Highest resolution chemical imaging based on secondary ion mass spectrometry performed on the helium ion microscope.

This paper is a review on the combination between Helium Ion Microscopy (HIM) and Secondary Ion Mass Spectrometry (SIMS), which is a recently developed technique that is of particular relevance in the context of the quest for high-resolution high-sensitivity nano-analytical solutions. We start by giving an overview on the HIM-SIMS concept and the underlying fundamental principles of both HIM and SIMS. We then present and discuss instrumental aspects of the HIM and SIMS techniques, highlighting the advantage of the integrated HIM-SIMS instrument. We give an overview on the performance characteristics of the HIM-SIMS technique, which is capable of producing elemental SIMS maps with lateral resolution below 20 nm, approaching the physical resolution limits, while maintaining a sub-nanometric resolution in the secondary electron microscopy mode. In addition, we showcase different strategies and methods allowing to take profit of both capabilities of the HIM-SIMS instrument (high-resolution imaging using secondary electrons and mass filtered secondary sons) in a correlative approach. Since its development HIM-SIMS has been successfully applied to a large variety of scientific and technological topics. Here, we will present and summarise recent applications of nanoscale imaging in materials research, life sciences and geology.

Significant enhancement of negative secondary ion yields by cluster ion bombardment combined with cesium flooding.

In secondary ion mass spectrometry (SIMS), the beneficial effect of cesium implantation or flooding on the enhancement of negative secondary ion yields has been investigated in detail for various semiconductor and metal samples. All results have been obtained for monatomic ion bombardment. Recent progress in SIMS is based to a large extent on the development and use of cluster primary ions. In this work we show that the enhancement of negative secondary ions induced by the combination of ion bombardment with simultaneous cesium flooding is valid not only for monatomic ion bombardment but also for cluster primary ions. Experiments carried out using C60+ and Ar4000+ bombardment on silicon show that yields of negative secondary silicon ions can be optimized in the same way as by Ga+ and Cs+ bombardment. Both for monatomic and cluster ion bombardment, the optimization does not depend on the primary ion species. Hence, it can be assumed that the silicon results are also valid for other cluster primary ions and that results obtained for monatomic ion bombardment on other semiconductor and metal samples are also valid for cluster ion bombardment. In SIMS, cluster primary ions are also largely used for the analysis of organic matter. For polycarbonate, our results show that Ar4000+ bombardment combined with cesium flooding enhances secondary ion signals by a factor of 6. This can be attributed to the removal of charging effects and/or reduced fragmentation, but no major influence on ionization processes can be observed. The use of cesium flooding for the imaging of cells was also investigated and a significant enhancement of secondary ion yields was observed. Hence, cesium flooding has also a vast potential for SIMS analyses with cluster ion bombardment.

Use of next generation sequencing data to develop a qPCR method for specific detection of EU-unauthorized genetically modified Bacillus subtilis overproducing riboflavin.

BACKGROUND: Recently, the presence of an unauthorized genetically modified (GM) Bacillus subtilis bacterium overproducing vitamin B2 in a feed additive was notified by the Rapid Alert System for Food and Feed (RASFF). This has demonstrated that a contamination by a GM micro-organism (GMM) may occur in feed additives and has confronted for the first time,the enforcement laboratories with this type of RASFF. As no sequence information of this GMM nor any specific detection or identification method was available, Next GenerationSequencing (NGS) was used to generate sequence information. However, NGS data analysis often requires appropriate tools, involving bioinformatics expertise which is not alwayspresent in the average enforcement laboratory. This hampers the use of this technology to rapidly obtain critical sequence information in order to be able to develop a specific qPCRdetection method. METHODS: Data generated by NGS were exploited using a simple BLAST approach. A TaqMan® qPCR method was developed and tested on isolated bacterial strains and on the feed additive directly. RESULTS: In this study, a very simple strategy based on the common BLAST tools that can be used by any enforcement lab without profound bioinformatics expertise, was successfully used toanalyse the B. subtilis data generated by NGS. The results were used to design and assess a new TaqMan® qPCR method, specifically detecting this GM vitamin B2 overproducing bacterium. The method complies with EU critical performance parameters for specificity, sensitivity, PCR efficiency and repeatability. The VitB2-UGM method also could detect the B. subtilis strain in genomic DNA extracted from the feed additive, without prior culturing step. CONCLUSIONS: The proposed method, provides a crucial tool for specifically and rapidly identifying this unauthorized GM bacterium in food and feed additives by enforcement laboratories. Moreover, this work can be seen as a case study to substantiate how the use of NGS data can offer an added value to easily gain access to sequence information needed to develop qPCR methods to detect unknown andunauthorized GMO in food and feed.

Experimental and numerical study of submonolayer sputter deposition of polystyrene fragments on silver for the storing matter technique.

In static secondary ion mass spectrometry (SIMS), quantification and high ionization probabilities are difficult to obtain. The Storing Matter technique has been developed to circumvent these issues and has already been applied to deposit inorganic and organic samples. For organic samples, the effect of fragmentation during sputter deposition and changing coverage on time-of-flight (TOF)-SIMS mass spectra has not been investigated. In this work, polystyrene (PS) was sputter deposited on silver using an argon ion beam in order to investigate these parameters and to get a better control of the whole process. For this purpose, we introduce a multitechnique characterization approach for the submonolayer deposition of PS. Experimental methods (TOF-SIMS, X-ray photoelectron spectroscopy (XPS)) were used in combination with simulations (density functional theory (DFT) calculations) in order to obtain information about the molecular and structural changes and the interactions of organic matter with the metal surface. Alterations of the PS surface and PS sputter deposit as a function of surface coverage and Ar(+) ion fluence are addressed. A major finding is that this approach can be used to identify surface reactions between different fragments on the collector surface. Indeed, in the dynamic regime, the ratio of large to small fragments is increasing although the fragmentation during the sputter deposition should lead to increasingly smaller fragments. Hence, for Storing Matter, the coverage on the collector must be kept low in order to minimize the reactions between fragments and to preserve the information on the original sample.

Ag-organic layered samples for optoelectronic applications: interface width and roughening using a 500 eV Cs+ probe in dynamic secondary ion mass spectrometry.

The performance of organic optoelectronic devices depends a lot on interface structure and width. Dynamic secondary ion mass spectrometry (SIMS) has been widely used to investigate interfaces in classical semiconductor devices and limitations are quite well understood. For low-energy dynamic SIMS on organic optoelectronic devices, sputter-induced diffusion processes and roughness formation have only been investigated sparsely. In this work we use low-energy dynamic SIMS depth profiling on metal-organic multilayered model samples with compositions similar to organic optoelectronic devices to investigate limitations in the calculation of interface widths due to sputter-induced roughness formation. The samples consist of silver and organic compounds (e.g., tris(8-hydroxyquinolinato) aluminum (Alq(3)) and metal phthalocyanines) sequentially deposited by thermal evaporation in vacuum onto a Si substrate. They are analyzed by a 500 eV Cs(+) primary ion beam. Surface roughness at the SIMS crater bottoms is characterized by AFM as a function of crater depth. We find that the roughness in SIMS craters is limited to approximately 1.5 nm, which is much smaller than the interface width of the as-deposited interfaces. Thus, for the studied organic-inorganic interfaces, low-energy dynamic SIMS can yield accurate information about interface morphology, allowing the study of its dependence on sample preparation conditions and its implication on device properties.

Ultralow-energy amorphization of contaminated silicon samples investigated by molecular dynamics.

Ion beam processes related to focused ion beam milling, surface patterning, and secondary ion mass spectrometry require precision and control. Quality and cleanliness of the sample are also crucial factors. Furthermore, several domains of nanotechnology and industry use nanoscaled samples that need to be controlled to an extreme level of precision. To reduce the irradiation-induced damage and to limit the interactions of the ions with the sample, low-energy ion beams are used because of their low implantation depths. Yet, low-energy ion beams come with a variety of challenges. When such low energies are used, the residual gas molecules in the instrument chamber can adsorb on the sample surface and impact the ion beam processes. In this paper we pursue an investigation on the effects of the most common contaminant, water, sputtered by ultralow-energy ion beams, ranging from 50 to 500 eV and covering the full range of incidence angles, using molecular dynamics simulations with the ReaxFF potential. We show that the expected sputtering yield trends are maintained down to the lowest sputtering yields. A region of interest with low damage is obtained for incidence angles around 60° to 75°. We also demonstrate that higher energies induce a larger removal of the water contaminant and, at the same time, induce an increased amorphization, which leads to a trade-off between sample cleanliness and damage.

Responses of patients with cancer to mRNA vaccines depend on the time interval between vaccination and last treatment.

BACKGROUND: Personalized mRNA vaccines are promising new therapeutic options for patients with cancer. Because mRNA vaccines are not yet approved for first-line therapy, the vaccines are presently applied to individuals that received prior therapies that can have immunocompromising effects. There is a need to address how prior treatments impact mRNA vaccine outcomes. METHOD: Therefore, we analyzed the response to BioNTech/Pfizer's anti-SARS-CoV-2 mRNA vaccine in 237 oncology outpatients, which cover a broad spectrum of hematologic malignancies and solid tumors and a variety of treatments. Patients were stratified by the time interval between the last treatment and first vaccination and by the presence or absence of florid tumors and IgG titers and T cell responses were analyzed 14 days after the second vaccination. RESULTS: Regardless of the last treatment time point, our data indicate that vaccination responses in patients with checkpoint inhibition were comparable to healthy controls. In contrast, patients after chemotherapy or cortisone therapy did not develop an immune response until 6 months after the last systemic therapy and patients after Cht-immune checkpoint inhibitor and tyrosine kinase inhibitor therapy only after 12 months. CONCLUSION: Accordingly, our data support that timing of mRNA-based therapy is critical and we suggest that at least a 6-months or 12-months waiting interval should be observed before mRNA vaccination in systemically treated patients.

Influence of water contamination on the sputtering of silicon with low-energy argon ions investigated by molecular dynamics simulations.

Focused ion beams (FIB) are a common tool in nanotechnology for surface analysis, sample preparation for electron microscopy and atom probe tomography, surface patterning, nanolithography, nanomachining, and nanoprinting. For many of these applications, a precise control of ion-beam-induced processes is essential. The effect of contaminations on these processes has not been thoroughly explored but can often be substantial, especially for ultralow impact energies in the sub-keV range. In this paper we investigate by molecular dynamics (MD) simulations how one of the most commonly found residual contaminations in vacuum chambers (i.e., water adsorbed on a silicon surface) influences sputtering by 100 eV argon ions. The incidence angle was changed from normal incidence to close to grazing incidence. For the simulation conditions used in this work, the adsorption of water favours the formation of defects in silicon by mixing hydrogen and oxygen atoms into the substrate. The sputtering yield of silicon is not significantly changed by the contamination, but the fraction of hydrogen and oxygen atoms that is sputtered largely depends on the incidence angle. This fraction is the largest for incidence angles between 70 and 80° defined with respect to the sample surface. Overall, it changes from 25% to 65%.

High-Throughput Direct Writing of Metallic Micro- and Nano-Structures by Focused Ga+ Beam Irradiation of Palladium Acetate Films.

Metallic nanopatterns are ubiquitous in applications that exploit the electrical conduction at the nanoscale, including interconnects, electrical nanocontacts, and small gaps between metallic pads. These metallic nanopatterns can be designed to show additional physical properties (optical transparency, plasmonic effects, ferromagnetism, superconductivity, heat evacuation, etc.). For these reasons, an intense search for novel lithography methods using uncomplicated processes represents a key on-going issue in the achievement of metallic nanopatterns with high resolution and high throughput. In this contribution, we introduce a simple methodology for the efficient decomposition of Pd3(OAc)6 spin-coated thin films by means of a focused Ga+ beam, which results in metallic-enriched Pd nanostructures. Remarkably, the usage of a charge dose as low as 30 µC/cm2 is sufficient to fabricate structures with a metallic Pd content above 50% (at.) exhibiting low electrical resistivity (70 µΩ·cm). Binary-collision-approximation simulations provide theoretical support to this experimental finding. Such notable behavior is used to provide three proof-of-concept applications: (i) creation of electrical contacts to nanowires, (ii) fabrication of small (40 nm) gaps between large metallic contact pads, and (iii) fabrication of large-area metallic meshes. The impact across several fields of the direct decomposition of spin-coated organometallic films by focused ion beams is discussed.

Automated Assessment of Breast Positioning Quality in Screening Mammography.

Screening mammography is a widely used approach for early breast cancer detection, effectively increasing the survival rate of affected patients. According to the Food and Drug Administration's Mammography Quality Standards Act and Program statistics, approximately 39 million mammography procedures are performed in the United States each year. Therefore, breast cancer screening is among the most common radiological tasks. Interpretation of screening mammograms by a specialist radiologist includes primarily the review of breast positioning quality, which is a key factor affecting the sensitivity of mammography and thus the diagnostic performance. Each mammogram with inadequate positioning may lead to a missed cancer or, in case of false positive signal interpretation, to follow-up activities, increased emotional burden and potential over-therapy and must be repeated, requiring the return of the patient. In this study, we have developed deep convolutional neuronal networks to differentiate mammograms with inadequate breast positioning from the adequate ones. The aim of the proposed automated positioning quality evaluation is to assist radiology technologists in detecting poorly positioned mammograms during patient visits, improve mammography performance, and decrease the recall rate. The implemented models have achieved 96.5% accuracy in cranio-caudal view classification and 93.3% accuracy in mediolateral oblique view regarding breast positioning quality. In addition to these results, we developed a software module that allows the study to be applied in practice by presenting the implemented model predictions and informing the technologist about the missing quality criteria.

A new promising oncogenic target (p.C382R) for treatment with pemigatinib in patients with cholangiocarcinoma.

Point mutations of the fibroblast growth factor receptor (FGFR)2 receptor in intrahepatic cholangiocarcinoma (iCC) are mainly of unknown functional significance compared to FGFR2 fusions. Pemigatinib, a tyrosine kinase inhibitor, is approved for the treatment of cholangiocarcinoma with FGFR2 fusion/rearrangement. Although it is hypothesized that FGFR2 mutations may cause uncontrolled activation of the signaling pathway, the data for targeted therapies for FGFR2 mutations remain unclear. In vitro analyses demonstrated the importance of the p.C382R mutation for ligand-independent constitutive activation of FGFR2 with transforming potential. The following report describes the clinical case of a patient diagnosed with an iCC carrying a FGFR2 p.C382R point mutation which was detected in liquid, as well as in tissue-based biopsies. The patient was treated with pemigatinib, resulting in a sustained complete functional remission in fluorodeoxyglucose-positron emission tomography/computed tomography over 10 months to date. The reported case is the first description of a complete functional remission under the treatment with pemigatinib in a patient with p.C383R mutation.

Highly-efficient growth of cobalt nanostructures using focused ion beam induced deposition under cryogenic conditions: application to electrical contacts on graphene, magnetism and hard masking.

Emergent technologies are required in the field of nanoelectronics for improved contacts and interconnects at nano and micro-scale. In this work, we report a highly-efficient nanolithography process for the growth of cobalt nanostructures requiring an ultra-low charge dose (15 µC cm-2, unprecedented in single-step charge-based nanopatterning). This resist-free process consists in the condensation of a ∼28 nm-thick Co2(CO)8 layer on a substrate held at -100 °C, its irradiation with a Ga+ focused ion beam, and substrate heating up to room temperature. The resulting cobalt-based deposits exhibit sub-100 nm lateral resolution, display metallic behaviour (room-temperature resistivity of 200 µΩ cm), present ferromagnetic properties (magnetization at room temperature of 400 emu cm-3) and can be grown in large areas. To put these results in perspective, similar properties can be achieved by room-temperature focused ion beam induced deposition and the same precursor only if a 2 × 103 times higher charge dose is used. We demonstrate the application of such an ultra-fast growth process to directly create electrical contacts onto graphene ribbons, opening the route for a broad application of this technology to any 2D material. In addition, the application of these cryo-deposits for hard masking is demonstrated, confirming its structural functionality.

Technically Representing Clinical Knowledge for Rehabilitation Care.

Providing a suitable rehabilitation after an acute episode or a chronic disease helps people to live independently and enhance their quality of life. However, the continuity of care is often interrupted in the transition from hospital to home. Virtual coaches (VCs) could help these patients to engage in personalized home rehabilitation programs. These coaching systems need also to be fed with procedural precepts in order to work as intended. This, in turn, relates both to properly represent the clinical knowledge (as the VC somehow replaces the formal caregivers that cannot be fully present) as well guide the patient correctly (in order to follow the medically desired procedures given the need for personalisation according to individual needs). Therefore, we outline our technical approach to deal with this. In particular, clinical pathways in terms of semi-formal procedure models in combination with machine learning components processing and powerful user interfaces providing these pathway information and feeding the VC are presented. The system is currently under testing in a participatory design phase called Living Lab. Thus, initial user feedback for further improvements is about to come.

Synthetic Image Rendering Solves Annotation Problem in Deep Learning Nanoparticle Segmentation.

Nanoparticles occur in various environments as a consequence of man-made processes, which raises concerns about their impact on the environment and human health. To allow for proper risk assessment, a precise and statistically relevant analysis of particle characteristics (such as size, shape, and composition) is required that would greatly benefit from automated image analysis procedures. While deep learning shows impressive results in object detection tasks, its applicability is limited by the amount of representative, experimentally collected and manually annotated training data. Here, an elegant, flexible, and versatile method to bypass this costly and tedious data acquisition process is presented. It shows that using a rendering software allows to generate realistic, synthetic training data to train a state-of-the art deep neural network. Using this approach, a segmentation accuracy can be derived that is comparable to man-made annotations for toxicologically relevant metal-oxide nanoparticle ensembles which were chosen as examples. The presented study paves the way toward the use of deep learning for automated, high-throughput particle detection in a variety of imaging techniques such as in microscopies and spectroscopies, for a wide range of applications, including the detection of micro- and nanoplastic particles in water and tissue samples.

Landscape of Biomarkers and Actionable Gene Alterations in Adenocarcinoma of GEJ and Stomach-A Real World Data Analysis.

After several years of negative phase III trials in gastric and esophageal cancer, a significant breakthrough in the treatment of metastatic adenocarcinomas of the gastroesophageal junction (GEJ) and stomach (GC) is now becoming evident with the emerging of precision oncology and implementation of molecular targets in tumor treatment. In addition, new generation studies such as umbrella and basket trials are focused on these molecular targets, which makes an early molecular diagnosis based on IHC/ISH and NGS necessary. The required companion diagnostics of Her2neu overamplification or PD-L1 expression is based on immunohistochemistry (IHC) or additionally in situ hybridization (ISH) in case of an IHC Her2neu score of 2+. However, there are investigator-dependent differences in the assessment of Her2neu amplification and different PD-L1 scoring systems obtained by IHC/ISH. The use of high-throughput technologies such as next-generation sequencing (NGS) holds the potential to standardize the analysis and thus make them more comparable. In the presented study, real-world multigene sequencing data of 72 Caucasian patients diagnosed with metastatic adenocarcinomas of GEJ and stomach were analyzed. In the clinical companion diagnostics, we found ESCAT level I molecular targets in one-third of our patients, which directly determined the therapy. In addition, we found potential targets in 14/72 patients (19.4%) who potentially qualify for precision therapies in corresponding molecular studies. The study highlights the importance of comprehensive molecular profiling for precision treatment of GEJ/GC and indicates that a biomarker evaluation should be performed for all patients with metastatic adenocarcinomas before the initiation of first-line treatment and during second-line or subsequent treatment.

Erratum: De Teresa, J.M. et al. Comparison between Focused Electron/Ion Beam-Induced Deposition at Room Temperature and under Cryogenic Conditions. Micromachines 2019, 10, 799.

In Section 3 [...].

Optimization of Pt-C Deposits by Cryo-FIBID: Substantial Growth Rate Increase and Quasi-Metallic Behaviour.

The Focused Ion Beam Induced Deposition (FIBID) under cryogenic conditions (Cryo-FIBID) technique is based on obtaining a condensed layer of precursor molecules by cooling the substrate below the condensation temperature of the gaseous precursor material. This condensed layer is irradiated with ions according to a desired pattern and, subsequently, the substrate is heated above the precursor condensation temperature, revealing the deposits with the shape of the exposed pattern. In this contribution, the fast growth of Pt-C deposits by Cryo-FIBID is demonstrated. Here, we optimize various parameters of the process in order to obtain deposits with the lowest-possible electrical resistivity. Optimized ~30 nm-thick Pt-C deposits are obtained using ion irradiation area dose of 120 µC/cm2 at 30 kV. This finding represents a substantial increment in the growth rate when it is compared with deposits of the same thickness fabricated by standard FIBID at room temperature (40 times enhancement). The value of the electrical resistivity in optimized deposits (~4 × 104 µΩ cm) is suitable to perform electrical contacts to certain materials. As a proof of concept of the potential applications of this technology, a 100 µm × 100 µm pattern is carried out in only 43 s of ion exposure (area dose of 23 µC/cm2), to be compared with 2.5 h if grown by standard FIBID at room temperature. The ion trajectories and the deposit composition have been simulated using a binary-collision-approximation Monte Carlo code, providing a solid basis for the understanding of the experimental results.

Combining short and long read sequencing to characterize antimicrobial resistance genes on plasmids applied to an unauthorized genetically modified Bacillus.

Antimicrobial resistance (AMR) is a major public health threat. Plasmids are able to transfer AMR genes among bacterial isolates. Whole genome sequencing (WGS) is a powerful tool to monitor AMR determinants. However, plasmids are difficult to reconstruct from WGS data. This study aimed to improve the characterization, including the localization of AMR genes using short and long read WGS strategies. We used a genetically modified (GM) Bacillus subtilis isolated as unexpected contamination in a feed additive, and therefore considered unauthorized (RASFF 2014.1249), as a case study. In GM organisms, AMR genes are used as selection markers. Because of the concern of spread of these AMR genes when present on mobile genetic elements, it is crucial to characterize their location. Our approach resulted in an assembly of one chromosome and one plasmid, each with several AMR determinants of which five are against critically important antibiotics. Interestingly, we found several plasmids, containing AMR genes, integrated in the chromosome in a repetitive region of at least 53 kb. Our findings would have been impossible using short reads only. We illustrated the added value of long read sequencing in addressing the challenges of plasmid reconstruction within the context of evaluating the risk of AMR spread.

A Novel Virtual Coaching System Based on Personalized Clinical Pathways for Rehabilitation of Older Adults-Requirements and Implementation Plan of the vCare Project.

Home-based rehabilitation after an acute episode or following an exacerbation of a chronic disease is often problematic with a clear lack of continuity of care between hospital and home care. Secondary prevention is an essential element of long-term rehabilitation where strategies oriented toward risk reduction, treatment adherence, and optimization of quality of life need to be applied. Frail and sometimes isolated, the patient fails to adhere to the proposed post-discharge clinical pathway due to lack of appropriate clinical, emotional, and informational support. Providing a suitable rehabilitation after an acute episode or a chronic disease is a major issue, as it helps people to live independently and enhance their quality of life. However, as the rehabilitation period usually lasts some months, the continuity of care is often interrupted in the transition from hospital to home. Virtual coaches could help these patients to engage in a personalized rehabilitation program that complies with age-related conditions. These coaches could be a key technology for empowering patients toward increasing their adherence to the care plan and to improve their secondary prevention measures. In this paper, we are presenting a novel virtual coaching system that will address these challenges by combining recent technological advances with clinical pathways, based on joint research and validation activities from researchers from the medical and information and communication technology (ICT) domains.

Comparison between Focused Electron/Ion Beam-Induced Deposition at Room Temperature and under Cryogenic Conditions.

In this contribution, we compare the performance of Focused Electron Beam-induced Deposition (FEBID) and Focused Ion Beam-induced Deposition (FIBID) at room temperature and under cryogenic conditions (the prefix "Cryo" is used here for cryogenic). Under cryogenic conditions, the precursor material condensates on the substrate, forming a layer that is several nm thick. Its subsequent exposure to a focused electron or ion beam and posterior heating to 50 °C reveals the deposit. Due to the extremely low charge dose required, Cryo-FEBID and Cryo-FIBID are found to excel in terms of growth rate, which is typically a few hundred/thousand times higher than room-temperature deposition. Cryo-FIBID using the W(CO)6 precursor has demonstrated the growth of metallic deposits, with resistivity not far from the corresponding deposits grown at room temperature. This paves the way for its application in circuit edit and the fast and direct growth of micro/nano-electrical contacts with decreased ion damage. The last part of the contribution is dedicated to the comparison of these techniques with other charge-based lithography techniques in terms of the charge dose required and process complexity. The comparison indicates that Cryo-FIBID is very competitive and shows great potential for future lithography developments.