| 1. |
- Allentoft, Morten E., et al.
(författare)
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Population genomics of post-glacial western Eurasia
- 2024
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Ingår i: Nature. - 0028-0836 .- 1476-4687. ; 625:7994, s. 301-311
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Tidskriftsartikel (refereegranskat)abstract
- Western Eurasia witnessed several large-scale human migrations during the Holocene1–5. Here, to investigate the cross-continental effects of these migrations, we shotgun-sequenced 317 genomes—mainly from the Mesolithic and Neolithic periods—from across northern and western Eurasia. These were imputed alongside published data to obtain diploid genotypes from more than 1,600 ancient humans. Our analyses revealed a ‘great divide’ genomic boundary extending from the Black Sea to the Baltic. Mesolithic hunter-gatherers were highly genetically differentiated east and west of this zone, and the effect of the neolithization was equally disparate. Large-scale ancestry shifts occurred in the west as farming was introduced, including near-total replacement of hunter-gatherers in many areas, whereas no substantial ancestry shifts happened east of the zone during the same period. Similarly, relatedness decreased in the west from the Neolithic transition onwards, whereas, east of the Urals, relatedness remained high until around 4,000 bp, consistent with the persistence of localized groups of hunter-gatherers. The boundary dissolved when Yamnaya-related ancestry spread across western Eurasia around 5,000 bp, resulting in a second major turnover that reached most parts of Europe within a 1,000-year span. The genetic origin and fate of the Yamnaya have remained elusive, but we show that hunter-gatherers from the Middle Don region contributed ancestry to them. Yamnaya groups later admixed with individuals associated with the Globular Amphora culture before expanding into Europe. Similar turnovers occurred in western Siberia, where we report new genomic data from a ‘Neolithic steppe’ cline spanning the Siberian forest steppe to Lake Baikal. These prehistoric migrations had profound and lasting effects on the genetic diversity of Eurasian populations.
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| 2. |
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| 3. |
- Allentoft, Morten E., et al.
(författare)
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100 ancient genomes show repeated population turnovers in Neolithic Denmark
- 2024
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Ingår i: Nature. - 0028-0836 .- 1476-4687. ; 625, s. 329-337
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Tidskriftsartikel (refereegranskat)abstract
- Major migration events in Holocene Eurasia have been characterized genetically at broad regional scales1–4. However, insights into the population dynamics in the contact zones are hampered by a lack of ancient genomic data sampled at high spatiotemporal resolution5–7. Here, to address this, we analysed shotgun-sequenced genomes from 100 skeletons spanning 7,300 years of the Mesolithic period, Neolithic period and Early Bronze Age in Denmark and integrated these with proxies for diet (13C and 15N content), mobility (87Sr/86Sr ratio) and vegetation cover (pollen). We observe that Danish Mesolithic individuals of the Maglemose, Kongemose and Ertebølle cultures form a distinct genetic cluster related to other Western European hunter-gatherers. Despite shifts in material culture they displayed genetic homogeneity from around 10,500 to 5,900 calibrated years before present, when Neolithic farmers with Anatolian-derived ancestry arrived. Although the Neolithic transition was delayed by more than a millennium relative to Central Europe, it was very abrupt and resulted in a population turnover with limited genetic contribution from local hunter-gatherers. The succeeding Neolithic population, associated with the Funnel Beaker culture, persisted for only about 1,000 years before immigrants with eastern Steppe-derived ancestry arrived. This second and equally rapid population replacement gave rise to the Single Grave culture with an ancestry profile more similar to present-day Danes. In our multiproxy dataset, these major demographic events are manifested as parallel shifts in genotype, phenotype, diet and land use.
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| 4. |
- Beal, Jacob, et al.
(författare)
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Robust estimation of bacterial cell count from optical density
- 2020
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Ingår i: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1
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Tidskriftsartikel (refereegranskat)abstract
- Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data.
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| 5. |
- Bekoe, Samuel Oppong, et al.
(författare)
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Detection and quantification of antibiotic residues in urine samples of healthy individuals from rural and urban communities in Ghana using a validated SPE-LC-MS/MS method
- 2020
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Ingår i: SN APPLIED SCIENCES. - 2523-3963. ; 2:11
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Tidskriftsartikel (refereegranskat)abstract
- The role of unregulated and inappropriate dispensing, and use of antibiotics remains significant in the development of antimicrobial resistance in infectious disease endemic regions of developing countries. The exposure to antibiotics from unfamiliar and unsuspecting sources such as drinking water and food, and adulterated herbal medicines remains a cause for concern. A sensitive SPE-LC-MS/MS method was developed and validated for the quantification and qualification of 12 antibiotics, including amoxicillin, clavulanic acid, metronidazole, ampicillin, cefuroxime, tetracycline, ceftriaxone, sulphamethoxazole, trimethoprim, ciprofloxacin, benzylpenicillin, and erythromycin, in the urine of healthy volunteers. The method was linear (r(2) > 0.98) within the concentration range 50-5000 ngmL(-1) for all the analytes. Instrument precision of 8-27% and 4-21% at 100 and 1000 ngmL(-1) levels were demonstrated. High mean recoveries between 71 and 125% with minimal variations were obtained for all compounds in the accuracy study. Limits of detection and quantification ranged between 70.3-271.0 ngmL(-1) and 213-821 ngmL(-1) respectively. The validated method successfully detected and quantified 9 of the 12 analytes, with the exception of clavulanic acid, cefuroxime, and benzylpenicillin. Most of the samples contained one analyte (52, 86.7%), with a handful containing two (7, 11.7%) and three analytes (1, 1.7%). Ciprofloxacin was the modal analyte detected (17, 24.6%), with amoxicillin and trimethoprim recording the average lowest (22.76 x 10(3) ngmL(-1)) and highest concentrations (255.47 x 10(3) ngmL(-1)) respectively. The developed method is a useful tool for non-invasive monitoring of consumption and the irrational use of antibiotics in microbial resistant-prone regions of the world.
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| 6. |
- Bekoe, Samuel Oppong, et al.
(författare)
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Detection and quantification of antibiotic residues in urine samples of healthy individuals from rural and urban communities in Ghana using a validated SPE-LC-MS/MS method
- 2020
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Ingår i: SN APPLIED SCIENCES. - : Springer Science and Business Media LLC. - 2523-3963 .- 2523-3971. ; 2:11
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Tidskriftsartikel (refereegranskat)abstract
- The role of unregulated and inappropriate dispensing, and use of antibiotics remains significant in the development of antimicrobial resistance in infectious disease endemic regions of developing countries. The exposure to antibiotics from unfamiliar and unsuspecting sources such as drinking water and food, and adulterated herbal medicines remains a cause for concern. A sensitive SPE-LC-MS/MS method was developed and validated for the quantification and qualification of 12 antibiotics, including amoxicillin, clavulanic acid, metronidazole, ampicillin, cefuroxime, tetracycline, ceftriaxone, sulphamethoxazole, trimethoprim, ciprofloxacin, benzylpenicillin, and erythromycin, in the urine of healthy volunteers. The method was linear (r(2) > 0.98) within the concentration range 50-5000 ngmL(-1) for all the analytes. Instrument precision of 8-27% and 4-21% at 100 and 1000 ngmL(-1) levels were demonstrated. High mean recoveries between 71 and 125% with minimal variations were obtained for all compounds in the accuracy study. Limits of detection and quantification ranged between 70.3-271.0 ngmL(-1) and 213-821 ngmL(-1) respectively. The validated method successfully detected and quantified 9 of the 12 analytes, with the exception of clavulanic acid, cefuroxime, and benzylpenicillin. Most of the samples contained one analyte (52, 86.7%), with a handful containing two (7, 11.7%) and three analytes (1, 1.7%). Ciprofloxacin was the modal analyte detected (17, 24.6%), with amoxicillin and trimethoprim recording the average lowest (22.76 x 10(3) ngmL(-1)) and highest concentrations (255.47 x 10(3) ngmL(-1)) respectively. The developed method is a useful tool for non-invasive monitoring of consumption and the irrational use of antibiotics in microbial resistant-prone regions of the world.
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| 7. |
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| 8. |
- Hagen, Kristen, et al.
(författare)
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Does Concentrated Exposure Treatment for Obsessive-Compulsive Disorder Improve Insomnia Symptoms? : Results From a Randomized Controlled Trial
- 2021
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Ingår i: Frontiers in Psychiatry. - : Frontiers Media SA. - 1664-0640. ; 12
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Tidskriftsartikel (refereegranskat)abstract
- Insomnia is a substantial problem in patients with obsessive-compulsive disorder (OCD). There is, however, a lack of studies investigating changes in concurrent symptoms of insomnia in OCD after concentrated treatment. A recent randomized controlled trial randomized participants to the Bergen 4-day treatment (B4DT, n = 16), or 12 weeks of unguided self-help (SH, n = 16), or waitlist (WL, n = 16). Patients from the SH- and WL-group who wanted further treatment after the 12 weeks were then offered the B4DT (total of 42 patients treated with the B4DT). There were no significant differences in symptoms of insomnia between the conditions at post-treatment, but a significant moderate improvement at 3-month follow-up for patients who received the B4DT. Insomnia was not associated with OCD-treatment outcome, and change in symptoms of insomnia was mainly related to changes in depressive symptoms. The main conclusion is that concentrated exposure treatment is effective irrespective of comorbid insomnia, and that insomnia problems are moderately reduced following treatment.
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| 9. |
- Harris, Alison J. T., 1982-, et al.
(författare)
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Archives of human-dog relationships : Genetic and stable isotope analysis of Arctic fur clothing
- 2020
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Ingår i: Journal of Anthropological Archaeology. - : Elsevier BV. - 0278-4165 .- 1090-2686. ; 59
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Tidskriftsartikel (refereegranskat)abstract
- Among Indigenous populations of the Arctic, domestic dogs (Canislupus familiaris) were social actors aiding in traction and subsistence activities. Less commonly, dogs fulfilled a fur-bearing role in both the North American and Siberian Arctic. Examples of garments featuring dog skins were collected during the 19th-20th centuries and are now curated by the National Museum of Denmark. We sequenced the mitochondrial genomes of macroscopically identified dog skin garments. We conducted stable carbon and nitrogen isotope ratio analysis of the dog furs and of fur samples from contemporaneous pelts of Arctic (C. lupus arctos) and grey (C. lupus) wolves. Despite the presence of biocides used to protect the fur clothing during storage, we extracted well-preserved DNA using a minimally-invasive sampling protocol. Unexpectedly, the mtDNA genomes of one-third of the samples were consistent with wild taxa, rather than domestic dogs. The strong marine component in the diets of North American dogs distinguished them from Greenland and Canadian wolves, but Siberian dogs consumed diets that were isotopically similar to wild species. We found that dog provisioning practices were variable across the Siberian and North American Arctic, but in all cases, involved considerable human labor.
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| 10. |
- Kvale, Gerd, et al.
(författare)
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Effect of D-Cycloserine on the Effect of Concentrated Exposure and Response Prevention in Difficult-to-Treat Obsessive-Compulsive Disorder : A Randomized Clinical Trial
- 2020
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Ingår i: JAMA Network Open. - : American Medical Association (AMA). - 2574-3805. ; 3:8
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Tidskriftsartikel (refereegranskat)abstract
- IMPORTANCE: Evidence is lacking for viable treatment options for patients with difficult-to-treat obsessive-compulsive disorder (OCD). It has been suggested that D-cycloserine (DCS) could potentiate the effect of exposure and response prevention (ERP) treatment, but the hypothesis has not been tested among patients with difficult-to-treat OCD.OBJECTIVE: To evaluate whether DCS potentiates the effect of concentrated ERP among patients with difficult-to-treat OCD.DESIGN, SETTING, AND PARTICIPANTS: The study was a randomized placebo-controlled triple-masked study with a 12-month follow-up. Participants were adult outpatients with difficult-to-treat OCD. A total of 220 potential participants were referred, of whom 36 did not meet inclusion criteria and 21 declined to participate. Patients had either relapsed after (n = 100) or not responded to (n = 63) previous ERP treatment. A total of 9 specialized OCD teams within the public health care system in Norway participated, giving national coverage. An expert team of therapists from the coordinating site delivered treatment. Inclusion of patients started in January 2016 and ended in August 2017. Data analysis was conducted February to September 2019.INTERVENTIONS: All patients received individual, concentrated ERP treatment delivered during 4 consecutive days in a group setting (the Bergen 4-day treatment format) combined with 100 mg DCS, 250 mg DCS, or placebo.MAIN OUTCOMES AND MEASURES: Change in symptoms of OCD and change in diagnostic status. Secondary outcomes measures included self-reported symptoms of OCD, anxiety, depression, and quality of life.RESULTS: The total sample of 163 patients had a mean (SD) age of 34.5 (10.9) years, and most were women (117 [71.8%]). They had experienced OCD for a mean (SD) of 16.2 (10.2) years. A total of 65 patients (39.9%) were randomized to receive 100 mg DCS, 67 (41.1%) to 250 mg of DCS, and 31 (19.0%) to placebo. Overall, 91 (56.5%) achieved remission at posttreatment, while 70 (47.9%) did so at the 12-month follow-up. There was no significant difference in remission rates among groups. There was a significant reduction in symptoms at 12 months, and within-group effect sizes ranged from 3.01 (95% CI, 2.38-3.63) for the group receiving 250 mg DCS to 3.49 (95% CI, 2.78-4.18) for the group receiving 100 mg DCS (all P < .001). However, there was no significant effect of treatment group compared with placebo in obsessive-compulsive symptoms (250 mg group at posttreatment: d = 0.33; 95% CI, -0.10 to 0.76; 100 mg group at posttreatment: d = 0.36; 95% CI, -0.08 to 0.79), symptoms of depression and anxiety (eg, Patient Health Questionnaire-9 score among 250 mg group at 12-month follow-up: d = 0.30; 95% CI, -0.17 to 0.76; Generalized Anxiety Disorder-7 score among 100 mg group at 12-month follow-up: d = 0.27; 95% CI, -0.19 to 0.73), and well-being (250 mg group: d = 0.10; 95% CI, -0.42 to 0.63; 100 mg group: d = 0.34; 95% CI, -0.19 to 0.86). No serious adverse effects were reported.CONCLUSIONS AND RELEVANCE: In this study, DCS did not potentiate ERP treatment effect, but concentrated ERP treatment was associated with improvement. This randomized clinical trial evaluates whether D-cycloserine potentiates the effect of concentrated exposure and response prevention among patients with difficult-to-treat obsessive-compulsive disorder.
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