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Canada is exposed to rare but potentially destructive earthquakes that threaten densely settled metropolitan centers in many parts of the country. To assess the impacts and consequences of future natural-hazard events and help advance policy goals and objectives of the Sendai Framework for Disaster Risk Reduction, Natural Resources Canada, through a collaborative partnership with the Global Earthquake Model Foundation, produced a national seismic risk model. Developing this model has required the creation of a national exposure inventory, Canadian-specific fragility and vulnerability curves, and significant simplification of the Canadian Seismic Hazard Model which forms the basis for the design seismic hazard values of the National Building Code of Canada. Using the Global Earthquake Model Foundation’s OpenQuake Engine, probabilistic stochastic risk modeling is completed under baseline and simulated retrofit conditions to assess seismic risk at the neighborhood level for all settled areas in Canada. Output risk metrics include the expected immediate physical impacts of earthquake events such as building damage, casualties, and direct economic losses. This article documents the technical details of the modeling approach including a description of novel data sets in use, a summary of the extensive sensitivity testing undertaken, and characterization of quality control implemented in the absence of usable validating earthquake loss data. The results from this model, such as loss exceedance curves and annual average losses, provide an open, accessible and quantitative base of evidence for decision-making at local, regional, and national levels. As a large country with a complex seismic hazard model and dispersed populations, this Canadian study is unique. However, the challenges faced and solutions offered are likely to be of interest to other nations pursuing similar programs.

The accurate and complete assembly of both haplotype sequences of a diploid organism is essential to understanding the role of variation in genome functions, phenotypes and diseases1. Here, using a trio-binning approach, we present a high-quality, diploid reference genome, with both haplotypes assembled independently at the chromosome level, for the common marmoset (Callithrix jacchus), an primate model system that is widely used in biomedical research2,3. The full spectrum of heterozygosity between the two haplotypes involves 1.36% of the genome—much higher than the 0.13% indicated by the standard estimation based on single-nucleotide heterozygosity alone. The de novo mutation rate is 0.43 × 10−8per site per generation, and the paternal inherited genome acquired twice as many mutations as the maternal. Our diploid assembly enabled us to discover a recent expansion of the sex-differentiation region and unique evolutionary changes in the marmoset Y chromosome. In addition, we identified many genes with signatures of positive selection that might have contributed to the evolution of Callithrixbiological features. Brain-related genes were highly conserved between marmosets and humans, although several genes experienced lineage-specific copy number variations or diversifying selection, with implications for the use of marmosets as a model system.

High-quality and complete reference genome assemblies are fundamental for the application of genomics to biology, disease, and biodiversity conservation. However, such assemblies are available for only a few non-microbial species1–4. To address this issue, the international Genome 10K (G10K) consortium5,6has worked over a five-year period to evaluate and develop cost-effective methods for assembling highly accurate and nearly complete reference genomes. Here we present lessons learned from generating assemblies for 16 species that represent six major vertebrate lineages. We confirm that long-read sequencing technologies are essential for maximizing genome quality, and that unresolved complex repeats and haplotype heterozygosity are major sources of assembly error when not handled correctly. Our assemblies correct substantial errors, add missing sequence in some of the best historical reference genomes, and reveal biological discoveries. These include the identification of many false gene duplications, increases in gene sizes, chromosome rearrangements that are specific to lineages, a repeated independent chromosome breakpoint in bat genomes, and a canonical GC-rich pattern in protein-coding genes and their regulatory regions. Adopting these lessons, we have embarked on the Vertebrate Genomes Project (VGP), an international effort to generate high-quality, complete reference genomes for all of the roughly 70,000 extant vertebrate species and to help to enable a new era of discovery across the life sciences.

After two decades of improvements, the current human reference genome (GRCh38) is the most accurate and complete vertebrate genome ever produced. However, no single chromosome has been finished end to end, and hundreds of unresolved gaps persist1,2. Here we present a human genome assembly that surpasses the continuity of GRCh382, along with a gapless, telomere-to-telomere assembly of a human chromosome. This was enabled by high-coverage, ultra-long-read nanopore sequencing of the complete hydatidiform mole CHM13 genome, combined with complementary technologies for quality improvement and validation. Focusing our efforts on the human X chromosome3, we reconstructed the centromeric satellite DNA array (approximately 3.1 Mb) and closed the 29 remaining gaps in the current reference, including new sequences from the human pseudoautosomal regions and from cancer-testis ampliconic gene families (CT-X and GAGE). These sequences will be integrated into future human reference genome releases. In addition, the complete chromosome X, combined with the ultra-long nanopore data, allowed us to map methylation patterns across complex tandem repeats and satellite arrays. Our results demonstrate that finishing the entire human genome is now within reach, and the data presented here will facilitate ongoing efforts to complete the other human chromosomes.

Background: The Australian black swan (Cygnus atratus) is an iconic species with contrasting plumage to that of the closely related northern hemisphere white swans. The relative geographic isolation of the black swan may have resulted in a limited immune repertoire and increased susceptibility to infectious diseases, notably infectious diseases from which Australia has been largely shielded. Unlike mallard ducks and the mute swan (Cygnus olor), the black swan is extremely sensitive to highly pathogenic avian influenza. Understanding this susceptibility has been impaired by the absence of any available swan genome and transcriptome information. Results: Here, we generate the first chromosome-length black and mute swan genomes annotated with transcriptome data, all using long-read based pipelines generated for vertebrate species. We use these genomes and transcriptomes to show that unlike other wild waterfowl, black swans lack an expanded immune gene repertoire, lack a key viral pattern-recognition receptor in endothelial cells and mount a poorly controlled inflammatory response to highly pathogenic avian influenza. We also implicate genetic differences in SLC45A2gene in the iconic plumage of the black swan. Conclusion: Together, these data suggest that the immune system of the black swan is such that should any avian viral infection become established in its native habitat, the black swan would be in a significant peril.

We report full-length draft de novo genome assemblies for 16 widely used inbred mouse strains and find extensive strain-specific haplotype variation. We identify and characterize 2,567 regions on the current mouse reference genome exhibiting the greatest sequence diversity. These regions are enriched for genes involved in pathogen defence and immunity and exhibit enrichment of transposable elements and signatures of recent retrotransposition events. Combinations of alleles and genes unique to an individual strain are commonly observed at these loci, reflecting distinct strain phenotypes. We used these genomes to improve the mouse reference genome, resulting in the completion of 10 new gene structures. Also, 62 new coding loci were added to the reference genome annotation. These genomes identified a large, previously unannotated, gene (Efcab3-like) encoding 5,874 amino acids. Mutant Efcab3-likemice display anomalies in multiple brain regions, suggesting a possible role for this gene in the regulation of brain development.

Understanding the mechanisms driving lineage-specific evolution in both primates and rodents has been hindered by the lack of sister clades with a similar phylogenetic structure having high-quality genome assemblies. Here, we have created chromosome-level assemblies of the Mus caroliand Mus paharigenomes. Together with the Mus musculusand Rattus norvegicusgenomes, this set of rodent genomes is similar in divergence times to the Hominidae (human-chimpanzee-gorilla-orangutan). By comparing the evolutionary dynamics between the Muridae and Hominidae, we identified punctate events of chromosome reshuffling that shaped the ancestral karyotype of Mus musculusand Mus carolibetween 3 and 6 million yr ago, but that are absent in the Hominidae. Hominidae show between four- and sevenfold lower rates of nucleotide change and feature turnover in both neutral and functional sequences, suggesting an underlying coherence to the Muridae acceleration. Our system of matched, high-quality genome assemblies revealed how specific classes of repeats can play lineage-specific roles in related species. Recent LINE activity has remodeled protein-coding loci to a greater extent across the Muridae than the Hominidae, with functional consequences at the species level such as reproductive isolation. Furthermore, we charted a Muridae-specific retrotransposon expansion at unprecedented resolution, revealing how a single nucleotide mutation transformed a specific SINE element into an active CTCF binding site carrier specifically in Mus caroli, which resulted in thousands of novel, species-specific CTCF binding sites. Our results show that the comparison of matched phylogenetic sets of genomes will be an increasingly powerful strategy for understanding mammalian biology.

The human reference genome assembly plays a central role in nearly all aspects of today's basic and clinical research. GRCh38 is the first coordinate-changing assembly update since 2009; it reflects the resolution of roughly 1000 issues and encompasses modifications ranging from thousands of single base changes to megabase-scale path reorganizations, gap closures, and localization of previously orphaned sequences. We developed a new approach to sequence generation for targeted base updates and used data from new genome mapping technologies and single haplotype resources to identify and resolve larger assembly issues. For the first time, the reference assembly contains sequence-based representations for the centromeres. We also expanded the number of alternate loci to create a reference that provides a more robust representation of human population variation. We demonstrate that the updates render the reference an improved annotation substrate, alter read alignments in unchanged regions, and impact variant interpretation at clinically relevant loci. We additionally evaluated a collection of new de novo long-read haploid assemblies and conclude that although the new assemblies compare favorably to the reference with respect to continuity, error rate, and gene completeness, the reference still provides the best representation for complex genomic regions and coding sequences. We assert that the collected updates in GRCh38 make the newer assembly a more robust substrate for comprehensive analyses that will promote our understanding of human biology and advance our efforts to improve health.

Insights into the evolution of non-model organisms are limited by the lack of reference genomes of high accuracy, completeness, and contiguity. Here, we present a chromosome-level, karyotype-validated reference genome and pangenome for the barn swallow (Hirundo rustica). We complement these resources with a reference-free multialignment of the reference genome with other bird genomes and with the most comprehensive catalog of genetic markers for the barn swallow. We identify potentially conserved and accelerated genes using the multialignment and estimate genome-wide linkage disequilibrium using the catalog. We use the pangenome to infer core and accessory genes and to detect variants using it as a reference. Overall, these resources will foster population genomics studies in the barn swallow, enable detection of candidate genes in comparative genomics studies, and help reduce bias toward a single reference genome.

We have generated an improved assembly and gene annotation of the pig X Chromosome, and a first draft assembly of the pig Y Chromosome, by sequencing BAC and fosmid clones from Duroc animals and incorporating information from optical mapping and fiber-FISH. The X Chromosome carries 1033 annotated genes, 690 of which are protein coding. Gene order closely matches that found in primates (including humans) and carnivores (including cats and dogs), which is inferred to be ancestral. Nevertheless, several protein-coding genes present on the human X Chromosome were absent from the pig, and 38 pig-specific X-chromosomal genes were annotated, 22 of which were olfactory receptors. The pig Y-specific Chromosome sequence generated here comprises 30 megabases (Mb). A 15-Mb subset of this sequence was assembled, revealing two clusters of male-specific low copy number genes, separated by an ampliconic region including the HSFYgene family, which together make up most of the short arm. Both clusters contain palindromes with high sequence identity, presumably maintained by gene conversion. Many of the ancestral X-related genes previously reported in at least one mammalian Y Chromosome are represented either as active genes or partial sequences. This sequencing project has allowed us to identify genes—both single copy and amplified—on the pig Y Chromosome, to compare the pig X and Y Chromosomes for homologous sequences, and thereby to reveal mechanisms underlying pig X and Y Chromosome evolution.

IMPORTANCE: Patients with stage T2 multilesion angiosarcomas of the scalp and face that are larger than 10 cm demonstrate a 2-year survival rate of 0%. To our knowledge, major therapeutic advances against this disease have not been reported for decades. Preclinical data indicate that blocking β-adrenergic signaling with propranolol hydrochloride disrupts angiosarcoma cell survival and xenograft angiosarcoma progression. OBSERVATIONS: A patient presented with a β-adrenergic–positive multifocal stage T2 cutaneous angiosarcoma (≥20 cm) involving 80% of the scalp, left forehead, and left cheek, with no evidence of metastasis. The patient was immediately administered propranolol hydrochloride, 40 mg twice a day, as his workup progressed and treatment options were elucidated. Evaluation of the proliferative index of the tumor before and after only 1 week of propranolol monotherapy revealed a reduction in the proliferative index of the tumor by approximately 34%. A combination of propranolol hydrochloride, 40 mg 3 times a day, paclitaxel, 2 mg/m2 infused weekly, and radiotherapy during the subsequent 8 months resulted in extensive tumor regression with no detectable metastases. CONCLUSIONS AND RELEVANCE: Our data suggest that β-blockade alone substantially reduced angiosarcoma proliferation and, in combination with standard therapy, is effective for reducing the size of the tumor and preventing metastases. If successful, β-blockade could be the first major advancement in the treatment of angiosarcoma in decades.

Real-time information systems have been used in transit agencies around the world to inform passengers better of their estimated wait. In 2012, the Massachusetts Bay Transportation Authority (MBTA) activated new real-time information signage across its heavy rail system. These signs displayed the estimated arrival of the next two trains in each direction. The study reported in this paper examined whether the introduction of real-time arrival signage led to reduced expectations of wait time, improved satisfaction with MBTA, and increased ridership. In-station surveys were conducted before and after real-time information was introduced to gauge changes in passenger satisfaction and wait-time expectations. These expectations were compared against headways collected from automated train tracking data. Ridership changes were measured with automated fare collection data provided by MBTA. Survey results revealed that, after the introduction of the countdown signs, people reduced their overestimation of wait time by 50%. Satisfaction with MBTA did not change significantly as a result of the real-time signage. People reported that they felt more relaxed with real-time signage if the next train arrival occurred within a scheduled headway but less relaxed in cases in which the headways were much greater than scheduled. Minor improvements in ridership were detected in stations with the real-time information after other factors were controlled for, but these results were preliminary. This study suggests that real-time arrival signage would be a positive addition to heavy rail systems to increase passenger comfort and improve perceptions of system performance in a relatively cost-effective manner with the use of existing technologies.

We prospectively evaluated the accuracy of the 2007 World Health Organization (WHO) criteria for diagnosing polycythemia vera (PV), especially in “early-stage” patients. A total of 28 of 30 patients were diagnosed as PV owing to an elevated Cr-51 red cell mass (RCM), JAK2 positivity, and at least 1 minor criterion. A total of 18 PV patients did not meet the WHO criterion for an increased hemoglobin value and 8 did not meet the WHO criterion for an increased hematocrit value. Bone marrow morphology was very valuable for diagnosis. Low serum erythropoietin (EPO) values were specific for PV, but normal EPO values were found at presentation (20%). We recommend revision of the WHO criteria, especially to distinguish early-stage PV from essential thrombocythemia. Major criteria remain JAK2 positivity and increased red cell volume, but Cr-51 RCM is mandatory for patients who do not meet the defined elevated hemoglobin or hematocrit value (>18.5 g/dL and 60% in men and >16.5 g/dL and 56% in women, respectively). Minor criteria remain bone marrow histology or a low serum EPO value. For patients with a normal EPO value, marrow examination is mandatory for diagnostic confirmation. Because the therapies for myeloproliferative disorders differ, our data have major clinical implications.

We prospectively evaluated the accuracy of the 2007 World Health Organization (WHO) criteria for diagnosing polycythemia vera (PV), especially in “early-stage” patients. A total of 28 of 30 patients were diagnosed as PV owing to an elevated Cr-51 red cell mass (RCM), JAK2positivity, and at least 1 minor criterion. A total of 18 PV patients did not meet the WHO criterion for an increased hemoglobin value and 8 did not meet the WHO criterion for an increased hematocrit value. Bone marrow morphology was very valuable for diagnosis. Low serum erythropoietin (EPO) values were specific for PV, but normal EPO values were found at presentation (20%). We recommend revision of the WHO criteria, especially to distinguish early-stage PV from essential thrombocythemia. Major criteria remain JAK2positivity and increased red cell volume, but Cr-51 RCM is mandatory for patients who do not meet the defined elevated hemoglobin or hematocrit value (>18.5 g/dL and 60% in men and >16.5 g/dL and 56% in women, respectively). Minor criteria remain bone marrow histology or a low serum EPO value. For patients with a normal EPO value, marrow examination is mandatory for diagnostic confirmation. Because the therapies for myeloproliferative disorders differ, our data have major clinical implications.

Abstract: This paper presents an experimental method for measuring the displacement fields in extremely soft materials and the subsequent analysis of the data to yield the stress field. The stresses in soft materials are difficult to measure by transducers because the measurement device can easily alter the quantity to be measured. In this study, strains in seat cushions and in the buttock model are indicated by lead markers and recorded on X-ray films. The method is different from previous grid methods in that the strains can be measured in any plane inside a three dimensional model. The lead-ball matrix gives a clear picture of the overall displacement field and areas of high strain. The displacement data are converted to a digital form and analyzed on a computer. Two separate aspects of the computer analysis are discussed in detail in this paper. First, by curve fitting, the hydrostatic pressure gradient is obtained. Second, a finite-element model with the displacement data as input yields a set of stress contours.

1-Aminocyclopropane-1-carboxylic acid (ACC) synthase is the key regulatory enzyme in the biosynthetic pathway of the plant hormone ethylene. The enzyme is encoded by a divergent multigene family in Arabidopsis thaliana, comprising at least five genes, ACS1-5(Liang, X., Abel, S., Keller, J. A., Shen, N. F., and Theologis, A.(1992) Proc. Natl. Acad. Sci. U. S. A.89, 11046-11050). In etiolated seedlings, ACS4is specifically induced by indoleacetic acid (IAA). The response to IAA is rapid (within 25 min) and insensitive to protein synthesis inhibition, suggesting that the ACS4gene expression is a primary response to IAA. The ACS4mRNA accumulation displays a biphasic dose-response curve which is optimal at 10 μM of IAA. However, IAA concentrations as low as 100 nM are sufficient to enhance the basal level of ACS4mRNA. The expression of ACS4is defective in the Arabidopsisauxin-resistant mutant lines axr1-12, axr2-1, and aux1-7. ACS4mRNA levels are severely reduced in axr1-12and axr2-1but are only 1.5-fold lower in aux1-7. IAA inducibility is abolished in axr2-1.

Background: Large palindromes (inverted repeats) make up substantial proportions of mammalian sex chromosomes, often contain genes, and have high rates of structural variation arising via ectopic recombination. As a result, they underlie many genomic disorders. Maintenance of the palindromic structure by gene conversion between the arms has been documented, but over longer time periods, palindromes are remarkably labile. Mechanisms of origin and loss of palindromes have, however, received little attention. Results: Here, we use fiber-FISH, 10x Genomics Linked-Read sequencing, and breakpoint PCR sequencing to characterize the structural variation of the P8 palindrome on the human Y chromosome, which contains two copies of the VCY(Variable Charge Y) gene. We find a deletion of almost an entire arm of the palindrome, leading to death of the palindrome, a size increase by recruitment of adjacent sequence, and other complex changes including the formation of an entire new palindrome nearby. Together, these changes are found in ~?1% of men, and we can assign likely molecular mechanisms to these mutational events. As a result, healthy men can have 1–4 copies of VCY. Conclusions: Gross changes, especially duplications, in palindrome structure can be relatively frequent and facilitate the evolution of sex chromosomes in humans, and potentially also in other mammalian species.

The World Health Organization (WHO) published consensus criteria (2007) for the diagnosis of polycythemia vera (PV), which have never been objectively evaluated prospectively. Concern regarding limitations of these criteria and treatment algorithms based upon them has been documented. The WHO diagnosis for PV includes 2 major criteria, (1) increased red cell volume (RCV), now most often measured by an increased hemoglobin value, and (2) JAK2 mutation, and 3 minor criteria, hypercellular bone marrow with trilineage hyperplasia, low serum erythropoietin (EPO) level, and endogenous erythroid colony (EEC) formation in vitro. Diagnosis of PV requires that either both major criteria and 1 minor criterion, or increased RCV and 2 minor criteria must be met. Increased red cell volume was arbitrarily defined as: hemoglobin concentration (Hgb) >18.5 g/dL in men and >16.5 g/dL in women, or hematocrit value (Hct) >99th percentile of institutional normal range, or Hgb >17g/dL in men and >15 g/dL in women if a true sustained increase ≥2 g/dL from baseline exists, or elevated red cell mass (RCM) value >25% above mean normal predicted value according to Pearson, et al.We prospectively evaluated 30 patients with a clinical phenotype of PV using the WHO criteria for diagnosis. For measuring RCV, simultaneous Cr51 RCM and I125 plasma volume analyses were performed. The RCM of overweight patients (BMI >25 kg/m2) was determined by using a BMI of 22 kg/m2 (20% fat) for adjusted weight. JAK2V617F allele burden was determined both qualitatively by ARMS PCR assay and quantitatively by pyrosequencing. Bone marrow biopsy slides were prepared routinely and stained for reticulin and collagen. The Manoharan scale was used for evaluating fibrosis. Marrow interpretation by 2 observers was initially “blinded”. EEC assays were not performed. All patients have been followed regularly at our institution for a median of 4 years to allow confirmation of diagnosis.Of the 30 patients, 28 were diagnosed as PV because of an increased RCM and JAK2 positivity. The median phlebotomy requirement during the first year was 4 (range 2–13). The remaining 2 patients met the WHO criterion of JAK2 positivity and an increased hematocrit value but had a normal RCM and were diagnosed as essential thrombocythemia (ET), subsequently confirmed clinically by no increase in Hct or Hgb and no need for phlebotomy in the succeeding years. Eighteen PV patients, 4 women and 14 men, met major criterion #1 by elevated RCM only, but not by the WHO criteria for increased Hgb. The median Hgb count was 15.2 g/dL for the 4 women (range: 14.4–16.4) and 17.2 g/dL for the 14 men (range: 15.6–18.1). All 28 patients had marrow findings consistent with PV; the marrows of the 2 ET patients were interpreted as nonspecific myeloproliferative disease. Only 21 patients had a low EPO level (<5 mU/mL), as did 1 ET patient. There was no correlation between RCM and white blood cell, red blood cell, or platelet counts, or between RCM and JAK2V617F %, age, phlebotomy requirement, spleen size, or grade of myelofibrosis. Although in general, RCM increased with increasing Hgb and Hct, it was not possible to correlate RCM with a unique Hgb or Hct.We conclude, as have others, that Cr51 RCM determination remains critical for distinguishing absolute erythrocytosis and the subsequent diagnosis of PV. Using Hgb as a single criterion, 18 patients (64.3%) would not have been diagnosed as PV and using Hct as a single criterion, 9 patients (32.1%) would have not. We confirm marrow evaluation is highly valuable when performed by skilled hematopathologists. However, serum EPO levels are not diagnostic. EEC assays are rarely performed except in experimental laboratories. The frequency of performing RCM studies has decreased due to a reliance on hemoglobin concentration, but this is incorrect. Informal review of hematocrit ranges shows institutional variability. We recommend immediate revision of the WHO criteria for the diagnosis of PV patients with “early stage” disease, especially to distinguish it from ET. Criteria for the unequivocal diagnosis of PV should be increased RCM, as opposed to any form of increased RCV, and JAK2 mutation. In the rare cases of increased RCM and JAK2 negativity, marrow morphology plus other minor criteria to be discussed can be diagnostic. Since the therapies for myeloproliferative disorders differ, our data has major clinical implications.No relevant conflicts of interest to declare.

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