In forensic autopsies, accurately estimating the postmortem interval (PMI) is crucial. Traditional methods, relying on physical parameters and police data, often lack precision, particularly after approximately two days have passed since the person's death. New methods are increasingly focusing on analyzing postmortem metabolomics in biological systems, acting as a 'fingerprint' of ongoing processes influenced by internal and external molecules. By carefully analyzing these metabolomic profiles, which span a diverse range of information from events preceding death to postmortem changes, there is potential to provide more accurate estimates of the PMI. The limitation of available real human data has hindered comprehensive investigation until recently. Large-scale metabolomic data collected by the National Board of Forensic Medicine (RMV, Rättsmedicinalverket) presents a unique opportunity for predictive analysis in forensic science, enabling innovative approaches for improving  PMI estimation. However, the metabolomic data appears to be large, complex, and potentially nonlinear, making it difficult to interpret. This underscores the importance of effectively employing machine learning algorithms to manage metabolomic data for the purpose of PMI predictions, the primary focus of this project.  In this study, a dataset consisting of 4,866 human samples and 2,304 metabolites from the RMV was utilized to train a model capable of predicting the PMI. Random Forest (RF) and Artificial Neural Network (ANN) models were then employed for PMI prediction. Furthermore, feature selection and incorporating sex and age into the model were explored to improve the neural network's performance.  This master's thesis shows that ANN consistently outperforms RF in PMI estimation, achieving an R2 of 0.68 and an MAE of 1.51 days compared to RF's R2 of 0.43 and MAE of 2.0 days across the entire PMI-interval. Additionally, feature selection indicates that only 35% of total metabolites are necessary for comparable results with maintained predictive accuracy. Furthermore, Principal Component Analysis (PCA) reveals that these informative metabolites are primarily located within a specific cluster on the first and second principal components (PC), suggesting a need for further research into the biological context of these metabolites.  In conclusion, the dataset has proven valuable for predicting PMI. This indicates significant potential for employing machine learning models in PMI estimation, thereby assisting forensic pathologists in determining the time of death. Notably, the model shows promise in surpassing current methods and filling crucial gaps in the field, representing an important step towards achieving accurate PMI estimations in forensic practice. This project suggests that machine learning will play a central role in assisting with determining time since death in the future.

The subject of corpses from mass violence is surprisingly unexplored, even though the materiality of the corpse carries strong symbolic capital in conflicts. The aim of my PhD research is to create new knowledge about the implications of unburied corpses that stem from intergroup conflicts, and subsequently to add knowledge concerning how intergroup violence is organised to achieve desired social agendas. In the licentiate thesis presented here, I research the conditions for postmortem agency and how treatment of corpses can be studied in prehistory, specifically through the material remains of unburied corpses from the Sandby borg massacre. The Sandby borg case study is explored through a bioarchaeological perspective. Inside the Iron Age ringfort, the remains of at least 26 individuals have been recovered hitherto. Several of the dead display traces of lethal intergroup violence. By integrating osteology, archaeology, taphonomy and social theories, I show how bioarchaeological research can contribute to the understanding of past postmortem agency in relation to intergroup violence as a social process. The thesis is comprised of four articles.

Indiana University-Purdue University Indianapolis (IUPUI) / The black blow fly, Phormia regina (Diptera: Calliphoridae), is a widely abundant fly autochthonous to North America. Like many other Calliphorids, P. regina plays a key role in several disciplines particularly in estimating post-mortem intervals (PMI). The aim of this work was to better understand the population genetic structure of this important ecological species using microsatellites from populations collected in the U.S. during 2008 and 2013. Additionally, it sought to determine the effect of limited genetic diversity on a quantitative trait throughout immature development; larval length, a measurement used to estimate specimen age. Observed heterozygosity was lower than expected at five of the six loci and ranged from 0.529-0.880 compared to expected heterozygosity that ranged from 0.512-0.980, this is indicative of either inbreeding or the presence of null alleles. Kinship coefficients indicate that individuals within each sample are not strongly related to one another; values for the wild-caught populations ranged from 0.033-0.171 and a high proportion of the genetic variation (30%) can be found among samples within regions. The population structure of this species does not correlate well to geography; populations are different to one another resulting from a lack of gene flow irrespective of geographic distance, thus inferring temporal distance plays a greater role on the genetic variation of P. regina. Among colonized samples, flies lost much of their genetic diversity, ≥67% of alleles per locus were lost, and population samples became increasingly more related; kinship coefficient values increased from 0.036 for the wild-caught individuals to 0.261 among the F10 specimens. Colonized larvae also became shorter in length following repeated inbreeding events, with the longest recorded specimen in F1 18.75 mm in length while the longest larva measured in F11 was 1.5 mm shorter at 17.25 mm. This could have major implications in forensic entomology, as the largest specimen is often assumed to be the oldest on the corpse and is subsequently used to estimate a postmortem interval. The reduction in length ultimately resulted in a greater proportion of individuals of a similar length; the range of data became reduced. Consequently, the major reduction in genetic diversity indicates that the loss in the spread of length distributions of the larvae may have a genetic influence or control. Therefore, this data highlights the importance when undertaking either genetic or development studies, particularly of blow flies such as Phormia regina, that collections of specimens and populations take place not only from more than one geographic location, but more importantly from more than one temporal event.

Ce travail porte sur des approches translationnelles dans les synucléinopathies notamment l’atrophie multisystématisée (AMS). Au-delà de leur rôle dans la régulation du glucose, l’insulin et l’insulin like growth factor-1 (IGF-1) ont des propriétés neurotrophiques. Des études ont montrées que la signalisation de l’insuline/IGF-1 est altérée dans la maladie d'Alzheimer et des données suggèrent l’altération de l’insuline/IGF-1 dans la maladie de Parkinson (MP) et l’AMS. Nous avons mis en évidence une résistance à l’insuline dans les neurones des patients MP et AMS ainsi que dans les oligodendrocytes chez les patients AMS.Mon travail a également consisté à cibler la troncation de l’α-synuclein (α-syn) comme cible thérapeutique. Nous avons démontré dans un modèle murin d’AMS que la diminution de l’α-syn tronquée permettait de réduire l’agrégation d’α-syn et la dégénérescence des neurones dopaminergiques.Enfin, nous avons étudié l’implication dans l’AMS des métalloprotéinases matricielles (MMP), des enzymes impliquées dans remodelage de la matrice, la démyélinisation, la troncation de l’α-syn et la perméabilité de la barrière hémato-encéphalique. Ce travail nous a permis de montrer une augmentation de l’expression et de l’activité de MMPs chez les patients AMS. Nous avons également montré que les cellules gliales sont la source de cette augmentation et que la MMP-2 est retrouvée dans les agrégats des patients AMS.Nous montrons ici de caractéristiques distinctes de l’AMS comme des altérations qui se produisent dans les oligodendrocytes. Nous présentons aussi VX-765 comme un candidat prometteur pour ralentir la progression de la pathologie dans un contexte de synucléinopathie. / This work focused on translational approaches in synucleinopathies and more specifically in multiple system atrophy (MSA). Beyond their role in glucose homeostasis, insulin/IGF-1 are neurotrophic factors in the brain. Studies have shown altered insulin/IGF-1 signalling in Alzheimer’s disease and data suggest impaired insulin signaling/IGF-1 in Parkinson's disease (PD) and MSA. The aim of my work was to characterize insulin/IGF-1 signalling in MSA and PD brain tissue. Both groups showed neuronal insulin resistance. Oligodendrocytes in MSA patients were also insulin resistant.In line with the translational approach, we also targeted α-synuclein (α-syn) truncation pharmacologically in MSA transgenic mice, which led to reduced α-syn aggregation and the protection of dopaminergic neurons.We also assessed the activity and distribution of matrix metalloproteinases (MMPs) in the brain of MSA patients compared to healthy controls. MMPs are involved in the remodelling of the extracellular matrix, demyelination, α-syn truncation and blood brain barrier permeability. We showed altered expression and activity of MMPs in two distinct structures in MSA brains. We were also able to show that glial cells were the source of increased MMPs and show a unique expression of MMPs in α-syn aggregates of MSA patients compared to PD, evidence that might hint at a mechanism that is differently altered between PD and MSA.We here show distinct pathological features of MSA such as key alterations occurring in oligodendrocytes, further supporting MSA as a primary oligodendrogliopathy. We also present VX-765 as a candidate drug for disease modification in synucleinopathies.

Indiana University-Purdue University Indianapolis (IUPUI) / Phormia regina (Meigen), commonly known as the black blow fly is a dipteran that belongs to the family Calliphoridae. Calliphorids play an important role in various research fields including ecology, medical studies, veterinary and forensic sciences. P. regina, a non-model organism, is one of the most common forensically relevant insects in North America and is typically used to assist in estimating postmortem intervals (PMI). To better understand the roles P. regina plays in the numerous research fields, we re-constructed its genome using next generation sequencing technologies. The focus was on generating a reference genome through de novo assembly of high-throughput short read sequences. Following assembly, genetic markers were identified in the form of microsatellites and single nucleotide polymorphisms (SNPs) to aid in future population genetic surveys of P. regina. A total 530 million 100 bp paired-end reads were obtained from five pooled male and female P. regina flies using the Illumina HiSeq2000 sequencing platform. A 524 Mbp draft genome was assembled using both sexes with 11,037 predicted genes. The draft reference genome assembled from this study provides an important resource for investigating the genetic diversity that exists between and among blow fly species; and empowers the understanding of their genetic basis in terms of adaptations, population structure and evolution. The genomic tools will facilitate the analysis of genome-wide studies using modern genomic techniques to boost a refined understanding of the evolutionary processes underlying genomic evolution between blow flies and other insect species.

Les personnes qui vivent avec le VIH (PVVIH) doivent prendre un traitement d’antirétroviraux combinés (ART) pour contrôler la réplication virale et empêcher le développement d’une immunodéficience dont l’issue est fatale. Les ART protègent les cellules saines de l’infection et permettent ainsi de rendre la charge virale plasmatique indétectable. Cependant, l’arrêt des ART entraine presque inévitablement un rebond de la charge virale, puisque le virus n’est jamais complètement éliminé par le système immunitaire. En effet, de multiples cellules infectées, où le virus s’est intégré et demeure dans un état de latence, restent présentes tout au long de la vie des PVVIH. Une partie de ces cellules infectées forme le réservoir compétent pour la réplication. Les provirus responsables du rebond de la charge virale possèdent trois caractéristiques : ils gardent la capacité d’être réactivés (sortie de latence), ils sont génétiquement intacts, et ils peuvent produire de nouvelles particules virales infectieuses. Afin de guérir les PVVIH de l’infection, il faut donc cibler les quelques rares cellules portant un provirus intact et inductible. Pour ce faire, il est impératif de comprendre comment ces cellules sont maintenues pendant les années de ART, de les localiser dans tout l’organisme, et d’identifier ce qui peut les distinguer des autres. Ce sont ces trois aspects que nous avons abordés au cours des travaux de recherche présentés dans cette thèse, autant à l’échelle de la cellule unique que de l’organisme entier. Nos résultats montrent que les provirus compétents pour la réplication persistent dans des lymphocytes T CD4+ mémoires exprimant l’intégrine VLA-4 en grande quantité, que les provirus intacts peuvent subsister au sein de différents compartiments anatomiques, que les provirus inductibles et compétents pour la traduction de la protéine virale p24 sont majoritairement défectifs, et que l’expansion clonale est un mécanisme important qui favorise le maintien du réservoir viral dans le sang et dans les tissus tout en favorisant la diversité phénotypique de ces cellules. / People with HIV (PWH) must take combinational antiretroviral therapy (ART) to control viral replication and avoid developing fatal immunodeficiency. ART allows achieving undetectable plasma viral load, and thus protects uninfected cells from HIV. However, ART interruption will almost inevitably result in a viral rebound since HIV is never completely cleared by the immune system. Indeed, a group of infected cells, where the virus has integrated and remains in a latent state, persists throughout the life course of PWH, and some of these cells form the replicationcompetent reservoir. Proviruses responsible for viral rebound have three characteristics: they can be induced to exit their latent state, they are genetically intact, and they are able to produce new infectious viral particles. Therefore, in order to cure PWH, it is essential to target the few cells with intact and inducible provirus, and to be able to do so, it is imperative to understand how these cells are maintained during years of ART, to localize them throughout the body, and to identify what distinguishes them from other cells. These three aspects are the focus of the work presented in this thesis, whether at the single-cell level or looking through the whole body. Our results show that replication-competent proviruses persist in memory CD4+ T cells expressing high levels of the integrin VLA-4, that intact proviruses can persist among various anatomical compartments, that inducible and translation-competent proviruses are predominantly defective, and that clonal expansion is an important mechanism that favors the maintenance of reservoir cells both in the blood and in deep tissues in addition to diversify phenotypically those cells.