| 1. |
- Beal, Jacob, et al.
(författare)
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Robust estimation of bacterial cell count from optical density
- 2020
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Ingår i: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1
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Tidskriftsartikel (refereegranskat)abstract
- Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data.
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| 2. |
- Qi, Di, et al.
(författare)
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Climate change drives rapid decadal acidification in the Arctic Ocean from 1994 to 2020
- 2022
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 377:6614, s. 1544-1550
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Tidskriftsartikel (refereegranskat)abstract
- The Arctic Ocean has experienced rapid warming and sea ice loss in recent decades, becoming the first open-ocean basin to experience widespread aragonite undersaturation [saturation state of aragonite (Warag) < 1]. However, its trend toward long-term ocean acidification and the underlying mechanisms remain undocumented. Here, we report rapid acidification there, with rates three to four times higher than in other ocean basins, and attribute it to changing sea ice coverage on a decadal time scale. Sea ice melt exposes seawater to the atmosphere and promotes rapid uptake of atmospheric carbon dioxide, lowering its alkalinity and buffer capacity and thus leading to sharp declines in pH and Warag. We predict a further decrease in pH, particularly at higher latitudes where sea ice retreat is active, whereas Arctic warming may counteract decreases in Warag in the future.
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| 3. |
- Du, Xinyu, et al.
(författare)
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Distribution, behavior, and risk assessment of chlorinated paraffins in paddy plants throughout whole growth cycle
- 2022
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Ingår i: Environment International. - : Elsevier BV. - 0160-4120 .- 1873-6750. ; 167
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Tidskriftsartikel (refereegranskat)abstract
- Paddy plants provide staple food for 3 billion people worldwide. This study explores the environmental fate and behavior of a high-volume production emerging contaminants chlorinated paraffins (CPs) in the paddy ecosystem. Very-short-, short-, medium-, and long-chain CPs (vSCCPs, SCCPs, MCCPs, and LCCPs, respectively) were analyzed in specific tissue of paddy plants at four main growth stages and soils from the Yangtze River Delta, China throughout a full rice growing season. The total CP concentrations in the paddy roots, stalks, leaves, panicles, hulls, rice, and soils ranged from 181 to 1.74 × 103, 21.7–383, 19.6–585, 108–332, 245–470, 59.6–130, and 99.6–400 ng/g dry weight, respectively. The distribution profile indicated the translocation of SCCPs and MCCPs from soils to paddy tissue, highlighting their elevated bioaccumulative potential. The evolution of CP level/mass/pattern during the whole growth cycle suggested atmospheric CPs deposition on leaves and hulls, as well as stalk-rice transfer. CSOIL plant uptake model well predicted the level, distribution pattern, and bioconcentration factors (BCFs) of SCCPs and MCCPs in paddy shoot and recognized the soil-air-shoot pathway as the major contributor. Moreover, risk evaluation indicated that MCCPs intake and subsequent risks dominated the total exposure to CPs via rice ingestion. This is the first report on the occurrence, fate and risk assessment of all CPs classes in paddy ecosystems, and the results underline the potential health effects caused by the in-use MCCPs via rice ingestion.
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| 4. |
- Ji, Xinyu, et al.
(författare)
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Epigenetic–smoking interaction reveals histologically heterogeneous effects of TRIM27 DNA methylation on overall survival among early-stage NSCLC patients
- 2020
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Ingår i: Molecular Oncology. - : Wiley. - 1574-7891 .- 1878-0261. ; 14:11, s. 2759-2774
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Tidskriftsartikel (refereegranskat)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.
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| 5. |
- Ji, Xinyu, et al.
(författare)
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Epigenome-wide three-way interaction study identifies a complex pattern between TRIM27, KIAA0226, and smoking associated with overall survival of early-stage NSCLC
- 2022
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Ingår i: Molecular Oncology. - : Wiley. - 1574-7891 .- 1878-0261. ; 16:3, s. 717-731
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Tidskriftsartikel (refereegranskat)abstract
- The interaction between DNA methylation of tripartite motif containing 27 (cg05293407TRIM27) and smoking has previously been identified to reveal histologically heterogeneous effects of TRIM27 DNA methylation on early-stage non-small-cell lung cancer (NSCLC) survival. However, to understand the complex mechanisms underlying NSCLC progression, we searched three-way interactions. A two-phase study was adopted to identify three-way interactions in the form of pack-year of smoking (number of cigarettes smoked per day × number of years smoked) × cg05293407TRIM27 × epigenome-wide DNA methylation CpG probe. Two CpG probes were identified with FDR-q ≤ 0.05 in the discovery phase and P ≤ 0.05 in the validation phase: cg00060500KIAA0226 and cg17479956EXT2. Compared to a prediction model with only clinical information, the model added 42 significant three-way interactions using a looser criterion (discovery: FDR-q ≤ 0.10, validation: P ≤ 0.05) had substantially improved the area under the receiver operating characteristic curve (AUC) of the prognostic prediction model for both 3-year and 5-year survival. Our research identified the complex interaction effects among multiple environment and epigenetic factors, and provided therapeutic target for NSCLC patients.
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| 6. |
- Lin, Jiachun, et al.
(författare)
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Gear wear prediction based on the theorem of degradation entropy generation
- 2024
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Ingår i: Tribology International. - : Elsevier BV. - 0301-679X .- 1879-2464. ; 191
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Tidskriftsartikel (refereegranskat)abstract
- Tooth surface material loss caused by gear wear alters the surface morphology of gears, which impacts their vibration, noise, and remaining lifespan. Although gear wear modeling and prediction have been extensively studied, this paper proposes a novel approach based on the theorem of degradation entropy generation (DEG). A point-by-point calculation method is introduced to determine the degradation coefficient for each measurement point on the tooth profile, accounting for varying working conditions along the tooth profile during the actual meshing process of the gear pair. First, the FZG gear's bearing capacity is tested. Next, a surface roughness profilometer is employed to in-situ measure the tooth profile after each load stage. The profile deviation curve and the amount of profile wear following each load stage are obtained by processing the measured profile morphology data. Then, the pitting safety factor for each point on the tooth surface is calculated according to the ISO 6336–22:2018 standard and used to correct the degradation coefficient for that point. Finally, the entropy generation of the system during each load stage of the FZG gear is calculated. The degradation coefficient suggested in the DEG theorem is employed to link gear wear with system entropy generation, realizing gear wear modeling and prediction. The results demonstrate that the gear wear calculation method based on the DEG theorem can accurately predict the evolution of tooth profile surface morphology during the experimental process. This research provides a unified calculation method for surface morphology evolution caused by gear wear during service.
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| 7. |
- Ma, Yue, et al.
(författare)
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Acid suppressants use and risk of atherosclerotic cardiovascular disease in middle-aged and older adults
- 2022
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Ingår i: Atherosclerosis. - : Elsevier BV. - 0021-9150. ; 358, s. 47-54
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Tidskriftsartikel (refereegranskat)abstract
- Background and aims: Concerns regarding adverse events associated with the use of acid suppressants have increased. However, the impact of proton pump inhibitors (PPIs) and histamine‐2 receptor antagonists (H2RAs) on the risk of atherosclerotic cardiovascular disease (ASCVD) remains unknown. This study aimed to estimate the risk of ASCVD in association with the use of PPIs and H2RAs. Methods: This prospective cohort study included participants without cardiovascular diseases or anti-hypertensive treatment at baseline (2006–2010) in the UK Biobank. The outcomes were ASCVD and each subtype (coronary artery disease, myocardial infarction, peripheral artery disease, and ischemic stroke). The association was estimated by Cox proportional-hazards models. Results: Among 316,730 individuals (aged 50–88 years), during a median of 12.5 years of follow-up, we documented 13,503 (4.3%) incident ASCVD. Regular PPIs use was associated with a higher risk of ASCVD (HR: 1.16, 95% CI: 1.09–1.23) and every subtype of ASCVD. Among each type of PPIs, omeprazole (HR: 1.19, 95% CI: 1.11–1.28), lansoprazole (HR: 1.11, 95% CI: 1.02–1.22), and pantoprazole (HR: 1.40, 95% CI: 1.00–1.97) were associated with a higher risk of ASCVD. Stratification analysis showed that PPIs use was associated with a higher risk of ASCVD among individuals without indications of medications for PPIs. In addition, use of H2RAs was not related to the risk of ASCVD (HR: 0.97, 95% CI: 0.85–1.11). Conclusions: PPIs were associated with increased risk of ASCVD, particularly amongst participants without indications for medication. Our findings are of important practical significance and suggest that clinicians should be cautious in prophylactic use of PPIs.
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| 8. |
- Ng, Chun Chet, et al.
(författare)
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When IC meets text: Towards a rich annotated integrated circuit text dataset
- 2024
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Ingår i: Pattern Recognition. - 0031-3203. ; 147
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Tidskriftsartikel (refereegranskat)abstract
- Automated Optical Inspection (AOI) is a process that uses cameras to autonomously scan printed circuit boards for quality control. Text is often printed on chip components, and it is crucial that this text is correctly recognized during AOI, as it contains valuable information. In this paper, we introduce \textit{ICText}, the largest dataset for text detection and recognition on integrated circuits. Uniquely, it includes labels for character quality attributes such as low contrast, blurry, and broken. While loss-reweighting and Curriculum Learning (CL) have been proposed to improve object detector performance by balancing positive and negative samples and gradually training the model from easy to hard samples, these methods have had limited success with one-stage object detectors commonly used in industry. To address this, we propose Attribute-Guided Curriculum Learning (AGCL), which leverages the labeled character quality attributes in \textit{ICText}. Our extensive experiments demonstrate that AGCL can be applied to different detectors in a plug-and-play fashion to achieve higher Average Precision (AP), significantly outperforming existing methods on \textit{ICText} without any additional computational overhead during inference. Furthermore, we show that AGCL is also effective on the generic object detection dataset Pascal VOC. Our code and dataset will be publicly available at \href{https://github.com/chunchet-ng/ICText-AGCL}{https://github.com/chunchet-ng/ICText-AGCL}.
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| 9. |
- Niu, Dong, et al.
(författare)
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Novel brominated flame retardants in house dust from Shanghai, China : levels, temporal variation, and human exposure
- 2019
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Ingår i: Environmental Sciences Europe. - : Springer London. - 2190-4707 .- 2190-4715. ; 31:1
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Tidskriftsartikel (refereegranskat)abstract
- Background: Novel brominated flame retardants (NBFRs) have been increasingly used as alternatives to legacy BFRs (e.g., PBDEs and HBCDs) in consumer products, but are liable to emigrate and contaminate indoor dust. In this study, a total of 154 house dust samples including floor dust (FD) and elevated surface dust (ESD) were collected in the biggest metropolitan area (Shanghai) of East China in 2016. Limited information about temporal variation of NBFRs indoors is available, while the period of sampling is influential in human exposure estimates. Levels, temporal variation, and human exposure of seven target NBFRs such as decabromodiphenylethane (DBDPE), 1,2-bis(2,4,6-tribromophenoxy) ethane (BTBPE), 2-ethylhexyl 2,3,4,5-tetrabromobenzoate (EHTBB), and bis(2-ethylhexyl) tetrabromophthalate (BEHTEBP) were investigated in indoor house dust.Results: Concentrations of Sigma(7)NBFRs ranged from 19.11 to 3099ng/g with a geomean of 295.1ng/g in FD, and from 34.74 to 404.6ng/g with a geomean of 117.9ng/g in ESD. The geomeans of DBDPE were 219.6ng/g in FD and 76.89ng/g in ESD, accounting for 90.5% and 80.5% of Sigma(7)NBFRs. Levels of EHTBB, BTBPE, and DBDPE in FD exceeded significantly those in ESD. The temporal variation in Sigma(7)NBFRs in FD was ranked as summer>winter>autumn>spring. The daily exposure doses (DEDs) of Sigma(7)NBFRs via dust ingestion decreased as: infants>toddlers>children>teenagers>adults. Infants showed the highest DED in FD, 9.1ng/kg bw/day.Conclusions: DBDPE clearly dominated the NBFRs in both FD and ESD, but the concentrations of DBDPE in this study were generally moderate compared with the other international studies. Dust ingestion was the major pathway of human exposure to NBFRs indoors. About eightfold difference in exposure estimates between infants and adults showed that infants faced elevated exposure risks in FD. This study highlighted the necessity to estimate human exposure of NBFRs for different age groups using FD and ESD, respectively.
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| 10. |
- Vinel, Claire, et al.
(författare)
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Comparative epigenetic analysis of tumour initiating cells and syngeneic EPSC-derived neural stem cells in glioblastoma
- 2021
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Ingår i: Nature Communications. - : Springer Nature. - 2041-1723. ; 12:1
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Tidskriftsartikel (refereegranskat)abstract
- Epigenetic mechanisms which play an essential role in normal developmental processes, such as self-renewal and fate specification of neural stem cells (NSC) are also responsible for some of the changes in the glioblastoma (GBM) genome. Here we develop a strategy to compare the epigenetic and transcriptional make-up of primary GBM cells (GIC) with patient-matched expanded potential stem cell (EPSC)-derived NSC (iNSC). Using a comparative analysis of the transcriptome of syngeneic GIC/iNSC pairs, we identify a glycosaminoglycan (GAG)-mediated mechanism of recruitment of regulatory T cells (Tregs) in GBM. Integrated analysis of the transcriptome and DNA methylome of GBM cells identifies druggable target genes and patient-specific prediction of drug response in primary GIC cultures, which is validated in 3D and in vivo models. Taken together, we provide a proof of principle that this experimental pipeline has the potential to identify patient-specific disease mechanisms and druggable targets in GBM. The identification of patient-specific disease mechanisms and druggable targets is crucial for precision medicine in glioblastoma. Here, the authors show that comparing patients-matched glioma-initiating cells with neural stem cells enables the discovery of patient-specific mechanisms of disease and the identification of effective drugs
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