| 1. |
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| 2. |
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- 2019
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Tidskriftsartikel (refereegranskat)
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| 3. |
- Kristanl, Matej, et al.
(författare)
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The Seventh Visual Object Tracking VOT2019 Challenge Results
- 2019
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Ingår i: 2019 IEEE/CVF INTERNATIONAL CONFERENCE ON COMPUTER VISION WORKSHOPS (ICCVW). - : IEEE COMPUTER SOC. - 9781728150239 ; , s. 2206-2241
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Konferensbidrag (refereegranskat)abstract
- The Visual Object Tracking challenge VOT2019 is the seventh annual tracker benchmarking activity organized by the VOT initiative. Results of 81 trackers are presented; many are state-of-the-art trackers published at major computer vision conferences or in journals in the recent years. The evaluation included the standard VOT and other popular methodologies for short-term tracking analysis as well as the standard VOT methodology for long-term tracking analysis. The VOT2019 challenge was composed of five challenges focusing on different tracking domains: (i) VOT-ST2019 challenge focused on short-term tracking in RGB, (ii) VOT-RT2019 challenge focused on "real-time" short-term tracking in RGB, (iii) VOT-LT2019 focused on long-term tracking namely coping with target disappearance and reappearance. Two new challenges have been introduced: (iv) VOT-RGBT2019 challenge focused on short-term tracking in RGB and thermal imagery and (v) VOT-RGBD2019 challenge focused on long-term tracking in RGB and depth imagery. The VOT-ST2019, VOT-RT2019 and VOT-LT2019 datasets were refreshed while new datasets were introduced for VOT-RGBT2019 and VOT-RGBD2019. The VOT toolkit has been updated to support both standard short-term, long-term tracking and tracking with multi-channel imagery. Performance of the tested trackers typically by far exceeds standard baselines. The source code for most of the trackers is publicly available from the VOT page. The dataset, the evaluation kit and the results are publicly available at the challenge website(1).
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| 4. |
- 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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| 5. |
- Kristan, Matej, et al.
(författare)
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The Ninth Visual Object Tracking VOT2021 Challenge Results
- 2021
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Ingår i: 2021 IEEE/CVF INTERNATIONAL CONFERENCE ON COMPUTER VISION WORKSHOPS (ICCVW 2021). - : IEEE COMPUTER SOC. - 9781665401913 ; , s. 2711-2738
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Konferensbidrag (refereegranskat)abstract
- The Visual Object Tracking challenge VOT2021 is the ninth annual tracker benchmarking activity organized by the VOT initiative. Results of 71 trackers are presented; many are state-of-the-art trackers published at major computer vision conferences or in journals in recent years. The VOT2021 challenge was composed of four sub-challenges focusing on different tracking domains: (i) VOT-ST2021 challenge focused on short-term tracking in RGB, (ii) VOT-RT2021 challenge focused on "real-time" short-term tracking in RGB, (iii) VOT-LT2021 focused on long-term tracking, namely coping with target disappearance and reappearance and (iv) VOT-RGBD2021 challenge focused on long-term tracking in RGB and depth imagery. The VOT-ST2021 dataset was refreshed, while VOT-RGBD2021 introduces a training dataset and sequestered dataset for winner identification. The source code for most of the trackers, the datasets, the evaluation kit and the results along with the source code for most trackers are publicly available at the challenge website(1).
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| 6. |
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| 7. |
- Kristan, Matej, et al.
(författare)
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The Sixth Visual Object Tracking VOT2018 Challenge Results
- 2019
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Ingår i: Computer Vision – ECCV 2018 Workshops. - Cham : Springer Publishing Company. - 9783030110086 - 9783030110093 ; , s. 3-53
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Konferensbidrag (refereegranskat)abstract
- The Visual Object Tracking challenge VOT2018 is the sixth annual tracker benchmarking activity organized by the VOT initiative. Results of over eighty trackers are presented; many are state-of-the-art trackers published at major computer vision conferences or in journals in the recent years. The evaluation included the standard VOT and other popular methodologies for short-term tracking analysis and a “real-time” experiment simulating a situation where a tracker processes images as if provided by a continuously running sensor. A long-term tracking subchallenge has been introduced to the set of standard VOT sub-challenges. The new subchallenge focuses on long-term tracking properties, namely coping with target disappearance and reappearance. A new dataset has been compiled and a performance evaluation methodology that focuses on long-term tracking capabilities has been adopted. The VOT toolkit has been updated to support both standard short-term and the new long-term tracking subchallenges. Performance of the tested trackers typically by far exceeds standard baselines. The source code for most of the trackers is publicly available from the VOT page. The dataset, the evaluation kit and the results are publicly available at the challenge website (http://votchallenge.net).
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| 8. |
- Luo, Yifei, et al.
(författare)
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Technology Roadmap for Flexible Sensors
- 2023
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Ingår i: ACS Nano. - : American Chemical Society. - 1936-0851 .- 1936-086X. ; 17:6, s. 5211-5295
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Forskningsöversikt (refereegranskat)abstract
- Humans rely increasingly on sensors to address grand challenges and to improve quality of life in the era of digitalization and big data. For ubiquitous sensing, flexible sensors are developed to overcome the limitations of conventional rigid counterparts. Despite rapid advancement in bench-side research over the last decade, the market adoption of flexible sensors remains limited. To ease and to expedite their deployment, here, we identify bottlenecks hindering the maturation of flexible sensors and propose promising solutions. We first analyze challenges in achieving satisfactory sensing performance for real-world applications and then summarize issues in compatible sensor-biology interfaces, followed by brief discussions on powering and connecting sensor networks. Issues en route to commercialization and for sustainable growth of the sector are also analyzed, highlighting environmental concerns and emphasizing nontechnical issues such as business, regulatory, and ethical considerations. Additionally, we look at future intelligent flexible sensors. In proposing a comprehensive roadmap, we hope to steer research efforts towards common goals and to guide coordinated development strategies from disparate communities. Through such collaborative efforts, scientific breakthroughs can be made sooner and capitalized for the betterment of humanity.
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| 9. |
- Weinstein, John N., et al.
(författare)
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The cancer genome atlas pan-cancer analysis project
- 2013
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Ingår i: Nature Genetics. - : Springer Science and Business Media LLC. - 1061-4036 .- 1546-1718. ; 45:10, s. 1113-1120
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Forskningsöversikt (refereegranskat)abstract
- The Cancer Genome Atlas (TCGA) Research Network has profiled and analyzed large numbers of human tumors to discover molecular aberrations at the DNA, RNA, protein and epigenetic levels. The resulting rich data provide a major opportunity to develop an integrated picture of commonalities, differences and emergent themes across tumor lineages. The Pan-Cancer initiative compares the first 12 tumor types profiled by TCGA. Analysis of the molecular aberrations and their functional roles across tumor types will teach us how to extend therapies effective in one cancer type to others with a similar genomic profile. © 2013 Nature America, Inc. All rights reserved.
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| 10. |
- Jin, Ying-Hui, et al.
(författare)
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Chemoprophylaxis, diagnosis, treatments, and discharge management of COVID-19 : An evidence-based clinical practice guideline (updated version)
- 2020
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Ingår i: Military Medical Research. - : Springer Science and Business Media LLC. - 2054-9369. ; 7:1
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Tidskriftsartikel (refereegranskat)abstract
- The novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the cause of a rapidly spreading illness, coronavirus disease 2019 (COVID-19), affecting more than seventeen million people around the world. Diagnosis and treatment guidelines for clinicians caring for patients are needed. In the early stage, we have issued "A rapid advice guideline for the diagnosis and treatment of 2019 novel coronavirus (2019-nCoV) infected pneumonia (standard version)"; now there are many direct evidences emerged and may change some of previous recommendations and it is ripe for develop an evidence-based guideline. We formed a working group of clinical experts and methodologists. The steering group members proposed 29 questions that are relevant to the management of COVID-19 covering the following areas: chemoprophylaxis, diagnosis, treatments, and discharge management. We searched the literature for direct evidence on the management of COVID-19, and assessed its certainty generated recommendations using the Grading of Recommendations, Assessment, Development and Evaluation (GRADE) approach. Recommendations were either strong or weak, or in the form of ungraded consensus-based statement. Finally, we issued 34 statements. Among them, 6 were strong recommendations for, 14 were weak recommendations for, 3 were weak recommendations against and 11 were ungraded consensus-based statement. They covered topics of chemoprophylaxis (including agents and Traditional Chinese Medicine (TCM) agents), diagnosis (including clinical manifestations, reverse transcription-polymerase chain reaction (RT-PCR), respiratory tract specimens, IgM and IgG antibody tests, chest computed tomography, chest x-ray, and CT features of asymptomatic infections), treatments (including lopinavir-ritonavir, umifenovir, favipiravir, interferon, remdesivir, combination of antiviral drugs, hydroxychloroquine/chloroquine, interleukin-6 inhibitors, interleukin-1 inhibitors, glucocorticoid, qingfei paidu decoction, lianhua qingwen granules/capsules, convalescent plasma, lung transplantation, invasive or noninvasive ventilation, and extracorporeal membrane oxygenation (ECMO)), and discharge management (including discharge criteria and management plan in patients whose RT-PCR retesting shows SARS-CoV-2 positive after discharge). We also created two figures of these recommendations for the implementation purpose. We hope these recommendations can help support healthcare workers caring for COVID-19 patients.
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| 11. |
- Zhang, Huai, et al.
(författare)
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A global survey on the use of the international classification of diseases codes for metabolic dysfunction-associated fatty liver disease.
- 2024
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Ingår i: Hepatology international. - 1936-0541.
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Tidskriftsartikel (refereegranskat)abstract
- With the implementation of the 11th edition of the International Classification of Diseases (ICD-11) and the publication of the metabolic dysfunction-associated fatty liver disease (MAFLD) nomenclature in 2020, it is important to establish consensus for the coding of MAFLD in ICD-11. This will inform subsequent revisions of ICD-11.Using the Qualtrics XM and WJX platforms, questionnaires were sent online to MAFLD-ICD-11 coding collaborators, authors of papers, and relevant association members.A total of 890 international experts in various fields from 61 countries responded to the survey. We also achieved full coverage of provincial-level administrative regions in China. 77.1% of respondents agreed that MAFLD should be represented in ICD-11 by updating NAFLD, with no significant regional differences (77.3% in Asia and 76.6% in non-Asia, p=0.819). Over 80% of respondents agreed or somewhat agreed with the need to assign specific codes for progressive stages of MAFLD (i.e. steatohepatitis) (92.2%), MAFLD combined with comorbidities (84.1%), or MAFLD subtypes (i.e., lean, overweight/obese, and diabetic) (86.1%).This global survey by a collaborative panel of clinical, coding, health management and policy experts, indicates agreement that MAFLD should be coded in ICD-11. The data serves as a foundation for corresponding adjustments in the ICD-11 revision.
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| 12. |
- Zhang, Hong-Zhen, et al.
(författare)
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PINCH Protein Expression in Normal Endometrium, Atypical Endometrial Hyperplasia and Endometrioid Endometrial Carcinoma
- 2010
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Ingår i: CHEMOTHERAPY. - : S. Karger AG. - 0009-3157 .- 1421-9794. ; 56:4, s. 291-297
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Tidskriftsartikel (refereegranskat)abstract
- Background: Particularly interesting new cysteine-histidine rich protein ( PINCH), as an adapter protein of the LIM family for signal transduction in the integrin and growth factor pathway, is upregulated in the stroma of several common types of cancers and involved in promoting tumor progression. In the present study, we examined PINCH expression in normal endometrium, atypical endometrial hyperplasia and endometrioid carcinoma, and further studied the relationships of PINCH expression with clinicopathological variables in cancer patients. Methods: PINCH expression was examined by immunohistochemistry in 23 normal endometrial samples, 18 atypical endometrial hyperplasias and 48 endometrioid endometrial carcinomas. Results: The PINCH expression in the stroma of cancer (71%) was significantly increased compared to either normal endometrium (17%, p andlt; 0.0001) or atypical hyperplasia (39%, p = 0.017), along with 9 cancers that had stronger PINCH expressions at the invasive margin of the cancers compared to the inner cancers. PINCH expression in cancer was higher in the patients with hypertension (p = 0.041) and estrogen exposure time andgt;30 years (p = 0.021). On the other hand, PINCH expression was not related to menopausal status, gravid status, blood sugar/lipid, family background of cancer, histological grade, myometrial invasion, cervical involvement, lymph nodal metastases, growth pattern, estrogen and progestogen receptors (p andgt; 0.05). Conclusion: The results suggest that PINCH seems to play a role, presently unknown, in the tumorigenesis and development of endometrial cancer that merits further study.
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| 13. |
- Hu, Hai-Xi, et al.
(författare)
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Structural insights into HetR-PatS interaction involved in cyanobacterial pattern formation
- 2015
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Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 5
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Tidskriftsartikel (refereegranskat)abstract
- The one-dimensional pattern of heterocyst in the model cyanobacterium Anabaena sp. PCC 7120 is coordinated by the transcription factor HetR and PatS peptide. Here we report the complex structures of HetR binding to DNA, and its hood domain (HetR(Hood)) binding to a PatS-derived hexapeptide (PatS6) at 2.80 and 2.10 angstrom, respectively. The intertwined HetR dimer possesses a couple of novel HTH motifs, each of which consists of two canonical alpha-helices in the DNA-binding domain and an auxiliary alpha-helix from the flap domain of the neighboring subunit. Two PatS6 peptides bind to the lateral clefts of HetR(Hood), and trigger significant conformational changes of the flap domain, resulting in dissociation of the auxiliary alpha-helix and eventually release of HetR from the DNA major grove. These findings provide the structural insights into a prokaryotic example of Turing model.
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| 14. |
- Jiang, Bing-Xin, et al.
(författare)
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Fabrication and bonding of In bumps on Micro-LED with 8 μ m pixel pitch
- 2024
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Ingår i: ENGINEERING RESEARCH EXPRESS. - 2631-8695. ; 6:2
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Tidskriftsartikel (refereegranskat)abstract
- Indium (In) is currently used to fabricate metal bumps on micro-light-emitting diode (Micro-LED) chips due to its excellent physical properties. However, as Micro-LED pixel size and pitch decrease, achieving high-quality In bumps on densely packed Micro-LED chips often presents more challenges. This paper describes the process of fabricating In bumps on micro-LEDs using thermal evaporation, highlighting an issue where In tends to grow laterally within the photoresist pattern, ultimately blocking the pattern and resulting in undersized and poorly dense In bumps on the Micro-LED chip. To address this issue, we conducted numerous experiments to study the height variation of In bumps within a range of photoresist aperture sizes (3 mu m -7 mu m) under two different resist thickness conditions (3.8 mu m and 4.8 mu m). The results showed that the resist thickness had a certain effect on the height of In bumps on the Micro-LED chip electrodes. Moreover, we found that, with the photoresist pattern size increasing under constant resist thickness conditions, the height and quality of the bumps significantly improved. Based on this finding, we rationalized the adjustment of the photoresist pattern size within a limited emission platform range to compensate for the height difference of In bumps caused by different resist thicknesses between the cathode and anode regions. Consequently, well-shaped and dense In bumps with a maximum height of up to 4.4 mu m were fabricated on 8 mu m pitch Micro-LED chips. Afterwards, we bonded the Micro-LED chip with indium bumps to the CMOS chip, and we found that we could successfully control the CMOS chip to drive the Micro-LED chip to display specific characters through the Flexible Printed Circuit (FPC). This work is of significant importance for the fabrication of In bumps on Micro-LED chips with pitches below 10 mu m and subsequent bonding processes.
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| 15. |
- Li, Faji, et al.
(författare)
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Genetic architecture of grain yield in bread wheat based on genome-wide association studies
- 2019
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Ingår i: BMC Plant Biology. - : BioMed Central. - 1471-2229. ; 19
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Tidskriftsartikel (refereegranskat)abstract
- BackgroundIdentification of loci for grain yield (GY) and related traits, and dissection of the genetic architecture are important for yield improvement through marker-assisted selection (MAS). Two genome-wide association study (GWAS) methods were used on a diverse panel of 166 elite wheat varieties from the Yellow and Huai River Valleys Wheat Zone (YHRVWD) of China to detect stable loci and analyze relationships among GY and related traits.ResultsA total of 326,570 single nucleotide polymorphism (SNP) markers from the wheat 90K and 660K SNP arrays were chosen for GWAS of GY and related traits, generating a physical distance of 14,064.8Mb. One hundred and twenty common loci were detected using SNP-GWAS and Haplotype-GWAS, among which two were potentially functional genes underpinning kernel weight and plant height (PH), eight were at similar locations to the quantitative trait loci (QTL) identified in recombinant inbred line (RIL) populations in a previous study, and 78 were potentially new. Twelve pleiotropic loci were detected on eight chromosomes; among these the interval 714.4-725.8Mb on chromosome 3A was significantly associated with GY, kernel number per spike (KNS), kernel width (KW), spike dry weight (SDW), PH, uppermost internode length (UIL), and flag leaf length (FLL). GY shared five loci with thousand kernel weight (TKW) and PH, indicating significantly affected by two traits. Compared with the total number of loci for each trait in the diverse panel, the average number of alleles for increasing phenotypic values of GY, TKW, kernel length (KL), KW, and flag leaf width (FLW) were higher, whereas the numbers for PH, UIL and FLL were lower. There were significant additive effects for each trait when favorable alleles were combined. UIL and FLL can be directly used for selecting high-yielding varieties, whereas FLW can be used to select spike number per unit area (SN) and KNS.ConclusionsThe loci and significant SNP markers identified in the present study can be used for pyramiding favorable alleles in developing high-yielding varieties. Our study proved that both GWAS methods and high-density genetic markers are reliable means of identifying loci for GY and related traits, and provided new insight to the genetic architecture of GY.
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| 16. |
- Menkveld, Albert J., et al.
(författare)
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Nonstandard Errors
- 2024
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Ingår i: JOURNAL OF FINANCE. - : Wiley-Blackwell. - 0022-1082 .- 1540-6261. ; 79:3, s. 2339-2390
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Tidskriftsartikel (refereegranskat)abstract
- In statistics, samples are drawn from a population in a data-generating process (DGP). Standard errors measure the uncertainty in estimates of population parameters. In science, evidence is generated to test hypotheses in an evidence-generating process (EGP). We claim that EGP variation across researchers adds uncertainty-nonstandard errors (NSEs). We study NSEs by letting 164 teams test the same hypotheses on the same data. NSEs turn out to be sizable, but smaller for more reproducible or higher rated research. Adding peer-review stages reduces NSEs. We further find that this type of uncertainty is underestimated by participants.
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| 17. |
- Nie, Huizhen, et al.
(författare)
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The short isoform of PRLR suppresses the pentose phosphate pathway and nucleotide synthesis through the NEK9-Hippo axis in pancreatic cancer
- 2021
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Ingår i: Theranostics. - : Ivyspring International Publisher. - 1838-7640. ; 11:8, s. 3898-3915
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Tidskriftsartikel (refereegranskat)abstract
- Prolactin binding to the prolactin receptor exerts pleiotropic biological effects in vertebrates. The prolactin receptor (PRLR) has multiple isoforms due to alternative splicing. The biological roles and related signaling of the long isoform (PRLR-LF) have been fully elucidated. However, little is known about the short isoform (PRLR-SF), particularly in cancer development and metabolic reprogramming, a core hallmark of cancer. Here, we reveal the role and underlying mechanism of PRLR-SF in pancreatic ductal adenocarcinoma (PDAC). Methods: A human PDAC tissue array was used to investigate the clinical relevance of PRLR in PDAC. The in vivo implications of PRLR-SF in PDAC were examined in a subcutaneous xenograft model and an orthotopic xenograft model. Immunohistochemistry was performed on tumor tissue obtained from genetically engineered KPC (KrasG12D/+; Trp53R172H/+; Pdx1-Cre) mice with spontaneous tumors. 13C-labeled metabolite measures, LC-MS, EdU incorporation assays and seahorse analyses were used to identify the effects of PRLR-SF on the pentose phosphate pathway and glycolysis. We identified the molecular mechanisms by immunofluorescence, coimmunoprecipitation, proximity ligation assays, chromatin immunoprecipitation and promoter luciferase activity. Public databases (TCGA, GEO and GTEx) were used to analyze the expression and survival correlations of the related genes. Results: We demonstrated that PRLR-SF is predominantly expressed in spontaneously forming pancreatic tumors of genetically engineered KPC mice and human PDAC cell lines. PRLR-SF inhibits the proliferation of PDAC cells (AsPC-1 and BxPC-3) in vitro and tumor growth in vivo. We showed that PRLR-SF reduces the expression of genes in the pentose phosphate pathway (PPP) and nucleotide biosynthesis by activating Hippo signaling. TEAD1, a downstream transcription factor of Hippo signaling, directly regulates the expression of G6PD and TKT, which are PPP rate-limiting enzymes. Moreover, NEK9 directly interacts with PRLR-SF and is the intermediator between PRLR and the Hippo pathway. The PRLR expression level is negatively correlated with overall survival and TNM stage in PDAC patients. Additionally, pregnancy and lactation increase the ratio of PRLR-SF:PRLR-LF in the pancreas of wild-type mice and subcutaneous PDAC xenograft tumors. Conclusion: Our characterization of the relationship between PRLR-SF signaling, the NEK9-Hippo pathway, PPP and nucleotide synthesis explains a mechanism for the correlation between PRLR-SF and metabolic reprogramming in PDAC progression. Strategies to alter this pathway might be developed for the treatment or prevention of pancreatic cancer.
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| 18. |
- Proletov, Ian, et al.
(författare)
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Primary and secondary glomerulonephritides 1.
- 2014
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Ingår i: Nephrology, dialysis, transplantation : official publication of the European Dialysis and Transplant Association - European Renal Association. - : Oxford University Press (OUP). - 1460-2385. ; 29 Suppl 3:May, s. 186-200
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Tidskriftsartikel (refereegranskat)
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| 19. |
- Zhang, Su-Yun, et al.
(författare)
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Ionic organic cage-encapsulating phase-transferable metal clusters
- 2019
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Ingår i: Chemical Science. - : Royal Society of Chemistry (RSC). - 2041-6520 .- 2041-6539. ; 10:5, s. 1450-1456
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Tidskriftsartikel (refereegranskat)abstract
- Exploration of metal clusters (MCs) adaptive to both aqueous and oil phases without disturbing their size is promising for a broad scope of applications. The state-of-the-art approach via ligandbinding may perturb MCs' size due to varied metal-ligand binding strength when shuttling between solvents of different polarity. Herein, we applied physical confinement of a series of small noble MCs (<1 nm) inside ionic organic cages (I-Cages), which by means of anion exchange enables reversible transfer of MCs between aqueous and hydrophobic solutions without varying their ultrasmall size. Moreover, the MCs@I-Cage hybrid serves as a recyclable, reaction-switchable catalyst featuring high activity in liquid-phase NH3BH3 (AB) hydrolysis reaction with a turnover frequency (TOF) of 115 min(-1).
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| 20. |
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| 21. |
- Kanoni, Stavroula, et al.
(författare)
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Implicating genes, pleiotropy, and sexual dimorphism at blood lipid loci through multi-ancestry meta-analysis.
- 2022
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Ingår i: Genome biology. - : Springer Science and Business Media LLC. - 1474-760X .- 1465-6906 .- 1474-7596. ; 23:1
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Tidskriftsartikel (refereegranskat)abstract
- Genetic variants within nearly 1000 loci are known to contribute to modulation of blood lipid levels. However, the biological pathways underlying these associations are frequently unknown, limiting understanding of these findings and hindering downstream translational efforts such as drug target discovery.To expand our understanding of the underlying biological pathways and mechanisms controlling blood lipid levels, we leverage a large multi-ancestry meta-analysis (N=1,654,960) of blood lipids to prioritize putative causal genes for 2286 lipid associations using six gene prediction approaches. Using phenome-wide association (PheWAS) scans, we identify relationships of genetically predicted lipid levels to other diseases and conditions. We confirm known pleiotropic associations with cardiovascular phenotypes and determine novel associations, notably with cholelithiasis risk. We perform sex-stratified GWAS meta-analysis of lipid levels and show that 3-5% of autosomal lipid-associated loci demonstrate sex-biased effects. Finally, we report 21 novel lipid loci identified on the X chromosome. Many of the sex-biased autosomal and X chromosome lipid loci show pleiotropic associations with sex hormones, emphasizing the role of hormone regulation in lipid metabolism.Taken together, our findings provide insights into the biological mechanisms through which associated variants lead to altered lipid levels and potentially cardiovascular disease risk.
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| 22. |
- Kozhevnikov, Evgeny, et al.
(författare)
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A dual-transduction-integrated biosensing system to examine the 3D cell-culture for bone regeneration
- 2019
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Ingår i: Biosensors & bioelectronics. - : ELSEVIER ADVANCED TECHNOLOGY. - 0956-5663 .- 1873-4235. ; 141
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Tidskriftsartikel (refereegranskat)abstract
- Three-dimensional (3D) cell cultures developed with living cells and scaffolds have demonstrated outstanding potential for tissue engineering and regenerative medicine applications. However, no suitable tools are available to monitor dynamically variable cell behavior in such a complex microenvironment. In particular, simultaneously assessing cell behavior, cell secretion, and the general state of a 3D culture system is of a really challenging task. This paper presents our development of a dual-transduction-integrated biosensing system that assesses electrical impedance in conjunction with imaging techniques to simultaneously investigate the 3D cell-culture for bone regeneration. First, we created models to mimic the dynamic deposition of the extracellular matrix (ECM) in 3D culture, which underwent osteogenesis by incorporating different amounts of bone-ECM components (collagen, hydroxyapatite [HAp], and hyaluronic acid [HA]) into alginate-based hydrogels. The formed models were investigated by means of electrical impedance spectroscopy (EIS), with the results showing that the impedances increased linearly with collagen and hyaluronan, but changed in a more complex manner with HAp. Thereafter, we created two models that consisted of primary osteoblast cells (OBs), which expressed the enhanced green fluorescent protein (EGFP), and 4T1 cells, which secreted the EGFP-HA, in the alginate hydrogel. We found the capacitance (associated with impedance and measured by EIS) increased with the increases in initial embedded OBs, and also confirmed the cell proliferation over 3 days with the EGFP signal as monitored by the fluorescent imaging component in our system. Interestingly, the change in capacitance is found to be associated with OB migration following stimulation. Also, we show higher capacitance in 4T1 cells that secret HA when compared to control 4T1 cells after a 3-day culture. Taken together, we demonstrate that our biosensing system is able to investigate the dynamic process of 3D culture in a non-invasive and real-time manner.
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| 23. |
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| 24. |
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| 25. |
- Liu, Hui, et al.
(författare)
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Centromere-Specific Retrotransposons and Very-Long-Chain Fatty Acid Biosynthesis in the Genome of Yellowhorn (Xanthoceras sorbifolium, Sapindaceae), an Oil-Producing Tree With Significant Drought Resistance
- 2021
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Ingår i: Frontiers in Plant Science. - : Frontiers Media S.A.. - 1664-462X. ; 12
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Tidskriftsartikel (refereegranskat)abstract
- In-depth genome characterization is still lacking for most of biofuel crops, especially for centromeres, which play a fundamental role during nuclear division and in the maintenance of genome stability. This study applied long-read sequencing technologies to assemble a highly contiguous genome for yellowhorn (Xanthoceras sorbifolium), an oil-producing tree, and conducted extensive comparative analyses to understand centromere structure and evolution, and fatty acid biosynthesis. We produced a reference-level genome of yellowhorn, ∼470 Mb in length with ∼95% of contigs anchored onto 15 chromosomes. Genome annotation identified 22,049 protein-coding genes and 65.7% of the genome sequence as repetitive elements. Long terminal repeat retrotransposons (LTR-RTs) account for ∼30% of the yellowhorn genome, which is maintained by a moderate birth rate and a low removal rate. We identified the centromeric regions on each chromosome and found enrichment of centromere-specific retrotransposons of LINE1 and Gypsy in these regions, which have evolved recently (∼0.7 MYA). We compared the genomes of three cultivars and found frequent inversions. We analyzed the transcriptomes from different tissues and identified the candidate genes involved in very-long-chain fatty acid biosynthesis and their expression profiles. Collinear block analysis showed that yellowhorn shared the gamma (γ) hexaploidy event with Vitis vinifera but did not undergo any further whole-genome duplication. This study provides excellent genomic resources for understanding centromere structure and evolution and for functional studies in this important oil-producing plant.
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| 26. |
- Liu, Zhigang, et al.
(författare)
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Gut microbiota mediates intermittent-fasting alleviation of diabetes-induced cognitive impairment
- 2020
-
Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723 .- 2041-1723. ; 11:1, s. 855-
-
Tidskriftsartikel (refereegranskat)abstract
- Cognitive decline is one of the complications of type 2 diabetes (T2D). Intermittent fasting (IF) is a promising dietary intervention for alleviating T2D symptoms, but its protective effect on diabetes-driven cognitive dysfunction remains elusive. Here, we find that a 28-day IF regimen for diabetic mice improves behavioral impairment via a microbiota-metabolites-brain axis: IF enhances mitochondrial biogenesis and energy metabolism gene expression in hippocampus, re-structures the gut microbiota, and improves microbial metabolites that are related to cognitive function. Moreover, strong connections are observed between IF affected genes, microbiota and metabolites, as assessed by integrative modelling. Removing gut microbiota with antibiotics partly abolishes the neuroprotective effects of IF. Administration of 3-indolepropionic acid, serotonin, short chain fatty acids or tauroursodeoxycholic acid shows a similar effect to IF in terms of improving cognitive function. Together, our study purports the microbiota-metabolites-brain axis as a mechanism that can enable therapeutic strategies against metabolism-implicated cognitive pathophysiologies.
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| 27. |
- Sun, Xu, et al.
(författare)
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Elevated heparanase expression is associated with poor prognosis in breast cancer : a study based on systematic review and TCGA data
- 2017
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Ingår i: Oncotarget. - : IMPACT JOURNALS LLC. - 1949-2553. ; 8:26, s. 43521-43535
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Forskningsöversikt (refereegranskat)abstract
- Heparanase promotes tumorigenesis, angiogenesis, and metastasis. Here, we conducted a study based on systematic review and the Cancer Genome Atlas (TCGA) data that examined heparanase expression in clinical samples to determine its prognostic value. According to the meta-analysis and TCGA data, we found that heparanase expression was up-regulated in most breast cancer specimens, and elevated heparanase expression was associated with increased lymph node metastasis, larger tumor size, higher histological grade, and poor survival. These results suggest that targeting heparanase might improve treatments for breast cancer patients.
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| 28. |
- Wang, Chao-Jie, et al.
(författare)
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Prognostic value of nuclear FBI-1 in patients with rectal cancer with or without preoperative radiotherapy
- 2019
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Ingår i: Oncology Letters. - : Spandidos Publications. - 1792-1074 .- 1792-1082. ; 18:5, s. 5301-5309
-
Tidskriftsartikel (refereegranskat)abstract
- Factor that binds to the inducer of short transcripts of the human immunodeficiency virus-1 (FBI-1) represents as a crucial gene regulator in colorectal cancer; however, the correlation between FBI-1 and preoperative radiotherapy (RT) in rectal cancer (RC) has not yet been reported. The aim was to detect FBI-1 expression in patients with RC with or without RT, by immunohistochemistry and quantitative polymerase chain reaction, and to analyze its association with clinicopathological features and response to RT. The results from immunohistochemistry analysis (n=139) and reverse transcription-quantitative polymerase chain reaction (n=55) demonstrated that FBI-1 was overexpressed in patients with RC, whether they had received preoperative RT or not. Subsequently, the association between FBI-1 expression, and the clinicopathological features and response to RT in patients with RC was analyzed. Cytoplasmic FBI-1 was upregulated in non-RT (n=77) and RT (n=62) groups (17.7 vs. 74.0%, P<0.001; 41.1 vs. 69.4%, P=0.002, respectively) of patients with RC compared with normal mucosa. However, nuclear FBI-1 was downregulated (75.8 vs. 22.1%, P<0.001; 83.9 vs. 35.5%, P<0.001, respectively) in both groups. RT had no significant effect on FBI-1 expression in RC tissues. Furthermore, nuclear FBI-1 was positively associated with tumor-node-metastasis stage and distant recurrence (P=0.003 and P=0.010, respectively). In patients with stage I, II or III RC, higher nuclear FBI-1 expression was associated with poorer disease-free survival [hazard ratio (HR)=1.934, 95% confidence interval (CI): 1.055-3.579, P=0.033] and overall survival (HR=2.174, 95% CI: 1.102-4.290, P=0.025), independently of sex, age, growth pattern, differentiation and RT. In addition, FBI-1 was positively correlated with numerous biological factors, including p73 [Spearman's correlation coefficient (rs)=0.332, P=0.007], lysyl oxidase (rs=0.234, P=0.043), Wrap53 (rs=-0.425, P=0.0002) and peroxisome proliferator-activated receptor δ (rs=-0.294, P=0.026). In conclusion, the present study demonstrated that nuclear FBI-1 was an independent prognostic factor in patients with RC and correlated with numerous biological factors, which indicated that it may have multiple roles in RC.
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| 29. |
- Wang, Mengmeng, et al.
(författare)
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Statistical analysis of whistler precursors upstream of foreshock transient shocks : MMS observations
- 2024
-
Ingår i: Geophysical Research Letters. - : American Geophysical Union (AGU). - 0094-8276 .- 1944-8007. ; 51:8
-
Tidskriftsartikel (refereegranskat)abstract
- Using the high-time-resolution data from the Magnetospheric Multiscale mission, precursor waves upstream of foreshock transient (FT) shocks are statistically investigated using the four-spacecraft timing method. The wave frequencies and wave vectors determined in the plasma rest frame (PRF) are shown to follow the cold plasma dispersion relation for whistler waves. Combining with the feature of the right-hand polarization in the PRF, the precursors are identified as whistler-mode waves around the lower hybrid frequency. The occurrence of whistler precursors is independent of the Alfvén Mach number and the FT shock normal angle. More importantly, all the whistler precursors have group velocities pointing upstream in the shock frame, suggesting the dispersive radiation to be a possible generation mechanism. The study improves the understanding of not only the whistler precursors but also the overall FT shock dynamics.
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| 30. |
- Xu, Chao-Qun, et al.
(författare)
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Genome sequence of Malania oleifera, a tree with great value for nervonic acid production
- 2019
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Ingår i: GigaScience. - : Oxford University Press. - 2047-217X. ; 8:2
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Tidskriftsartikel (refereegranskat)abstract
- Background Malania oleifera, a member of the Olacaceae family, is an IUCN red listed tree, endemic and restricted to the Karst region of southwest China. This tree's seed is valued for its high content of precious fatty acids (especially nervonic acid). However, studies on its genetic makeup and fatty acid biogenesis are severely hampered by a lack of molecular and genetic tools. Findings We generated 51 Gb and 135Gb of raw DNA sequences, using Pacific Biosciences (PacBio) single-molecule real-time and 10x Genomics sequencing, respectively. A final genome assembly, with a scaffold N50 size of 4.65 Mb and a total length of 1.51Gb, was obtained by primary assembly based on PacBio long reads plus scaffolding with 10x Genomics reads. Identified repeats constituted approximate to 82% of the genome, and 24,064 protein-coding genes were predicted with high support. The genome has low heterozygosity and shows no evidence for recent whole genome duplication. Metabolic pathway genes relating to the accumulation of long-chain fatty acid were identified and studied in detail. Conclusions Here, we provide the first genome assembly and gene annotation for M. oleifera. The availability of these resources will be of great importance for conservation biology and for the functional genomics of nervonic acid biosynthesis.
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| 31. |
- Zhang, Hui, et al.
(författare)
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Homocysteine inhibits endothelial progenitor cells proliferation via DNMT1-mediated hypomethylation of Cyclin A
- 2018
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Ingår i: Experimental Cell Research. - : Elsevier BV. - 0014-4827. ; 362:1, s. 217-226
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Tidskriftsartikel (refereegranskat)abstract
- Endothelial progenitor cells (EPCs) contribute to neovasculogenesis and reendothelialization of damaged blood vessels to maintain the endothelium. Dysfunction of EPCs is implicated in the pathogenesis of vascular injury induced by homocysteine (Hcy). We aimed to investigate the role of Cyclin A in Hcy-induced EPCs dysfunction and explore its molecular mechanism. In this study, by treatment of EPCs with Hcy, we found that the expression of Cyclin A mRNA and protein were significantly downregulated in a dose-dependent manner. Knockdown of Cyclin A prominently reduced proliferation of EPCs, while over-expression of Cyclin A significantly promoted the cell proliferation, suggesting that Hcy inhibits EPCs proliferation through downregulation of Cyclin A expression. In addition, epigenetic study also demonstrated that Hcy induces DNA hypomethylation of the Cyclin A promoter in EPCs through downregulated expression of DNMT1. Moreover, we found that Hcy treatment of EPCs leads to increased SAM, SAH and MeCP2, while the ratio of SAM/SAH and MBD expression decrease. In summary, our results indicate that Hcy inhibits Cyclin A expression through hypomethylation of Cyclin A and thereby suppress EPCs proliferation. These findings demonstrate a novel mechanism of DNA methylation mediated by DNMT1 in prevention of Hcy associated cardiovascular disease.
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| 32. |
- Zhang, Jialin, et al.
(författare)
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Altered brain activities associated with cue reactivity during forced break in subjects with Internet gaming disorder
- 2020
-
Ingår i: Addictive Behaviours. - : Elsevier Ltd. - 0306-4603 .- 1873-6327. ; 102
-
Tidskriftsartikel (refereegranskat)abstract
- Background: Studies have proven that forced break can elicit strong psychological cravings for addictive behaviors. This phenomenon could create an excellent situation to study the neural underpinnings of addiction. The current study explores brain features during a cue-reactivity task in Internet gaming disorder (IGD) when participants were forced to stop their gaming behaviors. Methods: Forty-nine IGD subjects and forty-nine matched recreational Internet game users (RGU) were asked to complete a cue-reactivity task when their ongoing gaming behaviors were forced to break. We compared their brain responses to gaming cues and tried to find specific features associated with IGD. Results: Compared with RGU, the IGD subjects showed decreased activation in the anterior cingulate cortex (ACC), parahippocampal gyrus, and dorsolateral prefrontal cortex (DLPFC). Significant negative correlations were observed between self-reported gaming cravings and the baseline activation level (bate value) of the ACC, DLPFC, and parahippocampal gyrus. Conclusions: IGD subjects were unable to suppress their gaming cravings after unexpectedly forced break. This result could also explain why RGU subjects are able to play online games without developing dependence. © 2019 Elsevier Ltd
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| 33. |
- Zhang, Wei, et al.
(författare)
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Activation of nuclear factor-kappa B pathway is responsible for tumor necrosis factor-a-induced up-regulation of endothelin B2 receptor expression in vascular smooth muscle cells in vitro
- 2012
-
Ingår i: Toxicology Letters. - : Elsevier BV. - 1879-3169 .- 0378-4274. ; 209:2, s. 107-112
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Tidskriftsartikel (refereegranskat)abstract
- The endothelin B2 (ETB2) receptors are induced in vascular smooth muscle cells (VSMCs) in cardiovascular diseases. We tested if in vitro short-term exposure to the pro-inflammatory cytokine tumor necrosis factor-alpha (TNF-alpha) could up-regulate ETB2 receptors in rat mesenteric arteries, and if this effect is through activation of intracellular nuclear factor-kappa B (NF-kappa B) pathway. The mesenteric arteries were dissected from male Sprague-Dawley rats and the endothelium was removed. The arteries were co-incubated with TNF-alpha in serum-free Dulbecco's modified Eagle's medium. Real-time reverse transcription-PCR, Western blot and immunohistochemical staining were employed to assess the mRNA/protein expression of ETB2 receptors and activation of NF-kappa B pathway. The results showed that, during organ culture. TNF-alpha concentration-dependently enhanced ET52 receptors expression at both mRNA and protein levels, paralleled with activation of NF-kappa B pathway in VSMC. The up-regulated ETB2 receptor expression and NF-kappa B activation could be effectively suppressed by general transcriptional inhibitor actinomycin D, or either of the selective I kappa B kinase inhibitors wedelolactone and IMD-0354. Conclusively, the activation of intracellular NF-kappa B pathway is responsible for the up-regulation of ETB2 receptors induced by short-term exposure to TNF-alpha. This could partly explain the toxic effects of TNF-alpha on VSMCs that account for cardiovascular diseases. (C) 2011 Elsevier Ireland Ltd. All rights reserved.
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| 34. |
- Zhou, Wencai, et al.
(författare)
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The Role of Grain Boundaries on Ion Migration and Charge Recombination in Halide Perovskites
- 2024
-
Ingår i: Small. - : WILEY-V C H VERLAG GMBH. - 1613-6810 .- 1613-6829.
-
Tidskriftsartikel (refereegranskat)abstract
- Grain boundaries (GBs) have a significant role in polycrystalline perovskite solar cells (PSCs). However, there is ongoing debate regarding the impact of GBs on the performance and long-term stability of PSCs. Employing the first-principles molecular dynamics for perovskites, the iodine vacancy defect migrations both in bulk and at GBs are investigated. i) The positive iodine vacancy (VI+) is found that have both lower formation energy (1.4 eV) and activation energy (0.18 eV) than those of neutral iodine vacancy (VI), statistically. It indicated the VI+ acts as the dominant migrated iodine vacancy rather than VI; ii) the iodine vacancy at GBs has approximate to 0.48 eV higher activation energy than those in bulk, which leads to the accumulation of iodine vacancy at GBs; iii) the presence of VI+ result in a 3-fold increase in charge recombination ratio at GBs, compared to pristine PSCs. Based on quantum molecular dynamics statistical results, which are consistent with experimental measurements, insights into iodine vacancy migration both at GBs and in the bulk are gained. This understanding can be valuable for defects engineering related to ion migration, in order to improve the long-term stability and promote the performance of PSCs. Understanding defects engineering related to ion migration is crucial for enhancing the long-term stability and performance of hybrid perovskite solar cells. Iodine vacancies accumulate at grain boundaries due to lower formation energy and higher migration potential barrier compared to those in the bulk, which further increase the nonradiative recombination. image
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| 35. |
- Chen, Yao Tong, et al.
(författare)
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Giant-atom effects on population and entanglement dynamics of Rydberg atoms in the optical regime
- 2023
-
Ingår i: Physical Review Research. - 2643-1564. ; 5:4
-
Tidskriftsartikel (refereegranskat)abstract
- Giant atoms are attracting interest as an emerging paradigm in the quantum optics of engineered waveguides. At variance with the well-known artificial giant atoms for microwave photonics, here we propose the archetype of a giant atom working in the optical regime by considering a pair of interacting Rydberg atoms coupled to a photonic crystal waveguide (PCW) and also driven by a coherent field. Giant-atom effects are observed as a phase-dependent decay of the double Rydberg excitation during the initial evolution stage while a nontrivial internal entanglement is exhibited at later times. Such an entanglement onset occurs in the presence of intrinsic atomic decay toward nonguided vacuum modes and is accompanied by antibunching in the emitted photons. Our predictions should be observable in current Rydberg-PCW experiments and may open the way toward giant-atom optical photonics for quantum information processing.
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| 36. |
- Cheng, Shi-Ping, et al.
(författare)
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Haplotype-resolved genome assembly and allele-specific gene expression in cultivated ginger
- 2021
-
Ingår i: Horticulture Research. - : Springer Nature. - 2052-7276. ; 8:1
-
Tidskriftsartikel (refereegranskat)abstract
- Ginger (Zingiber officinale) is one of the most valued spice plants worldwide; it is prized for its culinary and folk medicinal applications and is therefore of high economic and cultural importance. Here, we present a haplotype-resolved, chromosome-scale assembly for diploid ginger anchored to 11 pseudochromosome pairs with a total length of 3.1 Gb. Remarkable structural variation was identified between haplotypes, and two inversions larger than 15 Mb on chromosome 4 may be associated with ginger infertility. We performed a comprehensive, spatiotemporal, genome-wide analysis of allelic expression patterns, revealing that most alleles are coordinately expressed. The alleles that exhibited the largest differences in expression showed closer proximity to transposable elements, greater coding sequence divergence, more relaxed selection pressure, and more transcription factor binding site differences. We also predicted the transcription factors potentially regulating 6-gingerol biosynthesis. Our allele-aware assembly provides a powerful platform for future functional genomics, molecular breeding, and genome editing in ginger.
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| 37. |
- Du, Lei, et al.
(författare)
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Giant Atoms in a Synthetic Frequency Dimension
- 2022
-
Ingår i: Physical Review Letters. - 1079-7114 .- 0031-9007. ; 128:22
-
Tidskriftsartikel (refereegranskat)abstract
- Giant atoms that interact with real-space waveguides at multiple spatial points have attracted extensive attention due to their unique interference effects. Here we propose a feasible scheme for constructing giant atoms in a synthetic frequency dimension with, e.g., a dynamically modulated superconducting resonator and a tailored three-level artificial atom. Both analytical and numerical calculations show good agreement between our scheme and real-space two-level giant atoms. In particular, the symmetry of the model in momentum space can be broken by tuning the phase of the external field applied on the atom, enabling chiral interactions between the atom and the frequency lattice. We further demonstrate the possibility of simulating cascaded interaction and directional excitation transfer in the frequency dimension by directly extending our model to involve more such effective giant atoms.
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| 38. |
- Gorski, Mathias, et al.
(författare)
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Meta-analysis uncovers genome-wide significant variants for rapid kidney function decline
- 2021
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Ingår i: Kidney International. - : Elsevier. - 0085-2538 .- 1523-1755. ; 99:4, s. 926-939
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Tidskriftsartikel (refereegranskat)abstract
- Rapid decline of glomerular filtration rate estimated from creatinine (eGFRcrea) is associated with severe clinical endpoints. In contrast to cross-sectionally assessed eGFRcrea, the genetic basis for rapid eGFRcrea decline is largely unknown. To help define this, we meta-analyzed 42 genome-wide association studies from the Chronic Kidney Diseases Genetics Consortium and United Kingdom Biobank to identify genetic loci for rapid eGFRcrea decline. Two definitions of eGFRcrea decline were used: 3 mL/min/1.73m2/year or more ("Rapid3"; encompassing 34,874 cases, 107,090 controls) and eGFRcrea decline 25% or more and eGFRcrea under 60 mL/min/1.73m2 at follow-up among those with eGFRcrea 60 mL/min/1.73m2 or more at baseline ("CKDi25"; encompassing 19,901 cases, 175,244 controls). Seven independent variants were identified across six loci for Rapid3 and/or CKDi25: consisting of five variants at four loci with genome-wide significance (near UMOD-PDILT (2), PRKAG2, WDR72, OR2S2) and two variants among 265 known eGFRcrea variants (near GATM, LARP4B). All these loci were novel for Rapid3 and/or CKDi25 and our bioinformatic follow-up prioritized variants and genes underneath these loci. The OR2S2 locus is novel for any eGFRcrea trait including interesting candidates. For the five genome-wide significant lead variants, we found supporting effects for annual change in blood urea nitrogen or cystatin-based eGFR, but not for GATM or LARP4B. Individuals at high compared to those at low genetic risk (8-14 vs 0-5 adverse alleles) had a 1.20-fold increased risk of acute kidney injury (95% confidence interval 1.08-1.33). Thus, our identified loci for rapid kidney function decline may help prioritize therapeutic targets and identify mechanisms and individuals at risk for sustained deterioration of kidney function.
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| 39. |
- Hu, Xian-Ge, et al.
(författare)
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Global transcriptome analysis of Sabina chinensis (Cupressaceae), a valuable reforestation conifer
- 2016
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Ingår i: Molecular breeding. - : Springer Science and Business Media LLC. - 1380-3743 .- 1572-9788. ; 36:7
-
Tidskriftsartikel (refereegranskat)abstract
- Sabina chinensis has broad distribution in China and is widely used in the reforestation and as an urban tree. The species is frost resistant and grows well on contaminated soils and is becoming valuable for soil remediation and protection against air pollution. Breeding programs aimed at exploiting the species' unique properties were handicapped by the lack of basic genetic information. Here, we established a transcriptomic profiling study from five different tissues using RNA-Seq to gain insight on the functional genes and the development of molecular markers for breeding and conservation purposes. In total 90,382,108 high-quality sequence reads (similar to 9.0 bp) were obtained, and 116,814 unigenes (>= 200 nt) were assembled. Of which, 45,026 and 15,589 unigenes were mapped to the Nr and KOG databases, 31,288 (26.78 %) and 17,596 (15.06 %) were annotated to GO and KEGG database, respectively. Additionally, 28,843 (24.68 %) and 43,033 (36.84 %) S. chinensis unigenes were aligned to the Pinus taeda draft genome and PLAZA2.5 database, respectively. A total of 4570 simple sequence repeat (SSR) motifs were identified in the unigenes. Furthermore, we obtained 6 (12.5 %) polymorphic and 21 (43.75 %) monomorphic loci in the verification of 48 randomly selected SSR loci. This study represents the first transcriptome data of S. chinensis and confirms that the transcriptome assembly data of S. chinensis are a useful resource for EST-SSR loci development. The substantial number of transcripts obtained will aid our understanding of the species adaptation mechanisms and provide valuable genomic information for conservation and breeding applications.
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| 40. |
- Jia, Kai-Hua, et al.
(författare)
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Chromosome-scale assembly and evolution of the tetraploid Salvia splendens (Lamiaceae) genome
- 2021
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Ingår i: Horticulture Research. - : Oxford University Press (OUP). - 2052-7276 .- 2662-6810. ; 8:1
-
Tidskriftsartikel (refereegranskat)abstract
- Polyploidization plays a key role in plant evolution, but the forces driving the fate of homoeologs in polyploid genomes, i.e., paralogs resulting from a whole-genome duplication (WGD) event, remain to be elucidated. Here, we present a chromosome-scale genome assembly of tetraploid scarlet sage (Salvia splendens), one of the most diverse ornamental plants. We found evidence for three WGD events following an older WGD event shared by most eudicots (the γ event). A comprehensive, spatiotemporal, genome-wide analysis of homoeologs from the most recent WGD unveiled expression asymmetries, which could be associated with genomic rearrangements, transposable element proximity discrepancies, coding sequence variation, selection pressure, and transcription factor binding site differences. The observed differences between homoeologs may reflect the first step toward sub- and/or neofunctionalization. This assembly provides a powerful tool for understanding WGD and gene and genome evolution and is useful in developing functional genomics and genetic engineering strategies for scarlet sage and other Lamiaceae species.
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| 41. |
- Lyu, Xinchen, et al.
(författare)
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Selective Offloading in Mobile Edge Computing for the Green Internet of Things
- 2018
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Ingår i: IEEE Network. - Piscataway : IEEE. - 0890-8044 .- 1558-156X. ; 32:1, s. 54-60
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Tidskriftsartikel (refereegranskat)abstract
- Mobile edge computing provides the radio access networks with cloud computing capabilities to fulfill the requirements of the Internet of Things services such as high reliability and low latency. Offloading services to edge servers can alleviate the storage and computing limitations and prolong the lifetimes of the IoT devices. However, offloading in MEC faces scalability problems due to the massive number of IoT devices. In this article, we present a new integration architecture of the cloud, MEC, and IoT, and propose a lightweight request and admission framework to resolve the scalability problem. Without coordination among devices, the proposed framework can be operated at the IoT devices and computing servers separately, by encapsulating latency requirements in offloading requests. Then a selective offloading scheme is designed to minimize the energy consumption of devices, where the signaling overhead can be further reduced by enabling the devices to be self-nominated or self-denied for offloading. Simulation results show that our proposed selective offloading scheme can satisfy the latency requirements of different services and reduce the energy consumption of IoT devices. © 2018 IEEE
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| 42. |
- Ma, Tao, et al.
(författare)
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Genomic insights into salt adaptation in a desert poplar
- 2013
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Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 4, s. 2797-
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Tidskriftsartikel (refereegranskat)abstract
- Despite the high economic and ecological importance of forests, our knowledge of the genomic evolution of trees under salt stress remains very limited. Here we report the genome sequence of the desert poplar, Populus euphratica, which exhibits high tolerance to salt stress. Its genome is very similar and collinear to that of the closely related mesophytic congener, P. trichocarpa. However, we find that several gene families likely to be involved in tolerance to salt stress contain significantly more gene copies within the P. euphratica lineage. Furthermore, genes showing evidence of positive selection are significantly enriched in functional categories related to salt stress. Some of these genes, and others within the same categories, are significantly upregulated under salt stress relative to their expression in another salt-sensitive poplar. Our results provide an important background for understanding tree adaptation to salt stress and facilitating the genetic improvement of cultivated poplars for saline soils.
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| 43. |
- Meng, Wen-Jian, et al.
(författare)
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Correlation of SATB1 overexpression with the progression of human rectal cancer
- 2012
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Ingår i: International Journal of Colorectal Disease. - : Springer Verlag (Germany). - 0179-1958 .- 1432-1262. ; 27:2, s. 143-150
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Tidskriftsartikel (refereegranskat)abstract
- To date, the association between special AT-rich sequence-binding protein 1 (SATB1) and colorectal cancer (CRC) has not been reported. This study was aimed at investigating the expression and potential role of SATB1 in human rectal cancers. less thanbrgreater than less thanbrgreater thanNinety-three paired samples of rectal cancer and distant normal rectal tissue were analyzed by quantitative real-time PCR (qRT-PCR) and immunohistochemistry (IHC), and the correlations between SATB1 expression and clinicopathological parameters were evaluated. The expression profiles of SATB1 were also investigated in a panel of five human colon carcinoma cell lines. less thanbrgreater than less thanbrgreater thanThe general level of SATB1 mRNA in rectal cancer tissues was statistically significantly higher than that in normal mucosa (P = 0.043). The rate of positive SATB1 protein expression in rectal cancers (44.1%) was significantly higher than that in normal tissues (25.8%) by IHC analysis (P = 0.009). Overexpression of SATB1 mRNA was more predominant in patients with earlier onset of rectal cancer (P = 0.033). SATB1 expression correlated with invasive depth and tumor node metastasis (TNM) stage at both protein and mRNA levels (P andlt; 0.05). Furthermore, SATB1 expression in the poorly metastatic KM12C cells was significantly lower than the highly metastatic KM12SM and KM12L4A cells and higher than the HCT116 and SW480 cells (P = 0.001). These results were further confirmed by Western blotting. less thanbrgreater than less thanbrgreater thanOur results indicate that SATB1 may play an important role in the progression of human rectal cancer, which represents a possible new mechanism underlying CRC.
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| 44. |
- Nie, Shuai, et al.
(författare)
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Gapless genome assembly of azalea and multi-omics investigation into divergence between two species with distinct flower color
- 2023
-
Ingår i: Horticulture Research. - : Oxford University Press. - 2662-6810 .- 2052-7276. ; 10:1
-
Tidskriftsartikel (refereegranskat)abstract
- The genus Rhododendron (Ericaceae), with more than 1000 species highly diverse in flower color, is providing distinct ornamental values and a model system for flower color studies. Here, we investigated the divergence between two parental species with different flower color widely used for azalea breeding. Gapless genome assembly was generated for the yellow-flowered azalea, Rhododendron molle. Comparative genomics found recent proliferation of long terminal repeat retrotransposons (LTR-RTs), especially Gypsy, has resulted in a 125 Mb (19%) genome size increase in species-specific regions, and a significant amount of dispersed gene duplicates (13 402) and pseudogenes (17 437). Metabolomic assessment revealed that yellow flower coloration is attributed to the dynamic changes of carotenoids/flavonols biosynthesis and chlorophyll degradation. Time-ordered gene co-expression networks (TO-GCNs) and the comparison confirmed the metabolome and uncovered the specific gene regulatory changes underpinning the distinct flower pigmentation. B3 and ERF TFs were found dominating the gene regulation of carotenoids/flavonols characterized pigmentation in R. molle, while WRKY, ERF, WD40, C2H2, and NAC TFs collectively regulated the anthocyanins characterized pigmentation in the red-flowered R simsii. This study employed a multi-omics strategy in disentangling the complex divergence between two important azaleas and provided references for further functional genetics and molecular breeding.
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| 45. |
- Qian, Yan, et al.
(författare)
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Quantification for total demethylation potential of environmental samples utilizing the EGFP reporter gene
- 2016
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Ingår i: Journal of Hazardous Materials. - : Elsevier. - 0304-3894 .- 1873-3336. ; 306, s. 278-285
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Tidskriftsartikel (refereegranskat)abstract
- Abstract The demethylation potential of pollutants is arguably an innate component of their toxicity in environmental samples. A method was developed for determining the total demethylation potential of food samples (TDQ). The demethylation epigenetic toxicity was determined using the Hep G2 cell line transfected with pEGFP-C3 plasmids containing a methylated promoter of the EGFP reporter gene. The total demethylation potential of the sample extracts (the 5-AZA-CdR demethylation toxic equivalency) can be quantified within one week by using a standard curve of the 5-AZA-CdR demethylation agent. To explore the applicability of TDQ for environmental samples, 17 groundwater samples were collected from heavy polluted Kuihe river and the total demethylation potentials of the sample extracts were measured successfully. Meaningful demethylation toxic equivalencies ranging from 0.00050 to 0.01747 μM were found in all groundwater sample extracts. Among 19 kinds of inorganic substance, As and Cd played important roles for individual contribution to the total demethylation epigenetic toxicity. The TDQ assay is reliable and fast for quantifying the DNA demethylation potential of environmental sample extracts, which may improve epigenetic toxicity evaluations for human risk assessment, and the consistent consuming of groundwater alongside the Kuihe river pose unexpected epigenetic health risk to the local residents.
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| 46. |
- Seland, Øyvind, et al.
(författare)
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Overview of the Norwegian Earth System Model (NorESM2) and key climate response of CMIP6 DECK, historical, and scenario simulations
- 2020
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Ingår i: Geoscientific Model Development. - : Copernicus GmbH. - 1991-959X .- 1991-9603. ; 13:12, s. 6165-6200
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Tidskriftsartikel (refereegranskat)abstract
- The second version of the coupled Norwegian Earth System Model (NorESM2) is presented and evaluated. NorESM2 is based on the second version of the Community Earth System Model (CESM2) and shares with CESM2 the computer code infrastructure and many Earth system model components. However, NorESM2 employs entirely different ocean and ocean biogeochemistry models. The atmosphere component of NorESM2 (CAM-Nor) includes a different module for aerosol physics and chemistry, including interactions with cloud and radiation; additionally, CAM-Nor includes improvements in the formulation of local dry and moist energy conservation, in local and global angular momentum conservation, and in the computations for deep convection and air-sea fluxes. The surface components of NorESM2 have minor changes in the albedo calculations and to land and sea-ice models. We present results from simulations with NorESM2 that were carried out for the sixth phase of the Coupled Model Intercomparison Project (CMIP6). Two versions of the model are used: one with lower (similar to 2 degrees) atmosphere-land resolution and one with medium (similar to 1 degrees) atmosphere-land resolution. The stability of the pre-industrial climate and the sen- sitivity of the model to abrupt and gradual quadrupling of CO2 are assessed, along with the ability of the model to simulate the historical climate under the CMIP6 forcings. Compared to observations and reanalyses, NorESM2 represents an improvement over previous versions of NorESM in most aspects. NorESM2 appears less sensitive to greenhouse gas forcing than its predecessors, with an estimated equilibrium climate sensitivity of 2.5 K in both resolutions on a 150-year time frame; however, this estimate increases with the time window and the climate sensitivity at equilibration is much higher. We also consider the model response to future scenarios as defined by selected Shared Socioeconomic Pathways (SSPs) from the Scenario Model Intercomparison Project defined under CMIP6. Under the four scenarios (SSP1-2.6, SSP2-4.5, SSP3-7.0, and SSP5-8.5), the warming in the period 2090-2099 compared to 1850-1879 reaches 1.3, 2.2, 3.0, and 3.9 K in NorESM2-LM, and 1.3, 2.1, 3.1, and 3.9 K in NorESM-MM, robustly similar in both resolutions. NorESM2-LM shows a rather satisfactory evolution of recent sea-ice area. In NorESM2-LM, an ice-free Arctic Ocean is only avoided in the SSP1-2.6 scenario.
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| 47. |
- Wang, Hui, et al.
(författare)
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A red- emissive mitochondrial probe for imaging of the viscosity in living cells
- 2019
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Ingår i: New Journal of Chemistry. - : ROYAL SOC CHEMISTRY. - 1144-0546 .- 1369-9261. ; 43:22, s. 8811-8815
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Tidskriftsartikel (refereegranskat)abstract
- A novel water- soluble fluorescent probe L based on indole salts has been designed, synthesized and fully characterized. The systematic investigations demonstrated that probe L shows red emission and the fluorescence intensity is linear with the viscosity of the medium. Probe L is able to selectively accumulate in mitochondria within 1 min without any additional reagents for membrane permeabilization. It has been used to distinguish the viscosity differences between mitochondria in normal and nystatin- treated HeLa cells. In addition, due to the good photostability, probe L can be used to monitor the dynamics of mitochondria. These results support that probe L might provide a promising approach for the fluorescence detection of mitochondrial viscosity in living biological systems.
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| 48. |
- Wang, Hui, et al.
(författare)
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A water-soluble "turn-on" fluorescent probe for specifically imaging mitochondria viscosity in living cells
- 2018
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Ingår i: Spectrochimica Acta Part A - Molecular and Biomolecular Spectroscopy. - : PERGAMON-ELSEVIER SCIENCE LTD. - 1386-1425 .- 1873-3557. ; 203, s. 127-131
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Tidskriftsartikel (refereegranskat)abstract
- Rational design of water-soluble probes for mitochondrial viscosity in practical biological applications remains a challenge. Herein, we described a novel hydro soluble benzothiazole salt derivative MitoSN, which exhibits specifically response and singular sensitivity to the mitochondria viscosity in living Hela cells. MitoSN displays an excellent fluorescence enhancement (ca. 35-fold) with the increase of the viscosity in the water-glycerol system. Moreover, confocal microscopy indicates that MitoSN is sensitive to the local viscosity and selectively stains mitochondria, the body of zebrafish as well. Importantly, MitoSN is capable to identify the viscosity difference of mitochondria in normal and nystatin treated Hela cells. The work provides a useful tool to monitor the changes of viscosity in the mitochondrial microenvironment. (C) 2018 Elsevier B.V. All rights reserved.
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| 49. |
- Wang, Kai, et al.
(författare)
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Large-scale Multiconfiguration Dirac-Hartree-Fock and Relativistic Configuration Interaction Calculations of Transition Data for B-like S XII
- 2018
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Ingår i: Astrophysical Journal. - : American Astronomical Society. - 0004-637X .- 1538-4357. ; 864:2
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Tidskriftsartikel (refereegranskat)abstract
- Excitation energies and lifetimes for the 213 lowest states of the n <= 5 configurations in B-like S XII are calculated using highly correlated wave functions, optimized with the fully relativistic multiconfiguration Dirac-Hartree-Fock method. Multipole transition rates and associated radiative data (line strengths and oscillator strengths) for transitions connecting these levels are also reported. The theoretical excitation energies are systematically compared with the NIST Atomic Spectra Database in which misidentifications are pointed out. After eliminating the latter, a mean energy difference with the standard deviation between computed and observed energies of 12 +/- 341 cm(-1) is obtained for the n >= 3 high-lying states. This level of accuracy confirms that elaborate ab initio calculations can assist in the identification of new emission lines in the solar and other astrophysical spectra. The present work provides atomic data of high accuracy for an ion of astrophysical interest, B-like S XII, for which experimental data are scarce.
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| 50. |
- Wang, Ming-Wei, et al.
(författare)
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Expression of PINCH protein in gliomas and its clinicopathological significance
- 2007
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Ingår i: Oncology. - : S. Karger AG. - 0890-9091 .- 0030-2414 .- 1423-0232. ; 72:5-6, s. 343-346
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Tidskriftsartikel (refereegranskat)abstract
- Objectives: Particularly interesting new cysteine-histidine-rich protein (PINCH), as a LIM domain adapter protein, functions in the integrin and growth factor signal transduction pathway, and is upregulated in tumor-associated stroma in several types of cancers. However, no study of PINCH has been carried out in gliomas, therefore we examined PINCH expression in gliomas and its clinicopathological significance. Methods: PINCH expression was immunohistochemically examined in 82 gliomas, along with 26 matched adjacent normal brain samples and 10 recurred gliomas. Results: PINCH was strongly expressed in the primary (35%, p = 0.0001) or recurred tumors (40%, p = 0.004) and weak in normal brain tissue. PINCH expression was significantly increased in high-grade gliomas (55 vs. 24%, high- vs. low-grade gliomas, p = 0.004). There was no association of PINCH expression with gender, age, tumor number, size, histological type and tumor location (p > 0.05). Conclusions: PINCH expression may be involved in glioma development and differentiation. Copyright © 2008 S. Karger AG.
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