Segmentation of Head and Neck Lymph Node Regions for Radiotherapy Planning Using Active Contour-Based Atlas Registration

In this paper, we present the segmentation of the headand neck lymph node regions using a new active contourbased atlas registration model. We propose to segment thelymph node regions without directly including them in theatlas registration process; instead, they are segmentedusing the dense deformation field computed from theregistration of the atlas structures with distinctboundaries. This approach results in robust and accuratesegmentation of the lymph node regions even in thepresence of significant anatomical variations between theatlas-image and the patient's image to be segmented. Wealso present a quantitative evaluation of lymph noderegions segmentation using various statistical as well asgeometrical metrics: sensitivity, specificity, dicesimilarity coefficient and Hausdorff distance. Acomparison of the proposed method with two other state ofthe art methods is presented. The robustness of theproposed method to the atlas selection, in segmenting thelymph node regions, is also evaluated.

Pseudogenes in the ENCODE regions: consensus annotation, analysis of transcription, and evolution.

Arising from either retrotransposition or genomic duplication of functional genes, pseudogenes are "genomic fossils" valuable for exploring the dynamics and evolution of genes and genomes. Pseudogene identification is an important problem in computational genomics, and is also critical for obtaining an accurate picture of a genome's structure and function. However, no consensus computational scheme for defining and detecting pseudogenes has been developed thus far. As part of the ENCyclopedia Of DNA Elements (ENCODE) project, we have compared several distinct pseudogene annotation strategies and found that different approaches and parameters often resulted in rather distinct sets of pseudogenes. We subsequently developed a consensus approach for annotating pseudogenes (derived from protein coding genes) in the ENCODE regions, resulting in 201 pseudogenes, two-thirds of which originated from retrotransposition. A survey of orthologs for these pseudogenes in 28 vertebrate genomes showed that a significant fraction ( approximately 80%) of the processed pseudogenes are primate-specific sequences, highlighting the increasing retrotransposition activity in primates. Analysis of sequence conservation and variation also demonstrated that most pseudogenes evolve neutrally, and processed pseudogenes appear to have lost their coding potential immediately or soon after their emergence. In order to explore the functional implication of pseudogene prevalence, we have extensively examined the transcriptional activity of the ENCODE pseudogenes. We performed systematic series of pseudogene-specific RACE analyses. These, together with complementary evidence derived from tiling microarrays and high throughput sequencing, demonstrated that at least a fifth of the 201 pseudogenes are transcribed in one or more cell lines or tissues.

Contrasting diffusion of Quaternary gene pools across Europe: the case of the arctic-alpine Gentiana nivalis L. (Gentianaceae).

The fate of European arctic-alpine species during Pleistocene climatic oscillations still remains debated. Did these cold-adapted species invade much of the continental steppe or did they remain restricted to warmer slopes of inner mountain massifs? To examine this question, we investigated the phylogeography of Gentiana nivalis, a typical European arctic-alpine plant species. Genome fingerprinting analyses revealed that four genetic pools are actually unevenly distributed across the continent. One cluster covers almost all mountain massifs as well as northern areas, and thus coincides with a scenario of past distribution covering a large part of the European glacial steppe. In contrast, the three other lineages are strongly restricted spatially to western, central, and eastern Alps, respectively, thus arguing towards a scenario of in situ glacial survival. The coexistence of lineages with such contrasting demographic histories in Europe challenges our classical view of refugia and corroborates several hypotheses of biogeographers from the twentieth century.

Lower Triassic bryozoan beds from Ellesmere Island, High Arctic, Canada

In the Sverdrup Basin (Canadian Arctic), the Lower Triassic Blind Fiord Formation, comprising siltstone and shale, overlies various Middle to Late Permian (post-Wordian) sedimentary units. This formation is subdivided into three members: the Confederation Point, Smith Creek and Svartfjeld members of, respectively, Griesbachian-Dienerian, Smithian-Spathian and Spathian ages. Lower Triassic bryozoan beds are known from many sections of Ellesmere Island, but have never been studied in detail. During the Early Triassic biotic recovery interval, immediately following the Permian/Triassic extinction event, only one new bryozoan genus evolved in the Boreal region: Arcticopora. The first lower Triassic bryozoan bed appears in the upper part of the Confederation Point Member, and is dated as late Dienerian. Succeeding bryozoan levels occur in the upper Smith Creek Member, and are late Smithian-early Spathian in age. Bryozoan beds occupy a similar stratigraphic position in Spitsbergen. There, they occur scattered in silt to coarse sandstone beds, but also in bryozoan-dominated packstone beds resembling the packstone units in the uppermost part of the Confederation Point Member of Ellesmere Island. Previously, bryozoan-rich beds of Triassic age have not been reported, and the present work fills an important time gap in the bryozoan carbonate database

Influence of row spacing reduction on maize grain yield in regions with a short summer

The interest in reducing maize row spacing in the short growing season regions of Brazil is increasing due to potential advantages such as higher radiation use efficiency. This experiment was conducted to evaluate the effect of row spacing reduction on grain yield of different maize cultivars planted at different dates. The trial was conducted in Lages, in the State of Santa Catarina, Brazil, during 1996/97 and 1997/98 growing seasons, in a split-split plot design. Early (October 1st) and normal (November 15) planting dates were tested in the main plot; two morphologically contrasting cultivars (an early single-cross and a late double-cross hybrids) were evaluated in the split plots and three row widths (100, 75 and 50 cm) were studied in the split-split plots. The reduction of row spacing from 100 to 50 cm increased linearly maize grain yield. The yield edge provided by narrow rows was higher when maize was sown earlier in the season. Differences in hybrid cycle and plant architecture did not alter maize response to the reduction of row spacing.

Thinning response and growth trends of seeded Scots pine stands at the arctic timberline

Abstract

Tagging reveals limited exchange of immature loggerhead sea turtles (Caretta caretta) between regions in the western Mediterranean.

Exchange of immature loggerhead sea turtles (Caretta caretta) between the northern and southern regions of the western Mediterranean was investigated using data obtained from several Spanish tagging programmes. Tagged turtles ranged in straight carapace length from 23.0 to 74.0 cm. Thirty-six turtles were recaptured after an average interval of 390.5±462.6 days (SD). As the mean dispersal distance (MDD) of a turtle population that spreads over the western Mediterranean would stabilize after 117 days (CI 95%: 98 to 149), two analyses were conducted that included data from turtles recaptured after 98 and 149 days respectively. In both analyses, turtles were recaptured more often than expected in the same region where they had been tagged. No difference was found in either of the two regions between the average distance between the capture and recapture locations and the expected MDD if the turtles were to remain in the region where they were first captured. Turtles recaptured after 15 and 25 days respectively were excluded from the analysis to ensure data independence. The overall evidence indicates that immature turtles exhibit strong site fidelity to certain areas and that there is a strong barrier to dispersal between the northern and southern parts of the western Mediterranean. Therefore, loggerhead turtles in the western Mediterranean should be split into at least two management units.

Dissecting the role of low-complexity regions in the evolution of vertebrate proteins

Low-complexity regions (LCRs) in proteins are tracts that are highly enriched in one or a few aminoacids. Given their high abundance, and their capacity to expand in relatively short periods of time through replication slippage, they can greatly contribute to increase protein sequence space and generate novel protein functions. However, little is known about the global impact of LCRs on protein evolution. We have traced back the evolutionary history of 2,802 LCRs from a large set of homologous protein families from H.sapiens, M.musculus, G.gallus, D.rerio and C.intestinalis. Transcriptional factors and other regulatory functions are overrepresented in proteins containing LCRs. We have found that the gain of novel LCRs is frequently associated with repeat expansion whereas the loss of LCRs is more often due to accumulation of amino acid substitutions as opposed to deletions. This dichotomy results in net protein sequence gain over time. We have detected a significant increase in the rate of accumulation of novel LCRs in the ancestral Amniota and mammalian branches, and a reduction in the chicken branch. Alanine and/or glycine-rich LCRs are overrepresented in recently emerged LCR sets from all branches, suggesting that their expansion is better tolerated than for other LCR types. LCRs enriched in positively charged amino acids show the contrary pattern, indicating an important effect of purifying selection in their maintenance. We have performed the first large-scale study on the evolutionary dynamics of LCRs in protein families. The study has shown that the composition of an LCR is an important determinant of its evolutionary pattern.

Maintenance of A/P body regions in planarians by TCEN49, a putative cystine-knot neurotrophin.

In freshwater planarians, the protein TCEN49 has been linked to the regional specification of the central body region, which includes the pharynx.

Development of stable cell lines for production or regulated expression using matrix attachment regions.

One of the major hurdles of isolating stable, inducible or constitutive high-level producer cell lines is the time-consuming selection procedure. Given the variation in the expression levels of the same construct in individual clones, hundreds of clones must be isolated and tested to identify one or more with the desired characteristics. Various boundary elements (BEs), matrix attachment regions, and locus control regions (LCRs) were screened for their ability to augment the expression of heterologous genes in Chinese hamster ovary (CHO) cells. Of the chromatin elements assayed, the chicken lysozyme matrix-attachment region (MAR) was the only element to significantly increase stable reporter expression. We found that the use of the MAR increases the proportion of high-producing clones, thus reducing the number of clones that need to be screened. These benefits are observed both for constructs with MARs flanking the transgene expression cassette, as well as when constructs are co-transfected with the MAR on a separate plasmid. Moreover, the MAR was co-transfected with a multicomponent regulatable beta-galactosidase expression system in C2C12 cells and several clones exhibiting regulated expression were identified. Hence, MARs are useful in the development of stable cell lines for production or regulated expression.

Tourism destination zoning in rural regions: a consumer-based approach in Terres de l’Ebre

This document puts into question the conventional way of delineating tourism destinations. It intends to show a model of spatial analysis, to find new interpretations of the reality, more balanced and more optimized, in comparison with other territorial views most of them based on administrative boundaries. This paper portrays a methodological exercise that aims to structure tourism geographies into new tourism areas on the basis of visitor’s consumption patterns, which would be better fitted to the needs of tourist demand

Synthesis and immunological characterization of 104-mer and 102-mer peptides corresponding to the N- and C-terminal regions of the Plasmodium falciparum CS protein.

We investigated the immunogenicity and the conformational properties of the non-repetitive sequences of the Plasmodium falciparum circumsporozoite (CS) protein. Two polypeptides of 104 and 102 amino acids long, covering, respectively, the N- and C-terminal regions of the CS protein, were synthesized using solid phase Fmoc chemistry. The crude polypeptides were purified by a combination of size exclusion chromatography and RP-HPLC. Sera of mice immunized with the free polypeptides emulsified in incomplete Freund's adjuvant strongly reacted with the synthetic polypeptides as well as with native CS protein as judged by ELISA and IFAT assays. Most importantly, these antisera inhibited the sporozoite invasion of hepatoma cells. In addition, sera derived from donors living in a malaria endemic area recognized the CS 104- and 102-mers. Conformational studies of the CS polypeptides were also performed by circular dichroism spectroscopy showing the presence of a weakly ordered structure that can be increased by addition of trifluoroethanol. The obtained results indicate that the synthetic CS polypeptides and the natural CS protein share some common antigenic determinants and probably have similar conformation. The approach used in this study might be useful for the development of a synthetic malaria vaccine.

Preliminary characterization of Psidium germplasm in different Brazilian ecogeographic regions

The objective of this work was to characterize 119 accessions of guava and 40 accessions of "araçá" sampled in 35 Brazilian ecoregions, according to the International Union for the Protection of New Varieties of Plants (UPOV) descriptors. The majority of "araçá" accessions presented wide spacing of leaf veins, while guava accessions presented medium to close spacing. Most fruits of "araçá" accessions were classified as small, contrasting with medium to large fruits of guava accessions. Most of "araçá" accessions (91%) presented white flesh fruit color, while 58% of guava accessions presented pale pink, pink and dark pink colors. Fruit differences among wild and cultivated Psidium species indicate fruit as the most altered trait under artificial selection.

Distribution and agroclimatic characterization of potential cultivation regions of physic nut in Mexico

The purposes of this study were to determine the distribution and climatic patterns of current and future physic nut (Jatropha curcas) cultivation regions in Mexico, and to identify possible locations for in vivo germplasm banks establishment, using geographic information systems. Current climatic data were processed by Floramap software to obtain distribution maps and climatic patterns of regions where wild physic nuts could be found. DIVA-GIS software analyzed current climatic data (Worldclim model) and climatic data generated by CCM3 model to identify current and future physic nut cultivation regions, respectively. The distribution map showed that physic nut was present in most of the tropical and subtropical areas of Mexico, which corresponded to three agroclimatic regions. Climate types were Aw2, Aw1, and Bs1, for regions 1, 2 and 3, respectively. Nontoxic genotypes were associated with region 2, and toxic genotypes were associated with regions 1 and 3. According to the current and future cultivation regions identified, the best suitable ones to establish in vivo germplasm collections were the coast of Michoacán and the Isthmus of Tehuantepec, located among the states of Veracruz, Oaxaca and Chiapas.