| 1. |
- Feng, Shaohong, et al.
(författare)
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Dense sampling of bird diversity increases power of comparative genomics
- 2020
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 587:7833
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Tidskriftsartikel (refereegranskat)abstract
- Whole-genome sequencing projects are increasingly populating the tree of life and characterizing biodiversity(1-4). Sparse taxon sampling has previously been proposed to confound phylogenetic inference(5), and captures only a fraction of the genomic diversity. Here we report a substantial step towards the dense representation of avian phylogenetic and molecular diversity, by analysing 363 genomes from 92.4% of bird families-including 267 newly sequenced genomes produced for phase II of the Bird 10,000 Genomes (B10K) Project. We use this comparative genome dataset in combination with a pipeline that leverages a reference-free whole-genome alignment to identify orthologous regions in greater numbers than has previously been possible and to recognize genomic novelties in particular bird lineages. The densely sampled alignment provides a single-base-pair map of selection, has more than doubled the fraction of bases that are confidently predicted to be under conservation and reveals extensive patterns of weak selection in predominantly non-coding DNA. Our results demonstrate that increasing the diversity of genomes used in comparative studies can reveal more shared and lineage-specific variation, and improve the investigation of genomic characteristics. We anticipate that this genomic resource will offer new perspectives on evolutionary processes in cross-species comparative analyses and assist in efforts to conserve species. A dataset of the genomes of 363 species from the Bird 10,000 Genomes Project shows increased power to detect shared and lineage-specific variation, demonstrating the importance of phylogenetically diverse taxon sampling in whole-genome sequencing.
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| 2. |
- Allansson, Jakob, et al.
(författare)
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Planeringsverktyg för Bus rapid Transit (BRT) i Sverige
- 2024
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Rapport (populärvet., debatt m.m.)abstract
- Rapporten presenterar ett uppdaterad planeringsverktyg för Bus Rapid Transit (BRT), anpassat för en svensk kontext. Planeringsverktyget är tänkt att fungera som ett samverkansstöd för planerare och består av 25 olika parametrar fördelat på 4 olika kategorier; Stadens utformning, Kollektivtrafikens infrastruktur, Fordon och stödsystem samt Trafikering.
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| 3. |
- Andersson, Joel B. H., et al.
(författare)
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Structural controls on sulphide (re)-distribution in Kiruna
- 2019
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Ingår i: Proceedings of the 15th SGA Biennial Meeting, 27-30 August. - : University of Glasgow Publicity Services. ; , s. 115-118
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Konferensbidrag (refereegranskat)abstract
- In this study, we investigate a potential structural control on sulphide distribution in phyllite from the Kiruna area, northern Norrbotten, Sweden. We use X-ray tomography and X-ray fluorescence analyzed in tandem on a 40 cm section of oriented drill core. Scanning Electron Microscopy and Energy Dispersive Spectrometry are used in combination with optical microscopy to analyze mineralogy and microstructures. The results show that sulphides are distributed along So bedding planes, re-distributed along S-2 axial planar cleavage planes, and trapped by F-2-hinge zones and shear bands visible as elevated sulphide concentrations. The results of this study underlines the strength of X-ray tomography to image 3D geological structures and their relation to mineral distributions.
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| 4. |
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| 5. |
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| 6. |
- Bridel, Claire, et al.
(författare)
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Diagnostic Value of Cerebrospinal Fluid Neurofilament Light Protein in Neurology : A Systematic Review and Meta-analysis
- 2019
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Ingår i: JAMA Neurology. - : American Medical Association (AMA). - 2168-6149 .- 2168-6157. ; 76:9, s. 1035-1048
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Forskningsöversikt (refereegranskat)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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| 7. |
- De Marinis, Yang, et al.
(författare)
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Serology assessment of antibody response to SARS-CoV-2 in patients with COVID-19 by rapid IgM/IgG antibody test
- 2020
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Ingår i: Infection Ecology and Epidemiology. - : Informa UK Limited. - 2000-8686. ; 10:1
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Tidskriftsartikel (refereegranskat)abstract
- The coronavirus disease 2019 (COVID-19) pandemic has created a global health- and economic crisis. Detection of antibodies to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) which causes COVID-19 by serological methods is important to diagnose a current or resolved infection. In this study, we applied a rapid COVID-19 IgM/IgG antibody test and performed serology assessment of antibody response to SARS-CoV-2. In PCR-confirmed COVID-19 patients (n = 45), the total antibody detection rate is 92% in hospitalized patients and 79% in non-hospitalized patients. The total IgM and IgG detection is 63% in patients with <2 weeks from disease onset; 85% in non-hospitalized patients with >2 weeks disease duration; and 91% in hospitalized patients with >2 weeks disease duration. We also compared different blood sample types and suggest a higher sensitivity by serum/plasma over whole blood. Test specificity was determined to be 97% on 69 sera/plasma samples collected between 2016-2018. Our study provides a comprehensive validation of the rapid COVID-19 IgM/IgG serology test, and mapped antibody detection patterns in association with disease progress and hospitalization. Our results support that the rapid COVID-19 IgM/IgG test may be applied to assess the COVID-19 status both at the individual and at a population level.
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| 8. |
- Hammad, Samir, et al.
(författare)
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Kollektivtrafikens sårbarhet i Covid-19-eran : En holistisk strategi framåt
- 2022
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Rapport (övrigt vetenskapligt/konstnärligt)abstract
- The role of public transport in society is crucial, particularly for those who do not have access to alternative transport modes. For public transport to be able to fulfil its societal role, it should not be perceived as unsafe or unhealthy by its (potential) users. Several studies from all over the world have shown that anxiety has increased remarkably during the pandemic, and it is likely to last much longer. Furthermore, the pandemic is expected to affect travel behaviour even when it will be over and all the restrictions will be lifted due to, among other things, increased teleworking, increased unemployment and the remaining effect of concerns about congestion and infection. This study aims to investigate how the public transport supply has adjusted during the different stages of the pandemic and what the result of these changes on the costs of public transport has been. The study also aims to identify today's challenges, the measures that have already been implemented and what needs to be done in the future to keep public transport functioning in similar circumstances and to help it recover quickly and fully after the pandemic. The method used to understand the pandemic's impact on public transport and thus be able to answer the study's first two questions, is a literature study. Thereafter, quantitative data on ridership, public transport supply and costs have been collected. The data has been analyzed and visualized to present it in an easy-to-understand way. To answer the final question about how to better adapt public transport to the covid-19 pandemic in the medium and long term, qualitative interviews have been conducted. Finally, the proposed strategies presented in this paper have been assessed using the multi-Criteria Analysis.
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| 9. |
- Hansson, Joel, et al.
(författare)
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Defining regional public transport
- 2018
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Rapport (övrigt vetenskapligt/konstnärligt)abstract
- When exploring preferences of existing and potential public transport passengers, it isrelevant to acknowledge differences between different geographic scales: local, regionaland interregional. However, the boundaries between these categories remain unclear.Some previous attempts have been made to define regional travel – and hence local andinterregional travel – but the resulting definitions are somewhat vague and use diversesets of metrics. In order to sort the terms, this paper aims to explore the perception ofthe concept regional travel through a survey among public transport professionals. Intotal, 290 completed questionnaires were collected. All continents are represented in thesurvey, but with a strong concentration of responses in North America and Europe. Theresults emphasise the importance of maintaining a distinction between functionality andtechnology, meaning that factors such as vehicle type or speed should not be included inthe definition. Instead, the survey indicates a clear preference for either anadministrative or a functional definition, depending on the purpose. The functionaldefinition is argued to best fit the purpose of exploring passengers’ preferences, andhence the following working definition of regional public transport can be adopted:Regional public transport targets passengers travelling between separate urban areasor to rural areas, and a majority of the trips are made on a regular basis (daily toweekly in general).
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| 10. |
- Hansson, Joel, et al.
(författare)
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Effects of rural bus stops on travel time and reliability
- 2021
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Ingår i: Public Transport. - : Springer Science and Business Media LLC. - 1613-7159 .- 1866-749X.
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Tidskriftsartikel (refereegranskat)abstract
- Due to relatively low patronage levels, rural bus stops are sometimes questioned in order to improve travel time and reliability on regional bus services. Previous research into stop spacing has focused on urban areas, which means that there is a lack of knowledge regarding the effects of bus stops in regional networks, with longer distances, higher speeds, and lower passenger volumes, in general. The present study addresses this knowledge gap by analysing the effects of bus stops on a regional bus service regarding average travel times, travel time variability, and on-time performance. This is done by statistical analysis of automatic vehicle location (AVL) data, using a combination of methods previously used for analysis of rail traffic and urban bus operations. The results reveal that bus stops that are only used sporadically have a limited impact on average travel times, in general. In contrast, they are all the more influential on travel time variability, and, in turn, on on-time performance. On the studied bus service, the number of stops made have a far greater impact on travel time variability than any of the other included variables, such as the weather or traffic conditions during peak hours. However, the results suggest that rural bus stops have a much lower impact than what we define as secondary bus stops in urban areas. Consequently, by primarily focusing on bus stop consolidation in urban areas, it is possible to significantly improve service reliability without impairing rural coverage.
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