Clonal composition of human adamantinomatous craniopharyngiomas and somatic mutation analyses of the patched (PTCH), Gsα and Gi2α genes

Craniopharyngioma is the most common childhood tumor and thought to arise from embryonic remnants of Rathke's pouch. The paucity of published data on the molecular basis of these tumors prompted us to examine 22 adamantinomatous craniopharyngiomas looking for genetic abnormalities. Using the X-linked polymorphic androgen receptor gene as a tool for X-chromosome inactivating analysis, we found that a subset of craniopharyngiomas are monoclonal and therefore are probably due to acquired somatic genetic defects. Thus, we investigated these tumours for mutations within three candidate genes, Gsα, Gi2α and patched (PTCH). Using single stranded conformational polymorphism (SSCP), denaturing gradient gel electrophoresis and direct sequencing, the presence of somatic mutations in these genes could not be demonstrated in any tumor. Our data indicate that a subset of craniopharyngiomas are monoclonal and the mutations in the PTCH, Gsα, and Gi2α contribute little if any to cranipharyngioma development.

Comparative genomic hybridization analysis of craniopharyngiomas

Object. Craniopharyngioma is the most common childhood brain tumor and is thought to arise from embryonic remnants of the Rathke pouch. Some craniopharyngiomas are monoclonal in origin and hence presumably harbor somatic genetic alterations, although the precise molecular mechanisms involved in craniopharyngioma development are unknown. The goal of this study was to identify genetic alterations in craniopharyngiomas. Methods. To gain insight into the molecular mechanisms involved in development of these tumors, the authors analyzed nine adamantinomatous craniopharyngiomas by using comparative genomic hybridization. Six tumors (67%) displayed at least one genomic alteration, and three had six or more alterations. Only two tumors displayed a decrease in DNA copy number, and in all others an increase in DNA copy number was noted. Conclusions. The authors conclude that a subset of craniopharyngiomas consists of monoclonal tumors arising from activation of oncogenes located at specific chromosomal loci.

Molecular markers and human history: A tale of two haplogroup systems

To chronicle demographic movement across African Asian corridors, a variety of molecular (sequence analysis, restriction mapping and denaturing high performance liquid chromatography etc.) and statistical (correspondence analysis, AMOVA, calculation of diversity indices and phylogenetic inference, etc.) techniques were employed to assess the phylogeographic patterns of mtDNA control region and Y chromosomal variation among 14 sub-Saharan, North African and Middle Eastern populations. The patterns of genetic diversity revealed evidence of multiple migrations across several African Asian passageways as well within the African continent itself. The two-part analysis uncovered several interesting results which include the following: (1) a north (Egypt and Middle East Asia) to south (sub-Saharan Africa) partitioning of both mtDNA and Y chromosomal haplogroup diversity, (2) a genetic diversity gradient in sub-Saharan Africa from east to west, (3) evidence in favor of the Levantine Corridor over the Horn of Africa as the major genetic conduit since the Last Glacial Maximum, (4) a substantially higher mtDNA versus Y chromosomal sub-Saharan component in the Middle East collections, (5) a higher representation of East versus West African mtDNA haplotypes in the Arabian Peninsula populations versus no such bias in the Levant groups and lastly, (6) genetic remnants of the Bantu demographic expansion in sub-Saharan Africa. ^

Life cycle of Deccan trap magma chambers: A crystal scale elemental and strontium isotopic investigation

The Deccan Trap basalts are the remnants of a massive series of lava flows that erupted at the K/T boundary and covered 1-2 million km2 of west-central India. This eruptive event is of global interest because of its possible link to the major mass extinction event, and there is much debate about the duration of this massive volcanic event. In contrast to isotopic or paleomagnetic dating methods, I explore an alternative approach to determine the lifecycle of the magma chambers that supplied the lavas, and extend the concept to obtain a tighter constraint on Deccan’s duration. My method relies on extracting time information from elemental and isotopic diffusion across zone boundaries in individual crystals. I determined elemental and Sr-isotopic variations across abnormally large (2-5 cm) plagioclase crystals from the Thalghat and Kashele “Giant Plagioclase Basalts” from the lowermost Jawhar and Igatpuri Formations respectively in the thickest Western Ghats section near Mumbai. I also obtained bulk rock major, trace and rare earth element chemistry of each lava flow from the two formations. Thalghat flows contain only 12% zoned crystals, with 87 Sr/86Sr ratios of 0.7096 in the core and 0.7106 in the rim, separated by a sharp boundary. In contrast, all Kashele crystals have a wider range of 87Sr/86Sr values, with multiple zones. Geochemical modeling of the data suggests that the two types of crystals grew in distinct magmatic environments. Modeling intracrystalline diffusive equilibration between the core and rim of Thalghat crystals led me to obtain a crystal growth rate of 2.03x10-10 cm/s and a residence time of 780 years for the crystals in the magma chamber(s). Employing some assumptions based on field and geochronologic evidence, I extrapolated this residence time to the entire Western Ghats and obtained an estimate of 25,000–35,000 years for the duration of Western Ghats volcanism. This gave an eruptive rate of 30–40 km3/yr, which is much higher than any presently erupting volcano. This result will remain speculative until a similarly detailed analytical-modeling study is performed for the rest of the Western Ghats formations.

The Experience of Dis-placed Communities: Mis-placed Educational Opportunities

Newfoundland and Labrador (NL) has a long history of out-migration and internal migration between communities in coastal areas within the province. Resettlement programs initiated by the NL government between 1954 and 1975 accounted for the internal migration of approximately 30,000 people from 300 communities. Modern-day encounters with these abandoned communities are relevant to understanding the loss of place and home, as significant numbers of students in NL today are affected by migration. This dissertation is a phenomenological study of the experiences of educators as they explored the remnants of an abandoned community. The participants of the study were six experienced public school educators with teaching experience at the primary, elementary, intermediate, and secondary levels. The study took place in eight abandoned communities located on the western shore of Placentia Bay, where mainly the remnants of Isle Valen, St. Leonard’s, St. Kyran’s, and Great Paradise were explored. Data collection consisted of two personal interviews and one group hermeneutic circle, with the aim to answer one fundamental question: What is the experience of educators exploring the remnants of an abandoned community? Data in this study are represented by lived experience descriptions, which were interpreted hermeneutically and guided by four phenomenological existentials: temporality, corporeality, spatiality, and relationality. The most prominent themes emerging from the educators’ anecdotes were determined to be attunement, tension, and intensity. The results of this study not only provide deeper insight into communities abandoned through resettlement; they also reveal the significance of place in our lives, place as heuristic teacher, the pedagogical power of place, the need for local, meaningful place-based experiences in a curriculum as lived, and their potential for furthering personal and educational insight no matter where in this world we live or dwell.

Follow-up of the sponge and asteroid populations at the station Larsen A south (PS69/724-1 and PS77/253-1), Antarctic Peninsula, between 2007 and 2011

Over 30% of the Antarctic continental shelf is permanently covered by floating ice shelves, providing aphotic conditions for a depauperate fauna sustained by laterally advected food. In much of the remaining Antarctic shallows (<300 m depth), seasonal sea-ice melting allows a patchy primary production supporting rich megabenthic communities dominated by glass sponges (Porifera, Hexactinellida). The catastrophic collapse of ice shelves due to rapid regional warming along the Antarctic Peninsula in recent decades has exposed over 23,000 km**2 of seafloor to local primary production. The response of the benthos to this unprecedented flux of food is, however, still unknown. In 2007, 12 years after disintegration of the Larsen A ice shelf, a first biological survey interpreted the presence of hexactinellids as remnants of a former under-ice fauna with deep-sea characteristics. Four years later, we revisited the original transect, finding 2- and 3-fold increases in glass sponge biomass and abundance, respectively, after only two favorable growth periods. Our findings, along with other long-term studies, suggest that Antarctic hexactinellids, locked in arrested growth for decades, may undergo boom-and-bust cycles, allowing them to quickly colonize new habitats. The cues triggering growth and reproduction in Antarctic glass sponges remain enigmatic.

(Table 1) Age determination of composite sediment record LO09-14

A sediment core from Reykjanes Ridge has been studied at 10- to 50-year time resolution to document variability of Holocene surface water conditions in the western North Atlantic and to evaluate effects of Holocene ice-rafting episodes. Diatom assemblages are converted to quantitative sea surface temperatures (SST) using three different transfer functions. Spectral and scale-space methods are also applied on the records to explore variability at different timescales. Diatom assemblage and SST records clearly show that decaying remnants of the Laurentide ice sheet strongly influenced early Holocene climate in the western North Atlantic. This overrode the predominance of Milankovitch forcing, which played a key role in the development of Holocene climate in the eastern North Atlantic and Nordic Seas. Superimposed on general Holocene climate change is high-frequency SST variability on the order of 1°-3°C. The record also documents climatic oscillations with 600- to 1000-, ~1500-, and 2500-year periodicities, with a time-dependent dominance of different periodicities through the Holocene; a clear change in variability occurred about 5 ka BP. The SST record also provides evidence for Holocene cooling events (HCE) that, in some cases, correlate to documented southward intrusions of ice into the North Atlantic.

Characterization of the Galactic White Dwarf Population in the Next Generation Virgo Cluster Survey

Halo white dwarfs remain one of the least studied stellar populations in the Milky Way because of their faint luminosities. Recent work has uncovered a population of hot white dwarfs which are thought to be remnants of low-mass Population II stars. This thesis uses optical data from the Next Generation Virgo Cluster Survey (NGVS) and ultravoilet data from the GALEX Ultraviolet Virgo Cluster Survey (GUViCS) to select candidates which may belong to this population of recently formed halo white dwarfs. A colour selection was used to separate white dwarfs from QSOs and main-sequence stars. Photometric distances are calculated using model colour-absolute magnitude relations. Proper motions are calculated by using the difference in positions between objects from the Sloan Digital Sky Survey and the NGVS. The proper motions are combined with the calculated photometric distances to calculate tangential velocities, as well as approximate Galactic space velocities. White dwarf candidates are characterized as belonging to either the disk or the halo using a variety of methods, including calculated scale heights (z> 1 kpc), tangential velocities (vt >200 km/s), and their location in (V,U) space. The 20 halo white dwarf candidates which were selected using Galactic space velocities are analyzed, and their colours and temperatures suggest that these objects represent some of the youngest white dwarfs in the Galactic halo.

Juniperus navicularis - a study of Portuguese population structure and fitness

Juniperus navicularis Gand. is a dioecious endemic conifer that constitutes the understory of seaside pine forests in Portugal, areas currently threatened by increasing urban expansion. The aim of this study is to assess the conservation status of previously known populations of this species located on its core area of distribution. The study was performed in south-west coast of Portugal. Three populations varying in size and pine density were analyzed. Number of individuals, population density, spatial distribution and individual characteristics of junipers were estimated. Female cone, seed characteristics and seed viability were also evaluated. Results suggest that J. navicularis populations are vulnerable because seminal recruitment is scarce, what may lead to a reduction of genetic variability due solely to vegetative propagation. This vulnerability seems to be strongly determined by climatic constraints toward increasing aridity. Ratio between male and female shrubs did not differ from 1:1 in any population. Deviations from 1:1 between mature and non-mature plants were found in all populations, denoting population ageing. Very low seed viability was observed. A major part of described Juniperus navicularis populations have disappeared through direct habitat loss to urban development, loss of fitness in drier and warmer locations and low seed viability. This study is the first to address J. navicularis conservation, and represents a valuable first step toward this species preservation. 

An assessment of data leakage in Firefox under different conditions.

Data leakage is a serious issue and can result in the loss of sensitive data, compromising user accounts and details, potentially affecting millions of internet users. This paper contributes to research in online security and reducing personal footprint by evaluating the levels of privacy provided by the Firefox browser. The aim of identifying conditions that would minimize data leakage and maximize data privacy is addressed by assessing and comparing data leakage in the four possible browsing modes: normal and private modes using a browser installed on the host PC or using a portable browser from a connected USB device respectively. To provide a firm foundation for analysis, a series of carefully designed, pre-planned browsing sessions were repeated in each of the various modes of Firefox. This included low RAM environments to determine any effects low RAM may have on browser data leakage. The results show that considerable data leakage may occur within Firefox. In normal mode, all of the browsing information is stored within the Mozilla profile folder in Firefox-specific SQLite databases and sessionstore.js. While passwords were not stored as plain text, other confidential information such as credit card numbers could be recovered from the Form history under certain conditions. There is no difference when using a portable browser in normal mode, except that the Mozilla profile folder is located on the USB device rather than the host's hard disk. By comparison, private browsing reduces data leakage. Our findings confirm that no information is written to the Firefox-related locations on the hard disk or USB device during private browsing, implying that no deletion would be necessary and no remnants of data would be forensically recoverable from unallocated space. However, two aspects of data leakage occurred equally in all four browsing modes. Firstly, all of the browsing history was stored in the live RAM and was therefore accessible while the browser remained open. Secondly, in low RAM situations, the operating system caches out RAM to pagefile.sys on the host's hard disk. Irrespective of the browsing mode used, this may include Firefox history elements which can then remain forensically recoverable for considerable time.

Life Cycle of Deccan Trap Magma Chambers: A Crystal Scale Elemental and Strontium Isotopic Investigation

The Deccan Trap basalts are the remnants of a massive series of lava flows that erupted at the K/T boundary and covered 1-2 million km2 of west-central India. This eruptive event is of global interest because of its possible link to the major mass extinction event, and there is much debate about the duration of this massive volcanic event. In contrast to isotopic or paleomagnetic dating methods, I explore an alternative approach to determine the lifecycle of the magma chambers that supplied the lavas, and extend the concept to obtain a tighter constraint on Deccan’s duration. My method relies on extracting time information from elemental and isotopic diffusion across zone boundary in an individual crystal. I determined elemental and Sr-isotopic variations across abnormally large (2-5 cm) plagioclase crystals from the Thalghat and Kashele “Giant Plagioclase Basalts” from the lowermost Jawhar and Igatpuri Formations respectively in the thickest Western Ghats section near Mumbai. I also obtained bulk rock major, trace and rare earth element chemistry of each lava flow from the two formations. Thalghat flows contain only 12% zoned crystals, with 87Sr/86Sr ratios of 0.7096 in the core and 0.7106 in the rim, separated by a sharp boundary. In contrast, all Kashele crystals have a wider range of 87Sr/86Sr values, with multiple zones. Geochemical modeling of the data suggests that the two types of crystals grew in distinct magmatic environments. Modeling intracrystalline diffusive equilibration between the core and rim of Thalghat crystals led me to obtain a crystal growth rate of 2.03x10-10 cm/s and a residence time of 780 years for the crystals in the magma chamber(s). Employing some assumptions based on field and geochronologic evidence, I extrapolated this residence time to the entire Western Ghats and obtained an estimate of 25,000 – 35,000 years for the duration of Western Ghats volcanism. This gave an eruptive rate of 30 – 40 km3/yr, which is much higher than any presently erupting volcano. This result will remain speculative until a similarly detailed analytical-modeling study is performed for the rest of the Western Ghats formations.

African Indigeneity

The current argument is that there exist no indigenous people in Africa because all Africans are indigenous. The obverse considers those Africans who have not been touched by colonialism and lost their traditional cultures commensurate with attachments to the lands or a distinguishable traditional lifestyle to be indigenous. This paper argues in favor of the latter. For example, modernism, materialism, ex-colonial socio-cultural impacts (as in the remnants of European legal structures, and cultural scarring), globalization, and technology are international social homogenizers. People who live in this telos and do not participate in a distinct traditional culture that has been attached to the land for centuries are not indigenous. It is argued that this cultural divergence between modern and traditional is the major identifying point to settle the indigenous-non indigenous African debate. Finally, the paper looks at inclusive development, how this helps to distinguish African indigeneity, and provides a new political analysis model for quantifying inclusivity.

Instability prolongs the chondral phase during bone healing in sheep

In this sheep study, we investigated the influence of fixation stability on the temporal and spatial distribution of tissues in the fracture callus. As the initial mechanical conditions have been cited as being especially important for the healing outcome, it was hypothesized that differences in the path of healing would be seen as early as the initial phase of healing. ----- ----- Sixty-four sheep underwent a mid-shaft tibial osteotomy that was treated with either a rigid or a semi-rigid external fixator. Animals were sacrificed at 2, 3, 6 and 9 weeks postoperatively and the fracture calluses were analyzed using radiological, biomechanical and histological techniques. Statistical comparison between the groups was performed using the Mann–Whitney U test for unpaired non-parametric data. ----- ----- In the callus of the tibia treated with semi-rigid fixation, remnants of the fracture haematoma remained present for longer, although new periosteal bone formation during early healing was similar in both groups. The mechanical competence of the healing callus at 6 weeks was inferior compared to tibiae treated with rigid fixation. Semi-rigid fixation resulted in a larger cartilage component of the callus, which persisted longer. Remodeling processes were initiated earlier in the rigid group, while new bone formation continued throughout the entire investigated period in the semi-rigid group. ----- ----- In this study, evidence is provided that less rigid fixation increased the time required for healing. The process of intramembranous ossification appeared during the initial stages of healing to be independent of mechanical stability. However, the delay in healing was related to a prolonged chondral phase.

Linking ecological condition and the soundscape in fragmented Australian forests

Natural landscapes are increasingly subjected to anthropogenic pressure and fragmentation resulting in reduced ecological condition. In this study we examined the relationship between ecological condition and the soundscape in fragmented forest remnants of south-east Queensland, Australia. The region is noted for its high biodiversity value and increased pressure associated with habitat fragmentation and urbanisation. Ten sites defined by a distinct open eucalypt forest community dominated by spotted gum (Corymbia citriodora ssp. variegata) were stratified based on patch size and patch connectivity. Each site underwent a series of detailed vegetation condition and landscape assessments, together with bird surveys and acoustic analysis using relative soundscape power. Univariate and multivariate analyses indicated that the measurement of relative soundscape power reflects ecological condition and bird species richness, and is dependent on the extent of landscape fragmentation. We conclude that acoustic monitoring technologies provide a cost effective tool for measuring ecological condition, especially in conjunction with established field observations and recordings.

Making scenes : Reggae, punk, and death metal in 1990s Bali

In 1996, Emma Baulch went to live in Bali to do research on youth culture. Her chats with young people led her to an enormously popular regular outdoor show dominated by local reggae, punk, and death metal bands. In this rich ethnography, she takes readers inside each scene: hanging out in the death metal scene among unemployed university graduates clad in black T-shirts and ragged jeans; in the punk scene among young men sporting mohawks, leather jackets, and hefty jackboots; and among the remnants of the local reggae scene in Kuta Beach, the island’s most renowned tourist area. Baulch tracks how each music scene arrived and grew in Bali, looking at such influences as the global extreme metal underground, MTV Asia, and the internationalization of Indonesia’s music industry. Making Scenes is an exploration of the subtle politics of identity that took place within and among these scenes throughout the course of the 1990s. Participants in the different scenes often explained their interest in death metal, punk, or reggae in relation to broader ideas about what it meant to be Balinese, which reflected views about Bali’s tourism industry and the cultural dominance of Jakarta, Indonesia’s capital and largest city. Through dance, dress, claims to public spaces, and onstage performances, participants and enthusiasts reworked “Balinese-ness” by synthesizing global media, ideas of national belonging, and local identity politics. Making Scenes chronicles the creation of subcultures at a historical moment when media globalization and the gradual demise of the authoritarian Suharto regime coincided with revitalized, essentialist formulations of the Balinese self.