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| 2. |
- Alström, Per, et al.
(författare)
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Description of a new species of Phylloscopus from Vietnam and Laos.
- 2010
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Ingår i: Ibis. - 0019-1019 .- 1474-919X. ; 152:1, s. 145-168
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Tidskriftsartikel (refereegranskat)abstract
- A new species of Phylloscopus warbler, which we name Phylloscopus calciatilis Limestone Leaf Warbler, is described from central and northern Vietnam and central and northern Laos; it probably also breeds in southernmost China. In morphology, the new species is very similar to Sulphur-breasted Warbler Phylloscopus ricketti, but it is smaller with a proportionately larger bill and rounder wing. Its song and calls are diagnostic. Based on mitochondrial and nuclear DNA, the new species is most closely related to P. ricketti and Yellow-vented Warbler Phylloscopus cantator, and it is inferred to be sister to the latter. The mitochondrial divergences between these three species are at the low end of the variation found in other species of Phylloscopus and Seicercus warblers, but greater than in other taxa generally treated as subspecies. Possible introgressive hybridization between the new species and P. ricketti is discussed, but more data are needed to establish whether it does occur and, if it does, to what extent. The new species appears to have a restricted breeding range in limestone karst environments, where it is locally common and therefore not under any immediate threat. In view of the recognition of the new species, all previous records of P. ricketti sensu lato need to be re-evaluated.
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| 5. |
- Fang, Li Tai, et al.
(författare)
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Establishing community reference samples, data and call sets for benchmarking cancer mutation detection using whole-genome sequencing
- 2021
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Ingår i: Nature Biotechnology. - : Springer Nature. - 1087-0156 .- 1546-1696. ; 39:9, s. 1151-1160
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Tidskriftsartikel (refereegranskat)abstract
- Tumor-normal paired DNA samples from a breast cancer cell line and a matched lymphoblastoid cell line enable calibration of clinical sequencing pipelines and benchmarking 'tumor-only' or 'matched tumor-normal' analyses. The lack of samples for generating standardized DNA datasets for setting up a sequencing pipeline or benchmarking the performance of different algorithms limits the implementation and uptake of cancer genomics. Here, we describe reference call sets obtained from paired tumor-normal genomic DNA (gDNA) samples derived from a breast cancer cell line-which is highly heterogeneous, with an aneuploid genome, and enriched in somatic alterations-and a matched lymphoblastoid cell line. We partially validated both somatic mutations and germline variants in these call sets via whole-exome sequencing (WES) with different sequencing platforms and targeted sequencing with >2,000-fold coverage, spanning 82% of genomic regions with high confidence. Although the gDNA reference samples are not representative of primary cancer cells from a clinical sample, when setting up a sequencing pipeline, they not only minimize potential biases from technologies, assays and informatics but also provide a unique resource for benchmarking 'tumor-only' or 'matched tumor-normal' analyses.
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| 6. |
- Hult, Jenny, et al.
(författare)
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A waiting time of 7 min is sufficient to reduce bleeding in oculoplastic surgery following the administration of epinephrine together with local anaesthesia
- 2018
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Ingår i: Acta Ophthalmologica. - : Wiley. - 1755-375X. ; 96:5, s. 499-502
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Tidskriftsartikel (refereegranskat)abstract
- OBJECTIVE: The time taken to reach maximal haemostatic effect following local anaesthesia with epinephrine is generally believed to be <10 min. This is based on clinical experience and indirect measurements of perfusion using methods such as laser Doppler flowmetry and oxygen spectroscopy. However, the only study in which bleeding has been measured quantitatively in an intra-operative setting in humans showed that the full haemostatic effect was not achieved until 30 min after anaesthesia. The aim of this study was to determine the time taken to reach maximum haemostatic effect when using epinephrine for local anaesthesia in oculoplastic surgery.METHODS: Intra-operative bleeding following infiltration anaesthesia with either lidocaine 20 mg/ml (2%) or lidocaine + epinephrine 12.5 μg/ml (1:80 000) was measured after 7, 15 and 30 min in the eyelids of 16 patients undergoing upper eyelid blepharoplasty.RESULTS: Bleeding was decreased by 74.6% (with 95% CI, 6.16-87.6%) 7 min after the injection of lidocaine + epinephrine (p = 0.0048) compared with lidocaine without epinephrine. There was no further decrease in bleeding after 15 or 30 min (p = n.s.).CONCLUSION: The optimal time for skin incision in eyelid surgery is within 7 min of injection of lidocaine with epinephrine. Waiting longer does not lead to a further decrease in bleeding.
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| 11. |
- Mansouri, L, et al.
(författare)
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Different prognostic impact of recurrent gene mutations in chronic lymphocytic leukemia depending on IGHV gene somatic hypermutation status: a study by ERIC in HARMONY
- 2023
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Ingår i: Leukemia. - : Springer Science and Business Media LLC. - 1476-5551 .- 0887-6924. ; 37:2, s. 339-347
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Tidskriftsartikel (refereegranskat)abstract
- Recent evidence suggests that the prognostic impact of gene mutations in patients with chronic lymphocytic leukemia (CLL) may differ depending on the immunoglobulin heavy variable (IGHV) gene somatic hypermutation (SHM) status. In this study, we assessed the impact of nine recurrently mutated genes (BIRC3, EGR2, MYD88, NFKBIE, NOTCH1, POT1, SF3B1, TP53, and XPO1) in pre-treatment samples from 4580 patients with CLL, using time-to-first-treatment (TTFT) as the primary end-point in relation to IGHV gene SHM status. Mutations were detected in 1588 (34.7%) patients at frequencies ranging from 2.3–9.8% with mutations in NOTCH1 being the most frequent. In both univariate and multivariate analyses, mutations in all genes except MYD88 were associated with a significantly shorter TTFT. In multivariate analysis of Binet stage A patients, performed separately for IGHV-mutated (M-CLL) and unmutated CLL (U-CLL), a different spectrum of gene alterations independently predicted short TTFT within the two subgroups. While SF3B1 and XPO1 mutations were independent prognostic variables in both U-CLL and M-CLL, TP53, BIRC3 and EGR2 aberrations were significant predictors only in U-CLL, and NOTCH1 and NFKBIE only in M-CLL. Our findings underscore the need for a compartmentalized approach to identify high-risk patients, particularly among M-CLL patients, with potential implications for stratified management.
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| 12. |
- Menicatti, Roberto, et al.
(författare)
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Collaborative Development Within a Social Robotic, Multi-Disciplinary Effort : the CARESSES Case Study
- 2018
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Ingår i: 2018 IEEE Workshop on Advanced Robotics and its Social Impacts (ARSO). - : IEEE. - 9781538680377 ; , s. 117-124
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Konferensbidrag (refereegranskat)abstract
- In many cases, complex multidisciplinary research projects may show a lack of coordinated development and integration, and a big effort is often required in the final phase of the projects in order to merge software developed by heterogeneous research groups. This is particularly true in advanced robotic projects: the objective here is to deliver a system that integrates all the hardware and software components, is capable of autonomous behaviour, and needs to be deployed in real-world scenarios toward providing an impact on future research and, ultimately, on society. On the other hand, in recent years there has been a growing interest for techniques related to software integration, but these have been mostly applied to the IT commercial domain.This paper presents the work performed in the context of the project CARESSES, a multidisciplinary research project focusing on socially assistive robotics that involves 9 partners from the EU and Japan. Given the complexity of the project, a huge importance has been placed on software integration, task planning and architecture definition since the first stages of the work: to this aim, some of the practices commonly used in the commercial domain for software integration, such as merging software from the early stage, have been applied. As a case study, the document describes the steps which have been followed in the first year of the project discussing strengths and weaknesses of this approach.
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| 13. |
- Nguyen, Cu Dinh, et al.
(författare)
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Blood Perfusion in Human Eyelid Skin Flaps Examined by Laser Speckle Contrast Imaging-Importance of Flap Length and the Use of Diathermy
- 2018
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Ingår i: Ophthalmic Plastic and Reconstructive Surgery. - 1537-2677. ; 39:4, s. 361-365
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Tidskriftsartikel (refereegranskat)abstract
- PURPOSE: It is well known that blood perfusion is important for the survival of skin flaps. As no study has been conducted to investigate how the blood perfusion in human eyelid skin flaps is affected by the flap length and diathermy, the present study was carried out to investigate these in patients.METHODS: Fifteen upper eyelids were dissected as part of a blepharoplastic procedure, releasing a 30-mm long piece of skin, while allowing the 5 mm wide distal part of the skin to remain attached, to mimic a skin flap (hereafter called a "skin flap"). Blood perfusion was measured before and after repeated diathermy, using laser speckle contrast imaging.RESULTS: Blood perfusion decreased from the base to the tip of the flap: 5 mm from the base, the perfusion was 69%, at 10 mm it was 40%, at 15 mm it was 20%, and at 20 mm it was only 13% of baseline values. Diathermy further decreased blood perfusion (measured 15 mm from the base) to 13% after applying diathermy for the first time, to 6% after the second and to 4% after the third applications of diathermy.CONCLUSIONS: Blood perfusion falls rapidly with distance from the base of skin flaps on the human eyelid, and diathermy reduces blood perfusion even further. Clinically, it may be advised that flaps with a width of 5 mm be no longer than 15 mm (i.e., a width:length ratio of 1:3), and that the use of diathermy should be carefully considered.
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| 15. |
- Tenland, Kajsa, et al.
(författare)
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Perfusion Monitoring Shows Minimal Blood Flow From the Flap Pedicle to the Tarsoconjunctival Flap
- 2019
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Ingår i: Ophthalmic Plastic and Reconstructive Surgery. - 1537-2677. ; 35:4, s. 346-349
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: A previous study in pigs has shown that the pedicle of the tarsoconjunctival flap does not appear to have adequate blood perfusion. The aim of this study was to monitor perfusion in tarsoconjunctival flaps in patients with large lower eyelid defects resulting from tumor surgery.METHODS: The modified Hughes procedure was performed in 13 patients. Blood perfusion was monitored using laser Doppler velocimetry and laser speckle-contrast imaging.RESULTS: Blood flow decreased gradually from the pedicle base to the end of the flap and was 19% at the flap base, 11% in the middle of the flap, and 4% in the distal end of the flap. The flaps survived, and there was no tissue necrosis.CONCLUSIONS: Tarsoconjunctival tissue survival does not seem to be dependent on a conjunctival flap. Free tarsoconjunctival grafts or composite grafts might be considered as viable alternatives in reconstruction of major eyelid defects.
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| 16. |
- Xiao, Wenming, et al.
(författare)
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Toward best practice in cancer mutation detection with whole-genome and whole-exome sequencing
- 2021
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Ingår i: Nature Biotechnology. - : Springer Nature. - 1087-0156 .- 1546-1696. ; 39:9, s. 1141-1150
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Tidskriftsartikel (refereegranskat)abstract
- Recommendations are given on optimal read coverage and selection of calling algorithm to maximize the reproducibility of cancer mutation detection in whole-genome or whole-exome sequencing. Clinical applications of precision oncology require accurate tests that can distinguish true cancer-specific mutations from errors introduced at each step of next-generation sequencing (NGS). To date, no bulk sequencing study has addressed the effects of cross-site reproducibility, nor the biological, technical and computational factors that influence variant identification. Here we report a systematic interrogation of somatic mutations in paired tumor-normal cell lines to identify factors affecting detection reproducibility and accuracy at six different centers. Using whole-genome sequencing (WGS) and whole-exome sequencing (WES), we evaluated the reproducibility of different sample types with varying input amount and tumor purity, and multiple library construction protocols, followed by processing with nine bioinformatics pipelines. We found that read coverage and callers affected both WGS and WES reproducibility, but WES performance was influenced by insert fragment size, genomic copy content and the global imbalance score (GIV; G > T/C > A). Finally, taking into account library preparation protocol, tumor content, read coverage and bioinformatics processes concomitantly, we recommend actionable practices to improve the reproducibility and accuracy of NGS experiments for cancer mutation detection.
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