| 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. |
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| 3. |
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- 2019
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Tidskriftsartikel (refereegranskat)
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| 4. |
- Li, Yuchen, et al.
(författare)
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Associations of parental and perinatal factors with subsequent risk of stress-related disorders : a nationwide cohort study with sibling comparison
- 2022
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Ingår i: Molecular Psychiatry. - : Springer Nature. - 1359-4184 .- 1476-5578. ; 27, s. 1712-1719
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Tidskriftsartikel (refereegranskat)abstract
- Little is known about the contribution of pregnancy-related parental and perinatal factors to the development of stress-related disorders. We aimed to investigate whether parental/perinatal adversities entail higher risks of stress-related disorders in the offspring, later in life, by accounting for genetic and early environmental factors. Based on the nationwide Swedish registers, we conducted a population-based cohort study of 3,435,747 singleton births (of which 2,554,235 were full siblings), born 1973-2008 and survived through the age of 5 years. Using both population- and sibling designs, we employed Cox regression to assess the association between parental and perinatal factors with subsequent risk of stress-related disorders. We identified 55,511 individuals diagnosed with stress-related disorders in the population analysis and 37,433 in the sibling analysis. In the population-based analysis we observed increased risks of stress-related disorders among offspring of maternal/paternal age <25, single mothers, parity >= 4, mothers with BMI >= 25 or maternal smoking in early pregnancy, gestational diabetes, and offspring born moderately preterm (GA 32-36 weeks), or small-for-gestational-age. These associations were significantly attenuated toward null in the sibling analysis. Cesarean-section was weakly associated with offspring stress-related disorders in population [hazard ratio (HR) 1.09, 95% confidence interval (CI) 1.06-1.12] and sibling analyses (HR 1.10, 95% CI 1.02-1.20). Our findings suggest that most of the observed associations between parental and perinatal factors and risk of stress-related disorders in the population analysis are driven by shared familial environment or genetics, and underscore the importance of family designs in epidemiological studies on the etiology of psychiatric disorders.
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| 5. |
- An, Rui, et al.
(författare)
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Photostability and Photodegradation Processes in Colloidal CsPbI3 Perovskite Quantum Dots
- 2018
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Ingår i: ACS Applied Materials and Interfaces. - : American Chemical Society (ACS). - 1944-8244 .- 1944-8252. ; 10:45, s. 39222-39227
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Tidskriftsartikel (refereegranskat)abstract
- All-inorganic CsPbI3 perovskite quantum dots (QDs) have attracted intense attention for their successful application in photovoltaics (PVs) and optoelectronics that are enabled by their superior absorption capability and great photoluminescence (PL) properties. However, their photostability remains a practical bottleneck and further optimization is highly desirable. Here, we studied the photostability of as-obtained colloidal CsPbI3 QDs suspended in hexane. We found that light illumination does induce photodegradation of CsPbI3 QDs. Steady-state spectroscopy, X-ray diffraction, Fourier transform infrared spectroscopy, transmission electron microscopy, and transient absorption spectroscopy verified that light illumination leads to detachment of the capping agent, collapse of the CsPbI3 QD surface, and finally aggregation of surface Pb0. Both dangling bonds containing surface and Pb0 serve as trap states causing PL quenching with a dramatic decrease of PL quantum yield. Our work provides a detailed insight about the correlation between the structural and photophysical consequences of the photodegradation process in CsPbI3 QDs and may lead to the optimization of such QDs toward device applications.
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| 6. |
- Bettegowda, Chetan, et al.
(författare)
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Detection of circulating tumor DNA in early- and late-stage human malignancies
- 2014
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Ingår i: Science Translational Medicine. - : American Association for the Advancement of Science (AAAS). - 1946-6234 .- 1946-6242. ; 6:224, s. 224ra24-
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Tidskriftsartikel (refereegranskat)abstract
- The development of noninvasive methods to detect and monitor tumors continues to be a major challenge in oncology. We used digital polymerase chain reaction-based technologies to evaluate the ability of circulating tumor DNA (ctDNA) to detect tumors in 640 patients with various cancer types. We found that ctDNA was detectable in >75% of patients with advanced pancreatic, ovarian, colorectal, bladder, gastroesophageal, breast, melanoma, hepatocellular, and head and neck cancers, but in less than 50% of primary brain, renal, prostate, or thyroid cancers. In patients with localized tumors, ctDNA was detected in 73, 57, 48, and 50% of patients with colorectal cancer, gastroesophageal cancer, pancreatic cancer, and breast adenocarcinoma, respectively. ctDNA was often present in patients without detectable circulating tumor cells, suggesting that these two biomarkers are distinct entities. In a separate panel of 206 patients with metastatic colorectal cancers, we showed that the sensitivity of ctDNA for detection of clinically relevant KRAS gene mutations was 87.2% and its specificity was 99.2%. Finally, we assessed whether ctDNA could provide clues into the mechanisms underlying resistance to epidermal growth factor receptor blockade in 24 patients who objectively responded to therapy but subsequently relapsed. Twenty-three (96%) of these patients developed one or more mutations in genes involved in the mitogen-activated protein kinase pathway. Together, these data suggest that ctDNA is a broadly applicable, sensitive, and specific biomarker that can be used for a variety of clinical and research purposes in patients with multiple different types of cancer.
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| 7. |
- Cao, Qi, et al.
(författare)
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Jointly estimating the most likely driving paths and destination locations with incomplete vehicular trajectory data
- 2023
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Ingår i: Transportation Research, Part C: Emerging Technologies. - 0968-090X. ; 155
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Tidskriftsartikel (refereegranskat)abstract
- With an ever-increasing deployment density of probe and fixed sensors, massive vehicular trajectory data is available and show a promising foundation to improve the observability of dynamic traffic demand pattern. However, due to technical and privacy issues, the raw trajectories are not always complete and the paths and destinations between discontinuous trajectory nodes are usually missing. This paper proposes a probabilistic method to jointly reconstruct the missing driving path and destination location of vehicles with incomplete trajectory data. One problem-specific HMM-structured model incorporating spatial and temporal analysis (ST-HMM) is constructed to define the matching probability between observed data and possible movement. Two algorithms, namely candidate set generation and best-match search algorithms, are developed to seek the most possible one as matching result. It can implement end-to-end processing from incomplete trajectory data to complete and connective paths and destinations for the target vehicle. The proposed method is tested based on field-test data and city-wide road network. Compared with two benchmark methods, the proposed method improved the matching accuracy in terms of both path identification and destination inference. Additionally, sensitivity analyses on the size of training dataset and candidate set were performed. We believe that experiment results of these sensitivity analyses can help to provide guidance on data sensing and candidate generation.
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| 8. |
- Dolinska, Monika, et al.
(författare)
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Characterization of Bone Marrow Niche in Chronic Myeloid Leukemia Patients Identifies CXCL14 as a New Therapeutic Option
- 2023
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Ingår i: Blood. - : American Society of Hematology. - 0006-4971 .- 1528-0020. ; 142:1, s. 73-89
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Tidskriftsartikel (refereegranskat)abstract
- Although tyrosine kinase inhibitors (TKIs) are effective in treating chronic myeloid leukemia (CML), they often fail to eradicate the leukemia-initiating stem cells (LSCs), causing disease persistence and relapse. Evidence indicates that LSC persistence may be because of bone marrow (BM) niche protection; however, little is known about the underlying mechanisms. Herein, we molecularly and functionally characterize BM niches in patients with CML at diagnosis and reveal the altered niche composition and function in these patients. Long-term culture initiating cell assay showed that the mesenchymal stem cells from patients with CML displayed an enhanced supporting capacity for normal and CML BM CD34+CD38- cells. Molecularly, RNA sequencing detected dysregulated cytokine and growth factor expression in the BM cellular niches of patients with CML. Among them, CXCL14 was lost in the BM cellular niches in contrast to its expression in healthy BM. Restoring CXCL14 significantly inhibited CML LSC maintenance and enhanced their response to imatinib in vitro, and CML engraftment in vivo in NSG-SGM3 mice. Importantly, CXCL14 treatment dramatically inhibited CML engraftment in patient-derived xenografted NSG-SGM3 mice, even to a greater degree than imatinib, and this inhibition persisted in patients with suboptimal TKI response. Mechanistically, CXCL14 upregulated inflammatory cytokine signaling but downregulated mTOR signaling and oxidative phosphorylation in CML LSCs. Together, we have discovered a suppressive role of CXCL14 in CML LSC growth. CXCL14 might offer a treatment option targeting CML LSCs.
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| 9. |
- Dolinska, Monika, et al.
(författare)
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Characterization of the bone marrow niche in patients with chronic myeloid leukemia identifies CXCL14 as a new therapeutic option
- 2023
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Ingår i: Blood. - : American Society of Hematology. - 0006-4971 .- 1528-0020. ; 142:1, s. 73-89
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Tidskriftsartikel (refereegranskat)abstract
- Although tyrosine kinase inhibitors (TKIs) are effective in treating chronic myeloid leukemia (CML), they often fail to eradicate the leukemia-initiating stem cells (LSCs), causing disease persistence and relapse. Evidence indicates that LSC persistence may be because of bone marrow (BM) niche protection; however, little is known about the underlying mechanisms. Herein, we molecularly and functionally characterize BM niches in patients with CML at diagnosis and reveal the altered niche composition and function in these patients. Long -term culture initiating cell assay showed that the mesenchymal stem cells from patients with CML displayed an enhanced supporting capacity for normal and CML BM CD34+CD38- cells. Molecularly, RNA sequencing detected dysregulated cytokine and growth factor expression in the BM cellular niches of patients with CML. Among them, CXCL14 was lost in the BM cellular niches in contrast to its expression in healthy BM. Restoring CXCL14 significantly inhibited CML LSC maintenance and enhanced their response to imatinib in vitro, and CML engraftment in vivo in NSG-SGM3 mice. Importantly, CXCL14 treatment dramatically inhibited CML engraftment in patient-derived xenografted NSG-SGM3 mice, even to a greater degree than imatinib, and this inhibition persisted in patients with suboptimal TKI response. Mechanistically, CXCL14 upregulated inflammatory cytokine signaling but downregulated mTOR signaling and oxidative phosphorylation in CML LSCs. Together, we have discovered a suppressive role of CXCL14 in CML LSC growth. CXCL14 might offer a treatment option targeting CML LSCs.
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| 10. |
- Han, Yuchen, et al.
(författare)
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Characteristics and Application Analysis of a Novel Full Fresh Air System Using Only Geothermal Energy for Space Cooling and Dehumidification
- 2024
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Ingår i: Buildings. - : MDPI. - 2075-5309. ; 14:5
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Tidskriftsartikel (refereegranskat)abstract
- To effectively reduce building energy consumption, a novel full fresh air system with a heat source tower (HST) and a borehole heat exchanger (BHE) was proposed for space cooling and dehumidification in this paper. The cooling system only adopts geothermal energy to produce dry and cold fresh air for space cooling and dehumidification through the BHE and HST, which has the advantage of non-condensate water compared to BHE systems integrated with a fan coil or chilled beam. Based on the established mathematical model of the cooling system, this paper analyzed the system characteristics, feasibility, operation strategy, energy performance, and cost-effectiveness of the proposed model in detail. The results show that the mathematical model has less than 10% error in estimating the system performance compared to the practical HST-BHE experimental set up. Under the specific boundary conditions, the cooling and dehumidification capacity of this system increases with the decrease in the air temperature, air moisture content, and inlet water temperature of the HST. The optimal cooling capacity and the system COP can be achieved when the air-water flow ratio is at 4:3. A case study was conducted in a residential building in Shenyang with an area of about 1800 m2. It was found that this system can fully meet the cooling and dehumidification demand in such a residential building. The operation strategy of the cooling system can be optimized by adjusting the air-water flow ratio from 4:3 to 3:2 during the early cooling season (7 June-1 July) and end cooling season (3 August-1 September). As a result, the average COP of the cooling system during the whole cooling season can be improved from 6.1 to 8.7. Compared with the air source heat pump (ASHP) and the ground source heat pump (GSHP) for space cooling, the proposed cooling system can achieve an energy saving rate of 123% and 26%, respectively. Considering that the BHE of the GSHP can be part of the proposed HST-BHE cooling system, the integration of the HST and GHSP for space cooling (and heating) is strongly recommended in actual applications.
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