This paper responds to a resurgence of interest in constructing long-term time proxies of human activity, especially but not limited to models of population change over the Pleistocene and/or ...Holocene. While very much agreeing with the need for this increased attention, we emphasize three important issues that can all be thought of as modifiable reporting unit problems: the impact of (i) archaeological periodization, (ii) uneven event durations and (iii) geographical nucleation-dispersal phenomena. Drawing inspiration from real-world examples from prehistoric Britain, Greece and Japan, we explore their consequences and possible mitigation via a reproducible set of tactical simulations. This article is part of the theme issue 'Cross-disciplinary approaches to prehistoric demography'.
The search for highly ionizing particles in nuclear track detectors (NTDs) traditionally requires experts to manually search through samples in order to identify regions of interest that could be a ...hint of physics beyond the standard model of particle physics. The advent of automated image acquisition and modern data science, including machine learning-based processing of data presents an opportunity to accelerate the process of searching for anomalies in NTDs that could be a hint of a new physics avatar. The potential for modern data science applied to this topic in the context of the MoEDAL experiment at the large Hadron collider at the European Centre for Nuclear Research, CERN, is discussed.
This article is part of a discussion meeting issue ‘Topological avatars of new physics’.
ABSTRACT
The large quantities of dust that have been found in a number of high-redshift galaxies have led to suggestions that core-collapse supernovae (CCSNe) are the main sources of their dust and ...have motivated the measurement of the dust masses formed by local CCSNe. For Cassiopeia A (Cas A), an oxygen-rich remnant of a Type IIb CCSN, a dust mass of 0.6–1.1 M⊙ has already been determined by two different methods, namely (a) from its far-infrared spectral energy distribution and (b) from analysis of the red–blue emission line asymmetries in its integrated optical spectrum. We present a third, independent, method for determining the mass of dust contained within Cas A. This compares the relative fluxes measured in similar apertures from O iii far-infrared and visual-region emission lines, taking into account foreground dust extinction, in order to determine internal dust optical depths, from which corresponding dust masses can be obtained. Using this method, we determine a dust mass within Cas A of at least 0.99$^{+0.10}_{-0.09}$ M⊙.
Nanoparticles (NPs) can add functionality (e.g., catalytic, optical, rheological) to an oil–water interface. Adsorption of ∼10 nm NPs can be reversible; however, the mechanisms for adsorption and its ...effects on surface pressure remain poorly understood. Here we demonstrate how the competitive reversible adsorption of NPs and surfactants at fluid interfaces can lead to independent control of both the adsorbed amount and surface pressure. In contrast to prior work, both species investigated (NPs and surfactants) interact reversibly with the interface and without the surface active species binding to NPs. Independent measurements of the adsorption and surface pressure isotherms allow determination of the equation of state (EOS) of the interface under conditions where the NPs and surfactants are both in dynamic equilibrium with the bulk phase. The adsorption and surface pressure measurements are performed with gold NPs of two different sizes (5 and 10 nm), at two pH values, and across a wide concentration range of surfactant (tetrapentylammonium, TPeA+) and NPs. We show that free surface active ions compete with NPs for the interface and give rise to larger surface pressures upon the adsorption of NPs. Through a competitive adsorption model, we decouple the contributions of NPs wetting at the interface and their surface activity on the measured surface pressure. We also demonstrate reversible control of adsorbed amount via changes in the surfactant concentration or the aqueous phase pH.
Many patients suffering from developmental disorders harbor submicroscopic deletions or duplications that, by affecting the copy number of dosage-sensitive genes or disrupting normal gene expression, ...lead to disease. However, many aberrations are novel or extremely rare, making clinical interpretation problematic and genotype-phenotype correlations uncertain. Identification of patients sharing a genomic rearrangement and having phenotypic features in common leads to greater certainty in the pathogenic nature of the rearrangement and enables new syndromes to be defined. To facilitate the analysis of these rare events, we have developed an interactive web-based database called DECIPHER (Database of Chromosomal Imbalance and Phenotype in Humans Using Ensembl Resources) which incorporates a suite of tools designed to aid the interpretation of submicroscopic chromosomal imbalance, inversions, and translocations. DECIPHER catalogs common copy-number changes in normal populations and thus, by exclusion, enables changes that are novel and potentially pathogenic to be identified. DECIPHER enhances genetic counseling by retrieving relevant information from a variety of bioinformatics resources. Known and predicted genes within an aberration are listed in the DECIPHER patient report, and genes of recognized clinical importance are highlighted and prioritized. DECIPHER enables clinical scientists worldwide to maintain records of phenotype and chromosome rearrangement for their patients and, with informed consent, share this information with the wider clinical research community through display in the genome browser Ensembl. By sharing cases worldwide, clusters of rare cases having phenotype and structural rearrangement in common can be identified, leading to the delineation of new syndromes and furthering understanding of gene function.
Summary Background Human genome sequencing has transformed our understanding of genomic variation and its relevance to health and disease, and is now starting to enter clinical practice for the ...diagnosis of rare diseases. The question of whether and how some categories of genomic findings should be shared with individual research participants is currently a topic of international debate, and development of robust analytical workflows to identify and communicate clinically relevant variants is paramount. Methods The Deciphering Developmental Disorders (DDD) study has developed a UK-wide patient recruitment network involving over 180 clinicians across all 24 regional genetics services, and has performed genome-wide microarray and whole exome sequencing on children with undiagnosed developmental disorders and their parents. After data analysis, pertinent genomic variants were returned to individual research participants via their local clinical genetics team. Findings Around 80 000 genomic variants were identified from exome sequencing and microarray analysis in each individual, of which on average 400 were rare and predicted to be protein altering. By focusing only on de novo and segregating variants in known developmental disorder genes, we achieved a diagnostic yield of 27% among 1133 previously investigated yet undiagnosed children with developmental disorders, whilst minimising incidental findings. In families with developmentally normal parents, whole exome sequencing of the child and both parents resulted in a 10-fold reduction in the number of potential causal variants that needed clinical evaluation compared to sequencing only the child. Most diagnostic variants identified in known genes were novel and not present in current databases of known disease variation. Interpretation Implementation of a robust translational genomics workflow is achievable within a large-scale rare disease research study to allow feedback of potentially diagnostic findings to clinicians and research participants. Systematic recording of relevant clinical data, curation of a gene–phenotype knowledge base, and development of clinical decision support software are needed in addition to automated exclusion of almost all variants, which is crucial for scalable prioritisation and review of possible diagnostic variants. However, the resource requirements of development and maintenance of a clinical reporting system within a research setting are substantial. Funding Health Innovation Challenge Fund, a parallel funding partnership between the Wellcome Trust and the UK Department of Health.
The DECIPHER database (https://decipher.sanger.ac.uk/) is an accessible online repository of genetic variation with associated phenotypes that facilitates the identification and interpretation of ...pathogenic genetic variation in patients with rare disorders. Contributing to DECIPHER is an international consortium of >200 academic clinical centres of genetic medicine and ≥1600 clinical geneticists and diagnostic laboratory scientists. Information integrated from a variety of bioinformatics resources, coupled with visualization tools, provides a comprehensive set of tools to identify other patients with similar genotype-phenotype characteristics and highlights potentially pathogenic genes. In a significant development, we have extended DECIPHER from a database of just copy-number variants to allow upload, annotation and analysis of sequence variants such as single nucleotide variants (SNVs) and InDels. Other notable developments in DECIPHER include a purpose-built, customizable and interactive genome browser to aid combined visualization and interpretation of sequence and copy-number variation against informative datasets of pathogenic and population variation. We have also introduced several new features to our deposition and analysis interface. This article provides an update to the DECIPHER database, an earlier instance of which has been described elsewhere Swaminathan et al. (2012) DECIPHER: web-based, community resource for clinical interpretation of rare variants in developmental disorders. Hum. Mol. Genet., 21, R37-R44.
Deposition of silica microparticles on glass substrates was measured as a function of cationic polymer-anionic surfactant composition and shear rate. Particles were initially deposited in quiescent ...conditions in different polymer-surfactant compositions, which were chosen based on prior measurements of composition-dependent polymer-surfactant interactions and deposition behavior (up to 0.5 wt % polymer and 12 wt % surfactant). Programmed shear and dilution profiles in a flow cell together with optical microscopy observation were used to continuously track particle deposition, detachment, and redeposition. Knowledge of the shear-dependent torque on each particle provides information on adhesive torque mediated by polymer-surfactant complexes. Detachment of colloids initially deposited by depletion interactions occurs at low shear rates (∼100 s–1) due to lack of tangential forces or an adhesive torque. Further dilution produced redeposition of particles that resisted detachment (up to ∼2000 s–1) as the result of strong cationic polymer bridge formation, presumably due to preferential surfactant removal. Dilution from different initial compositions indicates a pathway dependence of polymer-surfactant de-complexation into shear-resistant cationic bridges. These findings demonstrate the ability to program deposition behavior via the informed design of initial polymer-surfactant compositions and shear profiles. The particle trajectory analysis developed in this work provides an assay to screen composition-dependent colloidal deposition in diverse materials and applications.
The luminous Type IIn SN 2010jl shows strong signs of interaction between the SN ejecta and dense circumstellar material. Dust may be present in the unshocked ejecta; the cool, dense shell (CDS) ...between the shocks in the interaction region; or in the circumstellar medium (CSM). We present and model new optical and infrared photometry and spectroscopy of SN 2010jl from 82 to 1367 days since explosion. We evaluate the photometric and spectroscopic evolution using the radiative transfer codes mocassin and damocles, respectively. We propose an interaction scenario and investigate the resulting dust formation scenarios and dust masses. We find that SN 2010jl has been continuously forming dust based on the evolution of its infrared emission and optical spectra. There is evidence for preexisting dust in the CSM as well as new dust formation in the CDS and/or ejecta. We estimate that 0.005-0.01 M of predominantly carbon dust grains has formed in SN 2010jl by ∼1400 days post-outburst.
Controlling active colloidal particle swarms could enable useful microscopic functions in emerging applications at the interface of nanotechnology and robotics. Here, we present a computational study ...of controlling self-propelled colloidal particle propulsion speeds to cooperatively capture and transport cargo particles, which otherwise produce random dispersions. By sensing swarm and cargo coordinates, each particle's speed is actuated according to a control policy based on multiagent assignment and path planning strategies that navigate stochastic particle trajectories to targets around cargo. Colloidal swarms are shown to dynamically cage cargo at their center via inward radial forces while simultaneously translating via directional forces. Speed, power, and efficiency of swarm tasks display emergent coupled dependences on swarm size and pair interactions and approach asymptotic limits indicating near-optimal performance. This scheme exploits unique interactions and stochastic dynamics in colloidal swarms to capture and transport microscopic cargo in a robust, stable, error-tolerant, and dynamic manner.
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