bluuebunny/crossref_metadata_2025 huggingface dataset:
The place of the Local Group in the cosmic web
Authors: Forero-Romero Jaime E. , González Roberto
Published: October 2016

We use the Bolshoi Simulation to find the most probable location of the Local Group (LG) in the cosmic web. Our LG simulacra are pairs of halos with isolation and kinematic properties consistent with observations. The cosmic web is defined using a tidal tensor approach. We find that the LG's preferred location is regions with a dark matter overdensity close to the cosmic average. This makes filaments and sheets the preferred environment. We also find a strong alignment between the LG and the cosmic web. The orbital angular momentum is preferentially perpendicular to the smallest tidal eigenvector, while the vector connecting the two halos is strongly aligned along the the smallest tidal eigenvector and perpendicular to the largest tidal eigenvector; the pair lies and moves along filaments and sheets. We do not find any evidence for an alignment between the spin of each halo in the pair and the cosmic web.
Galaxy Group Properties in Observations and Simulations
Authors: Nurmi Pasi
Published: October 2016

In this project, we compare different properties of galaxy groups in cosmological N-body simulations and SDSS galaxy group catalogs. In the first part of the project (Nurmi et al. 2013) we compared the basic properties of the groups like the luminosity functions, group richness and velocity dispersion distributions and studied how good is the agreement between the mock group catalog and the SDSS group catalog. Here we continue the earlier study and use updated galaxy group catalog (SDSS DR10) and new simulation data (Guo et al. 2013). We reanalyse earlier group properties and include new properties in the analysis like group environment, star formation rates and group masses. Our analysis show that there are clear differences between the simulated and observed properties of galaxy groups, especially for small groups with a few members. Also, the high luminosities are clearly overestimated in the simulations compared with the SDSS group data.
The Adopted Morphological Types of 247 Rich PF Galaxy Clusters
Authors: Panko Elena , Bajan Katarzyna , Flin Piotr , Gotsulyak Alla
Published: October 2016

Morphological types were determined for 247 rich galaxy clusters from the PF Catalogue of Galaxy Clusters and Groups. The adopted types are based on classical morphological schemes and consider concentration to the cluster center, the signs of preferential direction or plane in the cluster, and the positions of the brightest galaxies. It is shown that both concentration and preferential plane are significant and independent morphological criteria.
Quantifying the Cosmic Web using the Shapefinder diagonistic
Authors: Sarkar Prakash
Published: October 2016

One of the most successful method in quantifying the structures in the Cosmic Web is the Minkowski Functionals. In 3D, there are four minkowski Functionals: Area, Volume, Integrated Mean Curvature and the Integrated Gaussian Curvature. For defining the Minkowski Functionals one should define a surface. We have developed a method based on Marching cube 33 algorithm to generate a surface from a discrete data sets. Next we calculate the Minkowski Functionals and Shapefinder from the triangulated polyhedral surface. Applying this methodology to different data sets , we obtain interesting results related to geometry, morphology and topology of the large scale structure
Color and magnitude dependence of galaxy clustering
Authors: Müller Volker
Published: October 2016

A quantitative study of the clustering properties of galaxies in the cosmic web as a function of absolute magnitude and colour is presented using the SDSS Data Release 7 galaxy redshift survey. We compare our results with mock galaxy samples obtained with four different semi-analytical models of galaxy formation imposed on the merger trees of the Millenium simulation.
Identification of Extremely Large Scale Structures in SDSS-III
Authors: Sankhyayan Shishir , Bagchi J. , Sarkar P. , Sahni V. , Jacob J.
Published: October 2016

We have initiated the search and detailed study of large scale structures present in the universe using galaxy redshift surveys. In this process, we take the volume-limited sample of galaxies from Sloan Digital Sky Survey III and find very large structures even beyond the redshift of 0.2. One of the structures is even greater than 600 Mpc which raises a question on the homogeneity scale of the universe. The shapes of voids-structures (adjacent to each other) seem to be correlated, which supports the physical existence of the observed structures. The other observational supports include galaxy clusters' and QSO distribution's correlation with the density peaks of the volume limited sample of galaxies.
Cosmological parameters from the comparison of peculiar velocities with predictions from the 2M++ density field
Authors: Hudson Michael J. , Carrick Jonathan , Turnbull Stephen J. , Lavaux Guilhem
Published: October 2016

Using redshifts from the 2M++ redshift compilation, we reconstruct the density of galaxies within 200 h−1 Mpc, and compare the predicted peculiar velocities Tully-Fisher and SNe peculiar velocities. The comparison yields a best-fit value of β ≡ Ωm0.55/b* = 0.431 ± 0.021, suggesting Ωm0.55σ8,lin = 0.401 ± 0.024, in good agreement with other probes. The predicted peculiar velocity of the Local Group from sources within the 2M++ volume is 540 ± 40 km s−1, towards l = 268° ± 4°, b = 38° ± 6°, which is misaligned by only 10° with the Cosmic Microwave Background dipole. To account for sources outside the 2M++ volume, we fit simultaneously for β* and an external bulk flow in our analysis. The external bulk flow has a velocity of 159 ± 23 km s−1 towards l = 304° ± 11°, b6° ± 13°.
The disks and spheroid of LTGs in the light of their early web-like organization
Authors: Domínguez-Tenreiro R. , Obreja A. , Brook C. , Martínez-Serrano F. J. , Serna A.
Published: October 2016

Cosmological hydrodynamical simulations show that the baryonic elements that at z = 0 form the stellar populations of late-type galaxies (LTGs), display, at high z, a gaseous web-like organization, where different singular structures (walls, filaments, nodes) show up. The analysis also shows that the spheroid-to-be elements are the first to be involved in the singular structures, while thick and thin disk-to-be elements chronologically follow them. We discuss how these differences at high z can explain the differences among these three components at z = 0.
Satellites are the main drivers of environmental effects at least to z = 0.7
Authors: Kovač Katarina ,   the zCOSMOS team
Published: October 2016

We study the role of environment in the evolution of galaxies up to z = 0.7 using the final zCOSMOS-bright data set. We use the colour as a proxy for the quenched population, and measure the dependence of the red fraction of galaxies on stellar mass and two environmental indicators: the local overdensity of galaxies δ and a demarcation of galaxies to centrals and satellites. The analysis is carried out by quantifying the role of different quenching processes. We find that the measured dependence of the red fraction of galaxies on stellar mass and environment can be well described by two quenching processes: one related only to stellar mass (mass quenching) and the other related to the local environment (environment quenching). Within the errors, these processes are independent of each other, and consistent with the z ~ 0 measurement. Moreover, the red fraction of centrals fr,cen (both singleton centrals and centrals in the groups) does not show any trend with δ and more than 95% of fr,cen is consistent with being produced through the mass quenching alone. The satellite galaxies are redder than the centrals at the same stellar mass and δ, requiring additional environment quenching. Given the observed fractional distribution of satellites at different overdensities, the normalized excess in the red fraction of satellites with respect to the red fraction of centrals is consistent with a scenario in which the satellites account for most of the δ-dependences observed in the overall population of galaxies covering 0.1 < z < 0.7.
It takes a supercluster to raise a galaxy
Authors: Lietzen Heidi , Einasto Maret
Published: October 2016

The properties of galaxies depend on their environment: red, passive elliptical galaxies are usually located in denser environments than blue, star-forming spiral galaxies. This difference in galaxy populations can be detected at all scales from groups of galaxies to superclusters. In this paper, we will discuss the effect of the large-scale environment on galaxies. Our results suggest that galaxies in superclusters are more likely to be passive than galaxies in voids even when they belong to groups with the same richness. In addition, the galaxies in superclusters are also affected by the morphology of the supercluster: filament-type superclusters contain relatively more red, passive galaxies than spider-type superclusters. These results suggest that the evolution of a galaxy is not determined by its local environment alone, but the large-scale environment also affects.
How the cosmic web induces intrinsic alignments of galaxies
Authors: Codis S. , Dubois Y. , Pichon C. , Devriendt J. , Slyz A.
Published: October 2016

Intrinsic alignments are believed to be a major source of systematics for future generation of weak gravitational lensing surveys like Euclid or LSST. Direct measurements of the alignment of the projected light distribution of galaxies in wide field imaging data seem to agree on a contamination at a level of a few per cent of the shear correlation functions, although the amplitude of the effect depends on the population of galaxies considered. Given this dependency, it is difficult to use dark matter-only simulations as the sole resource to predict and control intrinsic alignments. We report here estimates on the level of intrinsic alignment in the cosmological hydrodynamical simulation Horizon-AGN that could be a major source of systematic errors in weak gravitational lensing measurements. In particular, assuming that the spin of galaxies is a good proxy for their ellipticity, we show how those spins are spatially correlated and how they couple to the tidal field in which they are embedded. We will also present theoretical calculations that illustrate and qualitatively explain the observed signals.
Spin Alignment in Analogues of The Local Sheet
Authors: Conidis George J.
Published: October 2016

Tidal torque theory and simulations of large scale structure predict spin vectors of massive galaxies should be coplanar with sheets in the cosmic web. Recently demonstrated, the giants (Ks⩽ -22.5 mag) in the Local Volume beyond the Local Sheet have spin vectors directed close to the plane of the Local Supercluster, supporting the predictions of Tidal Torque Theory. However, the giants in the Local Sheet encircling the Local Group display a distinctly different arrangement, suggesting that the mass asymmetry of the Local Group or its progenitor torqued them from their primordial spin directions. To investigate the origin of the spin alignment of giants locally, analogues of the Local Sheet were identified in the SDSS DR9. Similar to the Local Sheet, analogues have an interacting pair of disk galaxies isolated from the remaining sheet members. Modified sheets in which there is no interacting pair of disk galaxies were identified as a control sample.

Galaxies in face-on control sheets do not display axis ratios predominantly weighted toward low values, contrary to the expectation of tidal torque theory. For face-on and edge-on sheets, the distribution of axis ratios for galaxies in analogues is distinct from that in controls with a confidence of 97.6% & 96.9%, respectively. This corroborates the hypothesis that an interacting pair can affect spin directions of neighbouring galaxies.
Galaxy alignment on large and small scales
Authors: Kang X. , Lin W.P. , Dong X. , Wang Y.O. , Dutton A. , Macciò A.
Published: October 2016

Galaxies are not randomly distributed across the universe but showing different kinds of alignment on different scales. On small scales satellite galaxies have a tendency to distribute along the major axis of the central galaxy, with dependence on galaxy properties that both red satellites and centrals have stronger alignment than their blue counterparts. On large scales, it is found that the major axes of Luminous Red Galaxies (LRGs) have correlation up to 30Mpc/h. Using hydro-dynamical simulation with star formation, we investigate the origin of galaxy alignment on different scales. It is found that most red satellite galaxies stay in the inner region of dark matter halo inside which the shape of central galaxy is well aligned with the dark matter distribution. Red centrals have stronger alignment than blue ones as they live in massive haloes and the central galaxy-halo alignment increases with halo mass. On large scales, the alignment of LRGs is also from the galaxy-halo shape correlation, but with some extent of mis-alignment. The massive haloes have stronger alignment than haloes in filament which connect massive haloes. This is contrary to the naive expectation that cosmic filament is the cause of halo alignment.
Giant radio galaxies and cosmic web
Authors: Heinämäki Pekka
Published: October 2016

Giant radio galaxies create the well
distinguishable class of sources.
These sources are characterized with edge-brightened radio lobes with
highly collimated radio jets and large linear sizes which make them
the largest individual structures in the Universe. They are also known
to be hosted by elliptical/disturbed host galaxies and avoid clusters
and high galaxy density regions. Because of GRG, large linear sizes
lobes extend well beyond the interstellar media and host galaxy
halo the evolution of the radio lobes may depend on interaction
with this environment. Using our method to extract filamentary
structure of the galaxies in our local universe we study whether
radio lobe properties in some giant radio galaxies are determined
on an interaction of this filament ambient.
Real-space density profile reconstruction of stacked voids
Authors: Pisani Alice , Sutter P. , Lavaux G. , Wandelt B.
Published: October 2016

Modern surveys allow us to access to high quality large scale structure measurements. In this framework, cosmic voids appear as a new potential probe of Cosmology. We discuss the use of cosmic voids as standard spheres and their capacity to constrain new physics, dark energy and cosmological models. We introduce the Alcock-Paczyński test and its use with voids. We discuss the main difficulties in treating with cosmic voids: redshift-space distortions, the sparsity of data, and peculiar velocities. We present a method to reconstruct the spherical density profiles of void stacks in real space, without redshift-space distortions. We show its application to a toy model and a dark matter simulation; as well as a first application to reconstruct real cosmic void stacks density profiles in real space from the Sloan Digital Sky Survey.
Strong limit on the spatial and temporal variations of the fine-structure constant
Authors: Le T. D.
Published: October 2016

Observed spectra of quasars provide a powerful tool to test the possible spatial and temporal variations of the fine-structure constant α = e2/ћc over the history of the Universe. It is demonstrated that high sensitivity to the variation of α can be obtained from a comparison of the spectra of quasars and laboratories. We reported a new constraint on the variation of the fine-structure constant based on the analysis of the optical spectra of the fine-structure transitions in [NeIII], [NeV], [OIII], [OI] and [SII] multiplets from 14 Seyfert 1.5 galaxies. The weighted mean value of the α-variation derived from our analysis over the redshift range 0.035 < z < 0.281 Δα/α= (4.50 ± 5.53) \times 10-5. This result presents strong limit improvements on the constraint on Δα/α compared to the published in the literature
The cosmic web and microwave background fossilize the first turbulent combustion
Authors: Gibson Carl H. , Keeler R. Norris
Published: October 2016

Collisional fluid mechanics theory predicts a turbulent hot big bang at Planck conditions from large, negative, turbulence stresses below the Fortov-Kerr limit (< −10113Pa). Big bang turbulence fossilized when quarks formed, extracting the mass energy of the universe by extreme negative viscous stresses of inflation, expanding to length scales larger than the horizon scale ct. Viscous-gravitational structure formation by fragmentation was triggered at big bang fossil vorticity turbulence vortex lines during the plasma epoch, as observed by the Planck space telescope. A cosmic web of protogalaxies, protogalaxyclusters, and protogalaxysuperclusters that formed in turbulent boundary layers of the spinning voids are hereby identified as expanding turbulence fossils that falsify CDMHC cosmology.
Legal Preparedness for the Facilitation of International Humanitarian Assistance in the Aftermath of Vanuatu’s Cyclone Pam
Authors: Barber REBECCA
Published: October 2016

This paper uses the response to Cyclone Pam in Vanuatu, 2015, as a case-study to review one country’s legal preparedness to manage a large influx of international humanitarian assistance, and the international humanitarian community’s respect for national laws and institutions. It describes provisions in international disaster response law and the developing international law on the protection of persons in the event of disaster regarding the role of the affected state, and juxtaposes this with what happened in the cyclone response—namely, the introduction by international actors of a range of international humanitarian tools and services that were neither described in national legislation nor rehearsed in national planning processes. It concludes by suggesting that national governments and international humanitarian responders advance their efforts to promote the inter-operability of their disaster management systems, and to develop an improved mutual understanding of each other’s roles and responsibilities under international law.
The Conceptualization and Measurement of Job Crafting
Authors: Lichtenthaler Philipp Wolfgang , Fischbach Andrea
Published: October 2016

Abstract. This research redefined the job demands–resources (JD-R) job crafting model ( Tims & Bakker, 2010 ) to resolve theoretical and empirical inconsistencies regarding the crafting of job demands and developed a German version of the Job Crafting Scale (JCS; Tims, Bakker, & Derks, 2012 ) in two separate studies (total N = 512). In Study 1 the German version of the JCS was developed and tested for its factor structure, reliability, and construct validity. Study 2 dealt with the validity of our redefined JD-R job crafting model. The results show that, like the original version, the German version comprises four job crafting types, and the German version of the JCS is a valid and reliable generic measure that can be used for future research with German-speaking samples. Evidence for the redefined JD-R job crafting model was based on findings relating job crafting to work engagement and emotional exhaustion.
CircRNAs in hematopoiesis and hematological malignancies
Authors: Bonizzato A , Gaffo E , te Kronnie G , Bortoluzzi S
Published: October 2016

Cell states in hematopoiesis are controlled by master regulators and by complex circuits of a growing family of RNA species impacting cell phenotype maintenance and plasticity. Circular RNAs (circRNAs) are rapidly gaining the status of particularly stable transcriptome members with distinctive qualities. RNA-seq identified thousands of circRNAs with developmental stage- and tissue-specific expression corroborating earlier suggestions that circular isoforms are a natural feature of the cell expression program. CircRNAs are abundantly expressed also in the hematopoietic compartment. There are a number of studies on circRNAs in blood cells, a specific overview is however lacking. In this review we first present current insight in circRNA biogenesis discussing the relevance for hematopoiesis of the highly interleaved processes of splicing and circRNA biogenesis. Regarding molecular functions circRNAs modulate host gene expression, but also compete for binding of microRNAs, RNA-binding proteins or translation initiation and participate in regulatory circuits. We examine circRNA expression in the hematopoietic compartment and in hematologic malignancies and review the recent breakthrough study that identified pathogenic circRNAs derived from leukemia fusion genes. CircRNA high and regulated expression in blood cell types indicate that further studies are warranted to inform the position of these regulators in normal and malignant hematopoiesis.
Direct observation of redox reactions in Candida parapsilosis ATCC 7330 by Confocal microscopic studies
Authors: Venkataraman Sowmyalakshmi , Narayan Shoba , Chadha Anju
Published: October 2016

Confocal microscopic studies with the resting cells of yeast, Candida parapsilosis ATCC 7330, a reportedly versatile biocatalyst for redox enzyme mediated preparation of optically pure secondary alcohols in high optical purities [enantiomeric excess (ee) up to >99%] and yields, revealed that the yeast cells had large vacuoles under the experimental conditions studied where the redox reaction takes place. A novel fluorescence method was developed using 1-(6-methoxynaphthalen-2-yl)ethanol to track the site of biotransformation within the cells. This alcohol, itself non-fluorescent, gets oxidized to produce a fluorescent ketone, 1-(6-methoxynaphthalen-2-yl)ethanone. Kinetic studies showed that the reaction occurs spontaneously and the products get released out of the cells in less time [5 mins]. The biotransformation was validated using HPLC.
Preclinical validation of the small molecule drug quininib as a novel therapeutic for colorectal cancer
Authors: Murphy Adrian G. , Casey Rory , Maguire Aoife , Tosetto Miriam , Butler Clare T. , Conroy Emer , Reynolds Alison L. , Sheahan Kieran , O’Donoghue Diarmuid , Gallagher William M. , Fennelly David , Kennedy Breandán N. , O’Sullivan Jacintha
Published: October 2016

Colorectal cancer (CRC) is a leading cause of cancer deaths. Molecularly targeted therapies (e.g. bevacizumab) have improved survival rates but drug resistance ultimately develops and newer therapies are required. We identified quininib as a small molecule drug with anti-angiogenic activity using in vitro, ex vivo and in vivo screening models. Quininib (2-[(E)-2-(Quinolin-2-yl) vinyl] phenol), is a small molecule drug (molecular weight 283.75 g/mol), which significantly inhibited blood vessel development in zebrafish embryos (p < 0.001). In vitro, quininib reduced endothelial tubule formation (p < 0.001), cell migration was unaffected by quininib and cell survival was reduced by quininib (p < 0.001). Using ex vivo human CRC explants, quininib significantly reduced the secretions of IL-6, IL-8, VEGF, ENA-78, GRO-α, TNF, IL-1β and MCP-1 ex vivo (all values p < 0.01). Quininib is well tolerated in mice when administered at 50 mg/kg intraperitoneally every 3 days and significantly reduced tumour growth of HT-29-luc2 CRC tumour xenografts compared to vehicle control. In addition, quininib reduced the signal from a αvβ3 integrin fluorescence probe in tumours 10 days after treatment initiation, indicative of angiogenic inhibition. Furthermore, quininib reduced the expression of angiogenic genes in xenografted tumours. Collectively, these findings support further development of quininib as a novel therapeutic agent for CRC.
Correction: Corrigendum: Pre-formulation and systematic evaluation of amino acid assisted permeability of insulin across in vitro buccal cell layers
Authors: Iyire Affiong , Alaayedi Maryam , Mohammed Afzal R.
Published: October 2016

Scientific Reports 6: Article number: 32498; published online: 01 September 2016; updated: 14 October 2016
FOXA and master transcription factors recruit Mediator and Cohesin to the core transcriptional regulatory circuitry of cancer cells
Authors: Fournier Michèle , Bourriquen Gaëlle , Lamaze Fabien C. , Côté Maxime C. , Fournier Éric , Joly-Beauparlant Charles , Caron Vicky , Gobeil Stéphane , Droit Arnaud , Bilodeau Steve
Published: October 2016

Controlling the transcriptional program is essential to maintain the identity and the biological functions of a cell. The Mediator and Cohesin complexes have been established as central cofactors controlling the transcriptional program in normal cells. However, the distribution, recruitment and importance of these complexes in cancer cells have not been fully investigated. Here we show that FOXA and master transcription factors are part of the core transcriptional regulatory circuitry of cancer cells and are essential to recruit M ediator and Cohesin. Indeed, Mediator and Cohesin occupied the enhancer and promoter regions of actively transcribed genes and maintained the proliferation and colony forming potential. Through integration of publically available ChIP-Seq datasets, we predicted the core transcriptional regulatory circuitry of each cancer cell. Unexpectedly, for all cells investigated, the pioneer transcription factors FOXA1 and/or FOXA2 were identified in addition to cell-specific master transcription factors. Loss of both types of transcription factors phenocopied the loss of Mediator and Cohesin. Lastly, the master and pioneer transcription factors were essential to recruit Mediator and Cohesin to regulatory regions of actively transcribed genes. Our study proposes that maintenance of the cancer cell state is dependent on recruitment of Mediator and Cohesin through FOXA and master transcription factors.
Magnetoresistance manipulation and sign reversal in Mn-doped ZnO nanowires
Authors: Sapkota Keshab R. , Chen Weimin , Maloney F. Scott , Poudyal Uma , Wang Wenyong
Published: October 2016

We report magnetoresistance (MR) manipulation and sign reversal induced by carrier concentration modulation in Mn-doped ZnO nanowires. At low temperatures positive magnetoresistance was initially observed. When the carrier concentration was increased through the application of a gate voltage, the magnetoresistance also increased and reached a maximum value. However, further increasing the carrier concentration caused the MR to decrease, and eventually an MR sign reversal from positive to negative was observed. An MR change from a maximum positive value of 25% to a minimum negative value of 7% was observed at 5 K and 50 KOe. The observed MR behavior was modeled by considering combined effects of quantum correction to carrier conductivity and bound magnetic polarons. This work could provide important insights into the mechanisms that govern magnetotransport in dilute magnetic oxides, and it also demonstrated an effective approach to manipulating magnetoresistance in these materials that have important spintronic applications.
A nuclear-replicating viroid antagonizes infectivity and accumulation of a geminivirus by upregulating methylation-related genes and inducing hypermethylation of viral DNA
Authors: Torchetti Enza Maria , Pegoraro Mattia , Navarro Beatriz , Catoni Marco , Di Serio Francesco , Noris Emanuela
Published: October 2016

DNA methylation and post-transcriptional gene silencing play critical roles in controlling infection of single-stranded (ss) DNA geminiviruses and ssRNA viroids, respectively, but both pathogens can counteract these host defense mechanisms and promote their infectivity. Moreover, a specific role of DNA methylation in viroid-host interactions is not yet confirmed. Here, using an experimental system where two nuclear-replicating agents, the geminivirus tomato yellow leaf curl Sardinia virus (TYLCSV) and potato spindle tuber viroid (PSTVd), co-infect their common host tomato, we observed that PSTVd severely interferes with TYLCSV infectivity and accumulation, most likely as a consequence of strong activation of host DNA methylation pathways. In fact, PSTVd alone or in co-infection with TYLCSV significantly upregulates the expression of key genes governing DNA methylation in plants. Using methylation-sensitive restriction and bisulfite conversion assays, we further showed that PSTVd infection promotes a strong hypermethylation of TYLCSV DNA, thus supporting a mechanistic link with the antagonism of the viroid on the virus in co-infected tomato plants. These results describe the interaction between two nuclear-replicating pathogens and show that they differentially interfere with DNA methylation pathways.
NMR based serum metabolomics reveals a distinctive signature in patients with Lupus Nephritis
Authors: Guleria Anupam , Pratap Avadhesh , Dubey Durgesh , Rawat Atul , Chaurasia Smriti , Sukesh Edavalath , Phatak Sanat , Ajmani Sajal , Kumar Umesh , Khetrapal Chunni Lal , Bacon Paul , Misra Ramnath , Kumar Dinesh
Published: October 2016

Management of patient with Lupus Nephritis (LN) continues to remain a challenge for the treating physicians because of considerable morbidity and even mortality. The search of biomarkers in serum and urine is a focus of researchers to unravel new targets for therapy. In the present study, the utility of NMR-based serum metabolomics has been evaluated for the first time in discriminating LN patients from non-nephritis lupus patients (SLE) and further to get new insights into the underlying disease processes for better clinical management. Metabolic profiling of sera obtained from 22 SLE patients, 40 LN patients and 30 healthy controls (HC) were performed using high resolution 1D1H-CPMG and diffusion edited NMR spectra to identify the potential molecular biomarkers. Using multivariate analysis, we could distinguish SLE and LN patients from HC and LN from SLE patients. Compared to SLE patients, the LN patients had increased serum levels of lipid metabolites (including LDL/VLDL lipoproteins), creatinine and decreased levels of acetate. Our results revealed that metabolic markers especially lipids and acetate derived from NMR spectroscopy has high sensitivity and specificity to distinguish LN among SLE patients and has the potential to be a useful adjunctive tool in diagnosis and clinical management of LN.
Novel CHM mutations identified in Chinese families with Choroideremia
Authors: Cai Xue-Bi , Huang Xiu-Feng , Tong Yi , Lu Qin-Kang , Jin Zi-Bing
Published: October 2016

Choroideremia is a bilateral and progressive X-linked inherited disease characterized by widespread chorioretinal atrophy with relative sparing of the macular region. It is caused by mutations in the ubiquitously expressed CHM gene, which lead to the absence of the Rab escort protein 1 (REP-1), resulting in prenylation deficiency. Typical fundus appearances for choroideremia were found in 3 probands from three unrelated Chinese families in our study. We firstly used the targeted exome sequencing (TES) technology to detect mutations in CHM gene. Based on an established filtering strategy of data analyses, along with confirmation by co-segregation, a previously reported mutation (c.1584_1587del TGTT, p.V529Hfs*7) was identified in one family, while two novel mutations (c.227_232delinsTGTCATTTCA, p.Q76Lfs*7; c.710dupA, p.Y237_S238delinsX) were identified in the other two families. These findings not only expands the currently limited spectrum of Chinese disease-causing variants in CHM gene, but also increases our understanding of the phenotypic and genotypic correlations of choroideremia, and may potentially lead to improved genetic counseling and specific treatment for families with choroideremia as well.
Interrogating the superconductor Ca10(Pt4As8)(Fe2−xPtxAs2)5 Layer-by-layer
Authors: Kim Jisun , Nam Hyoungdo , Li Guorong , Karki A. B. , Wang Zhen , Zhu Yimei , Shih Chih-Kang , Zhang Jiandi , Jin Rongying , Plummer E. W.
Published: October 2016

Ever since the discovery of high-Tc superconductivity in layered cuprates, the roles that individual layers play have been debated, due to difficulty in layer-by-layer characterization. While there is similar challenge in many Fe-based layered superconductors, the newly-discovered Ca10(Pt4As8)(Fe2As2)5 provides opportunities to explore superconductivity layer by layer, because it contains both superconducting building blocks (Fe2As2 layers) and intermediate Pt4As8 layers. Cleaving a single crystal under ultra-high vacuum results in multiple terminations: an ordered Pt4As8 layer, two reconstructed Ca layers on the top of a Pt4As8 layer, and disordered Ca layer on the top of Fe2As2 layer. The electronic properties of individual layers are studied using scanning tunneling microscopy/spectroscopy (STM/S), which reveals different spectra for each surface. Remarkably superconducting coherence peaks are seen only on the ordered Ca/Pt4As8 layer. Our results indicate that an ordered structure with proper charge balance is required in order to preserve superconductivity.
Line-scanning Brillouin microscopy for rapid non-invasive mechanical imaging
Authors: Zhang Jitao , Fiore Antonio , Yun Seok-Hyun , Kim Hanyoup , Scarcelli Giuliano
Published: October 2016

Brillouin spectroscopy probes the mechanical properties of material by measuring the optical frequency shift induced by photon-phonon scattering interactions. In traditional configurations, Brillouin spectrometers measure only one point of the sample at a time. This results in long acquisition times for mechanical imaging of large areas. In this work, we demonstrate a parallel detection configuration where the Brillouin shift of hundreds of points in a line can be measured simultaneously. In mm-sized samples, this novel configuration effectively shortens the acquisition time of two-dimensional Brillouin imaging from hours to tens of seconds, thus making it a powerful technology for label-free mechanical characterization of tissue and biomaterials.
Evaluation of the human adaptation of influenza A/H7N9 virus in PB2 protein using human and swine respiratory tract explant cultures
Authors: Chan Louisa L. Y. , Bui Christine T. H. , Mok Chris K. P. , Ng Mandy M. T. , Nicholls John M. , Peiris J. S. Malik , Chan Michael C. W. , Chan Renee W. Y.
Published: October 2016

Novel avian H7N9 virus emerged in China in 2013 resulting in a case fatality rate of around 39% and continues to pose zoonotic and pandemic risk. Amino acid substitutions in PB2 protein were shown to influence the pathogenicity and transmissibility of H7N9 following experimental infection of ferrets and mice. In this study, we evaluated the role of amino acid substitution PB2-627K or compensatory changes at PB2-591K and PB2-701N, on the tropism and replication competence of H7N9 viruses for human and swine respiratory tracts using ex vivo organ explant cultures. Recombinant viruses of A/Shanghai/2/2013 (rgH7N9) and its mutants with PB2-K627E, PB2-K627E + Q591K and PB2-K627E + D701N were generated by plasmid-based reverse genetics. PB2-E627K was essential for efficient replication of rgH7N9 in ex vivo cultures of human and swine respiratory tracts. Mutant rgPB2-K627E + D701N replicated better than rgPB2-K627E in human lung but not as well as rgH7N9 virus. The rgPB2-K627E mutant failed to replicate in human type I-like pneumocytes (ATI) and peripheral blood monocyte-derived macrophages (PMϕ) at 37 °C while the compensatory mutant rgPB2-K627E + Q591K and rgPB2-K627E + D701N had partly restored replication competence in PMϕ. Our results demonstrate that PB2-E627K was important for efficient replication of influenza H7N9 in both human and swine respiratory tracts.
The microRNA expression profile of mouse Müller glia in vivo and in vitro
Authors: Wohl Stefanie G. , Reh Thomas A.
Published: October 2016

The profile of miRNAs in mature glia is not well characterized, and most studies have been done in cultured glia. In order to identify the miRNAs in adult and young (postnatal day 11/12) Müller glia of the neural retina, we isolated the Müller glia from Rlbp-CreER: Stopf/f-tdTomato mice by means of fluorescent activated cell sorting and analyzed their miRNAs using NanoStrings Technologies®. In freshly isolated adult Müller glia, we identified 7 miRNAs with high expression levels in the glia, but very low levels in the retinal neurons. These include miR-204, miR-9, and miR-125–5p. We also found 15 miRNAs with high levels of expression in both neurons and glia, and many miRNAs that were enriched in neurons and expressed at lower levels in Müller glia, such as miR-124. We next compared miRNA expression of acutely isolated Müller glia with those that were maintained in dissociated culture for 8 and 14 days. We found that most miRNAs declined in vitro. Interestingly, some miRNAs that were not highly expressed in adult Müller glia increased in cultured cells. Our results thus show the miRNA profile of adult Müller glia and the effects of cell culture on their levels.
Scent marking in Sunda clouded leopards (Neofelis diardi): novel observations close a key gap in understanding felid communication behaviours
Authors: Allen Maximilian L. , Wittmer Heiko U. , Setiawan Endro , Jaffe Sarah , Marshall Andrew J.
Published: October 2016

Intraspecific communication is integral to the behavioural ecology of solitary carnivores, but observing and quantifying their communication behaviours in natural environments is difficult. Our systematic literature review found that basic information on scent marking is completely lacking for 23% of all felid species, and information on 21% of other felid species comes solely from one study of captive animals. Here we present results of the first systematic investigation of the scent marking behaviours of Sunda clouded leopards in the wild. Our observations using motion-triggered video cameras in Indonesian Borneo are novel for clouded leopards, and contrary to previous descriptions of their behaviour. We found that clouded leopards displayed 10 distinct communication behaviours, with olfaction, scraping, and cheek rubbing the most frequently recorded. We also showed that males make repeated visits to areas they previously used for marking and that multiple males advertise and receive information at the same sites, potentially enhancing our ability to document and monitor clouded leopard populations. The behaviours we recorded are remarkably similar to those described in other solitary felids, despite tremendous variation in the environments they inhabit, and close a key gap in understanding and interpreting communication behaviours of clouded leopards and other solitary felids.
Electronically-Controlled Beam-Steering through Vanadium Dioxide Metasurfaces
Authors: Hashemi Mohammed Reza M. , Yang Shang-Hua , Wang Tongyu , Sepúlveda Nelson , Jarrahi Mona
Published: October 2016

Engineered metamaterials offer unique functionalities for manipulating the spectral and spatial properties of electromagnetic waves in unconventional ways. Here, we report a novel approach for making reconfigurable metasurfaces capable of deflecting electromagnetic waves in an electronically controllable fashion. This is accomplished by tilting the phase front of waves through a two-dimensional array of resonant metasurface unit-cells with electronically-controlled phase-change materials embedded inside. Such metasurfaces can be placed at the output facet of any electromagnetic radiation source to deflect electromagnetic waves at a desired frequency, ranging from millimeter-wave to far-infrared frequencies. Our design does not use any mechanical elements, external light sources, or reflectarrays, creating, for the first time, a highly robust and fully-integrated beam-steering device solution. We demonstrate a proof-of-concept beam-steering metasurface optimized for operation at 100 GHz, offering up to 44° beam deflection in both horizontal and vertical directions. Dynamic control of electromagnetic wave propagation direction through this unique platform could be transformative for various imaging, sensing, and communication applications, among others.
Synthetic Aspects of Peptide– and Protein–Polymer Conjugates in the Post-click Era
Authors: Meißig;ler Maria , Wieczorek Sebastian , ten Brummelhuis Niels , Börner Hans G.
Published: October 2016

Biomacromolecules offer complex and precise functions embedded in their monomer sequence such as enzymatic activity or specific interactions towards other molecules. Their informational content and capability to organize in higher ordered structures is superior to those of synthetic molecules. In comparison, synthetic polymers are easy to access even at large production scales and they are chemically more diverse. Solubilization, shielding against enzymatic degradation to more advanced functions like switchability or protein mimicry, etc., are accessible through the world of polymer chemistry. Bio-inspired hybrid materials consisting of peptides or proteins and synthetic polymers thereby combine the properties of both molecules to give rise to a new class of materials with unique characteristics and performance. To obtain well-defined bioconjugate materials, high yielding and site-specific as well as biorthogonal ligation techniques are mandatory. Since the first attempts of protein PEGylation in the 1970s and the concept of “click” chemistry arising in 2001, continuous progress in the field of peptide– and protein–polymer conjugate preparation has been gained. Herein, we provide an overview on ligation techniques to prepare functional bioconjugates published in the last decade, also referred to as “post-click” methods. Furthermore, chemoenzymatic approaches and biotransformation reactions used in peptide or protein modification, as well as highly site-specific and efficient reactions originated in synthetic macromolecular chemistry, which could potentially be adapted for bioconjugation, are presented. Finally, future perspectives for the preparation and application of bioconjugates at the interface between biology and synthetic materials are given.
Glycopolymers
Authors: Hartmann Laura , Neuhaus Kira
Published: October 2016

This chapter presents a short overview of the synthesis, characterization, and application of linear glycopolymers. Focus is devoted to linear glycopolymers consisting of pendant sugar ligands on the side chains. Selected examples will highlight the different approaches for synthesizing glycopolymers, their multivalent binding modes, the characterization of their binding affinity, and the use in biotechnological and biomedical applications.
Polymeric Ionic Liquids with Micelle-like Topologies and Functions
Authors: Kerscher Benjamin , Schüler Fabian , Evers Anna-Katharina , Mülhaupt Rolf
Published: October 2016

Micelles and micelle-forming amphiphilic polymers play an important role in nature and in everyday life. Today, the bio-inspired development of synthetic polymers with micelle-like molecular architectures goes well beyond the scope of biological micellar systems. Particularly, amphiphilic core–shell polymeric electrolytes, equivalent to unimolecular micelles, are much more robust and less sensitive to shear-, temperature-, and pH-induced disintegration. Among amphiphilic materials, polymeric ionic liquids (PILs) are attracting great attention, since they combine the features of low-molecular-weight ionic liquids (ILs) with the properties and facile processing typical of polymers. Hence, the precise incorporation of IL moieties into macromolecular core–shell and onion-like architectures represents an attractive route to nanostructured PILs exhibiting functions typical for micelles. This chapter highlights the progress made in bio-inspired molecular systems engineering by designing micelle-like PILs comprising dendritic and hyperbranched polymers as cores and IL-moieties with variable alkyl substitution in their periphery. Special focus is placed upon the design of hyperbranched PILs with onion-like topologies, enabling tailoring specific functions. The wide applications of compartmentalized PIL systems span from the synthesis of particles and dispersions to catalysis and smart materials that respond with property changes to external stimuli.
Biological and Bio-inspired Heterogeneous Composites: From Resilient Palm Trees to Stretchable Electronics
Authors: Rüggeberg Markus , Studart André R. , Burgert Ingo
Published: October 2016

Structural hierarchy, heterogeneity, and an adapted interfacial design are hallmarks of biological materials and have been exploited in engineering to optimize the mechanical response of composite materials used in load-bearing applications. In this chapter, we first revisit the exquisite hierarchical structure of plants, in particular the palm tree, to show how multiscale gradients provide an elegant means to optimize the stress distribution and architecture of load-bearing, resilient biological materials. We then turn our attention to synthetic heterogeneous composites that harness the concept of graded designs to enable mechanical coupling between hard and soft components of interest in the emerging field of stretchable electronics. By discussing similarities and disparities between these selected natural and artificial systems, a critical analysis on the benefits and challenges in the field of biomimetic materials research is presented. While synthetic systems remain far from reaching the level of architectural control found in natural materials, recently developed fabrication technologies provide encouraging demonstrations that suggest a promising future for biologically inspired advanced materials.
Antimicrobial Polymers and Surfaces – Natural Mimics or Surpassing Nature?
Authors: Krumm Christian , Tiller Joerg C.
Published: October 2016

Fighting pathogenic microbes is one of the great current challenges of mankind. Nature has developed several techniques to counteract microbial attacks. Science has also yielded several technologies, including antimicrobial polymers as biocides and polymers used for microbe killing and repelling surfaces. Recent scientific antimicrobial approaches are mimicking natural concepts. In this chapter, current developments in antimicrobial and antifouling polymers and surfaces are reviewed and discussed regarding the question whether they mimic nature or surpass it.
Green-to-red primed conversion of Dendra2 using blue and red lasers
Authors: Klementieva N. V. , Lukyanov K. A. , Markina N. M. , Lukyanov S. A. , Zagaynova E. V. , Mishin A. S.
Published: October 2016

Primed photoconversion of Dendra2 in commonly available confocal and super-resolution microscopy setups equipped with blue and red lasers is described.
Sterically induced reductive linkage of iron polypnictides with bulky lanthanide complexes by ring-opening of THF
Authors: Schoo Christoph , Bestgen Sebastian , Schmidt Monika , Konchenko Sergey N. , Scheer Manfred , Roesky Peter W.
Published: October 2016

Two new 3d/4f polyphosphide and polyarsenide complexes in which [(DippForm)2Sm(thf)2] and [Cp*Fe(η5-E5)] (E = P, As) are linked by ring-opened thf molecule were obtained and structurally characterized.
Dynamic nitroxyl formation in the ammonia oxidation on platinum via Eley–Rideal reactions
Authors: Yao Yunxi , Giapis Konstantinos P.
Published: October 2016

Simultaneous production of HNO, NO, and OH via Eley–Rideal reactions during the dynamic oxidation of ammonia on Pt surfaces.
Catalytic hydrogenation of CO2 to methanol in a Lewis pair functionalized MOF
Authors: Ye Jingyun , Johnson J. Karl
Published: October 2016

Capture and conversion of CO2 to methanol using a renewable source of H2 is a promising way to reduce net CO2 emissions while producing valuable fuels.
Fate of microplastics and other small anthropogenic litter (SAL) in wastewater treatment plants depends on unit processes employed
Authors: Michielssen Marlies R. , Michielssen Elien R. , Ni Jonathan , Duhaime Melissa B.
Published: October 2016

The accumulation of microplastics (plastic particles less than 5 mm) and similarly sized small anthropogenic litter (SAL; e.g., cellulosic products manufactured from natural material) in aquatic ecosystems is a growing concern.
Ru/ceria-catalyzed direct formylation of amines and CO to produce formamides
Authors: Wang Yehong , Zhang Jian , Chen Haijun , Zhang Zhixin , Zhang Chaofeng , Li Mingrun , Wang Feng
Published: October 2016

We herein report a new strategy of directly converting amines and CO to formamides with 100% atom utilization efficiency.