Diagnostic Prediction Using Discomfort Drawings with IBTM

In this paper, we explore the possibility to apply machine learning to make diagnostic predictions using discomfort drawings. A discomfort drawing is an intuitive way for patients to express discomfort and pain related symptoms. These drawings have proven to be an effective method to collect patient data and make diagnostic decisions in real-life practice. A dataset from real-world patient cases is collected for which medical experts provide diagnostic labels. Next, we use a factorized multimodal topic model, Inter-Battery Topic Model (IBTM), to train a system that can make diagnostic predictions given an unseen discomfort drawing. The number of output diagnostic labels is determined by using mean-shift clustering on the discomfort drawing. Experimental results show reasonable predictions of diagnostic labels given an unseen discomfort drawing. Additionally, we generate synthetic discomfort drawings with IBTM given a diagnostic label, which results in typical cases of symptoms. The positive result indicates a significant potential of machine learning to be used for parts of the pain diagnostic process and to be a decision support system for physicians and other health care personnel.Comment: Presented at 2016 Machine Learning and Healthcare Conference (MLHC 2016), Los Angeles, C

Bilder av Fredrika

Syftet med uppsatsen är att undersöka hur en plats kan beskrivas och vilken mening som tillskrivs den. Fredrika är en mindre tätort i Västerbottens län beläget vid Viskasjöns strand. Här bor lite drygt 200 människor och i denna uppsats får vi möta sex av dem. I materialet som grundas på kvalitativa intervjuer beskrivs hur invånarna ser på sin bygd, hur det är att leva där och tankar kring framtidens utmaningar och möjligheter. För att göra detta sammankopplas ovannämnd information till teorier inom samhällsvetenskap och socialkonstruktivism och begrepp som space, imaginative geographies och reciprocitet blir satta i arbete i en analys av platsförståelse. Vidare diskuteras den gestaltning av Fredrika som sker i det offentliga rummet, som till exempel i tv, tidningar och radio. Hur ser framställningarna ut, varför ser de ut som de gör och hur relaterar invånarna till dessa bilder? För att möta dessa frågor blir begreppet representation användbart och bidrar till diskussionen om en stadsnorm. Detta innebär strukturer där staden blir ansett som det normala och landsbygden som det avvikande. Med stöd i uppsatsens upptäckter hävdar jag till sist att de strukturer och normer som ger staden företräde att representera landsbygden är både kraftfulla och destruktiva. Min slutsats är att när människors val kring vart man vill bosätta sig och leva sina liv inte längre blir ens egna innebär detta ett betydande problem ur frihets- och rättvisesynpunkt. Dessutom är detta inte bara ett problem som påverkar en plats som Fredrika, utan även svensk landsbygd i stort.This thesis aims to examine how a place may be described and what meanings that are attached to it. Fredrika is a village in the county of Västerbotten nestled by the shores of Lake Viskasjön. Just over 200 people reside here and in this thesis we get to meet six of them. Using material based on qualitative interviews, the ways in which these inhabitants understand their hometown, -in terms of what it is like to live there, and their thoughts regarding the challenges and possibilities of the future- are described. Upon doing so this paper then attempts to connect the aforementioned material to theories from the social science and the social constructionist schools of thought. Constructs such as space, imaginative geographies and reciprocity are utilized in an analysis of ways to understand place. Additionally, the image of Fredrika that is commonly portrayed in public spheres -such as television, newspapers and radio -is discussed. What does the image look like, why is it made to look this way and how do the inhabitants relate to it? In attempting to discuss these questions the construct of representation is useful and contributes to the discourse of an urban norm, -this norm being a structure which presents the city as the normal and the rural as the abnormal. Finally, I will summarize that the findings of the thesis suggest that the structures and norms that are granting the urban the authority to navigate the represent the rural are both powerful and destructive. My conclusion is that when individual’s choices regarding where to settle and live are no longer able to be made autonomously, there becomes a significant problem in terms of liberty and justice. Furthermore, this problem effects not only a place like Fredrika, but also the Swedish countryside at large

Isolation and characterization of Bacillus thuringiensis from soils in contrasting agroecological zones of Ethiopia

Phenotypic and molecular methods were used to isolate and characterize B. thuringiensis from diverse agro-ecological zones of Ethiopia. Bioassays were used to test the insecticidal activity of B. thuringiensis strains against the major malaria vector, Anopheles arabiensis (Diptera).  B. thuringiensis were isolated from 32% of the total 503 soil samples collected from the 16 agro-ecological zones. All sequenced isolates were 99%–100% identical to each other and to B. thuringiensis entries in Genbank. B. thuringiensis with similar 16S rRNA gene sequences from these different zones were characterized with regard to maximum growth rate and temperature optima for growth to test if there was local adaptation in these functional traits. The result showed a narrow temperature range around 30°C for maximal growth rate, and there were no significant differences between agro-ecological zones. Of 110 Bacillus thuringiensis isolates analyzed for the presence of crystal protein genes,  7 tested positive for cry 4, cry 11, and cyt toxin genes. Sequencing of these genes in positive strains demonstrated 99–100 % homology to known mosquitocidal cry and cyt genes in Bacillus thuringiensis subsp. israelensis. The present study shows that this biotechnologically important species is wide spread in Ethiopian soils and that it does not demonstrate local adaptation to temperature regimes, at least not for basic functions such as growth-temperature response. Our finding also pointed the potential for exploiting this species in vector control programs.

Neuropathic Pain Diagnosis Simulator for Causal Discovery Algorithm Evaluation

Discovery of causal relations from observational data is essential for many disciplines of science and real-world applications. However, unlike other machine learning algorithms, whose development has been greatly fostered by a large amount of available benchmark datasets, causal discovery algorithms are notoriously difficult to be systematically evaluated because few datasets with known ground-truth causal relations are available. In this work, we handle the problem of evaluating causal discovery algorithms by building a flexible simulator in the medical setting. We develop a neuropathic pain diagnosis simulator, inspired by the fact that the biological processes of neuropathic pathophysiology are well studied with well-understood causal influences. Our simulator exploits the causal graph of the neuropathic pain pathology and its parameters in the generator are estimated from real-life patient cases. We show that the data generated from our simulator have similar statistics as real-world data. As a clear advantage, the simulator can produce infinite samples without jeopardizing the privacy of real-world patients. Our simulator provides a natural tool for evaluating various types of causal discovery algorithms, including those to deal with practical issues in causal discovery, such as unknown confounders, selection bias, and missing data. Using our simulator, we have evaluated extensively causal discovery algorithms under various settings.Comment: Accepted by NeurIPS 2019, 6 figures, 10 table

Imaging of Vascular Smooth Muscle Cells with Soft X-Ray Spectromicroscopy

Using X-ray microscopy and spectromicroscopy, vascular smooth muscle cells (VSMCs) were imaged, prepared without using additional embedding material or staining, but by applying simple, noncryo fixation techniques. The cells were imaged with a compact source transmission X-ray microscope and a scanning transmission X-ray microscope (STXM). With the STXM, spectromicroscopy was performed at the C K-edge and the Ca LIII,II-edges. VSMCs were chosen because of their high amount of actin stress fibers, so that the actin cytoskeleton should be visible. Other parts of the cell, such as the nucleus and organelles, were also identified from the micrographs. Both in the spectra and the images, the effects of the different preparation procedures were observable. Furthermore, Ca hotspots were detected and their density is determine

Synovial neuronal changes in knee joint osteoarthritis

Abstract Purpose: The purpose is to study whether pain and inflammation in knee joint osteoarthritis (OA) are associated with local synovial neuronal changes. Methods: Synovial biopsies were harvested from the medial and lateral knee compartments from OA patients undergoing total joint replacement surgery. All patients had predominant pain at the medial joint compartment. Pain and knee joint function were evaluated by knee society score (KSS). Synovial inflammation was analyzed by histopathological analysis and expression of growth associated protein-43 (GAP-43), sensory (SP, CGRP) and autonomic (NPY, VIP, TH) neuropeptides was studied by single and double immunohistochemistry techniques. Results: We observed reduced KSS and increased inflammatory score in synovial membrane of medial knee compartment. A significant increase in GAP-43 [P = 0.001], SP [P = 0.05], CGRP [P = 0.05] and TH [P = 0.05] expression was observed and SP, CGRP and NPY were found to be co-existed predominantly with GAP-43 in synovial membrane collected from medial compared to the lateral knee compartment. Conclusions: Regenerating nerve fibers containing sensory and autonomic neuropeptides are associated with pain and inflammation in knee joint O

Compact Zernike phase contrast X-ray microscopy using a single-element optic

We demonstrate Zernike phase contrast in a compact soft x-ray microscope using a single-element optic. The optic is a combined imaging zone plate and a Zernike phase plate and does not require any additional alignment or components. Contrast is increased and inversed in an image of a test object using the Zernike zone plate. This type of optic may be implemented into any existing x-ray microscope where phase contrast is of interest

Compact Zernike phase contrast X-ray microscopy using a single-element optic

We demonstrate Zernike phase contrast in a compact soft x-ray microscope using a single-element optic. The optic is a combined imaging zone plate and a Zernike phase plate and does not require any additional alignment or components. Contrast is increased and inversed in an image of a test object using the Zernike zone plate. This type of optic may be implemented into any existing x-ray microscope where phase contrast is of interest