Integrated Disaster Reduction Approach: LforS Learning and Simulation Game

Main objective of the game is to increase the coping capacity of players and familiarise them with the Integrated Disaster Reduction Approach. The game is intended to prepare for and introduce the players to a subsequent Learning for Sustainability capacity building workshop for community leaders. The game represents a typical emergency situation resulting from a natural disaster. Before and after the event, adequate measures help to prevent or minimise potential damages. Once a disaster has occurred, concerted actions and immediate measures need to be taken to rescue as much as possible (human lives, livestock, material) and safeguard the village against further damage and losses. In the course of the game, each playing team can proof its knowledge on adequate measures that have to be taken in order to avoid or reduce losses related to natural disasters. Such measures relate to assessment and monitoring of risks, prevention and mitigation measures, preparedness and response as well as recovery and reconstruction.

Temporal trends in the systemic inflammatory response syndrome, sepsis, and medical coding of sepsis.

BACKGROUND Recent reports using administrative claims data suggest the incidence of community- and hospital-onset sepsis is increasing. Whether this reflects changing epidemiology, more effective diagnostic methods, or changes in physician documentation and medical coding practices is unclear. METHODS We performed a temporal-trend study from 2008 to 2012 using administrative claims data and patient-level clinical data of adult patients admitted to Barnes-Jewish Hospital in St. Louis, Missouri. Temporal-trend and annual percent change were estimated using regression models with autoregressive integrated moving average errors. RESULTS We analyzed 62,261 inpatient admissions during the 5-year study period. 'Any SIRS' (i.e., SIRS on a single calendar day during the hospitalization) and 'multi-day SIRS' (i.e., SIRS on 3 or more calendar days), which both use patient-level data, and medical coding for sepsis (i.e., ICD-9-CM discharge diagnosis codes 995.91, 995.92, or 785.52) were present in 35.3 %, 17.3 %, and 3.3 % of admissions, respectively. The incidence of admissions coded for sepsis increased 9.7 % (95 % CI: 6.1, 13.4) per year, while the patient data-defined events of 'any SIRS' decreased by 1.8 % (95 % CI: -3.2, -0.5) and 'multi-day SIRS' did not change significantly over the study period. Clinically-defined sepsis (defined as SIRS plus bacteremia) and severe sepsis (defined as SIRS plus hypotension and bacteremia) decreased at statistically significant rates of 5.7 % (95 % CI: -9.0, -2.4) and 8.6 % (95 % CI: -4.4, -12.6) annually. All-cause mortality, SIRS mortality, and SIRS and clinically-defined sepsis case fatality did not change significantly during the study period. Sepsis mortality, based on ICD-9-CM codes, however, increased by 8.8 % (95 % CI: 1.9, 16.2) annually. CONCLUSIONS The incidence of sepsis, defined by ICD-9-CM codes, and sepsis mortality increased steadily without a concomitant increase in SIRS or clinically-defined sepsis. Our results highlight the need to develop strategies to integrate clinical patient-level data with administrative data to draw more accurate conclusions about the epidemiology of sepsis.

Integrated mRNA and miRNA expression profiling in blood reveals candidate biomarkers associated with endurance exercise in the horse.

The adaptive response to extreme endurance exercise might involve transcriptional and translational regulation by microRNAs (miRNAs). Therefore, the objective of the present study was to perform an integrated analysis of the blood transcriptome and miRNome (using microarrays) in the horse before and after a 160 km endurance competition. A total of 2,453 differentially expressed genes and 167 differentially expressed microRNAs were identified when comparing pre- and post-ride samples. We used a hypergeometric test and its generalization to gain a better understanding of the biological functions regulated by the differentially expressed microRNA. In particular, 44 differentially expressed microRNAs putatively regulated a total of 351 depleted differentially expressed genes involved variously in glucose metabolism, fatty acid oxidation, mitochondrion biogenesis, and immune response pathways. In an independent validation set of animals, graphical Gaussian models confirmed that miR-21-5p, miR-181b-5p and miR-505-5p are candidate regulatory molecules for the adaptation to endurance exercise in the horse. To the best of our knowledge, the present study is the first to provide a comprehensive, integrated overview of the microRNA-mRNA co-regulation networks that may have a key role in controlling post-transcriptomic regulation during endurance exercise.

Assessing the improved discriminatory power of a new biomarker in prognostic models

Although the area under the receiver operating characteristic (AUC) is the most popular measure of the performance of prediction models, it has limitations, especially when it is used to evaluate the added discrimination of a new biomarker in the model. Pencina et al. (2008) proposed two indices, the net reclassification improvement (NRI) and integrated discrimination improvement (IDI), to supplement the improvement in the AUC (IAUC). Their NRI and IDI are based on binary outcomes in case-control settings, which do not involve time-to-event outcome. However, many disease outcomes are time-dependent and the onset time can be censored. Measuring discrimination potential of a prognostic marker without considering time to event can lead to biased estimates. In this dissertation, we have extended the NRI and IDI to survival analysis settings and derived the corresponding sample estimators and asymptotic tests. Simulation studies were conducted to compare the performance of the time-dependent NRI and IDI with Pencina’s NRI and IDI. For illustration, we have applied the proposed method to a breast cancer study.^ Key words: Prognostic model, Discrimination, Time-dependent NRI and IDI ^

Immune response to hepatitis B vaccination in drug using populations: A systematic review and meta-regression analysis

Hepatitis B virus (HBV) is a significant cause of liver diseases and related complications worldwide. Both injecting and non-injecting drug users are at increased risk of contracting HBV infection. Scientific evidence suggests that drug users have subnormal response to HBV vaccination and the seroprotection rates are lower than that in the general population; potentially due to vaccine factors, host factors, or both. The purpose of this systematic review is to examine the rates of seroprotection following HBV vaccination in drug using populations and to conduct a meta-analysis to identify the factors associated with varying seroprotection rates. Seroprotection is defined as developing an anti-HBs antibody level of ≥ 10 mIU/ml after receiving the HBV vaccine. Original research articles were searched using online databases and reference lists of shortlisted articles. HBV vaccine intervention studies reporting seroprotection rates in drug users and published in English language during or after 1989 were eligible. Out of 235 citations reviewed, 11 studies were included in this review. The reported seroprotection rates ranged from 54.5 – 97.1%. Combination vaccine (HAV and HBV) (Risk ratio 12.91, 95% CI 2.98-55.86, p = 0.003), measurement of anti-HBs with microparticle immunoassay (Risk ratio 3.46, 95% CI 1.11-10.81, p = 0.035) and anti-HBs antibody measurement at 2 months after the last HBV vaccine dose (RR 4.11, 95% CI 1.55-10.89, p = 0.009) were significantly associated with higher seroprotection rates. Although statistically nonsignificant, the variables mean age>30 years, higher prevalence of anti-HBc antibody and anti-HIV antibody in the sample population, and current drug use (not in drug rehabilitation treatment) were strongly associated with decreased seroprotection rates. Proportion of injecting drug users, vaccine dose and accelerated vaccine schedule were not predictors of heterogeneity across studies. Studies examined in this review were significantly heterogeneous (Q = 180.850, p = 0.000) and factors identified should be considered when comparing immune response across studies. The combination vaccine showed promising results; however, its effectiveness compared to standard HBV vaccine needs to be examined systematically. Immune response in DUs can possibly be improved by the use of bivalent vaccines, booster doses, and improving vaccine completion rates through integrated public programs and incentives.^

INTEGRATIVE BIOMARKER IDENTIFICATION AND CLASSIFICATION USING HIGH THROUGHPUT ASSAYS

It is well accepted that tumorigenesis is a multi-step procedure involving aberrant functioning of genes regulating cell proliferation, differentiation, apoptosis, genome stability, angiogenesis and motility. To obtain a full understanding of tumorigenesis, it is necessary to collect information on all aspects of cell activity. Recent advances in high throughput technologies allow biologists to generate massive amounts of data, more than might have been imagined decades ago. These advances have made it possible to launch comprehensive projects such as (TCGA) and (ICGC) which systematically characterize the molecular fingerprints of cancer cells using gene expression, methylation, copy number, microRNA and SNP microarrays as well as next generation sequencing assays interrogating somatic mutation, insertion, deletion, translocation and structural rearrangements. Given the massive amount of data, a major challenge is to integrate information from multiple sources and formulate testable hypotheses. This thesis focuses on developing methodologies for integrative analyses of genomic assays profiled on the same set of samples. We have developed several novel methods for integrative biomarker identification and cancer classification. We introduce a regression-based approach to identify biomarkers predictive to therapy response or survival by integrating multiple assays including gene expression, methylation and copy number data through penalized regression. To identify key cancer-specific genes accounting for multiple mechanisms of regulation, we have developed the integIRTy software that provides robust and reliable inferences about gene alteration by automatically adjusting for sample heterogeneity as well as technical artifacts using Item Response Theory. To cope with the increasing need for accurate cancer diagnosis and individualized therapy, we have developed a robust and powerful algorithm called SIBER to systematically identify bimodally expressed genes using next generation RNAseq data. We have shown that prediction models built from these bimodal genes have the same accuracy as models built from all genes. Further, prediction models with dichotomized gene expression measurements based on their bimodal shapes still perform well. The effectiveness of outcome prediction using discretized signals paves the road for more accurate and interpretable cancer classification by integrating signals from multiple sources.

CaCO3, foraminifer fragmentation, benthic carbon isotopes, coarse lithic counts and radiogenic isotopes (Sr, Nd, Pb) of the Pliocene and earliest Pleistocene terrigenous component (3.3-2.4 Ma) of IODP Site 306-U1313

We present Plio-Pleistocene records of sediment color, %CaCO3, foraminifer fragmentation, benthic carbon isotopes (d13C) and radiogenic isotopes (Sr, Nd, Pb) of the terrigenous component from IODP Site U1313, a reoccupation of benchmark subtropical North Atlantic Ocean DSDP Site 607. We show that (inter)glacial cycles in sediment color and %CaCO3 pre-date major northern hemisphere glaciation and are unambiguously and consistently correlated to benthic oxygen isotopes back to 3.3 million years ago (Ma) and intermittently so probably back to the Miocene/Pliocene boundary. We show these lithological cycles to be driven by enhanced glacial fluxes of terrigenous material (eolian dust), not carbonate dissolution (the classic interpretation). Our radiogenic isotope data indicate a North American source for this dust (~3.3-2.4 Ma) in keeping with the interpreted source of terrestrial plant wax-derived biomarkers deposited at Site U1313. Yet our data indicate a mid latitude provenance regardless of (inter)glacial state, a finding that is inconsistent with the biomarker-inferred importance of glaciogenic mechanisms of dust production and transport. Moreover, we find that the relation between the biomarker and lithogenic components of dust accumulation is distinctly non-linear. Both records show a jump in glacial rates of accumulation from Marine Isotope Stage, MIS, G6 (2.72 Ma) onwards but the amplitude of this signal is about 3-8 times greater for biomarkers than for dust and particularly extreme during MIS 100 (2.52 Ma). We conclude that North America shifted abruptly to a distinctly more arid glacial regime from MIS G6, but major shifts in glacial North American vegetation biomes and regional wind fields (exacerbated by the growth of a large Laurentide Ice Sheet during MIS 100) likely explain amplification of this signal in the biomarker records. Our findings are consistent with wetter-than-modern reconstructions of North American continental climate under the warm high CO2 conditions of the Early Pliocene but contrast with most model predictions for the response of the hydrological cycle to anthropogenic warming over the coming 50 years (poleward expansion of the subtropical dry zones).

Biomarker proxies on sediment cores in the central Arctic Ocean

Although the permanently to seasonally ice-covered Arctic Ocean is a unique and sensitive component in the Earth's climate system, the knowledge of its long-term climate history remains very limited due to the restricted number of pre-Quaternary sedimentary records. During Polarstern Expedition PS87/2014, we discovered multiple submarine landslides over a distance of >350 km along Lomonosov Ridge. Removal of younger sediments from steep headwalls has led to exhumation of Miocene to early Quaternary sediments close to the seafloor, allowing the retrieval of such old sediments with gravity cores. Multi-proxy biomarker analyses of these gravity cores reveal for the first time that the late Miocene central Arctic Ocean was relatively warm (4-7°C) and ice-free during summer, whereas sea ice occurred during spring and autumn/winter. A comparison of our proxy data with Miocene climate simulations seems to favour relatively high late Miocene atmospheric CO2 concentrations. These new findings from the Arctic region provide new benchmarks for groundtruthing global climate reconstructions and modeling.

Modeled integrated responses of ppERK1 and ppERK2 of normal and elevated ERK1 and ERK2 levels (Figure 5b)

The present dataset contain source data for Figure 5b from Schilling et al., 2009. Cell fate decisions are regulated by the coordinated activation of signalling pathways such as the extracellular signal-regulated kinase (ERK) cascade, but contributions of individual kinase isoforms are mostly unknown. The authors combined quantitative data from erythropoietin-induced pathway activation in primary erythroid progenitor (colony-forming unit erythroid stage, CFU-E) cells with mathematical modelling, in order to predict and experimentally confirmed a distributive ERK phosphorylation mechanism in CFU-E cells. The authors found evidences that double-phosphorylated ERK1 attenuates proliferation beyond a certain activation level, whereas activated ERK2 enhances proliferation with saturation kinetics. They show integrated responses of double-phosphorylated ERK1 and ERK2 that were calculated for different Epo concentrations for the original model as well as for models with elevated ERK1 or ERK2 levels.

Specific microbial biomarker signatures from Congo fan sediments of ODP site 175-1075, Congo soils, wetland and estuary sediments

Methane (CH4) is a strong greenhouse gas known to have perturbed global climate in the past, especially when released in large quantities over short time periods from continental or marine sources. It is therefore crucial to understand and, if possible, quantify the individual and combined response of these variable methane sources to natural climate variability. However, past changes in the stability of greenhouse gas reservoirs remain uncertain and poorly constrained by geological evidence. Here, we present a record from the Congo fan of a highly specific bacteriohopanepolyol (BHP) biomarker for aerobic methane oxidation (AMO), 35-aminobacteriohopane-30,31,32,33,34-pentol (aminopentol), that identifies discrete periods of increased AMO as far back as 1.2 Ma. Fluctuations in the concentration of aminopentol, and other 35-aminoBHPs, follow a pattern that correlates with late Quaternary glacial-interglacial climate cycles, with highest concentrations during warm periods. We discuss possible sources of aminopentol, and the methane consumed by the precursor methanotrophs, within the context of the Congo River setting, including supply of methane oxidation markers from terrestrial watersheds and/or marine sources (gas hydrate and/or deep subsurface gas reservoir). Compound-specific carbon isotope values of -30 per mil to -40 per mil for BHPs in ODP 1075 and strong similarities between the BHP signature of the core and surface sediments from the Congo estuary and floodplain wetlands from the interior of the Congo River Basin, support a methanotrophic and likely terrigenous origin of the 35-aminoBHPs found in the fan sediments. This new evidence supports a causal connection between marine sediment BHP records of tropical deep sea fans and wetland settings in the feeding river catchments, and thus tropical continental hydrology. Further research is needed to better constrain the different sources and pathways of methane emission. However, this study identifies the large potential of aminoBHPs, in particular aminopentol, to trace and, once better calibrated and understood, quantify past methane sources and fluxes from terrestrial and potentially also marine sources.

Stable carbon isotopic composition of biomarker lipids of DSDP Hole 31-302

The middle Paleocene through early Eocene long-term gradual warming was superimposed by several transient warming events, such as the Paleocene-Eocene Thermal Maximum (PETM) and Eocene Thermal Maximum 2 (ETM2). Both events show evidence for extreme global warming associated with a major injection of carbon into the ocean-atmosphere system, but the mechanisms of carbon injection and many aspects of the environmental response are still poorly understood. In this study, we analyzed the concentration and stable carbon isotopic (d13C) composition of several sulfur-bound biomarkers derived from marine photoautotrophs, deposited in the Arctic Ocean at ~85°N, during ETM2. The presence of sulfur-bound biomarkers across this event points toward high primary productivity and anoxic bottom water conditions. The previously reported presence of isorenieratene derivatives indicates euxinic conditions in the photic zone, likely caused by a combination of enhanced primary productivity and salinity stratification. The negative carbon isotope excursion measured at the onset of ETM2 for several biomarkers, ranges between 3 per mil and 4.5 per mil, much larger than the ~1.4 per mil recorded in marine carbonates elsewhere, suggesting substantial enhanced isotopic fractionation by the primary producers likely due to a significant rise in pCO2. In the absence of biogenic carbonates in the ETM2 section of our core we use coeval planktonic d13C from elsewhere to estimate surface water d13C in the Arctic Ocean and then apply the relation between isotopic fractionation and pCO2, originally calibrated for haptophyte alkenones, to three selected organic biomarkers (i.e., S-bound phytane, C35 hopane, and a C25 highly branched isoprenoid). This yields pCO2 values potentially in the range of four times preindustrial levels. However, these estimates are uncertain because of a lack of knowledge on the importance of pCO2 on photosynthetic isotopic fractionation.

Biomarker and XRD results for the last 3.4 Ma from IODP Site 306-U1313

Various types of abrupt/millennial-scale climate variability such as Dansgaard/Oeschger and Heinrich Events characterized the last glacial period. Over the last decade, a number of studies demonstrated that such millennial-scale climate variability was not limited to the last glacial but inherent to Quaternary climate. Here we review the occurrence and origin of millennial ice-rafting events in the North Atlantic during the late Pliocene and Pleistocene (last 3.4 Ma) with a special focus on North Atlantic Hudson Strait (HS) Heinrich(-like) Events. Besides a clear biomarker signature, we show that Heinrich Layers 5, 4, 2, and 1 in marine sediment cores from across the North Atlantic all bear the organic geochemical fingerprint of the Hudson area. Using this framework and combining previously published results, detailed investigations into the organic and inorganic chemistry of ice-rafted debris (IRD) found across the North Atlantic demonstrate that prior to MIS 16 (~ 650 ka) IRD in the North Atlantic did not originate from the Hudson area of northern Canada. The signature of this early IRD is distinctly different compared to that of HS Heinrich Layers. Rather ice-rafting events during the late Pliocene and early Pleistocene predominantly emanated from the calving of the Greenland and Fennoscandian ice sheets and possibly minor contributions from local ice streams from the North American and British ice sheets. Compared to North Atlantic HS Heinrich Events, these early Pleistocene IRD-events had a limited impact on surface water characteristics in the North Atlantic. North Atlantic HS Heinrich(-like) Events first occurred during MIS 16. At the same time, the dominant frequency in silicate-rich IRD accumulation shifted from the obliquity (41-ka) to a 100-ka frequency across the North Atlantic. Iceberg survivability or a change in iceberg trajectory likely did not control this change in IRD-regime. These results lend further support for the existing hypothesis that an increase in size (thickness) of the Laurentide ice sheet controls the occurrence of North Atlantic HS Heinrich Events, favoring an internal dynamic mechanism for their occurrence.

Biomarker and x-ray diffraction data from Site U1313 (MIS 16 - 9)

A reconstruction of Milankovitch to millennial-scale variability of sea-surface temperature (SST) and sea-surface productivity in the Pleistocene mid-latitude North Atlantic Ocean (MIS 16-9) and its relationship to ice sheet instability was carried out on sediments from IODP Site U1313. This reconstruction is based on alkenone and n-alkane concentrations, Uk37' index, total organic carbon (TOC) and carbonate contents, X-Ray diffraction (XRD) data, magnetic susceptibility, and accumulation rates. Increased input of ice-rafted debris (IRD) occurred during MIS 16, 12, and 10, characterized by high concentrations of dolomite, quartz, and feldspars and elevated accumulation rates of terrigenous matter. Minimum input values of terrigenous matter, on the other hand, were determined for MIS 13 and 11. Peak values of dolomite, coinciding with quartz, plagioclase, and kalifeldspar peaks and maxima in long-chain n-alkanes indicative for land plants, are interpreted as Heinrich-like Events related to sudden instability of the Laurentide Ice Sheet during early and late (deglacial) phases of the glacials. The coincidence of increased TOC values with elevated absolute concentrations of alkenones suggest increased glacial productivity, probably due to a more southern position of the Polar Front. Alkenone-based SST reached absolute maxima of about 19°C during MIS 11.3 and absolute minima of <10°C during MIS 12 and 10. Within MIS 11, prominent cooling events (MIS 11.22 and 11.24) occurred. The absolute SST minima recorded directly before and after the glacial maxima MIS 10.2 and 12.2, are related to Heinrich-like Event meltwater pulses, as supported by the coincidence of SST minima and maxima in C37:4 alkenones and dolomite. These sudden meltwater pulses - especially during Terminations IV and V - probably caused a collapse of phytoplankton productivity as indicated by the distinct drop in alkenone concentrations. Ice-sheet disintegration and subsequent surges and outbursts of icebergs and meltwater discharge may have been triggered by increased insolation in the Northern High Latitudes.