Anchoring historical sequences using a new source of astro-chronological tie-points

The discovery of past spikes in atmospheric radiocarbon activity, caused by major solar energetic particle events, has opened up new possibilities for high-precision chronometry. The two spikes, or Miyake Events, have now been widely identified in tree-rings that grew in the years 775 and 994 CE. Furthermore, all other plant material that grew in these years would also have incorporated the anomalously high concentrations of radiocarbon. Crucially, some plant-based artefacts, such as papyrus documents, timber beams and linen garments, can also be allocated to specific positions within long, currently unfixed, historical sequences. Thus, Miyake Events represent a new source of tie-points that could provide the means for anchoring early chronologies to the absolute timescale. Here, we explore this possibility, outlining the most expeditious approaches, the current challenges and obstacles, and how they might best be overcome.Comment: 11 pages, accepted to Royal Society Proc

Robust prediction of clinical outcomes using cytometry data.

MotivationFlow cytometry and mass cytometry are widely used to diagnose diseases and to predict clinical outcomes. When associating clinical features with cytometry data, traditional analysis methods require cell gating as an intermediate step, leading to information loss and susceptibility to batch effects. Here, we wish to explore an alternative approach that predicts clinical features from cytometry data without the cell-gating step. We also wish to test if such a gating-free approach increases the accuracy and robustness of the prediction.ResultsWe propose a novel strategy (CytoDx) to predict clinical outcomes using cytometry data without cell gating. Applying CytoDx on real-world datasets allow us to predict multiple types of clinical features. In particular, CytoDx is able to predict the response to influenza vaccine using highly heterogeneous datasets, demonstrating that it is not only accurate but also robust to batch effects and cytometry platforms.Availability and implementationCytoDx is available as an R package on Bioconductor (bioconductor.org/packages/CytoDx). Data and scripts for reproducing the results are available on bitbucket.org/zichenghu_ucsf/cytodx_study_code/downloads.Supplementary informationSupplementary data are available at Bioinformatics online

Greater data science at baccalaureate institutions

Donoho's JCGS (in press) paper is a spirited call to action for statisticians, who he points out are losing ground in the field of data science by refusing to accept that data science is its own domain. (Or, at least, a domain that is becoming distinctly defined.) He calls on writings by John Tukey, Bill Cleveland, and Leo Breiman, among others, to remind us that statisticians have been dealing with data science for years, and encourages acceptance of the direction of the field while also ensuring that statistics is tightly integrated. As faculty at baccalaureate institutions (where the growth of undergraduate statistics programs has been dramatic), we are keen to ensure statistics has a place in data science and data science education. In his paper, Donoho is primarily focused on graduate education. At our undergraduate institutions, we are considering many of the same questions.Comment: in press response to Donoho paper in Journal of Computational Graphics and Statistic

Optimizing optical Bragg scattering for single-photon frequency conversion

We develop a systematic theory for optimising single-photon frequency conversion using optical Bragg scattering. The efficiency and phase-matching conditions for the desired Bragg scattering conversion as well as spurious scattering and modulation instability are identified. We find that third-order dispersion can suppress unwanted processes, while dispersion above the fourth order limits the maximum conversion efficiency. We apply the optimisation conditions to frequency conversion in highly nonlinear fiber, silicon nitride waveguides and silicon nanowires. Efficient conversion is confirmed using full numerical simulations. These design rules will assist the development of efficient quantum frequency conversion between multicolour single photon sources for integration in complex quantum networks.Comment: 9 pages, 14 figure

Histone H1 is essential for mitotic chromosome architecture and segregation in Xenopus laevis egg extracts.

During cell division, condensation and resolution of chromosome arms and the assembly of a functional kinetochore at the centromere of each sister chromatid are essential steps for accurate segregation of the genome by the mitotic spindle, yet the contribution of individual chromatin proteins to these processes is poorly understood. We have investigated the role of embryonic linker histone H1 during mitosis in Xenopus laevis egg extracts. Immunodepletion of histone H1 caused the assembly of aberrant elongated chromosomes that extended off the metaphase plate and outside the perimeter of the spindle. Although functional kinetochores assembled, aligned, and exhibited poleward movement, long and tangled chromosome arms could not be segregated in anaphase. Histone H1 depletion did not significantly affect the recruitment of known structural or functional chromosomal components such as condensins or chromokinesins, suggesting that the loss of H1 affects chromosome architecture directly. Thus, our results indicate that linker histone H1 plays an important role in the structure and function of vertebrate chromosomes in mitosis