bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mapping the ‘Two-component system’ network in rice
Authors: Sharan Ashutosh , Soni Praveen , Nongpiur Ramsong Chantre , Singla-Pareek Sneh L. , Pareek Ashwani 
Published: August 2017

AbstractTwo-component system (TCS) in plants is a histidine to aspartate phosphorelay based signaling system. Rice genome has multifarious TCS signaling machinery comprising of 11 histidine kinases (OsHKs), 5 histidine phosphotransferases (OsHPTs) and 36 response regulators (OsRRs). However, how these TCS members interact with each other and comprehend diverse signaling cascades remains unmapped. Using a highly stringent yeast two-hybrid (Y2H) platform and extensive in planta bimolecular fluorescence complementation (BiFC) assays, distinct arrays of interaction between various TCS proteins have been identified in the present study. Based on these results, an interactome map of TCS proteins has been assembled. This map clearly shows a cross talk in signaling, mediated by different sensory OsHKs. It also highlights OsHPTs as the interaction hubs, which interact with OsRRs, mostly in a redundant fashion. Remarkably, interactions between type-A and type-B OsRRs have also been revealed for the first time. These observations suggest that feedback regulation by type-A OsRRs may also be mediated by interference in signaling at the level of type-B OsRRs, in addition to OsHPTs, as known previously. The interactome map presented here provides a starting point for in-depth molecular investigations for signal(s) transmitted by various TCS modules into diverse biological processes.
Quantum illumination reveals phase-shift inducing cloaking
Authors: Las Heras U. , Di Candia R. , Fedorov K. G. , Deppe F. , Sanz M. , Solano E. 
Published: August 2017

AbstractIn quantum illumination entangled light is employed to enhance the detection accuracy of an object when compared with the best classical protocol. On the other hand, cloaking is a stealth technology based on covering a target with a material deflecting the light around the object to avoid its detection. Here, we propose a quantum illumination protocol especially adapted to quantum microwave technology. This protocol seizes the phase-shift induced by some cloaking techniques, such as scattering reduction, allowing for a 3 dB improvement in the detection of a cloaked target. The method can also be employed for the detection of a phase-shift in bright environments in different frequency regimes. Finally, we study the minimal efficiency required by the photocounter for which the quantum illumination protocol still shows a gain with respect to the classical protocol.
Evaluation of the concentration of point defects in GaN
Authors: Reshchikov M. A. , Usikov A. , Helava H. , Makarov Yu. , Prozheeva V. , Makkonen I. , Tuomisto F. , Leach J. H. , Udwary K. 
Published: August 2017

AbstractPhotoluminescence (PL) was used to estimate the concentration of point defects in GaN. The results are compared with data from positron annihilation spectroscopy (PAS), secondary ion mass spectrometry (SIMS), and deep level transient spectroscopy (DLTS). Defect-related PL intensity in undoped GaN grown by hydride vapor phase epitaxy increases linearly with the concentration of related defects only up to 1016 cm−3. At higher concentrations, the PL intensity associated with individual defects tends to saturate, and accordingly, does not directly correlate with the concentration of defects. For this reason, SIMS analysis, with relatively high detection limits, may not be helpful for classifying unidentified point defects in GaN. Additionally, we highlight challenges in correlating defects identified by PL with those by PAS and DLTS methods.
Gene Expression Profiling of Cutaneous Injured and Non-Injured Nociceptors in SNI Animal Model of Neuropathic Pain
Authors: Berta Temugin , Perrin Florence E. , Pertin Marie , Tonello Raquel , Liu Yen-Chin , Chamessian Alexander , Kato Ann C. , Ji Ru-Rong , Decosterd Isabelle 
Published: August 2017

AbstractNociceptors are a particular subtype of dorsal root ganglion (DRG) neurons that detect noxious stimuli and elicit pain. Although recent efforts have been made to reveal the molecular profile of nociceptors in normal conditions, little is known about how this profile changes in pathological conditions. In this study we exploited laser capture microdissection to specifically collect individual injured and non-injured nociceptive DRG neurons and to define their gene profiling in rat spared nerve injury (SNI) model of neuropathic pain. We found minimal transcriptional changes in non-injured neurons at 7 days after SNI. In contrast, several novel transcripts were altered in injured nociceptors, and the global signature of these LCM-captured neurons differed markedly from that the gene expression patterns found previously using whole DRG tissue following SNI. Pathway analysis of the transcriptomic profile of the injured nociceptors revealed oxidative stress as a key biological process. We validated the increase of caspase-6 (CASP6) in small-sized DRG neurons and its functional role in SNI- and paclitaxel-induced neuropathic pain. Our results demonstrate that the identification of gene regulation in a specific population of DRG neurons (e.g., nociceptors) is an effective strategy to reveal new mechanisms and therapeutic targets for neuropathic pain from different origins.
Acute respiratory infections in hospitalized children in Vientiane, Lao PDR – the importance of Respiratory Syncytial Virus
Authors: Nguyen Van Hoan , Dubot-Pérès Audrey , Russell Fiona M. , Dance David A. B. , Vilivong Keoudomphone , Phommachan Souphatsone , Syladeth Chanthaphone , Lai Jana , Lim Ruth , Morpeth Melinda , Mayxay Mayfong , Newton Paul N. , Richet Hervé , De Lamballerie Xavier 
Published: August 2017

AbstractThe Human respiratory syncytial virus (RSV) is one of the most important viral pathogens, causing epidemics of acute respiratory infection (ARI), especially bronchiolitis and pneumonia, in children worldwide. To investigate the RSV burden in Laos, we conducted a one-year study in children <5 years old admitted to Mahosot Hospital, Vientiane Capital, to describe clinical and epidemiological characteristics and predictive factors for severity of RSV-associated ARI. Pooled nasal and throat swabs were tested using multiplex real-time PCR for 33 respiratory pathogens (FTD® kit). A total of 383 patients were included, 277 (72.3%) of whom presented with pneumonia. 377 (98.4%) patients were positive for at least one microorganism, of which RSV was the most common virus (41.0%), with a peak observed between June and September, corresponding to the rainy season. Most RSV inpatients had pneumonia (84.1%), of whom 35% had severe pneumonia. Children <3-months old were a high-risk group for severe pneumonia, independently of RSV infection. Our study suggests that RSV infection is frequent in Laos and commonly associated with pneumonia in hospitalized young children. Further investigations are required to provide a better overall view of the Lao nationwide epidemiology and public health burden of RSV infection over time.
Analytical performance of reagent for assaying tau protein in human plasma and feasibility study screening neurodegenerative diseases
Authors: Yang Shieh-Yueh , Chiu Ming-Jang , Chen Ta-Fu , Lin Chin-Hsien , Jeng Jiann-Shing , Tang Sung-Chun , Lee Yen-Fu , Yang Che-Chuan , Liu Bing-Hsien , Chen Hsin-Hsien , Wu Chau-Chung 
Published: August 2017

AbstractImmunomagnetic reduction (IMR), which involves the use of antibody-functionalized magnetic nanoparticles to specifically label target biomarkers, was utilized to develop an assay for total tau protein in human plasma. The analytic properties of the IMR assay on tau protein were investigated. The limit of detection was found to be 0.026 pg/ml. Other properties such as Hook effect, assay linearity, dilution recovery range, reagent stability, interference test, and spiked recovery were also characterized. The ultra-sensitive IMR assay was applied to detect the plasma tau protein levels of subjects with prevalent neurodegenerative diseases, such as Alzheimer’s disease (AD), mild cognitive impairment (MCI) due to AD, Parkinson’s disease (PD), frontotemporal dementia (FTD) and vascular dementia (VD). The concentrations of plasma tau protein in patients with VD, PD, MCI due to AD, FTD, and AD patients were higher than that of healthy controls. Using an ROC curve analysis, the cutoff value for discriminating dementia patients from healthy controls was 17.43 pg/ml, resulting in 0.856 and 0.727 for clinical sensitivity and specificity, respectively. The area under the ROC curve was 0.908. These results imply that the IMR plasma tau assay would be useful to screen for prevalent neurodegenerative diseases.
Metagenomic analysis reveals a green sulfur bacterium as a potential coral symbiont
Authors: Cai Lin , Zhou Guowei , Tian Ren-Mao , Tong Haoya , Zhang Weipeng , Sun Jin , Ding Wei , Wong Yue Him , Xie James Y. , Qiu Jian-Wen , Liu Sheng , Huang Hui , Qian Pei-Yuan 
Published: August 2017

AbstractCoral reefs are ecologically significant habitats. Coral-algal symbiosis confers ecological success on coral reefs and coral-microbial symbiosis is also vital to coral reefs. However, current understanding of coral-microbial symbiosis on a genomic scale is largely unknown. Here we report a potential microbial symbiont in corals revealed by metagenomics-based genomic study. Microbial cells in coral were enriched for metagenomic analysis and a high-quality draft genome of “Candidatus Prosthecochloris korallensis” was recovered by metagenome assembly and genome binning. Phylogenetic analysis shows “Ca. P. korallensis” belongs to the Prosthecochloris clade and is clustered with two Prosthecochloris clones derived from Caribbean corals. Genomic analysis reveals “Ca. P. korallensis” has potentially important ecological functions including anoxygenic photosynthesis, carbon fixation via the reductive tricarboxylic acid (rTCA) cycle, nitrogen fixation, and sulfur oxidization. Core metabolic pathway analysis suggests “Ca. P. korallensis” is a green sulfur bacterium capable of photoautotrophy or mixotrophy. Potential host-microbial interaction reveals a symbiotic relationship: “Ca. P. korallensis” might provide organic and nitrogenous nutrients to its host and detoxify sulfide for the host; the host might provide “Ca. P. korallensis” with an anaerobic environment for survival, carbon dioxide and acetate for growth, and hydrogen sulfide as an electron donor for photosynthesis.
Activation of autophagy attenuates EtOH-LPS-induced hepatic steatosis and injury through MD2 associated TLR4 signaling
Authors: Kong Xiaoxia , Yang Ying , Ren Li , Shao Tuo , Li Fengyuan , Zhao Cuiqing , Liu Liming , Zhang Hongyu , McClain Craig J. , Feng Wenke 
Published: August 2017

AbstractAutophagy serves as a protective mechanism to degrade damaged organelles and proteins. Acute alcohol exposure is known to activate the hepatic autophagy response, whereas chronic alcohol exposure slows autophagosome formation along with an elevation of gut-derived endotoxin. In the current study, we examined whether lipopolysaccharide (LPS) administration decreased autophagic response in the liver of mice treated by short-term alcohol and whether activation of autophagy by rapamycin attenuates EtOH-LPS-induced liver steatosis and injury. We demonstrated that ten-day alcohol feeding primed the liver to LPS-induced lipid accumulation and liver injury with significantly increased hepatic steatosis and serum AST level as well as hepatic cellular NF-κB activation. LPS increased alcohol-mediated reactive oxygen species (ROS) formation while reducing autophagy activation. These deleterious effects were attenuated by rapamycin administration in mice. The protective effects of rapamycin are associated with decreased cellular MD2/TLR4 expression and interaction in Raw264.7 cells. Taken together, our results demonstrated that enhanced gut-derived LPS decreases the hepatic autophagosome numbers in response to alcohol exposure, and activation of autophagy by rapamycin protects from EtOH-LPS-induced liver injury, probably through reduced macrophage expression and interaction of TLR4/MD2 signaling complex.
CLE peptide-encoding gene families in Medicago truncatula and Lotus japonicus, compared with those of soybean, common bean and Arabidopsis
Authors: Hastwell April H. , de Bang Thomas C. , Gresshoff Peter M. , Ferguson Brett J. 
Published: August 2017

AbstractCLE peptide hormones are critical regulators of many cell proliferation and differentiation mechanisms in plants. These 12-13 amino acid glycosylated peptides play vital roles in a diverse range of plant tissues, including the shoot, root and vasculature. CLE peptides are also involved in controlling legume nodulation. Here, the entire family of CLE peptide-encoding genes was identified in Medicago truncatula (52) and Lotus japonicus (53), including pseudogenes and non-functional sequences that were identified. An array of bioinformatic techniques were used to compare and contrast these complete CLE peptide-encoding gene families with those of fellow legumes, Glycine max and Phaseolus vulgaris, in addition to the model plant Arabidopsis thaliana. This approach provided insight into the evolution of CLE peptide families and enabled us to establish putative M. truncatula and L. japonicus orthologues. This includes orthologues of nodulation-suppressing CLE peptides and AtCLE40 that controls the stem cell population of the root apical meristem. A transcriptional meta-analysis was also conducted to help elucidate the function of the CLE peptide family members. Collectively, our analyses considerably increased the number of annotated CLE peptides in the model legume species, M. truncatula and L. japonicus, and substantially enhanced the knowledgebase of this critical class of peptide hormones.
The impact of immigration on microbial community composition in full-scale anaerobic digesters
Authors: Kirkegaard Rasmus H. , McIlroy Simon J. , Kristensen Jannie M. , Nierychlo Marta , Karst Søren M. , Dueholm Morten S. , Albertsen Mads , Nielsen Per H. 
Published: August 2017

AbstractAnaerobic digestion is widely applied to treat organic waste at wastewater treatment plants. Characterisation of the underlying microbiology represents a source of information to develop strategies for improved operation. Hence, we investigated microbial communities of thirty-two full-scale anaerobic digesters over a six-year period using 16S rRNA gene amplicon sequencing. Sampling of the sludge fed into these systems revealed that several of the most abundant populations were likely inactive and immigrating with the influent. This observation indicates that a failure to consider immigration will interfere with correlation analysis and give an inaccurate picture of the growing microbial community. Furthermore, several abundant OTUs could not be classified to genus level with commonly applied taxonomies, making inference of their function unreliable and comparison to other studies problematic. As such, the existing MiDAS taxonomy was updated to include these abundant phylotypes. The communities of individual digesters surveyed were remarkably similar – with only 300 OTUs representing 80% of the total reads across all plants, and 15% of these identified as non-growing and possibly inactive immigrating microbes. By identifying abundant and growing taxa in anaerobic digestion, this study paves the way for targeted characterisation of the process-important organisms towards an in-depth understanding of the microbiology.
A systematic model identification method for chemical transformation pathways – the case of heroin biomarkers in wastewater
Authors: Ramin Pedram , Valverde-Pérez Borja , Polesel Fabio , Locatelli Luca , Plósz Benedek Gy. 
Published: August 2017

AbstractThis study presents a novel statistical approach for identifying sequenced chemical transformation pathways in combination with reaction kinetics models. The proposed method relies on sound uncertainty propagation by considering parameter ranges and associated probability distribution obtained at any given transformation pathway levels as priors for parameter estimation at any subsequent transformation levels. The method was applied to calibrate a model predicting the transformation in untreated wastewater of six biomarkers, excreted following human metabolism of heroin and codeine. The method developed was compared to parameter estimation methods commonly encountered in literature (i.e., estimation of all parameters at the same time and parameter estimation with fix values for upstream parameters) by assessing the model prediction accuracy, parameter identifiability and uncertainty analysis. Results obtained suggest that the method developed has the potential to outperform conventional approaches in terms of prediction accuracy, transformation pathway identification and parameter identifiability. This method can be used in conjunction with optimal experimental designs to effectively identify model structures and parameters. This method can also offer a platform to promote a closer interaction between analytical chemists and modellers to identify models for biochemical transformation pathways, being a prominent example for the emerging field of wastewater-based epidemiology.
Light-patterning of synthetic tissues with single droplet resolution
Authors: Booth Michael J. , Restrepo Schild Vanessa , Box Stuart J. , Bayley Hagan 
Published: August 2017

AbstractSynthetic tissues can be generated by forming networks of aqueous droplets in lipid-containing oil. Each droplet contains a cell-free expression system and is connected to its neighbor through a lipid bilayer. In the present work, we have demonstrated precise external control of such networks by activating protein expression within single droplets, by using light-activated DNA to encode either a fluorescent or a pore-forming protein. By controlling the extent of activation, synthetic tissues were generated with graded levels of protein expression in patterns of single droplets. Further, we have demonstrated reversible activation within individual compartments in synthetic tissues by turning a fluorescent protein on-and-off. This is the first example of the high-resolution patterning of droplet networks, following their formation. Single-droplet control will be essential to power subsets of compartments within synthetic tissues or to stimulate subsets of cells when synthetic tissues are interfaced with living tissues.
Analysis and evaluation of the entropy indices of a static network structure
Authors: Cai Meng , Cui Ying , Stanley H. Eugene 
Published: August 2017

AbstractAlthough degree distribution entropy (DDE), SD structure entropy (SDSE), Wu structure entropy (WSE) and FB structure entropy (FBSE) are four static network structure entropy indices widely used to quantify the heterogeneity of a complex network, previous studies have paid little attention to their differing abilities to describe network structure. We calculate these four structure entropies for four benchmark networks and compare the results by measuring the ability of each index to characterize network heterogeneity. We find that SDSE and FBSE more accurately characterize network heterogeneity than WSE and DDE. We also find that existing benchmark networks fail to distinguish SDSE and FBSE because they cannot discriminate local and global network heterogeneity. We solve this problem by proposing an evolving caveman network that reveals the differences between structure entropy indices by comparing the sensitivities during the network evolutionary process. Mathematical analysis and computational simulation both indicate that FBSE describes the global topology variation in the evolutionary process of a caveman network, and that the other three structure entropy indices reflect only local network heterogeneity. Our study offers an expansive view of the structural complexity of networks and expands our understanding of complex network behavior.
Achievability of 3D planned bimaxillary osteotomies: maxilla-first versus mandible-first surgery
Authors: Liebregts Jeroen , Baan Frank , de Koning Martien , Ongkosuwito Edwin , Bergé Stefaan , Maal Thomas , Xi Tong 
Published: August 2017

AbstractThe present study was aimed to investigate the effects of sequencing a two-component surgical procedure for correcting malpositioned jaws (bimaxillary osteotomies); specifically, surgical repositioning of the upper jaw—maxilla, and the lower jaw—mandible. Within a population of 116 patients requiring bimaxillary osteotomies, the investigators analyzed whether there were statistically significant differences in postoperative outcome as measured by concordance with a preoperative digital 3D virtual treatment plan. In one group of subjects (n = 58), the maxillary surgical procedure preceded the mandibular surgery. In the second group (n = 58), the mandibular procedure preceded the maxillary surgical procedure. A semi-automated analysis tool (OrthoGnathicAnalyser) was applied to assess the concordance of the postoperative maxillary and mandibular position with the cone beam CT-based 3D virtual treatment planning in an effort to minimize observer variability. The results demonstrated that in most instances, the maxilla-first surgical approach yielded closer concordance with the 3D virtual treatment plan than a mandibular-first procedure. In selected circumstances, such as a planned counterclockwise rotation of both jaws, the mandible-first sequence resulted in more predictable displacements of the jaws.
BIRC3 is a biomarker of mesenchymal habitat of glioblastoma, and a mediator of survival adaptation in hypoxia-driven glioblastoma habitats
Authors: Wang Dapeng , Berglund Anders E. , Kenchappa Rajappa S. , MacAulay Robert J. , Mulé James J. , Etame Arnold B. 
Published: August 2017

AbstractTumor hypoxia is an established facilitator of survival adaptation and mesenchymal transformation in glioblastoma (GBM). The underlying mechanisms that direct hypoxia-mediated survival in GBM habitats are unclear. We previously identified BIRC3 as a mediator of therapeutic resistance in GBM to standard temozolomide (TMZ) chemotherapy and radiotherapy (RT). Here we report that BIRC3 is a biomarker of the hypoxia-mediated adaptive mesenchymal phenotype of GBM. Specifically, in the TCGA dataset elevated BIRC3 gene expression was identified as a superior and selective biomarker of mesenchymal GBM versus neural, proneural and classical subtypes. Further, BIRC3 protein was highly expressed in the tumor cell niches compared to the perivascular niche across multiple regions in GBM patient tissue microarrays. Tumor hypoxia was found to mechanistically induce BIRC3 expression through HIF1-alpha signaling in GBM cells. Moreover, in human GBM xenografts robust BIRC3 expression was noted within hypoxic regions of the tumor. Importantly, selective inhibition of BIRC3 reversed therapeutic resistance of GBM cells to RT in hypoxic microenvironments through enhanced activation of caspases. Collectively, we have uncovered a novel role for BIRC3 as a targetable biomarker and mediator of hypoxia-driven habitats in GBM.