Abstract
The Astropy Project supports and fosters the development of open-source and openly developed
Python
packages that provide commonly needed functionality to the astronomical community. A key ...element of the Astropy Project is the core package
astropy
, which serves as the foundation for more specialized projects and packages. In this article, we provide an overview of the organization of the Astropy project and summarize key features in the core package, as of the recent major release, version 2.0. We then describe the project infrastructure designed to facilitate and support development for a broader ecosystem of interoperable packages. We conclude with a future outlook of planned new features and directions for the broader Astropy Project.
Summary
The North Wyke Farm Platform was established as a United Kingdom national capability for collaborative research, training and knowledge exchange in agro‐environmental sciences. Its remit is ...to research agricultural productivity and ecosystem responses to different management practices for beef and sheep production in lowland grasslands. A system based on permanent pasture was implemented on three 21‐ha farmlets to obtain baseline data on hydrology, nutrient cycling and productivity for 2 years. Since then two farmlets have been modified by either (i) planned reseeding with grasses that have been bred for enhanced sugar content or deep‐rooting traits or (ii) sowing grass and legume mixtures to reduce nitrogen fertilizer inputs. The quantities of nutrients that enter, cycle within and leave the farmlets were evaluated with data recorded from sensor technologies coupled with more traditional field study methods. We demonstrate the potential of the farm platform approach with a case study in which we investigate the effects of the weather, field topography and farm management activity on surface runoff and associated pollutant or nutrient loss from soil. We have the opportunity to do a full nutrient cycling analysis, taking account of nutrient transformations in soil, and flows to water and losses to air. The NWFP monitoring system is unique in both scale and scope for a managed land‐based capability that brings together several technologies that allow the effect of temperate grassland farming systems on soil moisture levels, runoff and associated water quality dynamics to be studied in detail.
Highlights
Can meat production systems be developed that are productive yet minimize losses to the environment?
The data are from an intensively instrumented capability, which is globally unique and topical.
We use sensing technologies and surveys to show the effect of pasture renewal on nutrient losses.
Platforms provide evidence of the effect of meteorology, topography and farm activity on nutrient loss.
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BFBNIB, FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SAZU, SBCE, SBMB, UL, UM, UPUK
► We review soil issues relevant to global food security and ecosystem functioning. ► We suggest actions for each issue including policies, communication or research. ► Organic matter content is ...essential for improving many soil physical properties. ► Policies to make fertilizers affordable in developing countries are essential. ► Practices to cut greenhouse gas emissions from intensified agriculture are needed.
Requirements for research, practices and policies affecting soil management in relation to global food security are reviewed. Managing soil organic carbon (C) is central because soil organic matter influences numerous soil properties relevant to ecosystem functioning and crop growth. Even small changes in total C content can have disproportionately large impacts on key soil physical properties. Practices to encourage maintenance of soil C are important for ensuring sustainability of all soil functions. Soil is a major store of C within the biosphere – increases or decreases in this large stock can either mitigate or worsen climate change. Deforestation, conversion of grasslands to arable cropping and drainage of wetlands all cause emission of C; policies and international action to minimise these changes are urgently required. Sequestration of C in soil can contribute to climate change mitigation but the real impact of different options is often misunderstood. Some changes in management that are beneficial for soil C, increase emissions of nitrous oxide (a powerful greenhouse gas) thus cancelling the benefit. Research on soil physical processes and their interactions with roots can lead to improved and novel practices to improve crop access to water and nutrients. Increased understanding of root function has implications for selection and breeding of crops to maximise capture of water and nutrients. Roots are also a means of delivering natural plant-produced chemicals into soil with potentially beneficial impacts. These include biocontrol of soil-borne pests and diseases and inhibition of the nitrification process in soil (conversion of ammonium to nitrate) with possible benefits for improved nitrogen use efficiency and decreased nitrous oxide emission. The application of molecular methods to studies of soil organisms, and their interactions with roots, is providing new understanding of soil ecology and the basis for novel practical applications. Policy makers and those concerned with development of management approaches need to keep a watching brief on emerging possibilities from this fast-moving area of science. Nutrient management is a key challenge for global food production: there is an urgent need to increase nutrient availability to crops grown by smallholder farmers in developing countries. Many changes in practices including inter-cropping, inclusion of nitrogen-fixing crops, agroforestry and improved recycling have been clearly demonstrated to be beneficial: facilitating policies and practical strategies are needed to make these widely available, taking account of local economic and social conditions. In the longer term fertilizers will be essential for food security: policies and actions are needed to make these available and affordable to small farmers. In developed regions, and those developing rapidly such as China, strategies and policies to manage more precisely the necessarily large flows of nutrients in ways that minimise environmental damage are essential. A specific issue is to minimise emissions of nitrous oxide whilst ensuring sufficient nitrogen is available for adequate food production. Application of known strategies (through either regulation or education), technological developments, and continued research to improve understanding of basic processes will all play a part. Decreasing soil erosion is essential, both to maintain the soil resource and to minimise downstream damage such as sedimentation of rivers with adverse impacts on fisheries. Practical strategies are well known but often have financial implications for farmers. Examples of systems for paying one group of land users for ecosystem services affecting others exist in several parts of the world and serve as a model.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UL, UM, UPCLJ, UPUK
4.
Oral bacteria and cancer Whitmore, Sarah E; Lamont, Richard J
PLOS pathogens,
03/2014, Volume:
10, Issue:
3
Journal Article
Peer reviewed
Open access
OSCC surfaces have been reported to harbor significantly higher levels of Porphyromonas and Fusobacterium compared with contiguous healthy mucosa 3. ...immunohistochemistry with P. gingivalis ...antibodies revealed higher levels of detection and intensity of staining in gingival carcinomas compared with healthy gingival tissue, although only a small number of cases were examined 4. MMP-9 degrades basement membrane and extracellular matrix, which promotes carcinoma cell migration and invasion, thus allowing carcinoma cells to enter the lymphatic system and blood vessels for dissemination and metastatic growth at remote sites. ...since well-characterized virulence factors of P. gingivalis and F. nucleatum, such as the FimA and FadA adhesins, may function as effector molecules in the transition of normal epithelial cells to cancerous cells, they may provide novel targets for therapeutic intervention.
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DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
A catalogue of molecular aberrations that cause ovarian cancer is critical for developing and deploying therapies that will improve patients' lives. The Cancer Genome Atlas project has analysed ...messenger RNA expression, microRNA expression, promoter methylation and DNA copy number in 489 high-grade serous ovarian adenocarcinomas and the DNA sequences of exons from coding genes in 316 of these tumours. Here we report that high-grade serous ovarian cancer is characterized by TP53 mutations in almost all tumours (96%); low prevalence but statistically recurrent somatic mutations in nine further genes including NF1, BRCA1, BRCA2, RB1 and CDK12; 113 significant focal DNA copy number aberrations; and promoter methylation events involving 168 genes. Analyses delineated four ovarian cancer transcriptional subtypes, three microRNA subtypes, four promoter methylation subtypes and a transcriptional signature associated with survival duration, and shed new light on the impact that tumours with BRCA1/2 (BRCA1 or BRCA2) and CCNE1 aberrations have on survival. Pathway analyses suggested that homologous recombination is defective in about half of the tumours analysed, and that NOTCH and FOXM1 signalling are involved in serous ovarian cancer pathophysiology.
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DOBA, IJS, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
The human retina is a complex tissue responsible for detecting photons of light and converting information from these photons into the neurochemical signals interpreted as vision. Such visual ...signaling not only requires sophisticated interactions between multiple classes of neurons, but also spatially-dependent molecular specialization of individual cell types. In this study, we performed single-cell RNA sequencing on neural retina isolated from both the fovea and peripheral retina in three human donors. We recovered a total of 8,217 cells, with 3,578 cells originating from the fovea and 4,639 cells originating from the periphery. Expression profiles for all major retinal cell types were compiled, and differential expression analysis was performed between cells of foveal versus peripheral origin. Globally, mRNA for the serum iron binding protein transferrin (TF), which has been associated with age-related macular degeneration pathogenesis, was enriched in peripheral samples. Cone photoreceptor cells were of particular interest and formed two predominant clusters based on gene expression. One cone cluster had 96% of cells originating from foveal samples, while the second cone cluster consisted exclusively of peripherally isolated cells. A total of 148 genes were differentially expressed between cones from the fovea versus periphery. Interestingly, peripheral cones were enriched for the gene encoding Beta-Carotene Oxygenase 2 (BCO2). A relative deficiency of this enzyme may account for the accumulation of carotenoids responsible for yellow pigment deposition within the macula. Overall, this data set provides rich expression profiles of the major human retinal cell types and highlights transcriptomic features that distinguish foveal and peripheral cells.
Display omitted
•Gene expression characterization of human retinal cell types.•Foveal and peripheral retinal cell types have distinct gene expression patterns.•Transferrin is enriched in peripheral retina cell types.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
Purpose We compared the efficacy and safety of the currently recommended dose of pentosan polysulfate sodium with a third of the daily dose and with placebo. Materials and Methods In this ...multicenter, double-blind, randomized, placebo controlled study 368 adults with interstitial cystitis/bladder pain syndrome, defined as an ICSI total score of 8 or greater and a score of greater than 0 on the 4 ICSI component items, received pentosan polysulfate sodium 100 mg once daily or 3 times daily, or matching placebo for 24 weeks. Study eligibility was not based on cystoscopy findings. ICSI was administered at baseline, and at weeks 4, 8, 12, 18 and 24. Unblinded interim analysis performed at 6 years with 54% of the target number of 645 patients enrolled resulted in early study termination. Results There was no statistically significant difference between the pentosan polysulfate sodium group and the placebo group or between the 2 pentosan polysulfate sodium groups for the primary end point, defined as responder achieving a 30% or greater reduction from the baseline ICSI total score at study end. This primary end point was achieved by 48 of 118 patients (40.7%) in the placebo group, and by 51 of 128 (39.8%) and 52 of 122 (42.6%) in the pentosan polysulfate sodium 100 mg once daily and 3 times daily groups, respectively. Pentosan polysulfate sodium was well tolerated with a similar percent of patients (range 10.2% to 13.3%) across the groups discontinuing due to an adverse event. Conclusions Results of this study in a broad population of patients with symptoms consistent with interstitial cystitis revealed no treatment effect vs placebo for pentosan polysulfate sodium at the currently established dose or at a third of the daily dose.
This paper describes an agricultural model (Roth-CNP) that estimates carbon (C), nitrogen (N) and phosphorus (P) pools, pool changes, their balance and the nutrient fluxes exported from arable and ...grassland systems in the UK during 1800–2010. The Roth-CNP model was developed as part of an Integrated Model (IM) to simulate C, N and P cycling for the whole of UK, by loosely coupling terrestrial, hydrological and hydro-chemical models. The model was calibrated and tested using long term experiment (LTE) data from Broadbalk (1843) and Park Grass (1856) at Rothamsted. We estimated C, N and P balance and their fluxes exported from arable and grassland systems on a 5km×5km grid across the whole of UK by using the area of arable of crops and livestock numbers in each grid and their management. The model estimated crop and grass yields, soil organic carbon (SOC) stocks and nutrient fluxes in the form of NH4-N, NO3-N and PO4-P. The simulated crop yields were compared to that reported by national agricultural statistics for the historical to the current period. Overall, arable land in the UK have lost SOC by −0.18, −0.25 and −0.08MgCha−1y−1 whereas land under improved grassland SOC stock has increased by 0.20, 0.47 and 0.24MgCha−1y−1 during 1800–1950, 1950–1970 and 1970–2010 simulated in this study. Simulated N loss (by leaching, runoff, soil erosion and denitrification) increased both under arable (−15, −18 and −53kgNha−1y−1) and grass (−18, −22 and −36kgNha−1y−1) during different time periods. Simulated P surplus increased from 2.6, 10.8 and 18.1kgPha−1y−1 under arable and 2.8, 11.3 and 3.6kgPha−1y−1 under grass lands 1800–1950, 1950–1970 and 1970–2010.
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•Roth-CNP model estimates C, N and P cycling within the UK agriculture for 1800–2010.•Simulated crop yields were comparable to the yields of UK's agricultural statistics.•Simulated SOC stock decreased under arable and increased under improved grassland.•Simulated N and P losses increased under both arable and grasslands.•Results shows the effect of local agriculture in a larger context of space and time.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UL, UM, UPCLJ, UPUK, ZRSKP
Context
The concept of landscape heterogeneity is central to species conservation; yet understanding the processes by which heterogeneity affects species can be challenging in practice. Complex and ...sometimes difficult-to-measure responses of species may reflect the outcome of life-history trade-offs shaped by different landscape properties.
Objectives
We tested the hypothesis that a mosaic of forest stand types affected hunting and breeding success for California spotted owls (
Strix occidentailis occidentalis
).
Methods
We integrated high-temporal-resolution GPS tags, video monitoring of nest sites, long-term assessments of reproductive status, and high-resolution remotely sensed vegetation data in a mixed-ownership landscape in the Sierra Nevada, California to test our hypothesis.
Results
Spotted owls made shorter nocturnal movements in homogenous territories with large areas of medium-aged forest apparently because this forest type allowed direct movement paths to foraging sites. However, spotted owls delivered prey at a higher rate to nest sites when they had more forest edge in their territory, which presumably provided greater access to large-bodied woodrat (
Neotoma
spp.) prey. Further, spotted owl reproductive output was relatively high in heterogenous territories containing a mix of mature and open forest.
Conclusions
The benefits heterogenous forests provide to hunting success appeared to outweigh costs associated with additional commuting distance to foraging sites and provided potential fitness benefits to spotted owls. We suggest that the effects of landscape heterogeneity can vary not only among, but also within, species and can reflect the outcome of trade-offs among different life history activities. Understanding the effects of landscape properties on biological communities will benefit from additional empirical and mechanistic studies of individual species.
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EMUNI, FIS, FZAB, GEOZS, GIS, IJS, IMTLJ, KILJ, KISLJ, MFDPS, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, SBMB, SBNM, UKNU, UL, UM, UPUK, VKSCE, ZAGLJ
► Scope for increasing UK SOC by reduced tillage at best 310
±
180
kg
C
ha
−1
yr
−1. ► Potential sequestration from added OM largely limited by availability and current use. ► Many activities that ...benefit SOC are a part of current practice. ► Green compost offers greatest potential to increase SOC stock. ► Benefits from increasing soil carbon may be offset by N
2O emissions.
Results from the UK were reviewed to quantify the impact on climate change mitigation of soil organic carbon (SOC) stocks as a result of (1) a change from conventional to less intensive tillage and (2) addition of organic materials including farm manures, digested biosolids, cereal straw, green manure and paper crumble. The average annual increase in SOC deriving from reduced tillage was 310
kg C
±
180
kg
C
ha
−1
yr
−1. Even this accumulation of C is unlikely to be achieved in the UK and northwest Europe because farmers practice rotational tillage. N
2O emissions may increase under reduced tillage, counteracting increases in SOC. Addition of biosolids increased SOC (in
kg
C
ha
−1
yr
−1
t
−1 dry solids added) by on average 60
±
20 (farm manures), 180
±
24 (digested biosolids), 50
±
15 (cereal straw), 60
±
10 (green compost) and an estimated 60 (paper crumble). SOC accumulation declines in long-term experiments (>50 yr) with farm manure applications as a new equilibrium is approached. Biosolids are typically already applied to soil, so increases in SOC cannot be regarded as mitigation. Large increases in SOC were deduced for paper crumble (>6
t
C
ha
−1
yr
−1) but outweighed by N
2O emissions deriving from additional fertiliser. Compost offers genuine potential for mitigation because application replaces disposal to landfill; it also decreases N
2O emission.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UL, UM, UPCLJ, UPUK
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