bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fragile legitimacy: the rise and crisis of the EU’s ‘sustainable biofuels’ policy
Authors: Kupzok Nils 
Published: October 2018

AbstractThe EU’s biofuels policy has made a full normative turn: introduced to advance sustainable development, it was curtailed as a threat to the global environment. Central to the crisis of legitimation was a contested scientific idea, emissions from indirect land-use changes. This article takes up the large impact of this small idea to discuss a central question of contemporary institutionalist and constructivist scholarship: Why and under what conditions can ideas and events become catalysts for change? Tracing the rise and crisis of the EU’s biofuels policy, my central theoretical intervention is to conceptualize the fragile legitimacy of policies and institutions. In addition, I specify the scope condition that heighten or reduce a policy’s fragility, arguing that it depends on: (a) a tight/loose coupling of legitimacy to underlying authoritative discourses, (b) the volatility of these sources of authority and (c) the agenda-setting power of groups opposing the status quo.
Short article: Frequency, pathophysiology, and clinical classification of intestinal failure type II and III at a tertiary referral center
Authors: Rosas-Flota Ximena , Castillo-Martínez Lilia , Reyes-Ramírez Ana L. , Osorio-Alamillo Yahiel , Murguía-Vázquez Maria , Serralde-Zúñiga Aurora E. 
Published: October 2018

Objective
Intestinal failure (IF) is a complex disease that is gaining significance and attention throughout the world. In Mexico, there are no available data on this condition. The aim of this study was to determine the frequency and characteristics of patients with IF type II and III hospitalized at a tertiary referral center in our country.

Patients and methods
A cross-sectional study was carried out from August 2016 to July 2017. Adult patients hospitalized in noncritical areas with a recent diagnosis of IF type II or III according to the European Society for Clinical Nutrition and Metabolism classification were included. Demographic, anthropometric, nutritional therapy, biochemical, and clinical characteristics were registered. Nutritional risk was determined by the Nutritional Risk Score 2002.

Results
During the study, 4144 patients were admitted to noncritical areas; 21 (5/1000) of these patients were included. The mean age of the patients was 51±18.8 years, and the mean BMI was 17.6±5.5 kg/m2. Fifteen (71.5%) patients were diagnosed with IF type II and six (28.5%) with IF type III. The primary diagnosis was surgical complications in seven (33.3%) of the cases and the principal pathophysiological mechanism was short bowel syndrome in nine (42.8%) patients. The most frequent (37%) clinical classification was D2: more than 20 kcal/kg/day and 1001–2000 ml/day and parenteral nutrition and PN2: 1001–2000 ml/day (52.3%) based on the modified European Society for Clinical Nutrition and Metabolism clinical classification.

Conclusion
In this study, a high frequency of IF was found; surgical complications and short bowel syndrome were the main mechanisms involved, and D2 was the most frequent clinical category.
Rates of generation and destruction of the continental crust: implications for continental growth
Authors: Dhuime Bruno , Hawkesworth Chris J. , Delavault Hélène , Cawood Peter A. 
Published: October 2018

Less than 25% of the volume of the juvenile continental crust preserved today is older than 3 Ga, there are no known rocks older than approximately 4 Ga, and yet a number of recent models of continental growth suggest that at least 60–80% of the present volume of the continental crust had been generated by 3 Ga. Such models require that large volumes of pre-3 Ga crust were destroyed and replaced by younger crust since the late Archaean. To address this issue, we evaluate the influence on the rock record of changing the rates of generation and destruction of the continental crust at different times in Earth's history. We adopted a box model approach in a numerical model constrained by the estimated volumes of continental crust at 3 Ga and the present day, and by the distribution of crust formation ages in the present-day crust. The data generated by the model suggest that new continental crust was generated continuously, but with a marked decrease in the net growth rate at approximately 3 Ga resulting in a temporary reduction in the volume of continental crust at that time. Destruction rates increased dramatically around 3 billion years ago, which may be linked to the widespread development of subduction zones. The volume of continental crust may have exceeded its present value by the mid/late Proterozoic. In this model, about 2.6–2.3 times of the present volume of continental crust has been generated since Earth's formation, and approximately 1.6–1.3 times of this volume has been destroyed and recycled back into the mantle.
This article is part of a discussion meeting issue ‘Earth dynamics and the development of plate tectonics'.
Geological archive of the onset of plate tectonics
Authors: Cawood Peter A. , Hawkesworth Chris J. , Pisarevsky Sergei A. , Dhuime Bruno , Capitanio Fabio A. , Nebel Oliver 
Published: October 2018

Plate tectonics, involving a globally linked system of lateral motion of rigid surface plates, is a characteristic feature of our planet, but estimates of how long it has been the modus operandi of lithospheric formation and interactions range from the Hadean to the Neoproterozoic. In this paper, we review sedimentary, igneous and metamorphic proxies along with palaeomagnetic data to infer both the development of rigid lithospheric plates and their independent relative motion, and conclude that significant changes in Earth behaviour occurred in the mid- to late Archaean, between 3.2 Ga and 2.5 Ga. These data include: sedimentary rock associations inferred to have accumulated in passive continental margin settings, marking the onset of sea-floor spreading; the oldest foreland basin deposits associated with lithospheric convergence; a change from thin, new continental crust of mafic composition to thicker crust of intermediate composition, increased crustal reworking and the emplacement of potassic and peraluminous granites, indicating stabilization of the lithosphere; replacement of dome and keel structures in granite-greenstone terranes, which relate to vertical tectonics, by linear thrust imbricated belts; the commencement of temporally paired systems of intermediate and high dT/dP gradients, with the former interpreted to represent subduction to collisional settings and the latter representing possible hinterland back-arc settings or ocean plateau environments. Palaeomagnetic data from the Kaapvaal and Pilbara cratons for the interval 2780–2710 Ma and from the Superior, Kaapvaal and Kola-Karelia cratons for 2700–2440 Ma suggest significant relative movements. We consider these changes in the behaviour and character of the lithosphere to be consistent with a gestational transition from a non-plate tectonic mode, arguably with localized subduction, to the onset of sustained plate tectonics.
This article is part of a discussion meeting issue ‘Earth dynamics and the development of plate tectonics'.
Crustal evolution and mantle dynamics through Earth history
Authors: Korenaga Jun 
Published: October 2018

Resolving the modes of mantle convection through Earth history, i.e. when plate tectonics started and what kind of mantle dynamics reigned before, is essential to the understanding of the evolution of the whole Earth system, because plate tectonics influences almost all aspects of modern geological processes. This is a challenging problem because plate tectonics continuously rejuvenates Earth's surface on a time scale of about 100 Myr, destroying evidence for its past operation. It thus becomes essential to exploit indirect evidence preserved in the buoyant continental crust, part of which has survived over billions of years. This contribution starts with an in-depth review of existing models for continental growth. Growth models proposed so far can be categorized into three types: crust-based, mantle-based and other less direct inferences, and the first two types are particularly important as their difference reflects the extent of crustal recycling, which can be related to subduction. Then, a theoretical basis for a change in the mode of mantle convection in the Precambrian is reviewed, along with a critical appraisal of some popular notions for early Earth dynamics. By combining available geological and geochemical observations with geodynamical considerations, a tentative hypothesis is presented for the evolution of mantle dynamics and its relation to surface environment; the early onset of plate tectonics and gradual mantle hydration are responsible not only for the formation of continental crust but also for its preservation as well as its emergence above sea level. Our current understanding of various material properties and elementary processes is still too premature to build a testable, quantitative model for this hypothesis, but such modelling efforts could potentially transform the nature of the data-starved early Earth research by quantifying the extent of preservation bias.
This article is part of a discussion meeting issue ‘Earth dynamics and the development of plate tectonics’.
Global tectonic evolution of Venus, from exogenic to endogenic over time, and implications for early Earth processes
Authors: Hansen Vicki L. 
Published: October 2018

Venus provides a rich arena in which to stretch one's tectonic imagination with respect to non-plate tectonic processes of heat transfer on an Earth-like planet. Venus is similar to Earth in density, size, inferred composition and heat budget. However, Venus' lack of plate tectonics and terrestrial surficial processes results in the preservation of a unique surface geologic record of non-plate tectonomagmatic processes. In this paper, I explore three global tectonic domains that represent changes in global conditions and tectonic regimes through time, divided respectively into temporal eras. Impactors played a prominent role in the ancient era, characterized by thin global lithosphere. The Artemis superstructure era highlights sublithospheric flow processes related to a uniquely large super plume. The fracture zone complex era, marked by broad zones of tectonomagmatic activity, witnessed coupled spreading and underthrusting, since arrested. These three tectonic regimes provide possible analogue models for terrestrial Archaean craton formation, continent formation without plate tectonics, and mechanisms underlying the emergence of plate tectonics. A bolide impact model for craton formation addresses the apparent paradox of both undepleted mantle and growth of Archaean crust, and recycling of significant Archaean crust to the mantle.This article is part of a discussion meeting issue ‘Earth dynamics and the development of plate tectonics’.
The inception of plate tectonics: a record of failure
Authors: O'Neill Craig , Turner Simon , Rushmer Tracy 
Published: October 2018

The development of plate tectonics from a pre-plate tectonics regime requires both the initiation of subduction and the development of nascent subduction zones into long-lived contiguous features. Subduction itself has been shown to be sensitive to system parameters such as thermal state and the specific rheology. While generally it has been shown that cold-interior high-Rayleigh-number convection (such as on the Earth today) favours plates and subduction, due to the ability of the interior stresses to couple with the lid, a given system may or may not have plate tectonics depending on its initial conditions. This has led to the idea that there is a strong history dependence to tectonic evolution—and the details of tectonic transitions, including whether they even occur, may depend on the early history of a planet. However, intrinsic convective stresses are not the only dynamic drivers of early planetary evolution. Early planetary geological evolution is dominated by volcanic processes and impacting. These have rarely been considered in thermal evolution models. Recent models exploring the details of plate tectonic initiation have explored the effect of strong thermal plumes or large impacts on surface tectonism, and found that these ‘primary drivers’ can initiate subduction, and, in some cases, over-ride the initial state of the planet. The corollary of this, of course, is that, in the absence of such ongoing drivers, existing or incipient subduction systems under early Earth conditions might fail. The only detailed planetary record we have of this development comes from Earth, and is restricted by the limited geological record of its earliest history. Many recent estimates have suggested an origin of plate tectonics at approximately 3.0 Ga, inferring a monotonically increasing transition from pre-plates, through subduction initiation, to continuous subduction and a modern plate tectonic regime around that time. However, both numerical modelling and the geological record itself suggest a strong nonlinearity in the dynamics of the transition, and it has been noted that the early history of Archaean greenstone belts and trondhjemite–tonalite–granodiorite record many instances of failed subduction. Here, we explore the history of subduction failure on the early Earth, and couple these with insights from numerical models of the geodynamic regime at the time.
This article is part of a discussion meeting issue ‘Earth dynamics and the development of plate tectonics'.
The diversity of tectonic modes and thoughts about transitions between them
Authors: Lenardic A. 
Published: October 2018

Plate tectonics is a particular mode of tectonic activity that characterizes the present-day Earth. It is directly linked to not only tectonic deformation but also magmatic/volcanic activity and all aspects of the rock cycle. Other terrestrial planets in our Solar System do not operate in a plate tectonic mode but do have volcanic constructs and signs of tectonic deformation. This indicates the existence of tectonic modes different from plate tectonics. This article discusses the defining features of plate tectonics and reviews the range of tectonic modes that have been proposed for terrestrial planets to date. A categorization of tectonic modes relates to the issue of when plate tectonics initiated on Earth as it provides insights into possible pre-plate tectonic behaviour. The final focus of this contribution relates to transitions between tectonic modes. Different transition scenarios are discussed. One follows classic ideas of regime transitions in which boundaries between tectonic modes are determined by the physical and chemical properties of a planet. The other considers the potential that variations in temporal evolution can introduce contingencies that have a significant effect on tectonic transitions. The latter scenario allows for the existence of multiple stable tectonic modes under the same physical/chemical conditions. The different transition potentials imply different interpretations regarding the type of variable that the tectonic mode of a planet represents. Under the classic regime transition view, the tectonic mode of a planet is a state variable (akin to temperature). Under the multiple stable modes view, the tectonic mode of a planet is a process variable. That is, something that flows through the system (akin to heat). The different implications that follow are discussed as they relate to the questions of when did plate tectonics initiate on Earth and why does Earth have plate tectonics.This article is part of a discussion meeting issue ‘Earth dynamics and the development of plate tectonics’.
Structural connectivity analysis using Finsler geometry
Authors: Haije Tom Dela , Savadjiev Peter , Fuster Andrea , Schultz Robert T. , Verma Ragini , Florack Luc , Westin Carl-Fredrik 
Published: October 2018

AbstractIn this work we demonstrate how Finsler geometry—and specifically the related geodesic tractography— can be levied to analyze structural connections between different brain regions. We present new theoretical developments which support the definition of a novel Finsler metric and associated con-nectivity measures, based on closely related works on the Riemannian framework for diffusion MRI. Using data from the Human Connectome Project, as well as population data from an autism spectrum disorder study, we demonstrate that this new Finsler metric, together with the new connectivity measures, results in connectivity maps that are much closer to known tract anatomy compared to previous geodesic connectivity methods. Our implementation can be used to compute geodesic distance and connectivity maps for segmented areas, and is publicly available.
Vertical and horizontal integration of multi-omics data with miodin
Authors: Ulfenborg Benjamin 
Published: October 2018

AbstractBackgroundStudies on multiple modalities of omics data such as transcriptomics, genomics and proteomics are growing in popularity, since they allow us to investigate complex mechanisms across molecular layers. It is widely recognized that integrative omics analysis holds the promise to unlock novel and actionable biological insights to health and disease. Integration of multi-omics data remains challenging, however, and requires combination of several software tools and extensive technical expertise to account for the properties of heterogeneous data.ResultsThis paper presents the miodin R package, which provides a streamlined workflow-based syntax for multi-omics data analysis. The package allows users to perform analysis and integration of omics data either across experiments on the same samples, or across studies on the same variables. Workflows have been designed to promote transparent data analysis and reduce the technical expertise required to perform low-level data import and processing.ConclusionsThe miodin package is implemented in R and is freely available for use and extension under the GPL-3 license. Package source, reference documentation and user manual are available athttps://gitlab.com/algoromics/miodin.
Dynamic mode decomposition of resting-state and task fMRI
Authors: Casorso Jeremy , Kong Xiaolu , Chi Wang , Van De Ville Dimitri , Yeo B.T. Thomas , Liégeois Raphaël 
Published: October 2018

AbstractComponent analysis is a powerful tool to identify dominant patterns of interactions in multivariate datasets. In the context of fMRI data, methods such as principal component analysis or independent component analysis have been used to identify the brain networks shaping functional connectivity (FC). Importantly, these approaches are static in the sense that they ignore the temporal information contained in fMRI time series. Therefore, the corresponding components provide a static characterization of FC. Building upon recent findings suggesting that FC dynamics encode richer information about brain functional organization, we use a dynamic extension of component analysis to identify dynamic modes (DMs) of fMRI time series. We demonstrate the feasibility and relevance of this approach using resting-state and motor-task fMRI data of 730 healthy subjects of the Human Connectome Project (HCP). In resting-state, dominant DMs have strong resemblance with classical resting-state networks, with an additional temporal characterization of the networks in terms of oscillatory periods and damping times. In motor-task conditions, dominant DMs reveal interactions between several brain areas, including but not limited to the posterior parietal cortex and primary motor areas, that are not found with classical activation maps. Finally, we identify two canonical components linking the temporal properties of the resting-state DMs with 158 behavioral and demographic HCP measures. Altogether, these findings illustrate the benefits of the proposed dynamic component analysis framework, making it a promising tool to characterize the spatio-temporal organization of brain activity.
Crystal structure of aThermus aquaticusdiversity-generating retroelement variable protein
Authors: Handa Sumit , Shaw Kharissa L , Ghosh Partho 
Published: October 2018

AbstractDiversity-generating retroelements (DGRs) are widely distributed in bacteria, archaea, and microbial viruses, and bring about unparalleled levels of sequence variation in target proteins. While DGR variable proteins share low sequence identity, the structures of several such proteins have revealed the C-type lectin (CLec)-fold as a conserved scaffold for accommodating massive sequence variation. This conservation has led to the suggestion that the CLec-fold may be useful in molecular surface display applications. Thermostability is an attractive feature in such applications, and thus we studied the variable protein of a DGR encoded by the thermophileThermus aquaticus. We report here the 2.8 Å resolution crystal structure of the variable protein from theT. aquaticusDGR, called TaqVP, and confirm that it has a CLec-fold. Remarkably, its variable region is nearly identical in structure to those of several other CLec-fold DGR variable proteins despite low sequence identity among these. TaqVP was found to be thermostable, which appears to be a property shared by several CLec-fold DGR variable proteins. These results provide impetus for the pursuit of the DGR variable protein CLec-fold in molecular display applications.
Decreased integrity of exercise-induced plasma cell free nuclear DNA – negative association with the increased oxidants production by circulating phagocytes
Authors: Stawski Robert , Walczak Konrad , Perdas Ewelina , Wlodarczyk Anna , Sarniak Agata , Kosielski Piotr , Meissner Pawel , Budlewski Tomasz , Padula Gianluca , Nowak Dariusz 
Published: October 2018

AbstractStrenuous exercise increases circulating cell free DNA (cf DNA) and stimulates blood phagocytes to generate reactive oxygen species (ROS) which may induce DNA strand breaks. We tested whether: (A) elevated cf DNA in response to three repeated bouts of exhaustive exercise has decreased integrity; (B) each bout of exercise increases luminol enhanced whole blood chemiluminescence (LBCL) as a measure of ROS production by polymorphonuclear leukocytes. Eleven men performed three treadmill exercise tests to exhaustion separated by 72 hours of resting. Pre- and post-exercise concentrations and integrity of cf nuclear and mitochondrial DNA (cf n-DNA, cf mt-DNA) and resting and fMLP-stimulated LBCL were determined. Each bout increased concentrations of cf n-DNA by more than 10-times which was accompanied by about 2-times elevated post-exercise rLBCL and fMLP-LBCL. Post-exercise cf n-DNA integrity (integrity index, I206/78) decreased after the first (0.59±0.19 vs. 0.48±0.18) and second (0.53±0.14 vs. 0.44±0.17) bout of exercise. There were negative correlations between I206/78and rLBCL (ƍ=−0.37) and I206/78and fMLP-LBCL (ƍ=− 0.40) – analysis of pooled pre- and post-exercise data (n=66). cf-mt DNA integrity (I218/97) did not alter in response to exercise. This suggests an involvement of phagocyte ROS in cf n-DNA strand breaks in response to exhaustive exercise.