bluuebunny/crossref_metadata_2025_split huggingface dataset:
Application of Chemical Cross‐Linking/Mass Spectrometry to Probe Protein Structures
Authors: Leitner Alexander 
Published: December 2016

Abstract
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

AbstractMultidimensional (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.
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.
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.
A
NanoWorkshop
Toolkit for in situ Nanoassembly and Nanocharacterization
Authors: Jonathan Smith Andrew , Rummel Andreas , Schock Klaus , Kleindiek Stephan 
Published: December 2016

Fitting a Focussed Ion Beam / Scanning Electron Microscope (FIB/SEM) with a micromanipulators as well as a range of plug‐in tools transforms the microscope from a device purely used for observation to a workstation where materials can be manipulated, assembled, characterized, etc. ‐ at the micron, sub‐micron, and nano scale.
Typical applications include harvesting, arranging, and mechanically testing nanowires, nano tubes, and CNTs. It is also often of great interest to characterize nanowires, nanotubes, CNTs, etc. electrically.
Electrical and mechanical tests as well as structural investigations on MEMS devices are also commonly performed tasks.
This work will present a number of different experiments performed inside SEM or FIB/SEM tools. Among these are pick and place operations on sub‐micron sized particles, mechanical testing of nanowires and CNTs as well as in situ thermal experiments.
One of the described experiments entails mounting a strand of CNTs to a force measurement cantilever inside an SEM and subsequently performing a tensile experiment on the strand of CNTs. The CNTs are mounted to the force measurement cantilever using a special vacuum compatible adhesive. The adhesive can be applied in situ using a fine tip on the end of a micromanipulator. The tip is dipped into a small droplet of the adhesive in order to wet it. Next, some adhesive is transferred to the force measurement cantilever. In an additional step, some adhesive is used to extract a strand of CNTs from a large bundle. The extracted CNTs are brought into contact to the wetted force measurement cantilever and the adhesive is cured using the electron beam. Finally, the a force measurement is performed revealing the CNTs tensile strength.
Precise atomic column position measurements using ISTEM
Authors: H W van den Bos Karel , F Krause Florian , Béché Armand , Verbeeck Johan , Rosenauer Andreas , Van Aert Sandra 
Published: December 2016

Nowadays, high angle annular dark field (HAADF) scanning transmission electron microscopy (STEM) is one of the most popular materials' characterisation techniques because of its ability to provide direct structural images at the atomic resolution [1]. Recently, Rosenauer et al. proposed a new imaging technique called imaging STEM (ISTEM) combining the conventional TEM imaging with STEM illumination [2]. This new, spatially incoherent imaging mode is particularly interesting as it provides direct structural images and visualisation of light elements, while it is robust towards chromatic aberrations. In this work, the ISTEM and STEM precision with which atomic column positions can be measured in a quantitative manner are compared.
In HAADF STEM imaging, statistical parameter estimation theory is an excellent tool to quantitatively extract structure parameters [3]. Here, an empirical model is fitted to an experimental image by optimising a criterion of goodness of fit. In this model, the shape of an atomic column is described by a Gaussian peak. The parameters of this empirical model can be linked to the unknown structure parameters of the material under study. The precision with which those parameters can be measured is mainly determined by the presence of shot noise and scan noise in the images. While post‐processing techniques reduce both effects [4,5], scan noise errors and probe instabilities have no influence in the ISTEM imaging mode as images for all probe positions are integrated. Therefore, it is expected that without the use of post‐processing techniques, atomic column positions can be measured more precisely for ISTEM imaging as compared to STEM imaging.

This assumption is tested on experimental images of PbTiO
3
. The ISTEM image in Fig. 1a clearly resolves the light oxygen columns, while in the HAADF STEM image, Fig. 2a, these columns cannot be resolved. In order to extract the atomic column positions, Gaussian models are fitted to both images, shown in Figs. 1b and 2b. The precision with which individual column positions can be estimated is determined by calculating the standard deviation on the distance between the columns (Fig. 3). These results confirm that atomic column positions are measured more precise for ISTEM as compared to ADF STEM imaging. Furthermore, it demonstrates that the position of individual light atomic columns, like oxygen columns in the present example, can be estimated with a precision in the picometer range.

In conclusion, it is shown that ISTEM is a very promising technique for precise measurements of atomic column positions.
In situ observation of heat‐induced degradation of perovskite solar cells
Authors: Divitini Giorgio , Cacovich Stefania , Matteocci Fabio , Cina' Lucio , Carlo Aldo Di , Midgley Paul , Ducati Caterina 
Published: December 2016

The use of perovskite materials (particularly methylammonium lead iodide) in solar cells has become very attractive due to the fast increase in reported power conversion efficiencies over the last few years, leading to values above 20%. While this value is competitive with established photovoltaic technologies, the stability of perovskite‐based solar cells is still insufficient for commercial applications. In particular, it is very well known that some components, including the perovskite layer and the hole transporter, can degrade when exposed to a combination of heat and moisture. In situ TEM is an ideal tool for investigating such degradation and understanding the phenomena underpinning it.
In this work [1,2] we prepare methylammonium lead iodide cells using different approaches from the literature (with the perovskite conversion carried out in single‐ and double‐step in glovebox, in air or in vacuum); we prepare TEM cross‐sectional samples using focused ion beam milling.
For each cell, we carry out scanning TEM imaging and EDX elemental mapping (shown in Figure 1) as they are heated in situ in the TEM. This is a procedure that requires careful control over the temperature and the electron dose. To that aim we exploit recent advances in TEM‐related technology, such as Silicon Drift Detectors (SDD) for EDX, which collect energy‐dispersed X‐ray spectra with a good yield, and stable MEMS heaters, enabling the temperature to be cycled quickly and reproducibly. Moreover, we employ multivariate analysis (principal component analysis, PCA) to increase the signal‐to‐noise ratio of the spectral maps.

Cross‐sectional views acquired after heating are reported in Figure 2. We do not observe changes in the morphology or the elemental distribution in the perovskite layer for heating up to 150°C for short times (employing a heating ramp with 30' steps every 25°C). Since the ex‐situ heating of the same samples above 90°C causes a significant decay in cell performance, we attribute such decay to the degradation of the charge transport properties of the hole transporter (spiro‐OMeTAD in this case). Increasing the temperature further, different decomposition patterns emerge for the perovskite layer. In samples that had not been exposed to air, elemental migration of lead and iodine results in the formation of aggregates, which EDX suggests might be PbI
2
, clustering on the FTO electrode. In the sample exposed to air, a different phenomenon occurs – instead of forming aggregates, the elemental species diffuse from the perovskite into the hole transporter. This is visible both as an increased contrast in the high‐angle annular dark field images (HAADF) and as features in the EDX spectra; we hypothesise that the trapped moisture within the cell might be hindering the formation of PbI
2
and make elemental diffusion more favourable.