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The amount of data generated worldwide is constantly increasing. These data come from a wide variety of sources and systems, are processed differently, have a multitude of formats, and are stored in an untraceable and unstructured manner, predominantly in natural language in data silos. This problem can be equally applied to the heterogeneous research data from materials science and engineering. In this domain, ways and solutions are increasingly being generated to smartly link material data together with their contextual information in a uniform and well-structured manner on platforms, thus making them discoverable, retrievable, and reusable for research and industry. Ontologies play a key role in this context. They enable the sustainable representation of expert knowledge and the semantically structured filling of databases with computer-processable data triples.
In this perspective article, we present the project initiative Materials-open-Laboratory (Mat-o-Lab) that aims to provide a collaborative environment for domain experts to digitize their research results and processes and make them fit for data-driven materials research and development. The overarching challenge is to generate connection points to further link data from other domains to harness the promised potential of big materials data and harvest new knowledge.
Here we report on the accumulation of ground-state NH molecules in a static magnetic trap. A pulsed supersonic beam of NH (a1Δ) radicals is produced and brought to a near standstill at the center of a quadrupole magnetic trap using a Stark decelerator. There, optical pumping of the metastable NH radicals to the X3Σ- ground state is performed by driving the spin-forbidden A3Π ← a1Δ transition, followed by spontaneous A → X emission. The resulting population in the various rotational levels of the ground state is monitored via laser induced fluorescence detection. A substantial fraction of the groundstate NH molecules stays confined in the several milliKelvin deep magnetic trap. The loading scheme allows one to increase the phase-space density of trapped molecules by accumulating packets from consecutive deceleration cycles in the trap. In the present experiment, accumulation of six packets is demonstrated to result in an overall increase of only slightly over a factor of two, limited by the trap-loss and reloading rates.
Microscope slide collections represent extremely valuable depositories of research material in a natural history, forensic, veterinary, and medical context. Unfortunately, most mounting media of these slides deteriorate over time, with the reason for this not yet understood at all. In this study, Raman spectroscopy, ultraviolet–visible (UV–Vis) spectroscopy, and different types of light microscopy were used to investigate the ageing behaviour of naturally aged slides from museum collections and the experimentally aged media of Canada balsam and Permount™, representing a natural and a synthetic resin, respectively, with both being based on mixtures of various terpenes. Whereas Canada balsam clearly revealed chemical ageing processes, visible as increasing colouration, Permount™ showed physical deterioration recognisable by the increasing number of cracks, which even often impacted a mounted specimen. Noticeable changes to the chemical and physical properties of these mounting media take decades in the case of Canada balsam but just a few years in the case of Permount™. Our results question whether or not Canada balsam should really be regarded as a mounting medium that lasts for centuries, if its increasing degree of polymerisation can lead to a mount which is no longer restorable.
A novel ionization scheme for ambient mass spectrometry is presented and discussed. Desorption and ionization are achieved by a quasi-continuous laser induced plasma (LIP) ignited in front of the atmospheric pressure interface of a time-of-flight mass spectrometer. This setup comprises the advantages of i) an ambient probe, ii) electro neutrality, iii) low power consumption, iv) a sufficient duty cycle, v) a ubiquitous plasma medium (air) and vi) high sensitivity caused by the high electron number densities.
The plasma properties and operating conditions are investigated to understand the processes that lead to the formation of molecular ions. Comprehensive studies include optical emission spectroscopy, shadowgraphic shockwave visualization and time-of-flight mass spectrometry investigations. The observed MS signal (including reagent-ion signal, as well as analyte spectra) closely resembles the ionization behavior of other electrically-driven plasma-based ionization sources, such as DBD, LTP or DART. Conversely that means that although LIPs are commonly known to have temperatures way above 10.000 K and thus efficiently atomize and ionize molecules, MS spectra were obtained that showed the formation of intact molecular ions.
For an insight into the LIP properties the optical emission of the LIP is examined and exhibits a pronounced degree of dissociation into atomic and ionic species, which reflects the higher temperature and electron density inside a LIP. Accordingly, rather elemental (ICP-type) than molecular spectra should be expected. However due to the absence of such ions, we conclude that the analyte does not enter the hot center of the plasma itself. Moreover, the initial, highly-excited plasma species react cascade-like to lower energetic species via reactive collision with the surrounding atmosphere, which can then subsequently ionize molecules of interest. The concept potentially involves charge transfer, proton transfer, electron impact and photoionization.
These assumptions are confirmed via the shadowgraphs of the expanding shockwave around the LIP. An effective spatial separation between the two regions is maintained by concentrically expanding pressure waves resulting in a strongly unidirectional diffusion. Additionally, the strictly outbound matter transport suggests a rarefaction inside the plasma region for each plasma event.
A novel ionization scheme for ambient mass spectrometry is presented and discussed. Desorption and ionization are achieved by a quasi-continuous laser induced plasma (LIP) ignited in front of the atmospheric pressure interface of a time-of-flight mass spectrometer. This setup comprises the advantages of i) an ambient probe, ii) electro neutrality, iii) low power consumption, iv) a sufficient duty cycle, v) a ubiquitous plasma medium (air) and vi) high sensitivity caused by the high electron number densities.
The plasma properties and operating conditions are investigated to understand the processes that lead to the formation of molecular ions. Comprehensive studies include optical emission spectroscopy, shadowgraphic shockwave visualization and time-of-flight mass spectrometry investigations. The observed MS signal (including reagent-ion signal, as well as analyte spectra) closely resembles the ionization behavior of other electrically-driven plasma-based ionization sources, such as DBD, LTP or DART. Conversely that means that although LIPs are commonly known to have temperatures way above 10.000 K and thus efficiently atomize and ionize molecules, MS spectra were obtained that showed the formation of intact molecular ions. For an insight into the LIP properties the optical emission of the LIP is examined and exhibits a pronounced degree of dissociation into atomic and ionic species, which reflects the higher temperature and electron density inside a LIP. Accordingly, rather elemental (ICP-type) than molecular spectra should be expected. However due to the absence of such ions, we conclude that the analyte does not enter the hot center of the plasma itself. Moreover, the initial, highlyexcited plasma species react cascade-like to lower energetic species via reactive collision with the surrounding atmosphere, which can then subsequently ionize molecules of interest. The concept potentially involves charge transfer, proton transfer, electron impact and photoionization.
These assumptions are confirmed via the shadowgraphs of the expanding shockwave around the LIP. An effective spatial separation between the two regions is maintained by concentrically expanding pressure waves resulting in a strongly unidirectional diffusion. Additionally, the strictly outbound matter transport suggests a rarefaction inside the plasma region for each plasma event.
Laser-induced plasma (LIP) has drawn significant amount of attentions in the past decades, particular in elemental analyses for solid or liquid samples. Through proper focusing of the highly energetic laser beam, the plasma can also be ignited in the ambient air, where airborne analytes can be ionized. Such an effect enabled the use of airborne LIP as an ambient ionization source for mass spectrometric analyses. In contrast to other ambient desorption/ionization sources, airborne LIP does not require a specific discharge medium or expensive gas stream. Meanwhile, the airborne LIP produces reagent ion species for both proton-transfer and charge-transfer reactions in addition to the vacuum ultraviolent photons that are capable of promoting single photon ionization, which can be utilized to ionize polar and non-polar analytes. In order to gauge the analytical performance of airborne LIP, it is critical to understand the undergoing chemistry and physics during and after the plasma formation.
Due to the ambient nature of airborne LIP, the variations of air composition and flow strongly affect the plasma behaviors. Preliminary result suggested the addition of a laminar flow of nitrogen gas favored the formation of protonated species (MH+) against the molecular ones (M+). Although the gas addition approach cannot fully tune the ionization process towards the specific production of pseudo-molecular species versus molecular ones, the alternation of molecular ion formation can be used for analyte recognitions through post processing of the ion patterns. The pulsed character of the used lasers makes the reagent ion equilibrium both transient- and highly fluid-dynamically controlled. The acoustic shock-waves induced by the airborne LIP get affected by an applied gas streams towards the plasma center, influencing the molecular-ion and ion-ion interactions in the near proximity of the plasma.
To understand the airborne LIP formation, the temporally and spatially resolved optical emission spectra were recorded. The results will be correlated to time-resolved mass-spectrometric investigations of the ion profile during different stages of the plasma formation. As one example, the formation of pyrylium ion originating from aromatic compounds will be highlighted.
A novel direct sampling ionisation scheme for ambient mass spectrometry is presented. Desorption and ionisation are achieved by a quasi-continuous laser induced plasma in air. Since there are no solid or liquid electrodes involved the ion source does not suffer from chemical interferences or fatigue originating from erosive burning or from electrode consumption. The overall plasma maintains electro-neutrality, minimising charge effects and accompanying long term drift of the charged particles trajectories. In the airborne plasma approach the ambient air not only serves as the plasma medium but at the same time also slows down the nascent ions via collisional cooling. Ionisation of the analyte molecules does not occur in the plasma itself but is induced by interaction with nascent ionic fragments, electrons and/or far ultraviolet photons in the plasma vicinity. At each individual air-spark an audible shockwave is formed, providing new reactive species, which expands concentrically and, thus, prevents direct contact of the analyte with the hot region inside the plasma itself. As a consequence the interaction volume between plasma and analyte does not exceed the threshold temperature for thermal dissociation or fragmentation. Experimentally this indirect ionisation scheme is demonstrated to be widely unspecific to the chemical nature of the analyte and to hardly result in any fragmentation of the studied molecules. A vast ensemble of different test analytes including polar and non-polar hydrocarbons, sugars, low mass active ingredients of pharmaceuticals as well as natural biomolecules in food samples directly out of their complex matrices could be shown to yield easily accessible yet meaningful spectra. Since the plasma medium is humid air, the chemical reaction mechanism of the ionisation is likely to be similar to other ambient ionisation techniques.
The visualization of index-of-refraction (IoR) distribution is one of the common methods to investigate fluid flow or pressure fields. While schlieren and shadowgraphy imaging techniques are widely accepted, their inherent limitations often lead to difficulties in elucidating the IoR distribution and extracting the true IoR information from the resulting images. While sophisticated solutions exist, the IoR-gradient-to-image was achieved by purposely introducing a commonly avoided “defect” into the optical path of a conventional coincident schlieren/shadowgraphy setup; the defect is a combination of slight defocusing and the use of non-conjugate optical components. As such, the method presented in this work is referred to as defocusing shadowgraphy, or DF-shadowgraphy. While retaining the ease of a conventional schlieren/shadowgraphy geometry, this DF approach allows direct visualization of complicated resonant acoustic fields even without any data processing. For instance, the transient acoustic fields of a common linear acoustic resonator and a two-dimensional one were directly visualized without inversion. Moreover, the optical process involved in DF-shadowgraphy was investigated from a theoretical perspective. A numerical solution of the sophisticated impulse response function was obtained, which converts the phase distortion into intensity distributions. Based on this solution, the IoRs of various gas streams (e.g., CO2 and isopropanol vapor) were determined from single images.
A commercially available airbrush gun as a new source for spray ionization is presented. It is best operated employing moderate stagnation pressures, resulting in a sonic gas flow. A mass spectrometric investigation on the amino acid lysine and several peptides reveals that this inexpensive approach results in reproducible mass spectra. The ion patterns strongly resemble the results from other studies obtained with custom made sonic spray vaporizers. The patterns as well resemble the mass spectra recorded with electrospray devices. For a better understanding of the vaporization process, the mass spectrometry experiments are accompanied by laser induced fluorescence experiments. Inverse Abel transform of the obtained fluorescence maps allows the determination of the full 3D distribution of the spray cone. Furthermore, via exploitation of the solvatochromism of the used dye the solvation state distribution can be visualized. In addition, expansion parameters like droplet size and velocity are obtained by laser stroboscopy. The experiments demonstrate that the analyte is hardly desolvated throughout the expansion. This indicates a subsequent vaporization of the residual solvent in the intermediate pressure region of the mass spectrometer.
An airborne laser plasma is suggested as an ambient ion source for mass spectrometry. Its fundamental physical properties, such as an excellent spatial and temporal definition, high electron and ion densities and a high effective cross section in maintaining the plasma, make it a promising candidate for future applications. For deeper insights into the plasma properties, the optical plasma emission is examined and compared to mass spectra. The results show a seemingly contradictory behavior, since the emitted light reports the plasma to almost entirely consist of hot elemental ions, while the corresponding mass spectra exhibit the formation of intact molecular species. Further experiments, including time- resolved shadowgraphy, spatially resolved mass spectrometry, as well as flow-dependent emission spectroscopy and mass spectrometry, suggest the analyte molecules to be formed in the cold plasma vicinity upon interaction with reactive species formed inside the hot plasma center. Spatial separation is maintained by concentrically expanding pressure waves, inducing a strong unidirectional diffusion. The accompanying rarefaction inside the plasma center can be compensated by a gas stream application. This replenishing results in a strong increase in emission brightness, in local reactive species concentration, and eventually in direct mass spectrometric sensitivity. To determine the analytical performance of the new technique, a comparison with an atmospheric pressure chemical ionization (APCI) source was conducted. Two kitchen herbs, namely, spearmint and basil, were analyzed without any sample pretreatment. The presented results demonstrate a considerably higher sensitivity of the presented laser-spark ionization technique.
Among the large number of new ambient ionization schemes in the last few years, dielectric barrier discharge (DBD) has witnessed special attention. In this contribution a versatile dual mode DBD is introduced and characterized by means of optical emission spectroscopy and time-of-flight mass spectrometry. A direct comparison of the individual results from spectroscopy, spectrometry and transient current/voltage consumption gives evidence for the existence of two individual operational mechanisms. The first is driven by rapid transient changes in the potential difference between the two electrodes over time (usually denoted as the homogeneous mode), while the second is caused at high static potential differences (leading to filamentary discharges). The transient versus steady-state characteristics of the individual discharge origin suggest the driving force for the current flow to be inductive and capacitive, respectively. In most cases of dielectric barrier plasmas both discharge types coexist as competitive ion formation channels, however, detailed plasma characteristics of DBDs operated under different conditions allow for a clear distinction of the individual contributions. In this way, two characteristic product channels for the ionization of ambient water could be observed resulting in the generation of either preferentially protonated water clusters or ammonium water clusters. Careful tuning of the operation parameters of the discharge device allows an operation predominated by either of the two modes. As a consequence, facile switching into the desired operational mode results in either protonated molecules or ammoniated molecules of the analyte. Plasma characteristics for both moieties were evaluated and cross-correlated on the basis of several factors including: the production of reagent ions, the individual appearance of current/voltage profiles, UV/Vis spectroscopy, voltage and flux dependence and the individual response to test compounds. Although the filamentary mode has been already discussed in the literature to induce fragmentation processes, no experimental evidence for analyte dissociation could be found in the case of the test compounds used
Mass spectrometry is applied as a tool for the elucidation of molecular structures. This premises that gas-phase structures reflect the original geometry of the analytes, while it requires a thorough understanding and investigation of the forces controlling and affecting the gas-phase structures. However, only little is known about conformational changes of oligonucleotides in the gas phase. In this study, a series of multiply charged DNA oligonucleotides (n¼15–40) has been subjected to a comprehensive tandem mass spectrometric study to unravel transitions between different ionic gas-phase structures. The nucleobase sequence and the chain length were varied to gain insights into their influence on the geometrical oligonucleotide organization. Altogether, 23 oligonucleotides were analyzed using collision-induced fragmentation. All sequences showed comparable correlation regarding the characteristic collision energy. This value that is also a measure for stability, strongly correlates with the net charge density of the precursor ions. With decreasing charge of the oligonucleotides, an increase in the fragmentation energy was observed. At a distinct charge density, a deviation from linearity was observed for all studied species, indicating a structural reorganization. To corroborate the proposed geometrical change, collisional cross-sections of the oligonucleotides at different charge states were determined using ion mobility-mass spectrometry. The results clearly indicate that an increase in charge density and thus Coulomb repulsion results in the transition from a folded, compact form to elongated structures of the precursor ions. Our data show this structural transition to depend mainly on the charge density, whereas sequence and size do not have an influence.
For many analytical purposes, direct laser ionization of liquids is desirable. Several studies on supported droplets, free liquid jets, and ballistically dispensed microdroplets have been conducted, yet detailed knowledge of the underlying mechanistics in ion formation is still missing. This contribution introduces a simple combination of IR-MALDI mass spectrometry and an acoustical levitation device for contactless confinement of the liquid sample. The homebuilt ultrasonic levitator supports droplets of several millimeters in diameter. These droplets are vaporized by a carbon dioxide laser in the vicinity of the atmospheric pressure interface of a time of flight mass spectrometer. The evaporation process is studied by high repetition rate shadowgraphy experiments elucidating the ballistic evaporation of the sample and revealing strong confinement of the vapor by the ultrasonic field of the trap. Finally, typical mass spectra for pure glycerol/water matrix and lysine as an analyte are presented with and without the addition of trifluoracetic acid, and the ionization mechanism is briefly discussed. The technique is a promising candidate for a reproducible mass spectrometric detection scheme for the field of microfluidics.
A wide range of aspects concerning microscope slides, their preparation, long-time storage, curatorial measures in collections, deterioration, restoration, and study is summarized based on our own data and by analyzing more than 600 references from the 19th century until 2016, 15 patents, and about 100 Materials Safety Data Sheets. Information from systematic zoology, conservation sciences, chemistry, forensic sciences, pathology, paleopathology, applied sciences like food industry, and most recent advances in digital imaging are put together in order to obtain a better understanding of which and possibly why mounting media and coverslip seals deteriorate, how slides can be salvaged, which studies may be necessary to identify a range of ideal mounting media, and how microscope studies can benefit from improvements in developmental biology and related fields. We also elaborate on confusing usage of concepts like that of maceration and of clearing.
The chemical ingredients of a range of mounting media and coverslip seals are identified as much as possible from published data, but this information suffers in so far as the composition of a medium is often proprietary of the manufacturer and may vary over time. Advantages, disadvantages, and signs of deterioration are documented extensively for these media both from references and from our own observations. It turns out that many media degrade within a few years, or decades at the latest, except Canada balsam with a documented life-time of 150 years, Euparal with a documented life-time of 50 years, and glycerol-paraffin mounts sealed with Glyceel, which represents almost the only non-deteriorating and easily reversible mount. Deterioration reveals itself as a yellowing in natural resins and as cracking, crystallization, shrinkage on drying or possibly on loss of a plasticizer, detachment of the coverslip, segregation of the ingredients in synthetic polymers, as well as continued maceration of a specimen to a degree that the specimen virtually disappears. Confusingly, decay does not always appear equally within a collection of slides mounted at the same time in the same medium. The reasons for the deteriorative processes have been discussed but are controversial especially for gum-chloral media. Comparing data from conservation sciences, chemical handbooks, and documented ingredients, we discuss here how far chemical and physical deterioration probably are inherent to many media and are caused by the chemical and physical properties of their components and by chemicals dragged along from previous preparation steps like fixation, chemical maceration, and physical clearing. Some recipes even contain a macerating agent, which proceeds with its destructive work. We provide permeability data for oxygen and water vapor of several polymers contained in mounting media and coverslip seals. Calculation of the penetration rate of moisture in one example reveals that water molecules reach a specimen within a few days up to about a month; this lays to rest extensive discussions about the permanent protection of a mounted specimen by a mounting medium and a coverslip seal.
Based on the ever growing evidence of the unsuitable composition and application of many, and possibly almost all, mounting media, we strongly encourage changing the perspective on microscope slides from immediate usability and convenience of preparation towards durability and reversibility, concepts taken from conservation sciences. Such a change has already been suggested by Upton (1993) more than 20 years ago for gum-chloral media, but these media are still encouraged nowadays by scientists. Without a new perspective, taxonomic biology will certainly lose a large amount of its specimen basis for its research within the next few decades. Modern non-invasive techniques like Raman spectroscopy may help to identify mounting media and coverslip seals on a given slide as well as to understand ageing of the media. An outlook is given on potential future studies.
In order to improve the situation of existing collections of microscope slides, we transfer concepts as per the Smithsonian Collections Standards and Profiling System, developed for insect collections more than 25 years ago, to collections of slides. We describe historical and current properties and usage of glass slides, coverslips, labels, and adhesives under conservational aspects. In addition, we summarize and argue from published and our own experimental information about restorative procedures, including re-hydration of dried-up specimens previously mounted in a fluid medium. Alternatives to microscope slides are considered. We also extract practical suggestions from the literature concerning microscope equipment, cleaning of optical surfaces, health risks of immersion oil, and recent improvements of temporary observation media especially in connection with new developments in digital software.
DNA and locked nucleic acid (LNA) were characterized as single strands, as well as double stranded DNA-DNA duplexes and DNA-LNA hybrids using tandem mass spectrometry with collision-induced dissociation. Additionally, ion mobility spectrometry was carried out on selected species. Oligonucleotide duplexes of different sequences – bearing mismatch positions and abasic sites of complementary DNA 15-mers – were investigated to unravel general trends in their stability in the gas phase. Single stranded LNA oligonucleotides were also investigated with respect to their gas phase behavior and fragmentation upon collision-induced dissociation. In contrast to the collision-induced dissociation of DNA, almost no base loss was observed for LNAs. Here, backbone cleavages were the dominant dissociation pathways. This finding was further underlined by the need for higher activation energies. Base losses from the LNA strand were also absent in fragmentation experiments of the investigated DNA-LNA hybrid duplexes. While DNA-DNA duplexes dissociated easily into single stranded fragments, the high stability of DNA-LNA hybrids resulted in predominant fragmentation of the DNA part rather than the LNA, while base losses were only observed from the DNA single strand of the hybrid.
Optical elemental analysis in the gas phase typically relies on electrically driven plasmas. As an alternative approach, laser-induced plasmas (LIPs) have been suggested but have so far been only scarcely used.
Here, a novel signal enhancement strategy for laser-based airborne plasma optical Emission spectroscopy for gas phase analytics is presented. In contrast to an electrically driven plasma, in the laser-induced analogue dynamic matter transport equilibrium builds up. The latter results in a rarefied density regime in the plasma core itself, surrounded by an area of compressed matter. The central rarefaction leads to a decrease in plasma intensity and analyte number density, both of which are detrimental for analytical purposes. Since the repetitive ignition of LIPs is a transient process, a restoration of the former gaseous medium by other dynamically equilibrated diffusion processes would be favourable. The presented combination of an airborne LIP and an ultrasonic acoustic resonator yields a fourfold signal enhancement while the Background contribution of ubiquitous air is at the same time effectively suppressed. Since the entire enhancement effect occurs without contact, no additional sources for abrasive sample contamination are introduced.
A spatial heterodyne spectrometer (SHS) was combined with a flame atomic absorption (FAA) setup to reveal the analytical potential of SHS to be used as a tool for high-resolution atomic absorption studies. Exploiting the advances in modern computational power, the spectral information encoded in the interferograms was extracted and separated. Consequently, unseeable interferometric ingredients corresponding to narrow-band absorption lines could be recognized. Namely, a single SHS absorption interferogram simultaneously contains both illumination background and absorption information, which can be distinguished through a series of computational steps. In the examples given by this work, we demonstrate the construction of Na absorbance spectra from a single image. The described single-image approach can be used to investigate highly dynamic systems, whereby background collections can be obviated.
The therapeutic dose of lithium (Li) compounds, which are widely used for the treatment of psychiatric and hematologic disorders, is close to its toxic level; therefore, drug monitoring protocols are mandatory. Herein, we propose a fast, simple, and low-cost analytical procedure for the traceable determination of Li concentration in human serum, based on the monitoring of the Li isotope dilution through the partially resolved isotope shift in its electronic transition around 670.80 nm using a commercially available high-resolution continuum source graphite furnace atomic absorption spectrometer. With this technique, serum samples only require acidic digestion before analysis. The procedure requires three measurements—an enriched 6Li spike, a mixture of a certified standard solution and spike, and a mixture of the sample and spike with a nominal 7Li/6Li ratio of 0.82. Lanthanum has been used as an internal spectral standard for wavelength correction. The spectra are described as the linear superposition of the contributions of the respective isotopes, each consisting of a spin-orbit doublet, which can be expressed as Gaussian components with constant spectral position and width and different relative intensity, reflecting the isotope ratio in the sample. Both the spectral constants and the correlation between isotope ratio and relative band intensity have been experimentally obtained using commercially available materials enriched with Li isotopes. The Li characteristic mass (mc) obtained corresponds to 0.6 pg. The procedure has been validated using five human serum certified reference materials. The results are metrologically comparable and compatible to the certified values. The measurement uncertainties are comparable to those obtained by the more complex and expensive technique, isotope dilution mass spectrometry.