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1. Exploring FlyBase Data Using QuickSearch

   https://doi.org/10.1002/cpz1.731  

   Marygold, Steven J. ; the FlyBase Consortium ( April 2023 , Current Protocols)

   FlyBase (www.flybase.org) is the primary online database of genetic, genomic, and functional information aboutDrosophila melanogaster. The long and rich history ofDrosophilaresearch, combined with recent surges in genomic‐scale and high‐throughput technologies, means that FlyBase now houses a huge quantity of data. Researchers need to be able to query these data rapidly and intuitively, and the QuickSearch tool has been designed to meet these needs. This tool is conveniently located on the FlyBase homepage and is organized into a series of simple tabbed interfaces that cover the major data and annotation classes within the database. This article describes the functionality of all aspects of the QuickSearch tool. With this knowledge, FlyBase users will be equipped to take full advantage of all QuickSearch features and thereby gain improved access to data relevant to their research. © 2023 The Authors. Current Protocols published by Wiley Periodicals LLC.

   Basic Protocol 1: Using the “Search FlyBase” tab of QuickSearch

   Basic Protocol 2: Using the “Data Class” tab of QuickSearch

   Basic Protocol 3: Using the “References” tab of QuickSearch

   Basic Protocol 4: Using the “Gene Groups” tab of QuickSearch

   Basic Protocol 5: Using the “Pathways” tab of QuickSearch

   Basic Protocol 6: Using the “GO” tab of QuickSearch

   Basic Protocol 7: Using the “Protein Domains” tab of QuickSearch

   Basic Protocol 8: Using the “Expression” tab of QuickSearch

   Basic Protocol 9: Using the “GAL4 etc” tab of QuickSearch

   Basic Protocol 10: Using the “Phenotype” tab of QuickSearch

   Basic Protocol 11: Using the “Human Disease” tab of QuickSearch

   Basic Protocol 12: Using the “Homologs” tab of QuickSearch

   Support Protocol 1: Managing FlyBase hit lists

    

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2. The eigensplitting of the fiber of the cyclotomic trace for the sphere spectrum

   https://doi.org/10.1090/tran/8822  

   Blumberg, Andrew ; Mandell, Michael ( January 2022 , Transactions of the American Mathematical Society)

   Let p ∈ Z p\in {\mathbb {Z}} be an odd prime. We show that the fiber sequence for the cyclotomic trace of the sphere spectrum S {\mathbb {S}} admits an “eigensplitting” that generalizes known splittings on K K -theory and T C TC . We identify the summands in the fiber as the covers of Z p {\mathbb {Z}}_{p} -Anderson duals of summands in the K ( 1 ) K(1) -localized algebraic K K -theory of Z {\mathbb {Z}} . Analogous results hold for the ring Z {\mathbb {Z}} where we prove that the K ( 1 ) K(1) -localized fiber sequence is self-dual for Z p {\mathbb {Z}}_{p} -Anderson duality, with the duality permuting the summands by i ↦ p − i i\mapsto p-i (indexed mod p − 1 p-1 ). We explain an intrinsic characterization of the summand we call Z Z in the splitting T C ( Z ) p ∧ ≃ j ∨ Σ j ′ ∨ Z TC({\mathbb {Z}})^{\wedge }_{p}\simeq j \vee \Sigma j’\vee Z in terms of units in the p p -cyclotomic tower of Q p {\mathbb {Q}}_{p} . 

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3. The L p chord Minkowski problem

   https://doi.org/10.1515/ans-2022-0041  

   Xi, Dongmeng ; Yang, Deane ; Zhang, Gaoyong ; Zhao, Yiming ( January 2023 , Advanced Nonlinear Studies)

   Abstract Chord measures are newly discovered translation-invariant geometric measures of convex bodies in R n {{\mathbb{R}}}^{n} , in addition to Aleksandrov-Fenchel-Jessen’s area measures. They are constructed from chord integrals of convex bodies and random lines. Prescribing the L p {L}_{p} chord measures is called the L p {L}_{p} chord Minkowski problem in the L p {L}_{p} Brunn-Minkowski theory, which includes the L p {L}_{p} Minkowski problem as a special case. This article solves the L p {L}_{p} chord Minkowski problem when p > 1 p\gt 1 and the symmetric case of 0 < p < 1 0\lt p\lt 1 . 

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4. Gridded road network statistics and settlement age surfaces for core-based statistical areas in the conterminous U.S.

   https://doi.org/10.6084/m9.figshare.19593496.v1  

   Uhl, Johannes H. ; Burghardt, Keith ( January 2022 , figshare)

   These geotiff files represent road network statistics for each core-based statistical area (CBSA) in the conterminous U.S., within grid cells of 1km x 1km. The road network statistics are based on the National transportation dataset (USGS-NTD) v2019.

   These statistics include:

   gridcell_stats_azimuthvariety_1km_all_cbsas.tif: The number of unique road angles (azimuth / orientation) in bins of 10 degrees per 1 sqkm grid cell.

   gridcell_stats_deadendrate_1km_all_cbsas.tif: The proportion of dead ends (nodes of degree 1) of all nodes per 1 sqkm grid cell.

   gridcell_stats_kmroad_1km_all_cbsas.tif: The approximate total road network length per 1 sqkm grid cell. This is based on the road segment length appended to each road segment centroid and may be biased for very long road segments.

   gridcell_stats_meandegree_1km_all_cbsas.tif: The average nodal degree of all nodes per 1 sqkm grid cell.

   gridcell_stats_meangriddedness_1km_all_cbsas.tif: The average griddedness of all nodes per 1 sqkm grid cell.

   gridcell_stats_nodedensity_1km_all_cbsas.tif: The number of nodes per 1 sqkm grid cell.

   gridcell_stats_nodesperkmroad_1km_all_cbsas.tif: The number of nodes per km road within each 1 sqkm grid cell.

   gridcell_stats_firstbuiltup_1km_all_cbsas.tif: The approximate settlement age per 1 sqkm grid cell. This layer is derived from the HISDAC-US First-built-up year (FBUY) layer, which is derived from Zillow's Transaction and Assessment Dataset (ZTRAX). The FBUY data is available here: Leyk, Stefan; Uhl, Johannes H., 2018, "FBUY.tar.gz", Historical settlement composite layer for the U.S. 1810 - 2015, https://doi.org/10.7910/DVN/PKJ90M/BOA5YC, Harvard Dataverse, V2 

   gridcell_stats_1km_all_cbsas_arcmap10.8.mxd: ESRI ArcMap 10.8 MXD file for quick visualization of the gridded surfaces.

   Spatial resolution: 1x1km

   Spatial reference: SR-ORG:7480, USA_Contiguous_Albers_Equal_Area_Conic_USGS_version

   Source data: USGS-NTD, HISDAC-US.

   File format: GeoTIFF.

   Spatial coverage of the road network metrics: All CBSAs in the conterminous U.S.

   Spatial coverage of the "first built-up year" surface: all U.S. counties that are covered by the HISDAC-US  historical settlement layers. This datasets includes around 2,700 U.S.  counties. In the remaining counties, construction year coverage in the  underlying ZTRAX data (Zillow Transaction and Assessment Dataset) is  low. See Leyk & Uhl (2018) for details.

   All data created by Johannes H. Uhl, University of Colorado Boulder, USA. Code available at https://github.com/johannesuhl/USRoadNetworkEvolution.

   References:

   Burghardt, K., Uhl, J., Lerman, K.,  & Leyk, S. (2022). Road   Network Evolution in the Urban and Rural  United States Since 1900.   Computers, Environment and Urban Systems.

   Leyk, S., & Uhl, J. H. (2018). HISDAC-US, historical settlement   data  compilation for the conterminous United States over 200 years. Scientific data, 5(1), 1-14. DOI:  https://doi.org/10.1038/sdata.2018.175 

    

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5. High species richness in the lichen genus Peltigera (Ascomycota, Lecanoromycetes): 34 species in the dolichorhizoid and scabrosoid clades of section Polydactylon, including 24 new to science

   https://doi.org/10.3767/persoonia.2023.51.01  

   Magain, N. ; Miadlikowska, J. ; Goffinet, B. ; Goward, T. ; Pardo-De la Hoz, C.J. ; Jüriado, I. ; Simon, A. ; Mercado-Díaz, J.A. ; Barlow, T. ; Moncada, B. ; et al ( August 2023 , Persoonia - Molecular Phylogeny and Evolution of Fungi)

   Applying molecular methods to fungi establishing lichenized associations with green algae or cyanobacteria has repeatedly revealed the existence of numerous phylogenetic taxa overlooked by classical taxonomic approaches. Here, we report taxonomical conclusions based on multiple species delimitation and validation analyses performed on an eight-locus dataset that includes world-wide representatives of the dolichorhizoid and scabrosoid clades in section Polydactylon of the genus Peltigera . Following the recommendations resulting from a consensus species delimitation approach and additional species validation analysis (BPP) performed in this study, we present a total of 25 species in the dolichorhizoid clade and nine in the scabrosoid clade, including respectively 18 and six species that are new to science and formally described. Additionally, one combination and three varieties (including two new to science) are proposed in the dolichorhizoid clade. The following 24 new species are described: P. appalachiensis , P. asiatica , P. borealis , P. borinquensis , P. chabanenkoae , P. clathrata , P. elixii , P. esslingeri , P. flabellae , P. gallowayi , P. hawaiiensis , P. holtanhartwigii , P. itatiaiae , P. hokkaidoensis , P. kukwae , P. massonii , P. mikado , P. nigriventris , P. orientalis , P. rangiferina , P. sipmanii , P. stanleyensis , P. vitikainenii and P. willdenowii ; the following new varieties are introduced: P. kukwae var. phyllidiata and P. truculenta var. austroscabrosa ; and the following new combination is introduced: P. hymenina var. dissecta . Each species from the dolichorhizoid and scabrosoid clades is morphologically and chemically described, illustrated, and characterised with ITS sequences. Identification keys are provided for the main biogeographic regions where species from the two clades occur. Morphological and chemical characters that are commonly used for species identification in the genus Peltigera cannot be applied to unambiguously recognise most molecularly circumscribed species, due to high variation of thalli formed by individuals within a fungal species, including the presence of distinct morphs in some cases, or low interspecific variation in others. The four commonly recognised morphospecies: P. dolichorhiza , P. neopolydactyla , P. pulverulenta and P. scabrosa in the dolichorhizoid and scabrosoid clades represent species complexes spread across multiple and often phylogenetically distantly related lineages. Geographic origin of specimens is often helpful for species recognition; however, ITS sequences are frequently required for a reliable identification. 

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