bluuebunny/crossref_metadata_2025_split huggingface dataset:
Olig2 regulates Purkinje cell generation in the early developing mouse cerebellum
Authors: Ju Jun , Liu Qian , Zhang Yang , Liu Yuanxiu , Jiang Mei , Zhang Liguo , He Xuelian , Peng Chenchen , Zheng Tao , Lu Q. Richard , Li Hedong 
Published: July 2016

AbstractThe oligodendrocyte transcription factor Olig2 plays a crucial role in the neurogenesis of both spinal cord and brain. In the cerebellum, deletion of both Olig2 and Olig1 results in impaired genesis of Purkinje cells (PCs) and Pax2+ interneurons. Here, we perform an independent study to show that Olig2 protein is transiently expressed in the cerebellar ventricular zone (VZ) during a period when PCs are specified. Further analyses demonstrate that Olig2 is expressed in both cerebellar VZ progenitors and early-born neurons. In addition, unlike in the ganglionic eminence of the embryonic forebrain where Olig2 is mostly expressed in proliferating progenitors, Olig2+ cells in the cerebellar VZ are in the process of leaving the cell cycle and differentiating into postmitotic neurons. Functionally, deletion of Olig2 alone results in a preferential reduction of PCs in the cerebellum, which is likely mediated by decreased neuronal generation from their cerebellar VZ progenitors. Furthermore, our long-term lineage tracing experiments show that cerebellar Olig gene-expressing progenitors produce PCs but rarely Pax2+ interneurons in the developing cerebellum, which opposes the “temporal identity transition” model of the cerebellar VZ progenitors stating that majority of Pax2+ interneuron progenitors are transitioned from Olig2+ PC progenitors.
Novel combination of sorafenib and biochanin-A synergistically enhances the anti-proliferative and pro-apoptotic effects on hepatocellular carcinoma cells
Authors: Youssef Mohieldin M. , Tolba Mai F. , Badawy Noha N. , Liu Andrew W. , El-Ahwany Eman , Khalifa Amani E. , Zada Suher , Abdel-Naim Ashraf B. 
Published: July 2016

AbstractSorafenib (SOR) is the first-line treatment for hepatocellular carcinoma (HCC). However, its use is hindered by the recently expressed safety concerns. One approach for reducing SOR toxicity is to use lower doses in combination with other less toxic agents. Biochanin-A (Bio-A), a promising isoflavone, showed selective toxicity to liver cancer cells. We postulated that combining SOR and Bio-A could be synergistically toxic towards HCC cells. We further evaluated the underlying mechanism. Cytotoxicity assay was performed to determine the IC50 of Bio-A and SOR in HepG2, SNU-449 and Huh-7 cells. Then, combination index in HepG2 was evaluated using Calcusyn showing that the concurrent treatment with lower concentrations of SOR and Bio-A synergistically inhibited cell growth. Our combination induced significant arrest in pre-G and G0/G1 cell cycle phases and decrease in cyclin D1 protein level. Concomitantly, SOR/Bio-A reduced Bcl-2/Bax ratio. Furthermore, this co-treatment significantly increased caspase-3 & -9 apoptotic markers, while decreased anti-apoptotic and proliferative markers; survivin and Ki-67, respectively. Active caspase-3 in HepG2, SNU-449 and Huh-7 confirmed our synergism hypothesis. This study introduces a novel combination, where Bio-A synergistically enhanced the anti-proliferative and apoptotic effects of SOR in HCC cells, which could serve as a potential effective regimen for treatment.
Genomic analysis of three Bifidobacterium species isolated from the calf gastrointestinal tract
Authors: Kelly William J. , Cookson Adrian L. , Altermann Eric , Lambie Suzanne C. , Perry Rechelle , Teh Koon Hoong , Otter Don E. , Shapiro Nicole , Woyke Tanja , Leahy Sinead C. 
Published: July 2016

AbstractRuminant animals contribute significantly to the global value of agriculture and rely on a complex microbial community for efficient digestion. However, little is known of how this microbial-host relationship develops and is maintained. To begin to address this, we have determined the ability of three Bifidobacterium species isolated from the faeces of newborn calves to grow on carbohydrates typical of a newborn ruminant diet. Genome sequences have been determined for these bacteria with analysis of the genomes providing insights into the host association and identification of several genes that may mediate interactions with the ruminant gastrointestinal tract. The present study provides a starting point from which we can define the role of potential beneficial microbes in the nutrition of young ruminants and begin to influence the interactions between the microbiota and the host. The differences observed in genomic content hint at niche partitioning among the bifidobacterial species analysed and the different strategies they employ to successfully adapt to this habitat.
Optimally controlling the human connectome: the role of network topology
Authors: Betzel Richard F. , Gu Shi , Medaglia John D. , Pasqualetti Fabio , Bassett Danielle S. 
Published: July 2016

AbstractTo meet ongoing cognitive demands, the human brain must seamlessly transition from one brain state to another, in the process drawing on different cognitive systems. How does the brain’s network of anatomical connections help facilitate such transitions? Which features of this network contribute to making one transition easy and another transition difficult? Here, we address these questions using network control theory. We calculate the optimal input signals to drive the brain to and from states dominated by different cognitive systems. The input signals allow us to assess the contributions made by different brain regions. We show that such contributions, which we measure as energy, are correlated with regions’ weighted degrees. We also show that the network communicability, a measure of direct and indirect connectedness between brain regions, predicts the extent to which brain regions compensate when input to another region is suppressed. Finally, we identify optimal states in which the brain should start (and finish) in order to minimize transition energy. We show that the optimal target states display high activity in hub regions, implicating the brain’s rich club. Furthermore, when rich club organization is destroyed, the energy cost associated with state transitions increases significantly, demonstrating that it is the richness of brain regions that makes them ideal targets.
A phospholipid transfer function of ER-mitochondria encounter structure revealed in vitro
Authors: Kojima Rieko , Endo Toshiya , Tamura Yasushi 
Published: July 2016

AbstractAs phospholipids are synthesized mainly in the endoplasmic reticulum (ER) and mitochondrial inner membranes, how cells properly distribute specific phospholipids to diverse cellular membranes is a crucial problem for maintenance of organelle-specific phospholipid compositions. Although the ER-mitochondria encounter structure (ERMES) was proposed to facilitate phospholipid transfer between the ER and mitochondria, such a role of ERMES is still controversial and awaits experimental demonstration. Here we developed a novel in vitro assay system with isolated yeast membrane fractions to monitor phospholipid exchange between the ER and mitochondria. With this system, we found that phospholipid transport between the ER and mitochondria relies on membrane intactness, but not energy sources such as ATP, GTP or the membrane potential across the mitochondrial inner membrane. We further found that lack of the ERMES component impairs the phosphatidylserine transport from the ER to mitochondria, but not the phosphatidylethanolamine transport from mitochondria to the ER. This in vitro assay system thus offers a powerful tool to analyze the non-vesicular phospholipid transport between the ER and mitochondria.
Serial testing for latent tuberculosis using QuantiFERON-TB Gold In-Tube: A Markov model
Authors: Moses Mark W. , Zwerling Alice , Cattamanchi Adithya , Denkinger Claudia M. , Banaei Niaz , Kik Sandra V. , Metcalfe John , Pai Madhukar , Dowdy David 
Published: July 2016

AbstractHealthcare workers (HCWs) in low-incidence settings are often serially tested for latent TB infection (LTBI) with the QuantiFERON-TB Gold In-Tube (QFT) assay, which exhibits frequent conversions and reversions. The clinical impact of such variability on serial testing remains unknown. We used a microsimulation Markov model that accounts for major sources of variability to project diagnostic outcomes in a simulated North American HCW cohort. Serial testing using a single QFT with the recommended conversion cutoff (IFN-g > 0.35 IU/mL) resulted in 24.6% (95% uncertainty range, UR: 23.8–25.5) of the entire population testing false-positive over ten years. Raising the cutoff to >1.0 IU/mL or confirming initial positive results with a (presumed independent) second test reduced this false-positive percentage to 2.3% (95%UR: 2.0–2.6%) or 4.1% (95%UR: 3.7–4.5%), but also reduced the proportion of true incident infections detected within the first year of infection from 76.5% (95%UR: 66.3–84.6%) to 54.8% (95%UR: 44.6–64.5%) or 61.5% (95%UR: 51.6–70.9%), respectively. Serial QFT testing of HCWs in North America may result in tremendous over-diagnosis and over-treatment of LTBI, with nearly thirty false-positives for every true infection diagnosed. Using higher cutoffs for conversion or confirmatory tests (for initial positives) can mitigate these effects, but will also diagnose fewer true infections.
Protective Effect of Quercetin on Posttraumatic Cardiac Injury
Authors: Jing Zehao , Wang Zhuorun , Li Xiujie , Li Xintao , Cao Tingting , Bi Yue , Zhou Jicheng , Chen Xu , Yu Deqin , Zhu Liang , Li Shuzhuang 
Published: July 2016

AbstractQuercetin is an important dietary flavonoid present in fruits and vegetables and has attracted attention because of its anti-inflammatory and anti-oxidative properties. Inflammation and oxidative stress play important roles in posttraumatic cardiomyocyte apoptosis, which contributes to secondary cardiac dysfunction. This study investigates the protective effect of quercetin on trauma-induced secondary cardiac injury and the mechanisms involved. Widely accepted nonlethal mechanical trauma models were established. In vivo, cardiomyocyte apoptosis and cardiac dysfunction in rats were assessed using TUNEL staining and a biological mechanic experiment system. In vitro, cell viability, tumour necrosis factor-α (TNF-α), reactive oxygen species (ROS) and [Ca2+]i of H9c2 cells were detected using an MTT assay, ELISA and 2′,7′-dichlorofluorescin diacetate and fluo-4 acetoxymethyl ester assays respectively. Quercetin pretreatment (20 mg/kg i.p.; 0.5 h before trauma) significantly improved posttraumatic cardiomyocyte apoptosis and cardiac dysfunction. Pretreatment with quercetin (20 μM; 24 h before trauma plasma addition) significantly attenuated trauma-induced viability decreases, TNF-α increases, ROS overproduction and [Ca2+]i overload in H9c2 cells. In conclusion, quercetin may reverse posttraumatic cardiac dysfunction by reducing cardiomyocyte apoptosis through the suppression of TNF-α increases, ROS overproduction and Ca2+ overload in cardiomyocytes, representing a potential preventive approach for the treatment of secondary cardiac injury after mechanical trauma.
Reduced Protein Synthesis Fidelity Inhibits Flagellar Biosynthesis and Motility
Authors: Fan Yongqiang , Evans Christopher R. , Ling Jiqiang 
Published: July 2016

AbstractAccurate translation of the genetic information from DNA to protein is maintained by multiple quality control steps from bacteria to mammals. Genetic and environmental alterations have been shown to compromise translational quality control and reduce fidelity during protein synthesis. The physiological impact of increased translational errors is not fully understood. While generally considered harmful, translational errors have recently been shown to benefit cells under certain stress conditions. In this work, we describe a novel regulatory pathway in which reduced translational fidelity downregulates expression of flagellar genes and suppresses bacterial motility. Electron microscopy imaging shows that the error-prone Escherichia coli strain lacks mature flagella. Further genetic analyses reveal that translational errors upregulate expression of a small RNA DsrA through enhancing its transcription and deleting DsrA from the error-prone strain restores motility. DsrA regulates expression of H-NS and RpoS, both of which regulate flagellar genes. We demonstrate that an increased level of DsrA in the error-prone strain suppresses motility through the H-NS pathway. Our work suggests that bacteria are capable of switching on and off the flagellar system by altering translational fidelity, which may serve as a previously unknown mechanism to improve fitness in response to environmental cues.
Impact of magnetic topology on radial electric field profile in the scrape-off layer of the Large Helical Device
Authors: Suzuki Y. , Ida K. , Kamiya K. , Yoshinuma M. , Tsuchiya H. , Kobayashi M. , Kawamura G. , Ohdachi S. , Sakakibara S. , Watanabe K.Y. , Hudson S. , Feng Y. , Yamada I. , Yasuhara R. , Tanaka K. , Akiyama T. , Morisaki T. 
Published: July 2016

Abstract
The radial electric field in the plasma edge is studied in the Large Helical Device (LHD) experiments. When magnetic field lines become stochastic or open at the plasma edge and connected to the vessel, electrons are lost faster than ions along these field lines. Then, a positive electric field appears in the plasma edge. The radial electric field profile can be used to detect the effective plasma boundary. Magnetic topology is an important issue in stellarator and tokamak research because the 3D boundary has the important role of controlling MHD edge stability with respect to ELMs, and plasma detachment. Since the stochastic magnetic field layer can be controlled in the LHD by changing the preset vacuum magnetic axis, this device is a good platform to study the properties of the radial electric field that appear with the different stochastic layer width. Two magnetic configurations with different widths of the stochastic layer as simulated in vacuum are studied for low-β discharges. It has been found that a positive electric field appeared outside of the last closed flux surface. In fact the positions of the positive electric field are found in the boundary between of the stochastic layer and the scrape-off layer. To understand where is the boundary of the stochastic layer and the scrape-off layer, the magnetic field lines are analyzed statistically. The variance of the magnetic field lines in the stochastic layer is increased outwards for both configurations. However, the skewness, which means the asymmetry of the distribution of the magnetic field line, increases for only one configuration. If the skewness is large, the connection length becomes effectively short. Since that is consistent with the experimental observation, the radial electric field can be considered as an index of the magnetic topology.
Simulation of bootstrap current in 2D and 3D ideal magnetic fields in tokamaks
Authors: Raghunathan M. , Graves J.P. , Cooper W.A. , Pedro M. , Sauter O. 
Published: July 2016

Abstract
We aim to simulate the bootstrap current for a MAST-like spherical tokamak using two approaches for magnetic equilibria including externally caused 3D effects such as resonant magnetic perturbations (RMPs), the effect of toroidal ripple, and intrinsic 3D effects such as non-resonant internal kink modes. The first approach relies on known neoclassical coefficients in ideal MHD equilibria, using the Sauter (Sauter et al 1999 Phys. Plasmas
6 2834) expression valid for all collisionalities in axisymmetry, and the second approach being the quasi-analytic Shaing–Callen (Shaing and Callen 1983 Phys. Fluids
26 3315) model in the collisionless regime for 3D. Using the ideal free-boundary magnetohydrodynamic code VMEC, we compute the flux-surface averaged bootstrap current density, with the Sauter and Shaing–Callen expressions for 2D and 3D ideal MHD equilibria including an edge pressure barrier with the application of resonant magnetic perturbations, and equilibria possessing a saturated non-resonant 1/1 internal kink mode with a weak internal pressure barrier. We compare the applicability of the self-consistent iterative model on the 3D applications and discuss the limitations and advantages of each bootstrap current model for each type of equilibrium.
Plasma response to m/n  =  3/1 resonant magnetic perturbation at J-TEXT Tokamak
Authors: Hu Qiming , Li Jianchao , Wang Nengchao , Yu Q. , Chen Jie , Cheng Zhifeng , Chen Zhipeng , Ding Yonghua , Jin Hai , Li Da , Li Mao , Liu Yang , Rao Bo , Zhu Lizhi , Zhuang Ge 
Published: July 2016

Abstract
The influence of resonant magnetic perturbations (RMPs) with a large m/n  =  3/1 component on electron density has been studied at J-TEXT tokamak by using externally applied static and rotating RMPs, where m and n are the poloidal and toroidal mode number, respectively. The detailed time evolution of electron density profile, measured by the polarimeter–interferometer, shows that the electron density n
e first increases (decreases) inside (around/outside) of the 3/1 rational surface (RS), and it is increased globally later together with enhanced edge recycling. Associated with field penetration, the toroidal rotation around the 3/1 RS is accelerated in the co-I
p direction and the poloidal rotation is changed from the electron to ion diamagnetic drift direction. Spontaneous unlocking-penetration circles occur after field penetration if the RMPs amplitude is not strong enough. For sufficiently strong RMPs, the 2/1 locked mode is also triggered due to mode coupling, and the global density is increased. The field penetration threshold is found to be linearly proportional to n
eL (line-integrated density) at the 3/1 RS but to (n
eL)0.73 for n
e at the plasma core. In addition, for rotating RMPs with a large 3/1 component, field penetration causes a global increase in electron density.
Measurements and modelling of plasma response field to RMP on the COMPASS tokamak
Authors: Markovic T. , Liu Y.Q. , Cahyna P. , Pánek R. , Peterka M. , Aftanas M. , Bílková P. , Bohm P. , Imríšek M. , Háček P. , Havlicek J. , Havránek A. , Komm M. , Urban J. , Weinzettl V. 
Published: July 2016

Abstract
It has been shown on several tokamaks that application of a resonant magnetic perturbation (RMP) field to the plasma can lead to suppression or mitigation of edge-localized mode (ELM) instabilities. Due to the rotation of the plasma in the RMP field reference system, currents are induced on resonant surfaces within the plasma, consequently screening the original perturbation. In this work, the extensive set of 104 saddle loops installed on the COMPASS tokamak is utilized to measure the plasma response field for two n  =  2 RMP configurations of different poloidal mode m spectra. It is shown that spatially the response field is in opposite phase to the original perturbation, and that the poloidal profile of the measured response field does not depend on the poloidal profile of the applied RMP. Simulations of the plasma response by the linear MHD code MARS-F (Liu et al 2000 Phys. Plasmas
7 3681) reveal that both of the studied RMP configurations are well screened by the plasma. Comparison of measured plasma response field with the simulated one shows a good agreement across the majority of poloidal angles, with the exception of the midplane low-field side area, where discrepancy is seen.
Human Leukocyte Antigen-G: A Promising Prognostic Marker of Disease Progression to Improve the Control of Human African Trypanosomiasis
Authors: Gineau Laure , Courtin David , Camara Mamadou , Ilboudo Hamidou , Jamonneau Vincent , Dias Fabricio C. , Tokplonou Leonidas , Milet Jacqueline , Mendonça Priscila B. , Castelli Erick C. , Camara Oumou , Camara Mariam , Favier Benoit , Rouas-Freiss Nathalie , Moreau Philippe , Donadi Eduardo A. , Bucheton Bruno , Sabbagh Audrey , Garcia André 
Published: July 2016

Abstract
Background.  Human African trypanosomiasis (HAT) caused by Trypanosoma brucei gambiense can be diagnosed in the early hemolymphatic stage (stage 1 [S1]) or meningoencephalitic stage (stage 2 [S2]). Importantly, individuals harbouring high and specific antibody responses to Tbg antigens but negative parasitology are also diagnosed in the field (seropositive [SERO]). Whereas some develop the disease in the months following their initial diagnosis (SERO/HAT), others remain parasitologically negative for long periods (SERO) and are apparently able to control infection. Human leucocyte antigen (HLA)-G, an immunosuppressive molecule, could play a critical role in this variability of progression between infection and disease.
Methods.  Soluble HLA-G (sHLA-G) was measured in plasma for patients in the SERO (n = 65), SERO/HAT (n = 14), or HAT (n = 268) group and in cerebrospinal fluid for patients in S1 (n = 55), early S2 (n = 93), or late S2 (n = 110). Associations between these different statuses and the soluble level or genetic polymorphisms of HLA-G were explored.
Results.  Plasma sHLA-G levels were significantly higher in HAT (P = 6 × 10−7) and SERO/HAT (P = .007) than SERO patients. No difference was observed between the SERO/HAT and HAT groups. Within the HAT group, specific haplotypes (HG010102 and HG0103) displayed increased frequencies in S1 (P = .013) and late S2 (P = .036), respectively.
Conclusions.  These results strongly suggest the involvement of HLA-G in HAT disease progression. Importantly, high plasma sHLA-G levels in SERO patients could be predictive of subsequent disease development and could represent a serological marker to help guide therapeutic decision making. Further studies are necessary to assess the predictive nature of HLA-G and to estimate both sensitivity and specificity.