Machine learning classification of surgical pathology reports and chunk recognition for information extraction noise reduction

Background and aims: Machine learning techniques for the text mining of cancer-related clinical documents have not been sufficiently explored. Here some techniques are presented for the pre-processing of free-text breast cancer pathology reports, with the aim of facilitating the extraction of information relevant to cancer staging.

Materials and methods: The first technique was implemented using the freely available software RapidMiner to classify the reports according to their general layout: ‘semi-structured’ and ‘unstructured’. The second technique was developed using the open source language engineering framework GATE and aimed at the prediction of chunks of the report text containing information pertaining to the cancer morphology, the tumour size, its hormone receptor status and the number of positive nodes. The classifiers were trained and tested respectively on sets of 635 and 163 manually classified or annotated reports, from the Northern Ireland Cancer Registry.

Results: The best result of 99.4% accuracy – which included only one semi-structured report predicted as unstructured – was produced by the layout classifier with the k nearest algorithm, using the binary term occurrence word vector type with stopword filter and pruning. For chunk recognition, the best results were found using the PAUM algorithm with the same parameters for all cases, except for the prediction of chunks containing cancer morphology. For semi-structured reports the performance ranged from 0.97 to 0.94 and from 0.92 to 0.83 in precision and recall, while for unstructured reports performance ranged from 0.91 to 0.64 and from 0.68 to 0.41 in precision and recall. Poor results were found when the classifier was trained on semi-structured reports but tested on unstructured.

Conclusions: These results show that it is possible and beneficial to predict the layout of reports and that the accuracy of prediction of which segments of a report may contain certain information is sensitive to the report layout and the type of information sought.

Building a 'Repository of Science': the importance of integrating Biobanks within molecular pathology programmes

Repositories containing high quality human biospecimens linked with robust and relevant clinical and pathological information are required for the discovery and validation of biomarkers for disease diagnosis, progression and response to treatment. Current molecular based discovery projects using either low or high throughput technologies rely heavily on ready access to such sample collections. It is imperative that modern biobanks align with molecular diagnostic pathology practices not only to provide the type of samples needed for discovery projects but also to ensure requirements for ongoing sample collections and the future needs of researchers are adequately addressed. Biobanks within comprehensive molecular pathology programmes are perfectly positioned to offer more than just tumour derived biospecimens; for example, they have the ability to facilitate researchers gaining access to sample metadata such as digitised scans of tissue samples annotated prior to macrodissection for molecular diagnostics or pseudoanonymised clinical outcome data or research results retrieved from other users utilising the same or overlapping cohorts of samples. Furthermore, biobanks can work with molecular diagnostic laboratories to develop standardized methodologies for the acquisition and storage of samples required for new approaches to research such as ‘liquid biopsies’ which will ultimately feed into the test validations required in large prospective clinical studies in order to implement liquid biopsy approaches for routine clinical practice. We draw on our experience in Northern Ireland to discuss how this harmonised approach of biobanks working synergistically with molecular pathology programmes is key for the future success of precision medicine.

The Cardiovascular Pathology of Stimulant Overdose Decedents in King County, Washington

Thesis (Master's)--University of Washington, 2016-09

The pathology of command and control: a formal synthesis

One of the most important theories in the study of environmental governance and policy is the pathology of command and control, which describes the negative consequences of top-down, technocratic governance of social and ecological systems. However, to date, this theory has been expressed somewhat inconsistently and informally in the literature, even by the seminal works that have established its importance and popularized it. This presents a problem for the sustainability science community if it cannot be sure of the precise details of one of its most important theories. Without such precision, applications and tests of various elements of the theory cannot be conducted reliably to advance the knowledge of environmental governance. I address this problem by synthesizing several seminal works to formalize this theory. The formalization involves the identification of the individual elements of the theory and a diagrammatic description of their relationships with each other that unfold in a series of semi-independent causal paths. Ideally, with such a formalization, scholars can use this theory more reliably and more meaningfully in their future work. I conclude by discussing the implications this theory has for the governance of natural resources.

Spike-timing dependent plasticity and connectivity in primate sensorimotor cortex

Thesis (Ph.D.)--University of Washington, 2016-06

Organisation chimioanatomique des afférences pallidales chez le primate

L’élucidation de la position qu’occupent les projections sérotoninergique (5-HT), cholinergique (ACh) et dopaminergique (DA) du tronc cérébral dans l’organisation anatomofonctionelle du globus pallidus externe (GPe) et interne (GPi) au sein des ganglions de la base chez le primate est primordiale à la compréhension de ce système neuronal hautement complexe impliqué dans le contrôle du comportement moteur. Les travaux de recherche consolidés dans la présente thèse rapportent les résultats principalement obtenus chez le singe écureuil (Saimiri sciureus) à l’aide de marquages immunohistochimiques et de quantifications stéréologiques servant à évaluer la distribution régionale et les caractéristiques ultrastructurales des varicosités axonales 5-HT, ACh et DA observées dans le pallidum. Nos données ont permis l’éloboration d’un nouveau modèle du neurone pallidal en tenant compte de la hiérarchie et des caractéristiques neurochimiques de ses entrées synaptiques. Ainsi, l’analyse quantitative en microscopie optique révèle que le GPe et le GPi reçoivent des innervations 5-HT, ACh et DA de densités variables et distribuées de façon hétérogène. Plus particulièrement, le GPe est innervé par 600 000 varicosités 5-HT/mm3 de tissu, 500 000 varicosités ACh/mm3 et 170 000 varicosités DA/mm3. En revanche, le GPi reçoit 600 000 varicosités 5-HT/mm3, 250 000 varicosités ACh/mm3 et 190 000 varicosités DA/mm3. De plus, la 5-HT, l’ACh et la DA ciblent préférentiellement les secteurs correspondant aux territoires fonctionnels associatifs et limbiques du pallidum, suggérant un rôle de ces projections dans la planification du comportement moteur ainsi que dans la régulation de l’attention et de l’humeur. Nos analyses en microscopie électronique révèlent que très peu de ces varicosités axonales établissent un contact synaptique, puisque plus de 70% des varicosités 5-HT, ACh et DA sont complètement dépouvues de jonction synaptique. Ainsi, bien que la 5-HT, l’ACh et la DA seraient en mesure de moduler directement les neurones pallidaux grâce à la transmission synaptique, leur plus grande influence s’opérerait par la transmission volumique, permettant d’influencer à la fois les neurones pallidaux et leurs afférences, principalement du striatum et noyau subthalamique. L’ensemble de ces résultats indique que les projections 5-HT, ACh et DA du tronc cérébral agissent de concert avec les afférences plus robustes en provenance du striatum et du noyau subthalamique. Ces nouvelles données neuroanatomiques positionnent le tronc cérébral en tant qu’acteur important dans l’organisation anatomique et fonctionnelle du pallidum chez le primate et doivent être prises en considération dans l’élaboration de nouvelles approches thérapeutiques visant à contrer les processus neurodégénératifs qui affectent les ganglions de la base, tel que la maladie de Parkinson.

Investigating the Diabetic Brain: The Effects of Pioglitazone and Insulin on the Cellular Processes and Pathology of Alzheimer's Disease

Alzheimer’s disease (AD) is the sixth leading cause of death in the US. Some researchers refer to AD as “Type III Diabetes” because of reported glucose metabolism dysfunction. Preclinical studies suggest increasing insulin decreases AD pathology, although the mechanism remains unclear. To sensitize insulin signaling, this study activated Peroxisome Proliferator-Activated Receptor Gamma using intranasal co-administration of pioglitazone (PGZ) and insulin. This method targeted the site of action to reduce peripheral effects and to maximize impact in transgenic mice expressing AD pathology. Data from GC-MS fluxomics analysis suggested that PGZ+Insulin increased glucose metabolism in the brain. Immunohistochemistry with relevant antibodies was used to identify AD pathological markers in the subiculum, indicating that PGZ+Insulin decreased pathology compared to Insulin and Saline. This suggests that increasing glucose uptake in the brain alleviated AD pathology, further clarifying the role of insulin signaling in AD pathology.Gemstone

eLearning in the context of a one-year postgraduate course in macroscopy in pathology: benefits of a multifaceted and pluripotent concept

Performing Macroscopy in Pathology implies to plan and implement methods of selection, description and collection of biological material from human organs and tissues, actively contributing to the clinical pathology analysis by preparing macroscopic report and the collection and identification of fragments, according to the standardized protocols and recognizing the criteria internationally established for determining the prognosis. The Macroscopy in Pathology course is a full year program with theoretical and pratical components taught by Pathologists. It is divided by organ/system surgical pathology into weekly modules and includes a practical "hands-on" component in Pathology Departments. The students are 50 biomedical scientists aged from 22 to 50 years old from all across the country that want to acquire competences in macroscopy. A blended learning strategy was used in order to: give students the opportunity to attend from distance; support the contents, lessons and the interaction with colleagues and teachers; facilitate the formative/summative assessment.

How institutions shaped the last major evolutionary transition to large-scale human societies.

What drove the transition from small-scale human societies centred on kinship and personal exchange, to large-scale societies comprising cooperation and division of labour among untold numbers of unrelated individuals? We propose that the unique human capacity to negotiate institutional rules that coordinate social actions was a key driver of this transition. By creating institutions, humans have been able to move from the default ‘Hobbesian’ rules of the ‘game of life’, determined by physical/environmental constraints, into self-created rules of social organization where cooperation can be individually advantageous even in large groups of unrelated individuals. Examples include rules of food sharing in hunter–gatherers, rules for the usage of irrigation systems in agriculturalists, property rights and systems for sharing reputation between mediaeval traders. Successful institutions create rules of interaction that are self-enforcing, providing direct benefits both to individuals that follow them, and to individuals that sanction rule breakers. Forming institutions requires shared intentionality, language and other cognitive abilities largely absent in other primates. We explain how cooperative breeding likely selected for these abilities early in the Homo lineage. This allowed anatomically modern humans to create institutions that transformed the self-reliance of our primate ancestors into the division of labour of large-scale human social organization.

Survey on parasites of Rutilus frisii Kutum in South west of Caspian Sea with the emphasis of pathology of Dactylogyrus frisii and morphological identification of Paradiplozoon sp and Anisakis sp

Rutilus frisii Kutum is one of the most precious fish in the Caspian Sea. Investigation of the various aspects of its biocharactristics. Including its parasite fauna and ecological aspects are of prime importance. In this study the farmed kutum fry were on the focus of investigation in various seasons of the year and prior to their being released in the sea. This included also the study on the kutum spawners caught both from liver and the sea. The results were that 17 external and internal parasite species were distinct within different organs which were further identified down to genus and species. The single celled parasites identified included Ichthyophthirius multifilils, Chilodonella hexastica, Chilodonella pisicola, Trichodina sp Along with the monogene parasites that included Paradiplozoon chazaricum, D. rarissimus, D. turaliensis, D. nybelini, Dactylogyrus frisii. Meanwhile Diplostomum spathaceum constituted the single eyed parasites and the intestinal termatode were Aspidogaster limacoides, Asymphyoldora kubanicum as well as Bothriocephalus gowkongeniss as the sestads. The nematodes defrentiated were Raphidascaris acus, Dioctophyma renale, and Eustrongylides excisus followed by Lernaea cyprinacea as a crustacean. In this study, infestations by single celled parasites, crustaceans and sestod were found to be present only among the farmed kutum fry which varied in terms of percentage and intensity of infection as well as the parasite species and season of the year. The highest percentage of infection among kutum fry and spawners in both fresh water and in the sea during all seasons belonged to monogene parasites (33%). This was up to 100% among spawners. Infection caused by nematodes was exclusively detected among riverine spawners (7.5-5%) and the infection by Asymphyoldora kubanicum and Aspidogaster limacoides among Spawners caught at Sea and rivers varied within different seasons of the year. The infestation of Metacercer diplostomum spathaceum among kutum fry was 12% which compared to spawners was in slightly higher level. The study could identify Dioctophyma renale for the first time in the country and Eustrongylidis excisu was also detected among Rutilus frisii kutum.

Play behaviour in nonhuman animals and the animal welfare issue

The mission of defining animal welfare indicators is methodologically difficult, limited, and possibly impossible. A promising alternative, however, to evaluate suitable environmental conditions is the assessment of play behaviour. In the present review, we summarise the general aspects of play behaviour in nonhuman animals and propose its use as a potential indicator of animal welfare. Play behaviour probably occurs in most vertebrates and some invertebrates, but predominately in mammals. It is also more frequent in young males and is associated with the environmental context in which animals find themselves. Animals play if they are healthy and well-fed, but not if they are under stressful conditions or if they are in a stressful state. We can therefore use the prevalence of play behaviour as an indicator of suitable environmental conditions, considering the specificity associated with the above-mentioned modifying factors.

Epothilone-d rescues cognition and attenuates alzheimer’s disease-like pathology in APP/PS1 mice

AIMS: Cognitive decline in Alzheimer's disease (AD) patients has been linked to synaptic damage and neuronal loss. Hyperphosphorylation of tau protein destabilizes microtubules leading to the accumulation of autophagy/vesicular material and the generation of dystrophic neurites, thus contributing to axonal/synaptic dysfunction. In this study, we analyzed the effect of a microtubule-stabilizing compound in the progression of the disease in the hippocampus of APP751SL/PS1M146L transgenic model. METHODS: APP/PS1 mice (3 month-old) were treated with a weekly intraperitoneal injection of 2 mg/kg epothilone-D (Epo-D) for 3 months. Vehicle-injected animals were used as controls. Mice were tested on the Morris water maze, Y-maze and object-recognition tasks for memory performance. Abeta, AT8, ubiquitin and synaptic markers levels were analyzed by Western-blots. Hippocampal plaque, synaptic and dystrophic loadings were quantified by image analysis after immunohistochemical stainings. RESULTS: Epo-D treated mice exhibited a significant improvement in the memory tests compared to controls. The rescue of cognitive deficits was associated to a significant reduction in the AD-like hippocampal pathology. Levels of Abeta, APP and ubiquitin were significantly reduced in treated animals. This was paralleled by a decrease in the amyloid burden, and more importantly, in the plaque-associated axonal dystrophy pathology. Finally, synaptic levels were significantly restored in treated animals compared to controls. CONCLUSION: Epo-D treatment promotes synaptic and spatial memory recovery, reduces the accumulation of extracellular Abeta and the associated neuritic pathology in the hippocampus of APP/PS1 model. Therefore, microtubule stabilizing drugs could be considered therapeutical candidates to slow down AD progression. Supported by FIS-PI12/01431 and PI15/00796 (AG),FIS-PI12/01439 and PI15/00957(JV)

Clustering of tau-immunoreactive pathology in chronic traumatic encephalopathy

Chronic traumatic encephalopathy (CTE) is a neurodegenerative disorder which may result from repetitive brain injury. A variety of tau-immunoreactive pathologies are present, including neurofibrillary tangles (NFT), neuropil threads (NT), dot-like grains (DLG), astrocytic tangles (AT), and occasional neuritic plaques (NP). In tauopathies, cellular inclusions in the cortex are clustered within specific laminae, the clusters being regularly distributed parallel to the pia mater. To determine whether a similar spatial pattern is present in CTE, clustering of the tau-immunoreactive pathology was studied in the cortex, hippocampus, and dentate gyrus in 11 cases of CTE and 7 cases of Alzheimer’s disease neuropathologic change (ADNC) without CTE. In CTE: (1) all aspects of tau-immunoreactive pathology were clustered and the clusters were frequently regularly distributed parallel to the tissue boundary, (2) clustering was similar in two CTE cases with minimal co-pathology compared with cases with associated ADNC or TDP-43 proteinopathy, (3) in a proportion of cortical gyri, estimated cluster size was similar to that of cell columns of the cortico-cortical pathways, and (4) clusters of the tau-immunoreactive pathology were infrequently spatially correlated with blood vessels. The NFT and NP in ADNC without CTE were less frequently randomly or uniformly distributed and more frequently in defined clusters than in CTE. Hence, the spatial pattern of the tau-immunoreactive pathology observed in CTE is typical of the tauopathies but with some distinct differences compared to ADNC alone. The spread of pathogenic tau along anatomical pathways could be a factor in the pathogenesis of the disease.