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1.	Klionsky, Daniel J, et al. (author) Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition). 2016 In: Autophagy. - : Informa UK Limited. - 1554-8635 .- 1554-8627. ; 12:1, s. 1-222 Journal article (peer-reviewed)
2.	Klionsky, Daniel J., et al. (author) Guidelines for the use and interpretation of assays for monitoring autophagy 2012 In: Autophagy. - : Informa UK Limited. - 1554-8635 .- 1554-8627. ; 8:4, s. 445-544 Research review (peer-reviewed)abstract In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field.
3.	2019 Journal article (peer-reviewed)
4.	Jakobsson, J., et al. (author) Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition)1 2021 In: Autophagy. - : Informa UK Limited. - 1554-8635 .- 1554-8627. ; 17:1, s. 1-382 Journal article (peer-reviewed)
5.	Jin, Ying-Hui, et al. (author) Chemoprophylaxis, diagnosis, treatments, and discharge management of COVID-19 : An evidence-based clinical practice guideline (updated version) 2020 In: Military Medical Research. - : Springer Science and Business Media LLC. - 2054-9369. ; 7:1 Journal article (peer-reviewed)abstract The novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the cause of a rapidly spreading illness, coronavirus disease 2019 (COVID-19), affecting more than seventeen million people around the world. Diagnosis and treatment guidelines for clinicians caring for patients are needed. In the early stage, we have issued "A rapid advice guideline for the diagnosis and treatment of 2019 novel coronavirus (2019-nCoV) infected pneumonia (standard version)"; now there are many direct evidences emerged and may change some of previous recommendations and it is ripe for develop an evidence-based guideline. We formed a working group of clinical experts and methodologists. The steering group members proposed 29 questions that are relevant to the management of COVID-19 covering the following areas: chemoprophylaxis, diagnosis, treatments, and discharge management. We searched the literature for direct evidence on the management of COVID-19, and assessed its certainty generated recommendations using the Grading of Recommendations, Assessment, Development and Evaluation (GRADE) approach. Recommendations were either strong or weak, or in the form of ungraded consensus-based statement. Finally, we issued 34 statements. Among them, 6 were strong recommendations for, 14 were weak recommendations for, 3 were weak recommendations against and 11 were ungraded consensus-based statement. They covered topics of chemoprophylaxis (including agents and Traditional Chinese Medicine (TCM) agents), diagnosis (including clinical manifestations, reverse transcription-polymerase chain reaction (RT-PCR), respiratory tract specimens, IgM and IgG antibody tests, chest computed tomography, chest x-ray, and CT features of asymptomatic infections), treatments (including lopinavir-ritonavir, umifenovir, favipiravir, interferon, remdesivir, combination of antiviral drugs, hydroxychloroquine/chloroquine, interleukin-6 inhibitors, interleukin-1 inhibitors, glucocorticoid, qingfei paidu decoction, lianhua qingwen granules/capsules, convalescent plasma, lung transplantation, invasive or noninvasive ventilation, and extracorporeal membrane oxygenation (ECMO)), and discharge management (including discharge criteria and management plan in patients whose RT-PCR retesting shows SARS-CoV-2 positive after discharge). We also created two figures of these recommendations for the implementation purpose. We hope these recommendations can help support healthcare workers caring for COVID-19 patients.
6.	Chen, I-Hua, et al. (author) Problematic internet-related behaviors mediate the associations between levels of internet engagement and distress among schoolchildren during COVID-19 lockdown : A longitudinal structural equation modeling study 2021 In: Journal of Behavioral Addictions. - : AKJournals. - 2062-5871 .- 2063-5303. ; 10:1, s. 135-148 Journal article (peer-reviewed)abstract Background and aims: Due to the rapid spread of the novel coronavirus disease 2019 (COVID-19), policies based on the nature of “spatial distancing” have been implemented and have resulted in school suspensions and online learning among schoolchildren. In order to examine the impact of such policies on schoolchildren, the aims of the present study were to (i) assess changes in the level of engagement in three internet-related activities (smartphone use, social media use, and gaming) before and during the COVID-19 outbreak, including prolonged and problematic engagement in these activities; (ii) investigate the differences of psychological distress before and after COVID-19 outbreak; and (iii) to use structural equation modeling to investigate the mediating roles of problematic internet-related behaviors in the causal relationships of psychological distress and time spent on internet-related activities.Methods: Self-report measures were used to assess internet-related activities and psychological distress. Time spent on internet-related activities, problematic use of internet-related activities, and psychological distress were collected from primary school students (N = 535; 265 boys; M age = 10.32 years [SD = 0.84]). The data were first collected before the COVID-19 outbreak (i.e., early November 2019) and then collected again during the school suspension due to COVID-19 outbreak (i.e., end of March 2020) for comparisons of changes.Results: Schoolchildren spent significantly more time on the smartphone (increased 1.02 h daily; P < 0.001) and social media (increased 0.73 h daily; P < 0.001) but not gaming (increased 0.14 h daily; P = 0.07) during the school suspension compared to the baseline. Schoolchildren who increased by 15 or 30 min daily on internet-related activities showed an increased level of psychological distress. The association between problematic use of social media and psychological distress was stronger during the school suspension (β = 0.584) than at the baseline (β = 0.451; P < 0.001).Conclusion: Increased problematic use of internet-related activities among schoolchildren was associated with greater psychological distress. Parents should therefore monitor internet-related activities and psychological distress of their children to support their mental health.
7.	Kattge, Jens, et al. (author) TRY plant trait database - enhanced coverage and open access 2020 In: Global Change Biology. - : Wiley-Blackwell. - 1354-1013 .- 1365-2486. ; 26:1, s. 119-188 Journal article (peer-reviewed)abstract Plant traits-the morphological, anatomical, physiological, biochemical and phenological characteristics of plants-determine how plants respond to environmental factors, affect other trophic levels, and influence ecosystem properties and their benefits and detriments to people. Plant trait data thus represent the basis for a vast area of research spanning from evolutionary biology, community and functional ecology, to biodiversity conservation, ecosystem and landscape management, restoration, biogeography and earth system modelling. Since its foundation in 2007, the TRY database of plant traits has grown continuously. It now provides unprecedented data coverage under an open access data policy and is the main plant trait database used by the research community worldwide. Increasingly, the TRY database also supports new frontiers of trait-based plant research, including the identification of data gaps and the subsequent mobilization or measurement of new data. To support this development, in this article we evaluate the extent of the trait data compiled in TRY and analyse emerging patterns of data coverage and representativeness. Best species coverage is achieved for categorical traits-almost complete coverage for 'plant growth form'. However, most traits relevant for ecology and vegetation modelling are characterized by continuous intraspecific variation and trait-environmental relationships. These traits have to be measured on individual plants in their respective environment. Despite unprecedented data coverage, we observe a humbling lack of completeness and representativeness of these continuous traits in many aspects. We, therefore, conclude that reducing data gaps and biases in the TRY database remains a key challenge and requires a coordinated approach to data mobilization and trait measurements. This can only be achieved in collaboration with other initiatives.
8.	Wang, Fang, et al. (author) Emerging contaminants: A One Health perspective 2024 In: Innovation. - 2666-6758. ; 5 Research review (peer-reviewed)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.
9.	Abd Nikooie Pour, Mina, et al. (author) Results of the Ontology Alignment Evaluation Initiative 2022 2022 In: CEUR Workshop Proceedings. - : CEUR-WS. ; , s. 84-128, s. 84-128 Conference paper (peer-reviewed)abstract The Ontology Alignment Evaluation Initiative (OAEI) aims at comparing ontology matching systems on precisely defined test cases. These test cases can be based on ontologies of different levels of complexity and use different evaluation modalities. The OAEI 2022 campaign offered 14 tracks and was attended by 18 participants. This paper is an overall presentation of that campaign. © 2022 Copyright for this paper by its authors.
10.	Abd Nikooie Pour, Mina, et al. (author) Results of the Ontology Alignment Evaluation Initiative 2023 2023 In: Proceedings of the 18th International Workshop on Ontology Matching co-located with the 22nd International Semantic Web Conference (ISWC 2023), Athens, Greece, November 7, 2023.. - : CEUR Workshop Proceedings. ; , s. 97-139 Conference paper (peer-reviewed)
11.	Amagat, Jordi, et al. (author) Injectable 2D flexible hydrogel sheets for optoelectrical/biochemical dual stimulation of neurons 2023 In: Biomaterials Advances. - : Elsevier BV. - 2772-9516 .- 2772-9508. ; 146 Journal article (peer-reviewed)abstract Major challenges in developing implanted neural stimulation devices are the invasiveness, complexity, and cost of the implantation procedure. Here, we report an injectable, nanofibrous 2D flexible hydrogel sheet-based neural stimulation device that can be non-invasively implanted via syringe injection for optoelectrical and biochemical dual stimulation of neuron. Specifically, methacrylated gelatin (GelMA)/alginate hydrogel nanofibers were mechanically reinforced with a poly(lactide-co-ε-caprolactone) (PLCL) core by coaxial electrospinning. The lubricant hydrogel shell enabled not only injectability, but also facile incorporation of functional nanomaterials and bioactives. The nanofibers loaded with photocatatlytic g-C3N4/GO nanoparticles were capable of stimulating neural cells via blue light, with a significant 36.3 % enhancement in neurite extension. Meanwhile, the nerve growth factor (NGF) loaded nanofibers supported a sustained release of NGF with well-maintained function to biochemically stimulate neural differentiation. We have demonstrated the capability of an injectable, hydrogel nanofibrous, neural stimulation system to support neural stimulation both optoelectrically and biochemically, which represents crucial early steps in a larger effort to create a minimally invasive system for neural stimulation.
12.	Amagat, Jordi, et al. (author) Self-snapping hydrogel-based electroactive microchannels as nerve guidance conduits 2022 In: MATERIALS TODAY BIO. - : Elsevier BV. - 2590-0064. ; 16 Journal article (peer-reviewed)abstract Peripheral nerve regeneration with large defects needs innovative design of nerve guidance conduits (NGCs) which possess anisotropic guidance, electrical induction and right mechanical properties in one. Herein, we present, for the first time, facile fabrication and efficient neural differentiation guidance of anisotropic, conductive, self-snapping, hydrogel-based NGCs. The hydrogels were fabricated via crosslinking of graphitic carbon nitride (g-C3N4) upon exposure with blue light, incorporated with graphene oxide (GO). Incorporation of GO and in situ reduction greatly enhanced surface charges, while decayed light penetration endowed the hydrogel with an intriguing self-snapping feature by the virtue of a crosslinking gradient. The hydrogels were in the optimal mechanical stiffness range for peripheral nerve regeneration and supported normal viability and proliferation of neural cells. The PC12 cells differentiated on the electroactive g-C3N4 H/rGO3 (3 mg/mL GO loading) hydrogel presented 47% longer neurite length than that of the pristine g-C3N4 H hydrogel. Furthermore, the NGC with aligned microchannels was successfully fabricated using sacrificial melt electrowriting (MEW) moulding, the anisotropic microchannels of the 10 mu m width showed optimal neurite guidance. Such anisotropic, electroactive, self-snapping NGCs may possess great potential for repairing peripheral nerve injuries.
13.	Blunden, Jessica, et al. (author) State of the Climate in 2012 2013 In: Bulletin of The American Meteorological Society - (BAMS). - 0003-0007 .- 1520-0477. ; 94:8, s. S1-S258 Journal article (peer-reviewed)abstract For the first time in serveral years, the El Nino-Southern Oscillation did not dominate regional climate conditions around the globe. A weak La Ni a dissipated to ENSOneutral conditions by spring, and while El Nino appeared to be emerging during summer, this phase never fully developed as sea surface temperatures in the eastern conditions. Nevertheless, other large-scale climate patterns and extreme weather events impacted various regions during the year. A negative phase of the Arctic Oscillation from mid-January to early February contributed to frigid conditions in parts of northern Africa, eastern Europe, and western Asia. A lack of rain during the 2012 wet season led to the worst drought in at least the past three decades for northeastern Brazil. Central North America also experienced one of its most severe droughts on record. The Caribbean observed a very wet dry season and it was the Sahel's wettest rainy season in 50 years. Overall, the 2012 average temperature across global land and ocean surfaces ranked among the 10 warmest years on record. The global land surface temperature alone was also among the 10 warmest on record. In the upper atmosphere, the average stratospheric temperature was record or near-record cold, depending on the dataset. After a 30-year warming trend from 1970 to 1999 for global sea surface temperatures, the period 2000-12 had little further trend. This may be linked to the prevalence of La Ni a-like conditions during the 21st century. Heat content in the upper 700 m of the ocean remained near record high levels in 2012. Net increases from 2011 to 2012 were observed at 700-m to 2000-m depth and even in the abyssal ocean below. Following sharp decreases in to the effects of La Ni a, sea levels rebounded to reach records highs in 2012. The increased hydrological cycle seen in recent years continued, with more evaporation in drier locations and more precipitation in rainy areas. In a pattern that has held since 2004, salty areas of the ocean surfaces and subsurfaces were anomalously salty on average, while fresher areas were anomalously fresh. Global tropical cyclone activity during 2012 was near average, with a total of 84 storms compared with the 1981-2010 average of 89. Similar to 2010 and 2011, the North Atlantic was the only hurricane basin that experienced above-normal activity. In this basin, Sandy brought devastation to Cuba and parts of the eastern North American seaboard. All other basins experienced either near-or below-normal tropical cyclone activity. Only three tropical cyclones reached Category 5 intensity-all in Bopha became the only storm in the historical record to produce winds greater than 130 kt south of 7 N. It was also the costliest storm to affect the Philippines and killed more than 1000 residents. Minimum Arctic sea ice extent in September and Northern Hemisphere snow cover extent in June both reached new record lows. June snow cover extent is now declining at a faster rate (-17.6% per decade) than September sea ice extent (-13.0% per decade). Permafrost temperatures reached record high values in northernmost Alaska. A new melt extent record occurred on 11-12 July on the Greenland ice sheet; 97% of the ice sheet showed some form of melt, four times greater than the average melt for this time of year. The climate in Antarctica was relatively stable overall. The largest maximum sea ice extent since records begain in 1978 was observed in September 2012. In the stratosphere, warm air led to the second smallest ozone hole in the past two decades. Even so, the springtime ozone layer above Antarctica likely will not return to its early 1980s state until about 2060. Following a slight decline associated with the global 2 emissions from fossil fuel combustion and cement production reached a record 9.5 +/- 0.5 Pg C in 2011 and a new record of 9.7 +/- 0.5 Pg C is estimated for 2012. Atmospheric CO2 concentrations increased by 2.1 ppm in 2012, to 392.6 ppm. In spring 2012, 2 concentration exceeded 400 ppm at 7 of the 13 Arctic observation sites. Globally, other greenhouse gases including methane and nitrous oxide also continued to rise in concentration and the combined effect now represents a 32% increase in radiative forcing over a 1990 baseline. Concentrations of most ozone depleting substances continued to fall.
14.	Brenner, Darren R, et al. (author) Identification of lung cancer histology-specific variants applying Bayesian framework variant prioritization approaches within the TRICL and ILCCO consortia 2015 In: Carcinogenesis. - : Oxford University Press. - 0143-3334 .- 1460-2180. ; 36:11, s. 1314-1326 Journal article (peer-reviewed)abstract Large-scale genome-wide association studies (GWAS) have likely uncovered all common variants at the GWAS significance level. Additional variants within the suggestive range (0.0001> P > 5×10−8) are, however, still of interest for identifying causal associations. This analysis aimed to apply novel variant prioritization approaches to identify additional lung cancer variants that may not reach the GWAS level. Effects were combined across studies with a total of 33456 controls and 6756 adenocarcinoma (AC; 13 studies), 5061 squamous cell carcinoma (SCC; 12 studies) and 2216 small cell lung cancer cases (9 studies). Based on prior information such as variant physical properties and functional significance, we applied stratified false discovery rates, hierarchical modeling and Bayesian false discovery probabilities for variant prioritization. We conducted a fine mapping analysis as validation of our methods by examining top-ranking novel variants in six independent populations with a total of 3128 cases and 2966 controls. Three novel loci in the suggestive range were identified based on our Bayesian framework analyses: KCNIP4 at 4p15.2 (rs6448050, P = 4.6×10−7) and MTMR2 at 11q21 (rs10501831, P = 3.1×10−6) with SCC, as well as GAREM at 18q12.1 (rs11662168, P = 3.4×10−7) with AC. Use of our prioritization methods validated two of the top three loci associated with SCC (P = 1.05×10−4 for KCNIP4, represented by rs9799795) and AC (P = 2.16×10−4 for GAREM, represented by rs3786309) in the independent fine mapping populations. This study highlights the utility of using prior functional data for sequence variants in prioritization analyses to search for robust signals in the suggestive range.
15.	Cao, Yuehan, et al. (author) Dual Functions of O-Atoms in the g-C3N4/BO0.2N0.8Interface : Oriented Charge Flow In-Plane and Separation within the Interface to Collectively Promote Photocatalytic Molecular Oxygen Activation 2020 In: ACS Applied Materials and Interfaces. - : American Chemical Society (ACS). - 1944-8244 .- 1944-8252. ; 12:30, s. 34432-34440 Journal article (peer-reviewed)abstract The photocatalytic performance of two-dimensional materials is largely limited by the fast recombination of photogenerated charges. Herein, we design and fabricate a novel g-C3N4/BO0.2N0.8 van der Waals heterostructure to realize oriented charge flow in-plane and separation within the interface. On one hand, a B-C bond forms within the g-C3N4/BO0.2N0.8 interface after the introduction of O atoms. The B-C bond as the mediator bridges g-C3N4 and BO0.2N0.8 sides to enhance the effective separation of photogenerated charges. On the other hand, the existence of O atoms promotes the formation of a B-O-O-B intermediate to realize that molecular oxygen can directionally obtain electrons from the surface to generate O2-. As a result, BO0.2N0.8 instead of g-C3N4 is considered to be the main reaction side, and the energy barrier of NO3- generation is significantly decreased. The NO removal performance of g-C3N4/BO0.2N0.8 is enhanced and the NO2 generation is effectively controlled compared with that of g-C3N and g-C3N4/BN. This work could provide an effective and facile strategy to tune oriented charge transfer.
16.	Cao, Yuehan, et al. (author) Modulating electron density of vacancy site by single Au atom for effective CO2 photoreduction 2021 In: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 12:1 Journal article (peer-reviewed)abstract The surface electron density significantly affects the photocatalytic efficiency, especially the photocatalytic CO2 reduction reaction, which involves multi-electron participation in the conversion process. Herein, we propose a conceptually different mechanism for surface electron density modulation based on the model of Au anchored CdS. We firstly manipulate the direction of electron transfer by regulating the vacancy types of CdS. When electrons accumulate on vacancies instead of single Au atoms, the adsorption types of CO2 change from physical adsorption to chemical adsorption. More importantly, the surface electron density is manipulated by controlling the size of Au nanostructures. When Au nanoclusters downsize to single Au atoms, the strong hybridization of Au 5d and S 2p orbits accelerates the photo-electrons transfer onto the surface, resulting in more electrons available for CO2 reduction. As a result, the product generation rate of AuSA/Cd1−xS manifests a remarkable at least 113-fold enhancement compared with pristine Cd1−xS.
17.	Chen, Chao, et al. (author) Epigenome-wide gene-age interaction analysis reveals reversed effects of PRODH DNA methylation on survival between young and elderly early-stage NSCLC patients 2020 In: Aging. - : Impact Journals, LLC. - 1945-4589. ; 12:11, s. 10642-10662 Journal article (peer-reviewed)abstract DNA methylation changes during aging, but it remains unclear whether the effect of DNA methylation on lung cancer survival varies with age. Such an effect could decrease prediction accuracy and treatment efficacy. We performed a methylation-age interaction analysis using 1,230 early-stage lung adenocarcinoma patients from five cohorts. A Cox proportional hazards model was used to investigate lung adenocarcinoma and squamous cell carcinoma patients for methylation-age interactions, which were further confirmed in a validation phase. We identified one adenocarcinoma-specific CpG probe, cg14326354PRODH, with effects significantly modified by age (HRinteraction = 0.989; 95% CI: 0.986-0.994; P = 9.18×10-7). The effect of low methylation was reversed for young and elderly patients categorized by the boundary of 95% CI standard (HRyoung = 2.44; 95% CI: 1.26-4.72; P = 8.34×10-3; HRelderly = 0.58; 95% CI: 0.42-0.82; P = 1.67×10-3). Moreover, there was an antagonistic interaction between low cg14326354PRODH methylation and elderly age (HRinteraction = 0.21; 95% CI: 0.11-0.40; P = 2.20×10-6). In summary, low methylation of cg14326354PRODH might benefit survival of elderly lung adenocarcinoma patients, providing new insight to age-specific prediction and potential drug targeting.
18.	Chen, Ying, et al. (author) Enhanced colonic tumorigenesis in alkaline sphingomyelinase (NPP7) knockout mice. 2015 In: Molecular Cancer Therapeutics. - 1538-8514. ; 14:1, s. 259-267 Journal article (peer-reviewed)abstract Intestinal alkaline sphingomyelinase (alk-SMase) generates ceramide and inactivates platelet-activating factor (PAF) and is previously suggested to have anticancer properties. The direct evidence is still lacking. We studied colonic tumorigenesis in alk-SMase knockout (KO) mice. Formation of aberrant crypt foci (ACF) was examined after azoxymethane (AOM) injection. Tumor was induced by AOM alone, a conventional AOM/dextran sulfate sodium (DSS) treatment, and an enhanced AOM/DSS method. beta-catenin was determined by immunohistochemistry, PAF levels by ELISA and sphingomyelin metabolites by mass spectrometry. Without treatment, spontaneous tumorigenesis was not identified but the intestinal mucosa appeared thicker in KO than in wild type (WT) littermates. AOM alone induced more ACF in KO mice but no tumors 28 weeks after injection. However, combination of AOM/DSS treatments induced colonic tumors and the incidence was significantly higher in KO than in WT mice. By the enhanced AOM/DSS method tumor number per mouse increased 4.5 times and tumor size 1.8 times in KO compared to WT mice. While all tumors were adenomas in WT mice, 32% were adenocarcinomas in KO mice. Compared to WT mice, cytosol expression of beta-catenin was significantly decreased and nuclear translocation in tumors was more pronounced in KO mice. Lipid analysis showed decreased ceramide in small intestine and increased sphingosine-1-phosphate in both small intestine and colon in nontreated KO mice. PAF levels in feces were significantly higher in the KO mice after AOM/DSS treatment. In conclusion lack of alk-SMase markedly increases AOM/DSS induced colonic tumorigenesis associated with decreased ceramide and increased sphingosine-1-phosphate and PAF levels.
19.	Chen, Ying, et al. (author) Mevalonate inhibits acid sphingomyelinase activity, increases sphingomyelin levels and inhibits cell proliferation of HepG2 and Caco-2 cells. 2015 In: Lipids in Health and Disease. - : Springer Science and Business Media LLC. - 1476-511X. ; 14 Journal article (peer-reviewed)abstract Sphingomyelin (SM) and cholesterol are two types of lipid closely related biophysically. Treating the cells with exogenous sphingomyelinase (SMase) induces trafficking of cholesterol from membrane to intracellular pools and inhibition of cholesterol synthesis. In the present work, we address a question whether increased cholesterol synthesis affects hydrolysis of SM by endogenous SMases.
20.	Dong, Xuesi, et al. (author) Trans-omics biomarker model improves prognostic prediction accuracy for early-stage lung adenocarcinoma 2019 In: Aging. - : Impact Journals, LLC. - 1945-4589. ; 11:16, s. 6312-6335 Journal article (peer-reviewed)abstract Limited studies have focused on developing prognostic models with trans-omics biomarkers for early-stage lung adenocarcinoma (LUAD). We performed integrative analysis of clinical information, DNA methylation, and gene expression data using 825 early-stage LUAD patients from 5 cohorts. Ranger algorithm was used to screen prognosis-associated biomarkers, which were confirmed with a validation phase. Clinical and biomarker information was fused using an iCluster plus algorithm, which significantly distinguished patients into high- and low-mortality risk groups (Pdiscovery = 0.01 and Pvalidation = 2.71×10-3). Further, potential functional DNA methylation-gene expression-overall survival pathways were evaluated by causal mediation analysis. The effect of DNA methylation level on LUAD survival was significantly mediated through gene expression level. By adding DNA methylation and gene expression biomarkers to a model of only clinical data, the AUCs of the trans-omics model improved by 18.3% (to 87.2%) and 16.4% (to 85.3%) in discovery and validation phases, respectively. Further, concordance index of the nomogram was 0.81 and 0.77 in discovery and validation phases, respectively. Based on systematic review of published literatures, our model was superior to all existing models for early-stage LUAD. In summary, our trans-omics model may help physicians accurately identify patients with high mortality risk.
21.	Dong, Ying, et al. (author) Differential splicing of KLK5 and KLK7 in epithelial ovarian cancer produces novel variants with potential as cancer biomarkers 2003 In: Clinical Cancer Research. - : American Association for Cancer Research. - 1078-0432 .- 1557-3265. ; 9:5, s. 1710-20 Journal article (peer-reviewed)abstract PURPOSE: The wild-type or variant mRNAs of several kallikrein (KLK) genes, such as KLK4, are highly expressed in ovarian carcinomas and may have potential as tumor markers. Two of these KLK genes (KLK5 and KLK7) and their proteins (hK5 and hK7) were first identified in the skin epidermis, where hK5 may be the physiological activator of hK7. The purpose of this study was to reexamine the expression of KLK5/hK5 and KLK7/hK7 and their association and to determine whether cancer-related variant transcripts were expressed.EXPERIMENTAL DESIGN: The expression of KLK5/hK5 and KLK7/hK7 was analyzed in the same cohort (n = 37) of benign (n = 4) and malignant ovarian tissue (n = 23) samples and primary cultured cells (n = 21) and in 8 ovarian cancer cell lines using semiquantitative RT-PCR; Southern, Northern, and Western blot analyses; and immunohistochemistry techniques.RESULTS: We showed the concordant higher expression of both KLK5/hK5 and KLK7/hK7 in ovarian carcinomas, especially late-stage serous carcinomas, compared with normal ovaries and benign adenomas. We also found that one novel KLK5 transcript with a short 5'-untranslated region and a novel KLK7 transcript with a long 3'-untranslated region were highly expressed in the ovarian cancer cell lines OVCAR-3 and PEO1, respectively, but were expressed at very low levels in normal ovarian epithelial cells. Both Western blot and immunohistochemistry analyses showed that these two enzymes are secreted from ovarian carcinoma cells.CONCLUSIONS: Our study demonstrated that hK5 and hK7, or more specifically, the short KLK5 and long KLK7 transcripts, may be useful as tumor markers for epithelial-derived serous carcinomas. However, additional clinical studies assessing serum levels of these putative biomarkers are required to confirm their usefulness in the diagnosis and/or monitoring of these tumors.
22.	Du, Mingrun, et al. (author) High pressure and high temperature induced polymerization of C60 solvates : The effect of intercalated aromatic solvents 2021 In: The Journal of Physical Chemistry C. - : American Chemical Society (ACS). - 1932-7447 .- 1932-7455. ; 125:31, s. 17155-17163 Journal article (peer-reviewed)abstract The polymerization of three typical aromatic solvent-doped fullerene materials with similar hexagonal closest packed (hcp) structures (mesitylene/C60, m-dichlorobenzene/C60 and m-xylene/C60 solvates) is studied under high pressure and high temperature (HPHT, 1.5 GPa, 573 K and 2 GPa, 700 K, respectively). Raman and photoluminescence spectroscopies reveal that the intercalated aromatic solvents play a crucial role in tailoring the extent of polymerization of C60 molecules. In the solvates, the solvents confine formation of covalent bonds between C60 molecules to the 001 direction and the (001) plane of the hcp lattices, leading to the formation of mixed polymeric phases of monomers, dimers, one-dimensional (1D) chainlike oligomers, and two-dimensional (2D) tetragonal phase polymers under suitable HPHT conditions. The type and number of substituent groups of the aromatic solvents are found to have significant influence, determining the amounts and types of polymeric phases formed. Our studies enrich the understanding of the formation mechanisms for controllably fabricating polymeric fullerenes and facilitate targeted design and synthesis of unique fullerene-based carbon materials.
23.	Duan, Chen, et al. (author) Comparative analysis of gene expression profiles between primary knee osteoarthritis and an osteoarthritis endemic to Northwestern China, Kashin-Beck disease. 2010 In: Arthritis and Rheumatism. - : John Wiley & Sons. - 0004-3591 .- 1529-0131. ; 62:3, s. 771-780 Journal article (peer-reviewed)abstract OBJECTIVE: To investigate the differences in gene expression profiles of adult articular cartilage from patients with Kashin-Beck disease (KBD) versus those with primary knee osteoarthritis (OA).METHODS: The messenger RNA expression profiles of articular cartilage from patients with KBD, diagnosed according to the clinical criteria for KBD in China, were compared with those of cartilage from patients with OA, diagnosed according to the Western Ontario and McMaster Universities OA Index. Total RNA was isolated separately from 4 pairs of the KBD and OA cartilage samples, and the expression profiles were evaluated by Agilent 4x44k Whole Human Genome density oligonucleotide microarray analysis. The microarray data for selected transcripts were confirmed by quantitative real-time reverse transcription-polymerase chain reaction (RT-PCR) amplification.RESULTS: For 1.2 x 10(4) transcripts, corresponding to 58.4% of the expressed transcripts, 2-fold changes in differential expression were revealed. Expression levels higher in KBD than in OA samples were observed in a mean + or - SD 6,439 + or - 1,041 (14.6 + or - 2.4%) of the transcripts, and expression levels were lower in KBD than in OA samples in 6,147 + or - 1,222 (14.2 + or - 2.8%) of the transcripts. After application of the selection criteria, 1.85% of the differentially expressed genes (P < 0.001 between groups) were detected. These included 233 genes, of which 195 (0.4%) were expressed at higher levels and 38 (0.08%) were expressed at lower levels in KBD than in OA cartilage. Comparisons of the quantitative RT-PCR data supported the validity of our microarray data.CONCLUSION: Differences between KBD and OA cartilage exhibited a similar pattern among all 4 of the pairs examined, indicating the presence of disease mechanisms, mainly chondrocyte matrix metabolism, cartilage degeneration, and apoptosis induction pathways, which contribute to cartilage destruction in KBD.
24.	Fan, Zheyong, et al. (author) GPUMD: A package for constructing accurate machine-learned potentials and performing highly efficient atomistic simulations 2022 In: Journal of Chemical Physics. - : AIP Publishing. - 1089-7690 .- 0021-9606. ; 157:11 Journal article (peer-reviewed)abstract We present our latest advancements of machine-learned potentials (MLPs) based on the neuroevolution potential (NEP) framework introduced in Fan et al. [Phys. Rev. B 104, 104309 (2021)] and their implementation in the open-source package gpumd. We increase the accuracy of NEP models both by improving the radial functions in the atomic-environment descriptor using a linear combination of Chebyshev basis functions and by extending the angular descriptor with some four-body and five-body contributions as in the atomic cluster expansion approach. We also detail our efficient implementation of the NEP approach in graphics processing units as well as our workflow for the construction of NEP models and demonstrate their application in large-scale atomistic simulations. By comparing to state-of-the-art MLPs, we show that the NEP approach not only achieves above-average accuracy but also is far more computationally efficient. These results demonstrate that the gpumd package is a promising tool for solving challenging problems requiring highly accurate, large-scale atomistic simulations. To enable the construction of MLPs using a minimal training set, we propose an active-learning scheme based on the latent space of a pre-trained NEP model. Finally, we introduce three separate Python packages, viz., gpyumd, calorine, and pynep, that enable the integration of gpumd into Python workflows.
25.	Hou, Juan, et al. (author) Helium bubble nucleation in Laser Powder Bed Fusion processed 304L stainless steel 2020 In: Journal of Nuclear Materials. - : Elsevier BV. - 0022-3115. ; 542 Journal article (peer-reviewed)abstract The interest in application of Additive Manufacturing (AM) to nuclear industry stems not only from the benefits of design freedom and shortened lead time, but also from the possibility of enhancing the performance through microstructure control. One of the most important requirements for in-core structural material in nuclear power plants is helium resistance. The Laser Powder Bed Fusion (LPBF) processed 304L stainless steel possesses strong defect sinks such as high densities of dislocation-surrounded sub-grains and dispersed nano-inclusions. In this work the LPBF processed 304L in as-built and solution-annealed conditions along with a conventionally rolled counterpart were implanted with 350 keV He+ ion at 300 °C to 0.24 dpa (displacement per atom). Transmission Electron Microscopy (TEM) observations indicate significantly higher helium resistance of the as-built LPBF 304L compared to the other two samples. The sink strengths in the three samples are calculated based on the measurements of the microstructural features using simplified equations for the correlation between microstructural characteristics and helium tolerance. Based on the calculation, the cellular sub-grains and the dispersed nano-inclusions are the primary and secondary contributors to the helium resistance of LPBF 304L steel.
26.	Ji, Xinyu, et al. (author) Epigenetic–smoking interaction reveals histologically heterogeneous effects of TRIM27 DNA methylation on overall survival among early-stage NSCLC patients 2020 In: Molecular Oncology. - : Wiley. - 1574-7891 .- 1878-0261. ; 14:11, s. 2759-2774 Journal article (peer-reviewed)abstract Tripartite motif containing 27 (TRIM27) is highly expressed in lung cancer, including non-small-cell lung cancer (NSCLC). Here, we profiled DNA methylation of lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC) tumours from 613 early-stage NSCLC patients and evaluated associations between CpG methylation of TRIM27 and overall survival. Significant CpG probes were confirmed in 617 samples from The Cancer Genome Atlas. The methylation of the CpG probe cg05293407TRIM27 was significantly associated with overall survival in patients with LUSC (HR = 1.65, 95% CI: 1.30–2.09, P = 4.52 × 10−5), but not in patients with LUAD (HR = 1.08, 95% CI: 0.87–1.33, P = 0.493). As incidence of LUSC is associated with higher smoking intensity compared to LUAD, we investigated whether smoking intensity impacted on the prognostic effect of cg05293407TRIM27 methylation in NSCLC. LUSC patients had a higher average pack-year of smoking (37.49LUAD vs 54.79LUSC, P = 1.03 × 10−19) and included a higher proportion of current smokers than LUAD patients (28.24%LUAD vs 34.09%LUSC, P = 0.037). cg05293407TRIM27 was significantly associated with overall survival only in NSCLC patients with medium–high pack-year of smoking (HR = 1.58, 95% CI: 1.26–1.96, P = 5.25 × 10−5). We conclude that cg05293407TRIM27 methylation is a potential predictor of LUSC prognosis, and smoking intensity may impact on its prognostic value across the various types of NSCLC.
27.	Ju, Ying, et al. (author) Joint Secure Offloading and Resource Allocation for Vehicular Edge Computing Network : A Multi-Agent Deep Reinforcement Learning Approach 2023 In: IEEE transactions on intelligent transportation systems (Print). - : Institute of Electrical and Electronics Engineers (IEEE). - 1524-9050 .- 1558-0016. ; 24:5, s. 5555-5569 Journal article (peer-reviewed)abstract The mobile edge computing (MEC) technology can simultaneously provide high-speed computing services for multiple vehicular users (VUs) in vehicular edge computing (VEC) networks. Nevertheless, due to the open feature of the wireless offloading channels and the high mobility of the vehicles, the security and stability of the offloading process would be seriously degraded. In this paper, by utilizing the physical layer security (PLS) technique and spectrum sharing architecture, we propose a deep reinforcement learning based joint secure offloading and resource allocation (SORA) scheme to improve the secrecy performance and resource efficiency of the multi-user VEC networks, where the VU offloading links share the frequency spectrum preoccupied with the vehicle-to-vehicle (V2V) communication links. We use Wyner's wiretap coding scheme to obtain the achievable secrecy rate and guarantee that confidential information cannot be decoded by multiple mobile eavesdroppers. We aim at minimizing the system processing delay while securing the wireless offloading process, by jointly optimizing the transmit power, the frequency spectrum selection and the computation resource allocation. We formulate the optimization problem as a multi-agent collaborative optimal decision problem and solve it with a double deep Q-learning algorithm. Besides, we set a punishment mechanism for the rate degradation to guarantee the communication quality of each V2V link. Simulation results demonstrate that multiple VU agents adopting the SORA scheme can rapidly adapt to the highly dynamic VEC networks and cooperate to improve the system delay performance while increasing the secrecy probability.
28.	Kang, Ying, et al. (author) Weak Bonds Joint Effects Catalyze the Cleavage of Strong C−C Bond of Lignin‐Inspired Compounds and Lignin in Air by Ionic Liquids 2020 In: ChemSusChem. - : John Wiley & Sons. - 1864-5631 .- 1864-564X. ; 13:22, s. 5945-5953 Journal article (peer-reviewed)abstract Oxidation of lignin to value‐added aromatics through selective C−C bond cleavage via metal‐free and mild strategies is promising but challenging. It was discovered that the cations of ionic liquids (ILs) could effectively catalyze this kind of strong bond cleavage by forming multiple weak hydrogen bonds, enabling the reaction conducted in air at temperature lower than 373 K without metal‐containing catalysts. The cation [CPMim]+ (1‐propylronitrile‐3‐methylimidazolium) afforded the highest efficiency in C−C bond cleavage, in which high yields (>90 %) of oxidative products were achieved. [CPMim]+ could form three ipsilateral hydrogen bonds with the oxygen atom of C=O and ether bonds at both sides of the C−C bond. The weak bonds joint effects could promote adjacent C−H bond cleave to form free radicals and thereby catalyze the fragmentation of the strong C−C. This work opens up an eco‐friendly and energy‐efficient route for direct valorization of lignin by enhancing IL properties via tuning the cation.
29.	Klingstedt, Miia, et al. (author) Advanced electron microscopy characterization for pore structure of mesoporous materials; a study of FDU-16 and FDU-18 2011 In: Journal of Materials Chemistry. - : Royal Society of Chemistry (RSC). - 0959-9428 .- 1364-5501. ; 21:35, s. 13664-13671 Journal article (peer-reviewed)abstract We present a comprehensive analysis for pore structures of cage-type ordered mesoporous carbons (OMCs) using various electron microscopy techniques in addition to conventional nitrogen adsorption isotherm studies. The benefits and drawbacks of these techniques are evaluated, and it is shown that they are complementary to each other. Knowledge of the structural properties, pore sizes, and connectivity gives insight into the synthesis strategies and how they are affecting the material properties that are useful within the possible applications. Herein, focus is put on the two OMCs with Im (3) over barm and Fm (3) over barm symmetries specified by FDU-16 and FDU-18. The central techniques used in this study are high resolution scanning electron microscopy combined with cross-section polisher and three-dimensional reconstruction methods (electron tomography and electron crystallography) based on transmission electron microscopy observations.
30.	Lee, Dong Geon, et al. (author) Effect of Metal Electrodes on Aging-Induced Performance Recovery in Perovskite Solar Cells 2019 In: ACS Applied Materials and Interfaces. - : AMER CHEMICAL SOC. - 1944-8244 .- 1944-8252. ; 11:51, s. 48497-48504 Journal article (peer-reviewed)abstract For commercialization of perovskite solar cells (PSCs), it is important to substitute the alternative electrode for Au to decrease the unit cost. From the early stage, Ag exhibits a potential to be a good counter electrode in PSCs; however, there is an abnormal s-shaped J-V curve with the Ag electrode, and it is recovered as time passes. The perception of the aging-induced recovery process and refutation of the raised stability issues are required for commercial application of Ag electrodes. Herein, we compared the aging effect of PSCs with Ag and Au electrodes and found that only devices with Ag electrodes have a dramatical aging-induced recovery process. We observed the change of photoelectronic properties only in the devices with Ag electrodes as time passes, which mainly contributes to recovery of the s-shaped J-V curve. We verified the work function change of an aged Ag electrode and its mechanism by photoelectron spectroscopy analysis. By comparing the light stability under 1 sun intensity illumination, we can assure the practical stability of Ag electrodes in case of being encapsulated. This work suggests the profound understanding of the aging-induced recovery process of PSCs and the possibility of commercial application of Ag electrodes.
31.	Li, Zhao, et al. (author) Non-uniform seasonal warming regulates vegetation greening and atmospheric CO2 amplification over northern lands 2018 In: Environmental Research Letters. - : IOP Publishing. - 1748-9326. ; 13:12 Journal article (peer-reviewed)abstract The enhanced vegetation growth by climate warming plays a pivotal role in amplifying the seasonal cycle of atmospheric CO2 at northern lands (>50° N) since 1960s. However, the correlation between vegetation growth, temperature and seasonal amplitude of atmospheric CO2 concentration have become elusive with the slowed increasing trend of vegetation growth and weakened temperature control on CO2 uptake since late 1990s. Here, based on in situ atmospheric CO2 concentration records from the Barrow observatory site, we found a slowdown in the increasing trend of the atmospheric CO2 amplitude from 1990s to mid-2000s. This phenomenon was associated with the paused decrease in the minimum CO2 concentration ([CO2]min), which was significantly correlated with the slowdown of vegetation greening and growing-season length extension. We then showed that both the vegetation greenness and growing-season length were positively correlated with spring but not autumn temperature over the northern lands. Furthermore, such asymmetric dependences of vegetation growth upon spring and autumn temperature cannot be captured by the state-of-art terrestrial biosphere models. These findings indicate that the responses of vegetation growth to spring and autumn warming are asymmetric, and highlight the need of improving autumn phenology in the models for predicting seasonal cycle of atmospheric CO2 concentration.
32.	Liu, Yong, et al. (author) Deletion Of XIAP reduces the severity of acute pancreatitis via regulation of cell death and nuclear factor-kappa B activity 2017 In: Cell Death and Disease. - : NATURE PUBLISHING GROUP. - 2041-4889. ; 8 Journal article (peer-reviewed)abstract Severe acute pancreatitis (SAP) still remains a clinical challenge, not only for its high mortality but the uncontrolled inflammatory progression from acute pancreatitis (AP) to SAP. Cell death, including apoptosis and necrosis are critical pathology of AP, since the severity of pancreatitis correlates directly with necrosis and inversely with apoptosis Therefore, regulation of cell death from necrosis to apoptosis may have practicably therapeutic value. X-linked inhibitor of apoptosis protein (XIAP) is the best characterized member of the inhibitor of apoptosis proteins (IAP) family, but its function in AP remains unclear. In the present study, we investigated the potential role of XIAP in regulation of cell death and inflammation during acute pancreatitis. The in vivo pancreatitis model was induced by the administration of cerulein with or without lipopolysaccharide (LPS) or by the administration of L-arginine in wild-type or XIAP-deficient mice, and ex vivo model was induced by the administration of cerulein+LPS in AR42J cell line following XIAP inhibition. The severity of acute pancreatitis was determined by serum amylase activity and histological grading. XIAP deletion on cell apoptosis, necrosis and inflammatory response were examined. Caspases activities, nuclear factor kappa B (NF-kappa B) activation and receptor-interacting protein kinase1 (RIP1) degradation were assessed by western blot. Deletion of XIAP resulted in the reduction of amylase activity, decrease of NF-kappa B activation and less release of TNF-alpha and IL-6, together with increased caspases activities and RIP1 degradation, leading to enhanced apoptosis and reduced necrosis in pancreatic acinar cells and ameliorated the severity of acute pancreatitis. Our results indicate that deletion of XIAP switches cell death away from necrosis to apoptosis and decreases the inflammatory response, effectively attenuating the severity of AP/SAP. The critical role of XIAP in cell death and inflammation suggests that inhibition of XIAP represents a potential therapeutic strategy for the treatment of acute pancreatitis.
33.	Park, Kyoung Chul, et al. (author) The Highly Operational Team (HOT) toward f-Block Materials 2023 In: Angewandte Chemie International Edition. - : Wiley. - 1433-7851 .- 1521-3773. ; 62:32 Journal article (other academic/artistic)
34.	Qin, Haihong, et al. (author) A digital-controlled SiC-based solid state circuit breaker with soft switch-off method for DC power system 2019 In: Electronics (Switzerland). - : MDPI AG. - 2079-9292. ; 8:8 Journal article (peer-reviewed)abstract Due to the lower on-state resistance, direct current (DC) solid state circuit breakers (SSCBs) based on silicon-carbide (SiC) metal-oxide-semiconductor field-effect transistors (MOSFETs) can reduce on-state losses and the investment of the cooling system when compared to breakers based on silicon (Si) MOSFETs. However, SiC MOSFETs, with smaller die area and higher current density, lead to weaker short-circuit ability, shorter short-circuit withstand time and higher protection requirements. To improve the reliability and short-circuit capability of SiC-based DC solid state circuit breakers, the short-circuit fault mechanisms of Si MOSFETs and SiC MOSFETs are revealed. Combined with the desaturation detection (DESAT), a “soft turn-off” short-circuit protection method based on source parasitic inductor is proposed. When the DESAT protection is activated, the “soft turn-off” method can protect the MOSFET against short-circuit and overcurrent. The proposed SSCB, combined with the flexibility of the DSP, has the μs-scale ultrafast response time to overcurrent detection. Finally, the effectiveness of the proposed method is validated by the experimental platform. The method can reduce the voltage stress of the power device, and it can also suppress the short-circuit current.
35.	Ren, Luyao, et al. (author) Quartet DNA reference materials and datasets for comprehensively evaluating germline variant calling performance 2023 In: Genome Biology. - : BioMed Central (BMC). - 1465-6906 .- 1474-760X. ; 24:1 Journal article (peer-reviewed)abstract BACKGROUND: Genomic DNA reference materials are widely recognized as essential for ensuring data quality in omics research. However, relying solely on reference datasets to evaluate the accuracy of variant calling results is incomplete, as they are limited to benchmark regions. Therefore, it is important to develop DNA reference materials that enable the assessment of variant detection performance across the entire genome.RESULTS: We established a DNA reference material suite from four immortalized cell lines derived from a family of parents and monozygotic twins. Comprehensive reference datasets of 4.2 million small variants and 15,000 structural variants were integrated and certified for evaluating the reliability of germline variant calls inside the benchmark regions. Importantly, the genetic built-in-truth of the Quartet family design enables estimation of the precision of variant calls outside the benchmark regions. Using the Quartet reference materials along with study samples, batch effects are objectively monitored and alleviated by training a machine learning model with the Quartet reference datasets to remove potential artifact calls. Moreover, the matched RNA and protein reference materials and datasets from the Quartet project enables cross-omics validation of variant calls from multiomics data.CONCLUSIONS: The Quartet DNA reference materials and reference datasets provide a unique resource for objectively assessing the quality of germline variant calls throughout the whole-genome regions and improving the reliability of large-scale genomic profiling.
36.	Santos, Tracy Dos, et al. (author) Injection Limitations in a Series of Porphyrin Dye-Sensitized Solar Cells 2010 In: The Journal of Physical Chemistry C. ; 114:7, s. 3276-3279 Journal article (peer-reviewed)
37.	Sun, Ying, et al. (author) Asymmetrical effects of mesophyll conductance on fundamental photosynthetic parameters and their relationships estimated from leaf gas exchange measurements 2014 In: Plant, Cell and Environment. - : John Wiley & Sons. - 0140-7791 .- 1365-3040. ; 37:4, s. 978-994 Journal article (peer-reviewed)abstract Worldwide measurements of nearly 130 C3 species covering all major plant functional types are analysed in conjunction with model simulations to determine the effects of mesophyll conductance (gm) on photosynthetic parameters and their relationships estimated fromA/Ci curves. We find that an assumption of infinite gm results in up to 75% underestimation for maximum carboxylation rate Vcmax, 60% for maximum electron transport rate Jmax, and 40% for triose phosphate utilization rate Tu. Vcmax is most sensitive, Jmax is less sensitive, and Tuhas the least sensitivity to the variation of gm. Because of this asymmetrical effect of gm, the ratios of Jmax to Vcmax, Tu to Vcmax and Tu toJmax are all overestimated. An infinite gm assumption also limits the freedom of variation of estimated parameters and artificially constrains parameter relationships to stronger shapes. These findings suggest the importance of quantifying gm for understanding in situphotosynthetic machinery functioning. We show that a nonzero resistance to CO2 movement in chloroplasts has small effects on estimated parameters. A non-linear function with gm as input is developed to convert the parameters estimated under an assumption of infinite gm to proper values. This function will facilitate gm representation in global carbon cycle models.
38.	Vromman, Marieke, et al. (author) Large-scale benchmarking of circRNA detection tools reveals large differences in sensitivity but not in precision 2023 In: Nature Methods. - 1548-7091 .- 1548-7105. ; 20:8, s. 1159-1169 Journal article (peer-reviewed)abstract The detection of circular RNA molecules (circRNAs) is typically based on short-read RNA sequencing data processed using computational tools. Numerous such tools have been developed, but a systematic comparison with orthogonal validation is missing. Here, we set up a circRNA detection tool benchmarking study, in which 16 tools detected more than 315,000 unique circRNAs in three deeply sequenced human cell types. Next, 1,516 predicted circRNAs were validated using three orthogonal methods. Generally, tool-specific precision is high and similar (median of 98.8%, 96.3% and 95.5% for qPCR, RNase R and amplicon sequencing, respectively) whereas the sensitivity and number of predicted circRNAs (ranging from 1,372 to 58,032) are the most significant differentiators. Of note, precision values are lower when evaluating low-abundance circRNAs. We also show that the tools can be used complementarily to increase detection sensitivity. Finally, we offer recommendations for future circRNA detection and validation. This study describes benchmarking and validation of computational tools for detecting circRNAs, finding most to be highly precise with variations in sensitivity and total detection. The study also finds over 315,000 putative human circRNAs.
39.	Wang, Min, et al. (author) Apolipoprotein M induces inhibition of inflammatory responses via the S1PR1 and DHCR24 pathways 2019 In: Molecular Medicine Reports. - 1791-2997. ; 19:2, s. 1272-1283 Journal article (peer-reviewed)abstract © 2019 Spandidos Publications. All rights reserved. Apolipoprotein M (ApoM) is a type of apolipoprotein. It is well known that high-density lipoprotein (HDL) decreases inflammatory responses via the apoM-sphingosine-1-phosphate (S1P) pathway. The present study further investigated the importance of ApoM in the inhibitory effects of HDL on inflammation. Mice with an apoM gene deficiency (apoM-/-) were employed to investigate the effects of ApoM on the expression of interleukin-1β (IL-1β), monocyte chemotactic protein-1 (MCP-1), S1P receptor-1 (S1PR1) and 3β-hydroxysterol Δ-24-reductase (DHCR24), as compared with in wild-type mice (apoM+/+). Furthermore, cell culture experiments were performed using a permanent human hybrid endothelial cell line (EA.hy926). Cells were cultured in the presence of recombinant human apoM (rec-apoM) or were induced to overexpress apoM (apoMTg); subsequently, cells were treated with tumor necrosis factor-α (TNF-α), in order to investigate the effects of ApoM on IL-1β and MCP-1. The results demonstrated that the mRNA expression levels of IL-1β and MCP-1 were significantly higher in the liver following administration of lipopolysaccharide in apoM-/- mice compared with in apoM+/+ mice. In cell culture experiments, when cells were pre-cultured with rec-apoM or were engineered to overexpress apoM (apoMTg), they exhibited decreased expression levels of IL-1β and MCP-1 following TNF-α treatment compared with in normal apoM-expressing cells (apoMTgN). Furthermore, the mRNA expression levels of IL-1β and MCP-1 were significantly elevated following addition of the S1PR1 inhibitor W146, but not by the scavenger receptor class B type I inhibitor, block lipid transport-1 (BLT-1), in apoMTg cells prior to TNF-α treatment. Conversely, there were no differences in these inflammatory biomarkers under the same conditions in apoMTgN cells. The mRNA expression levels of DHCR24 were significantly reduced by the addition of BLT-1 prior to TNF-α treatment in apoMTg cells; however, there was no difference in the expression of this inflammatory biomarker in apoMTgN cells. In conclusion, ApoM displayed inhibitory effects against the inflammatory response in vivo and in vitro; these effects may be induced via the S1PR1 and DHCR24 pathways.
40.	Wang, Mei jun, et al. (author) SIRT1-dependent deacetylation of Txnip H3K9ac is critical for exenatide-improved diabetic kidney disease 2023 In: Biomedicine and Pharmacotherapy. - 0753-3322. ; 167 Journal article (peer-reviewed)abstract Glucagon-like peptide 1 receptor agonist exenatide (exendin-4) has potential protective capabilities against diabetic kidney disease (DKD). However, the underlying mechanism has not been fully elucidated. The expression of thioredoxin-interacting protein (Txnip) is upregulated during DKD progression by histone acetylation. Sirtuin 1 (SIRT1) is a deacetylase and is decreased in DKD, which indicates that it may regulate Txnip in this disease. Here, we used whole-body heterozygous Sirt1 knockout (Sirt1+/-) and kidney-specific Sirt1 knockout (KSK) mice to investigate whether SIRT1 regulates Txnip via histone deacetylation in DKD and exenatide-alleviated DKD. Exenatide substantially improved renal pathological damage, decreased the albumin-to-creatinine ratio (ACR), upregulated SIRT1 expression, and downregulated Txnip expression in kidneys of high-fat diet-treated C57BL/6J mice. However, these effects diminished in Sirt1+/- and KSK mice under exenatide treatment. The downregulation of Txnip expression by exendin-4 in high-glucose-treated SV40 MES13 cells was hampered during Sirt1 knockdown. These results demonstrate that kidney SIRT1 is indispensable in exenatide-improved DKD and downregulation of Txnip expression. Exendin-4 mechanistically downregulated Txnip histone 3 lysine 9 acetylation (H3K9ac) in a SIRT1-dependent manner and decreased spliced X-box binding protein 1 (XBP1s) recruitment to the Txnip promoter. These findings provide epigenetic evidence elucidating the specific mechanism for exenatide-mediated DKD alleviation and highlight the importance of Txnip as a promising therapeutic target for DKD.
41.	Xu, Ning, et al. (author) Effects of platelet-activating factor, tumor necrosis factor, and interleukin-1alpha on the expression of apolipoprotein M in HepG2 cells. 2002 In: Biochemical and Biophysical Research Communications. - : Elsevier BV. - 1090-2104 .- 0006-291X. ; 292:4, s. 944-950 Journal article (peer-reviewed)abstract Apolipoprotein M (apoM) is a recently discovered human apolipoprotein predominantly present in high-density lipoprotein (HDL) in plasma, exclusively expressed in liver and in kidney. The function of apoM is yet unknown. The human apoM gene is located in the major histocompatibility complex class III region on chromosome 6. Because many genes located in this region are related to the immune response, we have investigated whether apoM might also be involved in the host inflammatory response. In this study we examined effects of the platelet-activating factor (PAF), tumor necrosis factor (TNF-alpha), and interleukin-1alpha (IL-1alpha) on apoM expression in a hepatoblastoma cell line, HepG2 cells. PAF significantly enhanced the apoM mRNA levels and the secretion of apoM in HepG2 cell cultures. The enhancement of apoM secretion is seen at a low concentration of PAF (2 ng/ml), whereas a high concentration of PAF increases both the apoM mRNA levels and apoM secretion. Neither TNF-alpha nor IL-1alpha influenced apoM mRNA level and secretion. Furthermore, Lexipafant, a PAF-receptor (PAF-R) antagonist significantly suppressed the mRNA level and the secretion of apoM in HepG2 cells in a dose-dependent manner. Neither PAF nor Lexipafant influenced the mRNA levels and the secretion of apoA-I, apoB and apoE in HepG2 cells, indicating that the effects of PAF or Lexipafant on the apoM production on hepatic cells are selective for apoM. The cellular mechanism of the effects of PAF or Lexipafant on apoM metabolism requires further investigations.
42.	Ying, Yang, 1982- (author) Inclusion Behaviour under a Swirl Flow in a Continuous Casting Process 2014 Licentiate thesis (other academic/artistic)abstract A swirl flow generated in a submerged entry nozzle (SEN) can effectively improve a flow pattern and heat transfer in a continuous casting process by using the methods of “swirl blade type” and “electromagnetic type”. In order to obtain a further in-depth understanding with respect to the effect of a swirl flow on a continuous casting process, the inclusion behaviour in a SEN and a mold was studied in the present work. Moreover, the use of electromagnetics was adopted for to generate a rotating electromagnetic field in a continuous casting process of steel. Specifically, an electromagnetic swirl flow generator (EMSFG) was placed around a SEN.First of all, two kinds of a full type EMSFG and a half type EMSFG were designed based on mathematical modeling. Then, distributions of a magnetic flux intensity in an EMSFG as well as distributions of a Lorentz force in molten steel were simulated. It was found that the EMSFG structure and electromagnetic parameters have an important effect on the magnetic flux intensity and Lorentz force distributions. For both a full type and a half type EMSFG, the magnetic flux intensity and Lorentz force increases as the magnetomotive force increases. Especially, for a full type EMSFG, the magnetic flux intensity is distributed evenly in molten steel. Moreover, the Lorentz force increases along a radial direction in the molten steel in the SEN. However, for a half type EMSFG, the magnetic flux intensity and Lorentz force decreases gradually towards the region without an EMSFG. Consequently, a full type EMSFG with a 44000 AT magnetomotive force and a 50 Hz frequency is more suitable to apply in the operation of an EMSFG under actual production conditions.Secondly, the flow field, the temperature field of molten steel and the inclusion behaviour in a SEN and a square bloom mold were simulated under the influence of a rotating electromagnetic field (swirl generator). Also, the influences of different inclusion parameters such as the densities, sizes and boundary conditions, on the inclusion behavior were studied. The results show that a flow pattern in a SEN can be characterized into three distinct flow regions: an accelerating flow of molten steel from an electromagnetic swirl flow generator (EMSFG) inlet to an EMSFG center, a decelerating flow of molten steel from an EMSFG center to an EMSFG outlet, and a recirculation flow of molten steel from an EMSFG outlet to an SEN outlet. In addition, it was found that light Al2O3 inclusion moves towards the rotational center by a centrifugal force, and that a swirl flow prevents nozzle clogging. Moreover, it was also found that the inclusion separation to a mold meniscus increased and that the inclusions trap into a solidified shell wall decreased by using a swirl flow.
43.	Zhang, Cong, et al. (author) Association of Metabolic Syndrome with Macular Thickness and Volume in Older Adults : A Population-Based Optical Coherence Tomography Study 2024 In: Metabolic Syndrome and Related Disorders. - 1540-4196 .- 1557-8518. ; 22:2, s. 141-150 Journal article (peer-reviewed)abstract Background: To explore the associations of the metabolic syndrome (MetS) and individual components with macular thickness and volume among rural-dwelling Chinese older adults.Methods: This population-based cross-sectional study included 705 participants (age ≥60 years) derived from the MIND-China study. In 2018–2019, we collected data through face-to-face interview, clinical examination, optical coherence tomography (OCT) examination, and blood test. We measured macular thickness and volume using spectral-domain OCT. MetS was defined following the International Diabetes Federation (IDF) criteria, the IDF/American Heart Association (AHA) criteria, the National Cholesterol Education Program-Adult Treatment Panel III criteria, and the Chinese Diabetes Society (CDS) criteria. Data were analyzed with multivariable general linear models.Results: MetS was significantly associated with thinner macula in central (multivariable-adjusted β = −5.29; 95% confidence interval: −9.31 to −1.26), parafoveal (−2.85; −5.73 to 0.04) and perifoveal regions (−4.37; −6.79 to −1.95) when using the IDF criteria, in the perifoveal regions (−3.82; −6.18 to −1.47) when using the IDF/AHA criteria, and in the central region (−5.63; −10.25 to −1.02) when using the CDS criteria, and with reduced macular volume when using the IDF (−0.16; −0.26 to −0.07) and IDF/AHA (−0.13; −0.22 to −0.04) criteria. In the parafoveal region, the IDF-defined MetS was significantly associated with thinner retina in men (β = −6.25; −10.94 to −1.56) but not in women. Abdominal obesity (−2.83; −5.41 to −0.25) and elevated fasting blood glucose (−2.65; −5.08 to −0.21) were associated with thinner macular thickness in the perifoveal region.Conclusion: MetS is associated with macular thinning and reduced macular volume among rural-dwelling older adults, and the associations vary by the defining criteria of MetS.
44.	Zhang, Ping, et al. (author) Alkaline sphingomyelinase (NPP7) promotes cholesterol absorption by affecting sphingomyelin levels in the gut. A study with NPP7 knockout mice. 2014 In: American Journal of Physiology: Gastrointestinal and Liver Physiology. - : American Physiological Society. - 1522-1547 .- 0193-1857. ; 306:10, s. 903-908 Journal article (peer-reviewed)abstract We previously showed that dietary sphingomyelin (SM) inhibited cholesterol absorption in animals. The key enzyme hydrolyzing SM in the gut is alkaline sphingomyelinase (alk-SMase, NPP7). Here using fecal dual-isotope ratio method we compared cholesterol absorption in the wild type (WT) and alk-SMase knockout (KO) mice. The animals were fed an emulsion containing (14)C-cholesterol and (3)H-sitosterol. The radioactivities in the lipids of the fecal samples collected 4, 8 and 24 h thereafter were determined and the ratio of (14)C/(3)H calculated. We found that the fecal (14)C-cholesterol recovery in the KO mice was significantly higher than in the WT mice. Maximal 92% increase occurred 8 h after feeding. Recovery of (3)H-sitosterol did not differ between the two groups. Accordingly the (14)C/(3)H ratio of fecal lipids was 133% higher at 8 h and 75% higher at 24 h in the KO than in the WT mice. Decreased (14)C-cholesterol was also found in the serum of the KO mice 4 h after feeding. Supplement of SM in the emulsion reduced the differences in fecal (14)C-cholesterol recovery between the WT and KO mice due to a greater increase of (14)C-cholesterol recovery in the WT mice. Without treatment the KO mice had significantly higher SM levels in the intestinal content and feces, but not in the intestinal mucosa or serum. The expression of NPC1L1 in the small intestine was not changed. In conclusion, alk-SMase is a physiological factor promoting cholesterol absorption by reducing SM levels in the intestinal lumen.
45.	Zhang, Ping, et al. (author) Deficiency of alkaline SMase enhances dextran sulfate sodium-induced colitis in mice with upregulation of autotaxin 2018 In: Journal of Lipid Research. - 1539-7262. ; 59:10, s. 1841-1850 Journal article (peer-reviewed)abstract Intestinal alkaline SMase (Alk-SMase) cleaves phosphocholine from SM, platelet-activating factor (PAF), and lysophosphatidylcholine. We recently found that colitis-associated colon cancer was 4- to 5-fold enhanced in Alk-SMase KO mice. Here, we further studied the pathogenesis of colitis induced by dextran sulfate sodium (DSS) in WT and KO mice. Compared with WT mice, KO mice demonstrated greater body weight loss, more severe bloody diarrhea, broader inflammatory cell infiltration, and more serious epithelial injury. Higher levels of PAF and lower levels of interleukin (IL)10 were identified in KO mice 2 days after DSS treatment. A greater and progressive increase of lysophosphatidic acid (LPA) was identified. The change was associated with increased autotaxin expression in both small intestine and colon, which was identified by immunohistochemistry study, Western blot, and sandwich ELISA. The upregulation of autotaxin coincided with an early increase of PAF. IL6 and TNFα were increased in both WT and KO mice. At the later stage (day 8), significant decreases in IL6, IL10, and PAF were identified, and the decreases were greater in KO mice. In conclusion, deficiency of Alk-SMase enhances DSS-induced colitis by mechanisms related to increased autotaxin expression and LPA formation. The early increase of PAF might be a trigger for such reactions.
46.	Zhang, Ruyang, et al. (author) EGLN2 DNA methylation and expression interact with HIF1A to affect survival of early-stage NSCLC 2019 In: Epigenetics. - : Informa UK Limited. - 1559-2294 .- 1559-2308. ; 14:2, s. 118-129 Journal article (peer-reviewed)abstract Hypoxia occurs frequently in human cancers and promotes stabilization and activation of hypoxia inducible factor (HIF). HIF-1α is specific for the hypoxia response, and its degradation mediated by three enzymes EGLN1, EGLN2 and EGLN3. Although EGLNs expression has been found to be related to prognosis of many cancers, few studies examined DNA methylation in EGLNs and its relationship to prognosis of early-stage non-small cell lung cancer (NSCLC). We analyzed EGLNs DNA methylation data from tumor tissue samples of 1,230 early-stage NSCLC patients, as well as gene expression data from The Cancer Genome Atlas. The sliding windows sequential forward feature selection method and weighted random forest were used to screen out the candidate CpG probes in lung adenocarcinomas (LUAD) and lung squamous cell carcinomas patients, respectively, in both discovery and validation phases. Then Cox regression was performed to evaluate the association between DNA methylation and overall survival. Among the 34 CpG probes in EGLNs, DNA methylation at cg25923056EGLN2 was identified to be significantly associated with LUAD survival (HR = 1.02, 95% CI: 1.01–1.03, P = 9.90 × 10–5), and correlated with EGLN2 expression (r =–0.36, P = 1.52 × 10–11). Meanwhile, EGLN2 expression was negatively correlated with HIF1A expression in tumor tissues (r =–0.30, P = 4.78 × 10–8) and significantly (P = 0.037) interacted with HIF1A expression on overall survival. Therefore, DNA methylation of EGLN2- HIF1A is a potential marker for LUAD prognosis and these genes are potential treatment targets for further development of HIF-1α inhibitors in lung cancer therapy.
47.	Zhang, Ruyang, et al. (author) Independent Validation of Early-Stage Non-Small Cell Lung Cancer Prognostic Scores Incorporating Epigenetic and Transcriptional Biomarkers With Gene-Gene Interactions and Main Effects 2020 In: Chest. - : Elsevier BV. - 0012-3692. ; 158:2, s. 808-819 Journal article (peer-reviewed)abstract Background: DNA methylation and gene expression are promising biomarkers of various cancers, including non-small cell lung cancer (NSCLC). Besides the main effects of biomarkers, the progression of complex diseases is also influenced by gene-gene (G×G) interactions. Research Question: Would screening the functional capacity of biomarkers on the basis of main effects or interactions, using multiomics data, improve the accuracy of cancer prognosis? Study Design and Methods: Biomarker screening and model validation were used to construct and validate a prognostic prediction model. NSCLC prognosis-associated biomarkers were identified on the basis of either their main effects or interactions with two types of omics data. A prognostic score incorporating epigenetic and transcriptional biomarkers, as well as clinical information, was independently validated. Results: Twenty-six pairs of biomarkers with G×G interactions and two biomarkers with main effects were significantly associated with NSCLC survival. Compared with a model using clinical information only, the accuracy of the epigenetic and transcriptional biomarker-based prognostic model, measured by area under the receiver operating characteristic curve (AUC), increased by 35.38% (95% CI, 27.09%-42.17%; P = 5.10 × 10–17) and 34.85% (95% CI, 26.33%-41.87%; P = 2.52 × 10–18) for 3- and 5-year survival, respectively, which exhibited a superior predictive ability for NSCLC survival (AUC3 year, 0.88 [95% CI, 0.83-0.93]; and AUC5 year, 0.89 [95% CI, 0.83-0.93]) in an independent Cancer Genome Atlas population. G×G interactions contributed a 65.2% and 91.3% increase in prediction accuracy for 3- and 5-year survival, respectively. Interpretation: The integration of epigenetic and transcriptional biomarkers with main effects and G×G interactions significantly improves the accuracy of prognostic prediction of early-stage NSCLC survival.
48.	Zhang, Ruyang, et al. (author) SIPA1L3 methylation modifies the benefit of smoking cessation on lung adenocarcinoma survival : an epigenomic–smoking interaction analysis 2019 In: Molecular Oncology. - : Wiley. - 1574-7891 .- 1878-0261. ; 13:5, s. 1235-1248 Journal article (peer-reviewed)abstract Smoking cessation prolongs survival and decreases mortality of patients with non-small-cell lung cancer (NSCLC). In addition, epigenetic alterations of some genes are associated with survival. However, potential interactions between smoking cessation and epigenetics have not been assessed. Here, we conducted an epigenome-wide interaction analysis between DNA methylation and smoking cessation on NSCLC survival. We used a two-stage study design to identify DNA methylation–smoking cessation interactions that affect overall survival for early-stage NSCLC. The discovery phase contained NSCLC patients from Harvard, Spain, Norway, and Sweden. A histology-stratified Cox proportional hazards model adjusted for age, sex, clinical stage, and study center was used to test DNA methylation–smoking cessation interaction terms. Interactions with false discovery rate-q ≤ 0.05 were further confirmed in a validation phase using The Cancer Genome Atlas database. Histology-specific interactions were identified by stratification analysis in lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC) patients. We identified one CpG probe (cg02268510 SIPA 1L3 ) that significantly and exclusively modified the effect of smoking cessation on survival in LUAD patients [hazard ratio (HR) interaction = 1.12; 95% confidence interval (CI): 1.07–1.16; P = 4.30 × 10 –7 ]. Further, the effect of smoking cessation on early-stage LUAD survival varied across patients with different methylation levels of cg02268510 SIPA 1L3 . Smoking cessation only benefited LUAD patients with low methylation (HR = 0.53; 95% CI: 0.34–0.82; P = 4.61 × 10 –3 ) rather than medium or high methylation (HR = 1.21; 95% CI: 0.86–1.70; P = 0.266) of cg02268510 SIPA 1L3 . Moreover, there was an antagonistic interaction between elevated methylation of cg02268510 SIPA 1L3 and smoking cessation (HR interaction = 2.1835; 95% CI: 1.27–3.74; P = 4.46 × 10 −3 ). In summary, smoking cessation benefited survival of LUAD patients with low methylation at cg02268510 SIPA 1L3 . The results have implications for not only smoking cessation after diagnosis, but also possible methylation-specific drug targeting.
49.	Zhang, Wei, et al. (author) Activation of nuclear factor-kappa B pathway is responsible for tumor necrosis factor-a-induced up-regulation of endothelin B2 receptor expression in vascular smooth muscle cells in vitro 2012 In: Toxicology Letters. - : Elsevier BV. - 1879-3169 .- 0378-4274. ; 209:2, s. 107-112 Journal article (peer-reviewed)abstract The endothelin B2 (ETB2) receptors are induced in vascular smooth muscle cells (VSMCs) in cardiovascular diseases. We tested if in vitro short-term exposure to the pro-inflammatory cytokine tumor necrosis factor-alpha (TNF-alpha) could up-regulate ETB2 receptors in rat mesenteric arteries, and if this effect is through activation of intracellular nuclear factor-kappa B (NF-kappa B) pathway. The mesenteric arteries were dissected from male Sprague-Dawley rats and the endothelium was removed. The arteries were co-incubated with TNF-alpha in serum-free Dulbecco's modified Eagle's medium. Real-time reverse transcription-PCR, Western blot and immunohistochemical staining were employed to assess the mRNA/protein expression of ETB2 receptors and activation of NF-kappa B pathway. The results showed that, during organ culture. TNF-alpha concentration-dependently enhanced ET52 receptors expression at both mRNA and protein levels, paralleled with activation of NF-kappa B pathway in VSMC. The up-regulated ETB2 receptor expression and NF-kappa B activation could be effectively suppressed by general transcriptional inhibitor actinomycin D, or either of the selective I kappa B kinase inhibitors wedelolactone and IMD-0354. Conclusively, the activation of intracellular NF-kappa B pathway is responsible for the up-regulation of ETB2 receptors induced by short-term exposure to TNF-alpha. This could partly explain the toxic effects of TNF-alpha on VSMCs that account for cardiovascular diseases. (C) 2011 Elsevier Ireland Ltd. All rights reserved.
50.	Zhang, Ying, et al. (author) Capture of novel sp3 hybridized Z-BN by compressing boron nitride nanotubes with small diameter 2022 In: Diamond and related materials. - : Elsevier. - 0925-9635 .- 1879-0062. ; 130 Journal article (peer-reviewed)abstract Experimental synthesis of new sp3 hybridized carbon/boron nitride structures remains challenging despite that numerous sp3 structures have been proposed in theory. Here, we showed that compressed multi-walled boron nitride nanotubes (MWBNNTs) and boron nitride peapods (C60@BNNTs) with small diameters could transform into a new sp3 hybridized boron nitride allotrope (Z-BN). This strategy is considered from the topological transition point of view in boron nitride nanotubes upon compression. Due to the increased curvature in compressed small-diameter MWBNNTs, the uncommon 4- and 8-membered rings in Z-BN could be more favorably formed. And the irreversible tube collapse is proved to be a critical factor for the capture of the formed Z-BN, because of the competition between the resilience of tube before collapse and the stress limitation for the lattice stabilization of Z-BN upon decompression. In this case, Z-BN starts to form above 19.0 GPa, which is fully reversible below 45 GPa and finally becomes quenchable at 93.5 GPa. This collapse-induced capture of the high-pressure phase could also be extended to other tubular materials for quenching novel sp3 structures.

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