Porcine intestinal innate lymphoid cells and lymphocyte spatial context revealed through single-cell RNA sequencing

Intestinal lymphocytes are crucial members of the mucosal immune system with impact over outcomes of intestinal health versus dysbiosis. Resolving intestinal lymphocyte complexity and function is a challenge, as the intestine provides cellular snapshots of a diverse spectrum of immune states. In pigs, intestinal lymphocytes are poorly described relative to humans or traditional model species. Enhanced understanding of porcine intestinal lymphocytes will promote food security and improve utility of pigs as a biomedical model for intestinal research. Single-cell RNA sequencing (scRNA-seq) was performed to provide transcriptomic profiles of lymphocytes in the porcine ileum, with 31,983 cells annotated into 26 cell types. Deeper interrogation revealed previously undescribed cells in porcine ileum, including SELLhi γδ T cells, group 1 and group 3 innate lymphoid cells (ILCs), and four subsets of B cells. Single-cell transcriptomes in ileum were compared to those in porcine blood, and subsets of activated lymphocytes were detected in ileum but not periphery. Comparison to scRNA-seq human and murine ileum data revealed a general consensus of ileal lymphocytes across species. Lymphocyte spatial context in porcine ileum was conferred through differential tissue dissection prior to scRNA-seq. Antibody-secreting cells, B cells, follicular αβ T cells, and cycling T/ILCs were enriched in ileum with Peyer's patches, while non-cycling γδ T, CD8 αβ T, and group 1 ILCs were enriched in ileum without Peyer's patches. scRNA-seq findings were leverages to develop advanced toolsets for further identification of ILCs in porcine ileum via flow cytometry and in situ staining. Porcine ileal ILCs identified via scRNA-seq did not transcriptionally mirror peripheral ILCs (corresponding to natural killer cells) but instead had gene signatures indicative of tissue- and activation-specific functions, indicating potentially similar roles to intestinal ILCs identified in humans. Overall, the data serve as a highly-resolved transcriptomic atlas of the porcine intestinal immune landscape and will be useful in further understanding intestinal immune cell function.

Multi-Scale Presentation of Spatial Context for Cultural Heritage Applications

An approach to the representation and presentation of spatial and geographical context of cultural heritage sites is proposed. The goal is to combine semantic representations of social and historical context with 3D representations of cultural heritage sites acquired through 3D reconstruction and 3D modeling technologies, to support their interpretation and presentation in education and tourism. Several use cases support and demonstrate the application of the proposed approach including immersive craft and context demonstration environment and interactive games.

Context awareness in process monitoring of additive manufacturing using a digital twin

Wire Arc Additive Manufacturing allows the cost-effective manufacturing of customized, large-scale metal parts. As the post-process quality assurance of large parts is costly and time-consuming, process monitoring is inevitable. In the present study, a context-aware monitoring solution was investigated by integrating machine, temporal, and spatial context in the data analysis. By analyzing the voltage patterns of each cycle in the oscillating cold metal transfer process with a deep neural network, temporal context was included. Spatial context awareness was enabled by building a digital twin of the manufactured part using an Octree as spatial indexing data structure. By means of the spatial context awareness, two quality metrics—the defect expansion and the local anomaly density—were introduced. The defect expansion was tracked in-process by assigning detected defects to the same defect cluster in case of spatial correlation. The local anomaly density was derived by defining a spherical region of interest which enabled the detection of aggregations of anomalies. By means of the context aware monitoring system, defects were detected in-process with a higher sensitivity as common defect detectors for welding applications, showing less false-positives and false-negatives. A quantitative evaluation of defect expansion and densities of various defect types such as pore nests was enabled.

Attributing and Defining an Unbuilt 1859 Architectural Plan for the Site of Trogir’s Medieval Walls

This paper discusses the attribution of an anonymous and unbuilt 1859 plan for a four-storey apartment building with commercial spaces on the ground floor, located on the site of the old town walls in Trogir. It proposes Josip Slade as the architect of the plan, interpreting Slade’s architectural language and the development of his approach to architectural heritage. An analysis of the project in a historical socio-political and spatial context, moreover, supports the conclusion that this was intended as rental property, and this paper therefore offers insights into the first known example of the tenement housing building typology in the nineteenth-century Trogir

The annotation and analysis of complex 3D plant organs using 3DCoordX

A fundamental question in biology concerns how molecular and cellular processes become integrated during morphogenesis. In plants, characterization of 3D digital representations of organs at single-cell resolution represents a promising approach to addressing this problem. A major challenge is to provide organ-centric spatial context to cells of an organ. We developed several general rules for the annotation of cell position and embodied them in 3DCoordX, a user-interactive computer toolbox implemented in the open-source software MorphoGraphX. It enables rapid spatial annotation of cells even in highly curved biological shapes. With the help of 3DCoordX we obtained new insight by analyzing cellular growth patterns in organs of several species. For example, the data indicated the presence of a basal cell proliferation zone in the ovule primordium of Arabidopsis thaliana. Proof-of-concept analyses suggested a preferential increase in cell length associated with neck elongation in the archegonium of Marchantia polymorpha and variations in cell volume linked to central morphogenetic features of a trap of the carnivorous plant Utricularia gibba. Our work demonstrates the broad applicability of the developed strategies as they provide organ-centric spatial context to cellular features in plant organs of diverse shape complexity.

Spatial Causalities in Geographies of Scientific Knowledge

This paper tries to discuss the efforts of geographers of science to put science in its geographical contexts. Geographers of science have studied the socio-spatial settings in which scientific knowledge has been generated, displayed, and legitimated. For them, science is socially constructed in “spatialities” and “temporalities”. The major question of this study is how “spatialities” construct scientific knowledge via its “causalities”. The fundamental idea is that geography of science does not only deal with places, locations, and regions where scientific knowledge is produced or distributed; it also deals with a variety set of spatial causalities through which scientific knowledge can be formed and transformed. This means that the development of innovative knowledge and ideas take place not only within a spatial context but also occur due to the spatial causalities associated with the myriad interlinkages and interdependencies among places. These imperatives of spatial significance operate across many spatial scales from body/local to the planet/global. Hence, in our increasingly globalized world, we must seek knowledge in spatial encounters and in-between places, not merely within spaces and places. In addition, when we are living in an unprecedented transformation period which transfers the terrestrial spatial causalities to the virtual spatial causalities via intelligent and digital technologies, we should be more aware of the difference that new algorithms make in our daily life through hacking virtual spatial causalities.

Light Distribution and Perceived Spaciousness: Light Patterns in Scale Models

Previous research showed that light distribution can affect the perception of spatial size and shape. However, most studies are limited to quantitative assessment of a few scenarios without explaining possible causes behind peoples’ experiences. This exploratory study aimed to reveal complex relationships between light patterns and perceived size, and to investigate how light patterns affect perceived spaciousness. A qualitative approach was used with pair-wise comparisons between systematic visual observations of scale models. The observations confirmed that illuminated walls increase spaciousness. Yet, darkness impacts the perception of spaciousness as well. Both compound and separated light zones can expand depth, height, or width, depending on the interpretation of these patterns of light seen in relation to the whole spatial context. Furthermore, the position of illuminated areas, with placements on edge or in the center, may additionally influence perceived size.