bluuebunny/crossref_metadata_2025_split huggingface dataset:
Urbanization, resources stabilization and the temporal persistence of bird species: A review
Authors: Leveau Lucas Matías 
Published: February 2018

Background. A scarcely studied consequence of urbanization is the effect of the temporal stabilization of habitat structure and resources on bird communities. This alteration is thought to dampen environmental variations between day and night, seasons and years, promoting a temporal persistence of bird composition in urban environments. The aim of this study is to review actual evidence of temporal stabilization of habitats and resources in urban environments, and its potential effects on the temporal variation of bird species presence among different temporal scales.
Methods. Selection of literature was made by searching published articles and book chapters using Google scholar. I only included articles that compared the temporal variation of bird composition or resources between different levels of urbanization.
Results. In general, there is evidence of temporal stabilization of habitat structure and resources along the three scales considered. At the diurnal scale, the main factor considered was artificial light in the context of light pollution. At the seasonal and interannual scales, several case studies found a lesser temporal variation of primary productivity in urban areas compared with natural and rural areas. Bird species composition showed more stabilization in urban environments at the three temporal scales: 1) several case studies reported bird feeding at night, associated with artificial light; 2) studies in urban parks and along urbanization gradients showed lower seasonal variation of bird composition in the more urbanized areas; and 3) in general, case studies along urbanization gradients showed lower interannual variation of bird composition in the more urbanized areas, although some studies showed no relationships or opposed trends than expected.
Discussion. The published evidence suggests that urban areas dampen the natural cycles at several temporal scales. The stabilization of biotic and abiotic factors, such as light, temperature, food and habitat structure are desynchronized from natural diurnal, seasonal and interannual cycles. However, there is a dearth of studies that simultaneously analyze the relationship between resources and bird composition stabilization. I also emphasize the need to differentiate spatial and temporal homogenization of avifaunas for a future research agenda. Moreover, the relationship between urbanization and other taxa is also commented. Finally, I propose suggestions for future work at different spatial scales.
ENSO‐Like Modulated Tropical Pacific Climate Changes Since 2.36 Myr and Its Implication for the Middle Pleistocene Transition
Authors: Yu Zhaojie , Wan Shiming , Colin Christophe , Song Lina , Zhao Debo , Huang Jie , Sun Hanjie , Xu Zhaokai , Li Anchun , Li Tiegang 
Published: February 2018

AbstractEl Niño/Southern Oscillation (ENSO) activity and the Pacific Walker Circulation are controlled by the zonal sea surface temperature (SST) gradient between the western and Eastern Equatorial Pacific (EEP) and the corresponding barometric difference. Variations in the zonal SST gradient since the early Pleistocene have primarily been triggered by changes in the SST in the Eastern Equatorial Pacific. However, the response of the ENSO‐like long‐term state to the cooling of the EEP and its coupling role with tropical Pacific climate changes are still not well established. Here we present a high‐resolution grain‐size record spanning the last 2.36 Myr, obtained from marine core sediment located in the West Philippine Sea in order to decipher the tropical pacific climate changes and reveal its controlling mechanism. By combining our data with other long‐term climatic records from the Equatorial Pacific, we demonstrate that the cooling of SST and enhanced upwelling in the EEP resulted in the development of the Walker Circulation and increased monsoon precipitation in Luzon from 2.2 to 1.6 Myr, from 1.2 to 0.8 Myr, and since 0.2 Myr ago. The progressive cooling of the high‐latitudes in the Quaternary may be responsible for our observation here. A newly identified 100 kyr dominant period between 2.2 and 1.6 Myr in the ENSO‐like modulated Pacific climate records indicates that the ENSO‐like system may play a key role in facilitating or responding to the global climate changes.
Calcium Isotopic Compositions of Normal Mid‐Ocean Ridge Basalts From the Southern Juan de Fuca Ridge
Authors: Zhu Hongli , Liu Fang , Li Xin , Wang Guiqin , Zhang Zhaofeng , Sun Weidong 
Published: February 2018

AbstractMantle peridotites show that Ca is isotopically heterogeneous in Earth's mantle, but the mechanism for such heterogeneity remains obscure. To investigate the effect of partial melting on Ca isotopic fractionation and the mechanism for Ca isotopic heterogeneity in the mantle, we report high‐precision Ca isotopic compositions of the normal Mid‐Ocean Ridge Basalts (N‐MORB) from the southern Juan de Fuca Ridge. δ44/40Ca of these N‐MORB samples display a small variation ranging from 0.75 ± 0.05 to 0.86 ± 0.03‰ (relative to NIST SRM 915a, a standard reference material produced by the National Institute of Standards and Technology), which are slightly lower than the estimated Upper Mantle value of 1.05 ± 0.04‰ and the Bulk Silicate Earth (BSE) value of 0.94 ± 0.05‰. This phenomenon cannot be explained by fractional crystallization, because olivine and orthopyroxene fractional crystallization has limited influence on δ44/40Ca of N‐MORB due to their low CaO contents, while plagioclase fractional crystallization cannot lead to light Ca isotopic compositions of the residue magma. Instead, the lower δ44/40Ca of N‐MORB samples compared to their mantle source is most likely caused by partial melting. The offset in δ44/40Ca between N‐MORB and BSE indicates that at least 0.1–0.2‰ fractionation would occur during partial melting and light Ca isotopes are preferred to be enriched in magma melt, which is in accordance with the fact that δ44/40Ca of melt‐depleted peridotites are higher than fertile peridotites in literature. Therefore, partial melting is an important process that can decrease δ44/40Ca in basalts and induce Ca isotopic heterogeneity in Earth's mantle.
Impact of Physics Parameterization Ordering in a Global Atmosphere Model
Authors: Donahue Aaron S. , Caldwell Peter M. 
Published: February 2018

AbstractBecause weather and climate models must capture a wide variety of spatial and temporal scales, they rely heavily on parameterizations of subgrid‐scale processes. The goal of this study is to demonstrate that the assumptions used to couple these parameterizations have an important effect on the climate of version 0 of the Energy Exascale Earth System Model (E3SM) General Circulation Model (GCM), a close relative of version 1 of the Community Earth System Model (CESM1). Like most GCMs, parameterizations in E3SM are sequentially split in the sense that parameterizations are called one after another with each subsequent process feeling the effect of the preceding processes. This coupling strategy is noncommutative in the sense that the order in which processes are called impacts the solution. By examining a suite of 24 simulations with deep convection, shallow convection, macrophysics/microphysics, and radiation parameterizations reordered, process order is shown to have a big impact on predicted climate. In particular, reordering of processes induces differences in net climate feedback that are as big as the intermodel spread in phase 5 of the Coupled Model Intercomparison Project. One reason why process ordering has such a large impact is that the effect of each process is influenced by the processes preceding it. Where output is written is therefore an important control on apparent model behavior. Application of k‐means clustering demonstrates that the positioning of macro/microphysics and shallow convection plays a critical role on the model solution.
A Comparison of the Diel Cycle of Modeled and Measured Latent Heat Flux During the Warm Season in a Colorado Subalpine Forest
Authors: Burns Sean P. , Swenson Sean C. , Wieder William R. , Lawrence David M. , Bonan Gordon B. , Knowles John F. , Blanken Peter D. 
Published: February 2018

AbstractPrecipitation changes the physiological characteristics of an ecosystem. Because land‐surface models are often used to project changes in the hydrological cycle, modeling the effect of precipitation on the latent heat flux λE is an important aspect of land‐surface models. Here we contrast conditionally sampled diel composites of the eddy‐covariance fluxes from the Niwot Ridge Subalpine Forest AmeriFlux tower with the Community Land Model (CLM, version 4.5). With respect to measured λE during the warm season: for the day following above‐average precipitation, λE was enhanced at midday by ≈40 W m−2 (relative to dry conditions), and nocturnal λE increased from ≈10 W m−2 in dry conditions to over 20 W m−2 in wet conditions. With default settings, CLM4.5 did not successfully model these changes. By increasing the amount of time that rainwater was retained by the canopy/needles, CLM was able to match the observed midday increase in λE on a dry day following a wet day. Stable nighttime conditions were problematic for CLM4.5. Nocturnal CLM λE had only a small (≈3 W m−2) increase during wet conditions, CLM nocturnal friction velocity u∗ was smaller than observed u∗, and CLM canopy air temperature was 2°C less than those measured at the site. Using observed u∗ as input to CLM increased λE; however, this caused CLM λE to be increased during both wet and dry periods. We suggest that sloped topography and the ever‐present drainage flow enhanced nocturnal u∗ and λE. Such phenomena would not be properly captured by topographically blind land‐surface models, such as CLM.
Effective Representation of River Geometry in Hydraulic Flood Forecast Models
Authors: Grimaldi S. , Li Y. , Walker J. P. , Pauwels V. R. N. 
Published: February 2018

AbstractBathymetric data are a critical input to hydraulic models. However, river depth and shape cannot be systematically observed remotely, and field data are both scarce and expensive to collect. In flood modeling, river roughness and geometry compensate for each other, with different parameter sets often being able to map model predictions equally well to the observed data, commonly known as equifinality. This study presents a numerical experiment to investigate an effective yet parsimonious representation of channel geometry that can be used for operational flood forecasting. The LISFLOOD‐FP hydraulic model was used to simulate a hypothetical flood event in the Clarence catchment (Australia). A high‐resolution model simulation based on accurate bathymetric field data was used to benchmark coarser model simulations based on simplified river geometries. These simplified river geometries were derived from a combination of globally available empirical formulations, remote sensing data, and a limited number of measurements. Model predictive discrepancy between simulations with field data and simplified geometries allowed an assessment of the geometry impact on inundation dynamics. In this study site, the channel geometrical representation for a reliable inundation forecast could be achieved using remote sensing‐derived river width values combined with a few measurements of river depth sampled at strategic locations. Furthermore, this study showed that spatially distributed remote sensing‐derived inundation levels at the very early stages of a flood event have the potential to support the effective diagnosis of errors in model implementations.
The TNF‐α‐induced expression of miR‐130b protects cervical cancer cells from the cytotoxicity of TNF‐α
Authors: Yang Lei , Wang Yanli , Shi Shuainan , Xie Lili , Liu Tao , Wang Yuliang , Mu Hong 
Published: February 2018

Tumour necrosis factor alpha (TNF‐α) is a multifunctional cytokine and has the capacity both to promote cell growth and to kill tumour cells by inducing cell apoptosis. However, many tumour cells develop resistance to the toxic effects of TNF‐α. Thus, understanding the mechanism underlying the resistance of tumours to TNF‐α toxicity and finding ways to overcome this resistance are urgently needed. In this study, we discovered that two cervical cancer cell lines, Hela and Siha, showed null responses to TNF‐α cytotoxicity. However, in these cell lines, TNF‐α stimulation promoted the expression of miR‐130b and downregulated the expression of PTEN gene, which encodes a dual‐specificity phosphatase that acts as a tumour suppressor. Blockade of miR‐130b function or overexpression of PTEN gene sensitized cells to TNF‐α cytotoxicity. Regression analyses revealed that there were reverse relationships between the cellular levels of miR‐130b and PTEN mRNA in cervical cancer cells. Gain‐ and loss‐of‐function assays demonstrated that there were causal relationships between the increase in miR‐130b levels and the reduction in PTEN mRNA or PTEN protein levels. In silico analysis revealed that there were two miR‐130b target sites within the 3′UTR of PTEN mRNA and experimental evidences demonstrated that miR‐130b repressed the expression of PTEN gene by binding directly to the 3′UTR of PTEN mRNA. These data suggest miR‐130b expression as a target to be inhibited to make tumour cells more sensitive to the toxic impact of TNF‐α.
The Cross‐Talk between Genomes: How Co‐Evolution Shaped Plant Mitochondrial Gene Expression
Authors: Budar Françoise , Mireau Hakim 
Published: February 2018

AbstractThis chapter first details studies that provide evidence for the variability of factors involved in plant mt gene expression, either cis‐elements or nuclear‐encoded products. It then shows how very different evolutionary processes of co‐evolution can explain some of the peculiarities of plant gene expression. Co‐evolution implies co‐ordinated genetic changes in two interacting entities, due to selection exerted by each on the other. The physical interaction between elements originating from the different genetic compartments is a prerequisite for co‐adaptation. Mitochondrial genes involved in cytoplasmic male sterility (CMS) and their nuclear restorers constitute the best‐known illustration of the role of co‐evolution in the variability of mitochondrial gene expression. The variation in CMS mitochondrial gene expression is driven by a genomic conflict. The chapter further explores the clues that suggest there has been a significant impact of co‐evolution on gene expression in plant mitochondria and discusses this in terms of possible evolutionary scenarios.
RNAMetabolism and Transcript Regulation
Authors: Zmudjak Michal , Ostersetzer‐Biran Oren 
Published: February 2018

AbstractMitochondria house the tricarboxylic acid (TCA) cycle, the oxidative phosphorylation (OXPHOS) machinery and are also the sites of numerous other essential metabolic pathways in plants. This chapter describes the principal components of the transcription and post‐transcriptional regulatory steps in mitochondrial gene expression. It then summarizes the current state of knowledge of mitochondrial RNA processing and maturation in plants. The chapter also describes the main pathways of ribosome maturation in bacteria and plant mitochondria. It reviews recent significant progress in editing factors research in plant mitochondria. Furthermore the chapter focuses on group I and group II introns that are predominant in angiosperm mitochondria. Analysis of group II introns splicing in wheat mitochondria indicates multiple group II splicing mechanisms, as evidenced by the presence of linear and circular forms of excised intron moleculesin vivo. The splicing of group II introns is mechanistically identical to that of the nuclear spliceosomal introns.
Ecophysiology of Plant Respiration
Authors: Del‐Saz Néstor Fernández , Ribas‐Carbo Miquel 
Published: February 2018

AbstractThis chapter discusses the two respiration parameters, including O2and CO2. A new technique based on cavity‐enhanced Raman multi‐gas spectrometry (CERS) that claims to have the potential to measure both O2consumption and CO2production on large closed systems which is a great leap forward in respiration studies, especially for the measurement of respiratory quotient (RQ). The chapter explains treatment of the O2/CO2paradigm, there are many situations where the amount of CO2produced during respiration is similar to the amount of O2consumed. Furthermore, the chapter describes the plant carbon balance resulting from contributions from photosynthesis, photorespiration and respiration. The eddy co‐variance (EC) method allows estimations to be made of the net global carbon balance through the assessment of CO2, water and temperature fluxes under a broad range of both temporal and spatial scales.
Honeycomb‐Like Spherical Cathode Host Constructed from Hollow Metallic and Polar Co9S8 Tubules for Advanced Lithium–Sulfur Batteries
Authors: Dai Chunlong , Lim Jin‐Myoung , Wang Minqiang , Hu Linyu , Chen Yuming , Chen Zhaoyang , Chen Hao , Bao Shu‐Juan , Shen Bolei , Li Yi , Henkelman Graeme , Xu Maowen 
Published: February 2018

AbstractThe practical application of lithium‐sulfur (Li‐S) batteries remains remote because of rapid capacity fade caused by the low conductivity of sulfur, dissolution of intermediate lithium polysulfides, severe volumetric expansion, and slow redox kinetics of polysulfide intermediates. Here, to address these obstacles, a new sulfiphilic and highly conductive honeycomb‐like spherical cathode host constructed from hollow metallic and polar Co9S8 tubes is designed. Co9S8 can effectively bind polar polysulfides for prolonged cycle life, due to the strong chemisorptive capability for immobilizing the polysulfide species. The hollow structure, as the sulfur host, can further prevent polysulfide dissolution and offer sufficient space to accommodate the necessary volume expansion. Well‐aligned tubular arrays provide a conduit for rapid conduction of electrons and Li‐ions. More importantly, the experimental results and theoretical calculations show that Co9S8 plays an important catalytic role in improving the electrochemical reaction kinetics. When used as cathode materials for Li–S batteries, the S@Co9S8 composite cathode exhibits high capacity and an exceptional stable cycling life demonstrated by tests of 600 cycles at 1 C with a very low capacity decay rate of only ≈0.026% per cycle.
Programmable and Multifunctional DNA‐Based Materials for Biomedical Applications
Authors: Zhang Yuezhou , Tu Jing , Wang Dongqing , Zhu Haitao , Maity Sajal Kumar , Qu Xiangmeng , Bogaert Bram , Pei Hao , Zhang Hongbo 
Published: February 2018

AbstractDNA encodes the genetic information; recently, it has also become a key player in material science. Given the specific Watson–Crick base‐pairing interactions between only four types of nucleotides, well‐designed DNA self‐assembly can be programmable and predictable. Stem‐loops, sticky ends, Holliday junctions, DNA tiles, and lattices are typical motifs for forming DNA‐based structures. The oligonucleotides experience thermal annealing in a near‐neutral buffer containing a divalent cation (usually Mg2+) to produce a variety of DNA nanostructures. These structures not only show beautiful landscape, but can also be endowed with multifaceted functionalities. This Review begins with the fundamental characterization and evolutionary trajectory of DNA‐based artificial structures, but concentrates on their biomedical applications. The coverage spans from controlled drug delivery to high therapeutic profile and accurate diagnosis. A variety of DNA‐based materials, including aptamers, hydrogels, origamis, and tetrahedrons, are widely utilized in different biomedical fields. In addition, to achieve better performance and functionality, material hybridization is widely witnessed, and DNA nanostructure modification is also discussed. Although there are impressive advances and high expectations, the development of DNA‐based structures/technologies is still hindered by several commonly recognized challenges, such as nuclease instability, lack of pharmacokinetics data, and relatively high synthesis cost.
Vertically Aligned Graphene Coating is Bactericidal and Prevents the Formation of Bacterial Biofilms
Authors: Pandit Santosh , Cao Zhejian , Mokkapati Venkata R. S. S. , Celauro Emanuele , Yurgens Avgust , Lovmar Martin , Westerlund Fredrik , Sun Jie , Mijakovic Ivan 
Published: February 2018

AbstractThe key first step in developing bacterial infections related to implants and medical devices is the attachment of planktonic bacterial cells, and subsequent formation of biofilms. Herein, it is reported that graphene, a 2D carbon‐based material, can be effectively used to prevent bacterial attachment. The key parameter for this effect is the orientation of graphene with respect to the coated surface. Chemical vapor deposition (CVD) graphene, deposited horizontally on the surface, exhibits no antibacterial effect. By contrast, an array of graphene flakes grown perpendicularly to the surface by a plasma‐enhanced CVD (PECVD) process prevent biofilm formation. Electron microscopy reveals that the exposed edges of vertically aligned graphene flakes penetrate the bacterial membrane and drain the cytosolic content. Bacteria are not able to develop resistance to this killing mechanism during multiple exposures. By keeping the height of the vertical graphene coating between 60 and 100 nm, the coating is able to effectively kill bacteria, while being completely harmless to mammalian cells.
A Two‐Electron Storage Nonaqueous Organic Redox Flow Battery
Authors: Huang Jinhua , Yang Zheng , Vijayakumar Murugesan , Duan Wentao , Hollas Aaron , Pan Baofei , Wang Wei , Wei Xiaoliang , Zhang Lu 
Published: February 2018

AbstractNonaqueous redox flow batteries based on redox‐active organic materials (ROMs) are attractive for stationary energy storage applications, but inferior energy densities are demonstrated in reported systems. To address this limitation, a nonaqueous organic flow battery using two‐electron anthraquinone anolyte and phenothiazine catholyte materials is developed. Structural tailoring leads to greatly improved solubilities with the cell potentials of 1.63 and 2.80 V for the first and second electron transfer reactions, respectively, of optimized ROMs. Doubled charge storage capacities indicative of 2e− reactions are achieved in proof‐of‐concept bulk electrolyte and flow cell demonstrations, albeit with only modest cyclability due to the limited stability of the second redox event. Although further improvement is still needed to attract practical interest, this study opens a promising pathway to increase the energy density for organic flow batteries and is expected to inspire more in‐depth studies of energy dense, stable ROMs.