bluuebunny/crossref_metadata_2025 huggingface dataset:
Differential fecal microbiota are retained in broiler chicken lines divergently selected for fatness traits
Authors: Hou Qiangchuan , Kwok Lai-Yu , Zheng Yi , Wang Lifeng , Guo Zhuang , Zhang Jiachao , Huang Weiqiang , Wang Yuxiang , Leng Li , Li Hui , Zhang Heping
Published: November 2016

Our study combined 16S rRNA-pyrosequencing and whole genome sequencing to analyze the fecal metagenomes of the divergently selected lean (LL) and fat (FL) line chickens. Significant structural differences existed in both the phylogenic and functional metagenomes between the two chicken lines. At phylum level, the FL group had significantly less Bacteroidetes. At genus level, fourteen genera of different relative abundance were identified, with some known short-chain fatty acid producers (including Subdoligranulum, Butyricicoccus, Eubacterium, Bacteroides, Blautia) and a potentially pathogenic genus (Enterococcus). Redundancy analysis identified 190 key responsive operational taxonomic units (OTUs) that accounted for the structural differences between the phylogenic metagenome of the two groups. Four Cluster of Orthologous Group (COG) categories (Amino acid transport and metabolism, E; Nucleotide transport and metabolism, F; Coenzyme transport and metabolism, H; and Lipid transport and metabolism, I) were overrepresented in LL samples. Fifteen differential metabolic pathways (Biosynthesis of amino acids, Pyruvate metabolism, Nitrotoluene degradation, Lipopolysaccharide biosynthesis, Peptidoglycan biosynthesis, Pantothenate and CoA biosynthesis, Glycosaminoglycan degradation, Thiamine metabolism, Phosphotransferase system, Two-component system, Bacterial secretion system, Flagellar assembly, Bacterial chemotaxis, Ribosome, Sulfur relay system) were identified. Our data highlighted interesting variations between the gut metagenomes of these two chicken lines.
Lymphocytic Microparticles Modulate Angiogenic Properties of Macrophages in Laser-induced Choroidal Neovascularization
Authors: Tahiri Houda , Omri Samy , Yang Chun , Duhamel François , Samarani Suzanne , Ahmad Ali , Vezina Mark , Bussières Martin , Vaucher Elvire , Sapieha Przemyslaw , Hickson Gilles , Hammamji Karim , Lapointe Réjean , Rodier Francis , Tremblay Sophie , Royal Isabelle , Cailhier Jean-François , Chemtob Sylvain , Hardy Pierre
Published: November 2016

Pathological choroidal neovascularization (CNV) is the common cause of vision loss in patients with age-related macular degeneration (AMD). Macrophages possess potential angiogenic function in CNV. We have demonstrated that human T lymphocyte-derived microparticles (LMPs) exert a potent antiangiogenic effect in several pathological neovascularization models. In this study, we investigated the alteration of proangiogenic properties of macrophages by LMPs treatment in vitro and in vivo models. LMPs regulated the expression of several angiogenesis-related factors in macrophages and consequently stimulated their antiangiogenic effects evidenced by the suppression of the proliferation of human retinal endothelial cells in co-culture experiments. The involvement of CD36 receptor in LMPs uptake by macrophages was demonstrated by in vitro assays and by immunostaining of choroidal flat mounts. In addition, ex vivo experiments showed that CD36 mediates the antiangiogenic effect of LMPs in murine and human choroidal explants. Furthermore, intravitreal injection of LMPs in the mouse model of laser-induced CNV significantly suppressed CNV in CD36 dependent manner. The results of this study suggested an ability of LMPs to alter the gene expression pattern of angiogenesis-related factors in macrophages, which provide important information for a new therapeutic approach for efficiently interfering with both vascular and extravascular components of CNV.
Changes of bivalent chromatin coincide with increased expression of developmental genes in cancer
Authors: Bernhart Stephan H. , Kretzmer Helene , Holdt Lesca M. , Jühling Frank , Ammerpohl Ole , Bergmann Anke K. , Northoff Bernd H. , Doose Gero , Siebert Reiner , Stadler Peter F. , Hoffmann Steve
Published: November 2016

Bivalent (poised or paused) chromatin comprises activating and repressing histone modifications at the same location. This combination of epigenetic marks at promoter or enhancer regions keeps genes expressed at low levels but poised for rapid activation. Typically, DNA at bivalent promoters is only lowly methylated in normal cells, but frequently shows elevated methylation levels in cancer samples. Here, we developed a universal classifier built from chromatin data that can identify cancer samples solely from hypermethylation of bivalent chromatin. Tested on over 7,000 DNA methylation data sets from several cancer types, it reaches an AUC of 0.92. Although higher levels of DNA methylation are often associated with transcriptional silencing, counter-intuitive positive statistical dependencies between DNA methylation and expression levels have been recently reported for two cancer types. Here, we re-analyze combined expression and DNA methylation data sets, comprising over 5,000 samples, and demonstrate that the conjunction of hypermethylation of bivalent chromatin and up-regulation of the corresponding genes is a general phenomenon in cancer. This up-regulation affects many developmental genes and transcription factors, including dozens of homeobox genes and other genes implicated in cancer. Thus, we reason that the disturbance of bivalent chromatin may be intimately linked to tumorigenesis.
Development of Commercial Thermo-sensitive Genic Male Sterile Rice Accelerates Hybrid Rice Breeding Using the CRISPR/Cas9-mediated TMS5 Editing System
Authors: Zhou Hai , He Ming , Li Jing , Chen Liang , Huang Zhifeng , Zheng Shaoyan , Zhu Liya , Ni Erdong , Jiang Dagang , Zhao Bingran , Zhuang Chuxiong
Published: November 2016

Hybrid rice breeding offers an important strategy to improve rice production, in which the cultivation of a male sterile line is the key to the success of cross-breeding. CRISPR/Cas9 systems have been widely used in target-site genome editing, whereas their application for crop genetic improvement has been rarely reported. Here, using the CRISPR/Cas9 system, we induced specific mutations in TMS5, which is the most widely applied thermo-sensitive genic male sterility (TGMS) gene in China, and developed new “transgene clean” TGMS lines. We designed 10 target sites in the coding region of TMS5 for targeted mutagenesis using the CRISPR/Cas9 system and assessed the potential rates of on- and off-target effects. Finally, we established the most efficient construct, the TMS5ab construct, for breeding potentially applicable “transgene clean” TGMS lines. We also discussed factors that affect the editing efficiency according to the characteristics of different target sequences. Notably, using the TMS5ab construct, we developed 11 new “transgene clean” TGMS lines with potential applications in hybrid breeding within only one year in both rice subspecies. The application of our system not only significantly accelerates the breeding of sterile lines but also facilitates the exploitation of heterosis.
Correlation analysis of the mRNA and miRNA expression profiles in the nascent synthetic allotetraploid Raphanobrassica
Authors: Ye Bingyuan , Wang Ruihua , Wang Jianbo
Published: November 2016

Raphanobrassicais an allopolyploid species derived from inter-generic hybridization that combines the R genome fromR. sativusand the C genome fromB. oleraceavar.alboglabra. In the present study, we used a high-throughput sequencing method to identify the mRNA and miRNA profiles inRaphanobrassicaand its parents. A total of 33,561 mRNAs and 283 miRNAs were detected, 9,209 mRNAs and 134 miRNAs were differentially expressed respectively, 7,633 mRNAs and 39 miRNAs showed ELD expression, 5,219 mRNAs and 57 miRNAs were non-additively expressed inRaphanobrassica. Remarkably, differentially expressed genes (DEGs) were up-regulated and maternal bias was detected inRaphanobrassica. In addition, a miRNA-mRNA interaction network was constructed based on reverse regulated miRNA-mRNAs, which included 75 miRNAs and 178 mRNAs, 31 miRNAs were non-additively expressed target by 13 miRNAs. The related target genes were significantly enriched in the GO term ‘metabolic processes’. Non-additive related target genes regulation is involved in a range of biological pathways, like providing a driving force for variation and adaption in this allopolyploid. The integrative analysis of mRNA and miRNA profiling provides more information to elucidate gene expression mechanism and may supply a comprehensive and corresponding method to study genetic and transcription variation of allopolyploid.
Structural basis of TRPA1 inhibition by HC-030031 utilizing species-specific differences
Authors: Gupta Rupali , Saito Shigeru , Mori Yoshiharu , Itoh Satoru G. , Okumura Hisashi , Tominaga Makoto
Published: November 2016

Pain is a harmful sensation that arises from noxious stimuli. Transient receptor potential ankyrin 1 (TRPA1) is one target for studying pain mechanisms. TRPA1 is activated by various stimuli such as noxious cold, pungent natural products and environmental irritants. Since TRPA1 is an attractive target for pain therapy, a few TRPA1 antagonists have been developed and some function as analgesic agents. The responses of TRPA1 to agonists and antagonists vary among species and these species differences have been utilized to identify the structural basis of activation and inhibition mechanisms. The TRPA1 antagonist HC-030031 (HC) failed to inhibit frog TRPA1 (fTRPA1) and zebrafish TRPA1 activity induced by cinnamaldehyde (CA), but did inhibit human TRPA1 (hTRPA1) in a heterologous expression system. Chimeric studies between fTRPA1 and hTRPA1, as well as analyses using point mutants, revealed that a single amino acid residue (N855 in hTRPA1) significantly contributes to the inhibitory action of HC. Moreover, the N855 residue and the C-terminus region exhibited synergistic effects on the inhibition by HC. Molecular dynamics simulation suggested that HC stably binds to hTRPA1-N855. These findings provide novel insights into the structure-function relationship of TRPA1 and could lead to the development of more effective analgesics targeted to TRPA1.
Crosstalk among proteome, acetylome and succinylome in colon cancer HCT116 cell treated with sodium dichloroacetate
Authors: Zhu Danxi , Hou Lidan , Hu Bin , Zhao Hang , Sun Jie , Wang Jianhua , Meng Xiangjun
Published: November 2016

Protein lysine acetylation and succinylation play important regulatory roles in cells, both of which or each other has a close relationship. Dichloroacetate (DCA), a well-known pyruvate dehydrogenase kinase (PDK) inhibitor, has the potential to be used as anti-cancer drugs for several tumors including colorectal cancer. However, little is known about the potential mechanism of DCA-based cancer therapy by protein posttranslational modifications (PTM) including global proteome, acetylome and succinylome. Here the combinations with stable isotope labeling (SILAC), antibody affinity enrichment and high resolution LC-MS/MS analysis were performed in human colon cancer HCT116 cells. The quantifiable proteome was annotated using bioinformatics. In total, 4,518 proteins, 1,436 acetylation sites, and 671 succinylation sites were quantified, respectively to DCA treatment. Among the quantified acetylated sites, 158 were with increased level (quantification ratio >1.5) and 145 with decreased level (quantification ratio <0.67). Meanwhile, 179 up-regulated and 114 down-regulated succinylated sites were identified. The bioinformatics analyses initially showed acetylation and succinylation were involved in a wide range of cellular functions upon DCA-based anti-cancer effects. Notably, protein-protein interaction network analyses demonstrated widespread interactions modulated by protein acetylation and succinylation. Taken together, this study may shed a light on understanding the mechanism of DCA-based cancer treatment.
Characterization of two distinct early post-entry blocks to HIV-1 in common marmoset lymphocytes
Authors: Pacheco Beatriz , Menéndez-Arias Luis , Sodroski Joseph
Published: November 2016

In nature, primate lentiviruses infect humans and several Old World monkeys and apes. However, to date, lentiviruses infecting New World monkeys have not been described. We studied the susceptibility of common marmoset cells to HIV-1 infection and observed the presence of post-entry blocks to the early phase of HIV-1 infection in peripheral blood lymphocytes (PBLs) and a B lymphocytic cell line (B-LCL). The blocks present in these cells are dominant and phenotypically different from each other. In PBLs, the block occurs at the level of reverse transcription, reducing the accumulation of early and late transcripts, similar to the block imposed by TRIM5α. However, we have found that marmoset TRIM5α does not block HIV-1. In contrast, the restriction factor present in B-LCLs blocks HIV-1 replication at a later step, after nuclear entry, and inhibits integration. Additionally, we have identified an HIV-1 capsid mutant, N74D, that is able to escape the restriction in the marmoset B-LCLs. Our results suggest that the factors responsible for the blocks present in marmoset PBLs and B-LCLs are different. We propose the existence of at least two new restriction factors able to block HIV-1 infection in marmoset lymphocytes.
The coordinated roles of miR-26a and miR-30c in regulating TGFβ1-induced epithelial-to-mesenchymal transition in diabetic nephropathy
Authors: Zheng Zongji , Guan Meiping , Jia Yijie , Wang Dan , Pang Ruoyu , Lv Fuping , Xiao Zhizhou , Wang Ling , Zhang Hongbin , Xue Yaoming
Published: November 2016

MicroRNAs (miRNAs) play vital roles in the development of diabetic nephropathy. Here, we compared the protective efficacies of miR-26a and miR-30c in renal tubular epithelial cells (NRK-52E) and determined whether they demonstrated additive effects in the attenuation of renal fibrosis. TGFβ1 suppressed miR-26a and miR-30c expression but up-regulated pro-fibrotic markers in NRK-52E cells, and these changes were also found in the kidney cortex of 40-week-old diabetic Otsuka Long-Evans Tokushima fatty (OLETF) rats. Bioinformatic analyses and luciferase assays further demonstrated that both miR-26a and miR-30c targeted connective tissue growth factor (CTGF); additionally, Snail family zinc finger 1 (Snail1), a potent epithelial-to-mesenchymal transition (EMT) inducer, was targeted by miR-30c. Overexpression of miR-26a and miR-30c coordinately decreased CTGF protein levels and subsequently ameliorated TGFβ1-induced EMT in NRK-52E cells. Co-silencing of miR-26a and miR-30c exhibited the opposite effect. Moreover, miR-26a and miR-30c co-silenced CTGF to decrease ERK1/2 and p38 MAPK activation. Furthermore, miR-26a was up-regulated in urinary extracellular vesicles of diabetic nephropathy patients. Our study provides evidence for the cooperative roles of miR-26a and miR-30c in the pathogenesis of diabetic nephropathy, and the co-targeting of miR-26a and miR-30c could provide a new direction for diabetic nephropathy treatment.
Close relationship between a dry-wet transition and a bubble rearrangement in two-dimensional foam
Authors: Furuta Yujiro , Oikawa Noriko , Kurita Rei
Published: November 2016

Liquid foams are classified into a dry foam and a wet foam, empirically judging from the liquid fraction or the shape of the gas bubbles. It is known that physical properties such as elasticity and diffusion are different between the dry foam and the wet foam. Nevertheless, definitions of those states have been vague and the dry-wet transition of foams has not been clarified yet. Here we show that the dry-wet transition is closely related to rearrangement of the gas bubbles, by simultaneously analysing the shape change of the bubbles and that of the entire foam in two dimensional foam. In addition, we also find a new state in quite low liquid fraction, which is named “superdry foam”. Whereas the shape change of the bubbles strongly depends on the change of the liquid fraction in the superdry foam, the shape of the bubbles does not change with changing the liquid fraction in the dry foam. Our results elucidate the relationship between the transitions and the macroscopic mechanical properties.
miR-706 inhibits the oxidative stress-induced activation of PKCα/TAOK1 in liver fibrogenesis
Authors: Yin Ruili , Guo Duo , Zhang Shuxian , Zhang Xiuying
Published: November 2016

Oxidative stress induces the activation of liver fibrogenic cells (myofibroblasts), thus promoting the expression of fibrosis-related genes, leading to hepatic fibrogenesis. MicroRNAs (miRNAs) are a new class of small RNAs ~18–25 nucleotides in length involved in post-transcriptional regulation of gene expression. Wound-healing and remodeling processes in liver fibrosis have been associated with changes in hepatic miRNA expression. However, the role of miR-706 in liver fibrogenesis is currently unknown. In the present study, we show that miR-706 is abundantly expressed in hepatocytes. Moreover, oxidative stress leads to a significant downregulation of miR-706, and the further reintroduction of miR-706 inhibits oxidative stress-induced expression of fibrosis-related markers such as α-SMA. Subsequent studies revealed that miR-706 directly inhibits PKCα and TAOK1 expression via binding to the 3′-untranslated region, preventing epithelial mesenchymal transition. In vivo studies showed that intravenous injection of miR-706 agomir successfully increases hepatic miR-706 and decreases α-SMA, PKCα, and TAOK1 protein levels in livers of carbon tetrachloride (CCl4)-treated mice. In summary, this study reveals a protective role for miR-706 by blocking the oxidative stress-induced activation of PKCα/TAOK1. Our results further identify a major implication for miR-706 in preventing hepatic fibrogenesis and suggest that miR-706 may be a suitable molecular target for anti-fibrosis therapy.
Inverse changes in L1 retrotransposons between blood and brain in major depressive disorder
Authors: Liu Shu , Du Tingfu , Liu Zeyue , Shen Yan , Xiu Jianbo , Xu Qi
Published: November 2016

Long interspersed nuclear element-1 (LINE-1 or L1) is a type of retrotransposons comprising 17% of the human and mouse genome, and has been found to be associated with several types of neurological disorders. Previous post-mortem brain studies reveal increased L1 copy number in the prefrontal cortex from schizophrenia patients. However, whether L1 retrotransposition occurs similarly in major depressive disorder (MDD) is unknown. Here, L1 copy number was measured by quantitative PCR analysis in peripheral blood of MDD patients (n = 105) and healthy controls (n = 105). The results showed that L1 copy number was increased in MDD patients possibly due to its hypomethylation. Furthermore, L1 copy number in peripheral blood and five brain regions (prefrontal cortex, hippocampus, amygdala, nucleus accumbens and paraventricular hypothalamic nucleus) was measured in the chronic unpredictable mild stress (CUMS) model of depression in mice. Intriguingly, increased L1 copy number in blood and the decreased L1 copy number in the prefrontal cortex were observed in stressed mice, while no change was found in other brain regions. Our results suggest that the changes of L1 may be associated with the pathophysiology of MDD, but the biological mechanism behind dysfunction of L1 retrotransposition in MDD remains to be further investigated.
The genome, transcriptome, and proteome of the nematode Steinernema carpocapsae: evolutionary signatures of a pathogenic lifestyle
Authors: Rougon-Cardoso Alejandra , Flores-Ponce Mitzi , Ramos-Aboites Hilda Eréndira , Martínez-Guerrero Christian Eduardo , Hao You-Jin , Cunha Luis , Rodríguez-Martínez Jonathan Alejandro , Ovando-Vázquez Cesaré , Bermúdez-Barrientos José Roberto , Abreu-Goodger Cei , Chavarría-Hernández Norberto , Simões Nelson , Montiel Rafael
Published: November 2016

The entomopathogenic nematode Steinernema carpocapsae has been widely used for the biological control of insect pests. It shares a symbiotic relationship with the bacterium Xenorhabdus nematophila, and is emerging as a genetic model to study symbiosis and pathogenesis. We obtained a high-quality draft of the nematode’s genome comprising 84,613,633 bp in 347 scaffolds, with an N50 of 1.24 Mb. To improve annotation, we sequenced both short and long RNA and conducted shotgun proteomic analyses. S. carpocapsae shares orthologous genes with other parasitic nematodes that are absent in the free-living nematode C. elegans, it has ncRNA families that are enriched in parasites, and expresses proteins putatively associated with parasitism and pathogenesis, suggesting an active role for the nematode during the pathogenic process. Host and parasites might engage in a co-evolutionary arms-race dynamic with genes participating in their interaction showing signatures of positive selection. Our analyses indicate that the consequence of this arms race is better characterized by positive selection altering specific functions instead of just increasing the number of positively selected genes, adding a new perspective to these co-evolutionary theories. We identified a protein, ATAD-3, that suggests a relevant role for mitochondrial function in the evolution and mechanisms of nematode parasitism.
Navigation by anomalous random walks on complex networks
Authors: Weng Tongfeng , Zhang Jie , Khajehnejad Moein , Small Michael , Zheng Rui , Hui Pan
Published: November 2016

Anomalous random walks having long-range jumps are a critical branch of dynamical processes on networks, which can model a number of search and transport processes. However, traditional measurements based on mean first passage time are not useful as they fail to characterize the cost associated with each jump. Here we introduce a new concept of mean first traverse distance (MFTD) to characterize anomalous random walks that represents the expected traverse distance taken by walkers searching from source node to target node, and we provide a procedure for calculating the MFTD between two nodes. We use Lévy walks on networks as an example, and demonstrate that the proposed approach can unravel the interplay between diffusion dynamics of Lévy walks and the underlying network structure. Moreover, applying our framework to the famous PageRank search, we show how to inform the optimality of the PageRank search. The framework for analyzing anomalous random walks on complex networks offers a useful new paradigm to understand the dynamics of anomalous diffusion processes, and provides a unified scheme to characterize search and transport processes on networks.
The Mediterranean Plastic Soup: synthetic polymers in Mediterranean surface waters
Authors: Suaria Giuseppe , Avio Carlo G. , Mineo Annabella , Lattin Gwendolyn L. , Magaldi Marcello G. , Belmonte Genuario , Moore Charles J. , Regoli Francesco , Aliani Stefano
Published: November 2016

The Mediterranean Sea has been recently proposed as one of the most impacted regions of the world with regards to microplastics, however the polymeric composition of these floating particles is still largely unknown. Here we present the results of a large-scale survey of neustonic micro- and meso-plastics floating in Mediterranean waters, providing the first extensive characterization of their chemical identity as well as detailed information on their abundance and geographical distribution. All particles >700 μm collected in our samples were identified through FT-IR analysis (n = 4050 particles), shedding for the first time light on the polymeric diversity of this emerging pollutant. Sixteen different classes of synthetic materials were identified. Low-density polymers such as polyethylene and polypropylene were the most abundant compounds, followed by polyamides, plastic-based paints, polyvinyl chloride, polystyrene and polyvinyl alcohol. Less frequent polymers included polyethylene terephthalate, polyisoprene, poly(vinyl stearate), ethylene-vinyl acetate, polyepoxide, paraffin wax and polycaprolactone, a biodegradable polyester reported for the first time floating in off-shore waters. Geographical differences in sample composition were also observed, demonstrating sub-basin scale heterogeneity in plastics distribution and likely reflecting a complex interplay between pollution sources, sinks and residence times of different polymers at sea.
Growth Mechanisms of Inductively-Coupled Plasma Torch Synthesized Silicon Nanowires and their associated photoluminescence properties
Authors: Agati M. , Amiard G. , Le Borgne V. , Castrucci P. , Dolbec R. , De Crescenzi M. , El Khakani M. A. , Boninelli S.
Published: November 2016

Ultra-thin Silicon Nanowires (SiNWs) were produced by means of an industrial inductively-coupled plasma (ICP) based process. Two families of SiNWs have been identified, namely long SiNWs (up to 2–3 micron in length) and shorter ones (~100 nm). SiNWs were found to consist of a Si core (with diameter as thin as 2 nm) and a silica shell, of which the thickness varies from 5 to 20 nm. By combining advanced transmission electron microscopy (TEM) techniques, we demonstrate that the growth of the long SiNWs occurred via the Oxide Assisted Growth (OAG) mechanism, while the Vapor Liquid Solid (VLS) mechanism is responsible for the growth of shorter ones. Energy filtered TEM analyses revealed, in some cases, the existence of chapelet-like Si nanocrystals embedded in an otherwise silica nanowire. Such nanostructures are believed to result from the exposure of some OAG SiNWs to high temperatures prevailing inside the reactor. Finally, the intense photoluminescence (PL) of these ICP-grown SiNWs in the 620–950 nm spectral range is a clear indication of the occurrence of quantum confinement. Such a PL emission is in accordance with the TEM results which revealed that the size of nanostructures are indeed below the exciton Bohr radius of silicon.
Experimental investigation into the oxidation reactivity and nanostructure of particulate matter from diesel engine fuelled with diesel/polyoxymethylene dimethyl ethers blends
Authors: Yang Hao , Li Xinghu , Wang Yan , Mu Mingfei , Li Xuehao , Kou Guiyue
Published: November 2016

This paper focuses on oxidation reactivity and nanostructural characteristics of particulate matter (PM) emitted from diesel engine fuelled with different volume proportions of diesel/polyoxymethylene dimethyl ethers (PODEn) blends (P0, P10 and P20). PM was collected using a metal filter from the exhaust manifold. The collected PM samples were characterized using thermogravimetric analysis (TGA), scanning electron microscopy (SEM), transmission electron microscopy (TEM) and Raman spectroscopy. The TGA results indicated that the PM produced by P20 had the highest moisture and volatility contents and the fastest oxidation rate of solid carbon followed by P10 and P0 derived PM. SEM analysis showed that PM generated from P20 was looser with a lower mean value than PM emitted from P10 and P0. Quantitative analysis of high-resolution TEM images presented that fringe length was reduced along with increased separation distance and tortuosity with an increase in PODEnconcentration. These trends improved the oxidation reactivity. According to Raman spectroscopy data, the intensity, full width at half-maximum and intensity ratio of the bands also changed demonstrating that PM nanostructure disorder was correlated with a faster oxidation rate. The results show the use of PODEnaffects the oxidation reactivity and nanostructure of PM that is easier to oxidize.
High-Acquisition-Rate Single-Shot Pump-Probe Measurements Using Time-Stretching Method
Authors: Kobayashi Masataka , Minami Yasuo , Johnson Courtney L. , Salmans Parker D. , Ellsworth Nicholas R. , Takeda Jun , Johnson Jeremy A. , Katayama Ikufumi
Published: November 2016

Recent advances of ultrafast spectroscopy allow the capture of an entire ultrafast signal waveform in a single probe shot, which greatly reduces the measurement time and opens the door for the spectroscopy of unrepeatable phenomena. However, most single-shot detection schemes rely on two-dimensional detectors, which limit the repetition rate of the measurement and can hinder real-time visualization and manipulation of signal waveforms. Here, we demonstrate a new method to circumvent these difficulties and to greatly simplify the detection setup by using a long, single-mode optical fiber and a fast photodiode. Initially, a probe pulse is linearly chirped (the optical frequency varies linearly across the pulse in time), and the temporal profile of an ultrafast signal is then encoded in the probe spectrum. The probe pulse and encoded temporal dynamics are further chirped to nanosecond time scales using the dispersion in the optical fiber, thus, slowing down the ultrafast signal to time scales easily recorded with fast detectors and high-bandwidth electronics. We apply this method to three distinct ultrafast experiments: investigating the power dependence of the Kerr signal in LiNbO3, observing an irreversible transmission change of a phase change material, and capturing terahertz waveforms.
HMGA1P7-pseudogene regulates H19 and Igf2 expression by a competitive endogenous RNA mechanism
Authors: De Martino Marco , Forzati Floriana , Marfella Marianna , Pellecchia Simona , Arra Claudio , Terracciano Luigi , Fusco Alfredo , Esposito Francesco
Published: November 2016

Recent studies have revealed that pseudogene transcripts can function as competing endogenous RNAs, and thereby can also contribute to cancer when dysregulated. We have recently identified two pseudogenes, HMGA1P6 and HMGA1P7 for the HMGA1 gene whose overexpression has a critical role in cancer progression. These pseudogenes work as competitive endogenous RNA decoys for HMGA1 and other cancer related genes suggesting their role in carcinogenesis. Looking for new HMGA1 pseudogene ceRNAs, we performed RNA sequencing technology on mouse embryonic fibroblasts deriving from transgenic mice overexpressing HMGA1P7. Here, we report that HMGA1P7 mRNA sustains the H19 and Igf2 overexpression by acting as miRNA decoy. Lastly, the expression of HMGA1P7 was significantly correlated with H19 and IGF2 levels in human breast cancer thereby suggesting a role for HMGA1P7 deregulation in this neoplasia.
Direct observation of electronic-liquid-crystal phase transitions and their microscopic origin in La1/3Ca2/3MnO3
Authors: Tao J. , Sun K. , Yin W.-G. , Wu L. , Xin H. , Wen J. G. , Luo W. , Pennycook S. J. , Tranquada J. M. , Zhu Y.
Published: November 2016

The ground-state electronic order in doped manganites is frequently associated with a lattice modulation, contributing to their many interesting properties. However, measuring the thermal evolution of the lattice superstructure with reciprocal-space probes alone can lead to ambiguous results with competing interpretations. Here we provide direct observations of the evolution of the superstructure in La1/3Ca2/3MnO3 in real space, as well as reciprocal space, using transmission electron microscopic (TEM) techniques. We show that the transitions are the consequence of a proliferation of dislocations plus electronic phase separation. The resulting states are well described by the symmetries associated with electronic-liquid-crystal (ELC) phases. Moreover, our results resolve the long-standing controversy over the origin of the incommensurate superstructure and suggest a new structural model that is consistent with recent theoretical calculations.
Bph32, a novel gene encoding an unknown SCR domain-containing protein, confers resistance against the brown planthopper in rice
Authors: Ren Juansheng , Gao Fangyuan , Wu Xianting , Lu Xianjun , Zeng Lihua , Lv Jianqun , Su Xiangwen , Luo Hong , Ren Guangjun
Published: November 2016

An urgent need exists to identify more brown planthopper (Nilaparvata lugensStål, BPH) resistance genes, which will allow the development of rice varieties with resistance to BPH to counteract the increased incidence of this pest species. Here, using bioinformatics and DNA sequencing approaches, we identified a novel BPH resistance gene, LOC_Os06g03240 (MSU LOCUS ID), from the rice variety Ptb33 in the interval between the markers RM19291 and RM8072 on the short arm of chromosome 6, where a gene for resistance to BPH was mapped by Jirapong Jairinet al.and renamed as “Bph32”. This gene encodes a unique short consensus repeat (SCR) domain protein. Sequence comparison revealed that theBph32gene shares 100% sequence identity with its allele inOryza latifolia. The transgenic introgression ofBph32into a susceptible rice variety significantly improved resistance to BPH. Expression analysis revealed thatBph32was highly expressed in the leaf sheaths, where BPH primarily settles and feeds, at 2 and 24 h after BPH infestation, suggesting thatBph32may inhibit feeding in BPH. Western blotting revealed the presence of Pph (Ptb33) and Tph (TN1) proteins using a Penta-His antibody, and both proteins were insoluble. This study provides information regarding a valuable gene for rice defence against insect pests.
Spatially differentiated trends in urbanization, agricultural land abandonment and reclamation, and woodland recovery in Northern China
Authors: Wang Chao , Gao Qiong , Wang Xian , Yu Mei
Published: November 2016

Uncovering magnitude, trend, and spatial pattern of land cover/land use changes (LCLUC) is crucial for understanding mechanisms of LCLUC and assisting land use planning and conservation. China has been undergoing unprecedented economic growth, massive rural-to-urban migration, and large-scale policy-driven ecological restoration, and therefore encountering enormous LCLUC in recent decades. However, comprehensive understandings of spatiotemporal LCLUC dynamics and underlying mechanisms are still lacking. Based on classification of annual LCLU maps from MODIS satellite imagery, we proposed a land change detection method to capture significant land change hotspots over Northern China during 2001–2013, and further analyzed temporal trends and spatial patterns of LCLUC. We found rapid decline of agricultural land near urban was predominantly caused by urban expansion. The process was especially strong in North China Plain with 14,057 km2 of urban gain and −21,017 km2 of agricultural land loss. To offset the loss of agricultural land, Northeast China Plain and Xinjiang were reclaimed. Substantial recovery of forests (49,908 km2) and closed shrubland (60,854 km2) occurred in mountainous regions due to abandoned infertile farmland, secondary succession, and governmental conservation policies. The spatial patterns and trends of LCLUC in Northern China provide information to support effective environmental policies towards sustainable development.
Active Brownian particles and run-and-tumble particles separate inside a maze
Authors: Khatami Maryam , Wolff Katrin , Pohl Oliver , Ejtehadi Mohammad Reza , Stark Holger
Published: November 2016

A diverse range of natural and artificial self-propelled particles are known and are used nowadays. Among them, active Brownian particles (ABPs) and run-and-tumble particles (RTPs) are two important classes. We numerically study non-interacting ABPs and RTPs strongly confined to different maze geometries in two dimensions. We demonstrate that by means of geometrical confinement alone, ABPs are separable from RTPs. By investigating Matryoshka-like mazes with nested shells, we show that a circular maze has the best filtration efficiency. Results on the mean first-passage time reveal that ABPs escape faster from the center of the maze, while RTPs reach the center from the rim more easily. According to our simulations and a rate theory, which we developed, ABPs in steady state accumulate in the outermost region of the Matryoshka-like mazes, while RTPs occupy all locations within the maze with nearly equal probability. These results suggest a novel technique for separating different types of self-propelled particles by designing appropriate confining geometries without using chemical or biological agents.
Molecular Insight into Affinities of Gallated and Nongallated Proanthocyanidins Dimers to Lipid Bilayers
Authors: Zhu Wei , Xiong Le , Peng Jinming , Deng Xiangyi , Gao Jun , Li Chun-mei
Published: November 2016

Experimental studies have proved the beneficial effects of proanthocyanidins (Pas) relating to interaction with the cell membrane. But the detailed mechanisms and structure-function relationship was unclear. In present study, molecular dynamics (MD) simulations were used to study the interactions of four PA dimers with a lipid bilayer composed of 1:1 mixed 1-palmitoyl-2-oleoyl phosphatidylcholine (POPC) and 1-palmitoyl-2-oleoyl phosphatidylethanolamine (POPE). The results showed that the gallated PA dimers had much higher affinities to the bilayer with lower binding free energies compared with nongallated PA dimers. The gallated PA dimers penetrated deeper into the bilayer and formed more hydrogen bonds (H-bonds) with bilayer oxygen atoms, especially the deeper oxygen atoms of the lipids simultaneously, thus inducing stronger lateral expansion of the membrane and lipid tails disorder. The present results provided molecular insights into the interactions between PA dimers and bio-membranes and agreed with our experimental results well. These molecular interactions helped to elucidate the structure-function relationship of the PA dimers and provided a foundation for a better understanding of the underlying mechanisms of the bioactivities of PA oligomers.
Rubber–Rectorite Composites with High Gas Barrier Properties
Authors: He Shaojian , Zhang Liqun
Published: November 2016

Rubber–clay nanocomposites have attracted considerable attention in the fields of materials science and engineering due to their high performance, especially their high gas barrier property. Rectorite, a kind of clay mineral, has a higher aspect ratio compared with montmorillonite, and is expected to endow the rubber–clay nanocomposites with a larger enhancement in composite performance. In this chapter, we describe the dominant mechanisms for the transport of gas molecules in rubbers and rubber nanocomposites, and the influence of the characteristics of the inorganic particles on the barrier properties of the composite is discussed. The emphasis is placed on the gas permeability of the various reported rubber–rectorite nanocomposites, and the potential approaches to further improve the gas barrier properties are also presented. Additionally, some other properties of rubber–rectorite nanocomposites are also introduced.
SIproc: an open-source biomedical data processing platform for large hyperspectral images
Authors: Berisha Sebastian , Chang Shengyuan , Saki Sam , Daeinejad Davar , He Ziqi , Mankar Rupali , Mayerich David
Published: November 2016

There has recently been significant interest within the vibrational spectroscopy community to apply quantitative spectroscopic imaging techniques to histology and clinical diagnosis.
A sensitive immunosensor for microcystin-(leucine–arginine) based on fluorescent self-assembled multilayers
Authors: Liu B. , Wang X. P. , Sun X. Y. , Yang C. X. , Li P.
Published: November 2016

In this paper, a novel fluorescent immunosensor based on self-assembled multilayers was constructed to detect microcystin-(leucine–arginine).
The macroscopic wettable surface: fabricated by calix[4]arene-based host–guest interaction and chiral discrimination of glucose
Authors: Sun Yue , Mei Yuxiao , Quan Jiaxin , Xiao Xuan , Zhang Lin , Tian Demei , Li Haibing
Published: November 2016

Herein, we reported a new strategy based on self-assembly chemistry for chiral discrimination of glucose on a new S-mandelic acid-appended calix[4]arene (S-MC4) modified nanostructure, which exhibits macroscopic chiral preference for d-glucose via contact angle measurements (CA).
A cationic iridium complex meets an electron-transporting counter-anion: enhanced performances of solution-processed phosphorescent light-emitting diodes
Authors: Luo Ningzi , Lan Ying , Tang Ruiren , He Lei , Duan Lian
Published: November 2016

A cationic iridium complex with an electron-transporting counter-anion was developed, which showed superior performance in solution-processed phosphorescent light-emitting diodes.
Electrochemical investigation of [Co4(μ3-O)4(μ-OAc)4(py)4] and peroxides by cyclic voltammetry
Authors: Clatworthy Edwin B. , Li Xiaobo , Masters Anthony F. , Maschmeyer Thomas
Published: November 2016

Electrochemical investigation of the cobalt cubane Co4(μ3-O)4(μ-OAc)4(py)4reveals a second quasi-reversible oxidation which can oxidise peroxides.
Improved slow magnetic relaxation in optically pure helicene-based DyIII single molecule magnets
Authors: Ou-Yang J.-K. , Saleh N. , Fernandez Garcia G. , Norel L. , Pointillart F. , Guizouarn T. , Cador O. , Totti F. , Ouahab L. , Crassous J. , Le Guennic B.
Published: November 2016

Racemic and optically pure [Dy(hfac)3(L)] complexes with L = 3-(2-pyridyl)-4-aza[6]-helicene have been synthesized and characterized.
Regarding the torsional flexibility of the dihydrolipoic acid's pharmacophore: 1,3-propanedithiol
Authors: Vigorito Annalisa , Calabrese Camilla , Paltanin Ettore , Melandri Sonia , Maris Assimo
Published: November 2016

The great flexibility of 1,3-propanedithiol is probed using freejet absorption microwave spectroscopy and quantum chemistry calculations.
Conformational adjustment for high-pressure glass formation of 1-alkyl-3-methylimidazolium tetrafluoroborate
Authors: Takekiyo Takahiro , Koyama Yoshihiro , Shigemi Machiko , Matsuishi Kiyoto , Abe Hiroshi , Hamaya Nozomu , Yoshimura Yukihiro
Published: November 2016

The role of the alkyl-chain length (the conformational adjustment effect) in high pressure glass formation of 1-alkyl-3-methylimidazolum tetrafluoroborate.
Unravelling the dissociation pathways of acetic acid upon electron transfer in potassium collisions: experimental and theoretical studies
Authors: Meneses G. , Widmann C. , Cunha T. , Gil A. , Ferreira da Silva F. , Calhorda M. J. , Limão-Vieira P.
Published: November 2016

A direct dissociation or concerted mechanism via a diol intermediate, leading to OH− formation in potassium acetic acid collisions?
Understanding dispersive charge-transport in crystalline organic-semiconductors
Authors: Yavuz Ilhan , Lopez Steven A.
Published: November 2016

The effect of short-range order and dispersivity on charge-transport for organic crystalline semiconductors are important and unresolved questions.
The intramolecular H-bonding effect on the growth and stability of Schiff-base surface covalent organic frameworks
Authors: Mo Yi-Ping , Liu Xuan-He , Sun Bing , Yan Hui-Juan , Wang Dong , Wan Li-Jun
Published: November 2016

The role of intramolecular H-bonding in on-surface synthesis and stability of imine based surface covalent organic frameworks is explored.
A computational study of self-assembled hexapeptide inhibitors against amyloid-β (Aβ) aggregation
Authors: Qiao Yuan , Zhang Mingzhen , Liang Ya'nan , Zheng Jie , Liang Guizhao
Published: November 2016

We explore the structure, dynamics, and interaction between 3 identified hexapeptides and different Aβ-derived fragments and an Aβ17–42 pentamer.
A theoretical study on the unusual square-planar structure of bis(imino)pyridine-ligated Group 13 complexes
Authors: Li Weiyi , Lyu Yajing , Zhang Huifang , Zhu Maoqin , Tang Hanping
Published: November 2016

The stronger aromaticity of the M-imidazolate ring and the small strain energy on the ligand backbone collectively drive the square-planar structure.
Dependence of magnetic coupling on ligands at the axial positions of NiII in phenoxido bridged dimers: experimental observations and DFT studies
Authors: Mondal Monotosh , Giri Sanjib , Guha Pampa M. , Ghosh Ashutosh
Published: November 2016

Experimental and theoretical results reveal that the magnetic coupling in diphenoxido bridged dinuclear NiII compounds is strongly dependent on the axially coordinated non-bridging ligands.
The new role of 1,1-diamino-2,2-dinitroethylene (FOX-7): two unexpected reactions
Authors: Zhou Tianhong , Li Yanfeng , Xu Kangzhen , Song Jirong , Zhao Fengqi
Published: November 2016

Two unexpected reactions of FOX-7 were studied. The reaction to form MNTzA is unusual among the syntheses of 2,4,5-trisubstituted 1,2,3-triazole compounds.
Diastereoselective synthesis of trifluoromethylated 1,3-dioxanes by intramolecular oxa-Michael reaction
Authors: Becerra-Figueroa Liliana , Brun Elodie , Mathieson Michael , Farrugia Louis J. , Wilson Claire , Prunet Joëlle , Gamba-Sánchez Diego
Published: November 2016

A rapid and simple method to access trifluoromethylated 1,3-dioxanes by a sequence of addition/oxa-Michael reaction has been developed; the reaction proceeds smoothly with excellent stereoselectivity.
Pseudopeptidic compounds for the generation of dynamic combinatorial libraries of chemically diverse macrocycles in aqueous media
Authors: Atcher Joan , Solà Jordi , Alfonso Ignacio
Published: November 2016

The combination of pseudopeptidic dithiol building blocks leads to the generation of highly diverse dynamic libraries of macrocycles in aqueous media.
Aqueous SARA ATRP using inorganic sulfites
Authors: Abreu Carlos M. R. , Fu Liye , Carmali Sheiliza , Serra Arménio C. , Matyjaszewski Krzysztof , Coelho Jorge F. J.
Published: November 2016

Aqueous SARA ATRP using inorganic sulfites was successfully carried out for the first time.
Metathesis polymerization of cystine-based macrocycles
Authors: Behrendt Felix N. , Schlaad Helmut
Published: November 2016

Entropy-driven ring-opening metathesis polymerization (ED-ROMP) of cystine-based macrocycles yields multifunctional poly(ester-amine-disulfide-alkene)s.
Correction: Acid and base dual-controlled cargo molecule release from polyaniline gated-hollow mesoporous silica nanoparticles
Authors: Zhu Xinyun , Zhao Jianliang , Wang Caiqi
Published: November 2016

Correction for ‘Acid and base dual-controlled cargo molecule release from polyaniline gated-hollow mesoporous silica nanoparticles’ by Xinyun Zhu, et al., Polym. Chem., 2016, 7, 6467–6474.
Facile construction of butadiynylene based conjugated porous polymers by cost-effective Glaser coupling
Authors: Xie Zhen , Wei Yabo , Zhao Xiaoyu , Li Yang , Ding Sanyuan , Chen Long
Published: November 2016

Four butadiynylene-based conjugated porous polymer gels with hierarchical pores and high CO2 uptake capacities were facilely synthesized via Glaser coupling.
Transition-metal free direct difluoromethylthiolation of electron-rich aromatics with difluoromethanesulfonyl chloride
Authors: Zhao Xia , Wei Aoqi , Li Tianjiao , Su Zhiyang , Chen Jun , Lu Kui
Published: November 2016

A new method for phosphine-mediated difluoromethylthiolation of indoles and other electron-rich aromatics using difluoromethanesulfonyl chloride was developed.
Restoring the osteogenic activity of bacterial debris contaminated titanium by doping with magnesium
Authors: Zhao Yaochao , Cao Huiliang , Wang Jiaxing , Qin Hui , Li Bin , Wang Donghui , Meng Fanhao , Zhang Xianlong , Liu Xuanyong
Published: November 2016

Bacterial debris can impair the osseointegration of implants and co-doping with magnesium and silver is a promising method to solve this issue.
Quantum mechanical based approaches for predicting pKavalues of carboxylic acids: evaluating the performance of different strategies
Authors: Rebollar-Zepeda Aida Mariana , Galano Annia
Published: November 2016

The FP method is recommended for estimating pKavalues of carboxylic acids for which this information is still unknown, especially in combination with the PBE0 functional (MUE = 0.26) and the SMD solvent model.
Ultrafine N-doped carbon nanoparticles with controllable size to enhance electrocatalytic activity for oxygen reduction reaction
Authors: Wang Wenxi , Shi Yang , Li Minchan , Wang Zhenyu , Wu Shaofei , Lyu Fucong , Shang Chaoqun , Lu Zhouguang
Published: November 2016

The ORR electrocatalytic activity of ultrafine nanoparticles prepared from carbonization ofSterculia scaphigerais significantly improved through a simple hydrothermal treatment.
A unique opportunity for the utilization of glass wastes as a resource for catalytic applications: toward a cleaner environment
Authors: Zolfagharinia Somayeh , Koukabi Nadiya , Kolvari Eskandar
Published: November 2016

n-glass-waste-SO3H at the service of catalytic application.