Diving into the vertical dimension of elasmobranch movement ecology

Knowledge of the three-dimensional movement patterns of elasmobranchs is vital to understand their ecological roles and exposure to anthropogenic pressures. To date, comparative studies among species at global scales have mostly focused on horizontal movements. Our study addresses the knowledge gap of vertical movements by compiling the first global synthesis of vertical habitat use by elasmobranchs from data obtained by deployment of 989 biotelemetry tags on 38 elasmobranch species. Elasmobranchs displayed high intra- and interspecific variability in vertical movement patterns. Substantial vertical overlap was observed for many epipelagic elasmobranchs, indicating an increased likelihood to display spatial overlap, biologically interact, and share similar risk to anthropogenic threats that vary on a vertical gradient. We highlight the critical next steps toward incorporating vertical movement into global management and monitoring strategies for elasmobranchs, emphasizing the need to address geographic and taxonomic biases in deployments and to concurrently consider both horizontal and vertical movements

Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network

Using the Cap Analysis of Gene Expression (CAGE) technology, the FANTOM5 consortium provided one of the most comprehensive maps of transcription start sites (TSSs) in several species. Strikingly, ~72% of them could not be assigned to a specific gene and initiate at unconventional regions, outside promoters or enhancers. Here, we probe these unassigned TSSs and show that, in all species studied, a significant fraction of CAGE peaks initiate at microsatellites, also called short tandem repeats (STRs). To confirm this transcription, we develop Cap Trap RNA-seq, a technology which combines cap trapping and long read MinION sequencing. We train sequence-based deep learning models able to predict CAGE signal at STRs with high accuracy. These models unveil the importance of STR surrounding sequences not only to distinguish STR classes, but also to predict the level of transcription initiation. Importantly, genetic variants linked to human diseases are preferentially found at STRs with high transcription initiation level, supporting the biological and clinical relevance of transcription initiation at STRs. Together, our results extend the repertoire of non-coding transcription associated with DNA tandem repeats and complexify STR polymorphism

Factors Associated with Revision Surgery after Internal Fixation of Hip Fractures

Background: Femoral neck fractures are associated with high rates of revision surgery after management with internal fixation. Using data from the Fixation using Alternative Implants for the Treatment of Hip fractures (FAITH) trial evaluating methods of internal fixation in patients with femoral neck fractures, we investigated associations between baseline and surgical factors and the need for revision surgery to promote healing, relieve pain, treat infection or improve function over 24 months postsurgery. Additionally, we investigated factors associated with (1) hardware removal and (2) implant exchange from cancellous screws (CS) or sliding hip screw (SHS) to total hip arthroplasty, hemiarthroplasty, or another internal fixation device. Methods: We identified 15 potential factors a priori that may be associated with revision surgery, 7 with hardware removal, and 14 with implant exchange. We used multivariable Cox proportional hazards analyses in our investigation. Results: Factors associated with increased risk of revision surgery included: female sex, [hazard ratio (HR) 1.79, 95% confidence interval (CI) 1.25-2.50; P = 0.001], higher body mass index (fo

Learning Signaling Network Structures with Sparsely Distributed Data

Flow cytometric measurement of signaling protein abundances has proved particularly useful for elucidation of signaling pathway structure. The single cell nature of the data ensures a very large dataset size, providing a statistically robust dataset for structure learning. Moreover, the approach is easily scaled to many conditions in high throughput. However, the technology suffers from a dimensionality constraint: at the cutting edge, only about 12 protein species can be measured per cell, far from sufficient for most signaling pathways. Because the structure learning algorithm (in practice) requires that all variables be measured together simultaneously, this restricts structure learning to the number of variables that constitute the flow cytometer's upper dimensionality limit. To address this problem, we present here an algorithm that enables structure learning for sparsely distributed data, allowing structure learning beyond the measurement technology's upper dimensionality limit for simultaneously measurable variables. The algorithm assesses pairwise (or n-wise) dependencies, constructs “Markov neighborhoods” for each variable based on these dependencies, measures each variable in the context of its neighborhood, and performs structure learning using a constrained search.Leukemia & Lymphoma Society of AmericaNational Institutes of Health (U.S.) (grant AI06584)National Institutes of Health (U.S.) (grant GM68762)Burroughs Wellcome FundNational Institutes of Health (U.S.) (grant N01-HV-28183)National Institutes of Health (U.S.) (U19 AI057229)National Institutes of Health (U.S.) (2P01 AI36535)National Institutes of Health (U.S.) (U19 AI062623)National Institutes of Health (U.S.) (R01-AI065824)National Institutes of Health (U.S.) (2P01 CA034233-22A1)National Institutes of Health (U.S.) (HHSN272200700038C)National Institutes of Health (U.S.) (NCI grant U54 RFA-CA-05-024)National Institutes of Health (U.S.) (LLS grant 7017-6

Minimal atomic complexes

We define <I>minimal atomic complexes</I> and <I>irreducible complexes</I>, and we prove that they are the same. The irreducible complexes admit homological characterizations that make them easy to recognize. These concepts apply both to spaces and to spectra. On the spectrum level, our characterizations allow us to show that such familiar spectra as <I>ko</I>, <I>eo</I><SUB>2</SUB>, and <I>BoP</I> at the prime 2, all <I>BP</I><<I>n</I>> at any prime <I>p</I>, and the indecomposable wedge summands of <IMG height="13" alt="Image" src="http://eprints.gla.ac.uk/images/sigmacp.gif" width="51" align="absBottom" border="0" /> and <IMG height="13" alt="Image" src="http://eprints.gla.ac.uk/images/sigmahp.gif" width="53" align="absBottom" border="0" /> at any prime <I>p</I> are irreducible and therefore minimal atomic. Up to equivalence, the minimal atomic complexes admit escriptions as CW complexes with restricted attaching maps, called <I>nuclear complexes</I>, and this description can be refined further to <I>nuclear minimal complexes</I>, which are nuclear and have zero differential on their mod <I>p</I> chains. As an illustrative example, we construct <I>BoP</I> as a nuclear complex