Quality assessment of gene repertoire annotations with OMArk

In the era of biodiversity genomics, it is crucial to ensure that annotations of protein-coding gene repertoires are accurate. State-of-the-art tools to assess genome annotations measure the completeness of a gene repertoire but are blind to other errors, such as gene overprediction or contamination. We introduce OMArk, a software package that relies on fast, alignment-free sequence comparisons between a query proteome and precomputed gene families across the tree of life. OMArk assesses not only the completeness but also the consistency of the gene repertoire as a whole relative to closely related species and reports likely contamination events. Analysis of 1,805 UniProt Eukaryotic Reference Proteomes with OMArk demonstrated strong evidence of contamination in 73 proteomes and identified error propagation in avian gene annotation resulting from the use of a fragmented zebra finch proteome as a reference. This study illustrates the importance of comparing and prioritizing proteomes based on their quality measures.ISSN:1546-1696ISSN:1087-015

Stuck in the driver's seat: a conceptualisation for understanding car dependence and its determinants

Car dependence brings along many negative social and environmental externalities that policymakers and stakeholders need to consider. Nonetheless, the concept is not well defined and lacks a clear framework regarding its determinants and mechanisms, which also leads to problems in terms of its operationalisation. Therefore, this paper proposes a conceptualisation and operationalisation of car dependence, which can serve as a basis for further research and policy. We define car dependence as the extent to which an individual is incapable to participate in location-based activities without a car in a satisfactory way. This definition is based on the theoretical background of the capabilities approach and the concept of motility and also linked to the concept of accessibility. Our conceptual model consists of seven components, most of which have been considered separately in previous conceptualisations, namely the land use system, transport system, natural environment, temporal component, social environment, and individual objective/subjective characteristics. These components range from being external to the individual (e.g. the land use system) to internal (e.g. individual features). Considering these components jointly emphasises the importance of looking at car dependence in a holistic, unifying way. This approach contributes to a better understanding of car dependence that goes beyond the explicit analysis of components in previous research. In addition, we provide a systematic approach to operationalising car dependence that contributes to a more comparable approach to measuring car dependence. Researchers have to decide whether they want to examine car dependence via its components or via self-report by individuals, whether they want to study the full set of components or only a subset, and whether they want to consider perceptions or factual information about external components. Therefore, our conceptualisation and operationalisation provide valuable new insights into car dependence regarding new research directions and policy approaches.ISSN:0144-1647ISSN:1464-532

A comprehensive investigation into the effect of vertical component of ground motion on response of sliding unanchored blocks

This study aims to quantify the effect of the vertical component of ground motion on the seismic response of sliding rigid blocks, in terms of maximum and residual displacements. A multi-stripe analysis approach is employed to examine the response with and without the vertical component under various levels of ground motion intensity. First, a parametric study is conducted using a Coulomb friction model with a constant coefficient of friction that does not account for any dependence of the friction coefficient on velocity or pressure. It is shown that the effect of the vertical component on maximum and residual displacement is more pronounced for ground motions that can barely initiate sliding. Moreover, the influence of the vertical component on the residual sliding displacement is higher than that on the maximum displacement. Subsequently, to account for the friction coefficient dependence on pressure and sliding velocity, two interface cases (steel-steel, and concrete-concrete) are analyzed. It is found that even when a variable coefficient of friction is used, the overall trends observed for a constant coefficient of friction do not change.ISSN:0141-029

A Supramolecular Wire Able to Self-Assemble on Gold Surface: Controlling the Film Length to Optimize the Device Lifetime and Electron Transfer Efficiency

A chemical "lego nanoset" has been used to realize different structures on gold surfaces. Three building blocks have been designed, in order to chemically link the surface and self-assemble in an ordered manner. Self-assembled films are arranged on a gold surface into 3D suprastructures via consecutive deposition of different mono-layers, taken together by thymine-adenine hydrogen bonds. Three films, composed of one, two, and three helical peptide layers, both containing a zinc-tetraphenylporphyrin dye as an external sheet, are built and characterized by spectro-electrochemical and spectroscopic techniques. All films are found to generate current under illumination, and their photoresponse and stability are studied as a function of the number of peptide layers. The efficiency of the photoconversion process has been correlated to the molecular organization of the porphyrin dyes in the film and to the templating role of the bridge between the porphyrin and the gold surface.ISSN:2196-735

Inverse Design of Singlet-Fission Materials with Uncertainty-Controlled Genetic Optimization

Singlet fission has shown potential for boosting the efficiency of solar cells, but the scarcity of suitable molecular materials hinders its implementation. We introduce an uncertainty-controlled genetic algorithm (ucGA) based on ensemble machine learning predictions from different molecular representations that concurrently optimizes excited state energies, synthesizability, and exciton size for the discovery of singlet fission materials. The ucGA allows us to efficiently explore the chemical space spanned by the reFORMED fragment database, which consists of 45,000 cores and 5,000 substituents derived from crystallographic structures assembled in the FORMED repository. Running the ucGA in an exploitative setup performs local optimization on variations of known singlet fission scaffolds, such as acenes. In an explorative mode, hitherto unknown candidates displaying excellent excited state properties for singlet fission are generated. We suggest a class of heteroatom-rich mesoionic compounds as acceptors for charge-transfer mediated singlet fission. When included in larger donor-acceptor systems, these units exhibit localization of the triplet state, favorable diradicaloid character and suitable triplet energies for exciton injection into semiconductor solar cells.ISSN:1433-7851ISSN:1521-3773ISSN:0570-083

Molecular epidemiology of Cercospora leaf spot on resistant and susceptible sugar beet hybrids

Cercospora leaf spot (CLS), caused by Cercospora beticola, is a major foliar disease impacting sugar beet production worldwide. The development of new resistant sugar beet hybrids is a powerful tool to better manage the disease, but it is unclear how these hybrids affect CLS epidemiology. We used a molecular epidemiology approach to study natural epidemics of CLS affecting two susceptible and two resistant sugar beet hybrids at two field sites. Infected plants were geotagged on a weekly basis. Isolations of C. beticola were made from infected leaves and genotyped using six simple-sequence repeat loci to identify clones. We determined that CLS epidemics had a later onset in plots planted to resistant hybrids, but once the pathogen established an infection, there was little difference between resistant and susceptible hybrids in the probability of localized spread and dispersal. We found that different clones often infected the same leaf and that clusters of infected plants were often colonized by a mixture of clones. There was little overall difference in genetic diversity of C. beticola collected on resistant and susceptible hybrids; however, genotypic diversity was lower on the resistant hybrid at one site, suggestive of a selection bottleneck. At the end of the epidemic infections were not randomly distributed across the fields and we found that a single clone could spread over a distance of 100 m during a growing season.ISSN:0032-0862ISSN:1365-305

Three Years of High-contrast Imaging of the PDS 70 b and c Exoplanets at Hα with MagAO-X: Evidence of Strong Protoplanet Hα Variability and Circumplanetary Dust

We present 3 yr of high-contrast imaging of the PDS 70 b and c accreting protoplanets with the new extreme AO system MagAO-X as part of the MaxProtoPlanetS survey of Hα protoplanets. In 2023 and 2024, our sharp (25-27 mas FWHM), well-AO-corrected (20%-26% Strehl), deep (2-3.6 hr) images detected compact (r ∼ 30 mas; r ∼ 3 au) circumplanetary disks (CPDs) surrounding both protoplanets. Starlight scattering off the front edge of these dusty CPDs is the likely source of the bright compact continuum light detected within ∼30 mas of both planets in our simultaneously obtained continuum 668 nm filter images. After subtraction of contaminating continuum and point-spread function residuals with pyKLIP angular differential imaging and spectral differential imaging, we obtained high-contrast ASDI Hα images of both planets in 2022, 2023, and 2024. We find the Hα line flux of planet b fell by (8.1 ± 1.6) × 10−16 erg s−1 cm−2, a factor of 4.6 drop in flux from 2022 to 2023. In 2024 March, planet b continued to be faint with just a slight 1.6× rise to an Hα line flux of (3.64 ± 0.87) × 10−16 erg s−1 cm−2. For c, we measure a significant increase of (2.74 ± 0.51) × 10−16 erg s−1 cm−2 from 2023 to 2024, which is a factor of 2.3 increase. So both protoplanets have recently experienced significant Hα variability with ∼1 yr sampling. In 2024, planet c is brighter than b: as c is brightening and b generally fading. We also tentatively detect one new point source “CC3” inside the inner disk (∼49 mas; at PA ∼ 295°; 2024) with orbital motion roughly consistent with a ∼5.6 au orbit.ISSN:0004-6256ISSN:1538-388

Microring quantum cascade surface emitting lasers

We miniaturize a vertically coupled in-plane whispering gallery mode cavity incorporating a quantum cascade gain medium, aiming to realize the mid-infrared counterpart to the vertical cavity surface emitting laser. Building on previous work with linear microcavities, we introduce a new type of quantum cascade surface emitting laser (QCSEL) by miniaturizing a buried heterostructure ring cavity. At wavelengths of 4.5 and 8 μm, we investigate the optical losses for decreasing ring diameters while benchmarking the device performance against linear microcavities. We achieve an equivalent mirror reflectivity of 0.95 and demonstrate lasing with ring diameters as small as 50 μm. Finally, we report a continuous-wave threshold power dissipation of 274 mW for a 100 μm diameter ring QCSEL, characterized on wafer level at 20 °C.ISSN:2378-096