| 1. |
- Vicari, Marco, et al.
(författare)
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Spatial multimodal analysis of transcriptomes and metabolomes in tissues
- 2024
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Ingår i: Nature Biotechnology. - : Nature Research. - 1087-0156 .- 1546-1696. ; 42:7, s. 1046-1050
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Tidskriftsartikel (refereegranskat)abstract
- We present a spatial omics approach that combines histology, mass spectrometry imaging and spatial transcriptomics to facilitate precise measurements of mRNA transcripts and low-molecular-weight metabolites across tissue regions. The workflow is compatible with commercially available Visium glass slides. We demonstrate the potential of our method using mouse and human brain samples in the context of dopamine and Parkinson’s disease.
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| 2. |
- Hernández-Neuta, Iván, 1986-, et al.
(författare)
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Highly multiplexed targeted sequencing strategy for infectious disease surveillance
- 2023
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Ingår i: BMC Biotechnology. - 1472-6750. ; 23
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Tidskriftsartikel (refereegranskat)abstract
- Background Global efforts to characterize diseases of poverty are hampered by lack of affordable and comprehensive detection platforms, resulting in suboptimal allocation of health care resources and inefficient disease control. Next generation sequencing (NGS) can provide accurate data and high throughput. However, shotgun and metagenome-based NGS approaches are limited by low concentrations of microbial DNA in clinical samples, requirements for tailored sample and library preparations plus extensive bioinformatics analysis. Here, we adapted molecular inversion probes (MIPs) as a cost-effective target enrichment approach to characterize microbial infections from blood samples using short-read sequencing. We designed a probe panel targeting 2 bacterial genera, 21 bacterial and 6 fungi species and 7 antimicrobial resistance markers (AMRs).Results Our approach proved to be highly specific to detect down to 1 in a 1000 pathogen DNA targets contained in host DNA. Additionally, we were able to accurately survey pathogens and AMRs in 20 out of 24 samples previously profiled with routine blood culture for sepsis.Conclusions Overall, our targeted assay identifies microbial pathogens and AMRs with high specificity at high throughput, without the need for extensive sample preparation or bioinformatics analysis, simplifying its application for characterization and surveillance of infectious diseases in medium- to low- resource settings.
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| 3. |
- Bro, Tomas, et al.
(författare)
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Two point four million cataract surgeries: 30 years with the Swedish National Cataract Register, 1992-2021
- 2023
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Ingår i: Journal of cataract and refractive surgery. - : Wolters Kluwer. - 1873-4502 .- 0886-3350. ; 49:8, s. 879-884
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Tidskriftsartikel (refereegranskat)abstract
- The present review summarizes data collected by the Swedish National Cataract Register (NCR), which by the end of 2021 contained data for more than 2.4 million cataract surgeries between 1992 and 2021. During these 30 years, the cataract surgery rate rose from 3700 to 12800. The coverage of NCR is very high including 93% of all cataract procedures in Sweden between 2010 and 2021. Independently of demographic changes, the proportion of operations of patients age 60 to 79 has increased while the proportion of 80 to 90+ has decreased. The median visual acuity of the first eye planned for surgery was 0.1 decimal in 1992 and has increased to 0.5 decimal in 2021. Patient-reported outcome measures have been registered with the Catquest-9SF questionnaire since 2008, demonstrating intervention at an earlier stage, but consistently favorable outcomes. Surgical complications have decreased; endophthalmitis has decreased from 0.10% to below 0.02%, and posterior capsule rupture from 2.8% to 0.6%.
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| 4. |
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| 5. |
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| 6. |
- Johnsson, Anders, et al.
(författare)
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Anal cancer in Sweden 2015-2019. Implementation of guidelines, structural changes, national registry and early results
- 2022
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Ingår i: Acta Oncologica. - : Taylor & Francis Group. - 0284-186X .- 1651-226X. ; 61:5, s. 575-582
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Tidskriftsartikel (refereegranskat)abstract
- Background Squamous cell cancer of the anus is an uncommon malignancy, usually caused by human papilloma virus (HPV). Chemoradiotherapy (CRT) is the recommended treatment in localized disease with cure rates of 60-80%. Local failures should be considered for salvage surgery. With the purpose of improving and equalizing the anal cancer care in Sweden, a number of actions were taken between 2015 and 2017. The aim of this study was to describe the implementation of guidelines and organizational changes and to present early results from the first 5 years of the Swedish anal cancer registry (SACR). Methods The following were implemented: (1) the first national care program with treatment guidelines, (2) standardized care process, (3) centralization of CRT to four centers and salvage surgery to two centers, (4) weekly national multidisciplinary team meetings where all new cases are discussed, (5) the Swedish anal cancer registry (SACR) was started in 2015. Results The SACR included 912 patients with a diagnosis of anal cancer from 2015 to 2019, reaching a national coverage of 95%. We could show that guidelines issued in 2017 regarding staging procedures and radiotherapy dose modifications were rapidly implemented. At baseline 52% of patients had lymph node metastases and 9% had distant metastases. Out of all patients in the SACR 89% were treated with curative intent, most of them with CRT, after which 92% achieved a local complete remission and the estimated overall 3-year survival was 85%. Conclusions This is the first report from the SACR, demonstrating rapid nation-wide implementation of guidelines and apparently good treatment outcome in patients with anal cancer in Sweden. The SACR will hopefully be a valuable source for future research.
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| 7. |
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| 8. |
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| 9. |
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| 10. |
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| 11. |
- Kukanja, Petra, et al.
(författare)
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Cellular architecture of evolving neuroinflammatory lesions and multiple sclerosis pathology
- 2024
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Ingår i: Cell. - : Cell Press. - 0092-8674 .- 1097-4172. ; 187:8, s. 1990-2009
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Tidskriftsartikel (refereegranskat)abstract
- Multiple sclerosis (MS) is a neurological disease characterized by multifocal lesions and smoldering pathology. Although single -cell analyses provided insights into cytopathology, evolving cellular processes underlying MS remain poorly understood. We investigated the cellular dynamics of MS by modeling temporal and regional rates of disease progression in mouse experimental autoimmune encephalomyelitis (EAE). By performing single -cell spatial expression profiling using in situ sequencing (ISS), we annotated disease neighborhoods and found centrifugal evolution of active lesions. We demonstrated that disease -associated (DA)-glia arise independently of lesions and are dynamically induced and resolved over the disease course. Single -cell spatial mapping of human archival MS spinal cords confirmed the differential distribution of homeostatic and DA-glia, enabled deconvolution of active and inactive lesions into sub -compartments, and identified new lesion areas. By establishing a spatial resource of mouse and human MS neuropathology at a single -cell resolution, our study unveils the intricate cellular dynamics underlying MS.
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| 12. |
- Li, Xiaofei, et al.
(författare)
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Profiling spatiotemporal gene expression of the developing human spinal cord and implications for ependymoma origin
- 2023
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Ingår i: Nature Neuroscience. - : Springer Nature. - 1097-6256 .- 1546-1726. ; 26:5, s. 891-901
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Tidskriftsartikel (refereegranskat)abstract
- The authors created a comprehensive developmental cell atlas for spatiotemporal gene expression of the human spinal cord, revealed species-specific regulation during development and used the atlas to infer novel markers for pediatric ependymomas. The spatiotemporal regulation of cell fate specification in the human developing spinal cord remains largely unknown. In this study, by performing integrated analysis of single-cell and spatial multi-omics data, we used 16 prenatal human samples to create a comprehensive developmental cell atlas of the spinal cord during post-conceptional weeks 5-12. This revealed how the cell fate commitment of neural progenitor cells and their spatial positioning are spatiotemporally regulated by specific gene sets. We identified unique events in human spinal cord development relative to rodents, including earlier quiescence of active neural stem cells, differential regulation of cell differentiation and distinct spatiotemporal genetic regulation of cell fate choices. In addition, by integrating our atlas with pediatric ependymomas data, we identified specific molecular signatures and lineage-specific genes of cancer stem cells during progression. Thus, we delineate spatiotemporal genetic regulation of human spinal cord development and leverage these data to gain disease insight.
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| 13. |
- Liu, Ilon, et al.
(författare)
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The landscape of tumor cell states and spatial organization in H3-K27M mutant diffuse midline glioma across age and location
- 2022
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Ingår i: Nature Genetics. - : Springer Science and Business Media LLC. - 1061-4036 .- 1546-1718. ; 54:12, s. 1881-1894
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Tidskriftsartikel (refereegranskat)abstract
- Histone 3 lysine27-to-methionine (H3-K27M) mutations most frequently occur in diffuse midline gliomas (DMGs) of the childhood pons but are also increasingly recognized in adults. Their potential heterogeneity at different ages and midline locations is vastly understudied. Here, through dissecting the single-cell transcriptomic, epigenomic and spatial architectures of a comprehensive cohort of patient H3-K27M DMGs, we delineate how age and anatomical location shape glioma cell-intrinsic and -extrinsic features in light of the shared driver mutation. We show that stem-like oligodendroglial precursor-like cells, present across all clinico-anatomical groups, display varying levels of maturation dependent on location. We reveal a previously underappreciated relationship between mesenchymal cancer cell states and age, linked to age-dependent differences in the immune microenvironment. Further, we resolve the spatial organization of H3-K27M DMG cell populations and identify a mitotic oligodendroglial-lineage niche. Collectively, our study provides a powerful framework for rational modeling and therapeutic interventions.
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| 14. |
- Lundström, Mats, et al.
(författare)
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Catquest-9SF functioning over a decade - a study from the Swedish National Cataract Register
- 2020
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Ingår i: Eye and Vision. - : Springer Science and Business Media LLC. - 2326-0254. ; 7:1
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Tidskriftsartikel (refereegranskat)abstract
- BackgroundThe Swedish National Cataract Register (NCR) collects data on cataract surgery outcomes during March, including patient-reported outcomes using the Catquest-9SF questionnaire for over 11years. Previous studies from NCR have shown that the preoperative visual acuity has improved over time. The main purpose of this study was to evaluate the Catquest-9SF Rasch scoring performance in this changing environment. A second purpose was to describe clinical data over the same period for those who completed the questionnaire.MethodsThe performance of the Catquest-9SF was analysed by a separate Rasch analysis for each year, resulting in a preoperative and postoperative score for each participating patient in the annual cohorts. The clinical data and questionnaire scoring were analysed for each year in the period 2008-2018 inclusive.ResultsData were available for 42,023 eyes for 11 annual cohorts (2008-2018). The psychometric properties of the questionnaire were stable during the study period. Person separation (precision) for the whole period was 2.58 and varied between 2.45 and 2.72. The person reliability was 0.87 and varied between 0.86 and 0.88. The targeting of question difficulty to person ability became less accurate over time meaning that the item activities became easier to carry out without difficulty. The average targeting for the whole period was -2.06 and changed from -1.92 in 2008 to -2.31 in 2018. The person score improved both before surgery and after surgery, indicating that patients are undergoing surgery at a more able level and getting better outcomes. The average improvement by surgery decreased from 3.41 logits in 2008 to 3.21 logits in 2018 (p=0.003).Over time, patient age decreased from 75 to 74years (p<0.001) and the proportion of women decreased from 63.9 to 57.9% (p<0.001). The mean preoperative visual acuity in both the operated eye and the better eye improved over time (0.47 to 0.40 logMAR, p<0.001 and 0.22 to 0.19 logMAR, p<0.001, respectively), as did the mean postoperative visual acuity in the operated eye (0.14 to 0.09 logMAR, p<0.001).ConclusionsThe Catquest-9SF retained stable psychometric properties over this 11-year period although more recent cohorts included slightly younger patients with somewhat better vision.
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| 15. |
- Lundström, Mats, et al.
(författare)
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Ten-year trends of immediate sequential bilateral cataract surgery (ISBCS) as reflected in the Swedish National Cataract Register
- 2024
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Ingår i: Acta Ophthalmologica. - : WILEY. - 1755-375X .- 1755-3768. ; 102:1, s. 68-73
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Tidskriftsartikel (refereegranskat)abstract
- Purpose: To analyse trends of ISBCS reported to the Swedish National Cataract Register (NCR) over a 10-year period.Methods: Since 2010 the NCR contains social security number of all individuals in the list of parameters reported to NCR after each cataract procedure. Bilateral surgeries were mapped out using social security numbers. When dates of both-eye surgeries are identical for an individual it is classified as an immediate sequential bilateral cataract surgery (ISBCS). This study includes all data reported during the period 1st of January 2010 to 31st of December 2019. During the study period 113 cataract surgery clinics affiliated to the NCR reported their data on consecutive cataract cases.Results: For the whole period 54 194 ISBCS were reported. The total number of bilateral cataract extractions was 422 300. There was a significant trend of increasing ISBCS over time with linear regression (Beta = 1.75, p < 0.001). In ISBCS the occurrence of an ocular comorbidity decreased over time. The use of a capsular tension ring was significantly more common in ISBCS than in delayed sequential bilateral cataract surgery (DSBCS). All other measures taken during surgery were more common in DSBCS. The use of multifocal IOL was significantly more frequent in ISBCS compared to DSBCS (p < 0.001).Conclusions: The use of ISBCS has increased over the study period. The operated eyes have less risk factors than eyes going through a DSBCS, but both ocular comorbidities and surgical complications occur in ISBCS eyes.
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| 16. |
- Magoulopoulou, Anastasia, 1986-, et al.
(författare)
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Padlock Probe-Based Targeted In Situ Sequencing : Overview of Methods and Applications
- 2023
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Ingår i: Annual review of genomics and human genetics (Print). - 1527-8204 .- 1545-293X. ; 24, s. 133-150
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Forskningsöversikt (refereegranskat)abstract
- Elucidating spatiotemporal changes in gene expression has been an essential goal in studies of health, development, and disease. In the emerging field of spatially resolved transcriptomics, gene expression profiles are acquired with the tissue architecture maintained, sometimes at cellular resolution. This has allowed for the development of spatial cell atlases, studies of cell-cell interactions, and in situ cell typing. In this review, we focus on padlock probe-based in situ sequencing, which is a targeted spatially resolved transcriptomic method. We summarize recent methodological and computational tool developments and discuss key applications. We also discuss compatibility with other methods and integration with multiomic platforms for future applications.
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| 17. |
- Marco Salas, Sergio, 1996-
(författare)
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From pixels to comprehensive cellular atlases : Applications of in situ sequencing to understand tissue biology
- 2024
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The development of single-cell RNA sequencing enabled the high throughput characterization of cell populations with unprecedented detail. Yet, it failed in capturing the spatial localization of individual cells. Overcoming this, different spatial profiling methods have been developed in recent years, with in situ sequencing (ISS) being among the most powerful solutionsISS is a targeted spatially-resolved transcriptomics method designed to detect the expression of hundreds of genes in situ in a single experiment. For this, ISS employs padlock probes, a type of oligonucleotide designed to specifically hybridize on the targeted regions, with rolling circle amplification and a combinatorial detection of the transcripts imaged. Due to its throughput and resolution, ISS is seen as a useful tool to create high content molecular maps of tissues, being of special use for building spatial atlases. However, due to its recent development, it’s still unclear how this should be done. The work presented in this thesis explores ISS as a tool for building large spatially-resolved atlases of cell types. In paper I, we compare the performance of cDNA-based ISS with the High Sensitivity Library Preparation Kit, developed by CARTANA AB. We identify this product to be fivefold more sensitive than cDNA-based ISS due to its improved chemistry. In addition, we show that this increased sensitivity enhances the analytical capabilities of the resulting data. In paper II, we build a topographic atlas of the developmental human lung. We identify 83 different cell types and states, including a novel type of GHRL-positive neuroendocrine cell. We further elucidate the developmental origin multiple populations, defining their location in situ and predicting potential interactions. In paper III, we create a topographic atlas of the adult human lung. We combine multiple spatial transcriptomic technologies to generate spatial maps of the populations found in the adult lung. We decipher regional differences in terms of cell type composition and cell type-specific expression. Finally, we also characterize the spatial context of rare cell types.In paper IV, we employ large-scale data integration to construct a scRNA-seq-based cellular map of glioblastoma, an aggressive brain malignancy. In addition, we use ISS to generate single-cell resolution cell type maps of 13 glioblastoma patients, identifying consistent niches across patients and uncovering the cellular organization of these tumors. In paper V, we explore the quality of the data generated by the Xenium In Situ Platform, a product based on ISS and commercialized by 10X Genomics. We explore the main characteristics of the data and benchmark it against other technologies. Finally, we also define best practices for the most common analysis done using these datasets. Collectively, the studies presented in this thesis serve as evidence of the efficacy of ISS in constructing comprehensive cellular atlases with a single-cell resolution.
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| 18. |
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| 19. |
- Ridderskär, Lucas, et al.
(författare)
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Outcome of cataract surgery in eyes with diabetic retinopathy: a Swedish national cataract register report
- 2022
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Ingår i: Acta Ophthalmologica. - : Wiley. - 1755-375X .- 1755-3768. ; 100:2
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Tidskriftsartikel (refereegranskat)abstract
- Purpose To analyse if patients with diabetic retinopathy (DR) subjected to cataract surgery differ in outcome compared to patients without DR with regard to best-corrected visual acuity (BCVA), deviation from target refraction, intraoperative difficulties and risk of complications. Methods A register-based study from the Swedish National Cataract Register (NCR) during the years 2015-2017 including 358 040 cataract procedures. Patients with other ocular pathology than cataract and DR were omitted from outcome analyses. Results Diabetic retinopathy was reported in 13 724 of all eyes (3.8%). Preoperative BCVA was significantly worse in DR patients than in patients without DR, 0.54 +/- 0.33 compared to 0.40 +/- 0.27 (logMAR, mean +/- SD, p < 0.001). The same was evident for postoperative BCVA, 0.15 +/- 0.25 for DR patients versus 0.06 +/- 0.13 (p < 0.001). The improvement in BCVA was slightly better in DR than in non-DR, -0.40 +/- 0.32 (logMAR; mean +/- SD) versus -0.35 +/- 0.27, p < 0.001. The absolute mean biometry prediction error was 0.42 +/- 0.50 diopters (D) in DR and 0.43 +/- 0.71 D in non-DR patients, p = 0.768. One or more intraoperative difficulties, including mechanical pupil dilation, capsular stain, hooks at capsulorhexis margin or capsular tension ring, had an adjusted odds ratio (OR) of 1.75 (95% confidence interval [CI] 1.61-1.90, p < 0.001) in DR versus non-DR cases and the rate of posterior capsular tears (PCR) had an adjusted OR of 1.76 (95% CI 1.40-2.20, p < 0.001). Conclusion Eyes with DR have inferior pre- and postoperative BCVA compared to non-DR eyes. There is little difference in improvement of BCVA and no difference in absolute mean biometry prediction error. Importantly, intraoperative difficulties and PCRs are almost twice as common in DR patients, strongly indicating that these patients should be managed by experienced surgeons.
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| 20. |
- Sabel, Ellinor, 1969-
(författare)
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Deltagande arkeologi : Värden och praktiker
- 2022
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Licentiatavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Denna licentiatuppsats utforskar vilka värden som uppstår när allmänheten, tillsammans med professionella arkeologer, får möjlighet att engagera sig i arkeologiskt fältarbete. Projektformen där professionella arkeologer arbetar tillsammans med aktörer ur allmänheten kallas i denna studie för Deltagande arkeologi. Uppsatsen utforskar även vilka praktiker som omgärdar denna projektform samt vilka traditioner och politiska beslut som har påverkat allmänhetens möjligheter för praktiskt deltagande inom kulturmiljöarbetet. Forskningen baseras till stor del på studierna av tre svenska arkeologiprojekt, som alla bygger på allmänhetens deltagande, vilka utforskas genom enkätstudier, intervjuer och deltagande observation. Resultaten visar att projektformen genererar flera olika former av värden och vinster. För den arkeologiska vetenskapen bidrar projektformen till att platser som ligger långt från uppdragsarkeologins verksamhetsområden kan uppmärksammas och undersökas vilket resulterar i en bättre geografisk spridning av arkeologiska undersökningar och därmed en jämnare kunskapsuppbyggnad. För arrangörerna (arkeologer) är projekten en möjlighet att få ägna sig åt långvarig forskning och för deltagarna (allmänheten) en möjlighet att få ägna sig åt sina intressen, skapa värdefulla kontaktnät och vänskaper. Samtidigt uppger båda aktörsgrupperna att deltagandet bidrar till en förbättrad hälsa och välbefinnande samt till att förstärka känslorna av delaktighet till, och i arbetet kring, det materiella kulturarvet.
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| 21. |
- Sallinger, Katja, et al.
(författare)
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Spatial tumour gene signature discriminates neoplastic from non-neoplastic compartments in colon cancer : unravelling predictive biomarkers for relapse
- 2023
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Ingår i: Journal of Translational Medicine. - 1479-5876. ; 21:1
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Tidskriftsartikel (refereegranskat)abstract
- Background: Opting for or against the administration of adjuvant chemotherapy in therapeutic management of stage II colon cancer remains challenging. Several studies report few survival benefits for patients treated with adjuvant therapy and additionally revealing potential side effects of overtreatment, including unnecessary exposure to chemotherapy-induced toxicities and reduced quality of life. Predictive biomarkers are urgently needed. We, therefore, hypothesise that the spatial tissue composition of relapsed and non-relapsed colon cancer stage II patients reveals relevant biomarkers.Methods: The spatial tissue composition of stage II colon cancer patients was examined by a novel spatial transcriptomics technology with sub-cellular resolution, namely in situ sequencing. A panel of 176 genes investigating specific cancer-associated processes such as apoptosis, proliferation, angiogenesis, stemness, oxidative stress, hypoxia, invasion and components of the tumour microenvironment was designed to examine differentially expressed genes in tissue of relapsed versus non-relapsed patients. Therefore, FFPE slides of 10 colon cancer stage II patients either classified as relapsed (5 patients) or non-relapsed (5 patients) were in situ sequenced and computationally analysed.Results: We identified a tumour gene signature that enables the subclassification of tissue into neoplastic and non-neoplastic compartments based on spatial expression patterns obtained through in situ sequencing. We developed a computational tool called Genes-To-Count (GTC), which automates the quantification of in situ signals, accurately mapping their position onto the spatial tissue map and automatically identifies neoplastic and non-neoplastic tissue compartments. The GTC tool was used to quantify gene expression of biological processes upregulated within the neoplastic tissue in comparison to non-neoplastic tissue and within relapsed versus non-relapsed stage II colon patients. Three differentially expressed genes (FGFR2, MMP11 and OTOP2) in the neoplastic tissue compartments of relapsed patients in comparison to non-relapsed patients were identified predicting recurrence in stage II colon cancer.Conclusions: In depth spatial in situ sequencing showed potential to provide a deeper understanding of the underlying mechanisms involved in the recurrence of disease and revealed novel potential predictive biomarkers for disease relapse in colon cancer stage II patients. Our open-access GTC-tool allowed us to accurately capture the tumour compartment and quantify spatial gene expression in colon cancer tissue.
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| 22. |
- Samadi, Behrad, et al.
(författare)
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Anti-inflammatory treatment after cataract surgery in Sweden : Changes in prescribing patterns from 2010 to 2017
- 2021
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Ingår i: BMJ Open Ophthalmology. - : BMJ. - 2397-3269. ; 6:1
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Tidskriftsartikel (refereegranskat)abstract
- Aims To investigate changes in the prescribing patterns of postoperative eye drops following cataract surgery in Sweden from 2010 to 2017. Methods Data from cataract procedures registered in the National Cataract Register during the month of March from 2010 to 2017 were record linked and sent to the Swedish Prescribed Drug Register, which allowed us to determine which eye drops the patients had obtained from 3 months presurgery to 2 weeks post surgery. Results During the 8-year study period, 54 889 surgeries were registered. Combination treatment with steroid and non-steroidal anti-inflammatory drug (NSAID) eye drops increased from 12% in 2010 to 60% in 2017 (p<0.001) while monotherapy with steroids decreased from 71% in 2010 to 26% in 2017 (p<0.001). Monotherapy with NSAIDs after surgery was fairly stable, at 17% in 2010 and 13% in 2017 (p<0.001). Combination treatment was more frequent in patients with diabetic retinopathy (p<0.001) or age-related macular degeneration (p<0.001), while monotherapy with steroids was more frequent in patients with glaucoma (p<0.001). The proportion of monotherapy or combination therapy varied widely between ophthalmic clinics. The prescription of antibiotic eye drops after surgery also varied greatly between clinics, from 0% to 63%, with a national average of 4.9%. Conclusion There is a change in the prescription pattern of anti-inflammatory eye drops after cataract surgery in Sweden, with less monotherapy and an increasing proportion of patients receiving a combination of steroid and NSAID eye drops.
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| 23. |
- Wernersson, Erik, et al.
(författare)
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Deconwolf enables high-performance deconvolution of widefield fluorescence microscopy images
- 2024
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Ingår i: Nature Methods. - 1548-7091 .- 1548-7105. ; 21:7, s. 1245-1256
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Tidskriftsartikel (refereegranskat)abstract
- Microscopy-based spatially resolved omic methods are transforming the life sciences. However, these methods rely on high numerical aperture objectives and cannot resolve crowded molecular targets, limiting the amount of extractable biological information. To overcome these limitations, here we develop Deconwolf, an open-source, user-friendly software for high-performance deconvolution of widefield fluorescence microscopy images, which efficiently runs on laptop computers. Deconwolf enables accurate quantification of crowded diffraction limited fluorescence dots in DNA and RNA fluorescence in situ hybridization images and allows robust detection of individual transcripts in tissue sections imaged with ×20 air objectives. Deconvolution of in situ spatial transcriptomics images with Deconwolf increased the number of transcripts identified more than threefold, while the application of Deconwolf to images obtained by fluorescence in situ sequencing of barcoded Oligopaint probes drastically improved chromosome tracing. Deconwolf greatly facilitates the use of deconvolution in many bioimaging applications.
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| 24. |
- Zetterberg, Madeleine, 1969, et al.
(författare)
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Cataract Surgery Volumes and Complications per Surgeon and Clinical Unit Data from the Swedish National Cataract Register 2007 to 2016
- 2020
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Ingår i: Ophthalmology. - : Elsevier BV. - 0161-6420 .- 1549-4713. ; 127:3, s. 305-314
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Tidskriftsartikel (refereegranskat)abstract
- Purpose: To investigate the change in proportion of high-volume cataract surgeons during the period 2007 to 2016 and determine the impact of operation volume per surgeon and clinical unit on the rate of capsule complications. Design: Retrospective, register-based study. Participants: Patients undergoing and surgeons performing cataract surgery at Swedish ophthalmologic departments 2007-2016. Methods: All cataract procedures performed during a 10-year period were analyzed, and the change in operation volume of individual surgeons over time was determined. The yearly incidence of capsule complications was correlated to the operation volume of individual surgeons and clinical units. Main Outcome Measures: The number of cataract procedures yearly per surgeon and clinical unit, proportion of capsule complications, and change over time in operation volume and complication rate. Results: The proportion of high-volume (>= 500 procedures yearly) and very high-volume (>= 1000 procedures yearly) surgeons increased from 15.0% to 34.0% and 2.1% to 10.9%, respectively (P < 0.001 for both categories). The proportion of all cataract procedures performed by high-volume surgeons was 36.9% in 2007, increasing to 68.1 % in 2016. The yearly incidence of capsule complications decreased with increasing number of procedures; from a mean of 2.15% (standard deviation [SD], 3.17) for low-volume surgeons (10-99 procedures/ year) to 1.32% (1.28) for medium-volume (100-499 procedures/year) surgeons and 0.59% (0.49) for high-volume surgeons (P = 0.016). Preoperative best-corrected visual acuity was significantly better in eyes operated on by high-volume and very high-volume cataract surgeons; the median best-corrected visual acuity (BCVA) was 0.5 (decimal) compared with a BCVA of 0.4 for patients who had their surgery performed by low- or medium-volume surgeons (overall P < 0.001). No significant difference in rate of capsule complications was seen between clinical units with high or low operation volume (P = 0.804). The overall incidence of capsule complications decreased gradually from 1.5% in 2007 to 0.8% in 2016, and preoperative BCVA increased from 0.46 +/- 0.10 (logarithm of the minimum angle of resolution) to 0.40 +/- 0.05 (P = 0.030). Conclusions: There is a strong association of rate of capsule complications with operation volume of individual surgeons but not with operation volume of individual clinical units. The decreased rate of capsule complications seen between 2007 and 2016 may be explained in part by a dramatic increase in the proportion of high-volume cataract surgeons during the period. (C) 2019 by the American Academy of Ophthalmology
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