bluuebunny/crossref_metadata_2025_split huggingface dataset:
Predictable evolution towards larger brains in birds colonizing oceanic islands
Authors: Sayol Ferran , Downing Philip A. , Iwaniuk Andrew N. , Maspons Joan , Sol Daniel 
Published: July 2018

AbstractTheory and evidence suggest that some selective pressures are more common on islands than in adjacent mainland habitats, leading evolution to follow predictable trends. The existence of predictable evolutionary trends has nonetheless been difficult to demonstrate, mainly because of the challenge of separating in situ evolution from sorting processes derived from colonization events. Here we use brain size measurements of >1900 avian species to reveal the existence of one such trend: increased brain size in island dwellers. Based on sister-taxa comparisons and phylogenetic ancestral trait estimations, we show that species living on islands have relatively larger brains than their mainland relatives and that these differences mainly reflect in situ evolution rather than varying colonization success. Our findings reinforce the view that in some instances evolution may be predictable, and yield insight into why some animals evolve larger brains despite substantial energetic and developmental costs.
Genomic inference of the metabolism and evolution of the archaeal phylum Aigarchaeota
Authors: Hua Zheng-Shuang , Qu Yan-Ni , Zhu Qiyun , Zhou En-Min , Qi Yan-Ling , Yin Yi-Rui , Rao Yang-Zhi , Tian Ye , Li Yu-Xian , Liu Lan , Castelle Cindy J. , Hedlund Brian P. , Shu Wen-Sheng , Knight Rob , Li Wen-Jun 
Published: July 2018

AbstractMicrobes of the phylum Aigarchaeota are widely distributed in geothermal environments, but their physiological and ecological roles are poorly understood. Here we analyze six Aigarchaeota metagenomic bins from two circumneutral hot springs in Tengchong, China, to reveal that they are either strict or facultative anaerobes, and most are chemolithotrophs that can perform sulfide oxidation. Applying comparative genomics to the Thaumarchaeota and Aigarchaeota, we find that they both originated from thermal habitats, sharing 1154 genes with their common ancestor. Horizontal gene transfer played a crucial role in shaping genetic diversity of Aigarchaeota and led to functional partitioning and ecological divergence among sympatric microbes, as several key functional innovations were endowed by Bacteria, including dissimilatory sulfite reduction and possibly carbon monoxide oxidation. Our study expands our knowledge of the possible ecological roles of the Aigarchaeota and clarifies their evolutionary relationship to their sister lineage Thaumarchaeota.
Host-linked soil viral ecology along a permafrost thaw gradient
Authors: Emerson Joanne B. , Roux Simon , Brum Jennifer R. , Bolduc Benjamin , Woodcroft Ben J. , Jang Ho Bin , Singleton Caitlin M. , Solden Lindsey M. , Naas Adrian E. , Boyd Joel A. , Hodgkins Suzanne B. , Wilson Rachel M. , Trubl Gareth , Li Changsheng , Frolking Steve , Pope Phillip B. , Wrighton Kelly C. , Crill Patrick M. , Chanton Jeffrey P. , Saleska Scott R. , Tyson Gene W. , Rich Virginia I. , Sullivan Matthew B. 
Published: July 2018

AbstractClimate change threatens to release abundant carbon that is sequestered at high latitudes, but the constraints on microbial metabolisms that mediate the release of methane and carbon dioxide are poorly understood1–7. The role of viruses, which are known to affect microbial dynamics, metabolism and biogeochemistry in the oceans8–10, remains largely unexplored in soil. Here, we aimed to investigate how viruses influence microbial ecology and carbon metabolism in peatland soils along a permafrost thaw gradient in Sweden. We recovered 1,907 viral populations (genomes and large genome fragments) from 197 bulk soil and size-fractionated metagenomes, 58% of which were detected in metatranscriptomes and presumed to be active. In silico predictions linked 35% of the viruses to microbial host populations, highlighting likely viral predators of key carbon-cycling microorganisms, including methanogens and methanotrophs. Lineage-specific virus/host ratios varied, suggesting that viral infection dynamics may differentially impact microbial responses to a changing climate. Virus-encoded glycoside hydrolases, including an endomannanase with confirmed functional activity, indicated that viruses influence complex carbon degradation and that viral abundances were significant predictors of methane dynamics. These findings suggest that viruses may impact ecosystem function in climate-critical, terrestrial habitats and identify multiple potential viral contributions to soil carbon cycling.
The lincRNA MIRAT binds to IQGAP1 and modulates the MAPK pathway in NRAS mutant melanoma
Authors: Sanlorenzo Martina , Vujic Igor , Esteve-Puig Rosaura , Lai Kevin , Vujic Marin , Lin Kevin , Posch Christian , Dimon Michelle , Moy Adrian , Zekhtser Mitchell , Johnston Katia , Gho Deborah , Ho Wilson , Gajjala Abhinay , Oses Prieto Juan , Burlingame Alma , Daud Adil , Rappersberger Klemens , Ortiz-Urda Susana 
Published: July 2018

AbstractDespite major advances in targeted melanoma therapies, drug resistance limits their efficacy. Long noncoding RNAs (lncRNAs) are transcriptome elements that do not encode proteins but are important regulatory molecules. LncRNAs have been implicated in cancer development and response to different therapeutics and are thus potential treatment targets; however, the majority of their functions and molecular interactions remain unexplored. In this study, we identify a novel cytoplasmic intergenic lincRNA (MIRAT), which is upregulated following prolonged MAPK inhibition in NRAS mutant melanoma and modulates MAPK signaling by binding to the MEK scaffold protein IQGAP1. Collectively, our results present MIRAT’s direct modulatory effect on the MAPK pathway and highlight the relevance of cytoplasmic lncRNAs as potential targets in drug resistant cancer.
Tuning the structure of the Josephson vortex lattice in Bi2Sr2CaCu2O8+δ single crystals with pancake vortices
Authors: Curran P. J. , Mohammed H. A. , Bending S. J. , Koshelev A. E. , Tsuchiya Y. , Tamegai T. 
Published: July 2018

AbstractIn extremely anisotropic cuprate superconductors a lattice of stacks of pancake vortices nucleates when a magnetic field is applied perpendicular to the copper oxide layers, while an orthogonal lattice of highly elliptical Josephson vortices forms when the applied field is parallel to the layers. Under tilted magnetic fields these sublattices can interact in complex ways to form systems of vortex chains and composite vortex lattices. Here we have used high-resolution scanning Hall microscopy (SHM) to map the rich tilted-field vortex phase diagram in an underdoped Bi2Sr2CaCu2O8+δ single crystal. We find that the Josephson vortex lattice spacing has an unexpected non-monotonic dependence on the pancake vortex density reflecting the delicate balance between attractive and repulsive vortex interactions, and actually undergoes a field-driven structural transformation with increasing out-of-plane fields. We also identify particularly stable composite structures composed of vortex chains separated by an integer number of rows of interstitial pancake vortex stacks and are able to establish the precise evolution of vortex-chain phases as the out-of-plane field is increased at small in-plane fields. Our results are in good semi-quantitative agreement with theoretical models and could enable the development of vortex ratchets and lenses based on the interactions between Josephson and pancake vortices.
Cellular stress induces erythrocyte assembly on intravascular von Willebrand factor strings and promotes microangiopathy
Authors: Nicolay Jan P. , Thorn Verena , Daniel Christoph , Amann Kerstin , Siraskar Balasaheb , Lang Florian , Hillgruber Carina , Goerge Tobias , Hoffmann Stefan , Gorzelanny Christian , Huck Volker , Mess Christian , Obser Tobias , Schneppenheim Reinhard , Fleming Ingrid , Schneider Matthias F. , Schneider Stefan W. 
Published: July 2018

AbstractMicroangiopathy with subsequent organ damage represents a major complication in several diseases. The mechanisms leading to microvascular occlusion include von Willebrand factor (VWF), notably the formation of ultra-large von Willebrand factor fibers (ULVWFs) and platelet aggregation. To date, the contribution of erythrocytes to vascular occlusion is incompletely clarified. We investigated the platelet-independent interaction between stressed erythrocytes and ULVWFs and its consequences for microcirculation and organ function under dynamic conditions. In response to shear stress, erythrocytes interacted strongly with VWF to initiate the formation of ULVWF/erythrocyte aggregates via the binding of Annexin V to the VWF A1 domain. VWF-erythrocyte adhesion was attenuated by heparin and the VWF-specific protease ADAMTS13. In an in vivo model of renal ischemia/reperfusion injury, erythrocytes adhered to capillaries of wild-type but not VWF-deficient mice and later resulted in less renal damage. In vivo imaging in mice confirmed the adhesion of stressed erythrocytes to the vessel wall. Moreover, enhanced eryptosis rates and increased VWF binding were detected in blood samples from patients with chronic renal failure. Our study demonstrates that stressed erythrocytes have a pronounced binding affinity to ULVWFs. The discovered mechanisms suggest that erythrocytes are essential for the pathogenesis of microangiopathies and renal damage by actively binding to ULVWFs.
Soil evaporation and organic matter turnover in the Sub-Taiga and Forest-Steppe of southwest Siberia
Authors: Kayler Zachary E. , Brédoire Félix , McMillan Helene , Barsukov Pavel A. , Rusalimova Olga , Nikitich Polina , Bakker Mark R. , Zeller Bernd , Fontaine Sébastien , Derrien Delphine 
Published: July 2018

AbstractSouthwest Siberia encompasses the forest-steppe and sub-taiga climatic zones and has historically been utilized for agriculture. Coinciding with predicted changes in climate for the region is the pressure of agricultural development; however, a characterization of the soil water and carbon dynamics is lacking. We assessed current soil water properties and soil organic carbon turnover in forests and grasslands for two sites that span the forest steppe and sub-taiga bioclimatic zones. Soil evaporation was 0.62 ± 0.17 mm d−1 (mean ± standard error) in grasslands and 0.45 ± 0.08 mm d−1 in the forests of the forest-steppe site. Evaporation at the sub-taiga site was 1.80 ± 1.70 mm d−1 in grasslands and 0.96 ± 0.05 mm d−1 in forest plots. Evaporation was significantly greater at the sub-taiga site than the forest-steppe site. The density of fine roots explained the soil water isotopic patterns between vegetation types and sites. We found soil organic matter turnover to be three times faster in the sub-taiga site than in the forest-steppe site. Our results show that while climate factors, in particular snow levels, between the two sites are drivers for water and carbon cycles, site level hydrology, soil characteristics, and vegetation directly interact to influence the water and carbon dynamics.
A Poly(ionic liquid) Gel Electrolyte for Efficient all Solid Electrochemical Double-Layer Capacitor
Authors: Taghavikish M. , Subianto S. , Gu Y. , Sun X. , Zhao X. S. , Choudhury N. Roy 
Published: July 2018

AbstractPolyionic liquid based gels have stimulated significant interest due to their wide applications in flexible electronics, such as wearable electronics, roll-up displays, smart mobile devices and implantable biosensors. Novel supported liquid gel electrolyte using polymerisable ionic liquid and an acrylate monomer, has been developed in this work by entrapping ionic liquid during polymerisation instead of post polymerisation impregnation. The chemically crosslinked polyionic liquid gel electrolyte (PIL) is prepared using 2-hydroxyethylmethacrylate (HEMA) monomer and a polymerisable ionic liquid, 1,4-di(vinylimidazolium)butane bisbromide (DVIMBr) in an ionic liquid (IL- 1-butyl-3 methylimidazolium hexafluorophosphate) as the polymerisation solvent, which resulted in in-situ entrapment of the IL in the gel during polymerisation and crosslinking of the polymer. The supported liquid gel electrolyte (SLG) material was characterised with thermal analysis, infrared spectroscopy, and dynamic mechanical analysis, and was found to be stable with good mechanical properties. The electrochemical analysis showed that these chemically cross-linked PIL gel electrolyte-supported ILs are suitable for solid-state, flexible supercapacitor applications.
Contrasting biogeography and diversity patterns between diatoms and haptophytes in the central Pacific Ocean
Authors: Endo Hisashi , Ogata Hiroyuki , Suzuki Koji 
Published: July 2018

AbstractDiatoms and haptophytes are two major phytoplankton groups, playing pivotal roles in global biogeochemical cycles and marine ecosystems. In general, diatoms have higher growth rates than haptophytes, whereas haptophytes tend to have higher nutrient uptake affinity. However, precise linkages between their ecological traits and geographical distributions remain poorly understood. Herein, we examined the basin-scale variability of the abundance and taxonomic composition of these two phytoplankton groups across 35 sites in the Pacific Ocean using DNA metabarcoding. The diatom community was generally dominated by a few genera at each sample site, whereas the haptophyte community consisted of a large number of genera in most of the sites. The coexistence of various haptophyte genera might be achieved by diversification of their ecophysiological traits such as mixotrophy. On the other hand, the diatom community might experience greater inter-genus competition due to the rapid uptake of nutrients. Our data further supports the notion that their distinct ecological strategies underlie the emergence of contrasting diversity patterns of these phytoplankton groups in the central Pacific at a basin scale.
Large body size constrains dispersal assembly of communities even across short distances
Authors: Bailey Richard I. , Molleman Freerk , Vasseur Chloe , Woas Steffen , Prinzing Andreas 
Published: July 2018

AbstractDispersal limitation has been considered to decrease with body size in animals and to be an important factor limiting community assembly on spatially isolated patches. Here we hypothesize that for flightless bark-dwelling oribatid mites dispersal limitation onto young trees might increase with body size (due to a decrease in aerial dispersal capacities), and it might occur even within a spatially contiguous forest canopy. We suppressed dispersal limitation towards branches from young trees by physically connecting them to branches from old trees and analyzed the impacts on community composition, accounting for branch microhabitat variables. Suppression of dispersal limitation increased community evenness and mean body size of mites on branches from young trees. Across all species, large species body-size corresponds to an abundance increase after suppression of dispersal limitation. Consistently, on no-contact control branches, mite body-sizes were larger on branches from old compared to young trees. Our study suggests that colonization/performance trade-offs might affect community assembly even across seemingly contiguous habitats. Overall, a previously underappreciated factor selecting against large body size in flightless canopy-dwelling invertebrates might be that large bodies makes these invertebrates fall faster and disperse less, not more.
Chronic Electrical Stimulation Promotes the Excitability and Plasticity of ESC-derived Neurons following Glutamate-induced Inhibition In vitro
Authors: Latchoumane Charles-Francois V. , Jackson LaDonya , Sendi Mohammad S. Eslampanah , Tehrani Kayvan F. , Mortensen Luke J. , Stice Steven L. , Ghovanloo Maysam , Karumbaiah Lohitash 
Published: July 2018

AbstractFunctional electrical stimulation (FES) is rapidly gaining traction as a therapeutic tool for mediating the repair and recovery of the injured central nervous system (CNS). However, the underlying mechanisms and impact of these stimulation paradigms at a molecular, cellular and network level remain largely unknown. In this study, we used embryonic stem cell (ESC)-derived neuron and glial co-cultures to investigate network maturation following acute administration of L-glutamate, which is a known mediator of excitotoxicity following CNS injury. We then modulated network maturation using chronic low frequency stimulation (LFS) and direct current stimulation (DCS) protocols. We demonstrated that L-glutamate impaired the rate of maturation of ESC-derived neurons and glia immediately and over a week following acute treatment. The administration of chronic LFS and DCS protocols individually following L-glutamate infusion significantly promoted the excitability of neurons as well as network synchrony, while the combination of LFS/DCS did not. qRT-PCR analysis revealed that LFS and DCS alone significantly up-regulated the expression of excitability and plasticity-related transcripts encoding N-methyl-D-aspartate (NMDA) receptor subunit (NR2A), brain-derived neurotrophic factor (BDNF) and Ras-related protein (RAB3A). In contrast, the simultaneous administration of LFS/DCS down-regulated BDNF and RAB3A expression. Our results demonstrate that LFS and DCS stimulation can modulate network maturation excitability and synchrony following the acute administration of an inhibitory dose of L-glutamate, and upregulate NR2A, BDNF and RAB3A gene expression. Our study also provides a novel framework for investigating the effects of electrical stimulation on neuronal responses and network formation and repair after traumatic brain injury.
Comprehensive map of age-associated splicing changes across human tissues and their contributions to age-associated diseases
Authors: Wang Kun , Wu Di , Zhang Haoyue , Das Avinash , Basu Mahashweta , Malin Justin , Cao Kan , Hannenhalli Sridhar 
Published: July 2018

AbstractAlternative splicing contributes to phenotypic diversity at multiple biological scales, and its dysregulation is implicated in both ageing and age-associated diseases in human. Cross-tissue variability in splicing further complicates its links to age-associated phenotypes and elucidating these links requires a comprehensive map of age-associated splicing changes across multiple tissues. Here, we generate such a map by analyzing ~8500 RNA-seq samples across 48 tissues in 544 individuals. Employing a stringent model controlling for multiple confounders, we identify 49,869 tissue-specific age-associated splicing events of 7 distinct types. We find that genome-wide splicing profile is a better predictor of biological age than the gene and transcript expression profiles, and furthermore, age-associated splicing provides additional independent contribution to age-associated complex diseases. We show that the age-associated splicing changes may be explained, in part, by concomitant age-associated changes of the upstream splicing factors. Finally, we show that our splicing-based model of age can successfully predict the relative ages of cells in 8 of the 10 paired longitudinal data as well as in 2 sets of cell passage data. Our study presents the first systematic investigation of age-associated splicing changes across tissues, and further strengthening the links between age-associated splicing and age-associated diseases.
Predictors of Early Onset Multiple Organ Dysfunction in Major Burn Patients with Ventilator Support: Experience from A Mass Casualty Explosion
Authors: Feng Jia-Yih , Chien Jung-Yien , Kao Kuo-Chin , Tsai Cheng-Liang , Hung Fang Ming , Lin Fan-Min , Hu Han-Chung , Huang Kun-Lun , Yu Chong-Jen , Yang Kuang-Yao 
Published: July 2018

AbstractOrgan dysfunction is common in patients with major burns and associated with poor outcomes. The risk factors for early onset multiple organ dysfunction syndrome (MODS) in major burn patients with invasive ventilator support has rarely been evaluated before. In this study, major burn patients with invasive ventilator support from 499 victims suffered in a mass casualty color dust explosion were retrospectively enrolled. The development of early MODS that occurred within 5 days after burn injury was determined and the risk factors associated with early MODS were analyzed. A total of 88 patients from five medical centers were included. Their mean total body surface area (TBSA) was 60.9 ± 15.8%, and 45 (51.1%) patients had early MODS. Hematologic failure was the most common organ failure (68.6%), followed by respiratory failure (48.9%). Independent clinical factors associated with early MODS included TBSA ≥55% (OR: 3.83; 95% CI: 1.29–11.37) and serum albumin level <2.1 g/dL upon admission (OR: 3.43; 95% CI: 1.01–11.57). Patients with early MODS had prolonged ventilator dependence and longer ICU admission than those without early MODS. Our results showed that early MODS in major burn patients with invasive ventilator support is very common and can be predicted early on admission.
Phytolith assemblage analysis for the identification of rice paddy
Authors: Huan Xiujia , Lu Houyuan , Zhang Jianping , Wang Can 
Published: July 2018

AbstractThe rice arable system is of importance to both society and the environment. The emergence of rice paddies was a crucial step in the transition from pre-domestic cultivation to systematic land use and management. However, many aspects of the formation of rice farming systems remain unclear. An important reason is the lack of reliable methods for identifying early rice paddies. One possible means of remedying this knowledge deficit is through analysis of phytolith assemblages, which are closely related to their parent plant communities. In this study, phytolith assemblages from 27 surface soil samples from wild rice fields, 91 surface soil samples from modern rice paddies, and 50 soil samples from non-rice fields were analysed to establish a discriminant function. This discriminant function enabled classification of 89.3% of the samples into appropriate groups. Further, the results suggested that phytolith assemblages can be used to identify rice fields and differentiate between wild rice fields and domesticated rice fields. The method was demonstrated to be an effective way of utilising the large amounts of unidentifiable phytoliths discovered at archaeological sites to provide a modern analogue that may be a valuable key to unlocking the past.
Impact of honey on dental erosion and adhesion of early bacterial colonizers
Authors: Habluetzel Alexandra , Schmid Christoph , Carvalho Thiago S. , Lussi Adrian , Eick Sigrun 
Published: July 2018

AbstractThe aim was to investigate if honey causes erosion and if salivary pellicle modified with honey, or its components, or the by-product propolis has a protective effect against dental erosion and adhesion of early bacterial colonizers. The tested substances were: 3 types of honey, methylglyoxal (MGO), hydrogen peroxide, propolis. First in the erosion experiment, 120 human enamel specimens were covered with salivary pellicle and modified with the substances. Then they were eroded with 1% citric acid, pH 3.6 for 2 min, before surface hardness was measured. In the microbiological assay, the enamel specimens (n = 126) covered with modified salivary pellicle were contaminated with bacterial suspensions. The antimicrobial activity of each substance and their effect on early bacterial colonizer adhesion and biofilm formation were determined. Despite a low pH, honey did not cause erosion. On the other hand, pellicle modification with the tested solutions did not protect the enamel from erosion. Microbiologically, the 3 honeys inhibited species-specific growth of oral bacteria. Propolis decreased initial attachment of Streptococcus gordonii, while one honey inhibited demineralization of enamel by biofilm. In conclusion, pellicle modification with honey, or its components, or propolis did neither protect against erosion nor promote it. Propolis presented some bacterial adhesion inhibition.