Global carbon budget 2013

Accurate assessment of anthropogenic carbon dioxide (CO2) emissions and their redistribution among the atmosphere, ocean, and terrestrial biosphere is important to better understand the global carbon cycle, support the development of climate policies, and project future climate change. Here we describe data sets and a methodology to quantify all major components of the global carbon budget, including their uncertainties, based on the combination of a range of data, algorithms, statistics and model estimates and their interpretation by a broad scientific community. We discuss changes compared to previous estimates, consistency within and among components, alongside methodology and data limitations. CO2 emissions from fossil-fuel combustion and cement production (EFF) are based on energy statistics, while emissions from land-use change (ELUC), mainly deforestation, are based on combined evidence from land-cover change data, fire activity associated with deforestation, and models. The global atmospheric CO2 concentration is measured directly and its rate of growth (GATM) is computed from the annual changes in concentration. The mean ocean CO2 sink (SOCEAN) is based on observations from the 1990s, while the annual anomalies and trends are estimated with ocean models. The variability in SOCEAN is evaluated for the first time in this budget with data products based on surveys of ocean CO2 measurements. The global residual terrestrial CO2 sink (SLAND) is estimated by the difference of the other terms of the global carbon budget and compared to results of independent dynamic global vegetation models forced by observed climate, CO2 and land cover change (some including nitrogen–carbon interactions). All uncertainties are reported as ± 1 σ, reflecting the current capacity to characterise the annual estimates of each component of the global carbon budget. For the last decade available (2003–2012), EFF was 8.6 ± 0.4 GtC yr − 1, ELUC 0.9 ± 0.5 GtC yr − 1, GATM 4.3 ± 0.1 GtC yr − 1, S OCEAN 2.5 ± 0.5 GtC yr − 1, and S LAND 2.8 ± 0.8 GtC yr − 1. For year 2012 alone, EFF grew to 9.7 ± 0.5 GtC yr − 1, 2.2 % above 2011, reflecting a continued growing trend in these emissions, GATM was 5.1 ± 0.2 GtC yr − 1, SOCEANwas 2.9 ± 0.5 GtC yr −1, and assuming an ELU Cof 1.0 ± 0.5 GtC yr − 1 (based on the 2001–2010 average), SLAND was 2.7 ± 0.9 GtC yr − 1. GATM was high in 2012 compared to the 2003–2012 average, almost entirely reflecting the high EFF. The global atmospheric CO2 con- centration reached 392.52 ± 0.10 ppm averaged over 2012. We estimate that EFF will increase by 2.1 % (1.1–3.1 %) to 9.9 ± 0.5 GtC in 2013, 61 % above emissions in 1990, based on projections of world gross domestic product and recent changes in the carbon intensity of the economy. With this projection, cumulative emissions of CO2 will reach about 535 ± 55 GtC for 1870–2013, about 70 % from EFF (390 ± 20 GtC) and 30 % from ELUC (145 ± 50 GtC). This paper also documents any changes in the methods and data sets used in this new carbon budget from previous budgets (Le Quéré et al., 2013). All observations presented here can be downloaded from the Carbon Dioxide Information Analysis Center.

Wet deposition of fossil and non-fossil derived particulate carbon: insights from radiocarbon measurement

Radiocarbon (14C) measurements of both organic carbon (OC) and elemental carbon (EC) allow a more detailed source apportionment, leading to a full and unambiguous distinction and quantification of the contributions from non-fossil and fossil sources. A thermal-optical method with a commercial OC/EC analyzer to isolate water-insoluble OC (WIOC) and EC for their subsequent 14C measurement was applied for the first time to filtered precipitation samples collected at a costal site in Portugal and at a continental site in Switzerland. Our results show that WIOC in precipitation is dominated by non-fossil sources such as biogenic and biomass-burning emissions regardless of rain origins and seasons, whereas EC sources are shared by fossil-fuel combustion and biomass burning. In addition, monthly variation of WIOC in Switzerland was characterized by higher abundance in warm than in cold seasons, highlighting the importance of biogenic emissions to particulate carbon in rainwater. Samples with high particulate carbon concentrations in Portugal were found to be associated with increased biogenic input. Despite the importance of non-fossil sources, fossil emissions account for approximately 20% of particulate carbon in wet deposition for our study, which is in line with fossil contribution in bulk rainwater dissolved organic carbon as well as aerosol WIOC and EC estimated by the 14C approach from other studies.

Cold Microwave-Enabled Protein Detection and Quantification.

Protein screening/detection is an essential tool in many laboratories. Owing to the relatively large time investments that are required by standard protocols, the development of methods with higher throughput while maintaining an at least comparable signal-to-noise ratio is highly beneficial in many research areas. This chapter describes how cold microwave technology can be used to enhance the rate of molecular interactions and provides protocols for dot blots, Western blots, and ELISA procedures permitting a completion of all incubation steps (blocking and antibody steps) within 24-45 min.

Titanium and hydroxyapatite coating of polyetheretherketone and carbon fiber-reinforced polyetheretherketone: A pilot study in sheep

Purpose: The purpose of this study was to evaluate the bone formation capability of polyetheretherketone (PEEK) and carbon fiber-reinforced PEEK (CFR-PEEK) implants coated with different titanium and hydroxyapatite plasma-sprayed layers after 2 and 12 weeks. Methods: In six sheep 108 implants were placed in the pelvis. Altogether six different surface modifications were tested. After 2 and 12 weeks, n = 3 implants per group were examined histologically and n = 6 implants per group were tested by a pull-out test. Results: Biomechanically (p = 0.001) as well as histologically (p > 0.05) surface coating of PEEK/CFR-PEEK led to an increase of osseointegration from 2 to 12 weeks. After 12 weeks, coated implants demonstrated significant (p < 0.001) higher pull-out values in comparison to uncoated implants. Overall, the double coating (titanium bond layer and hydroxyapatite top layer) showed the most favorable results after 2 and 12 weeks. Conclusions: Plasma-sprayed titanium and hydroxyapatite coatings on PEEK or CFR-PEEK demonstrated a significant improvement of osseointegration.

Video-based quantification of body movement indicates negative symptoms: a replication

Objective: In schizophrenia, abnormalities in nonverbal behaviors have always been considered as highly relevant. However, due to methodological limitations, nonverbal behavior was rarely quantified objectively. Recent methodological advances now allow a quantification of body movement from ordinary video recordings. We showed that patients’ objectively measured amount of movement in social role-play interactions was closely associated with their symptom profiles (Kupper, Ramseyer, Hoffmann, & Tschacher, Schizophrenia Research 2010). In the present study, a replication of these results in the context of semi-standardized PANSS (Positive and Negative Syndrome Scale) interviews was intended. Methods: 17 patients with schizophrenia were analyzed during the initial 15-min sequence of a videotaped PANSS interview using Motion Energy Analysis (MEA). The amount of patients’ movement was then correlated with their PANSS symptom scores. Results: Sizeable and significant correlations between negative symptoms and reduced movements (r = -.68, p<0.01) and reduced movement speed (r = -.80, p<0.001) were found. Moreover, cognitive symptoms were related to reduced movement speed (r = -.70, p<.01). Conclusion: Negative symptoms were reliably indicated by patients’ nonverbal behavior in psychopathology interviews. Hence, the main result of our earlier study, examining patients’ nonverbal behavior in role play tests, was replicated for the less structured interactions in psychopathological interviews. Results could encourage the use of MEA in a wide range of videotaped social interactions of patients with schizophrenia and other psychiatric disorders.

Gaseous radiocarbon measurements of small samples

Radiocarbon dating by means of accelerator mass spectrometry (AMS) is a well-established method for samples containing carbon in the milligram range. However, the measurement of small samples containing less than 50 lg carbon often fails. It is difficult to graphitise these samples and the preparation is prone to contamination. To avoid graphitisation, a solution can be the direct measurement of carbon dioxide. The MICADAS, the smallest accelerator for radiocarbon dating in Zurich, is equipped with a hybrid Cs sputter ion source. It allows the measurement of both, graphite targets and gaseous CO2 samples, without any rebuilding. This work presents experiences dealing with small samples containing 1-40 lg carbon. 500 unknown samples of different environmental research fields have been measured yet. Most of the samples were measured with the gas ion source. These data are compared with earlier measurements of small graphite samples. The performance of the two different techniques is discussed and main contributions to the blank determined. An analysis of blank and standard data measured within years allowed a quantification of the contamination, which was found to be of the order of 55 ng and 750 ng carbon (50 pMC) for the gaseous and the graphite samples, respectively. For quality control, a number of certified standards were measured using the gas ion source to demonstrate reliability of the data.

Pulmonary lymphangioleiomyomatosis: analysis of disease manifestation by region-based quantification of lung parenchyma

PURPOSE Lymphangioleiomyomatosis (LAM) is characterized by proliferation of smooth muscle tissue that causes bronchial obstruction and secondary cystic destruction of lung parenchyma. The aim of this study was to evaluate the typical distribution of cystic defects in LAM with quantitative volumetric chest computed tomography (CT). MATERIALS AND METHODS CT examinations of 20 patients with confirmed LAM were evaluated with region-based quantification of lung parenchyma. Additionally, 10 consecutive patients were identified who had recently undergone CT imaging of the lung at our institution, in which no pathologies of the lung were found, to serve as a control group. Each lung was divided into three regions (upper, middle and lower thirds) with identical number of slices. In addition, we defined a "peel" and "core" of the lung comprising the 2 cm subpleural space and the remaining inner lung area. Computerized detection of lung volume and relative emphysema was performed with the PULMO 3D software (v3.42, Fraunhofer MEVIS, Bremen, Germany). This software package enables the quantification of emphysematous lung parenchyma by calculating the pixel index, which is defined as the ratio of lung voxels with a density <-950HU to the total number of voxels in the lung. RESULTS Cystic changes accounted for 0.1-39.1% of the total lung volume in patients with LAM. Disease manifestation in the central lung was significantly higher than in peripheral areas (peel median: 15.1%, core median: 20.5%; p=0.001). Lower thirds of lung parenchyma showed significantly less cystic changes than upper and middle lung areas combined (lower third: median 13.4, upper and middle thirds: median 19.0, p=0.001). CONCLUSION The distribution of cystic lesions in LAM is significantly more pronounced in the central lung compared to peripheral areas. There is a significant predominance of cystic changes in apical and intermediate lung zones compared to the lung bases.

RNA-SEQUENCING APPLICATIONS: GENE EXPRESSION QUANTIFICATION AND METHYLATOR PHENOTYPE IDENTIFICATION

My dissertation focuses on two aspects of RNA sequencing technology. The first is the methodology for modeling the overdispersion inherent in RNA-seq data for differential expression analysis. This aspect is addressed in three sections. The second aspect is the application of RNA-seq data to identify the CpG island methylator phenotype (CIMP) by integrating datasets of mRNA expression level and DNA methylation status. Section 1: The cost of DNA sequencing has reduced dramatically in the past decade. Consequently, genomic research increasingly depends on sequencing technology. However it remains elusive how the sequencing capacity influences the accuracy of mRNA expression measurement. We observe that accuracy improves along with the increasing sequencing depth. To model the overdispersion, we use the beta-binomial distribution with a new parameter indicating the dependency between overdispersion and sequencing depth. Our modified beta-binomial model performs better than the binomial or the pure beta-binomial model with a lower false discovery rate. Section 2: Although a number of methods have been proposed in order to accurately analyze differential RNA expression on the gene level, modeling on the base pair level is required. Here, we find that the overdispersion rate decreases as the sequencing depth increases on the base pair level. Also, we propose four models and compare them with each other. As expected, our beta binomial model with a dynamic overdispersion rate is shown to be superior. Section 3: We investigate biases in RNA-seq by exploring the measurement of the external control, spike-in RNA. This study is based on two datasets with spike-in controls obtained from a recent study. We observe an undiscovered bias in the measurement of the spike-in transcripts that arises from the influence of the sample transcripts in RNA-seq. Also, we find that this influence is related to the local sequence of the random hexamer that is used in priming. We suggest a model of the inequality between samples and to correct this type of bias. Section 4: The expression of a gene can be turned off when its promoter is highly methylated. Several studies have reported that a clear threshold effect exists in gene silencing that is mediated by DNA methylation. It is reasonable to assume the thresholds are specific for each gene. It is also intriguing to investigate genes that are largely controlled by DNA methylation. These genes are called “L-shaped” genes. We develop a method to determine the DNA methylation threshold and identify a new CIMP of BRCA. In conclusion, we provide a detailed understanding of the relationship between the overdispersion rate and sequencing depth. And we reveal a new bias in RNA-seq and provide a detailed understanding of the relationship between this new bias and the local sequence. Also we develop a powerful method to dichotomize methylation status and consequently we identify a new CIMP of breast cancer with a distinct classification of molecular characteristics and clinical features.