Apples and pears? A comparison of two sources of national lung cancer audit data in England

In 2014, the method of data collection from NHS trusts in England for the National Lung Cancer Audit (NLCA) was changed from a bespoke dataset called LUCADA (Lung Cancer Data). Under the new contract, data are submitted via the Cancer Outcome and Service Dataset (COSD) system and linked additional cancer registry datasets. In 2014, trusts were given opportunity to submit LUCADA data as well as registry data. 132 NHS trusts submitted LUCADA data, and all 151 trusts submitted COSD data. This transitional year therefore provided the opportunity to compare both datasets for data completeness and reliability. We linked the two datasets at the patient level to assess the completeness of key patient and treatment variables. We also assessed the interdata agreement of these variables using Cohen’s kappa statistic, κ. We identified 26 001 patients in both datasets. Overall, the recording of sex, age, performance status and stage had more than 90% agreement between datasets, but there were more patients with missing performance status in the registry dataset. Although levels of agreement for surgery, chemotherapy and external-beam radiotherapy were high between datasets, the new COSD system identified more instances of active treatment. There seems to be a high agreement of data between the datasets, and the findings suggest that the registry dataset coupled with COSD provides a richer dataset than LUCADA. However, it lagged behind LUCADA in performance status recording, which needs to improve over time

Increased dry-season length over southern Amazonia in recent decades and its implication for future climate projection

RESUMEN: We have observed that the dry-season length (DSL) has increased over southern Amazonia since 1979, primarily owing to a delay of its ending dates (dry-season end, DSE), and is accompanied by a prolonged fire season. A poleward shift of the subtropical jet over South America and an increase of local convective inhibition energy in austral winter (June–August) seem to cause the delay of the DSE in austral spring (September–November). These changes cannot be simply linked to the variability of the tropical Pacific and Atlantic Oceans. Although they show some resemblance to the effects of anthropogenic forcings reported in the literature, we cannot attribute them to this cause because of inadequate representation of these processes in the global climate models that were presented in the Intergovernmental Panel on Climate Change’s Fifth Assessment Report. These models significantly underestimate the variability of the DSE and DSL and their controlling processes. Such biases imply that the future change of the DSE and DSL may be underestimated by the climate projections provided by the Intergovernmental Panel on Climate Change’s Fifth Assessment Report models. Although it is not clear whether the observed increase of the DSL will continue in the future, were it to continue at half the rate of that observed, the long DSL and fire season that contributed to the 2005 drought would become the new norm by the late 21st century. The large uncertainty shown in this study highlights the need for a focused effort to better understand and simulate these changes over southern Amazonia

A Low-Diversity Microbiota Inhabits Extreme Terrestrial Basaltic Terrains and Their Fumaroles : Implications for the Exploration of Mars

A major objective in the exploration of Mars is to test the hypothesis that the planet hosted life. Even in the absence of life, the mapping of habitable and uninhabitable environments is an essential task in developing a complete understanding of the geological and aqueous history of Mars and, as a consequence, understanding what factors caused Earth to take a different trajectory of biological potential. We carried out the aseptic collection of samples and comparison of the bacterial and archaeal communities associated with basaltic fumaroles and rocks of varying weathering states in Hawai'i to test four hypotheses concerning the diversity of life in these environments. Using high-throughput sequencing, we found that all these materials are inhabited by a low-diversity biota. Multivariate analyses of bacterial community data showed a clear separation between sites that have active fumaroles and other sites that comprised relict fumaroles, unaltered, and syn-emplacement basalts. Contrary to our hypothesis that high water flow environments, such as fumaroles with active mineral leaching, would be sites of high biological diversity, alpha diversity was lower in active fumaroles compared to relict or nonfumarolic sites, potentially due to high-temperature constraints on microbial diversity in fumarolic sites. A comparison of these data with communities inhabiting unaltered and weathered basaltic rocks in Idaho suggests that bacterial taxon composition of basaltic materials varies between sites, although the archaeal communities were similar in Hawai'i and Idaho. The taxa present in both sites suggest that most of them obtain organic carbon compounds from the atmosphere and from phototrophs and that some of them, including archaeal taxa, cycle fixed nitrogen. The low diversity shows that, on Earth, extreme basaltic terrains are environments on the edge of sustaining life with implications for the biological potential of similar environments on Mars and their exploration by robots and humans.Peer reviewe

From waste to food : optimising the breakdown of oil palm waste to provide substrate for insects farmed as animal feed

Waste biomass from the palm oil industry is currently burned as a means of disposal and solutions are required to reduce the environmental impact. Whilst some waste biomass can be recycled to provide green energy such as biogas, this investigation aimed to optimise experimental conditions for recycling palm waste into substrate for insects, farmed as a sustainable high-protein animal feed. NMR spectroscopy and LC-HRMS were used to analyse the composition of palm empty fruit bunches (EFB) under experimental conditions optimised to produce nutritious substrate rather than biogas. Statistical pattern recognition techniques were used to investigate differences in composition for various combinations of pre-processing and anaerobic digestion (AD) methods. Pre-processing methods included steaming, pressure cooking, composting, microwaving, and breaking down the EFB using ionic liquids. AD conditions which were modified in combination with pre-processing methods were ratios of EFB:digestate and pH. Results show that the selection of pre-processing method affects the breakdown of the palm waste and subsequently the substrate composition and biogas production. Although large-scale insect feeding trials will be required to determine nutritional content, we found that conditions can be optimised to recycle palm waste for the production of substrate for insect rearing. Pre-processing EFB using ionic liquid before AD at pH6 with a 2:1 digestate:EFB ratio were found to be the best combination of experimental conditions

Mendelian gene identification through mouse embryo viability screening.

BACKGROUND: The diagnostic rate of Mendelian disorders in sequencing studies continues to increase, along with the pace of novel disease gene discovery. However, variant interpretation in novel genes not currently associated with disease is particularly challenging and strategies combining gene functional evidence with approaches that evaluate the phenotypic similarities between patients and model organisms have proven successful. A full spectrum of intolerance to loss-of-function variation has been previously described, providing evidence that gene essentiality should not be considered as a simple and fixed binary property. METHODS: Here we further dissected this spectrum by assessing the embryonic stage at which homozygous loss-of-function results in lethality in mice from the International Mouse Phenotyping Consortium, classifying the set of lethal genes into one of three windows of lethality: early, mid, or late gestation lethal. We studied the correlation between these windows of lethality and various gene features including expression across development, paralogy and constraint metrics together with human disease phenotypes. We explored a gene similarity approach for novel gene discovery and investigated unsolved cases from the 100,000 Genomes Project. RESULTS: We found that genes in the early gestation lethal category have distinct characteristics and are enriched for genes linked with recessive forms of inherited metabolic disease. We identified several genes sharing multiple features with known biallelic forms of inborn errors of the metabolism and found signs of enrichment of biallelic predicted pathogenic variants among early gestation lethal genes in patients recruited under this disease category. We highlight two novel gene candidates with phenotypic overlap between the patients and the mouse knockouts. CONCLUSIONS: Information on the developmental period at which embryonic lethality occurs in the knockout mouse may be used for novel disease gene discovery that helps to prioritise variants in unsolved rare disease cases

Differential IRF8 Transcription Factor Requirement Defines Two Pathways of Dendritic Cell Development in Humans

The formation of mammalian dendritic cells (DCs) is controlled by multiple hematopoietic transcription factors, including IRF8. Loss of IRF8 exerts a differential effect on DC subsets, including plasmacytoid DCs (pDCs) and the classical DC lineages cDC1 and cDC2. In humans, cDC2-related subsets have been described including AXL+ SIGLEC6+ pre-DC, DC2 and DC3. The origin of this heterogeneity is unknown. Using highdimensional analysis, in vitro differentiation, and an allelic series of human IRF8 deficiency, we demonstrated that cDC2 (CD1c+ DC) heterogeneity originates from two distinct pathways of development. The lymphoidprimed IRF8hi pathway, marked by CD123 and BTLA, carried pDC, cDC1, and DC2 trajectories, while the common myeloid IRF8lo pathway, expressing SIRPA, formed DC3s and monocytes. We traced distinct trajectories through the granulocyte-macrophage progenitor (GMP) compartment showing that AXL+ SIGLEC6+ pre-DCs mapped exclusively to the DC2 pathway. In keeping with their lower requirement for IRF8, DC3s expand to replace DC2s in human partial IRF8 deficiency

Variable responses of individual species to tropical forest degradation

The functional stability of ecosystems depends greatly on interspecific differences in responses to environmental perturbation. However, responses to perturbation are not necessarily invariant among populations of the same species, so intraspecific variation in responses might also contribute. Such inter-population response diversity has recently been shown to occur spatially across species ranges, but we lack estimates of the extent to which individual populations across an entire community might have perturbation responses that vary through time. We assess this using 524 taxa that have been repeatedly surveyed for the effects of tropical forest logging at a focal landscape in Sabah, Malaysia. Just 39 % of taxa – all with non-significant responses to forest degradation – had invariant responses. All other taxa (61 %) showed significantly different responses to the same forest degradation gradient across surveys, with 6 % of taxa responding to forest degradation in opposite directions across multiple surveys. Individual surveys had low power (< 80 %) to determine the correct direction of response to forest degradation for one-fifth of all taxa. Recurrent rounds of logging disturbance increased the prevalence of intra-population response diversity, while uncontrollable environmental variation and/or turnover of intraspecific phenotypes generated variable responses in at least 44 % of taxa. Our results show that the responses of individual species to local environmental perturbations are remarkably flexible, likely providing an unrealised boost to the stability of disturbed habitats such as logged tropical forests

Proceedings of Patient Reported Outcome Measure’s (PROMs) Conference Oxford 2017: Advances in Patient Reported Outcomes Research

A33-Effects of Out-of-Pocket (OOP) Payments and Financial Distress on Quality of Life (QoL) of People with Parkinson’s (PwP) and their Carer