Ten Simple Rules for Reproducible Research in Jupyter Notebooks

Reproducibility of computational studies is a hallmark of scientific methodology. It enables researchers to build with confidence on the methods and findings of others, reuse and extend computational pipelines, and thereby drive scientific progress. Since many experimental studies rely on computational analyses, biologists need guidance on how to set up and document reproducible data analyses or simulations. In this paper, we address several questions about reproducibility. For example, what are the technical and non-technical barriers to reproducible computational studies? What opportunities and challenges do computational notebooks offer to overcome some of these barriers? What tools are available and how can they be used effectively? We have developed a set of rules to serve as a guide to scientists with a specific focus on computational notebook systems, such as Jupyter Notebooks, which have become a tool of choice for many applications. Notebooks combine detailed workflows with narrative text and visualization of results. Combined with software repositories and open source licensing, notebooks are powerful tools for transparent, collaborative, reproducible, and reusable data analyses

Chiral Estimates of Strong CP Violation Revisited

The effects of the CP violating $\theta$ term in the QCD Lagrangian upon low energy hadronic phenomenology are reconsidered. Strong CP violating interactions among Goldstone bosons and octet baryons are incorporated into an effective chiral Lagrangian framework. The $\theta$ term's impact upon the decays $\eta\to\pi\pi$ and $\pi^0\to\gamma\gamma$ is then investigated but found to be extremely small. A refined model independent estimate of nonanalytic contributions to the neutron electric dipole moment is also determined using velocity dependent Baryon Chiral Perturbation Theory. We obtain the approximate upper bound $|\theta| < 4.5 \times 10^{-10}$.Comment: 11 pages with 3 figures not included but available upon request, CALT-68-184

The Effect of Air on Granular Size Separation in a Vibrated Granular Bed

Using high-speed video and magnetic resonance imaging (MRI) we study the motion of a large sphere in a vertically vibrated bed of smaller grains. As previously reported we find a non-monotonic density dependence of the rise and sink time of the large sphere. We find that this density dependence is solely due to air drag. We investigate in detail how the motion of the intruder sphere is influenced by size of the background particles, initial vertical position in the bed, ambient pressure and convection. We explain our results in the framework of a simple model and find quantitative agreement in key aspects with numerical simulations to the model equations.Comment: 14 pages, 16 figures, submitted to PRE, corrected typos, slight change

Local multiresolution order in community detection

Community detection algorithms attempt to find the best clusters of nodes in an arbitrary complex network. Multi-scale ("multiresolution") community detection extends the problem to identify the best network scale(s) for these clusters. The latter task is generally accomplished by analyzing community stability simultaneously for all clusters in the network. In the current work, we extend this general approach to define local multiresolution methods, which enable the extraction of well-defined local communities even if the global community structure is vaguely defined in an average sense. Toward this end, we propose measures analogous to variation of information and normalized mutual information that are used to quantitatively identify the best resolution(s) at the community level based on correlations between clusters in independently-solved systems. We demonstrate our method on two constructed networks as well as a real network and draw inferences about local community strength. Our approach is independent of the applied community detection algorithm save for the inherent requirement that the method be able to identify communities across different network scales, with appropriate changes to account for how different resolutions are evaluated or defined in a particular community detection method. It should, in principle, easily adapt to alternative community comparison measures.Comment: 19 pages, 11 figure

Heart failure-associated anemia: bone marrow dysfunction and response to erythropoietin

Heart failure (HF)-associated anemia is common and has a poor outcome. Because bone marrow (BM) dysfunction may contribute to HF-associated anemia, we first investigated mechanisms of BM dysfunction in an established model of HF, the transgenic REN2 rat, which is characterized by severe hypertrophy and ventricular dilatation and SD rats as controls. Secondly, we investigated whether stimulation of hematopoiesis with erythropoietin (EPO) could restore anemia and BM dysfunction. After sacrifice, erythropoietic precursors (BFU-E) were isolated from the BM and cultured for 10 days. BFU-E were quantified and transcript abundance of genes involved in erythropoiesis were assayed. Number of BFU-E were severely decreased in BM of REN2 rats compared to SD rats (50 ± 6.2 vs. 6.4 ± 1.7, p < 0.01). EPO treatment increased hematocrit in the SD-EPO group (after 6 weeks, 49 ± 1 vs. 58 ± 1%, p < 0.01); however, in the mildly anemic REN2 rats, there was no effect (43 ± 1 vs. 44 ± 1%). This was paralleled by a 67% decrease in BFU-E in BM of REN2 rats compared to SD (p < 0.01). EPO significantly improved BFU-E in both SD and REN2 but could not restore this to control levels in the REN2 rats. Expression of several genes involved in differentiation (LMO2), mobilization (SDF-1), and iron incorporation (transferrin receptor) of the BM were differentially expressed in REN2 rats compared to SD rats, and EPO did not normalize this. Altogether, these results suggest that BM dysfunction is an important contributor to HF-associated anemia and that EPO is not an effective agent to treat HF-associated anemia

Cross-talk between epidermal growth factor receptor and protein kinase C during calcium-induced differentiation of keratinocytes

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/74029/1/j.1600-0625.2000.009003192.x.pd

Calculation of the Electron Self Energy for Low Nuclear Charge

We present a nonperturbative numerical evaluation of the one-photon electron self energy for hydrogenlike ions with low nuclear charge numbers Z=1 to 5. Our calculation for the 1S state has a numerical uncertainty of 0.8 Hz for hydrogen and 13 Hz for singly-ionized helium. Resummation and convergence acceleration techniques that reduce the computer time by about three orders of magnitude were employed in the calculation. The numerical results are compared to results based on known terms in the expansion of the self energy in powers of (Z alpha).Comment: 10 pages, RevTeX, 2 figure

Bumpy black holes from spontaneous Lorentz violation

We consider black holes in Lorentz violating theories of massive gravity. We argue that in these theories black hole solutions are no longer universal and exhibit a large number of hairs. If they exist, these hairs probe the singularity inside the black hole providing a window into quantum gravity. The existence of these hairs can be tested by future gravitational wave observatories. We generically expect that the effects we discuss will be larger for the more massive black holes. In the simplest models the strength of the hairs is controlled by the same parameter that sets the mass of the graviton (tensor modes). Then the upper limit on this mass coming from the inferred gravitational radiation emitted by binary pulsars implies that hairs are likely to be suppressed for almost the entire mass range of the super-massive black holes in the centers of galaxies.Comment: 40 pages, 4 figure