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- Holland, Linda Z, et al.
(författare)
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The amphioxus genome illuminates vertebrate origins and cephalochordate biology
- 2008
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Ingår i: Genome Research. - : Cold Spring Harbor Laboratory. - 1088-9051 .- 1549-5469. ; 18:7, s. 1100-1111
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Tidskriftsartikel (refereegranskat)abstract
- Cephalochordates, urochordates, and vertebrates evolved from a common ancestor over 520 million years ago. To improve our understanding of chordate evolution and the origin of vertebrates, we intensively searched for particular genes, gene families, and conserved noncoding elements in the sequenced genome of the cephalochordate Branchiostoma floridae, commonly called amphioxus or lancelets. Special attention was given to homeobox genes, opsin genes, genes involved in neural crest development, nuclear receptor genes, genes encoding components of the endocrine and immune systems, and conserved cis-regulatory enhancers. The amphioxus genome contains a basic set of chordate genes involved in development and cell signaling, including a fifteenth Hox gene. This set includes many genes that were co-opted in vertebrates for new roles in neural crest development and adaptive immunity. However, where amphioxus has a single gene, vertebrates often have two, three, or four paralogs derived from two whole-genome duplication events. In addition, several transcriptional enhancers are conserved between amphioxus and vertebrates--a very wide phylogenetic distance. In contrast, urochordate genomes have lost many genes, including a diversity of homeobox families and genes involved in steroid hormone function. The amphioxus genome also exhibits derived features, including duplications of opsins and genes proposed to function in innate immunity and endocrine systems. Our results indicate that the amphioxus genome is elemental to an understanding of the biology and evolution of nonchordate deuterostomes, invertebrate chordates, and vertebrates.
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- House, J, et al.
(författare)
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Climate and air quality
- 2006
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Ingår i: Millennium Ecosystem Assessment 2005 - Current State and Trends. Findings of the Condition and Trends Working Group (Ecosystems and Human Well-being). ; 1, s. 350-390
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Bokkapitel (övrigt vetenskapligt/konstnärligt)
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- Van Holsbeke, C, et al.
(författare)
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Imaging of gynecological disease (3): clinical and ultrasound characteristics of granulosa cell tumors of the ovary
- 2008
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Ingår i: Ultrasound in Obstetrics & Gynecology. - : Wiley. - 1469-0705 .- 0960-7692. ; 31:4, s. 450-456
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Tidskriftsartikel (refereegranskat)abstract
- Objectives To describe the clinical and ultrasound characteristics of granulosa cell tumors (GCTs) of the ovary, and to define the ultrasound appearance of GCTs based on pattern recognition. Methods Databases of four gynecological ultrasound centers were searched to identify patients with histologically proven GCTs who had undergone a standard preoperative ultrasound examination. Results A total of 23 women with confirmed GCT were identified. Twelve (52%) women were postmenopausal, nine (39%) were of fertile age and two (9%) were prepubertal. Clinical symptoms were abdominal distension (7/23, 30%), pain (5/23, 22%) and irregular vaginal bleeding (6/23, 26%). Seven patients (30%) were asymptomatic. Endometrial pathology was found in 54% (7/13) of the patients from whom endometrial biopsies were taken. On ultrasound scan 12/23 (52%) masses were multilocular-solid, 9/23 (39%) were purely solid, one mass (4%) was unilocular-solid and one mass was multilocular (4%). Multilocular and multilocular-solid cysts typically contained large numbers of small locules (> 10). The echogenicity of the cyst content was most often mixed (6/16, 38%) or low level (7/16, 44%). Papillary projections were found in only four women (17%). The GCTs were large tumors with a median largest diameter of 102 (range, 37-242) mm and manifested moderate or high color content at color Doppler examination (color score 3 in 13/23 tumors (57%); color score 4 in 8/23 tumors (35%)). Conclusions At ultrasound examination, most GCTs are large multilocular-solid masses with a large number of locules, or solid tumors with heterogeneous echogenicity of the solid tissue. Hemorrhagic components are common and increased vascularity is demonstrated at color/power Doppler ultrasound examination. The hyperestrogenic state that is created by the tumor often causes endometrial pathology with bleeding problems as a typical associated symptom.
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- Van Holsbeke, C., et al.
(författare)
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Real-time ultrasound vs. evaluation of static images in the preoperative assessment of adnexal masses
- 2008
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Ingår i: Ultrasound in Obstetrics & Gynecology. - : Wiley. - 1469-0705 .- 0960-7692. ; 32:6, s. 828-831
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Tidskriftsartikel (refereegranskat)abstract
- Objective To determine if the prediction of the Malignancy of all adnexal mass using pattern recognition, i.e. subjective evaluation of gray-scale and Doppler ultrasound findings, is as accurate when based on static images as it is when based on a real-time ultrasound examination. Methods The static images of 166 non-consecutive patients with 'difficult' adnexal masses, who all underwent surgery and for whom a histopathological diagnosis was available, were evaluated by three experts in gynecological ultrasound (image experts'). All ultrasound examinations bad been performed and the static images saved by a fourth expert sonologist ('real-time' sonologist). All four sonologists classified the adnexal masses as benign or malignant based on their subjective impression and stated with what degree of confidence their diagnosis was made. The diagnostic performance of the real-time sonologist was compared with that of each of The three image experts and with that of the 'consensus opinion' of the image experts (i.e. the diagnosis suggested by at least two of the latter). Results The real-time sonologist correctly predicted the diagnosis with an accuracy of 89% (148/166) vs. 85% (141/166) for the consensus opinion of static images (P = 0.0707). Equivalent values for sensitivity and specificity were 80% (56/170) vs. 83%, (58/70) (P = 0.4142) and 96%) (92/96) us. 86%, (83/96) (P = 0.0027), respectively. Conclusions The preoperative diagnosis of all adnexal mass made on the basis of a real-time ultrasound examination is more precise than a diagnosis made on the basis of saved static ultrasound images. Evaluation of static images is associated with lower diagnostic specificity. Copyright (c) 2008 ISUOG. Published by John Wiley & Sons, Ltd.
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- Van Holsbeke, C., et al.
(författare)
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Ultrasound methods to distinguish between malignant and benign adnexal masses in the hands of examiners with different levels of experience
- 2009
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Ingår i: Ultrasound in Obstetrics & Gynecology. - : Wiley. - 1469-0705 .- 0960-7692. ; 34:4, s. 454-461
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Tidskriftsartikel (refereegranskat)abstract
- Objectives To determine the effect of an ultrasound training course on the performance of pattern recognition when used by less experienced examiners and to compare the performance of pattern recognition, a logistic regression model and a scoring system to estimate the risk of malignancy between examiners with different levels of experience. Methods Using ultrasound images of selected adnexal masses, two trainees classified the masses as benign or malignant by using pattern recognition both before and after they bad attended a theoretical gynecological ultrasound course. They also classified the masses by using a logistic regression model and a scoring system, but only after they bad attended the course. The performance of these three methods when they were used by the trainees was then compared with that when they were used by experts. Results One hundred and sixty-five adnexal masses were included, of which 42% were malignant (21% invasive tumors and 21% borderline tumors). The area under the receiver- operating characteristics curve of pattern recognition when used by the trainees was similar before and after they had attended the course. Training decreased sensitivity (84% vs. 70% for Trainee 1, P = 0.004; 70% vs. 61% for Trainee2, P = 0.08) and increased specificity (77% vs. 92% for Trainee 1, P = 0.001; 89% vs. 95% for Trainee 2, P = 0.058). The performance of pattern recognition was poorer in the hands of the trainees than in the bands of the experts. The sensitivities of the logistic regression model were 70% and 54% for the trainees vs. 83% for an expert (P = 0.020 and < 0.001, respectively) and the specificities were 84% and 94% vs. 89% (P = 0.25 and 0.59, respectively). The sensitivities of the scoring system were 59% and 54% for the trainees vs. 75% for the expert (P = 0.002 and < 0.001, respectively), and the specificities were 90% and 93% vs. 85% (P = 0.103 and 0.008, respectively). Conclusion Theoretical ultrasound teaching did not seem to improve the performance of pattern recognition in the bands of trainees. A logistic regression model and a scoring system to classify adnexal masses as benign or malignant perform less well when they were used by inexperienced examiners than when used by an expert. Before using a model or a scoring system, experience and/or proper training are likely to be of paramount importance if diagnostic performance is to be optimized. Copyright (C) 2009 ISUOG. Published by John Wiley & Sons, Ltd.
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- Furlong, R. F., et al.
(författare)
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A degenerate ParaHox gene cluster in a degenerate vertebrate
- 2007
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Ingår i: Molecular Biology and Evolution. - 0737-4038. ; 24:12, s. 2681-2686
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Tidskriftsartikel (refereegranskat)abstract
- The ParaHox genes consist of 3 homeobox gene families, Gsx, Xlox, and Cdx, all of which have fundamental roles in development. Xlox (known as IPF1 or PDX1 in vertebrates), for example, is crucial for development of the vertebrate pancreas and is also involved in regulation of insulin expression. The invertebrate amphioxus has a gene cluster containing one gene from each of the gene families, whereas in all vertebrates examined to date there are additional copies resultant from ParaHox gene cluster duplications at the base of the vertebrate lineage. Extant vertebrates basal to bony and cartilaginous fish are central to the question of when and how these multiple genes arose in the vertebrate genome. Here, we report the mapping of a ParaHox gene cluster in 2 species of hagfishes. Unexpectedly, these basal vertebrates have lost a functional Xlox gene from this cluster, unlike every other vertebrate examined to date. Furthermore, our phylogenetic analyses suggest that hagfishes may have diverged from the vertebrate lineage before the duplications, which created the multiple ParaHox clusters in jawed vertebrates.
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