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.

Molecular dynamics simulations of the hydrophobin SC3 at a hydrophobic/hydrophilic interface

Hydrophobins are small (similar to 100 aa) proteins that have an important role in the growth and development of mycelial fungi. They are surface active and, after secretion by the fungi, self-assemble into amphipathic membranes at hydrophobic/hydrophilic interfaces, reversing the hydrophobicity of the surface. In this study, molecular dynamics simulation techniques have been used to model the process by which a specific class I hydrophobin, SC3, binds to a range of hydrophobic/ hydrophilic interfaces. The structure of SC3 used in this investigation was modeled based on the crystal structure of the class II hydrophobin HFBII using the assumption that the disulfide pairings of the eight conserved cysteine residues are maintained. The proposed model for SC3 in aqueous solution is compact and globular containing primarily P-strand and coil structures. The behavior of this model of SC3 was investigated at an air/water, an oil/water, and a hydrophobic solid/water interface. It was found that SC3 preferentially binds to the interfaces via the loop region between the third and fourth cysteine residues and that binding is associated with an increase in a-helix formation in qualitative agreement with experiment. Based on a combination of the available experiment data and the current simulation studies, we propose a possible model for SC3 self-assembly on a hydrophobic solid/water interface.

Connectivity of fragmented amphibian populations in a neotropical landscape

A high proportion of amphibian species are threatened with extinction globally, and habitat loss and degradation are the most frequently implicated causes. Rapid deforestation for the establishment of agricultural production is a primary driver of habitat loss in tropical zones where amphibian diversity is highest. Land-cover change affects native assemblages, in part, through the reduction of habitat area and the reduction of movement among remnant populations. Decreased gene flow contributes to loss of genetic diversity, which limits the ability of local populations to respond to further environmental changes. The focus of this dissertation is on the degree to which common land uses in Sarapiquí, Costa Rica impede the movement of two common amphibian species. First, I used field experiments, including displacement trials, and a behavioral landscape ecology framework to investigate the resistance of pastures to movement of Oophaga pumilio. Results from experiments demonstrate that pastures do impede movement of O. pumilio relative to forest. Microclimatic effects on movement performance as well as limited perceptual ranges likely contribute to reduced return rates through pastures. Next, I linked local processes to landscape scale estimates of resistance. I conducted experiments to measure habitat-specific costs to movement for O. pumilio and Craugastor bransfodrii, and then used experimental results to parameterize connectivity models. Model validation indicated highest support for resistance estimates generated from responses to land-use specific microclimates for both species and to predator encounters for O. pumilio. Finally, I used abundance and experiment-derived resistance estimates to analyze the effects of prevalent land uses on population genetic structure of the two focal species. While O. pumilio did not exhibit a strong response to landscape heterogeneity and was primarily structured by distances among sites, C. bransfordii genetic variation was explained by resistance estimates from abundance and experiment data. Collectivity, this work demonstrates that common land uses can offer different levels of resistance to amphibian movements in Sarapiquí and illustrates the value of investigating local scales processes to inform interpretation of landscape-scale patterns.^

Connectivity of fragmented amphibian populations in a Neotropical landscape

A high proportion of amphibian species are threatened with extinction globally, and habitat loss and degradation are the most frequently implicated causes. Rapid deforestation for the establishment of agricultural production is a primary driver of habitat loss in tropical zones where amphibian diversity is highest. Land-cover change affects native assemblages, in part, through the reduction of habitat area and the reduction of movement among remnant populations. Decreased gene flow contributes to loss of genetic diversity, which limits the ability of local populations to respond to further environmental changes. The focus of this dissertation is on the degree to which common land uses in Sarapiquí, Costa Rica impede the movement of two common amphibian species. First, I used field experiments, including displacement trials, and a behavioral landscape ecology framework to investigate the resistance of pastures to movement of Oophaga pumilio. Results from experiments demonstrate that pastures do impede movement of O. pumilio relative to forest. Microclimatic effects on movement performance as well as limited perceptual ranges likely contribute to reduced return rates through pastures. Next, I linked local processes to landscape scale estimates of resistance. I conducted experiments to measure habitat-specific costs to movement for O. pumilio and Craugastor bransfodrii, and then used experimental results to parameterize connectivity models. Model validation indicated highest support for resistance estimates generated from responses to land-use specific microclimates for both species and to predator encounters for O. pumilio. Finally, I used abundance and experiment-derived resistance estimates to analyze the effects of prevalent land uses on population genetic structure of the two focal species. While O. pumilio did not exhibit a strong response to landscape heterogeneity and was primarily structured by distances among sites, C. bransfordii genetic variation was explained by resistance estimates from abundance and experiment data. Collectivity, this work demonstrates that common land uses can offer different levels of resistance to amphibian movements in Sarapiquí and illustrates the value of investigating local scales processes to inform interpretation of landscape-scale patterns.

Sustainable Energy Production in the United States: Life Cycle Assessment of Biofuels and Bioenergy

The United States of America is making great efforts to transform the renewable and abundant biomass resources into cost-competitive, high-performance biofuels, bioproducts, and biopower. This is the key to increase domestic production of transportation fuels and renewable energy, and reduce greenhouse gas and other pollutant emissions. This dissertation focuses specifically on assessing the life cycle environmental impacts of biofuels and bioenergy produced from renewable feedstocks, such as lignocellulosic biomass, renewable oils and fats. The first part of the dissertation presents the life cycle greenhouse gas (GHG) emissions and energy demands of renewable diesel (RD) and hydroprocessed jet fuels (HRJ). The feedstocks include soybean, camelina, field pennycress, jatropha, algae, tallow and etc. Results show that RD and HRJ produced from these feedstocks reduce GHG emissions by over 50% compared to comparably performing petroleum fuels. Fossil energy requirements are also significantly reduced. The second part of this dissertation discusses the life cycle GHG emissions, energy demands and other environmental aspects of pyrolysis oil as well as pyrolysis oil derived biofuels and bioenergy. The feedstocks include waste materials such as sawmill residues, logging residues, sugarcane bagasse and corn stover, and short rotation forestry feedstocks such as hybrid poplar and willow. These LCA results show that as much as 98% GHG emission savings is possible relative to a petroleum heavy fuel oil. Life cycle GHG savings of 77 to 99% were estimated for power generation from pyrolysis oil combustion relative to fossil fuels combustion for electricity, depending on the biomass feedstock and combustion technologies used. Transportation fuels hydroprocessed from pyrolysis oil show over 60% of GHG reductions compared to petroleum gasoline and diesel. The energy required to produce pyrolysis oil and pyrolysis oil derived biofuels and bioelectricity are mainly from renewable biomass, as opposed to fossil energy. Other environmental benefits include human health, ecosystem quality and fossil resources. The third part of the dissertation addresses the direct land use change (dLUC) impact of forest based biofuels and bioenergy. An intensive harvest of aspen in Michigan is investigated to understand the GHG mitigation with biofuels and bioenergy production. The study shows that the intensive harvest of aspen in MI compared to business as usual (BAU) harvesting can produce 18.5 billion gallons of ethanol to blend with gasoline for the transport sector over the next 250 years, or 32.2 billion gallons of bio-oil by the fast pyrolysis process, which can be combusted to generate electricity or upgraded to gasoline and diesel. Intensive harvesting of these forests can result in carbon loss initially in the aspen forest, but eventually accumulates more carbon in the ecosystem, which translates to a CO2 credit from the dLUC impact. Time required for the forest-based biofuels to reach carbon neutrality is approximately 60 years. The last part of the dissertation describes the use of depolymerization model as a tool to understand the kinetic behavior of hemicellulose hydrolysis under dilute acid conditions. Experiments are carried out to measure the concentrations of xylose and xylooligomers during dilute acid hydrolysis of aspen. The experiment data are used to fine tune the parameters of the depolymerization model. The results show that the depolymerization model successfully predicts the xylose monomer profile in the reaction, however, it overestimates the concentrations of xylooligomers.

Deep crustal structure across a young passive margin from wide-angle and reflection seismic data (The Sardinia Experiment) - I. Gulf of Lion's margin

The conjugate margins system of the Gulf of Lion and West Sardinia (GLWS) represents a unique natural laboratory for addressing fundamental questions about rifting due to its landlocked situation, its youth, its thick sedimentary layers, including prominent palaeo-marker such as the MSC event, and the amount of available data and multidisciplinary studies. The main goals of the SARDINIA experiment, were to (i) investigate the deep structure of the entire system within the two conjugate margins: the Gulf of Lion and West Sardinia, (ii) characterize the nature of the crust, and (iii) define the geometry of the basin and provide important constrains on its genesis. This paper presents the results of P-wave velocity modelling on three coincident near-vertical reflection multi-channel seismic (MCS) and wide-angle seismic profiles acquired in the Gulf of Lion, to a depth of 35 km. A companion paper [part II Afilhado et al., 2015] addresses the results of two other SARDINIA profiles located on the oriental conjugate West Sardinian margin. Forward wide-angle modelling of both data sets confirms that the margin is characterised by three distinct domains following the onshore unthinned, 33 km-thick continental crust domain: Domain I is bounded by two necking zones, where the crust thins respectively from 30 to 20 and from 20 to 7 km over a width of about 170 km; the outermost necking is imprinted by the well-known T-reflector at its crustal base; Domain II is characterised by a 7 km-thick crust with anomalous velocities ranging from 6 to 7.5 km/s; it represents the transition between the thinned continental crust (Domain I) and a very thin (only 4-5 km) "atypical" oceanic crust (Domain III). In Domain II, the hypothesis of the presence of exhumed mantle is falsified by our results: this domain may likely consist of a thin exhumed lower continental crust overlying a heterogeneous, intruded lower layer. Moreover, despite the difference in their magnetic signatures, Domains II and III present the very similar seismic velocities profiles, and we discuss the possibility of a connection between these two different domains.

Deep crustal structure across a young passive margin from wide-angle and reflection seismic data (The Sardinia Experiment) - II. Sardinia's margin

Geophysical data acquired on the conjugate margins system of the Gulf of Lion and West Sardinia (GLWS) is unique in its ability to address fundamental questions about rifting (i.e. crustal thinning, the nature of the continent-ocean transition zone, the style of rifting and subsequent evolution, and the connection between deep and surface processes). While the Gulf of Lion (GoL) was the site of several deep seismic experiments, which occurred before the SARDINIA Experiment (ESP and ECORS Experiments in 1981 and 1988 respectively), the crustal structure of the West Sardinia margin remains unknown. This paper describes the first modeling of wide-angle and near-vertical reflection multi-channel seismic (MCS) profiles crossing the West Sardinia margin, in the Mediterranean Sea. The profiles were acquired, together with the exact conjugate of the profiles crossing the GoL, during the SARDINIA experiment in December 2006 with the French R/V L'Atalante. Forward wide-angle modeling of both data sets (wide-angle and multi-channel seismic) confirms that the margin is characterized by three distinct domains following the onshore unthinned, 26 km-thick continental crust : Domain V, where the crust thins from 26 to 6 km in a width of about 75 km; Domain IV where the basement is characterized by high velocity gradients and lower crustal seismic velocities from 6.8 to 7.25 km/s, which are atypical for either crustal or upper mantle material, and Domain III composed of "atypical" oceanic crust.The structure observed on the West Sardinian margin presents a distribution of seismic velocities that is symmetrical with those observed on the Gulf of Lion's side, except for the dimension of each domain and with respect to the initiation of seafloor spreading. This result does not support the hypothesis of simple shear mechanism operating along a lithospheric detachment during the formation of the Liguro-Provencal basin.

From a NoSQL data source to a business intelligence solution: An experiment

We are living in the era of Big Data. A time which is characterized by the continuous creation of vast amounts of data, originated from different sources, and with different formats. First, with the rise of the social networks and, more recently, with the advent of the Internet of Things (IoT), in which everyone and (eventually) everything is linked to the Internet, data with enormous potential for organizations is being continuously generated. In order to be more competitive, organizations want to access and explore all the richness that is present in those data. Indeed, Big Data is only as valuable as the insights organizations gather from it to make better decisions, which is the main goal of Business Intelligence. In this paper we describe an experiment in which data obtained from a NoSQL data source (database technology explicitly developed to deal with the specificities of Big Data) is used to feed a Business Intelligence solution.

Data quality in biofilm high-throughput routine analysis: intralaboratory protocol adaptation and experiment reproducibility

Biofilm research is growing more diverse and dependent on high-throughput technologies and the large-scale production of results aggravates data substantiation. In particular, it is often the case that experimental protocols are adapted to meet the needs of a particular laboratory and no statistical validation of the modified method is provided. This paper discusses the impact of intra-laboratory adaptation and non-rigorous documentation of experimental protocols on biofilm data interchange and validation. The case study is a non-standard, but widely used, workflow for Pseudomonas aeruginosa biofilm development, considering three analysis assays: the crystal violet (CV) assay for biomass quantification, the XTT assay for respiratory activity assessment, and the colony forming units (CFU) assay for determination of cell viability. The ruggedness of the protocol was assessed by introducing small changes in the biofilm growth conditions, which simulate minor protocol adaptations and non-rigorous protocol documentation. Results show that even minor variations in the biofilm growth conditions may affect the results considerably, and that the biofilm analysis assays lack repeatability. Intra-laboratory validation of non-standard protocols is found critical to ensure data quality and enable the comparison of results within and among laboratories.

Example of Data Telemetry for Biomedical Applications: An In Vivo Experiment

This letter describes a data telemetry biomedical experiment. An implant, consisting of a biometric data sensor, electronics, an antenna, and a biocompatible capsule, is described. All the elements were co-designed in order to maximize the transmission distance. The device was implanted in a pig for an in vivo experiment of temperature monitoring.

Imputation in data fusion of heterogeneous data sets a model-based numerical experiment

Given the very large amount of data obtained everyday through population surveys, much of the new research again could use this information instead of collecting new samples. Unfortunately, relevant data are often disseminated into different files obtained through different sampling designs. Data fusion is a set of methods used to combine information from different sources into a single dataset. In this article, we are interested in a specific problem: the fusion of two data files, one of which being quite small. We propose a model-based procedure combining a logistic regression with an Expectation-Maximization algorithm. Results show that despite the lack of data, this procedure can perform better than standard matching procedures.

An observing system simulation experiment for climate monitoring with GNSS radio occulation data: setup and testbed study

The long-term stability, high accuracy, all-weather capability, high vertical resolution, and global coverage of Global Navigation Satellite System (GNSS) radio occultation (RO) suggests it as a promising tool for global monitoring of atmospheric temperature change. With the aim to investigate and quantify how well a GNSS RO observing system is able to detect climate trends, we are currently performing an (climate) observing system simulation experiment over the 25-year period 2001 to 2025, which involves quasi-realistic modeling of the neutral atmosphere and the ionosphere. We carried out two climate simulations with the general circulation model MAECHAM5 (Middle Atmosphere European Centre/Hamburg Model Version 5) of the MPI-M Hamburg, covering the period 2001–2025: One control run with natural variability only and one run also including anthropogenic forcings due to greenhouse gases, sulfate aerosols, and tropospheric ozone. On the basis of this, we perform quasi-realistic simulations of RO observables for a small GNSS receiver constellation (six satellites), state-of-the-art data processing for atmospheric profiles retrieval, and a statistical analysis of temperature trends in both the “observed” climatology and the “true” climatology. Here we describe the setup of the experiment and results from a test bed study conducted to obtain a basic set of realistic estimates of observational errors (instrument- and retrieval processing-related errors) and sampling errors (due to spatial-temporal undersampling). The test bed results, obtained for a typical summer season and compared to the climatic 2001–2025 trends from the MAECHAM5 simulation including anthropogenic forcing, were found encouraging for performing the full 25-year experiment. They indicated that observational and sampling errors (both contributing about 0.2 K) are consistent with recent estimates of these errors from real RO data and that they should be sufficiently small for monitoring expected temperature trends in the global atmosphere over the next 10 to 20 years in most regions of the upper troposphere and lower stratosphere (UTLS). Inspection of the MAECHAM5 trends in different RO-accessible atmospheric parameters (microwave refractivity and pressure/geopotential height in addition to temperature) indicates complementary climate change sensitivity in different regions of the UTLS so that optimized climate monitoring shall combine information from all climatic key variables retrievable from GNSS RO data.