Open data, open science and transparency in the time of COVID 19.

A novel coronavirus now known as SARS-CoV-2 was first reported in Wuhan, China in December 2019. It targets the respiratory system, with a wide range of symptom severity and results in a comparatively high level of mortality. Crucially, it has rapidly spread across the globe, affecting people living on all the majorly populated continents. The rapid spread, high mortality, range of severity and other unknown factors, have resulted in huge uncertainty. This means there is an urgent necessity to understand the characteristics of the virus and develop strategies to reduce its impact. To make the best decisions in this developing situation, we need information. COVID-19, the disease caused by the SARS-CoV-2 virus, has fundamentally changed the way society interacts with health data. It has become a huge and dominating focus for both public and media interest and now guides a large proportion of research effort. Our media (both traditional and social) is dominated by daily updates on new figures, visualisations and discussion. At the same time, many academics have shifted or pivoted their work towards studying the ongoing pandemic, as funding calls from major sources are seeking to invest large sums of money into COVID-specific research projects. As interest and concern have escalated, our requirement for information to learn more and inform decision-making has also increased. Concurrently, the production and use of Open Data and wider Open Science practices has accelerated at an incredible rate

Characterization of U(VI) Sorption-Desoprtion Processes and Model Upscaling

In order to apply predictive reactive transport models to the Hanford site, detailed knowledge of the speciation of contaminants is required. Important speciation parameters include: (1) oxidation state; (2) the local molecular structure surrounding contaminant elements; (3) the type and binding of a contaminant ion sorption complex (if adsorbed); (4) the type(s) of phase within which a contaminant is structurally incorporated [e.g., present in a three-dimensional precipitate(s)]; (5) the phase associations of a contaminant; (6) the microscopic distribution of a contaminant within sediments and soils. In the present study, we have used synchrotron-based X-ray spectroscopic methods to study the speciation of U and Cu in contaminated soil and sediment samples from the Hanford Site. To complement and complete our initial XAFS investigation of U speciation in contaminated vadose zone sediments below tank BX-102, we have also performed mXRD studies of two sediment sample to identify the specific U(VI)-silicate phase present. Samples from the 300 Area were examined by mSXRF to determine the microscopic distribution and element associations of Cu and U. These samples were also analyzed by U LIII- and Cu K-edge XAFS spectroscopy to determine the chemical speciation of these elements

Belief Maintenance Systems: Initial Prototype Specification

A fundamental need in future information systems is an effective method of accurately representing and monitoring dynamic, real-world situations inside a computer. Information is represented using an Extended Open World Assumption (EOWA), in which the data are explicitly true or false. Reasoning within the EOWA is done through the use of a dynamic dependency net which only represents those beliefs and justifications that are both currently valid and in current use. In this paper, we present definitions and uses of the EOWA and dynamic dependency net in our current research of developing a database with which we can use deductive reasoning with limited resources. A prototype has been implemented for determining the existing problems of creating such a belief management system for operation in real-world applications

Characterization of U(VI) Sorption-Desorption Processes and Model Upscaling

The objectives of the overall collaborative EMSP effort (with which this project is associated) were to characterize sorption and desorption processes of U(VI) on pristine and contaminated Hanford sediments over a range of sediment facies and materials properties and to relate such characterization both to fundamental molecular-scale understanding and field-scale models of geochemistry and mass transfer. The research was intended to provide new insights on the mechanisms of U(VI) retardation at Hanford, and to allow the development of approaches by which laboratory-developed geochemical models could be upscaled for defensible field-scale predictions of uranium transport in the environment. Within this broader context, objectives of the JHU-based project were to test hypotheses regarding the coupled roles of adsorption and impermeable-zone diffusion in controlling the fate and transport of U(VI) species under conditions of comparatively short-term exposure. In particular, this work tested the following hypotheses: (1) the primary adsorption processes in the Hanford sediment over the pH range of 7 to 10 are surface complexation reactions of aqueous U(VI) hydroxycarbonate and carbonate complexes with amphoteric edge sites on detrital phyllosilicates in the silt/clay size fraction; (2) macroscopic adsorption intensity (at given aqueous conditions) is a function of mineral composition and aquatic chemistry; and (3) equilibrium sorption and desorption to apply in short-term, laboratory-spiked pristine sediments; and (4) interparticle diffusion can be fully understood in terms of a model that couples molecular diffusion of uranium species in the porewater with equilibrium sorption under the relevant aqueous conditions. The primary focus of the work was on developing and applying both models and experiments to test the applicability of "local equilibrium" assumptions in the modeling interpretation of sorption retarded interparticle diffusion, as relevant to processes of U(VI) diffusion in silt/clay layers. Batch isotherm experiments were first used to confirm sorption isotherms under the intended test conditions and diffusion cell experiments were then conducted to explore the diffusion hypotheses. Important new information was obtained about the role of aqueous calcium and solid calcium carbonate in controlling sorption equilibrium with Hanford sediments. The retarded interparticle diffusion model with local sorption equilibrium was shown to very successfully simulate diffusion at high aqueous concentration of U(VI). By contrast, however, diffusion data obtained at low concentration suggested nonequilibrium of sorption even at diffusion time scales. Such nonequilibrium effects at low concentration are likely to be the result of sorption retarded intraparticle diffusion, and strong U(VI) sorption in the low concentration range

Use of short-tandem repeat (STR) fingerprinting to validate sample origins in hepatitis C virus molecular epidemiology studies

Sequence analysis is used to define the molecular epidemiology and evolution of the hepatitis C virus. Whilst most studies have shown that individual patients harbour viruses that are derived from a limited number of highly related strains, some recent reports have shown that some patients can be co-infected with very distinct variants whose frequency can fluctuate greatly. Whilst co-infection with highly divergent strains is possible, an alternative explanation is that such data represent contamination or sample mix-up. In this study, we have shown that DNA fingerprinting techniques can accurately assess sample provenance and differentiate between samples that are truly exhibiting mixed infection from those that harbour distinct virus populations due to sample mix-up. We have argued that this approach should be adopted routinely in virus sequence analyses to validate sample provenance

The clinically extremely vulnerable to COVID: identification and changes in healthcare while self-isolating (shielding) during the coronavirus pandemic.

In March 2020, the government of Scotland identified people deemed clinically extremely vulnerable to COVID due to their pre-existing health conditions. These people were advised to strictly self-isolate (shield) at the start of the pandemic, except for necessary healthcare. We examined who was identified as clinically extremely vulnerable, how their healthcare changed during isolation, and whether this process exacerbated healthcare inequalities. We linked those on the shielding register in NHS Grampian, a health authority in Scotland, to healthcare records from 2015-2020. We described the source of identification, demographics, and clinical history of the cohort. We measured changes in out-patient, in-patient, and emergency healthcare during isolation in the shielding population and compared to the general non-shielding population. The register included 16,092 people (3% of the population), clinically vulnerable primarily due to a respiratory disease, immunosuppression, or cancer. Among them, 42% were not identified by national healthcare record screening but added ad hoc, with these additions including more children and fewer economically-deprived. During isolation, all forms of healthcare use decreased (25%-46%), with larger decreases in scheduled care than in emergency care. However, people shielding had better maintained scheduled care compared to the non-shielding general population: out-patient visits decreased 35% vs 49%; in-patient visits decreased 46% vs 81%. Notably, there was substantial variation in whose scheduled care was maintained during isolation: younger people and those with cancer had significantly higher visit rates, but there was no difference between sexes or socioeconomic levels. Healthcare changed dramatically for the clinically extremely vulnerable population during the pandemic. The increased reliance on emergency care while isolating indicates that continuity of care for existing conditions was not optimal. However, compared to the general population, there was success in maintaining scheduled care, particularly in young people and those with cancer. We suggest that integrating demographic and primary care data would improve identification of the clinically vulnerable and could aid prioritising their care

Entanglement can increase asymptotic rates of zero-error classical communication over classical channels

It is known that the number of different classical messages which can be communicated with a single use of a classical channel with zero probability of decoding error can sometimes be increased by using entanglement shared between sender and receiver. It has been an open question to determine whether entanglement can ever increase the zero-error communication rates achievable in the limit of many channel uses. In this paper we show, by explicit examples, that entanglement can indeed increase asymptotic zero-error capacity, even to the extent that it is equal to the normal capacity of the channel. Interestingly, our examples are based on the exceptional simple root systems E7 and E8.Comment: 14 pages, 2 figur

Serious mental health diagnoses in children on the child protection register: a record linkage study.

Children with experience of maltreatment, abuse or neglect are known to have a higher prevalence of poor mental health. Child Protection Services identify children most at risk of harm and in need of intervention. Mental healthcare usage in this population is not well understood as registration data is not routinely linked to health records. We undertook data linkage to describe the population on the register, their mental healthcare usage and to calculate age- and sex-specific incidence rates of mental health outcomes. We analysed records from the Aberdeen City Council Child Protection Register and for mental health prescribing and referrals to child and adolescent mental health services (CAMHS) for the NHS Grampian region between 1st January 2012 and 31st December 2022. We identified 1,498 individuals with a Child Protection Register registration, of which 70% were successfully matched to health records. 20% of registrations occurred before birth and the median age of registration was 3 years. 10.1% of children with a registration ever received a mental health prescription, 5.1% for treatment of attention deficit hyperactivity disorder and 1.7% for treatment of depression. 18.9% received a referral to specialist outpatient Child and Adolescent Mental Health Services. Age- and sex- standardised incidence rates for mental health prescribing and referrals are higher for children with a child protection registration compared to the general population. Children identified as being at significant risk of harm and involved with child protection services are at greater risk of seeking or receiving professional mental health support than their peers. Clinical services should investigate additional ways to support this population’s mental well-being as a priority. Efforts to reduce the exposure of children to potentially harmful environments at a societal level should also be pursued

Meteorite evidence for partial differentiation and protracted accretion of planetesimals.

Modern meteorite classification schemes assume that no single planetary body could be source of both unmelted (chondritic) and melted (achondritic) meteorites. This dichotomy is a natural outcome of formation models assuming that planetesimal accretion occurred nearly instantaneously. However, it has recently been proposed that the accretion of many planetesimals lasted over ≳1 million years (Ma). This could have resulted in partially differentiated internal structures, with individual bodies containing iron cores, achondritic silicate mantles, and chondritic crusts. This proposal can be tested by searching for a meteorite group containing evidence for these three layers. We combine synchrotron paleomagnetic analyses with thermal, impact, and collisional evolution models to show that the parent body of the enigmatic IIE iron meteorites was such a partially differentiated planetesimal. This implies that some chondrites and achondrites simultaneously coexisted on the same planetesimal, indicating that accretion was protracted and that apparently undifferentiated asteroids may contain melted interiors

Recombinant human L-ficolin directly neutralizes hepatitis C virus entry

L-ficolin is a soluble pattern recognition molecule expressed by the liver that contributes to innate immune defense against microorganisms. It is well described that binding of L-ficolin to specific pathogen-associated molecular patterns activates the lectin complement pathway, resulting in opsonization and lysis of pathogens. In this study, we demonstrated that in addition to this indirect effect, L-ficolin has a direct neutralizing effect against hepatitis C virus (HCV) entry. Specific, dose-dependent binding of recombinant L-ficolin to HCV glycoproteins E1 and E2 was observed. This interaction was inhibited by soluble L-ficolin ligands. Interaction of L-ficolin with E1 and E2 potently inhibited entry of retroviral pseudoparticles bearing these glycoproteins. L-ficolin also inhibited entry of cell-cultured HCV in a calcium-dependent manner. Neutralizing concentrations of L-ficolin were found to be circulating in the serum of HCV-infected individuals. This is the first description of direct neutralization of HCV entry by a ficolin and highlights a novel role for L-ficolin as a virus entry inhibitor