Malformations of the sacculus and the semicircular canals in spider morph pythons

Spider morph ball pythons are a frequently-bred designer morph with striking alterations of the skin color pattern. We created high-resolution μCT-image series through the otic region of the skulls, used 3D-reconstruction software for rendering anatomical models, and compared the anatomy of the semicircular ducts, sacculus and ampullae of wildtype Python regius (ball python) with spider morph snakes. All spider morph snakes showed the wobble condition (i.e., twisting movements of the head, impaired locomotion, difficulty striking or constricting prey items). We describe the inner ear structures in wildtype and spider morph snakes and report a deviant morphology of semicircular canals, ampullae and sacculus in the latter. We also report about associated differences in the desmal skull bones of spider morph snakes, which were characterized by wider semicircular canals, ampullae widened and difficult to discern in μCT, a deformed crus communis, and a small sacculus with a highly deviant X-ray morphology as compared to wildtype individuals. We observed considerable intra- and interindividual variability of these features. This deviant morphology in spider morph snakes could easily be associated with an impairment of sense of equilibrium and the observed neurological wobble condition. Limitations in sample size prevent statistical analyses, but the anatomical evidence is strong enough to support an association between the wobble condition and a malformation of the inner ear structures. A link between artificially selected alterations in pattern and specific color design with neural-crest associated developmental malformations of the statoacoustic organ as known from other vertebrates is discussed

MCALab: Reproducible Research in Signal and Image Decomposition and Inpainting

International audienceMorphological Component Analysis (MCA) of signals and images is an ambitious and important goal in signal processing; successful methods for MCA have many far-reaching applications in science and technology. Because MCA is related to solving underdetermined systems of linear equations it might also be considered, by some, to be problematic or even intractable. Reproducible research is essential to to give such a concept a firm scientific foundation and broad base of trusted results. MCALab has been developed to demonstrate key concepts of MCA and make them available to interested researchers and technologists. MCALab is a library of Matlab routines that implement the decomposition and inpainting algorithms that we previously proposed in [1], [2], [3], [4]. The MCALab package provides the research community with open source tools for sparse decomposition and inpainting and is made available for anonymous download over the Internet. It contains a variety of scripts to reproduce the figures in our own articles, as well as other exploratory examples not included in the papers. One can also run the same experiments on one's own data or tune the parameters by simply modifying the scripts. The MCALab is under continuing development by the authors; who welcome feedback and suggestions for further enhancements, and any contributions by interested researchers

Three genetically distinct ferlaviruses have varying effects on infected corn snakes (Pantherophis guttatus)

Ferlaviruses are important pathogens in snakes and other reptiles. They cause respiratory and neurological disease in infected animals and can cause severe disease outbreaks. Isolates from this genus can be divided into four genogroups-A, B, and C, as well as a more distantly related sister group, "tortoise". Sequences from large portions (5.3 kb) of the genomes of a variety of ferlavirus isolates from genogroups A, B, and C, including the genes coding the surface glycoproteins F and HN as well as the L protein were determined and compared. In silico analyses of the glycoproteins of genogroup A, B, and C isolates were carried out. Three isolates representing these three genogroups were used in transmission studies with corn snakes (Pantherophis guttatus), and clinical signs, gross and histopathology, electronmicroscopic changes in the lungs, and isolation of bacteria from the lungs were evaluated. Analysis of the sequences supported the previous categorization of ferlaviruses into four genogroups, and criteria for definition of ferlavirus genogroups and species were established based on sequence identities (80% resp. 90%). Analysis of the ferlavirus glycoprotein models showed parallels to corresponding regions of other paramyxoviruses. The transmission studies showed clear differences in the pathogenicities of the three virus isolates used. The genogroup B isolate was the most and the group A virus the least pathogenic. Reasons for these differences were not clear based on the differences in the putative structures of their respective glycoproteins, although e.g. residue and consequential structure variation of an extended cleavage site or changes in electrostatic charges at enzyme binding sites could play a role. The presence of bacteria in the lungs of the infected animals also clearly corresponded to increased pathogenicity. This study contributes to knowledge about the structure and phylogeny of ferlaviruses and lucidly demonstrates differences in pathogenicity between strains of different genogroups

UNIONS: The impact of systematic errors on weak-lensing peak counts

UNIONS is an ongoing deep photometric multi-band survey of the Northern sky. As part of UNIONS, CFIS provides r-band data which we use to study weak-lensing peak counts for cosmological inference. We assess systematic effects for weak-lensing peak counts and their impact on cosmological parameters for the UNIONS survey. In particular, we present results on local calibration, metacalibration shear bias, baryonic feedback, the source galaxy redshift estimate, intrinsic alignment, and the cluster member dilution. For each uncertainty and systematic effect, we describe our mitigation scheme and the impact on cosmological parameter constraints. We obtain constraints on cosmological parameters from MCMC using CFIS data and MassiveNuS N-body simulations as a model for peak counts statistics. Depending on the calibration (local versus global, and the inclusion of the residual multiplicative shear bias), the mean matter density parameter $\Omega_m$ can shift up to $-0.024$ ($-0.5\sigma$). We also see that including baryonic corrections can shift $\Omega_m$ by $+0.027$ ($+0.5 \sigma$) with respect to the DM-only simulations. Reducing the impact of the intrinsic alignment and cluster member dilution through signal-to-noise cuts can lead to a shift in $\Omega_m$ of $+0.027$ ($+0.5 \sigma$). Finally, with a mean redshift uncertainty of $\Delta \bar{z} = 0.03$, we see that the shift of $\Omega_m$ ($+0.001$ which corresponds to $+0.02 \sigma$) is not significant. This paper investigates for the first time with UNIONS weak-lensing data and peak counts the impact of systematic effects. The value of $\Omega_m$ is the most impacted and can shift up to $\sim 0.03$ which corresponds to $0.5\sigma$ depending on the choices for each systematics. We expect constraints to become more reliable with future (larger) data catalogues, for which the current pipeline will provide a starting point.Comment: 17 pages, 17 figure

Loss-of-function but not dominant-negative intragenic IKZF1 deletions are associated with an adverse prognosis in adult BCR-ABL-negative acute lymphoblastic leukemia

Genetic alterations of the transcription factor IKZF1 (“IKAROS”) are detected in around 15–30% of cases of BCR-ABL-negative B-cell precursor acute lymphoblastic leukemia. Different types of intragenic deletions have been observed, resulting in a functionally inactivated allele (“loss-of-function”) or in “dominant-negative” isoforms. The prognostic impact of these alterations especially in adult acute lymphoblastic leukemia is not well defined. We analyzed 482 well-characterized cases of adult BCR-ABL-negative B-precursor acute lymphoblastic leukemia uniformly treated in the framework of the GMALL studies and detected IKZF1 alterations in 128 cases (27%). In 20%, the IKZF1 alteration was present in a large fraction of leukemic cells (“high deletion load”) while in 7% it was detected only in small subclones (“low deletion load”). Some patients showed more than one IKZF1 alteration (8%). Patients exhibiting a loss-of-function isoform with high deletion load had a shorter overall survival (OS at 5 years 28% vs. 59%; P<0.0001), also significant in a subgroup analysis of standard risk patients according to GMALL classification (OS at 5 years 37% vs. 68%; P=0.0002). Low deletion load or dominant-negative IKZF1 alterations had no prognostic impact. The results thus suggest that there is a clear distinction between loss-of-function and dominant-negative IKZF1 deletions. Affected patients should thus be monitored for minimal residual disease carefully to detect incipient relapses at an early stage and they are potential candidates for alternative or intensified treatment regimes. (clinicaltrials.gov identifiers: 00199056 and 00198991)

Political masculinities, crisis tendencies, and social transition: Toward an understanding of change

This introduction to the special issue on “Political Masculinities and Social Transition” rethinks the notion of “crisis in masculinity” and points to its weaknesses, such as cyclical patterns and chronicity. Rather than viewing key moments in history as points of rupture, we understand social change as encompassing ongoing transitions marked by a “fluid nature” (Montecinos 2017, 2). In line with this, the contributions examine how political masculinities are implicated within a wide range of social transitions, such as nation building after war, the founding of a new political party in response to an economic crisis, an “authoritarian relapse” of a democracy, attempts at changing society through terrorism, rapid industrialization as well as peace building in conflict areas. Building on Starck and Sauer’s definition of “political masculinities” we suggest applying the concept to instances in which power is explicitly either being (re)produced or challenged. We distinguish between political masculinities that are more readily identified as such (e.g., professional politicians) and less readily identified political masculinities (e.g., citizens), emphasizing how these interact with each other. We ask whether there is a discernible trajectory in the characteristics of political masculinities brought about by social transition that can be confirmed across cultures. The contributors’ findings indicate that these political masculinities can contribute to different kinds of change that either maintain the status quo, are progressive, retrogressive, or a mixture of these. Revolutionary transitions, it seems, often promote the adherence to traditional forms of political masculinity, whereas more reformatory transition leaves discursive spaces for argument

Templates for Convex Cone Problems with Applications to Sparse Signal Recovery

This paper develops a general framework for solving a variety of convex cone problems that frequently arise in signal processing, machine learning, statistics, and other fields. The approach works as follows: first, determine a conic formulation of the problem; second, determine its dual; third, apply smoothing; and fourth, solve using an optimal first-order method. A merit of this approach is its flexibility: for example, all compressed sensing problems can be solved via this approach. These include models with objective functionals such as the total-variation norm, ||Wx||_1 where W is arbitrary, or a combination thereof. In addition, the paper also introduces a number of technical contributions such as a novel continuation scheme, a novel approach for controlling the step size, and some new results showing that the smooth and unsmoothed problems are sometimes formally equivalent. Combined with our framework, these lead to novel, stable and computationally efficient algorithms. For instance, our general implementation is competitive with state-of-the-art methods for solving intensively studied problems such as the LASSO. Further, numerical experiments show that one can solve the Dantzig selector problem, for which no efficient large-scale solvers exist, in a few hundred iterations. Finally, the paper is accompanied with a software release. This software is not a single, monolithic solver; rather, it is a suite of programs and routines designed to serve as building blocks for constructing complete algorithms.Comment: The TFOCS software is available at http://tfocs.stanford.edu This version has updated reference

GREAT3 results I: systematic errors in shear estimation and the impact of real galaxy morphology

We present first results from the third GRavitational lEnsing Accuracy Testing (GREAT3) challenge, the third in a sequence of challenges for testing methods of inferring weak gravitational lensing shear distortions from simulated galaxy images. GREAT3 was divided into experiments to test three specific questions, and included simulated space- and ground-based data with constant or cosmologically-varying shear fields. The simplest (control) experiment included parametric galaxies with a realistic distribution of signal-to-noise, size, and ellipticity, and a complex point spread function (PSF). The other experiments tested the additional impact of realistic galaxy morphology, multiple exposure imaging, and the uncertainty about a spatially-varying PSF; the last two questions will be explored in Paper II. The 24 participating teams competed to estimate lensing shears to within systematic error tolerances for upcoming Stage-IV dark energy surveys, making 1525 submissions overall. GREAT3 saw considerable variety and innovation in the types of methods applied. Several teams now meet or exceed the targets in many of the tests conducted (to within the statistical errors). We conclude that the presence of realistic galaxy morphology in simulations changes shear calibration biases by $\sim 1$ per cent for a wide range of methods. Other effects such as truncation biases due to finite galaxy postage stamps, and the impact of galaxy type as measured by the S\'{e}rsic index, are quantified for the first time. Our results generalize previous studies regarding sensitivities to galaxy size and signal-to-noise, and to PSF properties such as seeing and defocus. Almost all methods' results support the simple model in which additive shear biases depend linearly on PSF ellipticity.Comment: 32 pages + 15 pages of technical appendices; 28 figures; submitted to MNRAS; latest version has minor updates in presentation of 4 figures, no changes in content or conclusion