bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fabrication of all-transparent polymer-based and encapsulated nanofluidic devices using nano-indentation lithography
Authors: Wu Cong , Lin Tiffany G. , Zhan Zhikun , Li Yi , Tung Steve C.H. , Tang William C. , Li Wen J. 
Published: March 2017

AbstractIn this paper, we describe a novel and simple process for the fabrication of all-transparent and encapsulated polymeric nanofluidic devices using nano-indentation lithography. First, a nanomechanical probe is used to ‘scratch’ nanoscale channels on polymethylmethacrylate (PMMA) substrates with sufficiently high hardness. Next, polydimethylsiloxane (PDMS) is used twice to duplicate the nanochannels onto PDMS substrates from the ‘nano-scratched’ PMMA substrates. A number of experiments are conducted to explore the relationships between the nano-indentation parameters and the nanochannel dimensions and to control the aspect ratio of the fabricated nanochannels. In addition, traditional photolithography combined with soft lithography is employed to fabricate microchannels on another PDMS ‘cap’ substrate. After manually aligning the substrates, all uncovered channels on two separate PDMS substrates are bonded to achieve a sealed and transparent nanofluidic device, which makes the dimensional transition from microscale to nanoscale feasible. The smallest dimensions of the achievable nanochannels that we have demonstrated thus far are of ~20 nm depth and ~800 nm width, with lengths extendable beyond 100 μm. Fluid flow experiments are performed to verify the reliability of the device. Two types of colloidal solution are used to visualize the fluid flow through the nanochannels, that is, ethanol is mixed with gold colloid or fluorescent dye (fluorescein isothiocyanate), and the flow rate and filling time of liquid in the nanochannels are estimated based on time-lapsed image data. The simplicity of the fabrication process, bio-compatibility of the polymer substrates, and optical transparency of the nanochannels for flow visualization are key characteristics of this approach that will be very useful for nanofluidic and biomolecular research applications in the future.
Terahertz and mid-infrared plasmons in three-dimensional nanoporous graphene
Authors: D’Apuzzo Fausto , Piacenti Alba R. , Giorgianni Flavio , Autore Marta , Guidi Mariangela Cestelli , Marcelli Augusto , Schade Ulrich , Ito Yoshikazu , Chen Mingwei , Lupi Stefano 
Published: March 2017

AbstractTwo-dimensional (2D) graphene emerged as an outstanding material for plasmonic and photonic applications due to its charge-density tunability, high electron mobility, optical transparency and mechanical flexibility. Recently, novel fabrication processes have realised a three-dimensional (3D) nanoporous configuration of high-quality monolayer graphene which provides a third dimension to this material. In this work, we investigate the optical behaviour of nanoporous graphene by means of terahertz and infrared spectroscopy. We reveal the presence of intrinsic 2D Dirac plasmons in 3D nanoporous graphene disclosing strong plasmonic absorptions tunable from terahertz to mid-infrared via controllable doping level and porosity. In the far-field the spectral width of these absorptions is large enough to cover most of the mid-Infrared fingerprint region with a single plasmon excitation. The enhanced surface area of nanoporous structures combined with their broad band plasmon absorption could pave the way for novel and competitive nanoporous-graphene based plasmonic-sensors.
Positive affect, surprise, and fatigue are correlates of network flexibility
Authors: Betzel Richard F. , Satterthwaite Theodore D. , Gold Joshua I. , Bassett Danielle S. 
Published: March 2017

AbstractAdvances in neuroimaging have made it possible to reconstruct functional networks from the activity patterns of brain regions distributed across the cerebral cortex. Recent work has shown that flexible reconfiguration of human brain networks over short timescales supports cognitive flexibility and learning. However, modulating network flexibility to enhance learning requires an understanding of an as-yet unknown relationship between flexibility and brain state. Here, we investigate the relationship between network flexibility and affect, leveraging an unprecedented longitudinal data set. We demonstrate that indices associated with positive mood and surprise are both associated with network flexibility – positive mood portends a more flexible brain while increased levels of surprise portend a less flexible brain. In both cases, these relationships are driven predominantly by a subset of brain regions comprising the somatomotor system. Our results simultaneously suggest a network-level mechanism underlying learning deficits in mood disorders as well as a potential target – altering an individual’s mood or task novelty – to improve learning.
Anomalous evolution of broadband optical absorption reveals dynamic solid state reorganization during eumelanin build-up in thin films
Authors: Bonavolontà Carmela , Lisio Corrado de , d’Ischia Marco , Maddalena Pasqualino , Manini Paola , Pezzella Alessandro , Valentino Massimo 
Published: March 2017

AbstractThe origin of eumelanin optical properties remains a formidable conundrum preventing a detailed understanding of the complex photo-protective role of these widespread natural pigments and the rational design of innovative bioinspired materials for optoelectronic applications. Here we report the unusual kinetic and thickness-dependent evolution of the optical properties of black eumelanin polymers generated by spontaneous aerial polymerization of 5,6-dihydroxyindole (DHI) thin films (0.1–1 μm), consistent with peculiar solid state reorganization mechanisms governing broadband absorption. The complete reversal of eumelanin UV-visible transmittance spectrum curvature on passing from 0.2 to 0.5 μm thick films, the marked increase in visible extinction coefficients with increasing film thickness and the higher UV extinction coefficients in slowly vs. rapidly generated polymers concur to support distinct dynamic regimes of solid-state molecular reorganization at the nanoscale level and to do affect the development of broadband visible absorption. Solid state control of molecular reorganization disclosed herein may delineate new rational strategies for tuning optical properties in eumelanin thin films for optoelectronic applications.
A Circulating MicroRNA Signature Capable of Assessing the Risk of Hepatocellular Carcinoma in Cirrhotic Patients
Authors: Huang Ya-Hui , Liang Kung-Hao , Chien Rong-Nan , Hu Tsung-Hui , Lin Kwang-Huei , Hsu Chao-Wei , Lin Chih-Lang , Pan Tai-Long , Ke Po-Yuan , Yeh Chau-Ting 
Published: March 2017

AbstractWith the availability of potent antiviral therapies, complete suppression of hepatitis B virus (HBV) replication and total eradication of hepatitis C virus (HCV) can now be achieved. Despite these advances, hepatocellular carcinoma (HCC) still develops in a substantial proportion of cirrhotic patients, suggesting that host factors remain critical. Dysregulation of miRNAs is noted in many cancers, and circulating miRNAs can be readily assayed. In this study, we aimed to develop a circulating miRNA signature to assess the risk of HCC in cirrhotic patients. We first discovered that HBV- and HCV-related cirrhotic patients had distinguishable circulating miRNA profiles. A cohort of 330 cirrhotic patients was then compared against a cohort of 42 early HCC patients with complete remission. A score comprising 5 miRNAs and a binary etiology variable was established that was capable of differentiating between these two groups (AUC = 72.5%, P < 0.001). The 330 cirrhotic patients were further stratified into high- and low-risk groups, and all patients were longitudinally followed for 752 (11–891) days. Of them, 19 patients developed HCC. The high-risk group had significantly higher cumulative HCC incidence (P = 0.038). In summary, a circulating miRNA-based score was developed that is capable of assessing HCC risks in cirrhotic patients.
The Evolution and Expression Pattern of Human Overlapping lncRNA and Protein-coding Gene Pairs
Authors: Ning Qianqian , Li Yixue , Wang Zhen , Zhou Songwen , Sun Hong , Yu Guangjun 
Published: March 2017

AbstractLong non-coding RNA overlapping with protein-coding gene (lncRNA-coding pair) is a special type of overlapping genes. Protein-coding overlapping genes have been well studied and increasing attention has been paid to lncRNAs. By studying lncRNA-coding pairs in human genome, we showed that lncRNA-coding pairs were more likely to be generated by overprinting and retaining genes in lncRNA-coding pairs were given higher priority than non-overlapping genes. Besides, the preference of overlapping configurations preserved during evolution was based on the origin of lncRNA-coding pairs. Further investigations showed that lncRNAs promoting the splicing of their embedded protein-coding partners was a unilateral interaction, but the existence of overlapping partners improving the gene expression was bidirectional and the effect was decreased with the increased evolutionary age of genes. Additionally, the expression of lncRNA-coding pairs showed an overall positive correlation and the expression correlation was associated with their overlapping configurations, local genomic environment and evolutionary age of genes. Comparison of the expression correlation of lncRNA-coding pairs between normal and cancer samples found that the lineage-specific pairs including old protein-coding genes may play an important role in tumorigenesis. This work presents a systematically comprehensive understanding of the evolution and the expression pattern of human lncRNA-coding pairs.
Increased soil nutrition and decreased light intensity drive species loss after eight years grassland enclosures
Authors: Li Jingpeng , Zheng Zhirong , Xie Hongtao , Zhao Nianxi , Gao Yubao 
Published: March 2017

AbstractEnclosures (fenced, grazing or clipping) within a certain period of years are the most common tools for restoration of degraded grasslands in temperate regions. Short-term enclosures can improve biodiversity and productivity by effectively relieving grazing pressure, while long-term enclosures can reduce species diversity. We therefore carried out a field experiment to investigate the specific causes of the reduced species diversity in Hulunbeier grassland of northern China. After eight years of enclosure, the significantly increased soil available nitrogen (AN) and available phosphorus (AvP) in enclosure community reduced nitrogen (N) limitation but most vegetation was still N limited. Many environmental factors led to decreased species richness, but increased soil AN and decreased light intensity at the community bottom were the most significant ones. Community density decreased independently of soil nutrition but significantly related to decreased species richness. Density of dominant canopy species increased, while dominant understory species decreased during assemblage-level thinning; therefore, the random-loss hypothesis was not supported. The dominant understory species responded to lower light availability by increasing their height, leaf area, and chlorophyll content. Moreover, our results were expected to provide some specific guidance for the restoration mode selection of degraded grasslands in northern China.
Mutual information model for link prediction in heterogeneous complex networks
Authors: Shakibian Hadi , Moghadam Charkari Nasrollah 
Published: March 2017

AbstractRecently, a number of meta-path based similarity indices like PathSim, HeteSim, and random walk have been proposed for link prediction in heterogeneous complex networks. However, these indices suffer from two major drawbacks. Firstly, they are primarily dependent on the connectivity degrees of node pairs without considering the further information provided by the given meta-path. Secondly, most of them are required to use a single and usually symmetric meta-path in advance. Hence, employing a set of different meta-paths is not straightforward. To tackle with these problems, we propose a mutual information model for link prediction in heterogeneous complex networks. The proposed model, called as Meta-path based Mutual Information Index (MMI), introduces meta-path based link entropy to estimate the link likelihood and could be carried on a set of available meta-paths. This estimation measures the amount of information through the paths instead of measuring the amount of connectivity between the node pairs. The experimental results on a Bibliography network show that the MMI obtains high prediction accuracy compared with other popular similarity indices.
Influenza A virus hemagglutinin and neuraminidase act as novel motile machinery
Authors: Sakai Tatsuya , Nishimura Shin I. , Naito Tadasuke , Saito Mineki 
Published: March 2017

AbstractInfluenza A virus (IAV) membrane proteins hemagglutinin (HA) and neuraminidase (NA) are determinants of virus infectivity, transmissibility, pathogenicity, host specificity, and major antigenicity. HA binds to a virus receptor, a sialoglycoprotein or sialoglycolipid, on the host cell and mediates virus attachment to the cell surface. The hydrolytic enzyme NA cleaves sialic acid from viral receptors and accelerates the release of progeny virus from host cells. In this study, we identified a novel function of HA and NA as machinery for viral motility. HAs exchanged binding partner receptors iteratively, generating virus movement on a receptor-coated glass surface instead of a cell surface. The virus movement was also dependent on NA. Virus movement mediated by HA and NA resulted in a three to four-fold increase in virus internalisation by cultured cells. We concluded that cooperation of HA and NA moves IAV particles on a cell surface and enhances virus infection of host cells.
Experimental demonstration of a fully inseparable quantum state with nonlocalizable entanglement
Authors: Mičuda M. , Koutný D. , Miková M. , Straka I. , Ježek M. , Mišta L. 
Published: March 2017

AbstractLocalizability of entanglement in fully inseparable states is a key ingredient of assisted quantum information protocols as well as measurement-based models of quantum computing. We investigate the existence of fully inseparable states with nonlocalizable entanglement, that is, with entanglement which cannot be localized between any pair of subsystems by any measurement on the remaining part of the system. It is shown, that the nonlocalizable entanglement occurs already in suitable mixtures of a three-qubit GHZ state and white noise. Further, we generalize this set of states to a two-parametric family of fully inseparable three-qubit states with nonlocalizable entanglement. Finally, we demonstrate experimentally the existence of nonlocalizable entanglement by preparing and characterizing one state from the family using correlated single photons and linear optical circuit.
HDAC1-3 inhibitor MS-275 enhances IL10 expression in RAW264.7 macrophages and reduces cigarette smoke-induced airway inflammation in mice
Authors: Leus Niek G. J. , van den Bosch Thea , van der Wouden Petra E. , Krist Kim , Ourailidou Maria E. , Eleftheriadis Nikolaos , Kistemaker Loes E. M. , Bos Sophie , Gjaltema Rutger A. F. , Mekonnen Solomon A. , Bischoff Rainer , Gosens Reinoud , Haisma Hidde J. , Dekker Frank J. 
Published: March 2017

AbstractChronic obstructive pulmonary disease (COPD) constitutes a major health burden. Studying underlying molecular mechanisms could lead to new therapeutic targets. Macrophages are orchestrators of COPD, by releasing pro-inflammatory cytokines. This process relies on transcription factors such as NF-κB, among others. NF-κB is regulated by lysine acetylation; a post-translational modification installed by histone acetyltransferases and removed by histone deacetylases (HDACs). We hypothesized that small molecule HDAC inhibitors (HDACi) targeting class I HDACs members that can regulate NF-κB could attenuate inflammatory responses in COPD via modulation of the NF-κB signaling output. MS-275 is an isoform-selective inhibitor of HDAC1-3. In precision-cut lung slices and RAW264.7 macrophages, MS-275 upregulated the expression of both pro- and anti-inflammatory genes, implying mixed effects. Interestingly, anti-inflammatory IL10 expression was upregulated in these model systems. In the macrophages, this was associated with increased NF-κB activity, acetylation, nuclear translocation, and binding to the IL10 promoter. Importantly, in an in vivo model of cigarette smoke-exposed C57Bl/6 mice, MS-275 robustly attenuated inflammatory expression of KC and neutrophil influx in the lungs. This study highlights for the first time the potential of isoform-selective HDACi for the treatment of inflammatory lung diseases like COPD.
Rational Design of 1-D Co3O4 Nanofibers@Low content Graphene Composite Anode for High Performance Li-Ion Batteries
Authors: Cho Su-Ho , Jung Ji-Won , Kim Chanhoon , Kim Il-Doo 
Published: March 2017

AbstractCobalt oxide that has high energy density, is the next-generation candidate as the anode material for LIBs. However, the practical use of Co3O4 as anode material has been hindered by limitations, especially, low electrical conductivity and pulverization from large volume change upon cycling. These features lead to hindrance to its electrochemical properties for lithium-ion batteries. To improve electrochemical properties, we synthesized one-dimensional (1-D) Co3O4 nanofibers (NFs) overed with reduced graphene oxide (rGO) sheets by electrostatic self-assembly (Co3O4 NFs@rGO). The flexible graphene oxide sheets not only prevent volume changes of active materials upon cycling as a clamping layer but also provide efficient electrical pathways by three-dimensional (3-D) network architecture. When applied as an anode for LIBs, the Co3O4 NFs@rGO exhibits superior electrochemical performance: (i) high reversible capacity (615 mAh g−1 and 92% capacity retention after 400 cycles at 4.0 A g−1) and (ii) excellent rate capability. Herein, we highlighted that the enhanced conversion reaction of the Co3O4 NFs@rGO is attributed to effective combination of 1-D nanostructure and low content of rGO (~3.5 wt%) in hybrid composite.
Assortative Mating: Encounter-Network Topology and the Evolution of Attractiveness
Authors: Dipple S. , Jia T. , Caraco T. , Korniss G. , Szymanski B. K. 
Published: March 2017

AbstractWe model a social-encounter network where linked nodes match for reproduction in a manner depending probabilistically on each node’s attractiveness. The developed model reveals that increasing either the network’s mean degree or the “choosiness” exercised during pair formation increases the strength of positive assortative mating. That is, we note that attractiveness is correlated among mated nodes. Their total number also increases with mean degree and selectivity during pair formation. By iterating over the model’s mapping of parents onto offspring across generations, we study the evolution of attractiveness. Selection mediated by exclusion from reproduction increases mean attractiveness, but is rapidly balanced by skew in the offspring distribution of highly attractive mated pairs.
Liposomes loaded with bioactive lipids enhance antibacterial innate immunity irrespective of drug resistance
Authors: Poerio Noemi , Bugli Francesca , Taus Francesco , Santucci Marilina B. , Rodolfo Carlo , Cecconi Francesco , Torelli Riccardo , Varone Francesco , Inchingolo Riccardo , Majo Fabio , Lucidi Vincenzina , Mariotti Sabrina , Nisini Roberto , Sanguinetti Maurizio , Fraziano Maurizio 
Published: March 2017

AbstractPhagocytosis is a key mechanism of innate immunity, and promotion of phagosome maturation may represent a therapeutic target to enhance antibacterial host response. Phagosome maturation is favored by the timely and coordinated intervention of lipids and may be altered in infections. Here we used apoptotic body-like liposomes (ABL) to selectively deliver bioactive lipids to innate cells, and then tested their function in models of pathogen-inhibited and host-impaired phagosome maturation. Stimulation of macrophages with ABLs carrying phosphatidic acid (PA), phosphatidylinositol 3-phosphate (PI3P) or PI5P increased intracellular killing of BCG, by inducing phagosome acidification and ROS generation. Moreover, ABLs carrying PA or PI5P enhanced ROS-mediated intracellular killing ofPseudomonas aeruginosa, in macrophages expressing a pharmacologically-inhibited or a naturally-mutated cystic fibrosis transmembrane conductance regulator. Finally, we show that bronchoalveolar lavage cells from patients with drug-resistant pulmonary infections increased significantly their capacity to killin vivoacquired bacterial pathogens whenex vivostimulated with PA- or PI5P-loaded ABLs. Altogether, these results provide the proof of concept of the efficacy of bioactive lipids delivered by ABL to enhance phagosome maturation dependent antimicrobial response, as an additional host-directed strategy aimed at the control of chronic, recurrent or drug-resistant infections.
Zinc deficiency and low enterocyte zinc transporter expression in human patients with autism related mutations in SHANK3
Authors: Pfaender Stefanie , Sauer Ann Katrin , Hagmeyer Simone , Mangus Katharina , Linta Leonhard , Liebau Stefan , Bockmann Juergen , Huguet Guillaume , Bourgeron Thomas , Boeckers Tobias M. , Grabrucker Andreas M. 
Published: March 2017

AbstractPhelan McDermid Syndrome (PMDS) is a genetic disorder characterized by features of Autism spectrum disorders. Similar to reports of Zn deficiency in autistic children, we have previously reported high incidence of Zn deficiency in PMDS. However, the underlying mechanisms are currently not well understood. Here, using inductively coupled plasma mass-spectrometry to measure the concentration of Zinc (Zn) and Copper (Cu) in hair samples from individuals with PMDS with 22q13.3 deletion including SHANK3 (SH3 and multiple ankyrin repeat domains 3), we report a high rate of abnormally low Zn/Cu ratios. To investigate possible underlying mechanisms, we generated enterocytes from PMDS patient-derived induced pluripotent stem cells and used Caco-2 cells with knockdown of SHANK3. We detected decreased expression of Zn uptake transporters ZIP2 and ZIP4 on mRNA and protein level correlating with SHANK3 expression levels, and found reduced levels of ZIP4 protein co-localizing with SHANK3 at the plasma membrane. We demonstrated that especially ZIP4 exists in a complex with SHANK3. Furthermore, we performed immunohistochemistry on gut sections from Shank3αβ knockout mice and confirmed a link between enterocytic SHANK3, ZIP2 and ZIP4. We conclude that apart from its well-known role in the CNS, SHANK3 might play a specific role in the GI tract.
Cyclophilins and nucleoporins are required for infection mediated by capsids from circulating HIV-2 primary isolates
Authors: Mamede João I. , Damond Florence , Bernardo Ariel de , Matheron Sophie , Descamps Diane , Battini Jean-Luc , Sitbon Marc , Courgnaud Valérie 
Published: March 2017

AbstractHIV-2 groups have emerged from sooty mangabey SIV and entered the human population in Africa on several separate occasions. Compared to world pandemic HIV-1 that arose from the chimpanzee SIVcpz virus, the SIVsm-derived HIV-2, largely confined to West Africa, is less replicative, less transmissible and less pathogenic. Here, we evaluated the interactions between host cellular factors, which control HIV-1 infection and target the capsid, and HIV-2 capsids obtained from primary isolates from patients with different disease progression status. We showed that, like HIV-1, all HIV-2 CA we tested exhibited a dependence on cyclophilin A. However, we observed no correlation between HIV-2 viremia and susceptibility to hu-TRIM5alpha or dependence to CypA. Finally, we found that all CA from HIV-2 primary isolates exploit Nup358 and Nup153 for nucleus transposition. Altogether, these findings indicate that the ability to use the two latter nucleoporins is essential to infection of human cells for both HIV-1 and HIV-2. This dependence provides another molecular target that could be used for antiviral strategies against both HIV-1 and 2, based on both nucleoporins.