A high-resolution 3D atlas of the spectrum of tuberculous and COVID-19 lung lesions.

Our current understanding of the spectrum of TB and COVID-19 lesions in the human lung is limited by a reliance on low-resolution imaging platforms that cannot provide accurate 3D representations of lesion types within the context of the whole lung. To characterize TB and COVID-19 lesions in 3D, we applied micro/nanocomputed tomography to surgically resected, postmortem, and paraffin-embedded human lung tissue. We define a spectrum of TB pathologies, including cavitary lesions, calcium deposits outside and inside necrotic granulomas and mycetomas, and vascular rearrangement. We identified an unusual spatial arrangement of vasculature within an entire COVID-19 lobe, and 3D segmentation of blood vessels revealed microangiopathy associated with hemorrhage. Notably, segmentation of pathological anomalies reveals hidden pathological structures that might otherwise be disregarded, demonstrating a powerful method to visualize pathologies in 3D in TB lung tissue and whole COVID-19 lobes. These findings provide unexpected new insight into the spatial organization of the spectrum of TB and COVID-19 lesions within the framework of the entire lung.

Micro-Computed Tomography Analysis of the Human Tuberculous Lung Reveals Remarkable Heterogeneity in Three-dimensional Granuloma Morphology.

Rationale: Our current understanding of tuberculosis (TB) pathophysiology is limited by a reliance on animal models, the paucity of human TB lung tissue, and traditional histopathological analysis, a destructive two-dimensional approach that provides limited spatial insight. Determining the three-dimensional (3D) structure of the necrotic granuloma, a characteristic feature of TB, will more accurately inform preventive TB strategies.Objectives: To ascertain the 3D shape of the human tuberculous granuloma and its spatial relationship with airways and vasculature within large lung tissues.Methods: We characterized the 3D microanatomical environment of human tuberculous lungs by using micro computed tomography, histopathology, and immunohistochemistry. By using 3D segmentation software, we accurately reconstructed TB granulomas, vasculature, and airways in three dimensions and confirmed our findings by using histopathology and immunohistochemistry.Measurements and Main Results: We observed marked heterogeneity in the morphology, volume, and number of TB granulomas in human lung sections. Unlike depictions of granulomas as simple spherical structures, human necrotic granulomas exhibit complex, cylindrical, branched morphologies that are connected to the airways and shaped by the bronchi. The use of 3D imaging of human TB lung sections provides unanticipated insight into the spatial organization of TB granulomas in relation to the airways and vasculature.Conclusions: Our findings highlight the likelihood that a single, structurally complex lesion could be mistakenly viewed as multiple independent lesions when evaluated in two dimensions. In addition, the lack of vascularization within obstructed bronchi establishes a paradigm for antimycobacterial drug tolerance. Lastly, our results suggest that bronchogenic spread of Mycobacterium tuberculosis reseeds the lung.

Data for 3D printing enlarged museum specimens for the visually impaired.

Museums are embracing new technologies and one of these is the use of 3D printing. 3D printing allows for creating physical replicas of items which may, due to great value or significance, not be handled by the public, or which are too small or fragile to be handled or even seen with the naked eye. One such application of new technologies has been welcomed by the National Museum in Bloemfontein, Free State, South Africa. Here, blown-up (enlarged) Museum specimens were 3D printed for various interactive exhibits that are aimed at increasing the accessibility of their permanent displays for visually impaired visitors who rely greatly on touch as a source of observation. A selection of scorpions, pseudoscorpions, mites and archetypal bird skulls were scanned, processed and 3D printed to produce enlarged, highly functional nylon models. This data paper provides the raw micro Computed Tomography (micro-CT) scan data and print ready STL files processed from this data. The STL files may be used in their current format and details of the printing are provided.

Physico-elemental analysis of roasted organic coffee beans from Ethiopia, Colombia, Honduras, and Mexico using X-ray micro-computed tomography and external beam particle induced X-ray emission.

The physico-elemental profiles of commercially attained and roasted organic coffee beans from Ethiopia, Colombia, Honduras, and Mexico were compared using light microscopy, X-ray micro-computed tomography, and external beam particle induced X-ray emission. External beam PIXE analysis detected P, S, Cl, K, Ca, Ti, Mn, Fe, Cu, Zn, Br, Rb, and Sr in samples. Linear discriminant analysis showed that there was no strong association between elemental data and production region, whilst a heatmap combined with hierarchical clustering showed that soil-plant physico-chemical properties may influence regional elemental signatures. Physical trait data showed that Mexican coffee beans weighed significantly more than beans from other regions, whilst Honduras beans had the highest width. X-ray micro-computed tomography qualitative data showed heterogeneous microstructural features within and between beans representing different regions. In conclusion, such multi-dimensional analysis may present a promising tool in assessing the nutritional content and qualitative characteristics of food products such as coffee.

A micro X-ray computed tomography dataset of fossil echinoderms in an ancient obrution bed: a robust method for taphonomic and palaeoecologic analyses.

BACKGROUND: Taphonomic and palaeoecologic studies of obrution beds often employ conventional methods of investigation such as physical removal and extraction of fossils from their host rock (matrix) by mechanical preparation. This often-destructive method is not suitable for studying mold fossils, which are voids left in host rocks due to dissolution of the original organism in post-depositional processes. FINDINGS: Microcomputed tomography (µCT) scan data of 24 fossiliferous rock samples revealed thousands of Paleozoic echinoderms. Digitally "stitching" together individually µCT scanned rock samples within three-dimensional (3D) space allows for quantifiable taphonomic data on a fossil echinoderm-rich obrution deposit from the Devonian (Emsian) of South Africa. Here, we provide a brief step-by-step guide on creating, segmenting, and ultimately combining sections of richly fossiliferous beds to create virtual models suited for the quantitative and qualitative taphonomic analyses of fossil invertebrate assemblages. CONCLUSIONS: Visualizing the internal features of fossiliferous beds in 3D is an invaluable taphonomic tool for analyzing delicate fossils, accounting for all specimens irrespective of their preservation stages and with minimal damage. This technique is particularly useful for analyzing fossiliferous deposits with mold fossils that prove to be difficult to study with traditional methods, because the method relies on the large density contrast between the mold and host rock.

Standard method for microCT-based additive manufacturing quality control 4: Metal powder analysis.

X-ray micro computed tomography (microCT) can be applied to analyse powder feedstock used in additive manufacturing. In this paper, we demonstrate a dedicated workflow for this analysis method, specifically for Ti6Al4V powder typically used in commercial powder bed fusion (PBF) additive manufacturing (AM) systems. The methodology presented includes sample size requirements, scan conditions and settings, reconstruction and image analysis procedures. We envisage this method will support standardization in powder analysis in the additive manufacturing community. This is aimed at ultimately improving the quality of additively manufactured parts, through the identification of impurities and defects in powders. •MicroCT analysis of metal powders for additive manufacturing•Method describes a standard workflow simplifying usage of the technique•Sample requirements and image analysis workflow is described.

Standard method for microCT-based additive manufacturing quality control 1: Porosity analysis.

MicroCT is a well-established technique that is used to analyze the interior of objects non-destructively, and it is especially useful for void or porosity analysis. Besides its widespread use, few standards exist and none for additive manufacturing as yet. This is due to the inherent differences in part design, sizes and geometries, which results in different scan resolutions and qualities. This makes direct comparison between different scans of additively manufactured parts almost impossible. In addition, different image analysis methodologies can produce different results. In this method paper, we present a simplified 10 mm cube-shaped coupon sample as a standard size for detailed analysis of porosity using microCT, and a simplified workflow for obtaining porosity information. The aim is to be able to obtain directly comparable porosity information from different samples from the same AM system and even from different AM systems, and to potentially correlate detailed morphologies of the pores or voids with improper process parameters. The method is applied to two examples of different characteristic types of voids in AM: sub-surface lack of fusion due to improper contour scanning, and tree-like pores growing in the build direction. This standardized method demonstrates the capability for microCT to not only quantify porosity, but also identify void types which can be used to improve AM process optimization.

Standard method for microCT-based additive manufacturing quality control 3: Surface roughness.

The use of microCT of 10 mm coupon samples produced by AM has the potential to provide useful information of mean density and detailed porosity information of the interior of the samples. In addition, the same scan data can be used to provide surface roughness analysis of the as-built surfaces of the same coupon samples. This can be used to compare process parameters or new materials. While surface roughness is traditionally done using tactile probes or with non-contact interferometric techniques, the complex surfaces in AM are sometimes difficult to access and may be very rough, with undercuts and may be difficult to accurately measure using traditional techniques which are meant for smoother surfaces. This standard workflow demonstrates on a coupon sample how to acquire surface roughness results, and compares the results from roughly the same area of the same sample with tactile probe results. The same principle can be applied to more complex parts, keeping in mind the resolution limit vs sample size of microCT.

Standard method for microCT-based additive manufacturing quality control 2: Density measurement.

MicroCT is best known for its ability to detect and quantify porosity or defects, and to visualize its 3D distribution. However, it is also possible to obtain accurate volumetric measurements from parts - this can be used in combination with the part mass to provide a good measure of its average density. The advantage of this density-measurement method is the ability to combine the density measurement with visualization and other microCT analyses of the same sample. These other analyses may include detailed porosity or void analysis (size and distribution) and roughness assessment, obtainable with the same scan data. Simple imaging of the interior of the sample allows the detection of unconsolidated powder, open porosity to the surface or the presence of inclusions. The CT density method presented here makes use of a 10 mm cube sample and a simple data analysis workflow, facilitating standardization of the method. A laboratory microCT scanner is required at 15 µm voxel size, suitable software to allow sub-voxel precise edge determination of the scanned sample and hence an accurate total volume measurement, and a scale with accuracy to 3 digits. •MicroCT-based mean density measurement method.•Accurate volume measurement and scale mass.•10 mm cube sample allows standardization and automation of workflow.

Analyzing nature's protective design: The glyptodont body armor.

Many animal species evolved some form of body armor, such as scales of fish and bony plates or osteoderms of reptiles. Although a protective function is often taken for granted, recent studies show that body armor might comprise multiple functionalities and is shaped by trade-offs among these functionalities. Hence, despite the fact that natural body armor might serve as bio-inspiration for the development of artificial protective materials, focussing on model systems in which body armor serves a solely protective function might be pivotal. In this study, we investigate the osteoderms of Glyptotherium arizonae, an extinct armadillo-like mammal in which body armor evolved as protection against predators and/or tail club blows of conspecifics. By using a combination of micro-computed tomography, reverse-engineering, stress simulations and mechanical testing of 3D printed models, we show that the combination of dense compact layers and porous lattice core might provide an optimized combination of strength and high energy absorption.

Snake fangs: 3D morphological and mechanical analysis by microCT, simulation, and physical compression testing.

This Data Note provides data from an experimental campaign to analyse the detailed internal and external morphology and mechanical properties of venomous snake fangs. The aim of the experimental campaign was to investigate the evolutionary development of 3 fang phenotypes and investigate their mechanical behaviour. The study involved the use of load simulations to compare maximum Von Mises stress values when a load is applied to the tip of the fang. The conclusions of this study have been published elsewhere, but in this data note we extend the analysis, providing morphological comparisons including details such as curvature comparisons, thickness, etc. Physical compression results of individual fangs, though reported in the original paper, were also extended here by calculating the effective elastic modulus of the entire snake fang structure including internal cavities for the first time. This elastic modulus of the entire fang is significantly lower than the locally measured values previously reported from indentation experiments, highlighting the possibility that the elastic modulus is higher on the surface than in the rest of the material. The micro-computed tomography (microCT) data are presented both in image stacks and in the form of STL files, which simplifies the handling of the data and allows its re-use for future morphological studies. These fangs might also serve as bio-inspiration for future hypodermic needles.

Laboratory x-ray micro-computed tomography: a user guideline for biological samples.

Laboratory x-ray micro-computed tomography (micro-CT) is a fast-growing method in scientific research applications that allows for non-destructive imaging of morphological structures. This paper provides an easily operated "how to" guide for new potential users and describes the various steps required for successful planning of research projects that involve micro-CT. Background information on micro-CT is provided, followed by relevant setup, scanning, reconstructing, and visualization methods and considerations. Throughout the guide, a Jackson's chameleon specimen, which was scanned at different settings, is used as an interactive example. The ultimate aim of this paper is make new users familiar with the concepts and applications of micro-CT in an attempt to promote its use in future scientific studies.

Corneal transplantation: study of the data of a regional eye bank for the year 2013 and analysis of the evolution of the adverse events reported in France since 2010.

To analyze the data of the adverse events collected in a single major eye bank (EFS Bourgogne Franche Comté, Besançon, France) for the year 2013 and to report the French data of biovigilance provided by the French National Agency for Medicines and Health Products Safety (ANSM) between 2010 and 2013. we have set up a study of adverse events in 2013, in collaboration with a single eye bank (EFS Bourgogne Franche Comté, Besançon, France). A survey was sent to the surgeon for each delivered corneal button by the eye bank in 2013. They were asked for each grafted patient performed in their center, the type of graft (penetrating keratoplasty, anterior keratoplasty or endothelial keratoplasty), the occurrence of adverse events (primary failure, infectious keratis, endophthalmitis, immune rejection, and other events) and the time interval between surgery and events (Less than 1 postoperative month, between 1 month and 1 year postoperatively, >1 year postoperatively). In 2013, 407 corneal buttons were delivered by the eye bank of Besançon in 21 medical centers which performed corneal grafts and we sent 407 surveys. We received 243 completed questionnaires (59.75%) from 11 centers (52.38%). The global reported rate of adverse events was 27.54% of the graft (n = 65/236 corneal grafts performed in 11 centers in 2013; 20% of Primary graft failure, 11% of infectious keratitis, 1% of endophthalmitis, 34% of rejection, 34% of other incidents). 30.16% of complications were noticed before the first month after surgery versus 52.38% of complications noticed between the first month and the first year after surgery and 17.46% of complications noticed after the post-operative first year The most common causes of adverse events after PK were Immune rejection (13.17%), surgical causes (5.98%) and infection (4.79%) and after EK were Primary graft failure (8.2%) and surgical causes (19.67%). In 2013, in France 0.83% of adverse events were notified in ANSM. For the 236 performed graft issued from a major eye bank (EFS Besançon) in 2013 the global reported rate of post-graft adverse events was 27.54% of the grafts (20% of Primary graft failure, 11% of infectious keratitis, 1% of endophthalmitis, 34% of rejection and 34% of other incidents). Compared to the ANSM data (0.83% of adverse events reported in 2013) this rate is high. This difference can be explained by the low rate of annual notification to the ANSM and shows that biovigilance in France must be more developed. Since biovigilance needs constant improvement for the safety of the graft system, training, information for practitioners, simplifications of procedures and international standardization of the definition are the main points that could be improved.

In vitro characterization of patches of human mesenchymal stromal cells.

Stem cells may represent an excellent strategy to improve the healing of skin ulcers. Today the administration mode of stem cells to skin defects remains unsatisfactory. Delivering stem cells with topical treatments represents a new strategy and answering the patients' need. Mesenchymal stromal cells (MSC) have been shown to improve wound healing of cutaneous lesions and amniotic membrane (AM) is known to represent a natural scaffold for cells. The aim of this study is to develop a tissue-engineered product combining MSC and AM for clinical use. In this work we investigated whether the stromal matrix of intact human AM could constitute a scaffold for human MSC derived from either bone marrow (BM) or adipose tissue (AT). For this purpose, clinical-grade AM, MSC, and culture medium were used. We performed experiments of short-term adherence and proliferation for 15 days after the seeding of the cells. Morphological aspects and secretion profiles of MSC onto AM were studied, respectively, by scanning electron microscopy and Luminex analysis. Results demonstrated that the stromal matrix allow the adherence in much greater amount of MSC from BM or AT compared to 2D material. Experiments of proliferation showed that both kinds of MSC could proliferate on the stromal matrix and remain viable 15 days after the seeding of the cells. The 3D analysis of MSC culture demonstrated that both types of MSC invaded the stromal matrix and grew in multiple layers while retaining their fibroblastic morphology. By studying the secretion profile of MSC onto the stromal matrix, we found that both kinds of MSC secrete important cytokines and growth factors for wound healing of cutaneous lesions, such as vascular endothelial growth factor, hepatocyte growth factor, and basic fibroblast growth factor. In conclusion, these results suggest that the stromal matrix of AM seeded with MSC represents a bioactive scaffold that should be evaluated in patients with a nonhealing cutaneous wound.

In vivo and in vitro comparison of three different allografts vitalized with human mesenchymal stromal cells.

Bone allografts are commonly used by orthopedists to provide a mechanical support and template for cellular colonization and tissue repair. There is an increasing demand for bone graft substitutes that are safe and easy to store but which are equally effective in supporting new bone growth. In this study, we compared three different human bone allografts: (1) the cryopreserved allograft (frozen), (2) the gamma-irradiated and cryopreserved allograft (γ-irradiated), and (3) the solvent dehydrated and γ-irradiated-processed bone allograft (Tutoplast(®) Process Bone [TPB]). Human mesenchymal stromal cells (hMSCs) have the potential to differentiate into osteogenic, chondrogenic, and adipogenic lineages. Our results showed that hMSC seeding efficiency was equivalent among the three bone allografts. However, differences were observed in terms of cell metabolism (viability), osteoblastic gene expression, and in vivo bone formation. Frozen allografts had the higher frequency of new bone formation in vivo (89%). Compared with frozen allografts, we demonstrated that TPB allografts allowed optimal hMSC viability, osteoblastic differentiation, and bone formation to occur in vivo (72%). Further, the frequency of successful bone formation was higher than that obtained with the γ-irradiated allograft (55%). Moreover, after hMSC osteoinduction, 100% of the TPB and frozen allografts formed bone in vivo whereas only 61% of the γ-irradiated allografts did. As healthcare teams around the world require bone-grafting scaffolds that are safe and easy to store, the TPB allograft appears to be a good compromise between efficient bone formation in vivo and convenient storage at room temperature.

Alternatively spliced NKp30 isoforms affect the prognosis of gastrointestinal stromal tumors.

The natural killer (NK) cell receptor NKp30 is involved in the recognition of tumor and dendritic cells (DCs). Here we describe the influence of three NKp30 splice variants on the prognosis of gastrointestinal sarcoma (GIST), a malignancy that expresses NKp30 ligands and that is treated with NK-stimulatory KIT tyrosine kinase inhibitors. Healthy individuals and those with GIST show distinct patterns of transcription of functionally different NKp30 isoforms. In a retrospective analysis of 80 individuals with GIST, predominant expression of the immunosuppressive NKp30c isoform (over the immunostimulatory NKp30a and NKp30b isoforms) was associated with reduced survival of subjects, decreased NKp30-dependent tumor necrosis factor-α (TNF-α) and CD107a release, and defective interferon-γ (IFN-γ) and interleukin-12 (IL-12) secretion in the NK-DC cross-talk that could be restored by blocking of IL-10. Preferential NKp30c expression resulted partly from a single-nucleotide polymorphism at position 3790 in the 3' untranslated region of the gene encoding NKp30. The genetically determined NKp30 status predicts the clinical outcomes of individuals with GIST independently from KIT mutation.

CD4+CD25+ Tregs control the TRAIL-dependent cytotoxicity of tumor-infiltrating DCs in rodent models of colon cancer.

Tumors that progress do so via their ability to escape the antitumor immune response through several mechanisms, including developing ways to induce the differentiation and/or recruitment of CD4(+)CD25(+) Tregs. The Tregs, in turn, inhibit the cytotoxic function of T cells and NK cells, but whether they have an effect on the cytotoxic function of tumor-infiltrating DCs (TIDCs) has not been determined. Here we have shown, in 2 rodent models of colon cancer, that CD4(+)CD25(+) Tregs inhibit the ability of CD11b(+) TIDCs to mediate TNF-related apoptosis-inducing ligand-induced (TRAIL-induced) tumor cell death. In both models of cancer, combination treatment with Mycobacterium bovis Bacillus Calmette-Guérin (BCG), which activates the innate immune system via TLR2, TLR4, and TLR9, and cyclophosphamide (CTX), which depletes Tregs, eradicated the tumors. Further analysis revealed that the treatment led to a marked increase in the number of CD11b(+) TIDCs that killed the tumor cells via a TRAIL-dependent mechanism. Furthermore, acquisition of TRAIL expression by the CD11b(+) TIDCs was induced by BCG and dependent on signaling through TLR2, TLR4, and TLR9. In vivo transfer of Tregs abrogated the ability of BCG to induce CD11b(+) TIDCs to express TRAIL and thereby nullified the efficacy of the CTX-BCG treatment. Our data have therefore delineated what we believe to be a novel mechanism by which Tregs inhibit the antitumor immune response.

Ctla-4 blockade confers lymphocyte resistance to regulatory T-cells in advanced melanoma: surrogate marker of efficacy of tremelimumab?

PURPOSE: Anti-CTL antigen-4 (CTLA-4) monoclonal antibody (mAb) has led to encouraging antitumor activity associated with immune-related adverse events in patients with heavily pretreated melanoma. However, mechanisms of action and surrogate immunologic markers of efficacy have not been reported thus far. EXPERIMENTAL DESIGN: We monitored the immune responses of 10 melanoma patients included in a phase II clinical trial, which evaluated the efficacy of a second line of therapy of tremelimumab anti-CTLA-4 mAb in patients with metastatic melanoma. The frequency of blood leukocyte populations in association with T cell and regulatory T cell (Treg) functions were evaluated. RESULTS: Prior to therapy, patients with advanced melanoma presented with a severe CD4+ and CD8+ T cell lymphopenia associated with blunted T-cell proliferative capacities that could be assigned to Treg. Tremelimumab rapidly restored the effector and memory CD4+ and CD8+ T-cell pool and TCR-dependent T-cell proliferation that became entirely resistant to Treg-mediated suppression. Progression-free survival and overall survival was directly correlated with the acquisition of a biological response defined as the resistance of peripheral lymphocytes to Treg-inhibitory effects (obtained in 7 of 10 patients). CONCLUSION: CTLA-4 blockade seems to be a valuable strategy to revive reactive memory T cells anergized in the context of stage IV melanoma, and our work suggests that memory T-cell resistance to Treg resulting from anti-CTLA-4 treatment might be a biological activity marker for tremelimumab in patients with melanoma.

Tumor destruction using electrochemotherapy followed by CpG oligodeoxynucleotide injection induces distant tumor responses.

PURPOSE: Electrochemotherapy (ECT) is an effective local therapy of human cutaneous cancers but has no effect on distant untreated tumors. We addressed whether tumor-associated antigens released after ECT could induce an efficient systemic immunity when associated with an appropriate immunoadjuvant. METHODS AND RESULTS: We first studied the nature of the cellular recruitment and the expression of various toll-like receptors (TLRs) in tumors treated by ECT. We found that ECT induced a massive recruitment of CD11c and CD11b positive cells in the tumors and a strong increase of TLR9 expression. We then tested antitumor effects of the combination: ECT followed by TLR-9 ligands, CpG oligodeoxynucleotides (CpG ODN), in three murine tumor models. We found that this combination triggered both potent local synergistic antitumor effects, on the ipsi-lateral ECT-treated tumor, and more interestingly, a systemic antitumor response on the contra-lateral untreated tumor, in the three models. The systemic protection was T-cell dependent as it was not observed in nude littermates. The combination induced tumor-specific T cell effectors in the tumor-draining lymph nodes and in the spleen which secreted significantly more gamma-interferon upon activation than with ECT or CpG ODN alone. CONCLUSIONS: Our data show that ECT and CpG ODN synergize and induce a significant increase of the local effect and a systemic T-dependent antitumor response. Such combination constitutes a potential innovative vaccination strategy using in situ tumor-associated antigens that could eventually be translated into the clinic.