Deletion mapping suggests that the 1p22 melanoma susceptibility gene is a tumor suppressor localized to a 9-Mb interval

Loss of the short arm of chromosome 1 is frequently observed in many tumor types, including melanoma. We recently localized a third melanoma susceptibility locus to chromosome band 1p22. Critical recombinants in linked families localized the gene to a 15-Mb region between D1S430 and D1S2664. To map the locus more finely we have performed studies to assess allelic loss across the region in a panel of melanomas from 1p22-linked families, sporadic melanomas, and melanoma cell lines. Eighty percent of familial melanomas exhibited loss of heterozygosity (LOH) within the region, with a smallest region of overlapping deletions (SRO) of 9 Mb between D1S207 and D1S435. This high frequency of LOH makes it very likely that the susceptibility locus is a tumor suppressor. In sporadic tumors, four SROs were defined. SRO1 and SRO2 map within the critical recombinant and familial tumor region, indicating that one or the other is likely to harbor the susceptibility gene. However, SRO3 may also be significant because it overlaps with the markers with the highest 2-point LOD score (D1S2776), part of the linkage recombinant region, and the critical region defined in mesothelioma. The candidate genes PRKCL2 and GTF2B, within SRO2, and TGFBR3, CDC7, and EVI5, in a broad region encompassing SRO3, were screened in 1p22-linked melanoma kindreds, but no coding mutations were detected. Allelic loss in melanoma cell lines was significantly less frequent than in fresh tumors, indicating that this gene may not be involved late in progression, such as in overriding cellular senescence, necessary for the propagation of melanoma cells in culture.

Pedagogy of introductory computer programming : a people-first approach

Students struggle with learning to program. In recent years, not only has there been a dramatic drop in the number of students enrolling in IT and Computer Science courses, but attrition from these courses continues to be significant. Introductory programming subjects traditionally have high failure rates and as they tend to be core to IT and Computer Science courses can be a road block for many students to their university studies. Is programming really that difficult — or are there other barriers to learning that have a serious and detrimental effect on student progression? In-class experiments were conducted in introductory programming units to confirm our hypothesis that that pair-programming would benefit students' learning to program. We investigated the social and cultural barriers to learning programming by questioning students' perceptions of confidence, difficulty and enjoyment of programming. The results of paired and non-paired students were compared to determine the effect of pair-programming on learning outcomes. Both the empirical and anecdotal results of our experiments strongly supported our hypothesis.

Formation mechanisms of secondary organic aerosols in relation to laser printer emissions

Due to their large surface area, complex chemical composition and high alveolar deposition rate, ultrafine particles (UFPs) (< 0.1 ìm) pose a significant risk to human health and their toxicological effects have been acknowledged by the World Health Organisation. Since people spend most of their time indoors, there is a growing concern about the UFPs present in some indoor environments. Recent studies have shown that office machines, in particular laser printers, are a significant indoor source of UFPs. The majority of printer-generated UFPs are organic carbon and it is unlikely that these particles are emitted directly from the printer or its supplies (such as paper and toner powder). Thus, it was hypothesised that these UFPs are secondary organic aerosols (SOA). Considering the widespread use of printers and human exposure to these particles, understanding the processes involved in particle formation is of critical importance. However, few studies have investigated the nature (e.g. volatility, hygroscopicity, composition, size distribution and mixing state) and formation mechanisms of these particles. In order to address this gap in scientific knowledge, a comprehensive study including state-of-art instrumental methods was conducted to characterise the real-time emissions from modern commercial laser printers, including particles, volatile organic compounds (VOCs) and ozone (O3). The morphology, elemental composition, volatility and hygroscopicity of generated particles were also examined. The large set of experimental results was analysed and interpreted to provide insight into: (1) Emissions profiles of laser printers: The results showed that UFPs dominated the number concentrations of generated particles, with a quasi unimodal size distribution observed for all tests. These particles were volatile, non-hygroscopic and mixed both externally and internally. Particle microanalysis indicated that semi-volatile organic compounds occupied the dominant fraction of these particles, with only trace quantities of particles containing Ca and Fe. Furthermore, almost all laser printers tested in this study emitted measurable concentrations of VOCs and O3. A positive correlation between submicron particles and O3 concentrations, as well as a contrasting negative correlation between submicron particles and total VOC concentrations were observed during printing for all tests. These results proved that UFPs generated from laser printers are mainly SOAs. (2) Sources and precursors of generated particles: In order to identify the possible particle sources, particle formation potentials of both the printer components (e.g. fuser roller and lubricant oil) and supplies (e.g. paper and toner powder) were investigated using furnace tests. The VOCs emitted during the experiments were sampled and identified to provide information about particle precursors. The results suggested that all of the tested materials had the potential to generate particles upon heating. Nine unsaturated VOCs were identified from the emissions produced by paper and toner, which may contribute to the formation of UFPs through oxidation reactions with ozone. (3) Factors influencing the particle emission: The factors influencing particle emissions were also investigated by comparing two popular laser printers, one showing particle emissions three orders of magnitude higher than the other. The effects of toner coverage, printing history, type of paper and toner, and working temperature of the fuser roller on particle number emissions were examined. The results showed that the temperature of the fuser roller was a key factor driving the emission of particles. Based on the results for 30 different types of laser printers, a systematic positive correlation was observed between temperature and particle number emissions for printers that used the same heating technology and had a similar structure and fuser material. It was also found that temperature fluctuations were associated with intense bursts of particles and therefore, they may have impact on the particle emissions. Furthermore, the results indicated that the type of paper and toner powder contributed to particle emissions, while no apparent relationship was observed between toner coverage and levels of submicron particles. (4) Mechanisms of SOA formation, growth and ageing: The overall hypothesis that UFPs are formed by reactions with the VOCs and O3 emitted from laser printers was examined. The results proved this hypothesis and suggested that O3 may also play a role in particle ageing. In addition, knowledge about the mixing state of generated particles was utilised to explore the detailed processes of particle formation for different printing scenarios, including warm-up, normal printing, and printing without toner. The results indicated that polymerisation may have occurred on the surface of the generated particles to produce thermoplastic polymers, which may account for the expandable characteristics of some particles. Furthermore, toner and other particle residues on the idling belt from previous print jobs were a very clear contributing factor in the formation of laser printer-emitted particles. In summary, this study not only improves scientific understanding of the nature of printer-generated particles, but also provides significant insight into the formation and ageing mechanisms of SOAs in the indoor environment. The outcomes will also be beneficial to governments, industry and individuals.

Lingodroids : studies in spatial cognition and language

The Lingodroids are a pair of mobile robots that evolve a language for places and relationships between places (based on distance and direction). Each robot in these studies has its own understanding of the layout of the world, based on its unique experiences and exploration of the environment. Despite having different internal representations of the world, the robots are able to develop a common lexicon for places, and then use simple sentences to explain and understand relationships between places even places that they could not physically experience, such as areas behind closed doors. By learning the language, the robots are able to develop representations for places that are inaccessible to them, and later, when the doors are opened, use those representations to perform goal-directed behavior.

Six degrees of cohesion in patent citation network

While the phrase “six degrees of separation” is widely used to characterize a variety of humanderived networks, in this study we show that in patent citation network, related patents are connected with an average distance of 6, whereas an average distance for a random pair of nodes in the graph is approximately 15. We use this information to improve the recall level in prior-art retrieval in the setting of blind relevance feedback without any textual knowledge.

A novel duplication polymorphism in the FANCA promoter and its association with breast and ovarian cancer

The FANCA gene is one of the genes in which mutations lead to Fanconi anaemia, a rare autosomal recessive disorder characterised by congenital abnormalities, bone marrow failure, and predisposition to malignancy. FANCA is also a potential breast and ovarian cancer susceptibility gene. A novel allele was identified which has a tandem duplication of a 13 base pair sequence in the promoter region. Methods: We screened germline DNA from 352 breast cancer patients, 390 ovarian cancer patients and 256 normal controls to determine if the presence of either of these two alleles was associated with an increased risk of breast or ovarian cancer. Results: The duplication allele had a frequency of 0.34 in the normal controls. There was a nonsignificant decrease in the frequency of the duplication allele in breast cancer patients. The frequency of the duplication allele was significantly decreased in ovarian cancer patients. However, when malignant and benign tumours were considered separately, the decrease was only significant in benign tumours. Conclusion: The allele with the tandem duplication does not appear to modify breast cancer risk but may act as a low penetrance protective allele for ovarian cancer.

Reduced variance in monozygous twins for multiple MR parameters : implications for disease studies and the genetic basis of brain structure

Twin studies offer the opportunity to determine the relative contribution of genes versus environment in traits of interest. Here, we investigate the extent to which variance in brain structure is reduced in monozygous twins with identical genetic make-up. We investigate whether using twins as compared to a control population reduces variability in a number of common magnetic resonance (MR) structural measures, and we investigate the location of areas under major genetic influences. This is fundamental to understanding the benefit of using twins in studies where structure is the phenotype of interest. Twenty-three pairs of healthy MZ twins were compared to matched control pairs. Volume, T2 and diffusion MR imaging were performed as well as spectroscopy (MRS). Images were compared using (i) global measures of standard deviation and effect size, (ii) voxel-based analysis of similarity and (iii) intra-pair correlation. Global measures indicated a consistent increase in structural similarity in twins. The voxel-based and correlation analyses indicated a widespread pattern of increased similarity in twin pairs, particularly in frontal and temporal regions. The areas of increased similarity were most widespread for the diffusion trace and least widespread for T2. MRS showed consistent reduction in metabolite variation that was significant in the temporal lobe N-acetylaspartate (NAA). This study has shown the distribution and magnitude of reduced variability in brain volume, diffusion, T2 and metabolites in twins. The data suggest that evaluation of twins discordant for disease is indeed a valid way to attribute genetic or environmental influences to observed abnormalities in patients since evidence is provided for the underlying assumption of decreased variability in twins.

Probabilistic matching of image sets for video-based face recognition

We address the problem of face recognition on video by employing the recently proposed probabilistic linear discrimi-nant analysis (PLDA). The PLDA has been shown to be robust against pose and expression in image-based face recognition. In this research, the method is extended and applied to video where image set to image set matching is performed. We investigate two approaches of computing similarities between image sets using the PLDA: the closest pair approach and the holistic sets approach. To better model face appearances in video, we also propose the heteroscedastic version of the PLDA which learns the within-class covariance of each individual separately. Our experi-ments on the VidTIMIT and Honda datasets show that the combination of the heteroscedastic PLDA and the closest pair approach achieves the best performance.

Dual-band Decoupling and Matching Network Design for very Closely Spaced Antennas

A practical method for the design of dual-band decoupling and matching networks (DMN) for two closely spaced antennas using discrete components is presented. The DMN reduces the port-to-port coupling and enhances the diversity of the antennas. By applying the DMN, the radiation efficiency can also be improved when one port is fed and the other port is match terminated. The proposed DMN works at two frequencies simultaneously without the need for any switch. As a proof of concept, a dual-band DMN for a pair of monopoles spaced 0.05λ apart is designed. The measured return loss and port isolation exceed 10 dB from 1.71 GHz to 1.76 GHz and from 2.27 GHz to 2.32 GHz.

PLDA based speaker verification with weighted LDA techniques

This paper investigates the use of the dimensionality-reduction techniques weighted linear discriminant analysis (WLDA), and weighted median fisher discriminant analysis (WMFD), before probabilistic linear discriminant analysis (PLDA) modeling for the purpose of improving speaker verification performance in the presence of high inter-session variability. Recently it was shown that WLDA techniques can provide improvement over traditional linear discriminant analysis (LDA) for channel compensation in i-vector based speaker verification systems. We show in this paper that the speaker discriminative information that is available in the distance between pair of speakers clustered in the development i-vector space can also be exploited in heavy-tailed PLDA modeling by using the weighted discriminant approaches prior to PLDA modeling. Based upon the results presented within this paper using the NIST 2008 Speaker Recognition Evaluation dataset, we believe that WLDA and WMFD projections before PLDA modeling can provide an improved approach when compared to uncompensated PLDA modeling for i-vector based speaker verification systems.

Analysis of involved parties in port water conflicts

With increasing rate of shipping traffic, the risk of collisions in busy and congested port waters is expected to rise. However, due to low collision frequencies it is difficult to analyze such risk in a sound statistical manner. This study aims at examining the occurrence of traffic conflicts in order to understand the characteristics of vessels involved in navigational hazards. A binomial logit model was employed to evaluate the association of vessel attributes and the kinematic conditions with conflict severity levels. Results show a positive association for vessels of small gross tonnage, overall vessel length, vessel height and draft with conflict risk. Conflicts involving a pair of dynamic vessels sailing at low speeds also have similar effects.

Evaluation of fibroin-based scaffolds for ocular tissue reconstruction

The epithelium of the corneolimbus contains stem cells for regenerating the corneal epithelium. Diseases and injuries affecting the limbus can lead to a condition known as limbal stem cell deficiency (LSCD), which results in loss of the corneal epithelium, and subsequent chronic inflammation and scarring of the ocular surface. Advances in the treatment of LSCD have been achieved through use of cultured human limbal epithelial (HLE) grafts to restore epithelial stem cells of the ocular surface. These epithelial grafts are usually produced by the ex vivo expansion of HLE cells on human donor amniotic membrane (AM), but this is not without limitations. Although AM is the most widely accepted substratum for HLE transplantation, donor variation, risk of disease transfer, and rising costs have led to the search for alternative biomaterials to improve the surgical outcome of LSCD. Recent studies have demonstrated that Bombyx mori silk fibroin (hereafter referred to as fibroin) membranes support the growth of primary HLE cells, and thus this thesis aims to explore the possibility of using fibroin as a biomaterial for ocular surface reconstruction. Optimistically, the grafted sheets of cultured epithelium would provide a replenishing source of epithelial progenitor cells for maintaining the corneal epithelium, however, the HLE cells lose their progenitor cell characteristics once removed from their niche. More severe ocular surface injuries, which result in stromal scarring, damage the epithelial stem cell niche, which subsequently leads to poor corneal re-epithelialisation post-grafting. An ideal solution to repairing the corneal limbus would therefore be to grow and transplant HLE cells on a biomaterial that also provides a means for replacing underlying stromal cells required to better simulate the normal stem cell niche. The recent discovery of limbal mesenchymal stromal cells (L-MSC) provides a possibility for stromal repair and regeneration, and therefore, this thesis presents the use of fibroin as a possible biomaterial to support a three dimensional tissue engineered corneolimbus with both an HLE and underlying L-MSC layer. Investigation into optimal scaffold design is necessary, including adequate separation of epithelial and stromal layers, as well as direct cell-cell contact. Firstly, the attachment, morphology and phenotype of HLE cells grown on fibroin were directly compared to that observed on donor AM, the current clinical standard substrate for HLE transplantation. The production, transparency, and permeability of fibroin membranes were also evaluated in this part of the study. Results revealed that fibroin membranes could be routinely produced using a custom-made film casting table and were found to be transparent and permeable. Attachment of HLE cells to fibroin after 4 hours in serum-free medium was similar to that supported by tissue culture plastic but approximately 6-fold less than that observed on AM. While HLE cultured on AM displayed superior stratification, epithelia constructed from HLE on fibroin maintained evidence of corneal phenotype (cytokeratin pair 3/12 expression; CK3/12) and displayed a comparable number and distribution of ÄNp63+ progenitor cells to that seen in cultures grown on AM. These results confirm the suitability of membranes constructed from silk fibroin as a possible substrate for HLE cultivation. One of the most important aspects in corneolimbal tissue engineering is to consider the reconstruction of the limbal stem cell niche to help form the natural limbus in situ. MSC with similar properties to bone marrow derived-MSC (BM-MSC) have recently been grown from the limbus of the human cornea. This thesis evaluated methods for culturing L-MSC and limbal keratocytes using various serum-free media. The phenotype of resulting cultures was examined using photography, flow cytometry for CD34 (keratocyte marker), CD45 (bone marrow-derived cell marker), CD73, CD90, CD105 (collectively MSC markers), CD141 (epithelial/vascular endothelial marker), and CD271 (neuronal marker), immunocytochemistry (alpha-smooth muscle actin; á-sma), differentiation assays (osteogenesis, adipogenesis and chrondrogenesis), and co-culture experiments with HLE cells. While all techniques supported to varying degrees establishment of keratocyte and L-MSC cultures, sustained growth and serial propagation was only achieved in serum-supplemented medium or the MesenCult-XF„¥ culture system (Stem Cell Technologies). Cultures established in MesenCult-XF„¥ grew faster than those grown in serum-supplemented medium and retained a more optimal MSC phenotype. L-MSC cultivated in MesenCult-XFR were also positive for CD141, rarely expressed £\-sma, and displayed multi-potency. L-MSC supported growth of HLE cells, with the largest epithelial islands being observed in the presence of L-MSC established in MesenCult-XF„¥ medium. All HLE cultures supported by L-MSC widely expressed the progenitor cell marker £GNp63, along with the corneal differentiation marker CK3/12. Our findings conclude that MesenCult-XFR is a superior culture system for L-MSC, but further studies are required to explore the significance of CD141 expression in these cells. Following on from the findings of the previous two parts, silk fibroin was tested as a novel dual-layer construct containing both an epithelium and underlying stroma for corneolimbal reconstruction. In this section, the growth and phenotype of HLE cells on non-porous versus porous fibroin membranes was compared. Furthermore, the growth of L-MSC in either serum-supplemented medium or the MesenCult-XFR culture system within fibroin fibrous mats was investigated. Lastly, the co-culture of HLE and L-MSC in serum-supplemented medium on and within fibroin dual-layer constructs was also examined. HLE on porous membranes displayed a flattened and squamous monolayer; in contrast, HLE on non-porous fibroin appeared cuboidal and stratified closer in appearance to a normal corneal epithelium. Both constructs maintained CK3/12 expression and distribution of £GNp63+ progenitor cells. Dual-layer fibroin scaffolds consisting of HLE cells and L-MSC maintained a similar phenotype as on the single layers alone. Overall, the present study proposed to create a three dimensional limbal tissue substitute of HLE cells and L-MSC together, ultimately for safe and beneficial transplantation back into the human eye. The results show that HLE and L-MSC can be cultivated separately and together whilst maintaining a clinically feasible phenotype containing a majority of progenitor cells. In addition, L-MSC were able to be cultivated routinely in the MesenCult-XF® culture system while maintaining a high purity for the MSC characteristic phenotype. However, as a serum-free culture medium was not found to sustain growth of both HLE and L-MSC, the combination scaffold was created in serum-supplemented medium, indicating that further refinement of this cultured limbal scaffold is required. This thesis has also demonstrated a potential novel marker for L-MSC, and has generated knowledge which may impact on the understanding of stromal-epithelial interactions. These results support the feasibility of a dual-layer tissue engineered corneolimbus constructed from silk fibroin, and warrant further studies into the potential benefits it offers to corneolimbal tissue regeneration. Further refinement of this technology should explore the potential benefits of using epithelial-stromal co-cultures with MesenCult-XF® derived L-MSC. Subsequent investigations into the effects of long-term culture on the phenotype and behaviour of the cells in the dual-layer scaffolds are also required. While this project demonstrated the feasibility in vitro for the production of a dual-layer tissue engineered corneolimbus, further studies are required to test the efficacy of the limbal scaffold in vivo. Future in vivo studies are essential to fully understand the integration and degradation of silk fibroin biomaterials in the cornea over time. Subsequent experiments should also investigate the use of both AM and silk fibroin with epithelial and stromal cell co-cultures in an animal model of LSCD. The outcomes of this project have provided a foundation for research into corneolimbal reconstruction using biomaterials and offer a stepping stone for future studies into corneolimbal tissue engineering.

Alkyl radical geometry controls geminate cage recombination in alkylcobalamins

Abstract: The radical pair that results from photolysis of adenosylcob(II1)alamin (AdoCbl"') undergoes primary geminate recombination with a first-order rate constant of 1 x lo9 s-l. In contrast, methylcob(II1)alamin (CH3Cbl"') and aristeromicylcob(II1)alamin (AriCblII', the carbocyclic analogue of AdoCbl"' in which the ribofuranose ring oxygen has been replaced with a methylene group) does not undergo primary geminate recombination. The ribofwanose group enables a high rate of geminate recombination in the [Ado' Cbl"'] radical pair. This may be due to a stereoelectronic (p-anomeric) effect that maintains a pyramidal geometry at the 5'-carbon of the 5'-deoxyadenosyl radical, or it may be due to hindered rotation about the C4t-C5, bond such that /?-elimination to the olefin is prevented. Recombination in the geminate singlet radical pair is in competition with diffusive escape to form a solvent-separated radical pair. Hyperfine coupling from Co" promotes intersystem crossing to the triplet radical pair (Chagovetz, A. M.; Grissom, C. B. J. Am. Chem. SOC. 1993, 115, 12152). Recombination of the [CH3' Cbl"] radical pair is not prevented by a lack of intersystem crossing, as neither unlabeled or I3C-labeled CH3Cbl"' undergoes geminate recombination. There is only a small difference in the rate of diffusive recombination in the solvent cage for AdoCbl"', AriCbl"', and CH3Cbl"' following photolysis: 2.01 x 10" s-l, 2.20 x lo4 s-l, and 1.16 x lo4 s-l. The rate of diffusive recombination is limited by productive collisions and not by radical geometry or intersystem crossing. The CF3' radical that results from photolysis of (trifluoromethyl)cob(III)alamin (CF3Cbl"') maintains its pyramidal geometry and undergoes faster diffusive recombination in the solvent cage at 51 x lo4 s-l. The C-Co bond dissociation enthalpy in AriCbl"' is 37 f 1.4 kcaymol. The profound difference in geminate recombination rates for AdoCbl"' and CH3Cbl"' is consistent with their different biological roles as enzymatic cofactors: AdoCbl"' is an initiator of radical chain chemistry in the active site, whereas CH3Cbl"' is a methyl group donor in an S~2-type process.

Piecing together an integrative taxonomic puzzle: microsatellite, wing shape and aedeagus length analyses of Bactrocera dorsalis s.l. (Diptera: Tephritidae) find no evidence of multiple lineages in a proposed contact zone along the Thai/Malay Peninsula

Bactrocera dorsalis (Hendel) and B. papayae Drew & Hancock represent a closely related sibling species pair for which the biological species limits are unclear; i.e., it is uncertain if they are truely two biological species, or one biological species which has been incorrectly taxonomically split. The geographic ranges of the two taxa are thought to abut or overlap on or around the Isthmus of Kra, a recognised biogeographic barrier located on the narrowest portion of the Thai Peninsula. We collected fresh material of B. dorsalis sensu lato (i.e., B. dorsalis sensu stricto + B. papayae) in a north-south transect down the Thai Peninsula, from areas regarded as being exclusively B. dorsalis s.s., across the Kra Isthmus, and into regions regarded as exclusively B. papayae. We carried out microsatellite analyses and took measurements of male genitalia and wing shape. Both the latter morphological tests have been used previously to separate these two taxa. No significant population structuring was found in the microsatellite analysis and results were consistent with an interpretation of one, predominantly panmictic population. Both morphological datasets showed consistent, clinal variation along the transect, with no evidence for disjunction. No evidence in any tests supported historical vicariance driven by the Isthmus of Kra, and none of the three datasets supported the current taxonomy of two species. Rather, within and across the area of range overlap or abutment between the two species, only continuous morphological and genetic variation was recorded. Recognition that morphological traits previously used to separate these taxa are continuous, and that there is no genetic evidence for population segregation in the region of suspected species overlap, is consistent with a growing body of literature that reports no evidence of biological differentiation between these taxa.

Dual-frequency decoupling for two distinct antennas

Constant development of new wireless standards increases the demand for more radiating elements in compact end-user platforms. A decrease in antenna separation gives rise to increased antenna coupling, resulting in a reduction of the signal-to-interference-plus-noise-ratio (SINR) between transmitter and receiver. This paper proposes a decoupling network which provides dual band port isolation for a pair of distinct antennas. A prototype has been fabricated to verify the theory.