bluuebunny/crossref_metadata_2025_split huggingface dataset:
Eddy Compensation Dampens Southern Ocean Sea Surface Temperature Response to Westerly Wind Trends
Authors: Doddridge Edward W. , Marshall John , Song Hajoon , Campin Jean‐Michel , Kelley Maxwell , Nazarenko Larissa 
Published: April 2019

AbstractAnthropogenic influences have led to a strengthening and poleward shift of westerly winds over the Southern Ocean, especially during austral summer. We use observations, an idealized eddy‐resolving ocean sea ice channel model, and a global coupled model to explore the Southern Ocean response to a step change in westerly winds. Previous work hypothesized a two time scale response for sea surface temperature. Initially, Ekman transport cools the surface before sustained upwelling causes warming on decadal time scales. The fast response is robust across our models and the observations: We find Ekman‐driven cooling in the mixed layer, mixing‐driven warming below the mixed layer, and a small upwelling‐driven warming at the temperature inversion. The long‐term response is inaccessible from observations. Neither of our models shows a persistent upwelling anomaly, or long‐term, upwelling‐driven subsurface warming. Mesoscale eddies act to oppose the anomalous wind‐driven upwelling, through a process known as eddy compensation, thereby preventing long‐term warming.
“CandidatusMacondimonas diazotrophica”, a novel gammaproteobacterial genus dominating crude-oil-contaminated coastal sediments
Authors: Karthikeyan Smruthi , Rodriguez-R Luis M , Heritier-Robbins Patrick , Kim Minjae , Overholt Will A , Gaby John C , Hatt Janet K , Spain Jim C , Rosselló-Móra Ramon , Huettel Markus , Kostka Joel E , Konstantinidis Konstantinos T 
Published: April 2019

AbstractModeling crude-oil biodegradation in sediments remains a challenge due in part to the lack of appropriate model organisms. Here we report the metagenome-guided isolation of a novel organism that represents a phylogenetically narrow (&gt;97% 16S rRNA gene identity) group of previously uncharacterized, crude-oil degraders. Analysis of available sequence data showed that these organisms are highly abundant in oiled sediments of coastal marine ecosystems across the world, often comprising ~30% of the total community, and virtually absent in pristine sediments or seawater. The isolate genome encodes functional nitrogen fixation and hydrocarbon degradation genes together with putative genes for biosurfactant production that apparently facilitate growth in the typically nitrogen-limited, oiled environment. Comparisons to available genomes revealed that this isolate represents a novel genus within the Gammaproteobacteria, for which we propose the provisional name “Candidatus Macondimonas diazotrophica” gen. nov., sp. nov. “Ca. M. diazotrophica” appears to play a key ecological role in the response to oil spills around the globe and could be a promising model organism for studying ecophysiological responses to oil spills.
Rare earth element alcohol dehydrogenases widely occur among globally distributed, numerically abundant and environmentally important microbes
Authors: Huang Jing , Yu Zheng , Groom Joseph , Cheng Jan-Fang , Tarver Angela , Yoshikuni Yasuo , Chistoserdova Ludmila 
Published: April 2019

Abstract
Lanthanides (Ln3+), known as rare earth elements, have recently emerged as enzyme cofactors, contrary to prior assumption of their biological inertia. Several bacterial alcohol dehydrogenases have been characterized so far that depend on Ln3+ for activity and expression, belonging to the methanol dehydrogenase clade XoxF and the ethanol dehydrogenase clade ExaF/PedH. Here we compile an inventory of genes potentially encoding Ln3+-dependent enzymes, closely related to the previously characterized XoxF and ExaF/PedH enzymes. We demonstrate their wide distribution among some of the most numerically abundant and environmentally important taxa, such as the phylogenetically disparate rhizobial species and metabolically versatile bacteria inhabiting world’s oceans, suggesting that reliance on Ln3+-mediated biochemistry is much more widespread in the microbial world than previously assumed. Through protein expression and analysis, we here more than double the extant collection of the biochemically characterized Ln3+-dependent enzymes, demonstrating a range of catalytic properties and substrate and cofactor specificities. Many of these enzymes reveal propensity for oxidation of methanol. This observation, in combination with genome-based reconstruction of methylotrophy pathways for select species suggests a much wider occurrence of this metabolic capability among bacterial species, and thus further suggests the importance of methylated compounds as parts of the global carbon cycling.
Electronic transport in planar atomic-scale structures measured by two-probe scanning tunneling spectroscopy
Authors: Kolmer Marek , Brandimarte Pedro , Lis Jakub , Zuzak Rafal , Godlewski Szymon , Kawai Hiroyo , Garcia-Lekue Aran , Lorente Nicolas , Frederiksen Thomas , Joachim Christian , Sanchez-Portal Daniel , Szymonski Marek 
Published: April 2019

AbstractMiniaturization of electronic circuits into the single-atom level requires novel approaches to characterize transport properties. Due to its unrivaled precision, scanning probe microscopy is regarded as the method of choice for local characterization of atoms and single molecules supported on surfaces. Here we investigate electronic transport along the anisotropic germanium (001) surface with the use of two-probe scanning tunneling spectroscopy and first-principles transport calculations. We introduce a method for the determination of the transconductance in our two-probe experimental setup and demonstrate how it captures energy-resolved information about electronic transport through the unoccupied surface states. The sequential opening of two transport channels within the quasi-one-dimensional Ge dimer rows in the surface gives rise to two distinct resonances in the transconductance spectroscopic signal, consistent with phase-coherence lengths of up to 50 nm and anisotropic electron propagation. Our work paves the way for the electronic transport characterization of quantum circuits engineered on surfaces.
The parasitic worm product ES-62 normalises the gut microbiota bone marrow axis in inflammatory arthritis
Authors: Doonan James , Tarafdar Anuradha , Pineda Miguel A. , Lumb Felicity E. , Crowe Jenny , Khan Aneesah M. , Hoskisson Paul A. , Harnett Margaret M. , Harnett William 
Published: April 2019

AbstractThe human immune system has evolved in the context of our colonisation by bacteria, viruses, fungi and parasitic helminths. Reflecting this, the rapid eradication of pathogens appears to have resulted in reduced microbiome diversity and generation of chronically activated immune systems, presaging the recent rise of allergic, autoimmune and metabolic disorders. Certainly, gastrointestinal helminths can protect against gut and lung mucosa inflammatory conditions by modulating the microbiome and suppressing the chronic inflammation associated with dysbiosis. Here, we employ ES-62, an immunomodulator secreted by tissue-dwellingAcanthocheilonema viteaeto show that helminth-modulation of the gut microbiome does not require live infection with gastrointestinal-based worms nor is protection restricted to mucosal diseases. Specifically, subcutaneous administration of this defined immunomodulator affords protection against joint disease in collagen-induced arthritis, a mouse model of rheumatoid arthritis, which is associated with normalisation of gut microbiota and prevention of loss of intestinal barrier integrity.
Adjustment for index event bias in genome-wide association studies of subsequent events
Authors: Dudbridge Frank , Allen Richard J. , Sheehan Nuala A. , Schmidt A. Floriaan , Lee James C. , Jenkins R. Gisli , Wain Louise V. , Hingorani Aroon D. , Patel Riyaz S. 
Published: April 2019

AbstractFollowing numerous genome-wide association studies of disease susceptibility, there is increasing interest in genetic associations with prognosis, survival or other subsequent events. Such associations are vulnerable to index event bias, by which selection of subjects according to disease status creates biased associations if common causes of incidence and prognosis are not accounted for. We propose an adjustment for index event bias using the residuals from the regression of genetic effects on prognosis on genetic effects on incidence. Our approach eliminates this bias when direct genetic effects on incidence and prognosis are independent, and otherwise reduces bias in realistic situations. In a study of idiopathic pulmonary fibrosis, we reverse a paradoxical association of the strong susceptibility gene MUC5B with increased survival, suggesting instead a significant association with decreased survival. In re-analysis of a study of Crohn’s disease prognosis, four regions remain associated at genome-wide significance but with increased standard errors.
FoxK1 and FoxK2 in insulin regulation of cellular and mitochondrial metabolism
Authors: Sakaguchi Masaji , Cai Weikang , Wang Chih-Hao , Cederquist Carly T. , Damasio Marcos , Homan Erica P. , Batista Thiago , Ramirez Alfred K. , Gupta Manoj K. , Steger Martin , Wewer Albrechtsen Nicolai J. , Singh Shailendra Kumar , Araki Eiichi , Mann Matthias , Enerbäck Sven , Kahn C. Ronald 
Published: April 2019

AbstractA major target of insulin signaling is the FoxO family of Forkhead transcription factors, which translocate from the nucleus to the cytoplasm following insulin-stimulated phosphorylation. Here we show that the Forkhead transcription factors FoxK1 and FoxK2 are also downstream targets of insulin action, but that following insulin stimulation, they translocate from the cytoplasm to nucleus, reciprocal to the translocation of FoxO1. FoxK1/FoxK2 translocation to the nucleus is dependent on the Akt-mTOR pathway, while its localization to the cytoplasm in the basal state is dependent on GSK3. Knockdown of FoxK1 and FoxK2 in liver cells results in upregulation of genes related to apoptosis and down-regulation of genes involved in cell cycle and lipid metabolism. This is associated with decreased cell proliferation and altered mitochondrial fatty acid metabolism. Thus, FoxK1/K2 are reciprocally regulated to FoxO1 following insulin stimulation and play a critical role in the control of apoptosis, metabolism and mitochondrial function.
Unifying scrambling, thermalization and entanglement through measurement of fidelity out-of-time-order correlators in the Dicke model
Authors: Lewis-Swan R. J. , Safavi-Naini A. , Bollinger J. J. , Rey A. M. 
Published: April 2019

AbstractScrambling is the process by which information stored in local degrees of freedom spreads over the many-body degrees of freedom of a quantum system, becoming inaccessible to local probes and apparently lost. Scrambling and entanglement can reconcile seemingly unrelated behaviors including thermalization of isolated quantum systems and information loss in black holes. Here, we demonstrate that fidelity out-of-time-order correlators (FOTOCs) can elucidate connections between scrambling, entanglement, ergodicity and quantum chaos (butterfly effect). We compute FOTOCs for the paradigmatic Dicke model, and show they can measure subsystem Rényi entropies and inform about quantum thermalization. Moreover, we illustrate why FOTOCs give access to a simple relation between quantum and classical Lyapunov exponents in a chaotic system without finite-size effects. Our results open a path to experimental use FOTOCs to explore scrambling, bounds on quantum information processing and investigation of black hole analogs in controllable quantum systems.
The class 3 PI3K coordinates autophagy and mitochondrial lipid catabolism by controlling nuclear receptor PPARα
Authors: Iershov Anton , Nemazanyy Ivan , Alkhoury Chantal , Girard Muriel , Barth Esther , Cagnard Nicolas , Montagner Alexandra , Chretien Dominique , Rugarli Elena I. , Guillou Herve , Pende Mario , Panasyuk Ganna 
Published: April 2019

AbstractThe class 3 phosphoinositide 3-kinase (PI3K) is required for lysosomal degradation by autophagy and vesicular trafficking, assuring nutrient availability. Mitochondrial lipid catabolism is another energy source. Autophagy and mitochondrial metabolism are transcriptionally controlled by nutrient sensing nuclear receptors. However, the class 3 PI3K contribution to this regulation is unknown. We show that liver-specific inactivation of Vps15, the essential regulatory subunit of the class 3 PI3K, elicits mitochondrial depletion and failure to oxidize fatty acids. Mechanistically, transcriptional activity of Peroxisome Proliferator Activated Receptor alpha (PPARα), a nuclear receptor orchestrating lipid catabolism, is blunted in Vps15-deficient livers. We find PPARα repressors Histone Deacetylase 3 (Hdac3) and Nuclear receptor co-repressor 1 (NCoR1) accumulated in Vps15-deficient livers due to defective autophagy. Activation of PPARα or inhibition of Hdac3 restored mitochondrial biogenesis and lipid oxidation in Vps15-deficient hepatocytes. These findings reveal roles for the class 3 PI3K and autophagy in transcriptional coordination of mitochondrial metabolism.
Bidirectional contraction of a type six secretion system
Authors: Szwedziak Piotr , Pilhofer Martin 
Published: April 2019

AbstractContractile injection systems (CISs) mediate cell-cell interactions by a phage tail-like apparatus. Their conserved mechanism relies on the anchoring of the proximal end of a sheath-tube module to a membrane, followed by contraction of the sheath towards the attachment site and ejection of the inner tube. Here we reveal a major variation of the CIS mechanism in the type six secretion system (T6SS) of enteroaggregative Escherichia coli (EAEC). We show that both ends of the sheath-tube module are attached to opposite sides of the cell, enabling the structure to contract in two opposite directions. The protein TssA1 mediates the interaction of the distal end with the cell envelope, the termination of tail elongation, and non-canonical contraction towards the distal end. We provide a framework for the molecular processes at the T6SS distal end. Further research will address whether bidirectional contraction allows for bidirectional effector secretion. The unrecognized concept of non-canonical contractions could be relevant to biofilms of the human intestine.
Evidence for a prolonged Permian–Triassic extinction interval from global marine mercury records
Authors: Shen Jun , Chen Jiubin , Algeo Thomas J. , Yuan Shengliu , Feng Qinglai , Yu Jianxin , Zhou Lian , O’Connell Brennan , Planavsky Noah J. 
Published: April 2019

AbstractThe latest Permian mass extinction, the most devastating biocrisis of the Phanerozoic, has been widely attributed to eruptions of the Siberian Traps Large Igneous Province, although evidence of a direct link has been scant to date. Here, we measure mercury (Hg), assumed to reflect shifts in volcanic activity, across the Permian-Triassic boundary in ten marine sections across the Northern Hemisphere. Hg concentration peaks close to the Permian-Triassic boundary suggest coupling of biotic extinction and increased volcanic activity. Additionally, Hg isotopic data for a subset of these sections provide evidence for largely atmospheric rather than terrestrial Hg sources, further linking Hg enrichment to increased volcanic activity. Hg peaks in shallow-water sections were nearly synchronous with the end-Permian extinction horizon, while those in deep-water sections occurred tens of thousands of years before the main extinction, possibly supporting a globally diachronous biotic turnover and protracted mass extinction event.
New frontiers for the materials genome initiative
Authors: de Pablo Juan J. , Jackson Nicholas E. , Webb Michael A. , Chen Long-Qing , Moore Joel E. , Morgan Dane , Jacobs Ryan , Pollock Tresa , Schlom Darrell G. , Toberer Eric S. , Analytis James , Dabo Ismaila , DeLongchamp Dean M. , Fiete Gregory A. , Grason Gregory M. , Hautier Geoffroy , Mo Yifei , Rajan Krishna , Reed Evan J. , Rodriguez Efrain , Stevanovic Vladan , Suntivich Jin , Thornton Katsuyo , Zhao Ji-Cheng 
Published: April 2019

AbstractThe Materials Genome Initiative (MGI) advanced a new paradigm for materials discovery and design, namely that the pace of new materials deployment could be accelerated through complementary efforts in theory, computation, and experiment. Along with numerous successes, new challenges are inviting researchers to refocus the efforts and approaches that were originally inspired by the MGI. In May 2017, the National Science Foundation sponsored the workshop “Advancing and Accelerating Materials Innovation Through the Synergistic Interaction among Computation, Experiment, and Theory: Opening New Frontiers” to review accomplishments that emerged from investments in science and infrastructure under the MGI, identify scientific opportunities in this new environment, examine how to effectively utilize new materials innovation infrastructure, and discuss challenges in achieving accelerated materials research through the seamless integration of experiment, computation, and theory. This article summarizes key findings from the workshop and provides perspectives that aim to guide the direction of future materials research and its translation into societal impacts.
Multi-year whole-blood transcriptome data for the study of onset and progression of Parkinson’s Disease
Authors: Valentine Matthew N. Z. , Hashimoto Kosuke , Fukuhara Takeshi , Saiki Shinji , Ishikawa Kei-ichi , Hattori Nobutaka , Carninci Piero 
Published: April 2019

AbstractParkinson’s disease (PD) is an age-related, chronic and progressive neurodegenerative disorder characterized by a loss of multifocal neurons, resulting in both non-motor and motor symptoms. While several genetic and environmental contributory risk factors have been identified, more exact methods for diagnosing and assessing prognosis of PD have yet to be established. Here we describe the generation and validation of a dataset comprising whole-blood transcriptomes originally intended for use in detection of blood biomarkers and transcriptomic network changes indicative of PD. Whole-blood samples extracted from both early-stage PD patients and healthy controls were sequenced using no-amplification non-tagging cap analysis of gene expression (nAnT-iCAGE) to analyse differences in global RNA expression patterns across the conditions. Subsequent sampling of a subset of PD patients one-year later provides the opportunity to study changes in transcriptomes arising due to disease progression.
Multi-channel EEG recordings during a sustained-attention driving task
Authors: Cao Zehong , Chuang Chun-Hsiang , King Jung-Kai , Lin Chin-Teng 
Published: April 2019

AbstractWe describe driver behaviour and brain dynamics acquired from a 90-minute sustained-attention task in an immersive driving simulator. The data included 62 sessions of 32-channel electroencephalography (EEG) data for 27 subjects driving on a four-lane highway who were instructed to keep the car cruising in the centre of the lane. Lane-departure events were randomly induced to cause the car to drift from the original cruising lane towards the left or right lane. A complete trial included events with deviation onset, response onset, and response offset. The next trial, in which the subject was instructed to drive back to the original cruising lane, began 5–10 seconds after finishing the previous trial. We believe that this dataset will lead to the development of novel neural processing methodology that can be used to index brain cortical dynamics and detect driving fatigue and drowsiness. This publicly available dataset will be beneficial to the neuroscience and brain-computer interface communities.
Dry season habitat use of fishes in an Australian tropical river
Authors: Keller K. , Allsop Q. , Brim Box J. , Buckle D. , Crook D. A. , Douglas M. M. , Jackson S. , Kennard M. J. , Luiz O. J. , Pusey B. J. , Townsend S. A. , King A. J. 
Published: April 2019

AbstractThe modification of river flow regimes poses a significant threat to the world’s freshwater ecosystems. Northern Australia’s freshwater resources, particularly dry season river flows, are being increasingly modified to support human development, potentially threatening aquatic ecosystems and biodiversity, including fish. More information is urgently needed on the ecology of fishes in this region, including their habitat requirements, to support water policy and management to ensure future sustainable development. This study used electrofishing and habitat survey methods to quantify the dry season habitat use of 20 common freshwater fish taxa in the Daly River in Australia’s wet-dry tropics. Of twenty measured habitat variables, water depth and velocity were the two most important factors discriminating fish habitat use for the majority of taxa. Four distinct fish habitat guilds were identified, largely classified according to depth, velocity and structural complexity. Ontogenetic shifts in habitat use were also observed in three species. This study highlights the need to maintain dry season river flows that support a diversity of riverine mesohabitats for freshwater fishes. In particular, shallow fast-flowing areas provided critical nursery and refuge habitats for some species, but are vulnerable to water level reductions due to water extraction. By highlighting the importance of a diversity of habitats for fishes, this study assists water managers in future decision making on the ecological risks of water extractions from tropical rivers, and especially the need to maintain dry season low flows to protect the habitats of native fish.
Point-dipole approximation for small systems of strongly coupled radiating nanorods
Authors: Watson Derek W. , Jenkins Stewart D. , Fedotov Vassili A. , Ruostekoski Janne 
Published: April 2019

AbstractSystems of closely-spaced resonators can be strongly coupled by interactions mediated by scattered electromagnetic fields. In large systems the resulting response has been shown to be more sensitive to these collective interactions than to the detailed structure of individual resonators. Attempts to describe such systems have resulted in point-dipole approximations to resonators that are computationally efficient for large resonator ensembles. Here we provide a detailed study for the validity of point dipole approximations in small systems of strongly coupled plasmonic nanorods, including the cases of both super-radiant and subradiant excitations, where the characteristics of the excitation depends on the spatial separation between the nanorods. We show that over an appreciable range of rod lengths centered on 210 nm, when the relative separation kl in terms of the resonance wave number of light k satisfies $$kl\gtrsim \pi /2$$
k
l
≳
π
/
2
, the point electric dipole model becomes accurate. However, when the resonators are closer, the finite-size and geometry of the resonators modifies the excitation modes, in particular the cooperative mode line shifts of the point dipole approximation begin to rapidly diverge at small separations. We also construct simplified effective models by describing a pair of nanorods as a single effective metamolecule.