bluuebunny/crossref_metadata_2025_split huggingface dataset:
Microbial community dynamics in the rhizosphere of a cadmium hyper-accumulator
Authors: Wood J. L. , Zhang C. , Mathews E. R. , Tang C. , Franks A. E. 
Published: November 2016

AbstractPhytoextraction is influenced by the indigenous soil microbial communities during the remediation of heavy metal contaminated soils. Soil microbial communities can affect plant growth, metal availability and the performance of phytoextraction-assisting inocula. Understanding the basic ecology of indigenous soil communities associated with the phytoextraction process, including the interplay between selective pressures upon the communities, is an important step towards phytoextraction optimization. This study investigated the impact of cadmium (Cd), and the presence of a Cd-accumulating plant, Carpobrotus rossii (Haw.) Schwantes, on the structure of soil-bacterial and fungal communities using automated ribosomal intergenic spacer analysis (ARISA) and quantitative PCR (qPCR). Whilst Cd had no detectable influence upon fungal communities, bacterial communities underwent significant structural changes with no reduction in 16S rRNA copy number. The presence of C. rossii influenced the structure of all communities and increased ITS copy number. Suites of operational taxonomic units (OTUs) changed in abundance in response to either Cd or C. rossii, however we found little evidence to suggest that the two selective pressures were acting synergistically. The Cd-induced turnover in bacterial OTUs suggests that Cd alters competition dynamics within the community. Further work to understand how competition is altered could provide a deeper understanding of the microbiome-plant-environment and aid phytoextraction optimization.
Increasing trend of diabetes combined with hypertension or hypercholesterolemia: NHANES data analysis 1999–2012
Authors: Song Yongfeng , Liu Xiaoyun , Zhu Xiaolin , Zhao Bin , Hu Bo , Sheng Xia , Chen Lan , Yu Miao , Yang Tao , Zhao Jiajun 
Published: November 2016

AbstractIn order to prevent cardiovascular endpoints, control of diabetes, hypertension and hypercholesterolemia is a necessity as those risk factors frequently occur in combination. Prevalence trends of concurrent diabetes, hypertension and hypercholesterolemia in 36,673 subjects were obtained from the National Health and Nutrition Examination Survey (NHANES) from 1999–2012. The prevalence of concurrent diabetes, hypertension and hypercholesterolemia increased from 3% in 1999–2000 to 6.3% in 2011–2012 (P < 0.001). The diabetes with concurrent hypertension or hypercholesterolemia incidences also increased significantly, while the occurrence of concurrent hypertension and hypercholesterolemia was stable over the study period. Overall medical drug treatments for concurrent diabetes, hypertension, hypercholesterolemia were improved from 69.8% in 1999–2006, to 82.4% in 2007–2012 (P = 0.002). Treatment cost coverage rates in any combinations with diabetes were 79–82.4% and 90.7% in the subgroup of concurrent hypertension and hypercholesterolemia. General treatment goal achievement rates were <25%, the lowest rate being 14.2% in the subject groups with three combined risk factors. The treatment goal achievement rates in two subgroups with concurrent diabetes were 20.1% (with hypertension) and 17% (with hypercholesterolemia) and 24.5% in the group without diabetes. Cost coverage improved in all combinations, but the general treatment goal achievement rates were low, especially in the groups with concurrent diabetes.
Performance Metrics for Selecting Single Nucleotide Polymorphisms in Late-onset Alzheimer’s Disease
Authors: Chen Yen-Ching , Hsiao Chi-Jung , Jung Chien-Cheng , Hu Hui-Han , Chen Jen-Hau , Lee Wen-Chung , Chiou Jeng-Min , Chen Ta-Fu , Sun Yu , Wen Li-Li , Yip Ping-Keung , Chu Yi-Min , Chen Chien-Jen , Yang Hwai-I 
Published: November 2016

AbstractPrevious genome-wide association studies using P-values to select single nucleotide polymorphisms (SNPs) have suffered from high false-positive and false-negative results. This case-control study recruited 713 late-onset Alzheimer’s disease (LOAD) cases and controls aged ≥65 from three teaching hospitals in northern Taiwan from 2007 to 2010. Performance metrics were used to select SNPs in stage 1, which were then genotyped to another dataset (stage 2). Four SNPs (CPXM2 rs2362967, APOC1 rs4420638, ZNF521 rs7230380, and rs12965520) were identified for LOAD by both traditional P-values (without correcting for multiple tests) and performance metrics. After correction for multiple tests, no SNPs were identified by traditional P-values. Simultaneous testing of APOE e4 and APOC1 rs4420638 (the SNP with the best performance in the performance metrics) significantly improved the low sensitivity of APOE e4 from 0.50 to 0.78. A point-based genetic model including these 2 SNPs and important covariates was constructed. Compared with elders with low-risks score (0–6), elders belonging to moderate-risk (score = 7–11) and high-risk (score = 12–18) groups showed a significantly increased risk of LOAD (adjusted odds ratio = 7.80 and 46.93, respectively; Ptrend < 0.0001). Performance metrics allow for identification of markers with moderate effect and are useful for creating genetic tests with clinical and public health implications.
High-speed quantum networking by ship
Authors: Devitt Simon J. , Greentree Andrew D. , Stephens Ashley M. , Van Meter Rodney 
Published: November 2016

AbstractNetworked entanglement is an essential component for a plethora of quantum computation and communication protocols. Direct transmission of quantum signals over long distances is prevented by fibre attenuation and the no-cloning theorem, motivating the development of quantum repeaters, designed to purify entanglement, extending its range. Quantum repeaters have been demonstrated over short distances, but error-corrected, global repeater networks with high bandwidth require new technology. Here we show that error corrected quantum memories installed in cargo containers and carried by ship can provide a exible connection between local networks, enabling low-latency, high-fidelity quantum communication across global distances at higher bandwidths than previously proposed. With demonstrations of technology with sufficient fidelity to enable topological error-correction, implementation of the quantum memories is within reach, and bandwidth increases with improvements in fabrication. Our approach to quantum networking avoids technological restrictions of repeater deployment, providing an alternate path to a worldwide Quantum Internet.
Synthesis and Application of Ferroelectric Poly(Vinylidene Fluoride-co-Trifluoroethylene) Films using Electrophoretic Deposition
Authors: Ryu Jeongjae , No Kwangsoo , Kim Yeontae , Park Eugene , Hong Seungbum 
Published: November 2016

AbstractIn this study, we investigated the deposition kinetics of polyvinylidene fluoride copolymerized with trifluoroethylene (P(VDF-TrFE)) particles on stainless steel substrates during the electrophoretic deposition (EPD) process. The effect of applied voltage and deposition time on the structure and ferroelectric property of the P(VDF-TrFE) films was studied in detail. A method of repeated EPD and heat treatment above melting point were employed to fabricate crack-free P(VDF-TrFE) thick films. This method enabled us to fabricate P(VDF-TrFE) films with variable thicknesses. The morphology of the obtained films was investigated by scanning electron microscopy (SEM), and the formation of β-phase was confirmed by X-ray diffraction (XRD) and Fourier transform infrared (FTIR) spectroscopy. P(VDF-TrFE) films prepared with various thicknesses showed remnant polarization (Pr) of around 4 μC/cm2. To demonstrate the applicability of our processing recipe to complex structures, we fabricated a spring-type energy harvester by depositing P(VDF-TrFE) films on stainless steel springs using EPD process. Our preliminary results show that an electrophoretic deposition can be applied to produce high-quality P(VDF-TrFE) films on planar as well as three-dimensional (3-D) substrates.
CathepsinKCre mediated deletion of βcatenin results in dramatic loss of bone mass by targeting both osteoclasts and osteoblastic cells
Authors: Ruiz Paula , Martin-Millan Marta , Gonzalez-Martin M. C. , Almeida Maria , González-Macias Jesús , Ros Maria A. 
Published: November 2016

AbstractIt is well established that activation of Wnt/βcatenin signaling in the osteoblast lineage leads to an increase in bone mass through a dual mechanism: increased osteoblastogenesis and decreased osteoclastogenesis. However, the effect of this pathway on the osteoclast lineage has been less explored. Here, we aimed to examine the effects of Wnt/βcatenin signaling in mature osteoclasts by generating mice lacking βcatenin in CathepsinK-expressing cells (Ctnnb1f/f;CtsKCre mice). These mice developed a severe low-bone-mass phenotype with onset in the second month and in correlation with an excessive number of osteoclasts, detected by TRAP staining and histomorphometric quantification. We found that WNT3A, through the canonical pathway, promoted osteoclast apoptosis and therefore attenuated the number of M-CSF and RANKL-derived osteoclasts in vitro. This reveals a cell-autonomous effect of Wnt/βcatenin signaling in controlling the life span of mature osteoclasts. Furthermore, bone Opg expression in Ctnnb1f/f;CtsKCre mice was dramatically decreased pointing to an additional external activation of osteoclasts. Accordingly, expression of CathepsinK was detected in TRAP-negative cells of the inner periosteal layer also expressing Col1. Our results indicate that the bone phenotype of Ctnnb1f/f;CtsKCre animals combines a cell-autonomous effect in the mature osteoclast with indirect effects due to the additional targeting of osteoblastic cells.
Colour formation on the wings of the butterfly Hypolimnas salmacis by scale stacking
Authors: Siddique Radwanul Hasan , Vignolini Silvia , Bartels Carolin , Wacker Irene , Hölscher Hendrik 
Published: November 2016

AbstractThe butterfly genusHypolimnasfeatures iridescent blue colouration in some areas of its dorsal wings. Here, we analyse the mechanisms responsible for such colouration on the dorsal wings ofHypolimnas salmacisand experimentally demonstrate that the lower thin lamina in the white cover scales causes the blue iridescence. This outcome contradicts other studies reporting that the radiant blue inHypolimnasbutterflies is caused by complex ridge-lamellar architectures in the upper lamina of the cover scales. Our comprehensive optical study supported by numerical calculation however shows that scale stacking primarily induces the observed colour appearance ofHypolimnas salmacis.
Coral symbioses under prolonged environmental change: living near tolerance range limits
Authors: Sampayo Eugenia M. , Ridgway Tyrone , Franceschinis Lorenzo , Roff George , Hoegh-Guldberg Ove , Dove Sophie 
Published: November 2016

AbstractAs climate change progresses, understanding the long-term response of corals and their endosymbionts (Symbiodinium) to prolonged environmental change is of immediate importance. Here, a total of 1152 fragments from 72 colonies of three common coral species (Stylophora pistillata, Pocillopora damicornis, Seriatopora hystrix) underwent a 32-month reciprocal depth transplantation. Genetic analysis showed that while S. hystrix maintained its generalist symbiont, some S. pistillata and P. damicornis underwent temporary changes in resident symbionts immediately after stress (transplantation; natural bleaching). These temporary changes were phylogenetically constrained to ‘host-compatible’ symbionts only and reversion to original symbionts occurred within 7 to 12 months, indicating long-term fidelity and stability of adult symbioses. Measurements of symbiont photo-physiology (dark adapted yield, pressure over photosystem II) and coral health (host protein, bleaching status, mortality) indicated a broad acclimatory capacity. However, this came at an apparent energetic expense as disproportionate mortality amongst symbioses that persisted outside their distribution range was observed following a natural bleaching event. As environmental changes due to climate change become more continuous in nature, sub-lethal effects linked to the existence near tolerance range limits coupled with the inability of adult coral colonies to change resident symbionts makes corals particularly susceptible to additional environmental fluctuations or stress events and reduces the resilience of coral populations.
Surface micro- and nano-texturing of stainless steel by femtosecond laser for the control of cell migration
Authors: Martínez-Calderon M. , Manso-Silván M. , Rodríguez A. , Gómez-Aranzadi M. , García-Ruiz J. P. , Olaizola S. M. , Martín-Palma R. J. 
Published: November 2016

AbstractThe precise control over the interaction between cells and the surface of materials plays a crucial role in optimizing the integration of implanted biomaterials. In this regard, material surface with controlled topographic features at the micro- and nano-scales has been proved to affect the overall cell behavior and therefore the final osseointegration of implants. Within this context, femtosecond (fs) laser micro/nano machining technology was used in this work to modify the surface structure of stainless steel aiming at controlling cell adhesion and migration. The experimental results show that cells tend to attach and preferentially align to the laser-induced nanopatterns oriented in a specific direction. Accordingly, the laser-based fabrication method here described constitutes a simple, clean, and scalable technique which allows a precise control of the surface nano-patterning process and, subsequently, enables the control of cell adhesion, migration, and polarization. Moreover, since our surface-patterning approach does not involve any chemical treatments and is performed in a single step process, it could in principle be applied to most metallic materials.
X-Ray based Lung Function measurement–a sensitive technique to quantify lung function in allergic airway inflammation mouse models
Authors: Dullin C. , Markus M. A. , Larsson E. , Tromba G. , Hülsmann S. , Alves F. 
Published: November 2016

AbstractIn mice, along with the assessment of eosinophils, lung function measurements, most commonly carried out by plethysmography, are essential to monitor the course of allergic airway inflammation, to examine therapy efficacy and to correlate animal with patient data. To date, plethysmography techniques either use intubation and/or restraining of the mice and are thus invasive, or are limited in their sensitivity. We present a novel unrestrained lung function method based on low-dose planar cinematic x-ray imaging (X-Ray Lung Function, XLF) and demonstrate its performance in monitoring OVA induced experimental allergic airway inflammation in mice and an improved assessment of the efficacy of the common treatment dexamethasone. We further show that XLF is more sensitive than unrestrained whole body plethysmography (UWBP) and that conventional broncho-alveolar lavage and histology provide only limited information of the efficacy of a treatment when compared to XLF. Our results highlight the fact that a multi-parametric imaging approach as delivered by XLF is needed to address the combined cellular, anatomical and functional effects that occur during the course of asthma and in response to therapy.
Experimental piscine alphavirus RNA recombination in vivo yields both viable virus and defective viral RNA
Authors: Petterson Elin , Guo Tz-Chun , Evensen Øystein , Mikalsen Aase B. 
Published: November 2016

AbstractRNA recombination in non-segmented RNA viruses is important for viral evolution and documented for several virus species through in vitro studies. Here we confirm viral RNA recombination in vivo using an alphavirus, the SAV3 subtype of Salmon pancreas disease virus. The virus causes pancreas disease in Atlantic salmon and heavy losses in European salmonid aquaculture. Atlantic salmon were injected with a SAV3 6K-gene deleted cDNA plasmid, encoding a non-viable variant of SAV3, together with a helper cDNA plasmid encoding structural proteins and 6K only. Later, SAV3-specific RNA was detected and recombination of viral RNA was confirmed. Virus was grown from plasmid-injected fish and shown to infect and cause pathology in salmon. Subsequent cloning of PCR products confirming recombination, documented imprecise homologous recombination creating RNA deletion variants in fish injected with cDNA plasmid, corresponding with deletion variants previously found in SAV3 from the field. This is the first experimental documentation of alphavirus RNA recombination in an animal model and provides new insight into the production of defective virus RNA.
Identification of DNA primase inhibitors via a combined fragment-based and virtual screening
Authors: Ilic Stefan , Akabayov Sabine R. , Arthanari Haribabu , Wagner Gerhard , Richardson Charles C. , Akabayov Barak 
Published: November 2016

AbstractThe structural differences between bacterial and human primases render the former an excellent target for drug design. Here we describe a technique for selecting small molecule inhibitors of the activity of T7 DNA primase, an ideal model for bacterial primases due to their common structural and functional features. Using NMR screening, fragment molecules that bind T7 primase were identified and then exploited in virtual filtration to select larger molecules from the ZINC database. The molecules were docked to the primase active site using the available primase crystal structure and ranked based on their predicted binding energies to identify the best candidates for functional and structural investigations. Biochemical assays revealed that some of the molecules inhibit T7 primase-dependent DNA replication. The binding mechanism was delineated via NMR spectroscopy. Our approach, which combines fragment based and virtual screening, is rapid and cost effective and can be applied to other targets.
Large-scale identification of adverse drug reaction-related proteins through a random walk model
Authors: Chen Xiaowen , Shi Hongbo , Yang Feng , Yang Lei , Lv Yingli , Wang Shuyuan , Dai Enyu , Sun Dianjun , Jiang Wei 
Published: November 2016

AbstractAdverse drug reactions (ADRs) are responsible for drug failure in clinical trials and affect life quality of patients. The identification of ADRs during the early phases of drug development is an important task. Therefore, predicting potential protein targets eliciting ADRs is essential for understanding the pathogenesis of ADRs. In this study, we proposed a computational algorithm,Integrated Network for Protein-ADR relations (INPADR), to infer potential protein-ADR relations based on an integrated network. First, the integrated network was constructed by connecting the protein-protein interaction network and the ADR similarity network using known protein-ADR relations. Then, candidate protein-ADR relations were further prioritized by performing a random walk with restart on this integrated network. Leave-one-out cross validation was used to evaluate the ability of the INPADR. An AUC of 0.8486 was obtained, which was a significant improvement compared to previous methods. We also applied the INPADR to two ADRs to evaluate its accuracy. The results suggested that the INPADR is capable of finding novel protein-ADR relations. This study provides new insight to our understanding of ADRs. The predicted ADR-related proteins will provide a reference for preclinical safety pharmacology studies and facilitate the identification of ADRs during the early phases of drug development.
Possible flat band bending of the Bi1.5Sb0.5Te1.7Se1.3 crystal cleaved in an ambient air probed by terahertz emission spectroscopy
Authors: Park Soon Hee , Hamh Sun Young , Park Joonbum , Kim Jun Sung , Lee Jong Seok 
Published: November 2016

AbstractWe investigate an evolution of the surface electronic state of the Bi1.5Sb0.5Te1.7Se1.3 single crystal, which is one of the most bulk insulating topological insulators, by examining terahertz light emitted from the sample surface upon the illumination of the near-infrared femtosecond laser pulses. We find that the surface state with a flat band bending can appear in the course of the natural maturation process of the surface state in an ambient air. Furthermore, we demonstrate that the evolution of the surface electronic state can be accelerated, decelerated, or even stopped by controlling environmental conditions to contain different amount of H2O, in particular.
Unraveling the differential dynamics of developmental fate in central and peripheral nervous systems
Authors: Sengupta Dola , Kar Sandip 
Published: November 2016

AbstractBone morphogenetic protein 2 (BMP2), differentially regulates the developmental lineage commitment of neural stem cells (NSC’s) in central and peripheral nervous systems. However, the precise mechanism beneath such observations still remains illusive. To decipher the intricacies of this mechanism, we propose a generic mathematical model of BMP2 driven differentiation regulation of NSC’s. The model efficiently captures the dynamics of the wild-type as well as various mutant and over-expression phenotypes for NSC’s in central nervous system. Our model predicts that the differential developmental dynamics of the NSC’s in peripheral nervous system can be reconciled by altering the relative positions of the two mutually interconnected bi-unstable switches inherently present in the steady state dynamics of the crucial developmental fate regulatory proteins as a function of BMP2 dose. This model thus provides a novel mechanistic insight and has the potential to deliver exciting therapeutic strategies for neuronal regeneration from NSC’s of different origin.
A novel enzyme with antioxidant capacity produced by the ubiquitous skin colonizer Propionibacterium acnes
Authors: Allhorn Maria , Arve Sabine , Brüggemann Holger , Lood Rolf 
Published: November 2016

AbstractThe role of the skin microbiota in human health is poorly understood. Here, we identified and characterized a novel antioxidant enzyme produced by the skin microbiota, designated RoxP for radical oxygenase of Propionibacterium acnes. RoxP is uniquely produced by the predominant skin bacterium P. acnes, with no homologs in other bacteria; it is highly expressed and strongly secreted into culture supernatants. We show that RoxP binds heme, reduces free radicals, and can protect molecules from oxidation. Strikingly, RoxP is crucial for the survival of P. acnes in oxic conditions and for skin colonization of P. acnes ex vivo. Taken together, our study strongly suggests that RoxP facilitates P. acnes’ survival on human skin, and is an important beneficial factor for the host-commensal interaction. Thus, RoxP is the first described skin microbiota-derived mutualistic factor that potentially can be exploited for human skin protection.