bluuebunny/crossref_metadata_2025_split huggingface dataset:
A catalogue of 136 microbial draft genomes from Red Sea metagenomes
Authors: Haroon Mohamed F. , Thompson Luke R. , Parks Donovan H. , Hugenholtz Philip , Stingl Ulrich 
Published: July 2016

AbstractEarth is expected to continue warming and the Red Sea is a model environment for understanding the effects of global warming on ocean microbiomes due to its unusually high temperature, salinity and solar irradiance. However, most microbial diversity analyses of the Red Sea have been limited to cultured representatives and single marker gene analyses, hence neglecting the substantial uncultured majority. Here, we report 136 microbial genomes (completion minus contamination is ≥50%) assembled from 45 metagenomes from eight stations spanning the Red Sea and taken from multiple depths between 10 to 500 m. Phylogenomic analysis showed that most of the retrieved genomes belong to seven different phyla of known marine microbes, but more than half representing currently uncultured species. The open-access data presented here is the largest number of Red Sea representative microbial genomes reported in a single study and will help facilitate future studies in understanding the physiology of these microorganisms and how they have adapted to the relatively harsh conditions of the Red Sea.
Long non-coding RNA expression profiling in the NCI60 cancer cell line panel using high-throughput RT-qPCR
Authors: Mestdagh Pieter , Lefever Steve , Volders Pieter-Jan , Derveaux Stefaan , Hellemans Jan , Vandesompele Jo 
Published: July 2016

AbstractLong non-coding RNAs (lncRNAs) form a new class of RNA molecules implicated in various aspects of protein coding gene expression regulation. To study lncRNAs in cancer, we generated expression profiles for 1707 human lncRNAs in the NCI60 cancer cell line panel using a high-throughput nanowell RT-qPCR platform. We describe how qPCR assays were designed and validated and provide processed and normalized expression data for further analysis. Data quality is demonstrated by matching the lncRNA expression profiles with phenotypic and genomic characteristics of the cancer cell lines. This data set can be integrated with publicly available omics and pharmacological data sets to uncover novel associations between lncRNA expression and mRNA expression, miRNA expression, DNA copy number, protein coding gene mutation status or drug response
ATRA modulates mechanical activation of TGF-β by pancreatic stellate cells
Authors: Sarper Muge , Cortes Ernesto , Lieberthal Tyler J. , del Río Hernández Armando 
Published: July 2016

AbstractThe hallmark of pancreatic ductal adenocarcinoma (PDAC) is abundant desmoplasia, which is orchestrated by pancreatic stellate cells (PSCs) and accounts for the majority of the stroma surrounding the tumour. Healthy PSCs are quiescent, but upon activation during disease progression, they adopt a myofibroblast-contractile phenotype and secrete and concomitantly reorganise the stiff extracellular matrix (ECM). Transforming growth factor β (TGF-β) is a potent activator of PSCs, and its activation requires spatiotemporal organisation of cellular and extracellular cues to liberate it from an inactive complex with latent TGF-β binding protein (LTBP). Here we study the mechanical activation of TGF-β by PSCs in vitro by investigating LTBP-1 organisation with fibrillar fibronectin and show that all trans-retinoic acid (ATRA), which induces PSC quiescence, down-regulates the ability of PSCs to mechanically organise LTBP-1 and activate TGF-β through a mechanism involving myosin II dependent contractility. Therefore, ATRA inhibits the ability of PSCs to mechanically release active TGF-β, which might otherwise act in an autocrine manner to sustain PSCs in an active state and a tumour-favouring stiff microenvironment.
Ecosystem experiment reveals benefits of natural and simulated beaver dams to a threatened population of steelhead (Oncorhynchus mykiss)
Authors: Bouwes Nicolaas , Weber Nicholas , Jordan Chris E. , Saunders W. Carl , Tattam Ian A. , Volk Carol , Wheaton Joseph M. , Pollock Michael M. 
Published: July 2016

AbstractBeaver have been referred to as ecosystem engineers because of the large impacts their dam building activities have on the landscape; however, the benefits they may provide to fluvial fish species has been debated. We conducted a watershed-scale experiment to test how increasing beaver dam and colony persistence in a highly degraded incised stream affects the freshwater production of steelhead (Oncorhynchus mykiss). Following the installation of beaver dam analogs (BDAs), we observed significant increases in the density, survival and production of juvenile steelhead without impacting upstream and downstream migrations. The steelhead response occurred as the quantity and complexity of their habitat increased. This study is the first large-scale experiment to quantify the benefits of beavers and BDAs to a fish population and its habitat. Beaver mediated restoration may be a viable and efficient strategy to recover ecosystem function of previously incised streams and to increase the production of imperiled fish populations.
The minimization of mechanical work in vibrated granular matter
Authors: Clewett James P. D. , Wade Jack , Bowley R. M. , Herminghaus Stephan , Swift Michael R. , Mazza Marco G. 
Published: July 2016

AbstractExperiments and computer simulations are carried out to investigate phase separation in a granular gas under vibration. The densities of the dilute and the dense phase are found to follow a lever rule and obey an equation of state. Here we show that the Maxwell equal-areas construction predicts the coexisting pressure and binodal densities remarkably well, even though the system is far from thermal equilibrium. This construction can be linked to the minimization of mechanical work associated with density fluctuations without invoking any concept related to equilibrium-like free energies.
Habitat use of bats in relation to wind turbines revealed by GPS tracking
Authors: Roeleke Manuel , Blohm Torsten , Kramer-Schadt Stephanie , Yovel Yossi , Voigt Christian C. 
Published: July 2016

AbstractWorldwide, many countries aim at countering global climate change by promoting renewable energy. Yet, recent studies highlight that so-called green energy, such as wind energy, may come at environmental costs, for example when wind turbines kill birds and bats. Using miniaturized GPS loggers, we studied how an open-space foraging bat with high collision risk with wind turbines, the common noctule Nyctalus noctula (Schreber, 1774), interacts with wind turbines. We compared actual flight trajectories to correlated random walks to identify habitat variables explaining the movements of bats. Both sexes preferred wetlands but used conventionally managed cropland less than expected based on availability. During midsummer, females traversed the land on relatively long flight paths and repeatedly came close to wind turbines. Their flight heights above ground suggested a high risk of colliding with wind turbines. In contrast, males recorded in early summer commuted straight between roosts and foraging areas and overall flew lower than the operating range of most turbine blades, suggesting a lower collision risk. Flight heights of bats suggest that during summer the risk of collision with wind turbines was high for most studied bats at the majority of currently installed wind turbines. For siting of wind parks, preferred bat habitats and commuting routes should be identified and avoided.
Effects of landscape anthropization on mosquito community composition and abundance
Authors: Ferraguti Martina , Martínez-de la Puente Josué , Roiz David , Ruiz Santiago , Soriguer Ramón , Figuerola Jordi 
Published: July 2016

AbstractAnthropogenic landscape transformation has an important effect on vector-borne pathogen transmission. However, the effects of urbanization on mosquito communities are still only poorly known. Here, we evaluate how land-use characteristics are related to the abundance and community composition of mosquitoes in an area with endemic circulation of numerous mosquito-borne pathogens. We collected 340 829 female mosquitoes belonging to 13 species at 45 localities spatially grouped in 15 trios formed by 1 urban, 1 rural and 1 natural area. Mosquito abundance and species richness were greater in natural and rural areas than in urban areas. Environmental factors including land use, vegetation and hydrological characteristics were related to mosquito abundance and community composition. Given the differing competences of each species in pathogen transmission, these results provide valuable information on the transmission potential of mosquito-borne pathogens that will be of great use in public and animal health management by allowing, for instance, the identification of the priority areas for pathogen surveillance and vector control.
Programmed activation of cancer cell apoptosis: A tumor-targeted phototherapeutic topoisomerase I inhibitor
Authors: Shin Weon Sup , Han Jiyou , Kumar Rajesh , Lee Gyung Gyu , Sessler Jonathan L. , Kim Jong-Hoon , Kim Jong Seung 
Published: July 2016

AbstractWe report here a tumor-targeting masked phototherapeutic agent 1 (PT-1). This system contains SN-38—a prodrug of the topoisomerase I inhibitor irinotecan. Topoisomerase I is a vital enzyme that controls DNA topology during replication, transcription, and recombination. An elevated level of topoisomerase I is found in many carcinomas, making it an attractive target for the development of effective anticancer drugs. In addition, PT-1 contains both a photo-triggered moiety (nitrovanillin) and a cancer targeting unit (biotin). Upon light activation in cancer cells, PT-1 interferes with DNA re-ligation, diminishes the expression of topoisomerase I, and enhances the expression of inter alia mitochondrial apoptotic genes, death receptors, and caspase enzymes, inducing DNA damage and eventually leading to apoptosis. In vitro and in vivo studies showed significant inhibition of cancer growth and the hybrid system PT-1 thus shows promise as a programmed photo-therapeutic (“phototheranostic”).
Human neural stem cell-induced endothelial morphogenesis requires autocrine/paracrine and juxtacrine signaling
Authors: Chou Chung-Hsing , Modo Michel 
Published: July 2016

AbstractTransplanted neural stem cells (NSC) interact with the host brain microenvironment. A neovascularization is commonly observed in the vicinity of the cell deposit, which is correlated with behavioral improvements. To elucidate the signaling mechanisms between human NSCs and endothelial cells (ECs), these were cocultured in an in vitro model in which NSC-induced endothelial morphogenesis produced a neurovascular environment. Soluble (autocrine/paracrine) and contact–mediated (juxtacrine) signaling molecules were evaluated for two conditionally immortalized fetal NSC lines derived from the cortical anlage (CTXOE03) and ganglionic eminence (STROC05), as well as an adult EC line (D3) derived from the cerebral microvasculature of a hippocampal biopsy. STROC05 were 4 times as efficient to induce endothelial morphogenesis compared to CTXOE03. The cascade of reciprocal interactions between NSCs and ECs in this process was determined by quantifying soluble factors, receptor mapping and immunocytochemistry for extracellular matrix molecules. The mechanistic significance of these was further evaluated by pharmacological blockade. The sequential cell-specific regulation of autocrine/paracrine and juxtacrine signaling accounted for the differential efficiency of NSCs to induce endothelial morphogenesis. These in vitro studies shed new light on the reciprocal interactions between NSCs and ECs, which are pivotal for our mechanistic understanding of the efficacy of NSC transplantation.
Monoclonal antibody with conformational specificity for a toxic conformer of amyloid β42 and its application toward the Alzheimer’s disease diagnosis
Authors: Murakami Kazuma , Tokuda Maki , Suzuki Takashi , Irie Yumi , Hanaki Mizuho , Izuo Naotaka , Monobe Yoko , Akagi Ken-ichi , Ishii Ryotaro , Tatebe Harutsugu , Tokuda Takahiko , Maeda Masahiro , Kume Toshiaki , Shimizu Takahiko , Irie Kazuhiro 
Published: July 2016

AbstractAmyloid β-protein (Aβ42) oligomerization is an early event in Alzheimer’s disease (AD). Current diagnostic methods using sequence-specific antibodies against less toxic fibrillar and monomeric Aβ42 run the risk of overdiagnosis. Hence, conformation-specific antibodies against neurotoxic Aβ42 oligomers have garnered much attention for developing more accurate diagnostics. Antibody 24B3, highly specific for the toxic Aβ42 conformer that has a turn at Glu22 and Asp23, recognizes a putative Aβ42 dimer, which forms stable and neurotoxic oligomers more potently than the monomer. 24B3 significantly rescues Aβ42-induced neurotoxicity, whereas sequence-specific antibodies such as 4G8 and 82E1, which recognizes the N-terminus, do not. The ratio of toxic to total Aβ42 in the cerebrospinal fluid of AD patients is significantly higher than in control subjects as measured by sandwich ELISA using antibodies 24B3 and 82E1. Thus, 24B3 may be useful for AD diagnosis and therapy.
Integrated Electrowetting Nanoinjector for Single Cell Transfection
Authors: Shekaramiz Elaheh , Varadarajalu Ganeshkumar , Day Philip J. , Wickramasinghe H. Kumar 
Published: July 2016

AbstractSingle cell transfection techniques are essential to understand the heterogeneity between cells. We have developed an integrated electrowetting nanoinjector (INENI) to transfect single cells. The high transfection efficiency, controlled dosage delivery and ease of INENI fabrication promote the widespread application of the INENI in cell transfection assays.
Mechanism of sodium chloride in promoting reduction of high-magnesium low-nickel oxide ore
Authors: Zhou Shiwei , Wei Yonggang , Li Bo , Wang Hua , Ma Baozhong , Wang Chengyan 
Published: July 2016

AbstractSodium chloride has been proved that it is an effective promoter for the reduction of high-magnesium, low-nickel oxide ore. The aim of current work is to clarify the promotion behavior of sodium chloride in the roasting reduction process. The influence of moisture on the reduction of ore in the presence of sodium chloride is studied to get clear comprehension of promotion process. In the presence of moisture, the HCl is produced by pyrohydrolysis of sodium chloride for chlorinating nickel and iron oxides, moreover, interactions between metallic oxides and sodium chloride are also a way for chlorination at high temperature (>802 °C); subsequently, the metal chloride would be reduced by reductant. In the absence of moisture, the magnetic separation results show that the recoveries of iron and nickel have a significant increase; moreover, olivine structure would be destroyed gradually with the increase of roasting temperature in the action of sodium chloride and the sodium chloride existed in high-magnesium, low-nickel oxide ore could make the NiO isolate from NiO-bearing minerals. The NiO reacts with Fe2O3 at high temperature to form NiFe2O4, which is conductive to the formation of Ni-Fe alloy during the reduction process.
New insights in Microbial Fuel Cells: novel solid phase anolyte
Authors: Tommasi Tonia , Salvador Gian Paolo , Quaglio Marzia 
Published: July 2016

AbstractFor the development of long lasting portable microbial fuel cells (MFCs) new strategies are necessary to overcome critical issues such as hydraulic pump system and the biochemical substrate retrieval overtime to sustain bacteria metabolism. The present work proposes the use of a synthetic solid anolyte (SSA), constituted by agar, carbonaceous and nitrogen sources dissolved into diluted seawater. Results of a month-test showed the potential of the new SSA-MFC as a long lasting low energy consuming system.
Factors favoring regain of the lost vertical spinal height through posterior spinal fusion in adolescent idiopathic scoliosis
Authors: Shi Benlong , Mao Saihu , Xu Leilei , Sun Xu , Liu Zhen , Zhu Zezhang , Lam Tsz Ping , Cheng Jack CY , Ng Bobby , Qiu Yong 
Published: July 2016

AbstractHeight gain is a common beneficial consequence following correction surgery in adolescent idiopathic scoliosis (AIS), yet little is known concerning factors favoring regain of the lost vertical spinal height (SH) through posterior spinal fusion. A consecutive series of AIS patients from February 2013 to August 2015 were reviewed. Surgical changes in SH (ΔSH), as well as the multiple coronal and sagittal deformity parameters were measured and correlated. Factors associated with ΔSH were identified through Pearson correlation analysis and multivariate regression analysis. A total of 172 single curve and 104 double curve patients were reviewed. The ΔSH averaged 2.5 ± 0.9 cm in single curve group and 2.9 ± 1.0 cm in double curve group. The multivariate regression analysis revealed the following pre-operative variables contributed significantly to ΔSH: pre-op Cobb angle, pre-op TK (single curve group only), pre-op GK (double curve group only) and pre-op LL (double curve group only) (p < 0.05). Thus change in height (in cm) = 0.044 × (pre-op Cobb angle) + 0.012 × (pre-op TK) (Single curve, adjusted R2 = 0.549) or 0.923 + 0.021 × (pre-op Cobb angle1) + 0.028 × (pre-op Cobb angle2) + 0.015 × (pre-op GK)-0.012 × (pre-op LL) (Double curve, adjusted R2 = 0.563). Severer pre-operative coronal Cobb angle and greater sagittal curves were beneficial factors favoring more contribution to the surgical lengthening effect in vertical spinal height in AIS.
VirusMapper: open-source nanoscale mapping of viral architecture through super-resolution microscopy
Authors: Gray Robert D. M. , Beerli Corina , Pereira Pedro Matos , Scherer Kathrin Maria , Samolej Jerzy , Bleck Christopher Karl Ernst , Mercer Jason , Henriques Ricardo 
Published: July 2016

AbstractThe nanoscale molecular assembly of mammalian viruses during their infectious life cycle remains poorly understood. Their small dimensions, generally bellow the 300nm diffraction limit of light microscopes, has limited most imaging studies to electron microscopy. The recent development of super-resolution (SR) light microscopy now allows the visualisation of viral structures at resolutions of tens of nanometers. In addition, these techniques provide the added benefit of molecular specific labelling and the capacity to investigate viral structural dynamics using live-cell microscopy. However, there is a lack of robust analytical tools that allow for precise mapping of viral structure within the setting of infection. Here we present an open-source analytical framework that combines super-resolution imaging and naïve single-particle analysis to generate unbiased molecular models. This tool, VirusMapper, is a high-throughput, user-friendly, ImageJ-based software package allowing for automatic statistical mapping of conserved multi-molecular structures, such as viral substructures or intact viruses. We demonstrate the usability of VirusMapper by applying it to SIM and STED images of vaccinia virus in isolation and when engaged with host cells. VirusMapper allows for the generation of accurate, high-content, molecular specific virion models and detection of nanoscale changes in viral architecture.
Topical and Targeted Delivery of siRNAs to Melanoma Cells Using a Fusion Peptide Carrier
Authors: Ruan Renquan , Chen Ming , Sun Sijie , Wei Pengfei , Zou Lili , Liu Jing , Gao Dayong , Wen Longping , Ding Weiping 
Published: July 2016

AbstractTopical application of siRNAs through the skin is a potentially effective strategy for the treatment of melanoma tumors. In this study, we designed a new and safe fusion peptide carrier SPACE-EGF to improve the skin and cell penetration function of the siRNAs and their targeting ability to B16 cells, such that the apoptosis of B16 cells can be induced. The results show that the carrier is stable and less toxic. The EGF motif does not affect the skin and cell penetration function of the SPACE. Because EGF can strongly bind EGFR, which is overexpressed in cancer cells, the targeting ability of the SPACE-EGF-siRNA complex is increased. In vitro experiments indicate that GAPDH siRNAs conjugated with SPACE-EGF can significantly reduce the GAPDH concentration in B16 cells and c-Myc siRNAs can cause the gene silencing of c-Myc and thus the apoptosis of cells. In vivo experiments show that the topical application of c-Myc siRNAs delivered by SPACE-EGF through the skin can significantly inhibit the growth of melanoma tumors. This work may provide insight into the development of new transdermal drug carriers to treat a variety of skin disorders.
RNA is an Adjuvanticity Mediator for the Lipid-Based Mucosal Adjuvant, Endocine
Authors: Hayashi Masayuki , Aoshi Taiki , Ozasa Koji , Kusakabe Takato , Momota Masatoshi , Haseda Yasunari , Kobari Shingo , Kuroda Etsushi , Kobiyama Kouji , Coban Cevayir , Ishii Ken J. 
Published: July 2016

AbstractNasal vaccination has the potential to elicit systemic and mucosal immunity against pathogens. However, split and subunit vaccines lack potency at stimulating mucosal immunity, and an adjuvant is indispensable for eliciting potent mucosal immune response to nasal vaccines. Endocine, a lipid-based mucosal adjuvant, potentiates both systemic and mucosal immune responses. Although Endocine has shown efficacy and tolerability in animal and clinical studies, its mechanism of action remains unknown. It has been reported recently that endogenous danger signals are essential for the effects of some adjuvants such as alum or MF59. However, the contribution of danger signals to the adjuvanticity of Endocine has not been explored. Here, we show that RNA is likely to be an important mediator for the adjuvanticity of Endocine. Administration of Endocine generated nucleic acids release, and activated dendritic cells (DCs) in draining lymph nodes in vivo. These results suggest the possibility that Endocine indirectly activates DCs via damage-associated molecular patterns. Moreover, the adjuvanticity of Endocine disappeared in mice lacking TANK-binding kinase 1 (Tbk1), which is a downstream molecule of nucleic acid sensing signal pathway. Furthermore, co-administration of RNase A reduced the adjuvanticity of Endocine. These data suggest that RNA is important for the adjuvanticity of Endocine.
Comparative Study of Carbon Materials Synthesized “Greenly” for 2-CP Removal
Authors: Ma Ying , Lu Nan , Lu Ying , Guan Jiu-nian , Qu Jiao , Liu Hai-yang , Cong Qiao , Yuan Xing 
Published: July 2016

AbstractCarbon nanotubes (CNTs), graphene (GA) and carbon nanospheres (CNSs) were prepared respectively using grass (Festucaarundinace) as the sole carbon resource by solvothermal method and characterized as adsorbent and photocatalyst for 2-chlorophenol (2-CP) removal in water. With H2O2/HNO3/H2SO4, the CNTs were firstly produced from grass (Festucaarundinace) at 300 °C by hydrolysis and oxidization, the CNTs were secondly opened to form the GA by oxidization at 400 °C and the GA was lastly rolled-up to form the CNSs by oxidization at 500 °C. All adsorption equilibration of the CNTs, GA and CNSs for 2-CP were achieved within 120 min and 60.35%, 20.12% and 76.22% of 2-CP (5 mg L−1, pH = 6.3) were adsorbed, respectively. Furthermore, the high removal rates of 2-CP were about 88.23%, 92.90% and 79.64% by the CNTs, GA and CNSs, after 120 min adsorption and 160 min irradiation. On the basis of these results, the CNSs were suitable for removal 2-CP as adsorbent and the GA was suitable as photocatalyst. The photooxidation of 2-CP was mainly initiated by O2·− or ·OH which was generated from the combine with simulated sunlight and the CNTs or GA, respectively. However, the CNTs was not suitable for removal 2-CP owing to the increasing toxicity.