Implications of sampling design and sample size for national carbon accounting systems

<p>Abstract</p> <p>Background</p> <p>Countries willing to adopt a REDD regime need to establish a national Measurement, Reporting and Verification (MRV) system that provides information on forest carbon stocks and carbon stock changes. Due to the extensive areas covered by forests the information is generally obtained by sample based surveys. Most operational sampling approaches utilize a combination of earth-observation data and in-situ field assessments as data sources.</p> <p>Results</p> <p>We compared the cost-efficiency of four different sampling design alternatives (simple random sampling, regression estimators, stratified sampling, 2-phase sampling with regression estimators) that have been proposed in the scope of REDD. Three of the design alternatives provide for a combination of in-situ and earth-observation data. Under different settings of remote sensing coverage, cost per field plot, cost of remote sensing imagery, correlation between attributes quantified in remote sensing and field data, as well as population variability and the percent standard error over total survey cost was calculated. The cost-efficiency of forest carbon stock assessments is driven by the sampling design chosen. Our results indicate that the cost of remote sensing imagery is decisive for the cost-efficiency of a sampling design. The variability of the sample population impairs cost-efficiency, but does not reverse the pattern of cost-efficiency of the individual design alternatives.</p> <p>Conclusions, brief summary and potential implications</p> <p>Our results clearly indicate that it is important to consider cost-efficiency in the development of forest carbon stock assessments and the selection of remote sensing techniques. The development of MRV-systems for REDD need to be based on a sound optimization process that compares different data sources and sampling designs with respect to their cost-efficiency. This helps to reduce the uncertainties related with the quantification of carbon stocks and to increase the financial benefits from adopting a REDD regime.</p

Improving the value of public RNA-seq expression data by phenotype prediction.

Publicly available genomic data are a valuable resource for studying normal human variation and disease, but these data are often not well labeled or annotated. The lack of phenotype information for public genomic data severely limits their utility for addressing targeted biological questions. We develop an in silico phenotyping approach for predicting critical missing annotation directly from genomic measurements using well-annotated genomic and phenotypic data produced by consortia like TCGA and GTEx as training data. We apply in silico phenotyping to a set of 70 000 RNA-seq samples we recently processed on a common pipeline as part of the recount2 project. We use gene expression data to build and evaluate predictors for both biological phenotypes (sex, tissue, sample source) and experimental conditions (sequencing strategy). We demonstrate how these predictions can be used to study cross-sample properties of public genomic data, select genomic projects with specific characteristics, and perform downstream analyses using predicted phenotypes. The methods to perform phenotype prediction are available in the phenopredict R package and the predictions for recount2 are available from the recount R package. With data and phenotype information available for 70,000 human samples, expression data is available for use on a scale that was not previously feasible

Continuous monitoring of natural CO2 emissions near Rome: lessons for low-level CO2 leakage detection

Continuous monitoring has been carried out at a fluvial flood-plain site near Rome for over a year. There is a mix of biogenic CO2 and deep geogenic CO2 at the site at relatively low concentrations and fluxes compared with other natural CO2 seepage sites studied previously. Factors such as temperature and soil moisture clearly affect the CO2 concentration and flux and seasonal and diurnal influences are apparent. Statistical approaches are being used to try to define these relationships and separate out the two gas components, which would be necessary in any quantification of leakage from CO2 storage

Genome-wide DNA methylation analysis for diabetic nephropathy in type 1 diabetes mellitus

BACKGROUND: Diabetic nephropathy is a serious complication of diabetes mellitus and is associated with considerable morbidity and high mortality. There is increasing evidence to suggest that dysregulation of the epigenome is involved in diabetic nephropathy. We assessed whether epigenetic modification of DNA methylation is associated with diabetic nephropathy in a case-control study of 192 Irish patients with type 1 diabetes mellitus (T1D). Cases had T1D and nephropathy whereas controls had T1D but no evidence of renal disease. METHODS: We performed DNA methylation profiling in bisulphite converted DNA from cases and controls using the recently developed Illumina Infinium(R) HumanMethylation27 BeadChip, that enables the direct investigation of 27,578 individual cytosines at CpG loci throughout the genome, which are focused on the promoter regions of 14,495 genes. RESULTS: Singular Value Decomposition (SVD) analysis indicated that significant components of DNA methylation variation correlated with patient age, time to onset of diabetic nephropathy, and sex. Adjusting for confounding factors using multivariate Cox-regression analyses, and with a false discovery rate (FDR) of 0.05, we observed 19 CpG sites that demonstrated correlations with time to development of diabetic nephropathy. Of note, this included one CpG site located 18 bp upstream of the transcription start site of UNC13B, a gene in which the first intronic SNP rs13293564 has recently been reported to be associated with diabetic nephropathy. CONCLUSION: This high throughput platform was able to successfully interrogate the methylation state of individual cytosines and identified 19 prospective CpG sites associated with risk of diabetic nephropathy. These differences in DNA methylation are worthy of further follow-up in replication studies using larger cohorts of diabetic patients with and without nephropathy

Results from the Wide Angle Search for Planets Prototype (WASP0) II: Stellar Variability in the Pegasus Field

Recent wide-field photometric surveys which target a specific field for long durations are ideal for studying both long and short period stellar variability. Here we report on 75 variable stars detected during observations of a field in Pegasus using the WASP0 instrument, 73 of which are new discoveries. The variables detected include 16 delta Scuti stars, 34 eclipsing binaries, 3 BY Draconis stars, and 4 RR Lyraes. We estimate that the fraction of stars in the field brighter than V ~ 13.5 exhibiting variable behaviour with an amplitude greater than 0.6% rms is ~ 0.4%. These results are compared with other wide-field stellar variability surveys and implications for detecting transits due to extra-solar planets are discussed.Comment: 10 pages, 8 figures, published in MNRA

Introductory programming: a systematic literature review

As computing becomes a mainstream discipline embedded in the school curriculum and acts as an enabler for an increasing range of academic disciplines in higher education, the literature on introductory programming is growing. Although there have been several reviews that focus on specific aspects of introductory programming, there has been no broad overview of the literature exploring recent trends across the breadth of introductory programming. This paper is the report of an ITiCSE working group that conducted a systematic review in order to gain an overview of the introductory programming literature. Partitioning the literature into papers addressing the student, teaching, the curriculum, and assessment, we explore trends, highlight advances in knowledge over the past 15 years, and indicate possible directions for future research

Photo-a-day: a digital photographic practice and its impact on wellbeing

The practice of taking and sharing one photo every day for a year, has become a popular new form of photography enabled by the Internet. The purpose of this study was to investigate how people use photo-a-day to enhance their wellbeing. The data for the study were sixteen interviews with people who practised photo-a-day, analysed by thematic analysis. The analysis showed how photos offer positive affordances because of the conventions to take aesthetically pleasing images, share positive events and comment positively. A seemingly simple activity, photo-a-day creates a new layer of interest woven around daily activities, and expands social relationships. Representations of identity are complex, emerging through photos taken, rather than a premeditated profile

Tourists' consumption and interpretation of sport event imagery

In an era when popular and mass cultures are positioned further up the symbolic hierarchy, sport events are deemed by cities to be a valuable image or branding tools. Event strategies are often justified by their envisaged image effects and the celebrities, iconic structures and media exposure associated with sport events means that they are viewed as being particularly effective for this purpose. This paper evaluates the image effects of strategies deployed by three English cities; Birmingham, Manchester and Sheffield. Each of these cities has used a combination of regular sport fixtures, ‘mega’ sport events and event bids to further their reputations as tourist destinations. Semi-structured interviews with a representative sample of potential tourists were used to provide evidence of the impacts of these initiatives. Despite some participants making connections with traffic chaos and violence, in general sport events appear to have encouraged positive connotations amongst potential tourists, including modernity, progress and vitality. Events seem to be regarded favourably at a cultural level, generating widespread positive meanings even when individual preferences vary. This has positive implications for cities deploying sport events as re-imaging or branding tools

Defects in ErbB-Dependent Establishment of Adult Melanocyte Stem Cells Reveal Independent Origins for Embryonic and Regeneration Melanocytes

Adult stem cells are responsible for maintaining and repairing tissues during the life of an organism. Tissue repair in humans, however, is limited compared to the regenerative capabilities of other vertebrates, such as the zebrafish (Danio rerio). An understanding of stem cell mechanisms, such as how they are established, their self-renewal properties, and their recruitment to produce new cells is therefore important for the application of regenerative medicine. We use larval melanocyte regeneration following treatment with the melanocytotoxic drug MoTP to investigate these mechanisms in Melanocyte Stem Cell (MSC) regulation. In this paper, we show that the receptor tyrosine kinase, erbb3b, is required for establishing the adult MSC responsible for regenerating the larval melanocyte population. Both the erbb3b mutant and wild-type fish treated with the ErbB inhibitor, AG1478, develop normal embryonic melanocytes but fail to regenerate melanocytes after MoTP-induced melanocyte ablation. By administering AG1478 at different time points, we show that ErbB signaling is only required for regeneration prior to MoTP treatment and before 48 hours of development, consistent with a role in establishing MSCs. We then show that overexpression of kitla, the Kit ligand, in transgenic larvae leads to recruitment of MSCs, resulting in overproliferation of melanocytes. Furthermore, kitla overexpression can rescue AG1478-blocked regeneration, suggesting that ErbB signaling is required to promote the progression and specification of the MSC from a pre–MSC state. This study provides evidence that ErbB signaling is required for the establishment of adult MSCs during embryonic development. That this requirement is not shared with the embryonic melanocytes suggests that embryonic melanocytes develop directly, without proceeding through the ErbB-dependent MSC. Moreover, the shared requirement of larval melanocyte regeneration and metamorphic melanocytes that develops at the larval-to-adult transition suggests that these post-embryonic melanocytes develop from the same adult MSC population. Lastly, that kitla overexpression can recruit the MSC to develop excess melanocytes raises the possibility that Kit signaling may be involved in MSC recruitment during regeneration