bluuebunny/crossref_metadata_2025_split huggingface dataset:
The crosstalk between Target of Rapamycin (TOR) and Jasmonic Acid (JA) signaling existing in Arabidopsis and cotton
Authors: Song Yun , Zhao Ge , Zhang Xueyan , Li Linxuan , Xiong Fangjie , Zhuo Fengping , Zhang Chaojun , Yang Zuoren , Datla Raju , Ren Maozhi , Li Fuguang 
Published: April 2017

AbstractTarget of rapamycin (TOR) acts as an important regulator of cell growth, development and stress responses in most examined diploid eukaryotes. However, little is known about TOR in tetraploid species such as cotton. Here, we show that TORC1-S6K-RPS6, the major signaling components, are conserved and further expanded in cotton genome. Though the cotton seedlings are insensitive to rapamycin, AZD8055, the second-generation inhibitor of TOR, can significantly suppress the growth in cotton. Global transcriptome analysis revealed that genes associated with jasmonic acid (JA) biosynthesis and transduction were significantly altered in AZD8055 treated cotton seedlings, suggesting the potential crosstalk between TOR and JA signaling. Pharmacological and genetic approaches have been employed to get further insights into the molecular mechanism of the crosstalk between TOR and JA. Combination of AZD8055 with methyl jasmonate can synergistically inhibit cotton growth, and additionally JA levels were significantly increased when cotton seedlings were subjected to AZD8055. JA biosynthetic and signaling mutants including jar1, coi1-2 and myc2-2 displayed TOR inhibitor-resistant phenotypes, whereas COI1 overexpression transgenic lines and jaz10 exhibited sensitivity to AZD8055. Consistently, cotton JAZ can partially rescue TOR-suppressed phenotypes in Arabidopsis. These evidences revealed that the crosstalk between TOR and JA pathway operates in cotton and Arabidopsis.
A semi-synchronous label propagation algorithm with constraints for community detection in complex networks
Authors: Hou Chin Jia , Ratnavelu Kuru 
Published: April 2017

AbstractCommunity structure is an important feature of a complex network, where detection of the community structure can shed some light on the properties of such a complex network. Amongst the proposed community detection methods, the label propagation algorithm (LPA) emerges as an effective detection method due to its time efficiency. Despite this advantage in computational time, the performance of LPA is affected by randomness in the algorithm. A modified LPA, called CLPA-GNR, was proposed recently and it succeeded in handling the randomness issues in the LPA. However, it did not remove the tendency for trivial detection in networks with a weak community structure. In this paper, an improved CLPA-GNR is therefore proposed. In the new algorithm, the unassigned and assigned nodes are updated synchronously while the assigned nodes are updated asynchronously. A similarity score, based on the Sørensen-Dice index, is implemented to detect the initial communities and for breaking ties during the propagation process. Constraints are utilised during the label propagation and community merging processes. The performance of the proposed algorithm is evaluated on various benchmark and real-world networks. We find that it is able to avoid trivial detection while showing substantial improvement in the quality of detection.
Microbial Biogeography and Core Microbiota of the Rat Digestive Tract
Authors: Li Dongyao , Chen Haiqin , Mao Bingyong , Yang Qin , Zhao Jianxin , Gu Zhennan , Zhang Hao , Chen Yong Q. , Chen Wei 
Published: April 2017

AbstractAs a long-standing biomedical model, rats have been frequently used in studies exploring the correlations between gastrointestinal (GI) bacterial biota and diseases. In the present study, luminal and mucosal samples taken along the longitudinal axis of the rat digestive tract were subjected to 16S rRNA gene sequencing-based analysis to determine the baseline microbial composition. Results showed that the community diversity increased from the upper to lower GI segments and that the stratification of microbial communities as well as shift of microbial metabolites were driven by biogeographic location. A greater proportion of lactate-producing bacteria (such as Lactobacillus, Turicibacter and Streptococcus) were found in the stomach and small intestine, while anaerobic Lachnospiraceae and Ruminococcaceae, fermenting carbohydrates and plant aromatic compounds, constituted the bulk of the large-intestinal core microbiota where topologically distinct co-occurrence networks were constructed for the adjacent luminal and mucosal compartments. When comparing the GI microbiota from different hosts, we found that the rat microbial biogeography might represent a new reference, distinct from other murine animals. Our study provides the first comprehensive characterization of the rat GI microbiota landscape for the research community, laying the foundation for better understanding and predicting the disease-related alterations in microbial communities.
A novel tool for monitoring endogenous alpha-synuclein transcription by NanoLuciferase tag insertion at the 3′end using CRISPR-Cas9 genome editing technique
Authors: Basu Sambuddha , Adams Levi , Guhathakurta Subhrangshu , Kim Yoon-Seong 
Published: April 2017

Abstractα-synuclein (α-SYN) is a major pathologic contributor to Parkinson’s disease (PD). Multiplication of α-SYN encoding gene (SNCA) is correlated with early onset of the disease underlining the significance of its transcriptional regulation. Thus, monitoring endogenous transcription of SNCA is of utmost importance to understand PD pathology. We developed a stable cell line expressing α-SYN endogenously tagged with NanoLuc luciferase reporter using CRISPR/Cas9-mediated genome editing. This allows efficient measurement of transcriptional activity of α-SYN in its native epigenetic landscape which is not achievable using exogenous transfection-based luciferase reporter assays. The NanoLuc activity faithfully monitored the transcriptional regulation of SNCA following treatment with different drugs known to regulate α-SYN expression; while exogenous promoter-reporter assays failed to reproduce the similar outcomes. To our knowledge, this is the first report showing endogenous monitoring of α-SYN transcription, thus making it an efficient drug screening tool that can be used for therapeutic intervention in PD.
Artificial spatiotemporal touch inputs reveal complementary decoding in neocortical neurons
Authors: Oddo Calogero M. , Mazzoni Alberto , Spanne Anton , Enander Jonas M. D. , Mogensen Hannes , Bengtsson Fredrik , Camboni Domenico , Micera Silvestro , Jörntell Henrik 
Published: April 2017

AbstractInvestigations of the mechanisms of touch perception and decoding has been hampered by difficulties in achieving invariant patterns of skin sensor activation. To obtain reproducible spatiotemporal patterns of activation of sensory afferents, we used an artificial fingertip equipped with an array of neuromorphic sensors. The artificial fingertip was used to transduce real-world haptic stimuli into spatiotemporal patterns of spikes. These spike patterns were delivered to the skin afferents of the second digit of rats via an array of stimulation electrodes. Combined with low-noise intra- and extracellular recordings from neocortical neurons in vivo, this approach provided a previously inaccessible high resolution analysis of the representation of tactile information in the neocortical neuronal circuitry. The results indicate high information content in individual neurons and reveal multiple novel neuronal tactile coding features such as heterogeneous and complementary spatiotemporal input selectivity also between neighboring neurons. Such neuronal heterogeneity and complementariness can potentially support a very high decoding capacity in a limited population of neurons. Our results also indicate a potential neuroprosthetic approach to communicate with the brain at a very high resolution and provide a potential novel solution for evaluating the degree or state of neurological disease in animal models.
640-Gbit/s fast physical random number generation using a broadband chaotic semiconductor laser
Authors: Zhang Limeng , Pan Biwei , Chen Guangcan , Guo Lu , Lu Dan , Zhao Lingjuan , Wang Wei 
Published: April 2017

AbstractAn ultra-fast physical random number generator is demonstrated utilizing a photonic integrated device based broadband chaotic source with a simple post data processing method. The compact chaotic source is implemented by using a monolithic integrated dual-mode amplified feedback laser (AFL) with self-injection, where a robust chaotic signal with RF frequency coverage of above 50 GHz and flatness of ±3.6 dB is generated. By using 4-least significant bits (LSBs) retaining from the 8-bit digitization of the chaotic waveform, random sequences with a bit-rate up to 640 Gbit/s (160 GS/s × 4 bits) are realized. The generated random bits have passed each of the fifteen NIST statistics tests (NIST SP800-22), indicating its randomness for practical applications.
A randomized controlled trial of an ambulatory approach versus the hospital-based approach in managing suspected obstructive sleep apnea syndrome
Authors: Hui David S. , Ng Susanna S. , To Kin-Wang , Ko Fanny W. , Ngai Jenny , Chan Ken K. P. , Yip Wing-Ho , Chan Tat-On , Yiu Karen , Tam Wilson W. S. 
Published: April 2017

AbstractComparisons of home-based versus hospital-based approach in managing patients with suspected obstructive sleep apnoea syndrome(OSAS). A prospective, controlled CPAP parallel study of new referrals with suspected OSAS randomized into group A) home-based or B) hospital-based approach. Following detection of AHI ≥ 15/hr by Embletta sleep study (group A) or polysomnography (group B), patients received CPAP for 3 months after an overnight autoCPAP titration at home or in hospital respectively. Modified intention-to-treat analysis of those with AHI ≥ 15/hr on CPAP (n = 86 vs 86) showed no difference in Epworth sleepiness score, the primary endpoint, but greater improvement in Sleep-Apnoea-Quality-of-Life-Index[difference 0.3,(95%CI 0.02, 0.6), p = 0.033] at 3 months in group A. The mean costs for the patients in group A and group B were HK$8479(989) and HK$22,248(2407) respectively. The mean difference between groups was HK$-13,769(USD 1770 equivalent) per patient with 95% CI. (−14324, −13213), p < 0.001. The waiting time of patients with AHI ≥ 15/hr who were started on CPAP treatment from the first clinic consultation to the diagnostic sleep test, autoCPAP titration, and CPAP treatment was 189.6, 148.8 and 145.0 days shorter in group A than group B respectively. Home-based approach is non-inferior to hospital-based approach in managing patients with suspected OSAS, with shorter waiting time, and substantial cost savings.
Disulfide Bond Formation and N-Glycosylation Modulate Protein-Protein Interactions in GPI-Transamidase (GPIT)
Authors: Yi Lina , Bozkurt Gunes , Li Qiubai , Lo Stanley , Menon Anant K. , Wu Hao 
Published: April 2017

AbstractGlycosylphosphatidylinositol (GPI) transamidase (GPIT), the enzyme that attaches GPI anchors to proteins as they enter the lumen of the endoplasmic reticulum, is a membrane-bound hetero-pentameric complex consisting of Gpi8, Gpi16, Gaa1, Gpi17 and Gab1. Here, we expressed and purified the luminal domain of Saccharomyces cerevisiae (S. cerevisiae) Gpi8 using different expression systems, and examined its interaction with insect cell expressed luminal domain of S. cerevisiae Gpi16. We found that the N-terminal caspase-like domain of Gpi8 forms a disulfide-linked dimer, which is strengthened by N-glycosylation. The non-core domain of Gpi8 following the caspase-like domain inhibits this dimerization. In contrast to the previously reported disulfide linkage between Gpi8 and Gpi16 in human and trypanosome GPIT, our data show that the luminal domains of S. cerevisiae Gpi8 and S. cerevisiae Gpi16 do not interact directly, nor do they form a disulfide bond in the intact S. cerevisiae GPIT. Our data suggest that subunit interactions within the GPIT complex from different species may vary, a feature that should be taken into account in future structural and functional studies.
Biotemplating pores with size and shape diversity for Li-oxygen Battery Cathodes
Authors: Oh Dahyun , Ozgit-Akgun Cagla , Akca Esin , Thompson Leslie E. , Tadesse Loza F. , Kim Ho-Cheol , Demirci Gökhan , Miller Robert D. , Maune Hareem 
Published: April 2017

AbstractSynthetic porogens provide an easy way to create porous structures, but their usage is limited due to synthetic difficulties, process complexities and prohibitive costs. Here we investigate the use of bacteria, sustainable and naturally abundant materials, as a pore template. The bacteria require no chemical synthesis, come in variable sizes and shapes, degrade easier and are approximately a million times cheaper than conventional porogens. We fabricate free standing porous multiwalled carbon nanotube (MWCNT) films using cultured, harmless bacteria as porogens, and demonstrate substantial Li-oxygen battery performance improvement by porosity control. Pore volume as well as shape in the cathodes were easily tuned to improve oxygen evolution efficiency by 30% and double the full discharge capacity in repeated cycles compared to the compact MWCNT electrode films. The interconnected pores produced by the templates greatly improve the accessibility of reactants allowing the achievement of 4,942 W/kg (8,649 Wh/kg) at 2 A/ge (1.7 mA/cm2).
iTRAQ-based Proteomic Analysis of Porcine Kidney Epithelial PK15 cells Infected with Pseudorabies virus
Authors: Yang Songbai , Pei Yue , Zhao Ayong 
Published: April 2017

AbstractPseudorabies virus (PRV) is one of the most important pathogens of swine, resulting in severe economic losses to the pig industry. To improve our understanding of the host responses to PRV infection, we applied isobaric tags for relative and absolute quantification (iTRAQ) labeling coupled with liquid chromatography-tandem mass spectrometry to quantitatively identify the differentially expressed cellular proteins in PRV-infected PK15 cells. In total, relative quantitative data were identified for 4333 proteins in PRV and mock- infected PK15 cells, among which 466 cellular proteins were differentially expressed, including 234 upregulated proteins and 232 downregulated proteins. Bioinformatics analysis disclosed that most of these differentially expressed proteins were involved in metabolic processes, cellular growth and proliferation, endoplasmic reticulum (ER) stress response, cell adhesion and cytoskeleton. Moreover, expression levels of four representative proteins, beta-catenin, STAT1, GRB2 and PCNA, were further confirmed by western blot analysis. This is the first attempt to analyze the protein profile of PRV-infected PK15 cells using iTRAQ technology, and our findings may provide valuable information to help understand the host response to PRV infection.
Effect of Vitamin D Replacement on Cognition in Multiple Sclerosis Patients
Authors: Darwish Hala , Haddad Ribal , Osman Sahar , Ghassan Stephanie , Yamout Bassem , Tamim Hani , Khoury Samia 
Published: April 2017

AbstractMultiple Sclerosis is associated with deficient serum 25 hydroxyvitamin D (25 (OH)D) level and cognitive impairment. The aim of this study is to evaluate cognitive performance in MS patients with deficient 25 (OH)D (<25 ng/ml) compared to patients with sufficient levels (>35 ng/ml), then to evaluate the change in cognitive performance after 3 months of vitamin D3 oral replacement. Eighty-eight MS patients with relapsing remitting and clinically isolated type of MS, older than 18 years treated with interferon beta were enrolled. Cognitive testing was performed at baseline and at 3 months using the Montreal Cognitive Assessment (MoCA), Stroop, Symbol Digit Modalities (SDMT) and Brief Visuospatial Memory Test (BVMT-R). Serum 25 (OH)D was measured at baseline and at the end of the study. Vitamin D3 replacement improved the MS patients’ cognitive performance after 3 months on the MoCA and BVMT-Delayed Recall (DR). Sufficient serum 25 (OH)D level predicted better cognitive performance on the BVMT-DR at baseline (β: 1.74, p: <0.008) and 3 months (β: 1.93, p: <0.01) after adjusting for all measured confounding variables. Vitamin D3 replacement could improve cognitive performance in MS patients and make a significant difference in the patient’s quality of life.
Efficient multiuser quantum cryptography network based on entanglement
Authors: Xue Peng , Wang Kunkun , Wang Xiaoping 
Published: April 2017

AbstractWe present an efficient quantum key distribution protocol with a certain entangled state to solve a special cryptographic task. Also, we provide a proof of security of this protocol by generalizing the proof of modified of Lo-Chau scheme. Based on this two-user scheme, a quantum cryptography network protocol is proposed without any quantum memory.
A UPF0118 family protein with uncharacterized function from the moderate halophile Halobacillus andaensis represents a novel class of Na+(Li+)/H+ antiporter
Authors: Dong Ping , Wang Lidan , Song Na , Yang Lina , Chen Jin , Yan Mingxue , Chen Huiwen , Zhang Rui , Li Jincheng , Abdel-motaal Heba , Jiang Juquan 
Published: April 2017

AbstractIn this study, genomic DNA was screened from Halobacillus andaensis NEAU-ST10-40T by selection in Escherichia coli KNabc lacking three major Na+/H+ antiporters. One gene designated upf0118 exhibiting Na+(Li+)/H+ antiport activity was finally cloned. Protein alignment showed that UPF0118 shares the highest identity of 81.5% with an unannotated gene encoding a protein with uncharacterized protein function belonging to UPF0118 family from H. kuroshimensis, but shares no identity with all known specific Na+(Li+)/H+ antiporter genes or genes with Na+(Li+)/H+ antiport activity. Growth test, western blot and Na+(Li+)/H+ antiport assay revealed that UPF0118 as a transmembrane protein exhibits pH-dependent Na+(Li+)/H+ antiport activity. Phylogenetic analysis indicated that UPF0118 clustered with all its homologs belonging to UPF0118 family at a wide range of 22–82% identities with the bootstrap value of 92%, which was significantly distant with all known specific single-gene Na+(Li+)/H+ antiporters and single-gene proteins with the Na+(Li+)/H+ antiport activity. Taken together, we propose that UPF0118 should represent a novel class of Na+(Li+)/H+ antiporter. To the best of our knowledge, this is the first report on the functional analysis of a protein with uncharacterized protein function as a representative of UPF0118 family containing the domain of unknown function, DUF20.
Structural basis for a novel type of cytokinin-activating protein
Authors: Seo Hogyun , Kim Kyung-Jin 
Published: April 2017

AbstractThe Lonely Guy (LOG) protein has been identified as a crucial enzyme involved in the production of cytokinins, which are important phytohormones, in plants and plant-interacting organisms. However, C. glutamicum has an isoform (Cg1261) of LOG that contains an extended N-terminal region compared to those of known LOGs, and this type of isoforms are also found in a variety of organisms. Nevertheless, these proteins are considered as lysine decarboxylases, without their functional characterization. To investigate the function of Cg1261, we determined its crystal structure at a resolution of 1.95 Å. Unlike known dimeric LOGs, Cg1261 was found to form a hexamer. The overall shape of the hexamer resembles a trillium flower, in which a twisted dimer constitutes each petal. The dimeric petal is well superposed with known LOG dimers, and its active site conformation is similar to those of LOG dimers, suggesting that the hexameric LOG-like protein also acts as a LOG. Biochemical and in vivo cytokinin production studies on Cg1261 confirms that Cg1261 functions as a cytokinin-activating protein. Phylogenetic tree analysis using 123 LOG-like proteins suggest that the LOG-like proteins can be categorized to the dimeric type-I LOG and the hexameric type-II LOG.
Stress and adolescent hippocampal neurogenesis: diet and exercise as cognitive modulators
Authors: Hueston C M , Cryan J F , Nolan Y M 
Published: April 2017

AbstractAdolescence is a critical period for brain maturation. Deciphering how disturbances to the central nervous system at this time affect structure, function and behavioural outputs is important to better understand any long-lasting effects. Hippocampal neurogenesis occurs during development and continues throughout life. In adulthood, integration of these new cells into the hippocampus is important for emotional behaviour, cognitive function and neural plasticity. During the adolescent period, maturation of the hippocampus and heightened levels of hippocampal neurogenesis are observed, making alterations to neurogenesis at this time particularly consequential. As stress negatively affects hippocampal neurogenesis, and adolescence is a particularly stressful time of life, it is important to investigate the impact of stressor exposure at this time on hippocampal neurogenesis and cognitive function. Adolescence may represent not only a time for which stress can have long-lasting effects, but is also a critical period during which interventions, such as exercise and diet, could ameliorate stress-induced changes to hippocampal function. In addition, intervention at this time may also promote life-long behavioural changes that would aid in fostering increased hippocampal neurogenesis and cognitive function. This review addresses both the acute and long-term stress-induced alterations to hippocampal neurogenesis and cognition during the adolescent period, as well as changes to the stress response and pubertal hormones at this time which may result in differential effects than are observed in adulthood. We hypothesise that adolescence may represent an optimal time for healthy lifestyle changes to have a positive and long-lasting impact on hippocampal neurogenesis, and to protect against stress-induced deficits. We conclude that future research into the mechanisms underlying the susceptibility of the adolescent hippocampus to stress, exercise and diet and the consequent effect on cognition may provide insight into why adolescence may be a vital period for correct conditioning of future hippocampal function.