The DUB/USP17 deubiquitinating enzymes: A gene family within a tandemly repeated sequence, is also embedded within the copy number variable Beta-defensin cluste

Background: The DUB/USP17 subfamily of deubiquitinating enzymes were originally identified as immediate early genes induced in response to cytokine stimulation in mice (DUB-1, DUB-1A, DUB-2, DUB-2A). Subsequently we have identified a number of human family members and shown that one of these (DUB-3) is also cytokine inducible. We originally showed that constitutive expression of DUB-3 can block cell proliferation and more recently we have demonstrated that this is due to its regulation of the ubiquitination and activity of the 'CAAX' box protease RCE1.

Results: Here we demonstrate that the human DUB/USP17 family members are found on both chromosome 4p16.1, within a block of tandem repeats, and on chromosome 8p23.1, embedded within the copy number variable betadefensin cluster. In addition, we show that the multiple genes observed in humans and other distantly related mammals have arisen due to the independent expansion of an ancestral sequence within each species. However, it is also apparent when sequences from humans and the more closely related chimpanzee are compared, that duplication events have taken place prior to these species separating.

Conclusions: The observation that the DUB/USP17 genes, which can influence cell growth and survival, have evolved from an unstable ancestral sequence which has undergone multiple and varied duplications in the species examined marks this as a unique family. In addition, their presence within the beta-defensin repeat raises the question whether they may contribute to the influence of this repeat on immune related conditions.

Targets of genome copy number reduction in primary breast cancers identified by integrative genomics

The identification of specific oncogenes and tumor suppressor genes in regions of recurrent aneuploidy is a major challenge of molecular cancer research. Using both oligonucleotide single-nucleotide polymorphism and mRNA expression arrays, we integrated genomic and transcriptional information to identify and prioritize candidate cancer genes in regions of increased and decreased chromosomal copy number in a cohort of primary breast cancers. Confirming the validity of this approach, several regions of previously-known copy number (CN) alterations in breast cancer could be successfully reidentified. Focusing on regions of decreased CN, we defined a prioritized list of eighteen candidate genes, which included ARPIN, FBNI, and LZTSI, previously shown to be associated with cancers in breast or other tissue types, and novel genes such as P29, MORF4LI, and TBCID5. One such gene, the RUNX3 transcription factor, was selected for further study. We show that RUNX3 is present at reduced CNs in proportion to the rest of the tumor genome and that RUNX3 CN reductions can also be observed in a breast cancer series from a different center. Using tissue microarrays, we demonstrate in an independent cohort of over 120 breast tissues that RUNX3 protein is expressed in normal breast epithelium but not fat and stromal tissue, and widely down-regulated in the majority of breast cancers (> 85%). In vitro, RUNX3 overexpression suppressed the invasive potential of MDA-MB-231 breast cancer cells in a matrigel assay. Our results demonstrate the utility of integrative genomic approaches to identify novel potential cancer-related genes in primary tumors. This article contains Supplementary Material available at http:// www.interscience.wiley.com/jpages/1045-2257/suppmat. (c) 2006 Wiley-Liss, Inc.

Genome-wide association of early-onset myocardial infarction with single nucleotide polymorphisms and copy number variants

We conducted a genome-wide association study testing single nucleotide polymorphisms (SNPs) and copy number variants (CNVs) for association with early-onset myocardial infarction in 2,967 cases and 3,075 controls. We carried out replication in an independent sample with an effective sample size of up to 19,492. SNPs at nine loci reached genome-wide significance: three are newly identified (21q22 near MRPS6-SLC5A3-KCNE2, 6p24 in PHACTR1 and 2q33 in WDR12) and six replicated prior observations1-4 (9p21, 1p13 near CELSR2-PSRC1-SORT1, 10q11 near CXCL12, 1q41 in MIA3, 19p13 near LDLR and 1p32 near PCSK9). We tested 554 common copy number polymorphisms (>1% allele frequency) and none met the pre-specified threshold for replication (P < 10-3). We identified 8,065 rare CNVs but did not detect a greater CNV burden in cases compared to controls, in genes compared to the genome as a whole, or at any individual locus. SNPs at nine loci were reproducibly associated with myocardial infarction, but tests of common and rare CNVs failed to identify additional associations with myocardial infarction risk.

Young children's food brand knowledge. Early development and associations with television viewing and parent's diet

Brand knowledge is a prerequisite of children's requests and choices for branded foods. We explored the development of young children's brand knowledge of foods highly advertised on television - both healthy and less healthy. Participants were 172 children aged 3-5 years in diverse socio-economic settings, from two jurisdictions on the island of Ireland with different regulatory environments. Results indicated that food brand knowledge (i) did not differ across jurisdictions; (ii) increased significantly between 3 and 4 years; and (iii) children had significantly greater knowledge of unhealthy food brands, compared with similarly advertised healthy brands. In addition, (iv) children's healthy food brand knowledge was not related to their television viewing, their mother's education, or parent or child eating. However, (v) unhealthy brand knowledge was significantly related to all these factors, although only parent eating and children's age were independent predictors. Findings indicate that effects of food marketing for unhealthy foods take place through routes other than television advertising alone, and are present before pre-schoolers develop the concept of healthy eating. Implications are that marketing restrictions of unhealthy foods should extend beyond television advertising; and that family-focused obesity prevention programmes should begin before children are 3 years of age.

Discovering subgroups of patients from DNA copy number data using NMF on compacted matrices

In the study of complex genetic diseases, the identification of subgroups of patients sharing similar genetic characteristics represents a challenging task, for example, to improve treatment decision. One type of genetic lesion, frequently investigated in such disorders, is the change of the DNA copy number (CN) at specific genomic traits. Non-negative Matrix Factorization (NMF) is a standard technique to reduce the dimensionality of a data set and to cluster data samples, while keeping its most relevant information in meaningful components. Thus, it can be used to discover subgroups of patients from CN profiles. It is however computationally impractical for very high dimensional data, such as CN microarray data. Deciding the most suitable number of subgroups is also a challenging problem. The aim of this work is to derive a procedure to compact high dimensional data, in order to improve NMF applicability without compromising the quality of the clustering. This is particularly important for analyzing high-resolution microarray data. Many commonly used quality measures, as well as our own measures, are employed to decide the number of subgroups and to assess the quality of the results. Our measures are based on the idea of identifying robust subgroups, inspired by biologically/clinically relevance instead of simply aiming at well-separated clusters. We evaluate our procedure using four real independent data sets. In these data sets, our method was able to find accurate subgroups with individual molecular and clinical features and outperformed the standard NMF in terms of accuracy in the factorization fitness function. Hence, it can be useful for the discovery of subgroups of patients with similar CN profiles in the study of heterogeneous diseases.

VIEWING LEED PATTERNS AS ELECTRON HOLOGRAMS

It is shown theoretically that LEED patterns from ordered overlayer systems bear a strong relationship to electron holograms, and that phase information is recorded in the diffraction intensities. It is, therefore, possible to obtain structural information by direct holographic inversion from conventional LEED I-V spectra.

Digital slide viewing for primary reporting in gastrointestinal pathology: a validation study

Despite the increasing availability of digital slide viewing, and numerous advantages associated with its application, a lack of quality validation studies is amongst the reasons for poor uptake in routine practice. This study evaluated primary digital pathology reporting in the setting of routine subspecialist gastrointestinal pathology, commonplace in most tissue pathology laboratories and representing one of the highest volume specialties in most laboratories. Individual digital and glass slide diagnoses were compared amongst three pathologists reporting in a gastrointestinal subspecialty team, in a prospective series of 100 consecutive diagnostic cases from routine practice in a large teaching hospital laboratory. The study included a washout period of at least 6 months. Discordant diagnoses were classified, and the study evaluated against recent College of American Pathologists (CAP) recommendations for evaluating digital pathology systems for diagnostic use. The study design met all 12 of the CAP recommendations. The 100 study cases generated 300 pairs of diagnoses, comprising 100 glass slide diagnoses and 100 digital diagnoses from each of the three study pathologists. 286 of 300 pairs of diagnoses were concordant, representing intraobserver concordance of 95.3 %, broadly comparable to rates previously published in this field. In ten of the 14 discordant pairs, the glass slide diagnosis was favoured; in four cases, the digital diagnosis was favoured, but importantly, the 14 discordant intraobserver diagnoses were considered to be of minor clinical significance. Interobserver, or viewing modality independent, concordance was found in 94 of the total of 100 study cases, providing a comparable baseline discordance rate expected in any second viewing of pathology material. These overall results support the safe use of digital pathology in primary diagnostic reporting in this setting

How Video Lecture Capture affects Student Engagement in a University Computer Programming Course: Attendance, Video Viewing Behaviours and Student Attitudes

Introduction
The use of video capture of lectures in Higher Education is not a recent occurrence with web based learning technologies including digital recording of live lectures becoming increasing commonly offered by universities throughout the world (Holliman and Scanlon, 2004). However in the past decade the increase in technical infrastructural provision including the availability of high speed broadband has increased the potential and use of videoed lecture capture. This had led to a variety of lecture capture formats including pod casting, live streaming or delayed broadcasting of whole or part of lectures.
Additionally in the past five years there has been a significant increase in the popularity of online learning, specifically via Massive Open Online Courses (MOOCs) (Vardi, 2014). One of the key aspects of MOOCs is the simulated recording of lecture like activities. There has been and continues to be much debate on the consequences of the popularity of MOOCs, especially in relation to its potential uses within established University programmes.
There have been a number of studies dedicated to the effects of videoing lectures.
The clustered areas of research in video lecture capture have the following main themes:
• Staff perceptions including attendance, performance of students and staff workload
• Reinforcement versus replacement of lectures
• Improved flexibility of learning
• Facilitating engaging and effective learning experiences
• Student usage, perception and satisfaction
• Facilitating students learning at their own pace
Most of the body of the research has concentrated on student and faculty perceptions, including academic achievement, student attendance and engagement (Johnston et al, 2012).
Generally the research has been positive in review of the benefits of lecture capture for both students and faculty. This perception coupled with technical infrastructure improvements and student demand may well mean that the use of video lecture capture will continue to increase in frequency in the next number of years in tertiary education. However there is a relatively limited amount of research in the effects of lecture capture specifically in the area of computer programming with Watkins 2007 being one of few studies . Video delivery of programming solutions is particularly useful for enabling a lecturer to illustrate the complex decision making processes and iterative nature of the actual code development process (Watkins et al 2007). As such research in this area would appear to be particularly appropriate to help inform debate and future decisions made by policy makers.
Research questions and objectives
The purpose of the research was to investigate how a series of lecture captures (in which the audio of lectures and video of on-screen projected content were recorded) impacted on the delivery and learning of a programme of study in an MSc Software Development course in Queen’s University, Belfast, Northern Ireland. The MSc is conversion programme, intended to take graduates from non-computing primary degrees and upskill them in this area. The research specifically targeted the Java programming module within the course. It also analyses and reports on the empirical data from attendances and various video viewing statistics. In addition, qualitative data was collected from staff and student feedback to help contextualise the quantitative results.
Methodology, Methods and Research Instruments Used
The study was conducted with a cohort of 85 post graduate students taking a compulsory module in Java programming in the first semester of a one year MSc in Software Development. A pre-course survey of students found that 58% preferred to have available videos of “key moments” of lectures rather than whole lectures. A large scale study carried out by Guo concluded that “shorter videos are much more engaging” (Guo 2013). Of concern was the potential for low audience retention for videos of whole lectures.
The lecturers recorded snippets of the lecture directly before or after the actual physical delivery of the lecture, in a quiet environment and then upload the video directly to a closed YouTube channel. These snippets generally concentrated on significant parts of the theory followed by theory related coding demonstration activities and were faithful in replication of the face to face lecture. Generally each lecture was supported by two to three videos of durations ranging from 20 – 30 minutes.
Attendance
The MSc programme has several attendance based modules of which Java Programming was one element. In order to assess the consequence on attendance for the Programming module a control was established. The control used was a Database module which is taken by the same students and runs in the same semester.
Access engagement
The videos were hosted on a closed YouTube channel made available only to the students in the class. The channel had enabled analytics which reported on the following areas for all and for each individual video; views (hits), audience retention, viewing devices / operating systems used and minutes watched.
Student attitudes
Three surveys were taken in regard to investigating student attitudes towards the videoing of lectures. The first was before the start of the programming module, then at the mid-point and subsequently after the programme was complete.
The questions in the first survey were targeted at eliciting student attitudes towards lecture capture before they had experienced it in the programme. The midpoint survey gathered data in relation to how the students were individually using the system up to that point. This included feedback on how many videos an individual had watched, viewing duration, primary reasons for watching and the result on attendance, in addition to probing for comments or suggestions. The final survey on course completion contained questions similar to the midpoint survey but in summative view of the whole video programme.
Conclusions and Outcomes
The study confirmed findings of other such investigations illustrating that there is little or no effect on attendance at lectures. The use of the videos appears to help promote continual learning but they are particularly accessed by students at assessment periods. Students respond positively to the ability to access lectures digitally, as a means of reinforcing learning experiences rather than replacing them. Feedback from students was overwhelmingly positive indicating that the videos benefited their learning. Also there are significant benefits to part recording of lectures rather than recording whole lectures. The behaviour viewing trends analytics suggest that despite the increase in the popularity of online learning via MOOCs and the promotion of video learning on mobile devices in fact in this study the vast majority of students accessed the online videos at home on laptops or desktops However, in part, this is likely due to the nature of the taught subject, that being programming.
The research involved prerecording the lecture in smaller timed units and then uploading for distribution to counteract existing quality issues with recording entire live lectures. However the advancement and consequential improvement in quality of in situ lecture capture equipment may well help negate the need to record elsewhere. The research has also highlighted an area of potentially very significant use for performance analysis and improvement that could have major implications for the quality of teaching. A study of the analytics of the viewings of the videos could well provide a quick response formative feedback mechanism for the lecturer. If a videoed lecture either recorded live or later is a true reflection of the face to face lecture an analysis of the viewing patterns for the video may well reveal trends that correspond with the live delivery.

Integration of copy number and transcriptomics provides risk stratification in prostate cancer: A discovery and validation cohort study

BACKGROUND: Understanding the heterogeneous genotypes and phenotypes of prostate cancer is fundamental to improving the way we treat this disease. As yet, there are no validated descriptions of prostate cancer subgroups derived from integrated genomics linked with clinical outcome.

METHODS: In a study of 482 tumour, benign and germline samples from 259 men with primary prostate cancer, we used integrative analysis of copy number alterations (CNA) and array transcriptomics to identify genomic loci that affect expression levels of mRNA in an expression quantitative trait loci (eQTL) approach, to stratify patients into subgroups that we then associated with future clinical behaviour, and compared with either CNA or transcriptomics alone.

FINDINGS: We identified five separate patient subgroups with distinct genomic alterations and expression profiles based on 100 discriminating genes in our separate discovery and validation sets of 125 and 103 men. These subgroups were able to consistently predict biochemical relapse (p = 0.0017 and p = 0.016 respectively) and were further validated in a third cohort with long-term follow-up (p = 0.027). We show the relative contributions of gene expression and copy number data on phenotype, and demonstrate the improved power gained from integrative analyses. We confirm alterations in six genes previously associated with prostate cancer (MAP3K7, MELK, RCBTB2, ELAC2, TPD52, ZBTB4), and also identify 94 genes not previously linked to prostate cancer progression that would not have been detected using either transcript or copy number data alone. We confirm a number of previously published molecular changes associated with high risk disease, including MYC amplification, and NKX3-1, RB1 and PTEN deletions, as well as over-expression of PCA3 and AMACR, and loss of MSMB in tumour tissue. A subset of the 100 genes outperforms established clinical predictors of poor prognosis (PSA, Gleason score), as well as previously published gene signatures (p = 0.0001). We further show how our molecular profiles can be used for the early detection of aggressive cases in a clinical setting, and inform treatment decisions.

INTERPRETATION: For the first time in prostate cancer this study demonstrates the importance of integrated genomic analyses incorporating both benign and tumour tissue data in identifying molecular alterations leading to the generation of robust gene sets that are predictive of clinical outcome in independent patient cohorts.