| 1. |
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| 2. |
- Klionsky, Daniel J., et al.
(författare)
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Guidelines for the use and interpretation of assays for monitoring autophagy
- 2012
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Ingår i: Autophagy. - : Informa UK Limited. - 1554-8635 .- 1554-8627. ; 8:4, s. 445-544
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Forskningsöversikt (refereegranskat)abstract
- In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field.
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| 3. |
- Kattge, Jens, et al.
(författare)
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TRY plant trait database - enhanced coverage and open access
- 2020
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Ingår i: Global Change Biology. - : Wiley-Blackwell. - 1354-1013 .- 1365-2486. ; 26:1, s. 119-188
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Tidskriftsartikel (refereegranskat)abstract
- Plant traits-the morphological, anatomical, physiological, biochemical and phenological characteristics of plants-determine how plants respond to environmental factors, affect other trophic levels, and influence ecosystem properties and their benefits and detriments to people. Plant trait data thus represent the basis for a vast area of research spanning from evolutionary biology, community and functional ecology, to biodiversity conservation, ecosystem and landscape management, restoration, biogeography and earth system modelling. Since its foundation in 2007, the TRY database of plant traits has grown continuously. It now provides unprecedented data coverage under an open access data policy and is the main plant trait database used by the research community worldwide. Increasingly, the TRY database also supports new frontiers of trait-based plant research, including the identification of data gaps and the subsequent mobilization or measurement of new data. To support this development, in this article we evaluate the extent of the trait data compiled in TRY and analyse emerging patterns of data coverage and representativeness. Best species coverage is achieved for categorical traits-almost complete coverage for 'plant growth form'. However, most traits relevant for ecology and vegetation modelling are characterized by continuous intraspecific variation and trait-environmental relationships. These traits have to be measured on individual plants in their respective environment. Despite unprecedented data coverage, we observe a humbling lack of completeness and representativeness of these continuous traits in many aspects. We, therefore, conclude that reducing data gaps and biases in the TRY database remains a key challenge and requires a coordinated approach to data mobilization and trait measurements. This can only be achieved in collaboration with other initiatives.
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| 4. |
- Kujala, Sari, et al.
(författare)
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Benchmarking usability of patient portals in Estonia, Finland, Norway, and Sweden
- 2024
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Ingår i: International Journal of Medical Informatics. - : Elsevier. - 1386-5056 .- 1872-8243. ; 181
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Tidskriftsartikel (refereegranskat)abstract
- INTRODUCTION: Poor usability is a barrier to widespread adoption of electronic health records (EHR). Providing good usability is especially challenging in the health care context, as there is a wide variety of patient users. Usability benchmarking is an approach for improving usability by evaluating and comparing the strength and weaknesses of systems. The main purpose of this study is to benchmark usability of patient portals across countries. METHODS: A mixed-methods survey approach was applied to benchmark the national patient portals offering patient access to EHR in Estonia, Finland, Norway, and Sweden. These Nordic countries have similar public healthcare systems, and they are pioneers in offering patients access to EHR for several years. In a survey of 29,334 patients, both patients' quantitative ratings of usability and their qualitative descriptions of very positive and very negative peak experiences of portal use were collected. RESULTS: The usability scores ranged from good to fair level of usability. The narratives of very positive and very negative experiences included the benefits of the patient portals and experienced usability issues. The regression analysis of results showed that very positive and negative experiences of patient portal use explain 19-35% of the variation of usability scores in the four countries. The percentage of patients who reported very positive or very negative experiences in each country was unrelated to the usability scores across countries. CONCLUSIONS: The survey approach could be used to evaluate usability with a wide variety of users and it supported learning from comparison across the countries. The combination of quantitative and qualitative data provided an approximation of the level of the perceived usability, and identified usability issues to be improved and useful features that patients appreciate. Further work is needed to improve the comparability of the varied samples across countries.
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| 5. |
- 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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| 6. |
- Bärkås, Annika, et al.
(författare)
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Errors, Omissions, and Offenses in the Health Record of Mental Health Care Patients : Results from a Nationwide Survey in Sweden
- 2023
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Ingår i: Journal of Medical Internet Research. - : JMIR Publications. - 1438-8871. ; 25
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: Previous research reports that patients with mental health conditions experience benefits, for example, increased empowerment and validation, from reading their patient-accessible electronic health records (PAEHRs). In mental health care (MHC), PAEHRs remain controversial, as health care professionals are concerned that patients may feel worried or offended by the content of the notes. Moreover, existing research has focused on specific mental health diagnoses, excluding the larger PAEHR userbase with experience in MHC. OBJECTIVE: The objective of this study is to establish if and how the experiences of patients with and those without MHC differ in using their PAEHRs by (1) comparing patient characteristics and differences in using the national patient portal between the 2 groups and (2) establishing group differences in the prevalence of negative experiences, for example, rates of errors, omissions, and offenses between the 2 groups. METHODS: Our analysis was performed on data from an online patient survey distributed through the Swedish national patient portal as part of our international research project, NORDeHEALTH. The respondents were patient users of the national patient portal 1177, aged 15 years or older, and categorized either as those with MHC experience or with any other health care experience (nonmental health care [non-MHC]). Patient characteristics such as gender, age, education, employment, and health status were gathered. Portal use characteristics included frequency of access, encouragement to read the record, and instances of positive and negative experiences. Negative experiences were further explored through rates of error, omission, and offense. The data were summarized through descriptive statistics. Group differences were analyzed through Pearson chi-square. RESULTS: Of the total sample (N=12,334), MHC respondents (n=3131) experienced errors (1586/3131, 50.65%, and non-MHC 3311/9203, 35.98%), omissions (1089/3131, 34.78%, and non-MHC 2427/9203, 26.37%) and offenses (1183/3131, 37.78%, and non-MHC 1616/9203, 17.56%) in the electronic health record at a higher rate than non-MHC respondents (n=9203). Respondents reported that the identified error (MHC 795/3131, 50.13%, and non-MHC 1366/9203, 41.26%) and omission (MHC 622/3131, 57.12%, and non-MHC 1329/9203, 54.76%) were "very important," but most did nothing to correct them (MHC 792/3131, 41.29%, and non-MHC 1838/9203, 42.17%). Most of the respondents identified as women in both groups. CONCLUSIONS: About 1 in 2 MHC patients identified an error in the record, and about 1 in 3 identified an omission, both at a much higher rate than in the non-MHC group. Patients with MHC also felt offended by the content of the notes more commonly (1 in 3 vs 1 in 6). These findings validate some of the worries expressed by health care professionals about providing patients with MHC with PAEHRs and highlight challenges with the documentation quality in the records.
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| 7. |
- Hägglund, Maria, Lektor, 1975-, et al.
(författare)
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A Nordic Perspective on Patient Online Record Access and the European Health Data Space
- 2024
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Ingår i: Journal of Medical Internet Research. - : JMIR Publications. - 1438-8871. ; 26:1
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Tidskriftsartikel (refereegranskat)abstract
- The Nordic countries are, together with the United States, forerunners in online record access (ORA), which has now become widespread. The importance of accessible and structured health data has also been highlighted by policy makers internationally. To ensure the full realization of ORA’s potential in the short and long term, there is a pressing need to study ORA from a cross-disciplinary, clinical, humanistic, and social sciences perspective that looks beyond strictly technical aspects. In this viewpoint paper, we explore the policy changes in the European Health Data Space (EHDS) proposal to advance ORA across the European Union, informed by our research in a Nordic-led project that carries out the first of its kind, large-scale international investigation of patients’ ORA—NORDeHEALTH (Nordic eHealth for Patients: Benchmarking and Developing for the Future). We argue that the EHDS proposal will pave the way for patients to access and control third-party access to their electronic health records. In our analysis of the proposal, we have identified five key principles for ORA: (1) the right to access, (2) proxy access, (3) patient input of their own data, (4) error and omission rectification, and (5) access control. ORA implementation today is fragmented throughout Europe, and the EHDS proposal aims to ensure all European citizens have equal online access to their health data. However, we argue that in order to implement the EHDS, we need more research evidence on the key ORA principles we have identified in our analysis. Results from the NORDeHEALTH project provide some of that evidence, but we have also identified important knowledge gaps that still need further exploration.
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| 8. |
- Hägglund, Maria, et al.
(författare)
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NORDeHEALTH – Learning from the Nordic Experiences of Patient Online Record Access
- 2023
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Ingår i: Journal of Medical Internet Research. - : JMIR Publications. - 1438-8871.
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- The Nordic countries are forerunners in online record access (ORA) which has now become widespread. The importance of accessible and structured health data has also been highlighted by policymakers internationally. To ensure the full realization of ORA’spotential in the short and long term, there is a pressing need to study ORA from a cross-disciplinary, technical, clinical, humanistic, and social sciences perspective that looks beyond strictly technical aspects. In this viewpoint paper, we explore the policy changes in the European Health Data Space (EHDS) proposal to advance ORA across the European Union, and introduce a Nordic-led research project that carries out the first of its kind, large-scale international investigation of patients’ ORA; NORDeHEALTH. We argue that the EHDS proposal will pave the way for patients to access and control third-party access to their electronic health records (EHRs). This will have implications within Europe and globally as it will further extend the boundaries for accessing and using EHRs for primary and secondary data use. Research such as that led by the NORDeHEALTH project is essential in guiding the design and implementation of solutions to meet the requirements of the EHDS proposal. Further international collaboration and research are needed to ensure that socio-technical and contextual factors are considered to ensure successful and secure implementation.
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| 9. |
- Hägglund, Maria, Lektor, 1975-, et al.
(författare)
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The NORDeHEALTH 2022 Patient Survey : Cross-Sectional Study of National Patient Portal Users in Norway, Sweden, Finland, and Estonia
- 2023
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Ingår i: Journal of Medical Internet Research. - : JMIR Publications. - 1438-8871. ; 25
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: Although many surveys have been conducted on patients accessing their own health records in recent years, there is a limited amount of nationwide cross-country data available on patients' views and preferences. To address this gap, an international survey of patient users was conducted in the Nordic eHealth project, NORDeHEALTH. OBJECTIVE: We aimed to investigate the sociodemographic characteristics and experiences of patients who accessed their electronic health records (EHRs) through national patient portals in Norway, Sweden, Finland, and Estonia. METHODS: A cross-sectional web-based survey was distributed using the national online health portals. The target participants were patients who accessed the national patient portals at the start of 2022 and who were aged ≥15 years. The survey included a mixture of close-ended and free-text questions about participant sociodemographics, usability experience, experiences with health care and the EHR, reasons for reading health records online, experience with errors, omissions and offense, opinions about security and privacy, and the usefulness of portal functions. In this paper, we summarized the data on participant demographics, past experience with health care, and the patient portal through descriptive statistics. RESULTS: In total, 29,334 users completed the survey, of which 9503 (32.40%) were from Norway, 13,008 (44.35%) from Sweden, 4713 (16.07%) from Finland, and 2104 (7.17%) from Estonia. National samples were comparable according to reported gender, with about two-thirds identifying as women (19,904/29,302, 67.93%). Age distributions were similar across the countries, but Finland had older users while Estonia had younger users. The highest attained education and presence of health care education varied among the national samples. In all 4 countries, patients most commonly rated their health as "fair" (11,279/29,302, 38.48%). In Estonia, participants were more often inclined to rate their health positively, whereas Norway and Sweden had the highest proportion of negative health ratings. Across the whole sample, most patients received some care in the last 2 years (25,318/29,254, 86.55%). Mental health care was more common (6214/29,254, 21.24%) than oncological care (3664/29,254, 12.52%). Overall, most patients had accessed their health record "2 to 9 times" (11,546/29,306, 39.4%), with the most frequent users residing in Sweden, where about one-third of patients accessed it "more than 20 times" (4571/13,008, 35.14%). CONCLUSIONS: This is the first large-scale international survey to compare patient users' sociodemographics and experiences with accessing their EHRs. Although the countries are in close geographic proximity and demonstrate similar advancements in giving their residents online records access, patient users in this survey differed. We will continue to investigate patients' experiences and opinions about national patient-accessible EHRs through focused analyses of the national and combined data sets from the NORDeHEALTH 2022 Patient Survey.
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| 10. |
- Nahse, Viola, et al.
(författare)
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ATPase activity of DFCP1 controls selective autophagy
- 2023
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Ingår i: Nature Communications. - : Springer Nature. - 2041-1723. ; 14:1
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Tidskriftsartikel (refereegranskat)abstract
- The endoplasmic reticulum protein DFCP1 is found on omegasomes implicated in autophagosome biogenesis, but its function has remained unknown. Here, Nahse et al. show that DFCP1 is an ATPase that mediates selective autophagy by promoting constriction of large omegasomes. Cellular homeostasis is governed by removal of damaged organelles and protein aggregates by selective autophagy mediated by cargo adaptors such as p62/SQSTM1. Autophagosomes can assemble in specialized cup-shaped regions of the endoplasmic reticulum (ER) known as omegasomes, which are characterized by the presence of the ER protein DFCP1/ZFYVE1. The function of DFCP1 is unknown, as are the mechanisms of omegasome formation and constriction. Here, we demonstrate that DFCP1 is an ATPase that is activated by membrane binding and dimerizes in an ATP-dependent fashion. Whereas depletion of DFCP1 has a minor effect on bulk autophagic flux, DFCP1 is required to maintain the autophagic flux of p62 under both fed and starved conditions, and this is dependent on its ability to bind and hydrolyse ATP. While DFCP1 mutants defective in ATP binding or hydrolysis localize to forming omegasomes, these omegasomes fail to constrict properly in a size-dependent manner. Consequently, the release of nascent autophagosomes from large omegasomes is markedly delayed. While knockout of DFCP1 does not affect bulk autophagy, it inhibits selective autophagy, including aggrephagy, mitophagy and micronucleophagy. We conclude that DFCP1 mediates ATPase-driven constriction of large omegasomes to release autophagosomes for selective autophagy.
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