bluuebunny/crossref_metadata_2025 huggingface dataset:
Silicon amendment to rice plants impairs sucking behaviors and population growth in the phloem feeder Nilaparvata lugens (Hemiptera: Delphacidae)
Authors: Yang Lang , Han Yongqiang , Li Pei , Wen Lizhang , Hou Maolin
Published: April 2017

The brown planthopper (BPH), Nilaparvata lugens (Stål), is a migratory and destructive sucking insect pest of rice. Silicon (Si) amendment to plants can confer enhanced resistance to herbivores and is emerging as a novel approach for pest management. In the present study, we tested the effects of Si addition at 0.16 (low) and 0.32 (high) g Si/kg soil on sucking behaviors and population growth in BPH. Si amendment increased Si content in rice stems and extended non-probing event and phloem puncture followed by sustained phloem ingestion over that in the no-Si-addition control. High Si addition rate prolonged the stylet pathway and the time needed to reach the first phloem puncture, shortened durations of phloem puncture and phloem ingestion, and decreased the proportion of individuals that produced sustained phloem ingestion. BPH female feeding on and preference for plants with the high Si addition rate were also reduced. As a result, Si application significantly decreased BPH population growth rates while increased population doubling time. These results indicate that Si amendment, especially at the high rate, confers enhanced rice plant resistance to BPH through impairment of BPH feeding. Our results highlight the potential of Si amendment as an alternative for BPH management.
Switch from ambient to focal processing mode explains the dynamics of free viewing eye movements
Authors: Ito Junji , Yamane Yukako , Suzuki Mika , Maldonado Pedro , Fujita Ichiro , Tamura Hiroshi , Grün Sonja
Published: April 2017

Previous studies have reported that humans employ ambient and focal modes of visual exploration while they freely view natural scenes. These two modes have been characterized based on eye movement parameters such as saccade amplitude and fixation duration, but not by any visual features of the viewed scenes. Here we propose a new characterization of eye movements during free viewing based on how eyes are moved from and to objects in a visual scene. We applied this characterization to data obtained from freely-viewing macaque monkeys. We show that the analysis based on this characterization gives a direct indication of a behavioral shift from ambient to focal processing mode along the course of free viewing exploration. We further propose a stochastic model of saccade sequence generation incorporating a switch between the two processing modes, which quantitatively reproduces the behavioral features observed in the data.
Long lasting neutralization of C5 by SKY59, a novel recycling antibody, is a potential therapy for complement-mediated diseases
Authors: Fukuzawa Taku , Sampei Zenjiro , Haraya Kenta , Ruike Yoshinao , Shida-Kawazoe Meiri , Shimizu Yuichiro , Gan Siok Wan , Irie Machiko , Tsuboi Yoshinori , Tai Hitoshi , Sakiyama Tetsushi , Sakamoto Akihisa , Ishii Shinya , Maeda Atsuhiko , Iwayanagi Yuki , Shibahara Norihito , Shibuya Mitsuko , Nakamura Genki , Nambu Takeru , Hayasaka Akira , Mimoto Futa , Okura Yuu , Hori Yuji , Habu Kiyoshi , Wada Manabu , Miura Takaaki , Tachibana Tatsuhiko , Honda Kiyofumi , Tsunoda Hiroyuki , Kitazawa Takehisa , Kawabe Yoshiki , Igawa Tomoyuki , Hattori Kunihiro , Nezu Junichi
Published: April 2017

Dysregulation of the complement system is linked to the pathogenesis of a variety of hematological disorders. Eculizumab, an anti-complement C5 monoclonal antibody, is the current standard of care for paroxysmal nocturnal hemoglobinuria (PNH) and atypical hemolytic uremic syndrome (aHUS). However, because of high levels of C5 in plasma, eculizumab has to be administered biweekly by intravenous infusion. By applying recycling technology through pH-dependent binding to C5, we generated a novel humanized antibody against C5, SKY59, which has long-lasting neutralization of C5. In cynomolgus monkeys, SKY59 suppressed C5 function and complement activity for a significantly longer duration compared to a conventional antibody. Furthermore, epitope mapping by X-ray crystal structure analysis showed that a histidine cluster located on C5 is crucial for the pH-dependent interaction with SKY59. This indicates that the recycling effect of SKY59 is driven by a novel mechanism of interaction with its antigen and is distinct from other known pH-dependent antibodies. Finally, SKY59 showed neutralizing effect on C5 variant p.Arg885His, while eculizumab does not inhibit complement activity in patients carrying this mutation. Collectively, these results suggest that SKY59 is a promising new anti-C5 agent for patients with PNH and other complement-mediated disorders.
Unravelling the drastic range retraction of an emblematic songbird of North Africa: potential threats to Afro-Palearctic migratory birds
Authors: Khelifa Rassim , Zebsa Rabah , Amari Hichem , Mellal Mohammed Khalil , Bensouilah Soufyane , Laouar Abdeldjalil , Mahdjoub Hayat
Published: April 2017

Understanding how culture may influence biodiversity is fundamental to ensure effective conservation, especially when the practice is local but the implications are global. Despite that, little effort has been devoted to documenting cases of culturally-related biodiversity loss. Here, we investigate the cultural domestication of the European goldfinch (Carduelis carduelis) in western Maghreb (Morocco, Algeria and Tunisia) and the effects of long-term poaching of wild populations (1990–2016) on range distribution, socio-economic value, international trading and potential collateral damage on Afro-Palearctic migratory birds. On average, we found that the European goldfinch lost 56.7% of its distribution range in the region which led to the increase of its economic value and establishment of international trading network in western Maghreb. One goldfinch is currently worth nearly a third of the average monthly income in the region. There has been a major change in poaching method around 2010, where poachers started to use mist nets to capture the species. Nearly a third of the 16 bird species captured as by-catch of the European goldfinch poaching are migratory, of which one became regularly sold as cage-bird. These results suggest that Afro-Palearctic migratory birds could be under serious by-catch threat.
Electron-phonon coupling in topological surface states: The role of polar optical modes
Authors: Heid Rolf , Sklyadneva Irina Yu. , Chulkov Evgueni V.
Published: April 2017

The use of topological edge states for spintronic applications could be severely hampered by limited lifetimes due to intrinsic many-body interactions, in particular electron-phonon coupling. Previous works to determine the intrinsic coupling strength did not provide a coherent answer. Here, the electron-phonon interaction in the metallic surface state of 3D topological insulators is revised within a first principles framework. For the archetypical cases of Bi2Se3 and Bi2Te3, we find an overall weak coupling constant of less than 0.15, but with a characteristic energy dependence. Derived electronic self-energies compare favorably with previous angle-resolved photoemission spectroscopy results. The prevailing coupling is carried by optical modes of polar character, which is weakly screened by the metallic surface state and can be reduced by doping into bulk bands. We do not find any indication of a strong coupling to the A1g
mode or the presence of a Kohn anomaly in the surface phonon spectrum. The weak intrinsic electron-phonon coupling guarantees long-lived quasiparticles at elevated temperatures.
Diabetes mellitus and the risk of multidrug resistant tuberculosis: a meta-analysis
Authors: Liu Qianqian , Li Wenzhang , Xue Miao , Chen Yunfeng , Du Xinmiao , Wang Chengdi , Han Lina , Tang Yin , Feng Yulin , Tao Chuanmin , He Jian-Qing
Published: April 2017

The high prevalence of diabetes mellitus (DM) among multidrug resistant tuberculosis (MDR-TB) patients is a serious cause for concern. We conducted a meta-analysis to determine whether DM is an independent risk factor for MDR-TB. Electronic literature searches of the PubMed, Web of Science and EMBASE databases up to July 12, 2016 were conducted. The pooled adjusted odds ratio (OR) and 95% confidence intervals (CIs) were calculated using the random effects model with STATA 12.0 software. In total 13 studies, including 9289 individuals with TB, were included in this meta-analysis. Significant association between DM and MDR-TB (OR = 1.71; 95% CI = 1.32, 2.22) was identified. Subgroup analyses showed that: 1) Pooled OR was 1.25 (95% CI: 0.82–1.91) for cross-sectional studies, and was 2.14 (95% CI: 1.51–3.02) for longitudinal studies; 2) The pooled OR was 1.69 (95% CI:1.09–2.62) for primary MDR-TB, 1.94 (95% CI:1.42–2.65) for any MDR-TB, and 0.85 for secondary MDR-TB (95% CI: 0.29–2.54); 3) DM was significantly associated with MDR-TB in both Caucasian (OR = 2.26, 95% CI: 1.66–3.07) and Asian (OR = 1.40, 95% CI: 1.01–1.95) subgroups. No evidence of publication bias was identified. In conclusion, the pooling analysis indicated that DM was an independent risk factor for MDR-TB, especially for primary MDR-TB.
Transcriptome analysis on the exoskeleton formation in early developmetal stages and reconstruction scenario in growth-moulting in Litopenaeus vannamei
Authors: Gao Yi , Wei Jiankai , Yuan Jianbo , Zhang Xiaojun , Li Fuhua , Xiang Jianhai
Published: April 2017

Exoskeleton construction is an important issue in shrimp. To better understand the molecular mechanism of exoskeleton formation, development and reconstruction, the transcriptome of the entire developmental process in Litopenaeus vannamei, including nine early developmental stages and eight adult-moulting stages, was sequenced and analysed using Illumina RNA-seq technology. A total of 117,539 unigenes were obtained, with 41.2% unigenes predicting the full-length coding sequence. Gene Ontology, Clusters of Orthologous Group (COG), the Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis and functional annotation of all unigenes gave a better understanding of the exoskeleton developmental process in L. vannamei. As a result, more than six hundred unigenes related to exoskeleton development were identified both in the early developmental stages and adult-moulting. A cascade of sequential expression events of exoskeleton-related genes were summarized, including exoskeleton formation, regulation, synthesis, degradation, mineral absorption/reabsorption, calcification and hardening. This new insight on major transcriptional events provide a deep understanding for exoskeleton formation and reconstruction in L. vannamei. In conclusion, this is the first study that characterized the integrated transcriptomic profiles cover the entire exoskeleton development from zygote to adult-moulting in a crustacean, and these findings will serve as significant references for exoskeleton developmental biology and aquaculture research.
Characterisation of a cell-free synthesised G-protein coupled receptor
Authors: Shilling Patrick J. , Bumbak Fabian , Scott Daniel J. , Bathgate Ross A. D. , Gooley Paul R.
Published: April 2017

G-protein coupled receptors are the largest family of integral membrane proteins found within the human genome. They function as receptors and modulators to a wide range of ligands and responses which are crucial for human health. GPCR study, specifically the investigation of structure and interaction to cognate ligands, is of high priority. Limitations for structural study can be traced in part, to obtaining suitable quantities of recombinant protein. We sought to address the limitations of traditional recombinant technologies by utilising an Escherichia coli based cell-free protein synthesis (CFPS) approach for production of a thermostable neurotensin receptor 1 (en2NTS1). Initial results were promising, with a high amount (up to 2 mg/mL) of en2NTS1 produced, that had attained correct secondary structure. Meanwhile, concurrent experiments indicated that CFPS produced en2NTS1 showed non-competitive binding to the peptide ligand neurotensin8–13 when compared to E. coli produced en2NTS1. 1H-13C HMQC SOFAST NMR spectra were indicative of disrupted tertiary structure for CFPS produced 13CH3-methionine labelled en2NTS1. The results obtained, indicate CFPS produced en2NTS1 is not forming a discrete tertiary structure and that further development of the CFPS technique needs to be carried out.
Selective Targeting of Cancer Cells by Oxidative Vulnerabilities with Novel Curcumin Analogs
Authors: Pignanelli Christopher , Ma Dennis , Noel Megan , Ropat Jesse , Mansour Fadi , Curran Colin , Pupulin Simon , Larocque Kristen , Wu Jianzhang , Liang Guang , Wang Yi , Pandey Siyaram
Published: April 2017

Recently, research has focused on targeting the oxidative and metabolic vulnerabilities in cancer cells. Natural compounds like curcumin that target such susceptibilities have failed further clinical advancements due to the poor stability and bioavailability as well as the need of high effective doses. We have synthesized and evaluated the anti-cancer activity of several monocarbonyl analogs of curcumin. Interestingly, two novel analogs (Compound A and I) in comparison to curcumin, have increased chemical stability and have greater anti-cancer activity in a variety of human cancer cells, including triple-negative, inflammatory breast cancer cells. In particular, the generation of reactive oxygen species was selective to cancer cells and occurred upstream of mitochondrial collapse and execution of apoptosis. Furthermore, Compound A in combination with another cancer-selective/pro-oxidant, piperlongumine, caused an enhanced anti-cancer effect. Most importantly, Compound A was well tolerated by mice and was effective in inhibiting the growth of human triple-negative breast cancer and leukemia xenografts in vivo when administered intraperitoneally. Thus, exploiting oxidative vulnerabilities in cancer cells could be a selective and efficacious means to eradicate malignant cells as demonstrated by the curcumin analogs presented in this report with high therapeutic potential.
A high-power and fast charging Li-ion battery with outstanding cycle-life
Authors: Agostini M. , Brutti S. , Navarra M. A. , Panero S. , Reale P. , Matic A. , Scrosati B.
Published: April 2017

Electrochemical energy storage devices based on Li-ion cells currently power almost all electronic devices and power tools. The development of new Li-ion cell configurations by incorporating innovative functional components (electrode materials and electrolyte formulations) will allow to bring this technology beyond mobile electronics and to boost performance largely beyond the state-of-the-art. Here we demonstrate a new full Li-ion cell constituted by a high-potential cathode material, i.e. LiNi0.5Mn1.5O4, a safe nanostructured anode material, i.e. TiO2, and a composite electrolyte made by a mixture of an ionic liquid suitable for high potential applications, i.e. Pyr1,4PF6, a lithium salt, i.e. LiPF6, and standard organic carbonates. The final cell configuration is able to reversibly cycle lithium for thousands of cycles at 1000 mAg−1 and a capacity retention of 65% at cycle 2000.
Preparation of heterostructured WO3/TiO2 catalysts from wood fibers and its versatile photodegradation abilities
Authors: Gao Likun , Gan Wentao , Qiu Zhe , Zhan Xianxu , Qiang Tiangang , Li Jian
Published: April 2017

A facile route was adopted to synthesize heterostructured WO3/TiO2 photocatalysts from wood fibers through a two-steps hydrothermal method and a calcination process. The prepared WO3/TiO2-wood fibers were used as photocatalysts under UV irradiation for photodegradation of rhodamine B, methylene blue and methyl orange. In calcination process, the wood fibers acted as carbon substrates to prepare the WO3/TiO2 photocatalysts with high surface area and unique morphology. Thus, the significant enhanced photodegradation efficiency of the organic pollutants with the WO3/TiO2-wood fibers under UV irradiation was obtained. The photodegradation rates are measured which confirms the highest performance of the WO3/TiO2-wood fibers after calcination in comparison to the TiO2-wood fibers after calcination and the pure WO3/TiO2 after calcination. Moreover, the photodegradation efficiency of the WO3/TiO2-wood fibers after calcination under visible light is high. Our results demonstrated that the WO3/TiO2-wood fibers after calcination are a promising candidate for wastewater treatment in practical application.
Recombinant Adeno-Associated Virus-mediated rescue of function in a mouse model of Dopamine Transporter Deficiency Syndrome
Authors: Illiano P. , Bass C.E. , Fichera L. , Mus L. , Budygin E.A. , Sotnikova T.D. , Leo D. , Espinoza S. , Gainetdinov R.R.
Published: April 2017

Dopamine Transporter Deficiency Syndrome (DTDS) is a rare autosomal recessive disorder caused by loss-of-function mutations in dopamine transporter (DAT) gene, leading to severe neurological disabilities in children and adults. DAT-Knockout (DAT-KO) mouse is currently the best animal model for this syndrome, displaying functional hyperdopaminergia and neurodegenerative phenotype leading to premature death in ~36% of the population. We used DAT-KO mouse as model for DTDS to explore the potential utility of a novel combinatorial adeno-associated viral (AAV) gene therapy by expressing DAT selectively in DA neurons and terminals, resulting in the rescue of aberrant striatal DA dynamics, reversal of characteristic phenotypic and behavioral abnormalities, and prevention of premature death. These data indicate the efficacy of a new combinatorial gene therapy aimed at rescuing DA function and related phenotype in a mouse model that best approximates DAT deficiency found in DTDS.
Nomograms for predicting the prognostic value of serological tumor biomarkers in colorectal cancer patients after radical resection
Authors: Li Qingguo , Dai Weixing , Li Yaqi , Xu Ye , Li Xinxiang , Cai Sanjun
Published: April 2017

A wide range of serum tumor biomarkers, including CA19-9, CA242, CA72-4, CA50, and CA125, has been studied in association with colorectal cancer (CRC). However, few previous studies have comprehensively considered the above tumor biomarkers to assess their clinical significance in predicting prognosis. Data from Fudan University Shanghai Cancer Center (FUSCC) between January 1, 2007 and December 30, 2012 was retrospectively analyzed. Univariate and multivariate analyses were performed to assess the association between prognostic factors and survival outcomes. Nomograms were established based on multivariate Cox regression model analysis for overall survival (OS) and disease free survival (DFS), and c-indexes were 0.772 (95% CI: 0.724-0.820) and 0.715 (95% CI: 0.678–0.752), respectively. Subgroup analyses according to CEA status (high/normal) suggested that CA724 was the only independent prognostic factor for OS (P = 0.001) and DFS (P < 0.001) in the CEA-high group, while, in the CEA-normal group, the only independent prognostic factor for OS (P = 0.031) and DFS (P = 0.043) was CA50. CA50 and CA724 could supplement CEA in monitoring recurrence and metastasis. Accordingly, nomograms based on CEA, CA50, CA724 and other clinical-pathological factors could improve prognosis prediction for colorectal cancer patients.
Investigating the molecular mechanism of positive and negative allosteric modulators in the calcium-sensing receptor dimer
Authors: Jacobsen Stine Engesgaard , Gether Ulrik , Bräuner-Osborne Hans
Published: April 2017

Allosteric modulators that are targeting the calcium-sensing receptor (CaSR) hold great therapeutic potential, and elucidating the molecular basis for modulation would thus benefit the development of novel therapeutics. In the present study, we aimed at investigating the mechanism of allosteric modulation in CaSR by testing dimers carrying mutations in the allosteric site of one or both of the subunits. To ensure measurements on a well-defined dimer composition, we applied a trans-activation system in which only the specific heterodimer of two loss-of-function mutants responded to agonist. Although one of these mutants was potentiated by a positive allosteric modulator, we showed that receptor activity was further potentiated in a trans-activation heterodimer containing a single allosteric site, however only when the allosteric site was located in the subunit responsible for G protein coupling. On the contrary, preventing activation in both subunits was necessary for obtaining full inhibition by a negative allosteric modulator. These findings correlate with the proposed activation mechanism of the metabotropic glutamate receptors (mGluRs), in which only a single transmembrane domain is activated at a time. CaSR and mGluRs belong to the class C G protein-coupled receptors, and our findings thus suggest that the activation mechanism is common to this subfamily.
Toll-like receptor polymorphisms compromise the inflammatory response against bacterial antigen translocation in cirrhosis
Authors: Piñero Paula , Juanola Oriol , Caparrós Esther , Zapater Pedro , Giménez Paula , González-Navajas José M. , Such José , Francés Rubén
Published: April 2017

Bacterial translocation is associated with clinically relevant complications in cirrhosis. We evaluated the effect of toll-like receptor polymorphisms in the soluble response against these episodes. Consecutive patients with cirrhosis and ascitic fluid were distributed by TLR2 rs4696480, TLR4 rs4986790, and TLR9 rs187084 single-nucleotide polymorphisms. Lipoteichoic acid, lipopolyssaccharide, bacterial-DNA, pro-inflammatory cytokines and nitric oxide levels were quantified in serum samples. In vitro response against specific ligands in variant TLR genotypes was evaluated. One hundred and fourteen patients were included. Variant TLR-2, TLR-4 and TLR-9 SNP genotypes were associated with significantly increased serum levels of LTA, LPS and bacterial-DNA. TNF-α, IL-6 and nitric oxide serum levels were significantly decreased in all variant TLR genotyped patients. Cytokine levels were significantly less upregulated in response to specific TLR-ligands in patients with all variant vs wildtype TLR genotypes. Although in vitro gene expression levels of all wildtype and variant TLRs were similar, MyD88 and NFkB were significantly downregulated in cells from TLR-variant genotyped patients in response to their ligands. Variant TLR genotypes are associated with an increased circulating antigen burden and a decreased proinflammatory response in cirrhosis. This immunodeficiency may facilitate bacteria-related complications in cirrhosis and enhance TLR targeting for its management.
Simulated climate effects of desert irrigation geoengineering
Authors: Cheng Wei , Moore John C. , Cao Long , Ji Duoying , Zhao Liyun
Published: April 2017

Geoengineering, the deliberate large-scale manipulation of earth’s energy balance to counteract global warming, is an attractive proposition for sparsely populated deserts. We use the BNU and UVic Earth system models to simulate the effects of irrigating deserts under the RCP8.5 scenario. Previous studies focused on increasing desert albedo to reduce global warming; in contrast we examine how extending afforestation and ecological projects, that successfully improve regional environments, fair for geoengineering purposes. As expected desert irrigation allows vegetation to grow, with bare soil or grass gradually becoming shrub or tree covered, with increases in terrestrial carbon storage of 90.3 Pg C (UVic-ESCM) – 143.9 Pg C (BNU-ESM). Irrigating global deserts makes the land surface temperature decrease by 0.48 °C and land precipitation increase by 100 mm yr−1. In the irrigated areas, BNU-ESM simulates significant cooling of up to 4.2 °C owing to the increases in low cloud and latent heat which counteract the warming effect due to decreased surface albedo. Large volumes of water would be required to maintain global desert irrigation, equivalent 10 mm/year of global sea level (BNU-ESM) compensate for evapotranspiration losses. Differences in climate responses between the deserts prompt research into tailored albedo-irrigation schemes.
Multicolour nanoscopy of fixed and living cells with a single STED beam and hyperspectral detection
Authors: Winter Franziska R. , Loidolt Maria , Westphal Volker , Butkevich Alexey N. , Gregor Carola , Sahl Steffen J. , Hell Stefan W.
Published: April 2017

The extension of fluorescence nanoscopy to larger numbers of molecular species concurrently visualized by distinct markers is of great importance for advanced biological applications. To date, up to four markers had been distinguished in STED experiments featuring comparatively elaborate imaging schemes and optical setups, and exploiting various properties of the fluorophores. Here we present a simple yet versatile STED design for multicolour imaging below the diffraction limit. A hyperspectral detection arrangement (hyperSTED) collects the fluorescence in four spectral channels, allowing the separation of four markers with only one excitation wavelength and a single STED beam. Unmixing of the different marker signals based on the simultaneous readout of all channels is performed with a non-negative matrix factorization algorithm. We illustrate the approach showing four-colour nanoscopy of fixed and living cellular samples.
Revealing inhibition difference between PFI-2 enantiomers against SETD7 by molecular dynamics simulations, binding free energy calculations and unbinding pathway analysis
Authors: Niu Yuzhen , Shi Danfeng , Li Lanlan , Guo Jingyun , Liu Huanxiang , Yao Xiaojun
Published: April 2017

SETD7 is associated with multiple diseases related signaling pathways. (R)-PFI-2 is the first SETD7 inhibitor with nanomolar inhibitory potency. The activity of (R)-PFI-2 is about 500 times over that of (S)-PFI-2. Understanding the mechanism behind this difference will be helpful to discovery and design of more potent SETD7 inhibitors. A computational study combining molecular dynamics simulation, binding free energy calculations, and residue interaction network (RIN) was performed on the (S)-PFI-2/SETD7 and (R)-PFI-2/SETD7 complexes to explore the molecular mechanism behind the different inhibition activity. The results from Molecular Mechanics/Generalized Born Surface Area (MM/GBSA) calculation show (R)-PFI-2 has lower binding free energy. Residues H252, D256, L267, Y335, G336 and H339 are responsible for the binding of SETD7 to the (R)-PFI-2. RIN analysis indicates van der Waals interaction is critical for the binding of (R)-PFI-2. The results from adaptive basing force (ABF) simulation confirm that the free energy barrier of (R)-PFI-2 dissociating from the SETD7 is larger than that of (S)-PFI-2. (S)-PFI-2 and (R)-PFI-2 dissociate from the SETD7 binding site along different reaction coordinate and have potential mean of force (PMF) depth. Our simulations results will be useful to understand molecular mechanism of activity difference between PFI-2 enantiomers against SETD7.
Genome sequence of Plasmopara viticola and insight into the pathogenic mechanism
Authors: Yin Ling , An Yunhe , Qu Junjie , Li Xinlong , Zhang Yali , Dry Ian , Wu Huijuan , Lu Jiang
Published: April 2017

Plasmopara viticolacauses downy mildew disease of grapevine which is one of the most devastating diseases of viticulture worldwide. Here we report a 101.3 Mb whole genome sequence ofP. viticolaisolate ‘JL-7-2’ obtained by a combination of Illumina and PacBio sequencing technologies. TheP. viticolagenome contains 17,014 putative protein-coding genes and has ~26% repetitive sequences. A total of 1,301 putative secreted proteins, including 100 putative RXLR effectors and 90 CRN effectors were identified in this genome. In the secretome, 261 potential pathogenicity genes and 95 carbohydrate-active enzymes were predicted. Transcriptional analysis revealed that most of the RXLR effectors, pathogenicity genes and carbohydrate-active enzymes were significantly up-regulated during infection. Comparative genomic analysis revealed thatP. viticolaevolved independently from the Arabidopsis downy mildew pathogenHyaloperonospora arabidopsidis. The availability of theP. viticolagenome provides a valuable resource not only for comparative genomic analysis and evolutionary studies among oomycetes, but also enhance our knowledge on the mechanism of interactions between this biotrophic pathogen and its host.
Light-Patterned Current Generation in a Droplet Bilayer Array
Authors: Restrepo Schild Vanessa , Booth Michael J. , Box Stuart J. , Olof Sam N. , Mahendran Kozhinjampara R. , Bayley Hagan
Published: April 2017

We have created a 4 × 4 droplet bilayer array comprising light-activatable aqueous droplet bio-pixels. Aqueous droplets containing bacteriorhodopsin (bR), a light-driven proton pump, were arranged on a common hydrogel surface in lipid-containing oil. A separate lipid bilayer formed at the interface between each droplet and the hydrogel; each bilayer then incorporated bR. Electrodes in each droplet simultaneously measured the light-driven proton-pumping activities of each bio-pixel. The 4 × 4 array derived by this bottom-up synthetic biology approach can detect grey-scale images and patterns of light moving across the device, which are transduced as electrical current generated in each bio-pixel. We propose that synthetic biological light-activatable arrays, produced with soft materials, might be interfaced with living tissues to stimulate neuronal pathways.
The pretreatment lymphocyte to monocyte ratio predicts clinical outcome for patients with hepatocellular carcinoma: A meta-analysis
Authors: Song Wei , Tian Chuan , Wang Kai , Zhang Run-jin , Zou Shu-bing
Published: April 2017

The lymphocyte-to-monocyte ratio (LMR) has been reported to predict clinical outcomes in multiple malignancies. The aim of this study was to assess the prognostic role of pretreatment LMR in hepatocellular carcinoma (HCC). A total of seven studies comprising 2,738 patients were included in the meta-analysis. Pooled results showed that elevated LMR was significantly associated with increased overall survival (OS) (HR: 0.31, 95% CI: 0.20–0.47, p < 0.001), disease-free survival (DFS)/recurrence-free survival (RFS) (HR: 0.57, 95% CI: 0.49–0.67, p < 0.001). The favorable prognostic impact of high LMR on OS was observed in all subgroup with different sample size, type of publication, NOS score, and the cut-off value of LMR. In addition, low LMR was significantly correlated with TNM stage and BCLC stage. We therefore conclude that elevated pretreatment LMR could be a favorable prognostic factor for clinical outcomes in patients with HCC.
Efficient Heat Dissipation of Uncooled 400-Gbps (16×25-Gbps) Optical Transceiver Employing Multimode VCSEL and PD Arrays
Authors: Shih Tien-Tsorng , Chi Yu-Chieh , Wang Ruei-Nian , Wu Chao-Hsin , Huang Jian-Jang , Jou Jau-Ji , Lee Tai-Cheng , Kuo Hao-Chung , Lin Gong-Ru , Cheng Wood-Hi
Published: April 2017

An effective heat dissipation of uncooled 400-Gbps (16×25-Gbps) form-factor pluggable (CDFP) optical transceiver module employing chip-on-board multimode 25-Gbps vertical-surface-emitting-laser (VCSEL) and 25-Gbps photodiode (PD) arrays mounted on a brass metal core embedded within a printed circuit board (PCB) is proposed and demonstrated. This new scheme of the hollow PCB filling with thermally-dissipated brass metal core was simulated and used for high temperature and long term stability operation of the proposed 400-Gbps CDFP transceiver. During one-hour testing, a red-shift of central wavelength by 0.4-nm corresponding temperature increment of 6.7 °C was observed with the brass core assisted cooler module. Such a temperature change was significantly lower than that of 28.3 °C for the optical transceiver driven with conventional circuit board. After 100-m distance transmission over a multimode fiber (OM4), the 400-Gbps CDFP transceiver exhibited dispersion penalty of 2.6-dB, power budget of ≧ 3-dB, link loss of ≦ 0.63-dB, mask margin of 20%, and bit error rate (BER) of <10−12 with maintained stability more than one hour. The developed 400-Gbps CDFP transceiver module employing low-power consumption VCSEL and PD arrays, effective coupling lens arrays, and well thermal-dissipation brass metal core is suitable for use in the low-cost and high-performance data center applications.
Predicting Protein–protein Association Rates using Coarse-grained Simulation and Machine Learning
Authors: Xie Zhong-Ru , Chen Jiawen , Wu Yinghao
Published: April 2017

Protein–protein interactions dominate all major biological processes in living cells. We have developed a new Monte Carlo-based simulation algorithm to study the kinetic process of protein association. We tested our method on a previously used large benchmark set of 49 protein complexes. The predicted rate was overestimated in the benchmark test compared to the experimental results for a group of protein complexes. We hypothesized that this resulted from molecular flexibility at the interface regions of the interacting proteins. After applying a machine learning algorithm with input variables that accounted for both the conformational flexibility and the energetic factor of binding, we successfully identified most of the protein complexes with overestimated association rates and improved our final prediction by using a cross-validation test. This method was then applied to a new independent test set and resulted in a similar prediction accuracy to that obtained using the training set. It has been thought that diffusion-limited protein association is dominated by long-range interactions. Our results provide strong evidence that the conformational flexibility also plays an important role in regulating protein association. Our studies provide new insights into the mechanism of protein association and offer a computationally efficient tool for predicting its rate.
Assessing the presence of shared genetic architecture between Alzheimer’s disease and major depressive disorder using genome-wide association data
Authors: Gibson J , Russ T C , Adams M J , Clarke T-K , Howard D M , Hall L S , Fernandez-Pujals A M , Wigmore E M , Hayward C , Davies G , Murray A D , Smith B H , Porteous D J , Deary I J , McIntosh A M
Published: April 2017

Major depressive disorder (MDD) and Alzheimer’s disease (AD) are both common in older age and frequently co-occur. Numerous phenotypic studies based on clinical diagnoses suggest that a history of depression increases risk of subsequent AD, although the basis of this relationship is uncertain. Both illnesses are polygenic, and shared genetic risk factors could explain some of the observed association. We used genotype data to test whether MDD and AD have an overlapping polygenic architecture in two large population-based cohorts, Generation Scotland’s Scottish Family Health Study (GS:SFHS; N=19 889) and UK Biobank (N=25 118), and whether age of depression onset influences any relationship. Using two complementary techniques, we found no evidence that the disorders are influenced by common genetic variants. Using linkage disequilibrium score regression with genome-wide association study (GWAS) summary statistics from the International Genomics of Alzheimer's Project, we report no significant genetic correlation between AD and MDD (rG=−0.103, P=0.59). Polygenic risk scores (PRS) generated using summary data from International Genomics of Alzheimer's Project (IGAP) and the Psychiatric Genomics Consortium were used to assess potential pleiotropy between the disorders. PRS for MDD were nominally associated with participant-recalled AD family history in GS:SFHS, although this association did not survive multiple comparison testing. AD PRS were not associated with depression status or late-onset depression, and a survival analysis showed no association between age of depression onset and genetic risk for AD. This study found no evidence to support a common polygenic structure for AD and MDD, suggesting that the comorbidity of these disorders is not explained by common genetic variants.
Weak associations between pubertal development and psychiatric and behavioral problems
Authors: Smith-Woolley E , Rimfeld K , Plomin R
Published: April 2017

Pubertal development has been associated with adverse outcomes throughout adolescence and adulthood. However, much of the previous literature has categorized outcome variables and pubertal timing measures for ease of mean difference or odds ratio interpretation. We use a UK-representative sample of over 5000 individuals drawn from the Twins Early Development Study to extend this literature by adopting an individual differences approach and emphasizing effect sizes. We investigate a variety of psychiatric and behavioral measures collected longitudinally at ages 11, 14 and 16, for multiple raters and for males and females separately. In addition, we use two measures of pubertal development: the Pubertal Development Scale at each age, as well as the age of menarche for girls. We found that pubertal development, however assessed, was linearly associated with a range of psychiatric and behavioral outcomes; however, the effect sizes of these associations were modest for both males and females with most correlations between −0.10 and 0.10. Our systematic analysis of associations between pubertal development, and psychiatric and behavioral problems is the most comprehensive to date. The results showing linearity of the effects of pubertal development support an individual differences approach, treating both pubertal development and associated outcomes as continuous rather than categorical variables. We conclude that pubertal development explains little variance in psychiatric and behavioral outcomes (<1% on average). The small effect sizes indicate that the associations are weak and should not warrant major concern at least in non-clinical populations.
Diamondoid-structured polymolybdate-based metal–organic frameworks as high-capacity anodes for lithium-ion batteries
Authors: Wang Yuan-Yuan , Zhang Mi , Li Shun-Li , Zhang Shu-Ran , Xie Wei , Qin Jun-Sheng , Su Zhong-Min , Lan Ya-Qian
Published: April 2017

Two novel isostructural polyoxometalate (POM)-based coordination polymers were obtained. The results reveal that NENU-507 could be directly utilized as an anode material for lithium-ion batteries with outstanding performance.
Hybrid micro-/nano-structures derived from metal–organic frameworks: preparation and applications in energy storage and conversion
Authors: Cao Xiehong , Tan Chaoliang , Sindoro Melinda , Zhang Hua
Published: April 2017

In this review, the recent progress on the preparation of hybrid micro-/nano-structures derived from metal–organic frameworks and their applications in energy storage and conversion is systematically summarized.
A review of the management and treatment of brine solutions
Authors: Pramanik Biplob Kumar , Shu Li , Jegatheesan Veeriah
Published: April 2017

This paper critically reviews current technologies for concentrate management including emerging membrane technologies, which could recover valuable minerals from brine solutions.
Identification of two novel antioxidant peptides from edible bird's nest (Aerodramus fuciphagus) protein hydrolysates
Authors: Ghassem Masomeh , Arihara Keizo , Mohammadi Salimeh , Sani Norrakiah Abdullah , Babji Abdul Salam
Published: April 2017

Two novel antioxidant pentapeptides were isolated from EBN hydrolysates with a protective effect against H2O2-induced oxidative damage in cancer cell lines.
l-Cysteine-capped CdTe quantum dots as a fluorescent probe for sequential detection of lysozyme and trypsin
Authors: Shi Fanping , Liu Siyu , Su Xingguang
Published: April 2017

A fluorescence assay for the sequential determination of lysozyme and trypsin was established based on l-cysteine capped CdTe quantum dots. Lysozyme with positive charges can interact with l-cysteine capped CdTe quantum dots. Lysozyme can be hydrolyzed into small fragments in the presence of trypsin, and the interaction between l-cysteine-capped CdTe QDs and lysozyme would be inhibited, which could be used for trypsin quantification.
Highly active Ni–Fe double hydroxides as anode catalysts for electrooxidation of urea
Authors: Xu Wei , Du Dongwei , Lan Rong , Humphreys John , Wu Zucheng , Tao Shanwen
Published: April 2017

Ni–Fe double hydroxide catalysts show the highest catalytic activity and excellent stability toward the electrooxidation of urea.
Direct deposition of MoSe2 nanocrystals onto conducting substrates: towards ultra-efficient electrocatalysts for hydrogen evolution
Authors: Damien Dijo , Anil Athira , Chatterjee Dipanwita , Shaijumon M. M.
Published: April 2017

Monodisperse single/few-layered MoSe2 nanocrystals are directly deposited onto conducting substrates, through electrochemical exfoliation of bulk MoSe2, which exhibit remarkable electrocatalytic activity for the hydrogen evolution reaction.
Au nanoparticles anchored on Ni(OH)2 nanowires with multiple cavities for selective electrochemical detection of dopamine
Authors: Fu Yanyi , Sheng Qinglin , Zheng Jianbin
Published: April 2017

Au nanoparticles supported on nickel hydroxide nanowires with multiple cavities (Au/m-Ni(OH)2) were synthesized and used for the enhanced electrochemical sensing of dopamine (DA).
Development and optimization of a fast method for the determination of statins in human plasma using microextraction by packed sorbent (MEPS) followed by ultra high-performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS)
Authors: Ortega S. N. , Santos-Neto A. J. , Lancas F. M.
Published: April 2017

Miniaturized sample preparation techniques are very attractive in bioanalysis since a reduced size of sample is required.
Dehydrogenative cross-coupling of o-carborane with thiophenes via Ir-catalyzed regioselective cage B–H and C(sp2)–H activation
Authors: Quan Yangjian , Lyu Hairong , Xie Zuowei
Published: April 2017

Iridium-catalyzed carboxylic acid directed site-selective B–H/C–H dehydrogenative cross-coupling of o-carborane with thiophenes has been achieved for the first time, leading to the preparation of 4-thienyl-o-carboranes in a simple one-pot process for potential applications in materials.
Rearrangement of an aniline linked perylene bisimide under acidic conditions and visible to near-infrared emission from the intramolecular charge-transfer state of its fused derivatives
Authors: Kojima Mitsuru , Tamoto Akira , Aratani Naoki , Yamada Hiroko
Published: April 2017

We have prepared a series of aniline-linked and fused perylene bisimides (PBIs) for making near-infrared (NIR) fluorophores.
A DNA–gold nanoparticle hybrid hydrogel network prepared by enzymatic reaction
Authors: Eguchi Yuka , Kato Tomoharu , Tanaka Tsutomu , Maruyama Tatsuo
Published: April 2017

We report a DNA–gold nanoparticle (AuNP) hydrogel in which the AuNPs crosslink enzymatically synthesized DNA.
A quaternary-ammonium-functionalized covalent organic framework for anion conduction
Authors: Guo Hongxia , Wang Junhua , Fang Qianrong , Zhao Yun , Gu Shuang , Zheng Jie , Yan Yushan
Published: April 2017

A new anion conducting covalent organic framework (COF) was prepared by covalently tethering quaternary ammonium (QA) ions onto the pore walls of COF 1,3,5-triformylphloroglucinol-o-tolidine (TpBD-Me) through bromination and quaternization.
Surface chemistry of methanol on different ZnO surfaces studied by vibrational spectroscopy
Authors: Jin Lanying , Wang Yuemin
Published: April 2017

We present a surface science study of methanol decomposition on three nonpolar and polar ZnO surfaces. The systematic HREELS data provide deep insights into reaction mechanisms including the formation of various intermediates (methoxy, hydroxyl and formate species), which depend strongly on surface structures.
Self-powered electrochemical systems as neurochemical sensors: toward self-triggered in vivo analysis of brain chemistry
Authors: Wu Fei , Yu Ping , Mao Lanqun
Published: April 2017

This review highlights recent development of self-powered electrochemical systems for in vivo neurochemical sensing.
Comparison of nucleophilic- and radical-based routes to the formation of manganese-main group element single bonds
Authors: Agnew Douglas W. , Moore Curtis E. , Rheingold Arnold L. , Figueroa Joshua S.
Published: April 2017

One-electron activation of main-group substrates by a stable manganese metalloradical provides a facile pathway to Mn-element single bonds.
Capsaicin presynaptically inhibits glutamate release through the activation of TRPV1 and calcineurin in the hippocampus of rats
Authors: Lu Cheng Wei , Lin Tzu Yu , Hsie Ting Yang , Huang Shu Kuei , Wang Su Jane
Published: April 2017

Capsaicin is the major ingredient in hot peppers of the plantCapsicum genuswith neuroprotective effects in several preclinical models; its effect on glutamate release has been investigated in the rat hippocampus using isolated nerve terminals (synaptosomes) and brain slices.
Effects of different oligosaccharides at various dosages on the composition of gut microbiota and short-chain fatty acids in mice with constipation
Authors: Wang Linlin , Hu Lujun , Yan Shuang , Jiang Tian , Fang Shuguang , Wang Gang , Zhao Jianxin , Zhang Hao , Chen Wei
Published: April 2017

Oligosaccharides administered as a dietary supplement increase the water content of feces, reduce intestinal transit time, modulate the composition of the gut microbiota and increase the concentration of short-chain fatty acids in the feces of mice with constipation.
Switchable (pH-driven) aqueous biphasic systems formed by ionic liquids as integrated production–separation platforms
Authors: Ferreira Ana M. , Cláudio Ana Filipa M. , Válega Mónica , Domingues Fernando M. J. , Silvestre Armando J. D. , Rogers Robin D. , Coutinho João A. P. , Freire Mara G.
Published: April 2017

Reversible production–separation systems can be prepared by varying the speciation of at least one of their components.
Incorporation of carbon dioxide into phthalides via ligand-free copper-catalyzed direct carboxylation of benzoxasiloles
Authors: Nguyen Thanh V. Q. , Rodríguez-Santamaría José A. , Yoo Woo-Jin , Kobayashi Shū
Published: April 2017

The synthesis of a wide range of phthalides was achieved through a copper-catalyzed carboxylation reaction of benzoxasiloles.
A new Schiff-based chemosensor for chromogenic sensing of Cu2+, Co2+and S2−in aqueous solution: experimental and theoretical studies
Authors: Min Cheol Hong , Na Sangkyun , Shin Jae Eun , Kim Jae Kyun , Jo Tae Geun , Kim Cheal
Published: April 2017

A new Schiff-based multifunctional colorimetric chemosensor1was developed for the detection of various analytes (Cu2+, Co2+and S2−).
Retraction: A facile strategy to fabricate nitrogen-doped graphene aerogel supported Fe3N nanoparticles as efficient electrocatalysts for the oxygen reduction reaction
Authors: Wang Shufeng , Yu Dingling , He Xingquan
Published: April 2017

Retraction of ‘A facile strategy to fabricate nitrogen-doped graphene aerogel supported Fe3N nanoparticles as efficient electrocatalysts for the oxygen reduction reaction’ by Shufeng Wang et al., New J. Chem., 2017, DOI: 10.1039/c6nj04114k.
[3,3]-Sigmatropic rearrangement of allenic alcohols: stereoselective synthesis of 1,3-diene-2-ol sulfonates
Authors: Zhao Yuyang , Wang Yurong , Gu Zhanshou , Wang Zhiming
Published: April 2017

An efficient synthetic pathway to 1,3-diene-2-ol sulfonates involving the [3,3]-sigmatropic rearrangement of allenic alcohols with sulfonic acids under mild reaction conditions is described.
Organoiodine reagent-promoted intermolecular oxidative amination: synthesis of cyclopropyl spirooxindoles
Authors: Zhang Zhiguo , Zhang Yongchao , Huang Guoqing , Zhang Guisheng
Published: April 2017

An organoiodine-promoted intramolecular direct oxidative C(sp2)–N cross-coupling reaction was developed for the preparation of cyclopropyl spirooxindoles from readily available secondary cyclopropyl carboxamides.
Halloysite clay nanotubes as effective nanocarriers for the adsorption and loading of vancomycin for sustained release
Authors: Pan Qingqing , Li Neng , Hong Yu , Tang Heng , Zheng Zongfu , Weng Shaohuang , Zheng Yanjie , Huang Liying
Published: April 2017

A simple and effective local drug delivery system with halloysite clay nanotubes as nanocarriers for vancomycin was prepared for the bacterial infection treatment.