Temporal Changes in Randomness of Bird Communities across Central Europe

Many studies have examined whether communities are structured by random or deterministic processes, and both are likely to play a role, but relatively few studies have attempted to quantify the degree of randomness in species composition. We quantified, for the first time, the degree of randomness in forest bird communities based on an analysis of spatial autocorrelation in three regions of Germany. The compositional dissimilarity between pairs of forest patches was regressed against the distance between them. We then calculated the y-intercept of the curve, i.e. the ‘nugget’, which represents the compositional dissimilarity at zero spatial distance. We therefore assume, following similar work on plant communities, that this represents the degree of randomness in species composition. We then analysed how the degree of randomness in community composition varied over time and with forest management intensity, which we expected to reduce the importance of random processes by increasing the strength of environmental drivers. We found that a high portion of the bird community composition could be explained by chance (overall mean of 0.63), implying that most of the variation in local bird community composition is driven by stochastic processes. Forest management intensity did not consistently affect the mean degree of randomness in community composition, perhaps because the bird communities were relatively insensitive to management intensity. We found a high temporal variation in the degree of randomness, which may indicate temporal variation in assembly processes and in the importance of key environmental drivers. We conclude that the degree of randomness in community composition should be considered in bird community studies, and the high values we find may indicate that bird community composition is relatively hard to predict at the regional scale.

Classification of interstitial lung disease patterns using local DCT features and random forest.

Over the last decade, a plethora of computer-aided diagnosis (CAD) systems have been proposed aiming to improve the accuracy of the physicians in the diagnosis of interstitial lung diseases (ILD). In this study, we propose a scheme for the classification of HRCT image patches with ILD abnormalities as a basic component towards the quantification of the various ILD patterns in the lung. The feature extraction method relies on local spectral analysis using a DCT-based filter bank. After convolving the image with the filter bank, q-quantiles are computed for describing the distribution of local frequencies that characterize image texture. Then, the gray-level histogram values of the original image are added forming the final feature vector. The classification of the already described patches is done by a random forest (RF) classifier. The experimental results prove the superior performance and efficiency of the proposed approach compared against the state-of-the-art.

Segmented filamentous bacterium uses secondary and tertiary lymphoid tissues to induce gut IgA and specific T helper 17 cell responses.

Segmented filamentous bacterium (SFB) is a symbiont that drives postnatal maturation of gut adaptive immune responses. In contrast to nonpathogenic E. coli, SFB stimulated vigorous development of Peyer's patches germinal centers but paradoxically induced only a low frequency of specific immunoglobulin A (IgA)-secreting cells with delayed accumulation of somatic mutations. Moreover, blocking Peyer's patch development abolished IgA responses to E. coli, but not to SFB. Indeed, SFB stimulated the postnatal development of isolated lymphoid follicles and tertiary lymphoid tissue, which substituted for Peyer's patches as inductive sites for intestinal IgA and SFB-specific T helper 17 (Th17) cell responses. Strikingly, in mice depleted of gut organized lymphoid tissue, SFB still induced a substantial but nonspecific intestinal Th17 cell response. These results demonstrate that SFB has the remarkable capacity to induce and stimulate multiple types of intestinal lymphoid tissues that cooperate to generate potent IgA and Th17 cell responses displaying only limited target specificity.

Pretreatment of mice with streptomycin provides a Salmonella enterica serovar Typhimurium colitis model that allows analysis of both pathogen and host.

Salmonella enterica subspecies 1 serovar Typhimurium is a principal cause of human enterocolitis. For unknown reasons, in mice serovar Typhimurium does not provoke intestinal inflammation but rather targets the gut-associated lymphatic tissues and causes a systemic typhoid-like infection. The lack of a suitable murine model has limited the analysis of the pathogenetic mechanisms of intestinal salmonellosis. We describe here how streptomycin-pretreated mice provide a mouse model for serovar Typhimurium colitis. Serovar Typhimurium colitis in streptomycin-pretreated mice resembles many aspects of the human infection, including epithelial ulceration, edema, induction of intercellular adhesion molecule 1, and massive infiltration of PMN/CD18(+) cells. This pathology is strongly dependent on protein translocation via the serovar Typhimurium SPI1 type III secretion system. Using a lymphotoxin beta-receptor knockout mouse strain that lacks all lymph nodes and organized gut-associated lymphatic tissues, we demonstrate that Peyer's patches and mesenteric lymph nodes are dispensable for the initiation of murine serovar Typhimurium colitis. Our results demonstrate that streptomycin-pretreated mice offer a unique infection model that allows for the first time to use mutants of both the pathogen and the host to study the molecular mechanisms of enteric salmonellosis.

Automatic X-ray landmark detection and shape segmentation via data-driven joint estimation of image displacements

In this paper, we propose a new method for fully-automatic landmark detection and shape segmentation in X-ray images. To detect landmarks, we estimate the displacements from some randomly sampled image patches to the (unknown) landmark positions, and then we integrate these predictions via a voting scheme. Our key contribution is a new algorithm for estimating these displacements. Different from other methods where each image patch independently predicts its displacement, we jointly estimate the displacements from all patches together in a data driven way, by considering not only the training data but also geometric constraints on the test image. The displacements estimation is formulated as a convex optimization problem that can be solved efficiently. Finally, we use the sparse shape composition model as the a priori information to regularize the landmark positions and thus generate the segmented shape contour. We validate our method on X-ray image datasets of three different anatomical structures: complete femur, proximal femur and pelvis. Experiments show that our method is accurate and robust in landmark detection, and, combined with the shape model, gives a better or comparable performance in shape segmentation compared to state-of-the art methods. Finally, a preliminary study using CT data shows the extensibility of our method to 3D data.

Localization and Segmentation of 3D Intervertebral Discs in MR Images by Data Driven Estimation

This paper addresses the problem of fully-automatic localization and segmentation of 3D intervertebral discs (IVDs) from MR images. Our method contains two steps, where we first localize the center of each IVD, and then segment IVDs by classifying image pixels around each disc center as foreground (disc) or background. The disc localization is done by estimating the image displacements from a set of randomly sampled 3D image patches to the disc center. The image displacements are estimated by jointly optimizing the training and test displacement values in a data-driven way, where we take into consideration both the training data and the geometric constraint on the test image. After the disc centers are localized, we segment the discs by classifying image pixels around disc centers as background or foreground. The classification is done in a similar data-driven approach as we used for localization, but in this segmentation case we are aiming to estimate the foreground/background probability of each pixel instead of the image displacements. In addition, an extra neighborhood smooth constraint is introduced to enforce the local smoothness of the label field. Our method is validated on 3D T2-weighted turbo spin echo MR images of 35 patients from two different studies. Experiments show that compared to state of the art, our method achieves better or comparable results. Specifically, we achieve for localization a mean error of 1.6-2.0 mm, and for segmentation a mean Dice metric of 85%-88% and a mean surface distance of 1.3-1.4 mm.

Is postmenopausal hormone replacement therapy suitable after a cardio- or cerebrovascular event?

PURPOSE Vascular disease is the leading cause of death in women. One-third of acute events affect women below age 60, when the prevalence of menopausal symptoms is high. This raises the question if hormone replacement therapy (HRT) may be an appropriate treatment for individual women although vascular disease is generally considered a contraindication. METHODS Selective literature search was used for this study. RESULTS In healthy women, HRT increases risks for venous thromboembolism and ischemic stroke, but for cardiovascular disease apparently only beyond 10 years after menopause or 60 years of age. Limited data in women with cardio or cerebrovascular disease have not demonstrated an increased risk for a vascular recurrent event, but for the first year after initiation. In HRT users affected by a cardiovascular event continuation of HRT has not been found to be associated with adverse outcome. Low dose estradiol--preferentially as transdermal patches, if necessary combined with metabolically neutral progestins--appears to convey lower risk. CONCLUSIONS Safety data on HRT in survivors of cardiovascular events or ischemic stroke are limited, but exceptionally increased risk appears to be excluded. If off-label use of HRT is considered to be initiated or continued in women with cardio- or cerebrovascular disease, extensive counseling on the pros and cons of HRT is mandatory.

Morphological ripening of fluid inclusions and coupled zone-refining in quartz crystals revealed by cathodoluminescence imaging: Implications for CL-petrography, fluid inclusion analysis and trace-element geothermometry

Cathodoluminescence (CL) studies have previously shown that some secondary fluid inclusions in luminescent quartz are surrounded by dark, non-luminescent patches, resulting from fracture-sealing by late, trace-element-poor quartz. This finding has led to the tacit generalization that all dark CL patches indicate influx of low temperature, late-stage fluids. In this study we have examined natural and synthetic hydrothermal quartz crystals using CL imaging supplemented by in-situ elemental analysis. The results lead us to propose that all natural, liquid-water-bearing inclusions in quartz, whether trapped on former crystal growth surfaces (i.e., of primary origin) or in healed fractures (i.e., of pseudosecondary or secondary origin), are surrounded by three-dimensional, non-luminescent patches. Cross-cutting relations show that the patches form after entrapment of the fluid inclusions and therefore they are not diagnostic of the timing of fluid entrapment. Instead, the dark patches reveal the mechanism by which fluid inclusions spontaneously approach morphological equilibrium and purify their host quartz over geological time. Fluid inclusions that contain solvent water perpetually dissolve and reprecipitate their walls, gradually adopting low-energy euhedral and equant shapes. Defects in the host quartz constitute solubility gradients that drive physical migration of the inclusions over distances of tens of μm (commonly) up to several mm (rarely). Inclusions thus sequester from their walls any trace elements (e.g., Li, Al, Na, Ti) present in excess of equilibrium concentrations, thereby chemically purifying their host crystals in a process analogous to industrial zone refining. Non-luminescent patches of quartz are left in their wake. Fluid inclusions that contain no liquid water as solvent (e.g., inclusions of low-density H2O vapor or other non-aqueous volatiles) do not undergo this process and therefore do not migrate, do not modify their shapes with time, and are not associated with dark-CL zone-refined patches. This new understanding has implications for the interpretation of solids within fluid inclusions (e.g., Ti- and Al-minerals) and for the elemental analysis of hydrothermal and metamorphic quartz and its fluid inclusions by microbeam methods such as LA-ICPMS and SIMS. As Ti is a common trace element in quartz, its sequestration by fluid inclusions and its depletion in zone-refined patches impacts on applications of the Ti-in-quartz geothermometer.

Genetic consequences of habitat fragmentation during a range expansion

We investigate the effect of habitat fragmentation on the genetic diversity of a species experiencing a range expansion. These two evolutionary processes have not been studied yet, at the same time, owing to the difficulties of deriving analytic results for non-equilibrium models. Here we provide a description of their interaction by using extensive spatial and temporal coalescent simulations and we suggest guidelines for a proper genetic sampling to detect fragmentation. To model habitat fragmentation, we simulated a two-dimensional lattice of demes partitioned into groups (patches) by adding barriers to dispersal. After letting a population expand on this grid, we sampled lineages from the lattice at several scales and studied their coalescent history. We find that in order to detect fragmentation, one needs to extensively sample at a local level rather than at a landscape level. This is because the gene genealogy of a scattered sample is less sensitive to the presence of genetic barriers. Considering the effect of temporal changes of fragmentation intensities, we find that at least 10, but often >100, generations are needed to affect local genetic diversity and population structure. This result explains why recent habitat fragmentation does not always lead to detectable signatures in the genetic structure of populations. Finally, as expected, long-distance dispersal increases local genetic diversity and decreases levels of population differentiation, efficiently counteracting the effects of fragmentation.

Lipid- and mechanosensitivities of sodium/hydrogen exchangers analyzed by electrical methods.

Sodium/hydrogen exchangers (NHEs) are ubiquitous ion transporters that serve multiple cell functions. We have studied two mammalian isoforms, NHE1 (ubiquitous) and NHE3 (epithelial-specific), by measuring extracellular proton (H+) gradients during whole-cell patch clamp with perfusion of the cell interior. Maximal Na(+)-dependent H+ fluxes (JH+) are equivalent to currents >20 pA for NHE1 in Chinese hamster ovary fibroblasts, >200 pA for NHE1 in guinea pig ventricular myocytes, and 5-10 pA for NHE3 in opossum kidney cells. The fluxes are blocked by an NHE inhibitor, ethylisopropylamiloride, and are absent in NHE-deficient AP-1 cells. NHE1 activity is stable with perfusion of nonhydrolyzable ATP [adenosine 5'-(beta,gamma-imido)triphosphate], is abolished by ATP depletion (2 deoxy-D-glucose with oligomycin or perfusion of apyrase), can be restored with phosphatidylinositol 4,5-bisphosphate, and is unaffected by actin cytoskeleton disruption (latrunculin or pipette perfusion of gelsolin). NHE3 (but not NHE1) is reversibly activated by phosphatidylinositol 3,4,5-trisphosphate. Both NHE1 and NHE3 activities are disrupted in giant patches during gigaohm seal formation. NHE1 (but not NHE3) is reversibly activated by cell shrinkage, even at neutral cytoplasmic pH without ATP, and inhibited by cell swelling. NHE1 in Chinese hamster ovary fibroblasts (but not NHE3 in opossum kidney cells) is inhibited by agents that thin the membrane (L-alpha-lysophosphatidylcholine and octyl-beta-D-glucopyranoside) and activated by cholesterol enrichment, which thickens membranes. Expressed in AP-1 cells, however, NHE1 is insensitive to these agents but remains sensitive to volume changes. Thus, changes of hydrophobic mismatch can modulate NHE1 but do not underlie its volume sensitivity.

Molecular control of cardiac sodium homeostasis in health and disease.

INTRODUCTION Cardiac myocytes utilize three high-capacity Na transport processes whose precise function can determine myocyte fate and the triggering of arrhythmias in pathological settings. We present recent results on the regulation of all three transporters that may be important for an understanding of cardiac function during ischemia/reperfusion episodes. METHODS AND RESULTS Refined ion selective electrode (ISE) techniques and giant patch methods were used to analyze the function of cardiac Na/K pumps, Na/Ca exchange (NCX1), and Na/H exchange (NHE1) in excised cardiac patches and intact myocytes. To consider results cohesively, simulations were developed that account for electroneutrality of the cytoplasm, ion homeostasis, water homeostasis (i.e., cell volume), and cytoplasmic pH. The Na/K pump determines the average life-time of Na ions (3-10 minutes) as well as K ions (>30 minutes) in the cytoplasm. The long time course of K homeostasis can determine the time course of myocyte volume changes after ion homeostasis is perturbed. In excised patches, cardiac Na/K pumps turn on slowly (-30 seconds) with millimolar ATP dependence, when activated for the first time. In steady state, however, pumps are fully active with <0.2 mM ATP and are nearly unaffected by high ADP (2 mM) and Pi (10 mM) concentrations as may occur in ischemia. NCX1s appear to operate with slippage that contributes to background Na influx and inward current in heart. Thus, myocyte Na levels may be regulated by the inactivation reactions of the exchanger which are both Na- and proton-dependent. NHE1 also undergo strong Na-dependent inactivation, whereby a brief rise of cytoplasmic Na can cause inactivation that persists for many minutes after cytoplasmic Na is removed. This mechanism is blocked by pertussis toxin, suggesting involvement of a Na-dependent G-protein. Given that maximal NCX1- and NHE1-mediated ion fluxes are much greater than maximal Na/K pump-mediated Na extrusion in myocytes, the Na-dependent inactivation mechanisms of NCX1 and NHE1 may be important determinants of cardiac Na homeostasis. CONCLUSIONS Na/K pumps appear to be optimized to continue operation when energy reserves are compromised. Both NCX1 and NHE1 activities are regulated by accumulation of cytoplasmic Na. These principles may importantly control cardiac cytoplasmic Na and promote myocyte survival during ischemia/reperfusion episodes by preventing Ca overload.

Age-Independent Cartilage Generation for Synovium-Based Autologous Chondrocyte Implantation.

The articular cartilage layer of synovial joints is commonly lesioned by trauma or by a degenerative joint disease. Attempts to repair the damage frequently involve the performance of autologous chondrocyte implantation (ACI). Healthy cartilage must be first removed from the joint, and then, on a separate occasion, following the isolation of the chondrocytes and their expansion in vitro, implanted within the lesion. The disadvantages of this therapeutic approach include the destruction of healthy cartilage-which may predispose the joint to osteoarthritic degeneration-the necessarily restricted availability of healthy tissue, the limited proliferative capacity of the donor cells-which declines with age-and the need for two surgical interventions. We postulated that it should be possible to induce synovial stem cells, which are characterized by high, age-independent, proliferative and chondrogenic differentiation capacities, to lay down cartilage within the outer juxtasynovial space after the transcutaneous implantation of a carrier bearing BMP-2 in a slow-release system. The chondrocytes could be isolated on-site and immediately used for ACI. To test this hypothesis, Chinchilla rabbits were used as an experimental model. A collagenous patch bearing BMP-2 in a slow-delivery vehicle was sutured to the inner face of the synovial membrane. The neoformed tissue was excised 5, 8, 11 and 14 days postimplantation for histological and histomorphometric analyses. Neoformed tissue was observed within the outer juxtasynovial space already on the 5th postimplantation day. It contained connective and adipose tissues, and a central nugget of growing cartilage. Between days 5 and 14, the absolute volume of cartilage increased, attaining a value of 12 mm(3) at the latter juncture. Bone was deposited in measurable quantities from the 11th day onwards, but owing to resorption, the net volume did not exceed 1.5 mm(3) (14th day). The findings confirm our hypothesis. The quantity of neoformed cartilage that is deposited after only 1 week within the outer juxtasynovial space would yield sufficient cells for ACI. Since the BMP-2-bearing patches would be implanted transcutaneously in humans, only one surgical or arthroscopic intervention would be called for. Moreover, most importantly, sufficient numbers of cells could be generated in patients of all ages.

Independence Day for IgA

IgA is induced through T-cell-dependent and -independent pathways. In this issue, Bunker et al. (2015) now show that the T-cell-independent pathway is sufficient to coat most small intestinal microbes specifically, and Fransen et al. (2015) find that IgA coating promotes uptake of microbes into Peyer's patches and drives further induction in a positive-feedback loop.

Food Recognition for Dietary Assessment Using Deep Convolutional Neural Networks

Diet management is a key factor for the prevention and treatment of diet-related chronic diseases. Computer vision systems aim to provide automated food intake assessment using meal images. We propose a method for the recognition of already segmented food items in meal images. The method uses a 6-layer deep convolutional neural network to classify food image patches. For each food item, overlapping patches are extracted and classified and the class with the majority of votes is assigned to it. Experiments on a manually annotated dataset with 573 food items justified the choice of the involved components and proved the effectiveness of the proposed system yielding an overall accuracy of 84.9%.

Lung Pattern Classification for Interstitial Lung Diseases Using a Deep Convolutional Neural Network

Automated tissue characterization is one of the most crucial components of a computer aided diagnosis (CAD) system for interstitial lung diseases (ILDs). Although much research has been conducted in this field, the problem remains challenging. Deep learning techniques have recently achieved impressive results in a variety of computer vision problems, raising expectations that they might be applied in other domains, such as medical image analysis. In this paper, we propose and evaluate a convolutional neural network (CNN), designed for the classification of ILD patterns. The proposed network consists of 5 convolutional layers with 2×2 kernels and LeakyReLU activations, followed by average pooling with size equal to the size of the final feature maps and three dense layers. The last dense layer has 7 outputs, equivalent to the classes considered: healthy, ground glass opacity (GGO), micronodules, consolidation, reticulation, honeycombing and a combination of GGO/reticulation. To train and evaluate the CNN, we used a dataset of 14696 image patches, derived by 120 CT scans from different scanners and hospitals. To the best of our knowledge, this is the first deep CNN designed for the specific problem. A comparative analysis proved the effectiveness of the proposed CNN against previous methods in a challenging dataset. The classification performance (~85.5%) demonstrated the potential of CNNs in analyzing lung patterns. Future work includes, extending the CNN to three-dimensional data provided by CT volume scans and integrating the proposed method into a CAD system that aims to provide differential diagnosis for ILDs as a supportive tool for radiologists.