Smart Tea Project

Conference poster. The lab book is a big block to publication@source, if it’s not digital, it’s difficult to share. Most experimental information is recorded in a lab book in a highly personal way. We have created a new analogy to fully understand the use of the lab book and successfully built and evaluated a working electronic replacement

The Sociogenomics of Polygenic Scores of Reproductive Behavior and Their Relationship to Other Fertility Traits

Human reproductive behavior until relatively recently has been explained exclusively via individual and social characteristics. This article applies results from a recent Genome-Wide Association Study that combined sixty-two data sources to isolate twelve genetic loci associated with reproductive behavior. We create polygenic scores that allow us to include a summary variable of genetic factors into our statistical models. We use four datasets: the U.S. Health and Retirement Study, Dutch LifeLines, TwinsUK and the Swedish Twin register. First, we provide a brief overview of the dominant explanations of reproductive behavior. Second, we test the predictive power of polygenic scores. Third, we interrogate the robustness of our models using a series of sensitivity analyses to take into account possible confounders due to population stratification and selection

Making tea: a human centred approach to designing a pervasive smart lab notebook

The methodology used to design a useful and workable laboratory electronic notebook is described along with some of the technology needed to implement the smart lab systems

Imaging the Black Hole Silhouette of M87: Implications for Jet Formation and Black Hole Spin

The silhouette cast by the horizon of the supermassive black hole in M87 can now be resolved with the emerging millimeter very-long baseline interferometry (VLBI) capability. Despite being ~2000 times farther away than SgrA* (the supermassive black hole at the center of the Milky-Way and the primary target for horizon-scale imaging), M87's much larger black hole mass results in a horizon angular scale roughly half that of SgrA*'s, providing another practical target for direct imaging. However, unlike SgrA*, M87 exhibits a powerful radio jet, providing an opportunity to study jet formation physics on horizon scales. We employ a simple, qualitatively correct force-free jet model to explore the expected high-resolution images of M87 at wavelengths of 1.3mm and 0.87mm (230GHz and 345GHz), for a variety of jet parameters. We show that future VLBI data will be able to constrain the size of the jet footprint, the jet collimation rate, and the black hole spin. Polarization will further probe the structure of the jet's magnetic field and its effect on the emitting gas. Horizon-scale imaging of M87 and SgrA* will enable for the first time the empirical exploration of the relationship between the mass and spin of a black hole and the characteristics of the gas inflow/outflow around it.Comment: 18 pages, 7 figures, accepted by Ap

A three-protein biomarker panel assessed in diagnostic tissue predicts death from prostate cancer for men with localized disease

Only a minority of prostate cancers lead to death. Because no tissue biomarkers of aggressiveness other than Gleason score are available at diagnosis, many nonlethal cancers are treated aggressively. We evaluated whether a panel of biomarkers, associated with a range of disease outcomes in previous studies, could predict death from prostate cancer for men with localized disease. Using a case-only design, subjects were identified from three Australian epidemiological studies. Men who had died of their disease, cases (N = 83), were matched to referents (N = 232), those who had not died of prostate cancer, using incidence density sampling. Diagnostic tissue was retrieved to assess expression of AZGP1, MUC1, NKX3.1, p53, and PTEN by semiquantitative immunohistochemistry (IHC). Poisson regression was used to estimate mortality rate ratios (MRRs) adjusted for age, Gleason score, and stage and to estimate survival probabilities. Expression of MUC1 and p53 was associated with increased mortality (MRR 2.51, 95% CI 1.14-5.54, P = 0.02 and 3.08, 95% CI 1.41-6.95, P = 0.005, respectively), whereas AZGP1 expression was associated with decreased mortality (MRR 0.44, 95% CI 0.20-0.96, P = 0.04). Analyzing all markers under a combined model indicated that the three markers were independent predictors of prostate cancer death and survival. For men with localized disease at diagnosis, assessment of AZGP1, MUC1, and p53 expression in diagnostic tissue by IHC could potentially improve estimates of risk of dying from prostate cancer based only on Gleason score and clinical stage

Signature of effective mass in crackling noise asymmetry

Crackling noise is a common feature in many dynamic systems [1-9], the most familiar instance of which is the sound made by a sheet of paper when crumpled into a ball. Although seemingly random, this noise contains fundamental information about the properties of the system in which it occurs. One potential source of such information lies in the asymmetric shape of noise pulses emitted by a diverse range of noisy systems [8-12], but the cause of this asymmetry has lacked explanation [1]. Here we show that the leftward asymmetry observed in the Barkhausen effect [2] - the noise generated by the jerky motion of domain walls as they interact with impurities in a soft magnet - is a direct consequence of a magnetic domain wall's negative effective mass. As well as providing a means of determining domain wall effective mass from a magnet's Barkhausen noise our work suggests an inertial explanation for the origin of avalanche asymmetries in crackling noise phenomena more generally.Comment: 13 pages, 4 figures, to appear in Nature Physic

Atrazine and cancer incidence among pesticide applicators in the agricultural health study (1994-2007).

Atrazine is a triazine herbicide used widely in the United States. Although it is an animal carcinogen, the mechanism in rodents does not appear to operate in humans. Few epidemiologic studies have provided evidence for an association

Does Collocation Inform the Impact of Collaboration?

Background It has been shown that large interdisciplinary teams working across geography are more likely to be impactful. We asked whether the physical proximity of collaborators remained a strong predictor of the scientific impact of their research as measured by citations of the resulting publications. Methodology/Principal Findings Articles published by Harvard investigators from 1993 to 2003 with at least two authors were identified in the domain of biomedical science. Each collaboration was geocoded to the precise three-dimensional location of its authors. Physical distances between any two coauthors were calculated and associated with corresponding citations. Relationship between distance of coauthors and citations for four author relationships (first-last, first-middle, last-middle, and middle-middle) were investigated at different spatial scales. At all sizes of collaborations (from two authors to dozens of authors), geographical proximity between first and last author is highly informative of impact at the microscale (i.e. within building) and beyond. The mean citation for first-last author relationship decreased as the distance between them increased in less than one km range as well as in the three categorized ranges (in the same building, same city, or different city). Such a trend was not seen in other three author relationships. Conclusions/Significance Despite the positive impact of emerging communication technologies on scientific research, our results provide striking evidence for the role of physical proximity as a predictor of the impact of collaborations.Ewing Marion Kauffman FoundationHarvard University. Office of the Provost (1992-

What guidance are researchers given on how to present network meta-analyses to end-users such as policymakers and clinicians? A systematic review

© 2014 Sullivan et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.Introduction: Network meta-analyses (NMAs) are complex methodological approaches that may be challenging for non-technical end-users, such as policymakers and clinicians, to understand. Consideration should be given to identifying optimal approaches to presenting NMAs that help clarify analyses. It is unclear what guidance researchers currently have on how to present and tailor NMAs to different end-users. Methods: A systematic review of NMA guidelines was conducted to identify guidance on how to present NMAs. Electronic databases and supplementary sources were searched for NMA guidelines. Presentation format details related to sample formats, target audiences, data sources, analysis methods and results were extracted and frequencies tabulated. Guideline quality was assessed following criteria developed for clinical practice guidelines. Results: Seven guidelines were included. Current guidelines focus on how to conduct NMAs but provide limited guidance to researchers on how to best present analyses to different end-users. None of the guidelines provided reporting templates. Few guidelines provided advice on tailoring presentations to different end-users, such as policymakers. Available guidance on presentation formats focused on evidence networks, characteristics of individual trials, comparisons between direct and indirect estimates and assumptions of heterogeneity and/or inconsistency. Some guidelines also provided examples of figures and tables that could be used to present information. Conclusions: Limited guidance exists for researchers on how best to present NMAs in an accessible format, especially for non-technical end-users such as policymakers and clinicians. NMA guidelines may require further integration with end-users' needs, when NMAs are used to support healthcare policy and practice decisions. Developing presentation formats that enhance understanding and accessibility of NMAs could also enhance the transparency and legitimacy of decisions informed by NMAs.The Canadian Institute of Health Research (CIHR) Drug Safety and Effectiveness Network (Funding reference number – 116573)