A new method to detect loss of heterozygosity using cohort heterozygosity comparisons

Background Loss of heterozygosity (LOH) is an important marker for one of the 'two-hits' required for tumor suppressor gene inactivation. Traditional methods for mapping LOH regions require the comparison of both tumor and patient-matched normal DNA samples. However, for many archival samples, patient-matched normal DNA is not available leading to the under-utilization of this important resource in LOH studies. Here we describe a new method for LOH analysis that relies on the genome-wide comparison of heterozygosity of single nucleotide polymorphisms (SNPs) between cohorts of cases and un-matched healthy control samples. Regions of LOH are defined by consistent decreases in heterozygosity across a genetic region in the case cohort compared to the control cohort. Methods DNA was collected from 20 Follicular Lymphoma (FL) tumor samples, 20 Diffuse Large B-cell Lymphoma (DLBCL) tumor samples, neoplastic B-cells of 10 B-cell Chronic Lymphocytic Leukemia (B-CLL) patients and Buccal cell samples matched to 4 of these B-CLL patients. The cohort heterozygosity comparison method was developed and validated using LOH derived in a small cohort of B-CLL by traditional comparisons of tumor and normal DNA samples, and compared to the only alternative method for LOH analysis without patient matched controls. LOH candidate regions were then generated for enlarged cohorts of B-CLL, FL and DLBCL samples using our cohort heterozygosity comparison method in order to evaluate potential LOH candidate regions in these non-Hodgkin's lymphoma tumor subtypes. Results Using a small cohort of B-CLL samples with patient-matched normal DNA we have validated the utility of this method and shown that it displays more accuracy and sensitivity in detecting LOH candidate regions compared to the only alternative method, the Hidden Markov Model (HMM) method. Subsequently, using B-CLL, FL and DLBCL tumor samples we have utilised cohort heterozygosity comparisons to localise LOH candidate regions in these subtypes of non-Hodgkin's lymphoma. Detected LOH regions included both previously described regions of LOH as well as novel genomic candidate regions. Conclusions We have proven the efficacy of the use of cohort heterozygosity comparisons for genome-wide mapping of LOH and shown it to be in many ways superior to the HMM method. Additionally, the use of this method to analyse SNP microarray data from 3 common forms of non-Hodgkin's lymphoma yielded interesting tumor suppressor gene candidates, including the ETV3 gene that was highlighted in both B-CLL and FL.

Current rural valuation practice : a survey of NSW valuers and agribusiness managers

Despite the advances that have been made in relation to the valuation of Commercial, Industrial and retail property, there has not been the same progress in relation to the valuation of rural property. Although number of rural property valuations also require the valuer to carry out a full analysis of the economic performance of the farming operations, as well as the long term environmental viability of the farm, this information is rarely used to assess the value of the property, nor is it even used for a secondary valuation method. Over the past 20 years the nature of rural valuation practice has required most rural valuers to undertake studies in both agriculture (farm management) and valuation, especially if carrying out valuation work for financial institutions. The additional farm financial and management information obtained by rural valuers exceeds that level of information required to value commercial, retail and industrial by the capitalisation of net rent/profit valuation method and is very similar to the level of information required for the valuation of commercial and retail property by the Discounted Cash Flow valuation method. On this basis the valuers specialising in rural valuation practice have the necessary skills and information to value rural properties by an income valuation method. Although the direct comparison method of valuation has been sufficient in the past to value rural properties the future use of the method as the main valuation method is limited and valuers need to adopt an income valuation method as at least a secondary valuation method to overcome the problems associated with the use of direct comparison as the only rural property valuation method, especially in view of the impact that farm technical, financial and environmental .management can have on rural property values. This paper will review the results of an extensive survey carried out by rural property valuers and agribusiness managers in NSW, in relation to the impact of farm management on rural property values and rural property valuation practice.

The use of income valuation methods to value rural property

Despite the advances that have been made in relation to the valuation of commercial, industrial and retail property, there has not been the same progress in relation to the valuation of rural property. Although the majority of rural property valuations also require the valuer to carry out a full analysis of the economic performance of the farming operations, this information is rarely used to assess the value of the property, nor is it even used for a secondary valuation method. Over the past 20 years the nature of rural valuation practice has required rural valuers to undertake studies in both agriculture (farm management) and valuation, especially if carrying out valuation work for financial institutions. The additional farm financial information obtained by rural valuers exceeds that level of information required to value commercial, retail and industrial by the capitalisation of net rent/profit valuation method and is very similar to the level of information required for the valuation of commercial and retail property by the Discounted Cash Flow valuation method. On this basis the valuers specialising in rural valuation practice should have the necessary skills and information to value rural properties by an income valuation method. Although the direct comparison method of valuation has been sufficient in the past to value rural properties the future use of the method as the main valuation method is limited and valuers need to adopt an income valuation method as at least a secondary valuation method to overcome the problems associated with the use of direct comparison as the only rural property valuation method. This paper will review the results of an extensive survey carried out by rural property valuers in New South Wales (NSW), Australia, in relation to the impact of farm management on rural property values and rural property income potential.

Students’ perceptions, experiences and beliefs about Facebook in subjects at an Australian university

This paper reports on students’ perceptions, experiences and beliefs about the voluntary use of Facebook in Advertising, Law, Nursing and Creative Industries’ subjects at an Australian University. The researchers conducted in-depth interviews with students and the transcriptions were analysed using the constant comparison method. This resulted in a number of emergent themes, of which six are explored in this paper. The findings suggest that students are quite divergent in their responses to academics using Facebook in their subjects. They do not always see its relevance to the subject and are somewhat ambivalent about how it facilitates peer-to-peer relationships or a better relationship with the lecturer. The study also identifies themes relating to cynicism and intrusion into social spaces.

Assessing the suitability of market approach valuation methods for mine and quarry valuations

An area of property valuation that has attracted less attention than other property markets over the past 20 years has been the mining and extractive industries. These operations can range from small operators on leased or private land to multinational companies. Although there are a number of national mining standards that indicate the type of valuation methods that can be adopted for this asset class, these standards do not specify how or when these methods are best suited to particular mine operations. The RICS guidance notes and the draft IVSC guidance notes also advise the various valuations methods that can be used to value mining properties; but, again they do not specify what methods should be applied where and when. One of the methods supported by these standards and guidelines is the market approach. This paper will carry out an analysis of all mine, extractive industry and waste disposal sites sale transactions in Queensland Australia, a major world mining centre, to determine if a market valuation approach such as direct comparison is actually suitable for the valuation of a mine or extractive industry. The analysis will cover the period 1984 to 2011 and covers sale transactions for minerals, petroleum and gas, waste disposal sites, clay, sand and stone. Based on this analysis, the suitability of direct comparison for valuation purposes in this property sector will be tested.

A critical analysis of business process management education and alignment with industry demand : an Australian perspective

Business Process Management (BPM) is accepted globally as an organizational approach to enhance productivity and drive cost efficiencies. Studies confirm a shortage of BPM skilled professionals with limited opportunities to develop the required BPM expertise. This study investigates this gap starting from a critical analysis of BPM courses offered by Australian universities and training institutions. These courses were analyzed and mapped against a leading BPM capability framework to determine how well current BPM education and training offerings in Australia address the core capabilities required by BPM professionals globally. To determine the BPM skill-sets sought by industry, online recruitment advertisements were collated, analyzed, and mapped against this BPM capability framework. The outcomes provide a detailed overview on the alignment of available BPM education/training and industry demand. These insights are useful for BPM professionals and their employers to build awareness of the BPM capabilities required for a BPM mature organization. Universities and other training institutions will benefit from these results by understanding where demand is, where the gaps are, and what other BPM education providers are supplying. This structured comparison method could continue to provide a common ground for future discussion across university-industry boundaries and continuous alignment of their respective practices.

Analysing the similarity of proteins based on a new approach to empirical mode decomposition

The function of a protein can be partially determined by the information contained in its amino acid sequence. It can be assumed that proteins with similar amino acid sequences normally have closer functions. Hence analysing the similarity of proteins has become one of the most important areas of protein study. In this work, a layered comparison method is used to analyze the similarity of proteins. It is based on the empirical mode decomposition (EMD) method, and protein sequences are characterized by the intrinsic mode functions (IMFs). The similarity of proteins is studied with a new cross-correlation formula. It seems that the EMD method can be used to detect the functional relationship of two proteins. This kind of similarity method is a complement of traditional sequence similarity approaches which focus on the alignment of amino acids

Children’s physical activity, health and physical education in isolated rural contexts : the views of parent educators in Queensland

This paper describes the views of parent educators of their children’s levels and types of physical activity. The study was conducted at two mini-schools in western Queensland. These are occasion where students who undertake formal education through various Schools Distance Education, come together for a week of educational activity. Parents (mostly mothers) were interviewed using a semi-structured approach. The interview data were then analysed for dominant themes using a constant comparison method. The emergent themes related to nutrition and physical activity. Within the physical activity theme, notions of the great outdoors, work and organised sport skill development also emerged.

Mechanical testing of internal fixation devices: A theoretical and practical examination of current methods

Successful healing of long bone fractures is dependent on the mechanical environment created within the fracture, which in turn is dependent on the fixation strategy. Recent literature reports have suggested that locked plating devices are too stiff to reliably promote healing. However, in vitro testing of these devices has been inconsistent in both method of constraint and reported outcomes, making comparisons between studies and the assessment of construct stiffness problematic. Each of the methods previously used in the literature were assessed for their effect on the bending of the sample and concordant stiffness. The choice of outcome measures used in in vitro fracture studies was also assessed. Mechanical testing was conducted on seven hole locked plated constructs in each method for comparison. Based on the assessment of each method the use of spherical bearings, ball joints or similar is suggested at both ends of the sample. The use of near and far cortex movement was found to be more comprehensive and more accurate than traditional centrally calculated inter fragmentary movement values; stiffness was found to be highly susceptible to the accuracy of deformation measurements and constraint method, and should only be used as a within study comparison method. The reported stiffness values of locked plate constructs from in vitro mechanical testing is highly susceptible to testing constraints and output measures, with many standard techniques overestimating the stiffness of the construct. This raises the need for further investigation into the actual mechanical behaviour within the fracture gap of these devices.

Some comparison on whole-proteome phylogeny of large dsDNA viruses based on dynamical language approach and feature frequency profiles method

There has been a growing interest in alignment-free methods for phylogenetic analysis using complete genome data. Among them, CVTree method, feature frequency profiles method and dynamical language approach were used to investigate the whole-proteome phylogeny of large dsDNA viruses. Using the data set of large dsDNA viruses from Gao and Qi (BMC Evol. Biol. 2007), the phylogenetic results based on the CVTree method and the dynamical language approach were compared in Yu et al. (BMC Evol. Biol. 2010). In this paper, we first apply dynamical language approach to the data set of large dsDNA viruses from Wu et al. (Proc. Natl. Acad. Sci. USA 2009) and compare our phylogenetic results with those based on the feature frequency profiles method. Then we construct the whole-proteome phylogeny of the larger dataset combining the above two data sets. According to the report of The International Committee on the Taxonomy of Viruses (ICTV), the trees from our analyses are in good agreement to the latest classification of large dsDNA viruses.

Comparison of active-set method deconvolution and matched-filtering for derivation of an ultrasound transit time spectrum

The quality of ultrasound computed tomography imaging is primarily determined by the accuracy of ultrasound transit time measurement. A major problem in analysis is the overlap of signals making it difficult to detect the correct transit time. The current standard is to apply a matched-filtering approach to the input and output signals. This study compares the matched-filtering technique with active set deconvolution to derive a transit time spectrum from a coded excitation chirp signal and the measured output signal. The ultrasound wave travels in a direct and a reflected path to the receiver, resulting in an overlap in the recorded output signal. The matched-filtering and deconvolution techniques were applied to determine the transit times associated with the two signal paths. Both techniques were able to detect the two different transit times; while matched-filtering has a better accuracy (0.13 μs vs. 0.18 μs standard deviation), deconvolution has a 3.5 times improved side-lobe to main-lobe ratio. A higher side-lobe suppression is important to further improve image fidelity. These results suggest that a future combination of both techniques would provide improved signal detection and hence improved image fidelity.

The exploration of consumer power in online brand communities : a comparison case study in Australia and China

Aided by the development of information technology, the balance of power in the market place is rapidly shifting from marketers towards consumers and nowhere is this more obvious than in the online environment (Denegri-Knott, Zwick, & Schroeder, 2006; Moynagh & Worsley, 2002; Newcomer, 2000; Samli, 2001). From the inception and continuous development of the Internet, consumers are becoming more empowered. They can choose what they want to click on the Internet, they can shop and transact payments, watch and download video, chat with others, be it friends or even total strangers. Especially in online communities, like-minded consumers share and exchange information, ideas and opinions. One form of online community is the online brand community, which gathers specific brand lovers. As with any social unit, people form different roles in the community and exert different effects on each other. Their interaction online can greatly influence the brand and marketers. A comprehensive understanding of the operation of this special group form is essential to advancing marketing thought and practice (Kozinets, 1999). While online communities have strongly shifted the balance of power from marketers to consumers, the current marketing literature is sparse on power theory (Merlo, Whitwell, & Lukas, 2004). Some studies have been conducted from an economic point of view (Smith, 1987), however their application to marketing has been limited. Denegri-Knott (2006) explored power based on the struggle between consumers and marketers online and identified consumer power formats such as control over the relationship, information, aggregation and participation. Her study has built a foundation for future power studies in the online environment. This research project bridges the limited marketing literature on power theory with the growing recognition of online communities among marketing academics and practitioners. Specifically, this study extends and redefines consumer power by exploring the concept of power in online brand communities, in order to better understand power structure and distribution in this context. This research investigates the applicability of the factors of consumer power identified by Denegri-Knott (2006) to the online brand community. In addition, by acknowledging the model proposed by McAlexander, Schouten, & Koenig (2002), which emphasized that community study should focus on the role of consumers and identifying multiple relationships among the community, this research further explores how member role changes will affect power relationships as well as consumer likings of the brand. As a further extension to the literature, this study also considers cultural differences and their effect on community member roles and power structure. Based on the study of Hofstede (1980), Australia and China were chosen as two distinct samples to represent differences in two cultural dimensions, namely individualism verses collectivism and high power distance verses low power distance. This contribution to the research also helps answer the research gap identified by Muñiz Jr & O'Guinn (2001), who pointed out the lack of cross cultural studies within the online brand community context. This research adopts a case study methodology to investigate the issues identified above. Case study is an appropriate research strategy to answer “how” and “why” questions of a contemporary phenomenon in real-life context (Yin, 2003). The online brand communities of “Haloforum.net” in Australia and “NGA.cn” in China were selected as two cases. In-depth interviews were used as the primary data collection method. As a result of the geographical dispersion and the preference of a certain number of participants, online synchronic interviews via MSN messenger were utilized along with the face-to-face interviews. As a supplementary approach, online observation was carried over two months, covering a two week period prior to the interviews and a six week period following the interviews. Triangulation techniques were used to strengthen the credibility and validity of the research findings (Yin, 2003). The findings of this research study suggest a new definition of power in an online brand community. This research also redefines the consumer power types and broadens the brand community model developed by McAlexander et al. (2002) in an online context by extending the various relationships between brand and members. This presents a more complete picture of how the perceived power relationships are structured in the online brand community. A new member role is discovered in the Australian online brand community in addition to the four member roles identified by Kozinets (1999), in contrast however, all four roles do not exist in the Chinese online brand community. The research proposes a model which links the defined power types and identified member roles. Furthermore, given the results of the cross-cultural comparison between Australia and China showed certain discrepancies, the research suggests that power studies in the online brand community should be country-specific. This research contributes to the body of knowledge on online consumer power, by applying it to the context of an online brand community, as well as considering factors such as cross cultural difference. Importantly, it provides insights for marketing practitioners on how to best leverage consumer power to serve brand objective in online brand communities. This, in turn, should lead to more cost effective and successful communication strategies. Finally, the study proposes future research directions. The research should be extended to communities of different sizes, to different extents of marketer control over the community, to the connection between online and offline activities within the brand community, and (given the cross-cultural findings) to different countries. In addition, a greater amount of research in this area is recommended to determine the generalizability of this study.

Loading applied on prosthetic knee of transfemoral amputee: comparison of inverse dynamics and direct measurements

Inverse dynamics is the most comprehensive method that gives access to the net joint forces and moments during walking. However it is based on assumptions (i.e., rigid segments linked by ideal joints) and it is known to be sensitive to the input data (e.g., kinematic derivatives, positions of joint centres and centre of pressure, inertial parameters). Alternatively, transducers can be used to measure directly the load applied on the residuum of transfemoral amputees. So, the purpose of this study was to compare the forces and moments applied on a prosthetic knee measured directly with the ones calculated by three inverse dynamics computations - corresponding to 3 and 2 segments, and « ground reaction vector technique » - during the gait of one patient. The maximum RMSEs between the estimated and directly measured forces (i.e., 56 N) and moment (i.e., 5 N.m) were relatively small. However the dynamic outcomes of the prosthetic components (i.e., absorption of the foot, friction and limit stop of the knee) were only partially assessed with inverse dynamic methods.