bluuebunny/crossref_metadata_2025_split huggingface dataset:
AVISA: anisotropic visco-ISA model and its performance at cyclic loading
Authors: Tafili Merita , Triantafyllidis Theodoros 
Published: February 2020

AbstractIn this work, a constitutive model able to capture the strain rate dependency, small strain effects and the inherent anisotropy is proposed considering the influence of the overconsolidation ratio (OCR). Small strain effects are captured by using an extended ISA plasticity formulation (Fuentes and Triantafyllidis in Int J Numer Anal Methods Geomech 39(11):1235–1254, 2015). The strain rate dependency is reproduced by incorporating a third strain rate mechanism (in addition to the elastic and hypoplastic strain rate). A loading surface has been incorporated to define a three-dimensional (3D) overconsolidation ratio and to account for its effects on the simulations. Experimental investigations using Kaolin Clay and Lower Rhine Clay with horizontal bedding plane have shown that under undrained cycles of small strain amplitudes ($$<10^{-4}$$

<

10

-
4

), the effective stress path in the p–q space is significantly inclined towards the left upper corner of the $$p - q$$

p
-
q

plane. Consequently, a transversely (hypo)elastic stiffness has been successfully formulated to capture this behaviour. The performance of the model has been inspected by simulating the database of approximately 50 cyclic undrained triaxial (CUT) tests on low-plasticity Kaolin Clay (Wichtmann and Triantafyllidis) considering different deviatoric stress amplitudes, initial stress ratios, displacement rate, overconsolidation ratio and cutting direction. Furthermore, 4 CUT tests conducted on high-plasticity Lower Rhine Clay were simulated, whereby the influence of the displacement rate, as well as the deviatoric stress amplitude, has been analysed. The simulations showed a good congruence with the experimental observations.
Collaboration, creativity, conflict and chaos: doing interdisciplinary sustainability research
Authors: Cairns Rose , Hielscher Sabine , Light Ann 
Published: February 2020

AbstractHow do the social dynamics within interdisciplinary research teams shape sustainability research? This paper presents a case study of interdisciplinary research projects at the University of Sussex, as part of a programme aimed at encouraging collaborative work to address intersections between the Sustainability Development Goals. Using data gathered during a series of participatory workshops at the start and end of the projects, combined with non-participant observation and analysis of project discussions during the lifetime of the projects, we examine the diverse ways in which research teams configure themselves to navigate the terrain of interdisciplinary sustainability research and the kinds of social and discursive dynamics that shape projects. In particular, we relate the emergence of distinct project team configurations to diverse problem framings, and aspirations for collaboration within these teams. We examine some of the challenges facing researchers attempting to work in these ways, and explore implications of these dynamics for knowledge production for sustainability. We conclude by drawing out and addressing some of the challenges for institutions funding and supporting interdisciplinary sustainability research.
Phase Transformation-Induced Changes in Microstructure and Residual Stresses in Thermally Sprayed MnCoFeO4 Protective Coatings
Authors: Back Hyoung Chul , Gibmeier Jens , Vaßen Robert 
Published: February 2020

AbstractThe contribution comprises the investigation of the microstructure and residual stresses in thermally sprayed Mn1.0Co1.9Fe0.1O4.0 (MCF) protective coatings for interconnectors of SOFC stacks, deposited on ferritic steel Crofer 22 APU via atmospheric plasma spraying (APS). The coatings are designated to prevent Cr evaporation during high operation temperature of the SOFCs. The local microstructure, pore distributions and pore shapes, phase fractions, micro-hardness, Youngs’ modulus and residual stresses through the coating thickness were characterized in as-sprayed state and compared with longtime (10-100 h) heat-treated samples (700 and 850 °C). The results show that the long-term thermal aging treatment causes a successive high sintering of the coatings characterized by a reduction in pore density, by phase transformation from the metastable rock salt structure that gradually transformed to a spinel structure and by a slight relaxation of the process-induced tensile residual stresses in the coating. For SOFC application of the MCF coating, this indicates an improvement in the coatings integrity. During operation, a self-repair proceeds leading to dense and gas-proof coatings, while the mechanical properties are mainly retained.
Structural Disjunctivism, Indistinguishability and Introspection
Authors: Franken Dirk 
Published: February 2020

Abstract1Perceptual disjunctivism, as I regard it in this paper, is the view that veridical perceptions and hallucinations, while indistinguishable via introspection, are states of fundamentally different kinds. This fundamental difference can be spelled out in various ways. According to the view I will be concerned with (structural disjunctivism, as I shall call it), it is a fundamental difference in the personal-level structure of both states. Against this version of disjunctivism, I will raise a new challenge. It is a variant of what can be seen as the standard challenge against disjunctivism: how to do justice to the indistinguishability of (corresponding) veridical perceptions and hallucinations. It differs, however, from common versions of this challenge in where it locates the potential incompatibility of disjunctivism with the relevant fact of indistinguishability. Commonly, it is the disjunctivist assumption of a fundamental difference between both kinds ofstateswhich is regarded as incompatible with the indistinguishability of these states. In contrast, I will suggest that (i) if hallucinations and veridical perceptions differed in the way proposed by structural disjunctivism, this difference would induce a corresponding difference in the psychological processes of theirintrospectionand that (ii) the assumption of such a difference in the manner of introspection is most likely incompatible with a properly formulated indistinguishability claim.
Functional characterization of the idtF and idtP genes in the Claviceps paspali indole diterpene biosynthetic gene cluster
Authors: Kozák László , Szilágyi Zoltán , Tóth László , Pócsi István , Molnár István 
Published: February 2020

AbstractClaviceps paspali is used in the pharmaceutical industry for the production of ergot alkaloids. This fungus also biosynthesizes paspalitrems, indole diterpene (IDT) mycotoxins that cause significant economic losses in agriculture and represent safety concerns for ergot alkaloid manufacture. Here, we use Agrobacterium-mediated transformation to replace the idtP and the idtF genes in the IDT biosynthetic gene cluster of C. paspali with a selectable marker gene. We show that the ΔidtP knockout mutant produces paspaline, the first IDT intermediate of the pathway. The ΔidtF strain produces unprenylated IDTs such as paspalinine and paspaline. These experiments validate the function of idtP as the gene encoding the cytochrome P450 monooxygenase that oxidizes and demethylates paspaline to produce 13-desoxypaxilline, and that of idtF as the gene that encodes the α-prenyltransferase that prenylates paspalinine at the C20 or the C21 positions to yield paspalitrems A and C, respectively. In addition, we also show that axenic cultures of the wild type, the ΔidtP and the ΔidtF mutant C. paspali strains fail to produce an assembly of IDTs that are present in C. paspali–Paspalum spp. associations.
Introduction: Urban Slavery in the Age of Abolition
Authors: Fatah-Black Karwan 
Published: February 2020

AbstractThis Special Issue collects articles on urban slavery in the Atlantic world during the time when the institution of slavery was being abolished globally (c.1770s–c.1880s). At the time of abolition, most slaves were held on plantations, but this did not mean that the urban context of slavery was unimportant. In the cities of the Atlantic world, slavery was pervasive, and the cities themselves played an important role in the functioning of the slave system. This Special Issue seeks to examine urban slavery in its connection to the wider slave-based economy, and to address how slavery in the cities changed when abolition appeared on the political agenda in the Atlantic world. The articles in this issue find that urban communities went through great changes in the age of abolition and these changes proved crucial to determining the legacies of slavery and its abolition. Recovering the history of urban slavery in this area should come to inform the current mainstreaming of the memory of slavery around the Atlantic world. Attention to its history can provide new layers of understanding to the persistence of inequity and historical silencing today.
Evidence for an Oceanic Source of Methyl Ethyl Ketone to the Atmosphere
Authors: Brewer J. F. , Fischer E. V. , Commane R. , Wofsy S. C. , Daube B.C. , Apel E. C. , Hills A. J. , Hornbrook R. S. , Barletta B. , Meinardi S. , Blake D. R. , Ray E. A. , Ravishankara A. R. 
Published: February 2020

AbstractMethyl ethyl ketone (MEK) is a relatively abundant but understudied oxygenated volatile organic compound that can serve as a source of both HOx and PAN when photooxidized. We use aircraft observations of MEK from the remote marine troposphere to show that the ocean serves as a source of MEK to the atmosphere during both meteorological winter and summer. There is pronounced seasonality in the MEK profiles in the extratropical troposphere, with higher MEK mixing ratios observed in summer than in winter. MEK in clean air over the remote oceans correlates with both acetone and acetaldehyde, whose primary sources in the ocean water are the photooxidation of organic material. We show that even a small (>1 nM) concentration of MEK in surface waters is sufficient to allow the ocean to be a net source of MEK to the atmosphere over ocean basins across multiple seasons.
Detecting Mesopelagic Organisms Using Biogeochemical‐Argo Floats
Authors: Haëntjens Nils , Della Penna Alice , Briggs Nathan , Karp‐Boss Lee , Gaube Peter , Claustre Hervé , Boss Emmanuel 
Published: February 2020

AbstractDuring the North Atlantic Aerosols and Marine Ecosystems Study in the western North Atlantic, float‐based profiles of fluorescent dissolved organic matter and backscattering exhibited distinct spike layers at
300 m. The locations of the spikes were at depths similar or shallower to where a ship‐based scientific echo sounder identified layers of acoustic backscatter, an Underwater Vision Profiler detected elevated concentration of zooplankton, and mesopelagic fish were sampled by a mesopelagic net tow. The collocation of spike layers in bio‐optical properties with mesopelagic organisms suggests that some can be detected with float‐based bio‐optical sensors. This opens the door to the investigation of such aggregations/layers in observations collected by the global biogeochemical‐Argo array allowing the detection of mesopelagic organisms in remote locations of the open ocean under‐sampled by traditional methods.
Where Is the Bottom of a Watershed?
Authors: Condon Laura E. , Markovich Katherine H. , Kelleher Christa A. , McDonnell Jeffrey J. , Ferguson Grant , McIntosh Jennifer C. 
Published: February 2020

AbstractWatersheds have served as one of our most basic units of organization in hydrology for over 300 years (Dooge, 1988, https://doi.org/10.1080/02626668809491223; McDonnell, 2017, https://doi.org/10.1038/ngeo2964; Perrault, 1674, https://www.abebooks.com/first‐edition/lorigine‐fontaines‐Perrault‐Pierre‐Petit‐Imprimeur/21599664536/bd). With growing interest in groundwater‐surface water interactions and subsurface flow paths, hydrologists are increasingly looking deeper. But the dialog between surface water hydrologists and groundwater hydrologists is still embryonic, and many basic questions are yet to be posed, let alone answered. One key question is: where is the bottom of a watershed? Knowing where to draw the bottom boundary has not yet been fully addressed in the literature, and how to define the watershed “bottom” is a fraught question. There is large variability across physical and conceptual models regarding how to implement a watershed bottom, and what counts as “deep” varies markedly in different communities. In this commentary, we seek to initiate a dialog on existing approaches to defining the bottom of the watershed. We briefly review the current literature describing how different communities typically frame the answer of just how deep we should look and identify situations where deep flow paths are key to developing realistic conceptual models of watershed systems. We then review the common conceptual approaches used to delineate the watershed lower boundary. Finally, we highlight opportunities to trigger this potential research area at the interface of catchment hydrology and hydrogeology.
Polysaccharide niche partitioning of distinct Polaribacter clades during North Sea spring algal blooms
Authors: Avcı Burak , Krüger Karen , Fuchs Bernhard M , Teeling Hanno , Amann Rudolf I 
Published: February 2020

Abstract
Massive releases of organic substrates during marine algal blooms trigger growth of many clades of heterotrophic bacteria. Algal polysaccharides represent the most diverse and structurally complex class of these substrates, yet their role in shaping the microbial community composition is poorly understood. We investigated, whether polysaccharide utilization capabilities contribute to niche differentiation of Polaribacter spp. (class Flavobacteriia; known to include relevant polysaccharide-degraders) that were abundant during 2009–2012 spring algal blooms in the southern North Sea. We identified six distinct Polaribacter clades using phylogenetic and phylogenomic analyses, quantified their abundances via fluorescence in situ hybridization, compared metagenome-assembled genomes, and assessed in situ gene expression using metaproteomics. Four clades with distinct polysaccharide niches were dominating. Polaribacter 2-a comprised typical first responders featuring small genomes with limited polysaccharide utilization capacities. Polaribacter 3-a were abundant only in 2010 and possessed a distinct sulfated α-glucoronomannan degradation potential. Polaribacter 3-b responded late in blooms and had the capacity to utilize sulfated xylan. Polaribacter 1-a featured high numbers of glycan degradation genes and were particularly abundant following Chattonella algae blooms. These results support the hypothesis that sympatric Polaribacter clades occupy distinct glycan niches during North Sea spring algal blooms.
A phylogenetic model for the recruitment of species into microbial communities and application to studies of the human microbiome
Authors: Darcy John L , Washburne Alex D , Robeson Michael S , Prest Tiffany , Schmidt Steven K , Lozupone Catherine A 
Published: February 2020

Abstract
Understanding when and why new species are recruited into microbial communities is a formidable problem with implications for managing microbial systems, for instance by helping us better understand whether a probiotic or pathogen would be expected to colonize a human microbiome. Much theory in microbial temporal dynamics is focused on how phylogenetic relationships between microbes impact the order in which those microbes are recruited; for example, species that are closely related may competitively exclude each other. However, several recent human microbiome studies have observed closely related bacteria being recruited into microbial communities in short succession, suggesting that microbial community assembly is historically contingent, but competitive exclusion of close relatives may not be important. To address this, we developed a mathematical model that describes the order in which new species are detected in microbial communities over time within a phylogenetic framework. We use our model to test three hypothetical assembly modes: underdispersion (species recruitment is more likely if a close relative was previously detected), overdispersion (recruitment is more likely if a close relative has not been previously detected), and the neutral model (recruitment likelihood is not related to phylogenetic relationships among species). We applied our model to longitudinal human microbiome data, and found that for the individuals we analyzed, the human microbiome generally follows the underdispersion (i.e., nepotism) hypothesis. Exceptions were oral communities and the fecal communities of two infants that had undergone heavy antibiotic treatment. None of the datasets we analyzed showed statistically significant phylogenetic overdispersion.
Defining variation in pre-human ecosystems can guide conservation: An example from a Caribbean coral reef
Authors: O’Dea Aaron , Lepore Mauro , Altieri Andrew H. , Chan Melisa , Morales-Saldaña Jorge Manuel , Muñoz Nicte-Ha , Pandolfi John M. , Toscano Marguerite A. , Zhao Jian-xin , Dillon Erin M. 
Published: February 2020

AbstractMany Caribbean coral reefs are heavily degraded, yet their pre-human, natural states are often assumed or estimated using space-for-time substitution approaches. Here we use an 11-hectare suite of fossilised mid-Holocene (7.2–5.6 ka) fringing reefs in Caribbean Panama to define natural variation in hard coral community structure before human-impact to provide context to the states of the same reefs today. We collected bulk samples from four trenches dug into the mid-Holocene fossil reef and surficial bulk samples from 2–10 m depths on five adjacent modern reefs extending over 5 km. Analysis of the abundances of coral taxa in fossil bulk samples define the Historical Range of Variation (HRV) in community structure of the reefs. When compared to the community structure of adjacent modern reefs, we find that most coral communities today fall outside the HRV, identifying them as novel ecosystems and corroborating the well-documented transition from acroporid-dominated Caribbean reefs to reefs dominated by stress-tolerant taxa (Porites and Agaricia). We find one modern reef, however, whose community composition remains within the HRV showing that it has not transitioned to a novel state. Reef-matrix cores extracted from this reef reveal that the coral community has remained in this state for over 800 years, suggesting long-term stability and resistance to the region-wide shift to novel states. Without these data to provide historical context, this potentially robust and stable reef would be overlooked since it does not fulfil expectations of what a Caribbean coral reef should look like in the absence of humans. This example illustrates how defining past variation using the fossil record can improve our understanding of modern degradation and guide conservation.
Patient Semi-specific Computational Modeling of Electromagnetic Stimulation Applied to Neuroprotective Treatments in Acute Ischemic Stroke
Authors: Colella Micol , Camera Francesca , Capone Fioravante , Setti Stefania , Cadossi Ruggero , Di Lazzaro Vincenzo , Apollonio Francesca , Liberti Micaela 
Published: February 2020

AbstractNeuroprotective effects of pulsed electromagnetic fields (PEMFs) have been demonstrated both in vivo and in vitro. Moreover, preliminary clinical studies have been conducted and suggested PEMFs as a possible alternative therapy to treat acute ischemic stroke. In this work, we show that it’s possible to build-up a patient semi-specific head model, where the 3D reconstruction of the ischemic lesion of the patient under treatment is inserted in the head of the human body model “Duke” (v.1.0, Zurich MedTech AG). The semi-specific model will be used in the randomized, placebo-controlled, double-blind study currently ongoing. Three patients were modelled and simulated, and results showed that each ischemic lesion experiences a magnetic flux density field comparable to the one for which biological effects have been attested. Such a kind of dosimetric analysis reveals a reliable tool to assess the correlation between levels of exposure and the beneficial effect. Thus, once the on-going double blind study is complete it will prove if PEMFs treatment triggers a clinical effect, and we will then be able to characterize a dose-response curve with the methodology arranged in this study.
Prevalence and association of single nucleotide polymorphisms with sarcopenia in older women depends on definition
Authors: Khanal Praval , He Lingxiao , Stebbings Georgina , Onambele-Pearson Gladys L. , Degens Hans , Williams Alun , Thomis Martine , Morse Christopher I. 
Published: February 2020

AbstractThe prevalence of sarcopenia depends on the definition used. There are, however, consistent sarcopenic characteristics, including a low muscle mass and muscle strength. Few studies have investigated the relationship between sarcopenia and genotype. A cross-sectional study was conducted with 307 community-dwelling ≥60-year-old women in South Cheshire, UK. Handgrip strength was assessed with a handgrip dynamometer and skeletal muscle mass was estimated using bioelectrical impedance. DNA was extracted from saliva (∼38%) or blood (∼62%) and 24 single-nucleotide polymorphisms (SNPs) were genotyped. Three established sarcopenia definitions - %Skeletal Muscle Mass (%SMM), Skeletal Muscle Mass Index (SMI) and European Working Group on Sarcopenia in Older People (EWGSOP) - were used to assess sarcopenia prevalence. Binary logistic regression with age as covariate was used to identify SNPs associated with sarcopenia. The prevalence of sarcopenia was: %SMM 14.7%, SMI 60.6% and EWGSOP 1.3%. Four SNPs were associated with the %SMM and SMI definitions of sarcopenia; FTO rs9939609, ESR1 rs4870044, NOS3 rs1799983 and TRHR rs7832552. The first three were associated with the %SMM definition, and TRHR rs7832552 with the SMI definition, but none were common to both sarcopenia definitions. The gene variants associated with sarcopenia may help proper counselling and interventions to prevent individuals from developing sarcopenia.
Analysis of asymmetry in lipid and content mixing assays with reconstituted proteoliposomes containing the neuronal SNAREs
Authors: Pan Yun-Zu , Liu Xiaoxia , Rizo Josep 
Published: February 2020

AbstractReconstitution assays with proteoliposomes provide a powerful tool to elucidate the mechanism of neurotransmitter release, but it is important to understand how these assays report on membrane fusion, and recent studies with yeast vacuolar SNAREs uncovered asymmetry in the results of lipid mixing assays. We have investigated whether such asymmetry also occurs in reconstitution assays with the neuronal SNAREs, using syntaxin-1-SNAP-25-containing liposomes and liposomes containing synaptobrevin (T and V liposomes, respectively), and fluorescent probes to monitor lipid and content mixing simultaneously. Switching the fluorescent probes placed on the T and V liposomes, we observed a striking asymmetry in both lipid and content mixing stimulated by a fragment spanning the two C2 domains of synaptotagmin-1, or by a peptide that spans the C-terminal half of the synaptobrevin SNARE motif. However, no such asymmetry was observed in assays performed in the presence of Munc18-1, Munc13-1, NSF and αSNAP, which coordinate the assembly-disassembly cycle of neuronal SNARE complexes. Our results show that switching fluorescent probes between the two types of liposomes provides a useful approach to better understand the reactions that occur between liposomes and detect heterogenous behavior in these reactions.