Complete determination of plant tissues based only on auto‐fluorescence and the advanced image analysis – study of needles and stamens

Proper determination of tissues is one of the challenging problems in modern medicine and histology. Currently, interpretation of the results mainly depends on the experience of a histologist, leading to high percentage of results misinterpretation. Bearing in mind potential application, we proposed the set of procedures that allow us to obtain precise, mathematically determined parameters for tissue discrimination. First, the method was tested on simulated set of images and compared with several other algorithms. As the set of experimentally obtained input data, auto‐fluorescence images of needle cross sections (Picea omorika) and stamens of common centaury (Centaurium erythraea) were used. Determination of cell types is based on inherent features of plant cells – auto‐fluorescence. As each cell type consists of various fluorescent components in different quantities for each type of tissue, its integral emission spectrum can be used as the fingerprint for identification. Cross sections were imaged using four sets of filters for detection of fluorescence (both excitation and emission). Such filter set is standard equipment for most fluorescence microscopes. One additional image was transmission image using the same optics. By applying ℓ₀‐norm‐constrained nonnegative matrix factorization in a space induced by explicit feature maps, it is possible to identify up to 11 tissues in needles and five in stamens (actual number of tissues). In comparison to other image analysis methods, the greatest advantage is the fact that the number of extracted components significantly exceeds the number of initial images while most other techniques can extract only as much components as the number of initial images. Copyright © 2015 John Wiley & Sons, Ltd.     

Surface orientation characterisation of rough mc‐silicon surfaces by confocal microscopy and EBSD

For many semiconductor and photovoltaic applications the quality of substrate surfaces is an important requirement for the development of new devices. Therefore, methods are needed to analyse the surface structure in detail. In the following a new method is described that allows a fast analysis of as‐cut or artificially modified and textured surfaces. It uses laser confocal microscopy images. Therefrom the orientation of small surface elements are detected and depicted in an orientation distribution function of surface normals. The method is applied to as‐sawn mc‐silicon surfaces. It will be shown that it is also possible to determine the grain orientation for grains near 〈111〉 crystal direction by this method. The combination of electron backscatter diffraction and orientation distribution function analysis enables the detailed investigation of surface elements of an anisotropic etched silicon wafer. Inhomogeneity of surface textures can easily and rapidly be visualised by this method. Copyright © 2012 John Wiley & Sons, Ltd.     

Summary of ISO/TC 201 standard: ISO 18115‐2:2013 – surface chemical analysis – vocabulary – terms used in scanning probe microscopy

Amendments have been made to International Standard ISO 18115‐2:2010, extending the number of terms and, in a few cases where usage has changed, incorporating revisions. Part 2 covers 277 terms used in scanning probe microscopy as well as 98 acronyms. The terms cover words or phrases used in describing the samples, instruments and theoretical concepts involved. © 2014 Crown copyright. Surface and Interface Analysis © 2014 John Wiley & Sons, Ltd.     

Summary of ISO/TC 201 Standard: ISO 18115‐2:2010 – Surface chemical analysis – Vocabulary—Terms used in scanning probe microscopy

This International Standard revises ISO 18115:2001 and the two subsequent amendments by bringing the material up to date and by separating the general terms and terms used in spectroscopy into Part 1 and terms relating to scanning probe microscopy into Part 2. This part, Part 2, covers 227 terms used in scanning probe microscopy as well as 86 acronyms. The terms cover words or phrases used in describing the samples, instruments and theoretical concepts involved in surface chemical analysis. Copyright © 2012 Crown copyright.     

Summary of ISO/TC 201 Standard: ISO 18115‐1:2010 – surface chemical analysis – vocabulary – general terms and terms used in spectroscopy

This International Standard revises ISO 18115:2001 and the two subsequent amendments by bringing the material up to date and separating out the general terms and terms used in spectroscopy into Part 1, and terms relating to scanning probe microscopy into Part 2. This part, Part 1, covers 548 terms used in Auger electron spectroscopy, elastic peak electron spectroscopy, reflected electron energy loss spectroscopy, secondary ion mass spectrometry, ultra‐violet photoelectron spectroscopy, X‐ray photoelectron spectroscopy, and so on, as well as 52 acronyms. The terms cover words or phrases used in describing the samples, instruments, and theoretical concepts involved in surface chemical analysis. Copyright © 2012 Crown copyright.     

Two‐way and three‐way approaches to ultra high performance liquid chromatography–photodiode array dataset for the quantitative resolution of a two‐component mixture containing ciprofloxacin and ornidazole

Two‐way and three‐way calibration models were applied to ultra high performance liquid chromatography with photodiode array data with coeluted peaks in the same wavelength and time regions for the simultaneous quantitation of ciprofloxacin and ornidazole in tablets. The chromatographic data cube (tensor) was obtained by recording chromatographic spectra of the standard and sample solutions containing ciprofloxacin and ornidazole with sulfadiazine as an internal standard as a function of time and wavelength. Parallel factor analysis and trilinear partial least squares were used as three‐way calibrations for the decomposition of the tensor, whereas three‐way unfolded partial least squares was applied as a two‐way calibration to the unfolded dataset obtained from the data array of ultra high performance liquid chromatography with photodiode array detection. The validity and ability of two‐way and three‐way analysis methods were tested by analyzing validation samples: synthetic mixture, interday and intraday samples, and standard addition samples. Results obtained from two‐way and three‐way calibrations were compared to those provided by traditional ultra high performance liquid chromatography. The proposed methods, parallel factor analysis, trilinear partial least squares, unfolded partial least squares, and traditional ultra high performance liquid chromatography were successfully applied to the quantitative estimation of the solid dosage form containing ciprofloxacin and ornidazole.     

Selective Sensing of Fe3+ and Al3+ Ions and Detection of 2,4,6‐Trinitrophenol by a Water‐Stable Terbium‐Based Metal–Organic Framework

A water‐stable luminescent terbium‐based metal–organic framework (MOF), {[Tb(L₁)_1.5(H₂O)] ? 3 H₂O}_n (Tb‐MOF), with rod‐shaped secondary building units (SBUs) and honeycomb‐type tubular channels has been synthesized and structurally characterized by single‐crystal X‐ray diffraction. The high green emission intensity and the microporous nature of the Tb‐MOF indicate that it can potentially be used as a luminescent sensor. In this work, we show that Tb‐MOF can selectively sense Fe³⁺ and Al³⁺ ions from mixed metal ions in water through different detection mechanisms. In addition, it also exhibits high sensitivity for 2,4,6‐trinitrophenol (TNP) in the presence of other nitro aromatic compounds in aqueous solution by luminescence quenching experiments.     

Coordination Polymer Flexibility Leads to Polymorphism and Enables a Crystalline Solid–Vapour Reaction: A Multi‐technique Mechanistic Study

Despite an absence of conventional porosity, the 1D coordination polymer [Ag₄(O₂C(CF₂)₂CF₃)₄(TMP)₃] ( 1 ; TMP=tetramethylpyrazine) can absorb small alcohols from the vapour phase, which insert into Ag?O bonds to yield coordination polymers [Ag₄(O₂C(CF₂)₂CF₃)₄(TMP)₃(ROH)₂] ( 1‐ROH ; R=Me, Et, iPr). The reactions are reversible single‐crystal‐to‐single‐crystal transformations. Vapour‐solid equilibria have been examined by gas‐phase IR spectroscopy (K=5.68(9)×10^?5 (MeOH), 9.5(3)×10^?6 (EtOH), 6.14(5)×10^?5 (iPrOH) at 295 K, 1 bar). Thermal analyses (TGA, DSC) have enabled quantitative comparison of two‐step reactions 1‐ROH → 1 → 2 , in which 2 is the 2D coordination polymer [Ag₄(O₂C(CF₂)₂CF₃)₄(TMP)₂] formed by loss of TMP ligands exclusively from singly‐bridging sites. Four polymorphic forms of 1 ( 1‐A^LT , 1‐A^HT , 1‐B^LT and 1‐B^HT ; HT=high temperature, LT=low temperature) have been identified crystallographically. In situ powder X‐ray diffraction (PXRD) studies of the 1‐ROH → 1 → 2 transformations indicate the role of the HT polymorphs in these reactions. The structural relationship between polymorphs, involving changes in conformation of perfluoroalkyl chains and a change in orientation of entire polymers (A versus B forms), suggests a mechanism for the observed reactions and a pathway for guest transport within the fluorous layers. Consistent with this pathway, optical microscopy and AFM studies on single crystals of 1‐MeOH / 1‐A^HT show that cracks parallel to the layers of interdigitated perfluoroalkyl chains develop during the MeOH release/uptake process.     

Summary of ISO/TC 201 Standard: XX ISO 18118: 2004 – Surface chemical analysis – Auger electron spectroscopy and X‐ray photoelectron spectroscopy – Guide to the use of experimentally determined relative sensitivity factors for the quantitative analysis of homogeneous materials

ISO 18118 provides guidance on the measurement and use of experimentally determined relative sensitivity factors for the quantitative analysis of homogeneous materials by Auger electron spectroscopy (AES) and X‐ray photoelectron spectroscopy (XPS). This article provides a brief summary of this International Standard. Copyright © 2005 John Wiley & Sons, Ltd.     

Summary of ISO/TC 201 Standard: ISO 18115‐1:2013 – Surface chemical analysis – Vocabulary – General terms and terms used in spectroscopy

Amendments have been made to International Standards Organization (ISO) 18115‐1:2010 extending the number of terms and, in a few cases where usage has changed, incorporating revisions. Part 1 covers 600 terms used in Auger electron spectroscopy, elastic peak electron spectroscopy, reflected electron energy loss spectroscopy, SIMS, UPS, XPS, etc. as well as 75 acronyms. The terms cover words or phrases used in describing the samples, instruments and theoretical concepts involved in surface chemical analysis. © 2014 Crown copyright. Surface and Interface Analysis © 2014 John Wiley & Sons, Ltd.     

SECM and SKPFM Studies of the Local Corrosion Mechanism of Al Alloys – A Pathway to an Integrated SKP‐SECM System

Scanning Kelvin Probe Force Microscopy and Scanning Electrochemical Microscopy were applied for the investigation of localized corrosion on heterogeneous aiming on the investigation of the possible correlation between the local surface potential differences, measured by the Kelvin probe technique in ambient conditions, and corrosion during immersion in a corrosive electrolyte. A model sample mimicking the interaction of Al and Cu in Al alloys was chosen to demonstrate the complementary nature of the information received from SKPFM and SECM. The necessary prerequisites for a future integration of SKP and SECM into a single set‐up are discussed.     

Identification of substances migrating from plastic baby bottles using a combination of low‐resolution and high‐resolution mass spectrometric analysers coupled to gas and liquid chromatography

This work presents a strategy for elucidation of unknown migrants from plastic food contact materials (baby bottles) using a combination of analytical techniques in an untargeted approach. First, gas chromatography (GC) coupled to mass spectrometry (MS) in electron ionisation mode was used to identify migrants through spectral library matching. When no acceptable match was obtained, a second analysis by GC‐(electron ionisation) high resolution mass spectrometry time of flight (TOF) was applied to obtain accurate mass fragmentation spectra and isotopic patterns. Databases were then searched to find a possible elemental composition for the unknown compounds. Finally, a GC hybrid quadrupole‐TOF‐MS with an atmospheric pressure chemical ionisation source was used to obtain the molecular ion or the protonated molecule. Accurate mass data also provided additional information on the fragmentation behaviour as two acquisition functions with different collision energies were available (MS^E approach). In the low‐energy function, limited fragmentation took place, whereas for the high‐energy function, fragmentation was enhanced. For less volatile unknowns, ultra‐high pressure liquid chromatography‐quadrupole‐TOF‐MS was additionally applied. Using a home‐made database containing common migrating compounds and plastic additives, tentative identification was made for several positive findings based on accurate mass of the (de)protonated molecule, product ion fragments and characteristic isotopic ions. Six illustrative examples are shown to demonstrate the modus operandi and the difficulties encountered during identification. The combination of these techniques was proven to be a powerful tool for the elucidation of unknown migrating compounds from plastic baby bottles. Copyright © 2015 John Wiley & Sons, Ltd.     

Summary of ISO/TC 201 Standard: XXIV,ISO 24237:2005—surface chemical analysis—X‐ray photoelectron spectroscopy—repeatability and constancy of intensity scale

This International Standard specifies a method for evaluating the repeatability and constancy of the intensity scale of X‐ray photoelectron spectrometers, for general analytical purposes, using non‐monochromated Al or Mg X‐rays or monochromated Al X‐rays. It is only applicable to instruments that incorporate an ion gun for sputter cleaning. It is not intended to be a calibration of the intensity/energy response function (Seah MP. J. Electron Spectrosc. 1995; 71: 191; http://www.npl.co.uk/nanoanalysis/a1calib.html [2006]). That calibration may be made by the instrument manufacturer or other organization. The present method provides data to evaluate and confirm the accuracy with which the intensity/energy response function remains constant with instrument usage. Guidance is given to some of the instrument settings that may affect this constancy. Copyright © 2006 John Wiley & Sons, Ltd.     

Imaging surfaces of nano‐scale roughness by atomic force microscopy with carbon nanotubes as tips: a comparative study

Accurate knowledge of the nanoroughness of surfaces is crucial for many applications related to optics, electronics or tribology. Although atomic force microscopy (AFM) can image surfaces with a nanometre spatial resolution, the finite size of standard tips means that pores, pits or grooves with dimensions similar to or smaller than the tip apex will not be accurately imaged. Furthermore, standard tips are made of silicon or silicon nitride and are prone to wear. Mitigation may arise from the availability of AFM tips with a carbon nanotube (CNT) at their foremost end. This study compares the imaging performance of ultrasharp Si tips, CNT AFM tips prepared by a Langmuir‐Blodgett (LB) technique, and of CNT AFM tips prepared by a chemical vapour deposition (CVD) technique. The free length of the CNT AFM tips is in the range 80–200 and 600–750 nm, respectively. A polycrystalline niobium film surface is imaged that shows nanoroughness. The measurements demonstrate that CNT AFM tips allow excellent imaging if the scan parameters are adjusted very carefully. Nevertheless, in some cases distortions are found. The measured average grain diameter is 19.9 ± 3.6 nm in the case of a CNT AFM tip made by the LB technique, and 18.0 ± 3.3 nm in the case of a CNT AFM tip made by CVD. In addition to cross‐sections of topography images, also the power spectral density (PSD) is analyzed. An empirical approach for the readout of the characteristic length is suggested that involves the first derivative of the decadic logarithm of the PSD. Copyright © 2011 John Wiley & Sons, Ltd.     

Quantitative analysis of trace levels of surface contamination by X‐ray photoelectron spectroscopy. Part II: Systematic uncertainties and absolute quantification

We discuss analyses of trace levels of surface contamination using X‐ray photoelectron spectroscopy (XPS). The problem of quantifying common sources of statistical and systematic uncertainties for these measurements is formulated in terms of the needs of extreme ultraviolet lithography, but the results and conclusions are applicable to a broad range of XPS applications. We quantify the systematic uncertainties introduced by particular cases of overlapping peaks on different substrate structures by simulating measured spectra with the National Institute of Standards and Technology Database for the Simulation of Electron Spectra for Surface Analysis (SESSA). One example demonstrates that the relative atomic concentrations of trace elements such as S, P, and halogens on a Ru surface could be dramatically overestimated if the fitting of the overlapping Ru 3d and C 1s peaks excludes the contribution from carbon. We also show how spectra generated by SESSA can be compared with measured spectra to determine absolute amounts of surface impurities on layered samples of the type used for extreme ultraviolet lithography. We provide estimates of the total uncertainty for such measurements by considering the systematic limitations of SESSA and the statistical uncertainties of the measurements. The same procedure can be employed for other multilayered materials. Finally, we describe two approaches for converting XPS detection limits for an elemental impurity in an elemental matrix to the corresponding detection limits for the impurity as a thin film on the surface of the matrix material.     

Synthesis and crystal structure of a new Cu3Au‐type ternary phase in the Au–In–Pd system: distribution of atoms over crystallographic positions

A new Cu₃Au‐type ternary phase (τ phase) is found in the AuPd‐rich part of the Au–In–Pd system. It has a broad homogeneity range based on extensive (Pd,Au) and (In,Au) replacement, with the composition varying between Au_17.7In_25.3Pd_57.0 and Au_50.8In_16.2Pd_33.0. The occupancies of the crystallographic positions were studied by single‐crystal X‐ray diffraction for three samples of different composition. The sites with mm symmetry are occupied by atoms with a smaller scattering power than the atoms located on 4/mmm sites. Two extreme structure models were refined. Within the first, the occupation type changes from (Au,In,Pd)₃(Pd,In) to (Au,Pd)₃(In,Pd,Au) with an increase in the Au gross content. For the second model, the occupation type (Au,In,Pd)₃(Pd,Au) remains essentially unchanged for all Au concentrations. Although the diffraction data do not allow the choice of one of these models, the latter model, where Au substitutes In on 4/mmm sites, seems to be preferable, since it agrees with the fact that the homogeneity range of the τ phase is inclined to the Au corner and provides the same occupation type for all the studied samples of different compositions.     

An effective method for determining the ingredients of Shuanghuanglian formula in blood samples using high‐resolution LC–MS coupled with background subtraction and a multiple data processing approach

Shuanghuanglian formula (SF) is a combination of Flos lonicerae japonicae, Radix scutellariae, and Fructus forsythiae, commonly used to treat viral or bacterial infections. However, the constituents absorbed into the blood after oral administration of SF are difficult to determine and thus remain unclear. Here, we report the application of an accurate background subtraction and multiple data processing approach (Bs‐Mpa) for the comprehensive detection of compounds of SF in vivo. A sensitive and reliable ultra‐performance LC coupled with ESI quadrupole TOF MS (UPLC–ESI‐Q‐TOF‐MS) approach coupled with Bs‐Mpa, which is implemented in the Strip tool from UPLC to remove nonrelated ion signals from accurate mass LC–MS data, was established to characterize the chemical constituents and rat metabolites of SF. In the loading plot of the principal component analysis, 68 ions of interest were extracted from blood samples, among them, 39 absorbed prototype components of SF and 29 metabolites were identified in vivo. It is concluded that the integrative Bs‐Mpa method can be successfully applied for the rapid discovery of multiple components from a traditional Chinese medicine. The above challenge was addressed by using the proposed Bs‐Mpa method and it was particularly suitable for applying to the global characterization of the constituents or metabolites in rat blood after oral administration of other well‐known formulae.     

Evaluation of a multi‐fiber exchange solid‐phase microextraction system and its application to on‐site sampling

Until recently, multiple solid‐phase microextraction fibers could not be automatically desorbed in a single gas chromatographic sequence without manual intervention from an operator. This drawback had been a critical issue, particularly during the analysis of numerous on‐site samples taken with various fiber assemblies. Recently, a Multi‐Fiber Exchange system, designed to overcome this flaw found in other commercially available autosamplers, was released. In the current research, a critical evaluation of the Multi‐Fiber Exchange system performance in terms of storage stability and long‐term operation is presented. It was established in the course of our research that the Multi‐Fiber Exchange system can operate continuously and precisely for multiple extraction/injection cycles. However, when the effect of residence time of commercial fibers on the Multi‐Fiber Exchange tray was evaluated, results showed that among the evaluated fiber coatings, Carboxen/polydimethylsiloxane was the only coating capable of efficient storage on the tray for up to 24 h after field sampling without suffering significant loss of analytes (≤10% for benzene, toluene, ethylbenzene, o‐xylene, decane, and limonene). Additionally, the system capability for high‐throughput analysis was demonstrated by the unattended desorption of multiple fibers after on‐site sampling of toluene, indoor air levels, in a polymer synthesis lab.