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21.
  • Bridel, Claire, et al. (creator_code:aut_t)
  • Diagnostic Value of Cerebrospinal Fluid Neurofilament Light Protein in Neurology : A Systematic Review and Meta-analysis
  • 2019
  • record:In_t: JAMA Neurology. - : American Medical Association (AMA). - 2168-6149 .- 2168-6157. ; 76:9, s. 1035-1048
  • swepub:Mat_researchreview_t (swepub:level_refereed_t)abstract
    • Importance  Neurofilament light protein (NfL) is elevated in cerebrospinal fluid (CSF) of a number of neurological conditions compared with healthy controls (HC) and is a candidate biomarker for neuroaxonal damage. The influence of age and sex is largely unknown, and levels across neurological disorders have not been compared systematically to date.Objectives  To assess the associations of age, sex, and diagnosis with NfL in CSF (cNfL) and to evaluate its potential in discriminating clinically similar conditions.Data Sources  PubMed was searched for studies published between January 1, 2006, and January 1, 2016, reporting cNfL levels (using the search terms neurofilament light and cerebrospinal fluid) in neurological or psychiatric conditions and/or in HC.Study Selection  Studies reporting NfL levels measured in lumbar CSF using a commercially available immunoassay, as well as age and sex.Data Extraction and Synthesis  Individual-level data were requested from study authors. Generalized linear mixed-effects models were used to estimate the fixed effects of age, sex, and diagnosis on log-transformed NfL levels, with cohort of origin modeled as a random intercept.Main Outcome and Measure  The cNfL levels adjusted for age and sex across diagnoses.Results  Data were collected for 10 059 individuals (mean [SD] age, 59.7 [18.8] years; 54.1% female). Thirty-five diagnoses were identified, including inflammatory diseases of the central nervous system (n = 2795), dementias and predementia stages (n = 4284), parkinsonian disorders (n = 984), and HC (n = 1332). The cNfL was elevated compared with HC in a majority of neurological conditions studied. Highest levels were observed in cognitively impaired HIV-positive individuals (iHIV), amyotrophic lateral sclerosis, frontotemporal dementia (FTD), and Huntington disease. In 33.3% of diagnoses, including HC, multiple sclerosis, Alzheimer disease (AD), and Parkinson disease (PD), cNfL was higher in men than women. The cNfL increased with age in HC and a majority of neurological conditions, although the association was strongest in HC. The cNfL overlapped in most clinically similar diagnoses except for FTD and iHIV, which segregated from other dementias, and PD, which segregated from atypical parkinsonian syndromes.Conclusions and Relevance  These data support the use of cNfL as a biomarker of neuroaxonal damage and indicate that age-specific and sex-specific (and in some cases disease-specific) reference values may be needed. The cNfL has potential to assist the differentiation of FTD from AD and PD from atypical parkinsonian syndromes.
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22.
  • Choin, Jeremy, et al. (creator_code:aut_t)
  • Genomic insights into population history and biological adaptation in Oceania
  • 2021
  • record:In_t: Nature. - : Springer Nature. - 0028-0836 .- 1476-4687. ; 592:7855, s. 583-589
  • swepub:Mat_article_t (swepub:level_refereed_t)abstract
    • The Pacific region is of major importance for addressing questions regarding human dispersals, interactions with archaic hominins and natural selection processes(1). However, the demographic and adaptive history of Oceanian populations remains largely uncharacterized. Here we report high-coverage genomes of 317 individuals from 20 populations from the Pacific region. We find that the ancestors of Papuan-related ('Near Oceanian') groups underwent a strong bottleneck before the settlement of the region, and separated around 20,000-40,000 years ago. We infer that the East Asian ancestors of Pacific populations may have diverged from Taiwanese Indigenous peoples before the Neolithic expansion, which is thought to have started from Taiwan around 5,000 years ago(2-4). Additionally, this dispersal was not followed by an immediate, single admixture event with Near Oceanian populations, but involved recurrent episodes of genetic interactions. Our analyses reveal marked differences in the proportion and nature of Denisovan heritage among Pacific groups, suggesting that independent interbreeding with highly structured archaic populations occurred. Furthermore, whereas introgression of Neanderthal genetic information facilitated the adaptation of modern humans related to multiple phenotypes (for example, metabolism, pigmentation and neuronal development), Denisovan introgression was primarily beneficial for immune-related functions. Finally, we report evidence of selective sweeps and polygenic adaptation associated with pathogen exposure and lipid metabolism in the Pacific region, increasing our understanding of the mechanisms of biological adaptation to island environments.
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23.
  • Chylenski, Maciej, et al. (creator_code:aut_t)
  • Late Danubian mitochondrial genomes shed light into the Neolithisation of Central Europe in the 5th millennium BC
  • 2017
  • record:In_t: BMC Evolutionary Biology. - : BIOMED CENTRAL LTD. - 1471-2148. ; 17
  • swepub:Mat_article_t (swepub:level_refereed_t)abstract
    • Background: Recent aDNA studies are progressively focusing on various Neolithic and Hunter-Gatherer (HG) populations, providing arguments in favor of major migrations accompanying European Neolithisation. The major focus was so far on the Linear Pottery Culture (LBK), which introduced the Neolithic way of life in Central Europe in the second half of 6th millennium BC. It is widely agreed that people of this culture were genetically different from local HGs and no genetic exchange is seen between the two groups. From the other hand some degree of resurgence of HGs genetic component is seen in late Neolithic groups belonging to the complex of the Funnel Beaker Cultures (TRB). Less attention is brought to various middle Neolithic cultures belonging to Late Danubian sequence which chronologically fall in between those two abovementioned groups. We suspected that genetic influx from HG to farming communities might have happened in Late Danubian cultures since archaeologists see extensive contacts between those two communities. Results: Here we address this issue by presenting 5 complete mitochondrial genomes of various late Danubian individuals from modern-day Poland and combining it with available published data. Our data show that Late Danubian cultures are maternally closely related to Funnel Beaker groups instead of culturally similar LBK. Conclusions: We assume that it is an effect of the presence of individuals belonging to U5 haplogroup both in Late Danubians and the TRB. The U5 haplogroup is thought to be a typical for HGs of Europe and therefore we argue that it is an additional evidence of genetic exchange between farming and HG groups taking place at least as far back as in middle Neolithic, in the Late Danubian communities.
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24.
  • Chylenski, Maciej, et al. (creator_code:aut_t)
  • Patrilocality and hunter-gatherer-related ancestry of populations in East-Central Europe during the Middle Bronze Age
  • 2023
  • record:In_t: Nature Communications. - : Springer Nature. - 2041-1723. ; 14
  • swepub:Mat_article_t (swepub:level_refereed_t)abstract
    • The demographic history of East-Central Europe after the Neolithic period remains poorly explored, despite this region being on the confluence of various ecological zones and cultural entities. Here, the descendants of societies associated with steppe pastoralists form Early Bronze Age were followed by Middle Bronze Age populations displaying unique characteristics. Particularly, the predominance of collective burials, the scale of which, was previously seen only in the Neolithic. The extent to which this re-emergence of older traditions is a result of genetic shift or social changes in the MBA is a subject of debate. Here by analysing 91 newly generated genomes from Bronze Age individuals from present Poland and Ukraine, we discovered that Middle Bronze Age populations were formed by an additional admixture event involving a population with relatively high proportions of genetic component associated with European hunter-gatherers and that their social structure was based on, primarily patrilocal, multigenerational kin-groups. By analysing 91 Bronze Age genomes from East-Central Europe, the authors discovered that Middle Bronze Age populations were formed by an admixture event involving hunter-gatherers and that the social structure of resulting population was primarily patrilocal.
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25.
  • Cotgreave, Ian, et al. (creator_code:aut_t)
  • Pyriproxifen and microcephaly: an investigation of potential ties to the ongoing "Zika epidemic"
  • 2016
  • swepub:Mat_report_t (swepub:level_scientificother_t)abstract
    • As part of the Swetox mission to react to emerging concerns in chemical health and environmental safety, a preliminary litterature investigation was undertaken to gather all readily available scientific information on PPF with respect to safety assessment, in order to better understand potential links between chemical exposure and the devopment of microcephaly in affected areas. Therefore the contents of the report do not constitute an attempt at either questioning the use of existing regulatory data in the manner prescribed by international regulatory proceedures, or as a new risk assessment, based on the scientific information and concepts discussed. Here we report our findings, with particular emphasis on exisiting regulatory information, potential for lack of translation of results from regulatory animal testing to humans, lack of human exposure data and suggestions on plausible mode(s) of action of PPF in human neurodevelopmental adversities such as microcephaly.
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26.
  • Coutinho, Alexandra, et al. (creator_code:aut_t)
  • Later Stone Age human hair from Vaalkrans Shelter, Cape Floristic Region of South Africa, reveals genetic affinity to Khoe groups
  • 2021
  • record:In_t: American Journal of Physical Anthropology. - : John Wiley & Sons. - 0002-9483 .- 1096-8644. ; 174:4, s. 701-713
  • swepub:Mat_article_t (swepub:level_refereed_t)abstract
    • Previous studies show that the indigenous people of the southern Cape of South Africa were dramatically impacted by the arrival of European colonists starting ~400 years ago and their descendants are today mixed with Europeans and Asians. To gain insight on the occupants of the Vaalkrans Shelter located at the southernmost tip of Africa, we investigated the genetic make-up of an individual who lived there about 200 years ago. We further contextualize the genetic ancestry of this individual among prehistoric and current groups. From a hair sample excavated at the shelter, which was indirectly dated to about 200 years old, we sequenced the genome (1.01 times coverage) of a Later Stone Age individual. We analyzed the Vaalkrans genome together with genetic data from 10 ancient (pre-colonial) individuals from southern Africa spanning the last 2000 years. We show that the individual from Vaalkrans was a man who traced ~80% of his ancestry to local southern San hunter–gatherers and ~20% to a mixed East African-Eurasian source. This genetic make-up is similar to modern-day Khoekhoe individuals from the Northern Cape Province (South Africa) and Namibia, but in the southern Cape, the Vaalkrans man's descendants have likely been assimilated into mixed-ancestry “Coloured” groups. The Vaalkrans man's genome reveals that Khoekhoe pastoralist groups/individuals lived in the southern Cape as late as 200 years ago, without mixing with non-African colonists or Bantu-speaking farmers. Our findings are also consistent with the model of a Holocene pastoralist migration, originating in Eastern Africa, shaping the genomic landscape of historic and current southern African populations.
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27.
  • Coutinho, Alexandra, et al. (creator_code:aut_t)
  • The Evolution of Adaptive traits in Indigenous human populations in Sub-Saharan Africa
  • swepub:Mat_publicationother_t (swepub:level_scientificother_t)abstract
    • Several well-known genetic variants that confer disease resistance or other adaptive advantages have been investigated in modern-day populations across the globe. In particular, sub-Saharan African populations display variation for many of these loci. In this study, we investigate allele frequencies underlying functional variants of interest in sub-Saharan African populations. By also investigating sequence data from ancient human remains from excavated sites in sub-Saharan Africa, we can start to get an indication of the allele frequency trajectories of adaptive variants, how they have diffused through the African genetic landscape, and how much migration and admixture played a role in the distribution of these variants in modern-day African populations. Our results show that as well as selection, migration has had a large influence on changing allele frequency through time in variants associated with disease resistance, salt sensitivity and metabolism. Yet in other variants, such as some associated with skin pigmentation, allele frequencies have changed little over time. Lastly, this study emphasizes the need for continued study of African populations, as due to the sheer genetic diversity present in Africa, different functional variants may confer similar means of adaptation than those we know for out-of-Africa populations. This study is the first to comprehensively investigate adaptive variants in both ancient and modern Africans, and further research will continue to reveal how the genetic landscape of modern humans has changed, and continues to change through time.
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28.
  • Coutinho, Alexandra, et al. (creator_code:aut_t)
  • The Neolithic Pitted Ware culture foragers were culturally but not genetically influenced by the Battle Axe culture herders
  • 2020
  • record:In_t: American Journal of Physical Anthropology. - : Wiley. - 0002-9483 .- 1096-8644. ; 172:4, s. 638-649
  • swepub:Mat_article_t (swepub:level_refereed_t)abstract
    • ObjectivesIn order to understand contacts between cultural spheres in the third millennium BC, we investigated the impact of a new herder culture, the Battle Axe culture, arriving to Scandinavia on the people of the sub‐Neolithic hunter‐gatherer Pitted Ware culture. By investigating the genetic make‐up of Pitted Ware culture people from two types of burials (typical Pitted Ware culture burials and Battle Axe culture‐influenced burials), we could determine the impact of migration and the impact of cultural influences.MethodsWe sequenced and analyzed the genomes of 25 individuals from typical Pitted Ware culture burials and from Pitted Ware culture burials with Battle Axe culture influences in order to determine if the different burial types were associated with different gene‐pools.ResultsThe genomic data show that all individuals belonged to one genetic population—a population associated with the Pitted Ware culture—irrespective of the burial style.ConclusionWe conclude that the Pitted Ware culture communities were not impacted by gene‐flow, that is, via migration or exchange of mates. These different cultural expressions in the Pitted Ware culture burials are instead a consequence of cultural exchange.
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29.
  • Coutinho, Alexandra (creator_code:aut_t)
  • Where our feet have taken us : Examples of human contact, migration, and adaptation as revealed by ancient DNA
  • 2019
  • swepub:Mat_doctoralthesis_t (swepub:level_scientificother_t)abstract
    • In spite of our extensive knowledge of the human past, certain key questions remain to be answered about human prehistory. One involves the nature of cultural change in material culture through time from the perspective of how different ancient human groups interacted with one another. The other is how humans have adapted to the different environments as they migrated and populated the rest of the world from their origin in Africa. For my thesis I have investigated examples of human evolutionary history using genetic information from ancient human remains. Chapter 1 focused on the nature of possible interaction between the Pitted Ware Culture (PWC) and Battle Axe Culture (BAC) on the island of Gotland, in the Baltic Sea. Through the analysis of 4500 year old human remains from three PWC burial sites, I found that the existence of BAC influences in these burial sites was the result of cultural and not demic influence from the BAC. In chapter 2, I investigated the ancestry of a Late Stone Age individual from the southwestern Cape of South Africa. Population genetic analyses revealed that this individual was genetically affiliated with Khoe groups in southern Africa, a genetic make-up that is today absent from the Cape. Chapter 3 investigated the genetic landscape of prehistoric individuals from southern Africa. Specifically, I explored frequencies of adaptive variants between Late Stone Age and Iron Age individuals. I found an increase in disease resistance alleles in Iron Age individuals and attributed this to the effects of the Bantu expansion. Chapter 4 incorporated a wider range of trait-associated variants among a greater number of modern-day populations and ancient individuals in Africa. I found that many allele frequency patterns found in modern populations follow the routes of major migrations which took place in the African Holocene. The thesis attests to the complexity of human demographic history in general, and how migration contributes to adaptation by dispersing novel adaptive variants to populations.
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30.
  • da Fonseca, Rute R., et al. (creator_code:aut_t)
  • The origin and evolution of maize in the Southwestern United States
  • 2015
  • record:In_t: Nature Plants. - 2055-026X. ; 1:1
  • swepub:Mat_article_t (swepub:level_refereed_t)abstract
    • The origin of maize (Zea mays mays) in the US Southwest remains contentious, with conflicting archaeological data supporting either coastal(1-4) or highland(5,6) routes of diffusion of maize into the United States. Furthermore, the genetics of adaptation to the new environmental and cultural context of the Southwest is largely uncharacterized(7). To address these issues, we compared nuclear DNA from 32 archaeological maize samples spanning 6,000 years of evolution to modern landraces. We found that the initial diffusion of maize into the Southwest about 4,000 years ago is likely to have occurred along a highland route, followed by gene flow from a lowland coastal maize beginning at least 2,000 years ago. Our population genetic analysis also enabled us to differentiate selection during domestication for adaptation to the climatic and cultural environment of the Southwest, identifying adaptation loci relevant to drought tolerance and sugar content.
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