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Introduction Decades of research have shown that affect, emotions and moods, significantly impact all aspects of health behaviors. This research utilized a novel digital analogue technology (Morphii) to assess eight affective domains: stress, anxiety, loneliness, irritability, depression, pain, energy and overall feelings of wellness. Objectives To demonstrate the feasibility of use and strength of relationship/comparison to validated measures. Methods A U.S. census-based sample of adults ages 18-80 (n=985) completed online assessments including the 8 Morphii’s and additional comparative mental/behavioral health assessments (PSS-4, GAD-7, UCLA Loneliness Scale V3, BITe, PHQ-8 & PHQ-2, P4 Pain Scale, WHO-5, CFQ-11, ESS, and Vitality Subscale SF-36) via the Prolific Academic online platform and were compensated nominally for their participation. The resulting sample was 51.6% female and 74.2% White. Results Each Morphii was compared with the common corresponding industry assessment (e.g., Depression Morphii with PHQ) resulting in Pearson correlations ranging from -.519 to .761, with 6 of the 8 showing correlations above .700. Pearson correlations between dysfunction and each of the 8 Morphiis were significant at the p < .000 level, ranging from a low of .421 (Loneliness) to a high of .607 (Depression). Internal reliability was very good (Cronbach’s Alpha = .862). Respondents who expressed an assessment modality preference (55.2%) chose the Morphii type over traditional assessment format at a 2.5:1 ratio. Conclusions Morphii provides a reliable and valid assessment option with the ability to obtain a comprehensive (8 domains at once), efficient (less than 60 second administration), assessment with increased patient/client preference and engagement. Disclosure Milanak - submitting author - I serve on the advisory board for ADoH Scientific to consult on scientific research of Morphii development. To date, I have not been paid any money for this advisory role.

The accuracy and precision of snow depth measurements depend on the measuring device and the conditions of the site and snowpack in which it is being used. This study compares collocated snow depth measurements from a magnaprobe snow depth probe and a Federal snow tube in an ephemeral snow environment. We conducted three snow depth sampling campaigns from December 2020 to February 2021 that included 39 open-field and coniferous-, mixed-, and deciduous-forest sampling sites in Durham, New Hampshire, United States. For all sampling campaigns and land cover types, with a total of 936 paired observations, the magnaprobe snow depth measurements were consistently deeper than those of the snow tube. There was a 12 % average difference between the magnaprobe (14.9 cm) and snow tube (13.2 cm) average snow depths with a greater difference in the forest (1.9 cm) than the field (1.3 cm). This study suggests that snow depth measurements using a Federal snow tube can avoid overprobing with an ephemeral snowpack in forested environments.

Abstract The Tara Pacific expedition (2016–2018) sampled coral ecosystems around 32 islands in the Pacific Ocean and the ocean surface waters at 249 locations, resulting in the collection of nearly 58 000 samples. The expedition was designed to systematically study warm-water coral reefs and included the collection of corals, fish, plankton, and seawater samples for advanced biogeochemical, molecular, and imaging analysis. Here we provide a complete description of the sampling methodology, and we explain how to explore and access the different datasets generated by the expedition. Environmental context data were obtained from taxonomic registries, gazetteers, almanacs, climatologies, operational biogeochemical models, and satellite observations. The quality of the different environmental measures has been validated not only by various quality control steps, but also through a global analysis allowing the comparison with known environmental large-scale structures. Such publicly released datasets open the perspective to address a wide range of scientific questions.

Abstract Background Over the last decade, several coral genomes have been sequenced allowing a better understanding of these symbiotic organisms threatened by climate change. Scleractinian corals are reef builders and are central to coral reef ecosystems, providing habitat to a great diversity of species. Results In the frame of the Tara Pacific expedition, we assemble two coral genomes, Porites lobata and Pocillopora cf. effusa, with vastly improved contiguity that allows us to study the functional organization of these genomes. We annotate their gene catalog and report a relatively higher gene number than that found in other public coral genome sequences, 43,000 and 32,000 genes, respectively. This finding is explained by a high number of tandemly duplicated genes, accounting for almost a third of the predicted genes. We show that these duplicated genes originate from multiple and distinct duplication events throughout the coral lineage. They contribute to the amplification of gene families, mostly related to the immune system and disease resistance, which we suggest to be functionally linked to coral host resilience. Conclusions At large, we show the importance of duplicated genes to inform the biology of reef-building corals and provide novel avenues to understand and screen for differences in stress resilience.

Abstract Heat waves are causing declines in coral reefs globally. Coral thermal responses depend on multiple, interacting drivers, such as past thermal exposure, endosymbiont community composition, and host genotype. This makes the understanding of their relative roles in adaptive and/or plastic responses crucial for anticipating impacts of future warming. Here, we extracted DNA and RNA from 102 Pocillopora colonies collected from 32 sites on 11 islands across the Pacific Ocean to characterize host-photosymbiont fidelity and to investigate patterns of gene expression across a historical thermal gradient. We report high host-photosymbiont fidelity and show that coral and microalgal gene expression respond to different drivers. Differences in photosymbiotic association had only weak impacts on host gene expression, which was more strongly correlated with the historical thermal environment, whereas, photosymbiont gene expression was largely determined by microalgal lineage. Overall, our results reveal a three-tiered strategy of thermal acclimatization in Pocillopora underpinned by host-photosymbiont specificity, host transcriptomic plasticity, and differential photosymbiotic association under extreme warming.

Abstract In general, individuals who are lesbian, gay, bisexual, transgender, queer or questioning, plus other identities (LGBTQ+) living with multiple sclerosis (MS) have less favorable healthcare experiences and poorer overall health than cisgendered heterosexual individuals. They may experience further challenges in addition to managing their MS, including psychological or emotional problems, and an increased risk of comorbid diseases and substance abuse. Transgender individuals specifically face additional unique challenges, including high rates of mental health distress and effects from long-term exogenous hormone use and gender affirmation surgery. These findings highlight disparities in both quality of care and health outcomes of LGBTQ+ individuals. Unmet needs and drivers of these disparities relate to a lack of inclusivity in healthcare environments, poor communication between healthcare professionals (HCPs) and LGBTQ+ patients, inadequate HCP knowledge of LGBTQ+ health issues, and gaps in research into the impact of sexual orientation and gender identity in MS. Although data are limited, recommendations to improve the experience and care of LGBTQ+ individuals with MS include increasing HCP awareness of the challenges LGBTQ+ individuals face and provision of inclusive care, with the overarching goal for HCPs to be allies to the LGBTQ+ community. Improvements may be achieved through diversity and cultural awareness training of HCPs on sexual orientation and gender identity, and ensuring a friendly, open, and supportive healthcare environment. Use of sensitive and gender-neutral language by HCPs, representation of LGBTQ+ individuals in patient materials, and access to LGBTQ+ MS support groups are also recommended. HCPs should aim to integrate discussion of sexual orientation and gender identity and sexual and mental health into routine assessments and collaborate with other HCPs as needed. By addressing the challenges and unmet needs of LGBTQ+ individuals with MS, this should help resolve disparities in their quality of care and improve their overall health.

Abstract Background Microbiomes are now recognized as the main drivers of ecosystem function ranging from the oceans and soils to humans and bioreactors. However, a grand challenge in microbiome science is to characterize and quantify the chemical currencies of organic matter (i.e., metabolites) that microbes respond to and alter. Critical to this has been the development of Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS), which has drastically increased molecular characterization of complex organic matter samples, but challenges users with hundreds of millions of data points where readily available, user-friendly, and customizable software tools are lacking. Results Here, we build on years of analytical experience with diverse sample types to develop MetaboDirect, an open-source, command-line-based pipeline for the analysis (e.g., chemodiversity analysis, multivariate statistics), visualization (e.g., Van Krevelen diagrams, elemental and molecular class composition plots), and presentation of direct injection high-resolution FT-ICR MS data sets after molecular formula assignment has been performed. When compared to other available FT-ICR MS software, MetaboDirect is superior in that it requires a single line of code to launch a fully automated framework for the generation and visualization of a wide range of plots, with minimal coding experience required. Among the tools evaluated, MetaboDirect is also uniquely able to automatically generate biochemical transformation networks (ab initio) based on mass differences (mass difference network-based approach) that provide an experimental assessment of metabolite connections within a given sample or a complex metabolic system, thereby providing important information about the nature of the samples and the set of microbial reactions or pathways that gave rise to them. Finally, for more experienced users, MetaboDirect allows users to customize plots, outputs, and analyses. Conclusion Application of MetaboDirect to FT-ICR MS-based metabolomic data sets from a marine phage-bacterial infection experiment and a Sphagnum leachate microbiome incubation experiment showcase the exploration capabilities of the pipeline that will enable the research community to evaluate and interpret their data in greater depth and in less time. It will further advance our knowledge of how microbial communities influence and are influenced by the chemical makeup of the surrounding system. The source code and User’s guide of MetaboDirect are freely available through ( https://github.com/Coayala/MetaboDirect ) and ( https://metabodirect.readthedocs.io/en/latest/ ), respectively. Video Abstract

Abstract Intensive research in electrochemical CO2 reduction reaction has resulted in the discovery of numerous high-performance catalysts selective to multi-carbon products, with most of these catalysts still being purely transition metal based. Herein, we present high and stable multi-carbon products selectivity of up to 76.6% across a wide potential range of 1 V on histidine-functionalised Cu. In-situ Raman and density functional theory calculations revealed alternative reaction pathways that involve direct interactions between adsorbed histidine and CO2 reduction intermediates at more cathodic potentials. Strikingly, we found that the yield of multi-carbon products is closely correlated to the surface charge on the catalyst surface, quantified by a pulsed voltammetry-based technique which proved reliable even at very cathodic potentials. We ascribe the surface charge to the population density of adsorbed species on the catalyst surface, which may be exploited as a powerful tool to explain CO2 reduction activity and as a proxy for future catalyst discovery, including organic-inorganic hybrids.

Abstract Remarkable potency has been demonstrated for mRNA vaccines in reducing the global burden of the ongoing COVID-19 pandemic. An alternative form of the mRNA vaccine is the self-amplifying mRNA (sa-mRNA) vaccine, which encodes an alphavirus replicase that self-amplifies the full-length mRNA and SARS-CoV-2 spike (S) transgene. However, early-phase clinical trials of sa-mRNA COVID-19 vaccine candidates have questioned the potential of this platform to develop potent vaccines. We examined the immune gene response to a candidate sa-mRNA vaccine against COVID-19, ARCT-021, and compared our findings to the host response to other forms of vaccines. In blood samples from healthy volunteers that participated in a phase I/II clinical trial, greater induction of transcripts involved in Toll-like receptor (TLR) signalling, antigen presentation and complement activation at 1 day post-vaccination was associated with higher anti-S antibody titers. Conversely, transcripts involved in T-cell maturation at day 7 post-vaccination informed the magnitude of eventual S-specific T-cell responses. The transcriptomic signature for ARCT-021 vaccination strongly correlated with live viral vector vaccines, adjuvanted vaccines and BNT162b2 1 day post-vaccination. Moreover, the ARCT-021 signature correlated with day 7 YF17D live-attenuated vaccine transcriptomic responses. Altogether, our findings show that sa-mRNA vaccination induces innate immune responses that are associated with the development of adaptive immunity from other forms of vaccines, supporting further development of this vaccine platform for clinical application.

Dispositional gratitude has been negatively associated with perceived stress (PS) and positively associated with higher well-being in both general and chronically ill people. Attempts to understand the relationship between gratitude and aspects of quality of life (QOL) have been documented; however, there is limited research on determining the potential mediating effect of PS on gratitude and QOL factors in individuals with Multiple Sclerosis (MS). In this cross-sectional study, participant demographics, dispositional gratitude, PS, and QOL factors were collected online via self-report measures from a sample of 68 participants diagnosed with MS. Results indicated that both dispositional gratitude and PS were associated with aspects of QOL and that PS was found to partially and indirectly account for the relationship between gratitude and improved QOL. Findings are consistent with existing research conducted with non-chronically ill samples. Clarifying relationships between PS and dispositional factors in MS is necessary to inform future interventions aimed at maintaining and enhancing an individual's QOL.

Abstract SARS-CoV-2 infection and disease severity are influenced by viral entry (VE) gene expression patterns in the airway epithelium. The similarities and differences of VE gene expression (ACE2, TMPRSS2, and CTSL) across nasal and bronchial compartments have not been fully characterized using matched samples from large cohorts. Gene expression data from 793 nasal and 1673 bronchial brushes obtained from individuals participating in lung cancer screening or diagnostic workup revealed that smoking status (current versus former) was the only clinical factor significantly and reproducibly associated with VE gene expression. The expression of ACE2 and TMPRSS2 was higher in smokers in the bronchus but not in the nose. scRNA-seq of nasal brushings indicated that ACE2 co-expressed genes were highly expressed in club and C15orf48+ secretory cells while TMPRSS2 co-expressed genes were highly expressed in keratinizing epithelial cells. In contrast, these ACE2 and TMPRSS2 modules were highly expressed in goblet cells in scRNA-seq from bronchial brushings. Cell-type deconvolution of the gene expression data confirmed that smoking increased the abundance of several secretory cell populations in the bronchus, but only goblet cells in the nose. The association of ACE2 and TMPRSS2 with smoking in the bronchus is due to their high expression in goblet cells which increase in abundance in current smoker airways. In contrast, in the nose, these genes are not predominantly expressed in cell populations modulated by smoking. In individuals with elevated lung cancer risk, smoking-induced VE gene expression changes in the nose likely have minimal impact on SARS-CoV-2 infection, but in the bronchus, smoking may lead to higher viral loads and more severe disease.

Analysis of 13 sediment cores from the Challenger Deep of Marian Trench (down to 11 kilometers depth) identified distinct operational taxonomic units and relevant auxiliary metabolic genes, providing further insight into deep-sea viral metabolic capabilities and ecology.

Abstract Background Microbes and their viruses are hidden engines driving Earth’s ecosystems from the oceans and soils to humans and bioreactors. Though gene marker approaches can now be complemented by genome-resolved studies of inter-(macrodiversity) and intra-(microdiversity) population variation, analytical tools to do so remain scattered or under-developed. Results Here, we introduce MetaPop, an open-source bioinformatic pipeline that provides a single interface to analyze and visualize microbial and viral community metagenomes at both the macro- and microdiversity levels. Macrodiversity estimates include population abundances and α- and β-diversity. Microdiversity calculations include identification of single nucleotide polymorphisms, novel codon-constrained linkage of SNPs, nucleotide diversity (π and θ), and selective pressures (pN/pS and Tajima’s D) within and fixation indices (F ST) between populations. MetaPop will also identify genes with distinct codon usage. Following rigorous validation, we applied MetaPop to the gut viromes of autistic children that underwent fecal microbiota transfers and their neurotypical peers. The macrodiversity results confirmed our prior findings for viral populations (microbial shotgun metagenomes were not available) that diversity did not significantly differ between autistic and neurotypical children. However, by also quantifying microdiversity, MetaPop revealed lower average viral nucleotide diversity (π) in autistic children. Analysis of the percentage of genomes detected under positive selection was also lower among autistic children, suggesting that higher viral π in neurotypical children may be beneficial because it allows populations to better “bet hedge” in changing environments. Further, comparisons of microdiversity pre- and post-FMT in autistic children revealed that the delivery FMT method (oral versus rectal) may influence viral activity and engraftment of microdiverse viral populations, with children who received their FMT rectally having higher microdiversity post-FMT. Overall, these results show that analyses at the macro level alone can miss important biological differences. Conclusions These findings suggest that standardized population and genetic variation analyses will be invaluable for maximizing biological inference, and MetaPop provides a convenient tool package to explore the dual impact of macro- and microdiversity across microbial communities. Video abstract

The oxidative tricarboxylic acid (TCA) cycle is a central mitochondrial pathway integrating catabolic conversions of NAD +to NADH and anabolic production of aspartate, a key amino acid for cell proliferation. Several TCA cycle components are implicated in tumorigenesis, including loss-of-function mutations in subunits of succinate dehydrogenase (SDH), also known as complex II of the electron transport chain (ETC), but mechanistic understanding of how proliferating cells tolerate the metabolic defects of SDH loss is still lacking. Here, we identify that SDH supports human cell proliferation through aspartate synthesis but, unlike other ETC impairments, the effects of SDH inhibition are not ameliorated by electron acceptor supplementation. Interestingly, we find aspartate production and cell proliferation are restored to SDH-impaired cells by concomitant inhibition of ETC complex I (CI). We determine that the benefits of CI inhibition in this context depend on decreasing mitochondrial NAD+/NADH, which drives SDH-independent aspartate production through pyruvate carboxylation and reductive carboxylation of glutamine. We also find that genetic loss or restoration of SDH selects for cells with concordant CI activity, establishing distinct modalities of mitochondrial metabolism for maintaining aspartate synthesis. These data therefore identify a metabolically beneficial mechanism for CI loss in proliferating cells and reveal how compartmentalized redox changes can impact cellular fitness.

A universal taxonomy of viruses is essential for a comprehensive view of the virus world and for communicating the complicated evolutionary relationships among viruses. However, there are major differences in the conceptualisation and approaches to virus classification and nomenclature among virologists, clinicians, agronomists, and other interested parties. Here, we provide recommendations to guide the construction of a coherent and comprehensive virus taxonomy, based on expert scientific consensus. Firstly, assignments of viruses should be congruent with the best attainable reconstruction of their evolutionary histories, i.e., taxa should be monophyletic. This fundamental principle for classification of viruses is currently included in the International Committee on Taxonomy of Viruses (ICTV) code only for the rank of species. Secondly, phenotypic and ecological properties of viruses may inform, but not override, evolutionary relatedness in the placement of ranks. Thirdly, alternative classifications that consider phenotypic attributes, such as being vector-borne (e.g., “arboviruses”), infecting a certain type of host (e.g., “mycoviruses,” “bacteriophages”) or displaying specific pathogenicity (e.g., “human immunodeficiency viruses”), may serve important clinical and regulatory purposes but often create polyphyletic categories that do not reflect evolutionary relationships. Nevertheless, such classifications ought to be maintained if they serve the needs of specific communities or play a practical clinical or regulatory role. However, they should not be considered or called taxonomies. Finally, while an evolution-based framework enables viruses discovered by metagenomics to be incorporated into the ICTV taxonomy, there are essential requirements for quality control of the sequence data used for these assignments. Combined, these four principles will enable future development and expansion of virus taxonomy as the true evolutionary diversity of viruses becomes apparent. Transforming an existing phenotypic classification of viruses into one based on evolutionary relationships that can accommodate the vast number of viruses characterized in metagenomics and environmental studies is an ongoing challenge. This Consensus View explains how such a taxonomy can be expanded to encapsulate viral diversity and to recognize independent biological origins of different virus groups.

Recently, sensors deployed on unpiloted aerial systems (UAS) have provided snow depth estimates with high spatial resolution over watershed scales. While light detection and ranging (LiDAR) produces precise snow depth estimates for areas without vegetation cover, there has generally been poorer precision in forested areas. At a constant flight speed, the poorest precision within forests is observed beneath tree canopies that retain foliage into or through winter. The precision of lidar-derived elevation products is improved by increasing the sample size of ground returns but doing so reduces the spatial coverage of a mission due to limitations of battery power. We address the influence of flight speed on ground return density for baseline and snow-covered conditions and the subsequent effect on precision of snow depth estimates across a mixed landscape, while evaluating trade-offs between precision and bias. Prior to and following a snow event in December 2020, UAS flights were conducted at four different flight speeds over a region consisting of three contrasting land types: (1) open field, (2) deciduous forest, (3) conifer forest. For all cover types, we observed significant improvements in precision as flight speeds were reduced to 2 m s−1, as well as increases in the area over which a 2 cm snow depth precision was achieved. On the other hand, snow depth estimate differences were minimized at baseline flight speeds of 2 m s−1 and 4 m s−1 and snow-on flight speeds of 6 m s−1 over open fields and between 2 and 4 m s−1 over forest areas. Here, with consideration to precision and estimate bias within each cover type, we make recommendations for ideal flight speeds based on survey ground conditions and vegetation cover.

Biogeographical studies have traditionally focused on readily visible organisms, but recent technological advances are enabling analyses of the large-scale distribution of microscopic organisms, whose biogeographical patterns have long been debated. Here we assessed the global structure of plankton geography and its relation to the biological, chemical, and physical context of the ocean (the ‘seascape’) by analyzing metagenomes of plankton communities sampled across oceans during the Tara Oceans expedition, in light of environmental data and ocean current transport. Using a consistent approach across organismal sizes that provides unprecedented resolution to measure changes in genomic composition between communities, we report a pan-ocean, size-dependent plankton biogeography overlying regional heterogeneity. We found robust evidence for a basin-scale impact of transport by ocean currents on plankton biogeography, and on a characteristic timescale of community dynamics going beyond simple seasonality or life history transitions of plankton.

To our knowledge, this is the first article to apply metagenomics to characterize changes in gut microbial population dynamics caused by a clinically relevant model of central nervous system (CNS) trauma. It also utilizes the most current approaches in genome-resolved metagenomics and viromics to maximize the biological inferences that can be made from these data.