bluuebunny/crossref_metadata_2025_split huggingface dataset:
Daytime temperature is sensed by phytochrome B in Arabidopsis through a transcriptional activator HEMERA
Authors: Qiu Yongjian , Li Meina , Kim Ruth Jean-Ae , Moore Carisha M. , Chen Meng 
Published: January 2019

AbstractAmbient temperature sensing by phytochrome B (PHYB) in Arabidopsis is thought to operate mainly at night. Here we show that PHYB plays an equally critical role in temperature sensing during the daytime. In daytime thermosensing, PHYB signals primarily through the temperature-responsive transcriptional regulator PIF4, which requires the transcriptional activator HEMERA (HMR). HMR does not regulate PIF4 transcription, instead, it interacts directly with PIF4, to activate the thermoresponsive growth-relevant genes and promote warm-temperature-dependent PIF4 accumulation. A missense allele hmr-22, which carries a loss-of-function D516N mutation in HMR’s transcriptional activation domain, fails to induce the thermoresponsive genes and PIF4 accumulation. Both defects of hmr-22 could be rescued by expressing a HMR22 mutant protein fused with the transcriptional activation domain of VP16, suggesting a causal relationship between HMR-mediated activation of PIF4 target-genes and PIF4 accumulation. Together, this study reveals a daytime PHYB-mediated thermosensing mechanism, in which HMR acts as a necessary activator for PIF4-dependent induction of temperature-responsive genes and PIF4 accumulation.
Single spin localization and manipulation in graphene open-shell nanostructures
Authors: Li Jingcheng , Sanz Sofia , Corso Martina , Choi Deung Jang , Peña Diego , Frederiksen Thomas , Pascual Jose Ignacio 
Published: January 2019

AbstractTurning graphene magnetic is a promising challenge to make it an active material for spintronics. Predictions state that graphene structures with specific shapes can spontaneously develop magnetism driven by Coulomb repulsion of π-electrons, but its experimental verification is demanding. Here, we report on the observation and manipulation of individual magnetic moments in graphene open-shell nanostructures on a gold surface. Using scanning tunneling spectroscopy, we detect the presence of single electron spins localized around certain zigzag sites of the carbon backbone via the Kondo effect. We find near-by spins coupled into a singlet ground state and quantify their exchange interaction via singlet-triplet inelastic electron excitations. Theoretical simulations picture how electron correlations result in spin-polarized radical states with the experimentally observed spatial distributions. Extra hydrogen atoms bound to radical sites quench their magnetic moment and switch the spin of the nanostructure in half-integer amounts. Our work demonstrates the intrinsic π-paramagnetism of graphene nanostructures.
A recent increase in global wave power as a consequence of oceanic warming
Authors: Reguero Borja G. , Losada Iñigo J. , Méndez Fernando J. 
Published: January 2019

AbstractWind-generated ocean waves drive important coastal processes that determine flooding and erosion. Ocean warming has been one factor affecting waves globally. Most studies have focused on studying parameters such as wave heights, but a systematic, global and long-term signal of climate change in global wave behavior remains undetermined. Here we show that the global wave power, which is the transport of the energy transferred from the wind into sea-surface motion, has increased globally (0.4% per year) and by ocean basins since 1948. We also find long-term correlations and statistical dependency with sea surface temperatures, globally and by ocean sub-basins, particularly between the tropical Atlantic temperatures and the wave power in high south latitudes, the most energetic region globally. Results indicate the upper-ocean warming, a consequence of anthropogenic global warming, is changing the global wave climate, making waves stronger. This identifies wave power as a potentially valuable climate change indicator.
Altered chemistry of oxygen and iron under deep Earth conditions
Authors: Liu Jin , Hu Qingyang , Bi Wenli , Yang Liuxiang , Xiao Yuming , Chow Paul , Meng Yue , Prakapenka Vitali B. , Mao Ho-Kwang , Mao Wendy L. 
Published: January 2019

AbstractA drastically altered chemistry was recently discovered in the Fe-O-H system under deep Earth conditions, involving the formation of iron superoxide (FeO2Hx with x = 0 to 1), but the puzzling crystal chemistry of this system at high pressures is largely unknown. Here we present evidence that despite the high O/Fe ratio in FeO2Hx, iron remains in the ferrous, spin-paired and non-magnetic state at 60–133 GPa, while the presence of hydrogen has minimal effects on the valence of iron. The reduced iron is accompanied by oxidized oxygen due to oxygen-oxygen interactions. The valence of oxygen is not –2 as in all other major mantle minerals, instead it varies around –1. This result indicates that like iron, oxygen may have multiple valence states in our planet’s interior. Our study suggests a possible change in the chemical paradigm of how oxygen, iron, and hydrogen behave under deep Earth conditions.
Phosphorylation of CENP-A on serine 7 does not control centromere function
Authors: Barra Viviana , Logsdon Glennis A. , Scelfo Andrea , Hoffmann Sebastian , Hervé Solène , Aslanian Aaron , Nechemia-Arbely Yael , Cleveland Don W. , Black Ben E. , Fachinetti Daniele 
Published: January 2019

AbstractCENP-A is the histone H3 variant necessary to specify the location of all eukaryotic centromeres via its CENP-A targeting domain and either one of its terminal regions. In humans, several post-translational modifications occur on CENP-A, but their role in centromere function remains controversial. One of these modifications of CENP-A, phosphorylation on serine 7, has been proposed to control centromere assembly and function. Here, using gene targeting at both endogenous CENP-A alleles and gene replacement in human cells, we demonstrate that a CENP-A variant that cannot be phosphorylated at serine 7 maintains correct CENP-C recruitment, faithful chromosome segregation and long-term cell viability. Thus, we conclude that phosphorylation of CENP-A on serine 7 is dispensable to maintain correct centromere dynamics and function.
A gene expression map of shoot domains reveals regulatory mechanisms
Authors: Tian Caihuan , Wang Ying , Yu Haopeng , He Jun , Wang Jin , Shi Bihai , Du Qingwei , Provart Nicholas J. , Meyerowitz Elliot M. , Jiao Yuling 
Published: January 2019

AbstractGene regulatory networks control development via domain-specific gene expression. In seed plants, self-renewing stem cells located in the shoot apical meristem (SAM) produce leaves from the SAM peripheral zone. After initiation, leaves develop polarity patterns to form a planar shape. Here we compare translating RNAs among SAM and leaf domains. Using translating ribosome affinity purification and RNA sequencing to quantify gene expression in target domains, we generate a domain-specific translatome map covering representative vegetative stage SAM and leaf domains. We discuss the predicted cellular functions of these domains and provide evidence that dome seemingly unrelated domains, utilize common regulatory modules. Experimental follow up shows that the RABBIT EARS and HANABA TARANU transcription factors have roles in axillary meristem initiation. This dataset provides a community resource for further study of shoot development and response to internal and environmental signals.
Metaepigenomic analysis reveals the unexplored diversity of DNA methylation in an environmental prokaryotic community
Authors: Hiraoka Satoshi , Okazaki Yusuke , Anda Mizue , Toyoda Atsushi , Nakano Shin-ichi , Iwasaki Wataru 
Published: January 2019

AbstractDNA methylation plays important roles in prokaryotes, and their genomic landscapes—prokaryotic epigenomes—have recently begun to be disclosed. However, our knowledge of prokaryotic methylation systems is focused on those of culturable microbes, which are rare in nature. Here, we used single-molecule real-time and circular consensus sequencing techniques to reveal the ‘metaepigenomes’ of a microbial community in the largest lake in Japan, Lake Biwa. We reconstructed 19 draft genomes from diverse bacterial and archaeal groups, most of which are yet to be cultured. The analysis of DNA chemical modifications in those genomes revealed 22 methylated motifs, nine of which were novel. We identified methyltransferase genes likely responsible for methylation of the novel motifs, and confirmed the catalytic specificities of four of them via transformation experiments using synthetic genes. Our study highlights metaepigenomics as a powerful approach for identification of the vast unexplored variety of prokaryotic DNA methylation systems in nature.
Pentatricopeptide repeat poly(A) binding protein KPAF4 stabilizes mitochondrial mRNAs in Trypanosoma brucei
Authors: Mesitov Mikhail V. , Yu Tian , Suematsu Takuma , Sement Francois M. , Zhang Liye , Yu Clinton , Huang Lan , Aphasizheva Inna 
Published: January 2019

AbstractIn Trypanosoma brucei, most mitochondrial mRNAs undergo editing, and 3′ adenylation and uridylation. The internal sequence changes and terminal extensions are coordinated: pre-editing addition of the short (A) tail protects the edited transcript against 3′-5′ degradation, while post-editing A/U-tailing renders mRNA competent for translation. Participation of a poly(A) binding protein (PABP) in coupling of editing and 3′ modification processes has been inferred, but its identity and mechanism of action remained elusive. We report identification of KPAF4, a pentatricopeptide repeat-containing PABP which sequesters the A-tail and impedes mRNA degradation. Conversely, KPAF4 inhibits uridylation of A-tailed transcripts and, therefore, premature A/U-tailing of partially-edited mRNAs. This quality check point likely prevents translation of incompletely edited mRNAs. We also find that RNA editing substrate binding complex (RESC) mediates the interaction between the 5′ end-bound pyrophosphohydrolase MERS1 and 3′ end-associated KPAF4 to enable mRNA circularization. This event appears to be critical for edited mRNA stability.
Suicide among cancer patients
Authors: Zaorsky Nicholas G. , Zhang Ying , Tuanquin Leonard , Bluethmann Shirley M. , Park Henry S. , Chinchilli Vernon M. 
Published: January 2019

AbstractOur purpose is to identify cancer patients at highest risk of suicide compared to the general population and other cancer patients. This is a retrospective, population-based study using nationally representative data from the Surveillance, Epidemiology, and End Results program, 1973-2014. Among 8,651,569 cancer patients, 13,311 committed suicide; the rate of suicide was 28.58/ 100,000-person years, and the standardized mortality ratio (SMR) of suicide was 4.44 (95% CI, 4.33, 4.55). The predominant patients who committed suicide were male (83%) and white (92%). Cancers of the lung, head and neck, testes, bladder, and Hodgkin lymphoma had the highest SMRs ( > 5-10) through the follow up period. Elderly, white, unmarried males with localized disease are at highest risk vs other cancer patients. Among those diagnosed at < 50 years of age, the plurality of suicides is from hematologic and testicular tumors; if > 50, from prostate, lung, and colorectal cancer patients.
Feature-specific prediction errors and surprise across macaque fronto-striatal circuits
Authors: Oemisch Mariann , Westendorff Stephanie , Azimi Marzyeh , Hassani Seyed Alireza , Ardid Salva , Tiesinga Paul , Womelsdorf Thilo 
Published: January 2019

AbstractTo adjust expectations efficiently, prediction errors need to be associated with the precise features that gave rise to the unexpected outcome, but this credit assignment may be problematic if stimuli differ on multiple dimensions and it is ambiguous which feature dimension caused the outcome. Here, we report a potential solution: neurons in four recorded areas of the anterior fronto-striatal networks encode prediction errors that are specific to feature values of different dimensions of attended multidimensional stimuli. The most ubiquitous prediction error occurred for the reward-relevant dimension. Feature-specific prediction error signals a) emerge on average shortly after non-specific prediction error signals, b) arise earliest in the anterior cingulate cortex and later in dorsolateral prefrontal cortex, caudate and ventral striatum, and c) contribute to feature-based stimulus selection after learning. Thus, a widely-distributed feature-specific eligibility trace may be used to update synaptic weights for improved feature-based attention.
Intensiometric biosensors visualize the activity of multiple small GTPases in vivo
Authors: Kim Jihoon , Lee Sangkyu , Jung Kanghoon , Oh Won Chan , Kim Nury , Son Seungkyu , Jo YoungJu , Kwon Hyung-Bae , Heo Won Do 
Published: January 2019

AbstractRas and Rho small GTPases are critical for numerous cellular processes including cell division, migration, and intercellular communication. Despite extensive efforts to visualize the spatiotemporal activity of these proteins, achieving the sensitivity and dynamic range necessary for in vivo application has been challenging. Here, we present highly sensitive intensiometric small GTPase biosensors visualizing the activity of multiple small GTPases in single cells in vivo. Red-shifted sensors combined with blue light-controllable optogenetic modules achieved simultaneous monitoring and manipulation of protein activities in a highly spatiotemporal manner. Our biosensors revealed spatial dynamics of Cdc42 and Ras activities upon structural plasticity of single dendritic spines, as well as a broad range of subcellular Ras activities in the brains of freely behaving mice. Thus, these intensiometric small GTPase sensors enable the spatiotemporal dissection of complex protein signaling networks in live animals.
Enhanced growth after extreme wetness compensates for post-drought carbon loss in dry forests
Authors: Jiang Peng , Liu Hongyan , Piao Shilong , Ciais Philippe , Wu Xiuchen , Yin Yi , Wang Hongya 
Published: January 2019

AbstractWhile many studies have reported that drought events have substantial negative legacy effects on forest growth, it remains unclear whether wetness events conversely have positive growth legacy effects. Here, we report pervasive and substantial growth enhancement after extreme wetness by examining tree radial growth at 1929 forest sites, satellite-derived vegetation greenness, and land surface model simulations. Enhanced growth after extreme wetness lasts for 1 to 5 years and compensates for 93 ± 8% of the growth deficit after extreme drought across global water-limited regions. Remarkable wetness-enhanced growths are observed in dry forests and gymnosperms, whereas the enhanced growths after extreme wetness are much smaller in wet forests and angiosperms. Limited or no enhanced growths are simulated by the land surface models after extreme wetness. These findings provide new evidence for improving climate-vegetation models to include the legacy effects of both drought and wet climate extremes.
Stout camphor tree genome fills gaps in understanding of flowering plant genome evolution
Authors: Chaw Shu-Miaw , Liu Yu-Ching , Wu Yu-Wei , Wang Han-Yu , Lin Chan-Yi Ivy , Wu Chung-Shien , Ke Huei-Mien , Chang Lo-Yu , Hsu Chih-Yao , Yang Hui-Ting , Sudianto Edi , Hsu Min-Hung , Wu Kun-Pin , Wang Ling-Ni , Leebens-Mack James H. , Tsai Isheng J. 
Published: January 2019

AbstractWe present reference-quality genome assembly and annotation for the stout camphor tree (Cinnamomum kanehirae (Laurales, Lauraceae)), the first sequenced member of the Magnoliidae comprising four orders (Laurales, Magnoliales, Canellales and Piperales) and over 9,000 species. Phylogenomic analysis of 13 representative seed plant genomes indicates that magnoliid and eudicot lineages share more recent common ancestry than monocots. Two whole-genome duplication events were inferred within the magnoliid lineage: one before divergence of Laurales and Magnoliales and the other within the Lauraceae. Small-scale segmental duplications and tandem duplications also contributed to innovation in the evolutionary history of Cinnamomum. For example, expansion of the terpenoid synthase gene subfamilies within the Laurales spawned the diversity of Cinnamomum monoterpenes and sesquiterpenes.
Population dynamics and transcriptomic responses of Pseudomonas aeruginosa in a complex laboratory microbial community
Authors: Cheng Yingying , Yam Joey Kuok Hoong , Cai Zhao , Ding Yichen , Zhang Lian-Hui , Deng Yinyue , Yang Liang 
Published: January 2019

AbstractPseudomonas aeruginosa tends to be among the dominant species in multi-species bacterial consortia in diverse environments. To understand P. aeruginosa’s physiology and interactions with co-existing bacterial species in different conditions, we established physiologically reproducible 18 species communities, and found that P. aeruginosa dominated in mixed-species biofilm communities but not in planktonic communities. P. aeruginosa’s H1 type VI secretion system was highly induced in mixed-species biofilm consortia, compared with its monospecies biofilm, which was further demonstrated to play a key role in P. aeruginosa's enhanced fitness over other bacterial species. In addition, the type IV pili and Psl exopolysaccharide were required for P. aeruginosa to compete with other bacterial species in the biofilm community. Our study showed that the physiology of P. aeruginosa is strongly affected by interspecies interactions, and both biofilm determinants and type VI secretion system contribute to higher P. aeruginosa's fitness over other species in complex biofilm communities.
From contextuality of a single photon to realism of an electromagnetic wave
Authors: Markiewicz Marcin , Kaszlikowski Dagomir , Kurzyński Paweł , Wójcik Antoni 
Published: January 2019

AbstractViolations of Bell inequalities have been an incontestable indicator of non-classicality since the seminal paper by John Bell. However, recent claims of Bell inequalities violations with classical light have cast some doubts on their significance as hallmarks of non-classicality. Here, we challenge those claims. The crux of the problem is that such classical experiments simulate quantum probabilities with intensities of classical fields. However, fields intensities measurements are radically different from single-photon detections, which are primitives of any genuine Bell experiment. We show that this fundamental difference between field intensities measurements and single photon detections shifts the classical bound of relevant Bell inequalities to its non-signaling limit, leaving no place for their violations.
Interaction between temperature and sublethal infection with the amphibian chytrid fungus impacts a susceptible frog species
Authors: Campbell Lachlan , Bower Deborah S. , Clulow Simon , Stockwell Michelle , Clulow John , Mahony Michael 
Published: January 2019

AbstractThe amphibian chytrid fungus Batrachochytrium dendrobatidis is an emerging infectious pathogen present on every continent except Antarctica. It causes the disease chytridiomycosis in a subset of species but does not always result in disease or death for every host. Ambient temperature influences both amphibian metabolism and chytrid pathogenicity, however the interactive effects on host physiology is not well understood. We investigated the sublethal effect of B. dendrobatidis infection on a susceptible host, Litoria aurea to test (1) whether the infection load, metabolic activity, body fat and gonad size differed in L. aurea at either 24 °C or 12 °C ambient temperatures and (2) whether previous Bd infection caused long-term changes to body fat and gonad size. Litoria aurea in 12 °C treatments had higher infection loads of B. dendrobatidis and lower survivorship. Metabolic rate was higher and fat mass was lower in infected individuals and in animals in 24 °C treatments. Male L. aurea previously infected with B. dendrobatidis had smaller testes 5 months-post clearance of infection, an effect likely to translate to fitness costs in wild populations. These experiments demonstrate a physiological cost to sublethal B. dendrobatidis infection, which suggests a reduction in host fitness mediated by temperature in the host’s environment regardless of whether infection leads to mortality.
Obesity Aggravates Acute Pancreatitis via Damaging Intestinal Mucosal Barrier and Changing Microbiota Composition in Rats
Authors: Ye Cheng , Liu Ling , Ma Xiao , Tong Huan , Gao Jinhang , Tai Yang , Huang Libin , Tang Chengwei , Wang Rui 
Published: January 2019

AbstractObesity may aggravate acute pancreatitis (AP) through damaging the intestinal mucosal barrier (IMB). The underlying mechanism remains unclear. This study was aimed to provide further data to clarify the mechanism. 48 rats were divided into 4 groups: 1) normal control (NC), chow-fed rats with sham operation, 2) no-obese rats with AP (NAP), chow-fed rats with taurocholate infusion, 3) obese control (OC), high-fat diet (HFD)-fed rats with sham operation, and 4) obese rats with AP (OAP), HFD-fed rats with taurocholate infusion. Pancreatic pathologic score (11.39 ± 1.76 vs. 14.11 ± 1.05, p = 0.005), intestinal permeability to FD4 (0.91 ± 0.25 μg/ml vs. 7.06 ± 3.67 μg/ml, p < 0.001), serum leptin (10.25 ± 5.59 ng/ml vs. 79.73 ± 38.44 ng/ml, p < 0.001) and ileal apoptosis (2.05 ± 0.73% vs. 4.53 ± 2.28%, p = 0.006) were significantly higher in OAP than in NAP group. The intestinal bacterial richness (Chao 1 and OTUs) was significantly lower in OAP than in NAP rats. The higher abundance of Proteobacteria and reduced proportions of intestinal Actinobacteria, Allobaculum and Barnesiella were detected in OAP group. Obesity may result in decreased intestinal leptin/ObR-b binding, distinct phylogenetic clusters of ileal bacterial communities, increased intestinal inflammatory injury and the insufficient intestinal epithelial cells proliferation during AP attack. Pancreatic injury was aggravated due to obesity associated dysfunction of IMB.
Tailored Interface Energetics for Efficient Charge Separation in Metal Oxide-Polymer Solar Cells
Authors: Ehrenreich Philipp , Groh Arthur , Goodwin Heather , Huster Jeldrik , Deschler Felix , Mecking Stefan , Schmidt-Mende Lukas 
Published: January 2019

AbstractHybrid organic-inorganic heterointerfaces in solar cells suffer from inefficient charge separation yet the origin of performance limitations are widely unknown. In this work, we focus on the role of metal oxide-polymer interface energetics in a charge generation process. For this purpose, we present novel benzothiadiazole based thiophene oligomers that tailor the surface energetics of the inorganic acceptor TiO2 systematically. In a simple bilayer structure with the donor polymer poly(3-hexylthiophene) (P3HT), we are able to improve the charge generation process considerably. By means of an electronic characterization of solar cell devices in combination with ultrafast broadband transient absorption spectroscopy, we demonstrate that this remarkable improvement in performance originates from reduced recombination of localized charge transfer states. In this context, fundamental design rules for interlayers are revealed, which assist the charge separation at organic-inorganic interfaces. Beside acting as a physical spacer in between electrons and holes, interlayers should offer (1) a large energy offset to drive exciton dissociation, (2) a push-pull building block to reduce the Coulomb binding energy of charge transfer states and (3) an energy cascade to limit carrier back diffusion towards the interface.