bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Simulation Study on the Time Delay of Daytime Thermospheric Temperature Response to the 27‐Day Solar EUV Flux Variation
Authors: Ren Dexin , Lei Jiuhou , Wang Wenbin , Burns Alan , Luan Xiaoli , Dou Xiankang 
Published: October 2019

AbstractIn this study, the National Center for Atmospheric Research Thermosphere Ionosphere Electrodynamic General Circulation Model is used to explore the physical mechanisms of the time delay of daytime thermospheric temperature response to the 27‐day solar extreme ultraviolet (EUV) flux variation. The contributions from different physical processes to the time delay of thermospheric temperature response, the peak perturbation of the thermospheric temperature with respect to the peak of 27‐day solar EUV flux variation, were examined by diagnostically analyzing the thermospheric energy equation in a fixed local time frame. It was found that the time delay of the thermospheric temperature response to the 27‐day solar EUV flux variation corresponds to the time needed for the total heating and cooling rates to be balanced. This time is slightly later than the times of the peaks of both the heating and cooling rates. Furthermore, the global circulation in the upper atmosphere plays a significant role in the delayed response of thermospheric temperature to solar EUV flux variations. Our simulation results show that the time delay of thermospheric temperature response to the 27‐day solar EUV flux variation is about 0.5–0.8 day, depending on the amplitude of solar EUV flux variations.
A Simulation of the Field‐Aligned Plasma Transport in the Plasmaspheric Plume During the 2015 St. Patrick's Day Storm
Authors: Qiao Zheng , Yuan Zhigang , Tu Jiannan 
Published: October 2019

AbstractIn this paper, based on a calculated open E × B convection passage of a flux tube with subauroral polarization streams (SAPS) electric field involved, we use the Dynamic Fluid‐Kinetic model to simulate the transport of major ion species (H+, He+, and O+) along magnetic field line (field‐aligned) within the flux tube during the 2015 St. Patrick's Day storm. The drift trajectory is confirmed to be quite realistic based on observations and empirical models, meanwhile, the foot print of flux tube is initiated from subauroral latitudes toward polar latitudes along this drift pass. The Dynamic Fluid‐Kinetic simulation displays interesting temporal evolution of the field‐aligned plasma distribution at subauroral latitudes: The storm‐enhanced density region continuously provides upward ion flux filling into plasmasphere, but the equatorial mass loading in plasmaspheric plume increases at first and then decreases. Further analyses found that the SAPS particularly impact the field‐aligned transport of O+ particles from ionosphere to plasmasphere but have much less effect on H+ and He+ particles at subauroral latitudes, which causes significant enhancements of equatorial O+ density. The results show that the SAPS have significant effects on both drifting trajectory of the flux tube and associated field‐aligned ion dynamics. This work reveals intimate storm time interaction between the inner magnetosphere and ionosphere which may affect the dynamics in outer magnetosphere or even at magnetopause with flux tube convection.
Ocean Dynamics Shapes the Structure and Timing of Atlantic Equatorial Modes
Authors: Martín‐Rey Marta , Polo Irene , Rodríguez‐Fonseca Belén , Lazar Alban , Losada Teresa 
Published: October 2019

AbstractA recent study has brought to light the co‐existence of two distinct Atlantic Equatorial Modes during negative phases of the Atlantic Multidecadal Variability: the Atlantic Niño and Horse‐Shoe (HS) mode. Nevertheless, the associated air‐sea interactions for HS mode have not been explored so far and the prevailing dynamic view of the Atlantic Niño has been questioned. Here, using a forced ocean model simulation, we find that for both modes, ocean dynamics is essential to explain the equatorial SST variations, while air‐sea fluxes control the off‐equatorial SST anomalies. Moreover, we demonstrate the key role played by ocean waves in shaping their distinct structure and timing. For the positive phase of both Atlantic Niño and HS, anomalous westerly winds trigger a set of equatorial downwelling Kelvin waves (KW) during spring‐summer. These dKWs deepen the thermocline, favouring the equatorial warming through vertical diffusion and horizontal advection. Remarkably, for the HS, an anomalous north‐equatorial wind stress curl excites an upwelling Rossby wave (RW), which propagates westward and is reflected at the western boundary becoming an equatorial upwelling KW. The uKW propagates to the east, activating the thermocline feedbacks responsible to cool the sea surface during summer months. This RW‐reflected mechanism acts as a negative feedback causing the early termination of the HS mode. Our results provide an improvement in the understanding of the TAV modes and emphasize the importance of ocean wave activity to modulate the equatorial SST variability. These findings could be very useful to improve the prediction of the Equatorial Modes.
The release of a distinct cell type from swarm colonies facilitates dissemination of Vibrio parahaemolyticus in the environment
Authors: Freitas Carolina , Glatter Timo , Ringgaard Simon 
Published: October 2019

Abstract
Bacteria experience changes in their environment and have developed various strategies to respond accordingly. To accommodate environmental changes, certain bacteria differentiate between specialized cell types. Vibrio parahaemolyticus is a marine bacterium, a worldwide human pathogen and the leading agent of seafood-borne gastroenteritis. It exists as swimmer or swarmer cells, specialized for life in liquid and on solid environments, respectively. Swarmer cells are characteristically highly elongated—a morphology important for swarming behavior. When attached to surfaces it forms swarm colonies, however, it is not known how cells within swarming populations respond to changes in the external milieu and how its distinct life cycle influences its ecological dissemination. The worldwide distribution of V. parahaemolyticus accentuates the need for understanding the factors contributing to its dissemination. Here we determine the stage-wise development of swarm colonies and show how the swarm colony architecture fluctuates with changing environmental conditions. Swarm colonies act as a continuous source of cells that are released from the swarm colony into the environment. Surprisingly, the cell length distribution of released cells was very homogenous and almost no long cells were detected, indicating that swarmer cells are not released into the liquid environment but stay surface attached during flooding. Released cells comprise a distinct cell type that is morphologically optimized for swimming behavior and is capable of spreading in the liquid environment and attach to new surfaces. Release of this distinct cell type facilitates the dissemination of V. parahaemolyticus in the environment and likely influences the ecology of this bacterium.
Extremophilic nitrite-oxidizing Chloroflexi from Yellowstone hot springs
Authors: Spieck Eva , Spohn Michael , Wendt Katja , Bock Eberhard , Shively Jessup , Frank Jeroen , Indenbirken Daniela , Alawi Malik , Lücker Sebastian , Hüpeden Jennifer 
Published: October 2019

Abstract
Nitrifying microorganisms occur across a wide temperature range from 4 to 84 °C and previous studies in geothermal systems revealed their activity under extreme conditions. Archaea were detected to be responsible for the first step of nitrification, but it is still a challenging issue to clarify the identity of heat-tolerant nitrite oxidizers. In a long-term cultivation approach, we inoculated mineral media containing ammonium and nitrite as substrates with biofilms and sediments of two hot springs in Yellowstone National Park (USA). The nitrifying consortia obtained at 70 °C consisted mostly of novel Chloroflexi as revealed by metagenomic sequencing. Among these, two deep-branching novel Chloroflexi were identified as putative nitrite-oxidizing bacteria (NOB) by the presence of nitrite oxidoreductase encoding genes in their genomes. Stoichiometric oxidation of nitrite to nitrate occurred under lithoautotrophic conditions, but was stimulated by organic matter. Both NOB candidates survived long periods of starvation and the more abundant one formed miniaturized cells and was heat resistant. This detection of novel thermophilic NOB exemplifies our still incomplete knowledge of nitrification, and indicates that nitrite oxidation might be an ancient and wide-spread form of energy conservation.
Archaeal nitrification is constrained by copper complexation with organic matter in municipal wastewater treatment plants
Authors: Gwak Joo-Han , Jung Man-Young , Hong Heeji , Kim Jong-Geol , Quan Zhe-Xue , Reinfelder John R , Spasov Emilie , Neufeld Josh D , Wagner Michael , Rhee Sung-Keun 
Published: October 2019

Abstract
Consistent with the observation that ammonia-oxidizing bacteria (AOB) outnumber ammonia-oxidizing archaea (AOA) in many eutrophic ecosystems globally, AOB typically dominate activated sludge aeration basins from municipal wastewater treatment plants (WWTPs). In this study, we demonstrate that the growth of AOA strains inoculated into sterile-filtered wastewater was inhibited significantly, in contrast to uninhibited growth of a reference AOB strain. In order to identify possible mechanisms underlying AOA-specific inhibition, we show that complex mixtures of organic compounds, such as yeast extract, were highly inhibitory to all AOA strains but not to the AOB strain. By testing individual organic compounds, we reveal strong inhibitory effects of organic compounds with high metal complexation potentials implying that the inhibitory mechanism for AOA can be explained by the reduced bioavailability of an essential metal. Our results further demonstrate that the inhibitory effect on AOA can be alleviated by copper supplementation, which we observed for pure AOA cultures in a defined medium and for AOA inoculated into nitrifying sludge. Our study offers a novel mechanistic explanation for the relatively low abundance of AOA in most WWTPs and provides a basis for modulating the composition of nitrifying communities in both engineered systems and naturally occurring environments.
Gene network analysis reveals a role for striatal glutamatergic receptors in dysregulated risk-assessment behavior of autism mouse models
Authors: Oron Oded , Getselter Dmitriy , Shohat Shahar , Reuveni Eli , Lukic Iva , Shifman Sagiv , Elliott Evan 
Published: October 2019

AbstractAutism spectrum disorder (ASD) presents a wide, and often varied, behavioral phenotype. Improper assessment of risks has been reported among individuals diagnosed with ASD. Improper assessment of risks may lead to increased accidents and self-injury, also reported among individuals diagnosed with ASD. However, there is little knowledge of the molecular underpinnings of the impaired risk-assessment phenotype. In this study, we have identified impaired risk-assessment activity in multiple male ASD mouse models. By performing network-based analysis of striatal whole transcriptome data from each of these ASD models, we have identified a cluster of glutamate receptor-associated genes that correlate with the risk-assessment phenotype. Furthermore, pharmacological inhibition of striatal glutamatergic receptors was able to mimic the dysregulation in risk-assessment. Therefore, this study has identified a molecular mechanism that may underlie risk-assessment dysregulation in ASD.
Chromatin profiling of cortical neurons identifies individual epigenetic signatures in schizophrenia
Authors: Gusev Fedor E. , Reshetov Denis A. , Mitchell Amanda C. , Andreeva Tatiana V. , Dincer Aslihan , Grigorenko Anastasia P. , Fedonin Gennady , Halene Tobias , Aliseychik Maria , Filippova Elena , Weng Zhiping , Akbarian Schahram , Rogaev Evgeny I. 
Published: October 2019

AbstractBoth heritability and environment contribute to risk for schizophrenia. However, the molecular mechanisms of interactions between genetic and non-genetic factors remain unclear. Epigenetic regulation of neuronal genome may be a presumable mechanism in pathogenesis of schizophrenia. Here, we performed analysis of open chromatin landscape of gene promoters in prefrontal cortical (PFC) neurons from schizophrenic patients. We cataloged cell-type-based epigenetic signals of transcriptional start sites (TSS) marked by histone H3-K4 trimethylation (H3K4me3) across the genome in PFC from multiple schizophrenia subjects and age-matched control individuals. One of the top-ranked chromatin alterations was found in the major histocompatibility (MHC) locus on chromosome 6 highlighting the overlap between genetic and epigenetic risk factors in schizophrenia. The chromosome conformation capture (3C) analysis in human brain cells revealed the architecture of multipoint chromatin interactions between the schizophrenia-associated genetic and epigenetic polymorphic sites and distantly locatedHLA-DRB5andBTNL2genes. In addition, schizophrenia-specific chromatin modifications in neurons were particularly prominent for non-coding RNA genes, including an uncharacterizedLINC01115gene and recently identifiedBNRNA_052780. Notably, protein-coding genes with altered epigenetic state in schizophrenia are enriched for oxidative stress and cell motility pathways. Our results imply the rare individual epigenetic alterations in brain neurons are involved in the pathogenesis of schizophrenia.
Hippocampal proteomic changes of susceptibility and resilience to depression or anxiety in a rat model of chronic mild stress
Authors: Tang Min , Huang Haojun , Li Shuiming , Zhou Mi , Liu Zhao , Huang Rongzhong , Liao Wei , Xie Peng , Zhou Jian 
Published: October 2019

AbstractChronic stressful occurrences are documented as a vital cause of both depression and anxiety disorders. However, the stress-induced molecular mechanisms underlying the common and distinct pathophysiology of these disorders remains largely unclear. We utilized a chronic mild stress (CMS) rat model to differentiate and subgroup depression-susceptible, anxiety-susceptible, and insusceptible rats. The hippocampus was analyzed for differential proteomes by combining mass spectrometry and the isobaric tags for relative and absolute quantitation (iTRAQ) labeling technique. Out of 2593 quantified proteins, 367 were aberrantly expressed. These hippocampal protein candidates might be associated with susceptibility to stress-induced depression or anxiety and stress resilience. They provide the potential protein systems involved in various metabolic pathways as novel investigative protein targets. Further, independent immunoblot analysis identified changes in Por, Idh2 and Esd; Glo1, G6pdx, Aldh2, and Dld; Dlat, Ogdhl, Anxal, Tpp2, and Sdha that were specifically associated to depression-susceptible, anxiety-susceptible, or insusceptible groups respectively, suggesting that identical CMS differently impacted the mitochondrial and metabolic processes in the hippocampus. Collectively, the observed alterations to protein abundance profiles of the hippocampus provided significant and novel insights into the stress regulation mechanism in a CMS rat model. This might serve as the molecular basis for further studies that would contributed to a better understanding of the similarities and differences in pathophysiologic mechanisms underlying stress-induced depression or anxiety, and stress resiliency.
Two-dimensional inorganic molecular crystals
Authors: Han Wei , Huang Pu , Li Liang , Wang Fakun , Luo Peng , Liu Kailang , Zhou Xing , Li Huiqiao , Zhang Xiuwen , Cui Yi , Zhai Tianyou 
Published: October 2019

AbstractTwo-dimensional molecular crystals, consisting of zero-dimensional molecules, are very appealing due to their novel physical properties. However, they are mostly limited to organic molecules. The synthesis of inorganic version of two-dimensional molecular crystals is still a challenge due to the difficulties in controlling the crystal phase and growth plane. Here, we design a passivator-assisted vapor deposition method for the growth of two-dimensional Sb2O3 inorganic molecular crystals as thin as monolayer. The passivator can prevent the heterophase nucleation and suppress the growth of low-energy planes, and enable the molecule-by-molecule lateral growth along high-energy planes. Using Raman spectroscopy and in situ transmission electron microscopy, we show that the insulating α-phase of Sb2O3 flakes can be transformed into semiconducting β-phase under heat and electron-beam irradiation. Our findings can be extended to the controlled growth of other two-dimensional inorganic molecular crystals and open up opportunities for potential molecular electronic devices.
Transforming protein-polymer conjugate purification by tuning protein solubility
Authors: Baker Stefanie L. , Munasinghe Aravinda , Kaupbayeva Bibifatima , Rebecca Kang Nin , Certiat Marie , Murata Hironobu , Matyjaszewski Krzysztof , Lin Ping , Colina Coray M. , Russell Alan J. 
Published: October 2019

AbstractAlmost all commercial proteins are purified using ammonium sulfate precipitation. Protein-polymer conjugates are synthesized from pure starting materials, and the struggle to separate conjugates from polymer, native protein, and from isomers has vexed scientists for decades. We have discovered that covalent polymer attachment has a transformational effect on protein solubility in salt solutions. Here, protein-polymer conjugates with a variety of polymers, grafting densities, and polymer lengths are generated using atom transfer radical polymerization. Charged polymers increase conjugate solubility in ammonium sulfate and completely prevent precipitation even at 100% saturation. Atomistic molecular dynamic simulations show the impact is driven by an anti-polyelectrolyte effect from zwitterionic polymers. Uncharged polymers exhibit polymer length-dependent decreased solubility. The differences in salting-out are then used to simply purify mixtures of conjugates and native proteins into single species. Increasing protein solubility in salt solutions through polymer conjugation could lead to many new applications of protein-polymer conjugates.
Daily blue-light exposure shortens lifespan and causes brain neurodegeneration in Drosophila
Authors: Nash Trevor R. , Chow Eileen S. , Law Alexander D. , Fu Samuel D. , Fuszara Elzbieta , Bilska Aleksandra , Bebas Piotr , Kretzschmar Doris , Giebultowicz Jadwiga M. 
Published: October 2019

AbstractLight is necessary for life, but prolonged exposure to artificial light is a matter of increasing health concern. Humans are exposed to increased amounts of light in the blue spectrum produced by light-emitting diodes (LEDs), which can interfere with normal sleep cycles. The LED technologies are relatively new; therefore, the long-term effects of exposure to blue light across the lifespan are not understood. We investigated the effects of light in the model organism, Drosophila melanogaster, and determined that flies maintained in daily cycles of 12-h blue LED and 12-h darkness had significantly reduced longevity compared with flies maintained in constant darkness or in white light with blue wavelengths blocked. Exposure of adult flies to 12 h of blue light per day accelerated aging phenotypes causing damage to retinal cells, brain neurodegeneration, and impaired locomotion. We report that brain damage and locomotor impairments do not depend on the degeneration in the retina, as these phenotypes were evident under blue light in flies with genetically ablated eyes. Blue light induces expression of stress-responsive genes in old flies but not in young, suggesting that cumulative light exposure acts as a stressor during aging. We also determined that several known blue-light-sensitive proteins are not acting in pathways mediating detrimental light effects. Our study reveals the unexpected effects of blue light on fly brain and establishes Drosophila as a model in which to investigate long-term effects of blue light at the cellular and organismal level.
Deciphering tea tree chloroplast and mitochondrial genomes of Camellia sinensis var. assamica
Authors: Zhang Fen , Li Wei , Gao Cheng-wen , Zhang Dan , Gao Li-zhi 
Published: October 2019

AbstractTea is the most popular non-alcoholic caffeine-containing and the oldest beverage in the world. In this study, we de novo assembled the chloroplast (cp) and mitochondrial (mt) genomes of C. sinensis var. assamica cv. Yunkang10 into a circular contig of 157,100 bp and two complete circular scaffolds (701719 bp and 177329 bp), respectively. We correspondingly annotated a total of 141 cp genes and 71 mt genes. Comparative analysis suggests repeat-rich nature of the mt genome compared to the cp genome, for example, with the characterization of 37,878 bp and 149 bp of long repeat sequences and 665 and 214 SSRs, respectively. We also detected 478 RNA-editing sites in 42 protein-coding mt genes, which are ~4.4-fold more than 54 RNA-editing sites detected in 21 protein-coding cp genes. The high-quality cp and mt genomes of C. sinensis var. assamica presented in this study will become an important resource for a range of genetic, functional, evolutionary and comparative genomic studies in tea tree and other Camellia species of the Theaceae family.
Linkage disequilibrium maps for European and African populations constructed from whole genome sequence data
Authors: Vergara-Lope Alejandra , Jabalameli M. Reza , Horscroft Clare , Ennis Sarah , Collins Andrew , Pengelly Reuben J. 
Published: October 2019

AbstractQuantification of linkage disequilibrium (LD) patterns in the human genome is essential for genome-wide association studies, selection signature mapping and studies of recombination. Whole genome sequence (WGS) data provides optimal source data for this quantification as it is free from biases introduced by the design of array genotyping platforms. The Malécot-Morton model of LD allows the creation of a cumulative map for each choromosome, analogous to an LD form of a linkage map. Here we report LD maps generated from WGS data for a large population of European ancestry, as well as populations of Baganda, Ethiopian and Zulu ancestry. We achieve high average genetic marker densities of 2.3–4.6/kb. These maps show good agreement with prior, low resolution maps and are consistent between populations. Files are provided in BED format to allow researchers to readily utilise this resource.
Folding Free Energy Landscape of Ordered and Intrinsically Disordered Proteins
Authors: Chong Song-Ho , Ham Sihyun 
Published: October 2019

AbstractFolding funnel is the essential concept of the free energy landscape for ordered proteins. How does this concept apply to intrinsically disordered proteins (IDPs)? Here, we address this fundamental question through the explicit characterization of the free energy landscapes of the representative α-helical (HP-35) and β-sheet (WW domain) proteins and of an IDP (pKID) that folds upon binding to its partner (KIX). We demonstrate that HP-35 and WW domain indeed exhibit the steep folding funnel: the landscape slope for these proteins is ca. −50 kcal/mol, meaning that the free energy decreases by ~5 kcal/mol upon the formation of 10% native contacts. On the other hand, the landscape of pKID is funneled but considerably shallower (slope of −24 kcal/mol), which explains why pKID is disordered in free environments. Upon binding to KIX, the landscape of pKID now becomes significantly steep (slope of −54 kcal/mol), which enables otherwise disordered pKID to fold. We also show that it is the pKID–KIX intermolecular interactions originating from hydrophobic residues that mainly confer the steep folding funnel. The present work not only provides the quantitative characterization of the protein folding free energy landscape, but also establishes the usefulness of the folding funnel concept to IDPs.