bluuebunny/crossref_metadata_2025_split huggingface dataset:
Climate oscillations reflected within the microbiome of Arabian Sea sediments
Authors: Orsi William D. , Coolen Marco J. L. , Wuchter Cornelia , He Lijun , More Kuldeep D. , Irigoien Xabier , Chust Guillem , Johnson Carl , Hemingway Jordon D. , Lee Mitchell , Galy Valier , Giosan Liviu 
Published: July 2017

AbstractSelection of microorganisms in marine sediment is shaped by energy-yielding electron acceptors for respiration that are depleted in vertical succession. However, some taxa have been reported to reflect past depositional conditions suggesting they have experienced weak selection after burial. In sediments underlying the Arabian Sea oxygen minimum zone (OMZ), we performed the first metagenomic profiling of sedimentary DNA at centennial-scale resolution in the context of a multi-proxy paleoclimate reconstruction. While vertical distributions of sulfate reducing bacteria and methanogens indicate energy-based selection typical of anoxic marine sediments, 5–15% of taxa per sample exhibit depth-independent stratigraphies indicative of paleoenvironmental selection over relatively short geological timescales. Despite being vertically separated, indicator taxa deposited under OMZ conditions were more similar to one another than those deposited in bioturbated intervals under intervening higher oxygen. The genomic potential for denitrification also correlated with palaeo-OMZ proxies, independent of sediment depth and available nitrate and nitrite. However, metagenomes revealed mixed acid and Entner-Dourdoroff fermentation pathways encoded by many of the same denitrifier groups. Fermentation thus may explain the subsistence of these facultatively anaerobic microbes whose stratigraphy follows changing paleoceanographic conditions. At least for certain taxa, our analysis provides evidence of their paleoenvironmental selection over the last glacial-interglacial cycle.
Extreme coastal erosion enhanced by anomalous extratropical storm wave direction
Authors: Harley Mitchell D. , Turner Ian L. , Kinsela Michael A. , Middleton Jason H. , Mumford Peter J. , Splinter Kristen D. , Phillips Matthew S. , Simmons Joshua A. , Hanslow David J. , Short Andrew D. 
Published: July 2017

AbstractExtratropical cyclones (ETCs) are the primary driver of large-scale episodic beach erosion along coastlines in temperate regions. However, key drivers of the magnitude and regional variability in rapid morphological changes caused by ETCs at the coast remain poorly understood. Here we analyze an unprecedented dataset of high-resolution regional-scale morphological response to an ETC that impacted southeast Australia, and evaluate the new observations within the context of an existing long-term coastal monitoring program. This ETC was characterized by moderate intensity (for this regional setting) deepwater wave heights, but an anomalous wave direction approximately 45 degrees more counter-clockwise than average. The magnitude of measured beach volume change was the largest in four decades at the long-term monitoring site and, at the regional scale, commensurate with that observed due to extreme North Atlantic hurricanes. Spatial variability in morphological response across the study region was predominantly controlled by alongshore gradients in storm wave energy flux and local coastline alignment relative to storm wave direction. We attribute the severity of coastal erosion observed due to this ETC primarily to its anomalous wave direction, and call for greater research on the impacts of changing storm wave directionality in addition to projected future changes in wave heights.
Cryopreservation protocol for human biliary tree stem/progenitors, hepatic and pancreatic precursors
Authors: Nevi Lorenzo , Cardinale Vincenzo , Carpino Guido , Costantini Daniele , Di Matteo Sabina , Cantafora Alfredo , Melandro Fabio , Brunelli Roberto , Bastianelli Carlo , Aliberti Camilla , Monti Marco , Bosco Daniela , Berloco Pasquale Bartolomeo , Panici Pierluigi Benedetti , Reid Lola , Gaudio Eugenio , Alvaro Domenico 
Published: July 2017

AbstractHuman biliary tree stem/progenitor cells (hBTSCs) are being used for cell therapies of patients with liver cirrhosis. A cryopreservation method was established to optimize sourcing of hBTSCs for these clinical programs and that comprises serum-free Kubota’s Medium (KM) supplemented with 10% dimethyl sulfoxide (DMSO), 15% human serum albumin (HSA) and 0.1% hyaluronans. Cryopreserved versus freshly isolated hBTSCs were similar in vitro with respect to self-replication, stemness traits, and multipotency. They were able to differentiate to functional hepatocytes,cholangiocytes or pancreatic islets, yielding similar levels of secretion of albumin or of glucose-inducible levels of insulin. Cryopreserved versus freshly isolated hBTSCs were equally able to engraft into immunocompromised mice yielding cells with human-specific gene expression and human albumin levels in murine serum that were higher for cryopreserved than for freshly isolated hBTSCs. The successful cryopreservation of hBTSCs facilitates establishment of hBTSCs cell banking offering logistical advantages for clinical programs for treatment of liver diseases.
Weakened IL-15 Production and Impaired mTOR Activation Alter Dendritic Epidermal T Cell Homeostasis in Diabetic Mice
Authors: Liu Zhongyang , Liang Guangping , Gui Li , Li Yashu , Liu Meixi , bai Yang , Zhang Xiaorong , Hu Xiaohong , Chen Jian , Huang Chibing , Liu Xusheng , Luo Gaoxing , Wu Jun , He Weifeng 
Published: July 2017

AbstractDiabetes is associated with impaired wound healing, which may be caused primarily by a deficiency in dendritic epidermal T cells (DETCs). In the epidermis, IL-15, IGF-1, and mTOR are known to regulate the maintenance of DETCs; however, it is unclear how these molecules may intersect to regulate DETC homeostasis in diabetes. Here, we show that the reduction of DETCs in the epidermis of diabetic mice is caused by altered homeostasis mediated by a reduction in IL-15 levels. Both impaired mTOR activation and reduction of IL-15 in the epidermis play important roles in DETC homeostasis. Moreover, IGF-1 drives keratinocytes to produce IL-15. The activation of IL-15 is dependent on mTOR, and conversely, mTOR regulates IGF-1 production in DETC, in a classic feedback regulatory loop. Our data suggest that in the setting of diabetes, reduced IGF-1, impaired mTOR pathway activation and reduced IL-15 in the epidermis function coordinately to promote altered DETC homeostasis and delayed skin wound closure.
Enhancement of perpendicular magnetic anisotropy and its electric field-induced change through interface engineering in Cr/Fe/MgO
Authors: Kozioł-Rachwał A. , Nozaki T. , Freindl K. , Korecki J. , Yuasa S. , Suzuki Y. 
Published: July 2017

AbstractRecently, perpendicular magnetic anisotropy (PMA) and its voltage control (VC) was demonstrated for Cr/Fe/MgO. In this study, we shed light on the origin of large voltage-induced anisotropy change in Cr/Fe/MgO. Analysis of the chemical structure of Cr/Fe/MgO revealed the existence of Cr atoms in the proximity of the Fe/MgO interface, which can affect both magnetic anisotropy (MA) and its VC. We showed that PMA and its VC can be enhanced by controlled Cr doping at the Fe/MgO interface. For Cr/Fe (5.9 Å)/Cr (0.7 Å)/MgO with an effective PMA of 0.8 MJ/m3, a maximum value of the voltage-controlled magnetic anisotropy (VCMA) effect of 370 fJ/Vm was demonstrated due to Cr insertion.
Distinct functional relevance of dynamic GTPase cysteine methylation in fission yeast
Authors: Franco Alejandro , Soto Teresa , Martín-García Rebeca , Madrid Marisa , Vázquez-Marín Beatriz , Vicente-Soler Jero , Coll Pedro M. , Gacto Mariano , Pérez Pilar , Cansado José 
Published: July 2017

AbstractThe final step in post-translational processing of Ras and Rho GTPases involves methylation of the prenylated cysteine residue by an isoprenylcysteine-O-carboxyl methyltransferase (ICMT). ICMT activity is essential for cell growth and development in higher eukaryotes, and inhibition of GTPase methylation has become an attractive target in cancer therapy to inactivate prenylated oncoproteins. However, the specificity and dynamics of the GTPase methylation process remain to be fully clarified. Notably, cells lacking Mam4, the ICMT ortholog in the fission yeast Schizosaccharomyces pombe, are viable. We have exploited this feature to analyze the role of methylation on GTPase localization and function. We show that methylation differentially affects GTPase membrane localization, being particularly relevant for plasma membrane tethering and downstream signaling of palmitoylated and farnesylated GTPases Ras1 and Rho2 lacking C-terminal polybasic motifs. Indeed, Ras1 and Rho2 cysteine methylation is required for proper regulation of differentiation elicited by MAPK Spk1 and for stress-dependent activation of the cell integrity pathway (CIP) and its main effector MAPK Pmk1. Further, Mam4 negatively regulates TORC2 signaling by a cross-inhibitory mechanism relying on Rho GTPase methylation. These results highlight the requirement for a tight control of GTPase methylation in vivo to allow adequate GTPase function.
Large-Scale Analysis of Drug Side Effects via Complex Regulatory Modules Composed of microRNAs, Transcription Factors and Gene Sets
Authors: Jia Xiaodong , Jin Qing , Liu Xiangqiong , Bian Xiusen , Wang Yunfeng , Liu Lei , Ma Hongzhe , Tan Fujian , Gu Mingliang , Chen Xiujie 
Published: July 2017

AbstractIdentifying the occurrence mechanism of drug-induced side effects (SEs) is critical for design of drug target and new drug development. The expression of genes in biological processes is regulated by transcription factors(TFs) and/or microRNAs. Most of previous studies were focused on a single level of gene or gene sets, while studies about regulatory relationships of TFs, miRNAs and biological processes are very rare. Discovering the complex regulating relations among TFs, gene sets and miRNAs will be helpful for researchers to get a more comprehensive understanding about the mechanism of side reaction. In this study, a framework was proposed to construct the relationship network of gene sets, miRNAs and TFs involved in side effects. Through the construction of this network, the potential complex regulatory relationship in the occurrence process of the side effects was reproduced. The SE-gene set network was employed to characterize the significant regulatory SE-gene set interaction and molecular basis of accompanied side effects. A total of 117 side effects complex modules including four types of regulating patterns were obtained from the SE-gene sets-miRNA/TF complex regulatory network. In addition, two cases were used to validate the complex regulatory modules which could more comprehensively interpret occurrence mechanism of side effects.
Linking Rheology and Printability for Dense and Strong Ceramics by Direct Ink Writing
Authors: M’Barki Amin , Bocquet Lydéric , Stevenson Adam 
Published: July 2017

AbstractDirect ink writing of dense and strong ceramic objects remains an important open challenge. We develop a universal dimensionless criterion for printing such objects. Boehmite, an Al2O3 precursor, was used to assess the rheological properties leading to dense structures in ceramics manufactured by direct ink writing. Boehmite suspensions undergo time dependent gelation, thus providing a rheological laboratory of flow behaviours that can be correlated with printability requirements. We measured the evolution of rheological properties over several days and quantified the deformation of simple printed shapes at different aging times. We then identified the relevant physical parameters leading to printable suspensions. We defined a dimensionless number, Ξ, based on measured rheological properties, that predicts deformation of the printed object and determines the printability criterion. An important difference with this criterion is that Ξ necessarily accounts for capillary forces and gravitational slumping. We show that boehmite inks reach a printed shape fidelity > 90% when Ξ > 1, and that Al2O3 bars printed under these conditions can be sintered to 97% density, without printing defects, and have flexural strengths (500–600 MPa) competitive with commercial aluminas. Using Ξ, researchers can rationally design inks for printing dense materials by tailoring their rheological properties such that Ξ ≈ 1.
Effective Methods of Restraining Diffusion in Terms of Epidemic Dynamics
Authors: Xiong Fei , Li Zhao-Yi 
Published: July 2017

AbstractRemoving influential nodes or shortcuts in a network restrains epidemic or information diffusion, but this method destroys the connectivity of the network and changes the topological structure. As an alternative, an additional field can be imposed in the network to affect node behaviors and slow down diffusion dynamics. However, little research has been performed systematically to analyze and compare these methods. This paper investigates epidemic dynamics and proposes the following four methods to restrain the diffusion process: blocking nodes, blocking edges, distracting node attention, and propagating opposite information. We compare differences in the actions of these methods, and investigate their joint effects. Through numerical experiments in a scale-free network and a real network, we observe that these methods change the spreading threshold and final extent with different conditions. The method of blocking nodes is more efficient and economical than blocking edges. Propagating opposite information can effectively prevent diffusion of target information that has a large spreading rate, whereas distracting node attention only takes effect for the information with a small rate. Meanwhile, the effects of these two methods mainly depend on their action time. From the joint effects, we can select the optimal method for different situations.
Structure of general-population antibody titer distributions to influenza A virus
Authors: Nhat Nguyen Thi Duy , Todd Stacy , de Bruin Erwin , Thao Tran Thi Nhu , Vy Nguyen Ha Thao , Quan Tran Minh , Vinh Dao Nguyen , van Beek Janko , Anh Pham Hong , Lam Ha Minh , Hung Nguyen Thanh , Thanh Nguyen Thi Le , Huy Huynh Le Anh , Ha Vo Thi Hong , Baker Stephen , Thwaites Guy E. , Lien Nguyen Thi Nam , Hong Tran Thi Kim , Farrar Jeremy , Simmons Cameron P. , Chau Nguyen Van Vinh , Koopmans Marion , Boni Maciej F. 
Published: July 2017

AbstractSeroepidemiological studies aim to understand population-level exposure and immunity to infectious diseases. Their results are normally presented as binary outcomes describing the presence or absence of pathogen-specific antibody, despite the fact that many assays measure continuous quantities. A population’s natural distribution of antibody titers to an endemic infectious disease may include information on multiple serological states – naiveté, recent infection, non-recent infection, childhood infection – depending on the disease in question and the acquisition and waning patterns of immunity. In this study, we investigate 20,152 general-population serum samples from southern Vietnam collected between 2009 and 2013 from which we report antibody titers to the influenza virus HA1 protein using a continuous titer measurement from a protein microarray assay. We describe the distributions of antibody titers to subtypes 2009 H1N1 and H3N2. Using a model selection approach to fit mixture distributions, we show that 2009 H1N1 antibody titers fall into four titer subgroups and that H3N2 titers fall into three subgroups. For H1N1, our interpretation is that the two highest-titer subgroups correspond to recent and historical infection, which is consistent with 2009 pandemic attack rates. Similar interpretations are available for H3N2, but right-censoring of titers makes these interpretations difficult to validate.
Differential control of dNTP biosynthesis and genome integrity maintenance by the dUTPase superfamily enzymes
Authors: Hirmondo Rita , Lopata Anna , Suranyi Eva Viola , Vertessy Beata G. , Toth Judit 
Published: July 2017

AbstractdUTPase superfamily enzymes generate dUMP, the obligate precursor for de novo dTTP biosynthesis, from either dUTP (monofunctional dUTPase, Dut) or dCTP (bifunctional dCTP deaminase/dUTPase, Dcd:dut). In addition, the elimination of dUTP by these enzymes prevents harmful uracil incorporation into DNA. These two beneficial outcomes have been thought to be related. Here we determined the relationship between dTTP biosynthesis (dTTP/dCTP balance) and the prevention of DNA uracilation in a mycobacterial model that encodes both the Dut and Dcd:dut enzymes, and has no other ways to produce dUMP. We show that, in dut mutant mycobacteria, the dTTP/dCTP balance remained unchanged, but the uracil content of DNA increased in parallel with the in vitro activity-loss of Dut accompanied with a considerable increase in the mutation rate. Conversely, dcd:dut inactivation resulted in perturbed dTTP/dCTP balance and two-fold increased mutation rate, but did not increase the uracil content of DNA. Thus, unexpectedly, the regulation of dNTP balance and the prevention of DNA uracilation are decoupled and separately brought about by the Dcd:dut and Dut enzymes, respectively. Available evidence suggests that the discovered functional separation is conserved in humans and other organisms.
Sex-based Differences in the Association between Body Composition and Incident Fracture Risk in Koreans
Authors: Kim Jung Hee , Hong A. Ram , Choi Hyung Jin , Ku Eu Jeong , Cho Nam H. , Shin Chan Soo 
Published: July 2017

AbstractThe relative contribution of lean mass and fat mass on bone health is inconclusive. We investigated the relative contributions of lean and fat masses on fragility fracture risk in Korean men and women. This was an ongoing prospective community-dwelling cohort study at Ansung beginning in 2001, which included 2,189 men and 2,625 women over 40 years old. Study subjects were classified into the following four groups according to lean mass (LM)/height2 and percentage fat mass (PF). Clinical fragility fracture events were assessed at baseline and biennially using self-reported questionnaires. During a median follow-up of 9.4 years, 77 (3.5%) men and 203 (7.7%) women experienced at least one incident fracture. In Cox proportional hazard models, men with low LM under normal and high PF had a 2.16 and 2.59- fold higher risk for fragility fractures than normal ones even after adjusting for covariates. However, in women, low LM or high FM was not associated with fracture risk. We demonstrated sex-based differences in the association of body composition and incident fracture risk in Koreans aged over 40 years during a 10-year follow-up duration. Maintaining muscle mass in men is vital to maintaining bone health and preventing fragility fractures in Koreans.
Microstructure Refinement in W-Y2O3 Alloy Fabricated by Wet Chemical Method with Surfactant Addition and Subsequent Spark Plasma Sintering
Authors: Dong Zhi , Liu Nan , Ma Zongqing , Liu Chenxi , Guo Qianying , Alothman Zeid Abdullah , Yamauchi Yusuke , Shahriar A. Hossain Md. , Liu Yongchang 
Published: July 2017

AbstractWith the aim of preparing high performance oxide-dispersion-strengthened tungsten based alloys by powder metallurgy, the W-Y2O3 composite nanopowder precursor was fabricated by an improved wet chemical method with anion surfactant sodium dodecyl sulfate (SDS) addition. It is found that the employment of SDS can dramatically decrease W grain size (about 40 nm) and improve the size uniformity. What’s more, SDS addition can also remarkably improve the uniform dispersion of Y2O3 particles during the synthesis process. For the alloy whose powder precursor was fabricated by traditional wet chemical method without SDS addition, only a few Y2O3 dispersoids with size of approximate 10–50 nm distribute unevenly within tungsten grains. Nevertheless, for the sintered alloy whose powder precursor was produced by improved wet chemical method, the Y2O3 dispersoids (about 2–10 nm in size) with near spherical shape are dispersed well within tungsten grains. Additionally, compared with the former, the alloy possesses smaller grain size (approximate 700 nm) and higher relative density (99.00%). And a Vickers microhardness value up to 600 Hv was also obtained for this alloy. Based on these results, the employment of SDS in traditional wet chemical method is a feasible way to fabricate high performance yttria-dispersion-strengthened tungsten based alloys.
Anti-asthmatic effect of pitavastatin through aerosol inhalation is associated with CD4+ CD25+ Foxp3+ T cells in an asthma mouse model
Authors: Wu Songquan , Yang Ruhui , Wang Guangli 
Published: July 2017

AbstractStatins are competitive inhibitors of 3-hydroxy-3-methylglutaryl-CoA (HMG-A) reductase, and studies have shown that statins also have anti-inflammatory and immunomodulatory properties. The purpose of this study was to investigate the anti-asthmatic effects of pitavastatin, a type of statin, in an asthma mouse model. Mice were sensitized and challenged with ovalbumin (OVA) to establish the asthma model. These mice were then treated with inhaled pitavastatin (5 mg/kg) or dexamethasone (2 mg/kg), the latter of which served as a positive control. The results of the study showed that pitavastatin reduced allergen-induced increases in airway resistance and alleviated bronchial tube thickness and goblet cell hyperplasia in lung tissues. In addition, the results showed that pitavastatin inhibited OVA-induced increases in eosinophil counts and total inflammatory cell counts in bronchoalveolar lavage fluid (BALF) and increased the percentage of CD4+ CD25+ Foxp3+ Treg in the BALF of asthmatic mice. IL-4 and IL-17 levels were decreased, whereas IFN-γ levels were significantly increased in the BALF of pitavastatin-treated mice compared with the BALF of OVA-challenged mice. These results suggest that pitavastatin has potential as a therapy for allergic airway disease and that its effects are associated with its ability to regulate CD4+ CD25+ Foxp3+ T cell counts.
Human hippocampal pre-activation predicts behavior
Authors: Jafarpour Anna , Piai Vitoria , Lin Jack J. , Knight Robert T. 
Published: July 2017

AbstractThe response to an upcoming salient event is accelerated when the event is expected given the preceding events – i.e. a temporal context effect. For example, naming a picture following a strongly constraining temporal context is faster than naming a picture after a weakly constraining temporal context. We used sentences as naturalistic stimuli to manipulate expectations on upcoming pictures without prior training. Here, using intracranial recordings from the human hippocampus we found more power in the high-frequency band prior to high-expected pictures than weakly expected ones. We applied pattern similarity analysis on the temporal pattern of hippocampal high-frequency band activity in single hippocampal contacts. We found that greater similarity in the pattern of hippocampal field potentials between pre-picture interval and expected picture interval in the high-frequency band predicted picture-naming latencies. Additional pattern similarity analysis indicated that the hippocampal representations follow a semantic map. The results suggest that hippocampal pre-activation of expected stimuli is a facilitating mechanism underlying the powerful contextual behavioral effect.