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  • About
  • The Global ETD Search service is a free service for researchers to find electronic theses and dissertations. This service is provided by the Networked Digital Library of Theses and Dissertations.
    Our metadata is collected from universities around the world. If you manage a university/consortium/country archive and want to be added, details can be found on the NDLTD website.
21

Molecular Radionuclide Imaging Using Site-specifically Labelled Recombinant Affibody Molecules : Preparation and Preclinical Evaluation

Ahlgren, Sara January 2010 (has links)
Radionuclide molecular imaging is an emerging multidisciplinary technique that is used in modern medicine to visualise diseases at cellular and molecular levels. This thesis is based on five papers (I-V) and focuses on the development of site-specific radiolabelled recombinant anti-HER2 Affibody molecules and preclinical evaluations in vitro and in vivo of the labelled conjugates. This work is part of a preclinical development of an Affibody molecule-based tracer for molecular imaging of HER2 expressing tumours. Papers I and II report the evaluation of the Affibody molecule ZHER2:2395-C, site-specifically labelled with the radiometals 111In (for SPECT) and 57Co (as a surrogate for 55Co, suitable for PET applications) using a thiol reactive DOTA derivative as a chelator. Both conjugates demonstrated very suitable biodistribution properties, enabling high contrast imaging just a few hours after injection. Papers III and IV report the development and optimization of a technique for site-specific labelling of ZHER2:2395-C with 99mTc using an N3S chelating peptide sequence. 99mTc-ZHER2:2395-C demonstrated high and specific tumour uptake and rapid clearance of non-bound tracer from the blood, resulting in high tumour-to-non-tumour ratios shortly after injection, enabling high contrast imaging. In addition, in the study described in paper IV, freeze-dried kits previously developed for 99mTc-labelling were optimised, resulting in the development of a kit in which all the reagents and protein needed for labelling of ZHER2:2395-C with 99mTc were contained in a single vial. Paper V reports the evaluation of an anti-HER2 Affibody molecule, ABY-025, with a fundamentally re-engineered scaffold. Despite the profound re-engineering, the biodistribution pattern of 111In-ABY-025 was very similar to that of two variants of the parental molecule. It seems reasonable to believe that these results will also be applicable to Affibody molecules towards other targets. Hopefully, this work will also be helpful in the development of other small proteinaceous tracers.
22

Prostate Cancer Diagnosis : experimental and Clinical Studies With HRMAS NMR Spectroscopy

Stenman, Katarina January 2011 (has links)
A few abnormal cells found in a small piece of prostate tissue are most consequential for a man’s future. The prevalence of prostate cancer (PCa) is increasing globally. The main instigating factor for this cancer is not yet known, but it appears to be the consequence of many variables such as an increasingly older population, more frequent PSA-testing, and factors involving lifestyle. Prostate cancer screening, as an equivalent for breast cancer screening, has been suggested but unfortunately there are no accurate diagnostic tools available for this type of screening. The reason for this is simply that the prostate is one of the most difficult organs to diagnose and, consequently, PCa screening would generate far too many false-positive and false-negative results.  The prostate is not easily accessible as it is deeply-seated in the male pelvic area, wrapped around the urethra and surrounded by sensitive vital organs.  Furthermore, PCa is frequently multi-focal, and the cancer cells have a tendency of assimilating among normal cells and, thus, do not always form solid lumps.  Therefore, prostate tumors are often not felt by digital rectal examination (DRE) or identified by imaging.  The PSA-test is not reliable as it is more prostate-specific than cancer-specific.  Due to increasing prostate awareness, more early-stage and locally confined PCa are being detected. This is saving lives, although there is a high risk of over treatment and unnecessary side-effects.  The increased detection of PCa requires sophisticated diagnostic methods and highly skilled clinicians who can discern between indolent and aggressive cancers.  The current “gold-standard” for PCa diagnosis is biopsy grading by pathologists using the Gleason score system, which is a difficult task.  Therefore, innovative methods to improve the precision of prostate diagnosis, by increased biopsy sensitivity and tumor localization, are of essence. In light of these difficulties, the metabolomic approach using 1D and 2D high-resolution magic angle spinning (HRMAS) NMR spectroscopy combined with histopathology on intact prostatectomy specimens was evaluated in this research project.  The non-destructive nature of HRMAS NMR enables spectroscopic analysis of intact tissue samples with consecutive histological examinations under light microscope. Metabolomics aids in the unraveling and the discovery of organ-specific endogenous metabolites that have the potential to be reliable indicators of organ function and viability, extrinsic and intrinsic perturbations, as well as valuable markers for treatment response. The results may, therefore, be applied clinically to characterize an organ by utilizing biomarkers that have the capacity to distinguish between disease and health. The aim was to characterize the human and the rat prostate in terms of its intermediary metabolism, which I show here to differ between species and anatomical regions.  Furthermore, the aim is to seek the verification of HRMAS NMR derived metabolites which are known to be a part of the prostate metabolome such as, citrate, choline, and the polyamines which were performed, but also the identification of metabolites not previously identified as part of the local prostate metabolism, such as Omega-6, which was detected in tumors.  The extended aim was to elucidate novel bio-markers with clinical potential. In this study, the common phyto-nutrient, inositol, which appears to possess protective properties, was identified as being a potentially important PCa bio-marker for the distinction between the more indolent Gleason score 6 and the more aggressive Gleason score 7 in non-malignant prostate tissues with tumors elsewhere in the organ. Further studies in this area of PCa research are therefore warranted.
23

Kvalitativ undersökning av diagnostisk och interaktiv kontroll i styrningen av högskolor : En beskrivande studie av styrdialogen / Qualitative research on diagnostic and interactive control of the management control in universities : A descriptive study of the management control

Delebeck, Maria, Ivarsson, Johan January 2021 (has links)
Problem description: The universities resources is allocated yearly through a regulation letter by the government which might make it more difficult to plan the organisation due to unforeseen events. The adaption and design of the management is a critical event that can cause negative consequences for the operation if made with deficient knowledge understanding about the cause and effect. We argue that this demands the management to clearly communicate the operations unique context, visions, goals and desired approach to create consensus within the organisation.  Research question: How does the balance between interactive and diagnostic control affect the management and the actions between top and local management in universities?  Purpose: The purpose with this research is to describe and understand how the balance between interactive and diagnostic controll in both the management and budget process affects actions in universities.  Methodology: This is a descriptive qualitative research which is mainly deductive. The empirical data is based on six different interviews from six different respondents that has been interviewed according to two different interview guides depending on which management level they were. The interview guide is based on semi structured questions that are well anchored in the theory through a operationalization scheme to fulfil the purpose of gathering the desired data to ensure a high validity.  Conclusions: Actions like budget games occurs despite reached balance between interactive and diagnostic control as a result of the universities context of being a part of the government since local savings is prohibited. / Problemdiskussion: Resursfördelningen i högskolan tilldelas varje år genom att regeringen skickar ut regleringsbrev vilket medför att förmågan att planera långsiktigt till följd av oförutsedda händelser kan försvåras. Anpassning och utformning av styrdialogen är en kritisk händelse som vid bristande förståelse kring orsak och verkan, kan resultera i negativa konsekvenser för verksamheten. Detta ställer krav på en styrdialog som förmår att tydligt förmedla verksamhetens unika kontext, vision, mål och önskat tillvägagångssätt för att skapa samsyn inom organisationen. Forskningsfråga: Hur påverkar balansen mellan interaktiv och diagnostisk kontroll styrdialog och ageranden mellan central och lokal ledning i högskolor? Syfte: Vår undersökning syftar till att beskriva och förstå hur balansen mellan interaktiv och diagnostisk kontroll i såväl styrdialog som budgetprocess påverkar ageranden i högskolor. Metod: Detta är en beskrivande kvalitativ studie med en huvudsaklig deduktiv ansats. Empirin grundar sig på intervjuer från sex olika respondenter som har intervjuats efter två olika intervjuguider beroende av ledningsnivå. Intervjuguiden är baserad på semistrukturerade frågor som är väl förankrade i teorin genom ett operationaliseringsschema i syfte att samla önskad information för att säkerställa en hög validitet. Slutsats: Ageranden såsom budgetspel uppstår trots uppnådd balans mellan interaktiv och diagnostisk kontroll till följd av högskolans kontext av att vara en statlig myndighet då lokalt sparande inte tillåts.
24

Att diagnostiseras med autismspektrumtillstånd i vuxen ålder : en litteraturöversikt / Diagnosis of autism spectrum condition in adulthood : a literature review

Källander, Unni, Murtada, Fanny January 2023 (has links)
Bakgrund Autismspektrumtillstånd [AST] har ökat i prevalens över tid. Tidigare har inte vuxna diagnostiserats med AST. Idag diagnostiseras allt fler i vuxen ålder. Att diagnostiseras med AST först i vuxen ålder medför en ökad risk för komorbida tillstånd. I och med att allt fler diagnostiseras med AST i vuxen ålder är det av intresse att förstå hur sen diagnostisering av AST kan upplevas. Syfte Syftet var att belysa personers upplevelser av att diagnostiseras med autismspektrumtillstånd i vuxen ålder. Metod En icke systematisk litteraturöversikt baserad på 16 vetenskapliga artiklar. Artikelsökningar utfördes i databaserna PubMed och CINAHL. Samtliga inkluderade artiklar genomgick en kvalitetsgranskning. De inkluderade artiklarna analyserades utifrån en integrerad analys. Resultat Datan resulterade i fyra huvudkategorier; Erfarenheter från livet före diagnosen, Den diagnostiska processen, Den känslomässiga upplevelsen av att få diagnosen samtDiagnosens påverkan på livet. Resultatet påvisade en komplex emotionell upplevelse med flertalet upplevda barriärer till diagnostisering av AST hos personer i vuxen ålder. Upplevelsen av diagnosens betydelse varierar. Flera studiedeltagare fann stort värde i sin diagnos och upplevde att diagnosen har stor påverkan på livet samt ger ett nytt perspektiv. Andra studiedeltagare upplevde att diagnosen inte förändrat deras liv särskilt mycket. Slutsats I föreliggande studie framkommer en ökad känsla av sammanhang för en majoritet av personer som diagnostiseras med AST i vuxen ålder. Vidare belyser denna litteraturöversikt att den komplexa upplevelse som en sen diagnostisering innebär kräver individuellt anpassade stödåtgärder som i dagsläget upplevs som bristfälliga. / Background Autism spectrum condition [ASC] or Autism spectrum disorder [ASD] is increasing in prevalence. Historically adults were not diagnosed with ASC. Today it is getting more common to receive the diagnosis as an adult. Comorbidities are common within the autism spectrum. Diagnosis of ASD in adulthood increases the risk of comorbidities. Since ASDs are getting more common world wide and more people are being diagnosed in adulthood it is of relevance to highlight the experiences of getting the diagnosis in early, mid and late adulthood.  Aim This study aimed to highlight experiences of being diagnosed with ASD in adulthood.  Method Non-systematic literature review based on 16 scientific articles with both qualitative and quantitative approaches. The articles were retrieved from the databases PubMed and CINAHL. All included scientific articles underwent a quality review. The included articles were analyzed through an integrated analysis. Results The data resulted in four main categories; Experiences from before the diagnosis, The diagnostic process, The emotional experience of receiving the diagnosis and The diagnosis’ impact on life. The results indicate a complex emotional experience. The results indicated a complex emotional experience with several perceived barriers to diagnosing ASC in adults. The experience of the significance of the diagnosis varies. Several study participants find great value in their diagnosis and feel that the diagnosis has a major impact on life and gives a new perspective. Other study participants felt that the diagnosis did not change their lives and their perspective.  Conclusions In the present study, an increased sense of coherence emerged for most individuals diagnosed with ASD in adulthood. Furthermore, this literature review highlights that the complex experience that a late diagnosis entails requires individually adapted support measures, of which are currently perceived as deficient.
25

Validation of anti-cytokeratin antibodies used in rapid cancer diagnostics by isoelectric focusing and QCM technology

Kostines, Reneh January 2021 (has links)
Antibodies are Y-shaped proteins. In the human body, antibodies areproduced by plasma cells, mainly T and B cells which are included inthe adaptive immune system. The production of antibodies is stimulatedby antigens. The binding between an antigen-specific antibody and itsantigen can be like the interconnect between a lock and a key.Therefore, antibodies are widely used as diagnostic tools for avariety of diseases but most importantly cancer. Some rapid diagnostictests are completely dependent on the specificity and reactivity ofantibodies such as UBC® Rapid produced by IDL Biotech AB. Therefore,the quality of these antibodies is important. This master thesis at IDL Biotech aimed to validate six anticytokeratinantibodies that are currently used in several rapid cancerdiagnostic tests produced by IDL. Antibody validation is a processwhere specificity, selectivity and reproductivity of an antibody isdemonstrated through specific laboratory investigations. During thisthesis, two laboratory methods were used to validate antibodies,namely, isoelectric focusing electrophoresis and the Attana QuartzCrystal Microbalance based biosensor. Isoelectric focusing electrophoresis (IEF) is a method that determinesproteins pI-values which can then reveal information about posttranslationalmodifications and protein sustainability during storage.IEF revealed changes in pI-values in two antibodies: AB2 and AB4. Attana biosensor analysis on AB1-5 showed that all antibodies havehigh specificity, reactivity and relatively high affinity to theircytokeratin targets. It also revealed that 4 antibodies (AB1 and AB3-5) have lower cross-reactivity with other cytokeratins than theirtarget cytokeratins compared to AB2. Keywords: Antibody validation, Isoelectric focusing, QCM, Attanabiosensor, biosensors, rapid diagnostics, epithelial carcinomas.
26

Neurocognitive and endocrine dysfunction in women with exhaustion syndrome

Sandström, Agneta January 2010 (has links)
Stress has emerged as one of the most important factors to consider in psychiatric diagnoses and has become a common reason for long-term sick leave (LTSL). Roughly 50% of LTSL due to psychiatric diseases are thought to be associated with work-related stress. The demarcation towards major depression is disputed, and no international consensus exists for how to diagnose and rehabilitate these individuals. The Swedish National Board of Health has suggested the term “exhaustion syndrome” to integrate these individuals into stress-related disorders. Prominent features of this syndrome are fatigue, sleeping disorders, and cognitive dysfunction. The cognitive dysfunction may be due to an interaction between personality features, environmental factors, the biological effects of stress hormones, and dysfunction in key brain areas, notably the hippocampus and prefrontal cortex. A consistent feature of chronic stress is activation of the cortisol, or hypothalamic-pituitary-adrenal, axis, which may be linked to cognitive dysfunction. Increased glucocorticoid levels, mainly cortisol in humans, are known to impair memory performance. The aim of this thesis was to investigate whether patients with exhaustion syndrome exhibit specific alterations in an extensive set of biological, psychological and immunological variables. Patients in Study 1 had significant cognitive impairment for specific tasks assumed to tap frontal lobe functioning. In Study 2 anxiety prone, worrying, pessimistic individuals with low executive drive and a persistent personality type were more likely to develop exhaustion syndrome. Decreased reactivity was found on the pituitary level after corticotropin releasing hormone (CRH) in exhaustion syndrome patients. The cortisol/adrenocorticotropic hormone response to CRH was slightly higher in patients compared to controls, indicating increased sensitivity at the adrenal cortex level. No differences were found in hippocampal volume. In Study 3, functional imaging revealed a different pattern of brain activation in working memory tests in patients with exhaustion syndrome compared to healthy individuals and patients with depression. In summary, our data suggests an intimate link between personality and wellbeing, cognitive performance and neuroendocrine dysfunction, in exhaustion syndrome. We thus find similarities with major depression but also distinct differences between the exhaustion syndrome and major depression.
27

Svensk översättning och validering av The Voice Symptom Scale (VoiSS)

Stölten, Katrin, Svanell, Klara January 2011 (has links)
Självskattningsformulär utgör ett viktigt kliniskt redskap för både utredning och intervention av röstproblem men i nuläget är tillgången till olika formulär i Sverige begränsad då antalet validerade svenska översättningar är få. Syfte med studien var att översätta och preliminärt validera The Voice Symptom Scale (VoiSS) som består av 30 frågor tilldelade komponenterna Nedsättning, Emotionellt och Fysiskt. Den svenska versionen av VoiSS framtogs genom ”Forward-backward Translation” med en efterföljande pilotstudie. Sammanlagt deltog 203 vuxna individer som rekryterades via webb- och pappersenkät. Av dessa uppgav 86 deltagare att de upplevde röstbesvär. Resultaten visade på tydliga gruppskillnader där gruppen Med upplevda röstproblem genererade högre genomsnittliga svarspoäng än gruppen Utan upplevda röstproblem. Inga överlappningar kunde konstateras. En principalkomponentanalys (PCA) var i stort sett förenlig med en trekomponentstruktur som tillsammans med gruppseparationen visade på hög konstruktvaliditet. Vidare noterades samstämmighet mellan den svenska versionen och VoiSS-originalet. Sensitivitets- och specificitetsvärden bekräftade en hög diagnostisk validitet. Slutsatsen drogs att formuläret med god validitet förmår att diagnosticera upplevelse av röstproblem. Den preliminära valideringen visade således att den svenska versionen av VoiSS kan användas som ett instrument vid utredning av röstproblem men att ytterligare forskning behövs för att säkerställa formulärets användbarhet i klinisk verksamhet. / Self-assessment questionnaires are important clinical instruments for both investigation and intervention of voice problems but at date access to various questionnaires in Sweden is limited due to few validated translations. The objective of this study was to translate and preliminary validate the Voice Symptom Scale (VoiSS) consisting of 30 questions assigned Impairment, Emotional and Physical. The Swedish version of VoiSS was developed through ”Forward-backward Translation” followed by a pilot study. The questionnaire was completed by a total of 203 adults who were recruited by web and paper survey. Out of these, 86 participants experienced voice problems. Obvious group differences were observed in that the group With experienced voice problems generated higher mean scores than the group Without experienced voice problems. No overlaps were observed. A principal component analysis (PCA) was largely consistent with a three component structure that, combined with the group separation, affirmed high construct validity. Moreover, concurrence between the Swedish version and the VoiSS-original was found. Calculated values of sensitivity and specificity confirmed a high diagnostic validity. The conclusion was made that the self-assessment questionnaire with good validity was able to diagnose experience of voice problems. In conclusion, preliminary validation showed that the Swedish version of VoiSS can be used as a diagnostic tool in assessing voice problems. However, more research needs to be done to ensure the questionnaires adaptation to clinical context.
28

Användbarheten av diffusionsviktade sekvenser vid MRT för att påvisa uteruscancer En litteraturstudie

Sveder, Anna, Lindberg, Martin January 2018 (has links)
Inledning: Uteruscancer är den sjätte vanligaste cancerformen hos kvinnor i världen. Ny forskning pekar på att diffusionsviktad magnetresonanstomografi (MRT) kan vara en tillförlitlig undersökningsmetod för att detektera patologiska förändringar i uterus. Syfte: Att skapa en översikt av användbarheten av diffusionsviktade sekvenser vid MRT för att påvisa uteruscancer. Metod: Allmän litteraturöversikt, tio kvantitativa studier inkluderades. Resultat: Diffusionsviktade sekvenser vid MRT har högre sensitivitet, specificitet samt diagnostisk noggrannhet för att påvisa patologiska förändringar i uterus än sekvenser utan diffusionsviktning. Apparent diffusion coefficient (ADC) och b-värden är viktiga markörer för att skilja malign från benign vävnad, indikera patologisk parametrieinvasion samt förutse överlevnad hos patienter med cervixcancer. Slutsats: Diffusionsviktade sekvenser är bättre än sekvenser utan diffusionsviktning och kontrastmedelsförstärkta sekvenser på att hitta samt stadieindela tidiga förändringar i uterus. Undersökningen görs non-invasiv och säker för patienter med känslighet eller allergi mot kontrastmedel, samt frigör tid för röntgensjuksköterskan till omvårdnad av patienten. / Background: Uterus cancer is the sixth most common form of cancer in women in the world. New research suggests that diffusion-weighted magnetic resonance imaging (MRI) can be a reliable method of investigation for detecting pathological changes in the uterus. Purpose: To provide an overview of the available scientific support for the use of diffusion-weighted sequences in MRI to detect uterine cancer. Method: Literature review that included ten quantitative studies. Results: Diffusion-weighted sequences in MRI have higher sensitivity, specificity and diagnostic accuracy to detect pathological changes in the uterus compared to non- diffusion-weighted sequences. Apparent diffusion coefficient (ADC) and b-values are important markers to distinguish malignant from benign tissue, indicate pathological parametric invasion, and predict survival in patients with cervical cancer. Conclusion: Diffusion-weighted sequences are better than sequences without diffusion-weighting and contrast-mediated sequences for identifying and staging early changes in the uterus. The examination is made non-invasive and safe for patients with sensitivity or allergies toward contrast media, as well as freeing time for the radiographer to care for the patient.
29

Electroanalytical devices with fluidic control using textile materials and methods

Öberg Månsson, Ingrid January 2020 (has links)
This thesis, written by Ingrid Öberg Månsson at KTH Royal Institute of Technology and entitled “Electroanalytical devices with fluidic control using textile materials and methods”, presents experimental studies on the development of textile based electronic devices and biosensors. One of the reasons why this is of interest is the growing demand for integrated smart products for wearable health monitoring or energy harvesting. To enable such products, new interdisciplinary fields arise combining traditional textile technology and electronics. Textile based devices have garnered much interest in recent years due to their innate ability to incorporate function directly into, for example, clothing or bandages by textile processes such as weaving, knitting or stitching. However, many modifications of yarns required for such applications are not available on an industrial scale. The major objective of this work has been to study how to achieve the performance necessary to create electronic textile devices by either coating yarns with conductive material or using commercially available conductive yarns that are functionalized to create sensing elements. Further, liquid transport within textile materials has been studied to be able to control the contact area between electrolyte and electrodes in electrochemical devices such as sensors and transistors. Yarns with specially designed cross-sections, traditionally used in sportswear to wick sweat away from the body and enhance evaporation, was used to transport electrolyte liquids to come in contact with yarn electrodes. The defined area of the junction where the fluidic yarn meets the conductive yarn was shown to increase stability of the measurements and the reproducibility between devices. The results presented in the two publications of this thesis as well as additional results presented in the thesis itself show the promising potential of using textile materials to integrate electronic and electrochemical functionality in our everyday life. This is shown by using basic textile materials and processing techniques to fabricate complex devices for various application areas such as sensors and diagnostics as well as electrical and energy harvesting components. / Denna avhandling, skriven av Ingrid Öberg Månsson vid Kungliga Tekniska Högskolan och titulerad ”Elektroanalytiska sensorer med vätskekontroll integrerad genom användande av textila material och metoder”, presenterar experimentella studier inom utvecklingen av textilbaserade elektroniska komponenter och biosensorer. Detta är av intresse på grund av den ökade efterfrågan på integrerade smarta produkter som till exempel bärbara sensorer för hälsoövervakning eller för att samla upp och konvertera energi till elektricitet. För att möjliggöra denna typ av produkter föds nya interdisciplinära fält där traditionell textilteknologi och elektronik möts. Textilbaserade enheter har väckt stort intresse under de senaste åren på grund av den naturliga förmågan att integrera funktion i till exempel kläder eller förband genom textila tillverkningsprocesser som väveri, stickning eller sömnad. Många modifikationer hos garner som krävs för att möjliggöra sådana tillämpningar är dock inte tillgängliga i större skala. Därför har det huvudsakliga syftet med denna studie varit att undersöka hur man kan uppnå den prestanda som krävs för att tillverka elektroniska textila komponenter, antingen genom att belägga garner med elektroniskt ledande material eller genom att använda kommersiellt tillgängliga ledande garner som sedan modifieras kemiskt för att skapa sensorer. Utöver detta har vätsketransport inom textila material studerats för att kunna styra och kontrollera kontaktytan mellan elektrolyt och elektroder i elektrokemiska enheter så som sensorer och transistorer. Garner med speciella tvärsnitt, som traditionellt använts i sportkläder för att transportera svett bort från kroppen och underlätta avdunstning, har använts för att transportera elektrolytvätska till elektroder av garn. Den definierade kontaktytan där det vätsketransporterade garnet korsar elektrodgarnet har visats öka stabiliteten av mätningen och reproducerbarheten mellan mätenheter. Resultaten som presenteras i de två artiklar som denna avhandling bygger på samt i avhandlingen själv visar på lovande potential för användandet av textila material för att integrera elektronisk och elektrokemisk funktionalitet i våra vardagsliv. Detta har uppnåtts genom att använda grundläggande textila material och tillverkningsprocesser för att tillverka komplexa enheter för olika tillämpningsområden så som sensorer för diagnostik samt elektroniska komponenter. / <p>QC 2020-08-21</p>
30

Ett sannolikhetsbaserat kvalitetsmått förbättrar klassificeringen av oförväntade sekvenser i in situ sekvensering / A probability-based quality measure improves the classification of unexpected sequences in in situ sequencing

Nordesjö, Olle, Pontén, Victor, Herman, Stephanie, Ås, Joel, Jamal, Sabri, Nyberg, Alona January 2014 (has links)
In situ sekvensering är en metod som kan användas för att lokalisera differentiellt uttryck av mRNA direkt i vävnadssnitt, vilket kan ge viktiga ledtrådar om många sjukdomstillstånd. Idag förloras många av sekvenserna från in situ sekvensering på grund av det kvalitetsmått man använder för att säkerställa att sekvenser är korrekta. Det finns troligtvis möjlighet att förbättra prestandan av den nuvarande base calling-metoden eftersom att metoden är i ett tidigt utvecklingsskede. Vi har genomfört explorativ dataanalys för att undersöka förekomst av systematiska fel och korrigerat för dessa med hjälp av statistiska metoder. Vi har framförallt undersökt tre metoder för att korrigera för systematiska fel: I) Korrektion av överblödning som sker på grund avöverlappande emissionsspektra mellan fluorescenta prober. II) En sannolikhetsbaserad tolkningav intensitetsdata som resulterar i ett nytt kvalitetsmått och en alternativ klassificerare baseradpå övervakad inlärning. III) En utredning om förekomst av cykelberoende effekter, exempelvisofullständig dehybridisering av fluorescenta prober. Vi föreslår att man gör följande saker: Implementerar och utvärderar det sannolikhetsbaserade kvalitetsmåttet Utvecklar och implementerar den föreslagna klassificeraren Genomför ytterligare experiment för att påvisa eller bestrida förekomst av ofullständigdehybridisering / In situ sequencing is a method that can be used to localize differential expression of mRNA directly in tissue sections, something that can give valuable insights to many statest of disease. Today, many of the registered sequences from in situ sequencing are lost due to a conservative quality measure used to filter out incorrect sequencing reads. There is room for improvement in the performance of the current method for base calling since the technology is in an early stage of development. We have performed exploratory data analysis to investigate occurrence of systematic errors, and corrected for these by using various statistical methods. The primary methods that have been investigated are the following: I) Correction of emission spectra overlap resulting in spillover between channels. II) A probability-based interpretation of intensity data, resulting in a novel quality measure and an alternative classifier based on supervised learning. III) Analysis of occurrence of cycle dependent effects, e.g. incomplete dehybridization of fluorescent probes. We suggest the following: Implementation and evaluation of the probability-based quality measure Development and implementation of the proposed classifier Additional experiments to investigate the possible occurrence of incomplete dehybridization

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