In this paper, we propose a supervised learning strategy for the fluid motion estimation problem (i.e., extracting the velocity fields from particle images). The purpose of this work is to design a ...convolutional neural network (CNN) for estimating dense motion field for particle image velocimetry (PIV), which allows to improve the computational efficiency without reducing the accuracy. First, the network model is developed based on FlowNetS, which is recently proposed for end-to-end optical flow estimation in the computer vision community. The input of the network is a particle image pair and the output is a velocity field with displacement vectors at every pixel. Second, a synthetic dataset of fluid flow images is generated to train the CNN model. To our knowledge, this is the first time a CNN has been used as a global motion estimator for particle image velocimetry. Experimental evaluations indicate that the trained CNN model can provide satisfactory results in both artificial and laboratory PIV images. The proposed estimator is also applied to the experiment of turbulent boundary layer. In addition, the computational efficiency of the CNN estimator is much superior to those of the traditional cross-correction and optical flow methods.
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EMUNI, FIS, FZAB, GEOZS, GIS, IJS, IMTLJ, KILJ, KISLJ, MFDPS, NLZOH, NUK, OBVAL, OILJ, PNG, SAZU, SBCE, SBJE, SBMB, SBNM, UKNU, UL, UM, UPUK, VKSCE, ZAGLJ
This study investigated the dependence of the early tropical cyclone (TC) weakening rate in response to an imposed moderate environmental vertical wind shear (VWS) on the warm‐core strength and ...height of the TC vortex using idealized numerical simulations. Results show that the weakening of the warm core by upper‐level ventilation is the primary factor leading to the early TC weakening in response to an imposed environmental VWS. The upper‐level ventilation is dominated by eddy radial advection of the warm‐core air. The TC weakening rate is roughly proportional to the warm‐core strength and height of the initial TC vortex. The boundary‐layer ventilation shows no relationship with the early weakening rate of the TC in response to an imposed moderate VWS. The findings suggest that some previous diverse results regarding the TC weakening in environmental VWS could be partly due to the different warm‐core strengths and heights of the initial TC vortex.
Plain Language Summary
The warm core is a basic structural feature of a tropical cyclone (TC), and TC intensity is closely related to the warm‐core strength and height. This study investigated the dependence of the initial TC weakening rate in response to an imposed moderate environmental vertical wind shear (VWS) on the strength and height of the TC vortex during the TC intensifying period using idealized numerical simulations. It is found that the weakening of the warm core is the primary factor leading to the early weakening of the TC, and the TC weakening rate is roughly proportional to the warm‐core strength and height of the TC vortex. It is also found that the boundary‐layer ventilation associated with VWS‐induced convective downdrafts show no relationship with the early weakening rate of the TC in response to an imposed moderate VWS. The findings of this study can help explain why some TCs can continuously develop under the influence of moderate environmental VWS while some others cannot, which are partly due to the different warm‐core strengths and heights of the initial TC vortex.
Key Points
The tropical cyclone (TC) weakening rate in response to an imposed moderate environmental vertical wind shear (VWS) is proportional to the strength and height of the TC warm core
The warm‐core weakening induced by upper‐level ventilation is the primary factor to the early TC weakening induced by the imposed VWS
The boundary‐layer ventilation shows no relationship with the early weakening rate of the TC in response to the imposed moderate VWS
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FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SBCE, SBMB, UL, UM, UPUK
Previous studies have investigated how the environmental vertical wind shear (VWS) may trigger the asymmetric structure in an initially axisymmetric tropical cyclone (TC) vortex and how TC intensity ...changes in response. In this study, the possible effect of the initial vortex asymmetric structure on the TC intensity change in response to an imposed environmental VWS is investigated based on idealized full‐physics model simulations. Results show that the effect of the asymmetric structure in the initial TC vortex can either enhance or suppress the initial weakening of the TC in response to the imposed environmental VWS. When the initial asymmetric structure is in phase of the VWS‐induced asymmetric structure, the TC weakening will be enhanced and vice versa. Our finding calls for realistic representation of initial TC asymmetric structure in numerical weather prediction models and observations to better resolve the asymmetric structure in TCs.
Plain Language Summary
Although a strong tropical cyclone (TC) is often treated as an axisymmetric vortex in most theoretical studies, asymmetric structure always exists in a TC in nature, such as that generated by the environmental vertical wind shear (VWS). However, it is unclear whether and how the asymmetric structure in the initial TC vortex may affect the TC intensity change in response to an imposed environmental VWS. This has been addressed in this study by conducting idealized high‐resolution numerical simulations. Results show that the asymmetric structure in the initial TC vortex can either enhance or suppress the initial weakening of the TC in response to an imposed environmental VWS depending on how the initial asymmetry is aligned with the asymmetry induced by the VWS. If they are in phase, the TC weakening would be enhanced and vice versa. Our finding highlights the importance of realistically representing the asymmetric structure in the initial TC vortex in numerical weather prediction models for TC forecasts and also the need to better resolve the TC asymmetric structure in observations.
Key Points
The initial asymmetric structure in a tropical cyclone (TC) vortex can either enhance or suppress the TC weakening induced by an imposed environmental vertical wind shear (VWS)
If the initial asymmetric structure is in phase with the VWS‐induced asymmetric structure, the TC weakening would be enhanced and vice versa
The TC asymmetric structure should be better observed in real time and realistically represented in numerical weather prediction models
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FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SBCE, SBMB, UL, UM, UPUK
Chenopodium quinoa Willd., a halophytic crop, shows great variability among different genotypes in response to salt. To investigate the salinity tolerance mechanisms, five contrasting quinoa ...cultivars belonging to highland ecotype were compared for their seed germination (under 0, 100 and 400 mM NaCl) and seedling's responses under five salinity levels (0, 100, 200, 300 and 400 mM NaCl).
Substantial variations were found in plant size (biomass) and overall salinity tolerance (plant biomass in salt treatment as % of control) among the different quinoa cultivars. Plant salinity tolerance was negatively associated with plant size, especially at lower salinity levels (< 300 mM NaCl), but salt tolerance between seed germination and seedling growth was not closely correlated. Except for shoot/root ratio, all measured plant traits responded to salt in a genotype-specific way. Salt stress resulted in decreased plant height, leaf area, root length, and root/shoot ratio in each cultivar. With increasing salinity levels, leaf superoxide dismutase (SOD) activity and lipid peroxidation generally increased, but catalase (CAT) and peroxidase (POD) activities showed non-linear patterns. Organic solutes (soluble sugar, proline and protein) accumulated in leaves, whereas inorganic ion (Na
and K
) increased but K
/Na
decreased in both leaves and roots. Across different salinity levels and cultivars, without close relationships with antioxidant enzyme activities (SOD, POD, or CAT), salinity tolerance was significantly negatively correlated with organic solute and malondialdehyde contents in leaves and inorganic ion contents in leaves or roots (except for root K
content), but positively correlated with K
/Na
ratio in leaves or roots.
Our results indicate that leaf osmoregulation, K
retention, Na
exclusion, and ion homeostasis are the main physiological mechanisms conferring salinity tolerance of these cultivars, rather than the regulations of leaf antioxidative ability. As an index of salinity tolerance, K
/Na
ratio in leaves or roots can be used for the selective breeding of highland quinoa cultivars.
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DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Heat stress induced by continuous high ambient temperatures or strenuous exercise in humans and animals leads to intestinal epithelial damage through the induction of intracellular stress response. ...However, the precise mechanisms involved in the regulation of intestinal epithelial cell injury, especially intestinal stem cells (ISCs), remain unclear. Thereby, in vitro a confluent monolayer of IPEC‐J2 cells was exposed to the high temperatures (39, 40, and 41°C), the IPEC‐J2 cell proliferation, apoptosis, differentiation, and barrier were determined, as well as the expression of GRP78, which is a marker protein of endoplasmic reticulum stress (ERS). The Wnt/β‐catenin pathway‐mediated regenerative response was validated using R‐spondin 1 (Rspo1). And ex‐vivo, three‐dimensional cultured enteroids were developed from piglet jejunal crypt and employed to assess the ISC activity under heat exposure. The results showed that exposure to 41°C for 72 hr, rather than 39°C and 40°C, decreased IPEC‐J2 cell viability, inhibited cell proliferation and differentiation, induced ERS and cell apoptosis, damaged barrier function and restricted the Wnt/β‐catenin pathway. Nevertheless, Wnt/β‐catenin reactivation via Rspo1 protects the intestinal epithelium from heat exposure‐induced injury. Furthermore, exposure to 41°C for 24 hr reduced ISC activity, stimulated crypt‐cell apoptosis, upregulated the expression of GRP78 and caspase‐3, and downregulated the expression of β‐catenin, Lgr5, Bmi1, Ki67, KRT20, ZO‐1, occludin, and claudin‐1. Taken together, we conclude that heat exposure induces ERS and downregulates the Wnt/β‐catenin signaling pathway to disrupt epithelial integrity by inhibiting the intestinal epithelial cell proliferation and stem cell expansion.
Heat‐exposure induced endoplasmic reticulum stress blocks the β‐catenin pathway in the intestinal stem cells, resulting in inhibition of the proliferation and differentiation and promotion of cell apoptosis of porcine intestinal epithelial cells. These processes lead to intestinal function impairment, including damage to the intestinal epithelial integrity.
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BFBNIB, FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SBCE, SBMB, UL, UM, UPUK
Recently a technique based on the interaction between adhesion proteins extracted from Streptococcus pyogenes, known as SpyRing, has been widely used to improve the thermal resilience of enzymes, the ...assembly of biostructures, cancer cell recognition and other fields. It was believed that the covalent cyclization of protein skeleton caused by SpyRing reduces the conformational entropy of biological structure and improves its rigidity, thus improving the thermal resilience of the target enzyme. However, the effects of SpyTag/ SpyCatcher interaction with this enzyme are poorly understood, and their regulation of enzyme properties remains unclear. Here, for simplicity, we took the single domain enzyme lichenase from Bacillus subtilis 168 as an example, studied the interface interactions in the SpyRing by molecular dynamics simulations, and examined the effects of the changes of electrostatic interaction and van der Waals interaction on the thermal resilience of target enzyme. The simulations showed that the interface between SpyTag/SpyCatcher and the target enzyme is different from that found by geometric matching method and highlighted key mutations at the interface that might have effect on the thermal resilience of the enzyme. Our calculations highlighted interfacial interactions between enzyme and SpyTag/SpyCatcher, which might be useful in rational designs of the SpyRing.
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DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
The recent deployment of ESA's Sentinel operational satellites has established a new paradigm for remote sensing applications. In this context, Sentinel-1 radar images have made it possible to ...retrieve surface soil moisture with a high spatial and temporal resolution. This paper presents two methodologies for the retrieval of soil moisture from remotely-sensed SAR images, with a spatial resolution of 100 m. These algorithms are based on the interpretation of Sentinel-1 data recorded in the VV polarization, which is combined with Sentinel-2 optical data for the analysis of vegetation effects over a site in Urgell (Catalunya, Spain). The first algorithm has already been applied to observations in West Africa by Zribi et al., 2008, using low spatial resolution ERS scatterometer data, and is based on change detection approach. In the present study, this approach is applied to Sentinel-1 data and optimizes the inversion process by taking advantage of the high repeat frequency of the Sentinel observations. The second algorithm relies on a new method, based on the difference between backscattered Sentinel-1 radar signals observed on two consecutive days, expressed as a function of NDVI optical index. Both methods are applied to almost 1.5 years of satellite data (July 2015-November 2016), and are validated using field data acquired at a study site. This leads to an RMS error in volumetric moisture of approximately 0.087 m³/m³ and 0.059 m³/m³ for the first and second methods, respectively. No site calibrations are needed with these techniques, and they can be applied to any vegetation-covered area for which time series of SAR data have been recorded.
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IZUM, KILJ, NUK, PILJ, PNG, SAZU, UL, UM, UPUK
Rheumatoid arthritis (RA) is an autoimmune disease that exhibits a high degree of heterogeneity, marked by unpredictable disease flares and significant variations in the response to available ...treatments. The lack of optimal stratification for RA patients may be a contributing factor to the poor efficacy of current treatment options. The objective of this study is to elucidate the molecular characteristics of RA through the utilization of mitochondrial genes and subsequently construct and authenticate a diagnostic framework for RA. Mitochondrial proteins were obtained from the MitoCarta database, and the R package limma was employed to filter for differentially expressed mitochondrial genes (MDEGs). Metascape was utilized to perform enrichment analysis, followed by an unsupervised clustering algorithm using the ConsensuClusterPlus package to identify distinct subtypes based on MDEGs. The immune microenvironment, biological pathways, and drug response were further explored in these subtypes. Finally, a multi-biomarker-based diagnostic model was constructed using machine learning algorithms. Utilizing 88 MDEGs present in transcript profiles, it was possible to classify RA patients into three distinct subtypes, each characterized by unique molecular and cellular signatures. Subtype A exhibited a marked activation of inflammatory cells and pathways, while subtype C was characterized by the presence of specific innate lymphocytes. Inflammatory and immune cells in subtype B displayed a more modest level of activation (Wilcoxon test P < 0.05). Notably, subtype C demonstrated a stronger correlation with a superior response to biologics such as infliximab, anti-TNF, rituximab, and methotrexate/abatacept (P = 0.001) using the fisher test. Furthermore, the mitochondrial diagnosis SVM model demonstrated a high degree of discriminatory ability in distinguishing RA in both training (AUC = 100%) and validation sets (AUC = 80.1%). This study presents a pioneering analysis of mitochondrial modifications in RA, offering a novel framework for patient stratification and potentially enhancing therapeutic decision-making.
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IZUM, KILJ, NUK, PILJ, PNG, SAZU, UL, UM, UPUK
Hypoxia in vivo induces oligozoospermia, azoospermia, and degeneration of the germinal epithelium, but the underlying molecular mechanism of this induction is not fully clarified. The aim of this ...study was to investigate the role of the death receptor pathway and the mitochondrial pathway in hypoxia‐induced apoptosis of mouse GC‐2spd (GC‐2) cells and the relationship between HIF‐1α and apoptosis of GC‐2 cells induced by hypoxia. GC‐2 cells were subjected to 1% oxygen for 48 hr. Apoptosis was detected by flow cytometry, TUNEL staining, LDH, caspase‐3/8/9 in the absence and presence of HIF‐1α siRNA. The protein levels of apoptosis‐related markers were determined by Western blot in the presence and absence of HIF‐1α siRNA. Mitochondrial transmembrane potential change was observed by in situ JC‐1 staining. Cell viability was assessed upon treatment of caspase‐8 and 9 inhibitors. The results indicated that hypoxia at 1% oxygen for 48 hr induced apoptosis of GC‐2 cells. A prolonged exposure of GC‐2 cells to hypoxic conditions caused downregulation of c‐FLIP, DcR2 and Bcl‐2 and upregulation of DR5, TRAIL, Fas, p53, and Bax, with an overproduction of caspase‐3/8/9. Moreover, hypoxia at this level had an effect on mitochondrial depolarization. In addition, specific inhibitors of caspase‐8/9 partially suppressed hypoxia‐induced GC‐2 cell apoptosis, and the anti‐apoptotic effects of the caspase inhibitors were additive. Of note, HIF‐1α knockdown attenuated hypoxia and induced apoptosis of GC‐2 cells. In conclusion, our data suggest that the death receptor pathway and mitochondrial pathway, which are likely mediated by HIF‐1α, contribute to hypoxia‐induced GC‐2 cell apoptosis.
It has been known that hypoxia induces male infertility with the underlying mechanisms to be clarified. This study determined that the death receptor pathway and mitochondrial pathway, which are likely mediated by HIF‐1α, contribute to hypoxia‐induced apoptosis of mouse pachytene spermatocytes.
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BFBNIB, FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SBCE, SBMB, UL, UM, UPUK
After flower pollination, a programmed process called abscission occurs in which unwanted floral organs are actively shed from the main plant body. We found that a member of the DOF (for DNA binding ...with one finger) transcription factor family, Arabidopsis (Arabidopsis thaliana) DOF4.7, was expressed robustly in the abscission zone. The Arabidopsis 35S::AtDOF4.7 lines with constitutive expression of AtDOF4.7 exhibited an ethylene-independent floral organ abscission deficiency. In these lines, anatomical analyses showed that the formation of the abscission zone was normal. However, dissolution of the middle lamella failed to separate between the cell walls. AtDOF4.7 was identified as a nucleus-localized transcription factor. This protein had both in vitro and in vivo binding activity to typical DOF cis-elements in the promoter of an abscission-related polygalacturonase (PG) gene, PGAZAT. Overexpression of AtDOF4.7 resulted in down-regulation of PGAZAT. AtDOF4.7 interacted with another abscission-related transcription factor, Arabidopsis ZINC FINGER PROTEIN2. Taken together, our results suggest that AtDOF4.7 participates in the control of abscission as part of the transcription complex that directly regulates the expression of cell wall hydrolysis enzymes.
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BFBNIB, NMLJ, NUK, PNG, SAZU, UL, UM, UPUK
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