Computing the output distribution and selection probabilities of a stack filter from the DNF of its positive Boolean function

Many nonlinear filters used in practise are stack filters. An algorithm is presented which calculates the output distribution of an arbitrary stack filter S from the disjunctive normal form (DNF) of its underlying positive Boolean function. The so called selection probabilities can be computed along the way.Comment: This is the version published in Journal of Mathematical Imaging and Vision, online first, 1 august 201

Early-career paleoscientists meet in the mountains of Aragon

Three days prior to the 5th PAGES Open Science Meeting (OSM), 80 ambitious early-career scientists (PhD students and postdoctoral researchers) met in the restored village of Morillo de Tou, Spain. The remote setting in the Pyrenees, the old style buildings constructed of turbidites, and the clear and sunny weather made this place an inspiring location to discuss past climate, environment and human interactions. Despite some grumblings about cold coffee served in small cups, the conference was a high-energy affair that promoted connections

Late Glacial and Holocene records of tree-killing conifer bark beetles in Europe and North America: Implications for forest disturbance dynamics

Outbreaks of conifer bark beetles in Europe and North America have increased in scale and severity in recent decades. In this study, we identify existing fossil records containing bark beetle remains from the end of the Last Glacial Maximum (~14,000 cal. yr BP) to present day using the online databases Neotoma and BugsCEP and literature searches, and compare these data with modern distribution data of selected tree-killing species. Modern-day observational data from the Global Biodiversity Information Facility (GBIF) database was used to map recorded distributions from AD 1750 to present day. A total of 53 fossil sites containing bark beetle remains, from both geological and archeological sites, were found during our searches. Fossil sites were fewer in Europe (n = 21) than North America (n = 32). In Europe, 29% of the samples in which remains were found were younger than 1000 cal. yr BP, while in North America, remains were mainly identified from late Glacial (~14,000–11,500 cal. yr BP) sites. In total, the fossil records contained only 8 of 20 species we consider important tree-killing bark beetles in Europe and North America based on their impacts during the last 100 years. In Europe, Ips sexdentatus was absent from the fossil record. In North America, Dendroctonus adjunctus, Dendroctonus frontalis, Dendroctonus jeffreyi, Dendroctonus pseudotsugae, Dryocoetes confusus, Ips calligraphus, Ips confusus, Ips grandicollis, Ips lecontei, Ips paraconfusus, and Scolytus ventralis were absent. Overall, preserved remains of tree-killing bark beetles are rare in the fossil record. However, by retrieving bulk material from new and existing sites and combining data from identified bark beetle remains with pollen, charcoal, tree rings, and geochemistry, the occurrence and dominance of bark beetles, their outbreaks, and other disturbance events can be reconstructed

What evidence exists for temporal variability in Arctic terrestrial and freshwater biodiversity throughout the Holocene? A systematic map protocol

Background: The Arctic tundra is subject to the greatest climate change-induced temperature rises of any biome. Both terrestrial and freshwater biota are responding to recent climate warming through variability in their distribution, abundance, and richness. However, uncertainty arises within models of future change when considering processes that operate over centennial timescales. A systematic evidence synthesis of centennial-scale variability in biodiversity does not currently exist for the Arctic biome. Here, we sought to address the primary research question: what evidence exists for temporal variability in Arctic terrestrial and freshwater biodiversity throughout the Holocene (11,650 years before present (yBP)-OyBP)? Methods: Consultation with stakeholders informed key definitions, scoping and the appropriateness of the research question. The research question was structured using a PECO framework-Arctic biota (P), a timestamped year in the Holocene (E), another year in the Holocene (C), and the dimensions of biodiversity that have been measured (O)-to inform the search strategy. Search strings were benchmarked against a test list of 100 known sources to ensure a specific and comprehensive return of literature. Searches will occur across 13 bibliographic databases. The eligibility criteria specify that sources must: (a) use 'proxy' methods to measure biodiversity; (b) fall within the spatial extent of the contemporary Arctic tundra biome; and (c) consist of a time-series that overlaps with 11,650yBP to OyBP (1950AD). Information coded from studies will include proxy-specific information to account for both temporal uncertainty (i.e., the characteristics of age-depth models and dating methods) and taxonomic uncertainty (i.e., the samples and processes used for taxonomic identification). We will assess temporal uncertainty within each source by determining the quality of dating methods and measures; this information will be used to harmonise dates onto the IntCa120 calibration curve and determine the available temporal resolution and extent of evidence through space. Key outputs of this systematic map will be: (1) a graph database containing the spatial-temporal properties of each study dataset with taxonomic harmonisation; and (2) a geographical map of the evidence base.Peer reviewe

Next-generation sequencing in a large pedigree segregating visceral artery aneurysms suggests potential role of COL4A1/COL4A2 in disease etiology

Background Visceral artery aneurysms (VAAs) can be fatal if ruptured. Although a relatively rare incident, it holds a contemporary mortality rate of approximately 12%. VAAs have multiple possible causes, one of which is genetic predisposition. Here, we present a striking family with seven individuals affected by VAAs, and one individual affected by a visceral artery pseudoaneurysm. Methods We exome sequenced the affected family members and the parents of the proband to find a possible underlying genetic defect. As exome sequencing did not reveal any feasible protein-coding variants, we combined whole-genome sequencing of two individuals with linkage analysis to find a plausible non-coding culprit variant. Variants were ranked by the deep learning framework DeepSEA. Results Two of seven top-ranking variants, NC_000013.11:g.108154659C>T and NC_000013.11:g.110409638C>T, were found in all VAA-affected individuals, but not in the individual affected by the pseudoaneurysm. The second variant is in a candidate cis-regulatory element in the fourth intron of COL4A2, proximal to COL4A1. Conclusions As type IV collagens are essential for the stability and integrity of the vascular basement membrane and involved in vascular disease, we conclude that COL4A1 and COL4A2 are strong candidates for VAA susceptibility genes.Peer reviewe