bluuebunny/crossref_metadata_2025 huggingface dataset:
Erratum: Human pressures and ecological status of European rivers
Authors: Grizzetti B. , Pistocchi A. , Liquete C. , Udias A. , Bouraoui F. , van de Bund W.
Published: July 2017

A correction to this article has been published and is linked from the HTML version of this paper. The error has not been fixed in the paper.
Heterogeneity of tumor-infiltrating lymphocytes ascribed to local immune status rather than neoantigens by multi-omics analysis of glioblastoma multiforme
Authors: Feng Lin , Qian Haipeng , Yu Xuexin , Liu Kan , Xiao Ting , Zhang Chengli , Kuang Manchao , Cheng Shujun , Li Xueji , Wan Jinghai , Zhang Kaitai
Published: July 2017

Hypothetically, intratumoral genomic heterogeneity has the potential to foster tumor-infiltrating lymphocyte (TIL) diversity; however, no study has directly tested this hypothesis by simultaneously investigating somatic mutations, TIL diversity, and immune response activity. Thus, we performed whole-exome sequencing, immune repertoire sequencing and gene expression on ten spatially separated tumor samples obtained from two tumor masses excised from a glioblastoma multiforme (GBM) patient, and we included peripheral blood as control. We found that although the multi-region samples from one tumor shared more common mutations than those from different tumors, the TIL populations did not. TIL repertoire diversity did not significantly correlate with the number of non-synonymous mutations; however, TIL diversity was highly correlated with local immune activity, as the pathways were all immune-related pathways that highly positive correlated with local TIL diversity. Twenty-three genes with expression largely unaffected by the intratumor heterogeneity were extracted from these pathways. Fifty GBM patients were stratified into two clusters by the expression of these genes with significant difference in prognosis. This finding was validated by The Cancer Genome Atlas (TCGA) GBM dataset, which indicated that despite the heterogeneity of intra-tumor immune status, the overall level of the immune response in GBM could be connected with prognosis.
Optoacoustic micro-tomography at 100 volumes per second
Authors: Deán-Ben X. Luís , López-Schier Hernán , Razansky Daniel
Published: July 2017

Optical microscopy remains a fundamental tool for modern biological discovery owing to its excellent spatial resolution and versatile contrast in visualizing cellular and sub-cellular structures. Yet, the time domain is paramount for the observation of biological dynamics in living systems. Commonly, acquisition of microscopy data involves scanning of a spherically- or cylindrically-focused light beam across the imaged volume, which significantly limits temporal resolution in 3D. Additional complications arise from intense light scattering of biological tissues, further restraining the effective penetration depth and field of view of optical microscopy techniques. To overcome these limitations, we devised a fast optoacoustic micro-tomography (OMT) approach based on simultaneous acquisition of 3D image data with a high-density hemispherical ultrasound array having effective detection bandwidth beyond 25 MHz. We demonstrate fast three-dimensional imaging of freely-swimming zebrafish larvae, achieving 3D imaging speed of 100 volumes per second with isotropic spatial resolution approaching the dimensions of large cells across a field of view exceeding 50mm3. As opposed to other microscopy techniques based on optical contrast, OMT resolves optical absorption acoustically using unfocused light excitation. Thus, no penetration barriers are imposed by light scattering in deep tissues, suggesting it as a powerful approach for multi-scale functional and molecular imaging applications.
Probing helicity and the topological origins of helicity via non-local Hanbury-Brown and Twiss correlations
Authors: Mani Arjun , Benjamin Colin
Published: July 2017

Quantum Hall edge modes are chiral while quantum spin Hall edge modes are helical. However, unlike chiral edge modes which always occur in topological systems, quasi-helical edge modes may arise in a trivial insulator too. These trivial quasi-helical edge modes are not topologically protected and therefore need to be distinguished from helical edge modes arising due to topological reasons. Earlier conductance measurements were used to identify these helical states, in this work we report on the advantage of using the non local shot noise as a probe for the helical nature of these states as also their topological or otherwise origin and compare them with chiral quantum Hall states. We see that in similar set-ups affected by same degree of disorder and inelastic scattering, non local shot noise “HBT” correlations can be positive for helical edge modes but are always negative for the chiral quantum Hall edge modes. Further, while trivial quasi-helical edge modes exhibit negative non-local”HBT” charge correlations, topological helical edge modes can show positive non-local “HBT” charge correlation. We also study the non-local spin correlations and Fano factor for clues as regards both the distinction between chirality/helicity as well as the topological/trivial dichotomy for helical edge modes.
Microfluidic sorting of intrinsically magnetic cells under visual control
Authors: Myklatun Ahne , Cappetta Michele , Winklhofer Michael , Ntziachristos Vasilis , Westmeyer Gil G.
Published: July 2017

Magnetic cell sorting provides a valuable complementary mechanism to fluorescent techniques, especially if its parameters can be fine-tuned. In addition, there has recently been growing interest in studying naturally occurring magnetic cells and genetic engineering of cells to render them magnetic in order to control molecular processes via magnetic fields. For such approaches, contamination-free magnetic separation is an essential capability. We here present a robust and tunable microfluidic sorting system in which magnetic gradients of up to 1700 T/m can be applied to cells flowing through a sorting channel by reversible magnetization of ferrofluids. Visual control of the sorting process allowed us to optimize sorting efficiencies for a large range of sizes and magnetic moments of cells. Using automated quantification based on imaging of fluorescent markers, we showed that macrophages containing phagocytosed magnetic nanoparticles, with cellular magnetic dipole moments on the order of 10 fAm2, could be sorted with an efficiency of 90 ± 1%. Furthermore, we successfully sorted intrinsically magnetic magnetotactic bacteria with magnetic moments of 0.1 fAm2. In distinction to column-based magnetic sorting devices, microfluidic systems can prevent sample contact with superparamagnetic material. This ensures contamination-free separation of naturally occurring or bioengineered magnetic cells and is essential for downstream characterization of their properties.
Blockade of dengue virus infection and viral cytotoxicity in neuronal cells in vitro and in vivo by targeting endocytic pathways
Authors: Ho Min-Ru , Tsai Tsung-Ting , Chen Chia-Ling , Jhan Ming-Kai , Tsai Cheng-Chieh , Lee Yi-Chao , Chen Chun-Han , Lin Chiou-Feng
Published: July 2017

Dengue virus (DENV) infection in neuronal cells was speculated to trigger neuropathy. Herein, we determined the blockade of DENV infection by targeting endocytic pathways in vitro and in vivo. In DENV-infected mouse brains, we previously showed that viral proteins are expressed in neuronal cells around the hippocampus with accompanying neurotoxicity. DENV caused infection, including entry, double-stranded (ds)RNA replication, protein expression, and virus release, followed by cytotoxicity in the mouse neuronal Neuro-2a cell line. Pharmacologically blocking clathrin-mediated endocytosis of the DENV retarded viral replication. Targeting vacuolar-type H+-ATPase (V-ATPase)-based endosomal acidification effectively blocked the DENV replication process, but had no direct effect on viral translation. Blockade of the clathrin- and V-ATPase-based endocytic pathways also attenuated DENV-induced neurotoxicity. Inhibiting endosomal acidification effectively retarded DENV infection, acute viral encephalitis, and mortality. These results demonstrate that clathrin mediated endocytosis of DENV followed by endosomal acidification-dependent viral replication in neuronal cells, which can lead to neurotoxicity.
Membrane Perfusion of Hydrophobic Substances Around Channels Embedded in the Contact Bubble Bilayer
Authors: Iwamoto Masayuki , Oiki Shigetoshi
Published: July 2017

In fluidic biomembranes, lipids and membrane proteins diffuse restlessly, and lipid compositions change steadily. To mimic dynamic behavior of the biomembranes, a method for introducing rapid changes in the constituents in the lipid bilayer was developed. In contact bubble bilayers (CBB), as a water-in-oil droplet bilayer system, the bilayer hydrophobic interior is contiguous with the bulk oil phase. Making use of this geometrical feature as an access route, hydrophobic substances were administered into the bilayer. Polytheonamide B, a cytotoxic hydrophobic peptide, was applied, and oriented incorporation and relevant single-channel current recordings were enabled. Nystatin was pre-loaded in the CBB, and sterol perfusion exhibited slow development of the macroscopic current. On the contrary, the reconstituted KcsA potassium channels immediately attenuate the channel activity when cholesterol was applied. This oil-phase route in the CBB allows rapid perfusion of hydrophobic substances around the bilayer-embedded channels during continuous recordings of channel currents.
An atypical strictosidine synthase, OsSTRL2, plays key roles in anther development and pollen wall formation in rice
Authors: Zou Ting , Li Shuangcheng , Liu Mingxing , Wang Tao , Xiao Qiao , Chen Dan , Li Qiao , Liang Yanling , Zhu Jun , Liang Yueyang , Deng Qiming , Wang Shiquan , Zheng Aiping , Wang Lingxia , Li Ping
Published: July 2017

Strictosidine synthase (STR) plays an important role in the biosynthesis of terpenoid indole alkaloids (TIAs) and is expressed in a range of active meristematic tissues of higher plants. STR proteins are involved in different physiological and biochemical pathways. However, the function of STR proteins in rice development remains poorly understood. In this study, we identified 21 possible STR-like (OsSTRL) family members in rice genome and found that only one gene, OsSTRL2, exhibited a pre-emergency specific florescence expression pattern. Tissue-specific expression profile analysis, β-glucuronidase histochemical (GUS) staining and RNA in situ hybridization confirmed that OsSTRL2 was highly expressed in tapetal cells and microspores. Comparative protein sequence analysis indicated that OsSTRL2 lacked the key catalytic residue found in a typical STR (STR1), although it possessed conserved β-propellers and α-helices formed the basic structure of STR1. OsSTRL2 knockout mutant resulted to male sterility because of the defects in anther development and pollen wall formation. Subcellular localization of OsSTRL2-YFP revealed that the OsSTRL2 protein was primarily localized in the endoplasmic reticulum (ER). Therefore, OsSTRL2 is an atypical strictosidine synthase that plays crucial roles in regulating anther development and pollen wall formation in rice.
GFusion: an Effective Algorithm to Identify Fusion Genes from Cancer RNA-Seq Data
Authors: Zhao Jian , Chen Qi , Wu Jing , Han Ping , Song Xiaofeng
Published: July 2017

Fusion gene derived from genomic rearrangement plays a key role in cancer initiation. The discovery of novel gene fusions may be of significant importance in cancer diagnosis and treatment. Meanwhile, next generation sequencing technology provide a sensitive and efficient way to identify gene fusions in genomic levels. However, there are still many challenges and limitations remaining in the existing methods which only rely on unmapped reads or discordant alignment fragments. In this work we have developed GFusion, a novel method using RNA-Seq data, to identify the fusion genes. This pipeline performs multiple alignments and strict filtering algorithm to improve sensitivity and reduce the false positive rate. GFusion successfully detected 34 from 43 previously reported fusions in four cancer datasets. We also demonstrated the effectiveness of GFusion using 24 million 76 bp paired-end reads simulation data which contains 42 artificial fusion genes, among which GFusion successfully discovered 37 fusion genes. Compared with existing methods, GFusion presented higher sensitivity and lower false positive rate. The GFusion pipeline can be accessed freely for non-commercial purposes at: https://github.com/xiaofengsong/GFusion.
Using latent class cluster analysis to screen high risk clusters of birth defects between 2009 and 2013 in Northwest China
Authors: Pei Leilei , Zeng Lingxia , Zhao Yaling , Wang Duolao , Yan Hong
Published: July 2017

In the study, we aimed to explore the synergistic effects of multiple risk factors on birth defects, and examine temporal trend of the synergistic effects over time. Two cross-sectional surveys conducted in 2009 and 2013 were merged and then latent class cluster analysis and generalized linear Poisson model were used. A total of 9085 and 29094 young children born within the last three years and their mothers were enrolled in 2009 and 2013 respectively. Three latent maternal exposure clusters were determined: a high-risk, a moderate-risk, and a low-risk cluster (88.97%, 1.49%, 9.54% in 2009 and 82.42%, 3.39%, 14.19% in 2013). The synthetic effects of maternal exposure to multiple risk factors could increase the risk of overall birth defects and cardiovascular system malformation among live births, and this risk is significantly higher in high-risk cluster than that in low-risk cluster. After adjusting for confounding factors using a generalized linear Poisson model, in high-risk cluster the prevalence of nervous system malformation decreased by approximately 2.71%, and the proportion of cardiovascular system malformation rose by 0.92% from 2009 to 2013. The Chinese government should make great efforts to provide primary prevention for those on high-risk cluster as a priority target population.
Epauletted fruit bats display exceptionally high infections with a Hepatocystis species complex in South Sudan
Authors: Schaer Juliane , Perkins Susan L. , Ejotre Imran , Vodzak Megan E. , Matuschewski Kai , Reeder DeeAnn M.
Published: July 2017

Hepatocystis parasites are closely related to mammalian Plasmodium species, the causative agents of malaria. Despite the close phylogenetic relationship, Hepatocystis parasites lack the intermittent erythrocytic replication cycles, the signature and exclusive cause of malaria-related morbidity and mortality. Hepatocystis population expansion in the mammalian host is thought to be restricted to the pre-erythrocytic liver phase. Complete differentiation of first generation blood stages into sexual stages for subsequent vector transmission indicates alternative parasite/host co-evolution. In this study, we identified a region of exceptionally high prevalence of Hepatocystis infections in Old World fruit bats in South Sudan. Investigations over the course of five consecutive surveys revealed an average of 93 percent prevalence in four genera of African epauletted fruit bats. We observed a clear seasonal pattern and tolerance of high parasite loads in these bats. Phylogenetic analyses revealed several cryptic Hepatocystis parasite species and, in contrast to mammalian Plasmodium parasites, neither host specificity nor strong geographical patterns were evident. Together, our study provides evidence for Pan-African distribution and local high endemicity of a Hepatocystis species complex in Pteropodidae.
Overall process of using a valerate-dominant sludge hydrolysate to produce high-quality polyhydroxyalkanoates (PHA) in a mixed culture
Authors: Hao Jiuxiao , Wang Xiujin , Wang Hui
Published: July 2017

The overall process of polyhydroxyalkanoates (PHA) production in a mixed culture fed by thermophilic fermented valerate-dominant sludge hydrolysate with high-level soluble organics (proteins and carbohydrates) and nutrients (nitrogen and phosphorus) was investigated in this study. The valerate-dominant hydrolysate was fed to enrich a PHA culture with an increasing concentration, and the enriched culture displayed a strong PHA-producing capacity under feast-famine conditions. Valerate in the feedstock was preferentially utilized over acetate and butyrate, and its uptake correlated with the production of 3-hydroxyvalerate (3HV) and 3-hydroxy-2-methylvalerate (3H2MV). The maximum PHA content (42.31%) was highest to date in a mixed culture with complex feedstock, and the PHA consisted of 3-hydroxybutyrate (3HB), 3HV, 3H2MV at 68.4, 23.7, 7.9 mmol C%. PHA production was inhibited when the nutrients exceeded a certain limit. Microbial analysis revealed that valerate-dominant feedstock caused Delftia (53%) to become the prevailing group over other PHA-producing bacteria. For long-term operation, 75% of the biomass at the end of feast phase was collected for PHA recovery, and the entire process exhibited a potential to produce 5 g PHA from 1 kg sludge. These findings indicate that the complex valerate-dominant sludge hydrolysate can be used to stably produce PHA containing high 3HV and 3H2MV.
Novel electrochemical route to cleaner fuel dimethyl ether
Authors: Cassone Giuseppe , Pietrucci Fabio , Saija Franz , Guyot François , Sponer Jiri , Sponer Judit E. , Saitta A. Marco
Published: July 2017

Methanol, the simplest alcohol, and dimethyl ether, the simplest ether, are central compounds in the search for alternative “green” combustion fuels. In fact, they are generally considered as the cornerstones of the envisaged “Methanol Economy” scenario, as they are able to efficiently produce energy in an environmentally friendly manner. However, despite a massive amount of research in this field, the synthesis of dimethyl ether from liquid methanol has never so far been reported. Here we present a computational study, based on ab initio Molecular Dynamics, which suggests a novel synthesis route to methanol dehydration – leading thus to the dimethyl ether synthesis – through the application of strong electric fields. Besides proving the impressive catalytic effects afforded by the field, our calculations indicate that the obtained dimethyl ether is stable and that it can be progressively accumulated thanks to the peculiar chemical pathways characterising the methanol reaction network under electric field. These results suggest that the experimental synthesis of dimethyl ether from liquid methanol could be achieved, possibly in the proximity of field emitter tips.
Effects of elevated CO2 on phytoplankton during a mesocosm experiment in the southern eutrophicated coastal water of China
Authors: Liu Xin , Li Yan , Wu Yaping , Huang Bangqin , Dai Minhan , Fu Feixue , Hutchins David A. , Gao Kunshan
Published: July 2017

There is a growing consensus that the ongoing increase in atmospheric CO2 level will lead to a variety of effects on marine phytoplankton and ecosystems. However, the effects of CO2 enrichment on eutrophic coastal waters are still unclear, as are the complex mechanisms coupled to the development of eutrophication. Here, we report the first mesocosm CO2 perturbation study in a eutrophic subtropical bay during summer by investigating the effect of rising CO2 on a model artificial community consisting of well-characterized cultured diatoms (Phaeodactylum tricornutum and Thalassiosira weissflogii) and prymnesiophytes (Emiliania huxleyi and Gephyrocapsa oceanica). These species were inoculated into triplicate 4 m3 enclosures with equivalent chlorophyll a (Chl-a) under present and higher partial pressures of atmospheric CO2 (pCO2 = 400 and 1000 ppmv). Diatom bloom events were observed in all enclosures, with enhanced organic carbon production and Chl-a concentrations under high CO2 treatments. Relative to the low CO2 treatments, the consumption of the dissolved inorganic nitrogen and uptake ratios of N/P and N/Si increased significantly during the bloom. These observed responses suggest more extensive and complex effects of higher CO2 concentrations on phytoplankton communities in coastal eutrophic environments.
PhosphoPredict: A bioinformatics tool for prediction of human kinase-specific phosphorylation substrates and sites by integrating heterogeneous feature selection
Authors: Song Jiangning , Wang Huilin , Wang Jiawei , Leier André , Marquez-Lago Tatiana , Yang Bingjiao , Zhang Ziding , Akutsu Tatsuya , Webb Geoffrey I. , Daly Roger J.
Published: July 2017

Protein phosphorylation is a major form of post-translational modification (PTM) that regulates diverse cellular processes.In silicomethods for phosphorylation site prediction can provide a useful and complementary strategy for complete phosphoproteome annotation. Here, we present a novel bioinformatics tool, PhosphoPredict, that combines protein sequence and functional features to predict kinase-specific substrates and their associated phosphorylation sites for 12 human kinases and kinase families, including ATM, CDKs, GSK-3, MAPKs, PKA, PKB, PKC, and SRC. To elucidate critical determinants, we identified feature subsets that were most informative and relevant for predicting substrate specificity for each individual kinase family. Extensive benchmarking experiments based on both five-fold cross-validation and independent tests indicated that the performance of PhosphoPredict is competitive with that of several other popular prediction tools, including KinasePhos, PPSP, GPS, and Musite. We found that combining protein functional and sequence features significantly improves phosphorylation site prediction performance across all kinases. Application of PhosphoPredict to the entire human proteome identified 150 to 800 potential phosphorylation substrates for each of the 12 kinases or kinase families. PhosphoPredict significantly extends the bioinformatics portfolio for kinase function analysis and will facilitate high-throughput identification of kinase-specific phosphorylation sites, thereby contributing to both basic and translational research programs.
Determination of the energy band gap of Bi2Se3
Authors: Martinez G. , Piot B. A. , Hakl M. , Potemski M. , Hor Y. S. , Materna A. , Strzelecka S. G. , Hruban A. , Caha O. , Novák J. , Dubroka A. , Drašar Č. , Orlita M.
Published: July 2017

Despite intensive investigations of Bi2Se3 in past few years, the size and nature of the bulk energy band gap of this well-known 3D topological insulator still remain unclear. Here we report on a combined magneto-transport, photoluminescence and infrared transmission study of Bi2Se3, which unambiguously shows that the energy band gap of this material is direct and reaches E
g
 = (220 ± 5) meV at low temperatures.
Load-separation curves for the contact of self-affine rough surfaces
Authors: Papangelo Antonio , Hoffmann Norbert , Ciavarella Michele
Published: July 2017

There are two main approximate theories in the contact of rough solids: Greenwood-Williamson asperity theories (GW) and Persson theories. Neither of them has been fully assessed so far with respect to load-separation curves. Focusing on the most important case of low fractal dimension (D
f
 = 2.2) with extensive numerical studies we find that: (i) Persson’s theory describes well the regime of intermediate pressures/contact area, but requires significant corrective factors: the latter depend also on upper wavevector cutoff of the roughness; hence, (ii) Persson’s theory does not predict the correct functional dependence on magnification; (iii) asperity theories in the discrete version even neglecting interaction effects are more appropriate in the range of relatively large separations, also to take into consideration of the large scatter in actual realization of the surface.
Spatial structure of TLR4 transmembrane domain in bicelles provides the insight into the receptor activation mechanism
Authors: Mineev Konstantin S. , Goncharuk Sergey A. , Goncharuk Marina V. , Volynsky Pavel E. , Novikova Ekaterina V. , Aresinev Alexander S.
Published: July 2017

Toll-like receptors (TLRs) play a key role in the innate and adaptive immune systems. While a lot of structural data is available for the extracellular and cytoplasmic domains of TLRs, and a model of the dimeric full-length TLR3 receptor in the active state was build, the conformation of the transmembrane (TM) domain and juxtamembrane regions in TLR dimers is still unclear. In the present work, we study the transmembrane and juxtamembrane parts of human TLR4 receptor using solution NMR spectroscopy in a variety of membrane mimetics, including phospholipid bicelles. We show that the juxtamembrane hydrophobic region of TLR4 includes a part of long TM α-helix. We report the dimerization interface of the TM domain and claim that long TM domains with transmembrane charged aminoacids is a common feature of human toll-like receptors. This fact is analyzed from the viewpoint of protein activation mechanism, and a model of full-length TLR4 receptor in the dimeric state has been proposed.
“Embodied Body Language”: an electrical neuroimaging study with emotional faces and bodies
Authors: Calbi Marta , Angelini Monica , Gallese Vittorio , Umiltà Maria Alessandra
Published: July 2017

To date, most investigations in the field of affective neuroscience mainly focused on the processing of facial expressions, overlooking the exploration of emotional body language (EBL), its capability to express our emotions notwithstanding. Few electrophysiological studies investigated the time course and the neural correlates of EBL and the integration of face and body emotion-related information. The aim of the present study was to investigate both the time course and the neural correlates underlying the integration of affective information conveyed by faces and bodies. We analysed EEG activities evoked during an expression matching task, requiring the judgment of emotional congruence between sequentially presented pairs of stimuli belonging to the same category (face-face or body-body), and between stimuli belonging to different categories (face-body or body-face). We focused on N400 time window and results showed that incongruent stimuli elicited a modulation of the N400 in all comparisons except for body-face condition. This modulation was mainly detected in the Middle Temporal Gyrus and within regions related to the mirror mechanism. More specifically, while the perception of incongruent facial expressions activates somatosensory-related representations, incongruent emotional body postures also require the activation of motor and premotor representations, suggesting a strict link between emotion and action.
Analysis of autophagy gene polymorphisms in Spanish patients with head and neck squamous cell carcinoma
Authors: Fernández-Mateos Javier , Seijas-Tamayo Raquel , Klain Juan Carlos Adansa , Borgoñón Miguel Pastor , Pérez-Ruiz Elisabeth , Mesía Ricard , del Barco Elvira , Coloma Carmen Salvador , Dominguez Antonio Rueda , Daroqui Javier Caballero , Fernández Ruiz Encarnación , Cruz-Hernández Juan Jesús , González-Sarmiento Rogelio
Published: July 2017

Head and neck squamous cell carcinoma (HNSCC) is the sixth cancer on incidence worldwide. Tobacco and alcohol consumption are the most classical risk factors associated with its development. Autophagy process has a dual effect both in tumourigenesis and tumour suppressing activity. To investigate the importance of this pathway in HNSCC susceptibility, a risk factor matched case-control association study was performed with four candidate polymorphisms in autophagy genes (ATG2B, ATG5, ATG10, ATG16L1). We found an association between the variant in ATG10 rs1864183 and a higher susceptibility to develop laryngeal cancer, ATG2B rs3759601 and pharyngeal cancer and ATG16L1 rs2241880 and oral carcinoma. ATG5 rs2245214 SNP was not associated with any location. Overall, our results indicate the importance of the autophagy pathway in the susceptibility of head and neck squamous cell carcinoma and demonstrate the heterogeneity between its locations encompassed under a single terminology.
Intravenous infusion of human bone marrow mesenchymal stromal cells promotes functional recovery and neuroplasticity after ischemic stroke in mice
Authors: Sammali Eliana , Alia Claudia , Vegliante Gloria , Colombo Valentina , Giordano Nadia , Pischiutta Francesca , Boncoraglio Giorgio B. , Barilani Mario , Lazzari Lorenza , Caleo Matteo , De Simoni Maria-Grazia , Gaipa Giuseppe , Citerio Giuseppe , Zanier Elisa R.
Published: July 2017

Transplantation of human bone marrow mesenchymal stromal cells (hBM-MSC) promotes functional recovery after stroke in animal models, but the mechanisms underlying these effects remain incompletely understood. We tested the efficacy of Good Manufacturing Practices (GMP) compliant hBM-MSC, injected intravenously 3.5 hours after injury in mice subjected to transient middle cerebral artery occlusion (tMCAo). We addressed whether hBM-MSC are efficacious and if this efficacy is associated with cortical circuit reorganization using neuroanatomical analysis of GABAergic neurons (parvalbumin; PV-positive cells) and perineuronal nets (PNN), a specialized extracellular matrix structure which acts as an inhibitor of neural plasticity. tMCAo mice receiving hBM-MSC, showed early and lasting improvement of sensorimotor and cognitive functions compared to control tMCAo mice. Furthermore, 5 weeks post-tMCAo, hBM-MSC induced a significant rescue of ipsilateral cortical neurons; an increased proportion of PV-positive neurons in the perilesional cortex, suggesting GABAergic interneurons preservation; and a lower percentage of PV-positive cells surrounded by PNN, indicating an enhanced plastic potential of the perilesional cortex. These results show that hBM-MSC improve functional recovery and stimulate neuroprotection after stroke. Moreover, the downregulation of “plasticity brakes” such as PNN suggests that hBM-MSC treatment stimulates plasticity and formation of new connections in the perilesional cortex.
Broadband and thin magnetic absorber with non-Foster metasurface for admittance matching
Authors: Mou Jinchao , Shen Zhongxiang
Published: July 2017

One of the long-standing and challenging problems in microwave engineering is the realization of ultra-wideband absorption using extremely-thin structures. Magnetic material can facilitate thickness reduction for microwave absorbers but also bring inherent narrowband admittance matching conundrum originating from its frequency-dispersive permeability and high permittivity. In this paper, we propose a simple and yet effective solution based on the concept of admittance matching with non-Foster metasurface (NFMS). Building on this concept, an ultra-wideband and extremely-thin magnetic absorber is achieved, with a simple structure consisting of a conductor-backed magnetic sheet (CMBS) coated by a NFMS. The NFMS with negatively inductive susceptance can properly cancel its positively frequency-dispersive counterpart from the CMBS so that constructive interference near the absorber can be obtained over a wide frequency band. Furthermore, the NFMS will compensate the surface conductance required for maximum incident power dissipation. As an example, we demonstrate an absorber with one-frequency decade bandwidth and a thickness of only 1/255 wavelength at the lowest operation frequency. The proposed concept enables versatile admittance matching techniques using a single-layered and has the potential to be used in the development of interesting low-profile and broadband microwave devices.
A short D-enantiomeric antimicrobial peptide with potent immunomodulatory and antibiofilm activity against multidrug-resistant Pseudomonas aeruginosa and Acinetobacter baumannii
Authors: Mohamed Mohamed F. , Brezden Anna , Mohammad Haroon , Chmielewski Jean , Seleem Mohamed N.
Published: July 2017

Antimicrobial peptides (AMPs) represent a promising therapeutic alternative for the treatment of antibiotic-resistant bacterial infections. The present study investigates the antimicrobial activity of new, rationally-designed derivatives of a short α-helical peptide, RR. From the peptides designed, RR4 and its D-enantiomer, D-RR4, emerged as the most potent analogues with a more than 32-fold improvement in antimicrobial activity observed against multidrug-resistant strains of Pseudomonas aeruginosa and Acinetobacter baumannii. Remarkably, D-RR4 demonstrated potent activity against colistin-resistant strains of P. aeruginosa (isolated from cystic fibrosis patients) indicating a potential therapeutic advantage of this peptide over several AMPs. In contrast to many natural AMPs, D-RR4 retained its activity under challenging physiological conditions (high salts, serum, and acidic pH). Furthermore, D-RR4 was more capable of disrupting P. aeruginosa and A. baumannii biofilms when compared to conventional antibiotics. Of note, D-RR4 was able to bind to lipopolysaccharide to reduce the endotoxin-induced proinflammatory cytokine response in macrophages. Finally, D-RR4 protected Caenorhabditis elegans from lethal infections of P. aeruginosa and A. baumannii and enhanced the activity of colistin in vivo against colistin-resistant P. aeruginosa.
A metagenomic survey of forest soil microbial communities more than a decade after timber harvesting
Authors: Wilhelm Roland C. , Cardenas Erick , Leung Hilary , Maas Kendra , Hartmann Martin , Hahn Aria , Hallam Steven , Mohn William W.
Published: July 2017

The scarcity of long-term data on soil microbial communities in the decades following timber harvesting limits current understanding of the ecological problems associated with maintaining the productivity of managed forests. The high complexity of soil communities and the heterogeneity of forest and soil necessitates a comprehensive approach to understand the role of microbial processes in managed forest ecosystems. Here, we describe a curated collection of well replicated, multi-faceted data from eighteen reforested sites in six different North American ecozones within the Long-term Soil Productivity (LTSP) Study, without detailed analysis of results or discussion. The experiments were designed to contrast microbial community composition and function among forest soils from harvested treatment plots with varying intensities of organic matter removal. The collection includes 724 bacterial (16S) and 658 fungal (ITS2) amplicon libraries, 133 shotgun metagenomic libraries as well as stable isotope probing amplicon libraries capturing the effects of harvesting on hemicellulolytic and cellulolytic populations. This collection serves as a foundation for the LTSP Study and other studies of the ecology of forest soil and forest disturbance.
A large-scale solar dynamics observatory image dataset for computer vision applications
Authors: Kucuk Ahmet , Banda Juan M. , Angryk Rafal A.
Published: July 2017

The National Aeronautics Space Agency (NASA) Solar Dynamics Observatory (SDO) mission has given us unprecedented insight into the Sun’s activity. By capturing approximately 70,000 images a day, this mission has created one of the richest and biggest repositories of solar image data available to mankind. With such massive amounts of information, researchers have been able to produce great advances in detecting solar events. In this resource, we compile SDO solar data into a single repository in order to provide the computer vision community with a standardized and curated large-scale dataset of several hundred thousand solar events found on high resolution solar images. This publicly available resource, along with the generation source code, will accelerate computer vision research on NASA’s solar image data by reducing the amount of time spent performing data acquisition and curation from the multiple sources we have compiled. By improving the quality of the data with thorough curation, we anticipate a wider adoption and interest from the computer vision to the solar physics community.
The DCDC2 deletion is not a risk factor for dyslexia
Authors: Scerri T S , Macpherson E , Martinelli A , Wa W C , Monaco A P , Stein J , Zheng M , Suk-Han Ho C , McBride C , Snowling M , Hulme C , Hayiou-Thomas M E , Waye M M Y , Talcott J B , Paracchini S
Published: July 2017

Dyslexia is a specific impairment in learning to read and has strong heritability. An intronic deletion within the DCDC2 gene, with ~8% frequency in European populations, is increasingly used as a marker for dyslexia in neuroimaging and behavioral studies. At a mechanistic level, this deletion has been proposed to influence sensory processing capacity, and in particular sensitivity to visual coherent motion. Our re-assessment of the literature, however, did not reveal strong support for a role of this specific deletion in dyslexia. We also analyzed data from five distinct cohorts, enriched for individuals with dyslexia, and did not identify any signal indicative of associations for the DCDC2 deletion with reading-related measures, including in a combined sample analysis (N=526). We believe we conducted the first replication analysis for a proposed deletion effect on visual motion perception and found no association (N=445 siblings). We also report that the DCDC2 deletion has a frequency of 37.6% in a cohort representative of the general population recruited in Hong Kong (N=220). This figure, together with a lack of association between the deletion and reading abilities in this cohort, indicates the low likelihood of a direct deletion effect on reading skills. Therefore, on the basis of multiple strands of evidence, we conclude that the DCDC2 deletion is not a strong risk factor for dyslexia. Our analyses and literature re-evaluation are important for interpreting current developments within multidisciplinary studies of dyslexia and, more generally, contribute to current discussions about the importance of reproducibility in science.
Cloud point extraction of rare earths and zinc using 1,10-phenanthroline and Triton X-114 coupled with microwave plasma torch-atomic emission spectrometry
Authors: Li Xuemei , Song Naizhong , Feng Wei , Jia Qiong
Published: July 2017

In the present work, cloud point extraction (CPE) of rare earths and zinc coupled with microwave plasma torch-atomic emission spectrometry (MPT-AES) was studied with 1,10-phenanthroline as the chelating agent and polyethylene glycoltert-octylphenyl ether (Triton X-114) as the surfactant.
Preparation of polyacrylic acid surface-crosslinked strong fluorescent polymer nanoparticles and their sensitive in vitro imaging of cancer cells and long-life in vivo imaging of in situ tumors
Authors: Cai Xue-Ping , He Huan-Huan , Ding Hai-Yang , Chen Xiao-Bo , Wei Tong-Hong , Song Tian-mei , You Si-Jia , Xie Hong-Ping , Min Chun-Yan
Published: July 2017

Preparation of polyacrylic acid surface-crosslinked fluorescent polymer nanoparticles and their sensitivein vitroand long-livedin vivoimaging for cancer cells.
UV-visible spectroscopic detection of kanamycin based on target-induced growth of gold nanoparticles
Authors: Wang Chunshuai , Liu Jing , Han Xuyan , Liu Chang , Tian Yaping , Zhou Nandi
Published: July 2017

A UV-visible spectroscopic detection method of kanamycin was successfully developed based on target-induced growth of gold nanoparticles (AuNPs), using AuNPs as the probe and a kanamycin-specific aptamer as the recognition element.
Redox-responsive xanthene–coumarin–chlorambucil-based FRET-guided theranostics for “activatable” combination therapy with real-time monitoring
Authors: Gangopadhyay Moumita , Mengji Rakesh , Paul Amrita , Venkatesh Yarra , Vangala Venugopal , Jana Avijit , Singh N. D. Pradeep
Published: July 2017

A FRET-based theranostic agent, xanthene–coumarin–chlorambucil, exhibited redox-responsive “activatable” synergic treatment involving PDT and chemotherapy with fluorescence-change from green to blue.
Transient structural and catalytic behaviour of Pt-particles probed by operando spectroscopy during a realistic driving cycle
Authors: Benzi Federico , Sheppard Thomas L. , Doronkin Dmitry E. , Meira Debora M. , Gänzler Andreas M. , Baier Sina , Grunwaldt Jan-Dierk
Published: July 2017

Pt catalysts investigated with operando XAS under rapid transient temperature automotive driving cycle conditions.
Self-assembled three-dimensional flowerlike Mn0.8Cd0.2S microspheres as efficient visible-light-driven photocatalysts for H2 evolution and CO2 reduction
Authors: Liu Hong , Meng Jingchai , Zhang Jiang
Published: July 2017

3D flowerlike Mn0.8Cd0.2S hierarchical microspheres assembled from nanosheets with excellent photocatalytic activity and stability were fabricated by a facile PVP-assisted solvothermal method.
Imidazolium cation transportation in a 1-D coordination polymer
Authors: Chen Wenqian , Ogiwara Naoki , Kadota Kentaro , Panyarat Kitt , Kitagawa Susumu , Horike Satoshi
Published: July 2017

We synthesized a coordination polymer, [EtMeIm][Cu(bpy)(Me2PO4)3], containing an anionic 1-D chain and an ethyl methyl imidazolium cation.
Fabrication of a phosphorylated graphene oxide–chitosan composite for highly effective and selective capture of U(vi)
Authors: Cai Yawen , Wu Chunfang , Liu Zhiyong , Zhang Linjuan , Chen Lanhua , Wang Jianqiang , Wang Xiangke , Yang Shitong , Wang Shuao
Published: July 2017

The synthesized GO–CS–P exhibits ultrafast removal kinetics, high sorption capacity and great selectivity towards U(vi).
Heterogeneous endotoxin detection bioassay using drug–nanoparticle bioconjugates: an optimization study
Authors: Kalita Prasanta , Bhola Ashwin , Goel Nitish , Sritharan Venkataraman , Gupta Shalini
Published: July 2017

Design and development of a simple and ultrasensitive dot blot bioassay for endotoxin detection in serum.
Recent advances in air electrodes for Zn–air batteries: electrocatalysis and structural design
Authors: Cai Xiaoyi , Lai Linfei , Lin Jianyi , Shen Zexiang
Published: July 2017

This review addresses the importance of the air–electrode structure and the microstructures of the catalyst for rechargeable zinc–air batteries.
Kinetic enhancement in high-activity enzyme complexes attached to nanoparticles
Authors: Malanoski Anthony P. , Breger Joyce C. , Brown Carl W. , Deschamps Jeffrey R. , Susumu Kimihiro , Oh Eunkeu , Anderson George P. , Walper Scott A. , Medintz Igor L.
Published: July 2017

Accumulating studies by many groups have found consistent enhancement in a wide variety of enzyme activities when they are displayed around nanoparticles.
Phase diagram and structural evolution of tin/indium (Sn/In) nanosolder particles: from a non-equilibrium state to an equilibrium state
Authors: Shu Yang , Ando Teiichi , Yin Qiyue , Zhou Guangwen , Gu Zhiyong
Published: July 2017

Tin/indium (Sn/In) nanosolder particles, synthesized by a surfactant-assisted chemical reduction method at room temperature, were not in an equilibrium state; however, the equilibrium state was effectively attained through post-synthesis heat treatment.
Magnetization reversal in circular vortex dots of small radius
Authors: Goiriena-Goikoetxea M. , Guslienko K. Y. , Rouco M. , Orue I. , Berganza E. , Jaafar M. , Asenjo A. , Fernández-Gubieda M. L. , Fernández Barquín L. , García-Arribas A.
Published: July 2017

Exploring the limits of magnetic vortex stability: detection ofextra-largevortex cores in Permalloy dots with 30 nm radius.
Phytic acid-assisted electrochemically synthesized three-dimensional O, P-functionalized graphene monoliths with high capacitive performance
Authors: Li Han-Yu , Liu Lang , Zhang Zhi-Wei , Wang Shu-Shen , Yu Yao , Liu Lin , Wu Yue
Published: July 2017

Three-dimensional functionalized graphene monoliths (3DFGMs) have attracted intensive attention as energy storage materials due to their unique interconnected porous structure, good electrical conductivity, excellent mechanical strength, and pseudocapacitive characteristic.
Phase and morphological control of MoO3−x nanostructures for efficient cancer theragnosis therapy
Authors: Li Bo , Wang Xin , Wu Xiaoyu , He Guanjie , Xu Ruoyu , Lu Xinwu , Wang Feng Ryan , Parkin Ivan P.
Published: July 2017

Changing the phases and morphologies of MoO3−x nanomaterials, the obtained MoO2 nanoclusters can be used in efficient cancer theragnosis therapy.
Shape control in ZIF-8 nanocrystals and metal nanoparticles@ZIF-8 heterostructures
Authors: Zheng Guangchao , Chen Zhuwen , Sentosun Kadir , Pérez-Juste Ignacio , Bals Sara , Liz-Marzán Luis M. , Pastoriza-Santos Isabel , Pérez-Juste Jorge , Hong Mei
Published: July 2017

Shape control in metal–organic frameworks still remains a challenge.
Synergetic effects of solution-processable fluorinated graphene and PEDOT as a hole-transporting layer for highly efficient and stable normal-structure perovskite solar cells
Authors: Yu Jae-Hun , Lee Cheol-Ho , Joh Han-Ik , Yeo Jun-Seok , Na Seok-In
Published: July 2017

The combination of fluorinated graphene and PEDOT as a bi-interlayer can lead to highly efficient and stable normal-structure perovskite solar cells.
Coumarin-containing thermoresponsive hyaluronic acid-based nanogels as delivery systems for anticancer chemotherapy
Authors: Stefanello Talitha F. , Couturaud Benoit , Szarpak-Jankowska Anna , Fournier David , Louage Benoit , Garcia Francielle P. , Nakamura Celso V. , De Geest Bruno G. , Woisel Patrice , van der Sanden Boudewijn , Auzély-Velty Rachel
Published: July 2017

Light- and thermoresponsive hyaluronic acid-based nanogels carry hydrophobic molecules to cancer cells.
Single gold bipyramids with sharp tips as sensitive single particle orientation sensors in biological studies
Authors: Lee So Young , Han Yeji , Hong Jong Wook , Ha Ji Won
Published: July 2017

Single gold bipyramids with sharp tips can be used as sensitive orientation probes in dynamic biological studies using DIC microscopy.
Highly conductive and environmentally stable gold/graphene yarns for flexible and wearable electronics
Authors: Yun Yong Ju , Ah Chil Seong , Hong Won G. , Kim Hae Jin , Shin Jong-Ho , Jun Yongseok
Published: July 2017

Highly conducting, stable, and weavable gold/graphene yarns were fabricated by the electroless gold nanoparticle deposition onto the surface of graphene yarns.
A comparison of the human and mouse protein corona profiles of functionalized SiO2nanocarriers
Authors: Solorio-Rodríguez A. , Escamilla-Rivera V. , Uribe-Ramírez M. , Chagolla A. , Winkler R. , García-Cuellar C. M. , De Vizcaya-Ruiz A.
Published: July 2017

Differential profile in human and mouse plasma protein corona on SiO2NP in immune and coagulation processes indicate careful interpretation for safer nanomedicine design.
An efficient one-pot approach for the regio- and diastereoselective synthesis of trans-dihydrofuran derivatives: cytotoxicity and DNA-binding studies
Authors: Tangella Yellaiah , Manasa Kesari Lakshmi , Laxma Nayak V. , Sathish Manda , Sridhar B. , Alarifi Abdullah , Nagesh Narayana , Kamal Ahmed
Published: July 2017

A facile one-pot, three component strategy has been developed for the construction oftrans-2,3-dihydrofuran derivatives. All the synthesized compounds have been evaluated for their cytotoxic activity.
To branch or not to branch: C–H selectivity of thiophene-based donor–acceptor–donor monomers in direct arylation polycondensation exemplified by PCDTBT
Authors: Lombeck Florian , Marx Franziska , Strassel Karen , Kunz Susanna , Lienert Caroline , Komber Hartmut , Friend Richard , Sommer Michael
Published: July 2017

The possibility for unselective C–H activation of a thiophene-based, donor–acceptor–donor monomer during direct arylation polycondensation is investigated.
Tunable emission of a tetraphenylethylene copolymer via polymer matrix assisted and aggregation-induced emission
Authors: Zhang Chengjie , Yao Xuyang , Wang Jie , Ma Xiang
Published: July 2017

A novel polyacrylamide copolymer possessing tetraphenylethylene AIEgens was synthesized, exhibiting tunable fluorescence emission. Hydrogen bonding in the copolymer matrix played an important role in providing a rigid environment and blocking the non-radiative pathway thereby strengthening fluorescence emission.
Conditions for multicompartment polymeric tadpoles via temperature directed self-assembly
Authors: Bobrin Valentin A. , Jia Zhongfan , Monteiro Michael J.
Published: July 2017

Conditions to form well-defined polymeric tadpole nanostructures.