bluuebunny/crossref_metadata_2025 huggingface dataset:
Dormancy-specific imprinting underlies maternal inheritance of seed dormancy in Arabidopsis thaliana
Authors: Piskurewicz Urszula , Iwasaki Mayumi , Susaki Daichi , Megies Christian , Kinoshita Tetsu , Lopez-Molina Luis
Published: December 2016

Mature seed dormancy is a vital plant trait that prevents germination out of season. In Arabidopsis, the trait can be maternally regulated but the underlying mechanisms sustaining this regulation, its general occurrence and its biological significance among accessions are poorly understood. Upon seed imbibition, the endosperm is essential to repress the germination of dormant seeds. Investigation of genomic imprinting in the mature seed endosperm led us to identify a novel set of imprinted genes that are expressed upon seed imbibition. Remarkably, programs of imprinted gene expression are adapted according to the dormancy status of the seed. We provide direct evidence that imprinted genes play a role in regulating germination processes and that preferential maternal allelic expression can implement maternal inheritance of seed dormancy levels.
Angiopoietin receptor Tie2 is required for vein specification and maintenance via regulating COUP-TFII
Authors: Chu Man , Li Taotao , Shen Bin , Cao Xudong , Zhong Haoyu , Zhang Luqing , Zhou Fei , Ma Wenjuan , Jiang Haijuan , Xie Pancheng , Liu Zhengzheng , Dong Ningzheng , Xu Ying , Zhao Yun , Xu Guoqiang , Lu Peirong , Luo Jincai , Wu Qingyu , Alitalo Kari , Koh Gou Young , Adams Ralf H , He Yulong
Published: December 2016

Mechanisms underlying the vein development remain largely unknown. Tie2 signaling mediates endothelial cell (EC) survival and vascular maturation and its activating mutations are linked to venous malformations. Here we show that vein formation are disrupted in mouse skin and mesentery when Tie2 signals are diminished by targeted deletion of Tek either ubiquitously or specifically in embryonic ECs. Postnatal Tie2 attenuation resulted in the degeneration of newly formed veins followed by the formation of haemangioma-like vascular tufts in retina and venous tortuosity. Mechanistically, Tie2 insufficiency compromised venous EC identity, as indicated by a significant decrease of COUP-TFII protein level, a key regulator in venogenesis. Consistently, angiopoietin-1 stimulation increased COUP-TFII in cultured ECs, while Tie2 knockdown or blockade of Tie2 downstream PI3K/Akt pathway reduced COUP-TFII which could be reverted by the proteasome inhibition. Together, our results imply that Tie2 is essential for venous specification and maintenance via Akt mediated stabilization of COUP-TFII.
Cryo-EM structures of the autoinhibited E. coli ATP synthase in three rotational states
Authors: Sobti Meghna , Smits Callum , Wong Andrew SW , Ishmukhametov Robert , Stock Daniela , Sandin Sara , Stewart Alastair G
Published: December 2016

A molecular model that provides a framework for interpreting the wealth of functional information obtained on the E. coli F-ATP synthase has been generated using cryo-electron microscopy. Three different states that relate to rotation of the enzyme were observed, with the central stalk’s ε subunit in an extended autoinhibitory conformation in all three states. The Fo motor comprises of seven transmembrane helices and a decameric c-ring and invaginations on either side of the membrane indicate the entry and exit channels for protons. The proton translocating subunit contains near parallel helices inclined by ~30° to the membrane, a feature now synonymous with rotary ATPases. For the first time in this rotary ATPase subtype, the peripheral stalk is resolved over its entire length of the complex, revealing the F1 attachment points and a coiled-coil that bifurcates toward the membrane with its helices separating to embrace subunit a from two sides.
An integrative systematic revision and biogeography ofRhynchocalamussnakes (Reptilia, Colubridae) with a description of a new species from Israel
Authors: Tamar Karin , Šmíd Jiří , Göçmen Bayram , Meiri Shai , Carranza Salvador
Published: December 2016

Background

The colubrid snakes of the genusRhynchocalamusare seldom studied and knowledge of their ecology and life history is scarce. Three species ofRhynchocalamusare currently recognized,R. satunini(from Turkey eastwards to Iran),R. arabicus(Yemen and Oman), andR. melanocephalus(from the Sinai Peninsula northwards to Turkey). All are slender, secretive, mainly nocturnal and rare fossorial snakes. This comprehensive study is the first to sample all knownRhynchocalamusspecies in order to review the intra-generic phylogenetic relationships and historical biogeography of the genus.

Methods

We revised the systematics ofRhynchocalamususing an integrative approach and evaluated its phylogeography. The phylogenetic position within the Colubridae and the phylogenetic relationships within the genus were inferred using 29 individuals belonging to the three known species, with additional sampling of two other closely-related genera,MuhtarophisandLytorhynchus. We analysed three mitochondrial (12S,16S, cytb) and one nuclear (c-mos) gene fragments. Phylogenetic trees were reconstructed using maximum likelihood and Bayesian inference methods; the latter method also used to provide the first time-calibrated molecular phylogeny of the genus. We generated a nuclear network and carried out a topology test and species delimitation analysis. Morphological comparisons were used to differentiate among species and to describe a new species from Israel. The studied material was comprised of 108 alcohol-preserved specimens, 15 photographs, and data from the literature for the examination of 17 mensural, 14 meristic, and two categorical characters.

Results

The molecular results supportRhynchocalamusas monophyletic, and as having split from its sister genusLytorhynchusduring the Late Oligocene. The three recognized species ofRhynchocalamuscomprise four independently evolving groups. The molecular results reveal that the genus began to diverge during the Middle Miocene. We revealed that the best-studied species,R. melanocephalus,is paraphyletic. A population, formally ascribed to this species, from the Negev Mountain area in southern Israel is phylogenetically closer toR. arabicusfrom Oman than to the northern populations of the species from Israel, Syria and Turkey. Herein we describe this population as a new species:Rhynchocalamus dayanaesp. nov.

Discussion

We identify four species withinRhynchocalamus:R. satunini, R. arabicus, R. melanocephalus, andR. dayanaesp. nov., the latter, to the best of our knowledge, is endemic to southern Israel. The onset ofRhynchocalamusdiversification is very old and estimated to have occurred during the Middle Miocene, possibly originating in the Levant region. Radiation probably resulted from vicariance and dispersal events caused by continuous geological instability, sea-level fluctuations and climatic changes within the Levant region.
Three new species ofBertolonia(Melastomataceae) from Espírito Santo, Brazil
Authors: Bacci Lucas F. , Amorim André M. , Goldenberg Renato
Published: December 2016

We describe and illustrate three new species ofBertolonia, all endemic to the state of Espírito Santo, Brazil.Bertolonia duasbocaensisandB. macrocalyxoccur close to each other, in the municipalities of Cariacica and Viana.Bertolonia ruschianahas a wider distribution, occurring in the municipalities of Santa Leopoldina, Santa Maria de Jetibá and Santa Teresa. The first two species are classified as critically endangered (CR), and the latter as endangered (EN). We also present an identification key for the species ofBertoloniathat occur in Espírito Santo.
Regional climate engineering by radiation management: Prerequisites and prospects
Authors: Quaas Johannes , Quaas Martin F. , Boucher Olivier , Rickels Wilfried
Published: December 2016

Radiation management (RM), as an option to engineer the climate, is highly controversial and suffers from a number of ethical and regulatory concerns, usually studied in the context of the objective to mitigate the global mean temperature. In this article, we discuss the idea that RM can be differentiated and scaled in several dimensions with potential objectives being to influence a certain climate parameter in a specific region. Some short‐lived climate forcers (e.g., tropospheric aerosols) exhibit strong geographical and temporal variability, potentially leading to limited‐area climate responses. Marine cloud brightening and thinning or dissolution of cirrus clouds could be operated at a rather local scale. It is therefore conceivable that such schemes could be applied with the objective to influence the climate at a regional scale. From a governance perspective, it is desirable to avoid any substantial climate effects of regional RM outside the target region. This, however, could prove impossible for a sustained, long‐term RM. In turn, regional RM during limited time periods could prove more feasible without effects beyond the target area. It may be attractive as it potentially provides the opportunity to target the suppression of some extreme events such as heat waves. Research is needed on the traceability of regional RM, for example, using detection and attribution methods. Incentives and implications of regional RM need to be examined, and new governance options have to be conceived.
Hydrologic and geomorphic changes resulting from episodic glacial lake outburst floods: Rio Colonia, Patagonia, Chile
Authors: Jacquet J. , McCoy S. W. , McGrath D. , Nimick D. A. , Fahey M. , O'kuinghttons J. , Friesen B. A. , Leidich J.
Published: December 2016

Glacial lake outburst floods (GLOFs) are a prominent but poorly understood cryospheric hazard in a warming climate. We quantify the hydrologic and geomorphic response to 21 episodic GLOFs that began in April 2008 using multitemporal satellite imagery and field observations. Peak discharge exiting the source lake became progressively muted downstream. At ~40–60 km downstream, where the floods entered and traveled down the main stem Rio Baker, peak discharges were generally < 2000 m3 s−1, although these flows were still >1–2 times the peak annual discharge of this system, Chile's largest river by volume. As such, caution must be applied to empirical relationships relating lake volume to peak discharge, as the latter is dependent on where this observation is made along the flood path. The GLOFs and subsequent periods of free drainage resulted in > 40 m of incision, the net removal of ~25 × 106 m3 of sediment from the source lake basin, and a nonsteady channel configuration downstream. These results demonstrate that GLOFs sourced from low‐order tributaries can produce significant floods on major main stem rivers, in addition to significantly altering sediment dynamics.
Baby, it's cold outside: Climate model simulations of the effects of the asteroid impact at the end of the Cretaceous
Authors: Brugger Julia , Feulner Georg , Petri Stefan
Published: December 2016

Sixty‐six million years ago, the end‐Cretaceous mass extinction ended the reign of the dinosaurs. Flood basalt eruptions and an asteroid impact are widely discussed causes, yet their contributions remain debated. Modeling the environmental changes after the Chicxulub impact can shed light on this question. Existing studies, however, focused on the effect of dust or used one‐dimensional, noncoupled atmosphere models. Here we explore the longer‐lasting cooling due to sulfate aerosols using a coupled climate model. Depending on aerosol stratospheric residence time, global annual mean surface air temperature decreased by at least 26°C, with 3 to 16 years subfreezing temperatures and a recovery time larger than 30 years. The surface cooling triggered vigorous ocean mixing which could have resulted in a plankton bloom due to upwelling of nutrients. These dramatic environmental changes suggest a pivotal role of the impact in the end‐Cretaceous extinction.
The fate of terrigenous dissolved organic carbon on the Eurasian shelves and export to the North Atlantic
Authors: Kaiser K. , Benner R. , Amon R. M. W.
Published: December 2016

Dissolved lignin phenols, chromophoric dissolved organic matter (CDOM) absorption, and fluorescence were analyzed along cross‐slope mooring locations in the Barents, Laptev, and East Siberian Seas to gain a better understanding of terrigenous dissolved organic carbon (tDOC) dynamics in Arctic shelf seas and the Arctic Ocean. A gradient of river water and tDOC was observed along the continental shelf eastward into the East Siberian Sea. Correlations of carbon‐normalized yields of lignin‐derived phenols supplied by Siberian rivers with river water fractions and known water residence times yielded in situ decay constants of 0.18–0.58 yr−1. Calculations showed ∼50% of annual tDOC discharged by Siberian rivers was mineralized in estuaries and on Eurasian shelves per year indicating extensive removal of tDOC. Bioassay experiments and in situ decay constants indicated a reactivity continuum for tDOC. CDOM parameters and acid/aldehyde ratios of vanillyl (V) and syringyl (S) lignin phenols showed biomineralization was the dominant mechanism for the removal of tDOC. Characteristic ratios of p‐hydroxy (P), S, and V phenols (P/V, S/V) also identified shelf regions in the Kara Sea and regions along the Western Laptev Sea shelf where formation of Low Salinity Halocline Waters (LSHW) and Lower Halocline Water (LHW) occurred. The efficient removal of tDOC demonstrates the importance of Eurasian margins as sinks of tDOC derived from the large Siberian Rivers and confirms tDOC mineralization has a major impact on nutrients budgets, air‐sea CO2 exchange, and acidification in the Siberian Shelf Seas.
Quantifying the stability of planktic foraminiferal physical niches between the Holocene and Last Glacial Maximum
Authors: Waterson A. M. , Edgar K. M. , Schmidt D. N. , Valdes P. J.
Published: December 2016

The application of transfer functions on fossil assemblages to reconstruct past environments is fundamentally based on the assumption of stable environmental niches in both space and time. We quantitatively test this assumption for six dominant planktic foraminiferal species (Globigerinoides ruber (pink), G. ruber (white), Trilobatus sacculifer, Truncorotalia truncatulinoides, Globigerina bulloides, and Neogloboquadrina pachyderma) by contrasting reconstructions of species realized and optimum distributions in the modern and during the Last Glacial Maximum (LGM) using an ecological niche model (ENM; MaxEnt) and ordination framework. Global ecological niche models calibrated in the modern ocean have high predictive performance when projected to the LGM for subpolar and polar species, indicating that the environmental niches of these taxa are largely stable at the global scale across this interval. In contrast, ENMs had much poorer predictive performance for the optimal niche of tropical‐dwelling species, T. sacculifer and G. ruber (pink). This finding is supported by independent metrics of niche margin change, suggesting that niche stability in environmental space was greatest for (sub)polar species, with greatest expansion of the niche observed for tropical species. We find that globally calibrated ENMs showed good predictions of species occurrences globally, whereas models calibrated in either the Pacific or Atlantic Oceans only and then projected globally performed less well for T. sacculifer. Our results support the assumption of environmental niche stability over the last ~21,000 years for most of our focal planktic foraminiferal species and, thus, the application of transfer function techniques for palaeoenvironmental reconstruction during this interval. However, the lower observed niche stability for (sub)tropical taxa T. sacculifer and G. ruber (pink) suggests that (sub)tropical temperatures could be underestimated in the glacial ocean with the strongest effect in the equatorial Atlantic where both species are found today.
On the occurrence of F region irregularities over Haikou retrieved from COSMIC GPS radio occultation and ground‐based ionospheric scintillation monitor observations
Authors: Yu Xiao , Yue Xinan , Zhen Weimin , Xu Jisheng , Liu Dun , Guo Shan
Published: December 2016

In this paper, the amplitude scintillation index (s4) derived from COSMIC (Constellation Observing System for Meteorology, Ionosphere, and Climate) radio occultation (RO) technique and ground‐based Ionospheric Scintillation Monitor (ISM) at Haikou station (geographic latitude: 20.0°N, geographic longitude: 110.3°E, and geomagnetic latitude: 10.02°N) is used to investigate the morphology of F region irregularities in the low latitudes of China. The RO events of tangent point within the range of 10–30°N latitude, 70–160°E longitude, and 150–500 km altitude are adopted to analyze the ionospheric scintillation characteristics. The percentage of ionospheric scintillation occurrence is computed to obtain its diurnal variations, seasonal trends, and the dependence on solar and geomagnetic activities. Based on a statistical analysis of a long‐term period data set (years 2007 to 2013), we found that the ionospheric scintillation occurrence from both techniques show similar variations. After sunset (18 LT), the scintillation occurrence increases rapidly and reaches the maximum 3 h later. Then it decreases rapidly till 04 LT and remains low level during the daytime. The ionospheric scintillation tends to occur more frequently during vernal and autumnal equinoxes, especially in March–April and September–October. The equinoctial asymmetry could be seen clearly from the ground‐based ISM observations. The peak ionospheric scintillation occurrence time varies with seasons. It is reached latest in summer, while in spring it is very close to that in autumn. The nighttime ionospheric scintillation occurrence tends to increase with increasing solar activities. The increasing tendency is more prominent in vernal and autumnal equinoxes than that in summer and winter. In general, the control of geomagnetic activities is apt to inhibit ionospheric scintillation at equinox nighttime. In summer and winter, the geomagnetic activities could either trigger or inhibit the generation of ionospheric irregularities in a much more complicated way. Thus, it can be concluded that the tangent point location does accurately represent the scattering region, at least in an average sense. The RO technique is demonstrated to be a useful tool for remotely sensing the terrestrial ionosphere on a global scale down to the regional scale in terms of scintillation occurrence.
Scattering by a zero‐thickness PEC disk: A new analytically regularizing procedure based on Helmholtz decomposition and Galerkin method
Authors: Lucido Mario , Panariello Gaetano , Schettino Fulvio
Published: December 2016

The aim of this paper is the introduction of a new analytically regularizing procedure, based on Helmholtz decomposition and Galerkin method, successfully employed to analyze the electromagnetic scattering by zero‐thickness perfectly electrically conducting circular disk. After expanding the fields in cylindrical harmonics, the problem is formulated as an electric field integral equation in the vector Hankel transform domain. Assuming as unknowns the surface curl‐free and divergence‐free contributions of the surface current density, a second‐kind Fredholm infinite matrix‐operator equation is obtained by means of Galerkin method with expansion functions reconstructing the expected physical behavior of the surface current density and with closed‐form spectral domain counterparts, which form a complete set of orthogonal eigenfunctions of the most singular part of the integral operator. The coefficients of the scattering matrix are single improper integrals which can be quickly computed by means of analytical asymptotic acceleration technique. Comparisons with the literature have been provided in order to show the accuracy and efficiency of the presented technique.
A new approximate fast method of computing the scattering from multilayer rough surfaces based on the Kirchhoff approximation
Authors: Tian Jiasheng , Tong Jian , Shi Jian , Gui Liangqi
Published: December 2016

In this paper a new approximate fast method of calculating the bistatic‐scattering coefficients of a multilayer structure with random rough interfaces was presented based on the Kirchhoff Approximation (KA) and the electromagnetic theory of stratified media. First, the electromagnetic scattering from a Gauss rough metal or dielectric surface was calculated by KA method and method of moment (MOM), and the effectiveness of KA method was confirmed and verified. Second, a new approximate fast method was presented to calculate electromagnetic scattering from a multilayer‐random‐rough surface based on electromagnetic reflection from multilayer parallel surfaces and KA. The calculated results by the new method were in good agreements with those by MOM, especially near the specular point. Finally, a comparison of the new method and MOM was carried out in consuming computing time, memory resources, and complexity. The comparison indicated that the new approximate method was faster by about 30–150 times than MOM. The new approximate fast method could avoid a large matrix inversion and greatly reduce the computation time and memory resources and thus improve the computational efficiency. It was an effective approximation fast analyzing method of electromagnetic scattering from multilayer rough surfaces.
Biological Samples in Environmental Analysis: Preparation and Cleanup
Authors: Lawton Zachary , Santee Christopher , Bruno Alessanda , Mulligan Christopher , Kong Jason , Foss Jamie , Elliott Noelle , Kero Frank
Published: December 2016

The characterization of biological systems on a molecular level has led to sweeping developments in industries including pharmaceuticals, consumer product manufacturing, and environmental monitoring. The integrity of the sample preparation process is critical for development and discovery efforts in these fields. The art of biological sample preparation is in a perpetual state of evolution where boundaries and limitations reflect the sophistication of contemporary technology. Historical methods required laborious multistep procedures that resulted in analytical measurements with limited throughput and poor detection limits due to analyte losses. Present efforts in the scientific community are moving toward automated methods that require minimal sample volume and minimal sample cleanup. This change in the approach is due to the increasing selectivity of analytical systems that allow analyte separation and purification to be performed online with a variety of detectors. Trends of this nature are consistent with the ‘green chemistry’ efforts, where less solvent consumption provides a more environmental friendly (and cost‐effective) platform for the next stage of development in this field. This article revisits historical approaches and describes current trends in the preparation of biological samples.
Particle‐InducedX‐Ray Emission (PIXE)
Authors: Mandò Pier A. , Przybyłowicz Wojciech J.
Published: December 2016

Particle‐induced X‐ray emission (PIXE) is the most popular among the ion beam analysis (IBA) techniques, which are based on the use of the specimen to be analyzed as a target for a beam of accelerated particles. The detection of the radiation induced by the beam bombardment is then used to discriminate and quantify the presence of the different elements in the specimen. In PIXE, what is exploited is in particular the X‐rays emitted from the target, whose energies are characteristic of the emitting atomic species. After a general, simple description of the main features of PIXE, with a short historical overview and a brief comparison to other X‐ray fluorescence (XRF) techniques, this article covers in greater depth all the specific aspects of this technique. The basic aspects of X‐ray emission from the atoms are first recalled; then, the extraction of quantitative compositional data from thin and thick specimens is explained, and a discussion is given of the excellent performance of PIXE in terms of minimum detection limits (MDLs) and the factors affecting them. A technical description then follows of how proper beams for PIXE are produced and of the experimental set‐ups commonly used. The X‐ray detector characteristics, the electronics for constructing the energy spectra, and the software processes for their deconvolution, leading to the extraction of quantitative data, are then briefly described. The last section surveys the main analytical applications of PIXE in various fields (environmental monitoring, biomedicine, earth sciences, cultural heritage, and materials analysis), with no intent of exhaustiveness but rather with the purpose of focusing on when and why PIXE may be particularly suitable in each of them.
Application of Chemical Cross‐Linking/Mass Spectrometry to Probe Protein Structures
Authors: Leitner Alexander
Published: December 2016

Studying the higher order organization of proteins and protein complexes is important to understand their function and their interactions in biological systems. Cross‐linking/mass spectrometry (XL‐MS) is one of the relatively new methods that complement classical techniques used in structural biology. Chemical cross‐linking (XL) connects reactive groups in proteins and larger assemblies under conditions that preserve their structural integrity. The precise location of the XL sites in the proteins' primary sequences is obtained by subjecting cross‐linked samples to an enzymatic cleavage step and sequencing the resulting cross‐linked peptides by tandem mass spectrometry (MS). XL can provide valuable structural information, ranging from the domain organization of individual proteins to the subunit arrangement of complexes made up of close to 100 individual proteins. This article introduces different XL strategies and describes the analytical workflow of a XL‐MS experiment. It also explains how XL data can be integrated in structural biology projects, illustrated by selected applications.
Multidimensional Capillary Electrophoresis
Authors: Grochocki Wojciech , Markuszewski Michał J. , Quirino Joselito P.
Published: December 2016

Multidimensional (MD) separation is a combination of two or more separation techniques that increases peak capacity. There are two requirements or criteria in MD as suggested by Giddings. First is orthogonality, which means that the separation mechanism in each step must be based on different molecular properties such as size, charge, hydrophobicity, or chirality. Second is that the separation obtained in the first dimension must be preserved in the subsequent dimensions. There are two types of MD separation, comprehensive and heart cutting. In the first type, all compounds present in the mixture are separated and detected, while in the second, only selected fractions in the mixture are analyzed. The connection between the dimensions that must be tight and dead‐volume free is the most important part of an MD separation system. The most common connection was an interface that joins two or more chromatographic columns and/or electrophoretic capillaries. In the case of capillary electrophoresis (CE), there is an alternative strategy to obtain MD separations without the use of an interface. This is the so‐called heart‐cutting MD‐CE in a single capillary or interface‐free MD‐CE. In interface‐free MD‐CE, mobilization of fractions between dimensions is achieved by manipulation of voltage and/or pressure. Although MD‐CE has been developed for more than 15 years, applications to real samples were not as prevalent as those reported for MD gas and liquid chromatography. MD‐CE research reports were on tighter interfaces development as well as sensitivity and performance enhancements in two‐dimension format (2D‐CE). This article is devoted to the wide range of interfaces and interface/interface‐free methods developed for 2D‐CE. CE separation modes used in 2D‐CE were also briefly discussed for readers not familiar with CE.
PH
and concentration effect on the optical absorption properties of porphyrin nanorods functionalized graphene oxide
Authors: Bajjou Omar , Maaza Malik , Khenfouch Mohammed , Mothudi B , LEKALA M , Baitoul Mimouna
Published: December 2016

Graphene oxide (FGO) decorated with nanostructured porphyrin (PN) was synthesized and the interfacial interaction between these two components were investigated by using Scanning electron microscopy (SEM), Transmission electron microscopy (TEM), Raman scattering, Fourier transform infrared (FT‐IR), X‐ray, and Uv‐visible. SEM and TEM showed good dispersion of GO and PN. FT‐ IR and Raman results revealed a π‐π intermolecular interaction confirming the energy/charge transfer. Moreover, X‐ray diffraction study confirmed the intercalation of PN in GO and their disaggregation. The Uv‐visible results showed an important interaction between GO and porphyrin nanorods under pH values and different concentrations resulting an effect on the optical absorption of GO‐PN. The findings presented here are important to achieve the functionalization of graphene oxide with PN for various optoelectronic applications.
RISE
Microscopy: Correlative
R
aman and
SEM
Imaging
Authors: Schmidt Ute , Ayasse Philippe , Hollricher Olaf
Published: December 2016

RISE Microscopy is a novel correlative microscopy technique that combines confocal Raman Imaging and Scanning Electron (RISE) microscopy within one microscope system (Fig. 1a). This unique combination provides distinct advantages with regard to comprehensive sample characterization: electron microscopy is an excellent technique for visualizing surface structures in the nanometer range and confocal Raman imaging is an established method for detection of the chemical and molecular components of a sample with diffraction‐limited resolution. In contrast to conventional systems in which individual Raman spectra are collected from areas several micrometers across, RISE can produce diffraction‐limited confocal Raman images from the same sub‐micron areas investigated by SEM. It can also generate 3D‐images and depth profiles to visualize the distribution of the molecular compounds within a sample volume. Both analytical methods are fully integrated into the RISE microscope. Between measurements a precise translation stage automatically transfers the sample inside the microscope's vacuum chamber and re‐positions it. The RISE software carries out the required parameter adjustments and instrument alignments. The acquired results can then be correlated and the Raman and SEM images overlaid.

The instrument itself as well as example measurements demonstrating the potential of its hybrid approach will be presented. An example of correlative Raman and SEM imaging is presented in Figure 1b‐d, showing the distribution of TiO2 nanoparticles. Fig. 1b shows the SEM image of TiO2, revealing nanoparticles of two different sizes. From the same sample area an array of 150 × 150 complete Raman spectra was acquired with an integration time per spectrum of 37 ms. From this array two distinct spectra were evaluated as shown in Fig. 1c. They show the two polymorphic phases of TiO2: rutile and anatase. The correlative Raman‐SEM image (Fig. 1d) reveals that the large particles correspond to the rutile phase of TiO2, whereas the small particles consist of anatase TiO2, enabling the fine crystallographic structure of the nanoparticles to be differentiated.
Diamond Shape Formation by Spontaneous Aggregation of Silver Clusters in Gels
Authors: Qiang Lin , Jinbing Li , Yongsheng Han , Wei Lin , Qiang Lin
Published: December 2016

Particles aggregations in liquid are of great interest because the random collisions of particles are sometimes accompanied with directional assembly, leading to the formation of highly ordered structures. In this work, we find a easy method to synthesize diamond‐shaped silver nano particles in gels solution. The time dependent structure characterization indicates that these diamond shape particles were assembled by the spontaneous aggregation of tiny primary Ag clusters. Since the diffusion of Ag clusters are limited in viscous gels solution, Each cluster approaching to the aggregates has more sufficient time and space to optimize its location. The minimization of surface free energy leads to a selective binding of two approaching nuclei. The high energy facets of each nuclei have priority to be the receiving surface for aggregation, while the low energy facets are largely exposed in the aggregation, which led to a oriented self‐assembling of Ag clusters. The findings in this paper indicate that the diffusion of building blocks plays an important role in the shape development of materials.
Structural and electrical characterization of
SnO2/CeO2
composite films
Authors: komy Gehan El , komy Gehan el , mandouh Zainab el
Published: December 2016

Pure SnO2 films and CeO2/SnO2 composite films were prepared via sol‐gel technique.The deposited films have film thicknesses range from 90 to 450 nm. the CeO2 added to SnO 2 with the amounts range from 2 mol% to 10 mol%. Polycrystalline structures of the prepared composites powder and films were characterized by x‐ray diffraction analysis. The microstructure of the prepared films was investigated by SEM and TEM respectively. The electrical properties such as the electrical conductivity has been studied. The electrical conductivity was measured as a function of temperature at film thickness 450 nm in case of air and vacuum. The results showed that the SnO2 films are absorptive in case of air. The sensing properties for the prepared films CeO2/SnO2 were characterized and compared with pure SnO2 towards the H2S, CO and LPG gases at room temperature. The sensitivity measured at different film thickness, showed that the film thickness and the film microstructure had noticeable effect on the value of sensitivity. The sensitivity of CeO 2/SnO2 films to CO gas is 0.990 % at a response time for the sample 6 mol% while is 0.995 at 50 sec for sample 6mol%. Through all the previous studies, it was found that there is a capability to improve the gas sensing properties of pure SnO2 by controlling the amount of additive and the good choice of the proper catalytic.
Investigation on Effects of Atorvastatin and Gliclazide Combination Therapy on Male Reproductive System on Streptozotocin‐Induced Diabetic Rats
Authors: Öztaş Ezgi , Yılmaz Tuğba Ekiz , Güzel Elif , Özhan Gül
Published: December 2016

Diabetes Mellitus is characterized by hyperglycemia resulting from abnormalities in insulin secretion, insulin action, or both. It is one of the most serious challanges of 21th century because of both increased prevalence due to industrialization, urbanization and changed lifestyle habits, and socio‐economic impacts. Lifestyle reforms, treatment of oral antidiabetics for glycemic control and of statins to improve the dyslipidemia are crucial in the prevention and treatment of cardiovascular diseases caused by diabetes. Numerous studies proved that diabetes has negative effects on male reproductive system, however, data obtained about atorvastatin and gliclazide are conflicted.

In this study diabetes was induced in 250‐300g young adult male Sprague‐Dawley rats by streptozotocin. Diabetic rats were given atorvastatin, gliclazide and atorvastatin/gliclazide combination by oral gavage for 28 days. Rats were sacrificed on day 28 and hormone analysis in heart blood, morphological evaluations in sperms, light microscopic and ultrastructural examinations in testes were conducted. The obtained data were analyzed by using one‐way ANOVA.

The following results were obtained: (i) diabetes and individually the drugs did not change the hormone levels, while atorvastatin/gliclazide combination reduced the testosterone level, (ii) diabetes decreased sperm count, altered sperm morphology, caused damage in testes and impaired spermatogenesis, (iii) in diabetic rats atorvastatin did not effect sperm count and not improve testes structure, yet ameliorated sperm morphology, (iv) in diabetic rats gliclazide increased sperm count, ameliorated sperm morphology, improved testes structure and spermatogenesis, (v) in diabetic rats atorvastatin/gliclazide combination did not effect sperm count, ameliorated sperm morphology, improved testes structure, however, the improvement has not reached to control level.

In conclusion, data obtained from the study, which the effects of atorvastatin and gliclazide combination in diabetes‐induced damage on male reproductive system were evaluated, is believed to contribute to the literature.
Effect of Systemic
D
Vitamin Supplementation on The Treatment of Full Thickness Articular Cartilage Defects
Authors: Tok Okan , Yılmaz Tuğba Ekiz , Güzel Elif , Aydıngöz Önder , Ünlü Mehmet Can
Published: December 2016

Although the articular cartilage is complex and thin structure it is crucial in the structure and function of the joint. Treatment of the articular cartilage injuries has an significant role in orthopedic practice. Nevertheless, to heal the damaged articular cartilage in hyaline cartilage has not yet been achieved. In this study it was aimed to evaluate not only the effects of vitamin D to the cellular and extracellular matrix components of the articular cartilage but also the effects of vitamin D in the healing of the damaged articular cartilage by the microfracture technique which is frequently used in the treatment of the articular cartilage injuries.

In this study, twenty‐four 18‐months‐old New Zealand rabbits were divided into four groups based on the treatment modality. Standart full thickness articular cartilage defect was applied in the medial femoral condile of the right knee of the all rabbits in the experimental groups. In group 1, only cartilage defect was established. After cartilage defect, in group 2, microfracture technique was applied. In Group 3, vitamin D was supplemented. And in group 4 both microfracture technique and vitamin D supplementation was applied as a treatment method. All animals were sacrified after 16 weeks and were evaluated histologically by ICRS, O′Driscoll and Pineda scoring systems.

It was not observed any improvement in the area of the tissue defect in group 1. In group 2, the recovery of the defected tissue was not pure hyaline cartilage character. It was in the fibrous cartilage structure. Moreover a few round cells resembling chondrocytes were observed especially in the deep part of the healing tissue within the fibrous matrix. In group 3, the healing tissue in the defect area was a fibrous matrix character and although most of the embedded cells in matrix were fibroblast character, the existence of cartilage‐like cells was also recognized. Fibrotic tissue was observed in the superficial part of the healing tissue in the cartilage defect area but also in the deep layer close to the bone hyaline cartilage‐like tissue repairing was detected. Even though all other groups were reached statistically significant better results compared with Group 1, hyalin‐like cartilage repair was observed in Group 4. But this repair degree could not reach statistical significance when compared with Group 2.

As a result, in this study it was shown that the systemic vitamin D supplementation has a positive effect in the treatment of local full‐thickness articular cartilage defects in rabbits. We suggest that more comprehensive and further long term studies are necessary for better understanding of the effects of vitamin D on the articular cartilage defects.
Diamond‐hexagonal silicon ribbons in silicon fins
Authors: Qiu Yang , Bender Hugo , Besien Els Van , Kim Min‐Soo , Richard Olivier , Vandervorst Wilfried
Published: December 2016

The formation of diamond‐hexagonal silicon [1‐3] or Ge [4] is recently reported under different experimental conditions. The dh‐phase has potential for application in optoelectronic devices. A transformation of diamond‐cubic (dc) to diamond‐hexagonal (dh) Si can occur during the wet oxidation treatment applied to densify the oxide fillings between silicon fins in nano‐electronic devices [3]. The phase change is induced by the compressive stress due to the expanding oxide. A similar transformation is reported in Ge nanowires [4] under non‐oxidizing conditions and related to tensile stress of the shrinking oxide filling.

In the finfet structures, the transformation occurs at the base of the outer fins where the lateral stress is the largest and unbalanced between the wide and narrow oxide spacings (Fig. 1). The outer fin moves outward and typically a step and bulge are formed at inner and outer side respectively. In about half of the fins a thin dh‐Si ribbon is formed across the full or partial width of the fin. In the other cases only steps/bulges are present with defect‐free dc‐silicon in between.

To increase the volume of the dh‐Si, in this work the oxidation time is doubled compared to the conditions in [3]. The phase transformation is investigated by high resolution HAADF‐STEM at 120 kV in order to minimize the beam damage during the observations. The longer treatment results in larger steps/bulges (Fig. 1b vs 1a). They are also formed for fins with larger spacings which are not modified in case of the standard oxidation time. The average thickness of the dh‐Si in the outer fins increases by a factor 2‐3 while the transformed material in the outer fins generally becomes a mixture of several Si‐polytypes (Fig. 2b). Additionally the transformation also occurs in the second outer fins with thinner transformed slabs that are pure dh‐Si phase (Fig. 2a). The dh‐Si is epitaxial to the silicon substrate with its c‐axis horizontally across the fins i.e. (110)
dc
//(0001)
dh
and [‐110]
dc
//[2‐1‐10]
dh
.
Both (001)
dc‐Si
and (115)
dc‐Si
interfaces are present which are characterized by stepped (Fig. 3a) and flat (Fig. 3b) interfaces. In the latter case the dh‐lattice is ~4º rotated. The doubling of the oxidation time does not result in further consumption of the silicon on the fin sidewalls (Fig. 1), i.e. the oxidation rate is reduced by the stress which is therefore also not further increasing. The continued transformation of dc to dh‐phase during the prolonged oxidation is therefore a time related phenomenon and indicates a relatively slow process. Stress‐retarded oxidation of Si sidewalls is previously reported in [5]. Although dh‐Si is a metastable phase, once present, it remains stable during subsequent high temperature treatments even up to 1050ºC. As the dh‐Si is situated at the base of the fins it does not affect the transistor structures.
Localized electrical resistance measurements of supported reduced graphene oxide using in‐situ
STM
‐
TEM
Authors: Nilsson Hanna , de Knoop Ludvig , Cumings John , Olsson Eva
Published: December 2016

The tunable electrical properties of reduced graphene oxide (RGO) make it an ideal candidate for many applications including energy storage.
1
However, in order to utilize the material in industrially applied systems it is essential to understand the behavior of the material on the nanoscale, especially how naturally occurring phenomenon like wrinkling effects the electronic transport. While there have been many theoretical investigations on the transport behavior, there are much fewer experimental measurements.
2, 3, 4
Here we used a transmission electron microscope (TEM) with scanning tunneling microscope (STM) probe
in‐situ
holder is used to perform localized electrical measurements on wrinkled, supported RGO flakes. The RGO flakes are deposited onto pre‐patterned Au electrodes on SiN membranes. The flakes are 1–3 layers thick and have lateral dimensions on the order of single micrometers. They are deposited through an ammonium laurate (AL) aqueous surfactant. The TEM allows for observation of the local wrinkling structure of the RGO and simultaneously a Nanofactory STM‐TEM holder is used to perform localized resistance measurements. The holder allows for manipulation with and positioning of Au STM probes, with diameters less than 100 nm, with sub‐nanometer precision. The results show that the overall resistance is low, on the order of single kΩ, if the contact between the probe and the RGO is optimized.  Wrinkles reduce the contact resistance between RGO and the probe. The overall trend for more than 70 measurements is that the total resistance decreases with increasing amount of wrinkles and that the contact resistance dominates the resistance when the probe makes contact with wrinkle free RGO. The sheet resistance and maximal contact resistance for our measurements range from 5–20 kΩ/ and 6‐20E‐7Ω cm
2
, respectively, which falls in line with other scanning probe measurements for graphene and metal contacts.
5, 6
  Here we use a bottom metal contact for the gold electrodes which eliminates the risk of resist contamination and metal doping of the graphene.
7
These measurements give evidence that RGO with large amounts of wrinkling on a substrate can transport electrons well and that it is thus not necessary to produce suspended, pristine graphene in order to benefit from its electrical transport properties.
Investigation of the near fields of sputtered
Au
thin films, used for surface enhanced
R
aman spectroscopy, using the
AFM
and
DDA
Authors: Fitzek Harald , Sattelkow Jürgen , Pölt Peter
Published: December 2016

Surface enhanced Raman spectroscopy (SERS) is a powerful technique that uses metal nanostructures (Au, Ag, Cu) to gain in the best case single molecule sensitivity [1], because these nanostructures give rise to a huge enhancement of the Raman signal of molecules in their immediate vicinity. Most of the enhancement is attributed to the enhancement of the electric field near the surface of the metal, because the Raman signal in this case scales approximately proportional to the fourth power of the electric filed strength [2]. Therefore a good knowledge of both the geometry of the metal nanostructure and the electric near field it causes is crucial for the understanding of a SERS‐substrate.

A combination of AFM and the discrete dipole approximation (DDA) is a promising approach for a better understanding of solid SERS substrates. Using the AFM the geometry of a nanostructure on a flat substrate or a structured surface can be measured very accurately and the DDA is a well‐established method for solving scattering problems for arbitrary shapes, which makes little assumptions about the sample other than the target geometry [3]. Furthermore, using the FFT‐accelerated DDA a very large number of dipoles (>10
6
) can be simulated on a desktop computer [4], allowing for a discretization of comparatively large scatters on a nm scale.

We have written a Matlab program that uses the DDA to calculate the near field from a given AFM image of a nanostructure composed of a single material. The incident field and dielectric constant of the material can be chosen arbitrarily. We have tested the program against Mie theory (fig. 1) and shown that the error of the electric field strength is reasonably small two discretization steps away from the surface (fig.2). The average error of the electric field strength two discretization steps away from the surface is smaller than 5 % (fig.2), with the maximum error being smaller than 10 % (fig.1; apart from the strip around x=0, where the relative error appears large due to |E
Mie
|≈0, but the absolute error is actually very small).

This program is used to simulate SERS substrates, produced by sputtering thin Au‐films on glass slides (fig. 3). These substrates give rise to small but regular (across the substrate) enhancement with enhancement factors of the order of 10
2
– 10
3
. Our goal is to demonstrate the feasibility of using AFM based DDA simulations to study near field enhancement, by predicting the enhancement factors of several substrates.