| 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. |
- Ching, Tao-Chung, et al.
(författare)
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The JCMT BISTRO-2 Survey: Magnetic Fields of the Massive DR21 Filament
- 2022
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Ingår i: Astrophysical Journal. - : American Astronomical Society. - 1538-4357 .- 0004-637X. ; 941:2
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Tidskriftsartikel (refereegranskat)abstract
- We present 850 mu m dust polarization observations of the massive DR21 filament from the B-fields In STar-forming Region Observations (BISTRO) survey, using the POL-2 polarimeter and the SCUBA-2 camera on the James Clerk Maxwell Telescope. We detect ordered magnetic fields perpendicular to the parsec-scale ridge of the DR21 main filament. In the subfilaments, the magnetic fields are mainly parallel to the filamentary structures and smoothly connect to the magnetic fields of the main filament. We compare the POL-2 and Planck dust polarization observations to study the magnetic field structures of the DR21 filament on 0.1-10 pc scales. The magnetic fields revealed in the Planck data are well-aligned with those of the POL-2 data, indicating a smooth variation of magnetic fields from large to small scales. The plane-of-sky magnetic field strengths derived from angular dispersion functions of dust polarization are 0.6-1.0 mG in the DR21 filament and similar to 0.1 mG in the surrounding ambient gas. The mass-to-flux ratios are found to be magnetically supercritical in the filament and slightly subcritical to nearly critical in the ambient gas. The alignment between column density structures and magnetic fields changes from random alignment in the low-density ambient gas probed by Planck to mostly perpendicular in the high-density main filament probed by James Clerk Maxwell Telescope. The magnetic field structures of the DR21 filament are in agreement with MHD simulations of a strongly magnetized medium, suggesting that magnetic fields play an important role in shaping the DR21 main filament and subfilaments.
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| 3. |
- Yue, Siyao, et al.
(författare)
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Brown carbon from biomass burning imposes strong circum-Arctic warming
- 2022
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Ingår i: ONE EARTH. - : Elsevier BV. - 2590-3330 .- 2590-3322. ; 5:3, s. 293-304
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Tidskriftsartikel (refereegranskat)abstract
- Rapid warming in the Arctic has a huge impact on the global environment. Atmospheric brown carbon (BrC) is one of the least understood and uncertain warming agents due to a scarcity of observations. Here, we performed direct observations of atmospheric BrC and quantified its light-absorbing properties during a 2 month circum-Arctic cruise in summer of 2017. Through observation-constrained modeling, we show that BrC, mainly originated from biomass burning in the mid-to high latitudes of the Northern Hemisphere (similar to 60%), can be a strong warming agent in the Arctic region, especially in the summer, with an average radiative forcing of-90 mW m(-2) (similar to 30% relative to black carbon). As climate change is projected to increase the frequency, intensity, and spread of wildfires, we expect BrC to play an increasing role in Arctic warming in the future.
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| 4. |
- Chen, Zhishan, et al.
(författare)
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Fine-mapping analysis including over 254 000 East Asian and European descendants identifies 136 putative colorectal cancer susceptibility genes
- 2024
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Ingår i: Nature Communications. - : Springer Nature. - 2041-1723. ; 15:1
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Tidskriftsartikel (refereegranskat)abstract
- Genome-wide association studies (GWAS) have identified more than 200 common genetic variants independently associated with colorectal cancer (CRC) risk, but the causal variants and target genes are mostly unknown. We sought to fine-map all known CRC risk loci using GWAS data from 100,204 cases and 154,587 controls of East Asian and European ancestry. Our stepwise conditional analyses revealed 238 independent association signals of CRC risk, each with a set of credible causal variants (CCVs), of which 28 signals had a single CCV. Our cis-eQTL/mQTL and colocalization analyses using colorectal tissue-specific transcriptome and methylome data separately from 1299 and 321 individuals, along with functional genomic investigation, uncovered 136 putative CRC susceptibility genes, including 56 genes not previously reported. Analyses of single-cell RNA-seq data from colorectal tissues revealed 17 putative CRC susceptibility genes with distinct expression patterns in specific cell types. Analyses of whole exome sequencing data provided additional support for several target genes identified in this study as CRC susceptibility genes. Enrichment analyses of the 136 genes uncover pathways not previously linked to CRC risk. Our study substantially expanded association signals for CRC and provided additional insight into the biological mechanisms underlying CRC development.
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| 5. |
- Cheng, Shi-Ping, et al.
(författare)
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Haplotype-resolved genome assembly and allele-specific gene expression in cultivated ginger
- 2021
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Ingår i: Horticulture Research. - : Springer Nature. - 2052-7276. ; 8:1
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Tidskriftsartikel (refereegranskat)abstract
- Ginger (Zingiber officinale) is one of the most valued spice plants worldwide; it is prized for its culinary and folk medicinal applications and is therefore of high economic and cultural importance. Here, we present a haplotype-resolved, chromosome-scale assembly for diploid ginger anchored to 11 pseudochromosome pairs with a total length of 3.1 Gb. Remarkable structural variation was identified between haplotypes, and two inversions larger than 15 Mb on chromosome 4 may be associated with ginger infertility. We performed a comprehensive, spatiotemporal, genome-wide analysis of allelic expression patterns, revealing that most alleles are coordinately expressed. The alleles that exhibited the largest differences in expression showed closer proximity to transposable elements, greater coding sequence divergence, more relaxed selection pressure, and more transcription factor binding site differences. We also predicted the transcription factors potentially regulating 6-gingerol biosynthesis. Our allele-aware assembly provides a powerful platform for future functional genomics, molecular breeding, and genome editing in ginger.
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| 6. |
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| 7. |
- Koenig, Julian, et al.
(författare)
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Cortical thickness and resting-state cardiac function across the lifespan : A cross-sectional pooled mega-analysis
- 2021
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Ingår i: Psychophysiology. - : Wiley. - 0048-5772 .- 1469-8986 .- 1540-5958. ; 58:7
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Tidskriftsartikel (refereegranskat)abstract
- Understanding the association between autonomic nervous system [ANS] function and brain morphology across the lifespan provides important insights into neurovisceral mechanisms underlying health and disease. Resting-state ANS activity, indexed by measures of heart rate [HR] and its variability [HRV] has been associated with brain morphology, particularly cortical thickness [CT]. While findings have been mixed regarding the anatomical distribution and direction of the associations, these inconsistencies may be due to sex and age differences in HR/HRV and CT. Previous studies have been limited by small sample sizes, which impede the assessment of sex differences and aging effects on the association between ANS function and CT. To overcome these limitations, 20 groups worldwide contributed data collected under similar protocols of CT assessment and HR/HRV recording to be pooled in a mega-analysis (N = 1,218 (50.5% female), mean age 36.7 years (range: 12–87)). Findings suggest a decline in HRV as well as CT with increasing age. CT, particularly in the orbitofrontal cortex, explained additional variance in HRV, beyond the effects of aging. This pattern of results may suggest that the decline in HRV with increasing age is related to a decline in orbitofrontal CT. These effects were independent of sex and specific to HRV; with no significant association between CT and HR. Greater CT across the adult lifespan may be vital for the maintenance of healthy cardiac regulation via the ANS—or greater cardiac vagal activity as indirectly reflected in HRV may slow brain atrophy. Findings reveal an important association between CT and cardiac parasympathetic activity with implications for healthy aging and longevity that should be studied further in longitudinal research.
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| 8. |
- Qin, Xingna, et al.
(författare)
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Does having vulnerable friends help vulnerable youth? The co-evolution of friendships, victimization, and depressive symptoms in Chinese adolescents social networks
- 2023
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Ingår i: Child Development. - : WILEY. - 0009-3920 .- 1467-8624.
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Tidskriftsartikel (refereegranskat)abstract
- This study examined whether having vulnerable friends helps or hurts victimized and depressed (i.e., vulnerable) adolescents and whether this depends on classroom supportive norms. Students (n = 1461, 46.7% girls, 93.4% Han nationality) were surveyed four times from seventh and eighth grade (M-age = 13 years) in 2015 and 2016 in Central China. Longitudinal social network analyses indicated that having vulnerable friends can both hurt and help vulnerable adolescents. Depressed adolescents with depressed friends increased in victimization over time. Victimized adolescents with victimized friends increased in victimization but decreased in depressive symptoms. These processes were most likely in classrooms with high supportive norms. Having friends and a supportive classroom may hurt vulnerable adolescents social position but help victims emotional development.
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| 9. |
- Qin, Xingna, et al.
(författare)
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Parents on the Sidelines: The Role of Parental Directing in Chinese Adolescents' Friendship Dynamics Related to Academic Achievement, Aggression, and Prosocial Behavior
- 2024
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Ingår i: Journal of Early Adolescence. - : SAGE PUBLICATIONS INC. - 0272-4316 .- 1552-5449.
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Tidskriftsartikel (refereegranskat)abstract
- Adolescents' peer interactions strongly influence their school behavior, raising the question of whether parents can still direct adolescents' friendship choices or whether they are mostly on the sidelines. Chinese cultural values emphasize the importance of having "good" friends, raising questions about adolescents' adherence to parental direction of friendships. This study examined friendship dynamics among seventh and eighth graders in central China (n = 1,454, 46.7% girls), focusing on achievement, aggression, and prosocial behavior. Social network analysis revealed that Chinese students tended to select friends who were more similar to them in achievement, aggression, and prosocial behavior. Interestingly, they avoided aggressive peers but were attracted to high-achieving and prosocial peers. Despite parental emphasis on friendship quality, the study found no parental direction in adolescent friendship selection. These findings underscore the central role of peer characteristics in friendship dynamics, while highlighting the limited impact of parental directing on Chinese adolescents' friendship selection.
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| 10. |
- Wang, Wenyu, et al.
(författare)
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Nanosecond-Pulsed Passively Q-Switched Fiber Laser by Using Photothermal Dynamics in a Dielectric Microcavity
- 2023
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Ingår i: ACS Photonics. - 2330-4022. ; 10:10, s. 3656-3663
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Tidskriftsartikel (refereegranskat)abstract
- Thermal nonlinear effects have been extensively studied in whispering-gallery optical microcavities. Photothermal effect originating from high light power buildup in the microcavities plays an important role in various applications, such as thermal tuning, thermal detection, and thermal imaging; however, they are often limited by the slow photothermal response time. Here, we demonstrate a nanosecond passively Q-switched fiber laser via photothermal dynamics in a dielectric microcavity and reveal the nanosecond-time-scale photothermal response in the microcavity. The passive Q-switched fiber laser is realized by a novel Q-switching mechanism, which is derived from the dynamic photothermal effect in an ultrahigh-quality silica microcavity. Q-switched pulses with a duration of 25.8 ns and a repetition rate of 653 kHz are achieved, and it indicates that the photothermal response time is far shorter than a microsecond, which is much faster than conventional thermo-optic switching based on dielectric photonic structures. We also provide rigorous theoretical analyses on the photothermal effect and generated Q-switched pulses, which agree well with the experimental results. Our work demonstrates a counterintuitive feature of the photothermal effect in a dielectric microcavity that paves the way to ultrafast thermo-optic switching and pulsed lasing.
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