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result(s) for
"Chen, Suyang"
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Full waveform inversion with smoothing of dilated convolutions
2024
Full waveform inversion (FWI) is a method for building subsurface models with high resolution by optimizing a data-fitting problem. However, it is still a challenge to apply the FWI method to complicated subsurface models, because FWI is a highly ill-fitting inversion problem. When the simulated data differ from the observed data by more than half a cycle, FWI tends to suffer from the cycle-skipping problems and get trapped in a local minimum. To help the inversion to converge to the accurate subsurface model, we typically build a reasonable initial model or use low-frequency data to start our inversion. Here, we developed a novel technique called smoothing of dilated convolutions inversion (SDCI) to generate low-frequency components from seismic data to recover low-wavenumber components of the subsurface. In the theory part, we first present the objective function of the SDCI method and then derive the gradient of the objective function relative to the velocity using the adjoint-state approach. We then apply the method to a set of simulated data from the Marmousi model. The SDCI method can reasonably estimate the subsurface model even if the simulated seismic record does not contain information below 5 Hz. The numerical examples prove the effectiveness and feasibility of the proposed method. From the SDCI results, the FWI method recovers the velocity with higher accuracy and resolution.
Journal Article
Resolution Sensitivity of the GRIST Nonhydrostatic Model From 120 to 5 km (3.75 km) During the DYAMOND Winter
2022
We investigated the resolution sensitivity of the Global‐to‐Regional Integrated forecast SysTem global nonhydrostatic model characterized by explicit dynamics–microphysics coupling using varying uniform resolutions (120, 60, 30, 15, and 5 km). The experiments followed the DYnamics of the Atmospheric general circulation Modeled On Non‐hydrostatic Domains (DYAMOND) winter protocol, which covers a 40‐day integration. These simulations did not activate parameterized convection. One 120 km test with parameterized convection was performed as a coarse‐resolution reference. Other model configurations for different simulations were kept as consistent as possible. Our results showed that the model gradually improved its representation of the fine‐scale features as the resolution increased. The 5 km simulation was overall close to a 3.75 km simulation during the first 12 days of the DYAMOND winter. With respect to the mean climate, the 5 km simulation had a more realistic rainfall distribution than the lower resolution explicit convection simulations. Cloud water and the related physical fields (e.g., shortwave cloud radiative forcing) had a large resolution sensitivity. The tropical rainfall frequency–intensity spectra became more realistic in the 5 km explicit convection simulation, but the 120 km run with parameterized convection showed a more realistic mean climate. As the resolution increases, the mean bulk effect of finely resolved model convection gradually converges to that of parameterized convection. The mean climate of this storm‐resolving model has slightly higher rainfall biases than a parameterized convection coarse‐resolution model, highlighting the importance of balancing resolved‐ and under‐resolved model convection for developing a unified multiscale global model. Key Points The resolution sensitivity of the Global‐to‐Regional Integrated forecast SysTem nonhydrostatic model with an explicit‐convection setup is assessed from O (100 km) to O (km) scales The model gradually improves its representation of fine‐scale fluid structures with increasing resolution The interaction between cumulus ensemble and large‐scale flow of a Global storm‐resolving model overall converges to that of a parameterized convection model
Journal Article
Photobacterium damselae subsp. damselae in mariculture
2022
Photobacterium damselae subsp. damselae affects many marine animals; it is currently considered an emerging pathogen because of its wide geographic distribution as well as its negative impact on aquaculture organisms, which continues to increase over the years. Due to numerous epidemics caused by the ever-increasing presence of P. damselae subsp. damselae in aquatic environments, substantial research has been carried out to elucidate its virulence mechanisms and develop rapid detection techniques, though effective prevention and control strategies for this pathogen are almost non-existent. In this review, we have expanded the understanding of the infective potential of P. damselae subsp. damselae, and describe its ability to cause disease in several animal phyla. In addition, we described the different virulence factors reported to date and presented the different types of detection methods, including molecular ones that were used to achieve precise and specific identification of P. damselae subsp. damselae. Preventive measures and useful therapeutic strategies to counter outbreaks of P. damselae subsp. damselae were also discussed. This paper aims to summarize the current state of knowledge on P. damselae subsp. damselae, in particular on pathogenesis, known virulence factors, and different diagnostics methods. In conclusion, this review suggests that future research will be required with a focus on prevention and control strategies for this pathogen that causes heavy losses in the aquaculture industry.
Journal Article
Higher rates of sex evolve during adaptation to more complex environments
by
Kim, Yun Seong
,
Agrawal, Aneil F.
,
Ho, Eddie Ka Ho
in
Acclimatization
,
Adaptation, Physiological
,
Animals
2017
A leading hypothesis for the evolutionary maintenance of sexual reproduction proposes that sex is advantageous because it facilitates adaptation. Changes in the environment stimulate adaptation but not all changes are equivalent; a change may occur along one or multiple environmental dimensions. In two evolution experiments with the facultatively sexual rotifer Brachionus calyciflorus, we test how environmental complexity affects the evolution of sex by adapting replicate populations to various environments that differ from the original along one, two, or three environmental dimensions. Three different estimates of fitness (growth, lifetime reproduction, and population density) confirmed that populations adapted to their new environment. Growth measures revealed an intriguing cost of complex adaptations: populations that adapted to more complex environments lost greater amounts of fitness in the original environment. Furthermore, both experiments showed that B. calyciflorus became more sexual when adapting to a greater number of environmental dimensions. Common garden experiments confirmed that observed changes in sex were heritable. As environments in nature are inherently complex these findings help explain why sex is maintained in natural populations.
Journal Article
Identification of Ebola virus microRNAs and their putative pathological function
by
LIANG HongWei ZHOU Zhen ZHANG SuYang ZEN Ke CHEN Xi ZHANG ChenYu
in
Biomarkers - metabolism
,
Biomedical and Life Sciences
,
Computational Biology
2014
Ebola virus (EBOV), a member of the filovirus family, is an enveloped negative-sense RNA virus that causes lethal infections in humans and primates. Recently, more than 1000 people have been killed by the Ebola virus disease in Africa, yet no specific treatment or diagnostic tests for EBOV are available. In this study, we identified two putative viral microRNA precursors (pre-miRNAs) and three putative mature microRNAs (miRNAs) derived from the EBOV genome. The production of the EBOV miRNAs was further validated in HEK293T cells transfected with a pcDNA6.2-GW/EmGFP-EBOV-pre-miRNA plasmid, indicating that EBOV miRNAs can be produced through the cellular miRNA processing machinery. We also predicted the potential target genes of these EBOV miRNAs and their possible biological functions. Overall, this study reports for the first time that EBOV may produce miRNAs, which could serve as non-invasive biomarkers for the diagnosis and prognosis of EBOV infection and as therapeutic targets for Ebola viral infection treatment.
Journal Article
Research on the Method of Counting Wheat Ears via Video Based on Improved YOLOv7 and DeepSort
2023
The number of wheat ears in a field is an important parameter for accurately estimating wheat yield. In a large field, however, it is hard to conduct an automated and accurate counting of wheat ears because of their density and mutual overlay. Unlike the majority of the studies conducted on deep learning-based methods that usually count wheat ears via a collection of static images, this paper proposes a counting method based directly on a UAV video multi-objective tracking method and better counting efficiency results. Firstly, we optimized the YOLOv7 model because the basis of the multi-target tracking algorithm is target detection. Simultaneously, the omni-dimensional dynamic convolution (ODConv) design was applied to the network structure to significantly improve the feature-extraction capability of the model, strengthen the interaction between dimensions, and improve the performance of the detection model. Furthermore, the global context network (GCNet) and coordinate attention (CA) mechanisms were adopted in the backbone network to implement the effective utilization of wheat features. Secondly, this study improved the DeepSort multi-objective tracking algorithm by replacing the DeepSort feature extractor with a modified ResNet network structure to achieve a better extraction of wheat-ear-feature information, and the constructed dataset was then trained for the re-identification of wheat ears. Finally, the improved DeepSort algorithm was used to calculate the number of different IDs that appear in the video, and an improved method based on YOLOv7 and DeepSort algorithms was then created to calculate the number of wheat ears in large fields. The results show that the mean average precision (mAP) of the improved YOLOv7 detection model is 2.5% higher than that of the original YOLOv7 model, reaching 96.2%. The multiple-object tracking accuracy (MOTA) of the improved YOLOv7–DeepSort model reached 75.4%. By verifying the number of wheat ears captured by the UAV method, it can be determined that the average value of an L1 loss is 4.2 and the accuracy rate is between 95 and 98%; thus, detection and tracking methods can be effectively performed, and the efficient counting of wheat ears can be achieved according to the ID value in the video.
Journal Article
Atomic-scale observation of non-classical nucleation-mediated phase transformation in a titanium alloy
2022
Two-phase titanium-based alloys are widely used in aerospace and biomedical applications, and they are obtained through phase transformations between a low-temperature hexagonal closed-packed α-phase and a high-temperature body-centred cubic β-phase. Understanding how a new phase evolves from its parent phase is critical to controlling the transforming microstructures and thus material properties. Here, we report time-resolved experimental evidence, at sub-ångström resolution, of a non-classically nucleated metastable phase that bridges the α-phase and the β-phase, in a technologically important titanium–molybdenum alloy. We observed a nanosized and chemically ordered superstructure in the α-phase matrix; its composition, chemical order and crystal structure are all found to be different from both the parent and the product phases, but instigating a vanishingly low energy barrier for the transformation into the β-phase. This latter phase transition can proceed instantly via vibrational switching when the molybdenum concentration in the superstructure exceeds a critical value. We expect that such a non-classical phase evolution mechanism is much more common than previously believed for solid-state transformations.
A full kinetic pathway of a non-classical nucleation-induced phase transformation through metastable states is elucidated at sub-ångström resolution in a technologically important titanium alloy.
Journal Article
Long noncoding RNA SAM promotes myoblast proliferation through stabilizing Sugt1 and facilitating kinetochore assembly
2020
The functional study of lncRNAs in skeletal muscle satellite cells (SCs) remains at the infancy stage. Here we identify
SAM
(Sugt1 asssociated muscle) lncRNA that is enriched in the proliferating myoblasts. Global deletion of
SAM
has no overt effect on mice but impairs adult muscle regeneration following acute damage; it also exacerbates the chronic injury-induced dystrophic phenotype in mdx mice. Consistently, inducible deletion of
SAM
in SCs leads to deficiency in muscle regeneration. Further examination reveals that
SAM
loss results in a cell-autonomous defect in the proliferative expansion of myoblasts. Mechanistically, we find
SAM
interacts and stabilizes Sugt1, a co-chaperon protein key to kinetochore assembly during cell division. Loss of
SAM
or Sugt1 both disrupts kinetochore assembly in mitotic cells due to the mislocalization of two components: Dsn1 and Hec1. Altogether, our findings identify
SAM
as a regulator of SC proliferation through facilitating Sugt1 mediated kinetochore assembly during cell division.
Long noncoding RNA
SAM
(Sugt1 associated muscle) is upregulated in the proliferating myoblast cells. Here the authors investigate
SAM
knockout mice and suggest that
SAM
binds and stabilizes Sugt1, a co-chaperone protein that regulates kinetochore assembly.
Journal Article
M2 macrophages independently promote beige adipogenesis via blocking adipocyte Ets1
Adipose tissue macrophages can promote beige adipose thermogenesis by altering local sympathetic activity. Here, we perform sympathectomy in mice and further eradicate subcutaneous adipose macrophages and discover that these macrophages have a direct beige-promoting function that is independent of sympathetic system. We further identify adipocyte Ets1 as a vital mediator in this process. The anti-inflammatory M2 macrophages suppress Ets1 expression in adipocytes, transcriptionally activate mitochondrial biogenesis, as well as suppress mitochondrial clearance, thereby increasing the mitochondrial numbers and promoting the beiging process. Male adipocyte Ets1 knock-in mice are completely cold intolerant, whereas male mice lacking Ets1 in adipocytes show enhanced energy expenditure and are resistant to metabolic disorders caused by high-fat-diet. Our findings elucidate a direct communication between M2 macrophages and adipocytes, and uncover a function for Ets1 in responding to macrophages and negatively governing mitochondrial content and beige adipocyte formation.
Adipose beiging is a positive biological change, which is often thought to be primarily sympathetically induced. Here, the authors show that M2 macrophages can independently promote beige adipogenesis, further revealing the adipocyte transcription factor Ets1 as a negative regulator of this process.
Journal Article
miR-143 and miR-145 synergistically regulate ERBB3 to suppress cell proliferation and invasion in breast cancer
2014
Introduction
ERBB3, one of the four members of the ErbB family of receptor tyrosine kinases, plays an important role in breast cancer etiology and progression. In the present study, we aimed to identify novel miRNAs that can potentially target ERBB3 and their biological functions.
Method
The expression levels of miR-143/145 and target mRNA were examined by relative quantification RT-PCR, and the expression levels of target protein were detected by Western blot. We used bioinformatic analyses to search for miRNAs that can potentially target ERBB3. Luciferase reporter plasmids were constructed to confirm direct targeting. Furthermore, the biological consequences of the targeting of ERBB3 by miR-143/145 were examined by cell proliferation and invasion assays in vitro and by the mouse xenograft tumor model in vivo.
Results
We identified an inverse correlation between miR-143/145 levels and ERBB3 protein levels, but not between miR-143/145 levels and ERBB3 mRNA levels, in breast cancer tissue samples. We identified specific targeting sites for miR-143 and miR-145 (miR-143/145) in the 3’-untranslated region (3’-UTR) of the ERBB3 gene and regulate ERBB3 expression. We demonstrated that the repression of ERBB3 by miR-143/145 suppressed the proliferation and invasion of breast cancer cells, and that miR-143/145 showed an anti-tumor effect by negatively regulating ERBB3 in the xenograft mouse model. Interestingly, miR-143 and miR-145 showed a cooperative repression of ERBB3 expression and cell proliferation and invasion in breast cancer cells, such that the effects of the two miRNAs were greater than with either miR-143 or miR-145 alone.
Conclusion
Taken together, our findings provide the first clues regarding the role of the miR-143/145 cluster as a tumor suppressor in breast cancer through the inhibition of ERBB3 translation. These results also support the idea that different miRNAs in a cluster can synergistically repress a given target mRNA.
Journal Article