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- Rheinbay, E, et al.
(författare)
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Analyses of non-coding somatic drivers in 2,658 cancer whole genomes
- 2020
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 1476-4687 .- 0028-0836. ; 578:7793, s. 102-
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Tidskriftsartikel (refereegranskat)abstract
- The discovery of drivers of cancer has traditionally focused on protein-coding genes1–4. Here we present analyses of driver point mutations and structural variants in non-coding regions across 2,658 genomes from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium5 of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). For point mutations, we developed a statistically rigorous strategy for combining significance levels from multiple methods of driver discovery that overcomes the limitations of individual methods. For structural variants, we present two methods of driver discovery, and identify regions that are significantly affected by recurrent breakpoints and recurrent somatic juxtapositions. Our analyses confirm previously reported drivers6,7, raise doubts about others and identify novel candidates, including point mutations in the 5′ region of TP53, in the 3′ untranslated regions of NFKBIZ and TOB1, focal deletions in BRD4 and rearrangements in the loci of AKR1C genes. We show that although point mutations and structural variants that drive cancer are less frequent in non-coding genes and regulatory sequences than in protein-coding genes, additional examples of these drivers will be found as more cancer genomes become available.
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- Carlevaro-Fita, J, et al.
(författare)
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Cancer LncRNA Census reveals evidence for deep functional conservation of long noncoding RNAs in tumorigenesis
- 2020
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Ingår i: Communications biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1, s. 56-
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Tidskriftsartikel (refereegranskat)abstract
- Long non-coding RNAs (lncRNAs) are a growing focus of cancer genomics studies, creating the need for a resource of lncRNAs with validated cancer roles. Furthermore, it remains debated whether mutated lncRNAs can drive tumorigenesis, and whether such functions could be conserved during evolution. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, we introduce the Cancer LncRNA Census (CLC), a compilation of 122 GENCODE lncRNAs with causal roles in cancer phenotypes. In contrast to existing databases, CLC requires strong functional or genetic evidence. CLC genes are enriched amongst driver genes predicted from somatic mutations, and display characteristic genomic features. Strikingly, CLC genes are enriched for driver mutations from unbiased, genome-wide transposon-mutagenesis screens in mice. We identified 10 tumour-causing mutations in orthologues of 8 lncRNAs, including LINC-PINT and NEAT1, but not MALAT1. Thus CLC represents a dataset of high-confidence cancer lncRNAs. Mutagenesis maps are a novel means for identifying deeply-conserved roles of lncRNAs in tumorigenesis.
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- Wang, XP, et al.
(författare)
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Measurement of rainfall interception by xerophytic shrubs in re-vegetated sand dunes
- 2005
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Ingår i: Hydrological Sciences Journal. - : Informa UK Limited. - 0262-6667 .- 2150-3435. ; 50:5, s. 897-910
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Tidskriftsartikel (refereegranskat)abstract
- More than 40 years of re-vegetation using mainly xerophytic shrubs Artemisia ordosica Krasch. and Caragana korshinskii Kom. at Shapotou Desert Experimental Research Station near Lanzhou, China has resulted in established dwarf-shrub and herbaceous cover on sand dunes. Precipitation, as the sole source of water replenishment in the semiarid area, plays a pertinent role in sustaining the desert ecosystem. A field study was conducted to (a) measure interception loss on shrub canopies during individual rainfall events, (b) determine the canopy storage capacity of individual plants, and (c) explore the relationship between interception and rainfall parameters. The total rainfall and its respective partitions as throughfall were determined and the interception losses in the studied ecosystem were quantified. Interception loss was shown to differ among the xerophyte taxa studied. During the growing seasons, the average shrub community interception loss is 6.9% and 11.7% of the simultaneous overall precipitation, for A. ordosica and C. korshinskii, respectively. Taking into account the observed rainfall conditions and vegetation cover characteristics, it was concluded that the interception loss was 2.7% of the total annual precipitation verified in the period for the A. ordosica community with an average cover of 30%, canopy projection area of 0.8 m(2) and canopy storage capacity of 0.75 mm. In contrast, interception loss for the C korshinskii community was 3.8% with an average cover of 46%, canopy projection area of 3.8 m(2) and canopy storage capacity of 0.71 mm. For individual plants of both shrubs, the proportion of interception loss to gross rainfall decreased notably as the rainfall intensity increased between 0 and 2 min h(-1), while it tended to remain constant at about 0.1-0.2 for A. ordosica and 0.1-0.3 for C. korshinskii when the rainfall intensity was > 2 mm h(-1).
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- Zhang, F, et al.
(författare)
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Evaluating children with vestibular migraine through vestibular test battery: A cross-sectional investigation
- 2022
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Ingår i: Frontiers in neurology. - : Frontiers Media SA. - 1664-2295. ; 13, s. 997217-
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Tidskriftsartikel (refereegranskat)abstract
- The present study aimed to investigate the status of vestibular function in children with vestibular migraine of childhood (VMC) reflected by vestibular function test battery and explore the pathophysiological implication of these instrument-based findings.MethodsThe clinical data of 22 children (mean age 10.7 ± 2.9 years) with VMC who met the diagnostic criteria of the Barany Society were collected from September 2021 to March 2022. A vestibular function test battery on these children included a caloric test, video head impulse test (vHIT), cervical vestibular-evoked myogenic potential (cVEMP), and ocular vestibular-evoked myogenic potential (oVEMP); these parameters were triggered by air-conducted sound (ACS) and galvanic vestibular stimulation (GVS). The subjects were further divided into two groups: <3 months and >3 months according to the disease duration from symptom onset. The functional abnormalities and their characteristics reflected by the vestibular test battery, as well as the outcomes in children with or without aura, were analyzed.Results(1) The abnormal rate of the caloric test was 15.8% and that of vHIT was 0%. The response rates of ACS-cVEMP and ACS-oVEMP were 100% and 90.5%, respectively. The response rates of GVS-cVEMP and GVS-oVEMP were 100% and 88.9%, respectively. (2) No statistical difference was observed in the abnormal rate of the caloric test (P = 0.55) and the response rate of ACS-oVEMP (P = 0.21) between the two groups, irrespective of the course duration. (3) No statistical difference was detected in the abnormal rate of the caloric test (P = 0.53) and the response rate of ACS-oVEMP (P = 1.00) in children with or without aura.ConclusionVestibular function status comprehensively reported by the vestibular test battery did not show an aggravation with the disease duration in children with VMC. Also, it was not affected by the existence of aura in children with VMC. The high abnormal rates of the caloric test and oVEMPs (ACS-oVEMP and GVS-oVEMP) suggested that the lateral semicircular canal (low-frequency function component), the utricle, and the superior vestibular conduction pathway might be involved in VMC.
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- Liang, M, et al.
(författare)
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Vestibular evoked myogenic potential may predict the hearing recovery in patients with unilateral idiopathic sudden sensorineural hearing loss
- 2022
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Ingår i: Frontiers in neurology. - : Frontiers Media SA. - 1664-2295. ; 13, s. 1017608-
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Tidskriftsartikel (refereegranskat)abstract
- This study investigates the association between vestibular function and prognosis in patients with unilateral idiopathic sudden sensorineural hearing loss (UISSNHL).DesignA retrospective analysis of 64 patients with UISSNHL was performed. Pure tone audiometry and vestibular function tests for otoliths and semicircular canals were performed to assess the influence of vestibular functional status on the outcome of patients with UISSNHL.ResultsPatients with abnormal cervical vestibular evoked myogenic potential (cVEMP) or ocular vestibular evoked myogenic potential (oVEMP) responded less favorably to treatment. In the ineffective group, cVEMP was normal in four patients (6.3%) and oVEMPs in three (4.7%). Meanwhile, cVEMP was abnormal in 32 patients (50.0%) and oVEMP in 33 (51.6%). Better hearing recovery occurred in those with normal cVEMP (33.76 ± 15.07 dB HL improvement) or oVEMP (32.55 ± 19.56 dB HL improvement), but this was not the case in those with normal caloric tests. Patients with abnormalities in both cVEMP and oVEMP were less responsive to treatment and had worse hearing recovery than those with normal results in only one of the two tests.ConclusionAbnormal oVEMP and/or cVEMP results indicate poor auditory outcomes in patients with UISSNHL. Patients with impaired otolith organ function are likely to have a larger and more severe pathological change in their inner ear.
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- Shen, JL, et al.
(författare)
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Cervical vestibular evoked myogenic potentials in 3-month-old infants: Comparative characteristics and feasibility for infant vestibular screening
- 2022
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Ingår i: Frontiers in neurology. - : Frontiers Media SA. - 1664-2295. ; 13, s. 992392-
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Tidskriftsartikel (refereegranskat)abstract
- We compared the characteristics of air-conducted sound cervical vestibular evoked myogenic potential (ACS-cVEMP) and bone-conducted vibration cVEMP (BCV-cVEMP) among 3-month-old infants with normal hearing and sensorineural hearing loss (SNHL), and healthy adults to explore the feasibility and optimal strategies for infant vestibular screening.Methods29 infants (58 ears) were divided into two groups according to hearing (group I: normal hearing ears; group II: SNHL ears), 20 healthy adults were defined as group III. The results of response rate, P13 and N23 latency, P13-N23 interval, amplitudes, and corrected interaural asymmetry ratio (IAR) were recorded and compared among three groups.ResultsThe response rates of ACS-cVEMP in three groups were 88.89, 62.00, 100%, respectively. The P13 and N23 latencies, and P13-N23 interval did not differ significantly between group I and II (p = 0.866, p = 0.190, p = 0.252). A significant difference was found between group I and III (p = 0.016, p < 0.001, p < 0.001). No significant difference was observed in raw or corrected amplitude between group I and II (p = 0.741, p = 0.525), while raw and corrected amplitudes in group III were significantly larger than group I (p < 0.001, p < 0.001). For BCV-cVEMP, the response rates in three groups were 100, 86.36, 100%, respectively, No significant difference existed in the P13 and N23 latency, or P13-N23 interval between group I and II (p = 0.665, p = 0.925, p = 0.806), however, P13 and N23 latencies were significantly longer in group III than group I (p < 0.001, p = 0.018), but not in P13-N23 interval (p = 0.110). There was no significant difference in raw or corrected amplitude between group I and II (p = 0.771, p = 0.155) or in raw amplitude between group I and III (p = 0.093), however, a significant difference existed in corrected amplitude between group I and III (p < 0.001).ConclusionsCompared with adults, 3-month-old infants with normal hearing presented with equivalent response rates, shorter P13 and N23 latencies, smaller corrected amplitudes, and a wider IAR range for both ACS and BCV-cVEMP. SNHL infants had equivalent response rates of BCV-cVEMP, lower response rates of ACS-cVEMP than normal hearing infants. When responses were present, characteristics of ACS and BCV-cVEMP in SNHL infants were similar with normal hearing infants. ACS combined with BCV-cVEMP are recommended to improve the accuracy of vestibular screening.
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| 44. |
- Vegvari, A, et al.
(författare)
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Toward Single Bacterium Proteomics
- 2023
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Ingår i: Journal of the American Society for Mass Spectrometry. - 1879-1123. ; 34:10, s. 2098-2106
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Tidskriftsartikel (refereegranskat)
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| 45. |
- Wang, XP, et al.
(författare)
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Evapotranspiration of Artemisia ordosica vegetation in stabilized arid desert dune in Shapotou, China
- 2004
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Ingår i: Arid Land Research and Management. - : Informa UK Limited. - 1532-4982 .- 1532-4990. ; 18:1, s. 63-76
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Tidskriftsartikel (refereegranskat)abstract
- More than 40 years of revegetation using mainly Artemisia ordosica, Hedysarum scoparium, and Caragana korshinskii at Shapotou Desert Experimental Research Station near Lanzhou has established a dwarf-shrub and herbaceous cover on the stabilized sand dunes. The evapotranspiration (ET) of the xerophyte dwarf-shrub A. ordosica plant vegetation was measured by the autoweighing lysimeter method during the growing seasons from 1990 to 1995, and 2002 on the southeast edge of the Tengger Desert at Shapotou, China. The study showed that the average ET rates were 0.88 mm d(-1), and they varied from 0.6 mm d(-1) to 1.31 mm d(-1) during the 7-year experimental period from 1990 to 1995, and 2002. The ratios of ET/Precipitation (P) varied from 69.8% to 120.9% with an average of 90.9%. The higher ET/P value in 1991 was associated with the properties of intra year distribution of rainfall events, and resulted in soil moisture depletion. The correlation between the accumulative P and the accumulative ET was quite high. For the years 1990, 1993, and 1995, the relationship between the accumulative ET and the accumulative P had a closed linear relationship, resulting from the higher intensity of monthly P exceeding 40% of the overall P during the growing season. Whatever the variation in the monthly P, statistics showed that the relationship between the accumulative P and ET could be expressed as an equation, ET=0.8003 P+5.8914, with a correlation coefficient of R-2=0.9035. Results suggest that in areas similar to Shapotou it is practical to establish an artificial protection belt using xerophytic shrubs.
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| 46. |
- Yang, Y, et al.
(författare)
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Abnormal posterior semicircular canal function may predict poor prognosis in patients with severe and profound ISSNHL
- 2023
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Ingår i: Frontiers in neurology. - : Frontiers Media SA. - 1664-2295. ; 14, s. 1123165-
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Tidskriftsartikel (refereegranskat)abstract
- Severe and profound idiopathic sudden sensorineural hearing loss (ISSNHL) generally leads to unfavorable prognosis, and has a considerable impact on patient quality of life. However, related prognostic factors remain controversial.ObjectiveTo elaborate the relationship between vestibular function impairment and the prognosis of patients with severe and profound ISSNHL, and investigated the relevant factors affecting prognosis.MethodsForty-nine patients with severe and profound ISSNHL were divided into good outcome group [GO group, pure tone average (PTA) improvement > 30 dB] and poor outcome group (PO group, PTA improvement ≤ 30 dB) according to hearing outcomes. The clinical characteristics and the proportion of abnormal vestibular function tests in these two groups were analyzed by univariate analysis, and multivariable logistic regression analysis was performed for parameters with significant differences.ResultsForty-six patients had abnormal vestibular function test results (46/49, 93.88%). The number of vestibular organ injuries was 1.82 ± 1.29 in all patients, with higher mean numbers in PO group (2.22 ± 1.37) than in GO group (1.32 ± 0.99). Univariate analysis revealed no statistical differences between the GO and PO groups in terms of gender, age, side of the affected ear, vestibular symptoms, delayed treatment, instantaneous gain value of horizontal semicircular canal, regression gain value of vertical semicircular canal, abnormal rates of oVEMP, cVEMP, caloric test and vHIT in anterior and horizontal semicircular canal, however, significant differences were found in the initial hearing loss and abnormal vHIT of posterior semicircular canal (PSC). Multivariable analysis revealed that only PSC injury was an independent risk factor for predicting the prognosis of patients with severe and profound ISSNHL. Patients with abnormal PSC function had worse initial hearing impairment and prognosis than patients with normal PSC function. The sensitivity of abnormal PSC function in predicting poor prognosis in patients with severe and profound ISSNHL was 66.67%, specificity was 95.45%, and positive and negative likelihood ratios were 14.65 and 0.35, respectively.ConclusionAbnormal PSC function is an independent risk factor for poor prognosis in patients with severe and profound ISSNHL. Ischemia in the branches of the internal auditory artery supplying the cochlea and PSC may be the underlying mechanism.
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