bluuebunny/crossref_metadata_2025_split huggingface dataset:
A multi-step transcriptional cascade underlies vascular regeneration in vivo
Authors: Shirali Aditya S. , Romay Milagros C. , McDonald Austin I. , Su Trent , Steel Michelle E. , Iruela-Arispe M. Luisa 
Published: March 2018

AbstractThe molecular mechanisms underlying vascular regeneration and repair are largely unknown. To gain insight into this process, we developed a method of intima denudation, characterized the progression of endothelial healing, and performed transcriptome analysis over time. Next-generation RNA sequencing (RNAseq) provided a quantitative and unbiased gene expression profile during in vivo regeneration following denudation injury. Our data indicate that shortly after injury, cells immediately adjacent to the wound mount a robust and rapid response with upregulation of genes like Jun, Fos, Myc, as well as cell adhesion genes. This was quickly followed by a wave of proliferative genes. After completion of endothelial healing a vigorous array of extracellular matrix transcripts were upregulated. Gene ontology enrichment and protein network analysis were used to identify transcriptional profiles over time. Further data mining revealed four distinct stages of regeneration: shock, proliferation, acclimation, and maturation. The transcriptional signature of those stages provides insight into the regenerative machinery responsible for arterial repair under normal physiologic conditions.
Outer membrane vesicles from β-lactam-resistant Escherichia coli enable the survival of β-lactam-susceptible E. coli in the presence of β-lactam antibiotics
Authors: Kim Si Won , Park Seong Bin , Im Se Pyeong , Lee Jung Seok , Jung Jae Wook , Gong Tae Won , Lazarte Jassy Mary S. , Kim Jaesung , Seo Jong-Su , Kim Jong-Hwan , Song Jong-Wook , Jung Hyun Suk , Kim Gwang Joong , Lee Young Ju , Lim Suk-Kyung , Jung Tae Sung 
Published: March 2018

AbstractOuter membrane vesicles (OMVs) containing various bacterial compounds are released from mainly gram-negative bacteria. Secreted OMVs play important roles in the ability of a bacterium to defend itself, and thus contribute to the survival of bacteria in a community. In this study, we collected OMVs from β-lactam antibiotic-resistant Escherichia coli established by conjugation assay and the parental β-lactam antibiotic-susceptible strain, and performed comparative proteomic analysis to examine whether these OMVs carried β-lactam-resistant compounds. We also investigated whether both types of OMVs could protect susceptible cells from β-lactam-induced death and/or directly degrade β-lactam antibiotics. Several proteins that can be involved in degrading β-lactam antibiotics were more abundant in OMVs from β-lactam-resistant E. coli, and thus OMVs from β-lactam resistant E. coli could directly and dose-dependently degrade β-lactam antibiotics and fully rescue β-lactam-susceptible E. coli and other bacterial species from β-lactam antibiotic-induced growth inhibition. Taken together, present study demonstrate that OMVs from β-lactam-resistant E. coli play important roles in survival of antibiotic susceptible bacteria against β-lactam antibiotics. This finding may pave the way for new efforts to combat the current global spread of antibiotic resistances, which is considered to be a significant public health threat.
Hybridization and differential introgression associated with environmental shifts in a mistletoe species complex
Authors: Baena-Díaz Fernanda , Ramírez-Barahona Santiago , Ornelas Juan Francisco 
Published: March 2018

AbstractHost specialization after host shifting is traditionally viewed as the pathway to speciation in parasitic plants. However, geographical and environmental changes can also influence parasite speciation, through hybridization processes. Here we investigated the impact of past climatic fluctuations, environment, and host shifts on the genetic structure and patterns of hybridization and gene flow betweenPsittacanthus calyculatusandP.schiedeanus, a Mesoamerican species complex. Using microsatellites (408 individuals), we document moderate genetic diversity but high genetic differentiation between widespread parental clusters,calyculatusin dry pine-oak forests andschiedeanusin cloud forests. Bayesian analyses identified a third cluster, with admixture between parental clusters in areas of xeric and tropical dry forests and high levels of migration rates following secondary contact. Coincidently host associations in these areas differ from those in areas of parental species, suggesting that past hybridization played a role in environmental and host shifts. Overall, the observed genetic and geographic patterns suggest that thesePsittacanthuspopulations could have entered a distinct evolutionary pathway. The results provide evidence for highlights on the importance of the Pleistocene climate changes, habitat differences, and potential host shifts in the evolutionary history of Neotropical mistletoes.
Lentiviral vector delivery of short hairpin RNA to NgR1 promotes nerve regeneration and locomotor recovery in injured rat spinal cord
Authors: Zhao Xiaoyang , Peng Zhiming , Long Lingli , Chen Ningning , Zheng Haichong , Deng David Y. B. , Wan Yong 
Published: March 2018

AbstractNogo receptor 1 (NgR1) is a high-affinity receptor of myelin-associated inhibitors (MAIs), and suppresses neurogenesis. Lentiviral vector are commonly used to alter the expression of targeted genes. However, little is known about the potential function of lentiviral vector harboring NgR1 shRNA (LV-NgR1 shRNA) on neurogenesis in spinal cord injury (SCI). In this study, the rats were randomly divided into three groups: including the LN (LV-NgR1 shRNA injection), LC (LV-control shRNA injection) and Sham (laminectomy only). Eight weeks post-injection of LV, spinal cords were examined by histology for changes in cavity size and by immunohistochemistry for changes in expression of NgR1, cell apoptosis, astrocytes, neurons and myelination. Motor function was assessed using the Basso, Beattie and Bresnahan (BBB) locomotor scale. Animals that received LV-NgR1 shRNA remarkably improved the motor function. These animals also showed an increase in levels of nerve fibers, synapses and myelination, a decrease in levels of lesion cavity and cell apoptosis at 8 weeks post-treatment. These findings give evidence that NgR1 may be a promising target for SCI treatment.
A statistical method for analyzing and comparing spatiotemporal cortical activation patterns
Authors: Krauss Patrick , Metzner Claus , Schilling Achim , Tziridis Konstantin , Traxdorf Maximilian , Wollbrink Andreas , Rampp Stefan , Pantev Christo , Schulze Holger 
Published: March 2018

AbstractInformation in the cortex is encoded in spatiotemporal patterns of neuronal activity, but the exact nature of that code still remains elusive. While onset responses to simple stimuli are associated with specific loci in cortical sensory maps, it is completely unclear how the information about a sustained stimulus is encoded that is perceived for minutes or even longer, when discharge rates have decayed back to spontaneous levels. Using a newly developed statistical approach (multidimensional cluster statistics (MCS)) that allows for a comparison of clusters of data points in n-dimensional space, we here demonstrate that the information about long-lasting stimuli is encoded in the ongoing spatiotemporal activity patterns in sensory cortex. We successfully apply MCS to multichannel local field potential recordings in different rodent models and sensory modalities, as well as to human MEG and EEG data, demonstrating its universal applicability. MCS thus indicates novel ways for the development of powerful read-out algorithms of spatiotemporal brain activity that may be implemented in innovative brain-computer interfaces (BCI).
Analysis of the CaMKIIα and β splice-variant distribution among brain regions reveals isoform-specific differences in holoenzyme formation
Authors: Cook Sarah G. , Bourke Ashley M. , O’Leary Heather , Zaegel Vincent , Lasda Erika , Mize-Berge Janna , Quillinan Nidia , Tucker Chandra L. , Coultrap Steven J. , Herson Paco S. , Bayer K. Ulrich 
Published: March 2018

AbstractFour CaMKII isoforms are encoded by distinct genes, and alternative splicing within the variable linker-region generates additional diversity. The α and β isoforms are largely brain-specific, where they mediate synaptic functions underlying learning, memory and cognition. Here, we determined the α and β splice-variant distribution among different mouse brain regions. Surprisingly, the nuclear variant αB was detected in all regions, and even dominated in hypothalamus and brain stem. For CaMKIIβ, the full-length variant dominated in most regions (with higher amounts of minor variants again seen in hypothalamus and brain stem). The mammalian but not fish CaMKIIβ gene lacks exon v3N that encodes the nuclear localization signal in αB, but contains three exons not found in the CaMKIIα gene (exons v1, v4, v5). While skipping of exons v1 and/or v5 generated the minor splice-variants β’, βe and βe’, essentially all transcripts contained exon v4. However, we instead detected another minor splice-variant (now termed βH), which lacks part of the hub domain that mediates formation of CaMKII holoenzymes. Surprisingly, in an optogenetic cellular assay of protein interactions, CaMKIIβH was impaired for binding to the β hub domain, but still bound CaMKIIα. This provides the first indication for isoform-specific differences in holoenzyme formation.
GLYI and D-LDH play key role in methylglyoxal detoxification and abiotic stress tolerance
Authors: Jain Muskan , Nagar Preeti , Sharma Ayush , Batth Rituraj , Aggarwal Sakshi , Kumari Sumita , Mustafiz Ananda 
Published: March 2018

AbstractMethylglyoxal(MG) is a potent cytotoxin that is produced as a byproduct of various metabolic reactions in the cell. The major enzymes for MG detoxification are Glyoxalase I(GLYI), Glyoxalase II(GLYII) and D-lactate dehydrogenase(D-LDH). These three enzymes work together and convert MG into D-pyruvate, which directly goes to TCA cycle. Here, a comparative study of the ability of MG detoxification of these three enzymes has been done in both E. coli and yeast. Ectopic expression of these three genes from Arabidopsis in E. coli in presence of different abiotic stress revealed the contribution of each of these genes in detoxifying MG. Yeast mutants of MG detoxification enzymes were also grown in different stress conditions to record the effect of each gene. These mutants were also used for complementation assays using the respective MG detoxifying genes from Arabidopsis in presence of various stress conditions. The MG content and the corresponding growth of cells was measured in all the bacterial as well as yeast strains. This study reveals differential contribution of MG detoxification enzymes in mitigating MG levels and alleviating stress in both prokaryotes as well as eukaryotes. GLYI and D-LDH were found to be key enzymes in MG detoxification under various abiotic stresses.
A water-based green approach to large-scale production of aqueous compatible graphene nanoplatelets
Authors: Ding Ji-Heng , Zhao Hong-Ran , Yu Hai-Bin 
Published: March 2018

AbstractThe unique properties of graphene are highly desired for printing electronics, coatings, energy storage, separation membranes, biomedicine, and composites. However, the high efficiency exfoliation of graphene into single- or few-layered nanoplates remains a grand challenge and becomes the bottleneck in essential studies and applications of graphene. Here, we report a scalable and green method to exfoliate graphene nanoplatelets (GNPs) from nature graphite in pure water without using any chemicals or surfactants. The essence of this strategy lies in the facile liquid exfoliation route with the assistance of vapor pretreatment for the preparation of edge hydroxylated graphene. The produced graphene consisted primarily of fewer than ten atomic layers. Such the water soluble graphene can be stored in the form of dispersion (~0.55 g L−1) or filter cake for more than 6 months without the risk of re-stacking. This method paves the way for the environmentally friendly and cost-effective production of graphene-based materials.
Numerical simulations of the effects of regional topography on haze pollution in Beijing
Authors: Zhang Ziyin , Xu Xiangde , Qiao Lin , Gong Daoyi , Kim Seong-Joong , Wang Yinjun , Mao Rui 
Published: March 2018

AbstractIn addition to weather conditions and pollutant emissions, the degree to which topography influences the occurrence and development of haze pollution in downtown Beijing and the mechanisms that may be involved remain open questions. A series of atmospheric chemistry simulations are executed by using the online-coupled Weather Research and Forecasting with Chemistry (WRF-Chem) model for November-December 2015 with different hypothetical topographic height scenarios. The simulation results show that topography exerts an important influence on haze pollution in downtown Beijing, particularly the typical development of haze pollution. A possible mechanism that underlies the response of haze pollution to topography is that the mountains that surround Beijing tend to produce anomalous southerly winds, high relative humidity, low boundary layer heights, and sinking motion over most of Beijing. These conditions favor the formation and development of haze pollution in downtown Beijing. Furthermore, the reduction percentage in PM2.5 concentrations due to reduced terrain height in the southerly wind (S) mode is almost three times larger than that in the northerly wind (N) mode. In the context of the regional topography, the simple S and N modes represent useful indicators for haze prediction in Beijing to some extent, especially over medium to long time scales.
Engineered optical and electrical performance of rf–sputtered undoped nickel oxide thin films for inverted perovskite solar cells
Authors: Lee Hyeonseok , Huang Yu-Ting , Horn Mark W. , Feng Shien-Ping 
Published: March 2018

AbstractInverted perovskite solar cells incorporating RF sputtered NiO thin films as a hole transport layer and window layer are demonstrated. The electrical and optical properties of the NiO thin films are engineered using varied sputtering conditions. The localized states within bandgap owing to its crystal disorder and nonstoichiometric features affect the transmittance and the optical bandgap of the NiO thin films which in turn influences the Jsc of the perovskite solar cells. In addition, the electrical properties of the NiO thin films can be also varied during sputtering condition affecting the concentration of nickel vacancies and the resulting hole concentration. The conductivity largely originates from the hole concentration relating to the density of states in the NiO thin films which influence the fill factor (FF) of the solar cells. The solar cells fabricated with the NiO thin films made at 4 Pa of deposition pressure show highest performance owing to excellent transmittance and wider bandgap along with moderate conductivity. With further optimization, the perovskite solar cells exhibit ~20 mA/cm2 of Jsc and a 12.4% PCE (11.3% of averaged PCE).
Rapid evaluation of seed vigor by the absolute content of protein in seed within the same crop
Authors: Wen Daxing , Hou Hongcun , Meng Aiju , Meng Jie , Xie Liuyong , Zhang Chunqing 
Published: March 2018

AbstractSeed vigor, an important index of seed quality, determines the potential for rapid and uniform emergence of plants. The objective of this study was to explore a rapid method for evaluating seed vigor. To analyze the correlation of seed traits and seedling traits related to seed vigor, we designed five experiments including nitrogen fertilizer, irrigation and seed sorting treatments in wheat. The results showed that only the absolute content of protein (ACP) in wheat seed was significantly correlated with plant dry weight in five experiments. Subsequently, another experiment including 30 wheat seed lots was used to validate the above results. Although 100-grain weight was also correlated with plant dry weight (R = 0.799, p < 0.01), the correlation coefficient was lower than that between ACP in seed and plant dry weight (R = 0.897, p < 0.01). Moreover, the results of three experiments using maize seeds was similar with above. The relative content of protein in seed detected by near-infrared spectrum combining with seed weight could realize rapid and nondestructive testing ACP in seed. Collectively, ACP in crop seed could be applied in rapid evaluation of seed vigor and could potentially be used for processing and screening high vigor seeds.
Preventive Effect of Low Intensity Pulsed Ultrasound against Experimental Cerebral Ischemia/Reperfusion Injury via Apoptosis Reduction and Brain-derived Neurotrophic Factor Induction
Authors: Chen Chang-Mu , Wu Cheng-Tien , Yang Ting-Hua , Liu Shing-Hwa , Yang Feng-Yi 
Published: March 2018

AbstractStroke is known as the top 10 causes of death worldwide. Development of effectively neuroprotective or preventive strategies for ischemia stroke is imperative. For the purpose of stroke prevention, we tested the neuroprotective effects of low-intensity pulsed ultrasound (LIPUS) on ischemic stroke. Adult C57BL/6 mice were used to daily treatment with LIPUS for 5 days on left hemisphere before middle cerebral artery occlusion (MCAO)-induced cerebral ischemia/reperfusion injury. Western blotting and immunohistochemistry were performed to assess the protein expressions of signaling molecules. Pretreatment with LIPUS significantly ameliorated the brain ischemic damage, including the reduction of neurological deficit score, infarct area, histopathological score, and showed a better performance in neurological and behavior functions. LIPUS pretreatment could also significantly decrease the neuronal cell apoptosis and upregulation of apoptosis-related signaling molecules and downregulation of brain-derived neurotrophic factor (BDNF) in brain tissues of MCAO-treated mice. Furthermore, LIPUS significantly prevented the decreased cell viability, the increased caspase-3 cleavage, and the decreased BDNF expression in ischemia/reperfusion-treated microglial cells. These results demonstrate that LIPUS effectively prevented the cerebral ischemia/reperfusion injury through apoptosis reduction and BDNF induction in a MCAO mouse model. The neuroprotective potential of LIPUS may provide a novel preventive strategy for ischemic stroke in high-risk patients.
Real-time Detection and Monitoring of Loop Mediated Amplification (LAMP) Reaction Using Self-quenching and De-quenching Fluorogenic Probes
Authors: Gadkar Vijay J. , Goldfarb David M. , Gantt Soren , Tilley Peter A. G. 
Published: March 2018

AbstractLoop-mediated isothermal amplification (LAMP) is an isothermal nucleic acid amplification (iNAAT) technique known for its simplicity, sensitivity and speed. Its low-cost feature has resulted in its wide scale application, especially in low resource settings. The major disadvantage of LAMP is its heavy reliance on indirect detection methods like turbidity and non-specific dyes, which often leads to the detection of false positive results. In the present work, we have developed a direct detection approach, whereby a labelled loop probe quenched in its unbound state, fluoresces only when bound to its target (amplicon). Henceforth, referred to as Fluorescence of Loop Primer Upon Self Dequenching-LAMP (FLOS-LAMP), it allows for the sequence-specific detection of LAMP amplicons. The FLOS-LAMP concept was validated for rapid detection of the human pathogen, Varicella-zoster virus, from clinical samples. The FLOS-LAMP had a limit of detection of 500 copies of the target with a clinical sensitivity and specificity of 96.8% and 100%, respectively. The high level of specificity is a major advance and solves one of the main shortcomings of the LAMP technology, i.e. false positives. Self-quenching/de-quenching probes were further used with other LAMP primer sets and different fluorophores, thereby demonstrating its versatility and adaptability.
Development and application of new composite grouting material for sealing groundwater inflow and reinforcing wall rock in deep mine
Authors: Jinpeng Zhang , Limin Liu , Futao Zhang , Junzhi Cao 
Published: March 2018

AbstractWith cement, bentonite, water glass, J85 accelerator, retarder and water as raw materials, a new composite grouting material used to seal groundwater inflow and reinforce wall rock in deep fractured rock mass was developed in this paper. Based on the reaction mechanism of raw material, the pumpable time, stone rate, initial setting time, plastic strength and unconfined compressive strength of multi-group proportion grouts were tested by orthogonal experiment. Then, the optimum proportion of composite grouting material was selected and applied to the grouting engineering for sealing groundwater inflow and reinforcing wall rock in mine shaft lining. The results show the mixing proportion of the maximum pumpable time, maximum stone rate and minimum initial setting time of grout are AK4BK1CK4DK2, AK3BK1CK1DK4 and AK3BK3CK4DK1, respectively. The mixing proportion of the maximum plastic strength and unconfined compressive strength of grouts concretion bodies are AK1BK1CK1DK3 and AK1BK1CK1DK1, respectively. Balanced the above 5 indicators overall and determined the optimum proportion of grouts: bentonite-cement ratio of 1.0, water-solid ratio of 3.5, accelerator content of 2.9% and retarder content of 1.45%. This new composite grouting material had good effect on the grouting engineering for sealing groundwater inflow and reinforcing wall rock in deep fractured rock mass.
Phosphorous fertilization alleviates drought effects on Alnus cremastogyne by regulating its antioxidant and osmotic potential
Authors: Tariq Akash , Pan Kaiwen , Olatunji Olusanya Abiodun , Graciano Corina , Li Zilong , Sun Feng , Zhang Lin , Wu Xiaogang , Chen Wenkai , Song Dagang , Huang Dan , Xue Tan , Zhang Aiping 
Published: March 2018

AbstractAlnus cremastogyne, a broad-leaved tree endemic to south-western China, has both commercial and restoration importance. However, little is known of its morphological, physiological and biochemical responses to drought and phosphorous (P) application. A randomized experimental design was used to investigate how drought affected A. cremastogyne seedlings, and the role that P applications play in these responses. Drought had significant negative effects on A. cremastogyne growth and metabolism, as revealed by reduced biomass (leaf, shoot and root), leaf area, stem diameter, plant height, photosynthetic rate, leaf relative water content, and photosynthetic pigments, and a weakened antioxidative defence mechanism and high lipid peroxidation level. However, the reduced leaf area and enhanced osmolyte (proline and soluble sugars) accumulation suggests drought avoidance and tolerance strategies in this tree. Applying P significantly improved the leaf relative water content and photosynthetic rate of drought-stressed seedlings, which may reflect increased anti-oxidative enzyme (superoxide dismutase, catalase and peroxidase) activities, osmolyte accumulation, soluble proteins, and decreased lipid peroxidation levels. However, P had only a slight or negligible effect on the well-watered plants. A. cremastogyne is sensitive to drought stress, but P facilitates and improves its metabolism primarily via biochemical and physiological rather than morphological adjustments, regardless of water availability.