This thesis is about new and improved computational methods to analyze complex biological data produced by advanced biotechnologies. Such data is not only very large but it also is characterized by very high numbers of features. Addressing these needs, we developed a set of methods and tools that are suitable to analyze large sets of data, including next generation sequencing data, and built transparent models that may be interpreted by researchers not necessarily expert in computing. We focused on brain related diseases. The first aim of the thesis was to employ the meta-server approach to finding peaks in ChIP-seq data. Taking existing peak finders we created an algorithm that produces consensus results better than any single peak finder. The second aim was to use supervised machine learning to identify features that are significant in predictive diagnosis of Alzheimer disease in patients with mild cognitive impairment. This experience led to a development of a better feature selection method for rough sets, a machine learning method.  The third aim was to deepen the understanding of the role that STAT3 transcription factor plays in gliomas. Interestingly, we found that STAT3 in addition to being an activator is also a repressor in certain glioma rat and human models. This was achieved by analyzing STAT3 binding sites in combination with epigenetic marks. STAT3 regulation was determined using expression data of untreated cells and cells after JAK2/STAT3 inhibition. The four papers constituting the thesis are preceded by an exposition of the biological, biotechnological and computational background that provides foundations for the papers. The overall results of this thesis are witness of the mutually beneficial relationship played by Bioinformatics in modern Life Sciences and Computer Science.

In this thesis work, I have used a comparative genomics approach to study a fungal model organism, Neurospora tetrasperma. My specific focus has been on genomic introgression, intron evolution, chromosomal structural rearrangements and codon usage. All of the studies are based on large-scale dataset generated by next-generation sequencing technology (NGS), combined with other techniques, such as Optical Mapping. In the introgression study, we detected large-scale introgression tracts in three N. tetrasperma lineages, and the introgression showed allele-specific and chromosomal-specific pattern. In the study of introns, we found indications of mRNA mediated intron loss and non-homologous end joining (NHEJ) mediated intron gains in N. tetrasperma. We found that selection is involved in shaping intron gains and losses, and associated with intron position, intron phase and GC content. In the study of chromosomal structural rearrangements, we found a lineage specific chromosomal inversion pattern in N. tetrasperma, which indicates that inversions are unlikely to associate with the origin of the suppressed recombination and the mating system transition in N. tetrasperma. The result suggests inversions are the consequences, rather than the causes, of suppressed recombination on the mating-type chromosome of N. tetrasperma. In the final study, analyses of codon usage indicated that the region of suppressed recombination in N. tetrasperma is subjected to genomic degeneration, and selection efficiency has been much reduced in this region.

Myoclonus-Dystonia (MD) is an inherited, rare, autosomal dominant movement disorder characterized by quick, involuntary muscle jerking or twitching (myoclonus) and involuntary muscle contractions that cause twisting and pulling movements, resulting in abnormal postures (dystonia). The first MD locus was mapped to 7q21-q31 and called DYT11; this locus corresponds to the SGCE gene. Our group previously identified a second MD locus (DYT15) which maps to a 3.18 Mb region on 18p11. Two patients were chosen to undergo next-generation sequencing, which identified 2,292 shared novel variants within the critical region. Analysis of these variants revealed a 3 bp duplication in a transcript referred to as CD108131, which is believed to be a long non-coding RNA. Characterization of this transcript determined that it is 863 bp in size, it is ubiquitously expressed, with high expression in the cerebellum, and it accounts for ~3% of MD cases.

Nära patienten i samband med hjärt- eller lungtransplantation finns ofta anhöriga. Anhöriga upplever påfrestningar och har ett kunskapsbehov i samband med transplantationen. Liksom patienten är anhöriga sårbara och det är av betydelse att undersöka anhörigas upplevelser, det kan medföra att anhöriga bättre förbereds för den påfrestning transplantationen innebär. Litteraturstudiens syfte var att undersöka upplevelsen av att vara anhörig i samband med hjärt- eller lungtransplantation. Studien genomfördes som en allmän litteraturstudie och analysen gjordes med stöd av hermeneutisk metod. Resultatet visar att anhörigas stöd till patienten var en akt av kärlek som medförde att anhöriga bland annat försakade vänner och förändrade det dagliga livet. Transplantationen innebar en väntan och mycket känslor för anhöriga, allt från glädje när samtalet om att det var dags för transplantation kom, till oro för att patientens tillstånd efter transplantationen kunde försämras igen. Anhöriga upplevde brist i tillgängligheten från vården gällande information, uppmärksamhet och stöd i sin roll. I litteraturen är omvårdnadsprocessen relaterat till anhörigas upplevelser i samband med hjärt- eller lungtransplantation bristande, därför är framtida forskning betydelsefull för att skapa ytterligare evidensbaserad kunskap till omvårdnadsprocessen om anhörigas upplevelser. / Next of kins are often close to patients in heart- or lung transplantation. In connection with transplantation next of kins experience strain and has a need for knowledge. Like patients next of kins are vulnerable and it is important to explore next of kins’ experiences, this to better prepare for the burden of transplantation. The aim of the study was to explore the experience of being a next of kin in connection with heart- or lung transplantation. The study was conducted as a general literature study and the analysis was guided by a hermeneutic method. The results show that next of kin’s support for the patient is an act of love resulting in sacrificed relationships with friends and changes in their daily lives. The transplantation generated waiting and a lot of feelings for next of kins, such as joy when the call came about transplant, and later on after the transplantation worries that the patient’s condition would worsen again. Furthermore, next of kins experienced lack of availability from the health care services regarding information, attention and support in their role. In the literature the nursing process regarding next of kins’ experiences in heart- or lung transplantation is inadequately described, therefore it is of importance that future research creates new evidence based knowledge.

Background: In the management of metastatic colorectal cancer (mCRC), KRAS, NRAS and BRAF mutational status individualizes therapeutic options and identify a cohort of patients (pts) with an aggressive clinical course. We hypothesized that relapsed and refractory mCRC pts develop unique mutational signatures that may guide therapy, predict for a response and highlight key signaling pathways important for clinical decision making. Methods: Relapsed and refractory mCRC pts (N=32) were molecularly profiled utilizing commercially available next generation sequencing (NGS) platforms. Web-based bioinformatics tools (Reactome/Enrichr) were utilized to elucidate mutational profile linked pathways-networks that have the potential to guide therapy. Results: Pts had progressed on fluoropyrimidines, oxaliplatin, irinotecan, bevacizumab, cetuximab and/or panitumumab. Most common histology was adenocarcinoma (colon N=29; rectal N=3). Of the mutations TP53 was the most common, followed by APC, KRAS, PIK3CA, BRAF, SMAD4, SPTA1, FAT1, PDGFRA, ATM, ROS1, ALK, CDKN2A, FBXW7, TGFBR2, NOTCH1 and HER3. Pts had on average had >= 5 unique mutations. The most frequent activated signaling pathways were: HER2, fibroblast growth factor receptor (FGFR), p38 through BRAF-MEK cascade via RIT and RIN, ARMS-mediated activation of MAPK cascade, and VEGFR2. Conclusions: Dominant driver oncogene mutations do not always equate to oncogenic dependence, hence understanding pathogenic ` interactome(s)' in individual pts is key to both clinically relevant targets and in choosing the next best therapy. Mutational signatures derived from corresponding ` pathway-networks' represent a meaningful tool to (I) evaluate functional investigation in the laboratory; (II) predict response to drug therapy; and (III) guide rational drug combinations in relapsed and refractory mCRC pts.

The human genome consists of over 3 billion nucleotides and would be around 2 meters long if uncoiled and laid out. Each human somatic cell contains all this in their nucleus which is only around 5 µm across. This extreme compaction is largely achieved by wrapping the DNA around a histone octamer, the nucleosome. Still, the DNA is accessible to the transcriptional machinery and this regulation is highly dynamic and change rapidly with, e.g. exposure to drugs. The individual histone proteins can carry specific modifications such as methylations and acetylations. These modifications are a major part of the epigenetic status of the DNA which contributes significantly to the transcriptional status of a gene - certain modifications repress transcription and others are necessary for transcription to occur. Specific histone methylations and acetylations have also been implicated in more detailed regulation such as inclusion/exclusion of individual exons, i.e. splicing. Thus, the nucleosome is involved in chromatin remodeling and transcriptional regulation – both directly from steric hindrance but also as a signaling platform via the epigenetic modifications. In this work, we have developed tools for storage (Paper I) and normalization (Paper II) of next generation sequencing data in general, and analyzed nucleosome locations and histone modification in particular (Paper I, III and IV). The computational tools developed allowed us as one of the first groups to discover well positioned nucleosomes over internal exons in such wide spread organisms as worm, mouse and human. We have also provided biological insight into how the epigenetic histone modifications can control exon expression in a combinatorial way. This was achieved by applying a Monte Carlo feature selection system in combination with rule based modeling of exon expression. The constructed model was validated on data generated in three additional cell types suggesting a general mechanism.

Aim: The overall aim of the thesis was to illuminate the meanings of intensive care units’ patient rooms as a place of care for critically ill patients and their loved ones. Moreover, it was aimed to develop photovoice as a data collection method for research in ICU context. Methods and materials: Data has been collected using photovoice methodology in combination with research interviews for all three empirical studies. In total 37 people participated. Nine patients, fourteen loved ones and fourteen nurses from three ICU settings. Study I examined the perspective of loved ones, for this purpose a phenomenological hermeneutic method rooted in the philosophy of Ricoeur was chosen. Study II and III examined patients’ respectively nurses’ perspective. Both studies are phenomenologically orientated guided by a reflective lifeworld approach rooted in continental philosophy. Study IV is a theoretical paper focusing on employing photovoice as a data collection method in ICU context. Main findings: The tone and touch of caring is vital for how ICU patient room is materialized for patients. The interior design and furnishing has a great impact on the wellbeing of the loved ones and also the support they can offer the critically ill patient. One major finding is that the ICU patient room is a taken for granted place for health care providers and the impact of it upon caring, patients’ and loved ones wellbeing is not reflected over. It also seems unclear who is responsible for the environment of ICU once it has been built. The environment of ICU affects nurses’ ability to care for the patients and their family in a genuine way and to promote their wellbeing during a fragile time in life. Conclusions: There is an urgent need to translate research findings into clinical practice in order to improve the environment of ICU patient rooms. There is also need of further research and policies for transforming the hostile environment of the patient rooms to a healing environment more conductive to people’s recovering process. / <p>Akademisk avhandling som för avläggande av filosofie doktorsexamen vid Linnéuniversitetet försvaras vid offentlig disputation, 13 juni 2014, klockan 14.00 i sal Wicksell, Hus K, Växjö</p>

Nursing research has been performed during the last 20-30 years, about the next of kin’s vulnerability. Despite this, the health care system has had difficulties to integrate the next of kin in a way that gives support. The overall aim of the thesis was to describe and further explore the life situation of the next of kin to persons who are long-term ill, disabled, and/or older, and in need of care. Method: Multiple methods were used. Study I had a descriptive design, 44 next of kin of patients with multiple sclerosis were interviewed, latent content analysis was used for the analysis. Study II had a mixed method approach; the descriptive core study was analyzed with directed content analysis. The supplementary study with descriptive, correlative design was analyzed with descriptive and correlative statistics. Forty-four next of kin of patients with multiple sclerosis were interviewed; thereafter 37 of them answered a questionnaire about Quality of Life. Study III had a descriptive, explorative design. Twelve next of kin of older persons were interviewed with repeated informal conversational interviews, analyzed with latent content analysis. Study IV was cross-sectional with a descriptive, correlative design. Eighty-four next of kin of persons who were long-term ill, disabled, and/or older answered two questionnaires about Burden and Quality of Life that were analyzed with descriptive and correlative statistics. Results and Conclusions: Next of kin described a balance/imbalance in their relations to others and a high burden, but in general a good Quality of Life. Some next of kin also experienced chronic sorrow. Significant correlations were found between interpersonal relations and Quality of Life as a whole. Love and obligations were two anchor points on a continuum, describing the next of kin’s relationship to the ill/disabled person. The relationship with the health care personnel was described through cooperation and obligations. Good communication was seen as the key to balance the relationship with others. One possibility to achieve symmetrical communications is to adapt the Partnership Model, as a tool for creating good relationships. Honest and specific communication between the health care personnel, the next of kin, and the care receiver are necessary.

Aim: The overall aim of the thesis was to explore and describe the concepts of guilt and shame and gain a greater understanding of the next-of-kin’s experiences of guilt and shame in end-of-life care. Methods: Study I was a qualitative secondary analysis of 47 interviews with next-of-kin searching for experiences of guilt and shame. In study II a semantic concept analysis of the two concepts guilt and shame was performed. In studies III and IV a hermeneutic approach inspired by Gadamer was used to analyze next-of-kin’s experiences of guilt (Study III), and shame (Study IV) in end-of-life care. Main findings: The concept of guilt focus on behaviour and the concept of shame on the influence on the self.  The situation of being next-of-kin in end-of-life care involves a commitment to make the remaining time for the loved one as good as possible. When, for some reason, the commitment cannot be accomplished there is a risk that the next-of-kin experience guilt such as not having done enough, not having been together during important events, not having talked enough to each other, or not having done the right things. Aspects such as not having fulfilled a commitment, omission, and being the cause of can be present in these experiences. The guilt experience has a focus on what the next-of-kin has, or has not done. The experiences of shame are also linked to a perception that the remaining time for the loved one should be as good as possible. Shame can occur when the next-of-kin is involved and actually causes harm to the loved one as well as in situations that are beyond their control. Shame that the next-of-kin experience can also emanate from being put in situations by other people. Feelings of inferiority and powerlessness, second order shame, and family conflicts that are brought into the open are experiences of shame found in the studies as well as ignominy, humiliation, and disgrace. The shame experience has a focus on the next-of-kin’s self. Conclusion: The situation of being next-of-kin in end-of-life care is complex and demanding, something that health professionals should be aware of. Acknowledgement of experiences of guilt and shame can help the next-of-kin in their adaptation to the end-of-life situation as a whole and maybe also give useful tools to support next-of-kin during bereavement.

Kaposi's sarcoma-associated herpesvirus (KSHV) causes several tumours and hyperproliferative disorders. Hypoxia plays an important role in KSHV lifecycle, as hypoxia-inducible factors (HIFs) are involved in the latent/lytic switch and affect other KSHV genes, and as KSHV infection can in turn enhance cellular levels of HIFs. Two KSHV-associated tumours tend to develop in settings of relative hypoxia; Kaposi's sarcoma (KS) often occurs in the lower extremities and primary effusion lymphoma (PEL) exists in pleural effusions. A better knowledge of the pathways that regulate KSHV infection in hypoxia is therefore essential for an improved understanding of viral infection and pathogenesis. MicroRNAs (miRNAs) have been shown to play important roles in regulating the expression of genes in oncogenesis, and herpesviruses, including KSHV, encode for miRNAs. This thesis describes a multidisciplinary approach toward understanding the mechanisms behind the hypoxia-regulated miRNA-mRNA networks in the context of KSHV infection. The question of miRNA and mRNA regulation through hypoxia, KSHV or both is addressed in this thesis by deep sequencing and gene expression assays as well as various transfection and functional assays. In chronically infected cells compared to uninfected controls, it is demonstrated that the majority of cellular miRNAs whose expression is affected are substantially down-regulated. A third of this down-regulation can be attributed to a single genomic region, 14q32 cluster, where miRNAs are lowly expressed in infected cells. In hypoxia, hsa-miR-210 is the only miRNA to be consistently up-regulated in the KSHVinfected cell lines subjected to deep sequencing in this study. Computational approaches additionally allowed for the investigation of mRNA targets. Inversely correlated miRNAmRNA target pairs were identified and distributed into canonical pathways and biological networks. Taken together, these results suggest that miRNAs affected by hypoxic stress and/or viral infection are implicated in the pathogenesis of KSHV-related diseases. It is expected that the outcomes of these studies will change our understanding of how KSHV uses the host RNA silencing machinery to its advantage and how this intersects with the use of the cell's response to hypoxia.