Estimating the number of change-points in a two-dimensional segmentation model without penalization

In computational biology, numerous recent studies have been dedicated to the analysis of the chromatin structure within the cell by two-dimensional segmentation methods. Motivated by this application, we consider the problem of retrieving the diagonal blocks in a matrix of observations. The theoretical properties of the least-squares estimators of both the boundaries and the number of blocks proposed by L\'evy-Leduc et al. [2014] are investigated. More precisely, the contribution of the paper is to establish the consistency of these estimators. A surprising consequence of our results is that, contrary to the onedimensional case, a penalty is not needed for retrieving the true number of diagonal blocks. Finally, the results are illustrated on synthetic data.Comment: 30 pages, 8 figure

Answering Conjunctive Queries under Updates

We consider the task of enumerating and counting answers to $k$-ary conjunctive queries against relational databases that may be updated by inserting or deleting tuples. We exhibit a new notion of q-hierarchical conjunctive queries and show that these can be maintained efficiently in the following sense. During a linear time preprocessing phase, we can build a data structure that enables constant delay enumeration of the query results; and when the database is updated, we can update the data structure and restart the enumeration phase within constant time. For the special case of self-join free conjunctive queries we obtain a dichotomy: if a query is not q-hierarchical, then query enumeration with sublinear$^\ast$ delay and sublinear update time (and arbitrary preprocessing time) is impossible. For answering Boolean conjunctive queries and for the more general problem of counting the number of solutions of k-ary queries we obtain complete dichotomies: if the query's homomorphic core is q-hierarchical, then size of the the query result can be computed in linear time and maintained with constant update time. Otherwise, the size of the query result cannot be maintained with sublinear update time. All our lower bounds rely on the OMv-conjecture, a conjecture on the hardness of online matrix-vector multiplication that has recently emerged in the field of fine-grained complexity to characterise the hardness of dynamic problems. The lower bound for the counting problem additionally relies on the orthogonal vectors conjecture, which in turn is implied by the strong exponential time hypothesis. $^\ast)$ By sublinear we mean $O(n^{1-\varepsilon})$ for some $\varepsilon>0$, where $n$ is the size of the active domain of the current database

Beyond Worst-Case Analysis for Joins with Minesweeper

We describe a new algorithm, Minesweeper, that is able to satisfy stronger runtime guarantees than previous join algorithms (colloquially, `beyond worst-case guarantees') for data in indexed search trees. Our first contribution is developing a framework to measure this stronger notion of complexity, which we call {\it certificate complexity}, that extends notions of Barbay et al. and Demaine et al.; a certificate is a set of propositional formulae that certifies that the output is correct. This notion captures a natural class of join algorithms. In addition, the certificate allows us to define a strictly stronger notion of runtime complexity than traditional worst-case guarantees. Our second contribution is to develop a dichotomy theorem for the certificate-based notion of complexity. Roughly, we show that Minesweeper evaluates $\beta$-acyclic queries in time linear in the certificate plus the output size, while for any $\beta$-cyclic query there is some instance that takes superlinear time in the certificate (and for which the output is no larger than the certificate size). We also extend our certificate-complexity analysis to queries with bounded treewidth and the triangle query.Comment: [This is the full version of our PODS'2014 paper.

A continuous non-linear shadowing model of columnar growth

We propose the first continuous model with long range screening (shadowing) that described columnar growth in one space dimension, as observed in plasma sputter deposition. It is based on a new continuous partial derivative equation with non-linear diffusion and where the shadowing effects apply on all the different processes.Comment: Fast Track Communicatio

Animal Models of Zika Virus Sexual Transmission

ZIKV was first identified in the 1940s as a mosquito-borne virus; however, sexual transmission, which is uncommon for arboviruses, was demonstrated more than 60 years later. Tissue culture and animal models have allowed scientists to study how this transmission is possible. Immunocompromised mice infected with ZIKV had high viral loads in their testes, and infection of immunocompetent female mice was achieved following intravaginal inoculation or inoculation via mating with an infected male. These mouse studies lead researchers to investigate the individual components of the male reproductive system. In cell culture and mouse models, ZIKV can persist in Sertoli and germ cells of the testes and epithelial cells in the epididymis, which may lead to sexual transmission even after ZIKV has been cleared from other tissues. ZIKV has also been studied in nonhuman primates (NHPs), which appears to mimic the limited human epidemiological data, with low rates of symptomatic individuals and similar clinical signs. Although refinement is needed, these animal models have proven to be key in ZIKV research and continue to help uncovering the mechanisms of sexual transmission. This review will focus on the animal models used to elucidate the mechanisms of sexual transmission and persistence of flaviviruses

Modeling Chromosomes in Mouse to Explore the Function of Genes, Genomic Disorders, and Chromosomal Organization

One of the challenges of genomic research after the completion of the human genome project is to assign a function to all the genes and to understand their interactions and organizations. Among the various techniques, the emergence of chromosome engineering tools with the aim to manipulate large genomic regions in the mouse model offers a powerful way to accelerate the discovery of gene functions and provides more mouse models to study normal and pathological developmental processes associated with aneuploidy. The combination of gene targeting in ES cells, recombinase technology, and other techniques makes it possible to generate new chromosomes carrying specific and defined deletions, duplications, inversions, and translocations that are accelerating functional analysis. This review presents the current status of chromosome engineering techniques and discusses the different applications as well as the implication of these new techniques in future research to better understand the function of chromosomal organization and structures

Ringing effects reduction by improved deconvolution algorithm Application to A370 CFHT image of gravitational arcs

We develop a self-consistent automatic procedure to restore informations from astronomical observations. It relies on both a new deconvolution algorithm called LBCA (Lower Bound Constraint Algorithm) and the use of the Wiener filter. In order to explore its scientific potential for strong and weak gravitational lensing, we process a CFHT image of the galaxies cluster Abell 370 which exhibits spectacular strong gravitational lensing effects. A high quality restoration is here of particular interest to map the dark matter within the cluster. We show that the LBCA turns out specially efficient to reduce ringing effects introduced by classical deconvolution algorithms in images with a high background. The method allows us to make a blind detection of the radial arc and to recover morphological properties similar to thoseobserved from HST data. We also show that the Wiener filter is suitable to stop the iterative process before noise amplification, using only the unrestored data.Comment: A&A in press 9 pages 9 figure

Argon I lines produced in a hollow cathode source, 332 nm to 5865 nm

We report precision measurements by Fourier transform spectroscopy of the vacuum wavenumber, line width, and relative signal strength of 928 lines in the Ar I spectrum. Wavelength in air and classification of the transition are supplied for each line. A comparison of our results with other precision measurements illustrates the sensitivity of Ar I wavelengths to conditions in the light source

Solar Carbon Monoxide, Thermal Profiling, and the Abundances of C, O, and their Isotopes

A solar photospheric "thermal profiling" analysis is presented, exploiting the infrared rovibrational bands of carbon monoxide (CO) as observed with the McMath-Pierce Fourier transform spectrometer (FTS) at Kitt Peak, and from above the Earth's atmosphere by the Shuttle-borne ATMOS experiment. Visible continuum intensities and center-limb behavior constrained the temperature profile of the deep photosphere, while CO center-limb behavior defined the thermal structure at higher altitudes. The oxygen abundance was self consistently determined from weak CO absorptions. Our analysis was meant to complement recent studies based on 3-D convection models which, among other things, have revised the historical solar oxygen (and carbon) abundance downward by a factor of nearly two; although in fact our conclusions do not support such a revision. Based on various considerations, an oxygen abundance of 700+/-100 ppm (parts per million relative to hydrogen) is recommended; the large uncertainty reflects the model sensitivity of CO. New solar isotopic ratios also are reported for 13C, 17O, and 18O.Comment: 90 pages, 19 figures (some with parts "a", "b", etc.); to be published in the Astrophysical Journal Supplement

Real-world Experience With Sunitinib Treatment in Patients With Metastatic Renal Cell Carcinoma: Clinical Outcome According to Risk Score.

BACKGROUND: ADONIS is an ongoing observational study in 9 European countries, designed to evaluate treatment patterns/outcomes in patients with metastatic renal cell carcinoma (mRCC) treated with first-line sunitinib and/or second-line axitinib post sunitinib. We present an evaluation of sunitinib efficacy by risk group, in the real-world setting examined in ADONIS. PATIENTS AND METHODS: Patients were enrolled at the start of first-line sunitinib treatment or second-line axitinib post sunitinib treatment. Evaluation of sunitinib efficacy was assessed by International Metastatic Renal Cell Carcinoma Database Consortium (IMDC) and Memorial Sloan Kettering Cancer Center risk criteria. RESULTS: For all patients in this analysis (N = 467), the median progression-free survival was 23.8 months (95% confidence interval [CI], 16.5-28.5 months), 11.8 months (95% CI, 8.1-17.4 months), and 4.6 months (95% CI, 2.5-7.7 months) for IMDC favorable-, intermediate-, and poor-risk groups, respectively. The median overall survival was 97.1 months (95% CI, 46.3 months-not evaluable [NE]), 33.5 months (95% CI, 20.5-46.6 months), and 10.0 months (95% CI, 4.5-19.8 months) for the respective risk groups. Data on individual risk factors were available for a subgroup of patients, allowing analysis by intermediate risk by 1 versus 2 risk factors. When including this subgroup (n = 120), the median overall survival for IMDC favorable-, intermediate-1, and intermediate-2 risk factors was 21.6 months (95% CI, 16.3 months-NE), 20.5 months (15.5 months-NE), and 15.1 months (4.1 months-NE), respectively. CONCLUSIONS: For patients overall and by risk-group stratification, survival estimates were aligned with previously published data. In patients with intermediate-1 risk, overall survival was very similar to patients with favorable risk. However, further exploration of outcome data from different sources is needed to confirm these observations