QUASII: QUery-Aware Spatial Incremental Index.

With large-scale simulations of increasingly detailed models and improvement of data acquisition technologies, massive amounts of data are easily and quickly created and collected. Traditional systems require indexes to be built before analytic queries can be executed efficiently. Such an indexing step requires substantial computing resources and introduces a considerable and growing data-to-insight gap where scientists need to wait before they can perform any analysis. Moreover, scientists often only use a small fraction of the data - the parts containing interesting phenomena - and indexing it fully does not always pay off. In this paper we develop a novel incremental index for the exploration of spatial data. Our approach, QUASII, builds a data-oriented index as a side-effect of query execution. QUASII distributes the cost of indexing across all queries, while building the index structure only for the subset of data queried. It reduces data-to-insight time and curbs the cost of incremental indexing by gradually and partially sorting the data, while producing a data-oriented hierarchical structure at the same time. As our experiments show, QUASII reduces the data-to-insight time by up to a factor of 11.4x, while its performance converges to that of the state-of-the-art static indexes

Space odyssey: efficient exploration of scientific data.

Advances in data acquisition---through more powerful supercomputers for simulation or sensors with better resolution---help scientists tremendously to understand natural phenomena. At the same time, however, it leaves them with a plethora of data and the challenge of analysing it. Ingesting all the data in a database or indexing it for an efficient analysis is unlikely to pay off because scientists rarely need to analyse all data. Not knowing a priori what parts of the datasets need to be analysed makes the problem challenging. Tools and methods to analyse only subsets of this data are rather rare. In this paper we therefore present Space Odyssey, a novel approach enabling scientists to efficiently explore multiple spatial datasets of massive size. Without any prior information, Space Odyssey incrementally indexes the datasets and optimizes the access to datasets frequently queried together. As our experiments show, through incrementally indexing and changing the data layout on disk, Space Odyssey accelerates exploratory analysis of spatial data by substantially reducing query-to-insight time compared to the state of the art

Morphological diversity of the speckled dace (Rhinichthys osculus) in Oregon's desert springs

The Speckled dace (Rhinichthys osculus) is the most widespread minnow in western North America (Gilbert and Williams, 2002). It has diversified widely across its range—both morphologically and genetically—and as such might rightly be called a species complex. Our ongoing work aims to determine where boundaries between potentially undescribed species lie in Oregon and to identify morphological differences that may help diagnose those taxonomic entities. Meristic and linear morphometric data were collected from preserved specimens originating in four major drainage basins in desert Oregon. Morphometric data points to some potential phenotypic differences between fish reared in springs (slow-moving water) and fish reared in streams (fast-moving water). In particular, spring fish from each basin tend to have shallower bodies and shorter heads than the stream fish from the same basin. The morphologic differences described by this study will give insight in to the evolutionary history of this species complex and how geography has influenced the diversification of R. osculus

Clinical impact of anti-inflammatory microglia and macrophage phenotypes at glioblastoma margins

Glioblastoma is a devastating brain cancer for which effective treatments are required. Tumour-associated microglia and macrophages promote glioblastoma growth in an immune-suppressed microenvironment. Most recurrences occur at the invasive margin of the surrounding brain, yet the relationships between microglia/macrophage phenotypes, T cells and programmed death-ligand 1 (an immune checkpoint) across human glioblastoma regions are understudied. In this study, we performed a quantitative immunohistochemical analysis of 15 markers of microglia/macrophage phenotypes (including anti-inflammatory markers triggering receptor expressed on myeloid cells 2 and CD163, and the low-affinity-activating receptor CD32a), T cells, natural killer cells and programmed death-ligand 1, in 59 human IDH1-wild-type glioblastoma multi-regional samples (n = 177; 1 sample at tumour core, 2 samples at the margins: the infiltrating zone and leading edge). Assessment was made for the prognostic value of markers; the results were validated in an independent cohort. Microglia/macrophage motility and activation (Iba1, CD68), programmed death-ligand 1 and CD4+ T cells were reduced, and homeostatic microglia (P2RY12) were increased in the invasive margins compared with the tumour core. There were significant positive correlations between microglia/macrophage markers CD68 (phagocytic)/triggering receptor expressed on myeloid cells 2 (anti-inflammatory) and CD8+ T cells in the invasive margins but not in the tumour core (P < 0.01). Programmed death-ligand 1 expression was associated with microglia/macrophage markers (including anti-inflammatory) CD68, CD163, CD32a and triggering receptor expressed on myeloid cells 2, only in the leading edge of glioblastomas (P < 0.01). Similarly, there was a positive correlation between programmed death-ligand 1 expression and CD8+ T-cell infiltration in the leading edge (P < 0.001). There was no relationship between CD64 (a receptor for autoreactive T-cell responses) and CD8+/CD4+ T cells, or between the microglia/macrophage antigen presentation marker HLA-DR and microglial motility (Iba1) in the tumour margins. Natural killer cell infiltration (CD335+) correlated with CD8+ T cells and with CD68/CD163/triggering receptor expressed on myeloid cells 2 anti-inflammatory microglia/macrophages at the leading edge. In an independent large glioblastoma cohort with transcriptomic data, positive correlations between anti-inflammatory microglia/macrophage markers (triggering receptor expressed on myeloid cells 2, CD163 and CD32a) and CD4+/CD8+/programmed death-ligand 1 RNA expression were validated (P < 0.001). Finally, multivariate analysis showed that high triggering receptor expressed on myeloid cells 2, programmed death-ligand 1 and CD32a expression at the leading edge were significantly associated with poorer overall patient survival (hazard ratio = 2.05, 3.42 and 2.11, respectively), independent of clinical variables. In conclusion, anti-inflammatory microglia/macrophages, CD8+ T cells and programmed death-ligand 1 are correlated in the invasive margins of glioblastoma, consistent with immune-suppressive interactions. High triggering receptor expressed on myeloid cells 2, programmed death-ligand 1 and CD32a expression at the human glioblastoma leading edge are predictors of poorer overall survival. Given substantial interest in targeting microglia/macrophages, together with immune checkpoint inhibitors in cancer, these data have major clinical implications

Speed Partitioning for Indexing Moving Objects

Indexing moving objects has been extensively studied in the past decades. Moving objects, such as vehicles and mobile device users, usually exhibit some patterns on their velocities, which can be utilized for velocity-based partitioning to improve performance of the indexes. Existing velocity-based partitioning techniques rely on some kinds of heuristics rather than analytically calculate the optimal solution. In this paper, we propose a novel speed partitioning technique based on a formal analysis over speed values of the moving objects. We first show that speed partitioning will significantly reduce the search space expansion which has direct impacts on query performance of the indexes. Next we formulate the optimal speed partitioning problem based on search space expansion analysis and then compute the optimal solution using dynamic programming. We then build the partitioned indexing system where queries are duplicated and processed in each index partition. Extensive experiments demonstrate that our method dramatically improves the performance of indexes for moving objects and outperforms other state-of-the-art velocity-based partitioning approaches

A new species of Sebastes (Scorpaeniformes: Sebastidae) from the northeastern Pacific, with a redescription of the blue rockfish, S. mystinus (Jordan and Gilbert, 1881)

The diverse predatory rockfishes (Sebastes spp.) support extensive commercial fisheries in the northeastern Pacific. Although 106 species of Sebastes are considered valid, many of the ecological, geographical, and morphological boundaries separating them lack clarity. We clarify one such boundary by separating the blue rockfish Sebastes mystinus (Jordan and Gilbert, 1881) into 2 species on the basis of molecular and morphological data. We redescribe S. mystinus, designate a lectotype, and describe the deacon rockfish, Sebastes diaconus n. sp. Aside from its unambiguous distinction at 6 microsatellite loci, the new species is most easily differentiated from S. mystinus by its possession of a solid in contrast with a blotched color pattern. Sebastes diaconus also possesses a prominent symphyseal knob versus a reduced or absent knob, a flat rather than rounded ventrum, and longer first and second anal-fin spines. Se bastes diaconus occurs from central California northward to British Columbia, Canada, and S. mystinus occurs from northern Oregon south to Baja California Sur, Mexico, indicating a broad region of sympatry in Oregon and northern California. Further collection and study are necessary to clarify distributional boundaries and to understand the ecology and mechanisms of segregation for this species. Additionally, fisheries assessments will need revision to account for the longstanding conflation of these 2 species.This is the publisher’s final pdf. The published article is copyrighted by United States Department of Commerce, National Oceanic and Atmospheric Administration, National Marine Fisheries Service and can be found at: http://fisherybulletin.nmfs.noaa.gov

A Target Enrichment Bait Set for Studying Relationships among Ostariophysan Fishes

© 2020 by the American Society of Ichthyologists and Herpetologists. Target enrichment of conserved nuclear loci has helped reconstruct evolutionary relationships among a wide variety of species. While there are preexisting bait sets to enrich a few hundred loci across all fishes or a thousand loci from acanthomorph fishes, no bait set exists to enrich large numbers (\u3e1,000 loci) of ultraconserved nuclear loci from ostariophysans, the second largest actinopterygian superorder. In this study, we describe how we designed a bait set to enrich 2,708 ultraconserved nuclear loci from ostariophysan fishes by combining an existing genome assembly with low coverage sequence data collected from two ostariophysan lineages. We perform a series of enrichment experiments using this bait set across the ostariophysan tree of life, from the deepest splits among the major groups (\u3e150 Ma) to more recent divergence events that have occurred during the last 50 million years. Our results demonstrate that the bait set we designed is useful for addressing phylogenetic questions from the origin of crown ostariophysans to more recent divergence events, and our in silico results suggest that this bait set may be useful for addressing evolutionary questions in closely related groups of fishes, like Clupeiformes

Convergence and divergence in the evolution of cat skulls: temporal and spatial patterns of morphological diversity

Background: Studies of biological shape evolution are greatly enhanced when framed in a phylogenetic perspective. Inclusion of fossils amplifies the scope of macroevolutionary research, offers a deep-time perspective on tempo and mode of radiations, and elucidates life-trait changes. We explore the evolution of skull shape in felids (cats) through morphometric analyses of linear variables, phylogenetic comparative methods, and a new cladistic study of saber-toothed cats. Methodology/Principal Findings: A new phylogenetic analysis supports the monophyly of saber-toothed cats (Machairodontinae) exclusive of Felinae and some basal felids, but does not support the monophyly of various sabertoothed tribes and genera. We quantified skull shape variation in 34 extant and 18 extinct species using size-adjusted linear variables. These distinguish taxonomic group membership with high accuracy. Patterns of morphospace occupation are consistent with previous analyses, for example, in showing a size gradient along the primary axis of shape variation and a separation between large and small-medium cats. By combining the new phylogeny with a molecular tree of extant Felinae, we built a chronophylomorphospace (a phylogeny superimposed onto a two-dimensional morphospace through time). The evolutionary history of cats was characterized by two major episodes of morphological divergence, one marking the separation between saber-toothed and modern cats, the other marking the split between large and small-medium cats. Conclusions/Significance: Ancestors of large cats in the ‘Panthera’ lineage tend to occupy, at a much later stage, morphospace regions previously occupied by saber-toothed cats. The latter radiated out into new morphospace regions peripheral to those of extant large cats. The separation between large and small-medium cats was marked by considerable morphologically divergent trajectories early in feline evolution. A chronophylomorphospace has wider applications in reconstructing temporal transitions across two-dimensional trait spaces, can be used in ecophenotypical and functional diversity studies, and may reveal novel patterns of morphospace occupation

The emerging structure of the Extended Evolutionary Synthesis: where does Evo-Devo fit in?

The Extended Evolutionary Synthesis (EES) debate is gaining ground in contemporary evolutionary biology. In parallel, a number of philosophical standpoints have emerged in an attempt to clarify what exactly is represented by the EES. For Massimo Pigliucci, we are in the wake of the newest instantiation of a persisting Kuhnian paradigm; in contrast, Telmo Pievani has contended that the transition to an EES could be best represented as a progressive reformation of a prior Lakatosian scientific research program, with the extension of its Neo-Darwinian core and the addition of a brand-new protective belt of assumptions and auxiliary hypotheses. Here, we argue that those philosophical vantage points are not the only ways to interpret what current proposals to ‘extend’ the Modern Synthesis-derived ‘standard evolutionary theory’ (SET) entail in terms of theoretical change in evolutionary biology. We specifically propose the image of the emergent EES as a vast network of models and interweaved representations that, instantiated in diverse practices, are connected and related in multiple ways. Under that assumption, the EES could be articulated around a paraconsistent network of evolutionary theories (including some elements of the SET), as well as models, practices and representation systems of contemporary evolutionary biology, with edges and nodes that change their position and centrality as a consequence of the co-construction and stabilization of facts and historical discussions revolving around the epistemic goals of this area of the life sciences. We then critically examine the purported structure of the EES—published by Laland and collaborators in 2015—in light of our own network-based proposal. Finally, we consider which epistemic units of Evo-Devo are present or still missing from the EES, in preparation for further analyses of the topic of explanatory integration in this conceptual framework

Reversal to air-driven sound production revealed by a molecular phylogeny of tongueless frogs, family Pipidae

<p>Abstract</p> <p>Background</p> <p>Evolutionary novelties often appear by conferring completely new functions to pre-existing structures or by innovating the mechanism through which a particular function is performed. Sound production plays a central role in the behavior of frogs, which use their calls to delimit territories and attract mates. Therefore, frogs have evolved complex vocal structures capable of producing a wide variety of advertising sounds. It is generally acknowledged that most frogs call by moving an air column from the lungs through the glottis with the remarkable exception of the family Pipidae, whose members share a highly specialized sound production mechanism independent of air movement.</p> <p>Results</p> <p>Here, we performed behavioral observations in the poorly known African pipid genus <it>Pseudhymenochirus </it>and document that the sound production in this aquatic frog is almost certainly air-driven. However, morphological comparisons revealed an indisputable pipid nature of <it>Pseudhymenochirus </it>larynx. To place this paradoxical pattern into an evolutionary framework, we reconstructed robust molecular phylogenies of pipids based on complete mitochondrial genomes and nine nuclear protein-coding genes that coincided in placing <it>Pseudhymenochirus </it>nested among other pipids.</p> <p>Conclusions</p> <p>We conclude that although <it>Pseudhymenochirus </it>probably has evolved a reversal to the ancestral non-pipid condition of air-driven sound production, the mechanism through which it occurs is an evolutionary innovation based on the derived larynx of pipids. This strengthens the idea that evolutionary solutions to functional problems often emerge based on previous structures, and for this reason, innovations largely depend on possibilities and constraints predefined by the particular history of each lineage.</p