How Many Subpopulations is Too Many? Exponential Lower Bounds for Inferring Population Histories

Reconstruction of population histories is a central problem in population genetics. Existing coalescent-based methods, like the seminal work of Li and Durbin (Nature, 2011), attempt to solve this problem using sequence data but have no rigorous guarantees. Determining the amount of data needed to correctly reconstruct population histories is a major challenge. Using a variety of tools from information theory, the theory of extremal polynomials, and approximation theory, we prove new sharp information-theoretic lower bounds on the problem of reconstructing population structure -- the history of multiple subpopulations that merge, split and change sizes over time. Our lower bounds are exponential in the number of subpopulations, even when reconstructing recent histories. We demonstrate the sharpness of our lower bounds by providing algorithms for distinguishing and learning population histories with matching dependence on the number of subpopulations. Along the way and of independent interest, we essentially determine the optimal number of samples needed to learn an exponential mixture distribution information-theoretically, proving the upper bound by analyzing natural (and efficient) algorithms for this problem.Comment: 38 pages, Appeared in RECOMB 201

Three Decades of Internet- and Computer-Based Interventions for the Treatment of Depression: Protocol for a Systematic Review and Meta-Analysis

Background: Depression is one of the leading causes of disability worldwide. Internet- and computer-based interventions (IBIs) have been shown to provide effective, scalable forms of treatment. More than 100 controlled trials and a growing number of meta-analyses published over the past 30 years have demonstrated the efficacy of IBIs in reducing symptoms in the short and long term. Despite the large body of research, no comprehensive review or meta-analysis has been conducted to date that evaluates how the effectiveness of IBIs has evolved over time.Objective: This systematic review and meta-analysis aims to evaluate whether there has been a change in the effectiveness of IBIs on the treatment of depression over the past 30 years and to identify potential variables moderating the effect size.Methods: A sensitive search strategy will be executed across the Cochrane Central Register of Controlled Trials (CENTRAL), MEDLINE, EMBASE, and PsycINFO. Data extraction and evaluation will be conducted by two independent researchers. Risk of bias will be assessed. A multilevel meta-regression model will be used to analyze the data and estimate effect size.Results: The search was completed in mid-2019. We expect the results to be submitted for publication in early 2020.Conclusions: The year 2020 will mark 30 years since the first paper was published on the use of IBIs for the treatment of depression. Despite the large and rapidly growing body of research in the field, evaluations of effectiveness to date are missing the temporal dimension. This review will address that gap and provide valuable analysis of how the effectiveness of interventions has evolved over the past three decades; which participant-, intervention-, and study-related variables moderate changes in effectiveness; and where research in the field may benefit from increased focus.</p

A novel isoform of the Ly108 gene ameliorates murine lupus

Studies of human systemic lupus erythematosus patients and of murine congenic mouse strains associate genes in a DNA segment on chromosome 1 with a genetic predisposition for this disease. The systematic analysis of lupus-prone congenic mouse strains suggests a role for two isoforms of the Ly108 receptor in the pathogenesis of the disease. In this study, we demonstrate that Ly108 is involved in the pathogenesis of lupus-related autoimmunity in mice. More importantly, we identified a third protein isoform, Ly108-H1, which is absent in two lupus-prone congenic animals. Introduction of an Ly108-H1–expressing transgene markedly diminishes T cell–dependent autoimmunity in congenic B6.Sle1b mice. Thus, an immune response–suppressing isoform of Ly108 can regulate the pathogenesis of lupus.Peer Reviewe

Measurements of neutrino oscillation in appearance and disappearance channels by the T2K experiment with 6.6 x 10(20) protons on target

111 pages, 45 figures, submitted to Physical Review D. Minor revisions to text following referee comments111 pages, 45 figures, submitted to Physical Review D. Minor revisions to text following referee comments111 pages, 45 figures, submitted to Physical Review D. Minor revisions to text following referee commentsWe thank the J-PARC staff for superb accelerator performance and the CERN NA61/SHINE Collaboration for providing valuable particle production data. We acknowledge the support of MEXT, Japan; NSERC, NRC, and CFI, Canada; CEA and CNRS/IN2P3, France; DFG, Germany; INFN, Italy; National Science Centre (NCN), Poland; RSF, RFBR and MES, Russia; MINECO and ERDF funds, Spain; SNSF and SER, Switzerland; STFC, UK; and the U. S. Deparment of Energy, USA. We also thank CERN for the UA1/NOMAD magnet, DESY for the HERA-B magnet mover system, NII for SINET4, the WestGrid and SciNet consortia in Compute Canada, GridPP, UK, and the Emerald High Performance Computing facility in the Centre for Innovation, UK. In addition, participation of individual researchers and institutions has been further supported by funds from ERC (FP7), EU; JSPS, Japan; Royal Society, UK; and DOE Early Career program, USA

Measurement of the electron neutrino charged-current interaction rate on water with the T2K ND280 pi(0) detector

10 pages, 6 figures, Submitted to PRDhttp://journals.aps.org/prd/abstract/10.1103/PhysRevD.91.112010© 2015 American Physical Society11 pages, 6 figures, as accepted to PRD11 pages, 6 figures, as accepted to PRD11 pages, 6 figures, as accepted to PR

Search for short baseline nu(e) disappearance with the T2K near detector

8 pages, 6 figures, submitted to PRD rapid communication8 pages, 6 figures, submitted to PRD rapid communicationWe thank the J-PARC staff for superb accelerator performance and the CERN NA61 collaboration for providing valuable particle production data. We acknowledge the support of MEXT, Japan; NSERC, NRC and CFI, Canada; Commissariat `a l’Energie Atomique and Centre National de la Recherche Scientifique–Institut National de Physique Nucle´aire et de Physique des Particules, France; DFG, Germany; INFN, Italy; National Science Centre (NCN), Poland; Russian Science Foundation, RFBR and Ministry of Education and Science, Russia; MINECO and European Regional Development Fund, Spain; Swiss National Science Foundation and State Secretariat for Education, Research and Innovation, Switzerland; STFC, UK; and DOE, USA. We also thank CERN for the UA1/NOMAD magnet, DESY for the HERA-B magnet mover system, NII for SINET4, the WestGrid and SciNet consortia in Compute Canada, GridPP, UK. In addition participation of individual researchers and institutions has been further supported by funds from ERC (FP7), EU; JSPS, Japan; Royal Society, UK; DOE Early Career program, USA

Chitin Modulates Innate Immune Responses of Keratinocytes

Chitin, after cellulose the second most abundant polysaccharide in nature, is an essential component of exoskeletons of crabs, shrimps and insects and protects these organisms from harsh conditions in their environment. Unexpectedly, chitin has been found to activate innate immune cells and to elicit murine airway inflammation. The skin represents the outer barrier of the human host defense and is in frequent contact with chitin-bearing organisms, such as house-dust mites or flies. The effects of chitin on keratinocytes, however, are poorly understood. We hypothesized that chitin stimulates keratinocytes and thereby modulates the innate immune response of the skin. Here we show that chitin is bioactive on primary and immortalized keratinocytes by triggering production of pro-inflammatory cytokines and chemokines. Chitin stimulation further induced the expression of the Toll-like receptor (TLR) TLR4 on keratinocytes at mRNA and protein level. Chitin-induced effects were mainly abrogated when TLR2 was blocked, suggesting that TLR2 senses chitin on keratinocytes. We speculate that chitin-bearing organisms modulate the innate immune response towards pathogens by upregulating secretion of cytokines and chemokines and expression of MyD88-associated TLRs, two major components of innate immunity. The clinical relevance of this mechanism remains to be defined

Adaptive Evolution in Ecological Communities

Multi-species interactions can influence evolution in ways that are unpredictable from studies that focus on simpler communities because direct and indirect species interactions alter the strength and direction of selection

The evolution of private provision in urban drinking water: New geographies, institutional ambiguity and the need for political economy

Empirical research paints a dynamic picture of the evolution of private provision in urban drinking water. A second wave of privatisation is clustered in a key group of countries, distinguished by the rise of new domestic private and quasi-private providers. This is, however, taking place in the presence of a counter-dynamic of remunicipalisation. In response to the complexity in provision arrangements revealed, three case studies are used to illustrate how different power balance configurations in the state-society-capital complex inform particular institutional arrangements. In Germany, civil society pressure challenged private capital resulting in the reinstatement of municipal control in Berlin, but at high long-term costs. In Russia, disempowered civil society has watched as the ruling regime exploits the support of international public agencies and foreign investors, while carefully safeguarding the interests of domestic private capital. In China, different levels of the state have promoted quasi-state actors into global corporations, managing the entry of international capital in order to bolster domestic support for desired political reforms. Public responsibility, and equally the re-assertion of public control after a period of private provision, may not in itself secure net social benefit where the right of capital to profit is put before broader social considerations