| 1. |
- 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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| 2. |
- 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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| 3. |
- Ding, Xue Bing, et al.
(författare)
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Impaired meningeal lymphatic drainage in patients with idiopathic Parkinson’s disease
- 2021
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Ingår i: Nature Medicine. - : Springer Science and Business Media LLC. - 1078-8956 .- 1546-170X. ; 27:3, s. 411-418
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Tidskriftsartikel (refereegranskat)abstract
- Animal studies implicate meningeal lymphatic dysfunction in the pathogenesis of neurodegenerative diseases such as Alzheimer’s disease and Parkinson’s disease (PD). However, there is no direct evidence in humans to support this role1–5. In this study, we used dynamic contrast-enhanced magnetic resonance imaging to assess meningeal lymphatic flow in cognitively normal controls and patients with idiopathic PD (iPD) or atypical Parkinsonian (AP) disorders. We found that patients with iPD exhibited significantly reduced flow through the meningeal lymphatic vessels (mLVs) along the superior sagittal sinus and sigmoid sinus, as well as a notable delay in deep cervical lymph node perfusion, compared to patients with AP. There was no significant difference in the size (cross-sectional area) of mLVs in patients with iPD or AP versus controls. In mice injected with α-synuclein (α-syn) preformed fibrils, we showed that the emergence of α-syn pathology was followed by delayed meningeal lymphatic drainage, loss of tight junctions among meningeal lymphatic endothelial cells and increased inflammation of the meninges. Finally, blocking flow through the mLVs in mice treated with α-syn preformed fibrils increased α-syn pathology and exacerbated motor and memory deficits. These results suggest that meningeal lymphatic drainage dysfunction aggravates α-syn pathology and contributes to the progression of PD.
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| 4. |
- Hua, Dong, et al.
(författare)
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Small interfering RNA-directed targeting of toll-like receptor 4 inhibits human prostate cancer cell invasion, survival, and tumorigenicity
- 2009
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Ingår i: Molecular Immunology. - : Elsevier BV. - 0161-5890 .- 1872-9142. ; 46:15, s. 2876-2884
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Tidskriftsartikel (refereegranskat)abstract
- A major cause of tumor treatment failure is cancer cell metastasis. Toll-like receptor 4 (TLR4)-mediated signaling has been implicated in tumor cell invasion, survival, and metastasis in a variety of cancers. In this study, we investigated the biological roles of TLR4 in prostate metastatic cell invasion and survival, and the potential of gene silencing of TLR4 using small interfering RNA (siRNA) for treatment of cancer. In cultured human prostate cancer cell lines, TLR4 were higher PC3 and DU145 as compared with the poorly metastatic LNCaP indicating that up-regulation of TLR4 was positively correlated with metastasis of tumor cell. In the highly metastatic cancer cell PC3, gene silencing of TLR4 using siRNA significantly inhibited TLR4 mRNA expression and protein level. Knockdown of TLR4 in PC3 cells resulted in a dramatic reduction of tumor cell migration and invasion as indicated by a Matrigel invasion assay. Furthermore, TLR4 siRNA suppressed cell viability and ultimately caused the induction of apoptotic cell death. The effects were associated with abrogating TLR4-mediated signaling to downstream target molecules such as myeloid differentiation factor 88 (MyD88), adaptor-inducing IFN-beta (TRIF), and interferon regulatory factor-1 (IRF-1). In a mouse prostate cancer model, administration with the plasmid construct expressing siRNA for TLR4 obviously inhibited established tumor growth and survival. These studies revealed evidence of a multifaceted signaling network operating downstream of TLR4-mediated tumor cell invasion, proliferation, and survival. Thus, RNA interference-directed targeting of TLR4 may raise the potential of its application for cancer therapy.
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| 5. |
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| 6. |
- Yuan, Qin, et al.
(författare)
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A late Eocene palynological record from the Nangqian Basin, TibetanPlateau: Implications for stratigraphy and paleoclimate
- 2017
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Ingår i: Palaeoworld. - Nanjing : Elsevier. - 1871-174X .- 1875-5887. ; 26, s. 369-379
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Tidskriftsartikel (refereegranskat)abstract
- With the uplifting, large-scale thrusting and striking of the Tibetan Plateau, several Paleogene intracontinental basins formed within the northernTibetan Plateau (TP). Stratigraphical and paleoenvironmental studies of the sedimentary successions within these basins are critical for understandingPaleogene climatological changes in Eurasia. The Nangqian Basin, one of such basins, formed in the Yushu area of the northeastern Tibetan Plateau.A set of lacustrine sediments, dominated by red clasolite, marlite, and gypsum, developed in the Yang Ala section in this basin. Paleontologicalrecords from the Nangqian Basin remain poorly known. Here, we investigate the palynological assemblages of one sedimentary succession at theYang Ala section that belongs to the Gongjue Formation, and their implications regarding the geological age and paleoclimate are discussed. Theresults reveal that the assemblages are dominated mainly by angiosperm pollen (tricolpates and tricolporate), includingNitrariadites (Pokrovskaja), Quercoidites, and Labitricolpites, followed by gymnosperm pollen taxa, such as Ephedripites and Taxodiaceaepollenites, and sparse pteridophytespores produced by ferns. A late Eocene age is inferred based on palynostratigraphy and comparison with other pollen assemblages in the TP. Arelatively dry climate with brief humid periods is indicated by the high abundance of xerophytic pollen taxa, such as Ephedripites and Nitrariadites,which are associated with broadleaved deciduous and evergreen plants. The characteristics of the pollen assemblages from the studied Yang Alasection are consistent with other Cenozoic palynofloras from the Mahalagou Formation in the Xining Basin and with those of the Yaxicuo Groupin the Hoh Xil Basin. These results provide an improved stratigraphical scheme for parts of the Cenozoic and enrich the current knowledge of thevegetation history of the northeastern Tibetan Plateau.
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| 7. |
- Abdoullaye, Doukary, et al.
(författare)
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Permanent genetic resources added to molecular ecology resources database 1 August 2009 - 30 September 2009
- 2010
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Ingår i: Molecular Ecology Resources. - : Wiley. - 1755-098X .- 1755-0998. ; 10:1, s. 232-236
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Tidskriftsartikel (refereegranskat)abstract
- This article documents the addition of 238 microsatellite marker loci and 72 pairs of Single Nucleotide Polymorphism (SNP) sequencing primers to the Molecular Ecology Resources Database. Loci were developed for the following species: Adelges tsugae, Artemisia tridentata, Astroides calycularis, Azorella selago, Botryllus schlosseri, Botrylloides violaceus, Cardiocrinum cordatum var. glehnii, Campylopterus curvipennis, Colocasia esculenta, Cynomys ludovicianus, Cynomys leucurus, Cynomys gunnisoni, Epinephelus coioides, Eunicella singularis, Gammarus pulex, Homoeosoma nebulella, Hyla squirella, Lateolabrax japonicus, Mastomys erythroleucus, Pararge aegeria, Pardosa sierra, Phoenicopterus ruber ruber and Silene latifolia. These loci were cross-tested on the following species: Adelges abietis, Adelges cooleyi, Adelges piceae, Pineus pini, Pineus strobi, Tubastrea micrantha, three other Tubastrea species, Botrylloides fuscus, Botrylloides simodensis, Campylopterus hemileucurus, Campylopterus rufus, Campylopterus largipennis, Campylopterus villaviscensio, Phaethornis longuemareus, Florisuga mellivora, Lampornis amethystinus, Amazilia cyanocephala, Archilochus colubris, Epinephelus lanceolatus, Epinephelus fuscoguttatus, Symbiodinium temperate-A clade, Gammarus fossarum, Gammarus roeselii, Dikerogammarus villosus and Limnomysis benedeni. This article also documents the addition of 72 sequencing primer pairs and 52 allele specific primers for Neophocaena phocaenoides.
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| 8. |
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| 9. |
- Chen, Shao-Chun, et al.
(författare)
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First nationwide study regarding ceftriaxone resistance and molecular epidemiology of Neisseria gonorrhoeae in China
- 2016
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Ingår i: Journal of Antimicrobial Chemotherapy. - : Oxford University Press. - 0305-7453 .- 1460-2091. ; 71:1, s. 92-99
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Tidskriftsartikel (refereegranskat)abstract
- Objectives: Antimicrobial resistance (AMR) in Neisseria gonorrhoeae is a major public health concern worldwide. This is the first nationwide study, performed within the China Gonococcal Antimicrobial Susceptibility Programme (China-GASP), regarding AMR, including ceftriaxone genetic resistance determinants, and molecular epidemiology of gonococci in China.Methods: Gonococcal isolates (naEuroS=aEuroS1257) from consecutive patients were collected at 11 sentinel sites distributed across China during 2012-13. Susceptibility to ceftriaxone, spectinomycin, ciprofloxacin and tetracycline was determined using the agar dilution method. Ceftriaxone resistance determinants penA and penB were examined using sequencing. N. gonorrhoeae multiantigen sequence typing (NG-MAST) was performed for molecular epidemiology.Results: Among isolates, 0.2% were resistant to spectinomycin, 4.4% to ceftriaxone, 42.9% to tetracyclines (high-level resistance) and 99.8% to ciprofloxacin. Among 890 sequenced isolates, 16 (1.8%) possessed a penA mosaic allele; 4 of these isolates belonged to the MDR internationally spread NG-MAST genogroup G1407 (first description in China). Non-mosaic penA alleles with an A501T mutation and an A102D alteration in porB1b were statistically associated with decreased susceptibility/resistance to ceftriaxone. NG-MAST G10339, G1424 and G1053 were associated with decreased susceptibility/resistance to ceftriaxone.Conclusions: In China, ceftriaxone and spectinomycin can continue to be recommended for gonorrhoea treatment, with the possible exception of Hainan and Sichuan provinces where ceftriaxone resistance exceeded 5% and AMR surveillance needs to be strengthened. Molecular approaches including genotyping and AMR determinant analysis can be valuable to supplement and enhance conventional surveillance of gonococcal AMR in China.
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| 10. |
- Chen, Shao-Chun, et al.
(författare)
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Prevalence and Molecular Epidemiological Typing of Penicillinase-Producing Neisseria gonorrhoeae and Their bla(TEM-135) Gene Variants in Nanjing, China
- 2013
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Ingår i: Sexually Transmitted Diseases. - 0148-5717 .- 1537-4521. ; 40:11, s. 872-876
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Tidskriftsartikel (refereegranskat)abstract
- Background: This study aimed to investigate the prevalence of penicillinase-producing Neisseria gonorrhoeae (PPNG) and their bla(TEM-135) gene variant in 2007 and 2012 in Nanjing, China. In addition, molecular epidemiological typing of all isolates was performed to elucidate the genetic relationships of the PPNG strains. Methods: A total of 199 and 77 N. gonorrhoeae isolates were collected at the National Center for STD Control in 2007 and 2012, respectively. Nitrocefin tests were performed to identify PPNG. Mismatch amplification mutation assay was used to identify bla(TEM-135). All isolates were genotyped using N. gonorrhoeae multiantigen sequence typing (NG-MAST), and additionally, porB-based phylogenetic analysis was performed for the PPNG isolates. Results: The total prevalence of PPNG isolates was 41% (114/276) and 58% (66/114) of these PPNG isolates possessed bla(TEM-135). In 2007, 45% (90/199) produced beta-lactamase, and of those PPNG, 58% (52/90) possessed bla(TEM-135). In 2012, 31% (24/77) were PPNG, and 58% (14/24) of those isolates contained bla(TEM-135). There were 162 NG-MAST STs among the 276 isolates, and 89 of those were novel STs. A strong association between specific NG-MAST STs and bla(TEM-135) was found, and the porB-based phylogenetic analysis showed a distant evolutionary relationship between isolates in 2007 and isolates in 2012. Conclusions: A high prevalence of PPNG and bla(TEM-135) was found in Nanjing, China. bla(TEM-135) might be a precursor in the evolution into an extended-spectrum beta-lactamase that can degrade ceftriaxone, which stresses the need to continuously monitor PPNG, bla(TEM-135), and additional evolving bla(TEM) gene variants.
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| 11. |
- Chen, Zexin, et al.
(författare)
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Transmitter optimization for PS-QAM signal in high spectral efficiency metro-transmission
- 2023
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Ingår i: Journal of Lightwave Technology. - 0733-8724 .- 1558-2213. ; , s. 1-10
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Tidskriftsartikel (refereegranskat)abstract
- Probabilistic constellation shaping (PCS) brings unprecedented flexibility to future optical networks. However, PCS combined with higher-order modulation formats and higher symbol rates puts more demands on the transmitter. For metro-transmission with high spectral efficiency (SE), transmitter impairments are responsible for a major portion of the system constraints. To address this issue, in this work we study the impact of transmitter impairments on probabilistically shaped quadrature amplitude modulation (PS-QAM) signals. First, we investigate the impact of transmitter impairments and radio frequency (RF) amplifier noise on the optimum shaping factor and the modulation depth within a fiber link. Then, we explore how generalized mutual information (GMI) and the shaping factor are affected by the noise from the transmitter. Next, we first jointly optimize the arcsine swing and the clipping ratio, in order to mitigate the transmitter impairments for the PS-QAM signal, when the modulation depth, the noise from the transmitter, the noise from the fiber optical channel, and the shaping factor are fixed. Then, we verify its validity for various configurations of transmission system. The optimized parameters primarily depend on the noise from the transmitter and turn out to be insensitive to the noise from the fiber optical link and the shaping factor. Finally, we experimentally verify the optimization strategy with PS-256QAM in back-to-back (B2B) transmission.
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| 12. |
- Elsik, Christine G., et al.
(författare)
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The Genome Sequence of Taurine Cattle : A Window to Ruminant Biology and Evolution
- 2009
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 324:5926, s. 522-528
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Tidskriftsartikel (refereegranskat)abstract
- To understand the biology and evolution of ruminants, the cattle genome was sequenced to about sevenfold coverage. The cattle genome contains a minimum of 22,000 genes, with a core set of 14,345 orthologs shared among seven mammalian species of which 1217 are absent or undetected in noneutherian (marsupial or monotreme) genomes. Cattle-specific evolutionary breakpoint regions in chromosomes have a higher density of segmental duplications, enrichment of repetitive elements, and species-specific variations in genes associated with lactation and immune responsiveness. Genes involved in metabolism are generally highly conserved, although five metabolic genes are deleted or extensively diverged from their human orthologs. The cattle genome sequence thus provides a resource for understanding mammalian evolution and accelerating livestock genetic improvement for milk and meat production.
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| 13. |
- Foote, Andrew D., et al.
(författare)
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Convergent evolution of the genomes of marine mammals
- 2015
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Ingår i: Nature Genetics. - : Springer Science and Business Media LLC. - 1061-4036 .- 1546-1718. ; 47:3, s. 272-275
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Tidskriftsartikel (refereegranskat)abstract
- Marine mammals from different mammalian orders share several phenotypic traits adapted to the aquatic environment and therefore represent a classic example of convergent evolution. To investigate convergent evolution at the genomic level, we sequenced and performed de novo assembly of the genomes of three species of marine mammals (the killer whale, walrus and manatee) from three mammalian orders that share independently evolved phenotypic adaptations to a marine existence. Our comparative genomic analyses found that convergent amino acid substitutions were widespread throughout the genome and that a subset of these substitutions were in genes evolving under positive selection and putatively associated with a marine phenotype. However, we found higher levels of convergent amino acid substitutions in a control set of terrestrial sister taxa to the marine mammals. Our results suggest that, whereas convergent molecular evolution is relatively common, adaptive molecular convergence linked to phenotypic convergence is comparatively rare.
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| 14. |
- Fu, Jinrong, et al.
(författare)
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Anti-ischemia/reperfusion of C1 inhibitor in myocardial cell injury via regulation of local myocardial C3 activity.
- 2006
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Ingår i: Biochemical and Biophysical Research Communications - BBRC. - : Elsevier BV. - 0006-291X .- 1090-2104. ; 350:1, s. 162-8
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Tidskriftsartikel (refereegranskat)abstract
- C3 is common to all pathways of complement activation augmenting ischemia/reperfusion (I/R)-induced myocardial injury and cardiac dysfunction. Complement inhibition with the complement regulatory protein, C1 inhibitor (C1INH), obviously exerts cardioprotective effects. Here, we examine whether C1INH regulates C3 activity in the ischemic myocardial tissue. C1INH markedly suppressed C3 mRNA expression and protein synthesis in both a model of I/R-induced rat acute myocardial infarction (AMI) and the cultured rat H9c2 heart myocytes. At least, this regulation was at the transcriptional level in response to oxygen tension. In vitro, C3 deposition on, and binding to, the surface of rat myocardial cells were significantly blocked by C1INH treatment. C1INH could inhibit classical complement-mediated cell lysis via suppressing the biological activity of C3. Therefore, C1INH, in addition to inhibition of the systemic complement activation, prevents myocardial cell injury via a direct inhibitory role in the local myocardial C3 activity.
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| 15. |
- Gao, Xiang, et al.
(författare)
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Planting Age Identification and Yield Prediction of Apple Orchard Using Time-Series Spectral Endmember and Logistic Growth Model
- 2023
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Ingår i: Remote Sensing. - : MDPI AG. - 2072-4292. ; 15:3, s. 642-642
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Tidskriftsartikel (refereegranskat)abstract
- In response to significant shifts in dietary and lifestyle preferences, the global demand for fruits has increased dramatically, especially for apples, which are consumed worldwide. Growing apple orchards of more productive and higher quality with limited land resources is the way forward. Precise planting age identification and yield prediction are indispensable for the apple market in terms of sustainable supply, price regulation, and planting management. The planting age of apple trees significantly determines productivity, quality, and yield. Therefore, we integrated the time-series spectral endmember and logistic growth model (LGM) to accurately identify the planting age of apple orchard, and we conducted planting age-driven yield prediction using a neural network model. Firstly, we fitted the time-series spectral endmember of green photosynthetic vegetation (GV) with the LGM. By using the four-points method, the environmental carrying capacity (ECC) in the LGM was available, which serves as a crucial parameter to determine the planting age. Secondly, we combined annual planting age with historical apple yield to train the back propagation (BP) neural network model and obtained the predicted apple yields for 12 counties. The results show that the LGM method can accurately estimate the orchard planting age, with Mean Absolute Error (MAE) being 1.76 and the Root Mean Square Error (RMSE) being 2.24. The strong correlation between orchard planting age and apple yield was proved. The results of planting age-driven yield prediction have high accuracy, with the MAE up to 2.95% and the RMSE up to 3.71%. This study provides a novel method to accurately estimate apple orchard planting age and yields, which can support policy formulation and orchard planning in the future.
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| 16. |
- Jiao, Xiang, et al.
(författare)
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PHIP - a novel candidate breast cancer susceptibility locus on 6q14.1
- 2017
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Ingår i: Oncotarget. - : IMPACT JOURNALS LLC. - 1949-2553. ; 8:61, s. 102769-102782
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Tidskriftsartikel (refereegranskat)abstract
- Most non-BRCA1/2 breast cancer families have no identified genetic cause. We used linkage and haplotype analyses in familial and sporadic breast cancer cases to identify a susceptibility locus on chromosome 6q. Two independent genome-wide linkage analysis studies suggested a 3 Mb locus on chromosome 6q and two unrelated Swedish families with a LOD > 2 together seemed to share a haplotype in 6q14.1. We hypothesized that this region harbored a rare high-risk founder allele contributing to breast cancer in these two families. Sequencing of DNA and RNA from the two families did not detect any pathogenic mutations. Finally, 29 SNPs in the region were analyzed in 44,214 cases and 43,532 controls from BCAC, and the original haplotypes in the two families were suggested as low-risk alleles for European and Swedish women specifically. There was also some support for one additional independent moderate-risk allele in Swedish familial samples. The results were consistent with our previous findings in familial breast cancer and supported a breast cancer susceptibility locus at 6q14.1 around the PHIP gene.
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| 17. |
- Kanoni, Stavroula, et al.
(författare)
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Implicating genes, pleiotropy, and sexual dimorphism at blood lipid loci through multi-ancestry meta-analysis.
- 2022
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Ingår i: Genome biology. - : Springer Science and Business Media LLC. - 1474-760X .- 1465-6906 .- 1474-7596. ; 23:1
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Tidskriftsartikel (refereegranskat)abstract
- Genetic variants within nearly 1000 loci are known to contribute to modulation of blood lipid levels. However, the biological pathways underlying these associations are frequently unknown, limiting understanding of these findings and hindering downstream translational efforts such as drug target discovery.To expand our understanding of the underlying biological pathways and mechanisms controlling blood lipid levels, we leverage a large multi-ancestry meta-analysis (N=1,654,960) of blood lipids to prioritize putative causal genes for 2286 lipid associations using six gene prediction approaches. Using phenome-wide association (PheWAS) scans, we identify relationships of genetically predicted lipid levels to other diseases and conditions. We confirm known pleiotropic associations with cardiovascular phenotypes and determine novel associations, notably with cholelithiasis risk. We perform sex-stratified GWAS meta-analysis of lipid levels and show that 3-5% of autosomal lipid-associated loci demonstrate sex-biased effects. Finally, we report 21 novel lipid loci identified on the X chromosome. Many of the sex-biased autosomal and X chromosome lipid loci show pleiotropic associations with sex hormones, emphasizing the role of hormone regulation in lipid metabolism.Taken together, our findings provide insights into the biological mechanisms through which associated variants lead to altered lipid levels and potentially cardiovascular disease risk.
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| 18. |
- Liu, Lingling, et al.
(författare)
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Uniform and perfectly linear current-voltage characteristics of nitrogen-doped armchair graphene nanoribbons for nanowires
- 2017
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Ingår i: Physical Chemistry, Chemical Physics - PCCP. - : Royal Society of Chemistry. - 1463-9076 .- 1463-9084. ; 19:1, s. 44-48
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Tidskriftsartikel (refereegranskat)abstract
- Metallic nanowires with desired properties for molecular integrated circuits (MICs) are especially significant in molectronics, but preparing such wires at a molecular level still remains challenging. Here, we propose, from first principles calculations, experimentally realizable edge-nitrogen-doped graphene nanoribbons (N-GNRs) as promising candidates for nanowires. Our results show that edge N-doping has distinct effects on the electronic structures and transport properties of the armchair GNRs and zigzag GNRs (AGNRs, ZGNRs), due to the formation of pyridazine and pyrazole rings at the edges. The pyridazine rings raise the Fermi level and introduce delocalized energy bands near the Fermi level, resulting in a highly enhanced conductance in N-AGNRs at the stable nonmagnetic ground state. Especially for the family of AGNRs with widths of n = 3p + 2, their semiconducting characteristics are transformed to metallic characteristics via N-doping, and they exhibit perfectly linear current-voltage (I-V) behaviors. Such uniform and excellent features indicate bright application prospects of the N-AGNRs as nanowires and electrodes in molectronics.
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| 19. |
- Liu, Rui, et al.
(författare)
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Associations of sleep timing and time in bed with dementia and cognitive decline among Chinese older adults : A cohort study
- 2022
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Ingår i: Journal of The American Geriatrics Society. - : Wiley. - 0002-8614 .- 1532-5415. ; 70:11, s. 3138-3151
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Tidskriftsartikel (refereegranskat)abstract
- Background: The longitudinal associations of sleep timing and time in bed (TIB) with dementia and cognitive decline in older adults are unclear.Methods: This population-based cohort study used data from 1982 participants who were aged >= 60 years, free of dementia, and living in rural communities in western Shandong, China. At the baseline (2014) and follow-up (2018) examinations, sleep parameters were assessed using standard questionnaires. Cognitive function was measured using the Mini-Mental State Examination (MMSE). Dementia was diagnosed following the DSM-IV criteria, and the NIA-AA criteria for Alzheimer disease (AD). Data were analyzed using restricted cubic splines, Cox proportional-hazards models, and general linear models.Results: During the mean follow-up of 3.7 years, dementia was diagnosed in 97 participants (68 with AD). Restricted cubic spline curves showed J-shaped associations of sleep duration, TIB, and rise time with dementia risk, and a reverse J-shaped association with mid-sleep time. When sleep parameters were categorized into tertiles, the multivariable-adjusted hazard ratio (HR) of incident dementia was 1.69 (95%CI 1.01-2.83) for baseline sleep duration >8 hours (vs. 7-8 h), 2.17 (1.22-3.87) for bedtime before 9 p.m. (vs. 10 p.m. or later), and 2.00 (1.23-3.24) for mid-sleep time before 1 a.m. (vs. 1-1.5 a.m.). Early bedtime and mid-sleep time were significantly associated with incident AD (HR range: 2.25-2.51; p < 0.05). Among individuals who were free of dementia at follow-up, baseline long TIB, early bedtime and mid-sleep time, early and late rise time, and prolonged TIB and advanced bedtime and mid-sleep time from baseline to follow-up were associated with a greater decline in MMSE score (p < 0.05). These associations with cognitive decline were statistically evident mainly among men or participants who were aged 60-74 years.Conclusions: Long TIB and early sleep timing are associated with an increased risk of dementia, and the associations with greater cognitive decline are evident only among older people aged 60-74 years and men.
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| 20. |
- Meng, Xiang-hai, et al.
(författare)
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Safety evaluation of freeway basic segment based on CPMs and LOSS
- 2016
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Konferensbidrag (refereegranskat)abstract
- Safety evaluation of basic segments of freeway plays an important role in freeway safety management. Common methods for dividing basic segments were introduced and compared at first, and then a dynamic cluster segment division method was put forward based on where crashes located. Based on the numbers of crashes on divided segments, the statistical distribution of crashes was analyzed, and the result showed that the number of crashes on the divided segments followed the Negative Binomial (i.e., NB) distribution. Hence, Crash Prediction Models (i.e., CPMs) based on the NB distribution were established, and a method to evaluate the safety situation of freeway was proposed. Furthermore level of service of safety (i.e., LOSS) was introduced and the classification standard was determined, then a segment safety evaluation method based on LOSS was put forward. Both methods based on CPMs and based on LOSS were applied to the Jingzhu freeway, and the comparison showed that 57.8% segments were under the same level while the other were different. What’s more, it also could be find that the evaluation result based on CPM methods is more in line with actual situation. Safety evaluation method based on NB distribution considers traffic volume and geometric alignment, so it is more suitable for the freeway with complex geometric alignment conditions, mountainous freeway as Jingzhu freeway for instance. On the other hand, the safety evaluation method based on LOSS considers traffic volume and crash number, so it is more suitable for the freeway with good geometric alignment conditions.
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| 21. |
- Moretti, Rocco, et al.
(författare)
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Community-wide evaluation of methods for predicting the effect of mutations on protein-protein interactions
- 2013
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Ingår i: Proteins. - : Wiley. - 0887-3585 .- 1097-0134. ; 81:11, s. 1980-1987
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Tidskriftsartikel (refereegranskat)abstract
- Community-wide blind prediction experiments such as CAPRI and CASP provide an objective measure of the current state of predictive methodology. Here we describe a community-wide assessment of methods to predict the effects of mutations on protein-protein interactions. Twenty-two groups predicted the effects of comprehensive saturation mutagenesis for two designed influenza hemagglutinin binders and the results were compared with experimental yeast display enrichment data obtained using deep sequencing. The most successful methods explicitly considered the effects of mutation on monomer stability in addition to binding affinity, carried out explicit side-chain sampling and backbone relaxation, evaluated packing, electrostatic, and solvation effects, and correctly identified around a third of the beneficial mutations. Much room for improvement remains for even the best techniques, and large-scale fitness landscapes should continue to provide an excellent test bed for continued evaluation of both existing and new prediction methodologies. Proteins 2013; 81:1980-1987.
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| 22. |
- Pan, Lang, et al.
(författare)
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8-Oxoguanine targeted by 8-oxoguanine DNA glycosylase 1 (OGG1) is central to fibrogenic gene activation upon lung injury
- 2023
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Ingår i: Nucleic Acids Research. - : Oxford University Press (OUP). - 0305-1048 .- 1362-4962. ; 51:3, s. 1087-1102
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Tidskriftsartikel (refereegranskat)abstract
- Reactive oxygen species (ROS) are implicated in epithelial cell-state transition and deposition of extracellular matrix upon airway injury. Of the many cellular targets of ROS, oxidative DNA modification is a major driving signal. However, the role of oxidative DNA damage in modulation profibrotic processes has not been fully delineated. Herein, we report that oxidative DNA base lesions, 8-oxoG, complexed with 8-oxoguanine DNA glycosylase 1 (OGG1) functions as a pioneer factor, contributing to transcriptional reprogramming within airway epithelial cells. We show that TGFβ1-induced ROS increased 8-oxoG levels in open chromatin, dynamically reconfigure the chromatin state. OGG1 complexed with 8-oxoG recruits transcription factors, including phosphorylated SMAD3, to pro-fibrotic gene promoters thereby facilitating gene activation. Moreover, 8-oxoG levels are elevated in lungs of mice subjected to TGFβ1-induced injury. Pharmacologic targeting of OGG1 with the selective small molecule inhibitor of 8-oxoG binding, TH5487, abrogates fibrotic gene expression and remodeling in this model. Collectively, our study implicates that 8-oxoG substrate-specific binding by OGG1 is a central modulator of transcriptional regulation in response to tissue repair.
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| 23. |
- Parbey, Joseph, et al.
(författare)
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High-performance solid oxide fuel cells with fiber-based cathodes for low-temperature operation
- 2020
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Ingår i: International Journal of Hydrogen Energy. - : Elsevier BV. - 0360-3199. ; 45:11, s. 6949-6957
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Tidskriftsartikel (refereegranskat)abstract
- Low-temperature operation of solid oxide fuel cells (SOFCs) results in deterioration in electrochemical performance due to sluggish oxygen reduction reaction (ORR) at the cathode. To enhance the reaction pathway for ORR, La0.8Sr0.2MnO3 (LSM) nanofibers were fabricated by electrospinning and used for low-temperature solid oxide fuel cells operated at 600–700 °C. The morphological and structural characteristics show that the electrospun LSM nanofiber has a highly crystallized perovskite structure with a uniform elemental distribution. The average diameter of the LSM nanofiber after sintering is 380 nm. A symmetric cell of nanofiber-based LSM cathode on scandia-stabilized zirconia (SSZ) electrolyte pellet exhibits much lower area specific resistances compared to commercial LSM powder-based cathode. A single cell based on the nanofiber LSM cathode on yttrium-doped barium cerate-zirconia (BCZY) electrolyte exhibits a power density of 0.35 Wcm−2 at 600 °C, which increases to 0.85 Wcm−2 at 700 °C. The cell has an area specific resistance (ASR) of 0.46 Ωcm2 at 600 °C, which decreases to 0.07 Ωcm2 at 700 °C. The results indicate that the LSM electrode fabricated by the electrospinning process produces a nanostructured porous electrode which optimizes the microstructure and significantly enhances the ORR at the cathode of SOFCs.
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| 24. |
- Qin, Changliang, et al.
(författare)
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Process optimizations to recessed e-SiGe source/drain for performance enhancement in 22 nm all-last high-k/metal-gate pMOSFETs
- 2016
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Ingår i: Solid-State Electronics. - : Elsevier. - 0038-1101 .- 1879-2405. ; 123, s. 38-43
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Tidskriftsartikel (refereegranskat)abstract
- In this paper, the technology of recessed embedded SiGe (e-SiGe) source/drain (S/D) module is optimized for the performance enhancement in 22 nm all-last high-k/metal-gate (HK/MG) pMOSFETs. Different Si recess-etch techniques were applied in S/D regions to increase the strain in the channel and subsequently, improve the performance of transistors. A new recess-etch method consists of a two-step etch method is proposed. This process is an initial anisotropic etch for the formation of shallow trench followed by a final isotropic etch. By introducing the definition of the upper edge distance (D) between the recessed S/D region and the channel region, the process advantage of the new approach is clearly presented. It decreases the value of D than those by conventional one-step isotropic or anisotropic etch of Si. Therefore, the series resistance is reduced and the channel strain is increased, which confirmed by the simulation results. The physical reason of D reducing is analyzed in brief. Applying this recess design, the implant conditions for S/D extension (SDE) are also optimized by using a two-step implantation of BF2 in SiGe layers. The overlap space between doping junction and channel region has great effect on the device's performance. The designed implantation profile decreases the overlap space while keeps a shallow junction depth for a controllable short channel effect. The channel resistance as well as the transfer ID-VG curves varying with different process conditions are demonstrated. It shows the drive current of the device with the optimized SDE implant condition and Si recess-etch process is obviously improved. The change trend of on-off current distributions extracted from a series of devices confirmed the conclusions. This study provides a useful guideline for developing high performance strained PMOS SiGe technology.
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| 25. |
- Qin, Haihong, et al.
(författare)
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Evaluation and Suppression Method of Turn-off Current Spike for SiC/Si Hybrid Switch
- 2023
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Ingår i: IEEE Access. - 2169-3536 .- 2169-3536. ; 11, s. 26832-26842
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Tidskriftsartikel (refereegranskat)abstract
- SiC MOSFET/Si IGBT (SiC/Si) hybrid switch usually selects the gate control pattern that SiC MOSFET turns on earlier and turns off later than Si IGBT, with the aim of making the hybrid switch show excellent switching characteristics of SiC MOSFET and reduce switching loss. However, when SiC MOSFET turns off, the fast slew rate of drain source voltage causes the current spike in Si IGBT due to the effects of parasitic capacitance charging and carrier recombination, which will produce additional turn-off loss, thus affecting the overall efficiency and temperature rise of the converter. Based on the double pulse test circuit of SiC/Si hybrid switch, the mathematical model of the turn-off transient process is established. The effects of the remnant carrier recombination degree of Si IGBT, the turn-off speed of SiC MOSFET and the working conditions on the turn-off current spike of hybrid switch are evaluated. Although adjusting these parameters can reduce the turn-off current spike somewhat, additional losses will be introduced. Therefore, a new method to suppress the turn-off current spike is proposed to balance the power loss and current stress.
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