bluuebunny/crossref_metadata_2025_split huggingface dataset:
Biological nitrogen fixation in the oxygen-minimum region of the eastern tropical North Pacific ocean
Authors: Jayakumar Amal , Chang Bonnie X , Widner Brittany , Bernhardt Peter , Mulholland Margaret R , Ward Bess B 
Published: July 2017

Abstract
Biological nitrogen fixation (BNF) was investigated above and within the oxygen-depleted waters of the oxygen-minimum zone of the Eastern Tropical North Pacific Ocean. BNF rates were estimated using an isotope tracer method that overcame the uncertainty of the conventional bubble method by directly measuring the tracer enrichment during the incubations. Highest rates of BNF (~4 nm day−1) occurred in coastal surface waters and lowest detectable rates (~0.2 nm day−1) were found in the anoxic region of offshore stations. BNF was not detectable in most samples from oxygen-depleted waters. The composition of the N2-fixing assemblage was investigated by sequencing of nifH genes. The diazotrophic assemblage in surface waters contained mainly Proteobacterial sequences (Cluster I nifH), while both Proteobacterial sequences and sequences with high identities to those of anaerobic microbes characterized as Clusters III and IV type nifH sequences were found in the anoxic waters. Our results indicate modest input of N through BNF in oxygen-depleted zones mainly due to the activity of proteobacterial diazotrophs.
Long-term microdystrophin gene therapy is effective in a canine model of Duchenne muscular dystrophy
Authors: Le Guiner Caroline , Servais Laurent , Montus Marie , Larcher Thibaut , Fraysse Bodvaël , Moullec Sophie , Allais Marine , François Virginie , Dutilleul Maeva , Malerba Alberto , Koo Taeyoung , Thibaut Jean-Laurent , Matot Béatrice , Devaux Marie , Le Duff Johanne , Deschamps Jack-Yves , Barthelemy Inès , Blot Stéphane , Testault Isabelle , Wahbi Karim , Ederhy Stéphane , Martin Samia , Veron Philippe , Georger Christophe , Athanasopoulos Takis , Masurier Carole , Mingozzi Federico , Carlier Pierre , Gjata Bernard , Hogrel Jean-Yves , Adjali Oumeya , Mavilio Fulvio , Voit Thomas , Moullier Philippe , Dickson George 
Published: July 2017

AbstractDuchenne muscular dystrophy (DMD) is an incurable X-linked muscle-wasting disease caused by mutations in the dystrophin gene. Gene therapy using highly functional microdystrophin genes and recombinant adeno-associated virus (rAAV) vectors is an attractive strategy to treat DMD. Here we show that locoregional and systemic delivery of a rAAV2/8 vector expressing a canine microdystrophin (cMD1) is effective in restoring dystrophin expression and stabilizing clinical symptoms in studies performed on a total of 12 treated golden retriever muscular dystrophy (GRMD) dogs. Locoregional delivery induces high levels of microdystrophin expression in limb musculature and significant amelioration of histological and functional parameters. Systemic intravenous administration without immunosuppression results in significant and sustained levels of microdystrophin in skeletal muscles and reduces dystrophic symptoms for over 2 years. No toxicity or adverse immune consequences of vector administration are observed. These studies indicate safety and efficacy of systemic rAAV-cMD1 delivery in a large animal model of DMD, and pave the way towards clinical trials of rAAV–microdystrophin gene therapy in DMD patients.
Seismological evidence for a localized mushy zone at the Earth’s inner core boundary
Authors: Tian Dongdong , Wen Lianxing 
Published: July 2017

AbstractAlthough existence of a mushy zone in the Earth’s inner core has been hypothesized several decades ago, no seismic evidence has ever been reported. Based on waveform modeling of seismic compressional waves that are reflected off the Earth’s inner core boundary, here we present seismic evidence for a localized 4–8 km thick zone across the inner core boundary beneath southwest Okhotsk Sea with seismic properties intermediate between those of the inner and outer core and of a mushy zone. Such a localized mushy zone is found to be surrounded by a sharp inner core boundary nearby. These seismic results suggest that, in the current thermo-compositional state of the Earth’s core, the outer core composition is close to eutectic in most regions resulting in a sharp inner core boundary, but deviation from the eutectic composition exists in some localized regions resulting in a mushy zone with a thickness of 4–8 km.
A dsRNA virus with filamentous viral particles
Authors: Jia Hengxia , Dong Kaili , Zhou Lingling , Wang Guoping , Hong Ni , Jiang Daohong , Xu Wenxing 
Published: July 2017

AbstractViruses with double-stranded RNA genomes form isometric particles or are capsidless. Here we report a double-stranded RNA virus, Colletotrichum camelliae filamentous virus 1 (CcFV-1) isolated from a fungal pathogen, that forms filamentous particles. CcFV-1 has eight genomic double-stranded RNAs, ranging from 990 to 2444 bp, encoding 10 putative open reading frames, of which open reading frame 1 encodes an RNA-dependent RNA polymerase and open reading frame 4 a capsid protein. When inoculated, the naked CcFV-1 double-stranded RNAs are infectious and induce the accumulation of the filamentous particles in vivo. CcFV-1 is phylogenetically related to Aspergillus fumigatus tetramycovirus-1 and Beauveria bassiana polymycovirus-1, but differs in morphology and in the number of genomic components. CcFV-1 might be an intermediate virus related to truly capsidated viruses, or might represent a distinct encapsidating strategy. In terms of genome and particle architecture, our findings are a significant addition to the knowledge of the virosphere diversity.
Oropharyngeal mucosal transmission of Zika virus in rhesus macaques
Authors: Newman Christina M. , Dudley Dawn M. , Aliota Matthew T. , Weiler Andrea M. , Barry Gabrielle L. , Mohns Mariel S. , Breitbach Meghan E. , Stewart Laurel M. , Buechler Connor R. , Graham Michael E. , Post Jennifer , Schultz-Darken Nancy , Peterson Eric , Newton Wendy , Mohr Emma L. , Capuano Saverio , O’Connor David H. , Friedrich Thomas C. 
Published: July 2017

AbstractZika virus is present in urine, saliva, tears, and breast milk, but the transmission risk associated with these body fluids is currently unknown. Here we evaluate the risk of Zika virus transmission through mucosal contact in rhesus macaques. Application of high-dose Zika virus directly to the tonsils of three rhesus macaques results in detectable plasma viremia in all animals by 2 days post-exposure; virus replication kinetics are similar to those observed in animals infected subcutaneously. Three additional macaques inoculated subcutaneously with Zika virus served as saliva donors to assess the transmission risk from contact with oral secretions from an infected individual. Seven naive animals repeatedly exposed to donor saliva via the conjunctivae, tonsils, or nostrils did not become infected. Our results suggest that there is a risk of Zika virus transmission via the mucosal route, but that the risk posed by oral secretions from individuals with a typical course of Zika virus infection is low.
Heterogeneity of tumor-infiltrating lymphocytes ascribed to local immune status rather than neoantigens by multi-omics analysis of glioblastoma multiforme
Authors: Feng Lin , Qian Haipeng , Yu Xuexin , Liu Kan , Xiao Ting , Zhang Chengli , Kuang Manchao , Cheng Shujun , Li Xueji , Wan Jinghai , Zhang Kaitai 
Published: July 2017

AbstractHypothetically, intratumoral genomic heterogeneity has the potential to foster tumor-infiltrating lymphocyte (TIL) diversity; however, no study has directly tested this hypothesis by simultaneously investigating somatic mutations, TIL diversity, and immune response activity. Thus, we performed whole-exome sequencing, immune repertoire sequencing and gene expression on ten spatially separated tumor samples obtained from two tumor masses excised from a glioblastoma multiforme (GBM) patient, and we included peripheral blood as control. We found that although the multi-region samples from one tumor shared more common mutations than those from different tumors, the TIL populations did not. TIL repertoire diversity did not significantly correlate with the number of non-synonymous mutations; however, TIL diversity was highly correlated with local immune activity, as the pathways were all immune-related pathways that highly positive correlated with local TIL diversity. Twenty-three genes with expression largely unaffected by the intratumor heterogeneity were extracted from these pathways. Fifty GBM patients were stratified into two clusters by the expression of these genes with significant difference in prognosis. This finding was validated by The Cancer Genome Atlas (TCGA) GBM dataset, which indicated that despite the heterogeneity of intra-tumor immune status, the overall level of the immune response in GBM could be connected with prognosis.
Optoacoustic micro-tomography at 100 volumes per second
Authors: Deán-Ben X. Luís , López-Schier Hernán , Razansky Daniel 
Published: July 2017

AbstractOptical microscopy remains a fundamental tool for modern biological discovery owing to its excellent spatial resolution and versatile contrast in visualizing cellular and sub-cellular structures. Yet, the time domain is paramount for the observation of biological dynamics in living systems. Commonly, acquisition of microscopy data involves scanning of a spherically- or cylindrically-focused light beam across the imaged volume, which significantly limits temporal resolution in 3D. Additional complications arise from intense light scattering of biological tissues, further restraining the effective penetration depth and field of view of optical microscopy techniques. To overcome these limitations, we devised a fast optoacoustic micro-tomography (OMT) approach based on simultaneous acquisition of 3D image data with a high-density hemispherical ultrasound array having effective detection bandwidth beyond 25 MHz. We demonstrate fast three-dimensional imaging of freely-swimming zebrafish larvae, achieving 3D imaging speed of 100 volumes per second with isotropic spatial resolution approaching the dimensions of large cells across a field of view exceeding 50mm3. As opposed to other microscopy techniques based on optical contrast, OMT resolves optical absorption acoustically using unfocused light excitation. Thus, no penetration barriers are imposed by light scattering in deep tissues, suggesting it as a powerful approach for multi-scale functional and molecular imaging applications.
Probing helicity and the topological origins of helicity via non-local Hanbury-Brown and Twiss correlations
Authors: Mani Arjun , Benjamin Colin 
Published: July 2017

AbstractQuantum Hall edge modes are chiral while quantum spin Hall edge modes are helical. However, unlike chiral edge modes which always occur in topological systems, quasi-helical edge modes may arise in a trivial insulator too. These trivial quasi-helical edge modes are not topologically protected and therefore need to be distinguished from helical edge modes arising due to topological reasons. Earlier conductance measurements were used to identify these helical states, in this work we report on the advantage of using the non local shot noise as a probe for the helical nature of these states as also their topological or otherwise origin and compare them with chiral quantum Hall states. We see that in similar set-ups affected by same degree of disorder and inelastic scattering, non local shot noise “HBT” correlations can be positive for helical edge modes but are always negative for the chiral quantum Hall edge modes. Further, while trivial quasi-helical edge modes exhibit negative non-local”HBT” charge correlations, topological helical edge modes can show positive non-local “HBT” charge correlation. We also study the non-local spin correlations and Fano factor for clues as regards both the distinction between chirality/helicity as well as the topological/trivial dichotomy for helical edge modes.
Microfluidic sorting of intrinsically magnetic cells under visual control
Authors: Myklatun Ahne , Cappetta Michele , Winklhofer Michael , Ntziachristos Vasilis , Westmeyer Gil G. 
Published: July 2017

AbstractMagnetic cell sorting provides a valuable complementary mechanism to fluorescent techniques, especially if its parameters can be fine-tuned. In addition, there has recently been growing interest in studying naturally occurring magnetic cells and genetic engineering of cells to render them magnetic in order to control molecular processes via magnetic fields. For such approaches, contamination-free magnetic separation is an essential capability. We here present a robust and tunable microfluidic sorting system in which magnetic gradients of up to 1700 T/m can be applied to cells flowing through a sorting channel by reversible magnetization of ferrofluids. Visual control of the sorting process allowed us to optimize sorting efficiencies for a large range of sizes and magnetic moments of cells. Using automated quantification based on imaging of fluorescent markers, we showed that macrophages containing phagocytosed magnetic nanoparticles, with cellular magnetic dipole moments on the order of 10 fAm2, could be sorted with an efficiency of 90 ± 1%. Furthermore, we successfully sorted intrinsically magnetic magnetotactic bacteria with magnetic moments of 0.1 fAm2. In distinction to column-based magnetic sorting devices, microfluidic systems can prevent sample contact with superparamagnetic material. This ensures contamination-free separation of naturally occurring or bioengineered magnetic cells and is essential for downstream characterization of their properties.
Blockade of dengue virus infection and viral cytotoxicity in neuronal cells in vitro and in vivo by targeting endocytic pathways
Authors: Ho Min-Ru , Tsai Tsung-Ting , Chen Chia-Ling , Jhan Ming-Kai , Tsai Cheng-Chieh , Lee Yi-Chao , Chen Chun-Han , Lin Chiou-Feng 
Published: July 2017

AbstractDengue virus (DENV) infection in neuronal cells was speculated to trigger neuropathy. Herein, we determined the blockade of DENV infection by targeting endocytic pathways in vitro and in vivo. In DENV-infected mouse brains, we previously showed that viral proteins are expressed in neuronal cells around the hippocampus with accompanying neurotoxicity. DENV caused infection, including entry, double-stranded (ds)RNA replication, protein expression, and virus release, followed by cytotoxicity in the mouse neuronal Neuro-2a cell line. Pharmacologically blocking clathrin-mediated endocytosis of the DENV retarded viral replication. Targeting vacuolar-type H+-ATPase (V-ATPase)-based endosomal acidification effectively blocked the DENV replication process, but had no direct effect on viral translation. Blockade of the clathrin- and V-ATPase-based endocytic pathways also attenuated DENV-induced neurotoxicity. Inhibiting endosomal acidification effectively retarded DENV infection, acute viral encephalitis, and mortality. These results demonstrate that clathrin mediated endocytosis of DENV followed by endosomal acidification-dependent viral replication in neuronal cells, which can lead to neurotoxicity.
Membrane Perfusion of Hydrophobic Substances Around Channels Embedded in the Contact Bubble Bilayer
Authors: Iwamoto Masayuki , Oiki Shigetoshi 
Published: July 2017

AbstractIn fluidic biomembranes, lipids and membrane proteins diffuse restlessly, and lipid compositions change steadily. To mimic dynamic behavior of the biomembranes, a method for introducing rapid changes in the constituents in the lipid bilayer was developed. In contact bubble bilayers (CBB), as a water-in-oil droplet bilayer system, the bilayer hydrophobic interior is contiguous with the bulk oil phase. Making use of this geometrical feature as an access route, hydrophobic substances were administered into the bilayer. Polytheonamide B, a cytotoxic hydrophobic peptide, was applied, and oriented incorporation and relevant single-channel current recordings were enabled. Nystatin was pre-loaded in the CBB, and sterol perfusion exhibited slow development of the macroscopic current. On the contrary, the reconstituted KcsA potassium channels immediately attenuate the channel activity when cholesterol was applied. This oil-phase route in the CBB allows rapid perfusion of hydrophobic substances around the bilayer-embedded channels during continuous recordings of channel currents.
An atypical strictosidine synthase, OsSTRL2, plays key roles in anther development and pollen wall formation in rice
Authors: Zou Ting , Li Shuangcheng , Liu Mingxing , Wang Tao , Xiao Qiao , Chen Dan , Li Qiao , Liang Yanling , Zhu Jun , Liang Yueyang , Deng Qiming , Wang Shiquan , Zheng Aiping , Wang Lingxia , Li Ping 
Published: July 2017

AbstractStrictosidine synthase (STR) plays an important role in the biosynthesis of terpenoid indole alkaloids (TIAs) and is expressed in a range of active meristematic tissues of higher plants. STR proteins are involved in different physiological and biochemical pathways. However, the function of STR proteins in rice development remains poorly understood. In this study, we identified 21 possible STR-like (OsSTRL) family members in rice genome and found that only one gene, OsSTRL2, exhibited a pre-emergency specific florescence expression pattern. Tissue-specific expression profile analysis, β-glucuronidase histochemical (GUS) staining and RNA in situ hybridization confirmed that OsSTRL2 was highly expressed in tapetal cells and microspores. Comparative protein sequence analysis indicated that OsSTRL2 lacked the key catalytic residue found in a typical STR (STR1), although it possessed conserved β-propellers and α-helices formed the basic structure of STR1. OsSTRL2 knockout mutant resulted to male sterility because of the defects in anther development and pollen wall formation. Subcellular localization of OsSTRL2-YFP revealed that the OsSTRL2 protein was primarily localized in the endoplasmic reticulum (ER). Therefore, OsSTRL2 is an atypical strictosidine synthase that plays crucial roles in regulating anther development and pollen wall formation in rice.
GFusion: an Effective Algorithm to Identify Fusion Genes from Cancer RNA-Seq Data
Authors: Zhao Jian , Chen Qi , Wu Jing , Han Ping , Song Xiaofeng 
Published: July 2017

AbstractFusion gene derived from genomic rearrangement plays a key role in cancer initiation. The discovery of novel gene fusions may be of significant importance in cancer diagnosis and treatment. Meanwhile, next generation sequencing technology provide a sensitive and efficient way to identify gene fusions in genomic levels. However, there are still many challenges and limitations remaining in the existing methods which only rely on unmapped reads or discordant alignment fragments. In this work we have developed GFusion, a novel method using RNA-Seq data, to identify the fusion genes. This pipeline performs multiple alignments and strict filtering algorithm to improve sensitivity and reduce the false positive rate. GFusion successfully detected 34 from 43 previously reported fusions in four cancer datasets. We also demonstrated the effectiveness of GFusion using 24 million 76 bp paired-end reads simulation data which contains 42 artificial fusion genes, among which GFusion successfully discovered 37 fusion genes. Compared with existing methods, GFusion presented higher sensitivity and lower false positive rate. The GFusion pipeline can be accessed freely for non-commercial purposes at: https://github.com/xiaofengsong/GFusion.
Using latent class cluster analysis to screen high risk clusters of birth defects between 2009 and 2013 in Northwest China
Authors: Pei Leilei , Zeng Lingxia , Zhao Yaling , Wang Duolao , Yan Hong 
Published: July 2017

AbstractIn the study, we aimed to explore the synergistic effects of multiple risk factors on birth defects, and examine temporal trend of the synergistic effects over time. Two cross-sectional surveys conducted in 2009 and 2013 were merged and then latent class cluster analysis and generalized linear Poisson model were used. A total of 9085 and 29094 young children born within the last three years and their mothers were enrolled in 2009 and 2013 respectively. Three latent maternal exposure clusters were determined: a high-risk, a moderate-risk, and a low-risk cluster (88.97%, 1.49%, 9.54% in 2009 and 82.42%, 3.39%, 14.19% in 2013). The synthetic effects of maternal exposure to multiple risk factors could increase the risk of overall birth defects and cardiovascular system malformation among live births, and this risk is significantly higher in high-risk cluster than that in low-risk cluster. After adjusting for confounding factors using a generalized linear Poisson model, in high-risk cluster the prevalence of nervous system malformation decreased by approximately 2.71%, and the proportion of cardiovascular system malformation rose by 0.92% from 2009 to 2013. The Chinese government should make great efforts to provide primary prevention for those on high-risk cluster as a priority target population.
Epauletted fruit bats display exceptionally high infections with a Hepatocystis species complex in South Sudan
Authors: Schaer Juliane , Perkins Susan L. , Ejotre Imran , Vodzak Megan E. , Matuschewski Kai , Reeder DeeAnn M. 
Published: July 2017

AbstractHepatocystis parasites are closely related to mammalian Plasmodium species, the causative agents of malaria. Despite the close phylogenetic relationship, Hepatocystis parasites lack the intermittent erythrocytic replication cycles, the signature and exclusive cause of malaria-related morbidity and mortality. Hepatocystis population expansion in the mammalian host is thought to be restricted to the pre-erythrocytic liver phase. Complete differentiation of first generation blood stages into sexual stages for subsequent vector transmission indicates alternative parasite/host co-evolution. In this study, we identified a region of exceptionally high prevalence of Hepatocystis infections in Old World fruit bats in South Sudan. Investigations over the course of five consecutive surveys revealed an average of 93 percent prevalence in four genera of African epauletted fruit bats. We observed a clear seasonal pattern and tolerance of high parasite loads in these bats. Phylogenetic analyses revealed several cryptic Hepatocystis parasite species and, in contrast to mammalian Plasmodium parasites, neither host specificity nor strong geographical patterns were evident. Together, our study provides evidence for Pan-African distribution and local high endemicity of a Hepatocystis species complex in Pteropodidae.
Overall process of using a valerate-dominant sludge hydrolysate to produce high-quality polyhydroxyalkanoates (PHA) in a mixed culture
Authors: Hao Jiuxiao , Wang Xiujin , Wang Hui 
Published: July 2017

AbstractThe overall process of polyhydroxyalkanoates (PHA) production in a mixed culture fed by thermophilic fermented valerate-dominant sludge hydrolysate with high-level soluble organics (proteins and carbohydrates) and nutrients (nitrogen and phosphorus) was investigated in this study. The valerate-dominant hydrolysate was fed to enrich a PHA culture with an increasing concentration, and the enriched culture displayed a strong PHA-producing capacity under feast-famine conditions. Valerate in the feedstock was preferentially utilized over acetate and butyrate, and its uptake correlated with the production of 3-hydroxyvalerate (3HV) and 3-hydroxy-2-methylvalerate (3H2MV). The maximum PHA content (42.31%) was highest to date in a mixed culture with complex feedstock, and the PHA consisted of 3-hydroxybutyrate (3HB), 3HV, 3H2MV at 68.4, 23.7, 7.9 mmol C%. PHA production was inhibited when the nutrients exceeded a certain limit. Microbial analysis revealed that valerate-dominant feedstock caused Delftia (53%) to become the prevailing group over other PHA-producing bacteria. For long-term operation, 75% of the biomass at the end of feast phase was collected for PHA recovery, and the entire process exhibited a potential to produce 5 g PHA from 1 kg sludge. These findings indicate that the complex valerate-dominant sludge hydrolysate can be used to stably produce PHA containing high 3HV and 3H2MV.