bluuebunny/crossref_metadata_2025 huggingface dataset:
Mineral Flaws Clarify How Diamonds Form
Authors: Coombs Amy
Published: June 2016

A study of nanoscale, iron- and sulfur-rich impurities in diamonds provides new clues to the chemical processes that produce the superhard crystals and at what depths they occur.
Qualitative Perspectives From African American Youth and Caregivers for Developing the Families Improving Together (FIT) for Weight Loss Intervention
Authors: Kitzman-Ulrich Heather E. , Wilson Dawn K. , Lyerly Jordan E.
Published: June 2016

This study obtained qualitative data from African American (AA) youth and caregiver dyads to inform the Families Improving Together (FIT) for Weight Loss Trial. Focus groups were conducted with 55 AA parent and caregiver dyads to gather perspectives on facilitators and barriers, motivators, and program preferences for health and weight loss using a socioecological framework. Four main themes emerged: (a) using a positive health promotion framework for weight loss programs, (b) social support and the role of parents in providing positive support, (c) using a socioecological approach to examine factors that contribute to weight, and (d) creating programs that are convenient and fun, and reduce barriers to participation. The findings from this study were used to develop the FIT intervention and indicate important individual, interpersonal, and environmental factors to consider when developing weight management and healthy lifestyle programs for AA families.
New insights into therapeutic strategies for gut microbiota modulation in inflammatory diseases
Authors: Vieira Angélica Thomaz , Fukumori Claudio , Ferreira Caroline Marcantonio
Published: June 2016

The interaction between the gut microbiota and the host immune system is very important for balancing and resolving inflammation. The human microbiota begins to form during childbirth; the complex interaction between bacteria and host cells becomes critical for the formation of a healthy or a disease‐promoting microbiota. C‐section delivery, formula feeding, a high‐sugar diet, a high‐fat diet and excess hygiene negatively affect the health of the microbiota. Considering that the majority of the global population has experienced at least one of these factors that can lead to inflammatory disease, it is important to understand strategies to modulate the gut microbiota. In this review, we will discuss new insights into gut microbiota modulation as potential strategies to prevent and treat inflammatory diseases. Owing to the great advances in tools for microbial analysis, therapeutic strategies such as prebiotic, probiotic and postbiotic treatment and fecal microbiota transplantation have gained popularity.
A survey of the sorghum transcriptome using single-molecule long reads
Authors: Abdel-Ghany Salah E. , Hamilton Michael , Jacobi Jennifer L. , Ngam Peter , Devitt Nicholas , Schilkey Faye , Ben-Hur Asa , Reddy Anireddy S. N.
Published: June 2016

Alternative splicing and alternative polyadenylation (APA) of pre-mRNAs greatly contribute to transcriptome diversity, coding capacity of a genome and gene regulatory mechanisms in eukaryotes. Second-generation sequencing technologies have been extensively used to analyse transcriptomes. However, a major limitation of short-read data is that it is difficult to accurately predict full-length splice isoforms. Here we sequenced the sorghum transcriptome using Pacific Biosciences single-molecule real-time long-read isoform sequencing and developed a pipeline called TAPIS (Transcriptome Analysis Pipeline for Isoform Sequencing) to identify full-length splice isoforms and APA sites. Our analysis reveals transcriptome-wide full-length isoforms at an unprecedented scale with over 11,000 novel splice isoforms. Additionally, we uncover APA of ∼11,000 expressed genes and more than 2,100 novel genes. These results greatly enhance sorghum gene annotations and aid in studying gene regulation in this important bioenergy crop. The TAPIS pipeline will serve as a useful tool to analyse Iso-Seq data from any organism.
Unveiling the complexity of the maize transcriptome by single-molecule long-read sequencing
Authors: Wang Bo , Tseng Elizabeth , Regulski Michael , Clark Tyson A , Hon Ting , Jiao Yinping , Lu Zhenyuan , Olson Andrew , Stein Joshua C. , Ware Doreen
Published: June 2016

Zea mays is an important genetic model for elucidating transcriptional networks. Uncertainties about the complete structure of mRNA transcripts limit the progress of research in this system. Here, using single-molecule sequencing technology, we produce 111,151 transcripts from 6 tissues capturing ∼70% of the genes annotated in maize RefGen_v3 genome. A large proportion of transcripts (57%) represent novel, sometimes tissue-specific, isoforms of known genes and 3% correspond to novel gene loci. In other cases, the identified transcripts have improved existing gene models. Averaging across all six tissues, 90% of the splice junctions are supported by short reads from matched tissues. In addition, we identified a large number of novel long non-coding RNAs and fusion transcripts and found that DNA methylation plays an important role in generating various isoforms. Our results show that characterization of the maize B73 transcriptome is far from complete, and that maize gene expression is more complex than previously thought.
Ecological responses to experimental glacier-runoff reduction in alpine rivers
Authors: Cauvy-Fraunié Sophie , Andino Patricio , Espinosa Rodrigo , Calvez Roger , Jacobsen Dean , Dangles Olivier
Published: June 2016

Glacier retreat is a worldwide phenomenon with important consequences for the hydrological cycle and downstream ecosystem structure and functioning. To determine the effects of glacier retreat on aquatic communities, we conducted a 4-year flow manipulation in a tropical glacier-fed stream. Compared with an adjacent reference stream, meltwater flow reduction induces significant changes in benthic fauna community composition in less than 2 weeks. Also, both algal and herbivore biomass significantly increase in the manipulated stream as a response to flow reduction. After the flow reduction ceased, the system requires 14–16 months to return to its pre-perturbation state. These results are supported by a multi-stream survey of sites varying in glacial influence, showing an abrupt increase in algal and herbivore biomass below 11% glacier cover in the catchment. This study shows that flow reduction strongly affects glacier-fed stream biota, prefiguring profound ecological effects of ongoing glacier retreat on aquatic systems.
Photon-efficient imaging with a single-photon camera
Authors: Shin Dongeek , Xu Feihu , Venkatraman Dheera , Lussana Rudi , Villa Federica , Zappa Franco , Goyal Vivek K. , Wong Franco N. C. , Shapiro Jeffrey H.
Published: June 2016

Reconstructing a scene’s 3D structure and reflectivity accurately with an active imaging system operating in low-light-level conditions has wide-ranging applications, spanning biological imaging to remote sensing. Here we propose and experimentally demonstrate a depth and reflectivity imaging system with a single-photon camera that generates high-quality images from ∼1 detected signal photon per pixel. Previous achievements of similar photon efficiency have been with conventional raster-scanning data collection using single-pixel photon counters capable of ∼10-ps time tagging. In contrast, our camera’s detector array requires highly parallelized time-to-digital conversions with photon time-tagging accuracy limited to ∼ns. Thus, we develop an array-specific algorithm that converts coarsely time-binned photon detections to highly accurate scene depth and reflectivity by exploiting both the transverse smoothness and longitudinal sparsity of natural scenes. By overcoming the coarse time resolution of the array, our framework uniquely achieves high photon efficiency in a relatively short acquisition time.
Prediction of pressure-promoted thermal rejuvenation in metallic glasses
Authors: Miyazaki Narumasa , Wakeda Masato , Wang Yun-Jiang , Ogata Shigenobu
Published: June 2016

Rejuvenation is the structural excitation of glassy materials, and is a promising approach for improving the macroscopic deformability of metallic glasses. This atomistic study proposes the application of compressive hydrostatic pressure during the glass-forming quenching process and demonstrates highly rejuvenated glass states that have not been attainable without the application of pressure. Surprisingly, the pressure-promoted rejuvenation process increases the characteristic short- and medium-range order, even though it leads to a higher-energy glassy state. This ‘local order’–‘energy’ relation is completely opposite to conventional thinking regarding the relation, suggesting the presence of a well-ordered high-pressure glass/high-energy glass phase. We also demonstrate that the rejuvenated glass made by the pressure-promoted rejuvenation exhibits greater plastic performance than as-quenched glass, and greater strength and stiffness than glass made without the application of pressure. It is thus possible to tune the mechanical properties of glass using the pressure-promoted rejuvenation technique.
No-cloning of quantum steering
Authors: Chiu Ching-Yi , Lambert Neill , Liao Teh-Lu , Nori Franco , Li Che-Ming
Published: June 2016

Einstein–Podolsky–Rosen (EPR) steering allows two parties to verify their entanglement, even if one party’s measurements are untrusted. This concept has not only provided new insights into the nature of non-local spatial correlations in quantum mechanics, but also serves as a resource for one-sided device-independent quantum information tasks. Here, we investigate how EPR steering behaves when one-half of a maximally entangled pair of qudits (multidimensional quantum systems) is cloned by a universal cloning machine. We find that EPR steering, as verified by a criterion based on the mutual information between qudits, can only be found in one of the copy subsystems but not both. We prove that this is also true for the single-system analogue of EPR steering. We find that this restriction, which we term ‘no-cloning of quantum steering’, elucidates the physical reason why steering can be used to secure sources and channels against cloning-based attacks when implementing quantum communication and quantum computation protocols.
Targeting duplex DNA with the reversible reactivity of quinone methides
Authors: Huang Chengyun , Liu Yang , Rokita Steven E
Published: June 2016

DNA alkylation and crosslinking remains a common and effective strategy for anticancer chemotherapy despite its infamous lack of specificity. Coupling a reactive group to a sequence-directing component has the potential to enhance target selectivity but may suffer from premature degradation or the need for an external signal for activation. Alternatively, quinone methide conjugates may be employed if they form covalent but reversible adducts with their sequence directing component. The resulting self-adducts transfer their quinone methide to a chosen target without an external signal and avoid off-target reactions by alternative intramolecular self-trapping. Efficient transfer is shown to depend on the nature of the quinone methide and the sequence-directing ligand in applications involving alkylation of duplex DNA through a triplex recognition motif. Success required an electron-rich derivative that enhanced the stability of the transient quinone methide intermediate and a polypyrimidine strand of DNA to associate with its cognate polypurine/polypyrimidine target. Related quinone methide conjugates with peptide nucleic acids were capable of quinone methide transfer from their initial precursor but not from their corresponding self-adduct. The active peptide nucleic acid derivatives were highly selective for their complementary target.
The anti-angiogenic effect and novel mechanisms of action of Combretastatin A-4
Authors: Su Min , Huang Jingjia , Liu Suyou , Xiao Yuhang , Qin Xiyuan , Liu Jia , Pi Chaoqiong , Luo Tiao , Li Jijia , Chen Xianghui , Luo Zhiyong
Published: June 2016

Combretastatin A-4 (CA4) is the lead compound of a relatively new class of vascular disrupting agents that target existing tumor blood vessels. Recent studies showed the CA4 might inhibit angiogenesis. However, the underlying molecular mechanisms by which CA4 exerts its anti-angiogenic effects are not fully understood. In this study, we revealed that CA4 inhibited vascular endothelial growth factor (VEGF)-induced proliferation, migration and capillary-like tube formation of human umbilical vascular endothelial cells (HUVECs). In in vivo assay, CA4 suppressed neovascularization in chicken chorioallantoic membrane (CAM) model and decreased the microvessel density in tumor tissues of a breast cancer MCF-7 xenograft mouse model. In addition, CA4 decreased the expression level and secretion of VEGF both in MCF-7 cells and HUVECs under hypoxia, as well as the activation of VEGFR-2 and its downstream signaling mediators following VEGF stimulation in HUVECs. Moreover, VEGF and VEGFR-2 expression in tumor tissues of the mouse xenograft model were down-regulated following CA4 treatment. Taken together, results from the current work provide clear evidence that CA4 functions in endothelial cell system to inhibit angiogenesis, at least in part, by attenuating VEGF/VEGFR-2 signaling pathway.
An engineered tale-transcription factor rescues transcription of factor VII impaired by promoter mutations and enhances its endogenous expression in hepatocytes
Authors: Barbon Elena , Pignani Silvia , Branchini Alessio , Bernardi Francesco , Pinotti Mirko , Bovolenta Matteo
Published: June 2016

Tailored approaches to restore defective transcription responsible for severe diseases have been poorly explored. We tested transcription activator-like effectors fused to an activation domain (TALE-TFs) in a coagulation factor VII (FVII) deficiency model. In this model, the deficiency is caused by the −94C > G or −61T > G mutation, which abrogate the binding of Sp1 or HNF-4 transcription factors. Reporter assays in hepatoma HepG2 cells naturally expressing FVII identified a single TALE-TF (TF4) that, by targeting the region between mutations, specifically trans-activated both the variant (>100-fold) and wild-type (20–40-fold) F7 promoters. Importantly, in the genomic context of transfected HepG2 and transduced primary hepatocytes, TF4 increased F7 mRNA and protein levels (2- to 3-fold) without detectable off-target effects, even for the homologous F10 gene. The ectopic F7 expression in renal HEK293 cells was modestly affected by TF4 or by TALE-TF combinations. These results provide experimental evidence for TALE-TFs as gene-specific tools useful to counteract disease-causing promoter mutations.
Adaptive tuning functions arise from visual observation of past movement
Authors: Howard Ian S. , Franklin David W.
Published: June 2016

Visual observation of movement plays a key role in action. For example, tennis players have little time to react to the ball, but still need to prepare the appropriate stroke. Therefore, it might be useful to use visual information about the ball trajectory to recall a specific motor memory. Past visual observation of movement (as well as passive and active arm movement) affects the learning and recall of motor memories. Moreover, when passive or active, these past contextual movements exhibit generalization (or tuning) across movement directions. Here we extend this work, examining whether visual motion also exhibits similar generalization across movement directions and whether such generalization functions can explain patterns of interference. Both the adaptation movement and contextual movement exhibited generalization beyond the training direction, with the visual contextual motion exhibiting much broader tuning. A second experiment demonstrated that this pattern was consistent with the results of an interference experiment where opposing force fields were associated with two separate visual movements. Overall, our study shows that visual contextual motion exhibits much broader (and shallower) tuning functions than previously seen for either passive or active movements, demonstrating that the tuning characteristics of past motion are highly dependent on their sensory modality.
Structural transitions in full-length human prion protein detected by xenon as probe and spin labeling of the N-terminal domain
Authors: Narayanan Sunilkumar Puthenpurackal , Nair Divya Gopalakrishnan , Schaal Daniel , Barbosa de Aguiar Marisa , Wenzel Sabine , Kremer Werner , Schwarzinger Stephan , Kalbitzer Hans Robert
Published: June 2016

Fatal neurodegenerative disorders termed transmissible spongiform encephalopathies (TSEs) are associated with the accumulation of fibrils of misfolded prion protein PrP. The noble gas xenon accommodates into four transiently enlarged hydrophobic cavities located in the well-folded core of human PrP(23–230) as detected by [1H, 15N]-HSQC spectroscopy. In thermal equilibrium a fifth xenon binding site is formed transiently by amino acids A120 to L125 of the presumably disordered N-terminal domain and by amino acids K185 to T193 of the well-folded domain. Xenon bound PrP was modelled by restraint molecular dynamics. The individual microscopic and macroscopic dissociation constants could be derived by fitting the data to a model including a dynamic opening and closing of the cavities. As observed earlier by high pressure NMR spectroscopy xenon binding influences also other amino acids all over the N-terminal domain including residues of the AGAAAAGA motif indicating a structural coupling between the N-terminal domain and the core domain. This is in agreement with spin labelling experiments at positions 93 or 107 that show a transient interaction between the N-terminus and the start of helix 2 and the end of helix 3 of the core domain similar to that observed earlier by Zn2+-binding to the octarepeat motif.
AurkA controls self-renewal of breast cancer-initiating cells promoting wnt3a stabilization through suppression of miR-128
Authors: Eterno V. , Zambelli A. , Villani L. , Tuscano A. , Manera S. , Spitaleri A. , Pavesi L. , Amato A.
Published: June 2016

AurkA overexpression was previously found in breast cancer and associated to its ability in controlling chromosome segregation during mitosis, however whether it may affect breast cancer cells, endorsed with stem properties (BCICs), is still unclear. Surprisingly, a strong correlation between AurkA expression and β-catenin localization in breast cancer tissues suggested a link between AurkA and Wnt signaling. In our study, AurkA knock-down reduced wnt3a mRNA and suppressed metastatic signature of MDA-MB-231 cells. As a consequence, the amount of BCICs and their migratory capability dramatically decreased. Conversely, wnt3a mRNA stabilization and increased CD44+/CD24low/− subpopulation was found in AurkA-overexpressing MCF7 cells. In vivo, AurkA-overexpressing primary breast cancer cells showed higher tumorigenic properties. Interestingly, we found that AurkA suppressed the expression of miR-128, inhibitor of wnt3a mRNA stabilization. Namely, miR-128 suppression realized after AurkA binding to Snail. Remarkably, a strong correlation between AurkA and miR-128 expression in breast cancer tissues confirmed our findings. This study provides novel insights into an undisclosed role for the kinase AurkA in self-renewal and migration of BCICs affecting response to cancer therapies, metastatic spread and recurrence. In addition, it suggests a new therapeutic strategy taking advantage of miR-128 to suppress AurkA-Wnt3a signaling.
Maximal mid-expiratory flow is a surrogate marker of lung clearance index for assessment of adults with bronchiectasis
Authors: Guan Wei-jie , Yuan Jing-jing , Gao Yong-hua , Li Hui-min , Zheng Jin-ping , Chen Rong-chang , Zhong Nan-shan
Published: June 2016

Little is known about the comparative diagnostic value of lung clearance index (LCI) and maximal mid-expiratory flow (MMEF) in bronchiectasis. We compared the diagnostic performance, correlation and concordance with clinical variables, and changes of LCI and MMEF% predicted during bronchiectasis exacerbations (BEs). Patients with stable bronchiectasis underwent history inquiry, chest high-resolution computed tomography (HRCT), multiple-breath nitrogen wash-out test, spirometry and sputum culture. Patients who experienced BEs underwent these measurements during onset of BEs and 1 week following antibiotics therapy. Sensitivity analyses were performed in mild, moderate and severe bronchiectasis. We recruited 110 bronchiectasis patients between March 2014 and September 2015. LCI demonstrated similar diagnostic value with MMEF% predicted in discriminating moderate-to-severe from mild bronchiectasis. LCI negatively correlated with MMEF% predicted. Both parameters had similar concordance in reflecting clinical characteristics of bronchiectasis and correlated significantly with forced expiratory flow in one second, age, HRCT score, Pseudomonas aeruginosa colonization, cystic bronchiectasis, ventilation heterogeneity and bilateral bronchiectasis. In exacerbation cohort (n = 22), changes in LCI and MMEF% predicted were equally minimal during BEs and following antibiotics therapy. In sensitivity analyses, both parameters had similar diagnostic value and correlation with clinical variables. MMEF% predicted is a surrogate of LCI for assessing bronchiectasis severity.
Effect of curcumin analogs onα-synuclein aggregation and cytotoxicity
Authors: Jha Narendra Nath , Ghosh Dhiman , Das Subhadeep , Anoop Arunagiri , Jacob Reeba S. , Singh Pradeep K. , Ayyagari Narasimham , Namboothiri Irishi N. N. , Maji Samir K.
Published: June 2016

Alpha-synuclein (α-Syn) aggregation into oligomers and fibrils is associated with dopaminergic neuron loss occurring in Parkinson’s disease (PD) pathogenesis. Compounds that modulate α-Syn aggregation and interact with preformed fibrils/oligomers and convert them to less toxic species could have promising applications in the drug development efforts against PD. Curcumin is one of the Asian food ingredient which showed promising role as therapeutic agent against many neurological disorders including PD. However, the instability and low solubility makes it less attractive for the drug development. In this work, we selected various curcumin analogs and studied their toxicity, stability and efficacy to interact with different α-Syn species and modulation of their toxicity. We found a subset of curcumin analogs with higher stability and showed that curcumin and its various analogs interact with preformed fibrils and oligomers and accelerate α-Syn aggregation to produce morphologically different amyloid fibrils in vitro. Furthermore, these curcumin analogs showed differential binding with the preformed α-Syn aggregates. The present data suggest the potential role of curcumin analogs in modulating α-Syn aggregation.
Mendelian Randomisation study of the influence of eGFR on coronary heart disease
Authors: Charoen Pimphen , Nitsch Dorothea , Engmann Jorgen , Shah Tina , White Jonathan , Zabaneh Delilah , Jefferis Barbara , Wannamethee Goya , Whincup Peter , Mulick Cassidy Amy , Gaunt Tom , Day Ian , McLachlan Stela , Price Jacqueline , Kumari Meena , Kivimaki Mika , Brunner Eric , Langenberg Claudia , Ben-Shlomo Yoav , Hingorani Aroon , Whittaker John , Pablo Casas Juan , Dudbridge Frank ,   the UCLEB Consortium, Dale Caroline , Finan Chris , Wong Andrew , Ong Ken , Drenos Fotios , Cooper Jackie , Sofat Reecha , Schmidt Floriaan , Lawlor Debbie A. , Talmud Philippa J. , Humphries Steve E. , Hardy Rebecca , Kuh Diana , Wareham Nicholas , Morris Richard , Plagno Vincent
Published: June 2016

Impaired kidney function, as measured by reduced estimated glomerular filtration rate (eGFR), has been associated with increased risk of coronary heart disease (CHD) in observational studies, but it is unclear whether this association is causal or the result of confounding or reverse causation. In this study we applied Mendelian randomisation analysis using 17 genetic variants previously associated with eGFR to investigate the causal role of kidney function on CHD. We used 13,145 participants from the UCL-LSHTM-Edinburgh-Bristol (UCLEB) Consortium and 194,427 participants from the Coronary ARtery DIsease Genome-wide Replication and Meta-analysis plus Coronary Artery Disease (CARDIoGRAMplusC4D) consortium. We observed significant association of an unweighted gene score with CHD risk (odds ratio = 0.983 per additional eGFR-increasing allele, 95% CI = 0.970–0.996, p = 0.008). However, using weights calculated from UCLEB, the gene score was not associated with disease risk (p = 0.11). These conflicting results could be explained by a single SNP, rs653178, which was not associated with eGFR in the UCLEB sample, but has known pleiotropic effects that prevent us from drawing a causal conclusion. The observational association between low eGFR and increased CHD risk was not explained by potential confounders and there was no evidence of reverse causation, therefore leaving the remaining unexplained association as an open question.
The Phosphorylation and Distribution of Cortactin Downstream of Integrin α9β1 Affects Cancer Cell Behaviour
Authors: Høye Anette M. , Couchman John R. , Wewer Ulla M. , Yoneda Atsuko
Published: June 2016

Integrins, a family of heterodimeric adhesion receptors are implicated in cell migration, development and cancer progression. They can adopt conformations that reflect their activation states and thereby impact adhesion strength and migration. Integrins in an intermediate activation state may be optimal for migration and we have shown previously that fully activated integrin α9β1 corresponds with less migratory behaviour in melanoma cells. Here, we aimed to identify components associated with the activation status of α9β1. Using cancer cell lines with naturally occuring high levels of this integrin, activation by α9β1-specific ligands led to upregulation of fibronectin matrix assembly and tyrosine phosphorylation of cortactin on tyrosine 470 (Y470). Specifically, cortactin phosphorylated on Y470, but not Y421, redistributed together with α9β1 to focal adhesions where active β1 integrin also localises, upon integrin activation. This was commensurate with reduced migration. The localisation and phosphorylation of cortactin Y470 was regulated by Yes kinase and PTEN phosphatase. Cortactin levels influenced fibronectin matrix assembly and active β1 integrin on the cell surface, being inversely correlated with migratory behaviour. This study underlines the complex interplay between cortactin and α9β1 integrin that regulates cell-extracellular matrix interactions.
Enhanced optical gradient forces between coupled graphene sheets
Authors: Xu Xinbiao , Shi Lei , Liu Yang , Wang Zheqi , Zhang Xinliang
Published: June 2016

Optical gradient forces between monolayer infinite-width graphene sheets as well as single-mode graphene nanoribbon pairs of graphene surface plasmons (GSPs) at mid-infrared frequencies were theoretically investigated. Although owing to the strongly enhanced optical field, the normalized optical force, fn, can reach 50 nN/μm/mW, which is the largest fn as we know, the propagation loss is also large. But we found that by changing the chemical potential of graphene, fn and the optical propagation loss can be balanced. The total optical force acted on the nanoribbon waveguides can thus enhance more than 1 order of magnitude than that in metallic surface plasmons (MSPs) waveguides with the same length and the loss can be lower. Owing to the enhanced optical force and the significant neff tuning by varying the chemical potential of graphene, we also propose an ultra-compact phase shifter.
The rubber tree genome shows expansion of gene family associated with rubber biosynthesis
Authors: Lau Nyok-Sean , Makita Yuko , Kawashima Mika , Taylor Todd D. , Kondo Shinji , Othman Ahmad Sofiman , Shu-Chien Alexander Chong , Matsui Minami
Published: June 2016

Hevea brasiliensis Muell. Arg, a member of the family Euphorbiaceae, is the sole natural resource exploited for commercial production of high-quality natural rubber. The properties of natural rubber latex are almost irreplaceable by synthetic counterparts for many industrial applications. A paucity of knowledge on the molecular mechanisms of rubber biosynthesis in high yield traits still persists. Here we report the comprehensive genome-wide analysis of the widely planted H. brasiliensis clone, RRIM 600. The genome was assembled based on ~155-fold combined coverage with Illumina and PacBio sequence data and has a total length of 1.55 Gb with 72.5% comprising repetitive DNA sequences. A total of 84,440 high-confidence protein-coding genes were predicted. Comparative genomic analysis revealed strong synteny between H. brasiliensis and other Euphorbiaceae genomes. Our data suggest that H. brasiliensis’s capacity to produce high levels of latex can be attributed to the expansion of rubber biosynthesis-related genes in its genome and the high expression of these genes in latex. Using cap analysis gene expression data, we illustrate the tissue-specific transcription profiles of rubber biosynthesis-related genes, revealing alternative means of transcriptional regulation. Our study adds to the understanding of H. brasiliensis biology and provides valuable genomic resources for future agronomic-related improvement of the rubber tree.
Cross-stacked carbon nanotubes assisted self-separation of free-standing GaN substrates by hydride vapor phase epitaxy
Authors: Wei Tongbo , Yang Jiankun , Wei Yang , Huo Ziqiang , Ji Xiaoli , Zhang Yun , Wang Junxi , Li Jinmin , Fan Shoushan
Published: June 2016

We report a novel method to fabricate high quality 2-inch freestanding GaN substrate grown on cross-stacked carbon nanotubes (CSCNTs) coated sapphire by hydride vapor phase epitaxy (HVPE). As nanoscale masks, these CSCNTs can help weaken the interface connection and release the compressive stress by forming voids during fast coalescence and also block the propagation of threading dislocations (TDs). During the cool-down process, thermal stress-induced cracks are initiated at the CSCNTs interface with the help of air voids and propagated all over the films which leads to full self-separation of FS-GaN substrate. Raman and photoluminescence spectra further reveal the stress relief and crystalline improvement of GaN with CSCNTs. It is expected that the efficient, low cost and mass-producible technique may enable new applications for CNTs in nitride optoelectronic fields.
XBP1 splicing triggers miR-150 transfer from smooth muscle cells to endothelial cells via extracellular vesicles
Authors: Zhao Yue , Li Yi , Luo Peiyi , Gao Yingtang , Yang Junyao , Lao Ka-Hou , Wang Gang , Cockerill Gillian , Hu Yanhua , Xu Qingbo , Li Tong , Zeng Lingfang
Published: June 2016

The interaction between endothelial cells (ECs) and smooth muscle cells (SMCs) plays a critical role in the maintenance of vessel wall homeostasis. The X-box binding protein 1 (XBP1) plays an important role in EC and SMC cellular functions. However, whether XBP1 is involved in EC-SMC interaction remains unclear. In this study, In vivo experiments with hindlimb ischemia models revealed that XBP1 deficiency in SMCs significantly attenuated angiogenesis in ischemic tissues, therefore retarded the foot blood perfusion recovery. In vitro studies indicated that either overexpression of the spliced XBP1 or treatment with platelet derived growth factor-BB up-regulated miR-150 expression and secretion via extracellular vesicles (EVs). The XBP1 splicing-mediated up-regulation of miR-150 might be due to increased stability. The SMC-derived EVs could trigger EC migration, which was abolished by miR-150 knockdown in SMCs, suggesting miR-150 is responsible for SMC-stimulated EC migration. The SMC-derived miR-150-containing EVs or premiR-150 transfection increased vascular endothelial growth factor (VEGF)-A mRNA and secretion in ECs. Both inhibitors SU5416 and LY294002 attenuated EVs-induced EC migration. This study demonstrates that XBP1 splicing in SMCs can control EC migration via SMC derived EVs-mediated miR-150 transfer and miR-150-driven VEGF-A/VEGFR/PI3K/Akt pathway activation, thereby modulating the maintenance of vessel wall homeostasis.
Increased CXCR3 Expression of Infiltrating Plasma Cells in Hunner Type Interstitial Cystitis
Authors: Akiyama Yoshiyuki , Morikawa Teppei , Maeda Daichi , Shintani Yukako , Niimi Aya , Nomiya Akira , Nakayama Atsuhito , Igawa Yasuhiko , Fukayama Masashi , Homma Yukio
Published: June 2016

An up-regulated CXCR3 pathway and affluent plasma cell infiltration are characteristic features of Hunner type interstitial cystitis (HIC). We further examined these two features using bladder biopsy samples taken from 27 patients with HIC and 15 patients with non-IC cystitis as a control. The number of CD3-positive T lymphocytes, CD20-positive B lymphocytes, CD138-positive plasma cells, and CXCR3-positive cells was quantified by digital image analysis. Double-immunofluorescence for CXCR3 and CD138 was used to detect CXCR3 expression in plasma cells. Correlations between CXCR3 positivity and lymphocytic and plasma cell numbers and clinical parameters were explored. The density of CXCR3-positive cells showed no significant differences between HIC and non-IC cystitis specimens. However, distribution of CXCR3-positivity in plasma cells indicated co-localization of CXCR3 with CD138 in HIC specimens, but not in non-IC cystitis specimens. The number of CXCR3-positive cells correlated with plasma cells in HIC specimens alone. Infiltration of CXCR3-positive cells was unrelated to clinical parameters of patients with HIC. These results suggest that infiltration of CXCR3-positive plasma cells is a characteristic feature of HIC. The CXCR3 pathway and specific immune responses may be involved in accumulation/retention of plasma cells and pathophysiology of the HIC bladder.
Efficiency Enhancement of InGaN-Based Solar Cells via Stacking Layers of Light-Harvesting Nanospheres
Authors: Al-Amri Amal M. , Fu Po-Han , Lai Kun-Yu , Wang Hsin-Ping , Li Lain-Jong , He Jr-Hau
Published: June 2016

An effective light-harvesting scheme for InGaN-based multiple quantum well solar cells is demonstrated using stacking layers of polystyrene nanospheres. Light-harvesting efficiencies on the solar cells covered with varied stacks of nanospheres are evaluated through numerical and experimental methods. The numerical simulation reveals that nanospheres with 3 stacking layers exhibit the most improved optical absorption and haze ratio as compared to those obtained by monolayer nanospheres. The experimental demonstration, agreeing with the theoretical analyses, shows that the application of 3-layer nanospheres improves the conversion efficiency of the solar cell by ~31%.
Intestinally-targeted TGR5 agonists equipped with quaternary ammonium have an improved hypoglycemic effect and reduced gallbladder filling effect
Authors: Cao Hua , Chen Zhi-Xiang , Wang Kai , Ning Meng-Meng , Zou Qing-An , Feng Ying , Ye Yang-Liang , Leng Ying , Shen Jian-Hua
Published: June 2016

TGR5 activation of enteroendocrine cells increases glucagon-like peptide 1 (GLP-1) release, which maintains glycemic homeostasis. However, TGR5 activation in the gallbladder and heart is associated with severe side effects. Therefore, intestinally-targeted TGR5 agonists were suggested as potential hypoglycemic agents with minimal side effects. However, until now no such compounds with robust glucose-lowering effects were reported, especially in diabetic animal models. Herein, we identify a TGR5 agonist, 26a, which was proven to be intestinally-targeted through pharmacokinetic studies. 26a was used as a tool drug to verify the intestinally-targeted strategy. 26a displayed a robust and long-lasting hypoglycemic effect in ob/ob mice (once a day dosing (QD) and 18-day treatment) owing to sustained stimulation of GLP-1 secretion, which suggested that robust hypoglycemic effect could be achieved with activation of TGR5 in intestine alone. However, the gallbladder filling effect of 26a was rather complicated. Although the gallbladder filling effect of 26a was decreased in mice after once a day dosing, this side effect was still not eliminated. To solve the problem above, several research strategies were raised for further optimization.
Polyester type polyHIPE scaffolds with an interconnected porous structure for cartilage regeneration
Authors: Naranda Jakob , Sušec Maja , Maver Uroš , Gradišnik Lidija , Gorenjak Mario , Vukasović Andreja , Ivković Alan , Rupnik Marjan Slak , Vogrin Matjaž , Krajnc Peter
Published: June 2016

Development of artificial materials for the facilitation of cartilage regeneration remains an important challenge in orthopedic practice. Our study investigates the potential for neocartilage formation within a synthetic polyester scaffold based on the polymerization of high internal phase emulsions. The fabrication of polyHIPE polymer (PHP) was specifically tailored to produce a highly porous (85%) structure with the primary pore size in the range of 50–170 μm for cartilage tissue engineering. The resulting PHP scaffold was proven biocompatible with human articular chondrocytes and viable cells were observed within the materials as evaluated using the Live/Dead assay and histological analysis. Chondrocytes with round nuclei were organized into multicellular layers on the PHP surface and were observed to grow approximately 300 μm into the scaffold interior. The accumulation of collagen type 2 was detected using immunohistochemistry and chondrogenic specific genes were expressed with favorable collagen type 2 to 1 ratio. In addition, PHP samples are biodegradable and their baseline mechanical properties are similar to those of native cartilage, which enhance chondrocyte cell growth and proliferation.
A practical online tool to estimate antiretroviral coverage for HIV infected and susceptible populations needed to reduce local HIV epidemics
Authors: Chaillon Antoine , Hoenigl Martin , Mehta Sanjay R. , Weibel Nadir , Little Susan J. , Smith Davey M.
Published: June 2016

It remains unclear what proportions of HIV-infected and uninfected people should receive effective antiretroviral therapy (ART) to control local HIV epidemics. We developed a flexible model to evaluate the impact of treatment as prevention (TasP) and pre-exposure prophylaxis (PrEP) on HIV incidence in local communities. We evaluated this tool for determining what TasP and PrEP targets are needed to substantially reduce the HIV epidemic in San Diego, which is predominately comprised of men who have sex with men. By increasing the proportion of HIV-infected individuals on ART from 30% to 50%, 686 new infections would be prevented over five years in San Diego. By providing PrEP to 30% of MSM to the age group that account for 90% of local HIV incident cases (21–52 years), we could prevent 433 infections over five years. When combining these initiatives, a PrEP coverage rate of 40% and TasP coverage rate of 34% would be expected to decrease the number of new infections by over half in one year. This online tool is designed to help local public health planners and policy makers to estimate program outcomes and costs that may lead to better control of their local HIV epidemics.
Fluorescence suppression using micro-scale spatially offset Raman spectroscopy
Authors: Conti Claudia , Botteon Alessandra , Colombo Chiara , Realini Marco , Matousek Pavel
Published: June 2016

We present a new concept of fluorescence suppression in Raman microscopy based on micro-spatially offset Raman spectroscopy which is applicable to thin stratified turbid (diffusely scattering) matrices permitting the retrieval of the Raman signals of sublayers below intensely fluorescing turbid over-layers.
Preparation of a molecularly imprinted fluorescent chemosensor using quinoline modified vinyl-β-cyclodextrin and acrylamide as monomers for the selective recognition of spermidine
Authors: Cheng Yang , Dong Xiangchao
Published: June 2016

A new molecularly imprinted fluorescent chemosensor with selectivity for spermidine has been developed using quinoline modified vinyl-β-cyclodextrin as a reporter and major functional monomer.
Sensing materials developed and applied for bio-active Fe3+ recognition in water environment
Authors: Yan Zhengquan , Hu Lei , You Jinmao
Published: June 2016

In this minireview, we highlight the main sensing materials/techniques developed, including fluorescence, colorimetry, atomic absorption, chromatography, electrochemistry, flow injection, and luminescent sensing materials for Fe3+ detection, and our own work in this area in recent years.
Effective separation of single-walled carbon nanotubes and their very different electrochemical behaviours
Authors: Zhang Xin , Chen Lin , Chen Xiang-Yu , Zhang Hanzhi , Yang Liuqing , Yang Fengchun
Published: June 2016

The electrochemical behaviors of m- and s-SWNTs obtained from as-prepared SWNTs using a novel binaphthyl based separation agent were very different, and can be further interconverted through changing the DOS via electron or hole doping.
The Pauson–Khand reaction using alkynylboronic esters: solving a long-standing regioselectivity issue
Authors: León Thierry , Fernández Elena
Published: June 2016

The first intermolecular Pauson–Khand reaction, conducted using internal alkynylboronic esters, allows the installation of the boronic ester moiety at the β-position of the cyclopentenone with total regio- and stereoselectivity.
Rational design and synthesis of an amino-functionalized hydrogen-bonded network with an ACO zeolite-like topology for gas storage
Authors: Guo Xiao-Qing , Wang Miao , Meng Fei , Tang Yan-Feng , Tian Shu , Yang Hua-Ling , Jiang Guo-Qing , Zhu Jin-Li
Published: June 2016

The modification of amino groups on the surface of In8 cubic SBUs comprising hydrogen-bonded networks with an ACO zeolite-like topology resulted in a great improvement in gas adsorption.
The formation mechanism of eutectic microstructures in NiAl–Cr composites
Authors: Tang Bin , Cogswell Daniel A. , Xu Guanglong , Milenkovic Srdjan , Cui Yuwen
Published: June 2016

Based on a thermodynamic foundation, a phase field model is developed for describing eutectic composites. The inherent complexity of NiAl–Cr microstructure is rationalized by modeling eutectic solidification that precedes conditional spinodal decomposition.
Magnetoresistive polyaniline–silicon carbide metacomposites: plasma frequency determination and high magnetic field sensitivity
Authors: Gu Hongbo , Guo Jiang , Khan Mojammel Alam , Young David P. , Shen T. D. , Wei Suying , Guo Zhanhu
Published: June 2016

Both negative permittivity and high magnetic field resistance sensitivity are observed in silicon carbide/polyaniline nanocomposites.
Low-field thermal mixing in [1-13C] pyruvic acid for brute-force hyperpolarization
Authors: Peat David T. , Hirsch Matthew L. , Gadian David G. , Horsewill Anthony J. , Owers-Bradley John R. , Kempf James G.
Published: June 2016

We detail the process of low-field thermal mixing (LFTM) between 1H and 13C nuclei in neat [1-13C] pyruvic acid at cryogenic temperatures (4–15 K).
Design and synthesis of ternary Co3O4/carbon coated TiO2 hybrid nanocomposites for asymmetric supercapacitors
Authors: Kim Myeongjin , Choi Jaeho , Oh Ilgeun , Kim Jooheon
Published: June 2016

Recently, attention has been focused on the synthesis and application of nanocomposites for supercapacitors, which can have superior electrochemical performance than single structured materials.
Selective hydrogenation of arenes to cyclohexanes in water catalyzed by chitin-supported ruthenium nanoparticles
Authors: Morioka Yuna , Matsuoka Aki , Binder Kellie , Knappett Benjamin R. , Wheatley Andrew E. H. , Naka Hiroshi
Published: June 2016

The selective hydrogenation of arenes to cyclohexanes is promoted by Ru/chitin under aqueous conditions without the loss of C–O/C–N linkages.
A novel hollow capsule-like recyclable functional ZnO/C/Fe3O4 endowed with three-dimensional oriented recognition ability for selectively photodegrading danofloxacin mesylate
Authors: Lu Ziyang , Zhao Xiaoxu , Zhu Zhi , Song Minshan , Gao Nailing , Wang Youshan , Ma Zhongfei , Shi Weidong , Yan Yongsheng , Dong Hongjun
Published: June 2016

The functional ZnO/C/Fe3O4 exhibits high photocatalytic activity and possesses good selectivity.
Cationic 5-phosphonio-substituted N-heterocyclic carbenes
Authors: Schwedtmann Kai , Schoemaker Robin , Hennersdorf Felix , Bauzá Antonio , Frontera Antonio , Weiss Robert , Weigand Jan J.
Published: June 2016

Cationic NHCs featuring a phosphonium moiety in the 5-position are prepared from the reaction of imidazolium salts with a tert. phosphane. They are used as ligands for the preparation of transition metal complexes, dehydrogenation reactions of prim. and sec. phosphanes and the preparation of a N-heterocyclic olefin (NHO).
A long-tethered (P–B–P)-pincer ligand: synthesis, complexation, and application to catalytic dehydrogenation of alkanes
Authors: Kwan Enrique Huang , Kawai Yasushi Jack , Kamakura Sei , Yamashita Makoto
Published: June 2016

A new long-tethered boron-containing (P–B–P)-pincer ligand has been synthesized. This ligand was introduced to Ir to form (P–B–P)Ir(H)Cl complex. Subsequent reaction with nBuLi led to the formation of dihydride complex (P–B–P)Ir(H)2. Both complexes were found to be moderately active for the catalytic dehydrogenation of alkanes.
Synthesis and catalytic applications of 1,2,3-triazolylidene gold(i) complexes in silver-free oxazoline syntheses and C–H bond activation
Authors: Pretorius René , Fructos Manuel R. , Müller-Bunz Helge , Gossage Robert A. , Pérez Pedro J. , Albrecht Martin
Published: June 2016

Novel triazolylidene gold(i) complexes were synthesized and activated by silver-free methodologies to generate catalysts for oxazoline synthesis and the C–H activation of arenes.
Dual gradients of light intensity and nutrient concentration for full-factorial mapping of photosynthetic productivity
Authors: Nguyen Brian , Graham Percival J. , Sinton David
Published: June 2016

Optimizing bioproduct generation from microalgae is complicated by the myriad of coupled parameters affecting photosynthetic productivity.
Atom economical synthesis of di- and trithiocarbonates by the lithium tert-butoxide catalyzed addition of carbon disulfide to epoxides and thiiranes
Authors: Diebler J. , Spannenberg A. , Werner T.
Published: June 2016

The lithiumtert-butoxide catalyzed addition of CS2to epoxides and thiiranes under mild conditions is reported. A mechanism has been proposed taking into account the regio- and stereochemical outcome of the reaction.
A metal-catalyzed enyne-cyclization step for the synthesis of bi- and tricyclic scaffolds amenable to molecular library production
Authors: Wu Peng , Petersen Michael Åxman , Cohrt A. Emil , Petersen Rico , Morgentin Rémy , Lemoine Hugues , Roche Carine , Willaume Anthony , Clausen Mads H. , Nielsen Thomas E.
Published: June 2016

A facile metal-catalyzed diversification step for the synthesis of novel bi- and tricyclic scaffolds from enyne substrates is reported in this study for molecular library production.
Sequence-regulated vinyl copolymers with acid and base monomer units via atom transfer radical addition and alternating radical copolymerization
Authors: Soejima Takamasa , Satoh Kotaro , Kamigaito Masami
Published: June 2016

Sequence-regulated vinyl copolymers with acid and base monomer units were prepared via atom transfer radical addition and alternating radical copolymerization.
Highly active and spherical natured mesoporous aluminosilicate nanoparticles materialized for t-butylation of phenol
Authors: Selvaraj M.
Published: June 2016

A green and recyclable AlSMSN material synthesised with enhanced hydrothermal stability has a rich tetrahedral Al ion coordination and reveals an unprecedented catalytic activity in t-butylation of phenol, among the other mesoporous catalysts.
Folate-decorated redox/pH dual-responsive degradable prodrug micelles for tumor triggered targeted drug delivery
Authors: Tabatabaei Rezaei Seyed Jamal , Sarbaz Laila , Niknejad Hassan
Published: June 2016

Multifunctional polymeric prodrug micelles, which allow the targeted intracellular delivery and facilitated release of conjugated drugs at cytoplasm in response to an intracellular glutathione and pH level, were developed.