One read per cell per gene is optimal for single-cell RNA-Seq

An underlying question for virtually all single-cell RNA sequencing experiments is how to allocate the limited sequencing budget: deep sequencing of a few cells or shallow sequencing of many cells? A mathematical framework reveals that, for estimating many important gene properties, the optimal allocation is to sequence at the depth of one read per cell per gene. Interestingly, the corresponding optimal estimator is not the widely-used plug-in estimator but one developed via empirical Bayes

Path integral Monte Carlo simulations of silicates

We investigate the thermal expansion of crystalline SiO$_2$ in the $\beta$-- cristobalite and the $\beta$-quartz structure with path integral Monte Carlo (PIMC) techniques. This simulation method allows to treat low-temperature quantum effects properly. At temperatures below the Debye temperature, thermal properties obtained with PIMC agree better with experimental results than those obtained with classical Monte Carlo methods.Comment: 27 pages, 10 figures, Phys. Rev. B (in press

Impact of boundaries on fully connected random geometric networks

Many complex networks exhibit a percolation transition involving a macroscopic connected component, with universal features largely independent of the microscopic model and the macroscopic domain geometry. In contrast, we show that the transition to full connectivity is strongly influenced by details of the boundary, but observe an alternative form of universality. Our approach correctly distinguishes connectivity properties of networks in domains with equal bulk contributions. It also facilitates system design to promote or avoid full connectivity for diverse geometries in arbitrary dimension.Comment: 6 pages, 3 figure

Glass-Like Heat Conduction in High-Mobility Crystalline Semiconductors

The thermal conductivity of polycrystalline semiconductors with type-I clathrate hydrate crystal structure is reported. Ge clathrates (doped with Sr and/or Eu) exhibit lattice thermal conductivities typical of amorphous materials. Remarkably, this behavior occurs in spite of the well-defined crystalline structure and relatively high electron mobility ($\sim 100 cm^2/Vs$). The dynamics of dopant ions and their interaction with the polyhedral cages of the structure are a likely source of the strong phonon scattering.Comment: 4 pages, 3 postscript figures, to be published, Phys. Rev. Let

Polarization of macrophages toward M2 phenotype is favored by reduction in iPLA2β (group VIA phospholipase A2)*

Macrophages are important in innate and adaptive immunity. Macrophage participation in inflammation or tissue repair is directed by various extracellular signals and mediated by multiple intracellular pathways. Activation of group VIA phospholipase A2 (iPLA2β) causes accumulation of arachidonic acid, lysophospholipids, and eicosanoids that can promote inflammation and pathologic states. We examined the role of iPLA2β in peritoneal macrophage immune function by comparing wild type (WT) and iPLA2β−/− mouse macrophages. Compared with WT, iPLA2β−/− macrophages exhibited reduced proinflammatory M1 markers when classically activated. In contrast, anti-inflammatory M2 markers were elevated under naïve conditions and induced to higher levels by alternative activation in iPLA2β−/− macrophages compared with WT. Induction of eicosanoid (12-lipoxygenase (12-LO) and cyclooxygenase 2 (COX2))- and reactive oxygen species (NADPH oxidase 4 (NOX4))-generating enzymes by classical activation pathways was also blunted in iPLA2β−/− macrophages compared with WT. The effects of inhibitors of iPLA2β, COX2, or 12-LO to reduce M1 polarization were greater than those to enhance M2 polarization. Certain lipids (lysophosphatidylcholine, lysophosphatidic acid, and prostaglandin E2) recapitulated M1 phenotype in iPLA2β−/− macrophages, but none tested promoted M2 phenotype. These findings suggest that (a) lipids generated by iPLA2β and subsequently oxidized by cyclooxygenase and 12-LO favor macrophage inflammatory M1 polarization, and (b) the absence of iPLA2β promotes macrophage M2 polarization. Reducing macrophage iPLA2β activity and thereby attenuating macrophage M1 polarization might cause a shift from an inflammatory to a recovery/repair milieu

Shrinking Point Bifurcations of Resonance Tongues for Piecewise-Smooth, Continuous Maps

Resonance tongues are mode-locking regions of parameter space in which stable periodic solutions occur; they commonly occur, for example, near Neimark-Sacker bifurcations. For piecewise-smooth, continuous maps these tongues typically have a distinctive lens-chain (or sausage) shape in two-parameter bifurcation diagrams. We give a symbolic description of a class of "rotational" periodic solutions that display lens-chain structures for a general $N$-dimensional map. We then unfold the codimension-two, shrinking point bifurcation, where the tongues have zero width. A number of codimension-one bifurcation curves emanate from shrinking points and we determine those that form tongue boundaries.Comment: 27 pages, 6 figure

Composite CDMA - A statistical mechanics analysis

Code Division Multiple Access (CDMA) in which the spreading code assignment to users contains a random element has recently become a cornerstone of CDMA research. The random element in the construction is particular attractive as it provides robustness and flexibility in utilising multi-access channels, whilst not making significant sacrifices in terms of transmission power. Random codes are generated from some ensemble, here we consider the possibility of combining two standard paradigms, sparsely and densely spread codes, in a single composite code ensemble. The composite code analysis includes a replica symmetric calculation of performance in the large system limit, and investigation of finite systems through a composite belief propagation algorithm. A variety of codes are examined with a focus on the high multi-access interference regime. In both the large size limit and finite systems we demonstrate scenarios in which the composite code has typical performance exceeding sparse and dense codes at equivalent signal to noise ratio.Comment: 23 pages, 11 figures, Sigma Phi 2008 conference submission - submitted to J.Stat.Mec

Why People Gamble: A Qualitative Study of Four New Zealand Ethnic Groups

In multicultural countries such as New Zealand, it is particularly important that gambling research take into account possible cultural differences. Many New Zealanders come from cultures that do not have a history of gambling, including the Mäori (New Zealand indigenous people), Pacific Islanders, and recent migrants. Little research has examined the reasons why people start and continue to gamble, especially among different ethnic groups. This research project thus aimed to develop a framework to explain how environmental, cultural, and social factors interact with personal attributes to determine gambling behaviors. In a qualitative study, 131 people broadly representative of Mäori, Pacific, Asian, and Päkehä/New Zealand European groups residing in New Zealand were interviewed individually or in focus groups. They included social and problem gamblers, families of problem gamblers, and professionals. Different personal, socioeconomic, environmental, and cultural factors were identified, summarized in a developmental framework, and compared to factors found for ethnic groups in other countries. Public health policy issues were raised, including greater control of gambling promotion. © 2012 The Author(s).published_or_final_versionSpringer Open Choice, 28 May 201