bluuebunny/crossref_metadata_2025_split huggingface dataset:
A TonB-dependent receptor regulates antifungal HSAF biosynthesis in Lysobacter
Authors: Wang Ruping , Xu Huiyong , Du Liangcheng , Chou Shan-Ho , Liu Hongxia , Liu Youzhou , Liu Fengquan , Qian Guoliang 
Published: May 2016

AbstractLysobacter species are Gram-negative bacteria that are emerging as new sources of antibiotics, including HSAF (Heat Stable Antifungal Factor), which was identified from L. enzymogenes with a new mode of action. LesR, a LuxR solo, was recently shown to regulate the HSAF biosynthesis via an unidentified mechanism in L. enzymogenes OH11. Here, we used a comparative proteomic approach to identify the LesR targets and found that LesR influenced the expression of 33 proteins belonging to 10 functional groups, with 9 proteins belonging to the TBDR (TonB-Dependent Receptor) family. The fundamental role of bacterial TBDR in nutrient uptake motivates us to explore their potential regulation on HSAF biosynthesis which is also modulated by nutrient condition. Six out of 9 TBDR coding genes were individually in-frame deleted. Phenotypic and gene-expression assays showed that TBDR7, whose level was lower in a strain overexpressing lesR, was involved in regulating HSAF yield. TBDR7 was not involved in the growth, but played a vital role in transcribing the key HSAF biosynthetic gene. Taken together, the current lesR-based proteomic study provides the first report that TBDR7 plays a key role in regulating antibiotic (HSAF) biosynthesis, a function which has never been found for TBDRs in bacteria.
Fire carbon emissions over maritime southeast Asia in 2015 largest since 1997
Authors: Huijnen V. , Wooster M. J. , Kaiser J. W. , Gaveau D. L. A. , Flemming J. , Parrington M. , Inness A. , Murdiyarso D. , Main B. , van Weele M. 
Published: May 2016

AbstractIn September and October 2015 widespread forest and peatland fires burned over large parts of maritime southeast Asia, most notably Indonesia, releasing large amounts of terrestrially-stored carbon into the atmosphere, primarily in the form of CO2, CO and CH4. With a mean emission rate of 11.3 Tg CO2 per day during Sept-Oct 2015, emissions from these fires exceeded the fossil fuel CO2 release rate of the European Union (EU28) (8.9 Tg CO2 per day). Although seasonal fires are a frequent occurrence in the human modified landscapes found in Indonesia, the extent of the 2015 fires was greatly inflated by an extended drought period associated with a strong El Niño. We estimate carbon emissions from the 2015 fires to be the largest seen in maritime southeast Asia since those associated with the record breaking El Niño of 1997. Compared to that event, a much better constrained regional total carbon emission estimate can be made for the 2015 fires through the use of present-day satellite observations of the fire’s radiative power output and atmospheric CO concentrations, processed using the modelling and assimilation framework of the Copernicus Atmosphere Monitoring Service (CAMS) and combined with unique in situ smoke measurements made on Kalimantan.
Differential effects of Cytomegalovirus carriage on the immune phenotype of middle-aged males and females
Authors: van der Heiden Marieke , van Zelm Menno C. , Bartol Sophinus J. W. , de Rond Lia G. H. , Berbers Guy A. M. , Boots Annemieke M. H. , Buisman Anne-Marie 
Published: May 2016

AbstractThe elderly population is more susceptible to infections as a result of an altered immune response, commonly referred to as immunosenescence. Cytomegalovirus (CMV)-infection associated changes in blood lymphocytes are known to impact this process, but the interaction with gender remains unclear. Therefore, we analysed the effects and interaction of gender and CMV on the absolute numbers of a comprehensive set of naive and memory T- and B-cell subsets in people between 50 and 65 years of age. Enumeration and characterisation of lymphocyte subsets by flow cytometry was performed on fresh whole blood samples from 255 middle-aged persons. CMV-IgG serostatus was determined by ELISA. Gender was a major factor affecting immune cell numbers. CMV infection was mainly associated with an expansion of late-differentiated T-cell subsets. CMV+ males carried lower numbers of total CD4+, CD4+ central memory (CM) and follicular helper T-cells than females and CMV− males. Moreover, CMV+ males had significantly lower numbers of regulatory T (Treg)-cells and memory B-cells than CMV+ females. We here demonstrate an interaction between the effects of CMV infection and gender on T- and B-cells in middle-aged individuals. These differential effects on adaptive immunity between males and females may have implications for vaccination strategies at middle-age.
Self-Assembly of Hydrofluorinated Janus Graphene Monolayer: A Versatile Route for Designing Novel Janus Nanoscrolls
Authors: Jin Yakang , Xue Qingzhong , Zhu Lei , Li Xiaofang , Pan Xinglong , Zhang Jianqiang , Xing Wei , Wu Tiantian , Liu Zilong 
Published: May 2016

AbstractWith remarkably interesting surface activities, two-dimensional Janus materials arouse intensive interests recently in many fields. We demonstrate by molecular dynamic simulations that hydrofluorinated Janus graphene (J-GN) can self-assemble into Janus nanoscroll (J-NS) at room temperature. The van der Waals (vdW) interaction and the coupling of C-H/π/C-F interaction and π/π interaction are proven to offer the continuous driving force of self-assembly of J-GN. The results show that J-GN can self-assemble into various J-NSs structures, including arcs, multi-wall J-NS and arm-chair-like J-NS by manipulating its original geometry (size and aspect ratio). Moreover, we also investigated self-assembly of hydrofluorinated J-GN and Fe nanowires (NWs), suggesting that Fe NW is a good alternative to activate J-GN to form J-NS. Differently, the strong vdW interaction between J-GN and Fe NW provides the main driving force of the self-assembly. Finally, we studied the hydrogen sorption over the formed J-NS with a considerable interlayer spacing, which reaches the US DOE target, indicating that J-NS is a promising candidate for hydrogen storage by controlling the temperature of system. Our theoretical results firstly provide a versatile route for designing novel J-NS from 2D Janus nanomaterials, which has a great potential application in the realm of hydrogen storage/separation.
Analysis of tigecycline resistance development in clinical Acinetobacter baumannii isolates through a combined genomic and transcriptomic approach
Authors: Liu Lin , Cui Yujun , Zheng Beiwen , Jiang Saiping , Yu Wei , Shen Ping , Ji Jinru , Li Lanjuan , Qin Nan , Xiao Yonghong 
Published: May 2016

AbstractTigecycline (Tgc) is considered a last-resort antibiotic for the treatment of multi-drug resistant bacteria. To study Tgc resistance development in the important nosocomial pathogen Acinetobacter baumannii, we adopted six clinical isolates from three patients undergoing antibiotic treatment, and bacterial genomic sequences and seven strand-specific transcriptomes were studied. Interestingly, the Tgc-intermediate 2015ZJAB1 only differed from Tgc-resistant 2015ZJAB2 in an SNP-clustered region including OprD, a sugar-type MFS permease, and a LuxR-type transcriptional regulator. Surprisingly, an almost identical region was found in 2015ZJAB3, which supports the possibility of a homologous recombination event that increased Tgc resistance. Furthermore, comparative transcriptomic analysis identified significantly regulated genes associated with Tgc resistance, which was verified using qRT-PCR. Three enriched COG categories included amino acid transport and metabolism, transcription, and inorganic ion transport and metabolism. KEGG analysis revealed common features under Tgc conditions, including up regulated benzoate degradation and a less active TCA cycle. This may be related to selective antimicrobial pressure in the environment and adaptation by lowering metabolism. This study provides the first report of an in vivo evolutionary process that included a putative homologous recombination event conferring Tgc resistance in clinical A. baumannii isolates in which transcriptome analysis revealed resistance-conferring genes and related metabolism characteristics.
Dissolved Organic Carbon in the North Atlantic Meridional Overturning Circulation
Authors: Fontela Marcos , García-Ibáñez Maribel I. , Hansell Dennis A. , Mercier Herlé , Pérez Fiz F. 
Published: May 2016

AbstractThe quantitative role of the Atlantic Meridional Overturning Circulation (AMOC) in dissolved organic carbon (DOC) export is evaluated by combining DOC measurements with observed water mass transports. In the eastern subpolar North Atlantic, both upper and lower limbs of the AMOC transport high-DOC waters. Deep water formation that connects the two limbs of the AMOC results in a high downward export of non-refractory DOC (197 Tg-C·yr−1). Subsequent remineralization in the lower limb of the AMOC, between subpolar and subtropical latitudes, consumes 72% of the DOC exported by the whole Atlantic Ocean. The contribution of DOC to the carbon sequestration in the North Atlantic Ocean (62 Tg-C·yr−1) is considerable and represents almost a third of the atmospheric CO2 uptake in the region.
Variation in serum biomarkers with sex and female hormonal status: implications for clinical tests
Authors: Ramsey Jordan M. , Cooper Jason D. , Penninx Brenda W. J. H. , Bahn Sabine 
Published: May 2016

AbstractFew serum biomarker tests are implemented in clinical practice and recent reports raise concerns about poor reproducibility of biomarker studies. Here, we investigated the potential role of sex and female hormonal status in this widespread irreproducibility. We examined 171 serum proteins and small molecules measured in 1,676 participants from the Netherlands Study of Depression and Anxiety. Concentrations of 96 molecules varied with sex and 66 molecules varied between oral contraceptive pill users, postmenopausal females and females in the follicular and luteal phases of the menstrual cycle (FDR-adjustedp-value <0.05). Simulations of biomarker studies yielded up to 40% false discoveries when patient and control groups were not matched for sex and up to 41% false discoveries when premenopausal females were not matched for oral contraceptive pill use. High accuracy (over 90%) classification tools were developed to label samples with sex and female hormonal status where this information was not collected.
Exact results for Schrödinger cats in driven-dissipative systems and their feedback control
Authors: Minganti Fabrizio , Bartolo Nicola , Lolli Jared , Casteels Wim , Ciuti Cristiano 
Published: May 2016

AbstractIn quantum optics, photonic Schrödinger cats are superpositions of two coherent states with opposite phases and with a significant number of photons. Recently, these states have been observed in the transient dynamics of driven-dissipative resonators subject to engineered two-photon processes. Here we present an exact analytical solution of the steady-state density matrix for this class of systems, including one-photon losses, which are considered detrimental for the achievement of cat states. We demonstrate that the unique steady state is a statistical mixture of two cat-like states with opposite parity, in spite of significant one-photon losses. The transient dynamics to the steady state depends dramatically on the initial state and can pass through a metastable regime lasting orders of magnitudes longer than the photon lifetime. By considering individual quantum trajectories in photon-counting configuration, we find that the system intermittently jumps between two cats. Finally, we propose and study a feedback protocol based on this behaviour to generate a pure cat-like steady state.
Encoding, training and retrieval in ferroelectric tunnel junctions
Authors: Xu Hanni , Xia Yidong , Xu Bo , Yin Jiang , Yuan Guoliang , Liu Zhiguo 
Published: May 2016

AbstractFerroelectric tunnel junctions (FTJs) are quantum nanostructures that have great potential in the hardware basis for future neuromorphic applications. Among recently proposed possibilities, the artificial cognition has high hopes, where encoding, training, memory solidification and retrieval constitute a whole chain that is inseparable. However, it is yet envisioned but experimentally unconfirmed. The poor retention or short-term store of tunneling electroresistance, in particular the intermediate states, is still a key challenge in FTJs. Here we report the encoding, training and retrieval in BaTiO3 FTJs, emulating the key features of information processing in terms of cognitive neuroscience. This is implemented and exemplified through processing characters. Using training inputs that are validated by the evolution of both barrier profile and domain configuration, accurate recalling of encoded characters in the retrieval stage is demonstrated.
Proteasome activity is required for the initiation of precancerous pancreatic lesions
Authors: Furuyama Takaki , Tanaka Shinji , Shimada Shu , Akiyama Yoshimitsu , Matsumura Satoshi , Mitsunori Yusuke , Aihara Arihiro , Ban Daisuke , Ochiai Takanori , Kudo Atsushi , Fukamachi Hiroshi , Arii Shigeki , Kawaguchi Yoshiya , Tanabe Minoru 
Published: May 2016

AbstractProteasome activity is significantly increased in advanced cancers, but its role in cancer initiation is not clear, due to difficulties in monitoring this process in vivo. We established a line of transgenic mice that carried the ZsGreen-degronODC (Gdeg) proteasome reporter to monitor the proteasome activity. In combination with Pdx-1-Cre;LSL-KrasG12D model, proteasome activity was investigated in the initiation of precancerous pancreatic lesions (PanINs). Normal pancreatic acini in Gdeg mice had low proteasome activity. By contrast, proteasome activity was increased in the PanIN lesions that developed in Gdeg;Pdx-1-Cre;LSL-KrasG12D mice. Caerulein administration to Gdeg;Pdx-1-Cre;LSL-KrasG12D mice induced constitutive elevation of proteasome activity in pancreatic tissues and accelerated PanIN formation. The proteasome inhibitor markedly reduced PanIN formation in Gdeg;Pdx-1-Cre;LSL-KrasG12D mice (P = 0.001), whereas it had no effect on PanIN lesions that had already formed. These observations indicated the significance of proteasome activity in the initiation of PanIN but not the maintenance per se. In addition, the expressions of pERK and its downstream factors including cyclin D1, NF-κB, and Cox2 were decreased after proteasome inhibition in PanINs. Our studies showed activation of proteasome is required specifically for the initiation of PanIN. The roles of proteasome in the early stages of pancreatic carcinogenesis warrant further investigation.
Rapid formation and evolution of an extreme haze episode in Northern China during winter 2015
Authors: Sun Yele , Chen Chen , Zhang Yingjie , Xu Weiqi , Zhou Libo , Cheng Xueling , Zheng Haitao , Ji Dongsheng , Li Jie , Tang Xiao , Fu Pingqing , Wang Zifa 
Published: May 2016

AbstractWe investigate the rapid formation and evolutionary mechanisms of an extremely severe and persistent haze episode that occurred in northern China during winter 2015 using comprehensive ground and vertical measurements, along with receptor and dispersion model analysis. Our results indicate that the life cycle of a severe winter haze episode typically consists of four stages: (1) rapid formation initiated by sudden changes in meteorological parameters and synchronous increases in most aerosol species, (2) persistent evolution with relatively constant variations in secondary inorganic aerosols and secondary organic aerosols, (3) further evolution associated with fog processing and significantly enhanced sulfate levels and (4) clearing due to dry, cold north-northwesterly winds. Aerosol composition showed substantial changes during the formation and evolution of the haze episode but was generally dominated by regional secondary aerosols (53–67%). Our results demonstrate the important role of regional transport, largely from the southwest but also from the east and of coal combustion emissions for winter haze formation in Beijing. Also, we observed an important downward mixing pathway during the severe haze in 2015 that can lead to rapid increases in certain aerosol species.
A pilot study on commonality and specificity of copy number variants in schizophrenia and bipolar disorder
Authors: Chen J , Calhoun V D , Perrone-Bizzozero N I , Pearlson G D , Sui J , Du Y , Liu J 
Published: May 2016

AbstractSchizophrenia (SZ) and bipolar disorder (BD) are known to share genetic risks. In this work, we conducted whole-genome scanning to identify cross-disorder and disorder-specific copy number variants (CNVs) for these two disorders. The Database of Genotypes and Phenotypes (dbGaP) data were used for discovery, deriving from 2416 SZ patients, 592 BD patients and 2393 controls of European Ancestry, as well as 998 SZ patients, 121 BD patients and 822 controls of African Ancestry. PennCNV and Birdsuite detected high-confidence CNVs that were aggregated into CNV regions (CNVRs) and compared with the database of genomic variants for confirmation. Then, large (size⩾500 kb) and small common CNVRs (size <500 kb, frequency⩾1%) were examined for their associations with SZ and BD. Particularly for the European Ancestry samples, the dbGaP findings were further evaluated in the Wellcome Trust Case Control Consortium (WTCCC) data set for replication. Previously implicated variants (1q21.1, 15q13.3, 16p11.2 and 22q11.21) were replicated. Some cross-disorder variants were noted to differentially affect SZ and BD, including CNVRs in chromosomal regions encoding immunoglobulins and T-cell receptors that were associated more with SZ, and the 10q11.21 small CNVR (GPRIN2) associated more with BD. Disorder-specific CNVRs were also found. The 22q11.21 CNVR (COMT) and small CNVRs in 11p15.4 (TRIM5) and 15q13.2 (ARHGAP11B and FAN1) appeared to be SZ-specific. CNVRs in 17q21.2, 9p21.3 and 9q21.13 might be BD-specific. Overall, our primary findings in individual disorders largely echo previous reports. In addition, the comparison between SZ and BD reveals both specific and common risk CNVs. Particularly for the latter, differential involvement is noted, motivating further comparative studies and quantitative models.
Optimal design of a 1 kW switched reluctance generator for wind power systems using a genetic algorithm
Authors: Shin Hye‐Ung , Lee Kyo‐Beum 
Published: May 2016

This study presents an optimal design for a 1 kW switched reluctance generator (SRG) for wind‐power applications. The design of the SRG is optimised to increase efficiency and reduce the volume of the generator compared with a basic model designed using the D2L method. To begin the optimisation, Latin hypercube sampling is employed to extract samples of the design variables for the design of experiment. The Kriging method of approximation modelling is used to interpolate the non‐linear characteristics for the optimal design. Finally, a genetic algorithm is utilised to optimise the original design model for efficiency and reduced volume. The optimal design of the SRG uses the shape parameters of the basic model. Design variables are selected to be at their maxima. The designed optimal model is compared with the basic model and prototype to verify the results.
Jasmonoyl-l-isoleucine is required for the production of a flavonoid phytoalexin but not diterpenoid phytoalexins in ultraviolet-irradiated rice leaves
Authors: Miyamoto Koji , Enda Isami , Okada Toshiki , Sato Yumiko , Watanabe Kohei , Sakazawa Tomoko , Yumoto Emi , Shibata Kyomi , Asahina Masashi , Iino Moritoshi , Yokota Takao , Okada Kazunori , Yamane Hisakazu 
Published: May 2016

Abstract
Rice produces low-molecular-weight antimicrobial compounds known as phytoalexins, in response to not only pathogen attack but also abiotic stresses including ultraviolet (UV) irradiation. Rice phytoalexins are composed of diterpenoids and a flavonoid. Recent studies have indicated that endogenous jasmonyl-l-isoleucine (JA-Ile) is not necessarily required for the production of diterpenoid phytoalexins in blast-infected or CuCl2-treated rice leaves. However, JA-Ile is required for the accumulation of the flavonoid phytoalexin, sakuranetin. Here, we investigated the roles of JA-Ile in UV-induced phytoalexin production. We showed that UV-irradiation induces the biosynthesis of JA-Ile and its precursor jasmonic acid. We also showed that rice jasmonate biosynthesis mutants produced diterpenoid phytoalexins but not sakuranetin in response to UV, indicating that JA-Ile is required for the production of sakuranetin but not diterpenoid phytoalexins in UV-irradiated rice leaves.
Cryopreservation of the edible alkalophilic cyanobacterium Arthrospira platensis
Authors: Shiraishi Hideaki 
Published: May 2016

Abstract
Efficient cryopreservation conditions for the edible alkalophilic cyanobacterium Arthrospira (Spirulina) platensis were investigated using a model strain A. platensis NIES-39. As a result, it was found that more than 60% of cells were viable upon thawing, when they had been frozen at a cooling rate of approximately −1 °C min−1 in the presence of 10% (v/v) dimethyl sulfoxide. Further examination with other Arthrospira strains showed that many of them had strain-dependent optimal conditions for cryopreservation. For example, the best freezing conditions for A. platensis SAG 21.99 were snap-freezing in liquid nitrogen in the presence of 5% (v/v) dimethyl sulfoxide, while they were slow cooling at approximately −1 °C min−1 in the presence of 10% (v/v) methanol for A. platensis NIES-46, NIES-2308 and UTEX 1926. The variety of successful cryopreservation conditions presented in this study is useful when attempting to cryopreserve various Arthrospira strains.
Highly selective electrodeposition of sub-10 nm crystalline noble metallic nanorods inside vertically aligned multiwall carbon nanotubes
Authors: Wang Xuyang , Wang Ranran , Wu Qiang , Zhang Xiaohua , Yang Zhaohui , Guo Jun , Chen Muzi , Tang Minghua , Cheng Yajun , Chu Haibin 
Published: May 2016

Abstract
In this paper crystalline noble metallic nanorods including Au and Ag with sub-10 nm diameter, are encapsulated within prealigned and open-ended multiwall carbon nanotubes (MWCNTs) through an electrodeposition method. As the external surface of CNTs has been insulated by the epoxy the CNT channel becomes the only path for the mass transport as well as the nanoreactor for the metal deposition. Highly crystallized Au and Ag2O nanorods parallel to the radial direction of CNTs are confirmed by high-resolution transmission electron microscopy, energy dispersive x-ray spectroscopy and x-ray powder diffraction spectroscopy. The Ag2O nanorods are formed by air oxidation on the Ag metals and show a single crystalline structure with (111) planes. The Au nanorods exhibit a complex crystalline structure including twin-crystal and lattice dislocation with (111) and (200) planes. These crystalline noble metallic nanostructures may have important applications for nanocatalysts for fuel cells as well as nanoelectronic and nanophotonic devices. This method is deemed to benefit the precise deposition of other crystalline nanostructures inside CNTs with a small diameter.