Three-dimensional digital template atlas of the Macaque brain

We present a new 3D template atlas of the anatomical subdivisions of the macaque brain, which is based on and aligned to the magnetic resonance imaging (MRI) data set and histological sections of the Saleem and Logothetis atlas. We describe the creation and validation of the atlas that, when registered with macaque structural or functional MRI scans, provides a straightforward means to estimate the boundaries between architectonic areas, either in a 3D volume with different planesof sections, or on an inflated brain surface (cortical flat map). As such, this new template atlas is intended for use as a reference standard for macaque brain research. Atlases and templates are available as both volumes and surfaces in standard NIFTI and GIFTI formats

An evaluation of noise reduction algorithms for particle-based fluid simulations in multi-scale applications

AbstractFiltering of particle-based simulation data can lead to reduced computational costs and enable more efficient information transfer in multi-scale modelling. This paper compares the effectiveness of various signal processing methods to reduce numerical noise and capture the structures of nano-flow systems. In addition, a novel combination of these algorithms is introduced, showing the potential of hybrid strategies to improve further the de-noising performance for time-dependent measurements. The methods were tested on velocity and density fields, obtained from simulations performed with molecular dynamics and dissipative particle dynamics. Comparisons between the algorithms are given in terms of performance, quality of the results and sensitivity to the choice of input parameters. The results provide useful insights on strategies for the analysis of particle-based data and the reduction of computational costs in obtaining ensemble solutions

The unexplored role of sedentary time and physical activity in glucose and lipid metabolism-related placental mRNAs in pregnant women who are obese: the DALI lifestyle randomised controlled trial

Objective: We aimed to explore: (i) the association of sedentary time (ST) and physical activity (PA) during pregnancy with the placental expression of genes related to glucose and lipid metabolism in pregnant women who are obese; (ii) maternal metabolic factors mediating changes in these placental transcripts; and (iii) cord blood markers related to the mRNAs mediating neonatal adiposity. Design: Multicentre randomised controlled trial. Setting: Hospitals in nine European countries. Population: A cohort of 112 pregnant women with placental tissue. Methods: Both ST and moderate-to-vigorous PA (MVPA) levels were measured objectively using accelerometry at three time periods during pregnancy. Main outcome measures: Placental mRNAs (FATP2, FATP3, FABP4, GLUT1 and PPAR-γ) were measured with NanoString technology. Maternal and fetal metabolic markers and neonatal adiposity were assessed. Results: Longer periods of ST, especially in early to middle pregnancy, was associated with lower placental FATP2 and FATP3 expression (P \u3c 0.05), whereas MVPA at baseline was inversely associated with GLUT1 mRNA (P = 0.02). Although placental FATP2 and FATP3 expression were regulated by the insulin–glucose axis (P \u3c 0.05), no maternal metabolic marker mediated the association of ST/MVPA with placental mRNAs (P \u3e 0.05). Additionally, placental FATP2 expression was inversely associated with cord blood triglycerides and free fatty acids (FFAs; P \u3c 0.01). No cord blood marker mediated neonatal adiposity except for cord blood leptin, which mediated the effects of PPAR-γ on neonatal sum of skinfolds (P \u3c 0.05). Conclusions: In early to middle pregnancy, ST is associated with the expression of placental genes linked to lipid transport. PA is hardly related to transporter mRNAs. Strategies aimed at reducing sedentary behaviour during pregnancy could modulate placental gene expression, which may help to prevent unfavourable fetal and maternal pregnancy outcomes. Tweetable abstract: Reducing sedentary behaviour in pregnancy might modulate placental expression of genes related to lipid metabolism in women who are obese

Deep learning system to predict the 5-year risk of high myopia using fundus imaging in children

Our study aims to identify children at risk of developing high myopia for timely assessment and intervention, preventing myopia progression and complications in adulthood through the development of a deep learning system (DLS). Using a school-based cohort in Singapore comprising 998 children (aged 6-12 years old), we train and perform primary validation of the DLS using 7456 baseline fundus images of 1878 eyes; with external validation using an independent test dataset of 821 baseline fundus images of 189 eyes together with clinical data (age, gender, race, parental myopia, and baseline spherical equivalent (SE)). We derive three distinct algorithms - image, clinical, and mix (image + clinical) models to predict high myopia development (SE ≤ -6.00 diopter) during teenage years (5 years later, age 11-17). Model performance is evaluated using the area under the receiver operating curve (AUC). Our image models (Primary dataset AUC 0.93-0.95; Test dataset 0.91-0.93), clinical models (Primary dataset AUC 0.90-0.97; Test dataset 0.93-0.94) and mixed (image + clinical) models (Primary dataset AUC 0.97; Test dataset 0.97-0.98) achieve clinically acceptable performance. The addition of 1 year SE progression variable has minimal impact on the DLS performance (clinical model AUC 0.98 versus 0.97 in the primary dataset, 0.97 versus 0.94 in the test dataset; mixed model AUC 0.99 versus 0.97 in the primary dataset, 0.95 versus 0.98 in test dataset). Thus, our DLS allows prediction of the development of high myopia by teenage years amongst school-going children. This has potential utility as a clinical decision support tool to identify "at-risk" children for early intervention.info:eu-repo/semantics/publishedVersio

Etiology of Pediatric Bacterial Meningitis Pre- and Post-PCV13 Introduction Among Children Under 5 Years Old in Lomé, Togo.

BACKGROUND: Pediatric bacterial meningitis (PBM) causes severe morbidity and mortality within Togo. Thus, as a member of the World Health Organization coordinated Invasive Bacterial Vaccine Preventable Diseases network, Togo conducts surveillance targeting Streptococcus pneumoniae (pneumococcus), Neisseria meningitidis (meningococcus), and Haemophilus influenzae, at a sentinel hospital within the capital city, Lomé, in the southernmost Maritime region. METHODS: Cerebrospinal fluid was collected from children <5 years with suspected PBM admitted to the Sylvanus Olympio Teaching Hospital. Phenotypic detection of pneumococcus, meningococcus, and H. influenzae was confirmed through microbiological techniques. Samples were shipped to the Regional Reference Laboratory to corroborate results by species-specific polymerase chain reaction. RESULTS: Overall, 3644 suspected PBM cases were reported, and 98 cases (2.7%: 98/3644) were confirmed bacterial meningitis. Pneumococcus was responsible for most infections (67.3%: 66/98), followed by H. influenzae (23.5%: 23/98) and meningococcus (9.2%: 9/98). The number of pneumococcal meningitis cases decreased by 88.1% (52/59) postvaccine introduction with 59 cases from July 2010 to June 2014 and 7 cases from July 2014 to June 2016. However, 5 cases caused by nonvaccine serotypes were observed. Fewer PBM cases caused by vaccine serotypes were observed in infants <1 year compared to children 2-5 years. CONCLUSIONS: Routine surveillance showed that PCV13 vaccination is effective in preventing pneumococcal meningitis among children <5 years of age in the Maritime region. This complements the MenAfriVac vaccination against meningococcal serogroup A to prevent meningitis outbreaks in the northern region of Togo. Continued surveillance is vital for estimating the prevalence of PBM, determining vaccine impact, and anticipating epidemics in Togo

Rapid creation of skin substitutes from human skin cells and biomimetic nanofibers for acute full-thickness wound repair

yesCreation of functional skin substitutes within a clinically acceptable time window is essential for timely repair and management of large wounds such as extensive burns. The aim of this study was to investigate the possibility of fabricating skin substitutes via a bottom-up nanofiber-enabled cell assembly approach and using such substitutes for full-thickness wound repair in nude mice. Following a layer-by-layer (L-b-L) manner, human primary skin cells (fibroblasts and keratinocytes) were rapidly assembled together with electrospun polycaprolactone (PCL)/collagen (3:1 w/w, 8% w/v) nanofibers into 3D constructs, in which fibroblasts and keratinocytes were located in the bottom and upper portion respectively. Following culture, the constructs developed into a skin-like structure with expression of basal keratinocyte markers and deposition of new matrix while exhibited good mechanical strength (as high as 4.0 MPa by 14 days). Treatment of the full-thickness wounds created on the back of nude mice with various grafts (acellular nanofiber meshes, dermal substitutes, skin substitutes and autografts) revealed that 14-day-cultured skin substitutes facilitated a rapid wound closure with complete epithelialization comparable to autografts. Taken together, skin-like substitutes can be formed by L-b-L assembling human skin cells and biomimetic nanofibers and they are effective to heal acute full-thickness wounds in nude mice

A threatened ecological community: Research advances and priorities for Banksia woodlands

The rapid expansion of urban areas worldwide is leading to native habitat loss and ecosystem fragmentation and degradation. Although the study of urbanisation\u27s impact on biodiversity is gaining increasing interest globally, there is still a disconnect between research recommendations and urbanisation strategies. Expansion of the Perth metropolitan area on the Swan Coastal Plain in south-western Australia, one of the world\u27s thirty-six biodiversity hotspots, continues to affect the Banksia Woodlands (BWs) ecosystem, a federally listed Threatened Ecological Community (TEC). Here, we utilise the framework of a 1989 review of the state of knowledge of BWs ecology and conservation to examine scientific advances made in understanding the composition, processes and functions of BWs and BWs\u27 species over the last 30 years. We highlight key advances in our understanding of the ecological function and role of mechanisms in BWs that are critical to the management of this ecosystem. The most encouraging change since 1989 is the integration of research between historically disparate ecological disciplines. We outline remaining ecological knowledge gaps and identify key research priorities to improve conservation efforts for this TEC. We promote a holistic consideration of BWs with our review providing a comprehensive document that researchers, planners and managers may reference. To effectively conserve ecosystems threatened by urban expansion, a range of stakeholders must be involved in the development and implementation of best practices to conserve and maintain both biodiversity and human wellbeing

Dense sampling of bird diversity increases power of comparative genomics

© 2020, The Author(s). Whole-genome sequencing projects are increasingly populating the tree of life and characterizing biodiversity1–4. Sparse taxon sampling has previously been proposed to confound phylogenetic inference5, and captures only a fraction of the genomic diversity. Here we report a substantial step towards the dense representation of avian phylogenetic and molecular diversity, by analysing 363 genomes from 92.4% of bird families—including 267 newly sequenced genomes produced for phase II of the Bird 10,000 Genomes (B10K) Project. We use this comparative genome dataset in combination with a pipeline that leverages a reference-free whole-genome alignment to identify orthologous regions in greater numbers than has previously been possible and to recognize genomic novelties in particular bird lineages. The densely sampled alignment provides a single-base-pair map of selection, has more than doubled the fraction of bases that are confidently predicted to be under conservation and reveals extensive patterns of weak selection in predominantly non-coding DNA. Our results demonstrate that increasing the diversity of genomes used in comparative studies can reveal more shared and lineage-specific variation, and improve the investigation of genomic characteristics. We anticipate that this genomic resource will offer new perspectives on evolutionary processes in cross-species comparative analyses and assist in efforts to conserve species

Insight into the Mechanisms of Adenovirus Capsid Disassembly from Studies of Defensin Neutralization

Defensins are effectors of the innate immune response with potent antibacterial activity. Their role in antiviral immunity, particularly for non-enveloped viruses, is poorly understood. We recently found that human alpha-defensins inhibit human adenovirus (HAdV) by preventing virus uncoating and release of the endosomalytic protein VI during cell entry. Consequently, AdV remains trapped in the endosomal/lysosomal pathway rather than trafficking to the nucleus. To gain insight into the mechanism of defensin-mediated neutralization, we analyzed the specificity of the AdV-defensin interaction. Sensitivity to alpha-defensin neutralization is a common feature of HAdV species A, B1, B2, C, and E, whereas species D and F are resistant. Thousands of defensin molecules bind with low micromolar affinity to a sensitive serotype, but only a low level of binding is observed to resistant serotypes. Neutralization is dependent upon a correctly folded defensin molecule, suggesting that specific molecular interactions occur with the virion. CryoEM structural studies and protein sequence analysis led to a hypothesis that neutralization determinants are located in a region spanning the fiber and penton base proteins. This model was supported by infectivity studies using virus chimeras comprised of capsid proteins from sensitive and resistant serotypes. These findings suggest a mechanism in which defensin binding to critical sites on the AdV capsid prevents vertex removal and thereby blocks subsequent steps in uncoating that are required for release of protein VI and endosomalysis during infection. In addition to informing the mechanism of defensin-mediated neutralization of a non-enveloped virus, these studies provide insight into the mechanism of AdV uncoating and suggest new strategies to disrupt this process and inhibit infection