up multiple perspectives from answering fundamental ecological questions to deriving guidelines for manipulation and control of biofilms. Here, we present a method for sampling and AHL identification and quantification from marine intertidal sediments. The use of contact cores for sediment sampling ensures reproducible sample surface area and volume at each location. Flash-freezing of the samples with liquid nitrogen prevents enzymatic AHL degradation between sampling and extraction. After solvent extraction, samples were analyzed with an ultra-high performance liquid chromatography-high resolution mass spectrometry (UHPLC-HRMS) method that allows to baseline-separate 16 different AHLs in less than 10 min. The sensitivity of the method is sufficient for detection and quantification of AHLs in environmental samples of less than 16 cm(3)

Recent and historical recombination in the admixed Norwegian Red cattle breed

<p>Abstract</p> <p>Background</p> <p>Comparison of recent patterns of recombination derived from linkage maps to historical patterns of recombination from linkage disequilibrium (LD) could help identify genomic regions affected by strong artificial selection, appearing as reduced recent recombination. Norwegian Red cattle (NRF) make an interesting case study for investigating these patterns as it is an admixed breed with an extensively recorded pedigree. NRF have been under strong artificial selection for traits such as milk and meat production, fertility and health.</p> <p>While measures of LD is also crucial for determining the number of markers required for association mapping studies, estimates of recombination rate can be used to assess quality of genomic assemblies.</p> <p>Results</p> <p>A dataset containing more than 17,000 genome-wide distributed SNPs and 2600 animals was used to assess recombination rates and LD in NRF. Although low LD measured by r²was observed in NRF relative to some of the breeds from which this breed originates, reports from breeds other than those assessed in this study have described more rapid decline in r²at short distances than what was found in NRF. Rate of decline in r²for NRF suggested that to obtain an expected r²between markers and a causal polymorphism of at least 0.5 for genome-wide association studies, approximately one SNP every 15 kb or a total of 200,000 SNPs would be required. For well known quantitative trait loci (QTLs) for milk production traits on <it>Bos Taurus </it>chromosomes 1, 6 and 20, map length based on historic recombination was greater than map length based on recent recombination in NRF.</p> <p>Further, positions for 130 previously unpositioned contigs from assembly of the bovine genome sequence (Btau_4.0) found using comparative sequence analysis were validated by linkage analysis, and 28% of these positions corresponded to extreme values of population recombination rate.</p> <p>Conclusion</p> <p>While LD is reduced in NRF compared to some of the breeds from which this admixed breed originated, it is elevated over short distances compared to some other cattle breeds. Genomic regions in NRF where map length based on historic recombination was greater than map length based on recent recombination coincided with some well known QTL regions for milk production traits.</p> <p>Linkage analysis in combination with comparative sequence analysis and detection of regions with extreme values of population recombination rate proved to be valuable for detecting problematic regions in the Btau_4.0 genome assembly.</p

The Shedding of CD62L (L-Selectin) Regulates the Acquisition of Lytic Activity in Human Tumor Reactive T Lymphocytes

CD62L/L-selectin is a marker found on naïve T cells and further distinguishes central memory (Tcm, CD62L+) from effector memory (Tem, CD62L−) T cells. The regulation of CD62L plays a pivotal role in controlling the traffic of T lymphocytes to and from peripheral lymph nodes. CD62L is shed from the cell membrane following T cell activation, however, the physiological significance of this event remains to be elucidated. In this study, we utilized in vitro generated anti-tumor antigen T cells and melanoma lines as a model to evaluate the dynamics of CD62L shedding and expression of CD107a as a marker of lytic activity. Upon encounter, with matched tumor lines, antigen reactive T cells rapidly lose CD62L expression and this was associated with the acquisition of CD107a. By CD62L ELISA, we confirmed that this transition was mediated by the shedding of CD62L when T cells encountered specific tumor antigen. The introduction of a shedding resistant mutant of CD62L into the tumor antigen-reactive T cell line JKF6 impaired CD107a acquisition following antigen recognition and this was correlated with decreased lytic activity as measured by 51Cr release assays. The linkage of the shedding of CD62L from the surface of anti-tumor T cells and acquisition of lytic activity, suggests a new function for CD62L in T cell effector functions and anti-tumor activity

Marine substrate response from the analysis of seismic attributes in CHIRP sub-bottom profiles

O presente trabalho tem por objetivo apresentar uma avaliação da resposta dos atributos sísmicos (Amplitude Instantânea, Amplitude RMS, Energia e Frequência Instantânea) em diferentes tipos de substratos marinhos, correlacionando-os com características sedimentológicas das amostras coletadas. Foram analisados perfis sísmicos obtidos com um perfilador de subsuperfície com sinal do tipo CHIRP modelo SB-216S da marca EdgeTech, com frequência de trabalho de 2 e 16 kHz. O método se deu a partir da análise estatística não-paramétrica de Kruskal-Wallis foi aplicada para comparar o comportamento dos atributos com as diferentes classes dos grãos das amostras (subagrupadas segundo o grau de seleção) e com diferentes feições. Com base na análise dos resultados, foi possível distinguir dois grupos distintos nas amostras, o grupo SAMF (silte e areia muito fina) e o grupo AFMG (areia fina, areia média e areia grossa). Como conclusão, pode-se dizer que os atributos não foram capazes de distinguir entre as classes mais próximas dos grãos. Utilizando o coeficiente de Spearman foi verificado que o atributo "Amplitude Instantânea" mostrou-se mais eficiente em separar os dois conjuntos. Comparando sedimentos, gás e rocha, os atributos que utilizaram o atributo "amplitude" foram eficazes em separar os sedimentos do gás e da rocha, porém não os distinguiram entre as duas feições, visto que elas apresentaram amplitudes muito altas, mas semelhantes entre si. O atributo "Frequência Instantânea" mostrou-se eficaz na diferenciação entre sedimento, rocha e gás, o sedimento apresentou uma maior banda de frequência, a rocha uma faixa intermediária e o gás a menor delas.This paper presents an evaluation of the response of seismic reflection attributes in different types of marine substrate (rock, shallow gas, sediments) using seafloor samples for ground-truth statistical comparisons. The data analyzed include seismic reflection profiles collected using two CHIRP subbottom profilers (Edgetech Model 3100 SB-216S), with frequency ranging between 2 and 16 kHz, and a number (38) of sediment samples collected from the seafloor. The statistical method used to discriminate between different substratum responses was the non-parametric Kruskal-Wallis analysis, carried out in two steps: 1) comparison of Seismic Attributes between different marine substrates (unconsolidated sediments, rock and shallow gas); 2) comparison of Seismic Attributes between different sediment classes in seafloors characterized by unconsolidated sediments (subdivided according to sorting). These analyses suggest that amplitude-related attributes were effective in discriminating between sediment and gassy/rocky substratum, but did not differentiate between rocks and shallow gas. On the other hand, the Instantaneous Frequency attribute was effective in differentiating sediments, rocks and shallow gas, with sediment showing higher frequency range, rock an intermediate range, and shallow gas the lowest response. Regarding grain-size classes and sorting, statistical analysis discriminated between two distinct groups of samples, the SVFS (silt and very fine sand) and the SFMC (fine, medium and coarse sand) groups. Using a Spearman coefficient, it was found that the Instantaneous Amplitude was more efficient in distinguishing between the two groups. None of the attributes was able to distinguish between the closest grain size classes such as those of silt and very fine sand

Limited congruence exhibited across microbial, meiofaunal and macrofaunal benthic assemblages in a heterogeneous coastal environment

One of the most common approaches for investigating the ecology of spatially complex environments is to examine a single biotic assemblage present, such as macroinvertebrates. Underlying this approach are assumptions that sampled and unsampled taxa respond similarly to environmental gradients and exhibit congruence across different sites. These assumptions were tested for five benthic groups of various sizes (archaea, bacteria, microbial eukaryotes/protists, meiofauna and macrofauna) in Plymouth Sound, a harbour with many different pollution sources. Sediments varied in granulometry, hydrocarbon and trace metal concentrations. Following variable reduction, canonical correspondence analysis did not identify any associations between sediment characteristics and assemblage composition of archaea or macrofauna. In contrast, variation in bacteria was associated with granulometry, trace metal variations and bioturbation (e.g. community bioturbation potential). Protists varied with granulometry, hydrocarbon and trace metal predictors. Meiofaunal variation was associated with hydrocarbon and bioturbation predictors. Taxon turnover between sites varied with only three out of 10 group pairs showing congruence (meiofauna-protists, meiofauna-macrofauna and protists-macrofauna). While our results support using eukaryotic taxa as proxies for others, the lack of congruence suggests caution should be applied to inferring wider indicator or functional interpretations from studies of a single biotic assemblage

Benthic pH gradients across a range of shelf sea sediment types linked to sediment characteristics and seasonal variability

This study used microelectrodes to record pH profiles in fresh shelf sea sediment cores collected across a range of different sediment types within the Celtic Sea. Spatial and temporal variability was captured during repeated measurements in 2014 and 2015. Concurrently recorded oxygen microelectrode profiles and other sedimentary parameters provide a detailed context for interpretation of the pH data. Clear differences in profiles were observed between sediment type, location and season. Notably, very steep pH gradients exist within the surface sediments (10–20 mm), where decreases greater than 0.5 pH units were observed. Steep gradients were particularly apparent in fine cohesive sediments, less so in permeable sandier matrices. We hypothesise that the gradients are likely caused by aerobic organic matter respiration close to the sediment–water interface or oxidation of reduced species at the base of the oxic zone (NH4+, Mn2+, Fe2+, S−). Statistical analysis suggests the variability in the depth of the pH minima is controlled spatially by the oxygen penetration depth, and seasonally by the input and remineralisation of deposited organic phytodetritus. Below the pH minima the observed pH remained consistently low to maximum electrode penetration (ca. 60 mm), indicating an absence of sub-oxic processes generating H+ or balanced removal processes within this layer. Thus, a climatology of sediment surface porewater pH is provided against which to examine biogeochemical processes. This enhances our understanding of benthic pH processes, particularly in the context of human impacts, seabed integrity, and future climate changes, providing vital information for modelling benthic response under future climate scenarios