Plant species richness and environmental heterogeneity in a mountain landscape: effects of variability and spatial configuration

The loss of biodiversity has become a matter of urgent concern and a better understanding of local drivers is crucial for conservation. Although environmental heterogeneity is recognized as an important determinant of biodiversity, this has rarely been tested using field data at management scale. We propose and provide evidence for the simple hypothesis that local species diversity is related to spatial environmental heterogeneity. Species partition the environment into habitats. Biodiversity is therefore expected to be influenced by two aspects of spatial heterogeneity: 1) the variability of environmental conditions, which will affect the number of types of habitat, and 2) the spatial configuration of habitats, which will affect the rates of ecological processes, such as dispersal or competition. Earlier, simulation experiments predicted that both aspects of heterogeneity will influence plant species richness at a particular site. For the first time, these predictions were tested for plant communities using field data, which we collected in a wooded pasture in the Swiss Jura mountains using a four-level hierarchical sampling design. Richness generally increased with increasing environmental variability and "roughness" (i.e. decreasing spatial aggregation). Effects occurred at all scales, but the nature of the effect changed with scale, suggesting a change in the underlying mechanisms, which will need to be taken into account if scaling up to larger landscapes. Although we found significant effects of environmental heterogeneity, other factors such as history could also be important determinants. If a relationship between environmental heterogeneity and species richness can be shown to be general, recently available high-resolution environmental data can be used to complement the assessment of patterns of local richness and improve the prediction of the effects of land use change based on mean site conditions or land use history.

On the Schoenberg transformations in data analysis: theory and illustrations

The class of Schoenberg transformations, embedding Euclidean distances into higher dimensional Euclidean spaces, is presented, and derived from theorems on positive definite and conditionally negative definite matrices. Original results on the arc lengths, angles and curvature of the transformations are proposed, and visualized on artificial data sets by classical multidimensional scaling. A distance-based discriminant algorithm and a robust multidimensional centroid estimate illustrate the theory, closely connected to the Gaussian kernels of Machine Learning.

Angiofil-mediated visualization of the vascular system by microcomputed tomography: a feasibility study.

Visualization of the vascular systems of organs or of small animals is important for an assessment of basic physiological conditions, especially in studies that involve genetically manipulated mice. For a detailed morphological analysis of the vascular tree, it is necessary to demonstrate the system in its entirety. In this study, we present a new lipophilic contrast agent, Angiofil, for performing postmortem microangiography by using microcomputed tomography. The new contrast agent was tested in 10 wild-type mice. Imaging of the vascular system revealed vessels down to the caliber of capillaries, and the digital three-dimensional data obtained from the scans allowed for virtual cutting, amplification, and scaling without destroying the sample. By use of computer software, parameters such as vessel length and caliber could be quantified and remapped by color coding onto the surface of the vascular system. The liquid Angiofil is easy to handle and highly radio-opaque. Because of its lipophilic abilities, it is retained intravascularly, hence it facilitates virtual vessel segmentation, and yields an enduring signal which is advantageous during repetitive investigations, or if samples need to be transported from the site of preparation to the place of actual analysis, respectively. These characteristics make Angiofil a promising novel contrast agent; when combined with microcomputed tomography, it has the potential to turn into a powerful method for rapid vascular phenotyping.

Dpp/BMP signaling in flies: From molecules to biology.

Decapentaplegic (Dpp), the fly homolog of the secreted mammalian BMP2/4 signaling molecules, is involved in almost all aspects of fly development. Dpp has critical functions at all developmental stages, from patterning of the eggshell to the determination of adult intestinal stem cell identity. Here, we focus on recent findings regarding the transcriptional regulatory logic of the pathway, on a new feedback regulator, Pentagone, and on Dpp's roles in scaling and growth of the Drosophila wing.

Typologies textuelles et partitions musicales : dissimilarités, classification et autocorrélation

Axée dans un premier temps sur le formalisme et les méthodes, cette thèse est construite sur trois concepts formalisés: une table de contingence, une matrice de dissimilarités euclidiennes et une matrice d'échange. À partir de ces derniers, plusieurs méthodes d'Analyse des données ou d'apprentissage automatique sont exprimées et développées: l'analyse factorielle des correspondances (AFC), vue comme un cas particulier du multidimensional scaling; la classification supervisée, ou non, combinée aux transformations de Schoenberg; et les indices d'autocorrélation et d'autocorrélation croisée, adaptés à des analyses multivariées et permettant de considérer diverses familles de voisinages. Ces méthodes débouchent dans un second temps sur une pratique de l'analyse exploratoire de différentes données textuelles et musicales. Pour les données textuelles, on s'intéresse à la classification automatique en types de discours de propositions énoncées, en se basant sur les catégories morphosyntaxiques (CMS) qu'elles contiennent. Bien que le lien statistique entre les CMS et les types de discours soit confirmé, les résultats de la classification obtenus avec la méthode K- means, combinée à une transformation de Schoenberg, ainsi qu'avec une variante floue de l'algorithme K-means, sont plus difficiles à interpréter. On traite aussi de la classification supervisée multi-étiquette en actes de dialogue de tours de parole, en se basant à nouveau sur les CMS qu'ils contiennent, mais aussi sur les lemmes et le sens des verbes. Les résultats obtenus par l'intermédiaire de l'analyse discriminante combinée à une transformation de Schoenberg sont prometteurs. Finalement, on examine l'autocorrélation textuelle, sous l'angle des similarités entre diverses positions d'un texte, pensé comme une séquence d'unités. En particulier, le phénomène d'alternance de la longueur des mots dans un texte est observé pour des voisinages d'empan variable. On étudie aussi les similarités en fonction de l'apparition, ou non, de certaines parties du discours, ainsi que les similarités sémantiques des diverses positions d'un texte. Concernant les données musicales, on propose une représentation d'une partition musicale sous forme d'une table de contingence. On commence par utiliser l'AFC et l'indice d'autocorrélation pour découvrir les structures existant dans chaque partition. Ensuite, on opère le même type d'approche sur les différentes voix d'une partition, grâce à l'analyse des correspondances multiples, dans une variante floue, et à l'indice d'autocorrélation croisée. Qu'il s'agisse de la partition complète ou des différentes voix qu'elle contient, des structures répétées sont effectivement détectées, à condition qu'elles ne soient pas transposées. Finalement, on propose de classer automatiquement vingt partitions de quatre compositeurs différents, chacune représentée par une table de contingence, par l'intermédiaire d'un indice mesurant la similarité de deux configurations. Les résultats ainsi obtenus permettent de regrouper avec succès la plupart des oeuvres selon leur compositeur.

Is it the grain size or the characteristic pore size that controls the induced polarization relaxation time of clean sands and sandstones?

There is a wide range of evidence to suggest that permeability can be constrained through of induced polarization measurements. For clean sands and sandstones, current mechanistic models of induced polarization predict a relationship between the low-frequency time constant inferred from induced polarization measurements and the grain diameter. A number of observations do, however, disagree with this and indicate that the observed relaxation behavior is rather governed by the so-called dynamic pore radius L. To test this hypothesis, we have developed a set of new scaling relationships, which allow the relaxation time to be computed from the pore size and the permeability to be computed from both the Cole-Cole time constant and the formation factor. Moreover, these new scaling relationships can be also used to predict the dependence of the Cole-Cole time constant as a function of the water saturation under unsaturated conditions. Comparative tests of the proposed new relationships with regard to various published experimental results for saturated clean sands and sandstones as well as for partially saturated clean sandstones, do indeed confirm that the dynamic pore radius L is a much more reliable indicator of the observed relaxation behavior than grain-size-based models.

Mechanisms of cross-modal plasticity in early-blind subjects.

A variety of studies have demonstrated enhanced blood oxygenation level dependent responses to auditory and tactile stimuli within occipital cortex as a result of early blindness. However, little is known about the organizational principles that drive this cross-modal plasticity. We compared BOLD responses to a wide variety of auditory and tactile tasks (vs. rest) in early-blind and sighted subjects. As expected, cross-modal responses were larger in blind than in sighted subjects in occipital cortex for all tasks (cross-modal plasticity). Within both blind and sighted subject groups, we found patterns of cross-modal activity that were remarkably similar across tasks: a large proportion of cross-modal responses within occipital cortex are neither task nor stimulus specific. We next examined the mechanisms underlying enhanced BOLD responses within early-blind subjects. We found that the enhancement of cross-modal responses due to early blindness was best described as an additive shift, suggesting that cross-modal plasticity within blind subjects does not originate from either a scaling or unmasking of cross-modal responsivities found in sighted subjects.

Gravity-driven slug motion in capillary tubes

The velocity of a liquid slug falling in a capillary tube is lower than predicted for Poiseuille flow due to presence of menisci, whose shapes are determined by the complex interplay of capillary, viscous, and gravitational forces. Due to the presence of menisci, a capillary pressure proportional to surface curvature acts on the slug and streamlines are bent close to the interface, resulting in enhanced viscous dissipation at the wedges. To determine the origin of drag-force increase relative to Poiseuille flow, we compute the force resultant acting on the slug by integrating Navier-Stokes equations over the liquid volume. Invoking relationships from differential geometry we demonstrate that the additional drag is due to viscous forces only and that no capillary drag of hydrodynamic origin exists (i.e., due to hydrodynamic deformation of the interface). Requiring that the force resultant is zero, we derive scaling laws for the steady velocity in the limit of small capillary numbers by estimating the leading order viscous dissipation in the different regions of the slug (i.e., the unperturbed Poiseuille-like bulk, the static menisci close to the tube axis and the dynamic regions close to the contact lines). Considering both partial and complete wetting, we find that the relationship between dimensionless velocity and weight is, in general, nonlinear. Whereas the relationship obtained for complete-wetting conditions is found in agreement with the experimental data of Bico and Quere [J. Bico and D. Quere, J. Colloid Interface Sci. 243, 262 (2001)], the scaling law under partial-wetting conditions is validated by numerical simulations performed with the Volume of Fluid method. The simulated steady velocities agree with the behavior predicted by the theoretical scaling laws in presence and in absence of static contact angle hysteresis. The numerical simulations suggest that wedge-flow dissipation alone cannot account for the entire additional drag and that the non-Poiseuille dissipation in the static menisci (not considered in previous studies) has to be considered for large contact angles.

The prevalence of accentuated palmoplantar markings and keratosis pilaris in atopic dermatitis, autosomal dominant ichthyosis and control dermatological patients.

The prevalence of keratosis pilaris and accentuated palmoplantar marking was evaluated in 61 patients with atopic dermatitis, 35 patients with dominant ichthyosis vulgaris and 247 other dermatological cases taken as controls. Our data showed that (1) these features are of no diagnostic significance for atopic dermatitis and (2) they are significantly more frequent in patients with ichthyosis vulgaris without associated eczema than in those with atopic dermatitis. Consequently, they should be considered as part of the phenotype of ichthyosis vulgaris rather than attributed to a concomitant atopic dermatitis as suggested by some. These findings should be taken into account when evaluating atopic dermatitis or ichthyosis. To assess the frequency of scaling under winter weather conditions, 155 control subjects were also examined for evidence of visible desquamation and 25.8% showed slight but definite scaling.

Contribution of neural networks to Alzheimer disease's progression.

The neuropathology of Alzheimer disease is characterized by senile plaques, neurofibrillary tangles and cell death. These hallmarks develop according to the differential vulnerability of brain networks, senile plaques accumulating preferentially in the associative cortical areas and neurofibrillary tangles in the entorhinal cortex and the hippocampus. We suggest that the main aetiological hypotheses such as the beta-amyloid cascade hypothesis or its variant, the synaptic beta-amyloid hypothesis, will have to consider neural networks not just as targets of degenerative processes but also as contributors of the disease's progression and of its phenotype. Three domains of research are highlighted in this review. First, the cerebral reserve and the redundancy of the network's elements are related to brain vulnerability. Indeed, an enriched environment appears to increase the cerebral reserve as well as the threshold of disease's onset. Second, disease's progression and memory performance cannot be explained by synaptic or neuronal loss only, but also by the presence of compensatory mechanisms, such as synaptic scaling, at the microcircuit level. Third, some phenotypes of Alzheimer disease, such as hallucinations, appear to be related to progressive dysfunction of neural networks as a result, for instance, of a decreased signal to noise ratio, involving a diminished activity of the cholinergic system. Overall, converging results from studies of biological as well as artificial neural networks lead to the conclusion that changes in neural networks contribute strongly to Alzheimer disease's progression.

An international validation study of the EORTC brain cancer module (EORTC QLQ-BN20) for assessing health-related quality of life and symptoms in brain cancer patients.

Aims: The psychometric properties of the EORTC QLQ-BN20, a brain cancer-specific HRQOL questionnaire, have been previously determined in an English-speaking sample of patients. This study examined the validity and reliability of the questionnaire in a multi-national, multi-lingual study. Methods: QLQ-BN20 data were selected from two completed phase III EORTC/NCIC clinical trials in brain cancer (N=891), including 12 languages. Experimental treatments were surgery followed by radiotherapy (RT) and adjuvant PCV chemotherapy or surgery followed by concomitant RT plus temozolomide (TMZ) chemotherapy and adjuvant TMZ chemotherapy. Standard treatment consisted of surgery and postoperative RT alone. The psychometrics of the QLQ-BN20 were examined by means of multi-trait scaling analyses, reliability estimation, known groups validity testing, and responsiveness analysis. Results: All QLQ-BN20 items correlated more strongly with their own scale (r>0.70) than with other QLQ-BN20 scales. Internal consistency reliability coefficients were high (all alpha0.70). Known-groups comparisons yielded positive results, with the QLQ-BN20 distinguishing between patients with differing levels of performance status and mental functioning. Responsiveness of the questionnaire to changes over time was acceptable. Conclusion: The QLQ-BN20 demonstrates adequate psychometric properties and can be recommended for use in conjunction with the QLQ-C30 in assessing the HRQOL of brain cancer patients in international studies.

Robustness of Drosophila early embryo and wing imaginal disc development

Within a developing organism, cells require information on where they are in order to differentiate into the correct cell-type. Pattern formation is the process by which cells acquire and process positional cues and thus determine their fate. This can be achieved by the production and release of a diffusible signaling molecule, called a morphogen, which forms a concentration gradient: exposure to different morphogen levels leads to the activation of specific signaling pathways. Thus, in response to the morphogen gradient, cells start to express different sets of genes, forming domains characterized by a unique combination of differentially expressed genes. As a result, a pattern of cell fates and specification emerges.Though morphogens have been known for decades, it is not yet clear how these gradients form and are interpreted in order to yield highly robust patterns of gene expression. During my PhD thesis, I investigated the properties of Bicoid (Bcd) and Decapentaplegic (Dpp), two morphogens involved in the patterning of the anterior-posterior axis of Drosophila embryo and wing primordium, respectively. In particular, I have been interested in understanding how the pattern proportions are maintained across embryos of different sizes or within a growing tissue. This property is commonly referred to as scaling and is essential for yielding functional organs or organisms. In order to tackle these questions, I analysed fluorescence images showing the pattern of gene expression domains in the early embryo and wing imaginal disc. After characterizing the extent of these domains in a quantitative and systematic manner, I introduced and applied a new scaling measure in order to assess how well proportions are maintained. I found that scaling emerged as a universal property both in early embryos (at least far away from the Bcd source) and in wing imaginal discs (across different developmental stages). Since we were also interested in understanding the mechanisms underlying scaling and how it is transmitted from the morphogen to the target genes down in the signaling cascade, I also quantified scaling in mutant flies where this property could be disrupted. While scaling is largely conserved in embryos with altered bcd dosage, my modeling suggests that Bcd trapping by the nuclei as well as pre-steady state decoding of the morphogen gradient are essential to ensure precise and scaled patterning of the Bcd signaling cascade. In the wing imaginal disc, it appears that as the disc grows, the Dpp response expands and scales with the tissue size. Interestingly, scaling is not perfect at all positions in the field. The scaling of the target gene domains is best where they have a function; Spalt, for example, scales best at the position in the anterior compartment where it helps to form one of the anterior veins of the wing. Analysis of mutants for pentagone, a transcriptional target of Dpp that encodes a secreted feedback regulator of the pathway, indicates that Pentagone plays a key role in scaling the Dpp gradient activity.

Relationships of basal metabolic rate, relative testis size and cycle length of spermatogenesis in shrews (Mammalia, Soricidae).

The aim of the present study was to determinate the cycle length of spermatogenesis in three species of shrew, Suncus murinus, Sorex coronatus and Sorex minutus, and to assess the relative influence of variation in basal metabolic rate (BMR) and mating system (level of sperm competition) on the observed rate of spermatogenesis, including data of shrew species studied before (Sorex araneus, Crocidura russula and Neomys fodiens). The dynamics of sperm production were determined by tracing 5-bromodeoxyuridine in the DNA of germ cells. As a continuous scaling of mating systems is not evident, the level of sperm competition was evaluated by the significantly correlated relative testis size (RTS). The cycle durations estimated by linear regression were 14.3 days (RTS 0.3%) in Suncus murinus, 9.0 days (RTS 0.5%) in Sorex coronatus and 8.5 days (RTS 2.8%) in Sorex minutus. In regression and multiple regression analyses including all six studied species of shrew, cycle length was significantly correlated with BMR (r2=0.73) and RTS (r2=0.77). Sperm competition as an ultimate factor obviously leads to a reduction in the time of spermatogenesis in order to increase sperm production. BMR may act in the same way, independently or as a proximate factor, revealed by the covariation, but other factors (related to testes size and thus to mating system) may also be involved.

Essential surgery: the way forward.

INTRODUCTION: Very little surgical care is performed in low- and middle-income countries (LMICs). An estimated two billion people in the world have no access to essential surgical care, and non-surgeons perform much of the surgery in remote and rural areas. Surgical care is as yet not recognized as an integral aspect of primary health care despite its self-demonstrated cost-effectiveness. We aimed to define the parameters of a public health approach to provide surgical care to areas in most need. METHODS: Consensus meetings were held, field experience was collected via targeted interviews, and a literature review on the current state of essential surgical care provision in Sub-Saharan Africa (SSA) was conducted. Comparisons were made across international recommendations for essential surgical interventions and a consensus-driven list was drawn up according to their relative simplicity, resource requirement, and capacity to provide the highest impact in terms of averted mortality or disability. RESULTS: Essential Surgery consists of basic, low-cost surgical interventions, which save lives and prevent life-long disability or life-threatening complications and may be offered in any district hospital. Fifteen essential surgical interventions were deduced from various recommendations from international surgical bodies. Training in the realm of Essential Surgery is narrow and strict enough to be possible for non-physician clinicians (NPCs). This cadre is already active in many SSA countries in providing the bulk of surgical care. CONCLUSION: A basic package of essential surgical care interventions is imperative to provide structure for scaling up training and building essential health services in remote and rural areas of LMICs. NPCs, a health cadre predominant in SSA, require training, mentoring, and monitoring. The cost of such training is vastly more efficient than the expensive training of a few polyvalent or specialist surgeons, who will not be sufficient in numbers within the next few generations. Moreover, these practitioners are used to working in the districts and are much less prone to gravitate elsewhere. The use of these NPCs performing "Essential Surgery" is a feasible route to deal with the almost total lack of primary surgical care in LMICs.

What to compare and how: Comparative transcriptomics for Evo-Devo.

Evolutionary developmental biology has grown historically from the capacity to relate patterns of evolution in anatomy to patterns of evolution of expression of specific genes, whether between very distantly related species, or very closely related species or populations. Scaling up such studies by taking advantage of modern transcriptomics brings promising improvements, allowing us to estimate the overall impact and molecular mechanisms of convergence, constraint or innovation in anatomy and development. But it also presents major challenges, including the computational definitions of anatomical homology and of organ function, the criteria for the comparison of developmental stages, the annotation of transcriptomics data to proper anatomical and developmental terms, and the statistical methods to compare transcriptomic data between species to highlight significant conservation or changes. In this article, we review these challenges, and the ongoing efforts to address them, which are emerging from bioinformatics work on ontologies, evolutionary statistics, and data curation, with a focus on their implementation in the context of the development of our database Bgee (http://bgee.org). J. Exp. Zool. (Mol. Dev. Evol.) 324B: 372-382, 2015. © 2015 Wiley Periodicals, Inc.