| 1. |
- Birney, Ewan, et al.
(författare)
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Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
- 2007
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 447:7146, s. 799-816
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Tidskriftsartikel (refereegranskat)abstract
- We report the generation and analysis of functional data from multiple, diverse experiments performed on a targeted 1% of the human genome as part of the pilot phase of the ENCODE Project. These data have been further integrated and augmented by a number of evolutionary and computational analyses. Together, our results advance the collective knowledge about human genome function in several major areas. First, our studies provide convincing evidence that the genome is pervasively transcribed, such that the majority of its bases can be found in primary transcripts, including non-protein-coding transcripts, and those that extensively overlap one another. Second, systematic examination of transcriptional regulation has yielded new understanding about transcription start sites, including their relationship to specific regulatory sequences and features of chromatin accessibility and histone modification. Third, a more sophisticated view of chromatin structure has emerged, including its inter-relationship with DNA replication and transcriptional regulation. Finally, integration of these new sources of information, in particular with respect to mammalian evolution based on inter- and intra-species sequence comparisons, has yielded new mechanistic and evolutionary insights concerning the functional landscape of the human genome. Together, these studies are defining a path for pursuit of a more comprehensive characterization of human genome function.
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| 2. |
- Kristan, Matej, et al.
(författare)
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The Visual Object Tracking VOT2013 challenge results
- 2013
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Ingår i: 2013 IEEE INTERNATIONAL CONFERENCE ON COMPUTER VISION WORKSHOPS (ICCVW). - : IEEE. - 9781479930227 ; , s. 98-111
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Konferensbidrag (refereegranskat)abstract
- Visual tracking has attracted a significant attention in the last few decades. The recent surge in the number of publications on tracking-related problems have made it almost impossible to follow the developments in the field. One of the reasons is that there is a lack of commonly accepted annotated data-sets and standardized evaluation protocols that would allow objective comparison of different tracking methods. To address this issue, the Visual Object Tracking (VOT) workshop was organized in conjunction with ICCV2013. Researchers from academia as well as industry were invited to participate in the first VOT2013 challenge which aimed at single-object visual trackers that do not apply pre-learned models of object appearance (model-free). Presented here is the VOT2013 benchmark dataset for evaluation of single-object visual trackers as well as the results obtained by the trackers competing in the challenge. In contrast to related attempts in tracker benchmarking, the dataset is labeled per-frame by visual attributes that indicate occlusion, illumination change, motion change, size change and camera motion, offering a more systematic comparison of the trackers. Furthermore, we have designed an automated system for performing and evaluating the experiments. We present the evaluation protocol of the VOT2013 challenge and the results of a comparison of 27 trackers on the benchmark dataset. The dataset, the evaluation tools and the tracker rankings are publicly available from the challenge website(1).
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| 3. |
- Lensink, Marc F., et al.
(författare)
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Impact of AlphaFold on structure prediction of protein complexes: The CASP15-CAPRI experiment
- 2023
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Ingår i: Proteins. - : WILEY. - 0887-3585 .- 1097-0134.
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Tidskriftsartikel (refereegranskat)abstract
- We present the results for CAPRI Round 54, the 5th joint CASP-CAPRI protein assembly prediction challenge. The Round offered 37 targets, including 14 homodimers, 3 homo-trimers, 13 heterodimers including 3 antibody-antigen complexes, and 7 large assemblies. On average similar to 70 CASP and CAPRI predictor groups, including more than 20 automatics servers, submitted models for each target. A total of 21 941 models submitted by these groups and by 15 CAPRI scorer groups were evaluated using the CAPRI model quality measures and the DockQ score consolidating these measures. The prediction performance was quantified by a weighted score based on the number of models of acceptable quality or higher submitted by each group among their five best models. Results show substantial progress achieved across a significant fraction of the 60+ participating groups. High-quality models were produced for about 40% of the targets compared to 8% two years earlier. This remarkable improvement is due to the wide use of the AlphaFold2 and AlphaFold2-Multimer software and the confidence metrics they provide. Notably, expanded sampling of candidate solutions by manipulating these deep learning inference engines, enriching multiple sequence alignments, or integration of advanced modeling tools, enabled top performing groups to exceed the performance of a standard AlphaFold2-Multimer version used as a yard stick. This notwithstanding, performance remained poor for complexes with antibodies and nanobodies, where evolutionary relationships between the binding partners are lacking, and for complexes featuring conformational flexibility, clearly indicating that the prediction of protein complexes remains a challenging problem.
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| 4. |
- Wang, Y., et al.
(författare)
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The Impact of Different Degrees of Intraventricular Hemorrhage on Mortality and Neurological Outcomes in Very Preterm Infants: A Prospective Cohort Study
- 2022
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Ingår i: Frontiers in Neurology. - : Frontiers Media SA. - 1664-2295. ; 13
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Tidskriftsartikel (refereegranskat)abstract
- ObjectiveIntraventricular hemorrhage (IVH) is a common complication in preterm infants and is related to neurodevelopmental outcomes. Infants with severe IVH are at higher risk of adverse neurological outcomes and death, but the effect of low-grade IVH remains controversial. The purpose of this study was to evaluate the impact of different degrees of IVH on mortality and neurodevelopmental outcomes in very preterm infants. MethodsPreterm infants with a gestational age of ResultsA total of 1,079 preterm infants were included, and 380 (35.2%) infants had grade I-II IVH, 74 (6.9%) infants had grade III-IV IVH, and 625 (57.9%) infants did not have IVH. The mortality in the non-IVH, I-II IVH, and III-IV IVH groups was 20.1, 19.7, and 55.2%, respectively (p < 0.05), and the incidence of neurodevelopmental disabilities was 13.9, 16.1, and 43.3%, respectively (p < 0.05), at 18-24 months of corrected age. After adjusting for confounding factors, preterm infants with III-IV IVH had higher rates of cerebral palsy [26.7 vs. 2.4%, OR = 6.10, 95% CI (1.840-20.231), p = 0.003], disability [43.3 vs. 13.9%, OR = 2.49, 95% CI (1.059-5.873), p = 0.037], death [55.2 vs. 20.1%, OR = 3.84, 95% CI (2.090-7.067), p < 0.001], and disability + death [73.7 vs. 28.7%, OR = 4.77, 95% CI (2.518-9.021), p < 0.001] compared to those without IVH. However, the mortality and the incidence of neurodevelopmental disability in infants with I-II IVH were similar to those without IVH (p > 0.05). ConclusionsSevere IVH but not mild IVH increased the risk of mortality and neurodevelopmental disability in very preterm infants.
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| 5. |
- Jin, Binghan, et al.
(författare)
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Abdominal Adiposity and Total Body Fat as Predictors of Cardiometabolic Health in Children and Adolescents With Obesity
- 2020
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Ingår i: Frontiers in Endocrinology. - : FRONTIERS MEDIA SA. - 1664-2392. ; 11
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Tidskriftsartikel (refereegranskat)abstract
- Objective:We aimed to assess the role of adipose tissue distribution in cardiometabolic risk (in particular insulin sensitivity) in a population of children and adolescents with obesity. Methods:In this cross-sectional study, participants were 479 children and adolescents with obesity (322 boys and 157 girls) aged 3 to 18 years attending the Children's Hospital at Zhejiang University School of Medicine (Hangzhou, China). Clinical assessments included anthropometry, body composition (DXA scans), carotid artery ultrasounds, and OGTT. Insulin sensitivity was assessed using the Matsuda index. Participants were stratified into groups by sex and pubertal stage. Key predictors were DXA-derived android-to-gynoid-fat ratio (A/G) and total body fat percentage (TBF%). Results:Irrespective of sex and pubertal stage, there was a strong association between increasing A/G (i.e., greater abdominal adiposity) and lower insulin sensitivity. In multivariable models, every 0.1 increase in A/G was associated with a reduction in insulin sensitivity in prepubertal boys [-29% (95% CI -36%, -20%);p< 0.0001], pubertal boys [-13% (95% CI -21%, -6%);p= 0.001], and pubertal girls [-16% (95% CI -24%, -6%);p= 0.002]. In contrast, TBF% was not associated with insulin sensitivity when A/G was adjusted for, irrespective of pubertal stage or sex. In addition, every 0.1 increase in A/G was associated with increased likelihood of dyslipidemia in prepubertal boys [adjusted odds ratio (aOR) 1.62 (95% CI 1.05, 2.49)], impaired glucose tolerance in pubertal boys [aOR 1.64 (95% CI 1.07, 2.51)] and pubertal girls [aOR 1.81 (95% CI 1.10, 2.98)], and odds of NAFLD in both prepubertal [aOR 2.57 (95% CI 1.56, 4.21)] and pubertal [aOR 1.69 (95% CI 1.18, 2.40)] boys. In contrast, higher TBF% was only associated with higher fasting insulin and ALT in pubertal boys, being also predictive of NAFLD in this group [aOR 1.15 per percentage point (95% CI 1.06, 1.26)], but was not associated with the likelihood of other cardiometabolic outcomes assessed in any group. Conclusions:A/G is a much stronger independent predictor of cardiometabolic risk factors in children and adolescents with obesity in China, particularly glucose metabolism.
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| 6. |
- Liu, Xiaoqin, et al.
(författare)
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Mapping of Nonhomologous End Joining-Mediated Integration Facilitates Genome-Scale Trackable Mutagenesis in Yarrowia lipolytica
- 2022
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Ingår i: ACS Synthetic Biology. - : American Chemical Society (ACS). - 2161-5063. ; 11:1, s. 216-227
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Tidskriftsartikel (refereegranskat)abstract
- Genome-scale mutagenesis, phenotypic screening, and tracking the causal mutations is a powerful approach for genetic analysis. However, classic mutagenesis approaches require extensive effort to identify causal mutations. It is desirable to demonstrate a powerful approach for rapid trackable mutagenesis. Here, we mapped the distribution of nonhomologous end joining (NHEJ)-mediated integration for the first time and demonstrated that it can be used for constructing the genome-scale trackable mutagenesis library in Yarrowia lipolytica. The sequencing of 9.15 x 10(5) insertions showed that NHEJ-mediated integration inserted DNA randomly across the chromosomes, and the transcriptional regulatory regions exhibited integration preference. The insertions were located in both nucleosome-occupancy regions and nucleosome-free regions. Using NHEJ-mediated integration to construct the genome-scale mutagenesis library, the new targets that improved beta-carotene biosynthesis and acetic acid tolerance were identified rapidly. This mutagenesis approach is readily applicable to other organisms with strong NHEJ preference and will contribute to cell factory construction.
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| 7. |
- Ma, Tan, et al.
(författare)
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Effects of In Utero Exposure to Di-n-Butyl Phthalate on Testicular Development in Rat
- 2017
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Ingår i: International Journal of Environmental Research and Public Health. - : MDPI AG. - 1661-7827 .- 1660-4601. ; 14:10
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Tidskriftsartikel (refereegranskat)abstract
- Humans are inevitably exposed to ubiquitous phthalate esters (PAEs). In utero exposure to di-n-butyl phthalate (DBP) induces abnormal development of the testis and reproductive tract in male offspring, which correspond closely with the human condition of testicular dysgenesis syndrome (TDS)-like syndrome. However, the underlying mechanisms have not been elucidated in detail. In this study, pregnant rats were orally exposed to either corn oil (controls) or DBP at three different doses by gavage during Gestational Days 12.5-21.5. Pathological examinations were performed for toxicity evaluation. Proliferation and apoptosis related proteins (ras related dexamethasone induced 1 (Rasd1), mitogen-activated protein kinase kinases1/2 (MEK1/2), Bcl-2, and Bax) were measured for mechanisms exploration. The results showed that different doses of DBP caused male developmental and reproductive toxicity in rats, including the decrease of anogenital distance (AGD), the histological damage of testis, and apoptosis of seminiferous tubule cells. Our data suggested that DBP played chronic and continuous toxic roles on male reproductive system by disrupting expression of Rasd1 and MEK1/2 as well as Bcl-2/Bax ratio. Further research is warranted.
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| 8. |
- Wang, Hao, et al.
(författare)
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In-situ growth of low-dimensional perovskite-based insular nanocrystals for highly efficient light emitting diodes
- 2023
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Ingår i: Light. - : SPRINGERNATURE. - 2095-5545 .- 2047-7538. ; 12:1
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Tidskriftsartikel (refereegranskat)abstract
- Regulation of perovskite growth plays a critical role in the development of high-performance optoelectronic devices. However, judicious control of the grain growth for perovskite light emitting diodes is elusive due to its multiple requirements in terms of morphology, composition, and defect. Herein, we demonstrate a supramolecular dynamic coordination strategy to regulate perovskite crystallization. The combined use of crown ether and sodium trifluoroacetate can coordinate with A site and B site cations in ABX(3) perovskite, respectively. The formation of supramolecular structure retard perovskite nucleation, while the transformation of supramolecular intermediate structure enables the release of components for slow perovskite growth. This judicious control enables a segmented growth, inducing the growth of insular nanocrystal consist of low-dimensional structure. Light emitting diode based on this perovskite film eventually brings a peak external quantum efficiency up to 23.9%, ranking among the highest efficiency achieved. The homogeneous nano-island structure also enables high-efficiency large area (1 cm(2)) device up to 21.6%, and a record high value of 13.6% for highly semi-transparent ones.
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| 9. |
- Yin, Xiaoqin, et al.
(författare)
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MiR-301b-3p/3584-5p enhances low-dose mono-n-butyl phthalate (MBP) induced proliferation by targeting Rasd1 in Sertoli cells
- 2018
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Ingår i: Toxicology in Vitro. - : PERGAMON-ELSEVIER SCIENCE LTD. - 0887-2333 .- 1879-3177. ; 47, s. 79-88
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Tidskriftsartikel (refereegranskat)abstract
- To investigate the possible molecular mechanism of low concentration plasticizer mono-n-butyl phthalate (MBP)-induced juvenile Sertoli cells (SCs) proliferation, we evaluated global alterations of miRNA and mRNA expression in rat SCs treated with 0.1 mM MBP. Microarray analysis revealed that miR-3584-5p and miR-301b-3p were up-regulated and their common target gene Dexamethasone-induced Ras-related protein 1 (Rasd1) was down-regulated. Further work suggested that SCs proliferation induced by low concentration MBP in vitro might be mediated by Rasd1 regulating ERK1/2 signaling pathway. The present study is first to investigate the effect of low-dose MBP on SCs proliferation and may enhance our understanding on the modes of action of low concentration MBP on male reproductive system. We hope the results will contribute to explain the causes of precocious puberty and testicular tumors induced by exogenous chemicals.
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| 10. |
- Zhou, Yongqiang, et al.
(författare)
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Rainstorms drive export of aromatic and concurrent bio-labile organic matter to a large eutrophic lake and its major tributaries
- 2023
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Ingår i: Water Research. - : Elsevier. - 0043-1354 .- 1879-2448. ; 229
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Tidskriftsartikel (refereegranskat)abstract
- Lakes are hotspots for global carbon cycling, yet few studies have explored how rainstorms alter the flux, composition, and bio-lability of dissolved organic matter (DOM) in inflowing rivers using high-frequency monitoring. We conducted extensive campaigns in the watershed of Lake Taihu and made daily observations for three years in its two largest inflowing tributaries, River Dapu and River Yincun. We found higher DOC, bio-labile DOC (BDOC), and specific UV absorbance (SUVA(254)) levels in the northwestern inflowing regions compared with the remaining lake regions. DOC and BDOC increased during rainstorms in River Dapu, and DOC declined due to local dilution and BDOC increased during rainstorms in River Yincun. We found that rainstorms resulted in increased DOM absorbance a(350), SUVA(254), and humification index (HIX) and enhanced percentages of humic-like fluorescent components, %polycyclic condensed aromatic and %polyphenolic compounds as revealed from ultrahigh-resolution mass spectrometry (FT-ICR MS), while spectral slope (S275-295) and the percentages of protein-like C1 and C3 declined during rainstorms compared with other seasons. This can be explained by a combined flushing of catchment soil organic matter and household effluents. The annual inflows of DOC and BDOC to Lake Taihu were 1.15 +/- 0.18 x 10(4) t C yr(-1) and 0.23 +/- 0.06 x 104 t C yr(-1) from River Dapu and 2.92 +/- 0.42 x 103 t C yr(-1) and 0.53 +/- 0.07 x 10(3) t C yr(-1) from River Yincun, respectively, and the fluxes of DOC and BDOC from both rivers increased during rainstorms. We found an elevated frequency of heavy rainfall and rainstorms in the lake watershed during the past six decades. We conclude that an elevated input of terrestrial organic-rich DOM with concurrent high aromaticity and high bio-lability from inflowing rivers is likely to occur in a future wetter climate.
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