bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genomic innovations linked to infection strategies across emerging pathogenic chytrid fungi
Authors: Farrer Rhys A. , Martel An , Verbrugghe Elin , Abouelleil Amr , Ducatelle Richard , Longcore Joyce E. , James Timothy Y. , Pasmans Frank , Fisher Matthew C. , Cuomo Christina A. 
Published: March 2017

AbstractTo understand the evolutionary pathways that lead to emerging infections of vertebrates, here we explore the genomic innovations that allow free-living chytrid fungi to adapt to and colonize amphibian hosts. Sequencing and comparing the genomes of two pathogenic species of Batrachochytrium to those of close saprophytic relatives reveals that pathogenicity is associated with remarkable expansions of protease and cell wall gene families, while divergent infection strategies are linked to radiations of lineage-specific gene families. By comparing the host–pathogen response to infection for both pathogens, we illuminate the traits that underpin a strikingly different immune response within a shared host species. Our results show that, despite commonalities that promote infection, specific gene-family radiations contribute to distinct infection strategies. The breadth and evolutionary novelty of candidate virulence factors that we discover underscores the urgent need to halt the advance of pathogenic chytrids and prevent incipient loss of biodiversity.
Hierarchical on-surface synthesis and electronic structure of carbonyl-functionalized one- and two-dimensional covalent nanoarchitectures
Authors: Steiner Christian , Gebhardt Julian , Ammon Maximilian , Yang Zechao , Heidenreich Alexander , Hammer Natalie , Görling Andreas , Kivala Milan , Maier Sabine 
Published: March 2017

AbstractThe fabrication of nanostructures in a bottom-up approach from specific molecular precursors offers the opportunity to create tailored materials for applications in nanoelectronics. However, the formation of defect-free two-dimensional (2D) covalent networks remains a challenge, which makes it difficult to unveil their electronic structure. Here we report on the hierarchical on-surface synthesis of nearly defect-free 2D covalent architectures with carbonyl-functionalized pores on Au(111), which is investigated by low-temperature scanning tunnelling microscopy in combination with density functional theory calculations. The carbonyl-bridged triphenylamine precursors form six-membered macrocycles and one-dimensional (1D) chains as intermediates in an Ullmann-type coupling reaction that are subsequently interlinked to 2D networks. The electronic band gap is narrowed when going from the monomer to 1D and 2D surface-confined π-conjugated organic polymers comprising the same building block. The significant drop of the electronic gap from the monomer to the polymer confirms an efficient conjugation along the triphenylamine units within the nanostructures.
Periodic potentials in hybrid van der Waals heterostructures formed by supramolecular lattices on graphene
Authors: Gobbi Marco , Bonacchi Sara , Lian Jian X. , Liu Yi , Wang Xiao-Ye , Stoeckel Marc-Antoine , Squillaci Marco A. , D’Avino Gabriele , Narita Akimitsu , Müllen Klaus , Feng Xinliang , Olivier Yoann , Beljonne David , Samorì Paolo , Orgiu Emanuele 
Published: March 2017

AbstractThe rise of 2D materials made it possible to form heterostructures held together by weak interplanar van der Waals interactions. Within such van der Waals heterostructures, the occurrence of 2D periodic potentials significantly modifies the electronic structure of single sheets within the stack, therefore modulating the material properties. However, these periodic potentials are determined by the mechanical alignment of adjacent 2D materials, which is cumbersome and time-consuming. Here we show that programmable 1D periodic potentials extending over areas exceeding 104 nm2 and stable at ambient conditions arise when graphene is covered by a self-assembled supramolecular lattice. The amplitude and sign of the potential can be modified without altering its periodicity by employing photoreactive molecules or their reaction products. In this regard, the supramolecular lattice/graphene bilayer represents the hybrid analogue of fully inorganic van der Waals heterostructures, highlighting the rich prospects that molecular design offers to create ad hoc materials.
Probing cytoskeletal modulation of passive and active intracellular dynamics using nanobody-functionalized quantum dots
Authors: Katrukha Eugene A. , Mikhaylova Marina , van Brakel Hugo X. , van Bergen en Henegouwen Paul M. , Akhmanova Anna , Hoogenraad Casper C. , Kapitein Lukas C. 
Published: March 2017

AbstractThe cytoplasm is a highly complex and heterogeneous medium that is structured by the cytoskeleton. How local transport depends on the heterogeneous organization and dynamics of F-actin and microtubules is poorly understood. Here we use a novel delivery and functionalization strategy to utilize quantum dots (QDs) as probes for active and passive intracellular transport. Rapid imaging of non-functionalized QDs reveals two populations with a 100-fold difference in diffusion constant, with the faster fraction increasing upon actin depolymerization. When nanobody-functionalized QDs are targeted to different kinesin motor proteins, their trajectories do not display strong actin-induced transverse displacements, as suggested previously. Only kinesin-1 displays subtle directional fluctuations, because the subset of microtubules used by this motor undergoes prominent undulations. Using actin-targeting agents reveals that F-actin suppresses most microtubule shape remodelling, rather than promoting it. These results demonstrate how the spatial heterogeneity of the cytoskeleton imposes large variations in non-equilibrium intracellular dynamics.
Real-time reliable determination of binding kinetics of DNA hybridization using a multi-channel graphene biosensor
Authors: Xu Shicai , Zhan Jian , Man Baoyuan , Jiang Shouzhen , Yue Weiwei , Gao Shoubao , Guo Chengang , Liu Hanping , Li Zhenhua , Wang Jihua , Zhou Yaoqi 
Published: March 2017

AbstractReliable determination of binding kinetics and affinity of DNA hybridization and single-base mismatches plays an essential role in systems biology, personalized and precision medicine. The standard tools are optical-based sensors that are difficult to operate in low cost and to miniaturize for high-throughput measurement. Biosensors based on nanowire field-effect transistors have been developed, but reliable and cost-effective fabrication remains a challenge. Here, we demonstrate that a graphene single-crystal domain patterned into multiple channels can measure time- and concentration-dependent DNA hybridization kinetics and affinity reliably and sensitively, with a detection limit of 10 pM for DNA. It can distinguish single-base mutations quantitatively in real time. An analytical model is developed to estimate probe density, efficiency of hybridization and the maximum sensor response. The results suggest a promising future for cost-effective, high-throughput screening of drug candidates, genetic variations and disease biomarkers by using an integrated, miniaturized, all-electrical multiplexed, graphene-based DNA array.
A high-throughput framework for determining adsorption energies on solid surfaces
Authors: Montoya Joseph H. , Persson Kristin A. 
Published: March 2017

AbstractIn this work, we present a high-throughput workflow for calculation of adsorption energies on solid surfaces using density functional theory. Using open-source computational tools from the Materials Project infrastructure, we automate the procedure of constructing symmetrically distinct adsorbate configurations for arbitrary slabs. These algorithms are further used to construct and run workflows in a standard, automated way such that user intervention in the simulation procedure is minimal. To validate our approach, we compare results from our workflow to previous experimental and theoretical benchmarks from the CE27 database of chemisorption energies on solid surfaces. These benchmarks also illustrate how the task of performing and managing over 200 individual density functional theory calculations may be reduced to a single submission procedure and subsequent analysis. By enabling more efficient high-throughput computations of adsorption energies, these tools will accelerate theory-guided discovery of advanced materials for applications in catalysis and surface science.
A short discourse on vascular tissue engineering
Authors: Chang William G. , Niklason Laura E. 
Published: March 2017

AbstractVascular tissue engineering has significant potential to make a major impact on a wide array of clinical problems. Continued progress in understanding basic vascular biology will be invaluable in making further advancements. Past and current achievements in tissue engineering of microvasculature to perfuse organ specific constructs, small vessels for dialysis grafts, and modified synthetic and pediatric large caliber-vessel grafts will be discussed. An emphasis will be placed on clinical trial results with small and large-caliber vessel grafts. Challenges to achieving engineered constructs that satisfy the physiologic, immunologic, and manufacturing demands of engineered vasculature will be explored.
When scientific paradigms lead to tunnel vision: lessons from the study of fear
Authors: Paré Denis , Quirk Gregory J. 
Published: March 2017

AbstractFor the past 30 years, research on the amygdala has largely focused on the genesis of defensive behaviors as its main function. This focus originated from early lesion studies and was supported by extensive anatomical, physiological, and pharmacological data. Here we argue that while much data is consistent with the fear model of amygdala function, it has never been directly tested, in part due to overreliance on the fear conditioning task. In support of the fear model, amygdala neurons appear to signal threats and/or stimuli predictive of threats. However, recent studies in a natural threat setting show that amygdala activity does not correlate with threats, but simply with the movement of the rat, independent of valence. This was true for both natural threats as well as conditioned stimuli; indeed there was no evidence of threat signaling in amygdala neurons. Similar findings are emerging for prefrontal neurons that modulate the amygdala. These recent developments lead us to propose a new conceptualization of amygdala function whereby the amygdala inhibits behavioral engagement. Moreover, we propose that the goal of understanding the amygdala will be best served by shifting away from fear conditioning toward naturalistic approach and avoidance paradigms that involve decision-making and a larger repertoire of spontaneous and learned behaviors, all the while keeping an open mind.
A novel technique to determine the cell type specific response within an in vitro co-culture model via multi-colour flow cytometry
Authors: Clift Martin J. D. , Fytianos Kleanthis , Vanhecke Dimitri , Hočevar Sandra , Petri-Fink Alke , Rothen-Rutishauser Barbara 
Published: March 2017

AbstractDetermination of the cell type specific response is essential towards understanding the cellular mechanisms associated with disease states as well as assessing cell-based targeting of effective therapeutic agents. Recently, there have been increased calls for advanced in vitro multi-cellular models that provide reliable and valuable tools correlative to in vivo. In this pursuit the ability to assess the cell type specific response is imperative. Herein, we report a novel approach towards resolving each specific cell type of a multi-cellular model representing the human lung epithelial tissue barrier via multi-colour flow cytometry (FACS). We proved via ≤ five-colour FACS that the manipulation of this in vitro model allowed each cell type to be resolved with no impact upon cell viability. Subsequently, four-colour FACS verified the ability to determine the biochemical effect (e.g. oxidative stress) of each specific cell type. This technique will be vital in gaining information upon cellular mechanics when using next-level, multi-cellular in vitro strategies.
A Strategy to Delay the Development of Cisplatin Resistance by Maintaining a Certain Amount of Cisplatin-Sensitive Cells
Authors: Duan Guihua , Tang Qianyuan , Yan Hongli , Xie Lijuan , Wang Yun , Zheng Xi Emily , Zhuge Yuzheng , Shen Shanshan , Zhang Bin , Zhang Xiaoqi , Wang Jun , Wang Wei , Zou Xiaoping 
Published: March 2017

AbstractCisplatin (ddp), which is commonly employed in the treatment of many advanced cancers, often results in initial therapeutic success; however, rapid progression of ddp-resistant cells remains the main reason for treatment failure. Facd with such a problem, we investigated the fitness differences between ddp-sensitive and ddp-resistant cell lines. We found that the growth of ddp-resistant cells was significantly slower than that of sensitive cells due to elevated ROS levels, which suggested that the ddp resistance mechanisms may have negative impacts on the growth of resistant cells. Furthermore, we observed that, when mixed with ddp-sensitive cells, ddp-resistant cells failed to compete, and the growth of ddp-resistant cells could therefore be suppressed by treatment in vivo. We propose a mathematical model parameterized based on in vivo experiments to describe the allometric growth of tumors consisting of two competing subclones. According to our model, a quantitative strategy with a variant drug-dosing interval is proposed to control tumor growth. Taking advantage of intratumoral competition, our strategy with appropriate dosing intervals could remarkably delay the development of ddp resistance and prolong overall survival. Maintaining a certain number of ddp-sensitive cells rather than eradicating the tumor with continuous treatment is feasible for future tumor treatment.
Transcriptome and functional analysis reveals hybrid vigor for oil biosynthesis in oil palm
Authors: Jin Jingjing , Sun Yanwei , Qu Jing , syah Rahmad , Lim Chin-Huat , Alfiko Yuzer , Rahman Nur Estya Bte , Suwanto Antonius , Yue Genhua , Wong Limsoon , Chua Nam-Hai , Ye Jian 
Published: March 2017

AbstractOil palm is the most productive oil crop in the world and composes 36% of the world production. However, the molecular mechanisms of hybrids vigor (or heterosis) between Dura, Pisifera and their hybrid progeny Tenera has not yet been well understood. Here we compared the temporal and spatial compositions of lipids and transcriptomes for two oil yielding organs mesocarp and endosperm from Dura, Pisifera and Tenera. Multiple lipid biosynthesis pathways are highly enriched in all non-additive expression pattern in endosperm, while cytokinine biosynthesis and cell cycle pathways are highly enriched both in endosperm and mesocarp. Compared with parental palms, the high oil content in Tenera was associated with much higher transcript levels of EgWRI1, homolog of Arabidopsis thaliana WRINKLED1. Among 338 identified genes in lipid synthesis, 207 (61%) has been identified to contain the WRI1 specific binding AW motif. We further functionally identified EgWRI1-1, one of three EgWRI1 orthologs, by genetic complementation of the Arabidopsis wri1 mutant. Ectopic expression of EgWRI1-1 in plant produced dramatically increased seed mass and oil content, with oil profile changed. Our findings provide an explanation for EgWRI1 as an important gene contributing hybrid vigor in lipid biosynthesis in oil palm.
Non-classical monocytes are biased progenitors of wound healing macrophages during soft tissue injury
Authors: Olingy Claire E. , San Emeterio Cheryl L. , Ogle Molly E. , Krieger Jack R. , Bruce Anthony C. , Pfau David D. , Jordan Brett T. , Peirce Shayn M. , Botchwey Edward A. 
Published: March 2017

AbstractSuccessful tissue repair requires the activities of myeloid cells such as monocytes and macrophages that guide the progression of inflammation and healing outcome. Immunoregenerative materials leverage the function of endogenous immune cells to orchestrate complex mechanisms of repair; however, a deeper understanding of innate immune cell function in inflamed tissues and their subsequent interactions with implanted materials is necessary to guide the design of these materials. Blood monocytes exist in two primary subpopulations, characterized as classical inflammatory or non-classical. While classical monocytes extravasate into inflamed tissue and give rise to macrophages or dendritic cells, the recruitment kinetics and functional role of non-classical monocytes remains unclear. Here, we demonstrate that circulating non-classical monocytes are directly recruited to polymer films within skin injuries, where they home to a perivascular niche and generate alternatively activated, wound healing macrophages. Selective labeling of blood monocyte subsets indicates that non-classical monocytes are biased progenitors of alternatively activated macrophages. On-site delivery of the immunomodulatory small molecule FTY720 recruits S1PR3-expressing non-classical monocytes that support vascular remodeling after injury. These results elucidate a previously unknown role for blood-derived non-classical monocytes as contributors to alternatively activated macrophages, highlighting them as key regulators of inflammatory response and regenerative outcome.
Novel molecular approach to define pest species status and tritrophic interactions from historical Bemisia specimens
Authors: Tay W. T. , Elfekih S. , Polaszek A. , Court L. N. , Evans G. A. , Gordon K. H. J. , De Barro P. J. 
Published: March 2017

AbstractMuseum specimens represent valuable genomic resources for understanding host-endosymbiont/parasitoid evolutionary relationships, resolving species complexes and nomenclatural problems. However, museum collections suffer DNA degradation, making them challenging for molecular-based studies. Here, the mitogenomes of a single 1912 Sri LankanBemisia emiliaecotype puparium, and of a 1942 JapaneseBemisiapuparium are characterised using a Next-Generation Sequencing approach. Whiteflies are small sap-sucking insects includingB.tabacipest species complex.Bemisia emiliae’s draft mitogenome showed a high degree of homology with publishedB.tabacimitogenomes, and exhibited 98–100% partial mitochondrial DNA Cytochrome Oxidase I (mtCOI) gene identity with theB.tabacispecies known as Asia II-7. The partial mtCOI gene of the Japanese specimen shared 99% sequence identity with theBemisia‘JpL’ genetic group. Metagenomic analysis identified bacterial sequences in bothBemisiaspecimens, while hymenopteran sequences were also identified in the JapaneseBemisiapuparium, including complete mtCOI and rRNA genes, and various partial mtDNA genes. At 88–90% mtCOI sequence identity to Aphelinidae wasps, we concluded that the 1942Bemisianymph was parasitized by anEretmocerusparasitoid wasp. Our approach enables the characterisation of genomes and associated metagenomic communities of museum specimens using 1.5 ng gDNA, and to infer historical tritrophic relationships inBemisiawhiteflies.
Feasible attack on detector-device-independent quantum key distribution
Authors: Wei Kejin , Liu Hongwei , Ma Haiqiang , Yang Xiuqing , Zhang Yong , Sun Yongmei , Xiao Jinghua , Ji Yuefeng 
Published: March 2017

AbstractRecently, to bridge the gap between security of Measurement-device-independent quantum key distribution (MDI-QKD) and a high key rate, a novel protocol, the so-called detector-device-independent QKD (DDI-QKD), has been independently proposed by several groups and has attracted great interest. A higher key rate is obtained, since a single photon bell state measurement (BSM) setup is applied to DDI-QKD. Subsequently, Qi has proposed two attacks for this protocol. However, the first attack, in which Bob’s BSM setup is assumed to be completely a “black box”, is easily prevented by using some additional monitoring devices or by specifically characterizing the BSM. The second attack, which combines the blinding attack and the detector wavelength-dependent efficiency, is not explicitly discussed, and its feasibility is not experimentally confirmed. Here, we show that the second attack is not technically viable because of an intrinsically wavelength-dependent property of a realistic beam splitter, which is an essential component in DDI-QKD. Moreover, we propose a feasible attack that combines a well-known attack—detector blinding attack with intrinsic imperfections of single-photon detectors. The experimental measurement and proof-of-principle test results confirm that our attack can allow Eve to get a copy of quantum keys without being detected and that it is feasible with current technology.
Fabrication of nanotweezers and their remote actuation by magnetic fields
Authors: Iss Cécile , Ortiz Guillermo , Truong Alain , Hou Yanxia , Livache Thierry , Calemczuk Roberto , Sabon Philippe , Gautier Eric , Auffret Stéphane , Buda-Prejbeanu Liliana D. , Strelkov Nikita , Joisten Hélène , Dieny Bernard 
Published: March 2017

AbstractA new kind of nanodevice that acts like tweezers through remote actuation by an external magnetic field is designed. Such device is meant to mechanically grab micrometric objects. The nanotweezers are built by using a top-down approach and are made of two parallelepipedic microelements, at least one of them being magnetic, bound by a flexible nanohinge. The presence of an external magnetic field induces a torque on the magnetic elements that competes with the elastic torque provided by the nanohinge. A model is established in order to evaluate the values of the balanced torques as a function of the tweezers opening angles. The results of the calculations are confronted to the expected values and validate the overall working principle of the magnetic nanotweezers.
X-ray ptychographic and fluorescence microscopy of frozen-hydrated cells using continuous scanning
Authors: Deng Junjing , Vine David J. , Chen Si , Jin Qiaoling , Nashed Youssef S. G. , Peterka Tom , Vogt Stefan , Jacobsen Chris 
Published: March 2017

AbstractX-ray microscopy can be used to image whole, unsectioned cells in their native hydrated state. It complements the higher resolution of electron microscopy for submicrometer thick specimens, and the molecule-specific imaging capabilites of fluorescence light microscopy. We describe here the first use of fast, continuous x-ray scanning of frozen hydrated cells for simultaneous sub-20 nm resolution ptychographic transmission imaging with high contrast, and sub-100 nm resolution deconvolved x-ray fluorescence imaging of diffusible and bound ions at native concentrations, without the need to add specific labels. By working with cells that have been rapidly frozen without the use of chemical fixatives, and imaging them under cryogenic conditions, we are able to obtain images with well preserved structural and chemical composition, and sufficient stability against radiation damage to allow for multiple images to be obtained with no observable change.