Rhodoliths and rhodolith beds

Rhodolith (maërl) beds, communities dominated by free living coralline algae, are a common feature of subtidal environments worldwide. Well preserved as fossils, they have long been recognized as important carbonate producers and paleoenvironmental indicators. Coralline algae produce growth bands with a morphology and chemistry that record environmental variation. Rhodoliths are hard but often fragile, and growth rates are only on the order of mm/yr. The hard, complex structure of living beds provides habitats for numerous associated species not found on otherwise entirely sedimentary bottoms. Beds are degraded locally by dredging and other anthropogenic disturbances, and recovery is slow. They will likely suffer severe impacts worldwide from the increasing acidity of the ocean. Investigations of rhodolith beds with scuba have enabled precise stratified sampling that has shown the importance of individual rhodoliths as hot spots of diversity. Observations, collections, and experiments by divers have revolutionized taxonomic studies by allowing comprehensive, detailed collection and by showing the large effects of the environment on rhodolith morphology. Facilitated by in situ collection and calibrations, corallines are now contributing to paleoclimatic reconstructions over a broad range of temporal and spatial scales. Beds are particularly abundant in the mesophotic zone of the Brazilian shelf where technical diving has revealed new associations and species. This paper reviews selected past and present research on rhodoliths and rhodolith beds that has been greatly facilitated by the use of scuba

Chemical and Physical Mechanisms of Fungal Bioweathering of Rock Phosphate

This research has investigated fungal transformations of rock phosphate (RP) by geoactive fungi, with particular emphasis on Aspergillus niger. Direct hyphal interaction with RP particles induced morphological and mineralogical changes, as revealed by scanning electron microscopy (SEM) and X-ray diffraction (XRD) analysis. The formation of the oxalate mineral calcium oxalate monohydrate (whewellite, CaC2O4 center dot H2O) on RP surfaces showed that mycogenic oxalic acid was driving the chemical dissolution of apatite, with consequent phosphate release and secondary mineral formation. This was supported by abiotic testing of common fungal excreted organic acids which confirmed that oxalic acid was the only effective RP transforming agent and therefore responsible for the morphological and mineralogical changes observed in RP when exposed to fungal colonization. Cryogenic SEM provided evidence of fungal penetration and tunneling through RP particles demonstrating that physical interactions are also important for RP bioweathering, as well as biochemical mechanisms. These findings emphasize the important role of fungi in P cycling, with active participation in the transformation of mineral phosphates through physicochemical mechanisms and secondary oxalate biomineral formation

Shelf morphology as an indicator of sedimentary regimes: a synthesis from a mixed siliciclastic-carbonate shelf on the eastern Brazilian margin

Modern shelf morphology is the result of the interplay between short and long term sedimentary processes. The relation between rates of sediment supply/carbonate growth and accommodation space creation will not only control coastal transgression and regression, but will also define the shelf sedimentary regimes acting to shape the seabed. Herein, shelf morphology and sedimentology are investigated in order to discuss how these characteristics can be representative of distinct sedimentary regimes. The study area is the eastern Brazilian shelf where coastal transgression and regression coexist with the most important coral reef system of the South Atlantic. A compilation of existing published and unpublished data was carried out in order to produce morphological and faciological maps and compare the mapped features with high-resolution seismic and sonographic data. The results show three major regions or morphological compartments: Abrolhos Shelf, Doce River Shelf and the Paleovalleys Shelf. In terms of shelf sedimentary domain, rhodolith beds predominate over the outer shelf along the entire area, coralline reefs are present along the northern Abrolhos inner shelf and a significant terrigenous mud deposit is observed associated to the Doce River adjacent inner shelf beds. The rest of the shelf is composed by bioclastic or terrigenous mud sand and gravel. Terrigenous sedimentation is always restricted to the shoreface or inner shelf shallower areas and carbonate sands and gravels are predominant elsewhere. The Abrolhos shelf shows two distinct sectors; the northern area is a typical mixed sediment environment that has a supply regime along the coast/shoreface, mainly due to longshore transport and a carbonate regime along the inner and outer shelf. The southern shelf morphology and sedimentation are controlled by the antecedent topography and is typically a accommodation regime shelf with associated rhodolith beds. The Doce river shelf is a supply regime environment with the formation of a 5 to 8m thick regressive deposit with downlapping clinoforms. Southward from the Doce river shelf, a significant shift in sedimentary regime is observed as the morphology becomes very irregular with associated hardbottoms and unfilled paleovalleys. This sector of the shelf (Paleovalley shelf) is characterized by an accommodation regime. The interpretation shows that the entire study area can be defined as a mixed sedimentation shelf, showing supply and accommodation regimes. Shelf morphology worked as an indicator of these changes. Carbonate/terrigenous deposition during a highstand/regressive phase coeval along the eastern Brazilian shelf, either laterally and across shelf. This lateral/along coast variation in sediment supply and carbonate production leads to distinct lateral facies and geometry. These spatial changes in morphology and facies, with coexistence of carbonate and siliciclastic sedimentation, are very important for the correlation and interpretation of the geological record, especially stratigraphic surfaces and sequence units

White matter abnormalities in the fornix are linked to cognitive performance in SZ but not in BD disorder: An exploratory analysis with DTI deterministic tractography

Background In psychosis, white matter (WM) microstructural changes have been detected previously; however, direct comparisons of findings between bipolar (BD) and schizophrenia (SZ) patients are scarce. In this study, we employed deterministic tractography to reconstruct WM tracts in BD and SZ patients. Methods Diffusion tensor imaging (DTI) data was carried out with n=32 euthymic BD type I patients, n=26 SZ patients and 30 matched healthy controls. Deterministic tractography using multiple indices of diffusion (fractional anisotropy (FA), tract volume (Vol), tract length (Le) and number of tracts (NofT)) were obtained from the fornix, the cingulum, the anterior thalamic radiation, and the corpus callosum bilaterally. Results We showed widespread WM microstructural changes in SZ, and changes in the corpus callosum, the left cingulum and the fornix in BD. Fornix fiber tracking scores were associated with cognitive performance in SZ, and with age and age at disease onset in the BD patient group. Limitations Although the influence of psychopharmacological drugs as biasing variables on morphological alterations has been discussed for SZ and BD, we did not observe a clear influence of drug exposure on our findings. Conclusions These results confirm the assumption that SZ patients have more severe WM changes than BD patients. The findings also suggest a major role of WM changes in the fornix as important fronto-limbic connections in the etiology of cognitive symptoms in SZ, but not in B

Completeness of Reporting in Diet- and Nutrition-Related Randomized Controlled Trials and Systematic Reviews With Meta-Analysis:Protocol for 2 Independent Meta-Research Studies

Background: Journal articles describing randomized controlled trials (RCTs) and systematic reviews with meta-analysis of RCTs are not optimally reported and often miss crucial details. This poor reporting makes assessing these studies’ risk of bias or reproducing their results difficult. However, the reporting quality of diet- and nutrition-related RCTs and meta-analyses has not been explored. Objective: We aimed to assess the reporting completeness and identify the main reporting limitations of diet- and nutrition-related RCTs and meta-analyses of RCTs, estimate the frequency of reproducible research practices among these RCTs, and estimate the frequency of distorted presentation or spin among these meta-analyses. Methods: Two independent meta-research studies will be conducted using articles published in PubMed-indexed journals. The first will include a sample of diet- and nutrition-related RCTs; the second will include a sample of systematic reviews with meta-analysis of diet- and nutrition-related RCTs. A validated search strategy will be used to identify RCTs of nutritional interventions and an adapted strategy to identify meta-analyses in PubMed. We will search for RCTs and meta-analyses indexed in 1 calendar year and randomly select 100 RCTs (June 2021 to June 2022) and 100 meta-analyses (July 2021 to July 2022). Two reviewers will independently screen the titles and abstracts of records yielded by the searches, then read the full texts to confirm their eligibility. The general features of these published RCTs and meta-analyses will be extracted into a research electronic data capture database (REDCap; Vanderbilt University). The completeness of reporting of each RCT will be assessed using the items in the CONSORT (Consolidated Standards of Reporting Trials), its extensions, and the TIDieR (Template for Intervention Description and Replication) statements. Information about practices that promote research transparency and reproducibility, such as the publication of protocols and statistical analysis plans will be collected. There will be an assessment of the completeness of reporting of each meta-analysis using the items in the Preferred Reporting Items for Systematic reviews and Meta-Analysis (PRISMA) statement and collection of information about spin in the abstracts and full-texts. The results will be presented as descriptive statistics in diagrams or tables. These 2 meta-research studies are registered in the Open Science Framework. Results: The literature search for the first meta-research retrieved 20,030 records and 2182 were potentially eligible. The literature search for the second meta-research retrieved 10,918 records and 850 were potentially eligible. Among them, random samples of 100 RCTs and 100 meta-analyses were selected for data extraction. Data extraction is currently in progress, and completion is expected by the beginning of 2023. Conclusions: Our meta-research studies will summarize the main limitation on reporting completeness of nutrition- or diet-related RCTs and meta-analyses and provide comprehensive information regarding the particularities in the reporting of intervention studies in the nutrition field

Completeness of reporting in diet- and nutrition-related randomized controlled trials and systematic reviews with meta-analysis: protocol for 2 independent meta-research studies

Background: Journal articles describing randomized controlled trials (RCTs) and systematic reviews with meta-analysis of RCTs are not optimally reported and often miss crucial details. This poor reporting makes assessing these studies’ risk of bias or reproducing their results difficult. However, the reporting quality of diet- and nutrition-related RCTs and meta-analyses has not been explored. Objective: We aimed to assess the reporting completeness and identify the main reporting limitations of diet- and nutrition-related RCTs and meta-analyses of RCTs, estimate the frequency of reproducible research practices among these RCTs, and estimate the frequency of distorted presentation or spin among these meta-analyses. Methods: Two independent meta-research studies will be conducted using articles published in PubMed-indexed journals. The first will include a sample of diet- and nutrition-related RCTs; the second will include a sample of systematic reviews with meta-analysis of diet- and nutrition-related RCTs. A validated search strategy will be used to identify RCTs of nutritional interventions and an adapted strategy to identify meta-analyses in PubMed. We will search for RCTs and meta-analyses indexed in 1 calendar year and randomly select 100 RCTs (June 2021 to June 2022) and 100 meta-analyses (July 2021 to July 2022). Two reviewers will independently screen the titles and abstracts of records yielded by the searches, then read the full texts to confirm their eligibility. The general features of these published RCTs and meta-analyses will be extracted into a research electronic data capture database (REDCap; Vanderbilt University). The completeness of reporting of each RCT will be assessed using the items in the CONSORT (Consolidated Standards of Reporting Trials), its extensions, and the TIDieR (Template for Intervention Description and Replication) statements. Information about practices that promote research transparency and reproducibility, such as the publication of protocols and statistical analysis plans will be collected. There will be an assessment of the completeness of reporting of each meta-analysis using the items in the Preferred Reporting Items for Systematic reviews and Meta-Analysis (PRISMA) statement and collection of information about spin in the abstracts and full-texts. The results will be presented as descriptive statistics in diagrams or tables. These 2 meta-research studies are registered in the Open Science Framework. Results: The literature search for the first meta-research retrieved 20,030 records and 2182 were potentially eligible. The literature search for the second meta-research retrieved 10,918 records and 850 were potentially eligible. Among them, random samples of 100 RCTs and 100 meta-analyses were selected for data extraction. Data extraction is currently in progress, and completion is expected by the beginning of 2023. Conclusions: Our meta-research studies will summarize the main limitation on reporting completeness of nutrition- or diet-related RCTs and meta-analyses and provide comprehensive information regarding the particularities in the reporting of intervention studies in the nutrition field. International Registered Report Identifier (IRRID): DERR1-10.2196/4353

Protocol for a meta-research study of protocols for diet or nutrition-related trials published in indexed journals:general aspects of study design, rationale and reporting limitations

INTRODUCTION: The Standard Protocol Items: Recommendations for Interventional Trials (SPIRIT) reporting guideline establishes a minimum set of items to be reported in any randomised controlled trial (RCT) protocol. The Template for Intervention Description and Replication (TIDieR) reporting guideline was developed to improve the reporting of interventions in RCT protocols and results papers. Reporting completeness in protocols of diet or nutrition-related RCTs has not been systematically investigated. We aim to identify published protocols of diet or nutrition-related RCTs, assess their reporting completeness and identify the main reporting limitations remaining in this field. METHODS AND ANALYSIS: We will conduct a meta-research study of RCT protocols published in journals indexed in at least one of six selected databases between 2012 and 2022. We have run a search in PubMed, Embase, CINAHL, Web of Science, PsycINFO and Global Health using a search strategy designed to identify protocols of diet or nutrition-related RCTs. Two reviewers will independently screen the titles and abstracts of records yielded by the search in Rayyan. The full texts will then be read to confirm protocol eligibility. We will collect general study features (publication information, types of participants, interventions, comparators, outcomes and study design) of all eligible published protocols in this contemporary sample. We will assess reporting completeness in a randomly selected sample of them and identify their main reporting limitations. We will compare this subsample with the items in the SPIRIT and TIDieR statements. For all data collection, we will use data extraction forms in REDCap. This protocol is registered on the Open Science Framework (DOI: 10.17605/OSF.IO/YWEVS). ETHICS AND DISSEMINATION: This study will undertake a secondary analysis of published data and does not require ethical approval. The results will be disseminated through journals and conferences targeting stakeholders involved in nutrition research

Lattice dynamics localization in low-angle twisted bilayer graphene

A low twist angle between the two stacked crystal networks in bilayer graphene enables self-organized lattice reconstruction with the formation of a periodic domain. This superlattice modulates the vibrational and electronic structures, imposing new rules for electron-phonon coupling and the eventual observation of strong correlation and superconductivity. Direct optical images of the crystal superlattice in reconstructed twisted bilayer graphene are reported here, generated by the inelastic scattering of light in a nano-Raman spectroscope. The observation of the crystallographic structure with visible light is made possible due to lattice dynamics localization, the images resembling spectral variations caused by the presence of strain solitons and topological points. The results are rationalized by a nearly-free-phonon model and electronic calculations that highlight the relevance of solitons and topological points, particularly pronounced for structures with small twist angles. We anticipate our discovery to play a role in understanding Jahn-Teller effects and electronic Cooper pairing, among many other important phonon-related effects, and it may be useful for characterizing devices in the most prominent platform for the field of twistronics.Comment: 9 pages, 8 figure

Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context

Long noncoding RNAs (lncRNAs) are commonly dys-regulated in tumors, but only a handful are known toplay pathophysiological roles in cancer. We inferredlncRNAs that dysregulate cancer pathways, onco-genes, and tumor suppressors (cancer genes) bymodeling their effects on the activity of transcriptionfactors, RNA-binding proteins, and microRNAs in5,185 TCGA tumors and 1,019 ENCODE assays.Our predictions included hundreds of candidateonco- and tumor-suppressor lncRNAs (cancerlncRNAs) whose somatic alterations account for thedysregulation of dozens of cancer genes and path-ways in each of 14 tumor contexts. To demonstrateproof of concept, we showed that perturbations tar-geting OIP5-AS1 (an inferred tumor suppressor) andTUG1 and WT1-AS (inferred onco-lncRNAs) dysre-gulated cancer genes and altered proliferation ofbreast and gynecologic cancer cells. Our analysis in-dicates that, although most lncRNAs are dysregu-lated in a tumor-specific manner, some, includingOIP5-AS1, TUG1, NEAT1, MEG3, and TSIX, synergis-tically dysregulate cancer pathways in multiple tumorcontexts

Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas

This integrated, multiplatform PanCancer Atlas study co-mapped and identified distinguishing molecular features of squamous cell carcinomas (SCCs) from five sites associated with smokin