| 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. |
- Bentley, Blair P., et al.
(författare)
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Divergent sensory and immune gene evolution in sea turtles with contrasting demographic and life histories
- 2023
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Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences (PNAS). - 0027-8424 .- 1091-6490. ; 120:7
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Tidskriftsartikel (refereegranskat)abstract
- Sea turtles represent an ancient lineage of marine vertebrates that evolved from terrestrial ancestors over 100 Mya. The genomic basis of the unique physiological and ecological traits enabling these species to thrive in diverse marine habitats remains largely unknown. Additionally, many populations have drastically declined due to anthropogenic activities over the past two centuries, and their recovery is a high global conservation priority. We generated and analyzed high-quality reference genomes for the leatherback (Dermochelys coriacea) and green (Chelonia mydas) turtles, representing the two extant sea turtle families. These genomes are highly syntenic and homologous, but localized regions of noncollinearity were associated with higher copy numbers of immune, zinc-finger, and olfactory receptor (OR) genes in green turtles, with ORs related to waterborne odorants greatly expanded in green turtles. Our findings suggest that divergent evolution of these key gene families may underlie immunological and sensory adaptations assisting navigation, occupancy of neritic versus pelagic environments, and diet specialization. Reduced collinearity was especially prevalent in microchromosomes, with greater gene content, heterozygosity, and genetic distances between species, supporting their critical role in vertebrate evolutionary adaptation. Finally, diversity and demographic histories starkly contrasted between species, indicating that leatherback turtles have had a low yet stable effective population size, exhibit extremely low diversity compared with other reptiles, and harbor a higher genetic load compared with green turtles, reinforcing concern over their persistence under future climate scenarios. These genomes provide invaluable resources for advancing our understanding of evolution and conservation best practices in an imperiled vertebrate lineage.
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| 3. |
- Accordini, Simone, et al.
(författare)
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Incidence trends of airflow obstruction among European adults without asthma : a 20-year cohort study
- 2020
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Ingår i: Scientific Reports. - : NATURE PUBLISHING GROUP. - 2045-2322. ; 10:1
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Tidskriftsartikel (refereegranskat)abstract
- Investigating COPD trends may help healthcare providers to forecast future disease burden. We estimated sex- and smoking-specific incidence trends of pre-bronchodilator airflow obstruction (AO) among adults without asthma from 11 European countries within a 20-year follow-up (ECRHS and SAPALDIA cohorts). We also quantified the extent of misclassification in the definition based on pre-bronchodilator spirometry (using post-bronchodilator measurements from a subsample of subjects) and we used this information to estimate the incidence of post-bronchodilator AO (AO(post-BD)), which is the primary characteristic of COPD. AO incidence was 4.4 (95% CI: 3.5-5.3) male and 3.8 (3.1-4.6) female cases/1,000/year. Among ever smokers (median pack-years: 20, males; 12, females), AO incidence significantly increased with ageing in men only [incidence rate ratio (IRR), 1-year increase: 1.05 (1.03-1.07)]. A strong exposure-response relationship with smoking was found both in males [IRR, 1-pack-year increase: 1.03 (1.02-1.04)] and females [1.03 (1.02-1.05)]. The positive predictive value of AO for AO(post-BD) was 59.1% (52.0-66.2%) in men and 42.6% (35.1-50.1%) in women. AO(post-BD) incidence was 2.6 (1.7-3.4) male and 1.6 (1.0-2.2) female cases/1,000/year. AO incidence was considerable in Europe and the sex-specific ageing-related increase among ever smokers was strongly related to cumulative tobacco exposure. AO(post-BD) incidence is expected to be half of AO incidence.
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| 4. |
- Allinson, James P, et al.
(författare)
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Changes in lung function in European adults born between 1884 and 1996 and implications for the diagnosis of lung disease: a cross-sectional analysis of ten population-based studies.
- 2022
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Ingår i: The Lancet. Respiratory medicine. - : Elsevier. - 2213-2619 .- 2213-2600. ; 10:1, s. 83-94
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Tidskriftsartikel (refereegranskat)abstract
- During the past century, socioeconomic and scientific advances have resulted in changes in the health and physique of European populations. Accompanying improvements in lung function, if unrecognised, could result in the misclassification of lung function measurements and misdiagnosis of lung diseases. We therefore investigated changes in population lung function with birth year across the past century, accounting for increasing population height, and examined how such changes might influence the interpretation of lung function measurements.In our analyses of cross-sectional data from ten European population-based studies, we included individuals aged 20-94 years who were born between 1884 and 1996, regardless of previous respiratory diagnoses or symptoms. FEV1, forced vital capacity (FVC), height, weight, and smoking behaviour were measured between 1965 and 2016. We used meta-regression to investigate how FEV1 and FVC (adjusting for age, study, height, sex, smoking status, smoking pack-years, and weight) and the FEV1/FVC ratio (adjusting for age, study, sex, and smoking status) changed with birth year. Using estimates from these models, we graphically explored how mean lung function values would be expected to progressively deviate from predicted values. To substantiate our findings, we used linear regression to investigate how the FEV1 and FVC values predicted by 32 reference equations published between 1961 and 2015 changed with estimated birth year.Across the ten included studies, we included 243465 European participants (mean age 51·4 years, 95% CI 51·4-51·5) in our analysis, of whom 136275 (56·0%) were female and 107190 (44·0%) were male. After full adjustment, FEV1 increased by 4·8 mL/birth year (95% CI 2·6-7·0; p<0·0001) and FVC increased by 8·8 mL/birth year (5·7-12·0; p<0·0001). Birth year-related increases in the FEV1 and FVC values predicted by published reference equations corroborated these findings. This height-independent increase in FEV1 and FVC across the last century will have caused mean population values to progressively exceed previously predicted values. However, the population mean adjusted FEV1/FVC ratio decreased by 0·11 per 100 birth years (95% CI 0·09-0·14; p<0·0001).If current diagnostic criteria remain unchanged, the identified shifts in European values will allow the easier fulfilment of diagnostic criteria for lung diseases such as chronic obstructive pulmonary disease, but the systematic underestimation of lung disease severity.The European Respiratory Society, AstraZeneca, Chiesi Farmaceutici, GlaxoSmithKline, Menarini, and Sanofi-Genzyme.
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| 5. |
- Apollonio, Benedetta, et al.
(författare)
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Tumor-activated lymph node fibroblasts suppress T cell function in diffuse large B cell lymphoma
- 2023
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Ingår i: Journal of Clinical Investigation. - : American Society for Clinical Investigation. - 0021-9738 .- 1558-8238. ; 133:13
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Tidskriftsartikel (refereegranskat)abstract
- Recent transcriptomic-based analysis of diffuse large B cell lymphoma (DLBCL) has highlighted the clinical relevance of LN fibroblast and tumor-infiltrating lymphocyte (TIL) signatures within the tumor microenvironment (TME). However, the immunomodulatory role of fibroblasts in lymphoma remains unclear. Here, by studying human and mouse DLBCL-LNs, we identified the presence of an aberrantly remodeled fibroblastic reticular cell (FRC) network expressing elevated fibroblast activated protein (FAP). RNA-Seq analyses revealed that exposure to DLBCL reprogrammed key immunoregulatory pathways in FRCs, including a switch from homeostatic to inflammatory chemokine expression and elevated antigen-presentation molecules. Functional assays showed that DLBCL-activated FRCs (DLBCL-FRCs) hindered optimal TIL and chimeric antigen receptor (CAR) T cell migration. Moreover, DLBCL-FRCs inhibited CD'+ TIL cytotoxicity in an antigen-specific manner. Notably, the interrogation of patient LNs with imaging mass cytometry identified distinct environments differing in their CD'+ TIL-FRC composition and spatial organization that associated with survival outcomes. We further demonstrated the potential to target inhibitory FRCs to rejuvenate interacting TILs. Cotreating organotypic cultures with FAP-targeted immunostimulatory drugs and a bispecific antibody (glofitamab) augmented antilymphoma TIL cytotoxicity. Our study reveals an immunosuppressive role of FRCs in DLBCL, with implications for immune evasion, disease pathogenesis, and optimizing immunotherapy for patients.
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| 6. |
- Dussex, Nicolas, et al.
(författare)
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Population genomics of the critically endangered kākāpō
- 2021
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Ingår i: Cell Genomics. - : Elsevier BV. - 2666-979X. ; 1:1
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Tidskriftsartikel (refereegranskat)abstract
- Summary The kākāpō is a flightless parrot endemic to New Zealand. Once common in the archipelago, only 201 individuals remain today, most of them descending from an isolated island population. We report the first genome-wide analyses of the species, including a high-quality genome assembly for kākāpō, one of the first chromosome-level reference genomes sequenced by the Vertebrate Genomes Project (VGP). We also sequenced and analyzed 35 modern genomes from the sole surviving island population and 14 genomes from the extinct mainland population. While theory suggests that such a small population is likely to have accumulated deleterious mutations through genetic drift, our analyses on the impact of the long-term small population size in kākāpō indicate that present-day island kākāpō have a reduced number of harmful mutations compared to mainland individuals. We hypothesize that this reduced mutational load is due to the island population having been subjected to a combination of genetic drift and purging of deleterious mutations, through increased inbreeding and purifying selection, since its isolation from the mainland ∼10,000 years ago. Our results provide evidence that small populations can survive even when isolated for hundreds of generations. This work provides key insights into kākāpō breeding and recovery and more generally into the application of genetic tools in conservation efforts for endangered species.
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| 7. |
- Fürsich, Laura, 1993-
(författare)
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The Urban Tapestry : Essays on the Relationship Between Social Networks and Residential Segregation
- 2024
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Dominant explanations of segregation argue that patterns of spatial residential sorting are shaped by the aggregation of individual residential choices, guided by discrimination, differences in resources, and preference-based explanations of neighborhood ethnic composition. However, research on social networks indicates that social influence can serve as a driver of collective outcomes that result in social organization. I reconsider interactive behavior in line with the sociological literature on networks and social influence to advance the literature on how social contexts shape opportunities for interaction and how the social influence of social contexts may affect residential choices and subsequent segregation. To this end, I present three essays that address: 1) the macro implications of networked behavior in space, 2) the social influence effects of school peers during adulthood, and 3) how social contexts in neighborhoods, particularly in the form of local social infrastructure, modify the effects of social influence. In doing so, I demonstrate that network and institutional effects are empirically observable and show how they operate as mechanisms of segregation.In the introductory chapter, I address the emerging literature on social structural sorting and detail how it can benefit from the adoption of an Analytical sociology perspective. In particular, I highlight the importance of considering interactions in space and social contexts and their importance to an understanding of persistent patterns of spatial residential segregation.In Essay I, I provide an analytical account of how network features can shape residential segregation. I develop an Agent-based simulation similar to the seminal Schelling model but with the agents embedded in a social network structure. This allows me to experimentally manipulate network homophily, clustering, and degree to measure how each of these network features shapes segregation levels, patterns, and the stability of the social-spatial system. I show that depending on the combination of each of these features, network models can lead to even higher levels of residential sorting, driven by the interactive behavior of agents, than the seminal Schelling model. The results tie in with the classic sociological literature on social networks and highlight the importance of weak ties in tipping a social system into a segregated state.Essay II examines the role of social influence among school peers in young adulthood. Scholarship has previously highlighted the role of kin in residential choices. However, there is less evidence about how non-kin ties can affect intra-urban residential choices. Drawing on the push-pull and housing-search model, our hypothesis posits that school peers serve as a potential pool of friends that influence one’s residential decisions. To unravel the dynamics of social influence and selection into neighborhoods, we utilize population register data and employ a cross-cohort design. Using conditional logistic regression models, we see that the influence of school peers from both the 9th and 12th grades affects residential choices during adulthood. Moreover, our analysis demonstrates that various life stages have distinct social foci, but that the persistent influence of school peers remains evident throughout.Essay III examines how social contexts can modify social influence effects by providing an opportunity for interaction. We combine population register data with OpenStreetMap data to map the amenity landscape in Stockholm and test whether neighborhood-level infrastructure mitigates tendencies towards white flight behavior. We employ coarsened exact matching to address selection bias into neighborhoods and estimate weighted linear probability regressions to assess the probability of majority group members’ out-mobility. We find that local social amenities located on the city block can indeed reduce tendencies towards white flight behavior. However, with increasing amenity density in the neighborhoods, majority group members become more likely to engage in white flight. We conclude that amenity density allows neighborhood residents to sort into different establishments, which does not promote intergroup contact. However, if amenities are local, which presumably facilitates frequent contact with neighbors, opportunities for interaction can reduce intolerant behavior, highlighting how social contexts are important mechanisms of segregation.
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| 8. |
- Jarvis, Benjamin, 1981-, et al.
(författare)
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Analytical sociology amidst a computational social science revolution
- 2022
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Ingår i: Handbook of Computational Social Science, Volume 1. - London : Routledge. - 9781003024583 - 9780367456535 - 9780367456528 ; , s. 33-52
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Bokkapitel (refereegranskat)abstract
- Analytical sociology is beginning to embrace a digital revolution in the collection and analysis of social data and is increasingly drawing on tools from computational social science (CSS) to pursue its goals of mechanism-based explanation of aggregate outcomes. In this chapter, we highlight the ways in which analytical sociologists are using CSS tools to further social research. Using agent-based modeling, large-scale online experiments, digital trace data, and natural language processing, analytical sociologists are identifying how large-scale properties of social systems emerge from the complex interactions of networked actors at lower scales. At the same time, we provide a perspective on how CSS techniques can be successfully deployed in social research, including ways in which they can be productively combined. Computational tools, when applied using a theory-grounded approach, offer sociologists a chance to transcend the limitations of the dominant survey-research paradigm and finally address “big” sociological questions about, for example, the nature of culture, the emergence of inequality, and the dynamics of segregation. We also discuss how computational social scientists can take cues from analytical sociology to further hone their own research and methods in the service of theoretically grounded, mechanism-based explanations, moving beyond theoretically thin descriptions or predictions of micro- and macro-level outcomes.
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| 9. |
- Peralta, Gabriela P., et al.
(författare)
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Body mass index and weight change are associated with adult lung function trajectories : the prospective ECRHS study
- 2020
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Ingår i: Thorax. - : BMJ Publishing Group Ltd. - 0040-6376 .- 1468-3296. ; 75:4, s. 313-320
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: Previous studies have reported an association between weight increase and excess lung function decline in young adults followed for short periods. We aimed to estimate lung function trajectories during adulthood from 20-year weight change profiles using data from the population-based European Community Respiratory Health Survey (ECRHS).METHODS: We included 3673 participants recruited at age 20-44 years with repeated measurements of weight and lung function (forced vital capacity (FVC), forced expiratory volume in 1 s (FEV1)) in three study waves (1991-93, 1999-2003, 2010-14) until they were 39-67 years of age. We classified subjects into weight change profiles according to baseline body mass index (BMI) categories and weight change over 20 years. We estimated trajectories of lung function over time as a function of weight change profiles using population-averaged generalised estimating equations.RESULTS: In individuals with normal BMI, overweight and obesity at baseline, moderate (0.25-1 kg/year) and high weight gain (>1 kg/year) during follow-up were associated with accelerated FVC and FEV1 declines. Compared with participants with baseline normal BMI and stable weight (±0.25 kg/year), obese individuals with high weight gain during follow-up had -1011 mL (95% CI -1.259 to -763) lower estimated FVC at 65 years despite similar estimated FVC levels at 25 years. Obese individuals at baseline who lost weight (<-0.25 kg/year) exhibited an attenuation of FVC and FEV1 declines. We found no association between weight change profiles and FEV1/FVC decline.CONCLUSION: Moderate and high weight gain over 20 years was associated with accelerated lung function decline, while weight loss was related to its attenuation. Control of weight gain is important for maintaining good lung function in adult life.
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