19 research outputs found
On park design : looking beyond the wars
No full textThe present book opens with an account of a buffalo hunt in the company of soldiers in one of the national parks in Uganda. One buffalo was hit close to the heart but fled away as if it was not fatally wounded. The soldiers seeing it flee, fired more rounds of ammunition at it until, with limbs broken, the buffalo fell down. This account is used to demonstrate some of the ravages of wars on parks. It is argued that most parks around the world are destined to perish because of defects in their design leading to institutional fights and inappropriate development programmes. The present book raises issues aimed at generating debates on the design of parks looking beyond the wars.The book is a synthesis of studies started while the author worked for the Uganda National Parks. It discusses why many parks in poor countries, especially those ravaged by wars, might not survive. The institutional setup is often not conducive to the accumulation and the deployment of resources necessary for the sustained development of the parks. The book differs from its predecessors with similar titles in four main respects. First, many studies of park design have been confined to the design of recreation parks found largely in urban areas, whereas this one focuses on nature reserves. Second, most studies on park design adopt one of the approaches which have been widely used in the design of recreation parks, whereas this one considers them inappropriate. Third, the book proposes that the design of a park should be perceived and treated as a puzzle. Finally, using case studies the book highlights some institutional aspects of park design. It is expected that ensuing debates generated by the issues raised by the book would contribute to science and hopefully improve its role in sustainable land development.It is shown in the book that for the parks to succeed their design requires clear objectives and deep understanding of their systems' dynamics. Prevailing instability, poverty, lack of know-how on the park system dynamics, widespread deterioration of the environmental conditions, and the complex and dynamic nature of park systems underline the urgent need to innovate appropriate institutions. Poor countries, especially those ravaged by wars, are emphasized because it is there that the need for institutional reform of the park systems is most apparent. Besides, it is more likely that such reforms can be incorporated in internationally funded post-war reconstruction and rehabilitation programmes, than it is under the usual development programmes. Cautiously the book also draws attention to the "wars" within and amongst groups of people (especially specialists) which make impossible serious collaboration. The latter wars are salient features of parks and it is essential that they are treated accordingly in the design of the parks. Against this background, institutional dimensions of park design receive much attention in the book.The book uses the word park within the context of category II, National Park, as defined in the "1990 United Nations List of National Parks and Protected Areas". This is land set aside primarily to preserve specific natural and/or cultural features. In this sense and as hereafter discussed, the parks are comparable to Noah's Ark in the Bible. With respect to wars, two main types are discussed: the one is violent the other non-violent, Both types of wars are portrayed as the results of conflicts of interests in the absence of appropriate institutional mechanisms to prevent and/or diffuse them. Prevalence of wars lead to many changes and tragedies in the midst of which the care for parks does not fit in with priorities. Hence, parks suffer from wars . The present book argues that with the war ravages as fait-accompli , the parks would gain most if the circumstances created by the wars were converted into opportunities to review their design. Such reviews could help to create a sound basis for the sustainable development of the parks. The book argues that the survival of the parks will depend on their design, i.e. their make-up. It is this make-up of a park as well as how this is defined that is, therefore, the focus of the book. Parks as living systems are portrayed as structurally and functionally complex and dynamic. In comparison to the design of a house, park design is complex. The manner in which a house is designed is a fairly straight-forward architectural process. As for a park, its complexity and dynamics render much of these approaches inappropriate and yet, as shown in the book, that is how parks are being designed habitually.The book proposes that the design of a park be treated as a puzzle because like in ordinary puzzles it is made up of parts which somehow must be correctly related for the puzzle to be solved. If the puzzle is wrongly handled the proofs of that will inevitably surface. Unlike ordinary puzzles the parts are not static and also have complex and dynamic interactions amongst themselves. In the book some of these are demonstrated to highlight the fallacies in design approaches which do not treat this reality with the seriousness it deserves. The book argues that given the above characteristics of a park its future would be ensured if greater emphasis were placed on the institutional dimensions of the park's development. Institutions are portrayed as living systems. As such they are made-up of parts which make them function as entities. The death of an individual person or the loss of one facility in the institution, is compared to the death of a cell in an multi-celled organism or of a tree in a forest. It is argued that if some of the parts (cf. organs in an organism) do not function properly, the growth and development of the institution will be affected. Similarly, an unfavourable external environment, despite normally functional internal systems, will hinder the normal growth and development of the institution. Instead of putting the emphasis on defining the details of management programmes (e.g. frequency of burning), park design should therefore focus on defining an appropriate institutional make-up that would favour a sustainable development of the park. Accordingly the design should enable the park to develop its capabilities and to increasingly be able to use experiences drawn from past attempts iteratively so as to solve the ceaselessly changing design puzzle. To accumulate experience on a long-term basis calls for the innovation of appropriate memory systems , and in building this "park organ" the computer-based information systems could play an important role.Viewing the design of a park as a puzzle calls for the innovation of tools to minimise the risks and expenses associated with failures to solve the puzzle. In this respect the potential role of computers is again highlighted. It is suggested that the use of computerbased information systems could facilitate desk-top testing and communicating of park design ideas. There remains, however, the need to define what would constitute appropriate information system models for such purposes.Through case studies on the Murchison Falls Park, Uganda, attention is drawn to the dynamic and complex nature of a park system. Murchison Falls Park is an example of a park that has witnessed drastic ecological changes and has been ravaged by wars. Looking beyond the wars the park region needs reconstruction and rehabilitation of its socio-economic infrastructure. With special reference to the park, key aspects of the design of a park has been examined. Amongst others aspects such as fire, vegetation dynamics, patterns in herbivore densities and poaching have been examined in a series of case studies on the park. Through these studies of the park system structure and processes various aspects on which park design should focus are highlighted. The studies highlight the need for deep insight into the patterns and processes of a system if a design is to succeed. Since in all parks such insight always is lacking, the book argues that park design is reduced to trial and error and should be formally treated as such. The book concludes there is an urgent need for new perceptions in the design of parks, that for this tools have yet to be innovated, and that the future of green design and with it sustainable land development will depend on the improved understanding of the dynamics of relevant institutions. It is recommended that park design should take advantage of the fast growing computer-based information systems to manage, process and feedback relevant data and to test model design in virtual versions before resources are committed to their implementation. Future research should help define appropriate park information system models. Looking beyond the wars these are some of the key areas on which park design should focus for sustainable progress to be made in the attempts to solve the park design puzzles
Evaluating Reproducibility in Computational Biology Research
No full textFor my Honors Senior Project, I read five research papers in the field of computational biology and attempted to reproduce the results. However, for the most part, this proved a challenge, as many details vital to utilizing relevant software and data had been excluded. Using Geir Kjetil Sandve\u27s paper Ten Simple Rules for Reproducible Computational Research as a guide, I discuss how authors of these five papers did and did not obey these rules of reproducibility and how this affected my ability to reproduce their results
CGAT: Cell Graph ATtention Network for Grading of Pancreatic Disease Histology Images
No full textEarly detection of Pancreatic Ductal Adenocarcinoma (PDAC), one of the most aggressive malignancies of the pancreas, is crucial to avoid metastatic spread to other body regions. Detection of pancreatic cancer is typically carried out by assessing the distribution and arrangement of tumor and immune cells in histology images. This is further complicated due to morphological similarities with chronic pancreatitis (CP), and the co-occurrence of precursor lesions in the same tissue. Most of the current automated methods for grading pancreatic cancers rely on extensive feature engineering involving accurate identification of cell features or utilising single number spatially informed indices for grading purposes. Moreover, sophisticated methods involving black-box approaches, such as neural networks, do not offer insights into the model’s ability to accurately identify the correct disease grade. In this paper, we develop a novel cell-graph based Cell-Graph Attention (CGAT) network for the precise classification of pancreatic cancer and its precursors from multiplexed immunofluorescence histology images into the six different types of pancreatic diseases. The issue of class imbalance is addressed through bootstrapping multiple CGAT-nets, while the self-attention mechanism facilitates visualization of cell-cell features that are likely responsible for the predictive capabilities of the model. It is also shown that the model significantly outperforms the decision tree classifiers built using spatially informed metric, such as the Morisita-Horn (MH) indices
DataSheet_1_CGAT: Cell Graph ATtention Network for Grading of Pancreatic Disease Histology Images.pdf
No full textEarly detection of Pancreatic Ductal Adenocarcinoma (PDAC), one of the most aggressive malignancies of the pancreas, is crucial to avoid metastatic spread to other body regions. Detection of pancreatic cancer is typically carried out by assessing the distribution and arrangement of tumor and immune cells in histology images. This is further complicated due to morphological similarities with chronic pancreatitis (CP), and the co-occurrence of precursor lesions in the same tissue. Most of the current automated methods for grading pancreatic cancers rely on extensive feature engineering involving accurate identification of cell features or utilising single number spatially informed indices for grading purposes. Moreover, sophisticated methods involving black-box approaches, such as neural networks, do not offer insights into the model’s ability to accurately identify the correct disease grade. In this paper, we develop a novel cell-graph based Cell-Graph Attention (CGAT) network for the precise classification of pancreatic cancer and its precursors from multiplexed immunofluorescence histology images into the six different types of pancreatic diseases. The issue of class imbalance is addressed through bootstrapping multiple CGAT-nets, while the self-attention mechanism facilitates visualization of cell-cell features that are likely responsible for the predictive capabilities of the model. It is also shown that the model significantly outperforms the decision tree classifiers built using spatially informed metric, such as the Morisita-Horn (MH) indices.</p
GWC-DCMB/curriculum-notebooks: v0.1.0
No full textThis version contains the manuscript submitted to JOSE
J Open Source Educ
No full textWe are bioinformatics trainees at the University of Michigan who started a local chapter of Girls Who Code to provide a fun and supportive environment for high school women to learn the power of coding. Our goal was to cover basic coding topics and data science concepts through live coding and hands-on practice. However, we could not find a resource that exactly met our needs. Therefore, over the past three years, we have developed a curriculum and instructional format using Jupyter notebooks to effectively teach introductory Python for data science. This method, inspired by The Carpentries organization, uses bite-sized lessons followed by independent practice time to reinforce coding concepts, and culminates in a data science capstone project using real-world data. We believe our open curriculum is a valuable resource to the wider education community and hope that educators will use and improve our lessons, practice problems, and teaching best practices. Anyone can contribute to our Open Educational Resources on GitHub.F31 LM012946/LM/NLM NIH HHSUnited States/T32 AI007528/AI/NIAID NIH HHSUnited States/T42 OH008455/OH/NIOSH CDC HHSUnited States/T32 DA007281/DA/NIDA NIH HHSUnited States/T32 HG000040/HG/NHGRI NIH HHSUnited States/T32 GM070449/GM/NIGMS NIH HHSUnited States/R01 ES028802/ES/NIEHS NIH HHSUnited States/T32 NS076401/NS/NINDS NIH HHSUnited States/T32 CA140044/CA/NCI NIH HHSUnited States
547 Identification of the immune landscape in penile squamous cell carcinoma using multiplex immunofluorescence and spatial image analysis
No full textMHC Class II Expression Influences the Composition and Distribution of Immune Cells in the Metastatic Colorectal Cancer Microenvironment
No full textDespite advances in therapy over the past decades, metastatic colorectal cancer (mCRC) remains a highly morbid disease. While the impact of MHC-I on immune infiltration in mCRC has been well studied, data on the consequences of MHC-II loss are lacking. Multiplex fluorescent immunohistochemistry (mfIHC) was performed on 149 patients undergoing curative intent resection for mCRC and stratified into high and low human leukocyte antigen isotype DR (HLA-DR) expressing tumors. Intratumoral HLA-DR expression was found in stromal bands, and its expression level was associated with different infiltrating immune cell makeup and distribution. Low HLA-DR expression was associated with increased intercellular distances and decreased population mixing of T helper cells and antigen-presenting cells (APC), suggestive of decreased interactions. This was associated with less co-localization of tumor cells and cytotoxic T lymphocytes (CTLs), which tended to be in a less activated state as determined by Ki67 and granzyme B expression. These findings suggest that low HLA-DR in the tumor microenvironment of mCRC may reflect a state of poor helper T-cell interactions with APCs and CTL-mediated anti-tumor activity. Efforts to restore/enhance MHC-II presentation may be a useful strategy to enhance checkpoint inhibition therapy in the future
MHC Class II Expression Influences the Composition and Distribution of Immune Cells in the Metastatic Colorectal Cancer Microenvironment
No full textDespite advances in therapy over the past decades, metastatic colorectal cancer (mCRC) remains a highly morbid disease. While the impact of MHC-I on immune infiltration in mCRC has been well studied, data on the consequences of MHC-II loss are lacking. Multiplex fluorescent immunohistochemistry (mfIHC) was performed on 149 patients undergoing curative intent resection for mCRC and stratified into high and low human leukocyte antigen isotype DR (HLA-DR) expressing tumors. Intratumoral HLA-DR expression was found in stromal bands, and its expression level was associated with different infiltrating immune cell makeup and distribution. Low HLA-DR expression was associated with increased intercellular distances and decreased population mixing of T helper cells and antigen-presenting cells (APC), suggestive of decreased interactions. This was associated with less co-localization of tumor cells and cytotoxic T lymphocytes (CTLs), which tended to be in a less activated state as determined by Ki67 and granzyme B expression. These findings suggest that low HLA-DR in the tumor microenvironment of mCRC may reflect a state of poor helper T-cell interactions with APCs and CTL-mediated anti-tumor activity. Efforts to restore/enhance MHC-II presentation may be a useful strategy to enhance checkpoint inhibition therapy in the future
