bluuebunny/crossref_metadata_2025 huggingface dataset:
Time domain parameters of heart rate variability in children born as small-for-gestational age
Authors: Zamecznik Agata , Stańczyk Jerzy , Wosiak Agnieszka , Niewiadomska-Jarosik Katarzyna
Published: July 2016

According to metabolic programming theory, small-for-gestational age patients are at high risk of cardiovascular diseases also because of the possible malfunction of the autonomic nervous system. Autonomic disorders can be assessed by heart rate variability. The aims of this study were to compare time domain parameters of heart rate variability in children born as small-for-gestational age and appropriate-for-gestational age and to assess the correlation of the postnatal and current somatic parameters with the time domain parameters. The small-for-gestational age group consisted of 68 children aged 5–10 years who were born with birth weight below the 10th percentile. The appropriate-for-gestational age group consisted of 30 healthy peers, matched in terms of gender and age. On the basis of Holter monitoring, slightly higher average heart rate was observed in the small-for-gestational age group than in the appropriate-for-gestational age group. It was found that all the time domain parameters (SDNN, SDNNi, SDANNi, rMSSD, pNN50) were lower in the small-for-gestational age group than in the appropriate-for-gestational age group. In the small-for-gestational age group, girls had lower heart rate and some of the heart rate variability parameters (SDNN, SDNNi, SDANNi) in comparison with boys.

Children born as small-for-gestational age have impaired function of the autonomic nervous system. Moreover, in the small-for-gestational age group, autonomic balance moved towards the sympathetic component, which was evidenced by higher heart rate. Children with faster heart rate and lower heart rate variability parameters may be at risk of cardiovascular disease.
Un cri de passion ne s'analyse pas: Olivier Messiaen's Harmonic Borrowings from Jules Massenet
Authors: BALMER YVES , LACÔTE THOMAS , MURRAY CHRISTOPHER BRENT
Published: July 2016

Until the present article, Massenet's influence upon the music of Olivier Messiaen has remained entirely unexplored. During the 1930 and 1940s, Messiaen professed his love for the music of Massenet and regularly used Massenet as a model in his teaching materials. Several examples of the way in which Messiaen selects and transforms passages from Massenet's Werther and Manon are considered. The inclusion of a harmonic formula borrowed from Massenet, contrasted with a melodic formula borrowed from Mozart, in ‘Amen du Désir’, the fourth movement of the Visions de l'Amen, reveals the operatic characters hidden behind the programme of one of Messiaen's best-known works. These intersecting source materials in Messiaen's teaching and composition open new roads for the analysis of the composer's music and pedagogy.
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.
A Cluster of Water Seeps on Mars?
Authors: Cook Terri
Published: July 2016

The discovery of dense concentrations of recurring flowlike features in two Valles Marineris chasms could aid in the search for life and influence future exploration of the Red Planet.
Honoring Earth and Space Scientists
Authors:   AGU
Published: July 2016

AGU members and others in the news
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

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

The 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

The 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

The 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

Traditionally, 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

Development 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

Cellular 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

Prokaryotes 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

Significance 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

Histone 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

How 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

A 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

Mutations 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

We 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

Monolayer 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.
Insulin secretion impairment in Sirt6 knockout pancreatic β cells is mediated by suppression of the FoxO1-Pdx1-Glut2 pathway
Authors: Song Mi-Young , Wang Jie , Ka Sun-O , Bae Eun Ju , Park Byung-Hyun
Published: July 2016

Sirtuin 6 (Sirt6), a chromatin associated class III deacetylase, controls whole-body energy homeostasis and has a critical role in glucose-stimulated insulin secretion (GSIS) in pancreatic β cells. However, its underlying molecular mechanism remains poorly understood. To gain further insights, we studied the pathway by which Sirt6 regulates GSIS utilizing mice lacking Sirt6 in their β cells (βS6KO). Further, we overexpressed wild type or deacetylase-inactive mutant Sirt6 in isolated islets as well as in MIN6 cells. We confirmed that βS6KO mice developed glucose intolerance with severely impaired GSIS. Gene expression analysis of knockout islets and overexpression studies demonstrated that Sirt6 deacetylates forkhead box protein O1 (FoxO1) to trigger its nuclear export and releases its transcriptional repression of key glucose sensing genes such as Pdx1 and Glut2. Ectopic overexpression of Sirt6 in knockout islets resulted in rescue of the defective insulin secretion and restoration of the expression of Pdx1 and Glut2. These results show that Sirt6 in pancreatic β cells deacetylates FoxO1 and subsequently increases the expression of Pdx1 and Glut2 to maintain the glucose-sensing ability of pancreatic β cells and systemic glucose tolerance.
Structure-Activity Analysis of Gram-positive Bacterium-producing Lasso Peptides with Anti-mycobacterial Activity
Authors: Inokoshi Junji , Koyama Nobuhiro , Miyake Midori , Shimizu Yuji , Tomoda Hiroshi
Published: July 2016

Lariatin A, an 18-residue lasso peptide encoded by the five-gene cluster larABCDE, displays potent and selective anti-mycobacterial activity. The structural feature is an N-terminal macrolactam ring, through which the C-terminal passed to form the rigid lariat-protoknot structure. In the present study, we established a convergent expression system by the strategy in which larA mutant gene-carrying plasmids were transformed into larA-deficient Rhodococcus jostii and generated 36 lariatin variants of the precursor protein LarA to investigate the biosynthesis and the structure-activity relationships. The mutational analysis revealed that four amino acid residues (Gly1, Arg7, Glu8 and Trp9) in lariatin A are essential for the maturation and production in the biosynthetic machinery. Furthermore, the study on structure-activity relationships demonstrated that Tyr6, Gly11 and Asn14 are responsible for the anti-mycobacterial activity and the residues at positions 15, 16 and 18 in lariatin A are critical for enhancing the activity. This study will not only provide a useful platform for genetically engineering Gram-positive bacterium-producing lasso peptides, but also an important foundation to rationally design more promising drug candidates for combatting tuberculosis.
Using CRISPR-Cas9 to quantify the contributions of O-glycans, N-glycans and Glycosphingolipids to human leukocyte-endothelium adhesion
Authors: Stolfa Gino , Mondal Nandini , Zhu Yuqi , Yu Xinheng , Buffone Alexander , Neelamegham Sriram
Published: July 2016

There is often interest in dissecting the relative contributions of the N-glycans, O-glycans and glycosphingolipids (GSLs) in regulating complex biological traits like cell signaling, adhesion, development and metastasis. To address this, we developed a CRISPR-Cas9 toolkit to selectively truncate each of these commonly expressed glycan-types. Here, O-glycan biosynthesis was truncated by knocking-out Core 1 β3Gal-T Specific Molecular Chaperone (COSMC), N-glycans by targeting the β1,2 GlcNAc-transferase (MGAT1) and GSLs by deleting UDP-glucose ceramide glucosyltransferase (UGCG). These reagents were applied to reveal the glycoconjugates regulating human myeloid cell adhesion to selectins under physiological shear-flow observed during inflammation. These functional studies show that leukocyte rolling on P- and L-selectin is ablated in cells lacking O-glycans, with N-glycan truncation also increasing cell rolling velocity on L-selectin. All three glycan families contributed to E-selectin dependent cell adhesion with N-glycans contributing to all aspects of the leukocyte adhesion cascade, O-glycans only being important during initial recruitment and GSLs stabilizing slow cell rolling and the transition to firm arrest. Overall, the genome editing tools developed here may be broadly applied in studies of cellular glycosylation.
Context-specific protection of TGFα null mice from osteoarthritis
Authors: Usmani Shirine E. , Ulici Veronica , Pest Michael A. , Hill Tracy L. , Welch Ian D. , Beier Frank
Published: July 2016

Transforming growth factor alpha (TGFα) is a growth factor involved in osteoarthritis (OA). TGFα induces an OA-like phenotype in articular chondrocytes, by inhibiting matrix synthesis and promoting catabolic factor expression. To better understand TGFα’s potential as a therapeutic target, we employed two in vivo OA models: (1) post-traumatic and (2) aging related OA. Ten-week old and six-month old male Tgfa null mice and their heterozygous (control) littermates underwent destabilization of the medial meniscus (DMM) surgery. Disease progression was assessed histologically using the Osteoarthritis Research Society International (OARSI) scoring system. As well, spontaneous disease progression was analyzed in eighteen-month-old Tgfa null and heterozygous mice. Ten-week old Tgfa null mice were protected from OA progression at both seven and fourteen weeks post-surgery. No protection was seen however in six-month old null mice after DMM surgery and no differences were observed between genotypes in the aging model. Thus, young Tgfa null mice are protected from OA progression in the DMM model, while older mice are not. In addition, Tgfa null mice are equally susceptible to spontaneous OA development during aging. Thus, TGFα might be a valuable therapeutic target in some post-traumatic forms of OA, however its role in idiopathic disease is less clear.
Coherent optical phonon oscillation and possible electronic softening in WTe2 crystals
Authors: He Bin , Zhang Chunfeng , Zhu Weida , Li Yufeng , Liu Shenghua , Zhu Xiyu , Wu Xuewei , Wang Xiaoyong , Wen Hai-hu , Xiao Min
Published: July 2016

A rapidly-growing interest in WTe2 has been triggered by the giant magnetoresistance effect discovered in this unique system. While many efforts have been made towards uncovering the electron- and spin-relevant mechanisms, the role of lattice vibration remains poorly understood. Here, we study the coherent vibrational dynamics in WTe2 crystals by using ultrafast pump-probe spectroscopy. The oscillation signal in time domain in WTe2 has been ascribed as due to the coherent dynamics of the lowest energy A1 optical phonons with polarization- and wavelength-dependent measurements. With increasing temperature, the phonon energy decreases due to anharmonic decay of the optical phonons into acoustic phonons. Moreover, a significant drop (15%) of the phonon energy with increasing pump power is observed which is possibly caused by the lattice anharmonicity induced by electronic excitation and phonon-phonon interaction.
Localized recovery of complex networks against failure
Authors: Shang Yilun
Published: July 2016

Resilience of complex networks to failure has been an important issue in network research for decades and recent studies have begun to focus on the inverse recovery of network functionality through strategically healing missing nodes or edges. However, the effect of network recovery is far from fully understood and a general theory is still missing. Here we propose and study a general model of localized recovery, where a group of neighboring nodes are restored in an invasive way from a seed node. We develop a theoretical framework to compare the effect of random recovery (RR) and localized recovery (LR) in complex networks including Erdős-Rényi networks, random regular networks and scale-free networks. We find detailed phase diagrams for the subnetwork of occupied nodes and the “complement network” of failed nodes under RR and LR. By identifying the two competitive forces behind LR, we present an analytical and numerical approach to guide us in choosing the appropriate recovery strategy and provide estimation on its effect by using the degree distribution of the original network as the only input. Our work therefore provides insight for quantitatively understanding recovery process and its implications in infrastructure protection in various complex systems.
MoS2-clad microfibre laser delivering conventional, dispersion-managed and dissipative solitons
Authors: Cui Yudong , Lu Feifei , Liu Xueming
Published: July 2016

Molybdenum disulfide (MoS2), whose monolayer possesses a direct band gap, displays promising applications in optoelectronics, photonics, and lasers. Recent researches have demonstrated that MoS2 has not only a significant broadband saturable absorption performance, but also a higher optical nonlinear response than graphene. However, MoS2 shows much lower optical damage threshold owing to the poorer thermal conductivity and mechanical property. Here, we exploit a MoS2-clad microfibre (MCM) as the saturable absorber (SA) for the generation of ultrashort pulses under different dispersion conditions. The improved evanescent field interaction scheme can overcome the laser-induced thermal damage, as well as take full advantage of the strong nonlinear effect of MoS2. With the MCM SA, conventional, dispersion-managed, and dissipative solitons are generated around 1600 nm in Er-doped fibre lasers with anomalous, near-zero, and normal cavity dispersions, respectively. Our work paves the way for applications of 2D layered materials in photonics, especially in laser sources.
Recent advances in the development and application of nanoelectrodes
Authors: Fan Yunshan , Han Chu , Zhang Bo
Published: July 2016

Nanoelectrodes have key advantages compared to electrodes of conventional size and are the tool of choice for numerous applications in both fundamental electrochemistry research and bioelectrochemical analysis.
Stimulation of electrocatalytic oxygen reduction activity on nitrogen doped graphene through noncovalent molecular functionalisation
Authors: Mohapatra Biswaranjan D. , Mantry Swarna P. , Behera Nibedita , Behera Bibhudatta , Rath Satchidananda , Varadwaj Kumar S. K.
Published: July 2016

Molecular doping on graphene, through noncovalent functionalization, offers a great opportunity to tune charge density on graphene for catalytic applications.
Copper-catalyzed oxyamination of electron-deficient alkenes with N-acyloxyamines
Authors: Ren Shichao , Song Shengjin , Ye Lu , Feng Chao , Loh Teck-Peng
Published: July 2016

An intermolecular version of copper-catalyzed oxyamination of electron-deficient alkenes by making use ofN-acyloxyamines as both amino and oxygen donors was developed.
Correction: Beyond “turn-on” readout: from zero background to signal amplification by combination of magnetic separation and plasmon enhanced fluorescence
Authors: Gong Suqin , Xia Yunsheng
Published: July 2016

Correction for ‘Beyond “turn-on” readout: from zero background to signal amplification by combination of magnetic separation and plasmon enhanced fluorescence’ by Suqin Gong and Yunsheng Xia, Chem. Commun., 2016, 52, 9660–9663.
The effect of moisture on the structures and properties of lead halide perovskites: a first-principles theoretical investigation
Authors: Zhang Lei , Ju Ming-Gang , Liang WanZhen
Published: July 2016

The degradation mechanism of perovskite materials when exposed to moisture and sunlight has been fully explored.
Probing non-covalent interactions with a second generation energy decomposition analysis using absolutely localized molecular orbitals
Authors: Horn Paul R. , Mao Yuezhi , Head-Gordon Martin
Published: July 2016

Second generation of variational energy decomposition analysis method based on absolutely localized molecular orbitals.
The Ti–Mn system revisited: experimental investigation and thermodynamic modelling
Authors: Khan A. U. , Brož P. , Premović M. , Pavlů J. , Vřeštál J. , Yan X. , Maccio D. , Saccone A. , Giester G. , Rogl P.
Published: July 2016

Thermodynamic modelling of the Ti–Mn system based on new experimental data backed by DFT calculations and structure determination for TiMn3.
Direct phase coexistence molecular dynamics study of the phase equilibria of the ternary methane–carbon dioxide–water hydrate system
Authors: Michalis Vasileios K. , Tsimpanogiannis Ioannis N. , Stubos Athanassios K. , Economou Ioannis G.
Published: July 2016

Grown mixed carbon dioxide–methane hydrate with molecular dynamics.
Calix[4]arenes containing a ureido functionality on the lower rim as highly efficient receptors for anion recognition
Authors: Klejch Tomáš , Slavíček Jan , Hudeček Oldřich , Eigner Václav , Gutierrez Natalia Andrea , Cuřínová Petra , Lhoták Pavel
Published: July 2016

Calix[4]arenes bearing diaryl urea moieties with electron-withdrawing substituents on both sides can bind selected anions (AcO−, BzO−, H2PO4−) even in highly competitive solvents such as DMSO-d6.
Development and optimization of a competitive binding assay for the galactophilic low affinity lectin LecA from Pseudomonas aeruginosa
Authors: Joachim Ines , Rikker Sebastian , Hauck Dirk , Ponader Daniela , Boden Sophia , Sommer Roman , Hartmann Laura , Titz Alexander
Published: July 2016

Inhibition of LecA with its carbohydrate ligands results in reduced biofilm mass, a potential Achilles heel for treatment.
Hollow-structured upconverting sesquioxide targeted nanoprobes for magnetic resonance and fluorescence combined imaging
Authors: Yin Jinchang , Li Chaorui , Yang Yubiao , Hu Wenyong , Liu Huan , Shao Yuanzhi
Published: July 2016

The designed hollow-structured Gd2O3 : RE3+/Yb3+ (RE = Er, Ho, Tm) nanoprobe exhibits highly efficient upconverting fluorescence and MR relaxation properties.
Photoresponsive nanostructured membranes
Authors: Madhavan P. , Sutisna B. , Sougrat R. , Nunes S. P.
Published: July 2016

The perspective of adding stimuli-response to isoporous membranes stimulates the development of separation devices with pores, which would open or close under control of environment chemical composition, temperature or exposure to light.
Thermoelectric properties of highly-mismatched alloys of GaNxAs1−xfrom first- to second-principles methods: energy conversion
Authors: Reshak A. H.
Published: July 2016

The transport properties of GaNxAs1−x(x= 0.0, 0.25, 0.5, 0.75 and 1.0) alloys are investigated using the semi-classical Boltzmann theory as implemented in the BoltzTraP code.
Fluorescence “turn on” detection of Cr3+ using N-doped-CDs and graphitic nanosheet hybrids
Authors: Wang Meiling , Meng Guowen
Published: July 2016

N-doped CDs and graphitic nanosheet hybrids were prepared and used for fluorescence “turn on” detection of Cr3+ based on FRET.
Mechanical behaviors of AlCrFeCuNi high-entropy alloys under uniaxial tension via molecular dynamics simulation
Authors: Li Jia , Fang QiHong , Liu Bin , Liu YouWen , Liu Yong
Published: July 2016

Although a high-entropy alloy has exhibited promising mechanical properties, little attention has been given to the dynamics deformation mechanism during uniaxial tension, which limits its widespread and practical utility.
Fast self-diffusion of ions in CH3NH3PbI3: the interstiticaly mechanism versus vacancy-assisted mechanism
Authors: Yang Ji-Hui , Yin Wan-Jian , Park Ji-Sang , Wei Su-Huai
Published: July 2016

The stability of organic–inorganic halide perovskites is a major challenge for their applications and has been extensively studied.
Formation of N-doped molybdenum carbide confined in hierarchical and hollow carbon nitride microspheres with enhanced sodium storage properties
Authors: Qiu Jiyicheng , Yang Zhanxu , Li Qiang , Li Yue , Wu Xian , Qi Chengyuan , Qiao Qingdong
Published: July 2016

The confinement effect and template role provided by metal–organic supramolecular frameworks are exploited to fabricate hollow carbon nitride hierarchical microspheres with ultrafine N-doped MoC (MoCxNy) uniformly dispersed within the network.
Mediator-free Z-scheme photocatalytic system based on ultrathin CdS nanosheets for efficient hydrogen evolution
Authors: Huang Yi , Liu Yang , Zhu Dongyang , Xin Yani , Zhang Bin
Published: July 2016

A mediator-free Z-scheme photocatalytic system based on ultrathin CdS nanosheets for efficient and stable H2 evolution was fabricated through electrostatic interaction.
Heterotypic supramolecular hydrogels
Authors: Yuan Dan , Xu Bing
Published: July 2016

We reviewed heterotypic supramolecular hydrogels containing more than one component to illustrate their promise as soft biomaterials.
An AIE-based bioprobe for differentiating the early and late stages of apoptosis mediated by H2O2
Authors: Leung Anakin C. S. , Zhao Engui , Kwok Ryan T. K. , Lam Jacky W. Y. , Leung Chris W. T. , Deng Haiqin , Tang Ben Zhong
Published: July 2016

A bioprobe, TPE–Zn2BDPA, with aggregation-induced emission characteristics was designed and synthesized to differentiate the early and late stages of apoptosis mediated by H2O2.
Fabrication of optomicrofluidics for real-time bioassays based on hollow sphere colloidal photonic crystals with wettability patterns
Authors: Zhong Kuo , Khorshid Mehran , Li Jiaqi , Markey Karen , Wagner Patrick Hermann , Song Kai , Van Cleuvenbergen Stijn , Clays Koen
Published: July 2016

An optomicrofluidic device for real-time bioassays was constructed by introducing 3D superhydrophilic channels into superhydrophobic hollow SiO2 colloidal photonic crystals.
Association of P16-RBSP3 inactivation with phosphorylated RB1 overexpression in basal–parabasal layers of normal cervix unchanged during CACX development
Authors: Chakraborty Chandraditya , Roychowdhury Anirban , Samadder Sudip , Roy Anup , Mandal Ranajit Kumar , Basu Partha , Roychoudhury Susanta , Panda Chinmay Kumar
Published: July 2016

To understand the molecular mechanism of RB1 phosphorylation in basal–parabasal layers of normal cervix and during cervical cancer (CACX) development, we analyzed the alterations (expression/methylation/deletion/mutation) of RB1/phosphorylated RB1 (p-RB1) (ser807/811 and ser567) and two RB1 phosphorylation inhibitors, P16 and RBSP3, in disease-free normal cervical epithelium (n = 9), adjacent normal cervical epithelium of tumors (n = 70), cervical intraepithelial neoplasia (CIN; n = 28), CACX (n = 102) samples and two CACX cell lines. Immunohistochemical analysis revealed high/medium expression of RB1/p-RB1 (ser807/811 and ser567) and low expression of P16 and RBSP3 in proliferating basal–parabasal layers of majority of normal cervical epitheliums, irrespective of HPV16 infection. Interestingly, 35–52% samples showed high/medium expression of P16 in basal–parabasal layers of normal and had significant association with deleterious non-synonimous SNPs of P16. Methylation of P16 and RBSP3 in basal–parabasal layers of normal cervix (32 and 62%, respectively) showed concordance with their respective expressions in basal–parabasal layers. The methylation frequency of P16 and RBSP3 in basal–parabasal layers of normal did not change significantly in CIN and CACX. The deletion frequency of P16 and RB1 increased significantly with CACX progression. While, deletion of RBSP3 was high in CIN and comparable during CACX progression. P16 showed scattered and infrequent mutation in CACX. The alteration of P16 and RBSP3 was synergistic and showed association with overexpression of p-RB1 in tumors and associated with poor prognosis of patients. Thus, our data suggest that overexpression of p-RB1 in basal–parabasal layers of normal cervical epithelium was due to methylation/low functional-linked non-synonimous SNPs of P16 and RBSP3. This pattern was maintained during cervical carcinogenesis by additional deletion/mutation.
Ablation of CD44 induces glycolysis-to-oxidative phosphorylation transition via modulation of the c-Src–Akt–LKB1–AMPKα pathway
Authors: Nam KeeSoo , Oh Sunhwa , Shin Incheol
Published: July 2016

Cluster of differentiation 44 (CD44) is a transmembrane glycoprotein that has been identified as a cancer stem cell marker in various cancer cells. Although many studies have focused on CD44 as a cancer stem cell marker, its effect on cancer cell metabolism remains unclear. To investigate the role of CD44 on cancer cell metabolism, we established CD44 knock-down cells via retroviral delivery of shRNA against CD44 in human breast cancer cells. Silencing of CD44 decreased the glycolytic phenotype of cancer cells, affecting glucose uptake, ATP production, and lactate production. We also found that ablation of the CD44-induced lactate dehydrogenase (LDH) isoenzyme results in a shift to LDH1 due to LDHA down-regulation and LDHB up-regulation, implying the importance of LDH isoenzyme modulation on cancer metabolism. The expression of glycolysis-related proteins including hypoxia inducible factor-1α (HIF-1α) and LDHA was decreased by CD44 silencing. These effects were due to the up-regulation of liver kinase B1 (LKB1)/AMP-activated protein kinase (AMPK)α activity by reduction in c-Src and Akt activity in CD44 knock-down cells. Finally, induction of LKB1/AMPKα activity blocked the expression of HIF-1α and its target gene, LDHA. Inversely, LDHB expression was repressed by HIF-1α. Collectively, these results indicate that the CD44 silencing-induced metabolic shift is mediated by the regulation of c-Src/Akt/LKB1/AMPKα/HIF-1α signaling in human breast cancer cells.