Temperature dependent hyperspectral terahertz imaging of human bone for disease diagnosis

Water is a fundamental component of many biological systems. The ability to detect water therefore provides great insight into system functionality, particularly in the development of disease. In this work, the high interaction of terahertz radiation with water, paired with the dependence of the dynamics of water molecules with varying temperature, is utilised to monitor changes in the composition of bone tissue. Heterotopic ossification (HO) bone samples and deionised free water are measured using terahertz time-domain spectroscopy for varying environmental temperatures, for prospective use in disease diagnosis

Compact High-Velocity Clouds at High Resolution

Six examples of the compact, isolated high-velocity clouds catalogued by Braun & Burton (1999) and identified with a dynamically cold ensemble of primitive objects falling towards the barycenter of the Local Group have been imaged with the Westerbork Synthesis Radio Telescope; an additional ten have been imaged with the Arecibo telescope. The imaging reveals a characteristic core/halo morphology: one or several cores of cool, relatively high-column-density material, are embedded in an extended halo of warmer, lower-density material. Several of the cores show kinematic gradients consistent with rotation; these CHVCs are evidently rotationally supported and dark-matter dominated. The imaging data allows several independent estimates of the distances to these objects, which lie in the range 0.3 to 1.0 Mpc. The CHVC properties resemble what might be expected from very dark dwarf irregular galaxies.Comment: 12 pages, 7 figures, to appear in "The Chemical Evolution of the Milky Way: Stars versus Clusters", eds. F. Matteuchi and F. Giovannelli, Kluwer Academic Publisher

The topology of vitronectin: A complementary feature for neuroblastoma risk classification based on computer‐aided detection

Tumors are complex networks of constantly interacting elements: tumor cells, stromal cells, immune and stem cells, blood/lympathic vessels, nerve fibers and extracellular matrix components. These elements can influence their microenvironment through mechanical and physical signals to promote tumor cell growth. To get a better understanding of tumor biology, cooperation between multidisciplinary fields is needed. Diverse mathematic computations and algorithms have been designed to find prognostic targets and enhance diagnostic assessment. In this work, we use computational digital tools to study the topology of vitronectin, a glycoprotein of the extracellular matrix. Vitronectin is linked to angiogenesis and migration, two processes closely related to tumor cell spread. Here, we investigate whether the distribution of this molecule in the tumor stroma may confer mechanical properties affecting neuroblastoma aggressiveness. Combining image analysis and graph theory, we analyze different topological features that capture the organizational cues of vitronectin in histopathological images taken from human samples. We find that the Euler number and the branching of territorial vitronectin, two topological features, could allow for a more precise pretreatment risk stratification to guide treatment strategies in neuroblastoma patients. A large amount of recently synthesized VN would create migration tracks, pinpointed by both topological features, for malignant neuroblasts, so that dramatic change in the extracellular matrix would increase tumor aggressiveness and worsen patient outcomes

Mapping opportunities and challenges for rewilding in Europe

Farmland abandonment takes place across the world due to socio-economic and ecological drivers. In Europe agricultural and environmental policies aim to prevent abandonment and halt ecological succession. Ecological rewilding has been recently proposed as an alternative strategy. We developed a framework to assess opportunities for rewilding across different dimensions of wilderness in Europe. We mapped artificial light, human accessibility based on transport infrastructure, proportion of harvested primary productivity (i.e., ecosystem productivity appropriated by humans through agriculture or forestry), and deviation from potential natural vegetation in areas projected to be abandoned by 2040. At the continental level, the levels of artificial light were low and the deviation from potential natural vegetation was high in areas of abandonment. The relative importance of wilderness metrics differed regionally and was strongly connected to local environmental and socio-economic contexts. Large areas of projected abandonment were often located in or around Natura 2000 sites. Based on these results, we argue that management should be tailored to restore the aspects of wilderness that are lacking in each region. There are many remaining challenges regarding biodiversity in Europe, but megafauna species are already recovering. To further potentiate large-scale rewilding, Natura 2000 management would need to incorporate rewilding approaches. Our framework can be applied to assessing rewilding opportunities and challenges in other world regions, and our results could guide redirection of subsidies to manage social-ecological systems

Hybrid reflection retrieval method for terahertz dielectric imaging of human bone

Terahertz imaging is becoming a biological imaging modality in its own right, alongside the more mature infrared and X-ray techniques. Nevertheless, extraction of hyperspectral, biometric information of samples is limited by experimental challenges. Terahertz time domain spectroscopy reflection measurements demand highly precise alignment and suffer from limitations of the sample thickness. In this work, a novel hybrid Kramers-Kronig and Fabry-Pérot based algorithm has been developed to overcome these challenges. While its application is demonstrated through dielectric retrieval of glass-backed human bone slices for prospective characterisation of metastatic defects or osteoporosis, the generality of the algorithm offers itself to wider application towards biological materials

Preimplantation development regulatory pathway construction through a text-mining approach

BACKGROUND: The integration of sequencing and gene interaction data and subsequent generation of pathways and networks contained in databases such as KEGG Pathway is essential for the comprehension of complex biological processes. We noticed the absence of a chart or pathway describing the well-studied preimplantation development stages; furthermore, not all genes involved in the process have entries in KEGG Orthology, important information for knowledge application with relation to other organisms. RESULTS: In this work we sought to develop the regulatory pathway for the preimplantation development stage using text-mining tools such as Medline Ranker and PESCADOR to reveal biointeractions among the genes involved in this process. The genes present in the resulting pathway were also used as seeds for software developed by our group called SeedServer to create clusters of homologous genes. These homologues allowed the determination of the last common ancestor for each gene and revealed that the preimplantation development pathway consists of a conserved ancient core of genes with the addition of modern elements. CONCLUSIONS: The generation of regulatory pathways through text-mining tools allows the integration of data generated by several studies for a more complete visualization of complex biological processes. Using the genes in this pathway as "seeds" for the generation of clusters of homologues, the pathway can be visualized for other organisms. The clustering of homologous genes together with determination of the ancestry leads to a better understanding of the evolution of such process

Phenotypic and molecular assessment of seven patients with 6p25 deletion syndrome: Relevance to ocular dysgenesis and hearing impairment

BACKGROUND: Thirty-nine patients have been described with deletions involving chromosome 6p25. However, relatively few of these deletions have had molecular characterization. Common phenotypes of 6p25 deletion syndrome patients include hydrocephalus, hearing loss, and ocular, craniofacial, skeletal, cardiac, and renal malformations. Molecular characterization of deletions can identify genes that are responsible for these phenotypes. METHODS: We report the clinical phenotype of seven patients with terminal deletions of chromosome 6p25 and compare them to previously reported patients. Molecular characterization of the deletions was performed using polymorphic marker analysis to determine the extents of the deletions in these seven 6p25 deletion syndrome patients. RESULTS: Our results, and previous data, show that ocular dysgenesis and hearing impairment are the two most highly penetrant phenotypes of the 6p25 deletion syndrome. While deletion of the forkhead box C1 gene (FOXC1) probably underlies the ocular dysgenesis, no gene in this region is known to be involved in hearing impairment. CONCLUSIONS: Ocular dysgenesis and hearing impairment are the two most common phenotypes of 6p25 deletion syndrome. We conclude that a locus for dominant hearing loss is present at 6p25 and that this locus is restricted to a region distal to D6S1617. Molecular characterization of more 6p25 deletion patients will aid in refinement of this locus and the identification of a gene involved in dominant hearing loss

Effective Dark Matter Model: Relic density, CDMS II, Fermi LAT and LHC

The Cryogenic Dark Matter Search recently announced the observation of two signal events with a 77% confidence level. Although statistically inconclusive, it is nevertheless suggestive. In this work we present a model-independent analysis on the implication of a positive signal in dark matter scattering off nuclei. Assuming the interaction between (scalar, fermion or vector) dark matter and the standard model induced by unknown new physics at the scale $\Lambda$, we examine various dimension-6 tree-level induced operators and constrain them using the current experimental data, e.g. the WMAP data of the relic abundance, CDMS II direct detection of the spin-independent scattering, and indirect detection data (Fermi LAT cosmic gamma-ray), etc. Finally, the LHC reach is also explored

Contrasting changes in the abundance and diversity of North American bird assemblages from 1971 to 2010

This article is based upon work from COST Action ES1101 "Harmonising Global Biodiversity Modelling" (Harmbio), supported by COST (European Cooperation in Science and Technology).Although it is generally recognized that global biodiversity is declining, few studies have examined long-term changes in multiple biodiversity dimensions simultaneously. In this study we quantified and compared temporal changes in the abundance, taxonomic diversity, functional diversity and phylogenetic diversity of bird assemblages, using roadside monitoring data of the North American Breeding Bird Survey from 1971 to 2010. We calculated 12 abundance and diversity metrics based on five year average abundances of 519 species for each of 768 monitoring routes. We did this for all bird species together as well as for four sub-groups based on breeding habitat affinity (grassland, woodland, wetland and shrubland breeders). The majority of the biodiversity metrics increased or remained constant over the study period, whereas the overall abundance of birds showed a pronounced decrease, primarily driven by declines of the most abundant species. These results highlight how stable or even increasing metrics of taxonomic, functional or phylogenetic diversity may occur in parallel with substantial losses of individuals. We further found that patterns of change differed among the species sub-groups, with both abundance and diversity increasing for woodland birds and decreasing for grassland breeders. The contrasting changes between abundance and diversity and among the breeding habitat groups underscore the relevance of a multi-faceted approach to measuring biodiversity change. Our findings further stress the importance of monitoring the overall abundance of individuals in addition to metrics of taxonomic, functional or phylogenetic diversity, thus confirming the importance of population abundance as an essential biodiversity variable.Publisher PDFPeer reviewe