bluuebunny/crossref_metadata_2025 huggingface dataset:
CYP6AE gene cluster knockout in Helicoverpa armigera reveals role in detoxification of phytochemicals and insecticides
Authors: Wang Huidong , Shi Yu , Wang Lu , Liu Shuai , Wu Shuwen , Yang Yihua , Feyereisen René , Wu Yidong
Published: November 2018

The cotton bollwormHelicoverpa armigera, is one of the world’s major pest of agriculture, feeding on over 300 hosts in 68 plant families. Resistance cases to most insecticide classes have been reported for this insect. Management of this pest in agroecosystems relies on a better understanding of how it copes with phytochemical or synthetic toxins. We have used genome editing to knock out a cluster of nine P450 genes and show that this significantly reduces the survival rate of the insect when exposed to two classes of host plant chemicals and two classes of insecticides. Functional expression of all members of this gene cluster identified the P450 enzymes capable of metabolism of these xenobiotics. The CRISPR-Cas9-based reverse genetics approach in conjunction with in vitro metabolism can rapidly identify the contributions of insect P450s in xenobiotic detoxification and serve to identify candidate genes for insecticide resistance.
Graphene mechanical pixels for Interferometric Modulator Displays
Authors: Cartamil-Bueno Santiago J. , Davidovikj Dejan , Centeno Alba , Zurutuza Amaia , van der Zant Herre S. J. , Steeneken Peter G. , Houri Samer
Published: November 2018

Electro-optic modulators based on micro-electromechanical systems have found success as elements for optical projectors, for simplified optical spectrometers, and as reflective-type screens that make use of light interference (Interferometric Modulator Display technology). The latter concept offers an exciting avenue for graphene nanomechanical structures to replace classical micro-electromechanical devices and bring about enhancement in performance, especially switching speed and voltage. In this work we study the optical response of electrically actuated graphene drumheads by means of spectrometric and stroboscopic experiments. The color reproducibility and speed of these membranes in producing the desired electro-optic modulation makes them suitable as pixels for high refresh rate displays. As a proof of concept, we demonstrate a Graphene Interferometric Modulator Display prototype with 5 μm-in-diameter pixels that compose a high resolution image (2500 pixels per inch)—equivalent to a 5″ display of 12K—whose color can be changed at frame rates of at least 400 Hz.
Cross-ecosystem carbon flows connecting ecosystems worldwide
Authors: Gounand Isabelle , Little Chelsea J. , Harvey Eric , Altermatt Florian
Published: November 2018

Ecosystems are widely interconnected by spatial flows of material, but the overall importance of these flows relative to local ecosystem functioning remains unclear. Here we provide a quantitative synthesis on spatial flows of carbon connecting ecosystems worldwide. Cross-ecosystem flows range over eight orders of magnitude, bringing between 10−3and 105 gC m−2 year−1to recipient ecosystems. Magnitudes are similar to local fluxes in freshwater and benthic ecosystems, but two to three orders of magnitude lower in terrestrial systems, demonstrating different dependencies on spatial flows among ecosystem types. The strong spatial couplings also indicate that ecosystems are vulnerable to alterations of cross-ecosystem flows. Thus, a reconsideration of ecosystem functioning, including a spatial perspective, is urgently needed.
Multi-color live-cell super-resolution volume imaging with multi-angle interference microscopy
Authors: Chen Youhua , Liu Wenjie , Zhang Zhimin , Zheng Cheng , Huang Yujia , Cao Ruizhi , Zhu Dazhao , Xu Liang , Zhang Meng , Zhang Yu-Hui , Fan Jiannan , Jin Luhong , Xu Yingke , Kuang Cuifang , Liu Xu
Published: November 2018

Imaging and tracking of near-surface three-dimensional volumetric nanoscale dynamic processes of live cells remains a challenging problem. In this paper, we propose a multi-color live-cell near-surface-volume super-resolution microscopy method that combines total internal reflection fluorescence structured illumination microscopy with multi-angle evanescent light illumination. We demonstrate that our approach of multi-angle interference microscopy is perfectly adapted to studying subcellular dynamics of mitochondria and microtubule architectures during cell migration.
Non-obstructive intracellular nanolasers
Authors: Fikouras Alasdair H. , Schubert Marcel , Karl Markus , Kumar Jothi D. , Powis Simon J. , Di Falco Andrea , Gather Malte C.
Published: November 2018

Molecular dyes, plasmonic nanoparticles and colloidal quantum dots are widely used in biomedical optics. Their operation is usually governed by spontaneous processes, which results in broad spectral features and limited signal-to-noise ratio, thus restricting opportunities for spectral multiplexing and sensing. Lasers provide the ultimate spectral definition and background suppression, and their integration with cells has recently been demonstrated. However, laser size and threshold remain problematic. Here, we report on the design, high-throughput fabrication and intracellular integration of semiconductor nanodisk lasers. By exploiting the large optical gain and high refractive index of GaInP/AlGaInP quantum wells, we obtain lasers with volumes 1000-fold smaller than the eukaryotic nucleus (Vlaser < 0.1 µm3), lasing thresholds 500-fold below the pulse energies typically used in two-photon microscopy (Eth ≈ 0.13 pJ), and excellent spectral stability (<50 pm wavelength shift). Multiplexed labeling with these lasers allows cell-tracking through micro-pores, thus providing a powerful tool to study cell migration and cancer invasion.
Over 1000-fold enhancement of upconversion luminescence using water-dispersible metal-insulator-metal nanostructures
Authors: Das Ananda , Mao Chenchen , Cho Suehyun , Kim Kyoungsik , Park Wounjhang
Published: November 2018

Rare-earth activated upconversion nanoparticles (UCNPs) are receiving renewed attention for use in bioimaging due to their exceptional photostability and low cytotoxicity. Often, these nanoparticles are attached to plasmonic nanostructures to enhance their photoluminescence (PL) emission. However, current wet-chemistry techniques suffer from large inhomogeneity and thus low enhancement is achieved. In this paper, we report lithographically fabricated metal-insulator-metal (MIM) nanostructures that show over 1000-fold enhancement of their PL. We demonstrate the potential for bioimaging applications by dispersing the MIMs into water and imaging bladder cancer cells with them. To our knowledge, our results represent one and two orders of magnitude improvement, respectively, over the best lithographically fabricated structures and colloidal systems in the literature. The large enhancement will allow for bioimaging and therapeutics using lower particle densities or lower excitation power densities, thus increasing the sensitivity and efficacy of such procedures while decreasing potential side effects.
Author Correction: Integrated molecular subtyping defines a curable oligometastatic state in colorectal liver metastasis
Authors: Pitroda Sean P. , Khodarev Nikolai N. , Huang Lei , Uppal Abhineet , Wightman Sean C. , Ganai Sabha , Joseph Nora , Pitt Jason , Brown Miguel , Forde Martin , Mangold Kathy , Xue Lai , Weber Christopher , Segal Jeremy P. , Kadri Sabah , Stack Melinda E. , Khan Sajid , Paty Philip , Kaul Karen , Andrade Jorge , White Kevin P. , Talamonti Mark , Posner Mitchell C. , Hellman Samuel , Weichselbaum Ralph R.
Published: November 2018

In the originally published version of this Article, the affiliation details for Kevin P. White inadvertently omitted ‘Tempus Labs, Chicago, IL, 60654, USA’. This has now been corrected in both the PDF and HTML versions of the Article.
Author Correction: A sulfotransferase dosage-dependently regulates mouthpart polyphenism in the nematode Pristionchus pacificus
Authors: Bui Linh T. , Ivers Nicholas A. , Ragsdale Erik J.
Published: November 2018

The original version of this Article contained errors in Figure 4. In panel a, the x axis labels of bars 6-11 were incorrect, as depicted in the associated Author Correction. These errors have been corrected in both the PDF and HTML versions of the Article.
Pressure-induced superconductivity in topological semimetal NbAs2
Authors: Li Yupeng , An Chao , Hua Chenqiang , Chen Xuliang , Zhou Yonghui , Zhou Ying , Zhang Ranran , Park Changyong , Wang Zhen , Lu Yunhao , Zheng Yi , Yang Zhaorong , Xu Zhu-An
Published: November 2018

Topological superconductivity with Majorana bound states, which are critical to implement nonabelian quantum computation, may be realized in three-dimensional semimetals with nontrivial topological feature, when superconducting transition occurs in the bulk. Here, we report pressure-induced superconductivity in a transition-metal dipnictide NbAs2. The emergence of superconductivity is not accompanied by any structural phase transition up to the maximum experimental pressure of 29.8 GPa, as supported by pressure-dependent synchrotron X-ray diffraction and Raman spectroscopy. Intriguingly, the Raman study reveals rapid phonon mode hardening and broadening above 10 GPa, in coincident with the superconducting transition. Using first-principle calculations, we determine Fermi surface change induced by pressure, which steadily increases the density of states without breaking the electron–hole compensation. Noticeably, the main hole pocket of NbAs2 encloses one time-reversal-invariant momenta of the monoclinic lattice, suggesting NbAs2 as a candidate of topological superconductors.
Carbenoxolone-mediated cytotoxicity inhibits Vaccinia virus replication in a human keratinocyte cell line
Authors: Haga Ismar R. , Simpson Jennifer L. , Hawes Philippa C. , Beard Philippa M.
Published: November 2018

The re-emergence of poxviral zoonotic infections and the threat of bioterrorism emphasise the demand for effective antipoxvirus therapies. Here, we show that carbenoxolone, a pharmacological inhibitor of gap junction function and a compound widely used in cell culture, is capable of hindering the replication of Vaccinia virus, the prototypical poxvirus, in a gap junction-independent manner in a human keratinocyte cell line. Viral protein synthesis occurs in the presence of carbenoxolone but infectious virion formation is minimal, indicating that carbenoxolone blocks viral morphogenesis. Initial viability tests suggested that carbenoxolone was not toxic to cells. However, electron microscopic analysis of carbenoxolone treated cells revealed that it alters the cellular endomembrane system. This widespread ultrastructural damage prevents Vaccinia virus virion assembly. These results strengthen the need for thorough characterisation of the effects of antiviral compounds on the cellular ultrastructure.
Direct mineralogical imaging of economic ore and rock samples with multi-modal nonlinear optical microscopy
Authors: Kao Mung-Chung , Pegoraro Adrian F. , Kingston David M. , Stolow Albert , Kuo Wen-Chuan , Mercier Patrick H. J. , Gogoi Ankur , Kao Fu-Jen , Ridsdale Andrew
Published: November 2018

Multi-modal nonlinear optical (NLO) microscopy, including stimulated Raman scattering (SRS) and second harmonic generation (SHG), was used to directly image mineralogical features of economic ore and rock samples. In SRS/SHG imaging, ore samples generally require minimal preparation and may be rapidly imaged, even in their wet state. 3D structural details, at submicron resolution, are revealed tens of microns deep within samples. Standard mineral imaging based on scanning electron microscopy (SEM), with elemental analysis via energy dispersive X-Ray spectroscopy, was used to independently validate the mineral composition of the samples. Spatially-resolved SRS from dominant Raman-resonant bands precisely maps the locations of specific minerals contained within the samples. SHG imaging reveals locally non-centrosymmetric structures, such as quartz grains. Competing absorption and nonlinear scattering processes, however, can reduce contrast in SRS imaging. Importantly, the correlation between standard electron microscopy and multi-modal NLO optical microscopy shows that the latter offers rapid image contrast based on the mineral content of the sample.
Effects of an Online Mind–Body Training Program on the Default Mode Network: An EEG Functional Connectivity Study
Authors: Lee Dasom , Kang Do-Hyung , Ha Na-hyun , Oh Chang-young , Lee Ulsoon , Kang Seung Wan
Published: November 2018

Online mind–body training (MBT) programs can improve the psychological capabilities of practitioners. Although there has been a lot of effort to understand the neural mechanisms underlying the therapeutic effects of meditation, little is known about changes in electroencephalographic (EEG) functional connectivity that accompany mind-body training. The present study aimed to investigate how an online MBT program alters EEG functional connectivity in the default mode network (DMN). We assessed a group of healthcare providers, including 14 females who participated in the 4-week MBT program and 15 females who underwent a 4-week of waiting period. EEG data and information about psychological states were obtained at baseline and 4 weeks. The result was that the intervention group showed significant reductions in anxiety and trait anger that were accompanied by increased global DMN network strengths in the theta and alpha (but not beta and delta) frequency bands; these changes were not observed in the control group. Other variables including state anger, positive and negative affect, and self-esteem have not been changed over time in both groups. These findings suggest that practicing the mind-body training could have a relevance to the functional differences in network related to stress and anxiety reaction.
Drivers for Livestock-Associated Methicillin-Resistant Staphylococcus Aureus Spread Among Danish Pig Herds - A Simulation Study
Authors: Schulz Jana , Boklund Anette , Toft Nils , Halasa Tariq
Published: November 2018

To gain insight into the rapid increase in the number of livestock-associated Methicillin-resistant Staphylococcus aureus (LA-MRSA)-positive herds in Denmark, we developed an individual-based Monte Carlo simulation model. We aimed to assess whether transmission of LA-MRSA via pig movements could explain the observed increase in the number of positive herds in Denmark, and to evaluate the effect of other between-herd transmission mechanisms. Pig movements alone were not sufficient to mimic the observed increase in LA-MRSA-positive herds in Denmark in any of the modelled scenarios. The model identified three factors that played important roles in the between-herd spread of LA-MRSA: (1) the within-herd dynamics, (2) the frequency and effectiveness of indirect transmissions, and (3) unexplainable introduction of LA-MRSA to swine herds. These factors can act as starting points for the development of LA-MRSA control programs in pig herds in order to limit the risk of its transmission to humans.
Sequential state discrimination of coherent states
Authors: Namkung Min , Kwon Younghun
Published: November 2018

Sequential state discrimination is a strategy for quantum state discrimination of a sender’s quantum states when N receivers are separately located. In this report, we propose optical designs that can perform sequential state discrimination of two coherent states. For this purpose, we consider not only binary phase-shifting-key (BPSK) signals but also general coherent states, with arbitrary prior probabilities. Since our optical designs do not include electric feedback, they can be implemented without difficulty. Furthermore, we analyze our proposal for the case of photon loss. We also demonstrate that sequential state discrimination of two coherent states performs better than the probabilistic quantum cloning strategy. This proposal can facilitate multiparty QKD based on coherent states.
Combining fish and benthic communities into multiple regimes reveals complex reef dynamics
Authors: Donovan Mary K. , Friedlander Alan M. , Lecky Joey , Jouffray Jean-Baptiste , Williams Gareth J. , Wedding Lisa M. , Crowder Larry B. , Erickson Ashley L. , Graham Nick A. J. , Gove Jamison M. , Kappel Carrie V. , Karr Kendra , Kittinger John N. , Norström Albert V. , Nyström Magnus , Oleson Kirsten L. L. , Stamoulis Kostantinos A. , White Crow , Williams Ivor D. , Selkoe Kimberly A.
Published: November 2018

Coral reefs worldwide face an uncertain future with many reefs reported to transition from being dominated by corals to macroalgae. However, given the complexity and diversity of the ecosystem, research on how regimes vary spatially and temporally is needed. Reef regimes are most often characterised by their benthic components; however, complex dynamics are associated with losses and gains in both fish and benthic assemblages. To capture this complexity, we synthesised 3,345 surveys from Hawai‘i to define reef regimes in terms of both fish and benthic assemblages. Model-based clustering revealed five distinct regimes that varied ecologically, and were spatially heterogeneous by island, depth and exposure. We identified a regime characteristic of a degraded state with low coral cover and fish biomass, one that had low coral but high fish biomass, as well as three other regimes that varied significantly in their ecology but were previously considered a single coral dominated regime. Analyses of time series data reflected complex system dynamics, with multiple transitions among regimes that were a function of both local and global stressors. Coupling fish and benthic communities into reef regimes to capture complex dynamics holds promise for monitoring reef change and guiding ecosystem-based management of coral reefs.
Single-molecule long-read sequencing facilitates shrimp transcriptome research
Authors: Zeng Digang , Chen Xiuli , Peng Jinxia , Yang Chunling , Peng Min , Zhu Weilin , Xie Daxiang , He Pingping , Wei Pinyuan , Lin Yong , Zhao Yongzhen , Chen Xiaohan
Published: November 2018

Although shrimp are of great economic importance, few full-length shrimp transcriptomes are available. Here, we used Pacific Biosciences single-molecule real-time (SMRT) long-read sequencing technology to generate transcripts from the Pacific white shrimp (Litopenaeus vannamei). We obtained 322,600 full-length non-chimeric reads, from which we generated 51,367 high-quality unique full-length transcripts. We corrected errors in the SMRT sequences by comparison with Illumina-produced short reads. We successfully annotated 81.72% of all unique SMRT transcripts against the NCBI non-redundant database, 58.63% against Swiss-Prot, 45.38% against Gene Ontology, 32.57% against Clusters of Orthologous Groups of proteins (COG), and 47.83% against Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. Across all transcripts, we identified 3,958 long non-coding RNAs (lncRNAs) and 80,650 simple sequence repeats (SSRs). Our study provides a rich set of full-length cDNA sequences for L. vannamei, which will greatly facilitate shrimp transcriptome research.
Genetic engineering a large animal model of human hypophosphatasia in sheep
Authors: Williams Diarra K. , Pinzón Carlos , Huggins Shannon , Pryor Jane H. , Falck Alyssa , Herman Forrest , Oldeschulte James , Chavez Michael B. , Foster Brian L. , White Sarah H. , Westhusin Mark E. , Suva Larry J. , Long Charles R. , Gaddy Dana
Published: November 2018

The availability of tools to accurately replicate the clinical phenotype of rare human diseases is a key step toward improved understanding of disease progression and the development of more effective therapeutics. We successfully generated the first large animal model of a rare human bone disease, hypophosphatasia (HPP) using CRISPR/Cas9 to introduce a single point mutation in the tissue nonspecific alkaline phosphatase (TNSALP) gene (ALPL) (1077 C > G) in sheep. HPP is a rare inherited disorder of mineral metabolism that affects bone and tooth development, and is associated with muscle weakness. Compared to wild-type (WT) controls, HPP sheep have reduced serum alkaline phosphatase activity, decreased tail vertebral bone size, and metaphyseal flaring, consistent with the mineralization deficits observed in human HPP patients. Computed tomography revealed short roots and thin dentin in incisors, and reduced mandibular bone in HPP vs. WT sheep, accurately replicating odonto-HPP. Skeletal muscle biopsies revealed aberrant fiber size and disorganized mitochondrial cristae structure in HPP vs. WT sheep. These genetically engineered sheep accurately phenocopy human HPP and provide a novel large animal platform for the longitudinal study of HPP progression, as well as other rare human bone diseases.
Asymmetry in Mechanosensitive Gene Expression during Aortic Arch Morphogenesis
Authors: Karakaya Cansu , Goktas Selda , Celik Merve , Kowalski William J. , Keller Bradley B. , Pekkan Kerem
Published: November 2018

Embryonic aortic arches (AA) are initially bilaterally paired, transitional vessels and failures in remodeling based on hemodynamic and growth-related adaptations cause a spectrum of congenital heart disease (CHD) anatomies. Identifying regulatory mechanisms and cross-talk between the genetic elements of these vessels are critical to understand the ethiology of CHD and refine predictive computational models. This study aims to screen expression profiles of fundamental biological pathways in AA at early stages of chick embryo morphogenesis and correlate them with our current understanding of growth and mechanical loading. Reverse transcription-quantitative PCR (RT-qPCR) was followed by correlation and novel peak expression analyses to compare the behaviour and activation period of the genes. Available protein networks were also integrated to investigate the interactions between molecules and highlight major hierarchies. Only wall shear stress (WSS) and growth-correlated expression patterns were investigated. Effect of WSS was seen directly on angiogenesis as well on structural and apoptosis-related genes. Our time-resolved network suggested that WSS-correlated genes coordinate the activity of critical growth factors. Moreover, differential gene expression of left and right AA might be an indicator of subsequent asymmetric morphogenesis. These findings may further our understanding of the complex processes of cardiac morphogenesis and errors resulting in CHD.
Inherited genetic predispositions in F13A1 and F13B genes predict abdominal adhesion formation: identification of gender prognostic indicators
Authors: Gemmati Donato , Occhionorelli Savino , Tisato Veronica , Vigliano Marco , Longo Giovanna , Gonelli Arianna , Sibilla Maria G. , Serino Maria L. , Zamboni Paolo
Published: November 2018

Abdominal adhesions (AA) account for the most common complication of peritoneal surgery with bowel obstruction being the severest problem in the absence of effective predicting biomarkers. Anti-AA-barriers or adhesiolysis did not completely prevent bowel obstruction, although there is evidence they might reduce related complications requiring reoperation. In addition, gender-related predispositions have not been adequately investigated. We explored the role of coagulation Factor XIII (F13A1 and F13B subunit-genes) in patients following laparotomy, mostly median/lower median incision line. Globally, 426 patients (54%,♀), were PCR-SNP-genotyped for FXIIIA V34L (rs5985), FXIIIA P564L (rs5982), FXIIIA Y204F (rs3024477) and FXIIIB H95R (rs6003). Patients’ clinical phenotypes were: Group-A (n = 212), those who developed AA, and 55.2% of them developed bowel obstruction (subgroup-A1), the remaining were subgroup-A2; Group B (n = 214) were those who did not develop AA (subgroup-B1; 53.3%) or symptoms/complications (subgroup-B2). Among different laparotomy, colon surgery associated with AA at a major extent (OR = 5.1; 3.24–7.8; P < 0.0001) with different gender scores (♀OR = 5.33; 2.32–12.23; P < 0.0001 and ♂OR = 3.44; 1.58–7.49; P < 0.0001). Among SNPs, P564L (OR = 4.42; 1.45–13.4; P = 0.008) and Y204F (OR = 7.78; 1.62–37.3; P = 0.01) significantly predicted bowel obstruction and survival-analyses yielded interesting gender distinctions (♀HR = 5.28; 2.36–11.8; P = 0.00005; ♂HR = 2.22; 1.31–3.85; P = 0.0034). Active compounds preventing AA belong to the anticoagulant/fibrinolysis areas, suggesting them candidate investigation targets. We identified novel prognostic markers to predict AA/bowel obstruction giving insights to design novel therapeutic and gender prevention programs.
Large-scale conformational changes and redistribution of surface negative charge upon sugar binding dictate the fidelity of phosphorylation in Vibrio cholerae fructokinase
Authors: Paul Rakhi , Chatterjee Shramana , Nath Seema , Sen Udayaditya
Published: November 2018

Fructokinase (FRK) catalyzes the first step of fructose metabolism i.e., D-fructose to D-fructose-6-phosphate (F6P), however, the mechanistic insights of this reaction are elusive yet. Here we demonstrate that the putative Vibrio cholerae fructokinase (VcFRK) exhibit strong fructose-6-kinase activity allosterically modulated by K+/Cs+. We have determined the crystal structures of apo-VcFRK and its complex with fructose, fructose-ADP-Ca2+, fructose-ADP-Ca2+-BeF3−. Collectively, we propose the catalytic mechanism and allosteric activation of VcFRK in atomistic details explaining why K+/Cs+ are better activator than Na+. Structural results suggest that apo VcFRK allows entry of fructose in the active site, sequester it through several conserved H-bonds and attains a closed form through large scale conformational changes. A double mutant (H108C/T261C-VcFRK), that arrests the closed form but unable to reopen for F6P release, is catalytically impotent highlighting the essentiality of this conformational change. Negative charge accumulation around ATP upon fructose binding, is presumed to redirect the γ-phosphate towards fructose for efficient phosphotransfer. Reduced phosphotransfer rate of the mutants E205Q and E110Q supports this view. Atomic resolution structure of VcFRK-fructose-ADP-Ca2+-BeF3−, reported first time for any sugar kinase, suggests that BeF3− moiety alongwith R176, Ca2+ and ‘anion hole’ limit the conformational space for γ-phosphate favoring in-line phospho-transfer.
Health behaviour changes after type 2 diabetes diagnosis: Findings from the English Longitudinal Study of Ageing
Authors: Hackett Ruth A. , Moore Catherine , Steptoe Andrew , Lassale Camille
Published: November 2018

Healthy lifestyle is key for type 2 diabetes (T2D) management. It is unclear whether individuals change health behaviours in response to T2D diagnosis. We compared smoking, physical activity, fruit and vegetable intake and alcohol consumption at three times (pre-diagnosis, at diagnosis, 2–4 years post-diagnosis) in individuals who developed T2D and controls. Behaviours were assessed in 6877 individuals at waves 3–7 of the English Longitudinal Study of Ageing. Generalized estimating equations were used to examine differences by group and time and group-by-time interactions. The T2D group were less active (p < 0.001) and consumed less alcohol (p < 0.001). Smoking (p < 0.001), alcohol consumption (p = 0.037) and physical activity (p = 0.042) decreased over time in the overall sample, fruit and vegetable intake (p = 0.012) and sedentary activity (p < 0.001) increased. A group-by-time interaction was found for smoking, with the T2D group having greater reductions in smoking over time (p < 0.001). No significant interactions were detected for other behaviours. We found limited evidence that T2D diagnosis encourages behaviour change, other than a reduction in smoking. Given the importance of lifestyle for T2D outcomes, strategies for motivating behaviour change need to be identified.
DLK proteins modulate NOTCH signaling to influence a brown or white 3T3-L1 adipocyte fate
Authors: Nueda María-Luisa , González-Gómez María-Julia , Rodríguez-Cano María-Milagros , Monsalve Eva-María , Díaz-Guerra María José M. , Sánchez-Solana Beatriz , Laborda Jorge , Baladrón Victoriano
Published: November 2018

The role of NOTCH signaling in adipogenesis is highly controversial, with data indicating null, positive or negative effects on this differentiation process. We hypothesize that these contradictory results could be due to the different global NOTCH signaling levels obtained in different experimental settings, because of a specific modulation of NOTCH receptors’ activity by their ligands. We have previously demonstrated that DLK1 and DLK2, two non-canonical NOTCH1 ligands that inhibit NOTCH1 signaling in a dose-dependent manner, modulate the adipogenesis process of 3T3-L1 preadipocytes. In this work, we show that over-expression of any of the four NOTCH receptors enhanced adipogenesis of 3T3-L1 preadipocytes. We also determine that DLK proteins inhibit not only the activity of NOTCH1, but also the activity of NOTCH2, 3 and 4 receptors to different degrees. Interestingly, we have observed, by different approaches, that NOTCH1 over-expression seems to stimulate the differentiation of 3T3-L1 cells towards a brown-like adipocyte phenotype, whereas cells over-expressing NOTCH2, 3 or 4 receptors or DLK proteins would rather differentiate towards a white-like adipocyte phenotype. Finally, our data also demonstrate a complex feed-back mechanism involving Notch and Dlk genes in the regulation of their expression, which suggest that a precise level of global NOTCH expression and NOTCH-dependent transcriptional activity of specific targets could be necessary to determine the final phenotype of 3T3-L1 adipocytes.
Femtosecond diffraction studies of solid and liquid phase changes in shock-compressed bismuth
Authors: Gorman M. G. , Coleman A. L. , Briggs R. , McWilliams R. S. , McGonegle D. , Bolme C. A. , Gleason A. E. , Galtier E. , Lee H. J. , Granados E. , Śliwa M. , Sanloup C. , Rothman S. , Fratanduono D. E. , Smith R. F. , Collins G. W. , Eggert J. H. , Wark J. S. , McMahon M. I.
Published: November 2018

Bismuth has long been a prototypical system for investigating phase transformations and melting at high pressure. Despite decades of experimental study, however, the lattice-level response of Bi to rapid (shock) compression and the relationship between structures occurring dynamically and those observed during slow (static) compression, are still not clearly understood. We have determined the structural response of shock-compressed Bi to 68 GPa using femtosecond X-ray diffraction, thereby revealing the phase transition sequence and equation-of-state in unprecedented detail for the first time. We show that shocked-Bi exhibits a marked departure from equilibrium behavior - the incommensurate Bi-III phase is not observed, but rather a new metastable phase, and the Bi-V phase is formed at significantly lower pressures compared to static compression studies. We also directly measure structural changes in a shocked liquid for the first time. These observations reveal new behaviour in the solid and liquid phases of a shocked material and give important insights into the validity of comparing static and dynamic datasets.
Genetic structure and differentiation in Dendrocalamus sinicus (Poaceae: Bambusoideae) populations provide insight into evolutionary history and speciation of woody bamboos
Authors: Yang Jun Bo , Dong Yu Ran , Wong Khoon Meng , Gu Zhi Jia , Yang Han Qi , Li De Zhu
Published: November 2018

Evolutionary processes, speciation in woody bamboos are presently little understood. Here we used Dendrocalamus sinicus Chia & J.L. Sun as a model species to investigate dispersal or vicariance speciation in woody bamboos. Variation in three chloroplast DNA (cpDNA) fragments and eight simple sequence repeat markers (SSR) among 232 individuals sampled from 18 populations across the known geographic range of D. sinicus was surveyed. D. sinicus populations exhibited a high level of genetic differentiation which divided them into two groups that are consistent with different culm types. Eleven haplotypes and two lineages (Straight-culm and Sinuous-culm lineages) were identified from phylogenetic analyses, and a strong phylogeographic structure across the distribution range was found. The demographic and spatial expansion times of the Straight-culm lineage were calculated as 11.3 Kya and 20.8 Kya, respectively. The populations of D. sinicus had experienced dispersal and long-term isolation, although this trace was diluted by contemporary gene flow revealed by SSR data. Our results provide an phylogeographic insight to better understand the speciation processes of woody bamboos.
Persistent metabolic changes in HIV-infected patients during the first year of combination antiretroviral therapy
Authors: Peltenburg N. Chantal , Schoeman Johannes C. , Hou Jun , Mora Fernando , Harms Amy C. , Lowe Selwyn H. , Bierau Jörgen , Bakker Jaap A. , Verbon Annelies , Hankemeier Thomas , Boonstra Andre
Published: November 2018

The HIV-human metabolic relationship is a complex interaction convoluted even more by antiretroviral therapy (cART) and comorbidities. The ability of cART to undo the HIV induced metabolic dysregulation is unclear and under-investigated. Using targeted metabolomics and multiplex immune biomarker analysis, we characterized plasma samples obtained from 18 untreated HIV-1-infected adult patients and compared these to a non-HIV infected (n = 23) control population. The biogenic amine perturbations during an untreated HIV infection implicated altered tryptophan- nitrogen- and muscle metabolism. Furthermore, the lipid profiles of untreated patients were also significantly altered compared to controls. In untreated HIV infection, the sphingomyelins and phospholipids correlated negatively to markers of infection IP-10 and sIL-2R whereas a strong association was found between triglycerides and MCP-1. In a second cohort, we characterized plasma samples obtained from 28 HIV-1-infected adult patients before and 12 months after the start of cART, to investigate the immune-metabolic changes associated with cART. The identified altered immune-metabolic pathways of an untreated HIV infection showed minimal change after 12 months of cART. In conclusion, 12 months of cART impacts only mildly on the metabolic dysregulation underlying an untreated HIV infection and provide insights into the comorbidities present in virally suppressed HIV patients.
Cued reactivation during slow-wave sleep induces brain connectivity changes related to memory stabilization
Authors: Berkers Ruud M. W. J. , Ekman Matthias , van Dongen Eelco. V. , Takashima Atsuko , Barth Markus , Paller Ken. A. , Fernández Guillén
Published: November 2018

Memory reprocessing following acquisition enhances memory consolidation. Specifically, neural activity during encoding is thought to be ‘replayed’ during subsequent slow-wave sleep. Such memory replay is thought to contribute to the functional reorganization of neural memory traces. In particular, memory replay may facilitate the exchange of information across brain regions by inducing a reconfiguration of connectivity across the brain. Memory reactivation can be induced by external cues through a procedure known as “targeted memory reactivation”. Here, we analysed data from a published study with auditory cues used to reactivate visual object-location memories during slow-wave sleep. We characterized effects of memory reactivation on brain network connectivity using graph-theory. We found that cue presentation during slow-wave sleep increased global network integration of occipital cortex, a visual region that was also active during retrieval of object locations. Although cueing did not have an overall beneficial effect on the retention of cued versus uncued associations, individual differences in overnight memory stabilization were related to enhanced network integration of occipital cortex. Furthermore, occipital cortex displayed enhanced connectivity with mnemonic regions, namely the hippocampus, parahippocampal gyrus, thalamus and medial prefrontal cortex during cue sound presentation. Together, these results suggest a neural mechanism where cue-induced replay during sleep increases integration of task-relevant perceptual regions with mnemonic regions. This cross-regional integration may be instrumental for the consolidation and long-term storage of enduring memories.
Quenched Stochastic Optical Reconstruction Microscopy (qSTORM) with Graphene Oxide
Authors: Li Ruiheng , Georgiades Pantelis , Cox Henry , Phanphak Sorasak , Roberts Ian S. , Waigh Thomas A. , Lu Jian R.
Published: November 2018

Quenched Stochastic Optical Reconstruction Microscopy (qSTORM) was demonstrated with graphene oxide sheets, peptides and bacteria; a method of contrast enhancement with super-resolution fluorescence microscopy. Individual sheets of graphene oxide (GO) were imaged with a resolution of 16 nm using the quenching of fluorescence emission by GO via its large Resonant Energy Transfer (RET) efficiency. The method was then extended to image self-assembled peptide aggregates (resolution 19 nm) and live bacterial cells (resolution 55 nm, the capsular structure of E. coli from urinary tract infections) with extremely low backgrounds and high contrasts (between one and two orders of magnitude contrast factor improvements that depended on the thickness of the graphene oxide layer used). Graphene oxide films combined with STORM imaging thus provide an extremely convenient method to image samples with large backgrounds due to non-specifically bound fluorophores (either due to excess labelling or autofluorescent molecules), which is a common occurrence in studies of both biological cells and soft-condensed matter. The GO quenches the fluorescence across a thin layer at distances of less than 15 nm. Graphene oxide films coated with thin layers (≤15 nm) of polystyrene, polymethylmethacrylate and polylysine are shown to be effective in producing high contrast qSTORM images, providing a convenient modulation of sample/substrate interactions. The GO coatings can also provide an increased image resolution and a factor of 2.3 improvement was observed with the peptide fibres using a feature of interest metric,when there was a large non-specifically bound background.
A sixfold rise in concurrent day and night-time heatwaves in India under 2 °C warming
Authors: Mukherjee Sourav , Mishra Vimal
Published: November 2018

Heatwaves with severe impacts have increased and projected to become more frequent under warming climate in India. Concurrent day and nighttime heatwaves can exacerbate human discomfort causing high morbidity and mortality; however, their changes in the observed and projected climate remain unrecognized. Here using observations and model simulations from climate of 20thcentury plus (C20C+) detection and attribution (D&A) and coupled model intercomparison project 5 (CMIP5) projects, we show that 1 and 3-day concurrent hot day and hot night (CHDHN) events have significantly increased during the observed climate in India. Our results show that the anthropogenic emissions contribute considerably to the increase of 1 and 3-day CHDHN events in India. The frequency of 3-day CHDHN events is projected to increase 12-fold of the current level by the end of 21stcentury and 4-fold by the mid 21stcentury under the high emission pathway of RCP 8.5. The increase in 3-day CHDHN events can be limited to only 2-fold by the end of 21stcentury under low emission scenario of RCP 2.6. One and 3-day CHDHN events are projected to increase by 4, 6, and 8 folds of the current level in India under the 1.5, 2, and 3 °C warming worlds, respectively. Restricting global mean temperature below 1.5° from the pre-industrial level can substantially reduce the risk of 1 and 3-day CHDHN events and associated implications in India.
Mycorrhizal fungi mediate the direction and strength of plant–soil feedbacks differently between arbuscular mycorrhizal and ectomycorrhizal communities
Authors: Kadowaki Kohmei , Yamamoto Satoshi , Sato Hirotoshi , Tanabe Akifumi S. , Hidaka Amane , Toju Hirokazu
Published: November 2018

Plants influence their soil environment, which affects the next generation of seedlings that can be established. While research has shown that such plant–soil feedbacks occur in the presence of mycorrhizal fungi, it remains unclear when and how mycorrhizal fungi mediate the direction and strength of feedbacks in tree communities. Here we show that arbuscular mycorrhizal and ectomycorrhizal fungal guilds mediate plant–soil feedbacks differently to influence large-scale patterns such as tree species coexistence and succession. When seedlings are grown under the same mycorrhizal type forest, arbuscular mycorrhizal plant species exhibit negative or neutral feedbacks and ectomycorrhizal plant species do neutral or positive feedbacks. In contrast, positive and neutral feedbacks dominate when seedlings are grown in associations within the same versus different mycorrhizal types. Thus, ectomycorrhizal communities show more positive feedbacks than arbuscular mycorrhizal communities, potentially explaining why most temperate forests are ectomycorrhizal.
An improved genome assembly for Larimichthys crocea reveals hepcidin gene expansion with diversified regulation and function
Authors: Mu Yinnan , Huo Jieying , Guan Yanyun , Fan Dingding , Xiao Xiaoqiang , Wei Jingguang , Li Qiuhua , Mu Pengfei , Ao Jingqun , Chen Xinhua
Published: November 2018

Larimichthys crocea(large yellow croaker) is a type of perciform fish well known for its peculiar physiological properties and economic value. Here, we constructed an improved version of theL. croceagenome assembly, which contained 26,100 protein-coding genes. Twenty-four pseudo-chromosomes ofL. croceawere also reconstructed, comprising 90% of the genome assembly. This improved assembly revealed several expansions in gene families associated with olfactory detection, detoxification, and innate immunity. Specifically, six hepcidin genes (LcHamps) were identified inL. crocea, possibly resulting from lineage-specific gene duplication. All LcHamps possessed similar genomic structures and functional domains, but varied substantially with respect to expression pattern, transcriptional regulation, and biological function. LcHamp1 was associated specifically with iron metabolism, while LcHamp2s were functionally diverse, involving in antibacterial activity, antiviral activity, and regulation of intracellular iron metabolism. This functional diversity among gene copies may have allowedL. croceato adapt to diverse environmental conditions.
Surface-enhanced Raman scattering on a silver-coated TiO2 nanopore core needle biopsy for three dimensional chemical profiling
Authors: Liu Renxuan , Sha Tao , Nie Bei
Published: November 2018

In vivo analyzing chemical significance under human skin has impinged a formidable challenge upon regular optical methods due to its intrinsic opaque property.
Degradable redox-responsive disulfide-based nanogel drug carriers via dithiol oxidation polymerization
Authors: Elkassih Sussana A. , Kos Petra , Xiong Hu , Siegwart Daniel J.
Published: November 2018

Stimuli-responsive nanogels degrade to small molecules in reducing environments to mediate controlled drug release.
Polymer–antibiotic conjugates as antibacterial additives in dental resins
Authors: Zhang Runsheng , Jones Megan M. , Moussa Hoda , Keskar Mayuresh , Huo Ningbo , Zhang Ziqi , Visser Michelle B. , Sabatini Camila , Swihart Mark T. , Cheng Chong
Published: November 2018

Dental resins containing polymer–antibiotic conjugates (PACs) demonstrate significant antibacterial properties.
Quantification of the liquid window of deep eutectic solvents
Authors: Kollau Laura J. B. M. , Vis Mark , van den Bruinhorst Adriaan , Esteves A. Catarina C. , Tuinier Remco
Published: November 2018

The non-ideality of the eutectic phase diagram is quantified using a single interaction parameter that could be determined directly from the experimental eutectic temperature of the mixture.
The first stages of oxide growth at the low index Al surfaces (100), (110), (111): clusters and stripes vs. homogeneous growth
Authors: Lousada Cláudio M. , Korzhavyi Pavel A.
Published: November 2018

The oxide growth at Al(100), Al(110) and Al(111) involves formation of structures that depend on the surface and O-atom coverage.
The sacrificial inactivation of the blue-light photosensor cryptochrome from Drosophila melanogaster
Authors: Kutta Roger Jan , Archipowa Nataliya , Scrutton Nigel Shaun
Published: November 2018

Photoactivation of Drosophila melanogaster cryptochrome results in tryptophan decomposition, conformational changes, and final FAD release.
The role of Anderson’s rule in determining electronic, optical and transport properties of transition metal dichalcogenide heterostructures
Authors: Xu Ke , Xu Yuanfeng , Zhang Hao , Peng Bo , Shao Hezhu , Ni Gang , Li Jing , Yao Mingyuan , Lu Hongliang , Zhu Heyuan , Soukoulis Costas M.
Published: November 2018

We have investigated the structure and electronic, mechanical, transport and optical properties of van der Waals transition metal dichalcogenide heterostructures using first-principles calculations.
Computer study of the solubilization of polymer chains in polyelectrolyte complex cores of polymeric nanoparticles in aqueous media
Authors: Šindelka Karel , Limpouchová Zuzana , Procházka Karel
Published: November 2018

The formation and structure of nanoparticles containing non-polar polymer chains solubilized in interpolyelectrolyte complex (IPC) cores and the partitioning of non-polar chains between bulk solvent and IPC cores were studied by coarse-grained computer simulations.
Feature optimization for atomistic machine learning yields a data-driven construction of the periodic table of the elements
Authors: Willatt Michael J. , Musil Félix , Ceriotti Michele
Published: November 2018

By representing elements as points in a low-dimensional chemical space it is possible to improve the performance of a machine-learning model for a chemically-diverse dataset. The resulting coordinates are reminiscent of the main groups of the periodic table.
Impact of nanogold morphology on interactions with human serum
Authors: Carnovale C. , Bryant G. , Shukla R. , Bansal V.
Published: November 2018

Following the synthesis of different shaped gold nanoparticles, their interaction with human serum albumin was studied to reveal shape affects both the affinity and strength of binding.
Recent advances and strategies to tailor the energy levels, active sites and electron mobility in titania and its doped/composite analogues for hydrogen evolution in sunlight
Authors: Shwetharani R. , Sakar M. , Fernando C. A. N. , Binas Vassilis , Balakrishna R. Geetha
Published: November 2018

Hydrogen production through photocatalytic water reduction, a potential path for future renewable and sustainable energy generation.
Imino-stabilised phosphinidene (or azaphosphole?) and some of its derivatives
Authors: Nguyen Minh Tho , Gabidullin Bulat , Nikonov Georgii I.
Published: November 2018

Diiminophenyl (dimph) proved to be an excellent ligand platform to stabilise a low-valent phosphorus centre.
Investigations of the capacity fading mechanism of Na0.44MnO2via ex situ XAS and magnetization measurements
Authors: Altin Serdar , Oz Erdinc , Altin Emine , Demirel Serkan , Bayri Ali , Avci Sevda
Published: November 2018

We propose a capacity fading mechanism for Na0.44MnO2via ex situ X-ray diffraction, X-ray absorption spectroscopy, Fourier transform infrared spectroscopy and magnetization measurements.
Aqueous-phase synthesis of layered double hydroxide nanoplates as catalysts for the oxygen evolution reaction
Authors: Jung Euiyoung , Kim Jae Kyeom , Choi Hyungsuk , Lee Min Hyung , Yu Taekyung
Published: November 2018

Transition metal LDH nanoplates were synthesized by heating an aqueous solution containing a metal salt, PEG, and octylamine. The LDH nanoplates showed comparable electrochemical catalytic performance for the oxygen evolution reaction.
A capping agent dissolution method for the synthesis of metal nanosponges and their catalytic activity towards nitroarene reduction under mild conditions
Authors: Ghosh Sourav , Jagirdar Balaji R.
Published: November 2018

We report a general strategy for the synthesis of metal nanosponges (M = Ag, Au, Pt, Pd, and Cu) using a capping agent dissolution method where addition of water to the M@BNHx nanocomposite affords the metal nanosponges.