bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characterization of multi-cellular dynamics of angiogenesis and vascular remodelling by intravital imaging of the wounded mouse cornea
Authors: Wang Yixin , Jin Yi , Laviña Bàrbara , Jakobsson Lars 
Published: July 2018

AbstractEstablishment of the functional blood vasculature involves extensive cellular rearrangement controlled by growth factors, chemokines and flow-mediated shear forces. To record these highly dynamic processes in mammalians has been technically demanding. Here we apply confocal and wide field time-lapse in vivo microscopy to characterize the remodelling vasculature of the wounded mouse cornea. Using mouse lines with constitutive or inducible endogenous fluorescent reporters, in combination with tracer injections and mosaic genetic recombination, we follow processes of sprouting angiogenesis, sprout fusion, vessel expansion and pruning in vivo, at subcellular resolution. We describe the migratory behaviour of endothelial cells of perfused vessels, in relation to blood flow directionality and vessel identity. Live-imaging following intravascular injection of fluorescent tracers, allowed for recording of VEGFA-induced permeability. Altogether, live-imaging of the remodelling vasculature of inflamed corneas of mice carrying endogenous fluorescent reporters and conditional alleles, constitutes a powerful platform for investigation of cellular behaviour and vessel function.
Radiocaesium transfer and radiation exposure of frogs in Fukushima Prefecture
Authors: Tagami Keiko , Uchida Shigeo , Wood Michael D. , Beresford Nicholas A. 
Published: July 2018

AbstractThe International Commission on Radiological Protection has proposed an environmental assessment framework. This includes ionising radiation exposure assessment for different frog life-stages, but radiocaesium transfer parameters are unavailable. We collate data from the Fukushima Prefecture (contaminated by the Fukushima accident) and estimate radiocaesium concentration ratio (CRwo-water) values for tadpoles and adult frogs, presenting the largest available amphibian CRwo-water dataset. In total, 513 adult frogs and 2540 tadpoles were analysed in 62 and 59 composite samples respectively. Results suggest that equilibrium was reached between water and amphibian radiocaesium activity concentrations circa one-year after the accident. Radiocaesium transfer to tadpoles was higher than to adult frogs. Dose rates were estimated for different life-stages and species in both the aquatic and terrestrial environment. Estimated dose rates to adults and tadpoles were typically similar because external exposure dominated for both organisms; frogspawn dose rates were estimated to be orders of magnitude lower than other life-stages. For the two sites assessed, which were outside of the most contaminated areas of the Fukushima Prefecture, estimated dose rates were below those anticipated to present a risk to wildlife populations; it is likely that dose rates in more contaminated areas were in excess of some effects benchmark values.
Vesicular stomatitis virus G protein transmembrane region is crucial for the hemi-fusion to full fusion transition
Authors: Ci Yali , Yang Yang , Xu Caimin , Shi Lei 
Published: July 2018

AbstractViral fusion proteins are essential for enveloped virus infection. These proteins mediate fusion between the virus envelope and host cellular membrane to release the viral genome into cells. Vesicular stomatitis virus G (VSV G) protein is a typical type III viral fusion protein. To study the mechanism of VSV G protein mediated membrane fusion, we set up a cell-cell fusion system in which cells are marked by different fluorescent proteins. Taking advantage of this system, we performed real-time recording and quantitative analysis of the cell fusion mediated by VSV G. We found that the time scale required for VSV G mediated cell-cell fusion was approximately 1–2 minutes. Next, we specifically examined the function of the transmembrane (TM) region of VSV G protein in membrane fusion by replacing the TM region with those of other fusion proteins. The TM region replacements dramatically impaired VSV G protein function in the cell-cell fusion assay and diminished VSV G mediated lentivirus and recombinant VSV infection efficiency. Further experiments implied that the TM region played a role in the transition from hemi-fusion to full fusion. Several residues within the TM region were identified as important for membrane fusion. Overall, our findings unraveled the important function of the TM region in VSV G mediated viral fusion.
Probiotics in human gut microbiota can degrade host glycosaminoglycans
Authors: Kawai Keigo , Kamochi Reiko , Oiki Sayoko , Murata Kousaku , Hashimoto Wataru 
Published: July 2018

AbstractGlycosaminoglycans (GAGs) (e.g. heparin, chondroitin sulfate, and hyaluronan) show various significant physiological functions as a major component of extracellular matrix in animals. Some bacteria target GAGs for adhesion and/or infection to host cells, although no probiotics have been known to degrade GAGs. Here, we show GAG degradation by probiotics from human gut microbiota and their adhesion to human intestinal cells through a GAG. GAG-degrading bacteria were isolated from human faeces and identified as Enterococcus faecium, and some typical probiotics such as Lactobacillus casei, Lactobacillus rhamnosus and Enterococcus faecalis were also found to degrade heparin. GAG-degrading lactobacilli and enterococci including the isolated E. faecium possessed a genetic cluster encoding GAG-degrading/metabolising enzymes in the bacterial genome. KduI and KduD enzymes encoded in the GAG cluster of L. rhamnosus functioned as 4-deoxy-l-threo-5-hexosulose-uronate ketol-isomerase and 2-keto-3-deoxy-d-gluconate dehydrogenase, respectively, both of which were crucial for GAG metabolism. GAG-degrading L. rhamnosus and E. faecium attached to human intestinal Caco-2 cells via heparin. Some species of Bacteroides, considered to be the next generation probiotics, degraded chondroitin sulfate C and hyaluronan, and genes coding for the Bacteroides GAG-degrading enzyme were frequently detected from human gut microbiota. This is the first report on GAG-degrading probiotics in human gut microbiota.
Planktonic fungal community structures and their relationship to water quality in the Danjiangkou Reservoir, China
Authors: Chen Zhaojin , Yuan Jian , Sun Feng , Zhang Fei , Chen Yan , Ding Chuanyu , Shi Jianwei , Li Yuying , Yao Lunguang 
Published: July 2018

AbstractPlanktonic fungi are important components of aquatic ecosystems, and analyses of their community composition and function have far-reaching significance for the ecological management and maintenance of reservoir environments. However, few studies have investigated the composition, distribution, and function of planktonic fungi in reservoir ecosystems and their relationship with water quality. Here, the composition of the planktonic fungal community in the surface water layer of the Danjiangkou Reservoir is investigated using Illumina MiSeq sequencing. According to the results, the reservoir community is primarily composed of 7 phyla, including Ascomycota, Rozellomycota, Basidiomycota, Chytridiomycota, and Zygomycota, comprising 294 genera, demonstrating the rich diversity of this community. Redundancy analysis (RDA) of the planktonic fungal community and environmental factors showed dissolved oxygen (DO), chemical oxygen demand (COD), total nitrogen (TN), chlorophyll a (Chl a), and permanganate (CODMn) to be important factors influencing the distribution of planktonic fungi. Spearman correlation analysis of the planktonic fungal community composition and diversity indices with physical and chemical water quality parameters showed that the impacts of TN, COD and DO were the most significant. The results of this study on the planktonic fungal community in the Danjiangkou Reservoir area using high-throughput sequencing revealed that the community is sensitive to water quality parameters. This result provides a reference for studying the composition and distribution of the planktonic fungal community in Danjiangkou Reservoir and its role in the biogeochemical cycle.
ACGH detects distinct genomic alterations of primary intrahepatic cholangiocarcinomas and matched lymph node metastases and identifies a poor prognosis subclass
Authors: Jansen Ruben , Moehlendick Birte , Bartenhagen Christoph , Tóth Csaba , Lehwald Nadja , Stoecklein Nikolas H. , Knoefel Wolfram T. , Lachenmayer Anja 
Published: July 2018

AbstractLymph node metastases (LNM) are an important prognostic factor for patients with intrahepatic cholangiocarcinoma, but underlying genetic alterations are poorly understood. Whole genome array comparative genomic hybridization (aCGH) was performed in 37 tumors and 14 matched LNM. Genomic analyses of tumors confirmed known and identified new (gains in 19q) copy number alterations (CNA). Tumors with LNM (N1) had more alterations and exclusive gains (3p, 4q, 5p, 13q) and losses (17p and 20p). LNM shared most alterations with their matched tumors (86%), but 79% acquired new isolated gains [12q14 (36%); 1p13, 2p23, 7p22, 7q11, 11q12, 13q13 and 14q12 (>20%)]. Unsupervised clustering revealed a poor prognosis subclass with increased alterations significantly associated to tumor differentiation and survival. TP53 and KRAS mutations occurred in 19% of tumors and 6% of metastases. Pathway analyses revealed association to cancer-associated pathways. Advanced tumor stage, microvascular/perineural invasion, and microscopic positive resection margin (R1) were significantly correlated to metastases, while N1-status, R1-resection, and poor tumor differentiation were significantly correlated to survival. ACGH identified clear differences between N0 (no LNM) and N1 tumors, while N1 tumors and matched LNM displayed high clonality with exclusive gains in the metastases. A novel subclass with increased CNAs and poor tumor differentiation was significantly correlated to survival.
Sub-nanoliter, real-time flow monitoring in microfluidic chips using a portable device and smartphone
Authors: Temiz Yuksel , Delamarche Emmanuel 
Published: July 2018

AbstractThe ever-increasing need for portable, easy-to-use, cost-effective, and connected point-of-care diagnostics (POCD) has been one of the main drivers of recent research on lab-on-a-chip (LoC) devices. A majority of these devices use microfluidics to manipulate precisely samples and reagents for bioanalysis. However, filling microfluidic devices with liquid can be prone to failure. For this reason, we have implemented a simple, yet efficient method for monitoring liquid displacement in microfluidic chips using capacitive sensing and a compact (75 mm × 30 mm × 10 mm), low-cost ($60), and battery-powered (10-hour autonomy) device communicating with a smartphone. We demonstrated the concept using a capillary-driven microfluidic chip comprising two equivalent flow paths, each with a total volume of 420 nL. Capacitance measurements from a pair of electrodes patterned longitudinally along the flow paths yielded 17 pL resolution in monitoring liquid displacement at a sampling rate of 1 data/s (~1 nL/min resolution in the flow rate). We characterized the system using human serum, biological buffers, and water, and implemented an algorithm to provide real-time information on flow conditions occurring in a microfluidic chip and interactive guidance to the user.
Damage to the myogenic differentiation of C2C12 cells by heat stress is associated with up-regulation of several selenoproteins
Authors: Tang Jiayong , He Aihua , Yan Hui , Jia Gang , Liu Guangmang , Chen Xiaoling , Cai Jingyi , Tian Gang , Shang Haiying , Zhao Hua 
Published: July 2018

AbstractThis study was conducted to profile the selenoprotein encoding genes or proteins in mouse C2C12 cells and integrate their roles in the skeletal cell damage induced by heat stress (HS). Cells were cultured at 37.0 °C or 41.5 °C for 4, 6 or 8 days. The mRNA expression of 24 selenoprotein encoding genes and abundance of 5 selenoproteins were investigated. HS suppressed myogenic differentiation and impaired the development of muscle myotubes. HS down-regulated (P < 0.01) mRNA abundance of MYOD and MYOGENIN, and decreased (P < 0.01) MYOGENIN protein expression, HS elevated (P < 0.01) HSP70 and (P < 0.01) the ratio of BCL-2 to BAX at both mRNA and protein level. Meanwhile, HS up-regulated (P < 0.01–0.05) expressions of 18, 11 and 8 selenoprotein encoding genes after 4, 6 and 8 days of hyperthermia, and only down-regulated (P < 0.01) DIO2 after 6 and 8 days of hyperthermia, respectively. Furthermore, HS influenced expression of selenoproteins and up-regulated (P < 0.01–0.05) GPX1, GPX4 and SEPN1 after 6 days of HS. The damage to development of mouse skeletal muscle myotubes by HS accompanied with the up-regulation of both selenoprotein encoding genes and proteins, which suggested a potential protective effect of selenoprotein on hyperthermia associated damage in C2C12 cells.
Long-term in vivo biodistribution and toxicity study of functionalized near-infrared persistent luminescence nanoparticles
Authors: Sun Xia , Shi Junpeng , Fu Xiaoyan , Yang Yi , Zhang Hongwu 
Published: July 2018

AbstractNear-infrared (NIR) persistent luminescence nanoparticles (NPLNPs) have become one of the most promising candidates for bioimaging. Different from the other fluorescence nanoprobes, the NIR persistent luminescence of NPLNPs can last for a long time after excitation, double exposure that is nanoparticles and light exist during the long-term bioimaging. However, to date, the potential risk of nanoparticles and NIR persistent luminescence of NPLNPs is still unknown. In this study, Cr3 + -doped zinc gallate, Zn1.1Ga1.8Sn0.1O4:Cr3+ (ZGO), the most promising NPLNPs in bioimaging, was chosen as a representative for potential risk assessment. We evaluated the potential risk of nanoparticles and NIR persistent luminescence of ZGO for a long period of time. In vitro study showed that the ZGO possessed a low cytotoxicity. In vivo biodistribution results showed that the ZGO mainly accumulated in the reticuloendothelial system after intravenous injection and could be gradually cleared from the body by digestive system. In addition, the ZGO did not exhibit appreciable toxicity in mice over a period of 60 days. It’s also worth mentioning that long-term NIR persistent luminescence of ZGO did not exhibit obvious toxicities both in vitro and in vivo. Our results provide important information with regards to the risk of NPLNPs in long-term bioimaging.
Genetic markers associated to arbuscular mycorrhizal colonization in durum wheat
Authors: De Vita Pasquale , Avio Luciano , Sbrana Cristiana , Laidò Giovanni , Marone Daniela , Mastrangelo Anna M. , Cattivelli Luigi , Giovannetti Manuela 
Published: July 2018

AbstractIn this work we investigated the variability and the genetic basis of susceptibility to arbuscular mycorrhizal (AM) colonization of wheat roots. The mycorrhizal status of wild, domesticated and cultivated tetraploid wheat accessions, inoculated with the AM speciesFunneliformis mosseae, was evaluated. In addition, to detect genetic markers in linkage with chromosome regions involved in AM root colonization, a genome wide association analysis was carried out on 108 durum wheat varieties and two AM fungal species (F.mosseaeandRhizoglomus irregulare). Our findings showed that a century of breeding on durum wheat and the introgression ofReduced height(Rht) genes associated with increased grain yields did not select against AM symbiosis in durum wheat. Seven putative Quantitative Trait Loci (QTLs) linked with durum wheat mycorrhizal susceptibility in both experiments, located on chromosomes 1A, 2B, 5A, 6A, 7A and 7B, were detected. The individual QTL effects (r2) ranged from 7 to 16%, suggesting a genetic basis for this trait. Marker functional analysis identified predicted proteins with potential roles in host-parasite interactions, degradation of cellular proteins, homeostasis regulation, plant growth and disease/defence. The results of this work emphasize the potential for further enhancement of root colonization exploiting the genetic variability present in wheat.
Carbohydrate Syntrophy enhances the establishment of Bifidobacterium breve UCC2003 in the neonatal gut
Authors: O’Connell Motherway Mary , O’Brien Frances , O’Driscoll Tara , Casey Patrick G. , Shanahan Fergus , van Sinderen Douwe 
Published: July 2018

AbstractThe non-digestible oligosaccharide fraction of maternal milk represents an important of carbohydrate and energy source for saccharolytic bifidobacteria in the gastrointestinal tract during early life. However, not all neonatal bifidobacteria isolates can directly metabolise the complex sialylated, fucosylated, sulphated and/or N-acetylglucosamine-containing oligosaccharide structures present in mothers milk. For some bifidobacterial strains, efficient carbohydrate syntrophy or crossfeeding is key to their establishment in the gut. In this study, we have adopted advanced functional genomic approaches to create single and double in-frame deletions of the N-acetyl glucosamine 6-phosphate deacetylase encoding genes, nagA1 and nagA2, of B. breve UCC2003. In vitro phenotypic analysis followed by in vivo studies on co-colonisation, mother to infant transmission, and evaluation of the relative co-establishment of B. bifidum and B. breve UCC2003 or UCC2003ΔnagA1ΔnagA2 in dam-reared neonatal mice demonstrates the importance of crossfeeding on sialic acid, fucose and N-acetylglucosamine-containing oligosaccharides for the establishment of B. breve UCC2003 in the neonatal gut. Furthermore, transcriptomic analysis of in vivo gene expression shows upregulation of genes associated with the utilisation of lactose, sialic acid, GlcNAc-6-S and fucose in B. breve UCC2003, while for UCC2003ΔnagA1ΔnagA2 only genes for lactose metabolism were upregulated.
Exploring hidden diversity in Southeast Asia’s Dermogenys spp. (Beloniformes: Zenarchopteridae) through DNA barcoding
Authors: Nurul Farhana Samsudin , Muchlisin Zainal Abidin , Duong Thuy Yen , Tanyaros Suwat , Page Larry M. , Zhao Yahui , Adamson Eleanor A. S. , Khaironizam Md. Zain , de Bruyn Mark , Siti Azizah Mohd Nor 
Published: July 2018

AbstractMembers of the freshwater halfbeak genusDermogenysare hard to identify to the species level, despite several previous attempts to isolate fixed meristic, morphometric and colour pattern differences. This has led to ongoing confusion in scientific literature, records of species occurrence, and entries in museum collections. Here, a DNA barcoding study was conducted on the genus to gain further understanding of its taxonomic status across the Southeast Asian region. Fish were collected from 33 localities, spanning freshwater and brackish habitats in Malaysia, Western Indonesia, Thailand and Vietnam. In total, 290 samples ofDermogenysspp. were amplified for a 651 base pair fragment of the mitochondrial cytochrome oxidasecsubunit I (COI) gene. Analysis was able to successfully differentiate the three species:D.collettei,D.siamensis,D.sumatrana; reveal the presence of a new putative species,Dermogenyssp., that was sampled in sympatry withD.colletteiat three locations; as well as uncovering two genetic lineages of a fifth species,D.bispina, that display non-overlapping geographical distributions in drainages of northern Borneo; Kudat and Sandakan. This study expands the barcode library for Zenarchopteridae, demonstrates the efficacy of DNA barcoding techniques for differentiatingDermogenysspecies, and the potential thereof in species discovery.
V902 Monocerotis: A likely disc-accreting intermediate polar
Authors: Worpel H. , Schwope A. D. , Traulsen I. , Mukai K. , Ok S. 
Published: July 2018

Aims. We aim to confirm whether the eclipsing cataclysmic variable (CV) V902 Mon is an intermediate polar (IP), to characterise its X-ray spectrum and flux, and to refine its orbital ephemeris and spin period.
Methods. We performed spectrographic observations of V902 Mon in 2016 with the 2.2 m Calar Alto telescope, and X-ray photometry and spectroscopy with XMM-Newton in October 2017. This data was supplemented by several years of AAVSO visual photometry.
Results. We confirmed V902 Mon as an IP based on detecting the spin period, which has a value of 2208 s, at multiple epochs. Spectroscopy of the donor star and Gaia parallax yield a distance of 3.5−0.9+1.3 kpc, suggesting an X-ray luminosity one or two orders of magnitude lower than the 1033 erg s−1 typical of previously known IPs. The X-ray to optical flux ratio is also very low. The inclination of the system is more than 79°, and is most likely a value of around 82°. We have refined the eclipse ephemeris, stable over 14 000 cycles. The Hα line is present throughout the orbital cycle and is clearly present during eclipse, suggesting an origin distant from the white dwarf, and shows radial velocity variations at the orbital period. The amplitude and overall recessional velocity seem inconsistent with an origin in the disc. The XMM-Newton observation reveals a partially absorbed plasma model typical of magnetic CVs, that has a fluorescent iron line at 6.4 keV showing a large equivalent width of 1.4 keV.
Conclusions. V902 Mon is an IP, and probably a member of the hypothesized X-ray underluminous class of IPs. It is likely to be a disc accretor, although the radial velocity behaviour of the Hα line remains puzzling. The large equivalent width of the fluorescent iron line, the small FX/Fopt ratio, and the only marginal detection of X-ray eclipses suggests that the X-ray emission arises from scattering.
Molecular Diagnostics in Pediatric Brain Tumors: Impact on Diagnosis and Clinical Decision-Making — A Selected Case Series
Authors: Bächli Heidi , Ecker Jonas , van Tilburg Cornelis , Sturm Dominik , Selt Florian , Sahm Felix , Koelsche Christian , Grund Kerstin , Sutter Christian , Pietsch Torsten , Witt Hendrik , Herold-Mende Christel , von Deimling Andreas , Jones David , Pfister Stefan , Witt Olaf , Milde Till 
Published: July 2018

AbstractCentral nervous system (CNS) tumors account for the highest mortality among pediatric malignancies. Accurate diagnosis is essential for optimal clinical management. The increasing use of molecular diagnostics has opened up novel possibilities for more precise classification of CNS tumors. We here report a single-institutional collection of pediatric CNS tumor cases that underwent a refinement or a change of diagnosis after completion of molecular analysis that affected clinical decision-making including the application of molecularly informed targeted therapies. 13 pediatric CNS tumors were analyzed by conventional histology, immunohistochemistry, and molecular diagnostics including DNA methylation profiling in 12 cases, DNA sequencing in 8 cases and RNA sequencing in 3 cases. 3 tumors had a refinement of diagnosis upon molecular testing, and 6 tumors underwent a change of diagnosis. Targeted therapy was initiated in 5 cases. An underlying cancer predisposition syndrome was detected in 5 cases. Although this case series, retrospective and not population based, has its limitations, insight can be gained regarding precision of diagnosis and clinical management of the patients in selected cases. Accuracy of diagnosis was improved in the cases presented here by the addition of molecular diagnostics, impacting clinical management of affected patients, both in the first-line as well as in the follow-up setting. This additional information may support the clinical decision making in the treatment of challenging pediatric CNS tumors. Prospective testing of the clinical value of molecular diagnostics is currently underway.