bluuebunny/crossref_metadata_2025_split huggingface dataset:
Similarity in viral and host promoters couples viral reactivation with host cell migration
Authors: Bohn-Wippert Kathrin , Tevonian Erin N. , Megaridis Melina R. , Dar Roy D. 
Published: May 2017

AbstractViral–host interactomes map the complex architecture of an evolved arms race during host cell invasion. mRNA and protein interactomes reveal elaborate targeting schemes, yet evidence is lacking for genetic coupling that results in the co-regulation of promoters. Here we compare viral and human promoter sequences and expression to test whether genetic coupling exists and investigate its phenotypic consequences. We show that viral–host co-evolution is imprinted within promoter gene sequences before transcript or protein interactions. Co-regulation of human immunodeficiency virus (HIV) and human C-X-C chemokine receptor-4 (CXCR4) facilitates migration of infected cells. Upon infection, HIV can actively replicate or remain dormant. Migrating infected cells reactivate from dormancy more than non-migrating cells and exhibit differential migration–reactivation responses to drugs. Cells producing virus pose a risk for reinitiating infection within niches inaccessible to drugs, and tuning viral control of migration and reactivation improves strategies to eliminate latent HIV. Viral–host genetic coupling establishes a mechanism for synchronizing transcription and guiding potential therapies.
Neurons and neuronal activity control gene expression in astrocytes to regulate their development and metabolism
Authors: Hasel Philip , Dando Owen , Jiwaji Zoeb , Baxter Paul , Todd Alison C. , Heron Samuel , Márkus Nóra M. , McQueen Jamie , Hampton David W. , Torvell Megan , Tiwari Sachin S. , McKay Sean , Eraso-Pichot Abel , Zorzano Antonio , Masgrau Roser , Galea Elena , Chandran Siddharthan , Wyllie David J. A. , Simpson T. Ian , Hardingham Giles E. 
Published: May 2017

AbstractThe influence that neurons exert on astrocytic function is poorly understood. To investigate this, we first developed a system combining cortical neurons and astrocytes from closely related species, followed by RNA-seq and in silico species separation. This approach uncovers a wide programme of neuron-induced astrocytic gene expression, involving Notch signalling, which drives and maintains astrocytic maturity and neurotransmitter uptake function, is conserved in human development, and is disrupted by neurodegeneration. Separately, hundreds of astrocytic genes are acutely regulated by synaptic activity via mechanisms involving cAMP/PKA-dependent CREB activation. This includes the coordinated activity-dependent upregulation of major astrocytic components of the astrocyte–neuron lactate shuttle, leading to a CREB-dependent increase in astrocytic glucose metabolism and elevated lactate export. Moreover, the groups of astrocytic genes induced by neurons or neuronal activity both show age-dependent decline in humans. Thus, neurons and neuronal activity regulate the astrocytic transcriptome with the potential to shape astrocyte–neuron metabolic cooperation.
Ion-specific ice recrystallization provides a facile approach for the fabrication of porous materials
Authors: Wu Shuwang , Zhu Chongqin , He Zhiyuan , Xue Han , Fan Qingrui , Song Yanlin , Francisco Joseph S. , Zeng Xiao Cheng , Wang Jianjun 
Published: May 2017

AbstractIce recrystallization is of great importance to both fundamental research and practical applications, however understanding and controlling ice recrystallization processes remains challenging. Here, we report the discovery of an ion-specific effect on ice recrystallization. By simply changing the initial type and concentration of ions in an aqueous solution, the size of ice grains after recrystallization can be tuned from 27.4±4.1 to 277.5±30.9 μm. Molecular dynamics simulations show that the ability of the ion to be incorporated into the ice phase plays a key role in the ultimate size of the ice grains after recrystallization. Moreover, by using recrystallized ice crystals as templates, 2D and 3D porous networks with tuneable pore sizes could be prepared from various materials, for example, NaBr, collagen, quantum dots, silver and polystyrene colloids. These porous materials are suitable for a wide range of applications, for example, in organic electronics, catalysis and bioengineering.
Light-inducible antimiR-92a as a therapeutic strategy to promote skin repair in healing-impaired diabetic mice
Authors: Lucas Tina , Schäfer Florian , Müller Patricia , Eming Sabine A. , Heckel Alexander , Dimmeler Stefanie 
Published: May 2017

AbstractMicroRNAs (miRs) are small non-coding RNAs that post-transcriptionally control gene expression. Inhibition of miRs by antisense RNAs (antimiRs) might be a therapeutic option for many diseases, but systemic inhibition can have adverse effects. Here we show that light-activatable antimiRs efficiently and locally restricted target miR activity in vivo. We use an antimiR-92a and establish a therapeutic benefit in diabetic wound healing. AntimiR-92a is modified with photolabile protecting groups, so called ‘cages’. Irradiation activates intradermally injected caged antimiR-92a without substantially affecting miR-92a expression in other organs. Light activation of caged antimiR-92a improves healing in diabetic mice to a similar extent as conventional antimiRs and derepresses the miR-92a targets Itga5 and Sirt1, thereby regulating wound cell proliferation and angiogenesis. These data show that light can be used to locally activate therapeutically active antimiRs in vivo.
Directly converting CO2 into a gasoline fuel
Authors: Wei Jian , Ge Qingjie , Yao Ruwei , Wen Zhiyong , Fang Chuanyan , Guo Lisheng , Xu Hengyong , Sun Jian 
Published: May 2017

AbstractThe direct production of liquid fuels from CO2 hydrogenation has attracted enormous interest for its significant roles in mitigating CO2 emissions and reducing dependence on petrochemicals. Here we report a highly efficient, stable and multifunctional Na–Fe3O4/HZSM-5 catalyst, which can directly convert CO2 to gasoline-range (C5–C11) hydrocarbons with selectivity up to 78% of all hydrocarbons while only 4% methane at a CO2 conversion of 22% under industrial relevant conditions. It is achieved by a multifunctional catalyst providing three types of active sites (Fe3O4, Fe5C2 and acid sites), which cooperatively catalyse a tandem reaction. More significantly, the appropriate proximity of three types of active sites plays a crucial role in the successive and synergetic catalytic conversion of CO2 to gasoline. The multifunctional catalyst, exhibiting a remarkable stability for 1,000 h on stream, definitely has the potential to be a promising industrial catalyst for CO2 utilization to liquid fuels.
Membraneless water filtration using CO2
Authors: Shin Sangwoo , Shardt Orest , Warren Patrick B. , Stone Howard A. 
Published: May 2017

AbstractWater purification technologies such as microfiltration/ultrafiltration and reverse osmosis utilize porous membranes to remove suspended particles and solutes. These membranes, however, cause many drawbacks such as a high pumping cost and a need for periodic replacement due to fouling. Here we show an alternative membraneless method for separating suspended particles by exposing the colloidal suspension to CO2. Dissolution of CO2 into the suspension creates solute gradients that drive phoretic motion of particles. Due to the large diffusion potential generated by the dissociation of carbonic acid, colloidal particles move either away from or towards the gas–liquid interface depending on their surface charge. Using the directed motion of particles induced by exposure to CO2, we demonstrate a scalable, continuous flow, membraneless particle filtration process that exhibits low energy consumption, three orders of magnitude lower than conventional microfiltration/ultrafiltration processes, and is essentially free from fouling.
Benchmarking of RNA-sequencing analysis workflows using whole-transcriptome RT-qPCR expression data
Authors: Everaert Celine , Luypaert Manuel , Maag Jesper L. V. , Cheng Quek Xiu , Dinger Marcel E. , Hellemans Jan , Mestdagh Pieter 
Published: May 2017

AbstractRNA-sequencing has become the gold standard for whole-transcriptome gene expression quantification. Multiple algorithms have been developed to derive gene counts from sequencing reads. While a number of benchmarking studies have been conducted, the question remains how individual methods perform at accurately quantifying gene expression levels from RNA-sequencing reads. We performed an independent benchmarking study using RNA-sequencing data from the well established MAQCA and MAQCB reference samples. RNA-sequencing reads were processed using five workflows (Tophat-HTSeq, Tophat-Cufflinks, STAR-HTSeq, Kallisto and Salmon) and resulting gene expression measurements were compared to expression data generated by wet-lab validated qPCR assays for all protein coding genes. All methods showed high gene expression correlations with qPCR data. When comparing gene expression fold changes between MAQCA and MAQCB samples, about 85% of the genes showed consistent results between RNA-sequencing and qPCR data. Of note, each method revealed a small but specific gene set with inconsistent expression measurements. A significant proportion of these method-specific inconsistent genes were reproducibly identified in independent datasets. These genes were typically smaller, had fewer exons, and were lower expressed compared to genes with consistent expression measurements. We propose that careful validation is warranted when evaluating RNA-seq based expression profiles for this specific gene set.
The first two complete mitochondrial genomes for the family Triglidae and implications for the higher phylogeny of Scorpaeniformes
Authors: Cui Lei , Dong Yuelei , Liu Fenghua , Gao Xingchen , Zhang Hua , Li Li , Cen Jingyi , Lu Songhui 
Published: May 2017

AbstractThe mitochondrial genome (mitogenome) can provide useful information for analyzing phylogeny and molecular evolution. Scorpaeniformes is one of the most diverse teleostean orders and has great commercial importance. To develop mitogenome data for this important group, we determined the complete mitogenomes of two gurnards Chelidonichthys kumu and Lepidotrigla microptera of Triglidae within Scorpaeniformes for the first time. The mitogenomes are 16,495 bp long in C. kumu and 16,610 bp long in L. microptera. Both the mitogenomes contain 13 protein-coding genes (PCGs), 2 ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes and two non-coding regions. All PCGs are initiated by ATG codons, except for the cytochrome coxidase subunit 1 (cox1) gene. All of the tRNA genes could be folded into typical cloverleaf secondary structures, with the exception of tRNASer(AGN) lacks a dihydrouracil (DHU) stem. The control regions are both 838 bp and contain several features common to Scorpaeniformes. The phylogenetic relationships of 33 fish mitogenomes using Bayesian Inference (BI) and Maximum Likelihood (ML) based on nucleotide and amino acid sequences of 13 PCGs indicated that the mitogenome sequences could be useful in resolving higher-level relationship of Scorpaeniformes. The results may provide more insight into the mitogenome evolution of teleostean species.
Exact firing time statistics of neurons driven by discrete inhibitory noise
Authors: Olmi Simona , Angulo-Garcia David , Imparato Alberto , Torcini Alessandro 
Published: May 2017

AbstractNeurons in the intact brain receive a continuous and irregular synaptic bombardment from excitatory and inhibitory pre- synaptic neurons, which determines the firing activity of the stimulated neuron. In order to investigate the influence of inhibitory stimulation on the firing time statistics, we consider Leaky Integrate-and-Fire neurons subject to inhibitory instantaneous post- synaptic potentials. In particular, we report exact results for the firing rate, the coefficient of variation and the spike train spectrum for various synaptic weight distributions. Our results are not limited to stimulations of infinitesimal amplitude, but they apply as well to finite amplitude post-synaptic potentials, thus being able to capture the effect of rare and large spikes. The developed methods are able to reproduce also the average firing properties of heterogeneous neuronal populations.
Synergic bactericidal effects of reduced graphene oxide and silver nanoparticles against Gram-positive and Gram-negative bacteria
Authors: Prasad Karthika , Lekshmi G. S. , Ostrikov Kola , Lussini Vanessa , Blinco James , Mohandas Mandhakini , Vasilev Krasimir , Bottle Steven , Bazaka Kateryna , Ostrikov Kostya 
Published: May 2017

AbstractReduced graphene oxide (rGO) is a promising antibacterial material, the efficacy of which can be further enhanced by the addition of silver nanoparticles (nAg). In this study, the mechanisms of antibacterial activity of rGO–nAg nanocomposite against several important human pathogenic multi-drug resistant bacteria, namely Gram-positive coccal Staphylococcus aureus and Gram-negative rod-shaped Escherichia coli and Proteus mirabilis are investigated. At the same concentration (100 µg/ml), rGO–nAg nanocomposite was significantly more effective against all three pathogens than either rGO or nAg. The nanocomposite was equally active against P. mirabilis and S. aureus as systemic antibiotic nitrofurantoin, and significantly more effective against E. coli. Importantly, the inhibition was much faster in the case of rGO–nAg nanocomposite compared to nitrofurantoin, attributed to the synergistic effects of rGO–nAg mediated contact killing and oxidative stress. This study may provide new insights for the better understanding of antibacterial actions of rGO–nAg nanocomposite and for the better designing of graphene-based antibiotics or other biomedical applications.
An all-in-one, Tet-On 3G inducible PiggyBac system for human pluripotent stem cells and derivatives
Authors: Randolph Lauren N. , Bao Xiaoping , Zhou Chikai , Lian Xiaojun 
Published: May 2017

AbstractHuman pluripotent stem cells (hPSCs) offer tremendous promise in tissue engineering and cell-based therapies due to their unique combination of two properties: pluripotency and unlimited proliferative capacity. However, directed differentiation of hPSCs to clinically relevant cell lineages is needed to achieve the goal of hPSC-based therapies. This requires a deep understanding of how cell signaling pathways converge on the nucleus to control differentiation and the ability to dissect gene function in a temporal manner. Here, we report the use of the PiggyBac transposon and a Tet-On 3G drug-inducible gene expression system to achieve versatile inducible gene expression in hPSC lines. Our new system, XLone, offers improvement over previous Tet-On systems with significantly reduced background expression and increased sensitivity to doxycycline. Transgene expression in hPSCs is tightly regulated in response to doxycycline treatment. In addition, the PiggyBac elements in our XLone construct provide a rapid and efficient strategy for generating stable transgenic hPSCs. Our inducible gene expression PiggyBac transposon system should facilitate the study of gene function and directed differentiation in human stem cells.
The antifungal effects and mechanical properties of silver bromide/cationic polymer nano-composite-modified Poly-methyl methacrylate-based dental resin
Authors: Zhang Yu , Chen Yin-yan , Huang Li , Chai Zhi-guo , Shen Li-juan , Xiao Yu-hong 
Published: May 2017

AbstractPoly-methyl methacrylate (PMMA)-based dental resins with strong and long-lasting antifungal properties are critical for the prevention of denture stomatitis. This study evaluated the antifungal effects on Candida albicans ATCC90028, the cytotoxicity toward human dental pulp cells (HDPCs), and the mechanical properties of a silver bromide/cationic polymer nano-composite (AgBr/NPVP)-modified PMMA-based dental resin. AgBr/NPVP was added to the PMMA resin at 0.1, 0.2, and 0.3 wt%, and PMMA resin without AgBr/NPVP served as the control. Fungal growth was inhibited on the AgBr/NPVP-modified PMMA resin compared to the control (P < 0.05), and the antifungal activity increased as the incorporation of the AgBr/NPVP antimicrobial composite increased. Confocal laser scanning microscopy (CLSM) showed that the number of fungal cells attached to the modified PMMA resin was considerably lower than in the control. The relative growth rate of HDPCs of modified groups were higher than 75%. The flexural strength (FS) and flexural modulus (FM) were not significantly different (P > 0.05) between the experimental and control groups. These data indicate that the incorporation of AgBr/NPVP conferred strong and long-lasting antifungal effects against Candida albicans to the PMMA resin, and it has low toxicity toward HDPCs, and its mechanical properties were not significantly affected.
Inhibition of Sp1 prevents ER homeostasis and causes cell death by lysosomal membrane permeabilization in pancreatic cancer
Authors: Dauer Patricia , Gupta Vineet K. , McGinn Olivia , Nomura Alice , Sharma Nikita S. , Arora Nivedita , Giri Bhuwan , Dudeja Vikas , Saluja Ashok K. , Banerjee Sulagna 
Published: May 2017

AbstractEndoplasmic reticulum (ER) stress initiates an important mechanism for cell adaptation and survival, named the unfolded protein response (UPR). Severe or chronic/prolonged UPR can breach the threshold for survival and lead to cell death. There is a fundamental gap in knowledge on the molecular mechanism of how chronic ER stress is stimulated and leads to cell death in pancreatic ductal adenocarcinoma (PDAC). Our study shows that downregulating specificity protein 1 (Sp1), a transcription factor that is overexpressed in pancreatic cancer, activates UPR and results in chronic ER stress. In addition, downregulation of Sp1 results in its decreased binding to the ER stress response element present in the promoter region of Grp78, the master regulator of ER stress, thereby preventing homeostasis. We further show that inhibition of Sp1, as well as induction of ER stress, leads to lysosomal membrane permeabilization (LMP), a sustained accumulation of cytosolic calcium, and eventually cell death in pancreatic cancer.
Effect of Canal Anastomosis on Periapical Fluid Pressure Build-up during Needle Irrigation in Single Roots with Double Canals using a Polycarbonate Model
Authors: Huang Qi , Barnes Jonathan B. , Schoeffel G. John , Fan Bing , Tay Candice , Bergeron Brian E. , Susin Lisiane F. , Ling Jun-qi , Niu Li-na , Tay Franklin R. 
Published: May 2017

AbstractSodium hypochlorite is an effective irrigant for chemical debridement of root canals. However, increasing the intracanal pressure during irrigant delivery may result in irrigant extrusion into the bone and soft tissues surrounding the tooth. Because clinicians often encounter teeth with intracanal communications, the objective of the present study was to examine the effects of canal anastomosis on the generation of periapical fluid pressure at different fluid flow rates and insertion depths. Two similar polycarbonate models were used to simulate a single root with double canals, one containing, and the other without communicating channels between the canals. For both models, periapical pressure increased with increasing irrigant flow rates and insertion depths of a 30-gauge side-venting needle. In the presence of communicating channels, the magnitude of pressure build-up decreased by almost 90% irrespective of the fluid flow rate or needle insertion depth. Pressure reduction in anastomoses-containing roots provides an explanation why pressure generation in single roots is considerably higher. Nevertheless, it is still possible in teeth with canal anastomoses for pressure exceeding the intraosseous pressure to be generated when the fluid flow rate is sufficiently high and when the needle tip is close to the apical terminus.
Multimodality analysis of Hyper-reflective Foci and Hard Exudates in Patients with Diabetic Retinopathy
Authors: Niu Sijie , Yu Chenchen , Chen Qiang , Yuan Songtao , Lin Jiang , Fan Wen , Liu Qinghuai 
Published: May 2017

AbstractTo investigate the correlations between hyper-reflective foci and hard exudates in patients with non-proliferative diabetic retinopathy (NPDR) and proliferative diabetic retinopathy (PDR) by spectral-domain optical coherence tomography (SD OCT) images. Hyper-reflective foci in retinal SD OCT images were automatically detected by the developed algorithm. Then, the cropped CFP images generated by the semi-automatic registration method were automatically segmented for the hard exudates and corrected by the experienced clinical ophthalmologist. Finally, a set of 5 quantitative imaging features were automatically extracted from SD OCT images, which were used for investigating the correlations of hyper-reflective foci and hard exudates and predicting the severity of diabetic retinopathy. Experimental results demonstrated the positive correlations in area and amount between hard exudates and hyper-reflective foci at different stages of diabetic retinopathy, with statistical significance (all p < 0.05). In addition, the area and amount can be taken as potential discriminant indicators of the severity of diabetic retinopathy.
Genomic evidence for local adaptation in the ovoviviparous marine fish Sebastiscus marmoratus with a background of population homogeneity
Authors: Xu Shengyong , Song Na , Zhao Linlin , Cai Shanshan , Han Zhiqiang , Gao Tianxiang 
Published: May 2017

AbstractAdvances in next-generation sequencing techniques have allowed for the generation of genome-wide sequence data, to gain insight into the dynamics influencing genetic structure and the local adaptation of marine fish. Here, using genotyping-by-sequencing (GBS) technique, we identified 31,119 single nucleotide polymorphisms (SNPs) for Sebastiscus marmoratus in 59 individuals from three populations in Chinese coastal waters. Based on all SNPs, there was little evidence of genetic differentiation among populations. However, outlier tests revealed 329 SNPs putatively under divergent selection across populations. Structural and phylogenetic topology analyses based on the outliers showed clear genetic differentiation among populations. Gene Ontology (GO) annotation results revealed that most of these outliers are known or hypothesized to be involved in metabolic process. Together with previous work using mitochondrial cytochrome b sequences, the present results further suggest that the population structure is strongly influenced by locally adaptive pressure. Overall, adaptive evolution in a heterogeneous environment plays an important role in inducing genetic differentiation among local populations. This study increases understanding of the factors (including gene flow and local adaptation) promoting and constraining population genetic differentiation in marine organisms.