Invading and expanding: range dynamics and ecological consequences of the greater white-toothed shrew (Crocidura russula) invasion in Ireland

Establishing how invasive species impact upon pre-existing species is a fundamental question in ecology and conservation biology. The greater white-toothed shrew (Crocidura russula) is an invasive species in Ireland that was first recorded in 2007 and which, according to initial data, may be limiting the abundance/distribution of the pygmy shrew (Sorex minutus), previously Ireland’s only shrew species. Because of these concerns, we undertook an intensive live-trapping survey (and used other data from live-trapping, sightings and bird of prey pellets/nest inspections collected between 2006 and 2013) to model the distribution and expansion of C. russula in Ireland and its impacts on Ireland’s small mammal community. The main distribution range of C. russula was found to be approximately 7,600 km2 in 2013, with established outlier populations suggesting that the species is dispersing with human assistance within the island. The species is expanding rapidly for a small mammal, with a radial expansion rate of 5.5 km/yr overall (2008–2013), and independent estimates from live-trapping in 2012–2013 showing rates of 2.4–14.1 km/yr, 0.5–7.1 km/yr and 0–5.6 km/yr depending on the landscape features present. S. minutus is negatively associated with C. russula. S. minutus is completely absent at sites where C. russula is established and is only present at sites at the edge of and beyond the invasion range of C. russula. The speed of this invasion and the homogenous nature of the Irish landscape may mean that S. minutus has not had sufficient time to adapt to the sudden appearance of C. russula. This may mean the continued decline/disappearance of S. minutus as C. russula spreads throughout the island.

How historical and present climat conditions affected the distribution of the mediterranean whter shrew?:a phylogeographical and ecological approach

Tese de doutoramento, Biologia (Biologia Evolutiva), Universidade de Lisboa, Faculdade de Ciências, 2014

Mediterranean populations of the lesser white-toothed shrew (Crocidura suaveolens group): an unexpected puzzle of Pleistocene survivors and prehistoric introductions.

An earlier study revealed the strong phylogeographical structure of the lesser white-toothed shrew (Crocidura suaveolens group) within the northern Palaearctic. Here, we aim to reconstruct the colonization history of Mediterranean islands and to clarify the biogeography and phylogeographical relationships of the poorly documented Middle East region with the northern Palaearctic. We performed analyses on 998-bp-long haplotypes of the mitochondrial cytochrome b gene of 143 samples collected around the Mediterranean basin, including islands and the Middle East. The analyses suggest that the Cypriot shrew belongs to the rare group of relict insular Pleistocene mammal taxa that have survived to the present day. In contrast, the Cretan, Corsican and Menorcan populations were independently introduced from the Middle East during the Holocene. The phylogeographical structure of this temperate Palaearctic species within the Middle East appears to be complex and rich in diversity, probably reflecting fragmentation of the area by numerous mountain chains. Four deeply divergent clades of the C. suaveolens group occur in the area, meaning that a hypothetical contact zone remains to be located in central western Iran.

Phylogeographic Structure and Karyotypic Diversity of the Brazilian Shrew Mouse (Blarinomys breviceps, Sigmodontinae) in the Atlantic Forest

Blarinomys breviceps possesses cryptic and burrowing habits with poorly documented genetics and life history traits. Due to its rarity, only a few specimens and DNA sequences have been deposited in collections worldwide. Here, we present the most comprehensive cytogenetic and molecular characterization of this rare genus. Phylogenetic analyses based on partial cytochrome b sequences were performed, attempting to establish the relationships among individuals with distinct karyotypes along the geographic distribution of the genus in the Atlantic Forest. Classical and molecular cytogenetics, using banding patterns and FISH of telomeric and whole chromosome X-specific painting probes (obtained from the Akodontini Akodon cursor) were used to characterize and compare the chromosomal complements. Molecular phylogenetic analyses recovered 2 main geographically structured clades, northeastern and southeastern with pair-wise sequence divergences among specimens varying between 4.9 and 8.4%. Eight distinct karyomorphs are described: (A) 2n = 52 (50A, XX), (B) 2n = 52 (48A, XY+2Bs), (C) 2n = 45 (42A, XY+1B), (D) 2n = 43 (37A, XX+4Bs), (E) 2n = 37 (34A, XY+1B), (F) 2n = 34 (32A, XX), (G) 2n = 31 (27A, XX+2Bs), (H) 2n = 28 (26A, XY), all with the same number of autosomal arms (FNA = 50). Variation of 0-4 supernumerary chromosomes (Bs) presenting heterogeneity in morphology and distribution of interstitial telomeric sequences (ITSs) is reported. ITSs are also found in some metacentric autosomes. The phylogeographic separation between 2 major lineages with high levels of genetic divergence, and the wide karyotypic diversity indicate that B. breviceps is a diverse group that warrants taxonomic re-evaluation. Copyright (C) 2012 S. Karger AG, Basel

On the postnatal development of the striate cortex (V1) in the tree shrew (Tupaia belangeri)

Histological serial sections, three-dimensional reconstructions and morphometry served to study the postnatal development of V1 in tree shrews. The main objectives were to evaluate the expansion of V1, the implications of its growth on the occipital cortex and, vice versa, the effects of the expanding neocortex on the topography of V1. The future V1 was identified on postnatal day 1 by its granular layer IV, covering the superior surface of the occipital cortices including the poles. A subdivision of layer IV, distinctive for the binocular part, was evident in the central region. V1 expanded continuously with age into all directions succeeded by the maturation of layering. The monocular part was recognized from day 15 onward, after the binocular part had reached its medial border. In reference to the retinotopic map of V1, regions emerged in a coherent temporo-spatial sequence delineating the retinal topography in a central to peripheral gradient beginning with the visual streak representation. The growth of V1 was greatest until tree shrews open their eyes, culminated during adolescence, and completed after a subsequent decrease in the young adult. Simultaneous expansion of the neocortex induced a shifting of V1. Translation and elongation of V1 entailed that the occipital cortex covered the superior colliculi along with a downward rotation of the poles. The enlargement of the occipital part of the hemispheres was in addition associated with the formation of a small occipital horn in the lateral ventricles, indicating an incipient 'true' occipital lobe harbouring mainly cortices involved in visual functions.

Theseus Taming the Bull of Marathon

Carle van Loo; 2 ft. 2 in.x 4 ft. 10 in.; oil on canvas

The works of Shakespeare: in seven volumes. Collated with the oldest copies, and corrected;

v. 1. The tempest. The midsummer-night's dream. The two gentlemen of Verona. Merry wives of Windsor. Measure for measure. Much ado about nothing.--v. 2. The merchant of Venice. Love's labour's lost. As you like it. Taming the shrew. All's well that ends well. Twelfthnight; or, What you will.--v. 3. Comedy of errors. Winter's tale. King John. King Richard II. 1st part of K. Henry IV. 2d part of K. Henry IV.--v. 4. K. Henry V. 1st part of K. Henry VI. 2d part of K. Henry VI. 3d part of K. Henry VI. K. Richard III.--v. 5. K. Henry VIII. K. Lear. Macbeth. Timon of Athens. Titus Andronicus.--v. 6. Coriolanus Julius Cæsar. Antomy and Cleopatra. Cymbeline.--v. 7. Troilus and Cressida. Romeo and Juliet. Hamlet, Prince of Denmark. Othello. A table of the several editions of Shakespeare's plays, collected by the editor (p. [495]-[503])

The art of taming horses /

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Areal specialization of pyramidal cell structure in the visual cortex of the tree shrew: a new twist revealed in the evolution of cortical circuitry

Cortical pyramidal cells, while having a characteristic morphology, show marked phenotypic variation in primates. Differences have been reported in their size, branching structure and spine density between cortical areas. In particular, there is a systematic increase in the complexity of the structure of pyramidal cells with anterior progression through occipito-temporal cortical visual areas. These differences reflect area-specific specializations in cortical circuitry, which are believed to be important for visual processing. However, it remains unknown as to whether these regional specializations in pyramidal cell structure are restricted to primates. Here we investigated pyramidal cell structure in the visual cortex of the tree shrew, including the primary (V1), second (V2) and temporal dorsal (TD) areas. As in primates, there was a trend for more complex branching structure with anterior progression through visual areas in the tree shrew. However, contrary to the trend reported in primates, cells in the tree shrew tended to become smaller with anterior progression through V1, V2 and TD. In addition, pyramidal cells in V1 of the tree shrew are more than twice as spinous as those in primates. These data suggest that variables that shape the structure of adult cortical pyramidal cells differ among species.

The monster chronicles : the role of children’s stories featuring monsters in managing childhood fears and promoting empowerment

Children’s fascination with monsters is a normal part of childhood development. Children’s literature reflects this with a wealth of stories featuring monsters, ranging from fairy tales to picture books to books for independent readers. These stories can raise concerns from educators, parents and other sections of the community such as political and religious institutions on the basis that they could be disturbing or harmful to children. In contrast, there is evidence to indicate the potential for managing fears and enhancing feelings of empowerment in children through the reading of stories featuring monsters. A reappraisal of these stories from a predominantly therapeutic perspective reveals that they may act as agents of positive change in six ways – catharsis, naming, taming, integration, transformation and moral empowerment. Two of these functions, transformation and moral empowerment, are examined further in three case studies of stories for the older reader that feature monsters, Wolf Brother by Michelle Paver, Monster Blood Tattoo, Book One: Foundling by D.M. Cornish and my manuscript, ‘The Monster Chronicles’. The insights from this research have been used to inform the writing and editing of ‘The Monster Chronicles’ and inherent to that, my goal of creating a children’s story featuring monsters that is sensitive to children’s fears and their desire for empowerment.

Improving Usability of Software Refactoring Tools

Post-deployment maintenance and evolution can account for up to 75% of the cost of developing a software system. Software refactoring can reduce the costs associated with evolution by improving system quality. Although refactoring can yield benefits, the process includes potentially complex, error-prone, tedious and time-consuming tasks. It is these tasks that automated refactoring tools seek to address. However, although the refactoring process is well-defined, current refactoring tools do not support the full process. To develop better automated refactoring support, we have completed a usability study of software refactoring tools. In the study, we analysed the task of software refactoring using the ISO 9241-11 usability standard and Fitts' List of task allocation. Expanding on this analysis, we reviewed 11 collections of usability guidelines and combined these into a single list of 38 guidelines. From this list, we developed 81 usability requirements for refactoring tools. Using these requirements, the software refactoring tools Eclipse 3.2, Condenser 1.05, RefactorIT 2.5.1, and Eclipse 3.2 with the Simian UI 2.2.12 plugin were studied. Based on the analysis, we have selected a subset of the requirements that can be incorporated into a prototype refactoring tool intended to address the full refactoring process.

Taming the terabytes : a human-centered approach to surviving the information deluge

A fear of imminent information overload predates the World Wide Web by decades. Yet, that fear has never abated. Worse, as the World Wide Web today takes the lion’s share of the information we deal with, both in amount and in time spent gathering it, the situation has only become more precarious. This chapter analyses new issues in information overload that have emerged with the advent of the Web, which emphasizes written communication, defined in this context as the exchange of ideas expressed informally, often casually, as in verbal language. The chapter focuses on three ways to mitigate these issues. First, it helps us, the users, to be more specific in what we ask for. Second, it helps us amend our request when we don't get what we think we asked for. And third, since only we, the human users, can judge whether the information received is what we want, it makes retrieval techniques more effective by basing them on how humans structure information. This chapter reports on extensive experiments we conducted in all three areas. First, to let users be more specific in describing an information need, they were allowed to express themselves in an unrestricted conversational style. This way, they could convey their information need as if they were talking to a fellow human instead of using the two or three words typically supplied to a search engine. Second, users were provided with effective ways to zoom in on the desired information once potentially relevant information became available. Third, a variety of experiments focused on the search engine itself as the mediator between request and delivery of information. All examples that are explained in detail have actually been implemented. The results of our experiments demonstrate how a human-centered approach can reduce information overload in an area that grows in importance with each day that passes. By actually having built these applications, I present an operational, not just aspirational approach.

Mechanisms and molecular regulation of mammalian tooth replacement

In most non-mammalian vertebrates, such as fish and reptiles, teeth are replaced continuously. However, tooth replacement in most mammals, including human, takes place only once and further renewal is apparently inhibited. It is not known how tooth replacement is genetically regulated, and little is known on the physiological mechanism and evolutionary reduction of tooth replacement in mammals. In this study I have attempted to address these questions. In a rare human condition cleidocranial dysplasia, caused by a mutation in a Runt domain transcription factor Runx2, tooth replacement is continued. Runx2 mutant mice were used to investigate the molecular mechanisms of Runx2 function. Microarray analysis from dissected embryonic day 14 Runx2 mutant and wild type dental mesenchymes revealed many downstream targets of Runx2, which were validated using in situ hybridization and tissue culture methods. Wnt signaling inhibitor Dkk1 was identified as a candidate target, and in tissue culture conditions it was shown that Dkk1 is induced by FGF4 and this induction is Runx2 dependent. These experiments demonstrated a connection between Runx2, FGF and Wnt signaling in tooth development and possibly also in tooth replacement. The role of Wnt signaling in tooth replacement was further investigated by using a transgenic mouse model where Wnt signaling mediator β-catenin is continuously stabilized in dental epithelium. This stabilization led to activated Wnt signaling and to the formation of multiple enamel knots. In vitro and transplantation experiments were performed to examine the process of extra tooth formation. We showed that new teeth were continuously generated and that new teeth form from pre-existing teeth. A morphodynamic activator-inhibitor model was used to simulate enamel knot formation. By increasing the intrinsic production rate of the activator (β-catenin), the multiple enamel knot phenotype was reproduced by computer simulations. It was thus concluded that β-catenin acts as an upstream activator of enamel knots, closely linking Wnt signaling to the regulation of tooth renewal. As mice do not normally replace teeth, we used other model animals to investigate the physiological and genetic mechanisms of tooth replacement. Sorex araneus, the common shrew was earlier reported to have non-functional tooth replacement in all antemolar tooth positions. We showed by histological and gene expression studies that there is tooth replacement only in one position, the premolar 4 and that the deciduous tooth is diminished in size and disappears during embryogenesis without becoming functional. The growth rates of deciduous and permanent premolar 4 were measured and it was shown by competence inference that the early initiation of the replacement tooth in relation to the developmental stage of the deciduous tooth led to the inhibition of deciduous tooth morphogenesis. It was concluded that the evolutionary loss of deciduous teeth may involve the early activation of replacement teeth, which in turn suppress their predecessors. Mustela putorius furo, the ferret, has a dentition that resembles that of the human as ferrets have teeth that belong to all four tooth families, and all the antemolar teeth are replaced once. To investigate the replacement mechanism, histological serial sections from different embryonic stages were analyzed. It was noticed that tooth replacement is a process which involves the growth and detachment of the dental lamina from the lingual cervical loop of the deciduous tooth. Detachment of the deciduous tooth leads to a free successional dental lamina, which grows deeper into the mesenchyme, and later buds the replacement tooth. A careful 3D analysis of serial histological sections was performed and it was shown that replacement teeth are initiated from the successional dental lamina and not from the epithelium of the deciduous tooth. The molecular regulation of tooth replacement was studied and it was shown by examination of expression patterns of candidate regulatory genes that BMP/Wnt inhibitor Sostdc1 was strongly expressed in the buccal aspect of the dental lamina, and in the intersection between the detaching deciduous tooth and the successional dental lamina, suggesting a role for Sostdc1 in the process of detachment. Shh was expressed in the enamel knot and in the inner enamel epithelium in both generations of teeth supporting the view that the morphogenesis of both generations of teeth is regulated by similar mechanisms. In summary, histological and molecular studies on different model animals and transgenic mouse models were used to investigate tooth replacement. This thesis work has significantly contributed to the knowledge on the physiological mechanisms and molecular regulation of tooth replacement and its evolutionary suppression in mammals.