Miracle-dz/UniFAR-FTUs huggingface dataset:
RAMP1 as a novel prognostic biomarker in pan-cancer and osteosarcoma

Receptor activity modifying protein 1 (RAMP1) facilitates the localization of the calcitonin-like receptor (CLR) to the plasma membrane, but its role in osteosarcoma (OS) remains unclear. We evaluated the RAMP1 expression and prognostic value across different cancers, studying tumor immune infiltration. The prognostic value was analyzed using the GSE39058 and TARGET datasets. Differential gene expression was evaluated. a protein-protein interaction network was constructed, and gene set enrichment analysis was performed. The function of RAMP1 in the tumor microenvironment was analyzed, and its expression in OS cell lines was validated using quantitative real-time PCR. High RAMP1 expression correlated with poor prognosis relative to low RAMP1 expression (p < 0.05). Low RAMP1 expression correlated with an abundance of CD4+ memory-activated T cells. whereas a high expression level correlated with a high proportion of gamma-delta T cells (γδ T cells). Differentially expressed genes from TARGET was enriched in olfactory transduction pathways (normalized enrichment scores [NES] = 1.6998, p < 0.0001). RAMP1 expression negatively correlated with CD44 expression but positively correlated with TNFSF9 expression. The RAMP1 gene is substantially expressed in OS cells compared to the normal osteoblast cell line hFOB1.19. Thus, RAMP1 may be a prognostic biomarker and potential therapeutic target in OS.
Exploratory study of risk factors related to SARS-CoV-2 prevalence in nursing homes in Flanders (Belgium) during the first wave of the COVID-19 pandemic

In a previous study in Belgian nursing homes (NH) during the first wave of the COVID-19 pandemic, we found a SARS-CoV-2 seroprevalence of 17% with a large variability (0–45%) between NH. The current exploratory study aimed to identify nursing home-specific risk factors for high SARS-CoV-2 seroprevalence. Between October 19th, 2020 and November 13th, 2020, during the second COVID-19 wave in Belgium, capillary blood was collected on dried blood spots from 60 residents and staff in each of the 20 participating NH in Flanders and Brussels. The presence of SARS-CoV-2-specific IgG antibodies was assessed by ELISA. Risk factors were evaluated using a questionnaire, filled in by the director or manager of the NH. Assessed risk factors comprised community-related factors, resident-related factors, management and performance features as well as building-related aspects. The relation between risk factors and seroprevalence was assessed by applying random forest modelling, generalized linear models and Bayesian linear regression. The present analyses showed that the prevalence of residents with dementia, the scarcity of personal protective equipment (surgical masks, FFP2 masks, glasses and face shields), and inadequate PCR test capacity were related to a higher seroprevalence. Generally, our study put forward that the various aspects of infection prevention in NH require more attention and investment. This exploratory study suggests that the ratio of residents with dementia, the availability of test capacity and personal protective equipment may have played a role in the SARS-CoV-2 seroprevalence of NH, after the first wave. It underscores the importance of the availability of PPE and education in infection prevention. Moreover, investments may also yield benefits in the prevention of other respiratory infections (such as influenza).
Microbial signatures in peritidal siliciclastic sediments: a catalogue

A catalogue of microbial structural signatures is presented, based upon the coupling of fundamental biogeochemical–microbial processes and local morphogenetic determinants. It summarizes a collection of sedimentary structures obtained from two modern siliciclastic peritidal environments in different climatic zones (temperate humid: Mellum Island, southern North Sea; subtropical arid: coast of southern Tunisia). Textural geometries reveal a high structural diversity, but their determinants are primarily based upon six major parameters: (1) intrinsic biofactors: structural diversification of sedimentary microbial films and mats inherent in the organisms, i.e. their construction morphology, growth, taxis and behaviour, and local abundance of specific morphotypes. Most prominent are the ensheathed filamentous cyanobacteria Microcoleus chthonoplastes and Lyngbya aestuarii, and the sheathless filamentous cyanobacterium Oscillatoria limosa. (2) Biological response to physical disturbances: sediment supply, erosion and fracturing of surface layers resulting from desiccation cause growth responses of biofilms and microbial mats. (3) Trapping/binding effects: physicobiological processes give rise to grain orientations and wavy to lenticular lamina, lamina‐specific grain arrangements and ‘sucrose’ calcium carbonate accumulations. (4) Secondary physical deformation of biogenic build‐ups: mechanical stresses acting upon sediments overgrown and biostabilized by biofilms and mats produce erosional and overthrust structures. (5) Post‐burial processes: textural fabrics that evolve from mechanical effects of gas formation from decaying mats, and features related to the formation of authigenic minerals (calcium carbonates, calcium sulphates, pyrite). (6) Bioturbation and grazing: post‐depositional structures, such as Skolithos‐type dwellings, traces of burrowing insects, gastropod grazing traces and faecal pellets. In synopsis, the catalogue firstly comprises a sound set of ubiquitous signatures. This uniformity in architectural characteristics is attributed to the presence and local dominance of certain microbes throughout the different settings. The catalogue secondly documents signatures that are extremely sensitive to tidal position, hydrodynamic regime and overall climatic conditions. These kinds of signature indicate narrow facies zones, which often coincide with the activity or dominance zones of certain organisms. An overview of structures of microbial origin from the fossil record underlines the potential of many of the signatures included in this catalogue to become fossilized and provide strong indicators of former siliciclastic tidal settings.
Analysis of a two-year meteorological dataset produced on Italian territory with a coupling procedure between a limited area atmospheric model and a sequential MSG-SEVIRI LST assimilation scheme

The sensible and latent heat exchanges at the interface between soil and atmosphere are fundamental components of the surface energy budget and constitute the lower boundary condition for atmospheric numerical models. These models often represent such phenomena in very simplified ways or employ a detailed description of these dynamics that require complex parameterization, difficult or impossible to retrieve with sufficient accuracy. The characterization of such variables on large areas is possible only through remote-sensing techniques by monitoring indirectly related variables, with particular reference to the land surface temperature (LST). In this work, the Regional Atmospheric Modeling System (RAMS), a limited area atmospheric model, was coupled with the 1-D LST variational assimilation scheme Assimilation Code for Hydrologic-Atmospheric Budget (ACHAB), which is able to provide optimal estimates of the surface energy budget. The source of the LST maps for this work was Meteosat Second Generation-Spinning Enhanced Visible and Infrared Imager (MSG-SEVIRI) imagery. A 2 year-long meteorological dataset (2005–2006) was produced on the Italian territory using this coupling framework. The purpose of the experiment was to evaluate how much the assimilation of satellite-derived LST in a simple surface energy budget model is able to affect the dynamics of the troposphere on the study area, considering both summer and winter. Evaluations of the results of the coupling framework were carried out by comparing with both observations of the ground sensors network and the atmospheric soundings available in the study period. The analysis showed significant improvements in terms of reconstructions of the surface and atmospheric states during summer, while a general worsening of the performances of the atmospheric model was observed in winter months.
An observational study of the presence and variability of the microbiota composition of goat herd milk related to mainstream and artisanal farm management

Goat milk is produced on mainstream and artisanal farms. It was expected that the farm management may influence the microbial population of the milk. Therefore, we investigated the bacterial content and microbiota composition of raw milk in relation to Dutch goat farm management. After amplicon sequencing we analyzed the taxa at phylum and genus levels, and used the relative values enabling to provide information about the variation among the different samples. On ten farms our results indicated that the number of bacterial colony forming units and microbiota composition of the milk, directly after milking was variable among farms and not related to the farm management system. At the phylum level the phyla Firmicutes, Actinobacteria, Proteobacteria, and to a minor extend Bacteriodota were the dominant phyla in the raw goat milk, together usually comprising 90% of the total bacterial phyla. The most dominant genera were Staphylococcus, Pseudomonas, Lactococcus, Microbacteria, Acinetobacteria, and Corinebacteria. The number of bacterial phyla and genera does not differ between the mainstream and artisanal farms, although the Shannon index may be numerically higher in the mainstream farms as compared to artisanal farms. In addition, the variability is higher among artisanal farms, which may be due to less standardization of the management. The milk microbiota composition differed among farms. Repeated sampling of a farm showed that this changed over time. The lactic acid producing bacteria showed a similar pattern. Variable microbiota richness amount and diversity of microorganisms were present in different farming systems. We concluded that farm-specific management and sampling moment were the major determining factors for the milk microbiota composition.
The association between maternal infection and intellectual disability in children: A systematic review and meta-analysis

Background There is arguing evidence regarding the association between maternal infections during pregnancy and the risk of intellectual disability (ID) in children. This systematic review and meta-analysis are essential to determine and address inconsistent findings between maternal infections during pregnancy and the risk of ID in children. Methods The MOOSE and PRISMA guidelines were followed to perform and report on this study. The Medline/PubMed, Web of Science, Embase, and Scopus databases were searched from inception up to March 15, 2023, to identify potentially eligible studies. Inclusion and exclusion criteria were applied, as well as the Newcastle-Ottawa Scale was used to assess the methodological quality of studies included. The included studies were divided into two types based on the participants: (1) ID-based studies, which involved children with ID as cases and healthy children as controls and evaluated maternal infection in these participants; (2) infection-based studies, which assessed the prevalence or incidence of ID in the follow-up of children with or without exposure to maternal infection. We used Random-effects models (REM) to estimate the overall pooled odds ratio (OR) and 95% confidence intervals (CIs). The between-studies heterogeneity was assessed with the χ2-based Q-test and I2 statistic. Subgroup and sensitivity analyses were applied to explore the source of heterogeneity and results consistency. Results A total of eight studies including 1,375,662 participants (60,479 cases and 1,315,183 controls) met the eligibility criteria. The REM found that maternal infection significantly increased the risk of ID in children (OR, 1.33; 95% CI, 1.21–1.46; I2 = 64.6). Subgroup analysis showed a significant association for both infection-based (OR, 1.27; 95%CI, 1.15–1.40; I2 = 51.2) and ID-based (OR, 1.44; 95%CI, 1.19–1.74; I2 = 77.1) studies. Furthermore, subgroup analysis based on diagnostic criteria revealed a significant association when maternal infection or ID were diagnosed using ICD codes (OR, 1.33; 95% CI, 1.20–1.48; I2 = 75.8). Conclusion Our study suggests that maternal infection during pregnancy could be associated with an increased risk of ID in children. This finding is consistent across different types of studies and diagnostic criteria. However, due to the heterogeneity and limitations of the included studies, we recommend further longitudinal studies to confirm the causal relationship and the underlying mechanisms.
Serpentines Close-Up and Intimate: An HRTEM View

High-resolution transmission electron microscopy (HRTEM) affords a close look at the complex structures and intergrowths of the serpentine minerals. All contain alternating sheets of cations in tetrahedral and octahedral coordination. Lizardite, the flat species, forms in sufficiently large and well-ordered crystals to permit reliable X-ray structure determinations, and it is the reference mineral for estimates of the structures of antigorite and chrysotile. However, even lizardite forms in a wide variety of polytypes, only some of which have been explored. It also forms polygonal serpentine, a roughly cylindrical variety that typically consists of 15 or 30 sectors, each of which consists of lizardite layers. HRTEM images of the structure at sector boundaries show offsets of fringes that we interpret as the result of inversions of the tetrahedral sheets. Using lizardite as the basis for an estimate of the curled chrysotile structure, we obtained atomic coordinates and used them to calculate fiber-axis X-ray and electron-diffraction patterns for polytypes. HRTEM images obtained viewing down the fiber axis show no ordering between layers. Chisholm (1988) reported 2mm symmetry for fibers when viewed perpendicular to their length, but most of our measured fibers show no symmetry for such orientations. Employing Fourier transforms of HRTEM images, we found a new one-layered orthorhombic chrysotile polytype with mirror symmetry perpendicular to the fiber axis. Antigorite is notable for its conspicuous, modulated structure. We observed the waves to be asymmetrical and infer that the asymmetry results from an inhomogeneous distribution of hydrogen bonding between the layers. This distribution helps with a long-standing problem by explaining some apparently anomalous features of HRTEM images. The abundant (001) faults in antigorite are produced by boundaries of lamellae having different modulation profiles. HRTEM images show the relations of serpentine minerals to each other as well as their host materials. Areas exist where layers of each of the serpentine minerals grade continuously and free of faults from one variety to another. The resulting intermediate or partial structures defy categorization into simple mineral types.
Life Story Book to enhance communication in persons with dementia: A systematic review of reviews

The Life Story Book has been commonly used in promoting person-centred care in older adults, especially for persons with dementia. This involves collecting the life stories and memories of the person living with dementia and compiling them into a book or folder, which is used by staff or family to assist the person recall these memories. Evidence on the use, benefits and influences of the Life Story Book in dementia care is limited. This systematic literature review aimed to collect past reviews and provide a thorough overview of the use, benefits, and impact of the Life Story Book for the person with dementia, the relatives, family, and caregivers. The electronic databases PubMed, Scopus, Science Direct and Web of Science as well as grey literature through Google Scholar were searched to select the relevant studies. Seven studies that meet the inclusion criteria were selected and data synthesised. Findings revealed that the use of the Life Story Book has no specific guidelines and has been described with numerous characteristics and varied implementation methods. The Life Story Book intervention is found to provide positive outcomes for the person with dementia and the carers involved. Six out of the seven studies reported that Life Story Book enhanced communication between persons with dementia, relatives, care staff, and residents. The review extends the current evidence on the usage of the Life Story Book in dementia care and confirms that the use of life stories leads to better care in various settings. However, more research is needed to reveal the potential of the Life Story Book in enhancing communication. Guidelines and training are also required to make the best use of the Life Story Book.
Modelling Oyster Population Response to Variation in Freshwater Input

Abstract This paper describes the linkage of a three-dimensional hydrodynamic circulation model with descriptive and experimental biological data concerning oyster ( Crassostrea virginica ) population dynamics in the Apalachicola Estuary (Florida, U.S.A.). Our intent was to determine the direct and indirect role of Apalachicola River flow in the maintenance of oyster production. Results of a monthly field sampling programme conducted on the oyster reefs in the Apalachicola system during 1985–1986 were used to develop statistical models relating several life-history characteristics of oysters to physical-chemical aspects of water quality. The same life-history characteristics were related statistically to output from a circulation model of Apalachicola Bay. Highest oyster densities and overall bar growth were found in the vicinity of the confluence of high salinity water moving westwards from St George Sound and river-dominated (low salinity) water moving south and eastwards from East Bay. With the exception of models for oyster mortality, the predictive capability of results from the parallel modelling efforts was low. A time-averaged model was developed for oyster mortality during the summer of 1985 by running a regression analysis with averaged predictors derived from the hydrodynamic model and observed (experimental) mortality rates throughout the estuary. A geographic information system was then used to depict the results spatially and to compare the extent of expected mortality in 1985 and 1986. High salinity, relatively low-velocity current patterns, and the proximity of a given oyster bar to entry points of saline Gulf water into the bay were important factors that contribute to increased oyster mortality. Mortality was a major determinant of oyster production in the Apalachicola Estuary with predation as a significant aspect of such mortality. By influencing salinity levels and current patterns throughout the bay, the Apalachicola River was important in controlling such mortality. Oyster production rates in the Apalachicola system depend on a combination of variables that are directly and indirectly associated with freshwater input as modified by wind, tidal factors, and the physiography of the bay. River flow reduction, whether through naturally occurring droughts, through increased upstream anthropogenous (consumptive) water use, or a combination of the two, could have serious adverse consequences for oyster populations. By coupling hydrodynamic modelling with descriptive and experimental biological data, we were able to determine the effects of potential freshwater diversions on oyster production in Apalachicola Bay.
Soil profile development in some alluvial deposits of eastern New South Wales

Soil profile data from river terrace sequences on the New South Wales coast and southern highlands have been summarized. In all sequences the profiles have a progressive increase in soil development from low alluvial benches to flood plains to terraces. The general similarity of soils among these and other alluvial sequences in eastern New South Wales is the basis of a descriptive generalization in terms of five profile stages: stratic stage on low alluvial benches; cumulic stage on flood plains; low-contrast solum stage on low terraces; high-contrast solum stage on high terraces; extended subsolum stage on highest terraces. Sufficient lack of correlation occurs between sequences to suggest that the profile stages are groupings within a continuous spectrum of profile variation, the whole representing the one pedogenetic pathway. Pedogenesis in these alluvial landscapes is considered to progress through the development, first of a biotic profile which reaches a maximum within 1000 years, which is then degraded with the onset of mineral weathering and B horizon development, to a maximum solum form within 30 000 years. The rates of change of biotic and mineral profile components are sufficiently slow that only broad limits of confidence can be applied to soil stratigraphic correlations based on field morphology alone.
Revisiting the factor structure of the Short-Form McGill Pain Questionnaire-2 (SF-MPQ-2): Evidence for a bifactor model in individuals with Chiari malformation

The Short-Form McGill Pain Questionnaire-2 (SF-MPQ-2; Dworkin et al., 2009) is intended to measure the multidimensional qualities of pain (i.e., continuous, intermittent, neuropathic, and affective) as well as total pain. Using structural equation modeling, we evaluated the fit of four competing measurement models of the SF-MPQ-2—an oblique 4-factor model, a 1-factor model, a higher-order model, and a bifactor model—in 552 adults diagnosed with Chiari malformation, a chronic health condition whose primary symptoms include head and neck pain. Results revealed the strongest support for the bifactor model, suggesting that SF-MPQ-2 item responses are due to both a general pain factor and a specific pain factor that is orthogonal to the general pain factor. Additional bifactor analyses of the SF-MPQ-2’s model-based reliability and dimensionality revealed that most of the SF-MPQ-2’s reliable variance is explained by a general pain factor, and that the instrument can be modeled unidimensionally and scored as a general pain measure. Results also indicated that the general and affective pain factors in the bifactor model uniquely predicted pain-related external criteria (e.g., depression, anxiety, and stress); however, the continuous, intermittent, and neuropathic factors did not.