Predictions for ASKAP Neutral Hydrogen Surveys

The Australian Square Kilometer Array Pathfinder (ASKAP) will revolutionise our knowledge of gas-rich galaxies in the Universe. Here we present predictions for two proposed extragalactic ASKAP neutral hydrogen (HI) emission-line surveys, based on semi-analytic models applied to cosmological N-body simulations. The ASKAP HI All-Sky Survey, known as WALLABY, is a shallow 3 Pi survey (z = 0 - 0.26) which will probe the mass and dynamics of over 600,000 galaxies. A much deeper small-area HI survey, called DINGO, aims to trace the evolution of HI from z = 0 - 0.43, a cosmological volume of 40 million Mpc^3, detecting potentially 100,000 galaxies. The high-sensitivity 30 antenna ASKAP core (diameter ~2 km) will provide an angular resolution of 30 arcsec (at z=0). Our simulations show that the majority of galaxies detected in WALLABY (87.5%) will be resolved. About 5000 galaxies will be well resolved, i.e. more than five beams (2.5 arcmin) across the major axis, enabling kinematic studies of their gaseous disks. This number would rise to 160,000 galaxies if all 36 ASKAP antennas could be used; the additional six antennas provide baselines up to 6 km, resulting in an angular resolution of 10 arcsec. For DINGO this increased resolution is highly desirable to minimise source confusion; reducing confusion rates from a maximum of 10% of sources at the survey edge to 3%. We estimate that the sources detected by WALLABY and DINGO will span four orders of magnitude in total halo mass (from 10^{11} to 10^{15} Msol) and nearly seven orders of magnitude in stellar mass (from 10^{5} to 10^{12} Msol), allowing us to investigate the process of galaxy formation across the last four billion years.Comment: 21 pages, accepted for publication in MNRAS, minor updates to published version and fixed links. Movies and images available at http://ict.icrar.org/store/Movies/Duffy12c

Tree diversity promotes insect herbivory in subtropical forests of south-east China

1.Insect herbivory can strongly affect ecosystem processes, and its relationship with plant diversity is a central topic in biodiversity–functioning research. However, very little is known about this relationship from complex ecosystems dominated by long-lived individuals, such as forests, especially over gradients of high plant diversity

Can parasites adapt to pollutants? A multigenerational experiment with a Daphnia x Metschnikowia model system exposed to the fungicide tebuconazole

There is increasing evidence about negative effects of fungicides on non-target organisms, including parasitic species, which are key elements in food webs. Previous experiments showed that environmentally relevant concentrations of fungicide tebuconazole are toxic to the microparasite Metschnikowia bicuspidata, a yeast species that infects the planktonic crustacean Daphnia spp. However, due to their short-term nature, this and other experimental studies were not able to test if parasites could potentially adapt to these contaminants. Here, we tested if M. bicuspidata parasite can adapt to tebuconazole selective pressure. Infected D. magna lineages were reared under control conditions (no tebuconazole) and environmentally realistic tebuconazole concentrations, for four generations, and their performance was compared in a follow-up reciprocal assay. Additionally, we assessed whether the observed effects were transient (phenotypic) or permanent (genetic), by reassessing parasite fitness after the removal of selective pressure. Parasite fitness was negatively affected throughout the multigenerational exposure to the fungicide: prevalence of infection and spore load decreased, whereas host longevity increased, in comparison to control (naive) parasite lineages. In a follow-up reciprocal assay, tebuconazole-conditioned (TEB) lineages performed worse than naive parasite lineages, both in treatments without and with tebuconazole, confirming the cumulative negative effect of tebuconazole. The underperformance of TEB lineages was rapidly reversed after removing the influence of the selective pressure (tebuconazole), demonstrating that the costs of prolonged exposure to tebuconazole were phenotypic and transient. The microparasitic yeast M. bicuspidata did not reveal potential for rapid evolution to an anthropogenic selective pressure; instead, the long-term exposure to tebuconazole was hazardous to this non-target species. These findings highlight the potential environmental risks of azole fungicides on non-target parasit- This work was supported by the European Regional Development Fund (programmes COMPETE2020 and PT2020) and by National Funds (Portuguese Science Foundation - FCT, I.P.), through the strategic programmes UID/AMB/50017/2013 and UID/BIA/04050/2019 (POCI-01-0145-FEDER-007569), as well as by the research projects FunG-Eye (POCI-01-0145-FEDER-029505) and EcoAgriFood (NORTE-01-0145-FEDER-000009). Part of the work presented here was developed during the PhD of Ana P. Cuco, who was supported by FCT (PhD grant SFRH/BD/81661/2011). JW was supported by Beethoven Life-1 grant from the German Science Foundation and Polish National Science Center (WO 1587/9-1). Nelson Abrantes is the recipient of an individual postdoctoral research contract (CEECIND/01653/2017)

An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics

For a decade, The Cancer Genome Atlas (TCGA) program collected clinicopathologic annotation data along with multi-platform molecular profiles of more than 11,000 human tumors across 33 different cancer types. TCGA clinical data contain key features representing the democratized nature of the data collection process. To ensure proper use of this large clinical dataset associated with genomic features, we developed a standardized dataset named the TCGA Pan-Cancer Clinical Data Resource (TCGA-CDR), which includes four major clinical outcome endpoints. In addition to detailing major challenges and statistical limitations encountered during the effort of integrating the acquired clinical data, we present a summary that includes endpoint usage recommendations for each cancer type. These TCGA-CDR findings appear to be consistent with cancer genomics studies independent of the TCGA effort and provide opportunities for investigating cancer biology using clinical correlates at an unprecedented scale. Analysis of clinicopathologic annotations for over 11,000 cancer patients in the TCGA program leads to the generation of TCGA Clinical Data Resource, which provides recommendations of clinical outcome endpoint usage for 33 cancer types

Early onset of breast cancer in a group of British black women

Since there are no published data on breast cancer in British black women, we sought to determine whether, like African-American women, they present at a younger age with biologically distinct disease patterns. The method involved a retrospective review of breast cancer to compare age distributions and clinicopathological features between black women and white women in the UK, while controlling for socioeconomic status. All women presented with invasive breast cancer, between 1994 and 2005, to a single East London hospital. Black patients presented significantly younger (median age of 46 years), than white patients (median age of 67 years (P=0.001)). No significant differences between black and white population structures were identified. Black women had a higher frequency of grade 3 tumours, lymph node-positive disease, negative oestrogen receptor and progesterone receptor status and basal-like (triple negative status) tumours. There were no differences in stage at presentation; however, for tumours of ⩽2 cm, black patients had poorer survival than white patients (HR=2.90, 95% CI 0.98–8.60, P=0.05). Black women presented, on average, 21 years younger than white women. Tumours in younger women were considerably more aggressive in the black population, more likely to be basal-like, and among women with smaller tumours, black women were more than twice as likely to die of their disease. There were no disparities in socioeconomic status or treatment received. Our findings could have major implications for the biology of breast cancer and the detection and treatment of the disease in black women

Temporal Dynamics of Intrahost Molecular Evolution for a Plant RNA Virus

[EN] Populations of plant RNA viruses are highly polymorphic in infected plants, which may allow rapid within-host evolution. To understand tobacco etch potyvirus (TEV) evolution, longitudinal samples from experimentally evolved populations in the natural host tobacco and from the alternative host pepper were phenotypically characterized and genetically analyzed. Temporal and compartmental variabilities of TEV populations were quantified using high throughput Illumina sequencing and population genetic approaches. Of the two viral phenotypic traits measured, virulence increased in the novel host but decreased in the original one, and viral load decreased in both hosts, though to a lesser extent in the novel one. Dynamics of population genetic diversity were also markedly different among hosts. Population heterozygosity increased in the ancestral host, with a dominance of synonymous mutations fixed, whereas it did not change or even decreased in the new host, with an excess of nonsynonymous mutations. All together, these observations suggest that directional selection is the dominant evolutionary force in TEV populations evolving in a novel host whereas either diversifying selection or random genetic drift may play a fundamental role in the natural host. To better understand these evolutionary dynamics, we developed a computer simulation model that incorporates the effects of mutation, selection, and drift. Upon parameterization with empirical data from previous studies, model predictions matched the observed patterns, thus reinforcing our idea that the empirical patterns of mutation accumulation represent adaptive evolution.The authors thank Francisca de la Iglesia and Paula Agudo for excellent technical assistance, our labmates for useful discussions and suggestions, and Dr Jose A. Daros for gifting us the pMTEV infectious clone. This work was supported by grants BFU2009-06993 and BFU2012-30805 from the Spanish Ministry of Economy and Competitiveness (MINECO), grant PROMETEOII/2014/021 from Generalitat Valenciana, and by the European Commission 7th Framework Programme (FP7-ICT-611640 FET Proactive: Evolving Living Technologies) EvoEvo project to S.F.E. J.M.C. was supported by a JAE-doc postdoctoral contract from CSIC. A.W. was supported by the EvoEvo project. J.H. was recipient of a predoctoral contract from MINECO. M.P.Z. was supported by a Juan de la Cierva postdoctoral contract from MINECO.Cuevas, JM.; Willemsen, A.; Hillung, J.; Zwart, MP.; Elena Fito, SF. (2015). Temporal Dynamics of Intrahost Molecular Evolution for a Plant RNA Virus. Molecular Biology and Evolution. 32(5):1132-1147. https://doi.org/10.1093/molbev/msv028S1132114732

Monitoring and evaluation of breast cancer screening programmes : Selecting candidate performance indicators

In the scope of the European Commission Initiative on Breast Cancer (ECIBC) the Monitoring and Evaluation (M&E) subgroup was tasked to identify breast cancer screening programme (BCSP) performance indicators, including their acceptable and desirable levels, which are associated with breast cancer (BC) mortality. This paper documents the methodology used for the indicator selection. The indicators were identified through a multi-stage process. First, a scoping review was conducted to identify existing performance indicators. Second, building on existing frameworks for making well-informed health care choices, a specific conceptual framework was developed to guide the indicator selection. Third, two group exercises including a rating and ranking survey were conducted for indicator selection using pre-determined criteria, such as: relevance, measurability, accurateness, ethics and understandability. The selected indicators were mapped onto a BC screening pathway developed by the M&E subgroup to illustrate the steps of BC screening common to all EU countries. A total of 96 indicators were identified from an initial list of 1325 indicators. After removing redundant and irrelevant indicators and adding those missing, 39 candidate indicators underwent the rating and ranking exercise. Based on the results, the M&E subgroup selected 13 indicators: screening coverage, participation rate, recall rate, breast cancer detection rate, invasive breast cancer detection rate, cancers > 20 mm, cancers ≤10 mm, lymph node status, interval cancer rate, episode sensitivity, time interval between screening and first treatment, benign open surgical biopsy rate, and mastectomy rate. This systematic approach led to the identification of 13 BCSP candidate performance indicators to be further evaluated for their association with BC mortality

How Can We Improve Oncofertility Care for Patients? A Systematic Scoping Review of Current International Practice and Models of Care

© The Author(s) 2018. Published by Oxford University Press on behalf of the European Society of Human Reproduction and Embryology. BACKGROUND: Fertility preservation (FP) is an important quality of life issue for cancer survivors of reproductive age. Despite the existence of broad international guidelines, the delivery of oncofertility care, particularly amongst paediatric, adolescent and young adult patients, remains a challenge for healthcare professionals (HCPs). The quality of oncofertility care is variable and the uptake and utilization of FP remains low. Available guidelines fall short in providing adequate detail on how oncofertility models of care (MOC) allow for the real-world application of guidelines by HCPs. OBJECTIVE AND RATIONALE: The aim of this study was to systematically review the literature on the components of oncofertility care as defined by patient and clinician representatives, and identify the barriers, facilitators and challenges, so as to improve the implementation of oncofertility services. SEARCH METHODS: A systematic scoping review was conducted on oncofertility MOC literature published in English between 2007 and 2016, relating to 10 domains of care identified through consumer research: communication, oncofertility decision aids, age-appropriate care, referral pathways, documentation, training, supportive care during treatment, reproductive care after cancer treatment, psychosocial support and ethical practice of oncofertility care. A wide range of electronic databases (CINAHL, Embase, PsycINFO, PubMed, AEIPT, Education Research Complete, ProQuest and VOCED) were searched in order to synthesize the evidence around delivery of oncofertility care. Related citations and reference lists were searched. The review was undertaken following registration (International prospective register of systematic reviews (PROSPERO) registration number CRD42017055837) and guidelines of Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA). OUTCOMES: A total of 846 potentially relevant studies were identified after the removal of duplicates. All titles and abstracts were screened by a single reviewer and the final 147 papers were screened by two reviewers. Ten papers on established MOC were identified amongst the included papers. Data were extracted from each paper and quality scores were then summarized in the oncofertility MOC summary matrix. The results identified a number of themes for improving MOC in each domain, which included: the importance of patients receiving communication that is of a higher quality and in different formats on their fertility risk and FP options; improving provision of oncofertility care in a timely manner; improving access to age-appropriate care; defining the role and scope of practice of all HCPs; and improving communication between different HCPs. Different forms of decision aids were found useful for assisting patients to understand FP options and weigh up choices. WIDER IMPLICATIONS: This analysis identifies core components for delivery of oncofertility MOC. The provision of oncofertility services requires planning to ensure services have safe and reliable referral pathways and that they are age-appropriate and include medical and psychological oncofertility care into the survivorship period. In order for this to happen, collaboration needs to occur between clinicians, allied HCPs and executives within paediatric and adult hospitals, as well as fertility clinics across both public and private services. Training of both cancer and non-cancer HCPs is needed to improve the knowledge of HCPs, the quality of care provided and the confidence of HCPs with these consultations