Final Project 3.0: A Student Virtual World Conference on the Future of Collaboration

There is currently little research of any kind on enterprise virtual worlds or using these collaborative tool ecosystems for geographically distributed education in organizational studies. In 2013, a group of multidisciplinary graduate students created and executed a conference in a 3D virtual world as a class project. The topics presented in the conference were crowdsourcing and mobile virtual worlds, but the overall experience resulted in learning well beyond those topics. The project team encountered a significant learning curve over planning and executing in person meetings as well as technical challenges that would threaten the success of the project. This paper describes the end-to-end process taken by the team to plan and execute the conference, and shows the challenges, successes, and the lessons learned that can be applied to future conferences in 3D virtual worlds, which promise incredible potential for improving collaboration across businesses

Immunoglobulin G from bovine milk primes intestinal epithelial cells for increased colonization of bifidobacteria

peer-reviewedAbstract A bovine colostrum fraction (BCF) was recently shown to enhance the adherence of several commensal organisms to intestinal epithelial cells through modulating the epithelial cell surface. In this study, the main components of the BCF were examined to investigate the active component/s responsible for driving the changes in the intestinal cells. The adherence of various bifidobacteria to HT-29 cells was increased when the intestinal cells were pre-incubated with immunoglobulin G (IgG). Modulation of the intestinal cells by IgG was concentration dependent with 16 mg/mL IgG resulting in a 43-fold increase in the adhesion of Bifidobacterium longum NCIMB 8809 to HT-29 cells. Periodate treatment of colostral IgG prior to performing the colonization studies resulted in a reduction in the adhesion of the strain to the intestinal cells demonstrating that the glycans of IgG may be important in modulating the intestinal cells for enhanced commensal adhesion. IgG isolated from mature milk also resulted in significant increases in adhesion of the Bifidobacterium strains tested albeit at reduced levels (3.9-fold). The impact of IgG on the HT-29 cells was also visualised via scanning electron microscopy. This study builds a strong case for the inclusion of IgG ingredients sourced from cow’s milk in functional foods aimed at increasing numbers of health promoting bacteria in the human gut

Evidence for a Long-period Planet Orbiting Epsilon Eridani

High precision radial velocity (RV) measurements spanning the years 1980.8--2000.0 are presented for the nearby (3.22 pc) K2 V star $\epsilon$ Eri. These data, which represent a combination of six independent data sets taken with four different telescopes, show convincing variations with a period of $\approx$ 7 yrs. A least squares orbital solution using robust estimation yields orbital parameters of period, $P$ = 6.9 yrs, velocity $K$-amplitude $=$ 19 {\ms}, eccentricity $e$ $=$ 0.6, projected companion mass $M$ sin $i$ = 0.86 $M_{Jupiter}$, and semi-major axis $a_2$ $=$ 3.3 AU. Ca II H&K S-index measurements spanning the same time interval show significant variations with periods of 3 and 20 yrs, yet none at the RV period. If magnetic activity were responsible for the RV variations then it produces a significantly different period than is seen in the Ca II data. Given the lack of Ca II variation with the same period as that found in the RV measurements, the long-lived and coherent nature of these variations, and the high eccentricity of the implied orbit, Keplerian motion due to a planetary companion seems to be the most likely explanation for the observed RV variations. The wide angular separation of the planet from the star (approximately 1 arc-second) and the long orbital period make this planet a prime candidate for both direct imaging and space-based astrometric measurements.Comment: To appear in Astrophysical Journal Letters. 9 pages, 2 figure

Improved annotation of 3' untranslated regions and complex loci by combination of strand-specific direct RNA sequencing, RNA-seq and ESTs

The reference annotations made for a genome sequence provide the framework for all subsequent analyses of the genome. Correct annotation is particularly important when interpreting the results of RNA-seq experiments where short sequence reads are mapped against the genome and assigned to genes according to the annotation. Inconsistencies in annotations between the reference and the experimental system can lead to incorrect interpretation of the effect on RNA expression of an experimental treatment or mutation in the system under study. Until recently, the genome-wide annotation of 3-prime untranslated regions received less attention than coding regions and the delineation of intron/exon boundaries. In this paper, data produced for samples in Human, Chicken and A. thaliana by the novel single-molecule, strand-specific, Direct RNA Sequencing technology from Helicos Biosciences which locates 3-prime polyadenylation sites to within +/- 2 nt, were combined with archival EST and RNA-Seq data. Nine examples are illustrated where this combination of data allowed: (1) gene and 3-prime UTR re-annotation (including extension of one 3-prime UTR by 5.9 kb); (2) disentangling of gene expression in complex regions; (3) clearer interpretation of small RNA expression and (4) identification of novel genes. While the specific examples displayed here may become obsolete as genome sequences and their annotations are refined, the principles laid out in this paper will be of general use both to those annotating genomes and those seeking to interpret existing publically available annotations in the context of their own experimental dataComment: 44 pages, 9 figure

Precise Doppler Monitoring of Barnard's Star

We present 248 precise Doppler measurements of Barnard's Star (Gl 699), the second nearest star system to Earth, obtained from Lick and Keck Observatories during 25 years between 1987 and 2012. The early precision was 20 \ms{} but was 2 \ms{} during the last 8 years, constituting the most extensive and sensitive search for Doppler signatures of planets around this stellar neighbor. We carefully analyze the 136 Keck radial velocities spanning 8 years by first applying a periodogram analysis to search for nearly circular orbits. We find no significant periodic Doppler signals with amplitudes above $\sim$2 \ms{}, setting firm upper limits on the minimum mass (\msini) of any planets with orbital periods from 0.1 to 1000 days. Using a Monte Carlo analysis for circular orbits, we determine that planetary companions to Barnard's Star with masses above 2 \mearth{} and periods below 10 days would have been detected. Planets with periods up to 2 years and masses above 10 \mearth{} (0.03 \mjup) are also ruled out. A similar analysis allowing for eccentric orbits yields comparable mass limits. The habitable zone of Barnard's Star appears to be devoid of roughly Earth-mass planets or larger, save for face-on orbits. Previous claims of planets around the star by van de Kamp are strongly refuted. The radial velocity of Barnard's Star increases with time at $4.515\pm0.002$ \msy{}, consistent with the predicted geometrical effect, secular acceleration, that exchanges transverse for radial components of velocity.Comment: 21 pages & 11 figures; accepted to ApJ for publication; revision comments: the conclusions and results remain unchanged, removed the last paragraph in section 4.2, a few minor changes to the text, replaced figure 7 with figures 7 and 8, corrected typos in the rv data tables (tables 2 and 3, data downloadable from ApJ

The assessment of vascular risk in men with erectile dysfunction: the role of the cardiologist and general physician.

Erectile dysfunction (ED) and cardiovascular disease (CVD) share risk factors and frequently coexist, with endothelial dysfunction believed to be the pathophysiologic link. ED is common, affecting more than 70% of men with known CVD. In addition, clinical studies have demonstrated that ED in men with no known CVD often precedes a CVD event by 2-5 years. ED severity has been correlated with increasing plaque burden in patients with coronary artery disease. ED is an independent marker of increased CVD risk including all-cause and especially CVD mortality, particularly in men aged 30-60 years. Thus, ED identifies a window of opportunity for CVD risk mitigation. We recommend that a thorough history, physical exam (including visceral adiposity), assessment of ED severity and duration and evaluation including fasting plasma glucose, lipids, resting electrocardiogram, family history, lifestyle factors, serum creatinine (estimated glomerular filtration rate) and albumin:creatinine ratio, and determination of the presence or absence of the metabolic syndrome be performed to characterise cardiovascular risk in all men with ED. Assessment of testosterone levels should also be considered and biomarkers may help to further quantify risk, even though their roles in development of CVD have not been firmly established. Finally, we recommend that a question about ED be included in assessment of CVD risk in all men and be added to CVD risk assessment guidelines

A high-resolution map of human evolutionary constraint using 29 mammals.

The comparison of related genomes has emerged as a powerful lens for genome interpretation. Here we report the sequencing and comparative analysis of 29 eutherian genomes. We confirm that at least 5.5% of the human genome has undergone purifying selection, and locate constrained elements covering ∼4.2% of the genome. We use evolutionary signatures and comparisons with experimental data sets to suggest candidate functions for ∼60% of constrained bases. These elements reveal a small number of new coding exons, candidate stop codon readthrough events and over 10,000 regions of overlapping synonymous constraint within protein-coding exons. We find 220 candidate RNA structural families, and nearly a million elements overlapping potential promoter, enhancer and insulator regions. We report specific amino acid residues that have undergone positive selection, 280,000 non-coding elements exapted from mobile elements and more than 1,000 primate- and human-accelerated elements. Overlap with disease-associated variants indicates that our findings will be relevant for studies of human biology, health and disease

Genome-wide analyses as part of the international FTLD-TDP whole-genome sequencing consortium reveals novel disease risk factors and increases support for immune dysfunction in FTLD

Frontotemporal lobar degeneration with neuronal inclusions of the TAR DNA-binding protein 43 (FTLD-TDP) represents the most common pathological subtype of FTLD. We established the international FTLD-TDP whole genome sequencing consortium to thoroughly characterize the known genetic causes of FTLD-TDP and identify novel genetic risk factors. Through the study of 1,131 unrelated Caucasian patients, we estimated that C9orf72 repeat expansions and GRN loss-of-function mutations account for 25.5% and 13.9% of FTLD-TDP patients, respectively. Mutations in TBK1 (1.5%) and other known FTLD genes (1.4%) were rare, and the disease in 57.7% of FTLD-TDP patients was unexplained by the known FTLD genes. To unravel the contribution of common genetic factors to the FTLD-TDP etiology in these patients, we conducted a two-stage association study comprising the analysis of whole-genome sequencing data from 517 FTLD-TDP patients and 838 controls, followed by targeted genotyping of the most associated genomic loci in 119 additional FTLD-TDP patients and 1653 controls. We identified three genome-wide significant FTLD-TDP risk loci: one new locus at chromosome 7q36 within the DPP6 gene led by rs118113626 (pvalue=4.82e-08, OR=2.12), and two known loci: UNC13A, led by rs1297319 (pvalue=1.27e-08, OR=1.50) and HLA-DQA2 led by rs17219281 (pvalue=3.22e-08, OR=1.98). While HLA represents a locus previously implicated in clinical FTLD and related neurodegenerative disorders, the association signal in our study is independent from previously reported associations. Through inspection of our whole genome sequence data for genes with an excess of rare loss-of-function variants in FTLD-TDP patients (n≥3) as compared to controls (n=0), we further discovered a possible role for genes functioning within the TBK1-related immune pathway (e.g. DHX58, TRIM21, IRF7) in the genetic etiology of FTLD-TDP. Together, our study based on the largest cohort of unrelated FTLD-TDP patients assembled to date provides a comprehensive view of the genetic landscape of FTLD-TDP, nominates novel FTLD-TDP risk loci, and strongly implicates the immune pathway in FTLD-TDP pathogenesis