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Here the Human Pangenome Reference Consortium presents a first draft of the human pangenome reference. The pangenome contains 47 phased, diploid assemblies from a cohort of genetically diverse individuals1. These assemblies cover more than 99% of the expected sequence in each genome and are more than 99% accurate at the structural and base pair levels. Based on alignments of the assemblies, we generate a draft pangenome that captures known variants and haplotypes and reveals new alleles at structurally complex loci. We also add 119 million base pairs of euchromatic polymorphic sequences and 1,115 gene duplications relative to the existing reference GRCh38. Roughly 90 million of the additional base pairs are derived from structural variation. Using our draft pangenome to analyse short-read data reduced small variant discovery errors by 34% and increased the number of structural variants detected per haplotype by 104% compared with GRCh38-based workflows, which enabled the typing of the vast majority of structural variant alleles per sample.

Aedes aegypti (Diptera: Culicidae) is the principal vector of dengue and other viruses that cause disease among 100 to 400 million people each year. The recent development of widespread insecticidal resistance has led to the rapid development of biological control solutions aimed at larval control. While the efficacy of Metarhizium brunneum has been shown against Aedes larvae, the impact of larval population dynamics will need to be determined to formulate effective control strategies. In this study, larvae were subjected to four concentrations of M. brunneum (105, 106, 107, 108 conidia ml−1). Larvae were found to be susceptible to M. brunneum with dose-dependent efficacy. When constant larval immigration was added as a parameter, peak mortality was consistently found to occur on the fourth day, before a significant reduction in control efficacy linked to a decline in conidial availability within the water column. This suggests that M. brunneum treatments should be applied at a concentration 1 × 107 conidia ml−1 every four days to effectively control mosquito larvae in the field, regardless of the fungal formulation, water volume, or larval density. Understanding fungal-mosquito dynamics is critical in developing appropriate control programs as it helps optimize the fungal control agent’s dose and frequency of application.

Numerous novel adaptations characterise the radiation of notothenioids, the dominant fish group in the freezing seas of the Southern Ocean. To improve understanding of the evolution of this iconic fish group, here we generate and analyse new genome assemblies for 24 species covering all major subgroups of the radiation, including five long-read assemblies. We present a new estimate for the onset of the radiation at 10.7 million years ago, based on a time-calibrated phylogeny derived from genome-wide sequence data. We identify a two-fold variation in genome size, driven by expansion of multiple transposable element families, and use the long-read data to reconstruct two evolutionarily important, highly repetitive gene family loci. First, we present the most complete reconstruction to date of the antifreeze glycoprotein gene family, whose emergence enabled survival in sub-zero temperatures, showing the expansion of the antifreeze gene locus from the ancestral to the derived state. Second, we trace the loss of haemoglobin genes in icefishes, the only vertebrates lacking functional haemoglobins, through complete reconstruction of the two haemoglobin gene clusters across notothenioid families. Both the haemoglobin and antifreeze genomic loci are characterised by multiple transposon expansions that may have driven the evolutionary history of these genes.

Since its initial release in 2000, the human reference genome has covered only the euchromatic fraction of the genome, leaving important heterochromatic regions unfinished. Addressing the remaining 8% of the genome, the Telomere-to-Telomere (T2T) Consortium presents a complete 3.055 billion–base pair sequence of a human genome, T2T-CHM13, that includes gapless assemblies for all chromosomes except Y, corrects errors in the prior references, and introduces nearly 200 million base pairs of sequence containing 1956 gene predictions, 99 of which are predicted to be protein coding. The completed regions include all centromeric satellite arrays, recent segmental duplications, and the short arms of all five acrocentric chromosomes, unlocking these complex regions of the genome to variational and functional studies.

Computational tools to study thermodynamic properties of magnetic materials have, until recently, been limited to phenomenological modeling or to small domain sizes limiting our mechanistic understanding of thermal transport in ferromagnets. Herein, we study the interplay of phonon and magnetic spin contributions to the thermal conductivity in $$\alpha$$ α -iron utilizing non-equilibrium molecular dynamics simulations. It was observed that the magnetic spin contribution to the total thermal conductivity exceeds lattice transport for temperatures up to two-thirds of the Curie temperature after which only strongly coupled magnon-phonon modes become active heat carriers. Characterizations of the phonon and magnon spectra give a detailed insight into the coupling between these heat carriers, and the temperature sensitivity of these coupled systems. Comparisons to both experiments and ab initio data support our inferred electronic thermal conductivity, supporting the coupled molecular dynamics/spin dynamics framework as a viable method to extend the predictive capability for magnetic material properties.

What role does visual experience play in the development of object recognition? Prior controlled-rearing studies suggest that newborn animals require slow and smooth visual experiences to develop object recognition. Here we examined whether the development of object recognition also requires experience with the surface features of objects. We raised newborn chicks in automated controlled-rearing chambers that contained a single virtual object, then tested their ability to recognize that object from familiar and novel viewpoints. When chicks were reared with an object that had surface features, the chicks developed view-invariant object recognition. In contrast, when chicks were reared with a line drawing of an object, the chicks failed to develop object recognition. The chicks reared with line drawings performed at chance level, despite acquiring over 100 hours of visual experience with the object. These results indicate that the development of object recognition requires experience with the surface features of objects.

Highlights • While optic nerves are part of the CSI target volume, lenses need to be spared. • Lens and optic disc movement for different gaze directions was evaluated in MRI scans. • Eye movement influence on lens and optic nerve CSI dose distribution was analyzed. • With modern radiotherapy techniques, any eye movement increases the mean lens dose. • Maximum eye movements decrease mean orbital optic nerve D98, Purpose Optic nerves are part of the craniospinal irradiation (CSI) target volume. Modern radiotherapy techniques achieve highly conformal target doses while avoiding organs-at-risk such as the lens. The magnitude of eye movement and its influence on CSI target- and avoidance volumes are unclear. We aimed to evaluate the movement-range of lenses and optic nerves and its influence on dose distribution of several planning techniques. Methods Ten volunteers underwent MRI scans in various gaze directions (neutral, left, right, cranial, caudal). Lenses, orbital optic nerves, optic discs and CSI target volumes were delineated. 36-Gy cranial irradiation plans were constructed on synthetic CT images in neutral gaze, with Volumetric Modulated Arc Therapy, pencil-beam scanning proton therapy, and 3D-conventional photons. Movement-amplitudes of lenses and optic discs were analyzed, and influence of gaze direction on lens and orbital optic nerve dose distribution. Results Mean eye structures’ shift from neutral position was greatest in caudal gaze; −5.8±1.2 mm (±SD) for lenses and 7.0±2.0 mm for optic discs. In 3D-conventional plans, caudal gaze decreased Mean Lens Dose (MLD). In VMAT and proton plans, eye movements mainly increased MLD and diminished D98 orbital optic nerve (D98OON) coverage; mean MLD increased up to 5.5 Gy [total ΔMLD range −8.1 to 10.0 Gy], and mean D98OON decreased up to 3.3 Gy [total ΔD98OON range −13.6 to 1.2 Gy]. VMAT plans optimized for optic disc Internal Target Volume and lens Planning organ-at-Risk Volume resulted in higher MLD over gaze directions. D98OON became ≥95% of prescribed dose over 95/100 evaluated gaze directions, while all-gaze bilateral D98OON significantly changed in 1 of 10 volunteers. Conclusion With modern CSI techniques, eye movements result in higher lens doses and a mean detriment for orbital optic nerve dose coverage of

A feminist critical gaze in analyses of images in popular media found that a patriarchal gaze in androcentric visual reconstructions of early biosocial hominin evolution persists despite some recen...

BackgroundThe blue whale, Balaenoptera musculus , is the largest animal known to have ever existed. Body size is tightly coupled to cell metabolism and environmental adaptations. A high-quality genome assembly of this magnificent animal will aid our understanding of body size regulation and related biological processes.ResultsWe report a reference-quality, long read based assembly of the blue whale genome. We sequenced genomic DNA using PacBio long-read, Illumina short-read, and 10X Genomics synthetic long-read technologies. We also obtained long-range mapping information using Bionano optical mapping and Dovetail Hi-C. Additionally, we sequenced the transcriptome of blue whale fibroblasts using Illumina RNA-seq and PacBio Iso-seq technologies. We also measured genome size using a flow cytometry technique. We report on: (1) comparison of alternative long-read and short-read-based assemblies; (2) segmental duplications within the blue whale genome, which have resulted in dramatic amplifications of several genes; (3) sites in IGF1 gene correlated to body size in cetaceans; and (4) heterozygosity and historical demography of Pacific and Atlantic blue whale populations.ConclusionsThis is one of the first high-quality reference genomes of a cetacean and the first baleen whale sequenced using a long-read technology. A high quality, annotated blue whale genome will serve as an important resource for biology, evolution, and conservation research.

This article is a form of activist archaeology in taking a feminist intersectional approach to suggest additional information and sites to increase the inclusiveness of Boston’s Freedom Trail and Black Heritage Trail. First a critical feminist approach is taken to analyze the biases of these trails. Critique of the dominance of elite white heterosexual men in Freedom Trail sites is needed to open the space for more inclusive intersectional information. The inclusion of more information about Native American men and women is suggested for existing sites on the Freedom Trail, and a statue commemorating their settlements in the area. Inclusion of more information about women of various intersectionalities is suggested for existing sites on the Freedom Trail and the Black Heritage Trail, as well as some additional women’s sites from the Boston Women’s Heritage Trails and survey of over 120 women’s public institutions in Boston. Inclusion of greater ethnic diversity is suggested with the addition of information from the Irish Heritage Trail and the addition of sites from Jewish heritage trails. Inclusion at existing Freedom Trail sites of information about non-heterosexuals is suggested from Boston’s Equality Trail.

Este artículo analiza la labor de promoción, teorización, producción y exhibición del cine en Bolivia a principios de la década de 1960 por parte del grupo de cineastas que posteriormente establecerían el Grupo Ukamau hacia finales de ese decenio. En primer lugar, el artículo debate las implicaciones del uso del término «Ukamau» por los propios realizadores y por la comunidad crítica y académica, para historizar y periodizar un episodio clave de la historia del cine boliviano. A continuación, el texto propone una interpretación de las actividades fílmicas de Jorge Sanjinés y de sus colaboradores que demuestra los vínculos culturales, políticos y estéticos entre la cultura cinematográfica en Bolivia a inicios de los años sesenta y otros modos nacionales y transnacionales de concebir el cine. Por último, el artículo insta al desarrollo de nuevos enfoques descentrados del estudio de tales materiales que trasciendan una historia del cine centrada en películas canónicas o en la figura del autor.

This article focuses on the productive tensions between the competing ideological discourses of post-war internationalism, Mexican post-revolutionary nationalism and local indigenous representational paradigms in the activities of the film unit of the UNESCO-sponsored adult education centre (CREFAL) in the town of Pátzcuaro, Mexico in the 1950s, which combined village screenings of educational, promotional and informative movies from the world over, with the local production of pedagogical documentary shorts by non-professional filmmakers from across Latin America. Inspired by the work of British documentarian Paul Rotha, whose United Nation picture World Without End (Mexico/Thailand/United Kingdom, 1953, codirected with Basil Wright) was partly filmed at CREFAL, these films frequently resorted to a docudrama format that enabled amateur documentary filmmakers to engage with the agendas of their indigenous subjects even as they subordinated them to the United Nation’s call to hygiene, progress and civic values. In doing so, they responded creatively to appeals by theorists such as Kracauer and Grierson for a critical realist cinema. They also acted as a link between the so-called ‘classical’ pre-war documentary movements in the United Kingdom, North America and elsewhere, and the later, socially committed new cinemas.

The special issue presented in this introduction focuses on the uses of documentary cinema in Mexico between 1930 and 1980 as part of the wider cultural policy of a variety of institutions that made films to express particular discourses or to promote their agendas. The institutions under study include state agencies, international bodies, private media companies and marginal political organizations.

Genome sequences are computationally assembled from millions of much shorter sequencing reads. Although this process can be impressively accurate with long reads, it is still subject to a variety of types of errors, including large structural misassembly errors in addition to localised base pair substitutions. Recent advances in long single molecule sequencing in combination with other long-range technologies such as synthetic long read clouds and Hi-C have dramatically increased the contiguity of assembly. This makes it all the more important to be able to validate the structural integrity of the chromosomal scale assemblies now being generated. Here we describe a novel assembly evaluation tool, Asset, which evaluates the consistency of a proposed genome assembly with multiple primary long-range data sets, identifying both supported regions and putative structural misassemblies. We present tests on three de novo assemblies from a human, a goat and a fish species, demonstrating that Asset can identify structural misassemblies accurately by combining regionally supported evidence from long read and other raw sequencing data. Not only can Asset be used to assess overall assembly confidence, and discover specific problematic regions for downstream genome curation, a process that leads to improvement in genome quality, but it can also provide feedback to automated assembly pipelines.

Tungsten (W) is a material of choice for the divertor material due to its high melting temperature, thermal conductivity, and sputtering threshold. However, W has a very high brittle-to-ductile transition temperature, and at fusion reactor temperatures (≥1000 K), it may undergo recrystallization and grain growth. Dispersion-strengthening W with zirconium carbide (ZrC) can improve ductility and limit grain growth, but much of the effects of the dispersoids on microstructural evolution and thermomechanical properties at high temperatures are still unknown. We present a machine learned Spectral Neighbor Analysis Potential for W–ZrC that can now be used to study these materials. In order to construct a potential suitable for large-scale atomistic simulations at fusion reactor temperatures, it is necessary to train on ab initio data generated for a diverse set of structures, chemical environments, and temperatures. Further accuracy and stability tests of the potential were achieved using objective functions for both material properties and high temperature stability. Validation of lattice parameters, surface energies, bulk moduli, and thermal expansion is confirmed on the optimized potential. Tensile tests of W/ZrC bicrystals show that although the W(110)–ZrC(111) C-terminated bicrystal has the highest ultimate tensile strength (UTS) at room temperature, observed strength decreases with increasing temperature. At 2500 K, the terminating C layer diffuses into the W, resulting in a weaker W–Zr interface. Meanwhile, the W(110)–ZrC(111) Zr-terminated bicrystal has the highest UTS at 2500 K.

Polars are highly magnetic cataclysmic variables which have been long observed to have both high and low brightness states. The duration of these states has been previously seen to vary from a number of days up to years. Despite this; these states and their physical origin has not been explained in a consistent manner. We present observations of the shortest duration states of a number of Polars observed by ZTF and TESS. This has allowed us to determine that short duration states are a relatively common feature across the population of Polars. Furthermore we have been able to generalise the model of star spot migration to explain both short lived high and low states in Polars by incorporating the interaction between the magnetic field of the white dwarf and that of the star spots., Comment: 16 pages, 9 Figures. Final accepted version to MNRAS