| 1. |
- Zamora, Juan Carlos, et al.
(författare)
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Considerations and consequences of allowing DNA sequence data as types of fungal taxa
- 2018
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Ingår i: IMA Fungus. - : INT MYCOLOGICAL ASSOC. - 2210-6340 .- 2210-6359. ; 9:1, s. 167-185
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Tidskriftsartikel (refereegranskat)abstract
- Nomenclatural type definitions are one of the most important concepts in biological nomenclature. Being physical objects that can be re-studied by other researchers, types permanently link taxonomy (an artificial agreement to classify biological diversity) with nomenclature (an artificial agreement to name biological diversity). Two proposals to amend the International Code of Nomenclature for algae, fungi, and plants (ICN), allowing DNA sequences alone (of any region and extent) to serve as types of taxon names for voucherless fungi (mainly putative taxa from environmental DNA sequences), have been submitted to be voted on at the 11th International Mycological Congress (Puerto Rico, July 2018). We consider various genetic processes affecting the distribution of alleles among taxa and find that alleles may not consistently and uniquely represent the species within which they are contained. Should the proposals be accepted, the meaning of nomenclatural types would change in a fundamental way from physical objects as sources of data to the data themselves. Such changes are conducive to irreproducible science, the potential typification on artefactual data, and massive creation of names with low information content, ultimately causing nomenclatural instability and unnecessary work for future researchers that would stall future explorations of fungal diversity. We conclude that the acceptance of DNA sequences alone as types of names of taxa, under the terms used in the current proposals, is unnecessary and would not solve the problem of naming putative taxa known only from DNA sequences in a scientifically defensible way. As an alternative, we highlight the use of formulas for naming putative taxa (candidate taxa) that do not require any modification of the ICN.
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| 2. |
- Barrefelt, Asa, et al.
(författare)
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Fluorescence labeled microbubbles for multimodal imaging
- 2015
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Ingår i: Biochemical and Biophysical Research Communications - BBRC. - : Elsevier BV. - 0006-291X .- 1090-2104. ; 464:3, s. 737-742
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Tidskriftsartikel (refereegranskat)abstract
- Air-filled polyvinyl alcohol microbubbles (PVA-MBs) were recently introduced as a contrast agent for ultrasound imaging. In the present study, we explore the possibility of extending their application in multimodal imaging by labeling them with a near infrared (NIR) fluorophore, VivoTag-680. PVA-MBs were injected intravenously into FVB/N female mice and their dynamic biodistribution over 24 h was determined by 3D-fluorescence imaging co-registered with 3D-mu CT imaging, to verify the anatomic location. To further confirm the biodistribution results from in vivo imaging, organs were removed and examined histologically using bright field and fluorescence microscopy. Fluorescence imaging detected PVA-MB accumulation in the lungs within the first 30 min post-injection. Redistribution to a low extent was observed in liver and kidneys at 4 h, and to a high extent mainly in the liver and spleen at 24 h. Histology confirmed PVA-MB localization in lung capillaries and macrophages. In the liver, they were associated with Kupffer cells; in the spleen, they were located mostly within the marginal-zone. Occasional MBs were observed in the kidney glomeruli and interstitium. The potential application of PVA-MBs as a contrast agent was also studied using ultrasound (US) imaging in subcutaneous and orthotopic pancreatic cancer mouse models, to visualize blood flow within the tumor mass. In conclusion, this study showed that PVA-MBs are useful as a contrast agent for multimodal imaging. (C) 2015 Elsevier Inc. All rights reserved.
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| 3. |
- Campbell, PJ, et al.
(författare)
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Pan-cancer analysis of whole genomes
- 2020
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 1476-4687 .- 0028-0836. ; 578:7793, s. 82-
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Tidskriftsartikel (refereegranskat)abstract
- Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale1–3. Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4–5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter4; identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation5,6; analyses timings and patterns of tumour evolution7; describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity8,9; and evaluates a range of more-specialized features of cancer genomes8,10–18.
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| 4. |
- Chen, Sa, 1967-, et al.
(författare)
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In vivo analysis of Suppressor of zeste 12´s different isoforms
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Polycomb Group (PcG) genes are known to encode a large chromatin-associated family of proteins which are involved in genomic regulation of many cellular processes. Su(z)12 is a key component in PcG silencing. It is needed for three levels of methylation of histone 3 lysine 27 in vivo in Drosophila. Here, we report that Su(z)12 may exist in different isoforms and that these isoforms are spatially and temporally regulated. The biological function of the Su(z)12-A and -B isoforms seems to be very different. For instance the transgenic Su(z)12-B and the human homolog SUZ12, but not Su(z)12-A, rescue Su(z)12 mutants. Furthermore, transgenic flies over-expressing Su(z)12-B show typical homeotic transformation phenotypes, while over-expression of Su(z)12-A does not. However, the two isoforms appears to be able to substitute for each other in some aspects. During larval and pupal stages, Su(z)12-A seems to play the main role.
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| 5. |
- Fröberg, Asa, et al.
(författare)
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High variability in strain estimation errors when using a commercial ultrasound speckle tracking algorithm on tendon tissue
- 2016
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Ingår i: Acta Radiologica. - : Sage Publications. - 0284-1851 .- 1600-0455. ; 57:10, s. 1223-1229
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Tidskriftsartikel (refereegranskat)abstract
- Background: Ultrasound speckle tracking offers a non-invasive way of studying strain in the free Achilles tendon where no anatomical landmarks are available for tracking. This provides new possibilities for studying injury mechanisms during sport activity and the effects of shoes, orthotic devices, and rehabilitation protocols on tendon biomechanics. Purpose: To investigate the feasibility of using a commercial ultrasound speckle tracking algorithm for assessing strain in tendon tissue. Material and Methods: A polyvinyl alcohol (PVA) phantom, three porcine tendons, and a human Achilles tendon were mounted in a materials testing machine and loaded to 4% peak strain. Ultrasound long-axis cine-loops of the samples were recorded. Speckle tracking analysis of axial strain was performed using a commercial speckle tracking software. Estimated strain was then compared to reference strain known from the materials testing machine. Two frame rates and two region of interest (ROI) sizes were evaluated. Results: Best agreement between estimated strain and reference strain was found in the PVA phantom (absolute error in peak strain: 0.21 +/- 0.08%). The absolute error in peak strain varied between 0.72 +/- 0.65% and 10.64 +/- 3.40% in the different tendon samples. Strain determined with a frame rate of 39.4Hz had lower errors than 78.6Hz as was the case with a 22mm compared to an 11mm ROI. Conclusion: Errors in peak strain estimation showed high variability between tendon samples and were large in relation to strain levels previously described in the Achilles tendon.
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| 6. |
- Håkansson, Stellan, et al.
(författare)
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Real-time PCR-assay in the delivery suite for determination of group B streptococcal colonization in a setting with risk-based antibiotic prophylaxis
- 2014
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Ingår i: Journal of Maternal-Fetal & Neonatal Medicine. - : Informa UK Limited. - 1476-7058 .- 1476-4954. ; 27:4, s. 328-332
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Tidskriftsartikel (refereegranskat)abstract
- Objective: Intrapartum antibiotic prophylaxis (IAP) reduces the incidence of neonatal early onset group B streptococcal infections. The present study investigated if an automated PCR-assay, used bedside by the labor ward personnel was manageable and could decrease the use of IAP in a setting with a risk-based IAP strategy. Methods: The study comprises two phases. Phase 1 was a multicenter, randomized, controlled trial. Women with selected risk-factors were allocated either to PCR-IAP (prophylaxis given if positive or indeterminate) or IAP. A vaginal/rectal swab and superficial swabs from the neonate for conventional culture were also obtained. Phase 2 was non-randomized, assessing an improved version of the assay. Results: Phase 1 included 112 women in the PCR-IAP group and 117 in the IAP group. Excluding indeterminate results, the assay showed a sensitivity of 89% and a specificity of 90%. In 44 % of the PCR assays the result was indeterminate. The use of IAP was lower in the PCR group (53 versus 92%). Phase 2 included 94 women. The proportion of indeterminate results was reduced (15%). The GBS colonization rate was 31%. Conclusion: The PCR assay, in the hands of labor ward personnel, can be useful for selection of women to which IAP should be offered.
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| 7. |
- Lagerqvist, Nina, et al.
(författare)
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Molecular Diagnosis of Hemorrhagic Fever with Renal Syndrome Caused by Puumala Virus
- 2016
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Ingår i: Journal of Clinical Microbiology. - 0095-1137 .- 1098-660X. ; 54:5, s. 1335-1339
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Tidskriftsartikel (refereegranskat)abstract
- Rodent-borne hantaviruses cause two severe acute diseases: hemorrhagic fever with renal syndrome (HFRS) in Eurasia, and hantavirus pulmonary syndrome (HPS; also called hantavirus cardiopulmonary syndrome [HCPS]) in the Americas. Puumala virus (PUUV) is the most common causative agent of HFRS in Europe. Current routine diagnostic methods are based on serological analyses and can yield inconclusive results. Hantavirus-infected patients are viremic during the early phase of disease; therefore, detection of viral RNA genomes can be a valuable complement to existing serological methods. However, the high genomic sequence diversity of PUUV has hampered the development of molecular diagnostics, and currently no real-time reverse transcription- quantitative (RT)-PCR assay is available for routine diagnosis of HFRS. Here, we present a novel PUUV RT-PCR assay. The assay was validated for routine diagnosis of HFRS on samples collected in Sweden during the winter season from 2013 to 2014. The assay allowed detection of PUUV RNA in 98.7% of confirmed clinical HFRS samples collected within 8 days after symptomatic onset. In summary, this study shows that real-time RT-PCR can be a reliable alternative to serological tests during the early phase of HFRS.
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| 8. |
- Larsson, Bo, et al.
(författare)
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Headache prevalence and characteristics among school children as assessed by prospective paper diary recordings
- 2012
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Ingår i: Journal of Headache and Pain. - : Springer Science and Business Media LLC. - 1129-2369 .- 1129-2377. ; 13:2, s. 129-136
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Tidskriftsartikel (refereegranskat)abstract
- In the present school-based study, a convenience sample of 477 students in grades 6-9 and second year in high school from a city and a smaller town recorded daily occurrence and intensity of headaches in a standard paper diary during a 3-week period. Total headache activity (headache sum), number of headache days, intensity level and duration for weekly headaches were estimated. Approximately 85% of the adolescents had experienced headache of any intensity level during the 3-week recording period. On the average, they reported 2.5 headache days per week and a mean intensity level for headache episodes of 1.7. Our estimates for headache of any intensity level (1-5) occurring at least once a week was surprisingly high (73.8%). For the highest intensity level across the whole 3-week period, almost identical proportions of mild and moderate headaches were reported by students (22.3-22.5%), while about twice as many (40.7%) had experienced severe headaches. Girls consistently reported more headaches than boys, in particular of the moderate and severe intensity types. Students in the city also reported more frequent and intense headaches than those in the town. Peak headache activity was observed at noon and in the afternoon and in the days from the middle of the week until weekend. The use of prospective recordings in diaries will further advance our knowledge on the prevalence and characteristics of recurrent headaches among children and adolescents in community samples.
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| 9. |
- Larsson, Bo, 1943, et al.
(författare)
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Relaxation treatment of adolescent headache sufferers: results from a school-based replication series.
- 2005
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Ingår i: Headache. - : Wiley. - 0017-8748. ; 45:6, s. 692-704
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: In recent reviews of psychological and drug treatment, relaxation training approaches have been found to be efficacious for children and adolescents suffering from recurrent tension-type headache (TTH), while biofeedback procedures provide effective help for migraine headache sufferers, primarily treated in tertiary clinics. OBJECTIVE: In a school-based replication series, the effectiveness and efficiency of relaxation training provided within school settings were examined, in addition to the effects on various headache features and the maintenance of treatment gains at a 6 to 10-month follow-up. METHODS: Over a 20-year period, 288 adolescents aged 10 to 18 years participated in seven randomized, controlled trials conducted within regular school health service settings. Subjects were included if they had suffered from frequent migraine or TTHs, or from both headache types for at least 1 year. Various formats of standardized relaxation training procedures were contrasted to different attention-control (ATCO) approaches or self-monitoring (SM) of headaches in prospective diary recordings. RESULTS: The results showed that a therapist-administered relaxation approach was superior to self-help or school-nurse administered relaxation training approaches, ATCO conditions or SM of headaches. Students with TTHs responded positively to any form of relaxation training, whereas those with frequent migraine responded well only to therapist-administered relaxation. However, school-nurse administered procedures were found to be the most efficient form of relaxation treatment, in particular for adolescents suffering from TTHs. Total headache activity, the number of headache days and peak headache intensity were significantly reduced after relaxation treatment, in addition to medication usage. Treatment gains were well maintained at the 6 to 10-month follow-up. CONCLUSION: Therapist-assisted relaxation training is an effective treatment for adolescents suffering from frequent TTHs or migraine. However, such treatment administered by school-nurses administered within school health care settings is an efficient treatment approach for adolescents suffering from the most common form of primary headache, ie, TTHs.
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| 10. |
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