The effects of charge transfer inefficiency (CTI) on galaxy shape measurements

(Abridged) We examine the effects of charge transfer inefficiency (CTI) during CCD readout on galaxy shape measurements required by studies of weak gravitational lensing. We simulate a CCD readout with CTI such as that caused by charged particle radiation damage. We verify our simulations on data from laboratory-irradiated CCDs. Only charge traps with time constants of the same order as the time between row transfers during readout affect galaxy shape measurements. We characterize the effects of CTI on various galaxy populations. We baseline our study around p-channel CCDs that have been shown to have charge transfer efficiency up to an order of magnitude better than several models of n-channel CCDs designed for space applications. We predict that for galaxies furthest from the readout registers, bias in the measurement of galaxy shapes, Delta(e), will increase at a rate of 2.65 +/- 0.02 x 10^(-4) per year at L2 for accumulated radiation exposure averaged over the solar cycle. If uncorrected, this will consume the entire shape measurement error budget of a dark energy mission within about 4 years. Software mitigation techniques demonstrated elsewhere can reduce this by a factor of ~10, bringing the effect well below mission requirements. CCDs with higher CTI than the ones we studeied may not meet the requirements of future dark energy missions. We discuss ways in which hardware could be designed to further minimize the impact of CTI.Comment: 11 pages, 6 figures, and 2 tables. Accepted for publication in PAS

Radiation Tolerance of Fully-Depleted P-Channel CCDs Designed for the SNAP Satellite

Thick, fully depleted p-channel charge-coupled devices (CCDs) have been developed at the Lawrence Berkeley National Laboratory (LBNL). These CCDs have several advantages over conventional thin, n-channel CCDs, including enhanced quantum efficiency and reduced fringing at near-infrared wavelengths and improved radiation tolerance. Here we report results from the irradiation of CCDs with 12.5 and 55 MeV protons at the LBNL 88-Inch Cyclotron and with 0.1-1 MeV electrons at the LBNL Co60 source. These studies indicate that the LBNL CCDs perform well after irradiation, even in the parameters in which significant degradation is observed in other CCDs: charge transfer efficiency, dark current, and isolated hot pixels. Modeling the radiation exposure over a six-year mission lifetime with no annealing, we expect an increase in dark current of 20 e/pixel/hr, and a degradation of charge transfer efficiency in the parallel direction of 3e-6 and 1e-6 in the serial direction. The dark current is observed to improve with an annealing cycle, while the parallel CTE is relatively unaffected and the serial CTE is somewhat degraded. As expected, the radiation tolerance of the p-channel LBNL CCDs is significantly improved over the conventional n-channel CCDs that are currently employed in space-based telescopes such as the Hubble Space Telescope.Comment: 11 pages, 10 figures, submitted to IEEE Transaction

Molecular sex-typing in shorebirds: a review of an essential method for research in evolution, ecology and conservation

Knowing the correct sex of individuals is essential both for research in evolutionary ecology and for practical conservation. Recent molecular advances have produced cheap, quick and reliable methods for sexing birds including chicks, juveniles, immatures and adults. Shorebird researchers have not yet fully utilised these advances. Here we provide an overview of work in this area to date with two objectives: (i) to review the major applications of molecular sexing and findings of shorebird research so far, and (ii) to provide an essential guide on how to carry out molecular sexing using current methods whilst avoiding methodological pitfalls. We encourage shorebird researchers to make better use of molecular sex-typing techniques in studies of conservation, migration, foraging ecology and breeding behaviour

A new marker based on the avian spindlin gene that is able to sex most birds, including species problematic to sex with CHD markers

We have developed a new marker (Z43B) that can be successfully used to identify the sex of most birds (69%), including species difficult or impossible to sex with other markers. We utilized the zebra finch Taeniopygia guttata EST microsatellite sequence (CK309496) which displays sequence homology to the 5′ untranslated region (UTR) of the avian spindlin gene. This gene is known to be present on the Z and W chromosomes. To maximize cross-species utility, the primer set was designed from a consensus sequence created from homologs of CK309496 that were isolated from multiple distantly related species. Both the forward and reverse primer sequences were 100% identical to 14 avian species, including the Z chromosome of eight species and the chicken Gallus gallus W chromosome, as well as the saltwater crocodile Crocodylus porosus. The Z43B primer set was assessed by genotyping individuals of known sex belonging to 61 non-ratite species and a single ratite. The Z and W amplicons differed in size making it possible to distinguish between males (ZZ) and females (ZW) for the majority (69%) of non-ratite species tested, comprising 10 orders of birds. We predict that this marker will be useful for obtaining sex-typing data for ca 6,869 species of birds (69% of non-ratites but not galliforms). A wide range of species could be sex-typed including passerines, shorebirds, eagles, falcons, bee-eaters, cranes, shags, parrots, penguins, ducks, and a ratite species, the brown kiwi, Apteryx australis. Those species sexed include species impossible or problematic to sex-type with other markers (magpie, albatross, petrel, eagle, falcon, crane, and penguin species)

Large-Scale Analysis Exploring Evolution of Catalytic Machineries and Mechanisms in Enzyme Superfamilies.

Enzymes, as biological catalysts, form the basis of all forms of life. How these proteins have evolved their functions remains a fundamental question in biology. Over 100 years of detailed biochemistry studies, combined with the large volumes of sequence and protein structural data now available, means that we are able to perform large-scale analyses to address this question. Using a range of computational tools and resources, we have compiled information on all experimentally annotated changes in enzyme function within 379 structurally defined protein domain superfamilies, linking the changes observed in functions during evolution to changes in reaction chemistry. Many superfamilies show changes in function at some level, although one function often dominates one superfamily. We use quantitative measures of changes in reaction chemistry to reveal the various types of chemical changes occurring during evolution and to exemplify these by detailed examples. Additionally, we use structural information of the enzymes active site to examine how different superfamilies have changed their catalytic machinery during evolution. Some superfamilies have changed the reactions they perform without changing catalytic machinery. In others, large changes of enzyme function, in terms of both overall chemistry and substrate specificity, have been brought about by significant changes in catalytic machinery. Interestingly, in some superfamilies, relatives perform similar functions but with different catalytic machineries. This analysis highlights characteristics of functional evolution across a wide range of superfamilies, providing insights that will be useful in predicting the function of uncharacterised sequences and the design of new synthetic enzymes

Improving Primary Care After Stroke (IPCAS) trial: protocol of a randomised controlled trial to evaluate a novel model of care for stroke survivors living in the community.

INTRODUCTION: Survival after stroke is improving, leading to increased demand on primary care and community services to meet the long-term care needs of people living with stroke. No formal primary care-based holistic model of care with clinical trial evidence exists to support stroke survivors living in the community, and stroke survivors report that many of their needs are not being met. We have developed a multifactorial primary care model to address these longer term needs. We aim to evaluate the clinical and cost-effectiveness of this new model of primary care for stroke survivors compared with standard care. METHODS AND ANALYSIS: Improving Primary Care After Stroke (IPCAS) is a two-arm cluster-randomised controlled trial with general practice as the unit of randomisation. People on the stroke registers of general practices will be invited to participate. One arm will receive the IPCAS model of care including a structured review using a checklist; a self-management programme; enhanced communication pathways between primary care and specialist services; and direct point of contact for patients. The other arm will receive usual care. We aim to recruit 920 people with stroke registered with 46 general practices. The primary endpoint is two subscales (emotion and handicap) of the Stroke Impact Scale (SIS) as coprimary outcomes at 12 months (adjusted for baseline). Secondary outcomes include: SIS Short Form, EuroQol EQ-5D-5L, ICEpop CAPability measure for Adults, Southampton Stroke Self-management Questionnaire, Health Literacy Questionnaire and medication use. Cost-effectiveness of the new model will be determined in a within-trial economic evaluation. ETHICS AND DISSEMINATION: Favourable ethical opinion was gained from Yorkshire and the Humber-Bradford Leeds NHS Research Ethics Committee. Approval to start was given by the Health Research Authority prior to recruitment of participants at any NHS site. Data will be presented at national and international conferences and published in peer-reviewed journals. Patient and public involvement helped develop the dissemination plan. TRIAL REGISTRATION NUMBER: NCT03353519.This study was funded by the National Institute for Health Research’s Programme Grant for Applied Research titled ‘Developing primary care services for stroke survivors’ reference PTC-RP-PG-0213 20001. The chief investigator for the study is JM, University of Cambridge email: [email protected]. The IPCAS trial is cosponsored by the University of Cambridge and NHS Cambridgeshire and Peterborough Clinical Commissioning Group. This research is covered by the Cambridge University's Public Liability and Professional Indemnity policy

Lessons Learned through Research Partnership and Capacity Enhancement in Inuit Nunangat

Facilitating research and enhancing community research capacity through a partnered approach in Inuit Nunangat (the Inuit homeland of Canada, located in Arctic Canada) presents learning opportunities and challenges for southern-based, non-Inuit researchers and community members alike. This article outlines lessons learned through the Arctic Corridors and Northern Voices (AC-NV) project, which involved 14 communities across Inuit Nunangat. The AC-NV focused on understanding community-identified impacts and potential management options of increased shipping in Inuit Nunangat due to sea ice reductions and a changing climate. The approach used to conduct the research involved visiting researchers and community partners working together with local organizations, and training and hiring northern youth as cultural liaisons and workshop co-facilitators. We strove to develop a model of collaborative partnership and strong north-south research relationships. In this paper, we draw on our broad learning experiences from four community case studies conducted as part of the AC-NV project: Arviat, Cambridge Bay, Gjoa Haven, and Pond Inlet, Nunavut. Close partnerships were formed in each of these communities, and 32 youth were trained in participatory mapping and workshop facilitation. For our diverse team of Inuit, northern- (i.e., non-Inuit, living in Inuit Nunangat), and southern-based non-Inuit researchers, our efforts to engage in partnered research were a critical component of the research and learning experience. In this article we share methodological reflections and lessons learned from what collaborative-partnered research means in practice. In so doing, we aim to contribute to the increasing dialogue and efforts around knowledge co-production and Inuit self-determination in research. Key conclusions of this reflective exercise include the importance of 1) conducting research that is relevant to local needs and interests, 2) visiting researchers and local organizations partnering together, 3) co-creating and refining knowledge documentation tools, 4) including youth cultural liaisons as co-facilitators, 5) conducting results validation and sharing exercises, and 6) being open to forming personal friendships. For the AC-NV, this community-based partnership approach resulted in more robust research results, strengthened north-south relations, and enhanced local capacity for community-led projects.Le fait de faciliter la recherche et de rehausser la capacité de recherche communautaire par le biais d’une démarche axée sur les partenariats dans l’Inuit Nunangat (la patrie des Inuits du Canada, dans l’Arctique canadien) présente des occasions d’apprentissage et des défis pour les chercheurs non inuits du Sud et les membres de la communauté. Cet article fait ressortir les leçons apprises grâce au projet « Arctic Corridors and Northern Voices (AC-NV) » ayant fait appel à 14 collectivités de l’Inuit Nunangat. Le projet AC-NV avait pour but de comprendre les incidences cernées par la communauté et les options de gestion éventuelles en matière d’intensification du transport des marchandises dans l’Inuit Nunangat en raison de l’amenuisement de la glace de mer et du changement climatique. La démarche de recherche s’est traduite par un travail mené en collaboration par des chercheurs invités, des partenaires communautaires et des organisations locales, de même que par la formation et l’embauche de jeunes du Nord à titre de liaisons culturelles et de coanimateurs d’ateliers. Nous nous sommes efforcés de concevoir un modèle de partenariat coopératif caractérisé par de solides relations de recherche entre le Nord et le Sud. Dans cet article, nous nous appuyons sur nos vastes expériences d’apprentissage découlant de quatre études de cas communautaires réalisées dans le cadre du projet AC-NV : Arviat, Cambridge Bay, Gjoa Haven et Pond Inlet, au Nunavut. Dans chacune de ces collectivités, des partenariats étroits ont été créés, et 32 jeunes ont été formés en cartographie participative et en animation d’ateliers. Grâce à notre équipe variée composée d’Inuits, de chercheurs du Nord (c’est-à-dire des chercheurs non inuits, mais qui vivent dans l’Inuit Nunangat) et de chercheurs non inuits du Sud, nos efforts de recherche en partenariat ont représenté une composante critique de l’expérience de recherche et d’apprentissage. Dans cet article, nous faisons part de nos réflexions méthodologiques et des leçons que nous avons tirées de la signification pratique de la recherche coopérative en partenariat. Ce faisant, nous voulons faire notre part dans le dialogue de plus en plus prépondérant et dans les efforts relatifs à la coproduction de connaissances et à l’autodétermination des Inuits en matière de recherche. Parmi les grandes conclusions de cet exercice de réflexion, notons l’importance 1) de faire des recherches qui se rapportent aux besoins et aux intérêts locaux, 2) de faire en sorte que les chercheurs invités et les organisations locales travaillent en collaboration, 3) de coproduire et de peaufiner des outils de documentation des connaissances, 4) d’inclure les jeunes à titre de liaisons culturelles et de coanimateurs, 5) de procéder à la validation des résultats et à des exercices de partage, et 6) d’être prêt à nouer des amitiés personnelles. Dans le cas du projet ACNV, la méthode du partenariat communautaire a permis d’obtenir des résultats de recherche plus solides, de renforcer les relations nord-sud et de rehausser la capacité locale en vue de projets communautaires

Internet-based cognitive and behavioural therapies for post-traumatic stress disorder (PTSD) in adults

Background Therapist‐delivered trauma‐focused psychological therapies are effective for post‐traumatic stress disorder (PTSD) and have become the accepted first‐line treatments. Despite the established evidence‐base for these therapies, they are not always widely available or accessible. Many barriers limit treatment uptake, such as the number of qualified therapists available to deliver the interventions; cost; and compliance issues, such as time off work, childcare, and transportation, associated with the need to attend weekly appointments. Delivering Internet‐based cognitive and behavioural therapy (I‐C/BT) is an effective and acceptable alternative to therapist‐delivered treatments for anxiety and depression. Objectives To assess the effects of I‐C/BT for PTSD in adults. Search methods We searched MEDLINE, Embase, PsycINFO and the Cochrane Central Register of Controlled Trials to June 2020. We also searched online clinical trial registries and reference lists of included studies and contacted the authors of included studies and other researchers in the field to identify additional and ongoing studies. Selection criteria We searched for RCTs of I‐C/BT compared to face‐to‐face or Internet‐based psychological treatment, psychoeducation, wait list, or care as usual. We included studies of adults (aged over 16 years), in which at least 70% of the participants met the diagnostic criteria for PTSD, according to the Diagnostic and Statistical Manual (DSM) or the International Classification of Diseases (ICD). Data collection and analysis Two review authors independently assessed abstracts, extracted data, and entered data into Review Manager 5. The primary outcomes were severity of PTSD symptoms and dropouts. Secondary outcomes included diagnosis of PTSD after treatment, severity of depressive and anxiety symptoms, cost‐effectiveness, adverse events, treatment acceptability, and quality of life. We analysed categorical outcomes as risk ratios (RRs), and continuous outcomes as mean differences (MD) or standardised mean differences (SMDs), with 95% confidence intervals (CI). We pooled data using a fixed‐effect meta‐analysis, except where heterogeneity was present, in which case we used a random‐effects model. We independently assessed the included studies for risk of bias and we evaluated the certainty of available evidence using the GRADE approach; we discussed any conflicts with at least one other review author, with the aim of reaching a unanimous decision

New functional families (FunFams) in CATH to improve the mapping of conserved functional sites to 3D structures.

CATH version 3.5 (Class, Architecture, Topology, Homology, available at http://www.cathdb.info/) contains 173 536 domains, 2626 homologous superfamilies and 1313 fold groups. When focusing on structural genomics (SG) structures, we observe that the number of new folds for CATH v3.5 is slightly less than for previous releases, and this observation suggests that we may now know the majority of folds that are easily accessible to structure determination. We have improved the accuracy of our functional family (FunFams) sub-classification method and the CATH sequence domain search facility has been extended to provide FunFam annotations for each domain. The CATH website has been redesigned. We have improved the display of functional data and of conserved sequence features associated with FunFams within each CATH superfamily