bluuebunny/crossref_metadata_2025_split huggingface dataset:
Microsatellite markers for multiple Pocillopora genetic lineages offer new insights about coral populations
Authors: Nakajima Yuichi , Wepfer Patricia H. , Suzuki Shohei , Zayasu Yuna , Shinzato Chuya , Satoh Noriyuki , Mitarai Satoshi 
Published: July 2017

AbstractPopulation genetics of the coral genus Pocillopora have been more intensively studied than those of any other reef-building taxon. However, recent investigations have revealed that the current morphological classification is inadequate to represent genetic lineages. In this study, we isolated and characterized novel microsatellite loci from morphological Pocillopora meandrina (Type 1) and Pocillopora acuta (Type 5). Furthermore, we characterized previously reported microsatellite loci. A total of 27 loci (13 novel loci) proved useful for population genetic analyses at two sites in the Ryukyu Archipelago, in the northwestern Pacific. Clonal diversity differed in each genetic lineage. Genetic structure suggested by microsatellites corresponded to clusters in a phylogenetic tree constructed from a mitochondrial open reading frame (mtORF). In addition, we found an unknown mitochondrial haplotype of this mtORF. These microsatellite loci will be useful for studies of connectivity and genetic diversity of Pocillopora populations, and will also support coral reef conservation.
Natural variations in the biofilm-associated protein BslA from the genus Bacillus
Authors: Morris Ryan J. , Schor Marieke , Gillespie Rachel M. C. , Ferreira Ana Sofia , Baldauf Lucia , Earl Chris , Ostrowski Adam , Hobley Laura , Bromley Keith M. , Sukhodub Tetyana , Arnaouteli Sofia , Stanley-Wall Nicola R. , MacPhee Cait E. 
Published: July 2017

AbstractBslA is a protein secreted by Bacillus subtilis which forms a hydrophobic film that coats the biofilm surface and renders it water-repellent. We have characterised three orthologues of BslA from Bacillus amyloliquefaciens, Bacillus licheniformis and Bacillus pumilus as well as a paralogue from B. subtilis called YweA. We find that the three orthologous proteins can substitute for BslA in B. subtilis and confer a degree of protection, whereas YweA cannot. The degree to which the proteins functionally substitute for native BslA correlates with their in vitro biophysical properties. Our results demonstrate the use of naturally-evolved variants to provide a framework for teasing out the molecular basis of interfacial self-assembly.
Reconstruction of local frequencies for recovering the unwrapped phase in optical interferometry
Authors: Estrada Julio C. , Marroquin Jose L. , Medina Orlando M. 
Published: July 2017

AbstractIn optics, when interferograms or digital holograms are recorded and their phase is recovered, it is common to obtain a wrapped phase with some errors, noise and artifacts such as singularities due to the non linearities of the demodulation process. This paper shows how to reconstruct the frequency field of the wrapped phase by using adaptive Gabor filters. Gabor filters are Gaussian quadrature filters tuned in at a certain frequency. We adapt these Gabor filters by tuning them locally and estimating the frequency using wrapped finite differences of the estimated phase. Doing this process iteratively, the frequency estimation is refined and smoothed. The unwrapped phase is easily recovered by integrating the recovered frequency field using, for example, a simple line raster integration. We don’t have problems with phase inconsistencies or residues while integrating the phase, because these are removed. The obtained unwrapped phase is clean, consistent and practically error-free. We show estimation errors with simulated data and the performance of the proposed method using real-world recorded wavefronts.
Glucocorticoid therapy regulates podocyte motility by inhibition of Rac1
Authors: McCaffrey James C. , Webb Nicholas J. , Poolman Toryn M. , Fresquet Maryline , Moxey Cressida , Zeef Leo A. H. , Donaldson Ian J. , Ray David W. , Lennon Rachel 
Published: July 2017

AbstractNephrotic syndrome (NS) occurs when the glomerular filtration barrier becomes excessively permeable leading to massive proteinuria. In childhood NS, immune system dysregulation has been implicated and increasing evidence points to the central role of podocytes in the pathogenesis. Children with NS are typically treated with an empiric course of glucocorticoid (Gc) therapy; a class of steroids that are activating ligands for the glucocorticoid receptor (GR) transcription factor. Although Gc-therapy has been the cornerstone of NS management for decades, the mechanism of action, and target cell, remain poorly understood. We tested the hypothesis that Gc acts directly on the podocyte to produce clinically useful effects without involvement of the immune system. In human podocytes, we demonstrated that the basic GR-signalling mechanism is intact and that Gc induced an increase in podocyte barrier function. Defining the GR-cistrome identified Gc regulation of motility genes. These findings were functionally validated with live-cell imaging. We demonstrated that treatment with Gc reduced the activity of the pro-migratory small GTPase regulator Rac1. Furthermore, Rac1 inhibition had a direct, protective effect on podocyte barrier function. Our studies reveal a new mechanism for Gc action directly on the podocyte, with translational relevance to designing new selective synthetic Gc molecules.
Limits of Risk Predictability in a Cascading Alternating Renewal Process Model
Authors: Lin Xin , Moussawi Alaa , Korniss Gyorgy , Bakdash Jonathan Z. , Szymanski Boleslaw K. 
Published: July 2017

AbstractMost risk analysis models systematically underestimate the probability and impact of catastrophic events (e.g., economic crises, natural disasters, and terrorism) by not taking into account interconnectivity and interdependence of risks. To address this weakness, we propose the Cascading Alternating Renewal Process (CARP) to forecast interconnected global risks. However, assessments of the model’s prediction precision are limited by lack of sufficient ground truth data. Here, we establish prediction precision as a function of input data size by using alternative long ground truth data generated by simulations of the CARP model with known parameters. We illustrate the approach on a model of fires in artificial cities assembled from basic city blocks with diverse housing. The results confirm that parameter recovery variance exhibits power law decay as a function of the length of available ground truth data. Using CARP, we also demonstrate estimation using a disparate dataset that also has dependencies: real-world prediction precision for the global risk model based on the World Economic Forum Global Risk Report. We conclude that the CARP model is an efficient method for predicting catastrophic cascading events with potential applications to emerging local and global interconnected risks.
Hydrogen sulphide donors selectively potentiate a green tea polyphenol EGCG-induced apoptosis of multiple myeloma cells
Authors: Bae Jaehoon , Kumazoe Motofumi , Yamashita Shuya , Tachibana Hirofumi 
Published: July 2017

AbstractHydrogen sulphide (H2S) is a colourless gas with the odour of rotten eggs and has recently been recognized as a signal mediator in physiological activities related with the regulation of homeostasis, the vascular system and the inflammatory system. Here we show that H2S donors, including sodium hydrogen sulphide (NaHS), GYY 4137 and diallyltrisulfide (DATS), synergistically enhanced the anti-cancer effect of a green tea polyphenol (−)-epigallocatechin-3-O-gallate (EGCG) against multiple myeloma cells without affecting normal cells. NaHS significantly potentiated the anti-cancer effect of EGCG and prolonged survival in a mouse xenograft model. In this mechanism, H2S enhanced apoptotic cell death through cyclic guanosine monophosphate (cGMP)/acid sphingomyelinase pathway induced by EGCG. Moreover, NaHS reduced the enzyme activity of cyclic nucleotide phosphodiesterase that is known as cGMP negative regulator. In conclusion, we identified H2S as a gasotransmitter that potentiates EGCG-induced cancer cell death.
CT-perfusion stroke imaging: a threshold free probabilistic approach to predict infarct volume compared to traditional ischemic thresholds
Authors: Flottmann Fabian , Broocks Gabriel , Faizy Tobias Djamsched , Ernst Marielle , Forkert Nils Daniel , Grosser Malte , Thomalla Götz , Siemonsen Susanne , Fiehler Jens , Kemmling André 
Published: July 2017

AbstractThe aim was to evaluate a novel method of threshold-free prediction of brain infarct from computed tomography perfusion (CTP) imaging in comparison to conventional ischemic thresholds. In a multicenter cohort of 161 patients with acute large vessel occlusion who received endovascular therapy, brain infarction was predicted by CTP using (1) optimized parameter cut-off values determined by ROC curve analysis and (2) probabilistic logistic regression threshold-free analysis. Predicted infarct volumes and prediction errors based on four perfusion parameter maps were compared against observed infarcts. In 93 patients with successful recanalization, the mean observed infarct volume was 35.7 ± 61.9 ml (the reference for core infarct not savable by reperfusion). Optimal parameter thresholds predicted mean infarct volumes between 53.2 ± 44.4 and 125.0 ± 95.4 ml whereas threshold-free analysis predicted mean volumes between 35.9 ± 28.5 and 36.1 ± 29.0 ml. In 68 patients with persistent occlusion, the mean observed infarct volume was 113.4 ± 138.3 ml (the reference to define penumbral infarct savable by reperfusion). Predicted mean infarct volumes by parameter thresholds ranged from 91.4 ± 81.5 to 163.8 ± 135.7 ml, by threshold-free analysis from 113.2 ± 89.9 to 113.5 ± 89.0 ml. Threshold-free prediction of infarct volumes had a higher precision and lower patient-specific prediction error than conventional thresholding. Penumbra to core lesion mismatch estimate may therefore benefit from threshold-free CTP analysis.
In vitro significance of SOCS-3 and SOCS-4 and potential mechanistic links to wound healing
Authors: Feng Yi , Sanders Andrew J. , Morgan Liam D. , Owen Sioned , Ruge Fiona , Harding Keith G. , Jiang Wen G. 
Published: July 2017

AbstractWound healing and the management of chronic wounds represent a significant burden on the NHS. Members of the suppressor of cytokine signalling (SOCS) family have been implicated in the regulation of a range of cellular processes. The current study aims to explore the importance of SOCS-3 and SOCS-4 in regulating cellular traits associated with wound healing. SOCS-3 over-expression and SOCS-4 knockdown mutant lines were generated and verified using q-PCR and western blotting in human keratinocytes (HaCaT) and endothelial cells (HECV). Over-expression of SOCS-3 resulted in a significantly reduced proliferative rate in HaCaT keratinocytes and also enhanced the tubule formation capacity of HECV cells. SOCS-4 knockdown significantly reduced HaCaT migration and HECV cell tubule formation. Suppression of SOCS-4 influenced the responsiveness of HaCaT and HECV cells to EGF and TGFβ and resulted in a dysregulation of phospho-protein expression in HaCaT cells. SOCS-3 and SOCS-4 appear to play regulatory roles in a number of keratinocyte and endothelial cellular traits associated with the wound healing process and may also be able to regulate the responsiveness of these cells to EGF and TGFβ. This implies a potential regulatory role in the wound healing process and, thus highlights their potential as novel therapies.
III-Nitride Digital Alloy: Electronics and Optoelectronics Properties of the InN/GaN Ultra-Short Period Superlattice Nanostructures
Authors: Sun Wei , Tan Chee-Keong , Tansu Nelson 
Published: July 2017

AbstractThe III-Nitride digital alloy (DA) is comprehensively studied as a short-period superlattice nanostructure consisting of ultra-thin III-Nitride epitaxial layers. By stacking the ultra-thin III-Nitride epitaxial layers periodically, these nanostructures are expected to have comparable optoelectronic properties as the conventional III-Nitride alloys. Here we carried out numerical studies on the InGaN DA showing the tunable optoelectronic properties of the III-Nitride DA. Our study shows that the energy gap of the InGaN DA can be tuned from ~0.63 eV up to ~2.4 eV, where the thicknesses and the thickness ratio of each GaN and InN ultra-thin binary layers within the DA structure are the key factors for tuning bandgap. Correspondingly, the absorption spectra of the InGaN DA yield broad wavelength tunability which is comparable to that of bulk InGaN ternary alloy. In addition, our investigation also reveals that the electron-hole wavefunction overlaps are remarkably large in the InGaN DA structure despite the existence of strain effect and build-in polarization field. Our findings point out the potential of III-Nitride DA as an artificially engineered nanostructure for optoelectronic device applications.
The LncRNA Connectivity Map: Using LncRNA Signatures to Connect Small Molecules, LncRNAs, and Diseases
Authors: Yang Haixiu , Shang Desi , Xu Yanjun , Zhang Chunlong , Feng Li , Sun Zeguo , Shi Xinrui , Zhang Yunpeng , Han Junwei , Su Fei , Li Chunquan , Li Xia 
Published: July 2017

AbstractWell characterized the connections among diseases, long non-coding RNAs (lncRNAs) and drugs are important for elucidating the key roles of lncRNAs in biological mechanisms in various biological states. In this study, we constructed a database called LNCmap (LncRNA Connectivity Map), available at http://www.bio-bigdata.com/LNCmap/, to establish the correlations among diseases, physiological processes, and the action of small molecule therapeutics by attempting to describe all biological states in terms of lncRNA signatures. By reannotating the microarray data from the Connectivity Map database, the LNCmap obtained 237 lncRNA signatures of 5916 instances corresponding to 1262 small molecular drugs. We provided a user-friendly interface for the convenient browsing, retrieval and download of the database, including detailed information and the associations of drugs and corresponding affected lncRNAs. Additionally, we developed two enrichment analysis methods for users to identify candidate drugs for a particular disease by inputting the corresponding lncRNA expression profiles or an associated lncRNA list and then comparing them to the lncRNA signatures in our database. Overall, LNCmap could significantly improve our understanding of the biological roles of lncRNAs and provide a unique resource to reveal the connections among drugs, lncRNAs and diseases.
Inclusion of Population-specific Reference Panel from India to the 1000 Genomes Phase 3 Panel Improves Imputation Accuracy
Authors: Ahmad Meraj , Sinha Anubhav , Ghosh Sreya , Kumar Vikrant , Davila Sonia , Yajnik Chittaranjan S. , Chandak Giriraj R. 
Published: July 2017

AbstractImputation is a computational method based on the principle of haplotype sharing allowing enrichment of genome-wide association study datasets. It depends on the haplotype structure of the population and density of the genotype data. The 1000 Genomes Project led to the generation of imputation reference panels which have been used globally. However, recent studies have shown that population-specific panels provide better enrichment of genome-wide variants. We compared the imputation accuracy using 1000 Genomes phase 3 reference panel and a panel generated from genome-wide data on 407 individuals from Western India (WIP). The concordance of imputed variants was cross-checked with next-generation re-sequencing data on a subset of genomic regions. Further, using the genome-wide data from 1880 individuals, we demonstrate that WIP works better than the 1000 Genomes phase 3 panel and when merged with it, significantly improves the imputation accuracy throughout the minor allele frequency range. We also show that imputation using only South Asian component of the 1000 Genomes phase 3 panel works as good as the merged panel, making it computationally less intensive job. Thus, our study stresses that imputation accuracy using 1000 Genomes phase 3 panel can be further improved by including population-specific reference panels from South Asia.
Graphene transistors for interfacing with cells: towards a deeper understanding of liquid gating and sensitivity
Authors: Kireev Dmitry , Brambach Max , Seyock Silke , Maybeck Vanessa , Fu Wangyang , Wolfrum Bernhard , Offenhäusser Andreas 
Published: July 2017

AbstractThis work is focused on the fabrication and analysis of graphene-based, solution-gated field effect transistor arrays (GFETs) on a large scale for bioelectronic measurements. The GFETs fabricated on different substrates, with a variety of gate geometries (width/length) of the graphene channel, reveal a linear relation between the transconductance and the width/length ratio. The area normalised electrolyte-gated transconductance is in the range of 1–2 mS·V−1·□ and does not strongly depend on the substrate. Influence of the ionic strength on the transistor performance is also investigated. Double contacts are found to decrease the effective resistance and the transfer length, but do not improve the transconductance. An electrochemical annealing/cleaning effect is investigated and proposed to originate from the out-of-plane gate leakage current. The devices are used as a proof-of-concept for bioelectronic sensors, recording external potentials from both: ex vivo heart tissue and in vitro cardiomyocyte-like HL-1 cells. The recordings show distinguishable action potentials with a signal to noise ratio over 14 from ex vivo tissue and over 6 from the cardiac-like cell line in vitro. Furthermore, in vitro neuronal signals are recorded by the graphene transistors with distinguishable bursting for the first time.
ApoE Influences the Blood-Brain Barrier Through the NF-κB/MMP-9 Pathway After Traumatic Brain Injury
Authors: Teng Zhipeng , Guo Zongduo , Zhong Jianjun , Cheng Chongjie , Huang Zhijian , Wu Yue , Tang Shuang , Luo Chao , Peng Xing , Wu Haitao , Sun Xiaochuan , Jiang Li 
Published: July 2017

AbstractApolipoprotein E (ApoE), encoded by the ApoE gene (APOE), influences the outcomes of traumatic brain injury (TBI), but the mechanism remains unclear. The present study aimed to investigate the effects of different ApoEs on the outcome of TBI and to explore the possible mechanisms. Controlled cortical impact (CCI) was performed on APOEε3 (E3) and APOEε4 (E4) transgenic mice, APOE-KO (KO) mice, and wild type (WT) mice to construct an in vivo TBI model. Neurological deficits, blood brain barrier (BBB) permeability and brain edema were detected at days 1, 3, and 7 after TBI. The results revealed no significant differences among the four groups at day 1 or day 3 after injury, but more severe deficits were found in E4 and KO mice than in E3 and WT mice. Furthermore, a significant loss of tight junction proteins was observed in E4 and KO mice compared with E3 and WT mice at day 7. Additionally, more expression and activation of NF-κB and MMP-9 were found in E4 mice compared with E3 mice. Different ApoEs had distinct effects on neuro-function and BBB integrity after TBI. ApoE3, but not E4, might inhibit the NF-κB/MMP-9 pathway to alleviate BBB disruption and improve TBI outcomes.
Translational roles of the C75 2′OH in an in vitro tRNA transcript at the ribosomal A, P and E sites
Authors: Wang Jinfan , Forster Anthony C. 
Published: July 2017

AbstractAminoacyl-tRNAs containing a deoxy substitution in the penultimate nucleotide (C75 2′OH → 2′H) have been widely used in translation for incorporation of unnatural amino acids (AAs). However, this supposedly innocuous modification surprisingly increased peptidyl-tRNAAlaugc drop off in biochemical assays of successive incorporations. Here we predict the function of this tRNA 2′OH in the ribosomal A, P and E sites using recent co-crystal structures of ribosomes and tRNA substrates and test these structure-function models by systematic kinetics analyses. Unexpectedly, the C75 2′H did not affect A- to P-site translocation nor peptidyl donor activity of tRNAAlaugc. Rather, the peptidyl acceptor activity of the A-site Ala-tRNAAlaugc and the translocation of the P-site deacylated tRNAAlaugc to the E site were impeded. Delivery by EF-Tu was not significantly affected. This broadens our view of the roles of 2′OH groups in tRNAs in translation.
Aggregated transthyretin is specifically packaged into placental nano-vesicles in preeclampsia
Authors: Tong Mancy , Cheng Shi-bin , Chen Qi , DeSousa Joana , Stone Peter R. , James Joanna L. , Chamley Lawrence W. , Sharma Surendra 
Published: July 2017

AbstractIn preeclampsia, the serum levels of transthyretin, a carrier protein for thyroxine, are elevated. Transthyretin isolated from preeclamptic serum is also aggregated and can induce preeclampsia-like symptoms in pregnant IL10−/− mice. Using western blotting, immunofluorescence, ELISA and qRT-PCR, we investigated the production of transthyretin by preeclamptic placentae and whether transthyretin is carried into the maternal circulation via placental extracellular vesicles. Both total and aggregated transthyretin were present in higher levels in preeclamptic placentae compared to normotensive placentae (p < 0.05, n = 7), however the levels of transythretin mRNA were not significantly different (n = 8). Preeclamptic placentae secreted similar levels of total transthyretin compared to normotensive placentae (2352 ± 2949 ng/mL vs. 3250 ± 1864 ng/mL, mean ± SD, p > 0.05, n = 8), however in preeclampsia, a significant proportion is vesicle-associated (~48% vs 0%). Increased levels of aggregated transthyretin were specifically associated to preeclamptic nano-vesicles (p < 0.02, n = 8). This study showed that the placenta actively produces transthyretin and in preeclampsia, a significant amount is extruded into the maternal circulation via placental exracellular vesicles. The increased aggregation of transthyretin in preeclampsia occurs at the post-transcriptional level and while preeclamptic nano-vesicles may be removing a toxic aggregated protein from the placenta, they may also be delivering aggregated transthyretin to specific maternal organs, contributing to the pathogenesis of preeclampsia.
Antiparallel RNA G-quadruplex Formed by Human Telomere RNA Containing 8-Bromoguanosine
Authors: Xiao Chao-Da , Ishizuka Takumi , Xu Yan 
Published: July 2017

AbstractIn this study, by combining nuclear magnetic resonance (NMR), circular dichroism (CD), liquid chromatography-electrospray ionization-mass spectrometry (LC-ESI-MS), and gel electrophoresis, we report an unusual topological structure of the RNA G-quadruplex motif formed by human telomere RNA r(UAGGGU) containing 8-bromoguanosine. Results showed that the RNA sequence formed an antiparallel tetramolecular G-quadruplex, in which each pair of diagonal strands run in opposite directions. Furthermore, guanosines were observed both in syn- and anti-conformations. In addition, two of these G-quadruplex subunits were found to be stacking on top of each other, forming a dimeric RNA G-quadruplex. Our findings provide a new insight into the behavior of RNA G-quadruplex structures.