bluuebunny/crossref_metadata_2025_split huggingface dataset:
The mitochondrial genome map of Nelumbo nucifera reveals ancient evolutionary features
Authors: Gui Songtao , Wu Zhihua , Zhang Hongyuan , Zheng Yinzhen , Zhu Zhixuan , Liang Dequan , Ding Yi 
Published: July 2016

AbstractNelumbo nucifera is an evolutionary relic from the Late Cretaceous period. Sequencing the N. nucifera mitochondrial genome is important for elucidating the evolutionary characteristics of basal eudicots. Here, the N. nucifera mitochondrial genome was sequenced using single molecule real-time sequencing technology (SMRT) and the mitochondrial genome map was constructed after de novo assembly and annotation. The results showed that the 524,797-bp N. nucifera mitochondrial genome has a total of 63 genes, including 40 protein-coding genes, three rRNA genes and 20 tRNA genes. Fifteen collinear gene clusters were conserved across different plant species. Approximately 700 RNA editing sites in the protein-coding genes were identified. Positively selected genes were identified with selection pressure analysis. Nineteen chloroplast-derived fragments were identified and seven tRNAs were derived from the chloroplast. These results suggest that the N. nucifera mitochondrial genome retains evolutionarily conserved characteristics, including ancient gene content and gene clusters, high levels of RNA editing and low levels of chloroplast-derived fragment insertions. As the first publicly available basal eudicot mitochondrial genome, the N. nucifera mitochondrial genome facilitates further analysis of the characteristics of basal eudicots and provides clues of the evolutionary trajectory from basal angiosperms to advanced eudicots.
Noninvasive, label-free, three-dimensional imaging of melanoma with confocal photothermal microscopy: Differentiate malignant melanoma from benign tumor tissue
Authors: He Jinping , Wang Nan , Tsurui Hiromichi , Kato Masashi , Iida Machiko , Kobayashi Takayoshi 
Published: July 2016

AbstractSkin cancer is one of the most common cancers. Melanoma accounts for less than 2% of skin cancer cases but causes a large majority of skin cancer deaths. Early detection of malignant melanoma remains the key factor in saving lives. However, the melanoma diagnosis is still clinically challenging. Here, we developed a confocal photothermal microscope for noninvasive, label-free, three-dimensional imaging of melanoma. The axial resolution of confocal photothermal microscope is ~3 times higher than that of commonly used photothermal microscope. Three-dimensional microscopic distribution of melanin in pigmented lesions of mouse skin is obtained directly with this setup. Classic morphometric and fractal analysis of sixteen 3D images (eight for benign melanoma and eight for malignant) showed a capability of pathology of melanoma: melanin density and size become larger during the melanoma growth and the melanin distribution also becomes more chaotic and unregulated. The results suggested new options for monitoring the melanoma growth and also for the melanoma diagnosis.
Mechanism and Effect of Temperature on Variations in Antibiotic Resistance Genes during Anaerobic Digestion of Dairy Manure
Authors: Sun Wei , Qian Xun , Gu Jie , Wang Xiao-Juan , Duan Man-Li 
Published: July 2016

AbstractAnimal manure comprises an important reservoir for antibiotic resistance genes (ARGs), but the variation in ARGs during anaerobic digestion at various temperatures and its underlying mechanism remain unclear. Thus, we performed anaerobic digestion using dairy manure at three temperature levels (moderate: 20 °C, mesophilic: 35 °C and thermophilic: 55 °C), to analyze the dynamics of ARGs and bacterial communities by quantitative PCR and 16S rRNA gene sequencing. We found that 8/10 detected ARGs declined and 5/10 decreased more than 1.0 log during thermophilic digestion, whereas only four and five ARGs decreased during moderate and mesophilic digestion, respectively. The changes in ARGs and bacterial communities were similar under the moderate and mesophilic treatments, but distinct from those in the thermophilic system. Potential pathogens such as Bacteroidetes, Proteobacteria and Corynebacterium were removed by thermophilic digestion but not by moderate and mesophilic digestion. The bacterial community succession was the dominant mechanism that influenced the variation in ARGs and integrons during anaerobic digestion. Thermophilic digestion decreased the amount of mesophilic bacteria (Bacteroidetes and Proteobacteria) carrying ARGs. Anaerobic digestion generally decreased the abundance of integrons by eliminating the aerobic hosts of integrons (Actinomycetales and Bacilli). Thermophilic anaerobic digestion is recommended for the treatment and reuse of animal manure.
A tunable acoustic metamaterial with double-negativity driven by electromagnets
Authors: Chen Zhe , Xue Cheng , Fan Li , Zhang Shu-yi , Li Xiao-juan , Zhang Hui , Ding Jin 
Published: July 2016

AbstractWith the advance of the research on acoustic metamaterials, the limits of passive metamaterials have been observed, which prompts the studies concerning actively tunable metamaterials with adjustable characteristic frequency bands. In this work, we present a tunable acoustic metamaterial with double-negativity composed of periodical membranes and side holes, in which the double-negativity pass band can be controlled by an external direct-current voltage. The tension and stiffness of the periodically arranged membranes are actively controlled by electromagnets producing additional stresses, and thus, the transmission and phase velocity of the metamaterial can be adjusted by the driving voltage of the electromagnets. It is demonstrated that a tiny direct-current voltage of 6V can arise a shift of double-negativity pass band by 40% bandwidth, which exhibits that it is an easily controlled and highly tunable acoustic metamaterial, and furthermore, the metamaterial marginally causes electromagnetic interference to the surroundings.
Nonlinear dynamics and instability of aqueous dissolution of silicate glasses and minerals
Authors: Wang Yifeng , Jove-Colon Carlos F. , Kuhlman Kristopher L. 
Published: July 2016

AbstractAqueous dissolution of silicate glasses and minerals plays a critical role in global biogeochemical cycles and climate evolution. The reactivity of these materials is also important to numerous engineering applications including nuclear waste disposal. The dissolution process has long been considered to be controlled by a leached surface layer in which cations in the silicate framework are gradually leached out and replaced by protons from the solution. This view has recently been challenged by observations of extremely sharp corrosion fronts and oscillatory zonings in altered rims of the materials, suggesting that corrosion of these materials may proceed directly through congruent dissolution followed by secondary mineral precipitation. Here we show that complex silicate material dissolution behaviors can emerge from a simple positive feedback between dissolution-induced cation release and cation-enhanced dissolution kinetics. This self-accelerating mechanism enables a systematic prediction of the occurrence of sharp dissolution fronts (vs. leached surface layers), oscillatory dissolution behaviors and multiple stages of glass dissolution (in particular the alteration resumption at a late stage of a corrosion process). Our work provides a new perspective for predicting long-term silicate weathering rates in actual geochemical systems and developing durable silicate materials for various engineering applications.
Reduction of the spatially mutual coupling between dual-polarized patch antennas using coupled metamaterial slabs
Authors: Pan Bai Cao , Tang Wen Xuan , Qi Mei Qing , Ma Hui Feng , Tao Zui , Cui Tie Jun 
Published: July 2016

AbstractMutual coupling inside antenna array is usually caused by two routes: signal leakage via conducting currents on the metallic background or surface wave along substrates; radio leakage received from space between antenna elements. The former one can be depressed by changing the distribution of surface currents, as reported in literatures. But when it comes to the latter one, the radiation-leakage-caused coupling, traditional approaches using circuit manipulation may be inefficient. In this article, we propose and design a new type of decoupling module, which is composed of coupled metamaterial (MTM) slabs. Two classes of MTM particles, the interdigital structure (IS) and the split-ring resonators (SRRs), are adopted to provide the first and second modulations of signal. We validate its function to reduce the radiation leakage between two dual-polarized patch antennas. A prototype is fabricated in a volume with subwavelength scale (0.6λ × 0.3λ × 0.053λ) to provide 7dB improvement for both co-polarization and cross-polarization isolations from 1.95 to 2.2 GHz. The design has good potential for wireless communication and radar systems.
Dysfunctional epileptic neuronal circuits and dysmorphic dendritic spines are mitigated by platelet-activating factor receptor antagonism
Authors: Musto Alberto E. , Rosencrans Robert F. , Walker Chelsey P. , Bhattacharjee Surjyadipta , Raulji Chittalsinh M. , Belayev Ludmila , Fang Zhide , Gordon William C. , Bazan Nicolas G. 
Published: July 2016

AbstractTemporal lobe epilepsy or limbic epilepsy lacks effective therapies due to a void in understanding the cellular and molecular mechanisms that set in motion aberrant neuronal network formations during the course of limbic epileptogenesis (LE). Here we show in in vivo rodent models of LE that the phospholipid mediator platelet-activating factor (PAF) increases in LE and that PAF receptor (PAF-r) ablation mitigates its progression. Synthetic PAF-r antagonists, when administered intraperitoneally in LE, re-establish hippocampal dendritic spine density and prevent formation of dysmorphic dendritic spines. Concomitantly, hippocampal interictal spikes, aberrant oscillations, and neuronal hyper-excitability, evaluated 15–16 weeks after LE using multi-array silicon probe electrodes implanted in the dorsal hippocampus, are reduced in PAF-r antagonist-treated mice. We suggest that over-activation of PAF-r signaling induces aberrant neuronal plasticity in LE and leads to chronic dysfunctional neuronal circuitry that mediates epilepsy.
Determination of oxygen extraction fraction using magnetic resonance imaging in canine models with internal carotid artery occlusion
Authors: Chang Fei-Yan , Xiao Jiang-Xi , Xie Sheng , Yu Lei , Zhang Zhen-Xia , Wang Wu , Luo Jie , Zhang Zhong-Ping , Guo Hua 
Published: July 2016

AbstractPerfusion of the penumbra tissue below the flow threshold for functional disturbance but above that for the maintenance of morphological integrity is the target for therapy in acute ischaemic stroke. The measurement of the oxygen extraction fraction (OEF) may provide a direct assessment of tissue viability, so that irreversible tissue damage and penumbra can be reliably identified. By using an asymmetric spin echo single-shot echo planar imaging (ASE-SSEPI) sequence, the quantitative OEF was obtained in the ischaemic brain tissues of canine models with internal carotid artery occlusion. TTC staining, which delineated the regions of infarct and penumbra, was used for defining the corresponding regions on OEF maps. The threshold of the OEF to discriminate the infarct cores and penumbral tissues was then determined according to the OEF values at different times. With repeated-measures ANOVA, the OEF of the infarcted regions was found to be time dependent. An OEF greater than 0.48 best predicted cortical infarction at 1.5 hr, with an area under the receiving operating characteristic curve of 0.968, a sensitivity of 97.5% and a specificity of 92.5%. Our results may be helpful in the evaluation of tissue viability during stroke events.
Ca(OH)2-Catalyzed Condensation of Aldehydes with Methyl ketones in Dilute Aqueous Ethanol: A Comprehensive Access to α,β-Unsaturated Ketones
Authors: Yu Lei , Han Mengting , Luan Jie , Xu Lin , Ding Yuanhua , Xu Qing 
Published: July 2016

AbstractCheap, abundant but seldom-employed Ca(OH)2 was found to be an excellent low-loading (5–10 mol%) catalyst for Claisen-Schmidt condensation of aldehydes with methyl ketones under mild conditions. It was interesting that dilute aqueous ethanol (20 v/v%) was unexpectedly discovered to be the optimal solvent. The reaction was scalable at least to 100 mmol and calcium could be precipitated by CO2 and removed by filtration. Evaporation of solvent directly afforded the product in the excellent 96% yield with high purity, as confirmed by its 1H NMR spectrum.
Preparation of transparent hydrophobic polymeric films spray-deposited on substrates
Authors: Viechineski F. N. , Kubaski E. T. , Schmidt S. , Sequinel T. , Varela J. A. , Tebcherani S. M. 
Published: July 2016

This paper describes the production of transparent hydrophobic polymeric films made of poly(vinyl chloride) and paraffin wax. A liquid polymeric solution was prepared and spray-deposited on silica glass and nonwoven fabric surfaces. The contact angle between water droplets and glass substrate was 102° while that between droplets and nonwoven fabric was 120°. The films exhibited hydrophobic behaviour regardless of the droplet size. Field emission gun scanning electron microscopy revealed complete adhesion of the film on the substrate and a film thickness of 0.16 µm. The atomic force microscopy micrographs showed a nanoscale rough film surface, which was responsible for air entrapment, preventing water from penetrating the film. This fact explains the high contact angle obtained. The raw materials also contributed to the film's hydrophobicity because of their non-polarity, which prevents miscibility between water droplets and film. GRAPHICAL ABSTRACT
Widespread Rift Valley Fever Emergence in Senegal in 2013–2014
Authors: Sow Abdourahmane , Faye Ousmane , Ba Yamar , Diallo Diawo , Fall Gamou , Faye Oumar , Bob Ndeye Sakha , Loucoubar Cheikh , Richard Vincent , Dia Anta Tal , Diallo Mawlouth , Malvy Denis , Sall Amadou Alpha 
Published: July 2016

Abstract
Rift Valley fever (RVF), which caused epizootics and epidemics among human and livestock populations, occurred in Senegal in 2013–2014. A multidisciplinary field investigation was carried out in 3 regions of Senegal. We found 11 confirmed human cases of Rift Valley fever, including severe cases with encephalitis and retinitis, 1 pool of mosquito (Aedes ochraceus), and 52 animals tested positive for the disease. Symptoms such as encephalitis and macular retinitis were the most severe cases reported so far in Senegal. The outbreak was widespread due to animals' movements, leading to the largest RVF outbreak in Senegal in terms of geographic spreading and reaching areas that never reported RVF activity previously.
Generalization of the Ewens sampling formula to arbitrary fitness landscapes
Authors: Khromov Pavel , Malliaris Constantin D. , Morozov Alexandre V. 
Published: July 2016

AbstractIn considering evolution of transcribed regions, regulatory modules, and other genomic loci of interest, we are often faced with a situation in which the number of allelic states greatly exceeds the population size. In this limit, the population eventually adopts a steady state characterized by mutation-selection-drift balance. Although new alleles continue to be explored through mutation, the statistics of the population, and in particular the probabilities of seeing specific allelic configurations in samples taken from a population, do not change with time. In the absence of selection, probabilities of allelic configurations are given by the Ewens sampling formula, widely used in population genetics to detect deviations from neutrality. Here we develop an extension of this formula to arbitrary, possibly epistatic, fitness landscapes. Although our approach is general, we focus on the class of landscapes in which alleles are grouped into two, three, or several fitness states. This class of landscapes yields sampling probabilities that are computationally more tractable, and can form a basis for the inference of selection signatures from sequence data. We demonstrate that, for a sizeable range of mutation rates and selection coefficients, the steady-state allelic diversity is not neutral. Therefore, it may be used to infer selection coefficients, as well as other key evolutionary parameters, using high-throughput sequencing of evolving populations to collect data on locus polymorphisms. We also carry out numerical investigation of various approximations involved in deriving our sampling formulas, such as the infinite allele limit and the “full connectivity” assumption in which each allele can mutate into any other allele. We find that our theory remains sufficiently accurate even if these assumptions are relaxed. Thus, our framework establishes a theoretical foundation for inferring selection signatures from samples of sequences produced by evolution on epistatic fitness landscapes.
Flexibility of co-evolutionary patterns in ectoparasite populations: genetic structure and diversity inApodemusmice and their lice
Authors: Martinů J. , Hypša V. , Štefka J. 
Published: July 2016

AbstractHost-parasite co-evolution belongs among the major processes governing evolution of biodiversity on the global scale. Numerous studies performed at inter-specific level revealed variety of patterns from strict co-speciation to lack of co-divergence and frequent host-switching, even in species tightly linked to their hosts. To explain these observations and formulate ecological hypotheses, we need to acquire better understanding to parasites’ population genetics and dynamics, and their main determinants. Here, we analyse the impact of co-evolutionary processes on genetic diversity and structure of parasite populations, using a model composed of the lousePolyplax serrataand its hosts, mice of the genusApodemus, collected from several dozens of localities across Europe. We use mitochondrial DNA sequences and microsatellite data to describe the level of genealogical congruence between hosts and parasites and to assess genetic diversity of the populations. We also explore links between the genetic assignment of the parasite and its host affiliation, and test the prediction that populations of the parasite possessing narrower host specificity show deeper pattern of population structure and lower level of genetic diversity as a result of limited dispersal and smaller effective population size. We demonstrate an overall complexity of the co-evolutionary processes and their variability even among closely related lineages of the parasites. In the analysis of several sympatric parasite populations, we find strong evidence for the link between the width of host specificity and genetic diversity of parasites.
Tissue-specificity of gene expression diverges slowly between orthologs, and rapidly between paralogs
Authors: Kryuchkova-Mostacci Nadezda , Robinson-Rechavi Marc 
Published: July 2016

AbstractThe ortholog conjecture implies that functional similarity between orthologous genes is higher than between paralogs. It has been supported using levels of expression and Gene Ontology term analysis, although the evidence was rather weak and there were also conflicting reports. In this study on 12 species we provide strong evidence of high conservation in tissue-specificity between orthologs, in contrast to low conservation between within-species paralogs. This allows us to shed a new light on the evolution of gene expression patterns. While there have been several studies of the correlation of expression between species, little is known about the evolution of tissue-specificity itself. Ortholog tissue-specificity is strongly conserved between all tetrapod species, with the lowest Pearson correlation between mouse and frog at r = 0.66. Tissue-specificity correlation decreases strongly with divergence time. Paralogs in human show much lower conservation, even for recent Primate-specific paralogs. When both paralogs from ancient whole genome duplication tissue-specific paralogs are tissue-specific, it is often to different tissues, while other tissue-specific paralogs are mostly specific to the same tissue. The same patterns are observed using human or mouse as focal species, and are robust to choices of datasets and of thresholds. Our results support the following model of evolution: in the absence of duplication, tissue-specificity evolves slowly, and tissue-specific genes do not change their main tissue of expression; after small-scale duplication the less expressed paralog loses the ancestral specificity, leading to an immediate difference between paralogs; over time, both paralogs become more broadly expressed, but remain poorly correlated. Finally, there is a small number of paralog pairs which stay tissue-specific with the same main tissue of expression, for at least 300 million years.Author summaryFrom specific examples, it has been assumed by comparative biologists that the same gene in different species has the same function, whereas duplication of a gene inside one species to create several copies allows them to acquire different functions. Yet this model was little tested until recently, and then has proven harder than expected to confirm. One of the problems is defining “function” in a way which can be easily studied. We introduce a new way of considering function: how specific is the activity (“expression”) of a gene? Genes which are specific to certain tissues have functions related to these tissues, whereas genes which are broadly active over many or all tissues have more general functions for the organism. We find that this “tissue-specificity” evolves very slowly in the absence of duplication, while immediately after duplication the new gene copy differs. This shows that indeed duplication leads to a strong increase in the evolution of new functions.
Dropout-based feature selection for scRNASeq
Authors: Andrews Tallulah S. , Hemberg Martin 
Published: July 2016

AbstractFeatures selection is a key step in many single-cell RNASeq (scRNASeq) analyses. Feature selection is intended to preserve biologically relevant information while removing genes only subject to technical noise. As it is frequently performed prior to dimensionality reduction, clustering and pseudotime analyses, feature selection can have a major impact on the results. Several different approaches have been proposed for unsupervised feature selection from unprocessed single-cell expression matrices, most based upon identifying highly variable genes in the dataset. We present two methods which take advantage of the prevalence of zeros (dropouts) in scRNASeq data to identify features. We show that dropout-based feature selection outperforms variance-based feature selection for multiple applications of single-cell RNASeq.