Hierarchical Joint Registration of Tissue Blocks With Soft Shape Constraints For Large-Scale Histology of The Human Brain

Large-scale 3D histology reconstruction of the human brain with MRI as volumetric reference generally requires reassembling the tissue blocks into the MRI space, prior to any further reconstruction of the histology of the individual blocks. This is a challenging registration problem, particularly in the frequent case that blockface photographs of paraffin embedded tissue are used as intermediate modality, as their contrast between white and gray matter is rather low. Here we propose a registration framework to address this problem, relying on two key components. First, blocks are simultaneously aligned to the MRI while exploiting the spatial constraints that they impose on each other, by means of a customized soft shape constraint (similarly to a jigsaw puzzle). And second, we adopt a hierarchical optimization strategy that capitalizes on our prior knowledge on the slicing and blocking procedure. Our framework is validated quantitatively on synthetic data, and qualitatively on the histology of a whole human hemisphere

Effect of Fluorinert on the Histological Properties of Formalin-Fixed Human Brain Tissue

Fluorinert (perfluorocarbon) represents an inexpensive option for minimizing susceptibility artifacts in ex vivo brain MRI scanning, and provides an alternative to Fomblin. However, its impact on fixed tissue and histological analysis has not been rigorously and quantitatively validated. In this study, we excised tissue blocks from 2 brain regions (frontal pole and cerebellum) of 5 formalin-fixed specimens (2 progressive supranuclear palsy cases, 3 controls). We excised 2 blocks per region per case (20 blocks in total), one of which was subsequently immersed in Fluorinert for a week and then returned to a container with formalin. The other block from each region was kept in formalin for use as control. The tissue blocks were then sectioned and histological analysis was performed on each, including routine stains and immunohistochemistry. Visual inspection of the stained histological sections by an experienced neuropathologist through the microscope did not reveal any discernible differences between any of the samples. Moreover, quantitative analysis based on automated image patch classification showed that the samples were almost indistinguishable for a state-of-the-art classifier based on a deep convolutional neural network. The results showed that Fluorinert has no effect on subsequent histological analysis of the tissue even after a long (1 week) period of immersion, which is sufficient for even the lengthiest scanning protocols

Institutional Management and Planning for Droughts: A Comparison of Ireland and Ontario, Canada

Severe drought conditions in 2018 prompted concerted efforts by Irish authorities to establish a formal planning process for drought risks as part of the wider national water management strategy. More than two decades had passed since Ireland had experienced a socioeconomically significant drought, but recently reconstructed long-term data have shown that drought is a much more frequent hazard here than previously thought. With climate change impacts likely to affect the temporal and spatial distribution of precipitation in coming decades, there is an ongoing need for further planning and preparation to reduce the vulnerability of the Irish water system to droughts. In this article we report results of a systematic comparison of Irish drought management plans and policies with those in southwestern Ontario, Canada, a region that shares many similar drought risk factors and management challenges but has longer established institutional practices for managing droughts. Key recommendations for Irish water managers emerging from this project include fostering a culture of water conservation among the Irish public; using catchments as the spatial unit for drought monitoring and management decisions; creation of standing drought management teams that involve and broaden key stakeholders and user groups; and further refining data collection to support planning for future challenges associated with climate change. Pursuing future opportunities for peer-to-peer learning between Irish water managers and their counterparts in other jurisdictions is a wider opportunity for developing best practices for drought management in the Irish context

A multimodal computational pipeline for 3D histology of the human brain

ABSTRACT: Ex vivo imaging enables analysis of the human brain at a level of detail that is not possible in vivo with MRI. In particular, histology can be used to study brain tissue at the microscopic level, using a wide array of different stains that highlight different microanatomical features. Complementing MRI with histology has important applications in ex vivo atlas building and in modeling the link between microstructure and macroscopic MR signal. However, histology requires sectioning tissue, hence distorting its 3D structure, particularly in larger human samples. Here, we present an open-source computational pipeline to produce 3D consistent histology reconstructions of the human brain. The pipeline relies on a volumetric MRI scan that serves as undistorted reference, and on an intermediate imaging modality (blockface photography) that bridges the gap between MRI and histology. We present results on 3D histology reconstruction of whole human hemispheres from two donors

The forgotten drought of 1765–1768: Reconstructing and re-evaluating historical droughts in the British and Irish Isles

Historical precipitation records are fundamental for the management of water resources, yet rainfall observations typically span 100–15 0 years at most, with considerable uncertainties surrounding earlier records. Here, we analyse some of the longest a vailabl e precipitation records globally, for England and Wales, Scotland and Ireland. To assess the credibility of these records and extend them further back in time, we statistically reconstruct (using independent predictors) monthly precipitation series representing these regions for the period 1748–2000. By applying the Standardized Precipi- tation Index at 12-month accumulations (SPI-12) to the observed and our reconstructed series we re-evaluate historical meteorological droughts. We find strong agreement between observed and reconstructed drought chronol- ogies in post-1870 records, but divergence in e arlier series due to biases in early precipitation observations. Hence, the 1800s decade was less drought prone in our reconstructions relative to observations. Overall, the drought of 1834–1836 was the most intense SPI-12 event in our reconstruction for England and Wales. Newspaper accounts and documentary sources confirm the extent of impacts across England in particular. We also identify a major, “forgotten” drought in 1765–1768 that affected the British-Irish Isles. This was the most intense event in our reconstructions for Ireland and Scotland, and ranks first for accumulated deficits a cross all three regional series. Moreover, the 1765–1768 event was also the most extreme multi-year drought across all regional series when considering 36-month a ccumulations (SPI-36). Newspaper and other sources confirm the occurrence and major socio- economic impact of this drought, such as major rivers like the Shannon being fordable by foot. Our results provide new insights into historical droughts across the British Irish Isles. Given the importance of historical droughts for stress-testing the resilience of water resources, drought plans and supply sys- tems, the forgotten drought of 1765–1 768 offers perhaps the most extreme benchmark scenario in more than 250-years

Governmentality and locality : an historical geography of rural district councils in Ireland, 1898-1925

THESIS 8403This thesis examines the introduction and operation of the rural district council network in Ireland between 1898 and 1925. Foucault?s theory of governmentality and Bellamy?s theory of central- local relations have been used to situate this study of Irish local government in a broader theoretical context. In so doing it has been possible to chart the changing geographies of power in Ireland as the state attempted to increase its control over the Irish population and territory through the introduction of local bodies under close central supervision. To date, few Irish historical geographies or histories have attempted to chart the development of the administrative state in Ireland in the early twentieth century. Historians and historical geographers alike have tended to focus more on the Irish quest for independence, than on the daily running of the state. This thesis addresses this gap by providing an account of an important low-level tier of local government, which is in grave danger of being forgotten

Gaming Display [An Exhibit from July 2014 through August 2014]

33 images from an exhibit developed by Camielle Swenson and Chris Crampsie to publicize board games and other games

Gaming Display [An Exhibit from July 2014 through August 2014]

33 images from an exhibit developed by Camielle Swenson and Chris Crampsie to publicize board games and other games