| 1. |
- Klionsky, Daniel J., et al.
(author)
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Guidelines for the use and interpretation of assays for monitoring autophagy
- 2012
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In: Autophagy. - : Informa UK Limited. - 1554-8635 .- 1554-8627. ; 8:4, s. 445-544
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Research review (peer-reviewed)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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| 2. |
- Kristan, Matej, et al.
(author)
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The Ninth Visual Object Tracking VOT2021 Challenge Results
- 2021
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In: 2021 IEEE/CVF INTERNATIONAL CONFERENCE ON COMPUTER VISION WORKSHOPS (ICCVW 2021). - : IEEE COMPUTER SOC. - 9781665401913 ; , s. 2711-2738
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Conference paper (peer-reviewed)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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| 3. |
- Liu, Zhigang, et al.
(author)
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Gut microbiota mediates intermittent-fasting alleviation of diabetes-induced cognitive impairment
- 2020
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In: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723 .- 2041-1723. ; 11:1, s. 855-
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Journal article (peer-reviewed)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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| 4. |
- Boeger, Carsten A., et al.
(author)
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CUBN Is a Gene Locus for Albuminuria
- 2011
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In: Journal of the American Society of Nephrology. - 1046-6673 .- 1533-3450. ; 22:3, s. 555-570
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Journal article (peer-reviewed)abstract
- Identification of genetic risk factors for albuminuria may alter strategies for early prevention of CKD progression, particularly among patients with diabetes. Little is known about the influence of common genetic variants on albuminuria in both general and diabetic populations. We performed a meta-analysis of data from 63,153 individuals of European ancestry with genotype information from genome-wide association studies (CKDGen Consortium) and from a large candidate gene study (CARe Consortium) to identify susceptibility loci for the quantitative trait urinary albumin-to-creatinine ratio (UACR) and the clinical diagnosis microalbuminuria. We identified an association between a missense variant (I2984V) in the CUBN gene, which encodes cubilin, and both UACR (P = 1.1 x 10(-11)) and microalbuminuria (P = 0.001). We observed similar associations among 6981 African Americans in the CARe Consortium. The associations between this variant and both UACR and microalbuminuria were significant in individuals of European ancestry regardless of diabetes status. Finally, this variant associated with a 41% increased risk for the development of persistent microalbuminuria during 20 years of follow-up among 1304 participants with type 1 diabetes in the prospective DCCT/EDIC Study. In summary, we identified a missense CUBN variant that associates with levels of albuminuria in both the general population and in individuals with diabetes.
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| 5. |
- Pettersson, Mats, et al.
(author)
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A chromosome-level assembly of the Atlantic herring : detection of a supergene and other signals of selection
- 2019
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In: Genome Research. - : Cold Spring Harbor Laboratory Press (CSHL). - 1088-9051 .- 1549-5469. ; 29:11, s. 1919-1928
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Journal article (peer-reviewed)abstract
- The Atlantic herring is a model species for exploring the genetic basis for ecological adaptation, due to its huge population size and extremely low genetic differentiation at selectively neutral loci. However, such studies have so far been hampered because of a highly fragmented genome assembly. Here, we deliver a chromosome-level genome assembly based on a hybrid approach combining a de novo Pacific Biosciences (PacBio) assembly with Hi-C-supported scaffolding. The assembly comprises 26 autosomes with sizes ranging from 12.4 to 33.1 Mb and a total size, in chromosomes, of 726 Mb, which has been corroborated by a high-resolution linkage map. A comparison between the herring genome assembly with other high-quality assemblies from bony fishes revealed few inter-chromosomal but frequent intra-chromosomal rearrangements. The improved assembly facilitates analysis of previously intractable large-scale structural variation, allowing, for example, the detection of a 7.8-Mb inversion on Chromosome 12 underlying ecological adaptation. This supergene shows strong genetic differentiation between populations. The chromosome-based assembly also markedly improves the interpretation of previously detected signals of selection, allowing us to reveal hundreds of independent loci associated with ecological adaptation.
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| 6. |
- Haghighi, Mona, et al.
(author)
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A Comparison of Rule-based Analysis with Regression Methods in Understanding the Risk Factors for Study Withdrawal in a Pediatric Study
- 2016
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In: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 6
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Journal article (peer-reviewed)abstract
- Regression models are extensively used in many epidemiological studies to understand the linkage between specific outcomes of interest and their risk factors. However, regression models in general examine the average effects of the risk factors and ignore subgroups with different risk profiles. As a result, interventions are often geared towards the average member of the population, without consideration of the special health needs of different subgroups within the population. This paper demonstrates the value of using rule-based analysis methods that can identify subgroups with heterogeneous risk profiles in a population without imposing assumptions on the subgroups or method. The rules define the risk pattern of subsets of individuals by not only considering the interactions between the risk factors but also their ranges. We compared the rule-based analysis results with the results from a logistic regression model in The Environmental Determinants of Diabetes in the Young (TEDDY) study. Both methods detected a similar suite of risk factors, but the rule-based analysis was superior at detecting multiple interactions between the risk factors that characterize the subgroups. A further investigation of the particular characteristics of each subgroup may detect the special health needs of the subgroup and lead to tailored interventions.
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| 7. |
- Klionsky, Daniel J., et al.
(author)
-
Guidelines for the use and interpretation of assays for monitoring autophagy in higher eukaryotes
- 2008
-
In: Autophagy. - : Landes Bioscience. - 1554-8627 .- 1554-8635. ; 4:2, s. 151-175
-
Research review (peer-reviewed)abstract
- Research in autophagy continues to accelerate,1 and as a result many new scientists are entering the field. Accordingly, it is important to establish a standard set of criteria for monitoring macroautophagy in different organisms. Recent reviews have described the range of assays that have been used for this purpose.2,3 There are many useful and convenient methods that can be used to monitor macroautophagy in yeast, but relatively few in other model systems, and there is much confusion regarding acceptable methods to measure macroautophagy in higher eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers of autophagosomes versus those that measure flux through the autophagy pathway; thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from fully functional autophagy that includes delivery to, and degradation within, lysosomes (in most higher eukaryotes) or the vacuole (in plants and fungi). Here, we present a set of guidelines for the selection and interpretation of the methods that can be used by investigators who are attempting to examine macroautophagy and related processes, as well as by reviewers who need to provide realistic and reasonable critiques of papers that investigate these processes. This set of guidelines is 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 verify an autophagic response.
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| 8. |
- Liu, Xiaomei, et al.
(author)
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Cognitive Benefit of a Multidomain Intervention for Older Adults at Risk of Cognitive Decline : A Cluster- Randomized Controlled Trial
- 2023
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In: The American journal of geriatric psychiatry. - : Elsevier BV. - 1064-7481 .- 1545-7214. ; 31:3, s. 197-209
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Journal article (peer-reviewed)abstract
- Objective: We sought to assess cognitive benefits of a community-based multi -domain intervention for improving cognition among older adults at risk of cog-nitive decline (COMBAT). Design: A two-armed cluster-randomized controlled trial. Setting and Participants: Community-dwelling older adults aged 60 years or older and were at risk of cognitive decline (n = 209). Intervention: In this 9-month intervention study, 10 community hospitals in Beijing, China, were randomized (1:1) to receive either a multidomain inter-vention of meditation, cognitive training, exercise, and nutrition counseling or usual care. The intervention was delivered with weekly 1-hour group training sessions and weekly home homework. Measurements: Primary outcome was change in cognition as measured by a composite Z score of seven cognitive tests. Secondary outcomes included subjective cognitive abilities, positive and nega-tive affective experiences, physical activity, and dietary habits. Assessments were administered at baseline, end of the intervention, and 1 year after com-pleting the intervention (1-year follow-up). Results: Immediately after the intervention, the intervention group showed significant enhancement in cogni-tive performance (p = 0.026). The between-group difference in the Z score of change of cognition was 0.20 (95% CI: 0.053, 0.35), with a Hedges' g of 0.40 (95% CI: 0.29, 0.50). However, this cognitive benefit was not significant at
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| 9. |
- Nie, Junyang, et al.
(author)
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Systematic study on size and temporal dependence of micro-LED arrays for display applications
- 2023
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In: Photonics Research. - 2327-9125. ; 11:4, s. 549-557
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Journal article (peer-reviewed)abstract
- Micro-LEDs are one of the most promising candidates for next-generation displays, yet they are inconvenienced by the efficiency reduction induced by the sidewall defects when pursuing further scaled-down device dimensions. We have systematically investigated both the size and temporal dependence of micro-LEDs. Micro-LED arrays with a mesa size ranging from 7 to 100 μm were prepared for display purposes. The luminance and external quantum efficiency (EQE) were measured and discussed. Surprisingly, micro-LED arrays with a smaller mesa size exhibit a higher EQE under 100 ns pulse duration operation when compared with longer pulse duration operations. Under certain short-pulsed excitation, a 7 × 7 μm2 micro-LED array even exhibits a >20% higher EQE as compared to the direct current (DC) or the long duration pulse operation condition.We thus concluded that the notorious efficiency reduction induced by sidewall defects in small-sized micro-LED arrays could be significantly reduced by applying short-pulse voltages.
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| 10. |
- Wang, Xiaoning, et al.
(author)
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Effectiveness of driver's bounded rationality and speed guidance on fuel-saving and emissions-reducing at a signalized intersection
- 2021
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In: Journal of Cleaner Production. - : Elsevier BV. - 0959-6526 .- 1879-1786. ; 325, s. 129343-
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Journal article (peer-reviewed)abstract
- To reduce the fuel consumption and emissions of drivers passing through signalized intersections, this research proposes a fuel-saving and emissions-reducing strategy at a signalized intersection which takes into account driver's bounded rationality and speed guidance, including the theoretical basis of strategy, the scenario division of vehicle speed guidance, and the solution of vehicle optimal trajectory. Drivers are divided into three types: aggressive, normal, and conservative. Bounded rationality is divided into three levels: low, medium, and high. And the 3 x 3 x 3 numerical simulation experiments are carried out under low, medium, and high traffic flow. The results show that when the speed guidance is received, aggressive drivers have the greatest fuel-saving and emissions-reducing benefits, followed by conservative drivers. When the bounded rationality level changes under high traffic flow or the level of traffic flow and bounded rationality change concurrently, the benefits will be greatly affected. The driver's bounded rationality harms fuel consumption and emissions, and this negative effect increases with the increase of traffic flow. Providing corrected speed guidance can effectively reduce the negative effect. This study can provide more effective guidance information for drivers in a manual driving environment.
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| 11. |
- Wang, Yanzhi, et al.
(author)
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Fe Single-atom Sites in Two-Dimensional Nitrogen-doped Porous Carbon for Electrocatalytic Oxygen Reduction
- 2022
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In: ChemCatChem. - : Wiley. - 1867-3880 .- 1867-3899. ; 14:14
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Journal article (peer-reviewed)abstract
- The development of electrocatalysts for oxygen reduction reaction (ORR) is important for energy conversion devices, such as fuel cells, and metal-air batteries. Here, we have developed a confined space strategy to prepare a two-dimensional (2D) leaf-like nitrogen (N)-containing porous carbon as a single-atom catalyst substrate. ZIF−L materials have been confined in a thin silica layer to regulate the pyrolysis. The obtained Fe single atoms doped N-containing porous carbons (Fe SAs/N−C) maintain the 2D morphology and have Fe single-atom active sites. Correspondingly, Fe SAs/N−C exhibits excellent ORR performance (E1/2 of 0.907 V), which is more positive than those of commercially available Pt/C (0.874 V) and most reported non-noble metal catalysts. The durability test shows that Fe SAs/N−C exhibits good stability during electrocatalytic process. This rational design shows a new strategy to prepare 2D catalyst supports with single-atom active sites.
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| 12. |
- Zhu, Haining, et al.
(author)
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EMMPRIN regulates cytoskeleton reorganization and cell adhesion in prostate cancer
- 2011
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In: The Prostate. - : Wiley. - 0270-4137 .- 1097-0045. ; 72:1, s. 72-81
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Journal article (peer-reviewed)abstract
- BACKGROUND: Proteins on cell surface play important roles during cancer progression and metastasis via their ability to mediate cell-to-cell interactions and navigate the communication between cells and the microenvironment. METHODS: In this study a targeted proteomic analysis was conducted to identify the differential expression of cell surface proteins in human benign (BPH-1) versus malignant (LNCaP and PC-3) prostate epithelial cells. We identified EMMPRIN (extracellular matrix metalloproteinase inducer) as a key candidate and shRNA functional approaches were subsequently applied to determine the role of EMMPRIN in prostate cancer cell adhesion, migration, invasion as well as cytoskeleton organization. RESULTS: EMMPRIN was found to be highly expressed on the surface of prostate cancer cells compared to BPH-1 cells, consistent with a correlation between elevated EMMPRIN and metastasis found in other tumors. No significant changes in cell proliferation, cell cycle progression, or apoptosis were detected in EMMPRIN knockdown cells compared to the scramble controls. Furthermore, EMMPRIN silencing markedly decreased the ability of PC-3 cells to form filopodia, a critical feature of invasive behavior, while it increased expression of cell-cell adhesion and gap junction proteins. CONCLUSIONS: Our results suggest that EMMPRIN regulates cell adhesion, invasion, and cytoskeleton reorganization in prostate cancer cells. This study identifies a new function for EMMPRIN as a contributor to prostate cancer cell-cell communication and cytoskeleton changes towards metastatic spread, and suggests its potential value as a marker of prostate cancer progression to metastasis.
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