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61.
  • Hollfelder, Nina, et al. (creator_code:aut_t)
  • Northeast African genomic variation shaped by the continuity of indigenous groups and Eurasian migrations
  • 2017
  • record:In_t: PLOS Genetics. - : PUBLIC LIBRARY SCIENCE. - 1553-7390 .- 1553-7404. ; 13:8
  • swepub:Mat_article_t (swepub:level_refereed_t)abstract
    • Northeast Africa has a long history of human habitation, with fossil-finds from the earliest anatomically modern humans, and housing ancient civilizations. The region is also the gateway out of Africa, as well as a portal for migration into Africa from Eurasia via the Middle East and the Arabian Peninsula. We investigate the population history of northeast Africa by genotyping similar to 3.9 million SNPs in 221 individuals from 18 populations sampled in Sudan and South Sudan and combine this data with published genome-wide data from surrounding areas. We find a strong genetic divide between the populations from the northeastern parts of the region (Nubians, central Arab populations, and the Beja) and populations towards the west and south (Nilotes, Darfur and Kordofan populations). This differentiation is mainly caused by a large Eurasian ancestry component of the northeast populations likely driven by migration of Middle Eastern groups followed by admixture that affected the local populations in a north-to-south succession of events. Genetic evidence points to an early admixture event in the Nubians, concurrent with historical contact between North Sudanese and Arab groups. We estimate the admixture in current-day Sudanese Arab populations to about 700 years ago, coinciding with the fall of Dongola in 1315/1316 AD, a wave of admixture that reached the Darfurian/Kordofanian populations some 400-200 years ago. In contrast to the northeastern populations, the current-day Nilotic populations from the south of the region display little or no admixture from Eurasian groups indicating long-term isolation and population continuity in these areas of northeast Africa.
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62.
  • Hollfelder, Nina, et al. (creator_code:aut_t)
  • Patterns of African and Asian admixture in the Afrikaner population of South Africa
  • 2020
  • record:In_t: BMC Biology. - : Springer Science and Business Media LLC. - 1741-7007. ; 18:1
  • swepub:Mat_article_t (swepub:level_refereed_t)abstract
    • BACKGROUND: The Afrikaner population of South Africa is the descendants of European colonists who started to colonize the Cape of Good Hope in the 1600s. In the early days of the colony, mixed unions between European males and non-European females gave rise to admixed children who later became incorporated into either the Afrikaner or the Coloured populations of South Africa. Differences in ancestry, social class, culture, sex ratio and geographic structure led to distinct and characteristic admixture patterns in the Afrikaner and Coloured populations. The Afrikaner population has a predominant European composition, whereas the Coloured population has more diverse ancestries. Genealogical records previously estimated the contribution of non-Europeans into the Afrikaners to be between 5.5 and 7.2%. RESULTS: To investigate the genetic ancestry of the Afrikaner population today (11-13 generations after initial colonization), we genotyped approximately five million genome-wide markers in 77 Afrikaner individuals and compared their genotypes to populations across the world to determine parental source populations and admixture proportions. We found that the majority of Afrikaner ancestry (average 95.3%) came from European populations (specifically northwestern European populations), but that almost all Afrikaners had admixture from non-Europeans. The non-European admixture originated mostly from people who were brought to South Africa as slaves and, to a lesser extent, from local Khoe-San groups. Furthermore, despite a potentially small founding population, there is no sign of a recent bottleneck in the Afrikaner compared to other European populations. Admixture amongst diverse groups from Europe and elsewhere during early colonial times might have counterbalanced the effects of a small founding population. CONCLUSIONS: While Afrikaners have an ancestry predominantly from northwestern Europe, non-European admixture signals are ubiquitous in the Afrikaner population. Interesting patterns and similarities could be observed between genealogical predictions and our genetic inferences. Afrikaners today have comparable inbreeding levels to current-day European populations.
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63.
  • Hollfelder, Nina, 1985- (creator_code:aut_t)
  • Population genetic history and patterns of admixture : Examples from northeastern and southern Africa
  • 2018
  • swepub:Mat_doctoralthesis_t (swepub:level_scientificother_t)abstract
    • The origin of humans lies in Africa, as has been shown by archaeology, paleontology and genetics. Here, we can find the largest genetic diversity and the deepest split among human populations. African genetic diversity has been shaped by a long and complex history. In this thesis, I applied population genomic methods to investigate different aspects of the demographic history of Africa, specifically northeast and southern Africa.Both of these regions are population melting-pots, with many historically known major migrations.In northeast African populations, Eurasian admixture in central, northern, and eastern Sudanese populations was identified to be of Middle Eastern origin and the admixture time coincides with the Arab expansion. In northeast Africa I also studied alleles associated with lactase persistence, the ability to digest milk at an adult age. A wide diversity of these alleles was detected in Sudan, most commonly among pastoralists. The presence of a Middle Eastern LP-allele and absence of a European LP-allele is consistent with the admixture pattern observed in the first paper.I deciphered the patterns of genetic admixture in the Afrikaner population of South Africa and compared admixture patterns of the X-chromosome and autosomes to disentangle sex-biased admixture in southern African populations.The Afrikaner were shown to carry on average 5% non-European admixture, mostly from Khoe-San, East and South Asian sources. The admixture was sex-biased, with larger contributions from European males and admixture with Africans can be dated to 9-10 generations ago – fitting previous genealogical estimates of the age and the history of the population.Bantu-speaker/Khoe-San contact shows a pattern of female Bantu-speaker bias, which is conflicting with previous mtDNA and Y-chromosome studies. A change in mate-choice over time could explain this discrepancy.This thesis contributes to a deeper understanding of African demographic history in general and of some previously understudied populations and geographic areas in particular.
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64.
  • Hollfelder, Nina, et al. (creator_code:aut_t)
  • The deep population history in Africa
  • 2021
  • record:In_t: Human Molecular Genetics. - : Oxford University Press. - 0964-6906 .- 1460-2083. ; 30:R1, s. R2-R10
  • swepub:Mat_researchreview_t (swepub:level_refereed_t)abstract
    • Africa is the continent with the greatest genetic diversity among humans and the level of diversity is further enhanced by incorporating non-majority groups, which are often understudied. Many of today's minority populations historically practiced foraging lifestyles, which were the only subsistence strategies prior to the rise of agriculture and pastoralism, but only a few groups practicing these strategies remain today. Genomic investigations of Holocene human remains excavated across the African continent show that the genetic landscape was vastly different compared to today's genetic landscape and that many groups that today are population isolate inhabited larger regions in the past. It is becoming clear that there are periods of isolation among groups and geographic areas, but also genetic contact over large distances throughout human history in Africa. Genomic information from minority populations and from prehistoric remains provide an invaluable source of information on the human past, in particular deep human population history, as Holocene large-scale population movements obscure past patterns of population structure. Here we revisit questions on the nature and time of the radiation of early humans in Africa, the extent of gene-flow among human populations as well as introgression from archaic and extinct lineages on the continent.
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65.
  • Hollfelder, Nina, et al. (creator_code:aut_t)
  • The Genetic Variation of Lactase Persistence Alleles in Sudan and South Sudan
  • 2021
  • record:In_t: Genome Biology and Evolution. - : Oxford University Press. - 1759-6653 .- 1759-6653. ; 13:5
  • swepub:Mat_article_t (swepub:level_refereed_t)abstract
    • Lactase persistence (LP) is a well-studied example of a Mendelian trait under selection in some human groups due to gene-culture coevolution. We investigated the frequencies of genetic variants linked to LP in Sudanese and South Sudanese populations. These populations have diverse subsistence patterns, and some are dependent on milk to various extents, not only from cows but also from other livestock such as camels and goats. We sequenced a 316-bp region involved in regulating the expression of the LCT gene on chromosome 2, which encompasses five polymorphisms that have been associated with LP. Pastoralist populations showed a higher frequency of LP-associated alleles compared with nonpastoralist groups, hinting at positive selection also among northeast African pastoralists. Among the LP variants, the -14009:G variant occurs at the highest frequency among the investigated populations, followed by the -13915:G variant, which is likely of Middle Eastern origin, consistent with Middle Eastern gene flow to the Sudanese populations. There was no incidence of the “East African” LP allele (-14010:C) in the Sudanese and South Sudanese groups, and only one heterozygous individual for the “European” LP allele (-13910:T), suggesting limited recent admixture from these geographic regions. The Beja population of the Beni Amer show three different LP variants at substantial and similar levels, resulting in one of the greatest aggregation of LP variants among all populations across the world.
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66.
  • Holm, Alexander, et al. (creator_code:aut_t)
  • Patients' perspective on prostatic artery embolization : A qualitative study
  • 2021
  • record:In_t: SAGE Open Medicine. - : SAGE Open. - 2050-3121. ; 9, s. 1-6
  • swepub:Mat_article_t (swepub:level_refereed_t)abstract
    • Objectives: The aim was to describe the patients' experience of undergoing prostatic artery embolization.Methods: A retrospective qualitative interview study was undertaken with 15 patients of mean age 73 years who had undergone prostatic artery embolization with a median duration of 210 min at two medium sized hospitals in Sweden. The reasons for conducting prostatic artery embolization were clean intermittent catheterization (n = 4), lower urinary tract symptoms (n = 10) or haematuria (n = 1). Data were collected through individual, semi-structured telephone interviews 1-12 months after treatment and analysed using qualitative content analysis.Results: Four categories with sub-categories were formulated to describe the results: a diverse experience; ability to control the situation; resumption of everyday activities and range of opinions regarding efficacy of outcomes. Overall, the patients described the procedure as painless, easy and interesting and reported that while the procedure can be stressful, a calm atmosphere contributed to achieving a good experience. Limitations on access to reliable information before, during and after the procedure were highlighted as a major issue. Practical ideas for improving patient comfort during the procedure were suggested. Improved communications between treatment staff and patients were also highlighted. Most patients could resume everyday activities, some felt tired and bruising caused unnecessary worry for a few. Regarding functional outcome, some patients described substantial improvement in urine flow while others were satisfied with regaining undisturbed night sleep. Those with less effect were considering transurethral resection of the prostate as a future option. Self-enrolment to the treatment and long median operation time may have influenced the results.Conclusions: From the patients' perspective, prostatic artery embolization is a well-tolerated method for treating benign prostate hyperplacia.
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67.
  • Huang, Lucy, et al. (creator_code:aut_t)
  • Haplotype variation and genotype imputation in African populations
  • 2011
  • record:In_t: Genetic Epidemiology. - : Wiley. - 0741-0395 .- 1098-2272. ; 35:8, s. 766-780
  • swepub:Mat_article_t (swepub:level_refereed_t)abstract
    • Sub-Saharan Africa has been identified as the part of the world with the greatest human genetic diversity. This high level of diversity causes difficulties for genome-wide association (GWA) studies in African populationsfor example, by reducing the accuracy of genotype imputation in African populations compared to non-African populations. Here, we investigate haplotype variation and imputation in Africa, using 253 unrelated individuals from 15 Sub-Saharan African populations. We identify the populations that provide the greatest potential for serving as reference panels for imputing genotypes in the remaining groups. Considering reference panels comprising samples of recent African descent in Phase 3 of the HapMap Project, we identify mixtures of reference groups that produce the maximal imputation accuracy in each of the sampled populations. We find that optimal HapMap mixtures and maximal imputation accuracies identified in detailed tests of imputation procedures can instead be predicted by using simple summary statistics that measure relationships between the pattern of genetic variation in a target population and the patterns in potential reference panels. Our results provide an empirical basis for facilitating the selection of reference panels in GWA studies of diverse human populations, especially those of African ancestry.
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68.
  • Jakobsson, Erik, et al. (creator_code:aut_t)
  • Automated Usage Characterization of Mining Vehicles For Life Time Prediction
  • 2020
  • record:In_t: IFAC PAPERSONLINE. - : ELSEVIER. - 2405-8963. ; , s. 11950-11955
  • swepub:Mat_conferencepaper_t (swepub:level_refereed_t)abstract
    • The life of a vehicle is heavily influenced by how it is used, and usage information is critical to predict the future condition of the machine. In this work we present a method to categorize what task an earthmoving vehicle is performing, based on a data driven model and a single standalone accelerometer. By training a convolutional neural network using a couple of weeks of labeled data, we show that a three axis accelerometer is sufficient to correctly classify between 5 different classes with an accuracy over 96% for a balanced dataset with no manual feature generation. The results are also compared against some other machine learning techniques, showing that the convolutional neural network has the highest performance, although other techniques are not far behind. An important conclusion is that methods and ideas from the area of Human Activity Recognition (HAR) are applicable also for vehicles. Copyright (C) 2020 The Authors.
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69.
  • Jakobsson, Erik, 1987- (creator_code:aut_t)
  • Condition Monitoring in Mobile Mining Machinery
  • 2022
  • swepub:Mat_doctoralthesis_t (swepub:level_scientificother_t)abstract
    • The global mining industry is currently facing a huge transition from manually operated individual vehicles, to autonomous vehicles being part of an industrial process-like environment. The change is driven by the never ending need for efficient, safe, and environmentally friendly operations. One intentional consequence is an increased distance between the operator, and the machine being operated. This enables safer working environments and reduced cost for ventilation and other supporting systems in a mine, but it also results in the loss of the systems most important sensor. The transition from manual to autonomous operation requires this gap to be filled from a system awareness perspective, which lately has become evident with the large resources that car manufacturers use to develop self-driving cars. This thesis also targets system awareness, but of the internal kind. By this we mean knowing the condition of the machine and its capabilities. The operator is the most important sensor also for internal condition, and if no operator is present on the machine, this gap needs to be filled.The mining industry is categorized by small series and significant customization of machinery. This is a direct result of the geological prerequisites, where differently shaped ore bodies cause large differences in mine layout and mining methods. This thesis explores how methods estimating the health of mining vehicles can be used in this setting, by utilizing sensor signals to make assessments of the current vehicle condition and tasks.The resulting health information can be used both to aid in tasks such as maintenance planning, but also as an important input to decision making for the planning system, i.e. how to run the vehicle for minimum wear and damage, while maintaining other mission objectives.Two applications are studied. Mine trucks have slow degradation modes, such as crack propagation and fatigue, that are difficult to handle with data driven approaches since data collection requires significant amounts of time. A contribution in this thesis, is a method to utilize short term measurement data together with data driven methods to obtain the loads of a vehicle, and then to use physics based approaches to estimate the actual damage.The second application considers monitoring faults in hydraulic rock drills using online measurements during operation. The rock drill is a specifically difficult case, since severe vibration levels limits the locations and types of sensors that can be used. The main contribution is a method to handle individual differences when classifying internal faults using a single pressure sensor on the hydraulic supply line. A complicating factor is the large influence of wave propagation, causing different individuals to show different behavior.
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70.
  • Jakobsson, Erik, 1987-, et al. (creator_code:aut_t)
  • Data driven modeling and estimation of accumulated damage in mining vehicles using on-board sensors
  • 2017
  • record:In_t: PHM 2017. Proceedings of the Annual Conference of the Prognostics and Health Management Society 2017, St. Petersburg, Florida, USA, October 2–5, 2017. - : Prognostics and Health Management Society. - 9781936263264 ; , s. 98-107
  • swepub:Mat_conferencepaper_t (swepub:level_refereed_t)abstract
    • The life and condition of a MT65 mine truck frame is to a large extent related to how the machine is used. Damage from different stress cycles in the frame are accumulated over time, and measurements throughout the life of the machine are needed to monitor the condition. This results in high demands on the durability of sensors used. To make a monitoring system cheap and robust enough for a mining application, a small number of robust sensors are preferred rather than a multitude of local sensors such as strain gauges. The main question to be answered is whether a low number of robust on-board sensors can give the required information to recreate stress signals at various locations of the frame. Also the choice of sensors among many different locations and kinds are considered. A final question is whether the data could also be used to estimate road condition. By using accelerometer, gyroscope and strain gauge data from field tests of an Atlas Copco MT65 mine truck, coherence and Lasso-regression were evaluated as means to select which signals to use. ARX-models for stress estimation were created using the same data. By simulating stress signals using the models, rain flow counting and damage accumulation calculations were performed. The results showed that a low number of on-board sensors like accelerometers and gyroscopes could give enough information to recreate some of the stress signals measured. Together with a linear model, the estimated stress was accurate enough to evaluate the accumulated fatigue damage in a mining truck. The accumulated damage was also used to estimate the condition of the road on which the truck was traveling. To make a useful road monitoring system some more work is required, in particular regarding how vehicle speed influences damage accumulation.
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