| 1. |
- Ablikim, M., et al.
(författare)
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Measurements of (XcJ)-> K+K-K+K- decays
- 2006
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Ingår i: Physics Letters B. - : Elsevier BV. - 0370-2693 .- 1873-2445. ; 642:3, s. 197-202
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Tidskriftsartikel (refereegranskat)abstract
- Using 14M psi(2S) events taken with the BESII detector, chi(cJ) -> 2(K+K-) decays are studied. For the four-kaon final state, the branching fractions are B(chi(c0,1,2) ->.2(K+K-)) = (3.48 +/- 0.23 +/- 0.47) x 10(-3), (0.70 +/- 0.13 +/- 0.10) x 10(-3), and (2.17 +/- 0.20 +/- 0.31) x 10(-3). For the phi K+K- final state, the branching fractions, which are measured for the first time, are B(chi(c0,1,2) -> phi K+K-) = (1.03 +/- 0.22 +/- 0.15) x 10(-3), (0.46 +/- 0.16 +/- 0.06) x 10(-3), and (1.67 +/- 0.26 +/- 0.24) x 10(-4). For the phi phi final state, B(chi(c0,2) -> phi phi) = (0.94 +/- 0.21 +/- 0.13) x 10(-3) and (1.70 +/- 0.30 +/- 0.25) x 10(-3).
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| 2. |
- 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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| 3. |
- Wang, Y., et al.
(författare)
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Erythropoietin prevents necrotizing enterocolitis in very preterm infants: a randomized controlled trial
- 2020
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Ingår i: Journal of Translational Medicine. - : Springer Science and Business Media LLC. - 1479-5876. ; 18:1
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Tidskriftsartikel (refereegranskat)abstract
- Background: Necrotizing enterocolitis (NEC) is one of the most severe complications in very preterm infants, but there are currently no accepted methods to prevent NEC. Studies have shown that erythropoietin (EPO) has the potential to prevent NEC or improve outcomes of preterm NEC. This study aimed to determine whether recombinant human EPO (rhEPO) could protect against NEC in very preterm infants. Methods: The study was a prospective randomized clinical trial performed among four NICU centers. A total of 1327 preterm infants with gestational age <= 32 weeks were admitted to the centers, and 42 infants were excluded leaving 1285 eligible infants to be randomized to the rhEPO or control group. Infants in the rhEPO group were given 500 IU/kg rhEPO intravenously every other day for 2 weeks, while the control group was given the same volume of saline. The primary outcome was the incidence of NEC in very preterm infants at 36 weeks of corrected gestational age. Results: A total of 1285 infants were analyzed at 36 weeks of corrected age for the incidence of NEC. rhEPO treatment significantly decreased the incidence of NEC (stage I, II and III) (12.0% vs. 17.1%, p = 0.010), especially confirmed NEC (stage II and III) (3.0% vs. 5.4%, p = 0.027). Meanwhile, rhEPO treatment significantly reduced the number of red blood cells transfusion in the confirmed NEC cases (1.2 +/- 0.4 vs. 2.7 +/- 1.0, p = 0.004). Subgroup analyses showed that rhEPO treatment significantly decreased the incidence of confirmed NEC at gestational age < 28 weeks (p = 0.019), and the incidence of all stages NEC in preterm infants with hemoglobin < 90 g/l (p = 0.000) and 5 min Apgar score > 5 (p = 0.028). Conclusion: Repeated low-dose rhEPO treatment is beneficial against NEC in very preterm infants.
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| 4. |
- Yang, X. M., et al.
(författare)
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Overexpression of Rac GTPase Activating Protein 1 Contributes to Proliferation of Cancer Cells by Reducing Hippo Signaling to Promote Cytokinesis
- 2018
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Ingår i: Gastroenterology. - : Elsevier BV. - 0016-5085. ; 155:4
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND & AIMS: Agents designed to block or alter cytokinesis can kill or stop proliferation of cancer cells. We aimed to identify cytokinesis-related proteins that are overexpressed in hepatocellular carcinoma (HCC) cells and might be targeted to slow liver tumor growth. METHODS: Using the Oncomine database, we compared the gene expression patterns in 16 cancer microarray datasets and assessed gene enrichment sets using gene ontology. We performed immunohistochemical analysis of an HCC tissue microarray and identified changes in protein levels that are associated with patient survival times. Candidate genes were overexpressed or knocked down with small hairpin RNAs in SMMC7721, MHCC97H, or HCCLM3 cell lines; we analyzed their proliferation, viability, and clone-formation ability and their growth as subcutaneous or orthotopic xenograft tumors in mice. We performed microarray analyses to identify alterations in signaling pathways and immunoblot and immunofluorescence assays to detect and localize proteins in tissues. Yeast 2-hybrid screens and mass spectrometry combined with co-immunoprecipitation experiments were used to identify binding proteins. Protein interactions were validated with co-immunoprecipitation and proximity ligation assays. Chromatin immunoprecipitation, promoter luciferase activity, and quantitative real-time polymerase chain reaction analyses were used to identify factors that regulate transcription of specific genes. RESULTS: The genes that were most frequently overexpressed in different types of cancer cells were involved in cell division processes. We identified 3 cytokinesis-regulatory proteins among the 10 genes most frequently overexpressed by all cancer cell types. Rac GTPase activating protein 1 (RACGAP1) was the cytokinesis-regulatory protein that was most highly overexpressed in multiple cancers. Increased expression of RACGAP1 in tumor tissues was associated with shorter survival times of patients with cancer. Knockdown of RACGAP1 in HCC cells induced cytokinesis failure and cell apoptosis. In microarray analyses, we found knockdown of RACGAP1 in SMMC7721 cells to reduce expression of genes regulated by yes-associated protein (YAP) and WW domain containing transcription regulator 1 (WWTR1 or TAZ). RACGAP1 reduced activation of the Hippo pathway in HCC cells by increasing activity of RhoA and polymerization of filamentous actin. Knockdown of YAP reduced phosphorylation of RACGAP1 and redistribution at the anaphase central spindle. We found transcription of the translocated promoter region, nuclear basket protein (TPR) to be regulated by YAP and coordinately expressed with RACGAP1 to promote proliferation of HCC cells. TPR redistributed upon nuclear envelope breakdown and formed complexes with RACGAP1 during mitosis. Knockdown of TPR in HCC cells reduced phosphorylation of RACGAP1 by aurora kinase B and impaired their redistribution at the central spindle during cytokinesis. STAT3 activated transcription of RACGAP in HCC cells. CONCLUSIONS: In an analysis of gene expression patterns of multiple tumor types, we found RACGAP1 to be frequently overexpressed, which is associated with shorter survival times of patients. RACGAP1 promotes proliferation of HCC cells by reducing activation of the Hippo and YAP pathways and promoting cytokinesis in coordination with TPR.
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| 5. |
- Mishra, A, et al.
(författare)
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Diminishing benefits of urban living for children and adolescents' growth and development
- 2023
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 1476-4687 .- 0028-0836. ; 615:7954, s. 874-883
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Tidskriftsartikel (refereegranskat)abstract
- Optimal growth and development in childhood and adolescence is crucial for lifelong health and well-being1–6. Here we used data from 2,325 population-based studies, with measurements of height and weight from 71 million participants, to report the height and body-mass index (BMI) of children and adolescents aged 5–19 years on the basis of rural and urban place of residence in 200 countries and territories from 1990 to 2020. In 1990, children and adolescents residing in cities were taller than their rural counterparts in all but a few high-income countries. By 2020, the urban height advantage became smaller in most countries, and in many high-income western countries it reversed into a small urban-based disadvantage. The exception was for boys in most countries in sub-Saharan Africa and in some countries in Oceania, south Asia and the region of central Asia, Middle East and north Africa. In these countries, successive cohorts of boys from rural places either did not gain height or possibly became shorter, and hence fell further behind their urban peers. The difference between the age-standardized mean BMI of children in urban and rural areas was <1.1 kg m–2 in the vast majority of countries. Within this small range, BMI increased slightly more in cities than in rural areas, except in south Asia, sub-Saharan Africa and some countries in central and eastern Europe. Our results show that in much of the world, the growth and developmental advantages of living in cities have diminished in the twenty-first century, whereas in much of sub-Saharan Africa they have amplified.
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| 6. |
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| 7. |
- Albrechtsen, A., et al.
(författare)
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Exome sequencing-driven discovery of coding polymorphisms associated with common metabolic phenotypes
- 2013
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Ingår i: Diabetologia. - : Springer Science and Business Media LLC. - 0012-186X .- 1432-0428. ; 56:2, s. 298-310
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Tidskriftsartikel (refereegranskat)abstract
- Human complex metabolic traits are in part regulated by genetic determinants. Here we applied exome sequencing to identify novel associations of coding polymorphisms at minor allele frequencies (MAFs) > 1% with common metabolic phenotypes. The study comprised three stages. We performed medium-depth (8x) whole exome sequencing in 1,000 cases with type 2 diabetes, BMI > 27.5 kg/m(2) and hypertension and in 1,000 controls (stage 1). We selected 16,192 polymorphisms nominally associated (p < 0.05) with case-control status, from four selected annotation categories or from loci reported to associate with metabolic traits. These variants were genotyped in 15,989 Danes to search for association with 12 metabolic phenotypes (stage 2). In stage 3, polymorphisms showing potential associations were genotyped in a further 63,896 Europeans. Exome sequencing identified 70,182 polymorphisms with MAF > 1%. In stage 2 we identified 51 potential associations with one or more of eight metabolic phenotypes covered by 45 unique polymorphisms. In meta-analyses of stage 2 and stage 3 results, we demonstrated robust associations for coding polymorphisms in CD300LG (fasting HDL-cholesterol: MAF 3.5%, p = 8.5 x 10(-14)), COBLL1 (type 2 diabetes: MAF 12.5%, OR 0.88, p = 1.2 x 10(-11)) and MACF1 (type 2 diabetes: MAF 23.4%, OR 1.10, p = 8.2 x 10(-10)). We applied exome sequencing as a basis for finding genetic determinants of metabolic traits and show the existence of low-frequency and common coding polymorphisms with impact on common metabolic traits. Based on our study, coding polymorphisms with MAF above 1% do not seem to have particularly high effect sizes on the measured metabolic traits.
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| 8. |
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| 9. |
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| 10. |
- Wang, X. F., et al.
(författare)
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Size distributions of aerosol sulfates and nitrates in Beijing during the 2008 Olympic Games: Impacts of pollution control measures and regional transport
- 2013
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Ingår i: Advances in Atmospheric Sciences. - : Springer Science and Business Media LLC. - 0256-1530 .- 1861-9533. ; 30:2, s. 341-353
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Tidskriftsartikel (refereegranskat)abstract
- For the 2008 Olympic Games, drastic control measures were implemented on industrial and urban emissions of sulfur dioxide (SO2), nitrogen oxides (NO (x) ) and other pollutants to address the issues of poor air quality in Beijing. To investigate the effects of SO2 and NO (x) reductions on the particulate sulfate and nitrate concentrations as well as their size distributions, size-segregated aerosol samples were collected using micro-orifice uniform deposit impactors (MOUDIs) at urban and downwind rural sites in Beijing before and after full-scale controls. During the sampling period, the mass concentrations of fine particles (PM1.8) at the urban and rural sites were 94.0 and 85.9 mu g m(-3), respectively. More than 90% of the sulfates and similar to 60% of nitrates formed as fine particles. Benefiting from the advantageous meteorological conditions and the source controls, sulfates were observed in rather low concentrations and primarily in condensation mode during the Olympics. The effects of the control measures were separately analyzed for the northerly and the southerly air-mass-dominated days to account for any bias. After the control measures were implemented, PM, sulfates, and nitrates were significantly reduced when the northerly air masses prevailed, with a higher percentage of reduction in larger particles. The droplet mode particles, which dominated the sulfates and nitrates before the controls were implemented, were remarkably reduced in mass concentration after the control measures were implemented. Nevertheless, when the polluted southerly air masses prevailed, the local source control measures in Beijing did not effectively reduce the ambient sulfate concentration due to the enormous regional contribution from the North China Plain.
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| 11. |
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- 2019
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Tidskriftsartikel (refereegranskat)
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| 12. |
- Chen, H., et al.
(författare)
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Unprecedented non-hysteretic superelasticity of [001]-oriented NiCoFeGa single crystals
- 2020
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Ingår i: Nature Materials. - : Nature Research. - 1476-1122 .- 1476-4660.
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Tidskriftsartikel (refereegranskat)abstract
- Superelasticity associated with the martensitic transformation has found a broad range of engineering applications1,2. However, the intrinsic hysteresis3 and temperature sensitivity4 of the first-order phase transformation significantly hinder the usage of smart metallic components in many critical areas. Here, we report a large superelasticity up to 15.2% strain in [001]-oriented NiCoFeGa single crystals, exhibiting non-hysteretic mechanical responses, a small temperature dependence and high-energy-storage capability and cyclic stability over a wide temperature and composition range. In situ synchrotron X-ray diffraction measurements show that the superelasticity is correlated with a stress-induced continuous variation of lattice parameter accompanied by structural fluctuation. Neutron diffraction and electron microscopy observations reveal an unprecedented microstructure consisting of atomic-level entanglement of ordered and disordered crystal structures, which can be manipulated to tune the superelasticity. The discovery of the large elasticity related to the entangled structure paves the way for exploiting elastic strain engineering and development of related functional materials.
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| 13. |
- Klionsky, Daniel J., et al.
(författare)
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Guidelines for the use and interpretation of assays for monitoring autophagy
- 2012
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Ingår i: Autophagy. - : Informa UK Limited. - 1554-8635 .- 1554-8627. ; 8:4, s. 445-544
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Forskningsöversikt (refereegranskat)abstract
- In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field.
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| 14. |
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| 15. |
- Zheng, H. G., et al.
(författare)
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Rosuvastatin Slows Progression of Carotic Intima-Media Thickness: The METEOR-China Randomized Controlled Study
- 2022
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Ingår i: Stroke. - : Ovid Technologies (Wolters Kluwer Health). - 0039-2499 .- 1524-4628. ; 53:10, s. 3004-3013
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND:Atherosclerosis is the leading cause of cardiovascular disease worldwide, including in China Primary prevention, through lipid-lowering, could avert development of atherosclerosis. Carotid intima-media thickness (CIMT) is a well-validated measure of atherosclerosis used in intervention studies as the primary outcome and alternative end point for cardiovascular disease events. METHODS: This randomized, double-blind, placebo-controlled, multicenter, parallel-group study assessed the effects of rosuvastatin 20 mg/d compared with placebo on progression of CIMT over 104 weeks in Chinese people with subclinical atherosclerosis. The primary end point was the annualized rate of change in mean of the maximum CIMT measurements taken 7x over the study period from each of 12 carotid artery sites (near and far walls of the right and left common carotid artery, carotid bulb, and internal carotid artery). Secondary end points included CIMT changes at different artery sites and lipid-parameter changes. Safety was also assessed. RESULTS: Participants were randomized (1:1) to receive rosuvastatin (n=272) or placebo (n=271). Baseline characteristics were well balanced between groups. The change in mean of the maximum CIMT of the 12 carotid sites was 0.0038 mm/y (95% CI, -0.0023-0.0100) for the rosuvastatin group versus 0.0142 mm/y (95% CI, 0.0080-0.0204) for the placebo group, with a difference of -0.0103 mm/y (95% CI, -0.0191 to -0.0016; P=0.020). For the CIMT secondary end points, the results were generally consistent with the primary end point. There were clinically relevant improvements in lipid parameters with rosuvastatin. We observed an adverse-event profile consistent with the known safety profile of rosuvastatin. CONCLUSIONS: Rosuvastatin 20 mg/d significantly reduced the progression of CIMT over 2 years in Chinese adults with subclinical atherosclerosis and was well tolerated.
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| 16. |
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| 17. |
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| 18. |
- Burr, S. P., et al.
(författare)
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Cell lineage-specific mitochondrial resilience during mammalian organogenesis
- 2023
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Ingår i: Cell. - : Elsevier BV. - 0092-8674. ; 186:6
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Tidskriftsartikel (refereegranskat)abstract
- Mitochondrial activity differs markedly between organs, but it is not known how and when this arises. Here we show that cell lineage-specific expression profiles involving essential mitochondrial genes emerge at an early stage in mouse development, including tissue-specific isoforms present before organ formation. However, the nuclear transcriptional signatures were not independent of organelle function. Genetically disrupting intra-mitochondrial protein synthesis with two different mtDNA mutations induced cell lineage-specific compensatory responses, including molecular pathways not previously implicated in organellar maintenance. We saw downregulation of genes whose expression is known to exacerbate the effects of exogenous mito-chondrial toxins, indicating a transcriptional adaptation to mitochondrial dysfunction during embryonic devel-opment. The compensatory pathways were both tissue and mutation specific and under the control of tran-scription factors which promote organelle resilience. These are likely to contribute to the tissue specificity which characterizes human mitochondrial diseases and are potential targets for organ-directed treatments.
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| 19. |
- Cao, S., et al.
(författare)
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3D Porous Pyramid Heterostructure Array Realizing Efficient Photo-Electrochemical Performance
- 2019
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Ingår i: Advanced Energy Materials. - : Wiley-VCH Verlag. - 1614-6832 .- 1614-6840.
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Tidskriftsartikel (refereegranskat)abstract
- Direct photo-electrochemical (PEC) water splitting is of great practical interest for developing a sustainable energy systems, but remains a big challenge owing to sluggish charge separation, low efficiency, and poor stability. Herein, a 3D porous In2O3/In2S3 pyramid heterostructure array on a fluorine-doped tin oxide substrate is fabricated by an ion exchange–induced synthesis strategy. Based on the synergistic structural and electronic modulations from density functional theory calculations and experimental observations, 3D porous In2O3/In2S3 photoanode by the protective layer delivers a low onset potential of ≈0.02 V versus reversible hydrogen electrode (RHE), the highest photocurrent density of 8.2 mA cm−2 at 1.23 V versus RHE among all the In2S3 photoanodes reported to date, an incident photon-to-current efficiency of 76% at 400 nm, and high stability over 20 h for PEC water splitting are reported. This work provides an alternative promising prototype for the design and construction of novel heterostructures in robust PEC water splitting applications.
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| 20. |
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| 21. |
- Gu, Y, et al.
(författare)
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Quick Hot Shot & Young Surgeon Presentation
- 2015
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Ingår i: Hernia : the journal of hernias and abdominal wall surgery. - 1248-9204. ; 19 Suppl 1, s. S77-84
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Tidskriftsartikel (refereegranskat)
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| 22. |
- Jia, N, et al.
(författare)
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Formation of Deformation Textures in Face-Centered-Cubic Materials Studied by In-Situ High-Energy X-Ray Diffraction and Self-Consistent Model
- 2010
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Ingår i: METALLURGICAL AND MATERIALS TRANSACTIONS A-PHYSICAL METALLURGY AND MATERIALS SCIENCE. - : Springer Science and Business Media LLC. - 1073-5623. ; 41A:5, s. 1246-1254
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Tidskriftsartikel (refereegranskat)abstract
- The evolution of deformation textures in copper and alpha brass that are representative of fcc metals with different stacking fault energies (SFEs) during cold rolling is predicted using a self-consistent (SC) model. The material parameters used for describing the micromechanical behavior of each metal are determined from the high-energy X-ray (HEXRD) diffraction data. At small reductions, a reliable prediction of the evolution of the grain orientation distribution that is represented as the continuous increase of the copper and brass components is achieved for both metals when compared with the experimental textures. With increasing deformation, the model could characterize the textures of copper, i.e., the strengthening of the copper component, when dislocation slip is still the dominant mechanism. For alpha brass at moderate and large reductions, a reliable prediction of its unique feature of texture evolution, i.e., the weakening of the copper component and the strengthening of the brass component, could only be achieved when proper boundary conditions together with some specified slip/twin systems are considered in the continuum micromechanics mainly containing twinning and shear banding. The present investigation suggests that for fcc metals with a low SFE, the mechanism of shear banding is the dominant contribution to the texture development at large deformations.
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| 23. |
- Jiang, X., et al.
(författare)
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An enhanced iot gateway in a broadcast system
- 2012
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Ingår i: Proceedings - IEEE 9th International Conference on Ubiquitous Intelligence and Computing and IEEE 9th International Conference on Autonomic and Trusted Computing, UIC-ATC 2012. - : IEEE. - 9780769548432 ; , s. 746-751
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Konferensbidrag (refereegranskat)abstract
- Internet of things (IOT) technology increasingly affects backbone network development. Aiming to reduce or weaken such effects on backbone networks from a traffic perspective and attain no discount on functions in a CobraNet based digital broadcast system, an enhanced IOT gateway and its evaluation system are presented. Based on the prototype evaluation system, experiments demonstrate the IOT gateway not only inherits the conventional functions previously often carried out by a PC platform or a server, but also develops additional abilities to cut down traffic under some cases and provides portable management for the system at the same time. According to the experimental results, it is possible from a traffic perspective to design an enhanced IOT gateway to provide value added service such as file transfer, message function, etc. in addition to high quality audio service by taking advantage of the verified sub-linear information addition mechanism. Such enhanced gateway can be properly adapted to other kinds of applications according to the nondemanding system requirements of the prototype evaluation system and proposed IOTGW design.
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| 24. |
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| 25. |
- Li, Y., et al.
(författare)
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VIP: an integrated pipeline for metagenomics of virus identification and discovery
- 2016
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Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 6
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Tidskriftsartikel (refereegranskat)abstract
- Identification and discovery of viruses using next-generation sequencing technology is a fast-developing area with potential wide application in clinical diagnostics, public health monitoring and novel virus discovery. However, tremendous sequence data from NGS study has posed great challenge both in accuracy and velocity for application of NGS study. Here we describe VIP ("Virus Identification Pipeline"), a one-touch computational pipeline for virus identification and discovery from metagenomic NGS data. VIP performs the following steps to achieve its goal: (i) map and filter out background-related reads, (ii) extensive classification of reads on the basis of nucleotide and remote amino acid homology, (iii) multiple k-mer based de novo assembly and phylogenetic analysis to provide evolutionary insight. We validated the feasibility and veracity of this pipeline with sequencing results of various types of clinical samples and public datasets. VIP has also contributed to timely virus diagnosis (similar to 10 min) in acutely ill patients, demonstrating its potential in the performance of unbiased NGS-based clinical studies with demand of short turnaround time. VIP is released under GPLv3 and is available for free download at: https://github.com/keylabivdc/VIP.
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