Governance of Indigenous data in open earth systems science.

In the age of big data and open science, what processes are needed to follow open science protocols while upholding Indigenous Peoples' rights? The Earth Data Relations Working Group (EDRWG), convened to address this question and envision a research landscape that acknowledges the legacy of extractive practices and embraces new norms across Earth science institutions and open science research. Using the National Ecological Observatory Network (NEON) as an example, the EDRWG recommends actions, applicable across all phases of the data lifecycle, that recognize the sovereign rights of Indigenous Peoples and support better research across all Earth Sciences.

A conceptual classification scheme of invasion science.

In the era of big data and global biodiversity decline, there is a pressing need to transform data and information into findable and actionable knowledge. We propose a conceptual classification scheme for invasion science that goes beyond hypothesis networks and allows to organize publications and data sets, guide research directions, and identify knowledge gaps. Combining expert knowledge with literature analysis, we identified five major research themes in this field: introduction pathways, invasion success and invasibility, impacts of invasion, managing biological invasions, and meta-invasion science.

A new leaf inhabiting ascomycete from the Jurassic (ca 170 Mya) of Yorkshire, UK, and insights into the appearance and diversification of filamentous Ascomycota.

Leaf-associated fungi, the fungi that depend on leaves to sporulate, have a rich Cenozoic record, however their earlier diversity is poorly characterized. Here we describe Harristroma eboracense gen. et sp.

Making Mathematical Research Data FAIR: Pathways to Improved Data Sharing.

The sharing and citation of research data is becoming increasingly recognized as an essential building block in scientific research across various fields and disciplines. Sharing research data allows other researchers to reproduce results, replicate findings, and build on them. Ultimately, this will foster faster cycles in knowledge generation.

Bragg Spot Finder (BSF): a new machine-learning-aided approach to deal with spot finding for rapidly filtering diffraction pattern images.

Macromolecular crystallography contributes significantly to understanding diseases and, more importantly, how to treat them by providing atomic resolution 3D structures of proteins. This is achieved by collecting X-ray diffraction images of protein crystals from important biological pathways. Spotfinders are used to detect the presence of crystals with usable data, and the spots from such crystals are the primary data used to solve the relevant structures.

Investigation of fast and efficient lossless compression algorithms for macromolecular crystallography experiments.

Structural biology experiments benefit significantly from state-of-the-art synchrotron data collection. One can acquire macromolecular crystallography (MX) diffraction data on large-area photon-counting pixel-array detectors at framing rates exceeding 1000 frames per second, using 200 Gbps network connectivity, or higher when available. In extreme cases this represents a raw data throughput of about 25 GB s, which is nearly impossible to deliver at reasonable cost without compression.

Getting your DUCs in a row - standardising the representation of Digital Use Conditions.

Improving patient care and advancing scientific discovery requires responsible sharing of research data, healthcare records, biosamples, and biomedical resources that must also respect applicable use conditions. Defining a standard to structure and manage these use conditions is a complex and challenging task. This is exemplified by a near unlimited range of asset types, a high variability of applicable conditions, and differing applications at the individual or collective level.

Parallel evolution of angiosperm-like venation in Peltaspermales: a reinvestigation of Furcula.

Leaf venation is a pivotal trait in the success of vascular plants. Whereas gymnosperms have single or sparsely branched parallel veins, angiosperms developed a hierarchical structure of veins that form a complex reticulum. Its physiological consequences are considered to have enabled angiosperms to dominate terrestrial ecosystems in the Late Cretaceous and Cenozoic.

Disparity of cycad leaves dispels the living fossil metaphor.

The living fossil metaphor is tightly linked with the cycads. This group of gymnosperms is supposed to be characterised by long-term morphological stasis, particularly after their peak of diversity and disparity in the Jurassic. However, no formal test of this hypothesis exists.

Embracing uncertainty: The way forward in plant fossil phylogenetics.

Although molecular phylogenetics remains the most widely used method of inferring the evolutionary history of living groups, the last decade has seen a renewed interest in morphological phylogenetics, mostly driven by the promises that integrating the fossil record in phylogenetic trees offers to our understanding of macroevolutionary processes and dynamics and the possibility that the inclusion of fossil taxa could lead to more accurate phylogenetic hypotheses. The plant fossil record presents some challenges to its integration in a phylogenetic framework. Phylogenies including plant fossils often retrieve uncertain relationships with low support, or lack of resolution.

An invertible seven-dimensional Dirichlet cell characterization of lattices.

Characterization of crystallographic lattices is an important tool in structure solution, crystallographic database searches and clustering of diffraction images in serial crystallography. Characterization of lattices by Niggli-reduced cells (based on the three shortest non-coplanar lattice vectors) or by Delaunay-reduced cells (based on four non-coplanar vectors summing to zero and all meeting at obtuse or right angles) is commonly performed. The Niggli cell derives from Minkowski reduction.

Reconciling fossils with phylogenies reveals the origin and macroevolutionary processes explaining the global cycad biodiversity.

The determinants of biodiversity patterns can be understood using macroevolutionary analyses. The integration of fossils into phylogenies offers a deeper understanding of processes underlying biodiversity patterns in deep time. Cycadales are considered a relict of a once more diverse and globally distributed group but are restricted to low latitudes today.

Editorial of the Special Issue "Neurobiological Mechanisms Implicated in Stress-Related Psychiatric Disorders".

Mental disorders may seriously impair the quality of life of affected individuals and cause a significant public health burden [...

Cenozoic migration of a desert plant lineage across the North Atlantic.

Previous paleobotanical work concluded that Paleogene elements of the sclerophyllous subhumid vegetation of western Eurasia and western North America were endemic to these disjunct regions, suggesting that the southern areas of the Holarctic flora were isolated at that time. Consequently, molecular studies invoked either parallel adaptation to dry climates from related ancestors, or long-distance dispersal in explaining disjunctions between the two regions, dismissing the contemporaneous migration of dry-adapted lineages via land bridges as unlikely. We report Vauquelinia (Rosaceae), currently endemic to western North America, in Cenozoic strata of western Eurasia.

Why there is no dilemma for the birth strategy: a response to Bobier and Omelianchuk.

Bobier and Omelianchuk argue that the Birth Strategy for addressing analogies between abortion and infanticide is saddled with a dilemma. It must be accepted that non-therapeutic late-term abortions are either, impermissible, or they are not. If accepted, then the Birth Strategy is undermined.

Variability of Steroid Prescription for COVID-19 Associated Pneumonia in Real-Life, Non-Trial Settings.

The RECOVERY study documented lower 28-day mortality with the use of dexamethasone in hospitalized patients on invasive mechanical ventilation or oxygen with COVID-19 Pneumonia. We aimed to examine the practice patterns of steroids use, and their impact on mortality and length of stay in ICU. We retrospectively examined records of all patients with confirmed Covid 19 pneumonia admitted to the ICU of Dubai hospital from January 1st, 2020 - June 30th, 2020.

Letter to the Editor: FHIR RDF - Why the world needs structured electronic health records.

This comment discusses the benefits of representing and reusing the information in Electronic Health Record databases as knowledge graphs in the RDF format based on the FHIR RDF specification. As a structured representation of clinical data, FHIR RDF-based electronic health records allow a simpler and more effective integration of biomedical information using semantic alignment, queries, interoperability, and federation to provide better support for health practice and research.

Homology Modeling and Molecular Dynamics-Driven Search for Natural Inhibitors That Universally Target Receptor-Binding Domain of Spike Glycoprotein in SARS-CoV-2 Variants.

The rapid spread of SARS-CoV-2 required immediate actions to control the transmission of the virus and minimize its impact on humanity. An extensive mutation rate of this viral genome contributes to the virus' ability to quickly adapt to environmental changes, impacts transmissibility and antigenicity, and may facilitate immune escape. Therefore, it is of great interest for researchers working in vaccine development and drug design to consider the impact of mutations on virus-drug interactions.

The relationship between chlorophyllous spores and mycorrhizal associations in ferns: evidence from an evolutionary approach.

Premise: Approximately 14% of all fern species have physiologically active chlorophyllous spores that are much more short-lived than the more common and dormant achlorophyllous spores. Most chlorophyllous-spored species (70%) are epiphytes and account for almost 37% of all epiphytic ferns. Chlorophyllous-spored ferns are also overrepresented among fern species in habitats with waterlogged soils, of which nearly 60% have chlorophyllous spores.

Serial crystallography with multi-stage merging of thousands of images.

KAMO and BLEND provide particularly effective tools to automatically manage the merging of large numbers of data sets from serial crystallography. The requirement for manual intervention in the process can be reduced by extending BLEND to support additional clustering options such as the use of more accurate cell distance metrics and the use of reflection-intensity correlation coefficients to infer `distances' among sets of reflections. This increases the sensitivity to differences in unit-cell parameters and allows clustering to assemble nearly complete data sets on the basis of intensity or amplitude differences.

Orphans cannot be after-birth aborted: a response to Bobier.

I offer a response to an objection to my account of the moral difference between fetuses and newborns, an account that seeks to address an analogy between abortion and infanticide, which is based on the apparent equality of moral value of fetuses and newborns.

A simple technique to classify diffraction data from dynamic proteins according to individual polymorphs.

One often observes small but measurable differences in the diffraction data measured from different crystals of a single protein. These differences might reflect structural differences in the protein and may reveal the natural dynamism of the molecule in solution. Partitioning these mixed-state data into single-state clusters is a critical step that could extract information about the dynamic behavior of proteins from hundreds or thousands of single-crystal data sets.