bluuebunny/crossref_metadata_2025_split huggingface dataset:
How warfare has evolved – a humanitarian organization's perception: The case of the ICRC, 1863–1960
Authors: Palmieri Daniel 
Published: July 2016

To understand how war is perceived and how it has evolved over time, we must first choose the right agent to study: one that is at once involved in the bellicosity, and yet keeps its distance. Such an agent will be better placed to maintain an objective and rational view of developments. The International Committee of the Red Cross (ICRC) would seem to fit the bill. As a humanitarian organization that has been working with the victims of armed conflict for more than 153 years, the ICRC has plenty of experience of war, yet it preserves its ability to interpret critically in its capacity as non-belligerent. It is therefore in a position to grasp the evolution of mankind's oldest activity over one and a half centuries – a period during which warfare has undergone incredible and deadly transformations in conjunction with technological breakthroughs and the rise of extremist political ideologies. On top of this, the ICRC was itself, in its early days, made up of people who had experienced war in one way or another. Of the five members who decided to found the organization in February 1863, three had personally experienced armed violence to varying degrees. This fact also made the nascent organization uniquely entitled to voice its views on a subject of which it had empirical experience.
Erratum: Fish gut microbiota analysis differentiates physiology and behavior of invasive Asian carp and indigenous American fish
Authors: Ye Lin , Amberg Jon , Chapman Duane , Gaikowski Mark , Liu Wen-Tso 
Published: July 2016

Abstract
Correction to: The ISME Journal (2014) 8, 541–551; doi:10.1038/ismej.2013.181 Sequencing information was missing from the published article. The data can be found here: http://www.ncbi.nlm.nih.gov/sra/SRX245252 [accn. The description of the data is linked to this corrigendum as Supplementary Information.
Chemical control over the energy-level alignment in a two-terminal junction
Authors: Yuan Li , Franco Carlos , Crivillers Núria , Mas-Torrent Marta , Cao Liang , Sangeeth C. S. Suchand , Rovira Concepció , Veciana Jaume , Nijhuis Christian A. 
Published: July 2016

AbstractThe energy-level alignment of molecular transistors can be controlled by external gating to move molecular orbitals with respect to the Fermi levels of the source and drain electrodes. Two-terminal molecular tunnelling junctions, however, lack a gate electrode and suffer from Fermi-level pinning, making it difficult to control the energy-level alignment of the system. Here we report an enhancement of 2 orders of magnitude of the tunnelling current in a two-terminal junction via chemical molecular orbital control, changing chemically the molecular component between a stable radical and its non-radical form without altering the supramolecular structure of the junction. Our findings demonstrate that the energy-level alignment in self-assembled monolayer-based junctions can be regulated by purely chemical modifications, which seems an attractive alternative to control the electrical properties of two-terminal junctions.
First-principles treatment of Mott insulators: linearized QSGW+DMFT approach
Authors: Choi Sangkook , Kutepov Andrey , Haule Kristjan , van Schilfgaarde Mark , Kotliar Gabriel 
Published: July 2016

AbstractThe theoretical understanding of emergent phenomena in quantum materials is one of the greatest challenges in condensed matter physics. In contrast to simple materials such as noble metals and semiconductors, macroscopic properties of quantum materials cannot be predicted by the properties of individual electrons. One of the examples of scientific importance is strongly correlated electron system. Neither localized nor itinerant behaviors of electrons in partially filled 3d, 4f, and 5f orbitals give rise to rich physics such as Mott insulators, high-temperature superconductors, and superior thermoelectricity, but hinder quantitative understanding of low-lying excitation spectrum. Here we present a new first-principles approach to strongly correlated solids. It is based on a combination of the quasiparticle self-consistent GW approximation and the dynamical mean-field theory. The sole input in this method is the projector to the set of correlated orbitals for which all local Feynman graphs are being evaluated. For that purpose, we choose very localized quasiatomic orbitals spanning large energy window, which contains most strongly hybridized bands, as well as upper and lower Hubbard bands. The self-consistency is carried out on the Matsubara axis. This method enables the first-principles study of Mott insulators in both their paramagnetic and antiferromagnetic phases. We illustrate the method on the archetypical charge transfer correlated insulators La2CuO4 and NiO, and obtain spectral properties and magnetic moments in good agreement with experiments.
Superconductivity in topologically nontrivial material Au2Pb
Authors: Xing Ying , Wang He , Li Chao-Kai , Zhang Xiao , Liu Jun , Zhang Yangwei , Luo Jiawei , Wang Ziqiao , Wang Yong , Ling Langsheng , Tian Mingliang , Jia Shuang , Feng Ji , Liu Xiong-Jun , Wei Jian , Wang Jian 
Published: July 2016

AbstractThe search for nontrivial superconductivity in novel quantum materials is currently a most attractive topic in condensed matter physics and material science. The experimental studies have progressed quickly over the past couple of years. In this article, we report systematic studies of superconductivity in Au2Pb single crystals. The bulk superconductivity (onset transition temperature, Tconset=1.3 K) of Au2Pb is characterised by both transport and diamagnetic measurements, where the upper critical field Hc2 shows unusual quasi-linear temperature dependence. The superconducting gap is revealed by point-contact measurement with gold tip. However, when using tungsten (W) tip, which is much harder, the superconducting gap probed is largely enhanced as demonstrated by the increases of both Tconset and upper critical field (Hc2). This can be interpreted as a result of increase in density of states under external anisotropic stress imposed by the tip, as revealed by first-principles calculations. Furthermore, novel phase winding of the pseudospin texture along k-space loops around the Fermi energy is uncovered from the calculations, indicating that the observed superconductivity in Au2Pb may have nontrivial topology.
Dissecting the hemagglutinin head and stalk-specific IgG antibody response in healthcare workers following pandemic H1N1 vaccination
Authors: Tete Sarah M , Krammer Florian , Lartey Sarah , Bredholt Geir , Wood John , Skrede Steinar , Cox Rebecca J 
Published: July 2016

AbstractTraditionally, neutralising antibodies that are directed to the major surface glycoprotein hemagglutinin (HA) head domain are measured as surrogate correlates of protection against influenza. In addition to neutralization, hemagglutinin-specific antibodies may provide protection by mediating antibody-dependent cellular cytotoxicity (ADCC). During the 2009 pandemic, vaccination induced HA-specific antibodies that were mostly directed to the conserved HA stalk domain. However, the protective role of these antibodies has not been investigated in detail. We quantified the HA head and stalk-specific antibodies, their avidity, ability to neutralise virus and activate natural killer cells in an ADCC assay. We analyzed sera obtained from 14 healthcare workers who had low hemagglutination inhibition (HI) antibody titres at 3 months after pandemic H1N1 vaccination as well as from 22 controls. Vaccination resulted in a HA stalk dominant antibody response in both low responders and controls. Revaccination of low responders, 5 months later, resulted in a boost in antibodies, with HA head-specific antibodies dominating the response. Comparative analysis of head and stalk antibody avidities revealed that stalk-specific antibodies were qualitatively superior. Furthermore, stalk-specific antibodies mediated virus neutralization and had significantly higher ADCC activity than head-specific antibodies. Despite the head and stalk-specific antibodies being lower in low responders, they had comparable antibody avidity, ADCC functionality and neutralising capacity to those of controls who had high HI titres post-vaccination. Thus, our study has demonstrated that HA stalk-specific antibodies may have an important role in protection through neutralization and ADCC in low responders who do not maintain seroprotective HI antibodies.
Identification of host transcriptional networks showing concentration-dependent regulation by HPV16 E6 and E7 proteins in basal cervical squamous epithelial cells
Authors: Smith Stephen P. , Scarpini Cinzia G. , Groves Ian J. , Odle Richard I. , Coleman Nicholas 
Published: July 2016

AbstractDevelopment of cervical squamous cell carcinoma requires increased expression of the major high-risk human-papillomavirus (HPV) oncogenes E6 and E7 in basal cervical epithelial cells. We used a systems biology approach to identify host transcriptional networks in such cells and study the concentration-dependent changes produced by HPV16-E6 and -E7 oncoproteins. We investigated sample sets derived from the W12 model of cervical neoplastic progression, for which high quality phenotype/genotype data were available. We defined a gene co-expression matrix containing a small number of highly-connected hub nodes that controlled large numbers of downstream genes (regulons), indicating the scale-free nature of host gene co-expression in W12. We identified a small number of ‘master regulators’ for which downstream effector genes were significantly associated with protein levels of HPV16 E6 (n = 7) or HPV16 E7 (n = 5). We validated our data by depleting E6/E7 in relevant cells and by functional analysis of selected genesin vitro. We conclude that the network of transcriptional interactions in HPV16-infected basal-type cervical epithelium is regulated in a concentration-dependent manner by E6/E7, via a limited number of central master-regulators. These effects are likely to be significant in cervical carcinogenesis, where there is competitive selection of cells with elevated expression of virus oncoproteins.
Mitochondrial Mg2+ homeostasis decides cellular energy metabolism and vulnerability to stress
Authors: Yamanaka Ryu , Tabata Sho , Shindo Yutaka , Hotta Kohji , Suzuki Koji , Soga Tomoyoshi , Oka Kotaro 
Published: July 2016

AbstractCellular energy production processes are composed of many Mg2+ dependent enzymatic reactions. In fact, dysregulation of Mg2+ homeostasis is involved in various cellular malfunctions and diseases. Recently, mitochondria, energy-producing organelles, have been known as major intracellular Mg2+ stores. Several biological stimuli alter mitochondrial Mg2+ concentration by intracellular redistribution. However, in living cells, whether mitochondrial Mg2+ alteration affect cellular energy metabolism remains unclear. Mg2+ transporter of mitochondrial inner membrane MRS2 is an essential component of mitochondrial Mg2+ uptake system. Here, we comprehensively analyzed intracellular Mg2+ levels and energy metabolism in Mrs2 knockdown (KD) cells using fluorescence imaging and metabolome analysis. Dysregulation of mitochondrial Mg2+ homeostasis disrupted ATP production via shift of mitochondrial energy metabolism and morphology. Moreover, Mrs2 KD sensitized cellular tolerance against cellular stress. These results indicate regulation of mitochondrial Mg2+via MRS2 critically decides cellular energy status and cell vulnerability via regulation of mitochondrial Mg2+ level in response to physiological stimuli.
Full transcription of the chloroplast genome in photosynthetic eukaryotes
Authors: Shi Chao , Wang Shuo , Xia En-Hua , Jiang Jian-Jun , Zeng Fan-Chun , Gao Li-Zhi 
Published: July 2016

AbstractProkaryotes possess a simple genome transcription system that is different from that of eukaryotes. In chloroplasts (plastids), it is believed that the prokaryotic gene transcription features govern genome transcription. However, the polycistronic operon transcription model cannot account for all the chloroplast genome (plastome) transcription products at whole-genome level, especially regarding various RNA isoforms. By systematically analyzing transcriptomes of plastids of algae and higher plants and cyanobacteria, we find that the entire plastome is transcribed in photosynthetic green plants and that this pattern originated from prokaryotic cyanobacteria — ancestor of the chloroplast genomes that diverged about 1 billion years ago. We propose a multiple arrangement transcription model that multiple transcription initiations and terminations combine haphazardly to accomplish the genome transcription followed by subsequent RNA processing events, which explains the full chloroplast genome transcription phenomenon and numerous functional and/or aberrant pre-RNAs. Our findings indicate a complex prokaryotic genome regulation when processing primary transcripts.
Loss-of-function screening to identify miRNAs involved in senescence: tumor suppressor activity of miRNA-335 and its new target CARF
Authors: Yu Yue , Gao Ran , Kaul Zeenia , Li Ling , Kato Yoshio , Zhang Zhenya , Groden Joanna , Kaul Sunil C , Wadhwa Renu 
Published: July 2016

AbstractSignificance of microRNAs (miRs), small non-coding molecules, has been implicated in a variety of biological processes. Here, we recruited retroviral insertional mutagenesis to obtain induction of an arbitrary noncoding RNAs and coupled it with a cell based loss-of-function (5-Aza-2′-deoxycytidine (5Aza-dC)-induced senescence bypass) screening system. Cells that escaped 5-Aza-dC-induced senescence were subjected to miR-microarray analysis with respect to the untreated control. We identified miR-335 as one of the upregulated miRs. In order to characterize the functional significance, we overexpressed miR-335 in human cancer cells and found that it caused growth suppression. We demonstrate that the latter accounted for inhibition of 5-Aza-dC incorporation into the cell genome, enabling them to escape from induction of senescence. We also report that CARF (Collaborator of ARF) is a new target of miR-335 that regulates its growth suppressor function by complex crosstalk with other proteins including p16INK4A, pRB, HDM2 and p21WAF1.
Dynamic phosphorylation of Histone Deacetylase 1 by Aurora kinases during mitosis regulates zebrafish embryos development
Authors: Loponte Sara , Segré Chiara V. , Senese Silvia , Miccolo Claudia , Santaguida Stefano , Deflorian Gianluca , Citro Simona , Mattoscio Domenico , Pisati Federica , Moser Mirjam A. , Visintin Rosella , Seiser Christian , Chiocca Susanna 
Published: July 2016

AbstractHistone deacetylases (HDACs) catalyze the removal of acetyl molecules from histone and non-histone substrates playing important roles in chromatin remodeling and control of gene expression. Class I HDAC1 is a critical regulator of cell cycle progression, cellular proliferation and differentiation during development; it is also regulated by many post-translational modifications (PTMs). Herein we characterize a new mitosis-specific phosphorylation of HDAC1 driven by Aurora kinases A and B. We show that this phosphorylation affects HDAC1 enzymatic activity and it is critical for the maintenance of a proper proliferative and developmental plan in a complex organism. Notably, we find that Aurora-dependent phosphorylation of HDAC1 regulates histone acetylation by modulating the expression of genes directly involved in the developing zebrafish central nervous system. Our data represent a step towards the comprehension of HDAC1 regulation by its PTM code, with important implications in unravelling its roles both in physiology and pathology.
A mechanistic stochastic framework for regulating bacterial cell division
Authors: Ghusinga Khem Raj , Vargas-Garcia Cesar A. , Singh Abhyudai 
Published: July 2016

AbstractHow exponentially growing cells maintain size homeostasis is an important fundamental problem. Recent single-cell studies in prokaryotes have uncovered the adder principle, where cells add a fixed size (volume) from birth to division, irrespective of their size at birth. To mechanistically explain the adder principle, we consider a timekeeper protein that begins to get stochastically expressed after cell birth at a rate proportional to the volume. Cell-division time is formulated as the first-passage time for protein copy numbers to hit a fixed threshold. Consistent with data, the model predicts that the noise in division timing increases with size at birth. Intriguingly, our results show that the distribution of the volume added between successive cell-division events is independent of the newborn cell size. This was dramatically seen in experimental studies, where histograms of the added volume corresponding to different newborn sizes collapsed on top of each other. The model provides further insights consistent with experimental observations: the distribution of the added volume when scaled by its mean becomes invariant of the growth rate. In summary, our simple yet elegant model explains key experimental findings and suggests a mechanism for regulating both the mean and fluctuations in cell-division timing for controlling size.
Perpendicular magnetic tunnel junction with a strained Mn-based nanolayer
Authors: Suzuki K. Z. , Ranjbar R. , Okabayashi J. , Miura Y. , Sugihara A. , Tsuchiura H. , Mizukami S. 
Published: July 2016

AbstractA magnetic tunnel junction with a perpendicular magnetic easy-axis (p-MTJ) is a key device for spintronic non-volatile magnetoresistive random access memory (MRAM). Co-Fe-B alloy-based p-MTJs are being developed, although they have a large magnetisation and medium perpendicular magnetic anisotropy (PMA), which make it difficult to apply them to a future dense MRAM. Here, we demonstrate a p-MTJ with an epitaxially strained MnGa nanolayer grown on a unique CoGa buffer material, which exhibits a large PMA of more than 5 Merg/cm3 and magnetisation below 500 emu/cm3; these properties are sufficient for application to advanced MRAM. Although the experimental tunnel magnetoresistance (TMR) ratio is still low, first principles calculations confirm that the strain-induced crystal lattice distortion modifies the band dispersion along the tetragonal c-axis into the fully spin-polarised state; thus, a huge TMR effect can be generated in this p-MTJ.
NF-E2, FLI1 and RUNX1 collaborate at areas of dynamic chromatin to activate transcription in mature mouse megakaryocytes
Authors: Zang Chongzhi , Luyten Annouck , Chen Justina , Liu X. Shirley , Shivdasani Ramesh A. 
Published: July 2016

AbstractMutations in mouse and human Nfe2, Fli1 and Runx1 cause thrombocytopenia. We applied genome-wide chromatin dynamics and ChIP-seq to determine these transcription factors’ (TFs) activities in terminal megakaryocyte (MK) maturation. Enhancers with H3K4me2-marked nucleosome pairs were most enriched for NF-E2, FLI and RUNX sequence motifs, suggesting that this TF triad controls much of the late MK program. ChIP-seq revealed NF-E2 occupancy near previously implicated target genes, whose expression is compromised in Nfe2-null cells and many other genes that become active late in MK differentiation. FLI and RUNX were also the motifs most enriched near NF-E2 binding sites and ChIP-seq implicated FLI1 and RUNX1 in activation of late MK, including NF-E2-dependent, genes. Histones showed limited activation in regions of single TF binding, while enhancers that bind NF-E2 and either RUNX1, FLI1 or both TFs gave the highest signals for TF occupancy and H3K4me2; these enhancers associated best with genes activated late in MK maturation. Thus, three essential TFs co-occupy late-acting cis-elements and show evidence for additive activity at genes responsible for platelet assembly and release. These findings provide a rich dataset of TF and chromatin dynamics in primary MK and explain why individual TF losses cause thrombopocytopenia.
On the origin of pure optical rotation in twisted-cross metamaterials
Authors: Barr Lauren E. , Díaz-Rubio Ana , Tremain Ben , Carbonell Jorge , Sánchez-Dehesa José , Hendry Euan , Hibbins Alastair P. 
Published: July 2016

AbstractWe present an experimental and computational study of the response of twisted-cross metamaterials that provide near dispersionless optical rotation across a broad band of frequencies from 19 GHz to 37 GHz. We compare two distinct geometries: firstly, a bilayer structure comprised of arrays of metallic crosses where the crosses in the second layer are twisted about the layer normal; and secondly where the second layer is replaced by the complementary to the original, i.e. an array of cross-shaped holes. Through numerical modelling we determine the origin of rotatory effects in these two structures. In both, pure optical rotation occurs in a frequency band between two transmission minima, where alignment of electric and magnetic dipole moments occurs. In the cross/cross metamaterial, the transmission minima occur at the symmetric and antisymmetric resonances of the coupled crosses. By contrast, in the cross/complementary-cross structure the transmission minima are associated with the dipole and quadrupole modes of the cross, the frequencies of which appear intrinsic to the cross layer alone. Hence the bandwidth of optical rotation is found to be relatively independent of layer separation.
Surface enhanced Raman scattering of monolayer MX2 with metallic nano particles
Authors: Zhang Duan , Wu Ye-Cun , Yang Mei , Liu Xiao , Coileáin Cormac Ó , Abid Mourad , Abid Mohamed , Wang Jing-Jing , Shvets Igor , Xu Hongjun , Chun Byong Sun , Liu Huajun , Wu Han-Chun 
Published: July 2016

AbstractMonolayer transition metal dichalcogenides MX2 (M = Mo, W; X = S) exhibit remarkable electronic and optical properties, making them candidates for application within flexible nano-optoelectronics. The ability to achieve a high optical signal, while quantitatively monitoring strain in real-time is the key requirement for applications in flexible sensing and photonics devices. Surface-enhanced Raman scattering (SERS) allows us to achieve both simultaneously. However, the SERS depends crucially on the size and shape of the metallic nanoparticles (NPs), which have a large impact on its detection sensitivity. Here, we investigated the SERS of monolayer MX2, with particular attention paid to the effect of the distribution of the metallic NPs. We show that the SERS depends crucially on the distribution of the metallic NPs and also the phonon mode of the MX2. Moreover, strong coupling between MX2 and metallic NPs, through surface plasmon excitation, results in splitting of the "Equation missing" and "Equation missing" modes and an additional peak becomes apparent. For a WS2-Ag system the intensity of the additional peak increases exponentially with local strain, which opens another interesting window to quantitatively measure the local strain using SERS. Our experimental study may be useful for the application of monolayer MX2 in flexible nano-optoelectronics.