bluuebunny/crossref_metadata_2025_split huggingface dataset:
Half-metre sea-level fluctuations on centennial timescales from mid-Holocene corals of Southeast Asia
Authors: Meltzner Aron J. , Switzer Adam D. , Horton Benjamin P. , Ashe Erica , Qiu Qiang , Hill David F. , Bradley Sarah L. , Kopp Robert E. , Hill Emma M. , Majewski Jędrzej M. , Natawidjaja Danny H. , Suwargadi Bambang W. 
Published: February 2017

AbstractSea-level rise is a global problem, yet to forecast future changes, we must understand how and why relative sea level (RSL) varied in the past, on local to global scales. In East and Southeast Asia, details of Holocene RSL are poorly understood. Here we present two independent high-resolution RSL proxy records from Belitung Island on the Sunda Shelf. These records capture spatial variations in glacial isostatic adjustment and paleotidal range, yet both reveal a RSL history between 6850 and 6500 cal years BP that includes two 0.6 m fluctuations, with rates of RSL change reaching 13±4 mm per year (2σ). Observations along the south coast of China, although of a lower resolution, reveal fluctuations similar in amplitude and timing to those on the Sunda Shelf. The consistency of the Southeast Asian records, from sites 2,600 km apart, suggests that the records reflect regional changes in RSL that are unprecedented in modern times.
IFI16 is required for DNA sensing in human macrophages by promoting production and function of cGAMP
Authors: Jønsson K. L. , Laustsen A. , Krapp C. , Skipper K. A. , Thavachelvam K. , Hotter D. , Egedal J. H. , Kjolby M. , Mohammadi P. , Prabakaran T. , Sørensen L. K. , Sun C. , Jensen S. B. , Holm C. K. , Lebbink R. J. , Johannsen M. , Nyegaard M. , Mikkelsen J. G. , Kirchhoff F. , Paludan S. R. , Jakobsen M. R. 
Published: February 2017

AbstractInnate immune activation by macrophages is an essential part of host defence against infection. Cytosolic recognition of microbial DNA in macrophages leads to induction of interferons and cytokines through activation of cyclic GMP-AMP synthase (cGAS) and stimulator of interferon genes (STING). Other host factors, including interferon-gamma inducible factor 16 (IFI16), have been proposed to contribute to immune activation by DNA. However, their relation to the cGAS-STING pathway is not clear. Here, we show that IFI16 functions in the cGAS-STING pathway on two distinct levels. Depletion of IFI16 in macrophages impairs cGAMP production on DNA stimulation, whereas overexpression of IFI16 amplifies the function of cGAS. Furthermore, IFI16 is vital for the downstream signalling stimulated by cGAMP, facilitating recruitment and activation of TANK-binding kinase 1 in STING complex. Collectively, our results suggest that IFI16 is essential for efficient sensing and signalling upon DNA challenge in macrophages to promote interferons and antiviral responses.
Mismatch between marine plankton range movements and the velocity of climate change
Authors: Chivers William J. , Walne Anthony W. , Hays Graeme C. 
Published: February 2017

AbstractThe response of marine plankton to climate change is of critical importance to the oceanic food web and fish stocks. We use a 60-year ocean basin-wide data set comprising >148,000 samples to reveal huge differences in range changes associated with climate change across 35 plankton taxa. While the range of dinoflagellates and copepods tended to closely track the velocity of climate change (the rate of isotherm movement), the range of the diatoms moved much more slowly. Differences in range shifts were up to 900 km in a recent warming period, with average velocities of range movement between 7 km per decade northwards for taxa exhibiting niche plasticity and 99 km per decade for taxa exhibiting niche conservatism. The differing responses of taxa to global warming will cause spatial restructuring of the plankton ecosystem with likely consequences for grazing pressures on phytoplankton and hence for biogeochemical cycling, higher trophic levels and biodiversity.
Ubiquitous strong electron–phonon coupling at the interface of FeSe/SrTiO3
Authors: Zhang Chaofan , Liu Zhongkai , Chen Zhuoyu , Xie Yanwu , He Ruihua , Tang Shujie , He Junfeng , Li Wei , Jia Tao , Rebec Slavko N. , Ma Eric Yue , Yan Hao , Hashimoto Makoto , Lu Donghui , Mo Sung-Kwan , Hikita Yasuyuki , Moore Robert G. , Hwang Harold Y. , Lee Dunghai , Shen Zhixun 
Published: February 2017

AbstractThe observation of replica bands in single-unit-cell FeSe on SrTiO3 (STO)(001) by angle-resolved photoemission spectroscopy (ARPES) has led to the conjecture that the coupling between FeSe electrons and the STO phonons are responsible for the enhancement of Tc over other FeSe-based superconductors. However the recent observation of a similar superconducting gap in single-unit-cell FeSe/STO(110) raised the question of whether a similar mechanism applies. Here we report the ARPES study of the electronic structure of FeSe/STO(110). Similar to the results in FeSe/STO(001), clear replica bands are observed. We also present a comparative study of STO(001) and STO(110) bare surfaces, and observe similar replica bands separated by approximately the same energy, indicating this coupling is a generic feature of the STO surfaces and interfaces. Our findings suggest that the large superconducting gaps observed in FeSe films grown on different STO surface terminations are likely enhanced by a common mechanism.
Responses of the cutworm Spodoptera litura (Lepidoptera: Noctuidae) to two Bt corn hybrids expressing Cry1Ab
Authors: Yinghua Shu , Yan Du , Jin Chen , Jiaxi Wei , Jianwu Wang 
Published: February 2017

AbstractTo examine the responses of the secondary lepidopteran pest Spodoptera litura to two Bacillus thuringiensis (Bt) corn hybrids [5422Bt1 (Event Bt11), 5422CBCL (MON810)] expressing Cry1Ab, larval bioassays with Cry1Ab toxin, corn leaves or kernels and bagging on corn plants were conducted. The results showed that larvae displayed a similar performance when fed kernels, but not leaves of 5422Bt1, 5422CBCL and their near-isogenic non-Bt corn (5422). Significantly higher Cry1Ab amounts were detected in larvae fed leaves than kernels of both Bt hybrids, with different molecular weights of protein band in plants (72 and 90 kDa for 5422Bt1 and 5422CBCL, respectively), gut contents (65 kDa), feces (50 kDa), which indicated that larvae had lower ingestion, higher degradation and excretion of Cry1Ab when fed kernels not leaves of both Bt hybrids. Significantly higher levels of cadherin-like receptors and alkaline phosphatase transcripts were detected in larvae fed leaves than kernels of two Bt hybrids. Catalase, superoxide dismutase and glutathione-S-transferase activities in larvae fed 5422Bt1 leaves were significantly higher than that of 5422 treatments. Therefore, S. litura had low susceptibility to 5422Bt1 and 5422CBCL when larvae fed kernels not leaves of Bt corn. Additionally, S. litura presented a much stronger tolerance to 5422CBCL than 5422Bt1.
The combination of the functionalities of feedback circuits is determinant for the attractors’ number and size in pathway-like Boolean networks
Authors: Azpeitia Eugenio , Muñoz Stalin , González-Tokman Daniel , Martínez-Sánchez Mariana Esther , Weinstein Nathan , Naldi Aurélien , Álvarez-Buylla Elena R. , Rosenblueth David A. , Mendoza Luis 
Published: February 2017

AbstractMolecular regulation was initially assumed to follow both a unidirectional and a hierarchical organization forming pathways. Regulatory processes, however, form highly interlinked networks with non-hierarchical and non-unidirectional structures that contain statistically overrepresented circuits or motifs. Here, we analyze the behavior of pathways containing non-unidirectional (i.e. bidirectional) and non-hierarchical interactions that create motifs. In comparison with unidirectional and hierarchical pathways, our pathways have a high diversity of behaviors, characterized by the size and number of attractors. Motifs have been studied individually showing that feedback circuit motifs regulate the number and size of attractors. It is less clear what happens in molecular networks that usually contain multiple feedbacks. Here, we find that the way feedback circuits couple to each other (i.e., the combination of the functionalities of feedback circuits) regulate both the number and size of the attractors. We show that the different expected results of epistasis analysis (a method to infer regulatory interactions) are produced by many non-hierarchical and non-unidirectional structures. Thus, these structures cannot be correctly inferred by epistasis analysis. Finally, we show that the combinations of functionalities, combined with other network properties, allow for a better characterization of regulatory structures.
Effect of lithographically-induced strain relaxation on the magnetic domain configuration in microfabricated epitaxially grown Fe81Ga19
Authors: Beardsley R. P. , Parkes D. E. , Zemen J. , Bowe S. , Edmonds K. W. , Reardon C. , Maccherozzi F. , Isakov I. , Warburton P. A. , Campion R. P. , Gallagher B. L. , Cavill S. A. , Rushforth A. W. 
Published: February 2017

AbstractWe investigate the role of lithographically-induced strain relaxation in a micron-scaled device fabricated from epitaxial thin films of the magnetostrictive alloy Fe81Ga19. The strain relaxation due to lithographic patterning induces a magnetic anisotropy that competes with the magnetocrystalline and shape induced anisotropies to play a crucial role in stabilising a flux-closing domain pattern. We use magnetic imaging, micromagnetic calculations and linear elastic modelling to investigate a region close to the edges of an etched structure. This highly-strained edge region has a significant influence on the magnetic domain configuration due to an induced magnetic anisotropy resulting from the inverse magnetostriction effect. We investigate the competition between the strain-induced and shape-induced anisotropy energies, and the resultant stable domain configurations, as the width of the bar is reduced to the nanoscale range. Understanding this behaviour will be important when designing hybrid magneto-electric spintronic devices based on highly magnetostrictive materials.
Stable Cretaceous sex chromosomes enable molecular sexing in softshell turtles (Testudines: Trionychidae)
Authors: Rovatsos Michail , Praschag Peter , Fritz Uwe , Kratochvšl Lukáš 
Published: February 2017

AbstractTurtles demonstrate variability in sex determination ranging from environmental sex determination (ESD) to highly differentiated sex chromosomes. However, the evolutionary dynamics of sex determining systems in this group is not well known. Differentiated ZZ/ZW sex chromosomes were identified in two species of the softshell turtles (Trionychidae) from the subfamily Trionychinae and Z-specific genes were identified in a single species. We tested Z-specificity of a subset of these genes by quantitative PCR comparing copy gene numbers in male and female genomes in 10 species covering the phylogenetic diversity of trionychids. We demonstrated that differentiated ZZ/ZW sex chromosomes are conserved across the whole family and that they were already present in the common ancestor of the extant trionychids. As the sister lineage,Carettochelys insculpta, possess ESD, we can date the origin of the sex chromosomes in trionychids between 200 Mya (split of Trionychidae and Carettochelyidae) and 120 Mya (basal splitting of the recent trionychids). The results support the evolutionary stability of differentiated sex chromosomes in some lineages of ectothermic vertebrates. Moreover, our approach determining sex-linkage of protein coding genes can be used as a reliable technique of molecular sexing across trionychids useful for effective breeding strategy in conservation projects of endangered species.
Impact of Dehydroepiandrosterone Sulfate on Newborn Leukocyte Telomere Length
Authors: Liu Han , Zhou Guangdi , Chen Qian , Ouyang Fengxiu , Little Julian , Zhang Jun , Chen Dan 
Published: February 2017

AbstractThe newborn setting of leukocyte telomere length (LTL) likely has important implications for telomere dynamics over the lifespan. However, its determinants are poorly understood. Hormones play an important role during pregnancy and delivery. We hypothesized that exposure to hormones may impact the fetal telomere biology system. To test this hypothesis, cortisol, estradiol, dehydroepiandrosterone sulfate (DHEAS) and reactive oxygen species (ROS) were measured in cord blood of 821 newborns from a prospective study. After accounting for the effects of potential determinants of newborn LTL, a 10-fold increase in DHEAS concentration was associated with a 0.021 increase in T/S ratio of newborn LTL (95% confidence interval: 0.009–0.034, P = 0.0008). For newborns who fell in the lowest quartile of DHEAS level, the mean newborn LTL was estimated to be approximately 2.0% shorter than the newborns in the highest DHEAS concentration quartile (P = 0.0014). However, no association was found between newborn LTL and cortisol or estradiol. As expected, newborns with higher ROS level (ROS > 260 mol/L) had lower LTL compared to that with lower ROS level (ROS ≤ 260 mol/L) (P = 0.007). There was also an inverse relationship between DHEAS and ROS (P < 1×10−4). Our findings suggest that exposure to DHEAS may exert a “programming” effect on the newborn telomere biology system.
Dimerisation induced formation of the active site and the identification of three metal sites in EAL-phosphodiesterases
Authors: Bellini Dom , Horrell Sam , Hutchin Andrew , Phippen Curtis W. , Strange Richard W. , Cai Yuming , Wagner Armin , Webb Jeremy S. , Tews Ivo , Walsh Martin A. 
Published: February 2017

AbstractThe bacterial second messenger cyclic di-3′,5′-guanosine monophosphate (c-di-GMP) is a key regulator of bacterial motility and virulence. As high levels of c-di-GMP are associated with the biofilm lifestyle, c-di-GMP hydrolysing phosphodiesterases (PDEs) have been identified as key targets to aid development of novel strategies to treat chronic infection by exploiting biofilm dispersal. We have studied the EAL signature motif-containing phosphodiesterase domains from the Pseudomonas aeruginosa proteins PA3825 (PA3825EAL) and PA1727 (MucREAL). Different dimerisation interfaces allow us to identify interface independent principles of enzyme regulation. Unlike previously characterised two-metal binding EAL-phosphodiesterases, PA3825EAL in complex with pGpG provides a model for a third metal site. The third metal is positioned to stabilise the negative charge of the 5′-phosphate, and thus three metals could be required for catalysis in analogy to other nucleases. This newly uncovered variation in metal coordination may provide a further level of bacterial PDE regulation.
Performance comparison of next-generation sequencing platforms for determining HIV-1 coreceptor use
Authors: Raymond Stéphanie , Nicot Florence , Jeanne Nicolas , Delfour Olivier , Carcenac Romain , Lefebvre Caroline , Cazabat Michelle , Sauné Karine , Delobel Pierre , Izopet Jacques 
Published: February 2017

AbstractThe coreceptor used by HIV-1 must be determined before a CCR5 antagonist, part of the arsenal of antiretroviral drugs, is prescribed because viruses that enter cells using the CXCR4 coreceptor are responsible for treatment failure. HIV-1 tropism is also correlated with disease progression and so must be determined for virological studies. Tropism can be determined by next-generation sequencing (NGS), but not all of these new technologies have been fully validated for use in clinical practice. The Illumina NGS technology is used in many laboratories but its ability to predict HIV-1 tropism has not been evaluated while the 454 GS-Junior (Roche) is used for routine diagnosis. The genotypic prediction of HIV-1 tropism is based on sequencing the V3 region and interpreting the results with an appropriate algorithm. We compared the performances of the MiSeq (Illumina) and 454 GS-Junior (Roche) systems with a reference phenotypic assay. We used clinical samples for the NGS tropism predictions and assessed their ability to quantify CXCR4-using variants. The data show that the Illumina platform can be used to detect minor CXCR4-using variants in clinical practice but technical optimization are needed to improve quantification.
Targeting of phage particles towards endothelial cells by antibodies selected through a multi-parameter selection strategy
Authors: Mandrup Ole A. , Lykkemark Simon , Kristensen Peter 
Published: February 2017

AbstractOne of the hallmarks of cancer is sustained angiogenesis. Here, normal endothelial cells are activated, and their formation of new blood vessels leads to continued tumour growth. An improved patient condition is often observed when angiogenesis is prevented or normalized through targeting of these genomically stable endothelial cells. However, intracellular targets constitute a challenge in therapy, as the agents modulating these targets have to be delivered and internalized specifically to the endothelial cells. Selection of antibodies binding specifically to certain cell types is well established. It is nonetheless a challenge to ensure that the binding of antibodies to the target cell will mediate internalization. Previously selection of such antibodies has been performed targeting cancer cell lines; most often using either monovalent display or polyvalent display. In this article, we describe selections that isolate internalizing antibodies by sequential combining monovalent and polyvalent display using two types of helper phages, one which increases display valence and one which reduces background. One of the selected antibodies was found to mediate internalization into human endothelial cells, although our results confirms that the single stranded nature of the DNA packaged into phage particles may limit applications aimed at targeting nucleic acids in mammalian cells.
Chemical Modification of Graphene Oxide by Nitrogenation: An X-ray Absorption and Emission Spectroscopy Study
Authors: Chuang Cheng-Hao , Ray Sekhar C. , Mazumder Debarati , Sharma Surbhi , Ganguly Abhijit , Papakonstantinou Pagona , Chiou Jau-Wern , Tsai Huang-Ming , Shiu Hung-Wei , Chen Chia-Hao , Lin Hong-Ji , Guo Jinghua , Pong Way-Faung 
Published: February 2017

AbstractNitrogen-doped graphene oxides (GO:Nx) were synthesized by a partial reduction of graphene oxide (GO) using urea [CO(NH2)2]. Their electronic/bonding structures were investigated using X-ray absorption near-edge structure (XANES), valence-band photoemission spectroscopy (VB-PES), X-ray emission spectroscopy (XES) and resonant inelastic X-ray scattering (RIXS). During GO:Nxsynthesis, different nitrogen-bonding species, such as pyrrolic/graphitic-nitrogen, were formed by replacing of oxygen-containing functional groups. At lower N-content (2.7 at%), pyrrolic-N, owing to surface and subsurface diffusion of C, N and NH is deduced from various X-ray spectroscopies. In contrast, at higher N-content (5.0 at%) graphitic nitrogen was formed in which each N-atom trigonally bonds to three distinctsp2-hybridized carbons with substitution of the N-atoms for C atoms in the graphite layer. Upon nitrogen substitution, the total density of state close to Fermi level is increased to raise the valence-band maximum, as revealed by VB-PES spectra, indicating an electron donation from nitrogen, molecular bonding C/N/O coordination or/and lattice structure reorganization in GO:Nx. The well-ordered chemical environments induced by nitrogen dopant are revealed by XANES and RIXS measurements.
Beam wander relieved orbital angular momentum communication in turbulent atmosphere using Bessel beams
Authors: Yuan Yangsheng , Lei Ting , Li Zhaohui , Li Yangjin , Gao Shecheng , Xie Zhenwei , Yuan Xiaocong 
Published: February 2017

AbstractOptical beam wander is one of the most important issues for free-space optical (FSO) communication. We theoretically derive a beam wander model for Bessel beams propagating in turbulent atmosphere. The calculated beam wander of high order Bessel beams with different turbulence strengths are consistent with experimental measurements. Both theoretical and experimental results reveal that high order Bessel beams are less influenced by the turbulent atmosphere. We also demonstrate the Bessel beams based orbital angular momentum (OAM) multiplexing/demultiplexing in FSO communication with atmospheric turbulence. Under the same atmospheric turbulence condition, the bit error rates of transmitted signals carried by high order Bessel beams show smaller values and fluctuations, which indicates that the high order Bessel beams have an advantage of mitigating the beam wander in OAM multiplexing FSO communication.
Pan-retinal characterisation of Light Responses from Ganglion Cells in the Developing Mouse Retina
Authors: Hilgen Gerrit , Pirmoradian Sahar , Pamplona Daniela , Kornprobst Pierre , Cessac Bruno , Hennig Matthias H. , Sernagor Evelyne 
Published: February 2017

AbstractWe have investigated the ontogeny of light-driven responses in mouse retinal ganglion cells (RGCs). Using a large-scale, high-density multielectrode array, we recorded from hundreds to thousands of RGCs simultaneously at pan-retinal level, including dorsal and ventral locations. Responses to different contrasts not only revealed a complex developmental profile for ON, OFF and ON-OFF responses, but also unveiled differences between dorsal and ventral RGC responses. At eye-opening, dorsal RGCs of all types were more responsive to light, perhaps indicating an environmental priority to nest viewing for pre-weaning pups. The developmental profile of ON and OFF responses exhibited antagonistic behaviour, with the strongest ON responses shortly after eye-opening, followed by an increase in the strength of OFF responses later on. Further, we found that with maturation receptive field (RF) center sizes decrease, spike-triggered averaged responses to white noise become stronger, and centers become more circular while maintaining differences between RGC types. We conclude that the maturation of retinal functionality is not spatially homogeneous, likely reflecting ecological requirements that favour earlier maturation of the dorsal retina.