Ecological enhancement of coastal engineering structures: passive enhancement techniques

The rock type used in coastal engineering structures impacts biodiversity, but its effect has been understudied to date. We report here on whether different combinations of rock material and rock mass properties can improve habitat suitability and early phase ecological outcomes on coastal engineering structures. We examine two coastal engineering schemes that used different granites during construction. At site one, Shap granite boulders with a high number of cm-dm2 surface features (e.g. ledges) were deliberately positioned during construction (called passive enhancement), to a) maximise the provision of cm-dm scale intertidal habitat and b) determine which scale of habitat is best for ecological enhancement. At site two, Norwegian granite boulders were installed without passive enhancement, allowing for a direct comparison. Passive positioning of Shap granite boulders led to an increase in limpet (Patella vulgata, Linnaeus, 1758) abundance within two years but few limpets were recorded on the non-enhanced Norwegian granite. Positioning of boulder thus exerts a strong control on the mm and mm-dm scale geomorphic features present, with clear ecological benefits when suitable features are selected for and optimally positioned (i.e. passive enhancement) to maximise habitat features. An EcoRock scoring matrix was developed to aid in the selection of the most ecologically suitable rock materials for coastal engineering worldwide; this can help improve habitat provision on engineered structures in a rapidly warming world

Maximising the ecological value of hard coastal structures using textured formliners

In order to enhance the ecological value of vertical hard coastal structures, hybrid designs with complex surface textures (such as a combination of grooves and pits) have been recommended. This strategy optimises ecological colonisation at two spatial scales: 1) at the mm-scale for barnacle abundance (shown to have bioprotective capabilities), and 2) at the cm-scale for species richness and abundance through the incorporation/creation of habitat features. To determine the optimal design for improving the intertidal habitat quality of vertical coastal defence structures, we conducted an ecological enhancement trial involving 160 artificial concrete tiles of different designs (and thus topographic complexity) and 24 cleared natural surfaces (150 × 150 mm) at three sites in the UK. Within 18 months, tile designs with intermediate levels of complexity (mm-scale surface roughness) were optimal in increasing barnacle cover compared to plain-cast tiles. Tiles with high complexity (with microhabitat recesses up to 30 mm deep) developed greatest species richness and mobile species abundance and had lowest peak air temperatures and highest humidity. Such textured ecological enhancements can help improve the habitat value of existing and future hard coastal structures by favouring the conservation of intertidal species in urban marine habitats and enhancing otherwise weak or absent ecosystem service provision

Datasheets for Machine Learning Sensors

Machine learning (ML) sensors offer a new paradigm for sensing that enables intelligence at the edge while empowering end-users with greater control of their data. As these ML sensors play a crucial role in the development of intelligent devices, clear documentation of their specifications, functionalities, and limitations is pivotal. This paper introduces a standard datasheet template for ML sensors and discusses its essential components including: the system's hardware, ML model and dataset attributes, end-to-end performance metrics, and environmental impact. We provide an example datasheet for our own ML sensor and discuss each section in detail. We highlight how these datasheets can facilitate better understanding and utilization of sensor data in ML applications, and we provide objective measures upon which system performance can be evaluated and compared. Together, ML sensors and their datasheets provide greater privacy, security, transparency, explainability, auditability, and user-friendliness for ML-enabled embedded systems. We conclude by emphasizing the need for standardization of datasheets across the broader ML community to ensure the responsible and effective use of sensor data

DFB Quantum Cascade Laser Arrays

DFB quantum cascade laser (DFB-QCL) arrays operating between 8.7 and 9.4 mum are investigated for their performance characteristics-single-mode selection of the DFB grating, and variability in threshold, slope efficiency, and output power of different lasers in the array. Single-mode selection refers to the ability to choose a desired mode/frequency of laser emission with a DFB grating. We apply a theoretical framework developed for general DFB gratings to analyze DFB-QCL arrays. We calculate how the performance characteristics of DFB-QCLs are affected by the coupling strength kappaL of the grating, and the relative position of the mirror facets at the ends of the laser cavity with respect to the grating. We discuss how single-mode selection can be improved by design. Several DFB-QCL arrays are fabricated and their performance examined. We achieve desired improvements in single-mode selection, and we observe the predicted variability in the threshold, slope efficiency, and output power of the DFB-QCLs. As a demonstration of potential applications, the DFB-QCL arrays are used to perform infrared absorption spectroscopy with fluids.Engineering and Applied Science

Transcription Factors Bind Thousands of Active and Inactive Regions in the Drosophila Blastoderm

Identifying the genomic regions bound by sequence-specific regulatory factors is central both to deciphering the complex DNA cis-regulatory code that controls transcription in metazoans and to determining the range of genes that shape animal morphogenesis. We used whole-genome tiling arrays to map sequences bound in Drosophila melanogaster embryos by the six maternal and gap transcription factors that initiate anterior–posterior patterning. We find that these sequence-specific DNA binding proteins bind with quantitatively different specificities to highly overlapping sets of several thousand genomic regions in blastoderm embryos. Specific high- and moderate-affinity in vitro recognition sequences for each factor are enriched in bound regions. This enrichment, however, is not sufficient to explain the pattern of binding in vivo and varies in a context-dependent manner, demonstrating that higher-order rules must govern targeting of transcription factors. The more highly bound regions include all of the over 40 well-characterized enhancers known to respond to these factors as well as several hundred putative new cis-regulatory modules clustered near developmental regulators and other genes with patterned expression at this stage of embryogenesis. The new targets include most of the microRNAs (miRNAs) transcribed in the blastoderm, as well as all major zygotically transcribed dorsal–ventral patterning genes, whose expression we show to be quantitatively modulated by anterior–posterior factors. In addition to these highly bound regions, there are several thousand regions that are reproducibly bound at lower levels. However, these poorly bound regions are, collectively, far more distant from genes transcribed in the blastoderm than highly bound regions; are preferentially found in protein-coding sequences; and are less conserved than highly bound regions. Together these observations suggest that many of these poorly bound regions are not involved in early-embryonic transcriptional regulation, and a significant proportion may be nonfunctional. Surprisingly, for five of the six factors, their recognition sites are not unambiguously more constrained evolutionarily than the immediate flanking DNA, even in more highly bound and presumably functional regions, indicating that comparative DNA sequence analysis is limited in its ability to identify functional transcription factor targets

Urban Biodiversity and Landscape Ecology: Patterns, Processes and Planning

Effective planning for biodiversity in cities and towns is increasingly important as urban areas and their human populations grow, both to achieve conservation goals and because ecological communities support services on which humans depend. Landscape ecology provides important frameworks for understanding and conserving urban biodiversity both within cities and considering whole cities in their regional context, and has played an important role in the development of a substantial and expanding body of knowledge about urban landscapes and communities. Characteristics of the whole city including size, overall amount of green space, age and regional context are important considerations for understanding and planning for biotic assemblages at the scale of entire cities, but have received relatively little research attention. Studies of biodiversity within cities are more abundant and show that longstanding principles regarding how patch size, configuration and composition influence biodiversity apply to urban areas as they do in other habitats. However, the fine spatial scales at which urban areas are fragmented and the altered temporal dynamics compared to non-urban areas indicate a need to apply hierarchical multi-scalar landscape ecology models to urban environments. Transferring results from landscape-scale urban biodiversity research into planning remains challenging, not least because of the requirements for urban green space to provide multiple functions. An increasing array of tools is available to meet this challenge and increasingly requires ecologists to work with planners to address biodiversity challenges. Biodiversity conservation and enhancement is just one strand in urban planning, but is increasingly important in a rapidly urbanising world

Improved imputation of low-frequency and rare variants using the UK10K haplotype reference panel

Imputing genotypes from reference panels created by whole-genome sequencing (WGS) provides a cost-effective strategy for augmenting the single-nucleotide polymorphism (SNP) content of genome-wide arrays. The UK10K Cohorts project has generated a data set of 3,781 whole genomes sequenced at low depth (average 7x), aiming to exhaustively characterize genetic variation down to 0.1% minor allele frequency in the British population. Here we demonstrate the value of this resource for improving imputation accuracy at rare and low-frequency variants in both a UK and an Italian population. We show that large increases in imputation accuracy can be achieved by re-phasing WGS reference panels after initial genotype calling. We also present a method for combining WGS panels to improve variant coverage and downstream imputation accuracy, which we illustrate by integrating 7,562 WGS haplotypes from the UK10K project with 2,184 haplotypes from the 1000 Genomes Project. Finally, we introduce a novel approximation that maintains speed without sacrificing imputation accuracy for rare variants

TCTEX1D2 mutations underlie Jeune asphyxiating thoracic dystrophy with impaired retrograde intraflagellar transport

Tiina Paunio on työryhmän UK10K jäsen.The analysis of individuals with ciliary chondrodysplasias can shed light on sensitive mechanisms controlling ciliogenesis and cell signalling that are essential to embryonic development and survival. Here we identify TCTEX1D2 mutations causing Jeune asphyxiating thoracic dystrophy with partially penetrant inheritance. Loss of TCTEX1D2 impairs retrograde intraflagellar transport (IFT) in humans and the protist Chlamydomonas, accompanied by destabilization of the retrograde IFT dynein motor. We thus define TCTEX1D2 as an integral component of the evolutionarily conserved retrograde IFT machinery. In complex with several IFT dynein light chains, it is required for correct vertebrate skeletal formation but may be functionally redundant under certain conditions.Peer reviewe