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Trajectory Modelling Techniques Useful to Epidemiological Research: A Comparative Narrative Review of Approaches
Trajectory modelling techniques have been developed to determine subgroups within a given population and are increasingly used to better understand intra- and inter-individual variability in health outcome patterns over time. The objectives of this narrative review are to explore various trajectory modelling approaches useful to epidemiological research and give an overview of their applications and differences. Guidance for reporting on the results of trajectory modelling is also covered. Trajectory modelling techniques reviewed include latent class modelling approaches, ie, growth mixture modelling (GMM), group-based trajectory modelling (GBTM), latent class analysis (LCA), and latent transition analysis (LTA). A parallel is drawn to other individual-centered statistical approaches such as cluster analysis (CA) and sequence analysis (SA). Depending on the research question and type of data, a number of approaches can be used for trajectory modelling of health outcomes measured in longitudinal studies. However, the various terms to designate latent class modelling approaches (GMM, GBTM, LTA, LCA) are used inconsistently and often interchangeably in the available scientific literature. Improved consistency in the terminology and reporting guidelines have the potential to increase researchers' efficiency when it comes to choosing the most appropriate technique that best suits their research questions.
Journal Article
DNA barcoding and taxonomy: dark taxa and dark texts
Both classical taxonomy and DNA barcoding are engaged in the task of digitizing the living world. Much of the taxonomic literature remains undigitized. The rise of open access publishing this century and the freeing of older literature from the shackles of copyright have greatly increased the online availability of taxonomic descriptions, but much of the literature of the mid- to late-twentieth century remains offline (‘dark texts’). DNA barcoding is generating a wealth of computable data that in many ways are much easier to work with than classical taxonomic descriptions, but many of the sequences are not identified to species level. These ‘dark taxa’ hamper the classical method of integrating biodiversity data, using shared taxonomic names. Voucher specimens are a potential common currency of both the taxonomic literature and sequence databases, and could be used to help link names, literature and sequences. An obstacle to this approach is the lack of stable, resolvable specimen identifiers. The paper concludes with an appeal for a global ‘digital dashboard’ to assess the extent to which biodiversity data are available online.
This article is part of the themed issue ‘From DNA barcodes to biomes’.
Journal Article
Prediction of gestational age based on genome-wide differentially methylated regions
Background
We explored the association between gestational age and cord blood DNA methylation at birth and whether DNA methylation could be effective in predicting gestational age due to limitations with the presently used methods. We used data from the Norwegian Mother and Child Birth Cohort study (MoBa) with Illumina HumanMethylation450 data measured for 1753 newborns in two batches: MoBa 1, n = 1068; and MoBa 2, n = 685. Gestational age was computed using both ultrasound and the last menstrual period. We evaluated associations between DNA methylation and gestational age and developed a statistical model for predicting gestational age using MoBa 1 for training and MoBa 2 for predictions. The prediction model was additionally used to compare ultrasound and last menstrual period-based gestational age predictions. Furthermore, both CpGs and associated genes detected in the training models were compared to those detected in a published prediction model for chronological age.
Results
There were 5474 CpGs associated with ultrasound gestational age after adjustment for a set of covariates, including estimated cell type proportions, and Bonferroni-correction for multiple testing. Our model predicted ultrasound gestational age more accurately than it predicted last menstrual period gestational age.
Conclusions
DNA methylation at birth appears to be a good predictor of gestational age. Ultrasound gestational age is more strongly associated with methylation than last menstrual period gestational age. The CpGs linked with our gestational age prediction model, and their associated genes, differed substantially from the corresponding CpGs and genes associated with a chronological age prediction model.
Journal Article
Serine peptidases: Classification, structure and function
Serine peptidases play key roles in human health and disease and their biochemical properties shaped the molecular evolution of these processes. Of known proteolytic enzymes, the serine peptidase family is the major cornerstone of the vertebrate degradome. We describe the known diversity of serine peptidases with respect to structure and function. Particular emphasis is placed on the S1 peptidase family, the trypsins, which underwent the most predominant genetic expansion yielding the enzymes responsible for vital processes in man such as digestion, blood coagulation, fibrinolysis, development, fertilization, apoptosis and immunity.
Journal Article
A comparison of biomonitoring methodologies for surf zone fish communities
Surf zones are highly dynamic marine ecosystems that are subject to increasing anthropogenic and climatic pressures, posing multiple challenges for biomonitoring. Traditional methods such as seines and hook and line surveys are often labor intensive, taxonomically biased, and can be physically hazardous. Emerging techniques, such as baited remote underwater video (BRUV) and environmental DNA (eDNA) are promising nondestructive tools for assessing marine biodiversity in surf zones of sandy beaches. Here we compare the relative performance of beach seines, BRUV, and eDNA in characterizing community composition of bony (teleost) and cartilaginous (elasmobranch) fishes of surf zones at 18 open coast sandy beaches in southern California. Seine and BRUV surveys captured overlapping, but distinct fish communities with 50% (18/36) of detected species shared. BRUV surveys more frequently detected larger species (e.g. sharks and rays) while seines more frequently detected one of the most abundant species, barred surfperch ( Amphistichus argenteus ). In contrast, eDNA metabarcoding captured 88.9% (32/36) of all fishes observed in seine and BRUV surveys plus 57 additional species, including 15 that frequent surf zone habitats. On average, eDNA detected over 5 times more species than BRUVs and 8 times more species than seine surveys at a given site. eDNA approaches also showed significantly higher sensitivity than seine and BRUV methods and more consistently detected 31 of the 32 (96.9%) jointly observed species across beaches. The four species detected by BRUV/seines, but not eDNA were only resolved at higher taxonomic ranks (e.g. Embiotocidae surfperches and Sygnathidae pipefishes). In frequent co-detection of species between methods limited comparisons of richness and abundance estimates, highlighting the challenge of comparing biomonitoring approaches. Despite potential for improvement, results overall demonstrate that eDNA can provide a cost-effective tool for long-term surf zone monitoring that complements data from seine and BRUV surveys, allowing more comprehensive surveys of vertebrate diversity in surf zone habitats.
Journal Article
Motor Control and Sensory Feedback Enhance Prosthesis Embodiment and Reduce Phantom Pain After Long-Term Hand Amputation
We quantified prosthesis embodiment and phantom pain reduction associated with motor control and sensory feedback from a prosthetic hand in one human with a long-term transradial amputation. Microelectrode arrays were implanted in the residual median and ulnar arm nerves and intramuscular electromyography recording leads were implanted in residual limb muscles to enable sensory feedback and motor control. Objective measures (proprioceptive drift) and subjective measures (survey answers) were used to assess prosthesis embodiment. For both measures, there was a significant level of embodiment of the physical prosthetic limb after open-loop motor control of the prosthesis (i.e., without sensory feedback), open-loop sensation from the prosthesis (i.e., without motor control), and closed-loop control of the prosthesis (i.e., motor control with sensory feedback). There was also a statistically significant reduction in reported phantom pain after experimental sessions that included open-loop nerve microstimulation, open-loop prosthesis motor control, or closed-loop prosthesis motor control. The closed-loop condition provided no additional significant improvements in phantom pain reduction or prosthesis embodiment relative to the open-loop sensory condition or the open-loop motor condition. This study represents the first long-term (14-month), systematic report of phantom pain reduction and prosthesis embodiment in a human amputee across a variety of prosthesis use cases.
Journal Article
Amino acid sensor conserved from bacteria to humans
Amino acids are the building blocks of life, and they are also recognized as signals by various receptors in bacteria, archaea, and eukaryotes. Despite their common basic structure, no universal mechanism for amino acid recognition is currently known. Here, we show that a subclass of dCache_1 (double domain found in calcium channels and chemotaxis receptors, family 1), a ubiquitous extracellular sensory domain, contains a simple motif, which recognizes the amino and carboxyl groups of amino acid ligands. We found this motif throughout the Tree of Life. In bacteria and archaea, this motif exclusively binds amino acids, including γ-aminobutyric acid (GABA), and it is present in all major receptor types. In humans, this motif is found in α2δ-subunits of voltage-gated calcium channels that are implicated in neuropathic pain and neurodevelopmental disorders and in a recently characterized CACHD1 protein. Our findings suggest that GABA-derived drugs bind to the same motif in human α2δ-subunits that binds natural GABA ligands in bacterial chemoreceptors. The exact location on the target protein and the mechanism of binding may enable future improvements of drugs targeting pain and neurobiological disorders.
Journal Article