| 1. |
- Beal, Jacob, et al.
(författare)
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Robust estimation of bacterial cell count from optical density
- 2020
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Ingår i: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1
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Tidskriftsartikel (refereegranskat)abstract
- Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data.
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| 2. |
- 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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| 3. |
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| 4. |
-
- 2019
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Tidskriftsartikel (refereegranskat)
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| 5. |
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| 6. |
- Kristan, Matej, et al.
(författare)
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The Visual Object Tracking VOT2015 challenge results
- 2015
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Ingår i: Proceedings 2015 IEEE International Conference on Computer Vision Workshops ICCVW 2015. - : IEEE. - 9780769557205 ; , s. 564-586
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Konferensbidrag (refereegranskat)abstract
- The Visual Object Tracking challenge 2015, VOT2015, aims at comparing short-term single-object visual trackers that do not apply pre-learned models of object appearance. Results of 62 trackers are presented. The number of tested trackers makes VOT 2015 the largest benchmark on short-term tracking to date. For each participating tracker, a short description is provided in the appendix. Features of the VOT2015 challenge that go beyond its VOT2014 predecessor are: (i) a new VOT2015 dataset twice as large as in VOT2014 with full annotation of targets by rotated bounding boxes and per-frame attribute, (ii) extensions of the VOT2014 evaluation methodology by introduction of a new performance measure. The dataset, the evaluation kit as well as the results are publicly available at the challenge website(1).
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| 7. |
- Kristan, Matej, et al.
(författare)
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The Visual Object Tracking VOT2017 challenge results
- 2017
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Ingår i: 2017 IEEE INTERNATIONAL CONFERENCE ON COMPUTER VISION WORKSHOPS (ICCVW 2017). - : IEEE. - 9781538610343 ; , s. 1949-1972
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Konferensbidrag (refereegranskat)abstract
- The Visual Object Tracking challenge VOT2017 is the fifth annual tracker benchmarking activity organized by the VOT initiative. Results of 51 trackers are presented; many are state-of-the-art published at major computer vision conferences or journals in recent years. The evaluation included the standard VOT and other popular methodologies and a new "real-time" experiment simulating a situation where a tracker processes images as if provided by a continuously running sensor. 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 VOT2017 goes beyond its predecessors by (i) improving the VOT public dataset and introducing a separate VOT2017 sequestered dataset, (ii) introducing a realtime tracking experiment and (iii) releasing a redesigned toolkit that supports complex experiments. The dataset, the evaluation kit and the results are publicly available at the challenge website(1).
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| 8. |
- Liu, Shicong, et al.
(författare)
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LEO Satellite Constellations for 5G and Beyond : How Will They Reshape Vertical Domains?
- 2021
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Ingår i: IEEE Communications Magazine. - : Institute of Electrical and Electronics Engineers (IEEE). - 0163-6804 .- 1558-1896. ; 59:7, s. 30-36
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Tidskriftsartikel (refereegranskat)abstract
- The rapid development of communication technologies in the past decades has provided immense vertical opportunities for individuals and enterprises. However, conventional terrestrial cellular networks have unfortunately neglected the huge geographical digital divide, since high-bandwidth wireless coverage is concentrated in urban areas. To meet the goal of 'connecting the unconnected,' integrating low Earth orbit (LEO) satellites with the terrestrial cellular networks has been widely considered as a promising solution. In this article, we first introduce the development roadmap of LEO satellite constellations (SatCons), including early attempts in LEO satellites with the emerging LEO constellations. Further, we discuss the unique opportunities of employing LEO SatCons for the delivery of integrating 5G networks. Specifically, we present their key performance indicators, which offer important guidelines for the design of associated enabling techniques, and then discuss the potential impact of integrating LEO SatCons with typical 5G use cases, where we engrave our vision of various vertical domains reshaped by LEO SatCons. Technical challenges are finally provided to specify future research directions.
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| 9. |
- 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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| 10. |
- Ma, Ruijie, et al.
(författare)
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Adding a Third Component with Reduced Miscibility and Higher LUMO Level Enables Efficient Ternary Organic Solar Cells
- 2020
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Ingår i: ACS Energy Letters. - : American Chemical Society (ACS). - 2380-8195. ; 5:8, s. 2711-2720
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Tidskriftsartikel (refereegranskat)abstract
- It is widely known that the miscibility between donor and acceptor is a crucial factor that affects the morphology and thus device performance of nonfullerene organic solar cells (OSCs). In this Letter, we show that incorporating a third component with lower miscibility and higher lowest unoccupied molecular orbital (LUMO) level into the state-of-the-art PM6:Y6 system can significantly enhance the performance of devices. The best results of the ternary devices are achieved by adding a small molecular acceptor named ITCPTC (similar to 5% w/w), which significantly improves the power conversion efficiency (PCE) of the host system from 16.44% to 17.42%. The higher LUMO of the third component increases the open-circuit voltage (V-oc), while the low miscibility enlarges the domains and leads to improved short-circuit current density (J(sc)) and fill factor (FF). The efficacy of this strategy is supported by using other nonfullerene third components including an asymmetric small molecule (N7IT) and a polymer acceptor (PF2-DTC), which play the same role as ITCPTC and boost the PCEs to 16.96% and 17.04%, respectively. Our approach can be potentially applied to a wide range of OSC material systems and should facilitate the development of the OSC field.
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| 11. |
- Wu, Ya-Ting, et al.
(författare)
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Monitoring bisphenol A and its biodegradation in water using a fluorescent molecularly imprinted chemosensor.
- 2015
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Ingår i: Chemosphere. - : Elsevier BV. - 1879-1298 .- 0045-6535. ; 119, s. 515-523
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Tidskriftsartikel (refereegranskat)abstract
- In this paper, we present a simple and rapid method for monitoring bisphenol A (BPA) and its biodegradation in environmental water using a fluorescent molecularly imprinted polymer chemosensor (fMIPcs). A fluorescent molecularly imprinted polymer (fMIP) was first synthesized by precipitation polymerization method using BPA as template, dansyl methacrylate as functional monomer. Then a fMIPcs was constructed by combining the fMIP with a fluorescent microplate reader. The fMIPcs displayed selective, concentration-dependent fluorescence quenching in response to BPA in water even in the existence of interferences, thereby allowing reliable high through-put quantification of BPA via simple fluorescence measurements. The fMIPcs was able to directly quantify BPA (from 10 to 2000μgL(-1)) in different environmental water samples (distilled water, distilled water containing heavy metals and humic acid, tap water, and river water) with high accuracy, and to monitor BPA biodegradation in real-time. Using the fMIPcs, it was possible to achieve fast analytical results with lower limit of detection for BPA (3μgL(-1)) from smaller sample volume (250μL), which are superior to many relevant methods reported in the literature. Moreover, BPA levels and biodegradation rates measured by fMIPcs are comparable to the instrument-based method (HPLC). The fMIPcs developed in this work offers a new solution for simple, rapid, accurate and high through-put BPA quantification, and makes it possible to monitor BPA biodegradation in real time.
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| 12. |
- Wuttke, Matthias, et al.
(författare)
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A catalog of genetic loci associated with kidney function from analyses of a million individuals
- 2019
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Ingår i: Nature Genetics. - : NATURE PUBLISHING GROUP. - 1061-4036 .- 1546-1718. ; 51:6, s. 957-972
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Tidskriftsartikel (refereegranskat)abstract
- Chronic kidney disease (CKD) is responsible for a public health burden with multi-systemic complications. Through transancestry meta-analysis of genome-wide association studies of estimated glomerular filtration rate (eGFR) and independent replication (n = 1,046,070), we identified 264 associated loci (166 new). Of these,147 were likely to be relevant for kidney function on the basis of associations with the alternative kidney function marker blood urea nitrogen (n = 416,178). Pathway and enrichment analyses, including mouse models with renal phenotypes, support the kidney as the main target organ. A genetic risk score for lower eGFR was associated with clinically diagnosed CKD in 452,264 independent individuals. Colocalization analyses of associations with eGFR among 783,978 European-ancestry individuals and gene expression across 46 human tissues, including tubulo-interstitial and glomerular kidney compartments, identified 17 genes differentially expressed in kidney. Fine-mapping highlighted missense driver variants in 11 genes and kidney-specific regulatory variants. These results provide a comprehensive priority list of molecular targets for translational research.
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| 13. |
- Andhikaputra, Gerry, et al.
(författare)
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The impact of temperature and precipitation on all-infectious-, bacterial-, and viral-diarrheal disease in Taiwan
- 2023
-
Ingår i: Science of the Total Environment. - : Elsevier BV. - 1879-1026 .- 0048-9697. ; 862
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: The ongoing climate change will elevate the incidence of diarrheal in 2030-2050 in Asia, including Taiwan. This study investigated associations between meteorological factors (temperature, precipitation) and burden of age-cause-specific diarrheal diseases in six regions of Taiwan using 13 years of (2004-2016) population-based data.METHODS: Weekly cause-specific diarrheal and meteorological data were obtained from 2004 to 2016. We used distributed lag non-linear model to assess age (under five, all age) and cause-specific (viral, bacterial) diarrheal disease burden associated with extreme high (99th percentile) and low (5th percentile) of climate variables up to lag 8 weeks in six regions of Taiwan. Random-effects meta-analysis was used to pool these region-specific estimates.RESULTS: Extreme low temperature (15.30 °C) was associated with risks of all-infectious and viral diarrhea, with the highest risk for all-infectious diarrheal found at lag 8 weeks among all age [Relative Risk (RR): 1.44; 95 % Confidence Interval (95 % CI): 1.24-1.67]. The highest risk of viral diarrheal infection was observed at lag 2 weeks regardless the age. Extreme high temperature (30.18 °C) was associated with risk of bacterial diarrheal among all age (RR: 1.07; 95 % CI: 1.02-1.13) at lag 8 weeks. Likewise, extreme high precipitation (290 mm) was associated with all infectious diarrheal, with the highest risk observed for bacterial diarrheal among population under five years (RR: 2.77; 95 % CI: 1.60-4.79) at lag 8 weeks. Extreme low precipitation (0 mm) was associated with viral diarrheal in all age at lag 1 week (RR: 1.08; 95 % CI: 1.01-1.15)].CONCLUSION: In Taiwan, extreme low temperature is associated with an increased burden of viral diarrheal, while extreme high temperature and precipitation elevated burden of bacterial diarrheal. This distinction in cause-specific and climate-hazard specific diarrheal disease burden underscore the importance of incorporating differences in public health preparedness measures designed to enhance community resilience against climate change.
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| 14. |
- Beijer, Kristina, et al.
(författare)
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Effluent from drug manufacturing affects cytochrome P450 1 regulation and function in fish
- 2013
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Ingår i: Chemosphere. - : Elsevier BV. - 0045-6535 .- 1879-1298. ; 90:3, s. 1149-1157
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Tidskriftsartikel (refereegranskat)abstract
- We have previously reported very high concentrations of pharmaceuticals in the effluent from a treatment plant receiving wastewater from about 90 bulk drug manufacturers near Hyderabad, India. The main objective of the present study was to examine how high dilutions of this effluent affect mRNA expression of cytochrome P450 (CYP) 1 family genes and ethoxyresorufin O-deethylase (EROD) activity in exposed wildlife, using the three-spined stickleback (Gasterosteus aculeatus) as a model. In gill filaments exposed to diluted effluent ex vivo, EROD activity was strongly inhibited in a concentration-dependent manner. In a subsequent in vivo study, groups of fish were exposed (24. h) to three concentrations of effluent, 0.8%, 1.6% or 3.2%. In this experiment, EROD in gills was induced 27-, 52- or 60-fold, respectively. Accordingly, CYP1A mRNA was markedly up-regulated in gill, liver and brain of fish exposed to all three effluent concentrations. Expression of mRNA for CYP1B1 and CYP1C1 was induced in gills at all concentrations while effects on these genes in liver and brain were weak or absent. The results of a time course study suggested that most CYP1-inducing substances in the effluent were readily metabolised or excreted, because the induced EROD activity and mRNA expression decreased when the fish were transferred to clean water. Considering that CYP1 enzymes play important roles in biotransformation of endogenous and foreign compounds, the observed dual effect of the effluent on CYP1 catalytic activity and mRNA expression suggests that multiple physiological functions could be affected in exposed wildlife.
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| 15. |
- Chai, Gaoda, et al.
(författare)
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Deciphering the Role of Chalcogen-Containing Heterocycles in Nonfullerene Acceptors for Organic Solar Cells
- 2020
-
Ingår i: ACS Energy Letters. - : AMER CHEMICAL SOC. - 2380-8195. ; 5:11, s. 3415-3425
-
Tidskriftsartikel (refereegranskat)abstract
- The field of organic solar cells has experienced paradigm-shifting changes in recent years because of the emergence of nonfullerene acceptors (NFAs). It is critically important to gain more insight into the structure-property relationship of the emerging A-DAD-A-type NFAs. In this Letter, a family of NFAs named BPF-4F, BPT-4F, and BPS-4F incorporating various chalcogen-containing heterocycles, i.e., furan, thiophene, and selenophene, respectively, was designed and synthesized. These NFAs exhibited dramatic differences in their photovoltaic performances with device efficiencies of 16.8% achieved by the thiophene-based cells, which was much higher than the furan-based ones (12.6%). In addition, the selenophene-based NFA showed a red-shifted absorption relative to the furan- and thiophene-based ones and obtained a decent efficiency of 16.3% owing to an improved J(SC). The reasons why these NFAs performed differently are systematically studied by comparing their optoelectronic properties and film morphology, which provides new understandings of the molecular design of high-performance NFAs.
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| 16. |
- Chen, Kai, et al.
(författare)
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Room-temperature multiferroic properties in NiBi2O4
- 2010
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Ingår i: Europhysics letters. - : European Physical Society. - 0295-5075 .- 1286-4854. ; 89:2
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Tidskriftsartikel (refereegranskat)abstract
- Magnetism and ferroelectricity at room temperature are observed in the NiBi2O4 ceramics. Both the time reversal and the inversion symmetry of the structure (space group F-43m) are broken. The saturation magnetization is 0.028 emu/g and the saturation polarization 2P(s) similar to 4.0 mu C/cm(2). NiBi2O4 also shows other room-temperature multiferroic properties, e. g. the piezoelectric coefficient (d(33)), the polarized dielectric character, the magneto-dielectric response and the magnetoelectric effect. Copyright (C) EPLA, 2010
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| 17. |
- Chen, Kai, et al.
(författare)
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Self-Assembled Core-Shell Polymer Dielectric Prepared by Solution Casting Process
- 2009
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Ingår i: Integrated Ferroelectrics. - : Taylor andamp; Francis: STM, Behavioural Science and Public Health Titles. - 1058-4587 .- 1607-8489. ; 113, s. 1-8
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Tidskriftsartikel (refereegranskat)abstract
- Giant permittivity at 1 MHz, which slightly changes with temperatures, is observed in a polymer composite. The dielectric spectroscopy demonstrates that the samples are electrically heterogeneous. The microstructure observation and the ingredient analysis evidence they self assemble the conducting cores surrounded by the insulating shells. The giant-dielectric phenomenon is therefore attributed to the percolation effect. The electrically heterogeneous microstructure with effective permittivity values about 10 000 can be fabricated by a simple solution casting process in air. The composite is an attractive option to the currently used printing dielectric and the future flexible electronics.
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| 18. |
- Chen, Xian-Kai, et al.
(författare)
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A unified description of non-radiative voltage losses in organic solar cells
- 2021
-
Ingår i: Nature Energy. - : Springer Nature. - 2058-7546. ; 6:8, s. 799-806
-
Tidskriftsartikel (refereegranskat)abstract
- Organic solar cells based on non-fullerene acceptors have enabled high efficiencies yet their charge dynamics and its impact on the photovoltaic parameters are not fully understood. Now, Chen et al. provide a general description of non-radiative voltage losses in both fullerene and non-fullerene solar cells. Recent advances in organic solar cells based on non-fullerene acceptors (NFAs) come with reduced non-radiative voltage losses (Delta V-nr). Here we show that, in contrast to the energy-gap-law dependence observed in conventional donor:fullerene blends, the Delta V-nr values in state-of-the-art donor:NFA organic solar cells show no correlation with the energies of charge-transfer electronic states at donor:acceptor interfaces. By combining temperature-dependent electroluminescence experiments and dynamic vibronic simulations, we provide a unified description of Delta V-nr for both fullerene- and NFA-based devices. We highlight the critical role that the thermal population of local exciton states plays in low-Delta V-nr systems. An important finding is that the photoluminescence yield of the pristine materials defines the lower limit of Delta V-nr. We also demonstrate that the reduction in Delta V-nr (for example, <0.2 V) can be obtained without sacrificing charge generation efficiency. Our work suggests designing donor and acceptor materials with high luminescence efficiency and complementary optical absorption bands extending into the near-infrared region.
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| 19. |
- Cheng, Shi-Ping, et al.
(författare)
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Haplotype-resolved genome assembly and allele-specific gene expression in cultivated ginger
- 2021
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Ingår i: Horticulture Research. - : Springer Nature. - 2052-7276. ; 8:1
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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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| 20. |
- Cui, Manying, et al.
(författare)
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Regulation of Lithium-Ion Flux by Nanotopology Lithiophilic Boron-Oxygen Dipole in Solid Polymer Electrolytes for Lithium-Metal Batteries
- 2023
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Ingår i: Energy & Environmental Materials. - 2575-0356.
-
Tidskriftsartikel (refereegranskat)abstract
- Inhomogeneous lithium-ion (Li+) deposition is one of the most crucial problems, which severely deteriorates the performance of solid-state lithium metal batteries (LMBs). Herein, we discovered that covalent organic framework (COF-1) with periodically arranged boron-oxygen dipole lithiophilic sites could directionally guide Li+ even deposition in asymmetric solid polymer electrolytes. This in situ prepared 3D cross-linked network Poly(ACMO-MBA) hybrid electrolyte simultaneously delivers outstanding ionic conductivity (1.02 × 10−3 S cm−1 at 30 °C) and excellent mechanical property (3.5 MPa). The defined nanosized channel in COF-1 selectively conducts Li+ increasing Li+ transference number to 0.67. Besides, The COF-1 layer and Poly(ACMO-MBA) also participate in forming a boron-rich and nitrogen-rich solid electrolyte interface to further improve the interfacial stability. The Li‖Li symmetric cell exhibits remarkable cyclic stability over 1000 h. The Li‖NCM523 full cell also delivers an outstanding lifespan over 400 cycles. Moreover, the Li‖LiFePO4 full cell stably cycles with a capacity retention of 85% after 500 cycles. the Li‖LiFePO4 pouch full exhibits excellent safety performance under pierced and cut conditions. This work thereby further broadens and complements the application of COF materials in polymer electrolyte for dendrite-free and high-energy-density solid-state LMBs.
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| 21. |
- Cui, Shaohua, 1995, et al.
(författare)
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Delay-throughput tradeoffs for signalized networks with finite queue capacity
- 2024
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Ingår i: Transportation Research Part B: Methodological. - 0191-2615. ; 180
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Tidskriftsartikel (refereegranskat)abstract
- Network-level adaptive signal control is an effective way to reduce delay and increase network throughput. However, in the face of asymmetric exogenous demand, the increase of network performance via adaptive signal control alone is at the expense of service fairness (i.e., phase actuation fairness and network resource utilization fairness). In addition, for oversaturated networks, arbitrary adaptive signal control seems to have little effect on improving network performance. Therefore, under the assumption that the mean routing proportions/turn ratios of vehicles at intersections are fixed, this study investigates the problem of optimally allocating input rates to entry links and simultaneously finding a stabilizing signal control policy with phase fairness. We model the stochastic optimization problem of maximizing network throughput subject to network stability (i.e., all queue lengths have finite means) and average phase actuation constraints to bridge the gap between stochastic network stability control and convex optimization. Moreover, we further propose a micro-level joint admission and bounded signal control algorithm to achieve network stability and throughput optimization simultaneously. Joint control is implemented in a fully decomposed and distributed manner. For any arrival rate, joint control provably achieves network throughput within O(1/V) of optimality while trading off average delay with O(V), where V is an adjusted control parameter. Through a comparative simulation of a real network with 256 O-D pairs, the proposed joint control keeps network throughput at maximum, guarantees service fairness, and fully utilizes network capacity (i.e., increases network throughput by 17.54%).
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| 22. |
- Dai, Tingyang, et al.
(författare)
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Sequential Polymer Precipitation of Core-Shell Microstructured Composites with Giant Permittivity
- 2010
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Ingår i: Macromolecular rapid communications. - : Wiley-VCH Verlag. - 1022-1336 .- 1521-3927. ; 31:5, s. 484-489
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Tidskriftsartikel (refereegranskat)abstract
- Polymeric core shell microstructures have been constructed through a new method, namely sequential precipitation, which is intrinsically a self-assembly and phase separation process. High-quality poly(vinyldene fluoride)-polycarbonate-lithium perchlorate composite films with spherical core shell microstructures have been prepared and determined to consist of conducting cores and insulating shells. Because of the percolation effect, the resulting materials present a dielectric constant as high as 10(4)-10(7) at the threshold.
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| 23. |
- Dong, Pingping, et al.
(författare)
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Receiver-Side TCP Countermeasure in Cellular Networks
- 2019
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Ingår i: Sensors. - : MDPI. - 1424-8220. ; 19:12
-
Tidskriftsartikel (refereegranskat)abstract
- Cellular-based networks keep large buffers at base stations to smooth out the bursty data traffic, which has a negative impact on the user’s Quality of Experience (QoE). With the boom of smart vehicles and phones, this has drawn growing attention. For this paper, we first conducted experiments to reveal the large delays, thus long flow completion time (FCT), caused by the large buffer in the cellular networks. Then, a receiver-side transmission control protocol (TCP) countermeasure named Delay-based Flow Control algorithm with Service Differentiation (DFCSD) was proposed to target interactive applications requiring high throughput and low delay in cellular networks by limiting the standing queue size and decreasing the amount of packets that are dropped in the eNodeB in Long Term Evolution (LTE). DFCSD stems from delay-based congestion control algorithms but works at the receiver side to avoid the performance degradation of the delay-based algorithms when competing with loss-based mechanisms. In addition, it is derived based on the TCP fluid model to maximize the network utility. Furthermore, DFCSD also takes service differentiation into consideration based on the size of competing flows to shorten their completion time, thus improving user QoE. Simulation results confirmed that DFCSD is compatible with existing TCP algorithms, significantly reduces the latency of TCP flows, and increases network throughput.
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| 24. |
- Felsberg, Michael, et al.
(författare)
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The Thermal Infrared Visual Object Tracking VOT-TIR2015 Challenge Results
- 2015
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Ingår i: Proceedings of the IEEE International Conference on Computer Vision. - : Institute of Electrical and Electronics Engineers (IEEE). - 9781467383905 ; , s. 639-651
-
Konferensbidrag (refereegranskat)abstract
- The Thermal Infrared Visual Object Tracking challenge 2015, VOTTIR2015, aims at comparing short-term single-object visual trackers that work on thermal infrared (TIR) sequences and do not apply prelearned models of object appearance. VOT-TIR2015 is the first benchmark on short-term tracking in TIR sequences. Results of 24 trackers are presented. For each participating tracker, a short description is provided in the appendix. The VOT-TIR2015 challenge is based on the VOT2013 challenge, but introduces the following novelties: (i) the newly collected LTIR (Linköping TIR) dataset is used, (ii) the VOT2013 attributes are adapted to TIR data, (iii) the evaluation is performed using insights gained during VOT2013 and VOT2014 and is similar to VOT2015.
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| 25. |
- Gao, Bin, et al.
(författare)
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An efficient first-principle approach for electronic structures calculations of nanomaterials
- 2008
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Ingår i: Journal of Computational Chemistry. - : Wiley. - 0192-8651 .- 1096-987X. ; 29:3, s. 434-444
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Tidskriftsartikel (refereegranskat)abstract
- An efficient parallel implementation has been realized for a recently proposed central insertion scheme (Jiang, Liu, Lu, Luo. J Chem Phys 2006,124,214711; J Chem Phys 2006,125, 149902) that allows to calculate electronic structures of nanomaterials at various density functional theory levels. It has adopted the sparse-matrix format for Fock/Kohn-Sham and overlap matrices, as well as a combination of implicitly restarted Arnoldi methods (IRAM) and spectral transformation for computing selected eigenvalues/eigenvectors. A systematic error analysis and control for the proposed method has been provided based on a strict mathematical basis. The efficiency and applicability of the new implementation have been demonstrated by calculations of electronic structures of two different nanomaterials consisting of one hundred thousand electrons.
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| 26. |
- Gao, Hong, et al.
(författare)
-
The landscape of tolerated genetic variation in humans and primates
- 2023
-
Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 380:6648
-
Tidskriftsartikel (refereegranskat)abstract
- Personalized genome sequencing has revealed millions of genetic differences between individuals, but our understanding of their clinical relevance remains largely incomplete. To systematically decipher the effects of human genetic variants, we obtained whole-genome sequencing data for 809 individuals from 233 primate species and identified 4.3 million common protein-altering variants with orthologs in humans. We show that these variants can be inferred to have nondeleterious effects in humans based on their presence at high allele frequencies in other primate populations. We use this resource to classify 6% of all possible human protein-altering variants as likely benign and impute the pathogenicity of the remaining 94% of variants with deep learning, achieving state-of-the-art accuracy for diagnosing pathogenic variants in patients with genetic diseases.
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| 27. |
- Gao, Kai, et al.
(författare)
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Application of Rainbow Trout CYP1 Gene Expression Patterns in Gill and Liver for Haihe River Bio-monitoring
- 2015
-
Ingår i: Huanjing Kexue. - 0250-3301. ; 36:10, s. 3878-3883
-
Tidskriftsartikel (refereegranskat)abstract
- CYP1 subfamily genes in gills and liver of rainbow trout as biomarkers were studied to establish methods for quantitative mRNA expression analysis of these genes and to determine their expression pattern. Fish caged in various waters in the Haihe River (Tianjin) were analyzed. The mRNA expression patterns observed in Machangjian River and estuary site of Haihe River were markedly similar but at different levels, reflecting that those sites shared the similar pollution components but with different local pollution load. CYP1C1 and 1C3 were only induced at Gegu site and estuary site of Haihe River, indicating different types of CYP1 agonists in Machangjian River. Response patterns of multiple CYP1 genes in gills and liver could be applied in the monitoring strategy. The response patterns of CYP1 genes could be used for better understanding the relationship between complex mixtures of pollutants and biological response of organisms in aquatic environments.
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| 28. |
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| 29. |
- Gao, Kai
(författare)
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Basal and Pollutant-induced Expression of CYP1A, 1B and 1C isoforms in Fish : Implications for Biomonitoring
- 2013
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Aquatic wildlife are exposed to contaminants in their natural habitats, and toxic pollutants may induce toxicity in sensitive target tissues and cells. There is therefore a need to establish biomarkers to determine exposure to certain classes of contaminants and the subsequent biological responses. In the present work the whole suite of cytochrome P450 1 (CYP1) genes expressed in fish were examined with regard to their inducibility and potential use as biomarkers. Complementary DNA of the CYP1A, 1B and 1C transcripts in rainbow trout and three-spined stickleback were cloned and characterized by quantitative mRNA expression analysis. All CYP1 transcripts could be induced by two selected aryl hydrocarbon receptor (AhR) agoinsts (indigo and PCB 126) in both species, suggesting that all genes were regulated by the AhR. CYP1 mRNA expression profiles induced by PCB 126 and indigo varied over time showing that PCB 126 gave rise to a high and persistent induction in gills and liver while induction by indigo was transient in both organs. The uptake and kinetics of 14C-indigo was studied by autoradiography in rainbow trout. A rapid uptake of 14C-indigo from the water and a subsequent elimination in bile and intestinal contents was observed, explaining the transient CYP1 induction. A high accumulation of 14C-indigo in the gills was completely blocked the CYP1 inhibitor ellipticine, suggesting a CYP1-dependent uptake. High dilutions of a sewage treatment plant effluent containing a complex mixture of pharmaceuticals were investigated. The same water sample both induced CYP1A mRNA expression and inhibited catalytic activity of CYP1A. A field study revealed different induction signatures of the CYP1 genes examined at various locations in Uppsala water environments. As concluded by the temporal and spatial responses obtained, the results of this work suggest that the CYP1 gene panel could be used for biomonitoring of environmental contaminants acting on the CYP system. Further field studies will be required to evaluate this possibility.
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| 30. |
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| 31. |
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| 32. |
- Gao, Kai, et al.
(författare)
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Cytochrome P450 1A, 1B, and 1C mRNA induction patterns in three-spined stickleback exposed to a transient and a persistent inducer
- 2011
-
Ingår i: Comparative Biochemistry and Physiology - Part C. - : Elsevier BV. - 1532-0456 .- 1878-1659. ; 154:1, s. 42-55
-
Tidskriftsartikel (refereegranskat)abstract
- Cytochrome P450 1 (CYP1) mRNA induction patterns in three-spined stickleback (Gasterosteus aculeatus) were explored for use in environmental monitoring of aryl hydrocarbon receptor (AHR) agonists. The cDNAs of stickleback CYP1A, CYP1B1, CYP1C1, and CYP1C2 were cloned and their basal and induced expression patterns were determined in the brain, gill, liver and kidney. Also, their induction time courses were compared after waterborne exposure to a transient (indigo) or a persistent (3,3',4,4',5-pentacholorbiphenyl PCB 126) AHR agonist. The cloned stickleback CYP1s exhibited a high amino acid sequence identity compared with their zebrafish orthologs and their constitutive tissue distribution patterns largely agreed with those reported in other species. PCB 126 (100 nM) induced different CYP1 expression patterns in the four tissues, suggesting tissue-specific regulation. Both indigo (1 nM) and PCB 126 (10 nM) induced a strong CYP1 expression in gills. However, while PCB 126 gave rise to a high and persistent induction in gills and liver, induction by indigo was transient in both organs. The number of putative dioxin response elements found in each CYP1 gene promoter roughly reflected the induction levels of the genes. The high responsiveness of CYP1A,CYP1B1, and CYP1C1 observed in several organs suggests that three-spined stickleback is suitable for monitoring of pollution with AHR agonists.
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| 33. |
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| 34. |
- Gao, Kai, et al.
(författare)
-
Induction of Cytochrome P4501 Genes by Various Inducers in Rainbow Trout (Oncorhynchus mykiss)
- 2020
-
Ingår i: Journal of Coastal Research. - : COASTAL EDUCATION & RESEARCH FOUNDATION. - 0749-0208 .- 1551-5036. ; 37:1, s. 143-148
-
Tidskriftsartikel (refereegranskat)abstract
- Juvenile rainbow trout is widely found in various aquatic systems, such as freshwater, coastal, and marine habitats all over the world. Expression patterns of the cytochrome P4501 (CYP1) genes exposed to various stressors in such fish could be informative and useful in biomonitoring. In the present study, the induction of CYP1 in rainbow trout by indigo, humic acid (HA), and benzo(a)pyrene (BaP) was studied through a 12-hour exposure experiment by using rainbow trout as an experimental object. First, 7-ethoxyresorufin O-deethylase (EROD) activity and CYP1 expression levels in fish exposed to different concentrations of indigo were analyzed. The EROD activities in fish gills were greatly affected by the concentration of indigo (1, 18, 50, and 80 nM). The expression level of CYP1A1 and CYP1A3 in gills was higher compared with CYP1B1 and CYP1Cs. Second, the gill EROD activity and CYP1 mRNA expressions levels were compared when induced by indigo, HA, and BaP at the same concentration (1 nM). Results indicated that rainbow trout were sensitive to all three inducers. Among them, the HA affected CYP1A1 and CYP1A3 most obviously. CYP1A, as an important biomarker, was more sensitive than CYP1B and CYP1C to those inducers. The observed effects of the different CYP1 inducers could provide a useful tool for monitoring of AhR-active pollutants in the aquatic environment.
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| 35. |
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| 36. |
- Gao, Rong, et al.
(författare)
-
Deep sequencing reveals global patterns of mRNA recruitment during translation initiation
- 2016
-
Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 6
-
Tidskriftsartikel (refereegranskat)abstract
- In this work, we developed a method to systematically study the sequence preference of mRNAs during translation initiation. Traditionally, the dynamic process of translation initiation has been studied at the single molecule level with limited sequencing possibility. Using deep sequencing techniques, we identified the sequence preference at different stages of the initiation complexes. Our results provide a comprehensive and dynamic view of the initiation elements in the translation initiation region (TIR), including the S1 binding sequence, the Shine-Dalgarno (SD)/anti-SD interaction and the second codon, at the equilibrium of different initiation complexes. Moreover, our experiments reveal the conformational changes and regional dynamics throughout the dynamic process of mRNA recruitment.
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| 37. |
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| 38. |
- Guo, Renjun, et al.
(författare)
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Degradation mechanisms of perovskite solar cells under vacuum and one atmosphere of nitrogen
- 2021
-
Ingår i: Nature Energy. - : Springer Nature. - 2058-7546. ; 6:10, s. 977-
-
Tidskriftsartikel (refereegranskat)abstract
- Extensive studies have focused on improving the operational stability of perovskite solar cells, but few have surveyed the fundamental degradation mechanisms. One aspect overlooked in earlier works is the effect of the atmosphere on device performance during operation. Here we investigate the degradation mechanisms of perovskite solar cells operated under vacuum and under a nitrogen atmosphere using synchrotron radiation-based operando grazing-incidence X-ray scattering methods. Unlike the observations described in previous reports, we find that light-induced phase segregation, lattice shrinkage and morphology deformation occur under vacuum. Under nitrogen, only lattice shrinkage appears during the operation of solar cells, resulting in better device stability. The different behaviour under nitrogen is attributed to a larger energy barrier for lattice distortion and phase segregation. Finally, we find that the migration of excessive PbI2 to the interface between the perovskite and the hole transport layer degrades the performance of devices under vacuum or under nitrogen. Understanding degradation mechanisms in perovskite solar cells is key to their development. Now, Guo et al. show a greater degradation of the perovskite structure and morphology for devices operated under vacuum than under nitrogen.
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| 39. |
- Havstorm, Tanja Elina, 1991-
(författare)
-
Cargo Cult in Agile Software Development
- 2023
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Software development (SD) projects are complex endeavors, and organizations employ software development methods (SDMs) both to add structure and to propel their projects. Nowadays, agile SDMs are the most used methods. Still, inefficient and ineffective use of SDMs is a challenge, and existing research shows cases of SD teams failing in their use of SDMs due to deviations made. Of course, methods should not be used in rigorous and textbook-like ways. Among practitioners, some of these deviations are referred to as cargo cult behavior; without, however, providing much of theoretical depth or any analytical tools to identify and characterize such behaviors. Although existing research has investigated SDM deviations, they have not been investigated as cargo cult behavior.Against this backdrop, the aim of this thesis is to understand the challenges in succeeding with SDM use by developing a theory called SDM cargo cult theory (SDMCCT), to identify, analyze, and describe the cargo cult phenomenon in agile SDM use. The journey of this thesis takes its starting point in practitioners’ use of the buzzwords “cargo cult” when referring to flawed SDM use. By returning to the field of social anthropology and its studies of cargo cult, a definition of SDM cargo cult and an analytical framework are iteratively crafted through a longitudinal ethnographic study to constitute the SDMCCT. The research approach has been abductive and the SDMCCT builds on social action theory and work motivation theory.The ethnographical study took place at an international industrial manufacturing company in Sweden that is using agile SDMs. This study includes three years of data collection, which includes observations, interviews, and gathering of business documents. The ethnographic study focused on three SD teams and their daily work using agile SDMs. The analysis using the analytical framework includes four agile SDM practices: daily scrum meeting, sprint demo, continuous integration, and visualization. In total, the analysis uncovered 36 deviations in the SD teams’ use of these practices, structured into 30 SDM cargo cult categories. In addition, this study shows that the framework is applicable to analyze and characterize effective SDM use as well, although it is not its main focus. The framework can be used by researchers to make similar analysis of cargo cult situations in other organizations, and the catalogue of cargo cult situations can serve as background knowledge for other organizations to study and improve their SD teams’ use of agile SDM practices.
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| 40. |
- Islam, M. Sirajul, 1974-, et al.
(författare)
-
Learners and their learning environment in Swedish higher education : Challenges in computer-mediated learning during COVID-19
- 2023
-
Ingår i: Nordic Journal of Digital Literacy. - Norway : Universitetsforlaget. - 1891-943X. ; 18:1, s. 35-47
-
Tidskriftsartikel (refereegranskat)abstract
- This paper aims at investigating the issues and challenges experienced by remote learning among the students of higher education in the context of Sweden during COVID-19. The pandemic situation influenced the emergence of a new learning context and the effectiveness of the computer-mediated remote learning from the sudden transition of traditional approaches poised many interesting issues. The empirical part of the study was based on a web-based survey conducted among 1767 anonymous students studied at 30 higher educational institutions in Sweden during the pandemic period in mid-2020. The results are presented in line with Zimmerman’s (2000) triadic (personal, environmental and behavioural) forms of self-regulation. The survey indicated that the perceived worries students experienced were oriented towards the students’ own personal situation, and future possibilities rather than the general state and welfare of the global society. The fast transition to online classes and seminars led to a lot of students being worried about their abilities to maintain efficiency in their studies. The findings of this study could provide refined insights into the issues that we should have in mind while formulating strategies for effective remote learning in such a changing environment during a crisis period not only in Sweden but also in some international contexts.
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| 41. |
- Jacobs, Kevin B, et al.
(författare)
-
Detectable clonal mosaicism and its relationship to aging and cancer.
- 2012
-
Ingår i: Nature Genetics. - New York : Nature Publishing Group. - 1061-4036 .- 1546-1718. ; 44:6, s. 651-658
-
Tidskriftsartikel (refereegranskat)abstract
- In an analysis of 31,717 cancer cases and 26,136 cancer-free controls from 13 genome-wide association studies, we observed large chromosomal abnormalities in a subset of clones in DNA obtained from blood or buccal samples. We observed mosaic abnormalities, either aneuploidy or copy-neutral loss of heterozygosity, of >2 Mb in size in autosomes of 517 individuals (0.89%), with abnormal cell proportions of between 7% and 95%. In cancer-free individuals, frequency increased with age, from 0.23% under 50 years to 1.91% between 75 and 79 years (P = 4.8 × 10(-8)). Mosaic abnormalities were more frequent in individuals with solid tumors (0.97% versus 0.74% in cancer-free individuals; odds ratio (OR) = 1.25; P = 0.016), with stronger association with cases who had DNA collected before diagnosis or treatment (OR = 1.45; P = 0.0005). Detectable mosaicism was also more common in individuals for whom DNA was collected at least 1 year before diagnosis with leukemia compared to cancer-free individuals (OR = 35.4; P = 3.8 × 10(-11)). These findings underscore the time-dependent nature of somatic events in the etiology of cancer and potentially other late-onset diseases.
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| 42. |
- Jiang, Jizhong, et al.
(författare)
-
Synergistic strain engineering of perovskite single crystals for highly stable and sensitive X-ray detectors with low-bias imaging and monitoring
- 2022
-
Ingår i: Nature Photonics. - : Nature Portfolio. - 1749-4885 .- 1749-4893. ; 16:8, s. 575-581
-
Tidskriftsartikel (refereegranskat)abstract
- X-ray detectors based on dual-site-doped perovskite single crystals exhibit excellent sensitivity of 2.6 x 10(4) mu C Gy(air)(-1) cm(-2) under a low field of 1 V cm(-1). The detectable dose rate is as low as 7.09 nGy(air) s(-1). The operational stability is beyond half a year. Although three-dimensional metal halide perovskite (ABX(3)) single crystals are promising next-generation materials for radiation detection, state-of-the-art perovskite X-ray detectors include methylammonium as A-site cations, limiting the operational stability. Previous efforts to improve the stability using formamidinium-caesium-alloyed A-site cations usually sacrifice the detection performance because of high trap densities. Here we successfully solve this trade-off between stability and detection performance by synergistic composition engineering, where we include A-site alloys to decrease the trap density and B-site dopants to release the microstrain induced by A-site alloying. As such, we develop high-performance perovskite X-ray detectors with excellent stability. Our X-ray detectors exhibit high sensitivity of (2.6 +/- 0.1) x 10(4) mu C Gy(air)(-1) cm(-2) under 1 V cm(-1) and ultralow limit of detection of 7.09 nGy(air) s(-1). In addition, they feature long-term operational stability over half a year and impressive thermal stability up to 125 degrees C. We further demonstrate the promise of our perovskite X-ray detectors for low-bias portable applications with high-quality X-ray imaging and monitoring prototypes.
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| 43. |
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| 44. |
- Jönsson, Maria E., et al.
(författare)
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Induction patterns of new CYP1 genes in environmentally exposed rainbow trout
- 2010
-
Ingår i: Aquatic Toxicology. - : Elsevier BV. - 0166-445X .- 1879-1514. ; 98:4, s. 311-321
-
Tidskriftsartikel (refereegranskat)abstract
- The cytochrome P4501 (CYP1) gene family comprises four subfamilies in fish: CYP1A, CYP1B, CYP1C, and CYP1D. Only two CYP1 genes, CYP1A1 and CYP1A3, are so far known in rainbow trout (Oncorhynchus mykiss). The present study aimed to identify other CYP1 subfamily genes in rainbow trout, to establish methods for quantitative mRNA expression analysis of these genes, and to determine their basal and induced mRNA expression in gills and liver. Another goal was to examine their mRNA expression in environmentally exposed fish. We cloned four new transcripts, denoted rbCYP1B1, rbCYP1C1, rbCYP1C2, and rbCYP1C3. Levels of these and the previously known rbCYP1A transcripts were determined by real-time PCR in unexposed fish, fish exposed to the potent aryl hydrocarbon receptor (AhR) agonist 3,3',4,4',5-pentachlorobiphenyl (PCB126), and fish caged in various waters in the Uppsala region (Sweden). The mRNA expression patterns observed in unexposed rainbow trout (basal levels) were markedly similar to those reported for orthologous genes in other species. All six transcripts were induced by PCB126 in gills and liver, suggesting all genes to be AhR regulated. The caged fish showed clear rbCYP1 induction in gills at all monitoring sites (up to 70-fold the basal level), whereas the liver responses were weak; induction (up to 5-fold) was recorded only at the Uppsala municipal sewage treatment plant outlet. Gill filament EROD activity was induced at all caging sites. Most interestingly, the rbCYP1 gene response patterns in gills differed among caging sites and among subfamilies. The EROD induction seemed to only reflect induction of rbCYP1A transcription. Response patterns of multiple CYP1 genes in gills and liver could provide an improved monitoring strategy. Such patterns could be used to characterize complex mixtures of AhR agonists and antagonists in aquatic environments.
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| 45. |
- Kuderna, Lukas F. K., et al.
(författare)
-
A global catalog of whole-genome diversity from 233 primate species
- 2023
-
Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 380:6648, s. 906-913
-
Tidskriftsartikel (refereegranskat)abstract
- The rich diversity of morphology and behavior displayed across primate species provides an informative context in which to study the impact of genomic diversity on fundamental biological processes. Analysis of that diversity provides insight into long-standing questions in evolutionary and conservation biology and is urgent given severe threats these species are facing. Here, we present high-coverage wholegenome data from 233 primate species representing 86% of genera and all 16 families. This dataset was used, together with fossil calibration, to create a nuclear DNA phylogeny and to reassess evolutionary divergence times among primate clades. We found within-species genetic diversity across families and geographic regions to be associated with climate and sociality, but not with extinction risk. Furthermore, mutation rates differ across species, potentially influenced by effective population sizes. Lastly, we identified extensive recurrence of missense mutations previously thought to be human specific. This study will open a wide range of research avenues for future primate genomic research.
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| 46. |
- Kuderna, Lukas F. K., et al.
(författare)
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Identification of constrained sequence elements across 239 primate genomes
- 2024
-
Ingår i: Nature. - : Springer Nature. - 0028-0836 .- 1476-4687. ; 625:7996, s. 735-742
-
Tidskriftsartikel (refereegranskat)abstract
- Noncoding DNA is central to our understanding of human gene regulation and complex diseases1,2, and measuring the evolutionary sequence constraint can establish the functional relevance of putative regulatory elements in the human genome3,4,5,6,7,8,9. Identifying the genomic elements that have become constrained specifically in primates has been hampered by the faster evolution of noncoding DNA compared to protein-coding DNA10, the relatively short timescales separating primate species11, and the previously limited availability of whole-genome sequences12. Here we construct a whole-genome alignment of 239 species, representing nearly half of all extant species in the primate order. Using this resource, we identified human regulatory elements that are under selective constraint across primates and other mammals at a 5% false discovery rate. We detected 111,318 DNase I hypersensitivity sites and 267,410 transcription factor binding sites that are constrained specifically in primates but not across other placental mammals and validate their cis-regulatory effects on gene expression. These regulatory elements are enriched for human genetic variants that affect gene expression and complex traits and diseases. Our results highlight the important role of recent evolution in regulatory sequence elements differentiating primates, including humans, from other placental mammals.
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| 47. |
- Li, Jing, et al.
(författare)
-
An obligatory role for neurotensin in high-fat-diet-induced obesity
- 2016
-
Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 533, s. 411-415
-
Tidskriftsartikel (refereegranskat)abstract
- Obesity and its associated comorbidities (for example, diabetes mellitus and hepatic steatosis) contribute to approximately 2.5 million deaths annually and are among the most prevalent and challenging conditions confronting the medical profession. Neurotensin (NT; also known as NTS), a 13-amino-acid peptide predominantly localized in specialized enteroendocrine cells of the small intestine and released by fat ingestion, facilitates fatty acid translocation in rat intestine, and stimulates the growth of various cancers. The effects of NT are mediated through three known NT receptors (NTR1, 2 and 3; also known as NTSR1, 2, and NTSR3, respectively). Increased fasting plasma levels of pro-NT (a stable NT precursor fragment produced in equimolar amounts relative to NT) are associated with increased risk of diabetes, cardiovascular disease and mortality; however, a role for NT as a causative factor in these diseases is unknown. Here we show that NT-deficient mice demonstrate significantly reduced intestinal fat absorption and are protected from obesity, hepatic steatosis and insulin resistance associated with high fat consumption. We further demonstrate that NT attenuates the activation of AMP-activated protein kinase (AMPK) and stimulates fatty acid absorption in mice and in cultured intestinal cells, and that this occurs through a mechanism involving NTR1 and NTR3 (also known as sortilin). Consistent with the findings in mice, expression of NT in Drosophila midgut enteroendocrine cells results in increased lipid accumulation in the midgut, fat body, and oenocytes (specialized hepatocyte-like cells) and decreased AMPK activation. Remarkably, in humans, we show that both obese and insulin-resistant subjects have elevated plasma concentrations of pro-NT, and in longitudinal studies among non-obese subjects, high levels of pro-NT denote a doubling of the risk of developing obesity later in life. Our findings directly link NT with increased fat absorption and obesity and suggest that NT may provide a prognostic marker of future obesity and a potential target for prevention and treatment.
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| 48. |
- Li, Jian, et al.
(författare)
-
Array Comparative Genomic Hybridization of Keratoacanthomas and Squamous Cell Carcinomas: Different Patterns of Genetic Aberrations Suggest Two Distinct Entities
- 2012
-
Ingår i: Journal of Investigative Dermatology. - : Elsevier BV. - 1523-1747 .- 0022-202X. ; 132:8, s. 2060-2066
-
Tidskriftsartikel (refereegranskat)abstract
- Keratoacanthoma (KA) is a benign keratinocytic neoplasm that spontaneously regresses after 3-6 months and shares features with squamous cell carcinomas (SCCs). Furthermore, there are reports of KAs that have metastasized, invoking the question of whether KA is a variant of SCC (Hodak et al., 1993). To date, no reported criteria are sensitive enough to discriminate reliably between KA and SCC, and consequently there is a clinical need for discriminating markers. Our previous study analyzed 132 KAs and 29 SCCs and revealed significantly different regions of genomic aberrations using chromosomal comparative genomic hybridization (CGH). In the present study, we applied array CGH to investigate 98 KAs and 22 SCCs from the above samples. The result shows that all KAs and SCCs have some degree of genetic aberrations. The distribution of numbers of aberrant clones per sample differed significantly between KAs and SCCs (P<0.02), which also demonstrated recurrent aberrations that differed significantly (P<0.001), as illustrated by unsupervised cluster analysis. Classifiers for clinicopathological parameters of KAs were established based on t-test statistics and permutation tests. Tumor size, fibrosis, and inflammation, which are related to the developmental stages of KAs, showed significant (t-test, permutation test) associations with aberrations of selected genomic regions. This suggests chromosomal instability during the whole life cycle of KAs.
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| 49. |
- Li, Kai, et al.
(författare)
-
A novel engine and battery coupled thermal management strategy for connected HEVs based on switched model predictive control under low temperature
- 2023
-
Ingår i: Energy. - : PERGAMON-ELSEVIER SCIENCE LTD. - 0360-5442 .- 1873-6785. ; 278
-
Tidskriftsartikel (refereegranskat)abstract
- Under a low-temperature environment, electric vehicles face serious environmental adaptability problems, and efficient vehicle thermal management strategies are urgently needed. This paper presents a novel engine- battery coupled thermal management strategy for connected hybrid electric vehicles (HEVs). An improved system structure for an engine-battery coupled thermal management system (engine-battery CTMS) is designed to avoid unnecessary heat loss. The control requirements of the engine-battery CTMS include minimum engine fuel consumption, minimum power battery aging damage and minimum system energy consumption, which constitutes a multi-objective optimal control problem in a finite time domain. Based on model predictive control (MPC) theory, a switched nonlinear MPC (NMPC) control strategy is proposed to solve the optimal control problem of the complex coupled multi-input multi-output system. To verify the effectiveness of the proposed strategy, three comparative experiments of the centralized NMPC-based and rule-based methods combined with the improved system structure and the unimproved system structure are designed. The results of the cosimulation experiment between MATLAB/Simulink and AMEsim under various driving cycles and different ambient temperatures show that the improved structure and switched control strategy confer great advantages in reducing the controller computation burden, engine fuel consumption, and power battery aging damage.
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| 50. |
- Li, Kai, et al.
(författare)
-
An advanced control strategy for engine thermal management systems with large pure time delay
- 2023
-
Ingår i: Applied Thermal Engineering. - : PERGAMON-ELSEVIER SCIENCE LTD. - 1359-4311 .- 1873-5606. ; 224
-
Tidskriftsartikel (refereegranskat)abstract
- Stable and precise temperature control can effectively improve the engines fuel consumption and emissions. An advanced engine thermal management system (AETMS) composed of electric actuators has great potential in increasing the temperature tracking control accuracy and decreasing the system energy consumption. Time -varying disturbance and pure time delay in the system make it challenging to harmoniously control multiple actuators to ensure efficient temperature tracking performance. In addition, a reasonable power distribution of the actuators is beneficial to reduce the parasitic energy consumption of the system and further improve the system efficiency. In this article, an adaptive optimization control strategy consisting of a state predictor, a disturbance estimator, an energy consumption optimization block and a state tracking controller is proposed for the temperature tracking and energy consumption optimization of AETMS. Experimental verification was performed on a range extender bench of an extended-range electric vehicle, and the results show that the system achieves high-precision temperature control and energy consumption near the theoretical optimal value under changing working conditions. The temperature steady-state error is within 0.3 oC, and the temperature adjustment time is within 100 s after the first overshoot.
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