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"Roland, C."
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Octopus : the ocean's intelligent invertebrate
A natural history of the octopus, featuring personal narratives, underwater research, and closeup photography that details mating and predatory behaviors, intelligence, and problem-solving abilities.
Book
Science and Technology of Rubber (4th Edition)
This book provides a broad survey of elastomers with special emphasis on materials with a rubber-like elasticity. As in the 3rd Edition, the emphasis remains on a unified treatment of the material; exploring topics from the chemical aspects such as elastomer synthesis and curing, through recent theoretical developments and characterization of equilibrium and dynamic properties, to the final applications of rubber, including tire engineering and manufacturing. Many advances have been made in polymer and elastomers research over the past ten years since the 3rd Edition was published. Updated material stresses the continuous relationship between the ongoing research in synthesis, physics, structure, and mechanics of rubber technology and industrial applications. Special attention is paid to recent advances in rubber-like elasticity theory and new processing techniques for elastomers. This new edition is comprised of 20% new material, including a new chapter on environmental issues and tire recycling.
eBook
Following the terrestrial tracks of Caulobacter - redefining the ecology of a reputed aquatic oligotroph
For the past 60 years
Caulobacter spp
. have been commonly attributed an aquatic and oligotrophic lifestyle yet are not uncommon in nutrient-rich or soil environments. This study evaluates the environmental and ecological associations of
Caulobacter
to reconcile past evidence, largely limited to culturing and microscopy, with currently available metagenomic and genomic data. The distribution of
Caulobacter
species and their characteristic adhesion-conferring genes, holdfast (
hfaAB
), were determined using collections of 10,641 16S rRNA gene libraries (196 studies) and 2625 shotgun metagenomes (190 studies) from a range of terrestrial and aquatic environments. Evidence for ecotypic variation was tested in 26 genomes sourced from soil, rhizosphere, plant, groundwater, and water.
Caulobacter
were, on average, fourfold more relatively abundant in soil than in aquatic environments, and abundant in decomposing wood, compost, and particulate matter (in air and water).
Caulobacter
holdfast genes were 35-fold more abundant in soils than aquatic environments. Ecotypic differences between soil and aquatic
Caulobacter
were evident in the environmental associations of several species and differences in genome size and content among isolates. However, most abundant species were common to both environments, suggesting populations exist in a continuum that was evident in the re-analysis of studies on the temporal dynamics of, and sources of bacterioplankton to, lakes and rivers. This study provides a new perspective on the ecological profile of
Caulobacter
, demonstrating that members of this genus are predominantly soil-borne, possess an overlooked role in plant matter decomposition and a dependency on water-mediated dispersal.
Journal Article
Calcium promotes persistent soil organic matter by altering microbial transformation of plant litter
Calcium (Ca) can contribute to soil organic carbon (SOC) persistence by mediating physico-chemical interactions between organic compounds and minerals. Yet, Ca is also crucial for microbial adhesion, potentially affecting colonization of plant and mineral surfaces. The importance of Ca as a mediator of microbe-mineral-organic matter interactions and resulting SOC transformation has been largely overlooked. We incubated
44
Ca labeled soils with
13
C
15
N labeled leaf litter to study how Ca affects microbial transformation of litter and formation of mineral associated organic matter. Here we show that Ca additions promote hyphae-forming bacteria, which often specialize in colonizing surfaces, and increase incorporation of litter into microbial biomass and carbon use efficiency by approximately 45% each. Ca additions reduce cumulative CO
2
production by 4%, while promoting associations between minerals and microbial byproducts of plant litter. These findings expand the role of Ca in SOC persistence from solely a driver of physico-chemical reactions to a mediator of coupled abiotic-biotic cycling of SOC.
Calcium drives soil organic carbon persistence through associations between organic compounds and minerals. Here, the authors expand the role of calcium by showing that it alters microbial conversion of plant carbon into persistent mineral fractions
Journal Article
Gradient forests: calculating importance gradients on physical predictors
In ecological analyses of species and community distributions there is interest in the nature of their responses to environmental gradients and in identifying the most important environmental variables, which may be used for predicting patterns of biodiversity. Methods such as random forests already exist to assess predictor importance for individual species and to indicate where along gradients abundance changes. However, there is a need to extend these methods to whole assemblages, to establish where along the range of these gradients the important compositional changes occur, and to identify any important thresholds or change points. We develop such a method, called \"gradient forest,\" which is an extension of the random forest approach. By synthesizing the cross-validated
R
2
and accuracy importance measures from univariate random forest analyses across multiple species, sampling devices, and surveys, gradient forest obtains a monotonic function of each predictor that represents the compositional turnover along the gradient of the predictor. When applied to a synthetic data set, the method correctly identified the important predictors and delineated where the compositional change points occurred along these gradients. Application of gradient forest to a real data set from part of the Great Barrier Reef identified mud fraction of the sediment as the most important predictor, with highest compositional turnover occurring at mud fraction values around 25%, and provided similar information for other predictors. Such refined information allows for more accurate capturing of biodiversity patterns for the purposes of bioregionalization, delineation of protected areas, or designing of biodiversity surveys.
Journal Article
Bacterial contributions to delignification and lignocellulose degradation in forest soils with metagenomic and quantitative stable isotope probing
Delignification, or lignin-modification, facilitates the decomposition of lignocellulose in woody plant biomass. The extant diversity of lignin-degrading bacteria and fungi is underestimated by culture-dependent methods, limiting our understanding of the functional and ecological traits of decomposers populations. Here, we describe the use of stable isotope probing (SIP) coupled with amplicon and shotgun metagenomics to identify and characterize the functional attributes of lignin, cellulose and hemicellulose-degrading fungi and bacteria in coniferous forest soils from across North America. We tested the extent to which catabolic genes partitioned among different decomposer taxa; the relative roles of bacteria and fungi, and whether taxa or catabolic genes correlated with variation in lignocellulolytic activity, measured as the total assimilation of
13
C-label into DNA and phospholipid fatty acids. We found high overall bacterial degradation of our model lignin substrate, particularly by gram-negative bacteria (Comamonadaceae and Caulobacteraceae), while fungi were more prominent in cellulose-degradation. Very few taxa incorporated
13
C-label from more than one lignocellulosic polymer, suggesting specialization among decomposers. Collectively, members of Caulobacteraceae could degrade all three lignocellulosic polymers, providing new evidence for their importance in lignocellulose degradation. Variation in lignin-degrading activity was better explained by microbial community properties, such as catabolic gene content and community structure, than cellulose-degrading activity. SIP significantly improved shotgun metagenome assembly resulting in the recovery of several high-quality draft metagenome-assembled genomes and over 7500 contigs containing unique clusters of carbohydrate-active genes. These results improve understanding of which organisms, conditions and corresponding functional genes contribute to lignocellulose decomposition.
Journal Article
Trawl impacts on the relative status of biotic communities of seabed sedimentary habitats in 24 regions worldwide
Bottom trawling is widespread globally and impacts seabed habitats. However, risks from trawling remain unquantified at large scales in most regions. We address these issues by synthesizing evidence on the impacts of different trawl-gear types, seabed recovery rates, and spatial distributions of trawling intensity in a quantitative indicator of biotic status (relative amount of pretrawling biota) for sedimentary habitats, where most bottom-trawling occurs, in 24 regions worldwide. Regional average status relative to an untrawled state (=1) was high (>0.9) in 15 regions, but <0.7 in three (European) regions and only 0.25 in the Adriatic Sea. Across all regions, 66% of seabed area was not trawled (status = 1), 1.5% was depleted (status = 0), and 93% had status > 0.8. These assessments are first order, based on parameters estimated with uncertainty from meta-analyses; we recommend regional analyses to refine parameters for local specificity. Nevertheless, our results are sufficiently robust to highlight regions needing more effective management to reduce exploitation and improve stock sustainability and seabed environmental status—while also showing seabed status was high (>0.95) in regions where catches of trawled fish stocks meet accepted benchmarks for sustainable exploitation, demonstrating that environmental benefits accrue from effective fisheries management. Furthermore, regional seabed status was related to the proportional area swept by trawling, enabling preliminary predictions of regional status when only the total amount of trawling is known. This research advances seascape-scale understanding of trawl impacts in regions around the world, enables quantitative assessment of sustainability risks, and facilitates implementation of an ecosystem approach to trawl fisheries management globally.
Journal Article
A transcriptomics data-driven gene space accurately predicts liver cytopathology and drug-induced liver injury
Predicting unanticipated harmful effects of chemicals and drug molecules is a difficult and costly task. Here we utilize a ‘big data compacting and data fusion’—concept to capture diverse adverse outcomes on cellular and organismal levels. The approach generates from transcriptomics data set a ‘predictive toxicogenomics space’ (PTGS) tool composed of 1,331 genes distributed over 14 overlapping cytotoxicity-related gene space components. Involving ∼2.5 × 10
8
data points and 1,300 compounds to construct and validate the PTGS, the tool serves to: explain dose-dependent cytotoxicity effects, provide a virtual cytotoxicity probability estimate intrinsic to omics data, predict chemically-induced pathological states in liver resulting from repeated dosing of rats, and furthermore, predict human drug-induced liver injury (DILI) from hepatocyte experiments. Analysing 68 DILI-annotated drugs, the PTGS tool outperforms and complements existing tests, leading to a hereto-unseen level of DILI prediction accuracy.
Predicting the hepatotoxic effects of new drugs is still a challenge. Using toxicogenomics data, the authors here define a predictive toxicogenomic space (PTGS), the component gene space capturing dose-dependent cytotoxicity, and demonstrate that it can be used to accurately predict drug-induced liver pathology, including human drug-induced liver injury from
in vitro
data.
Journal Article
Routine frailty assessment predicts postoperative complications in elderly patients across surgical disciplines – a retrospective observational study
Background
Frailty is a frequent and underdiagnosed functional syndrome involving reduced physiological reserves and an increased vulnerability against stressors, with severe individual and socioeconomic consequences. A routine frailty assessment was implemented at our preoperative anaesthesia clinic to identify patients at risk.
Objective
This study examines the relationship between frailty status and the incidence of in-hospital postoperative complications in elderly surgical patients across several surgical disciplines.
Design
Retrospective observational analysis.
Setting
Single center, major tertiary care university hospital. Data collection took place between June 2016 and March 2017.
Patients
Patients 65 years old or older were evaluated for frailty using Fried’s 5-point frailty assessment prior to elective non-cardiac surgery. Patients were classified into non-frail (0 criteria, reference group), pre-frail (1–2 positive criteria) and frail (3–5 positive criteria) groups.
Main outcome measures
The incidence of postoperative complications was assessed until discharge from the hospital, using the roster from the National VA Surgical Quality Improvement Program. Propensity score matching and logistic regression analysis were performed.
Results
From 1186 elderly patients, 46.9% were classified as pre-frail (
n
= 556), and 11.4% as frail (
n
= 135). The rate of complications were significantly higher in the pre-frail (34.7%) and frail groups (47.4%), as compared to the non-frail group (27.5%). Similarly, length of stay (non-frail: 5.0 [3.0;7.0], pre-frail: 7.0 [3.0;9.0], frail 8.0 [4.5;12.0];
p
< 0.001) and discharges to care facilities (non-frail:1.6%, pre-frail: 7.4%, frail: 17.8%); p < 0.001) were significantly associated with frailty status. After propensity score matching and logistic regression analysis, the risk for developing postoperative complications was approximately two-fold for pre-frail (OR 1.78; 95% CI 1.04–3.05) and frail (OR 2.08; 95% CI 1.21–3.60) patients.
Conclusions
The preoperative frailty assessment of elderly patients identified pre-frail and frail subgroups to have the highest rate of postoperative complications, regardless of age, surgical discipline, and surgical risk. Significantly increased length of hospitalisation and discharges to care facilities were also observed. Implementation of routine frailty assessments appear to be an effective tool in identifying patients with increased risk. Now future studies are needed to investigate whether patients benefit from optimization of patient counselling, process planning, and risk reduction protocols based on the application of risk stratification.
Journal Article