CZ CELLxGENE Discover: a single-cell data platform for scalable exploration, analysis and modeling of aggregated data.

Hundreds of millions of single cells have been analyzed using high-throughput transcriptomic methods. The cumulative knowledge within these datasets provides an exciting opportunity for unlocking insights into health and disease at the level of single cells. Meta-analyses that span diverse datasets building on recent advances in large language models and other machine-learning approaches pose exciting new directions to model and extract insight from single-cell data.

MAMS: matrix and analysis metadata standards to facilitate harmonization and reproducibility of single-cell data.

Many datasets are being produced by consortia that seek to characterize healthy and disease tissues at single-cell resolution. While biospecimen and experimental information is often captured, detailed metadata standards related to data matrices and analysis workflows are currently lacking. To address this, we develop the matrix and analysis metadata standards (MAMS) to serve as a resource for data centers, repositories, and tool developers.

Matrix and analysis metadata standards (MAMS) to facilitate harmonization and reproducibility of single-cell data.

A large number of genomic and imaging datasets are being produced by consortia that seek to characterize healthy and disease tissues at single-cell resolution. While much effort has been devoted to capturing information related to biospecimen information and experimental procedures, the metadata standards that describe data matrices and the analysis workflows that produced them are relatively lacking. Detailed metadata schema related to data analysis are needed to facilitate sharing and interoperability across groups and to promote data provenance for reproducibility.

How safe is this trip? Judging personal safety in a pandemic based on information from different sources.

In a preregistered experiment, we presented participants with information about the safety of traveling during a deadly pandemic and during a migration trip using five different sources (a news article, a family member, an official organization, someone with personal experience, and the travel organizer) and four different verbal descriptions of the likelihood of safety ( and ). We found that both for the pandemic and migration contexts, judgments about the likelihood of safely traveling and decisions to travel were most strongly influenced by information from the respective official organizations and that participants also indicated greater willingness to share information from official organizations with others. These results are consistent with the established finding that expert sources are more persuasive.

Ancient noeggerathialean reveals the seed plant sister group diversified alongside the primary seed plant radiation.

Noeggerathiales are enigmatic plants that existed during Carboniferous and Permian times, ∼323 to 252 Mya. Although their morphology, diversity, and distribution are well known, their systematic affinity remained enigmatic because their anatomy was unknown. Here, we report from a 298-My-old volcanic ash deposit, an in situ, complete, anatomically preserved noeggerathialean.

Reconstructing development of the earliest seed integuments raises a new hypothesis for the evolution of ancestral seed-bearing structures.

How plant seeds originated remains unresolved, in part due to disconnects between fossil intermediates and developmental genetics in extant species. The Carboniferous fossil Genomosperma is considered among the most primitive known seeds, with highly lobed integument and exposed nucellus. We have used this key fossil taxon to investigate the evolutionary origins of seed development.

The ENCODE Portal as an Epigenomics Resource.

The Encyclopedia of DNA Elements (ENCODE) web portal hosts genomic data generated by the ENCODE Consortium, Genomics of Gene Regulation, The NIH Roadmap Epigenomics Consortium, and the modENCODE and modERN projects. The goal of the ENCODE project is to build a comprehensive map of the functional elements of the human and mouse genomes. Currently, the portal database stores over 500 TB of raw and processed data from over 15,000 experiments spanning assays that measure gene expression, DNA accessibility, DNA and RNA binding, DNA methylation, and 3D chromatin structure across numerous cell lines, tissue types, and differentiation states with selected genetic and molecular perturbations.

How deep is the conflict between molecular and fossil evidence on the age of angiosperms?

The timing of the origin of angiosperms is a hotly debated topic in plant evolution. Molecular dating analyses that consistently retrieve pre-Cretaceous ages for crown-group angiosperms have eroded confidence in the fossil record, which indicates a radiation and possibly also origin in the Early Cretaceous. Here, we evaluate paleobotanical evidence on the age of the angiosperms, showing how fossils provide crucial data for clarifying the situation.

Prevention of data duplication for high throughput sequencing repositories.

https://www.encodeproject.org/.

The Encyclopedia of DNA elements (ENCODE): data portal update.

The Encyclopedia of DNA Elements (ENCODE) Data Coordinating Center has developed the ENCODE Portal database and website as the source for the data and metadata generated by the ENCODE Consortium. Two principles have motivated the design. First, experimental protocols, analytical procedures and the data themselves should be made publicly accessible through a coherent, web-based search and download interface.

Choosing the choice: Reflections on modelling decisions and behaviour in demographic agent-based models.

This paper investigates the issues associated with choosing appropriate models of choice for demographic agent-based models. In particular, we discuss the importance of context, time preference, and dealing with uncertainty in decision modelling, as well as the heterogeneity between agents in their decision-making strategies. The paper concludes by advocating empirically driven, modular, and multi-model approaches to designing simulations of human decision-making, given the lack of an agreed strategy for dealing with any of these issues.

SnoVault and encodeD: A novel object-based storage system and applications to ENCODE metadata.

The Encyclopedia of DNA elements (ENCODE) project is an ongoing collaborative effort to create a comprehensive catalog of functional elements initiated shortly after the completion of the Human Genome Project. The current database exceeds 6500 experiments across more than 450 cell lines and tissues using a wide array of experimental techniques to study the chromatin structure, regulatory and transcriptional landscape of the H. sapiens and M.

Anatomically preserved "strobili" and leaves from the Permian of China (Dorsalistachyaceae, fam. nov.) broaden knowledge of Noeggerathiales and constrain their possible taxonomic affinities.

Premise Of The Study: Noeggerathiales are an extinct group of heterosporous shrubs and trees that were widespread and diverse during the Pennsylvanian-Permian Epochs (323-252 Ma) but are of controversial taxonomic affinity. Groups proposed as close relatives include leptosporangiate ferns, sphenopsids, progymnosperms, or the extant eusporangiate fern Tmesipteris. Previously identified noeggerathialeans lacked anatomical preservation, limiting taxonomic comparisons to their external morphology and spore structure.

Surveying DNA Elements within Functional Genes of Heterocyst-Forming Cyanobacteria.

Some cyanobacteria are capable of differentiating a variety of cell types in response to environmental factors. For instance, in low nitrogen conditions, some cyanobacteria form heterocysts, which are specialized for N2 fixation. Many heterocyst-forming cyanobacteria have DNA elements interrupting key N2 fixation genes, elements that are excised during heterocyst differentiation.

Principles of metadata organization at the ENCODE data coordination center.

The Encyclopedia of DNA Elements (ENCODE) Data Coordinating Center (DCC) is responsible for organizing, describing and providing access to the diverse data generated by the ENCODE project. The description of these data, known as metadata, includes the biological sample used as input, the protocols and assays performed on these samples, the data files generated from the results and the computational methods used to analyze the data. Here, we outline the principles and philosophy used to define the ENCODE metadata in order to create a metadata standard that can be applied to diverse assays and multiple genomic projects.

Stratigraphy, palaeoenvironments and palaeoecology of the Loch Humphrey Burn lagerstätte and other Mississippian palaeobotanical localities of the Kilpatrick Hills, southwest Scotland.

Background and Aims. The largely Mississippian strata of the Kilpatrick Hills, located at the western end of the Scottish Midland Valley, enclose several macrofossil floras that together contain ca 21 organ-species of permineralised plants and ca 44 organ-species of compressed plants, here estimated to represent 25 whole-plant species (Glenarbuck = nine, Loch Humphrey Burn Lower = 11, Upper = seven). The most significant locality is the internationally important volcanigenic sequence that is reputedly intercalated within the Clyde Plateau Lava Formation at Loch Humphrey Burn, where ca 30 m of reworked tuffs and other clastic sediments enclose one of the world's most important terrestrial lagerstätten of this period.

Middle Jurassic evidence for the origin of Cupressaceae: A paleobotanical context for the roles of regulatory genetics and development in the evolution of conifer seed cones.

Premise Of The Study: Triassic and Jurassic fossils record structural changes in conifer seed cones through time, provide the earliest evidence for crown-group conifer clades, and further clarify sister-group relationships of modern conifer families. A new and distinct seed-cone from the Isle of Skye in western Scotland provides the oldest detailed evidence for the ancestral morphology of the phylogenetically contentious family Cupressaceae.

Methods: A single isolated cone was prepared as serial sections by the cellulose acetate peel technique, mounted on microscope slides, and viewed and photographed using transmitted light.

Metatranscriptomics of N2-fixing cyanobacteria in the Amazon River plume.

Biological N2 fixation is an important nitrogen source for surface ocean microbial communities. However, nearly all information on the diversity and gene expression of organisms responsible for oceanic N2 fixation in the environment has come from targeted approaches that assay only a small number of genes and organisms. Using genomes of diazotrophic cyanobacteria to extract reads from extensive meta-genomic and -transcriptomic libraries, we examined diazotroph diversity and gene expression from the Amazon River plume, an area characterized by salinity and nutrient gradients.

X-ray Synchrotron Microtomography of a silicified Jurassic Cheirolepidiaceae (Conifer) cone: histology and morphology of Pararaucaria collinsonae sp. nov.

We document a new species of ovulate cone (Pararaucaria collinsonae) on the basis of silicified fossils from the Late Jurassic Purbeck Limestone Group of southern England (Tithonian Stage: ca. 145 million years). Our description principally relies on the anatomy of the ovuliferous scales, revealed through X-ray synchrotron microtomography (SRXMT) performed at the Diamond Light Source (UK).

Reconstructing relative genome size of vascular plants through geological time.

The strong positive relationship evident between cell and genome size in both animals and plants forms the basis of using the size of stomatal guard cells as a proxy to track changes in plant genome size through geological time. We report for the first time a taxonomic fine-scale investigation into changes in stomatal guard-cell length and use these data to infer changes in genome size through the evolutionary history of land plants. Our data suggest that many of the earliest land plants had exceptionally large genome sizes and that a predicted overall trend of increasing genome size within individual lineages through geological time is not supported.

Peronosporomycetes (Oomycota) from a Middle Permian permineralised peat within the Bainmedart Coal Measures, Prince Charles Mountains, Antarctica.

The fossil record of Peronosporomycetes (water moulds) is rather sparse, though their distinctive ornamentation means they are probably better reported than some true fungal groups. Here we describe a rare Palaeozoic occurrence of this group from a Guadalupian (Middle Permian) silicified peat deposit in the Bainmedart Coal Measures, Prince Charles Mountains, Antarctica. Specimens are numerous and comprise two morphologically distinct kinds of ornamented oogonia, of which some are attached to hyphae by a septum.

Several developmental and morphogenetic factors govern the evolution of stomatal patterning in land plants.

We evaluate stomatal development in terms of its primary morphogenetic factors and place it in a phylogenetic context, including clarification of the contrasting specialist terms that are used by different sets of researchers. The genetic and structural bases for stomatal development are well conserved and increasingly well understood in extant taxa, but many phylogenetically crucial plant lineages are known only from fossils, in which it is problematic to infer development. For example, specialized lateral subsidiary cells that occur adjacent to the guard cells in some taxa can be derived either from the same cell lineage as the guard cells or from an adjacent cell file.