bluuebunny/crossref_metadata_2025_split huggingface dataset:
Exploratory Metabolomics Profiling in the Kainic Acid Rat Model Reveals Depletion of 25-Hydroxyvitamin D3 during Epileptogenesis
Authors: Heischmann Svenja , Quinn Kevin , Cruickshank-Quinn Charmion , Liang Li-Ping , Reisdorph Rick , Reisdorph Nichole , Patel Manisha 
Published: August 2016

AbstractCurrently, no reliable markers are available to evaluate the epileptogenic potential of a brain injury. The electroencephalogram is the standard method of diagnosis of epilepsy; however, it is not used to predict the risk of developing epilepsy. Biomarkers that indicate an individual’s risk to develop epilepsy, especially those measurable in the periphery are urgently needed. Temporal lobe epilepsy (TLE), the most common form of acquired epilepsy, is characterized by spontaneous recurrent seizures following brain injury and a seizure-free “latent” period. Elucidation of mechanisms at play during epilepsy development (epileptogenesis) in animal models of TLE could enable the identification of predictive biomarkers. Our pilot study using liquid chromatography-mass spectrometry metabolomics analysis revealed changes (p-value ≤ 0.05, ≥1.5-fold change) in lipid, purine, and sterol metabolism in rat plasma and hippocampus during epileptogenesis and chronic epilepsy in the kainic acid model of TLE. Notably, disease development was associated with dysregulation of vitamin D3 metabolism at all stages and plasma 25-hydroxyvitamin D3 depletion in the acute and latent phase of injury-induced epileptogenesis. These data suggest that plasma VD3 metabolites reflect the severity of an epileptogenic insult and that a panel of plasma VD3 metabolites may be able to serve as a marker of epileptogenesis.
microRNA regulatory circuits in a mouse model of inherited retinal degeneration
Authors: Palfi Arpad , Hokamp Karsten , Hauck Stefanie M. , Vencken Sebastian , Millington-Ward Sophia , Chadderton Naomi , Carrigan Mathew , Kortvely Elod , Greene Catherine M. , Kenna Paul F. , Farrar G. Jane 
Published: August 2016

AbstractmiRNA dysregulation is a hallmark of many neurodegenerative disorders, including those involving the retina. Up-regulation of miR-1/133 and miR-142, and down-regulation of miR-183/96/182 has been described in the RHO-P347S mouse retina, a model for a common form of inherited blindness. High-throughput LC-MS/MS was employed to analyse the protein expression of predicted targets for these miRNAs in RHO-P347S mouse retinas; 133 potential target genes were identified. Pathway over-representation analysis suggests G-protein signaling/visual transduction, and synaptic transmission for miR-1, and transmembrane transport, cell-adhesion, signal transduction and apoptosis for miR-183/96/182 as regulated functions in retina. Validation of miRNA-target mRNA interactions for miR-1, miR-96/182 and miR-96 targeting Ctbp2, Rac1 and Slc6a9, respectively, was demonstrated in vitro. In vivo interaction of miR-183/96/182 and Rac1 mRNA in retina was confirmed using miR-CATCH. Additional miRNAs (including miR-103-3p, miR-9-5p) were both predicted to target Rac1 mRNA and enriched by Rac1-miR-CATCH. Other Rac1-miR-CATCH-enriched miRNAs (including miR-125a/b-5p, miR-378a-3p) were not predicted to target Rac1. Furthermore, levels of ~25% of the retinal Rac1 interactors were determined by LC-MS/MS; expression of Rap1gds1 and Cav1 was elevated. Our data suggest significant utilisation of miRNA-based regulation in retina. Possibly more than 30 miRNAs interact with Rac1 in retina, targeting both UTRs and coding regions.
Neutrons describe ectoine effects on water H-bonding and hydration around a soluble protein and a cell membrane
Authors: Zaccai Giuseppe , Bagyan Irina , Combet Jérôme , Cuello Gabriel J. , Demé Bruno , Fichou Yann , Gallat François-Xavier , Galvan Josa Victor M. , von Gronau Susanne , Haertlein Michael , Martel Anne , Moulin Martine , Neumann Markus , Weik Martin , Oesterhelt Dieter 
Published: August 2016

AbstractUnderstanding adaptation to extreme environments remains a challenge of high biotechnological potential for fundamental molecular biology. The cytosol of many microorganisms, isolated from saline environments, reversibly accumulates molar concentrations of the osmolyte ectoine to counterbalance fluctuating external salt concentrations. Although they have been studied extensively by thermodynamic and spectroscopic methods, direct experimental structural data have, so far, been lacking on ectoine-water-protein interactions. In this paper,in vivodeuterium labeling, small angle neutron scattering, neutron membrane diffraction and inelastic scattering are combined with neutron liquids diffraction to characterize the extreme ectoine-containing solvent and its effects on purple membrane ofH. salinarumandE. colimaltose binding protein. The data reveal that ectoine is excluded from the hydration layer at the membrane surface and does not affect membrane molecular dynamics, and prove a previous hypothesis that ectoine is excluded from a monolayer of dense hydration water around the soluble protein. Neutron liquids diffraction to atomic resolution shows how ectoine enhances the remarkable properties of H-bonds in water—properties that are essential for the proper organization, stabilization and dynamics of biological structures.
Precipitation overrides warming in mediating soil nitrogen pools in an alpine grassland ecosystem on the Tibetan Plateau
Authors: Lin Li , Zhu Biao , Chen Chengrong , Zhang Zhenhua , Wang Qi-Bing , He Jin-Sheng 
Published: August 2016

AbstractSoils in the alpine grassland store a large amount of nitrogen (N) due to slow decomposition. However, the decomposition could be affected by climate change, which has profound impacts on soil N cycling. We investigated the changes of soil total N and five labile N stocks in the topsoil, the subsoil and the entire soil profile in response to three years of experimental warming and altered precipitation in a Tibetan alpine grassland. We found that warming significantly increased soil nitrate N stock and decreased microbial biomass N (MBN) stock. Increased precipitation reduced nitrate N, dissolved organic N and amino acid N stocks, but increased MBN stock in the topsoil. No change in soil total N was detected under warming and altered precipitation regimes. Redundancy analysis further revealed that soil moisture (26.3%) overrode soil temperature (10.4%) in explaining the variations of soil N stocks across the treatments. Our results suggest that precipitation exerted stronger influence than warming on soil N pools in this mesic and high-elevation grassland ecosystem. This indicates that the projected rise in future precipitation may lead to a significant loss of dissolved soil N pools by stimulating the biogeochemical processes in this alpine grassland.
A multi-similarity spectral clustering method for community detection in dynamic networks
Authors: Qin Xuanmei , Dai Weidi , Jiao Pengfei , Wang Wenjun , Yuan Ning 
Published: August 2016

AbstractCommunity structure is one of the fundamental characteristics of complex networks. Many methods have been proposed for community detection. However, most of these methods are designed for static networks and are not suitable for dynamic networks that evolve over time. Recently, the evolutionary clustering framework was proposed for clustering dynamic data, and it can also be used for community detection in dynamic networks. In this paper, a multi-similarity spectral (MSSC) method is proposed as an improvement to the former evolutionary clustering method. To detect the community structure in dynamic networks, our method considers the different similarity metrics of networks. First, multiple similarity matrices are constructed for each snapshot of dynamic networks. Then, a dynamic co-training algorithm is proposed by bootstrapping the clustering of different similarity measures. Compared with a number of baseline models, the experimental results show that the proposed MSSC method has better performance on some widely used synthetic and real-world datasets with ground-truth community structure that change over time.
Structural and physical properties of the dust particles in Qatar and their influence on the PV panel performance
Authors: Aïssa Brahim , Isaifan Rima J. , Madhavan Vinod E. , Abdallah Amir A. 
Published: August 2016

AbstractRecently, extensive R&D has been conducted, both by industry and academia, to significantly raise the conversion efficiency of commercial photovoltaic (PV) modules. The installation of PV systems aimed at optimizing solar energy yield is primarily dictated by its geographic location and installation design to maximize solar exposure. However, even when these characteristics have been addressed appropriately, there are other factors that adversely affect the performance of PV systems, namely the temperature-induced voltage decrease leading to a PV power loss and the dust accumulation (soiling). The latter is the lesser acknowledged factor that significantly influences the performance of PV installations especially in the Middle East region. In this paper we report on the investigation of the structural and physical properties of the desert-dust particles in the State of Qatar. The dust particles were collected directly from the PV panels installed in desert environment and characterized by different techniques, including scanning electron, optical and atomic force microscopies, X-ray diffraction, energy-dispersive, UV-Vis, micro-Raman and Fourier transform infrared spectroscopy. The vibrating sample magnetometry analyses were also conducted to study the magnetic properties of the dust particles. The influence of the dust accumulation on the PV panel performance was also presented and discussed.
Folding analysis of the most complex Stevedore’s protein knot
Authors: Wang Iren , Chen Szu-Yu , Hsu Shang-Te Danny 
Published: August 2016

AbstractDehI is a homodimeric haloacid dehalogenase from Pseudomonas putida that contains the most complex 61 Stevedore’s protein knot within its folding topology. To examine how DehI attains such an intricate knotted topology we combined far-UV circular dichroism (CD), intrinsic fluorescence spectroscopy and small angle X-ray scattering (SAXS) to investigate its folding mechanism. Equilibrium unfolding of DehI by chemical denaturation indicated the presence of two highly populated folding intermediates, I and I’. While the two intermediates vary in secondary structure contents and tertiary packing according to CD and intrinsic fluorescence, respectively, their overall dimension and compactness are similar according to SAXS. Three single-tryptophan variants (W34, W53, and W196) were generated to probe non-cooperative unfolding events localized around the three fluorophores. Kinetic fluorescence measurements indicated that the transition from the intermediate I’ to the unfolded state is rate limiting. Our multiparametric folding analyses suggest that DehI unfolds through a linear folding pathway with two distinct folding intermediates by initial hydrophobic collapse followed by nucleation condensation, and that knotting precedes the formation of secondary structures.
A self-enhanced transport mechanism through long noncoding RNAs for X chromosome inactivation
Authors: Li Chunhe , Hong Tian , Webb Chiu-Ho , Karner Heather , Sun Sha , Nie Qing 
Published: August 2016

AbstractX-chromosome inactivation (XCI) is the mammalian dosage compensation strategy for balancing sex chromosome content between females and males. While works exist on initiation of symmetric breaking, the underlying allelic choice mechanisms and dynamic regulation responsible for the asymmetric fate determination of XCI remain elusive. Here we combine mathematical modeling and experimental data to examine the mechanism of XCI fate decision by analyzing the signaling regulatory circuit associated with long noncoding RNAs (lncRNAs) involved in XCI. We describe three plausible gene network models that incorporate features of lncRNAs in their localized actions and rapid transcriptional turnovers. In particular, we show experimentally that Jpx (a lncRNA) is transcribed biallelically, escapes XCI and is asymmetrically dispersed between two X’s. Subjecting Jpx to our test of model predictions against previous experimental observations, we identify that a self-enhanced transport feedback mechanism is critical to XCI fate decision. In addition, the analysis indicates that an ultrasensitive response of Jpx signal on CTCF is important in this mechanism. Overall, our combined modeling and experimental data suggest that the self-enhanced transport regulation based on allele-specific nature of lncRNAs and their temporal dynamics provides a robust and novel mechanism for bi-directional fate decisions in critical developmental processes.
Expanding the molecular toolkit for the homoacetogen Clostridium ljungdahlii
Authors: Molitor Bastian , Kirchner Kristina , Henrich Alexander W. , Schmitz Simone , Rosenbaum Miriam A. 
Published: August 2016

AbstractIncreasing interest in homoacetogenic bacteria for the production of biochemicals and biofuels requisites the development of new genetic tools for these atypical production organisms. An attractive host for the conversion of synthesis gas or electricity into multi-carbon compounds is Clostridium ljungdahlii. So far only limited achievements in modifying this organism towards the production of industrially relevant compounds have been made. Therefore, there is still a strong need for developing new and optimizing existing genetic tools to efficiently access its metabolism. Here, we report on the development of a stable and reproducible transformation protocol that is applicable to C. ljungdahlii and several other clostridial species. Further, we demonstrate the functionality of a temperature-sensitive origin of replication in combination with a fluorescence marker system as important tools for future genetic engineering of this host for microbial bioproduction.
Common methods for fecal sample storage in field studies yield consistent signatures of individual identity in microbiome sequencing data
Authors: Blekhman Ran , Tang Karen , Archie Elizabeth A. , Barreiro Luis B. , Johnson Zachary P. , Wilson Mark E. , Kohn Jordan , Yuan Michael L. , Gesquiere Laurence , Grieneisen Laura E. , Tung Jenny 
Published: August 2016

AbstractField studies of wild vertebrates are frequently associated with extensive collections of banked fecal samples—unique resources for understanding ecological, behavioral and phylogenetic effects on the gut microbiome. However, we do not understand whether sample storage methods confound the ability to investigate interindividual variation in gut microbiome profiles. Here, we extend previous work on storage methods for gut microbiome samples by comparing immediate freezing, the gold standard of preservation, to three methods commonly used in vertebrate field studies: lyophilization, storage in ethanol and storage in RNAlater. We found that the signature of individual identity consistently outweighed storage effects: alpha diversity and beta diversity measures were significantly correlated across methods and while samples often clustered by donor, they never clustered by storage method. Provided that all analyzed samples are stored the same way, banked fecal samples therefore appear highly suitable for investigating variation in gut microbiota. Our results open the door to a much-expanded perspective on variation in the gut microbiome across species and ecological contexts.
Optical Addressing of Multi-Colour Photochromic Material Mixture for Volumetric Display
Authors: Hirayama Ryuji , Shiraki Atsushi , Naruse Makoto , Nakamura Shinichiro , Nakayama Hirotaka , Kakue Takashi , Shimobaba Tomoyoshi , Ito Tomoyoshi 
Published: August 2016

AbstractThis is the first study to demonstrate that colour transformations in the volume of a photochromic material (PM) are induced at the intersections of two control light channels, one controlling PM colouration and the other controlling decolouration. Thus, PM colouration is induced by position selectivity and therefore, a dynamic volumetric display may be realised using these two control lights. Moreover, a mixture of multiple PM types with different absorption properties exhibits different colours depending on the control light spectrum. Particularly, the spectrum management of the control light allows colour-selective colouration besides position selectivity. Therefore, a PM-based, full-colour volumetric display is realised. We experimentally construct a mixture of two PM types and validate the operating principles of such a volumetric display system. Our system is constructed simply by mixing multiple PM types; therefore, the display hardware structure is extremely simple and the minimum size of a volume element can be as small as the size of a molecule. Volumetric displays can provide natural three-dimensional (3D) perception; therefore, the potential uses of our system include high-definition 3D visualisation for medical applications, architectural design, human–computer interactions, advertising and entertainment.
Quantifying the evolution of flow boiling bubbles by statistical testing and image analysis: toward a general model
Authors: Xiao Qingtai , Xu Jianxin , Wang Hua 
Published: August 2016

AbstractA new index, the estimate of the error variance, which can be used to quantify the evolution of the flow patterns when multiphase components or tracers are difficultly distinguishable, was proposed. The homogeneity degree of the luminance space distribution behind the viewing windows in the direct contact boiling heat transfer process was explored. With image analysis and a linear statistical model, the F-test of the statistical analysis was used to test whether the light was uniform and a non-linear method was used to determine the direction and position of a fixed source light. The experimental results showed that the inflection point of the new index was approximately equal to the mixing time. The new index has been popularized and applied to a multiphase macro mixing process by top blowing in a stirred tank. Moreover, a general quantifying model was introduced for demonstrating the relationship between the flow patterns of the bubble swarms and heat transfer. The results can be applied to investigate other mixing processes that are very difficult to recognize the target.
De novo transcriptome assembly and analysis of differentially expressed genes of two barley genotypes reveal root-zone-specific responses to salt exposure
Authors: Hill Camilla Beate , Cassin Andrew , Keeble-Gagnère Gabriel , Doblin Monika S. , Bacic Antony , Roessner Ute 
Published: August 2016

AbstractPlant roots are the first organs sensing and responding to salinity stress, manifested differentially between different root types, and also at the individual tissue and cellular level. High genetic diversity and the current lack of an assembled map-based sequence of the barley genome severely limit barley research potential. We used over 580 and 600 million paired-end reads, respectively, to create twode novoassemblies of a barley landrace (Sahara) and a malting cultivar (Clipper) with known contrasting responses to salinity. Generalized linear models were used to statistically access spatial, treatment-related, and genotype-specific responses. This revealed a spatial gene expression gradient along the barley root, with more differentially expressed transcripts detected between different root zones than between treatments. The root transcriptome also showed a gradual transition from transcripts related to sugar-mediated signaling at the root meristematic zone to those involved in cell wall metabolism in the elongation zone, and defense response-related pathways toward the maturation zone, with significant differences between the two genotypes. The availability of these additional transcriptome reference sets will serve as a valuable resource to the cereal research community, and may identify valuable traits to assist in breeding programmes.
The loss of ATP2C1 impairs the DNA damage response and induces altered skin homeostasis: Consequences for epidermal biology in Hailey-Hailey disease
Authors: Cialfi Samantha , Le Pera Loredana , De Blasio Carlo , Mariano Germano , Palermo Rocco , Zonfrilli Azzurra , Uccelletti Daniela , Palleschi Claudio , Biolcati Gianfranco , Barbieri Luca , Screpanti Isabella , Talora Claudio 
Published: August 2016

AbstractMutation of the Golgi Ca2+-ATPase ATP2C1 is associated with deregulated calcium homeostasis and altered skin function. ATP2C1 mutations have been identified as having a causative role in Hailey-Hailey disease, an autosomal-dominant skin disorder. Here, we identified ATP2C1 as a crucial regulator of epidermal homeostasis through the regulation of oxidative stress. Upon ATP2C1 inactivation, oxidative stress and Notch1 activation were increased in cultured human keratinocytes. Using RNA-seq experiments, we found that the DNA damage response (DDR) was consistently down-regulated in keratinocytes derived from the lesions of patients with Hailey-Hailey disease. Although oxidative stress activates the DDR, ATP2C1 inactivation down-regulates DDR gene expression. We showed that the DDR response was a major target of oxidative stress-induced Notch1 activation. Here, we show that this activation is functionally important because early Notch1 activation in keratinocytes induces keratinocyte differentiation and represses the DDR. These results indicate that an ATP2C1/NOTCH1 axis might be critical for keratinocyte function and cutaneous homeostasis, suggesting a plausible model for the pathological features of Hailey-Hailey disease.
Overexpression of the Eggplant (Solanum melongena) NAC Family Transcription Factor SmNAC Suppresses Resistance to Bacterial Wilt
Authors: Na Chen , Shuanghua Wu , Jinglong Fu , Bihao Cao , Jianjun Lei , Changming Chen , Jin Jiang 
Published: August 2016

AbstractBacterial wilt (BW) is a serious disease that affects eggplant (Solanum melongena) production. Although resistance to this disease has been reported, the underlying mechanism is unknown. In this study, we identified a NAC family transcription factor (SmNAC) from eggplant and characterized its expression, its localization at the tissue and subcellular levels, and its role in BW resistance. To this end, transgenic eggplant lines were generated in which the expression of SmNAC was constitutively up regulated or suppressed using RNAi. The results indicated that overexpression of SmNAC decreases resistance to BW. Moreover, SmNAC overexpression resulted in the reduced accumulation of the plant immune signaling molecule salicylic acid (SA) and reduced expression of ICS1 (a gene that encode isochorismate synthase 1, which is involved in SA biosynthesis). We propose that reduced SA content results in increased bacterial wilt susceptibility in the transgenic lines. Our results provide important new insights into the regulatory mechanisms of bacterial wilt resistance in eggplant.