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Manganese-doped germanium films are model systems for the study of nanospinodal decomposition into Mn-rich nanostructures and its influence on the electronic and magnetic properties. Here we study a film of Ge0.9Mn0.1 forming self-organized nanocolumns perpendicular to a Ge substrate with high resolution scanning transmission electron microscopy combined with electron energy loss spectroscopy, bulk magnetization, and muon spin rotation and relaxation (μSR) measurements. The Mn-rich nanocolumns approximately form a triangular lattice with no detectable Mn atoms in the matrix. We find that they consist of cores surrounded by shells. The combined analysis of bulk magnetization and μSR data enables us to characterize the electronic and magnetic properties of both the cores and shells. We argue that the discovered phase separation of the columns between a core and a shell is relevant for other transition-metal-doped semiconductors. [ABSTRACT FROM AUTHOR]

Van der Waals heterostructures have been lately intensively studied because they offer a large variety of properties that can be controlled by selecting 2D materials and their sequence in the stack. The exact arrangement of the layers as well as the exact arrangement of the atoms within the layers, both are important for the properties of the resulting device. However, it is very difficult to control and characterize the exact position of the atoms and the layers in such heterostructures, in particular, along the vertical (z) dimension. Recently it has been demonstrated that convergent beam electron diffraction (CBED) allows quantitative three-dimensional mapping of atomic positions in three-dimensional materials from a single CBED pattern. In this study we investigate CBED in more detail by simulating and performing various CBED regimes, with convergent and divergent wavefronts, on a somewhat simplified system: a two-dimensional (2D) monolayer crystal. In CBED, each CBED spot is in fact an in-line hologram of the sample, where in-line holography is known to exhibit high intensity contrast in detection of weak phase objects that are not detectable in conventional in-focus imaging mode. Adsorbates exhibit strong intensity contrast in the zero and higher order CBED spots, whereas lattice deformation such as strain or rippling cause noticeable intensity contrast only in the first and higher order CBED spots. The individual CBED spots can thus be reconstructed as typical in-line holograms, and a resolution of 2.13 Å can in principle be achieved in the reconstructions. We provide simulated and experimental examples of CBED of a 2D monolayer crystal. The simulations show that individual CBED spots can be treated as in-line holograms and sample distributions such as adsorbates, can be reconstructed. Individual atoms can be reconstructed from a single CBED pattern provided the later exhibits high-order CBED spots. The experimental results were obtained in a transmission electron microscope (TEM) at 80 keV on free-standing monolayer hBN containing adsorbates. Examples of reconstructions obtained from experimental CBED patterns at a resolution of 2.7 Å are shown. CBED technique can be potentially useful for imaging individual biological macromolecules, because it provides a relatively high resolution and does not require additional scanning procedure or multiple image acquisitions and therefore allows minimizing the radiation damage. [ABSTRACT FROM AUTHOR]

In this letter, we study the structural and magnetic properties of Ge1-x-ySnxMny films grown on Ge(001) by low temperature molecular beam epitaxy using X-ray diffraction, high resolution transmission electron microscopy, and superconducting quantum interference device. Like in Mn doped Ge films, Mn atoms diffuse during the growth and aggregate into vertically aligned Mn-rich nanocolumns of a few nanometers in diameter. Transmission electron microscopy observations in plane view clearly indicate that the Sn incorporation is not uniform with concentration in Mn rich vertical nanocolumns lower than the detection limit of electron energy loss spectroscopy. The matrix exhibits a GeSn solid solution while there is a Sn-rich GeSn shell around GeMn nanocolumns. The magnetization in Ge1-x-ySnxMny layers is higher than in Ge1-xMnx films. This magnetic moment enhancement in Ge1-x-ySnxMny is probably related to the modification of the electronic structure of Mn atoms in the nanocolumns by the Sn-rich shell, which is formed around the nanocolumns. [ABSTRACT FROM AUTHOR]

Background: Failure of gastrointestinal acute graft- versus -host disease (GI-aGvHD) to respond to steroid therapy is associated with limited further therapeutic options. We aimed to assess the safety and efficacy of the first-in-human use of the pooled allogeneic faecal microbiota, MaaT013, for the treatment of steroid-refractory GI-aGvHD., Methods: This prospective, international, single-arm, phase 2a study reports clinical outcomes from a 24-patient cohort with grade III-IV, steroid refractory GI-aGvHD treated with the pooled allogeneic faecal microbiota MaaT013. MaaT013 involved pooling faecal matter from 3 to 8 screened donors then transplanting the pooled batches into patients to treat GI-aGVHD. The 24 patients were treated in the HERACLES study (Aug 2018 to Nov 2020) at 26 sites in Europe and an additional 52 patients were treated in a compassionate use/expanded access program (EAP) in France (July 2018 to April 2021). The primary endpoint was GI response at day 28, defined as the proportion of patients with GI-aGvHD who had a complete response (CR) or very good partial response (VGPR). GvHD grading and staging were assessed according to the revised Glucksberg criteria. Adverse events and severe adverse events were monitored for 6 months and 12 months, respectively. The HERACLES study was registered with ClinicalTrials.gov (NCT03359980)., Findings: Compared with single donors, MaaT013 is characterised by higher microbial richness and reduced variability across batches. At day 28 (D28), the GI-overall response rate (ORR) was 38% in the prospective population, including 5 complete responses (CR), 2 very good partial responses (VGPR) and 2 partial responses (PR). In the EAP, the GI-ORR was 58% (17 CR, 9 VGPR and 4 PR). The 12-month overall survival (OS) was 25% in the prospective study and 38% in the EAP. Regarding safety, five infectious complications, including 3 sepsis, could not be excluded from being related to the study procedure in HERACLES. Shotgun sequencing analyses of the identified strains suggest that none were found in MaaT013. In the EAP, 18 pharmacovigilance cases were reported among 52 treated patients, including 11 bacteraemia/sepsis. In HERACLES, we observed in stools from responding patients at D28 a higher microbiota richness and increased levels of beneficial bacteria, in particular butyrate producers, along with increased levels of short-chain fatty acid and bile acids. In contrast, stools from non-responding (NR) patients displayed increased levels of pathogenic pro-inflammatory bacteria along with increased systemic inflammatory parameters., Interpretation: Overall, MaaT013 was safe in this population of highly immunocompromised patients and was associated with responses in some patients with GI-aGvHD and deserves further investigation., Funding: MaaT Pharma., Competing Interests: FM reports honoraria from Therakos/Mallinckrodt, Sanofi and Novartis. TC reports consulting fee from Celgene, Abbvie, Jazz Pharma, Roche, Novartis, Agios and Servier and honoraria from Novartis, Amgen, Astellas, Celgene/BMS and Gilead/Kite. ED report payment for expert testimony from Astellas and support for attending meetings and/or travel from Neovii and Novartis. MJGTV report grants or contracts from MSD, Heel, Biontech and Roche, consulting fees from MaaT Pharma, Tillots, MSD/Merck, Roche and EUMEDICA and payment or honoraria from Merck/MSD, 3M, Ferring, Astellas, Uniklinik Karlsruhe, Uniklinik Köln, Akademie für Infektionsmedizin, Klinikum Essen, Pfizer, Universitätsklinikum Heidelberg, Uniklinik Frankfurt, Landesärztekammer Hessen, Janssen, Intitur Merieux, Forum für medizinische Fortbildung Gmbh, Universitätsklinikum Freiburg, Berliner Dialy Seminar, ADKA, Falk Foundation, St. Johannes Hospital, DiaLog Service, CED Service, Ärztekammer Niedersachsen, St. Josef Hospital, Limbach Gruppe SE, SUMIT OXFORD Ltd. EUMEDICA Kit Kongress, Tillots Pharma, Helios Kliniken, Lahn-Dill-Kliniken, GILEAD and Klinikum Leverkusen. CEB report honoraria from Astellas. EH report grants from Medac, payment for expert testimony from Novartis, participation on Advisory Board of Maat Pharma and Pharmabiome. JD is cofounder and member of the advisory board of MaaT Pharma, report consulting fees from MaaT Pharma, support for attending meetings and/or travel from MaaT Pharma and shares from MaaT Pharma. EPr, CG and EPl are MaaT Pharma employees and have patents as part of company inventor compensation policy MM reports grants and consulting fees from Sanofi, Novartis, and Janssen, honoraria from Sanofi, Novartis, Janssen, and MaaT Pharma, participation on Advisory Board of Janssen and leadership role in The European Group for Blood & Marrow Transplantation. All other authors declare no competing interests., (© 2023 The Author(s).)

An important aspect of immunotherapy is the ability of dendritic cells (DCs) to prime T cell immunity, an approach that has yielded promising results in some early phase clinical trials. However, novel approaches are required to improve DC therapeutic efficacy by enhancing their uptake of, and activation by, disease relevant antigens. The carbon nano-material graphene oxide (GO) may provide a unique way to deliver antigen to innate immune cells and modify their ability to initiate effective adaptive immune responses. We have assessed whether GO of various lateral sizes affects DC activation and function in vitro and in vivo , including their ability to take up, process and present the well-defined model antigen ovalbumin (OVA). We have found that GO flakes are internalised by DCs, while having minimal effect on their viability, activation phenotype or cytokine production. Although adsorption of OVA protein to either small or large GO flakes promoted its uptake into DCs, large GO interfered with OVA processing. In terms of modulation of DC function, delivery of OVA via small GO flakes significantly enhanced DC ability to induce proliferation of OVA-specific CD4 + T cells, promoting granzyme B secretion in vitro . On the other hand, delivery of OVA via large GO flakes augmented DC ability to induce proliferation of OVA-specific CD8 + T cells, and their production of IFN-γ and granzyme B. Together, these data demonstrate the capacity of GO of different lateral dimensions to act as a promising delivery platform for DC modulation of distinct facets of the adaptive immune response, information that could be exploited for future development of targeted immunotherapies.

This work presents the new template matching capabilities implemented in Pyxem, an open source Python library for analyzing four-dimensional scanning transmission electron microscopy (4D-STEM) data. Template matching is a brute force approach for deriving local crystal orientations. It works by comparing a library of simulated diffraction patterns to experimental patterns collected with nano-beam and precession electron diffraction (NBED and PED). This is a computationally demanding task, therefore the implementation combines efficiency and scalability by utilizing multiple CPU cores or a graphical processing unit (GPU). The code is built on top of the scientific Python ecosystem, and is designed to support custom and reproducible workflows that combine the image processing, template library generation, indexation and visualization all in one environment. The tools are agnostic to file size and format, which is significant in light of the increased adoption of pixelated detectors from different manufacturers. This paper details the implementation and validation of the method. The method is illustrated by calculating orientation maps of nanocrystalline materials and precipitates embedded in a crystalline matrix. The combination of speed and flexibility opens the door for automated parameter studies and real-time on-line orientation mapping inside the TEM., (Copyright © 2022 The Authors. Published by Elsevier B.V. All rights reserved.)

Stabilisers, such as surfactants, polymers and polyaromatic molecules, offer an effective way to produce graphene dispersions in water by Liquid Phase Exfoliation (LPE) without degrading the properties of graphene. In particular, pyrene derivatives provide better exfoliation efficiency than traditional surfactants and polymers. A stabiliser is expected to be relatively soluble in order to disperse hydrophobic graphene in water. Here, we show that exfoliation can also be achieved with insoluble pyrene stabilisers if appropriately designed. In particular, bis-pyrene stabilisers (BPSs) functionalised with pyrrolidine provide a higher exfoliation efficiency and percentage of single layers compared to traditional pyrene derivatives under the same experimental conditions. This is attributed to the enhanced interactions between BPS and graphene, provided by the presence of two pyrene binding groups. This approach is therefore attractive not only to produce highly concentrated graphene, but also to use graphene to disperse insoluble molecules in water. The enhanced adsorption of BPS on graphene, however, is reflected in higher toxicity towards human epithelial bronchial immortalized cells, limiting the use of this material for biomedical applications.

The human gut microbiota performs functions that are essential for the maintenance of the host physiology. However, characterizing the functioning of microbial communities in relation to the host remains challenging in reference-based metagenomic analyses. Indeed, as taxonomic and functional analyses are performed independently, the link between genes and species remains unclear. Although a first set of species-level bins was built by clustering co-abundant genes, no reference bin set is established on the most used gut microbiota catalog, the Integrated Gene Catalog (IGC). With the aim to identify the best suitable method to group the IGC genes, we benchmarked nine taxonomy-independent binners implementing abundance-based, hybrid and integrative approaches. To this purpose, we designed a simulated non-redundant gene catalog (SGC) and computed adapted assessment metrics. Overall, the best trade-off between the main metrics is reached by an integrative binner. For each approach, we then compared the results of the best-performing binner with our expected community structures and applied the method to the IGC. The three approaches are distinguished by specific advantages, and by inherent or scalability limitations. Hybrid and integrative binners show promising and potentially complementary results but require improvements to be used on the IGC to recover human gut microbial species., (© The Author(s) 2021. Published by Oxford University Press on behalf of NAR Genomics and Bioinformatics.)

The convergent beam electron diffraction (CBED) patterns of twisted bilayer samples exhibit interference patterns in their CBED spots. Such interference patterns can be treated as off-axis holograms and the phase of the scattered waves, meaning the interlayer distance can be reconstructed. A detailed protocol of the reconstruction procedure is provided in this study. In addition, we derive an exact formula for reconstructing the interlayer distance from the recovered phase distribution, which takes into account the different chemical compositions of the individual monolayers. It is shown that one interference fringe in a CBED spot is sufficient to reconstruct the distance between the layers, which can be practical for imaging samples with a relatively small twist angle or when probing small sample regions. The quality of the reconstructed interlayer distance is studied as a function of the twist angle. At smaller twist angles, the reconstructed interlayer distance distribution is more precise and artefact free. At larger twist angles, artefacts due to the moiré structure appear in the reconstruction. A method for the reconstruction of the average interlayer distance is presented. As for resolution, the interlayer distance can be reconstructed by the holographic approach at an accuracy of ±0.5 Å, which is a few hundred times better than the intrinsic z-resolution of diffraction limited resolution, as expressed through the spread of the measured k-values. Moreover, we show that holographic CBED imaging can detect variations as small as 0.1 Å in the interlayer distance, though the quantitative reconstruction of such variations suffers from large errors., (Copyright © 2020 The Authors. Published by Elsevier B.V. All rights reserved.)

Carbon nanomaterials, including 2D graphene-based materials, have shown promising applicability to drug delivery, tissue engineering, diagnostics, and various other biomedical areas. However, to exploit the benefits of these materials in some of the areas mentioned, it is necessary to understand their possible toxicological implications and long-term fate in vivo . We previously demonstrated that following intravenous administration, 2D graphene oxide (GO) nanosheets were largely excreted via the kidneys; however, a small but significant portion of the material was sequestered in the spleen. Herein, we interrogate the potential consequences of this accumulation and the fate of the spleen-residing GO over a period of nine months. We show that our thoroughly characterized GO materials are not associated with any detectable pathological consequences in the spleen. Using confocal Raman mapping of tissue sections, we determine the sub-organ biodistribution of GO at various time points after administration. The cells largely responsible for taking up the material are confirmed using immunohistochemistry coupled with Raman spectroscopy, and transmission electron microscopy (TEM). This combination of techniques identified cells of the splenic marginal zone as the main site of GO bioaccumulation. In addition, through analyses using both bright-field TEM coupled with electron diffraction and Raman spectroscopy, we reveal direct evidence of in vivo intracellular biodegradation of GO sheets with ultrastructural precision. This work offers critical information about biological processing and degradation of thin GO sheets by normal mammalian tissue, indicating that further development and exploitation of GO in biomedicine would be possible.

The outstanding properties of graphene offer high potential for biomedical applications. In this framework, positively charged nanomaterials show better interactions with the biological environment, hence there is strong interest in the production of positively charged graphene nanosheets. Currently, production of cationic graphene is either time consuming or producing dispersions with poor stability, which strongly limit their use in the biomedical field. In this study, we made a family of new cationic pyrenes, and have used them to successfully produce water-based, highly concentrated, stable, and defect-free graphene dispersions with positive charge. The use of different pyrene derivatives as well as molecular dynamics simulations allowed us to get insights on the nanoscale interactions required to achieve efficient exfoliation and stabilisation. The cationic graphene dispersions show outstanding biocompatibility and cellular uptake as well as exceptional colloidal stability in the biological medium, making this material extremely attractive for biomedical applications.

Convergent beam electron diffraction is routinely applied for studying deformation and local strain in thick crystals by matching the crystal structure to the observed intensity distributions. Recently, it has been demonstrated that CBED can be applied for imaging two-dimensional (2D) crystals where a direct reconstruction is possible and three-dimensional crystal deformations at a nanometre resolution can be retrieved. Here, we demonstrate that second-order effects allow for further information to be obtained regarding stacking arrangements between the crystals. Such effects are especially pronounced in samples consisting of multiple layers of 2D crystals. We show, using simulations and experiments, that twisted multilayer samples exhibit extra modulations of interference fringes in CBED patterns, i. e., a CBED moiré. A simple and robust method for the evaluation of the composition and the number of layers from a single-shot CBED pattern is demonstrated., (Copyright © 2020 The Authors. Published by Elsevier B.V. All rights reserved.)

Hybrids composed of liposomes (L) and metallic nanoparticles (NPs) hold great potential for imaging and drug delivery purposes. However, the efficient incorporation of metallic NPs into liposomes using conventional methodologies has so far proved to be challenging. In this study, we report the fabrication of hybrids of liposomes and hydrophobic gold NPs of size 2-4 nm (Au) using a microfluidic-assisted self-assembly process. The incorporation of increasing amounts of AuNPs into liposomes was examined using microfluidics and compared to L-AuNP hybrids prepared by the reverse-phase evaporation method. Our microfluidics strategy produced L-AuNP hybrids with a homogeneous size distribution, a smaller polydispersity index, and a threefold increase in loading efficiency when compared to those hybrids prepared using the reverse-phase method of production. Quantification of the loading efficiency was determined by ultraviolet spectroscopy, inductively coupled plasma mass spectroscopy, and centrifugal field flow fractionation, and qualitative validation was confirmed by transmission electron microscopy. The higher loading of gold NPs into the liposomes achieved using microfluidics produced a slightly thicker and more rigid bilayer as determined with small-angle neutron scattering. These observations were confirmed using fluorescent anisotropy and atomic force microscopy. Structural characterization of the liposomal-NP hybrids with cryo-electron microscopy revealed the coexistence of membrane-embedded and interdigitated NP-rich domains, suggesting AuNP incorporation through hydrophobic interactions. The microfluidic technique that we describe in this study allows for the automated production of monodisperse liposomal-NP hybrids with high loading capacity, highlighting the utility of microfluidics to improve the payload of metallic NPs within liposomes, thereby enhancing their application for imaging and drug delivery.