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Sökning: WFRF:(Zhang Huan)

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2.
  • Beal, Jacob, et al. (författare)
  • Robust estimation of bacterial cell count from optical density
  • 2020
  • Ingår i: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1
  • 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.
  • Klionsky, Daniel J., et al. (författare)
  • Guidelines for the use and interpretation of assays for monitoring autophagy
  • 2012
  • Ingår i: Autophagy. - : Informa UK Limited. - 1554-8635 .- 1554-8627. ; 8:4, s. 445-544
  • 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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4.
  • Wang, Fang, et al. (författare)
  • Emerging contaminants: A One Health perspective
  • 2024
  • Ingår i: Innovation. - 2666-6758. ; 5
  • Forskningsöversikt (refereegranskat)abstract
    • Environmental pollution is escalating due to rapid global development that often prioritizes human needs over planetary health. Despite global efforts to mitigate legacy pollutants, the continuous introduction of new substances remains a major threat to both people and the planet. In response, global initiatives are focusing on risk assessment and regulation of emerging contaminants, as demonstrated by the ongoing efforts to establish the UN's Intergovernmental Science-Policy Panel on Chemicals, Waste, and Pollution Prevention. This review identifies the sources and impacts of emerging contaminants on planetary health, emphasizing the importance of adopting a One Health approach. Strategies for monitoring and addressing these pollutants are discussed, underscoring the need for robust and socially equitable environmental policies at both regional and international levels. Urgent actions are needed to transition toward sustainable pollution management practices to safeguard our planet for future generations.
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5.
  • Zhang, Huan, et al. (författare)
  • Synergistic effects of warming and eutrophication alert zooplankton predator–prey interactions along the benthic–pelagic interface
  • 2021
  • Ingår i: Global Change Biology. - : Wiley. - 1354-1013 .- 1365-2486. ; 27:22, s. 5907-5919
  • Tidskriftsartikel (refereegranskat)abstract
    • Contemporary evidence suggests that climate change and other co-occurring large-scale environmental changes, such as eutrophication, will have a considerable impact on aquatic communities. However, the interactions of these environmental changes on trophic interactions among zooplankton remain largely unknown. Here we present results of a mesocosm experiment examining how a couple of zooplankton predator and prey taxa with different life-history strategies respond to the combined effect of an increase in temperature (4.5°C) and in eutrophication (phosphorus addition), during the crucial recruiting and growing season. We show that the addition of phosphorus alone significantly weakened the top-down effects by the cyclopoid copepod predators on their rotifer prey. In contrast, warming strengthened the top-down effects from the predator, leading to a reduction in the abundance of the rotifer prey. These effects of warming were enhanced by phosphorus addition. Together, our results demonstrate that warming made plankton prey organisms more susceptible to top-down effects from predators, but reduced their sensitivity to nutrient enrichment. In terms of the phenological effects, warming advanced the termination of diapause for both rotifers and cyclopoid copepods by about 2 weeks, but these temporal shifts, akin for both groups, resulted in no apparent trophic mismatch. Hence, from a future perspective, cyclopoid copepods are likely to benefit more from the combination of nutrient enrichment and climate warming to the detriment of their rotifer prey.
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6.
  • Chong, Hui, et al. (författare)
  • Organo-ptii complexes for potent photodynamic inactivation of multi-drug resistant bacteria and the influence of configuration
  • 2024
  • Ingår i: Advanced Science. - : John Wiley & Sons. - 2198-3844. ; 11:14
  • Tidskriftsartikel (refereegranskat)abstract
    • PtII based organometallic photosensitizers (PSs) have emerged as novel potent photodynamic inactivation (PDI) reagents through their enhanced intersystem crossing (ISC) processes. Currently, few PtII PSs have been investigated as antibacterial materials, with relatively poor performances reported and with structure-activity relationships not well described. Herein, a pair of configurational isomers are reported of Bis-BODIPY (4,4-difluoro-boradizaindacene) embedded PtII PSs. The cis-isomer (cis-BBP) displayed enhanced 1O2 generation and better bacterial membrane anchoring capability as compared to the trans-isomer (trans-BBP). The effective PDI concentrations (efficiency > 99.9%) for cis-BBP in Acinetobacter baumannii (multi-drug resistant (MDR)) and Staphylococcus aureus are 400 nM (12 J cm−2) and 100 nM (18 J cm−2), respectively; corresponding concentrations and light doses for trans-BBP in the two bacteria are 2.50 µM (30 J cm−2) and 1.50 µM (18 J cm−2), respectively. The 50% and 90% minimum inhibitory concentration (MIC50 and MIC90) ratio of trans-BBP to cis-BBP is 22.22 and 24.02 in A. baumannii (MDR); 21.29 and 22.36 in methicillin resistant S. aureus (MRSA), respectively. Furthermore, cis-BBP displays superior in vivo antibacterial performance, with acceptable dark and photoinduced cytotoxicity. These results demonstrate cis-BBP is a robust light-assisted antibacterial reagent at sub-micromolecular concentrations. More importantly, configuration of PtII PSs should be an important issue to be considered in further PDI reagents design.
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7.
  • Liu, Li, et al. (författare)
  • Involvement of yes-associated protein 1 activation in the matrix degradation of human-induced-pluripotent-stem-cell-derived chondrocytes induced by T-2 toxin and deoxynivalenol alone and in combination
  • 2024
  • Ingår i: International Journal of Molecular Sciences. - : MDPI. - 1661-6596 .- 1422-0067. ; 25:2
  • Tidskriftsartikel (refereegranskat)abstract
    • T-2 toxin and deoxynivalenol (DON) are two prevalent mycotoxins that cause cartilage damage in Kashin-Beck disease (KBD). Cartilage extracellular matrix (ECM) degradation in chondrocytes is a significant pathological feature of KBD. It has been shown that the Hippo pathway is involved in cartilage ECM degradation. This study aimed to examine the effect of YAP, a major regulator of the Hippo pathway, on the ECM degradation in the hiPS-derived chondrocytes (hiPS-Ch) model of KBD. The hiPS-Ch injury models were established via treatment with T-2 toxin/DON alone or in combination. We found that T-2 toxin and DON inhibited the proliferation of hiPS-Ch in a dose-dependent manner; significantly increased the levels of YAP, SOX9, and MMP13; and decreased the levels of COL2A1 and ACAN (all p values < 0.05). Immunofluorescence revealed that YAP was primarily located in the nuclei of hiPS-Ch, and its expression level increased with toxin concentrations. The inhibition of YAP resulted in the dysregulated expression of chondrogenic markers (all p values < 0.05). These findings suggest that T-2 toxin and DON may inhibit the proliferation of, and induce the ECM degradation, of hiPS-Ch mediated by YAP, providing further insight into the cellular and molecular mechanisms contributing to cartilage damage caused by toxins.
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8.
  • Yang, Yalan, et al. (författare)
  • Chemodiversity of Cyanobacterial Toxins Driven by Future Scenarios of Climate Warming and Eutrophication
  • 2023
  • Ingår i: Environmental Science and Technology. - 0013-936X. ; 57:32, s. 11767-11778
  • Tidskriftsartikel (refereegranskat)abstract
    • Climate change and eutrophication are two environmental threats that can alter the structure of freshwater ecosystems and their service functions, but we know little about how ecosystem structure and function will evolve in future scenarios of climate warming. Therefore, we created different experimental climate scenarios, including present-day conditions, a 3.0 °C increase in mean temperature, and a “heatwaves” scenario (i.e., an increase in temperature variability) to assess the effects of climate change on phytoplankton communities under simultaneous stress from eutrophication and herbicides. We show that the effects of climate warming, particularly heatwaves, are associated with elevated cyanobacterial abundances and toxin production, driven by a change from mainly nontoxic to toxic Microcystis spp. The reason for higher cyanobacterial toxin concentrations is likely an increase in abundances because under the dual pressures of climate warming and eutrophication individual Microcystis toxin-producing ability decreased. Eutrophication and higher temperatures significantly increased the biomass of Microcystis, leading to an increase in the cyanobacterial toxin concentrations. In contrast, warming alone did not produce higher cyanobacterial abundances or cyanobacterial toxin concentrations likely due to the depletion of the available nutrient pool. Similarly, the herbicide glyphosate alone did not affect abundances of any phytoplankton taxa. In the case of nutrient enrichment, cyanobacterial toxin concentrations were much higher than under warming alone due to a strong boost in biomass of potential cyanobacterial toxin producers. From a broader perspective our study shows that in a future warmer climate, nutrient loading has to be reduced if toxic cyanobacterial dominance is to be controlled.
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9.
  • Zhang, Ling, et al. (författare)
  • Roles of piRNAs in microcystin-leucine-arginine (MC-LR) induced reproductive toxicity in testis on male offspring
  • 2017
  • Ingår i: Food and Chemical Toxicology. - : PERGAMON-ELSEVIER SCIENCE LTD. - 0278-6915 .- 1873-6351. ; 105, s. 177-185
  • Tidskriftsartikel (refereegranskat)abstract
    • In the present study, we evaluated the toxic effects on the testis of the male offspring of MC-LR exposure during fetal and lactational periods. Pregnant females were distributed into two experimental groups: control group and MC-LR group which were exposed to 0 and 10 mu g/L of MC-LR, respectively, through drinking water separately during fetal and lactational periods. At the age of 30 days after birth, the male offspring were euthanized. The body weight, testis index, and histomorphology change were observed and the global changes of piwi-interacting RNA (piRNA) expression were evaluated. The results revealed that MC-LR was found in the testis of male offspring, body weight and testis index decreased significantly, and testicular tissue structure was damaged in the MC-LR group. In addition, the exposure to MCLR resulted in an altered piRNA expression profile and an increase of the cell apoptosis and a decrease of the cell proliferation in the testis of the male offspring. It was reasonable to speculate that the toxic effects on reproductive system of the male offspring in MC-LR group might be mediated by piRNAs through the regulation of the target genes. As far as we are aware, this is the first report showing that MC-LR could play a role in disorder of proliferative and cell apoptosis in the testis of the male offspring by the maternal transmission effect of toxicity. (C) 2017 Elsevier Ltd. All rights reserved.
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10.
  • Anderson, Cynthia M., et al. (författare)
  • Permanent Genetic Resources added to Molecular Ecology Resources Database 1 December 2009-31 January 2010
  • 2010
  • Ingår i: Molecular Ecology Resources. - : Wiley. - 1755-098X .- 1755-0998. ; 10:3, s. 576-579
  • Tidskriftsartikel (refereegranskat)abstract
    • This article documents the addition of 220 microsatellite marker loci to the Molecular Ecology Resources Database. Loci were developed for the following species: Allanblackia floribunda, Amblyraja radiata, Bactrocera cucurbitae, Brachycaudus helichrysi, Calopogonium mucunoides, Dissodactylus primitivus, Elodea canadensis, Ephydatia fluviatilis, Galapaganus howdenae howdenae, Hoplostethus atlanticus, Ischnura elegans, Larimichthys polyactis, Opheodrys vernalis, Pelteobagrus fulvidraco, Phragmidium violaceum, Pistacia vera, and Thunnus thynnus. These loci were cross-tested on the following species: Allanblackia gabonensis, Allanblackia stanerana, Neoceratitis cyanescens, Dacus ciliatus, Dacus demmerezi, Bactrocera zonata, Ceratitis capitata, Ceratitis rosa, Ceratits catoirii, Dacus punctatifrons, Ephydatia mulleri, Spongilla lacustris, Geodia cydonium, Axinella sp., Ischnura graellsii, Ischnura ramburii, Ischnura pumilio, Pistacia integerrima and Pistacia terebinthus.
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11.
  • Li, Yuchen, et al. (författare)
  • Public awareness, emotional reactions and human mobility in response to the COVID-19 outbreak in China : a population-based ecological study
  • 2022
  • Ingår i: Psychological Medicine. - : Cambridge University Press. - 0033-2917 .- 1469-8978. ; 52:9, s. 1793-1800
  • Tidskriftsartikel (refereegranskat)abstract
    • Background: The outbreak of COVID-19 generated severe emotional reactions, and restricted mobility was a crucial measure to reduce the spread of the virus. This study describes the changes in public emotional reactions and mobility patterns in the Chinese population during the COVID-19 outbreak.Methods: We collected data on public emotional reactions in response to the outbreak through Weibo, the Chinese Twitter, between January 1st and March 31st, 2020. Using anonymized location-tracking information, we analyzed the daily mobility patterns of approximately 90% of Sichuan residents.Results: There were three distinct phases of the emotional and behavioral reactions to the COVID-19 outbreak. The alarm phase (January 19th –26th) was a restriction-free period, characterized by few new daily cases, but enormous public negative emotions (the number of negative comments per Weibo post increased by 246.9 per day, 95%CI: 122.5–371.3), and a substantial increase in self-limiting mobility (from 45.6% to 54.5%, changing by 1.5% per day, 95%CI: 0.7%–2.3%). The epidemic phase (January 27th –February 15th) exhibited rapidly increasing numbers of new daily cases, decreasing expression of negative emotions (a decrease of 27.3 negative comments per post per day, 95%CI: −40.4–−14.2), and a stabilized level of self-limiting mobility. The relief phase (February 16th –March 31st) had a steady decline in new daily cases and decreasing levels of negative emotion and self-limiting mobility.Conclusions: During the COVID-19 outbreak in China, the public’s emotional reaction was strongest before the actual peak of the outbreak and declined thereafter. The change in human mobility patterns occurred before the implementation of restriction orders, suggesting a possible link between emotion and behavior.
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12.
  • Liu, Huan, et al. (författare)
  • The first human induced pluripotent stem cell line of Kashin–Beck disease reveals involvement of heparan sulfate proteoglycan biosynthesis and PPAR pathway
  • 2022
  • Ingår i: The FEBS Journal. - : John Wiley & Sons. - 1742-464X .- 1742-4658. ; 289:1, s. 279-293
  • Tidskriftsartikel (refereegranskat)abstract
    • OBJECTIVE: Kashin-Beck disease (KBD) is an endemic osteochondropathy. Due to a lack of suitable animal or cellular disease models, the research progress on KBD has been limited. Our goal was to establish the first disease-specific human induced pluripotent stem cells (hiPSCs) cellular disease model of KBD, and to explore its etiology and pathogenesis exploiting transcriptome sequencing.METHODS: HiPSCs were reprogrammed from dermal fibroblasts of two KBD and one healthy control donors via integration-free vectors. Subsequently, hiPSCs were differentiated into chondrocytes through three-week culture. Gene expression profiles in KBD, normal primary chondrocytes and hiPSC-derived chondrocytes were defined by RNA sequencing. A Venn diagram was constructed to show the number of shared differentially expressed genes (DEGs) between KBD and normal. Gene oncology and Kyoto Encyclopedia of Genes and Genomes annotations were performed, and six DEGs were further validated in other individuals by real-time quantitative reverse transcription PCR (RT-qPCR).RESULTS: KBD cellular disease models were successfully established by generation of hiPSC lines. Seventeen consistent and significant DEGs present in all compared groups (KBD and normal) were identified. RT-qPCR validation gave consistent results with the sequencing data. Glycosaminoglycan biosynthesis-heparan sulfate/heparin, PPAR signaling pathway and cell adhesion molecules (CAMs) pathways were identified to be significantly altered in KBD.CONCLUSION: Differentiated chondrocytes deriving from KBD-origin hiPSCs provide the first cellular disease model for etiological studies of KBD. This study also provides new sights into the pathogenesis and etiology of KBD and is likely to inform the development of targeted therapeutics for its treatment.
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13.
  • Sampson, Joshua N., et al. (författare)
  • Analysis of Heritability and Shared Heritability Based on Genome-Wide Association Studies for 13 Cancer Types
  • 2015
  • Ingår i: Journal of the National Cancer Institute. - : Oxford University Press (OUP). - 0027-8874 .- 1460-2105. ; 107:12
  • Tidskriftsartikel (refereegranskat)abstract
    • Background: Studies of related individuals have consistently demonstrated notable familial aggregation of cancer. We aim to estimate the heritability and genetic correlation attributable to the additive effects of common single-nucleotide polymorphisms (SNPs) for cancer at 13 anatomical sites. Methods: Between 2007 and 2014, the US National Cancer Institute has generated data from genome-wide association studies (GWAS) for 49 492 cancer case patients and 34 131 control patients. We apply novel mixed model methodology (GCTA) to this GWAS data to estimate the heritability of individual cancers, as well as the proportion of heritability attributable to cigarette smoking in smoking-related cancers, and the genetic correlation between pairs of cancers. Results: GWAS heritability was statistically significant at nearly all sites, with the estimates of array-based heritability, h(l)(2), on the liability threshold (LT) scale ranging from 0.05 to 0.38. Estimating the combined heritability of multiple smoking characteristics, we calculate that at least 24% (95% confidence interval [CI] = 14% to 37%) and 7% (95% CI = 4% to 11%) of the heritability for lung and bladder cancer, respectively, can be attributed to genetic determinants of smoking. Most pairs of cancers studied did not show evidence of strong genetic correlation. We found only four pairs of cancers with marginally statistically significant correlations, specifically kidney and testes (rho = 0.73, SE = 0.28), diffuse large B-cell lymphoma (DLBCL) and pediatric osteosarcoma (rho = 0.53, SE = 0.21), DLBCL and chronic lymphocytic leukemia (CLL) (rho = 0.51, SE = 0.18), and bladder and lung (rho = 0.35, SE = 0.14). Correlation analysis also indicates that the genetic architecture of lung cancer differs between a smoking population of European ancestry and a nonsmoking Asian population, allowing for the possibility that the genetic etiology for the same disease can vary by population and environmental exposures. Conclusion: Our results provide important insights into the genetic architecture of cancers and suggest new avenues for investigation.
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14.
  • Schouten, Stefan, et al. (författare)
  • An interlaboratory study of TEX86 and BIT analysis of sediments, extracts, and standard mixtures
  • 2013
  • Ingår i: Geochemistry Geophysics Geosystems. - 1525-2027. ; 14:12, s. 5263-5285
  • Tidskriftsartikel (refereegranskat)abstract
    • Two commonly used proxies based on the distribution of glycerol dialkyl glycerol tetraethers (GDGTs) are the TEX86 (TetraEther indeX of 86 carbon atoms) paleothermometer for sea surface temperature reconstructions and the BIT (Branched Isoprenoid Tetraether) index for reconstructing soil organic matter input to the ocean. An initial round-robin study of two sediment extracts, in which 15 laboratories participated, showed relatively consistent TEX86 values (reproducibility +/- 3-4 degrees C when translated to temperature) but a large spread in BIT measurements (reproducibility +/- 0.41 on a scale of 0-1). Here we report results of a second round-robin study with 35 laboratories in which three sediments, one sediment extract, and two mixtures of pure, isolated GDGTs were analyzed. The results for TEX86 and BIT index showed improvement compared to the previous round-robin study. The reproducibility, indicating interlaboratory variation, of TEX86 values ranged from 1.3 to 3.0 degrees C when translated to temperature. These results are similar to those of other temperature proxies used in paleoceanography. Comparison of the results obtained from one of the three sediments showed that TEX86 and BIT indices are not significantly affected by interlaboratory differences in sediment extraction techniques. BIT values of the sediments and extracts were at the extremes of the index with values close to 0 or 1, and showed good reproducibility (ranging from 0.013 to 0.042). However, the measured BIT values for the two GDGT mixtures, with known molar ratios of crenarchaeol and branched GDGTs, had intermediate BIT values and showed poor reproducibility and a large overestimation of the true (i.e., molar-based) BIT index. The latter is likely due to, among other factors, the higher mass spectrometric response of branched GDGTs compared to crenarchaeol, which also varies among mass spectrometers. Correction for this different mass spectrometric response showed a considerable improvement in the reproducibility of BIT index measurements among laboratories, as well as a substantially improved estimation of molar-based BIT values. This suggests that standard mixtures should be used in order to obtain consistent, and molar-based, BIT values.
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15.
  • Wang, Shu Min, 1963, et al. (författare)
  • Novel Dilute Bismides for IR Optoelectronics Applications
  • 2013
  • Ingår i: Asia Communications and Photonics Conference, ACP. - Washington, D.C. : OSA. - 2162-108X.
  • Konferensbidrag (refereegranskat)abstract
    • III-V-Bi compounds reveal a number of attractive physical properties promising for novel IR optoelectronic applications [1,2] and have received considerable attention as witnessed by the dedicated international workshops on this topic in the consecutive past four years. The isoelectronic nature of Bi atoms in III-Vs induces strong interactions with the energy bands of host materials leading to large band-gap reduction, less temperature sensitive band-gap and large spin-orbit split band. So far the most studied material is Ga(N)AsBi, while other dilute bismides have also been reported recently. In this paper, we shall briefly review several novel bismides: GaSbBi, InSbiBi, InAsBi, InPBi and InGaAsBi, and the Bi surfactant effect from our group, all grown by molecular beam epitaxy (MBE).
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16.
  • Wu, Zhenjing, et al. (författare)
  • Mathematical Modeling and Performance Analysis of Seawater Heat Exchanger in Closed-Loop Seawater-Source Heat Pump System
  • 2019
  • Ingår i: Journal of energy engineering. - : ASCE-AMER SOC CIVIL ENGINEERS. - 0733-9402 .- 1943-7897. ; 145:4
  • Tidskriftsartikel (refereegranskat)abstract
    • The seawater source heat pump (SWHP) utilizes low-grade energy from seawater to satisfy heating/cooling requirements of coastal buildings. Compared with the open-loop SWHP system, the closed-loop system is more stable and reliable when used in cold regions because the seawater heat exchanger can mitigate icing and corrosion problems. This study established mathematical modeling for the seawater heat exchanger, which was validated by the experimental results, to estimate the heat transfer performance. The thermal performance of the seawater heat exchanger under different operating conditions was predicted, and the effects of several key parameters on thermal resistance were analyzed. The results revealed that the pipe wall thermal resistance of the original heat exchanger was the most important factor limiting the heat transfer. Hence, a cost analysis of the heat exchangers with different pipe materials was conducted, and the steel pipe with anticorrosive coating was proven to be optimal in reducing pipe wall thermal resistance and economy. The findings are useful in designing and optimizing the seawater heat exchanger and promoting the application of ocean thermal energy.
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17.
  • Xu, Jun, et al. (författare)
  • Optimal response to habitat linkage of local fish diversity and mean trophic level
  • 2016
  • Ingår i: Limnology and Oceanography. - : Wiley. - 1939-5590 .- 0024-3590. ; 61:4, s. 1438-1448
  • Tidskriftsartikel (refereegranskat)abstract
    • Spatially segregated ecosystems are frequently subsidized by cross-habitat linkages, but the extent to which the functional links between habitats influence local community attributes, such as consumer and food web structure is still poorly understood. Using the bidirectional linkage between benthic and pelagic habitats in floodplain lakes, we address this important question by looking for evidence of an optimal extent of habitat linkage supporting maximum taxonomic richness and mean trophic level. We then ask if there are significant changes in these local community attributes between historical and current communities, and if these reflect the history of species loss resulting from the intense human alteration of these lakes. We found a strong optimal response of maximum richness and mean trophic level along the pelagic-benthic gradient, both across and within individual lakes. This is consistent with the expectation of optimal resource availability along the habitat linkage gradient supporting more and taxonomically richer communities. Comparison between historical and current assemblages revealed a significant decrease in the optimal linkage for maximum richness in response to the history of species loss, but not for maximum mean trophic level, probably a response to the increased habitat homogenization and enhanced productivity caused by the recent history of nutrient-enrichment and habitat alteration. Our study provides strong evidence of high diversity and trophic level occurring at intermediate levels of coupling between pelagic and benthic resources, suggesting assemblage reliance on multiple production sources, and offers novel insight into the responses of this relationship to species loss due to human activities.
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18.
  • Zhang, Yanan, et al. (författare)
  • Dysregulation of Cells Cycle and Apoptosis in Human Induced Pluripotent Stem Cells Chondrocytes Through p53 Pathway by HT-2 Toxin : An in vitro Study
  • 2021
  • Ingår i: Frontiers in Genetics. - : Frontiers Media S.A.. - 1664-8021. ; 12
  • Tidskriftsartikel (refereegranskat)abstract
    • Kashin–Beck disease (KBD) mainly damages growth plate of adolescents and is susceptible to both gene and gene–environmental risk factors. HT-2 toxin, which is a primary metabolite of T-2 toxin, was regarded as one of the environmental risk factors of KBD. We used successfully generated KBD human induced pluripotent stem cells (hiPSCs) and control hiPSCs, which carry different genetic information. They have potential significance in exploring the effects of HT-2 toxin on hiPSC chondrocytes and interactive genes with HT-2 toxin for the purpose of providing a cellular disease model for KBD. In this study, we gave HT-2 toxin treatment to differentiating hiPSC chondrocytes in order to investigate the different responses of KBD hiPSC chondrocytes and control hiPSC chondrocytes to HT-2 toxin. The morphology of HT-2 toxin-treated hiPSC chondrocytes investigated by transmission electron microscope clearly showed that the ultrastructure of organelles was damaged and type II collagen expression in hiPSC chondrocytes was downregulated by HT-2 treatment. Moreover, dysregulation of cell cycle was observed; and p53, p21, and CKD6 gene expressions were dysregulated in hiPSC chondrocytes after T-2 toxin treatment. Flow cytometry also demonstrated that there were significantly increased amounts of late apoptotic cells in KBD hiPSC chondrocytes and that the mRNA expression level of Fas was upregulated. In addition, KBD hiPSC chondrocytes presented stronger responses to HT-2 toxin than control hiPSC chondrocytes. These findings confirmed that HT-2 is an environmental risk factor of KBD and that p53 pathway interacted with HT-2 toxin, causing damaged ultrastructure of organelles, accelerating cell cycle in G1 phase, and increasing late apoptosis in KBD hiPSC chondrocytes.
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19.
  • Zhang, Yin-Ping, et al. (författare)
  • Cross-cultural adaptation and validation of the osteoporosis assessment questionnaire short version (OPAQ-SV) for Chinese osteoporotic fracture females
  • 2016
  • Ingår i: Clinical Rheumatology. - : Springer. - 0770-3198 .- 1434-9949. ; 35:4, s. 1003-1010
  • Tidskriftsartikel (refereegranskat)abstract
    • The Osteoporosis Assessment Questionnaire Short Version (OPAQ-SV) was cross-culturally adapted to measure health-related quality of life in Chinese osteoporotic fracture females and then validated in China for its psychometric properties. Cross-cultural adaptation, including translation of the original OPAQ-SV into Mandarin Chinese language, was performed according to published guidelines. Validation of the newly cross-culturally adapted OPAQ-SV was conducted by sampling 234 Chinese osteoporotic fracture females and also a control group of 235 Chinese osteoporotic females without fractures, producing robust content, construct, and discriminant validation results. Major categories of reliability were also met: the Cronbach alpha coefficient was 0.975, indicating good internal consistency; the test-retest reliability was 0.80; and principal component analysis resulted in a 6-factor structure explaining 75.847 % of the total variance. Further, the Comparative Fit Index result was 0.922 following the modified model confirmatory factor analysis, and the chi-squared test was 1.98. The root mean squared error of approximation was 0.078. Moreover, significant differences were revealed between females with fractures and those without fractures across all domains (p < 0.001). Overall, the newly cross-culturally adapted OPAQ-SV appears to possess adequate validity and reliability and may be utilized in clinical trials to assess the health-related quality of life in Chinese osteoporotic fracture females.
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20.
  • Zhou, Fang, et al. (författare)
  • A New Red-Emitting Fluorescence Probe for Rapid and Effective Visualization of Bisulfite in Food Samples and Live Animals
  • 2019
  • Ingår i: Journal of Agricultural and Food Chemistry. - : American Chemical Society (ACS). - 0021-8561 .- 1520-5118. ; 67:15, s. 4375-4383
  • Tidskriftsartikel (refereegranskat)abstract
    • The development of new methods for rapid and effective detection of bisulfite (HSO3-) in food samples and imaging of HSO3- intake in animals is of significant importance due to the key roles of HSO3- in food quality assurance and community health. In this work, a new responsive fluorescence probe, EQC, is reported for the quantitative detection of HSO3- in food samples and visualization of HSO3- intake in animals. Upon addition of HSO3-, the UV-vis absorption and red emission of EQC were significantly decreased within 120 s. The changes in absorption and emission spectra of EQC were rationalized by theoretical computations. The proposed reaction mechanism of EQC with HSO3- was confirmed by high-resolution mass spectrometry (HRMS) and spectroscopic titration measurements. EQC has the advantages of high sensitivity, selectivity (a detection limit of 18.1 nM), and fast response toward HSO3-, which enable rapid and effective HSO3- detection in buffer solution. The practical applications of EQC were demonstrated by the detection of HSO3- in food samples and the imaging of HSO3- intake in live animals.
  •  
21.
  • Bai, Ru, et al. (författare)
  • Clinical characteristics and phylogenetic analysis of human enteric adenovirus type 41 (HAdV-F41) from children with gastroenteritis during SARS-CoV-2 pandemic
  • 2024
  • Ingår i: Infection, Genetics and Evolution. - : Elsevier. - 1567-1348 .- 1567-7257. ; 123
  • Tidskriftsartikel (refereegranskat)abstract
    • Human adenovirus type 41 (HAdV-F41) usually causes pediatrics gastroenteritis. However, it was reported to be associated with the outbreaks of severe acute hepatitis of unknown aetiology (SAHUA) in pediatrics during COVID-19 pandemic. In this study, we investigated the prevalence of enteric HAdV-F41 in 37,920 paediatric gastroenteritis cases from 2017 to 2022 in Guangzhou, China. All children presented were tested negative for SARS-CoV-2 during the “zero-COVID” period. The main clinical symptom of the children was diarrhea (96.5%). No fatalities nor liver abnormal symptoms was found. In 2021, one year since the pandemic of COVID-19, the prevalence of HAdV-F41 abruptly increased from 3.71% to 8.64% (P < 0.001). All of HAdV-F41 circulating worldwide were classified into eight different subtypes (G1-G8) based on the phylogenetic clustering permutation of the four capsid genes of HAdV-F41. G3 was the predominant subtype (56.2%; 77/137). CRV5 isolates from SAHUA cases belong to this subtype, in which N312D and H335D mutations in the short fiber knob were identified in both Guangzhou and CRV5 isolates, presumably changing the virus tropism by directly interacting with the heparin sulfate (HS) receptor. Additionally, a novel recombinant G6 subtype, which is unique and only circulating in China was first identified in this study. This is the first study highlighting the prevalence of HAdV-F41 in paediatric cases of gastroenteritis during COVID-19 pandemic in China. The clinical and viral evolution finding of HAdV-F41 provide insight into the clinical characteristics of children with HAdV-F41 infections as well as the uncertain role of HAdV-F41 in the cause of SAHUA.
  •  
22.
  • Björnerås, Caroline, et al. (författare)
  • Inland blue holes of The Bahamas - chemistry and biology in a unique aquatic environment
  • 2020
  • Ingår i: Fundamental and Applied Limnology. - : Schweizerbart science publishers. - 1863-9135. ; 194:2, s. 95-106
  • Tidskriftsartikel (refereegranskat)abstract
    • While lake systems in temperate regions have been extensively studied, tropical and subtropical systems have received less attention. Here, we describe the water chemistry and biota of ten inland blue holes on Andros Island, The Bahamas, representative of the morphological, abiotic, and biotic variation among Androsian inland blue holes. The majority of the studied blue holes were vertically stratified with oxic freshwater overlying anoxic saline groundwater of marine origin. Water chemistry (e.g. total phosphorus and nitrogen) in shallow waters was similar among blue holes, while turbidity and water color varied. Presence of hydrogen sulfide and reduced iron in and below the halocline indicate reducing conditions in all stratified blue holes. The biota above the halocline was also similar among blue holes with a few taxa dominating the phytoplankton community, and the zooplankton community consisting of copepods and rotifers. The Bahamas mosquitofish (Gambusia hubbsi) was present in all investigated blue holes, often accompanied by other small planktivorous fish, while the piscivorous bigmouth sleeper (Gobiomorus donnitor) was only present in some of the blue holes. Our field study reinforces that inland blue holes are highly interesting for biogeochemical research, and provide naturally replicated systems for evolutionary studies.
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23.
  • Björnsson, Bergthor, et al. (författare)
  • Digital twins to personalize medicine
  • 2020
  • Ingår i: Genome Medicine. - : Springer Science and Business Media LLC. - 1756-994X. ; 12:1
  • Forskningsöversikt (refereegranskat)abstract
    • Personalized medicine requires the integration and processing of vast amounts of data. Here, we propose a solution to this challenge that is based on constructing Digital Twins. These are high-resolution models of individual patients that are computationally treated with thousands of drugs to find the drug that is optimal for the patient.
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24.
  • Bruhn, Sören, et al. (författare)
  • A Generally Applicable Translational Strategy Identifies S100A4 as a Candidate Gene in Allergy
  • 2014
  • Ingår i: Science Translational Medicine. - : American Association for the Advancement of Science (AAAS). - 1946-6234 .- 1946-6242. ; 6:218
  • Tidskriftsartikel (refereegranskat)abstract
    • The identification of diagnostic markers and therapeutic candidate genes in common diseases is complicated by the involvement of thousands of genes. We hypothesized that genes co-regulated with a key gene in allergy, IL13, would form a module that could help to identify candidate genes. We identified a T helper 2 (T(H)2) cell module by small interfering RNA-mediated knockdown of 25 putative IL13-regulating transcription factors followed by expression profiling. The module contained candidate genes whose diagnostic potential was supported by clinical studies. Functional studies of human TH2 cells as well as mouse models of allergy showed that deletion of one of the genes, S100A4, resulted in decreased signs of allergy including TH2 cell activation, humoral immunity, and infiltration of effector cells. Specifically, dendritic cells required S100A4 for activating T cells. Treatment with an anti-S100A4 antibody resulted in decreased signs of allergy in the mouse model as well as in allergen-challenged T cells from allergic patients. This strategy, which may be generally applicable to complex diseases, identified and validated an important diagnostic and therapeutic candidate gene in allergy.
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25.
  • Bruhn, Sören, 1976-, et al. (författare)
  • Combining gene expression microarray- and cluster analysis with sequence-based predictions to identify regulators of IL-13 in allergy
  • 2012
  • Ingår i: Cytokine. - : Elsevier. - 1043-4666 .- 1096-0023. ; 60:3, s. 736-740
  • Tidskriftsartikel (refereegranskat)abstract
    • The Th2 cytokine IL-13 plays a key role in allergy, by regulating IgE, airway hyper secretion, eosinophils and mast cells. In this study, we aimed to identify novel transcription factors (TFs) that potentially regulated IL-13. We analyzed Th2 polarized naïve T cells from four different blood donors with gene expression microarrays to find clusters of genes that were correlated or anti-correlated with IL13. These clusters were further filtered, by selecting genes that were functionally related. In these clusters, we identified three transcription factors (TFs) that were predicted to regulate the expression of IL13, namely CEBPB, E2F6 and AHR. siRNA mediated knockdowns of these TFs in naïve polarized T cells showed significant increases of IL13, following knockdown of CEBPB and E2F6, but not AHR. This suggested an inhibitory role of CEBPB and E2F6 in the regulation of IL13 and allergy. This was supported by analysis of E2F6, but not CEBPB, in allergen-challenged CD4+ T cells from six allergic patients and six healthy controls, which showed decreased expression of E2F6 in patients. In summary, our findings indicate an inhibitory role of E2F6 in the regulation of IL-13 and allergy. The analytical approach may be generally applicable to elucidate the complex regulatory patterns in Th2 cell polarization and allergy.
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26.
  • Cao, Lina, et al. (författare)
  • Atomically dispersed iron hydroxide anchored on Pt for preferential oxidation of CO in H-2
  • 2019
  • Ingår i: Nature. - : NATURE PUBLISHING GROUP. - 0028-0836 .- 1476-4687. ; 565:7741, s. 631-635
  • Tidskriftsartikel (refereegranskat)abstract
    • Proton-exchange-membrane fuel cells (PEMFCs) are attractive next-generation power sources for use in vehicles and other applications(1), with development efforts focusing on improving the catalyst system of the fuel cell. One problem is catalyst poisoning by impurity gases such as carbon monoxide (CO), which typically comprises about one per cent of hydrogen fuel(2-4). A possible solution is on-board hydrogen purification, which involves preferential oxidation of CO in hydrogen (PROX)(3-7). However, this approach is challenging(8-15) because the catalyst needs to be active and selective towards CO oxidation over a broad range of low temperatures so that CO is efficiently removed (to below 50 parts per million) during continuous PEMFC operation (at about 353 kelvin) and, in the case of automotive fuel cells, during frequent cold-start periods. Here we show that atomically dispersed iron hydroxide, selectively deposited on silica-supported platinum (Pt) nanoparticles, enables complete and 100 per cent selective CO removal through the PROX reaction over the broad temperature range of 198 to 380 kelvin. We find that the mass-specific activity of this system is about 30 times higher than that of more conventional catalysts consisting of Pt on iron oxide supports. In situ X-ray absorption fine-structure measurements reveal that most of the iron hydroxide exists as Fe-1(OH)(x) clusters anchored on the Pt nanoparticles, with density functional theory calculations indicating that Fe-1(OH)(x)-Pt single interfacial sites can readily react with CO and facilitate oxygen activation. These findings suggest that in addition to strategies that target oxide-supported precious-metal nanoparticles or isolated metal atoms, the deposition of isolated transition-metal complexes offers new ways of designing highly active metal catalysts.
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27.
  • Chen, Lan, et al. (författare)
  • A modified ionization difference UV-vis method for fast quantitation of guaiacyl-type phenolic hydroxyl groups in lignin
  • 2022
  • Ingår i: International Journal of Biological Macromolecules. - : Elsevier BV. - 0141-8130 .- 1879-0003. ; 201, s. 330-337
  • Tidskriftsartikel (refereegranskat)abstract
    • An ionization difference UV-Vis method (Delta epsilon-spectrum method) is the most potentially simple method for fast quantitation of phenolic hydroxyl groups (ph-OH) in lignin. However, the underestimated results were calculated from the conventional Delta epsilon-spectrum method using one- or two-point wavelengths measurement. In this study, a modified Delta epsilon-spectrum method using multi-point wavelengths measurement was developed and the negative absorbance was also considered. Four main typical lignin models, e.g. vanilla alcohol, 5-5 biphenyl, stilbenoid and vanillin, were applied as the guaiacyl-type (G-type) phenolic models for the determination of ph-OH by the modified Delta epsilon-spectrum method. The 2-methoxyethanol/water/acetic acid = 8/2/0.2 (V/V/V) was used as the acidic solvent system and the 2-methoxyethanol/0.2 M NaOH solution = 1/9 (V/V) was used as the alkaline solvent system. The ph-OH contents in the spruce milled wood lignin (SMWL) and the spruce Kraft lignin (SKL) were respectively quantified by the modified Delta epsilon-spectrum method as 1.078 and 4.348 mmol/g, which were comparable to the counterparts determined by P-31 Nuclear Magnetic Resonance Spectroscopy (P-31 NMR). The results revealed that the modified Delta epsilon-spectrum method can provide more accurate and reliable results compared to the conventional method.
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28.
  • Choudhury, Maidul I., et al. (författare)
  • Charophytes collapse beyond a critical warming and brownification threshold in shallow lake systems
  • 2019
  • Ingår i: Science of the Total Environment. - : Elsevier BV. - 0048-9697 .- 1879-1026. ; 661, s. 148-154
  • Tidskriftsartikel (refereegranskat)abstract
    • Charophytes play a critical role for the functioning of shallow lake ecosystems. Although growth of charophytes can be limited by many factors, such as temperature, nutrients and light availability, our understanding about concomitant effects of climate warming and other large-scale environmental perturbations, e.g. increases in humic matter content (‘brownification’) is still limited. Here we conducted an outdoor mesocosm experiment during 71 days with a common charophyte species, Chara vulgaris, along an increasing gradient of temperature and brownification. We hypothesized the growth of C. vulgaris to increase with temperature, but to level off along the combined temperature and brownification gradient when reaching a critical threshold for light limitation via brownification. We show that C. vulgaris increases the relative growth rate (RGR), main and total shoot elongation, as well as number of lateral shoots when temperature and brownification increased by +2 °C and + 100%, respectively above today's levels. However, the RGR, shoot elongation and number of lateral shoots declined at further increment of temperature and brownification. Macrophyte weight-length ratio decreased with increased temperature and brownification, indicating that C. vulgaris allocate more resources or energy for shoot elongation instead of biomass increase at warmer temperatures and higher brownification. Our study shows that C. vulgaris will initially benefit from warming and brownification but will then decline as a future scenario of increased warming and brownification reaches a certain threshold level, in case of our experiment at +4 °C and a 2-fold increase in brownification above today's levels.
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29.
  • Deng, Huan, et al. (författare)
  • Altered Expression of the Hedgehog Pathway Proteins BMP2, BMP4, SHH, and IHH Involved in Knee Cartilage Damage of Patients With Osteoarthritis and Kashin-Beck Disease
  • 2022
  • Ingår i: Cartilage. - : Sage Publications. - 1947-6035 .- 1947-6043. ; 13:1
  • Tidskriftsartikel (refereegranskat)abstract
    • OBJECTIVE: To investigate the expression of Hedgehog (HH) signaling pathway proteins in knee articular cartilage from Kashin-Beck disease (KBD) and osteoarthritis (OA) patients.METHODS: Knee articular cartilage samples were collected from normal (N), OA, and KBD adults (aged 38-60 years) and divided into 3 groups with 6 subjects in each group. The localization of the HH pathway proteins bone morphogenetic protein 2 (BMP2), bone morphogenetic protein 4 (BMP4), Sonic hedgehog (SHH), and Indian hedgehog (IHH) was observed with the microscope after immunohistochemical (IHC) staining. Positive staining cell rates of each proteins were compared.RESULTS: The strongest stainings of all proteins were observed in the middle zones of all 3 groups. The positive staining rates of BMP4 and IHH were significantly lower in the OA and KBD groups than those in the N group in all 3 zones. The positive staining rates of BMP2 and SHH tend to be lower in the OA and KBD groups than those in the N group in the deep zone, while higher in the OA and KBD groups than those in the N group in superficial and middle zones.CONCLUSIONS: Altered expression of the HH pathway proteins BMP2, BMP4, SHH, and IHH was found in OA and KBD articular cartilage. There seemed to be a compensatory effect between SHH and IHH in cartilage damage. Further studies on the pathogenesis of OA and KBD may be carried out from these aspects in the future.
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30.
  • Ferro, Ana, et al. (författare)
  • Alcohol intake and gastric cancer : Meta-analyses of published data versus individual participant data pooled analyses (StoP Project)
  • 2018
  • Ingår i: Cancer Epidemiology. - : ELSEVIER SCI LTD. - 1877-7821 .- 1877-783X. ; 54, s. 125-132
  • Tidskriftsartikel (refereegranskat)abstract
    • Background: Individual participant data pooled analyses allow access to non-published data and statistical reanalyses based on more homogeneous criteria than meta-analyses based on systematic reviews. We quantified the impact of publication-related biases and heterogeneity in data analysis and presentation in summary estimates of the association between alcohol drinking and gastric cancer.Methods: We compared estimates obtained from conventional meta-analyses, using only data available in published reports from studies that take part in the Stomach Cancer Pooling (StoP) Project, with individual participant data pooled analyses including the same studies.Results: A total of 22 studies from the StoP Project assessed the relation between alcohol intake and gastric cancer, 19 had specific data for levels of consumption and 18 according to cancer location; published reports addressing these associations were available from 18, 5 and 5 studies, respectively. The summary odds ratios [OR, (95%CI)] estimate obtained with published data for drinkers vs. non-drinkers was 10% higher than the one obtained with individual StoP data [18 vs. 22 studies: 1.21 (1.07-1.36) vs. 1.10 (0.99-1.23)] and more heterogeneous (1(2): 63.6% vs 54.4%). In general, published data yielded less precise summary estimates (standard errors up to 2.6 times higher). Funnel plot analysis suggested publication bias.Conclusion: Meta-analyses of the association between alcohol drinking and gastric cancer tended to overestimate the magnitude of the effects, possibly due to publication bias. Additionally, individual participant data pooled analyses yielded more precise estimates for different levels of exposure or cancer subtypes.
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31.
  • Ferro, Ana, et al. (författare)
  • Tobacco smoking and gastric cancer: : meta-analyses of published data versus pooled analyses of individual participant data (StoP Project).
  • 2018
  • Ingår i: European Journal of Cancer Prevention. - 0959-8278 .- 1473-5709. ; 27:3, s. 197-204
  • Tidskriftsartikel (refereegranskat)abstract
    • Tobacco smoking is one of the main risk factors for gastric cancer, but the magnitude of the association estimated by conventional systematic reviews and meta-analyses might be inaccurate, due to heterogeneous reporting of data and publication bias. We aimed to quantify the combined impact of publication-related biases, and heterogeneity in data analysis or presentation, in the summary estimates obtained from conventional meta-analyses. We compared results from individual participant data pooled-analyses, including the studies in the Stomach Cancer Pooling (StoP) Project, with conventional meta-analyses carried out using only data available in previously published reports from the same studies. From the 23 studies in the StoP Project, 20 had published reports with information on smoking and gastric cancer, but only six had specific data for gastric cardia cancer and seven had data on the daily number of cigarettes smoked. Compared to the results obtained with the StoP database, conventional meta-analyses overvalued the relation between ever smoking (summary odds ratios ranging from 7% higher for all studies to 22% higher for the risk of gastric cardia cancer) and yielded less precise summary estimates (SE ≤2.4 times higher). Additionally, funnel plot asymmetry and corresponding hypotheses tests were suggestive of publication bias. Conventional meta-analyses and individual participant data pooled-analyses reached similar conclusions on the direction of the association between smoking and gastric cancer. However, published data tended to overestimate the magnitude of the effects, possibly due to publication biases and limited the analyses by different levels of exposure or cancer subtypes.
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32.
  • Fu, Hong, et al. (författare)
  • Energetic Asymmetry Connected with Energy Flow Changes in Response to Eutrophication : A Study of Multiple Fish Species in Subtropical Shallow Lakes
  • 2019
  • Ingår i: Polish Journal of Ecology. - 1505-2249. ; 67:4, s. 305-315
  • Tidskriftsartikel (refereegranskat)abstract
    • Energy flow is a central characteristic in all ecosystems, and it has attracted considerable scientific attention due to its significant effects on the stability of food webs. Lake ecosystems that undergo regime shifts (clear water phase, phytoplankton dominated changed into turbid water, macrophytes dominated or vice versa) are characterized by a series of transformation in trophic structure. Although previous studies have mainly focused on the causes and consequences of regime shifts in shallow lakes, studies about responses of energy flow changes to regime shifts is far from complete. In this paper, we estimated trophic position and benthivory (i.e. degree of benthivory) of seventeen fish species from seven shallow lakes. Our data show that the trophic position and benthivory of fish species in clear water phase are significantly higher than in turbid water. This finding might help spark some ideas for subtropical lake eutrophication treatment.
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33.
  • Gawel, Danuta, et al. (författare)
  • A validated single-cell-based strategy to identify diagnostic and therapeutic targets in complex diseases
  • 2019
  • Ingår i: Genome Medicine. - : Springer Science and Business Media LLC. - 1756-994X. ; 11
  • Tidskriftsartikel (refereegranskat)abstract
    • Background: Genomic medicine has paved the way for identifying biomarkers and therapeutically actionable targets for complex diseases, but is complicated by the involvement of thousands of variably expressed genes across multiple cell types. Single-cell RNA-sequencing study (scRNA-seq) allows the characterization of such complex changes in whole organs. Methods: The study is based on applying network tools to organize and analyze scRNA-seq data from a mouse model of arthritis and human rheumatoid arthritis, in order to find diagnostic biomarkers and therapeutic targets. Diagnostic validation studies were performed using expression profiling data and potential protein biomarkers from prospective clinical studies of 13 diseases. A candidate drug was examined by a treatment study of a mouse model of arthritis, using phenotypic, immunohistochemical, and cellular analyses as read-outs. Results: We performed the first systematic analysis of pathways, potential biomarkers, and drug targets in scRNA-seq data from a complex disease, starting with inflamed joints and lymph nodes from a mouse model of arthritis. We found the involvement of hundreds of pathways, biomarkers, and drug targets that differed greatly between cell types. Analyses of scRNA-seq and GWAS data from human rheumatoid arthritis (RA) supported a similar dispersion of pathogenic mechanisms in different cell types. Thus, systems-level approaches to prioritize biomarkers and drugs are needed. Here, we present a prioritization strategy that is based on constructing network models of disease-associated cell types and interactions using scRNA-seq data from our mouse model of arthritis, as well as human RA, which we term multicellular disease models (MCDMs). We find that the network centrality of MCDM cell types correlates with the enrichment of genes harboring genetic variants associated with RA and thus could potentially be used to prioritize cell types and genes for diagnostics and therapeutics. We validated this hypothesis in a large-scale study of patients with 13 different autoimmune, allergic, infectious, malignant, endocrine, metabolic, and cardiovascular diseases, as well as a therapeutic study of the mouse arthritis model. Conclusions: Overall, our results support that our strategy has the potential to help prioritize diagnostic and therapeutic targets in human disease.
  •  
34.
  • Gawel, Danuta, et al. (författare)
  • An algorithm-based meta-analysis of genome- and proteome-wide data identifies a combination of potential plasma biomarkers for colorectal cancer
  • 2019
  • Ingår i: Scientific Reports. - : NATURE PUBLISHING GROUP. - 2045-2322. ; 9
  • Tidskriftsartikel (refereegranskat)abstract
    • Screening programs for colorectal cancer (CRC) often rely on detection of blood in stools, which is unspecific and leads to a large number of colonoscopies of healthy subjects. Painstaking research has led to the identification of a large number of different types of biomarkers, few of which are in general clinical use. Here, we searched for highly accurate combinations of biomarkers by meta-analyses of genome- and proteome-wide data from CRC tumors. We focused on secreted proteins identified by the Human Protein Atlas and used our recently described algorithms to find optimal combinations of proteins. We identified nine proteins, three of which had been previously identified as potential biomarkers for CRC, namely CEACAM5, LCN2 and TRIM28. The remaining proteins were PLOD1, MAD1L1, P4HA1, GNS, C12orf10 and P3H1. We analyzed these proteins in plasma from 80 patients with newly diagnosed CRC and 80 healthy controls. A combination of four of these proteins, TRIM28, PLOD1, CEACAM5 and P4HA1, separated a training set consisting of 90% patients and 90% of the controls with high accuracy, which was verified in a test set consisting of the remaining 10%. Further studies are warranted to test our algorithms and proteins for early CRC diagnosis.
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35.
  •  
36.
  • Gawel, Danuta, et al. (författare)
  • The Allergic Airway Inflammation Repository - a user-friendly, curated resource of mRNA expression levels in studies of allergic airways
  • 2014
  • Ingår i: Allergy. European Journal of Allergy and Clinical Immunology. - : Wiley. - 0105-4538 .- 1398-9995. ; 69:8, s. 1115-1117
  • Tidskriftsartikel (refereegranskat)abstract
    • Public microarray databases allow analysis of expression levels of candidate genes in different contexts. However, finding relevant microarray data is complicated by the large number of available studies. We have compiled a user-friendly, open-access database of mRNA microarray experiments relevant to allergic airway inflammation, the Allergic Airway Inflammation Repository (AAIR, http://aair.cimed.ike.liu.se/). The aim is to allow allergy researchers to determine the expression profile of their genes of interest in multiple clinical data sets and several experimental systems quickly and intuitively. AAIR also provides quick links to other relevant information such as experimental protocols, related literature and raw data files.
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37.
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38.
  • Gustafsson, Mika, et al. (författare)
  • A validated gene regulatory network and GWAS identifies early regulators of T cell-associated diseases
  • 2015
  • Ingår i: Science Translational Medicine. - : AMER ASSOC ADVANCEMENT SCIENCE. - 1946-6234 .- 1946-6242. ; 7:313
  • Tidskriftsartikel (refereegranskat)abstract
    • Early regulators of disease may increase understanding of disease mechanisms and serve as markers for presymptomatic diagnosis and treatment. However, early regulators are difficult to identify because patients generally present after they are symptomatic. We hypothesized that early regulators of T cell-associated diseases could be found by identifying upstream transcription factors (TFs) in T cell differentiation and by prioritizing hub TFs that were enriched for disease-associated polymorphisms. A gene regulatory network (GRN) was constructed by time series profiling of the transcriptomes and methylomes of human CD4(+) T cells during in vitro differentiation into four helper T cell lineages, in combination with sequence-based TF binding predictions. The TFs GATA3, MAF, and MYB were identified as early regulators and validated by ChIP-seq (chromatin immunoprecipitation sequencing) and small interfering RNA knockdowns. Differential mRNA expression of the TFs and their targets in T cell-associated diseases supports their clinical relevance. To directly test if the TFs were altered early in disease, T cells from patients with two T cell-mediated diseases, multiple sclerosis and seasonal allergic rhinitis, were analyzed. Strikingly, the TFs were differentially expressed during asymptomatic stages of both diseases, whereas their targets showed altered expression during symptomatic stages. This analytical strategy to identify early regulators of disease by combining GRNs with genome-wide association studies may be generally applicable for functional and clinical studies of early disease development.
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39.
  • Gustafsson, Mika, et al. (författare)
  • Integrated genomic and prospective clinical studies show the importance of modular pleiotropy for disease susceptibility, diagnosis and treatment
  • 2014
  • Ingår i: Genome Medicine. - : BioMed Central. - 1756-994X. ; 6:17
  • Tidskriftsartikel (refereegranskat)abstract
    • Background: Translational research typically aims to identify and functionally validate individual, disease-specific genes. However, reaching this aim is complicated by the involvement of thousands of genes in common diseases, and that many of those genes are pleiotropic, that is, shared by several diseases. Methods: We integrated genomic meta-analyses with prospective clinical studies to systematically investigate the pathogenic, diagnostic and therapeutic roles of pleiotropic genes. In a novel approach, we first used pathway analysis of all published genome-wide association studies (GWAS) to find a cell type common to many diseases. Results: The analysis showed over-representation of the T helper cell differentiation pathway, which is expressed in T cells. This led us to focus on expression profiling of CD4(+) T cells from highly diverse inflammatory and malignant diseases. We found that pleiotropic genes were highly interconnected and formed a pleiotropic module, which was enriched for inflammatory, metabolic and proliferative pathways. The general relevance of this module was supported by highly significant enrichment of genetic variants identified by all GWAS and cancer studies, as well as known diagnostic and therapeutic targets. Prospective clinical studies of multiple sclerosis and allergy showed the importance of both pleiotropic and disease specific modules for clinical stratification. Conclusions: In summary, this translational genomics study identified a pleiotropic module, which has key pathogenic, diagnostic and therapeutic roles.
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40.
  • Gustafsson, Mika, et al. (författare)
  • Modules, networks and systems medicine for understanding disease and aiding diagnosis
  • 2014
  • Ingår i: Genome Medicine. - : BioMed Central. - 1756-994X. ; 6:82
  • Forskningsöversikt (refereegranskat)abstract
    • Many common diseases, such as asthma, diabetes or obesity, involve altered interactions between thousands of genes. High-throughput techniques (omics) allow identification of such genes and their products, but functional understanding is a formidable challenge. Network-based analyses of omics data have identified modules of disease-associated genes that have been used to obtain both a systems level and a molecular understanding of disease mechanisms. For example, in allergy a module was used to find a novel candidate gene that was validated by functional and clinical studies. Such analyses play important roles in systems medicine. This is an emerging discipline that aims to gain a translational understanding of the complex mechanisms underlying common diseases. In this review, we will explain and provide examples of how network-based analyses of omics data, in combination with functional and clinical studies, are aiding our understanding of disease, as well as helping to prioritize diagnostic markers or therapeutic candidate genes. Such analyses involve significant problems and limitations, which will be discussed. We also highlight the steps needed for clinical implementation.
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41.
  • Han, Jing, et al. (författare)
  • Nano-elemental selenium particle developed via supramolecularself-assembly of chondroitin sulfate A and Na2SeO3 to repaircartilage lesions
  • 2023
  • Ingår i: Carbohydrate Polymers. - : Elsevier. - 0144-8617 .- 1879-1344. ; 316
  • Tidskriftsartikel (refereegranskat)abstract
    • Cartilage repair is a significant clinical issue due to its restricted ability to regenerate and self-heal after cartilage lesions or degenerative disease. Herein, a nano-elemental selenium particle (chondroitin sulfate A‑selenium nanoparticle, CSA-SeNP) is developed by the supramolecular self-assembly of Na2SeO3 and negatively charged chondroitin sulfate A (CSA) via electrostatic interactions or hydrogen bonds followed by in-situ reducing of l-ascorbic acid for cartilage lesions repair. The constructed micelle exhibits a hydrodynamic particle size of 171.50 ± 2.40 nm and an exceptionally high selenium loading capacity (9.05 ± 0.03 %) and can promote chondrocyte proliferation, increase cartilage thickness, and improve the ultrastructure of chondrocytes and organelles. It mainly enhances the sulfation modification of chondroitin sulfate by up-regulating the expression of chondroitin sulfate 4-O sulfotransferase-1, −2, −3, which in turn promotes the expression of aggrecan to repair articular and epiphyseal-plate cartilage lesions. The micelles combine the bio-activity of CSA with selenium nanoparticles (SeNPs), which are less toxic than Na2SeO3, and low doses of CSA-SeNP are even superior to inorganic selenium in repairing cartilage lesions in rats. Thus, the developed CSA-SeNP is anticipated to be a promising selenium supplementation preparation in clinical application to address the difficulty of healing cartilage lesions with outstanding repair effects.
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42.
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43.
  • Hansson, Lars Anders, et al. (författare)
  • Different climate scenarios alter dominance patterns among aquatic primary producers in temperate systems
  • 2020
  • Ingår i: Limnology and Oceanography. - : WILEY. - 0024-3590 .- 1939-5590. ; 65:10, s. 2328-2336
  • Tidskriftsartikel (refereegranskat)abstract
    • In a future climate change perspective, the interactions among different life-forms of primary producers will likely be altered, leading to changes in the relative dominance among macrophytes, filamentous, and planktonic algae. In order to improve the possibilities to forecast future ecosystem services and function, we therefore conducted a long-term mesocosm study where primary producers were exposed to different climate scenarios, including both a mean increase in temperature (4 degrees C) and a similar energy input, but delivered as "heat waves" (fluctuations 0-8 degrees C above ambient). We show that in shallow systems, future climate change scenarios will likely lead to higher total macrophyte biomasses, but also to considerable alterations in the macrophyte community composition. The biomass of filamentous algae (Cladophora) showed no significant difference among treatments, although effect size analyses identified a slight increase at heated conditions. We also show that future climate change will not necessarily lead to more phytoplankton blooms, although a considerable alteration in phytoplankton community composition is to be expected, with a dominance of cyanobacteria and Cryptophytes, whereas Chlorophyceae and diatoms will likely play a less pronounced role than at present. In a broader context, we conclude that the total biomass of macrophytes will likely increase in shallow areas, whereas phytoplankton may not show any strong changes in biomass in a future climate change scenario. Instead, the major changes among primary producers will likely be mirrored in a considerably different species composition than at present.
  •  
44.
  • Hellberg, Sandra, et al. (författare)
  • Dynamic Response Genes in CD4+ T Cells Reveal a Network of Interactive Proteins that Classifies Disease Activity in Multiple Sclerosis
  • 2016
  • Ingår i: Cell Reports. - : Cell Press. - 2211-1247. ; 16:11, s. 2928-2939
  • Tidskriftsartikel (refereegranskat)abstract
    • Multiple sclerosis (MS) is a chronic inflammatory disease of the CNS and has a varying disease course as well as variable response to treatment. Biomarkers may therefore aid personalized treatment. We tested whether in vitro activation of MS patient-derived CD4+ T cells could reveal potential biomarkers. The dynamic gene expression response to activation was dysregulated in patient-derived CD4+ T cells. By integrating our findings with genome-wide association studies, we constructed a highly connected MS gene module, disclosing cell activation and chemotaxis as central components. Changes in several module genes were associated with differences in protein levels, which were measurable in cerebrospinal fluid and were used to classify patients from control individuals. In addition, these measurements could predict disease activity after 2 years and distinguish low and high responders to treatment in two additional, independent cohorts. While further validation is needed in larger cohorts prior to clinical implementation, we have uncovered a set of potentially promising biomarkers.
  •  
45.
  • Jiang, Huanxiang, et al. (författare)
  • Appropriate Molecular Interaction Enabling Perfect Balance Between Induced Crystallinity and Phase Separation for Efficient Photovoltaic Blends
  • 2020
  • Ingår i: ACS Applied Materials and Interfaces. - : American Chemical Society. - 1944-8244 .- 1944-8252. ; 12:23, s. 26286-26292
  • Tidskriftsartikel (refereegranskat)abstract
    • Fluorination is a promising modification method to adjust the photophysical profiles of organic semiconductors. Notably, the fluorine modification on donor or acceptor materials could impact the molecular interaction, which is strongly related to the morphology of bulk heterojunction (BHJ) blends and the resultant device performance. Therefore, it is essential to investigate how the molecular interaction affects the morphology of BHJ films. In this study, a new fluorinated polymer PBDB-PSF is synthesized to investigate the molecular interaction in both nonfluorinated (ITIC) and fluorinated (IT-4F) systems. The results reveal that the F-F interaction in the PBDB-PSF:IT-4F system could effectively induce the crystallization of IT-4F while retaining the ideal phase separation scale, resulting in outstanding charge transport. On the contrary, poor morphology can be observed in the PBDB-PSF:ITIC system because of the unbalanced molecular interaction. As a consequence, the PBDB-PSF:IT-4F device delivers an excellent power conversion efficiency of 13.63%, which greatly exceeds that of the PBDB-PSF:ITIC device (9.84%). These results highlight manipulating the micromorphology with regard to molecular interaction.
  •  
46.
  • Jiao, Jian, et al. (författare)
  • Effectiveness of non-surgical periodontal therapy in a large Chinese population with chronic periodontitis
  • 2017
  • Ingår i: Journal of Clinical Periodontology. - : Wiley. - 0303-6979. ; 44:1, s. 42-50
  • Tidskriftsartikel (refereegranskat)abstract
    • Aim: The aim of this study was to evaluate the effectiveness of non-surgical periodontal treatment (NSPT) and its influential factors in a large Chinese population with chronic periodontitis. Methods: Periodontal examination data of 10,789 patients with at least one periodontal re-evaluation record were extracted from a hospital-based electronic periodontal charting record system. Probing depth (PD) and bleeding index (BI) reductions after NSPT and their influential factors were analysed by multilevel analysis. Results: Mean PD reductions at patient level and site level were 0.62 and 0.65 mm respectively. Mean reductions of percentage of tooth with BI > 1 and BI > 2 were 14.9% and 25.21%. Multilevel analysis demonstrated that PD and BI reductions were mainly influenced by baseline PD, baseline attachment loss (AL), baseline mobility, tooth type and frequency of periodontal maintenance (FPM). Besides, PD reduction was associated with baseline BI for all sites and was associated with gender and smoking status for sites with baseline PD ≥ 5 mm. Conclusion: The effectiveness of NSPT on patients with chronic periodontitis was proved in a large Chinese population. Outcomes of NSPT were mainly influenced by baseline PD, baseline AL, baseline mobility, tooth type and FPM.
  •  
47.
  • Jung Lee, Eun Jung, et al. (författare)
  • Analysis of expression profiling data suggests explanation for difficulties in finding biomarkers for nasal polyps
  • 2020
  • Ingår i: Rhinology. - : INT RHINOLOGIC SOC. - 0300-0729 .- 1996-8604. ; 58:4, s. 360-367
  • Tidskriftsartikel (refereegranskat)abstract
    • Background: Identification of clinically useful biomarkers for Nasal Polyposis in chronic rhinosinusitis (CRSwNP) has proven difficult. We analyzed gene expression profiling data to find explanations for this. Methods:We analyzed mRNA expression profiling data, GSE36830, of six uncinate tissues from healthy controls and six NP from CRSwNP patients. We performed Ingenuity Pathway Analysis (IPA) of differentially expressed genes to identify pathways and predicted upstream regulators. Results: We identified 1,608 differentially expressed genes and 177 significant pathways, of which Th1 and Th2 activation pathway and leukocyte extravasation signaling were most significant. We identified 75 upstream regulators whose activity was predicted to be upregulated.These included regulators of known pathogenic and therapeutic relevance, like IL-4. However, only seven of the 75 regulators were actually differentially expressed in NP, namely CSF1, TYROBP, CCL2, CCL11, SELP, ADORA3, ICAM1. Interestingly, these did not include IL-4, and four of the seven were receptors. This suggested a potential explanation for the discrepancy between the predicted and observed expression levels of the regulators, namely that the receptors, and not their ligands, were upregulated. Indeed, we found that 10 receptors of key predicted upstream regulators were upregulated, including IL4R. Conclusion: Our findings indicate that the difficulties in finding specific biomarkers for CRSwNP depend on the complex underlying mechanisms, which include multiple pathways and regulators, each of which may be subdivided into multiple components such as ligands, soluble and membrane-bound receptors. This suggests that combinations of biomarkers may be needed for CRSwNP diagnostics.
  •  
48.
  • Jung Lee, Eun Jung, et al. (författare)
  • Bulk and single cell transcriptomic data indicate that a dichotomy between inflammatory pathways in peripheral blood and arthritic joints complicates biomarker discovery
  • 2020
  • Ingår i: Cytokine. - : ACADEMIC PRESS LTD- ELSEVIER SCIENCE LTD. - 1043-4666 .- 1096-0023. ; 127
  • Tidskriftsartikel (refereegranskat)abstract
    • Background: Unbiased studies using different genome-wide methods have identified several novel biomarkers for diagnosis and treatment response in Rheumatoid Arthritis (RA). However, clinical translation has proven difficult. Here, we hypothesized that one reason could be that inflammatory responses in peripheral blood are different from those in the arthritic joint. Methods: We performed meta-analysis of gene expression microarray data from synovium, whole blood cells (WBC), peripheral blood mononuclear cells (PBMC), and CD4+ T cells from patients with RA and healthy controls in order to identify overlapping pathways, upstream regulators and potential biomarkers. We also analyzed single cell RNA-sequencing (scRNA-seq) data from peripheral blood and whole joints from a mouse model of antigen-induced arthritis. Results: Analyses of two profiling data sets from synovium from RA patients and healthy controls all showed significant activation of pathways with known pathogenic relevance, such as the Th1 pathway, the role of NFAT in regulation of the immune response, dendritic cell maturation, iCOS-iCOSL signaling in T helper cells, Fc gamma receptor-mediated phagocytosis, interferon signaling, Cdc42 signaling, and cytotoxic T lymphocyte-mediated apoptosis. The most activated upstream regulators included TNF, an important drug target, as well as IFN-gamma and CD40LG, all of which are known to play important pathogenic roles in RA. The differentially expressed genes from synovium included several potential biomarkers, such as CCL5, CCL13, CCL18, CX3CL1, CXCL6, CXCL9, CXCL10, CXCL13, ILLS, IL32, IL1RN, SPP1, and TNFSF11. By contrast, microarray studies of WBC, PBMC and CD4+ T cells showed variable pathways and limited pathway overlap with synovium. Similarly, scRNA-seq data from a mouse model of arthritis did not support that inflammatory responses in peripheral blood reflect those in the arthritic joints. These data showed pathway overlap between mouse joint cells and synovium from patients with RA, but not with cells in peripheral blood. Conclusions: Our findings indicate a dichotomy between gene expression changes, pathways, upstream regulators and biomarkers in synovium and cell types in peripheral blood, which complicates identification of biomarkers in blood.
  •  
49.
  •  
50.
  • L.Q.Zhang,, et al. (författare)
  • Fabrication of novel unipolar nanodiodes in InAs/AlSb for microwave detection
  • 2011
  • Ingår i: Infrared, Millimeter and Terahertz Waves (IRMMW-THz), 2011 36th International Conference on. - 2162-2027. - 9781457705083 ; :2-7 Oct. 2011, s. 1-2
  • Konferensbidrag (refereegranskat)abstract
    • Abstract—We report on the fabrication of unipolar nanodiodes into an InAs/AlxGa1-xSb quantum-well heterostructure for room temperature microwave detection up to 110 GHz. Electron-beam lithography was combined with both dry- and wet-etching, and we explored the differences in the electric and detection parameters with the two methods.
  •  
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