bluuebunny/crossref_metadata_2025_split huggingface dataset:
Succinate supplementation improves metabolic performance of mixed glial cell cultures with mitochondrial dysfunction
Authors: Giorgi-Coll Susan , Amaral Ana I. , Hutchinson Peter J. A. , Kotter Mark R. , Carpenter Keri L. H. 
Published: April 2017

AbstractMitochondrial dysfunction, the inability to efficiently utilise metabolic fuels and oxygen, contributes to pathological changes following traumatic spinal cord or traumatic brain injury (TBI). In the present study, we tested the hypothesis that succinate supplementation can improve cellular energy state under metabolically stressed conditions in a robust, reductionist in vitro model of mitochondrial dysfunction in which primary mixed glial cultures (astrocytes, microglia and oligodendrocytes) were exposed to the mitochondrial complex I inhibitor rotenone. Cellular response was determined by measuring intracellular ATP, extracellular metabolites (glucose, lactate, pyruvate), and oxygen consumption rate (OCR). Rotenone produced no significant changes in glial ATP levels. However, it induced metabolic deficits as evidenced by lactate/pyruvate ratio (LPR) elevation (a clinically-established biomarker for poor outcome in TBI) and decrease in OCR. Succinate addition partially ameliorated these metabolic deficits. We conclude that succinate can improve glial oxidative metabolism, consistent our previous findings in TBI patients’ brains. The mixed glial cellular model may be useful in developing therapeutic strategies for conditions involving mitochondrial dysfunction, such as TBI.
How visual experience impacts the internal and external spatial mapping of sensorimotor functions
Authors: Crollen Virginie , Albouy Geneviève , Lepore Franco , Collignon Olivier 
Published: April 2017

AbstractTactile perception and motor production share the use of internally- and externally-defined coordinates. In order to examine how visual experience affects the internal/external coding of space for touch and movement, early blind (EB) and sighted controls (SC) took part in two experiments. In experiment 1, participants were required to perform a Temporal Order Judgment task (TOJ), either with their hands in parallel or crossed over the body midline. Confirming previous demonstration, crossing the hands led to a significant decrement in performance in SC but did not affect EB. In experiment 2, participants were trained to perform a sequence of five-finger movements. They were tested on their ability to produce, with the same hand but with the keypad turned upside down, the learned (internal) or the mirror (external) sequence. We observed significant transfer of motor sequence knowledge in both EB and SC irrespective of whether the representation of the sequence was internal or external. Together, these results demonstrate that visual experience differentially impacts the automatic weight attributed to internal versus external coordinates depending on task-specific spatial requirements.
Efficacy of alprostadil for preventing of contrast-induced nephropathy: A meta-analysis
Authors: Zhang Jing-Zhan , Kang Xiao-Jing , Gao Ying , Zheng Ying-Ying , Wu Ting-Ting , Li Long , Liu Fen , Yang Yi-Ning , Li Xiao-Mei , Ma Yi-Tong , Xie Xiang 
Published: April 2017

AbstractContrast-induced nephropathy (CIN) has become the third-leading cause of hospital-acquired acute renal injury. Although alprostadil has been proposed as an effective preventative measure, this conclusion remains inconsistent. Thus, we performed a meta-analysis of the published studies on this topic to evaluate the preventative effect of alprostadil on CIN. Databases, including PubMed, the Web of Science, Cochrane Library, Wanfang, the China Biological Medicine Database (SinoMed) and the China National Knowledge Infrastructure (CNKI) were systematically searched. Nineteen clinical trials involving 2267 individuals were identified. We utilized a random or a fixed effect model to calculate the pooled odd ratios (ORs) and the standardized mean differences (SMD), respectively. Compared to the control group, the CIN risk decreased significantly in the alprostadil group (P < 0.00001, OR = 0.29, 95% CI = 0.21–0.39). In the subgroup of coronary angiography patients, the use of alprostadil also decreased the risk of CIN (P < 0.00001, OR = 0.27, 95% CI: 0.19–0.39). In conclusion, Alprostadil might be associated with a significant reduction in postcontrast Scr, BUN and CysC level and decrease the incidence of CIN.
Regulation of viral gene expression by duck enteritis virus UL54
Authors: Liu Chaoyue , Cheng Anchun , Wang Mingshu , Chen Shun , Jia Renyong , Zhu Dekang , Liu Mafeng , Sun Kunfeng , Yang Qiao , Wu Ying , Zhao Xinxin , Chen Xiaoyue 
Published: April 2017

AbstractDuck enteritis virus (DEV) UL54 is a homologue of human herpes simplex virus-1 (HSV-1) ICP27, which plays essential regulatory roles during infection. Our previous studies indicated that DEV UL54 is an immediate-early protein that can shuttle between the nucleus and the cytoplasm. In the present study, we found that UL54-deleted DEV (DEV-ΔUL54) exhibits growth kinetics, a plaque size and a viral DNA copy number that are significantly different from those of its parent wild-type virus (DEV-LoxP) and the revertant (DEV-ΔUL54 (Revertant)). Relative viral mRNA levels, reflecting gene expression, the transcription phase and the translation stage, are also significantly different between DEV-ΔUL54-infected cells and DEV-LoxP/DEV-ΔUL54 (Revertant)-infected cells. However, the localization pattern of UL30 mRNA is obviously changed in DEV-ΔUL54-infected cells. These findings suggest that DEV UL54 is important for virus growth and may regulate viral gene expression during transcription, mRNA export and translation.
Differential sensitivity to infections and antimicrobial peptide-mediated immune response in four silkworm strains with different geographical origin
Authors: Romoli Ottavia , Saviane Alessio , Bozzato Andrea , D’Antona Paola , Tettamanti Gianluca , Squartini Andrea , Cappellozza Silvia , Sandrelli Federica 
Published: April 2017

AbstractThe domesticated silkworm Bombyx mori has an innate immune system, whose main effectors are the antimicrobial peptides (AMPs). Silkworm strains are commonly grouped into four geographical types (Japanese, Chinese, European and Tropical) and are generally characterised by a variable susceptibility to infections. To clarify the genetic and molecular mechanisms on which the different responses to infections are based, we exposed one silkworm strain for each geographical area to oral infections with the silkworm pathogens Enterococcus mundtii or Serratia marcescens. We detected a differential susceptibility to both bacteria, with the European strain displaying the lowest sensitivity to E. mundtii and the Indian one to S. marcescens. We found that all the strains were able to activate the AMP response against E. mundtii. However, the highest tolerance of the European strain appeared to be related to the specific composition of its AMP cocktail, containing more effective variants such as a peculiar Cecropin B6 isoform. The resistance of the Indian strain to S. marcescens seemed to be associated with its prompt capability to activate the systemic transcription of AMPs. These data suggest that B. mori strains with distinct genetic backgrounds employ different strategies to counteract bacterial infections, whose efficacy appears to be pathogen-dependent.
Low-cost, Low-bias and Low-input RNA-seq with High Experimental Verifiability based on Semiconductor Sequencing
Authors: Mai Zhibiao , Xiao Chuanle , Jin Jingjie , Zhang Gong 
Published: April 2017

AbstractLow-input RNA-seq is powerful to represent the gene expression profiles with limited number of cells, especially when single-cell variations are not the aim. However, pre-amplification-based and molecule index-based library construction methods boost bias or require higher throughput. Here we demonstrate a simple, low-cost, low-bias and low-input RNA-seq with ion torrent semiconductor sequencing (LIEA RNA-seq). We also developed highly accurate and error-tolerant spliced mapping algorithm FANSe2splice to accurately map the single-ended reads to the reference genome with better experimental verifiability than the previous spliced mappers. Combining the experimental and computational advancements, our solution is comparable with the bulk mRNA-seq in quantification, reliably detects splice junctions and minimizes the bias with much less mappable reads.
COX-1/PGE2/EP4 alleviates mucosal injury by upregulating β-arr1-mediated Akt signaling in colitis
Authors: Peng Xiaojie , Li Jianzhong , Tan Siwei , Xu Minyi , Tao Jin , Jiang Jie , Liu Huiling , Wu Bin 
Published: April 2017

AbstractCOX-1/PGE2 is an important protective mediator in ulcerative colitis (UC). β-arrestin1 (β-arr1), which acts as a scaffold protein, is involved in PGE2-mediated signaling pathways. However, the interaction between PGE2 and β-arr1 in maintaining mucosal barrier integrity remains unexplored. In this study, we demonstrated that COX-1 and PGE2 were significantly decreased, and EP4 mRNA was downregulated in both UC patients and mice during the injury phase. PGE2 treatment was found to alleviate mucosal injury and induce EP4 expression during dextran sulfate sodium (DSS)-induced colitis in wild-type (WT) mice. Following DSS-induced injury, β-arr1 deficient mice showed increased signs of colitis compared to β-arr1 WT mice, and the expression of PI3K and p-Akt were remarkably downregulated in β-arr1 deficient mice. In parallel, HCT116 cells transfected with β-arr1 siRNA were examined in the presence or absence of PGE2in vitro. PGE2 treatment in the β-arr1 WT/KO DSS model and β-arr1 siRNA transfection of HCT116 cells confirmed that PGE2 upregulated β-arr1 in vivo and in vitro. Collectively, our results indicate that COX-1/PGE2/EP4 upregulates the β-arr1 mediated Akt signaling pathway to provide mucosal protection in colitis. Thus, these findings provide support for the future development and clinical application of COX-1/PGE2 in UC.
Enhancing the throughput and multiplexing capabilities of next generation sequencing for efficient implementation of pooled shRNA and CRISPR screens
Authors: Islam Md. Fahmid , Watanabe Atsushi , Wong Lai , Lazarou Conor , Vizeacoumar Frederick S. , Abuhussein Omar , Hill Wayne , Uppalapati Maruti , Geyer C. Ronald , Vizeacoumar Franco J. 
Published: April 2017

AbstractNext generation sequencing is becoming the method of choice for functional genomic studies that use pooled shRNA or CRISPR libraries. A key challenge in sequencing these mixed-oligo libraries is that they are highly susceptible to hairpin and/or heteroduplex formation. This results in polyclonal, low quality, and incomplete reads and reduces sequencing throughput. Unfortunately, this challenge is significantly magnified in low-to-medium throughput bench-top sequencers as failed reads significantly perturb the maximization of sequence coverage and multiplexing capabilities. Here, we report a methodology that can be adapted to maximize the coverage on a bench-top, Ion PGM System for smaller shRNA libraries with high efficiency. This ligation-based, half-shRNA sequencing strategy minimizes failed sequences and is also equally amenable to high-throughput sequencers for increased multiplexing. Towards this, we also demonstrate that our strategy to reduce heteroduplex formation improves multiplexing capabilities of pooled CRISPR screens using Illumina NextSeq 500. Overall, our method will facilitate sequencing of pooled shRNA or CRISPR libraries from genomic DNA and maximize sequence coverage.
A novel mechanism linking memory stem cells with innate immunity in protection against HIV-1 infection
Authors: Wang Yufei , Whittall Trevor , Neil Stuart , Britton Gary , Mistry Mukesh , Rerks-Ngarm Supachai , Pitisuttithum Punnee , Kaewkungwal Jaranit , Nitayaphan Sorachai , Yu Xuesong , Sato Alicia , O’Connell Robert J. , Michael Nelson L. , Robb Merlin L. , Kim Jerome H. , Lehner Thomas 
Published: April 2017

AbstractHIV infection affects 37 million people and about 1.7 million are infected annually. Among the phase III clinical trials only the RV144 vaccine trial elicited significant protection against HIV-1 acquisition, but the efficacy and immune memory were inadequate. To boost these vaccine functions we studied T stem cell memory (TSCM) and innate immunity. TSCM cells were identified by phenotypic markers of CD4+ T cells and they were further characterised into 4 subsets. These expressed the common IL-2/IL-15 receptors and another subset of APOBEC3G anti-viral restriction factors, both of which were upregulated. In contrast, CD4+ TSCM cells expressing CCR5 co-receptors and α4β7 mucosal homing integrins were decreased. A parallel increase in CD4+ T cells was recorded with IL-15 receptors, APOBEC3G and CC chemokines, the latter downmodulating CCR5 molecules. We suggest a novel mechanism of dual memory stem cells; the established sequential memory pathway, TSCM →Central →Effector memory CD4+ T cells and the innate pathway consisting of the 4 subsets of TSCM. Both pathways are likely to be activated by endogenous HSP70. The TSCM memory stem cell and innate immunity pathways have to be optimised to boost the efficacy and immune memory of protection against HIV-1 in the clinical trial.
Formation of CuO nano-flowered surfaces via submerged photo-synthesis of crystallites and their antimicrobial activity
Authors: Nishino Fumika , Jeem Melbert , Zhang Lihua , Okamoto Kazumasa , Okabe Satoshi , Watanabe Seiichi 
Published: April 2017

AbstractWe report the fabrication of flower-like CuO nanostructured surfaces via submerged photo-synthesis of crystallites (SPSC), which requires only UV illumination in neutral water. In this paper, we discuss the reaction mechanism of the photochemical formation of the SPSC-fabricated CuO nanostructures in detail based on surface microstructural analyses and a radiation-chemical consideration with additional gamma-ray irradiation. Since the SPSC method for surface nanostructural fabrication can work at low temperatures at atmospheric pressure without using harmful substances, it is a potential fabrication method for green nanotechnology applications. In this vein, the antibacterial activity of the nano-flowered CuO surfaces was tested against Gram-positive (Staphylococcus aureus) bacteria and Gram-negative (Escherichia coli K12) bacteria, and the results demonstrate that the nano-flowered CuO nanostructures act as an effective antimicrobial agent.
Simple Rectangular Gratings as a Near-Field “Anti-Reflection” Pattern for GaSb TPV Cells
Authors: Yu Haitong , Liu Dong , Yang Zhen , Duan Yuanyuan 
Published: April 2017

AbstractWe show theoretically that 2D rectangular gratings on the surface of GaSb can serve as an “anti-reflection” pattern for nano-gap thermophotovoltaic (TPV) devices, which significantly enhances near-field radiative flux from the emitter to a GaSb cell, thus improving output power and conversion efficiency. The system in this study is a 200-nm gap TPV power generation system with a planar infrared plasmonic emitter and GaSb cell. Rigorous coupled-wave analysis is used to calculate the spectral near-field radiative flux involving periodic structures. The simulation shows that when coupled with a near-infrared plasmonic bulk emitter, adding gratings on the GaSb cell surface results in strong spectral enhancement above the cell’s bandgap and suppression for low-energy photon transmission, an effect that cannot be fully predicted by the effective medium theory. The resultant peak spectral heat flux is 2.8 times as high as the case without surface structures and the radiative transfer efficiency increased to 24.8% from the original 14.5% with the emitter temperature at 1800 K. The influence of the grating’s geometry parameters on the enhancement and peak frequency is further discussed with rigorous calculation of the spatial distribution of thermal radiative transfer that provided insight into the physical mechanism.
Functionally interchangeable cis-acting RNA elements in both genome segments of a picorna-like plant virus
Authors: Guo Jiangbo , Han Junping , Lin Junyan , Finer John , Dorrance Anne , Qu Feng 
Published: April 2017

AbstractCis-acting RNA structures in the genomes of RNA viruses play critical roles in viral infection, yet their importance in the bipartite genomes of the picorna-like, plant-infecting comoviruses has not been carefully investigated. We previously characterized SLC, a stem-loop structure in the 5′ untranslated region (UTR) of the bean pod mottle comovirus (BPMV) RNA2, and found it to be essential for RNA2 accumulation in infected cells. Here we report the identification of SL1, a similar cis-acting element in the other BPMV genome segment - RNA1. SL1 encompasses a portion of RNA1 5′ UTR but extends into the coding sequence for nine nucleotides, thus was missed in the previous study. While the stems of SL1 and SLC share little sequence similarity, their end loops are of the same size and identical for 11 of 15 nucleotides. Importantly, SL1 and SLC are functionally interchangeable, and separate exchanges of the stem and loop portions were likewise well tolerated. By contrast, the conserved loop sequence tolerated minimal perturbations. Finally, stem-loop structures with similar configurations were identified in two other comoviruses. Therefore, SL1 and SLC are likely essential comoviral RNA structures that play a conserved function in viral infection cycles.
Targeting ornithine decarboxylase (ODC) inhibits esophageal squamous cell carcinoma progression
Authors: He Wei , Roh Eunmiri , Yao Ke , Liu Kangdong , Meng Xing , Liu Fangfang , Wang Penglei , Bode Ann M. , Dong Zigang 
Published: April 2017

AbstractTo explore the function of ornithine decarboxylase in esophageal squamous cell carcinoma progression and test the effectiveness of anti-ornithine decarboxylase therapy for esophageal squamous cell carcinoma. In this study, we examined the expression pattern of ornithine decarboxylase in esophageal squamous cell carcinoma cell lines and tissues using immunohistochemistry and Western blot analysis. Then we investigated the function of ornithine decarboxylase in ESCC cells by using shRNA and an irreversible inhibitor of ornithine decarboxylase, difluoromethylornithine. To gather more supporting pre-clinical data, a human esophageal squamous cell carcinoma patient-derived xenograft mouse model (C.B-17 severe combined immunodeficient mice) was used to determine the antitumor effects of difluoromethylornithine in vivo. Our data showed that the expression of the ornithine decarboxylase protein is increased in esophageal squamous cell carcinoma tissues compared with esophagitis or normal adjacent tissues. Polyamine depletion by ODC shRNA not only arrests esophageal squamous cell carcinoma cells in the G2/M phase, but also induces apoptosis, which further suppresses esophageal squamous cell carcinoma cell tumorigenesis. Difluoromethylornithine treatment decreases proliferation and also induces apoptosis of esophageal squamous cell carcinoma cells and implanted tumors, resulting in significant reduction in the size and weight of tumors. The results of this study indicate that ornithine decarboxylase is a promising target for esophageal squamous cell carcinoma therapy and difluoromethylornithine warrants further study in clinical trials to test its effectiveness against esophageal squamous cell carcinoma.
Restoring visual function to the blind retina with a potent, safe and long-lasting photoswitch
Authors: Tochitsky Ivan , Trautman Jay , Gallerani Nicholas , Malis Jonatan G. , Kramer Richard H. 
Published: April 2017

AbstractPhotoswitch compounds such as DENAQ confer light-sensitivity on endogenous neuronal ion channels, enabling photocontrol of neuronal activity without genetic manipulation. DENAQ treatment restores both retinal light responses and visual behaviors in rodent models of Retinitis pigmentosa. However, retinal photosensitization requires a high dose of DENAQ and disappears within several days after treatment. Here we report that BENAQ, an improved photoswitch, is 20-fold more potent than DENAQ and persists in restoring visual responses to the retina for almost 1 month after a single intraocular injection. Studies on mice and rabbits show that BENAQ is non-toxic at concentrations 10-fold higher than required to impart light-sensitivity. These favorable properties make BENAQ a potential drug candidate for vision restoration in patients with degenerative blinding diseases.
Role of Slow-Release Nanocomposite Fertilizers on Nitrogen and Phosphate Availability in Soil
Authors: Giroto Amanda S. , Guimarães Gelton G. F. , Foschini Milene , Ribeiro Caue 
Published: April 2017

AbstractDeveloping efficient crop fertilization practices has become more and more important due to the ever-increasing global demand for food production. One approach to improving the efficiency of phosphate and urea fertilization is to improve their interaction through nanocomposites that are able to control the release of urea and P in the soil. Nanocomposites were produced from urea (Ur) or extruded thermoplastic starch/urea (TPSUr) blends as a matrix in which hydroxyapatite particles (Hap) were dispersed at ratios 50% and 20% Hap. Release tests and two incubation experiments were conducted in order to evaluate the role played by nanocomposites in controlling the availability of nitrogen and phosphate in the soil. Tests revealed an interaction between the fertilizer components and the morphological changes in the nanocomposites. TPSUr nanocomposites provided a controlled release of urea and increased the release of phosphorus from Hap in citric acid solution. The TPSUr nanocomposites also had lower NH3 volatilization compared to a control. The interaction resulting from dispersion of Hap within a urea matrix reduced the phosphorus adsorption and provided higher sustained P availability after 4 weeks of incubation in the soil.
Daily touchscreen use in infants and toddlers is associated with reduced sleep and delayed sleep onset
Authors: Cheung Celeste H. M. , Bedford Rachael , Saez De Urabain Irati R. , Karmiloff-Smith Annette , Smith Tim J. 
Published: April 2017

AbstractTraditional screen time (e.g. TV and videogaming) has been linked to sleep problems and poorer developmental outcomes in children. With the advent of portable touchscreen devices, this association may be extending down in age to disrupt the sleep of infants and toddlers, an age when sleep is essential for cognitive development. However, this association has not been demonstrated empirically. This study aims to examine whether frequency of touchscreen use is associated with sleep in infants and toddlers between 6 and 36 months of age. An online survey was administered to 715 parents reporting on child media use (daily exposure to TV and use of touchscreens), sleep patterns (night-time and daytime sleep duration, sleep onset - time to fall asleep, and frequencies of night awakenings). Structural equation models controlling for age, sex, TV exposure and maternal education indicated a significant association between touchscreen use and night-time sleep, daytime sleep and sleep onset. No significant effect was observed for the number of night awakenings. To our knowledge, this is the first report linking the use of touchscreen with sleep problems in infants and toddlers. Future longitudinal studies are needed to clarify the direction of effects and the mechanisms underlying these associations using detailed sleep tracking.