A novel pathway-based distance score enhances assessment of disease heterogeneity in gene expression

Distance-based unsupervised clustering of gene expression data is commonly used to identify heterogeneity in biologic samples. However, high noise levels in gene expression data and the relatively high correlation between genes are often encountered, so traditional distances such as Euclidean distance may not be effective at discriminating the biological differences between samples. In this study, we developed a novel computational method to assess the biological differences based on pathways by assuming that ontologically defined biological pathways in biologically similar samples have similar behavior. Application of this distance score results in more accurate, robust, and biologically meaningful clustering results in both simulated data and real data when compared to traditional methods. It also has comparable or better performance compared to Pathifier

The Right to Stay Put: City Garden Montessori School and Neighborhood Change

This report presents findings from the Listening Project. A collaboration among St. Louis’ Forest Park Southeast Neighborhood Association, the Brown School of Social Work, and the Sam Fox School of Design and Visual Arts at Washington University, the project engaged underrepresented voices in the Forest Park Southeast, Botanical Heights, Tiffany, and Shaw neighborhoods neighborhood to identify priorities for community improvement

Monocular catadioptric panoramic depth estimation via improved end-to-end neural network model

In this paper, we propose a monocular catadioptric panoramic depth estimation algorithm based on an improved end-to-end neural network model. First, we use an enhanced concentric circle approximation unfolding algorithm to unfold the panoramic images captured by the catadioptric panoramic camera and then extract the effective regions. In addition, the integration of the Non-local attention mechanism is exploited to improve image understanding. Finally, a depth smoothness loss strategy is implemented to further enhance the reliability and precision of the estimated depths. Experimental results confirm that this refined algorithm is capable of providing highly accurate estimates of object depth

When Web 3.0 Meets Reality: A Hyperdimensional Fractal Polytope P2P Ecosystems

Web 3.0 opens the world of new existence of the crypto-network-entity, which is independently defined by the public key pairs for entities and the connection to the Web 3.0 cyberspace. In this paper, we first discover a spacetime coordinate system based on fractal polytope in any dimensions with discrete time offered by blockchain and consensus. Second, the novel network entities and functions are defined to make use of hyperdimensional deterministic switching and routing protocols and blockchain-enabled mutual authentication. In addition to spacetime network architecture, we also define a multi-tier identity scheme which extends the native Web 3.0 crypto-network-entity to outer cyber and physical world, offering legal-compliant anonymity and linkability to all derived identifiers of entities. In this way, we unify the holistic Web 3.0 network based on persistent spacetime and its entity extension to our cyber and physical world

Effect of dynamic threshold pressure gradient on production performance in water-bearing tight gas reservoir

AbstractWater content and distribution have important impacts on gas production in water-bearing tight gas reservoirs. However, due to the structural and chemical heterogeneity of tight reservoirs, the water phase exists in various states, which has complicated the analyses of the effects of water characteristics on tight gas production performance. In this work, the water phase is distinguished from immobile to mobile states and the term of constrained water saturation is proposed. It is established that water can flow when the driving pressure difference is larger than the critical driving pressure difference. A new theoretical model of threshold pressure gradient is derived to incorporate the influences of constrained water saturation and permeability. On this basis, a new prediction model considering the varied threshold pressure gradient is obtained, and the result indicates that when threshold pressure gradient is constant, the real gas production capacity of the reservoir will be weakened. Meanwhile, a dynamic supply boundary model is presented, which indicates that the permeability has a strong influence on the dynamic supply boundary, whereas the impact of initial water saturation is negligible. These findings provide insights into the understanding of the effects of water state and saturation on the threshold pressure gradient and gas production rate in tight gas reservoirs. Furthermore, this study provides useful guidance on the prediction of field-scale gas production.Cited as: Zhu, W., Liu, Y., Shi, Y., Zou, G., Zhang, Q., Kong, D. Effect of dynamic threshold pressure gradient on production performance in water-bearing tight gas reservoir. Advances in Geo-Energy Research, 2022, 6(4): 286-295. https://doi.org/10.46690/ager.2022.04.0

Green finance strategies for mitigating GHG emissions in China: Public spending as a new determinant of green economic development

In order to lessen China’s carbon footprint, the government has turned to environmentally friendly financing. A reduction in CO2 has been reported in some Chinese provinces where green finance has been developed. Numerous regions in China from 2010 to 2020 are selected for this study. Based on a Dynamic Seemingly Uncorrelated, fully modified ordinary least squares and dynamic ordinary least squares regressions model, empirical research is performed with per capita growth in the economy, public spending, and the relationship between economic growth, human resources, and industrial arrangement as core variables to test the influence of green financing on CO2 emission in Chinese provinces. According to the findings, green financing speeds up the reduction of carbon emissions. Moreover, the outcomes present that industrial structure, economic growth per capita, and trade openness increase carbon emissions. Likewise, public expenditures and human capital are significantly contributing to emissions reduction. The findings show that sustainable green environment can only be achieved by boosting the performance of green finance and increasing the level of green finance supported by the Chinese economy. Last but not least, policymakers should promote public health and education spending to fully engage in the protection of the environmental efforts to encourage green consumption while minimizing the structural problems resulting from economic activity

Microbial diversity and physicochemical properties in farmland soils amended by effective microorganisms and fulvic acid for cropping Asian ginseng

Demand for products made from the dry mass of Asian ginseng (Panax ginseng) is growing, but harvest is limited by fungal disease infection when ginseng is replanted in the same field. Rotated cropping with maize can cope with the replant limit, but it may take decades. We aimed to amend post-maize-cropping farmland soils for cultivating Asian ginseng, using effective microorganisms EMs and fulvic acid (FA) additives and detecting and comparing their effects on soil microbial diversity and physiochemical properties. Amendments promoted seedling survival and depressed disease-infection. Both EMs and FA increased the relative abundances of Pseudomonas, Flavobacterium, Duganella, and Massilia spp., but, decreased the relative abundances of Fusarium and Sistotrema. In addition, soil nutrient availability and properties that benefitted nutrient availabilities were promoted. In conclusion, amendments with EMs and FA improved the fertility of farmland soils, and the quality of Asian ginseng, and revealed the relationship between soil microbial diversity and physiochemical properties

Construction of an RNAi vector for knockdown of GM-ACS genes in the cotyledonary nodes of soybean

Background: Ethylene plays an important role in the regulation of floral organ development in soybean, and 1-aminocyclopropane-1-carboxylate synthase (ACS) is a rate-limiting enzyme for ethylene biosynthesis. However, whether ACS also regulates floral organ differentiation in soybean remains unknown. To address this, we constructed an RNAi vector to inhibit ACS expression in cotyledonary nodes. Linear DNA cassettes of RNAi-ACS obtained by PCR were used to transform soybean cotyledonary nodes. Results: In total, 131 of 139 transiently transformed plants acquired herbicide resistance and displayed GUS activities in the new buds. In comparison to untransformed seedling controls, a greater number of flower buds were differentiated at the cotyledonary node; GM-ACS1 mRNA expression levels and ethylene emission in the transformed buds were reduced. Conclusion: These results indicate that the cotyledonary node transient transformation system may be suitable for stable transformation and that the inhibition of ACS expression may be an effective strategy for promoting floral organ differentiation in soybean

The effects of ethylene on the HCl-extractability of trace elements during soybean seed germination

Background: Ethylene is capable of promoting seed germination in some plant species. Mobilization of metals such as Fe, Cu, Mn, and Zn in mature seeds takes place when seeds are germinating. However, whether ethylene is involved in the regulation of soybean seed germination and metal element mobilization during early seed germination stage remains unknown. In the present study, seeds were treated with ethylene synthesis inhibitor aminoethoxyvinylglycine (AVG) and ethylene precursor 1-aminocyclopropane-1-carboxylic acid (ACC), and double distilled H2O (ddH20) treatment was used as control. Ethylene emission, ACC synthase (ACS) expression, ACS enzyme activity and Ca, Zn, Mn, Cu and Fe content in hypocotyls were qualified to analyze the relationship between ethylene and mobilization of these elements. Results: The results showed that ACS expression, ACS enzyme activity and ethylene emission peaked at 1 and 7 d after sowing. AVG inhibited ethylene production, promoted the hypocotyls length, ACS expression and its activity, concentrations of total and HCl-extractable Zn, and HCl-extractable Fe in hypocotyls, while ACC caused opposite effects. AVG and ACC treatment had no significantly effects on total and HCl-extractable Ca, Cu and HCl-extractable Mn. Total Mn concentration was promoted by AVG at 1, 3, and 5 d significantly, while ACC treatment tended to have no significantly effects on Mn concentration. Conclusion: These findings suggested that ethylene is at least partly involved in the regulation of soybean seed germination. Remobilization of Zn and Fe may be negatively regulated by ethylene

Growth, Nutrient Uptake, and Foliar Gas Exchange in Pepper Cultured with Un-composted Fresh Spent Mushroom Residue

Spent mushroom substrate (SMS) can be used as the component of growing medium for the culture of crop plants. Fresh SMS may have the potential as an alternative to peat to raise horticultural plants. In this study, five container media characterized by the proportions of SMS to commercial peat in 0% (control), 25%, 50%, 75%, and 100% were used to raise pepper (Capsicum annum L.) plants. Initial SMS was found to have low available nitrogen (N) content (<20 mg kg-1) but moderate extractable phosphorus (P) content (900 mg kg-1). In the second month photosynthetic rate was found to decline in the 75% treatment. At harvest in the third month, plants in the 100% treatment nearly died out. The 25% treatment resulted in the highest height (19 cm) and diameter growth (0.3 cm), shoot (0.6 g) and root biomass accumulation (0.13 g), fruit weight (3 g), and shoot carbohydrate content (98 mg g-1), but lowest foliar acid phosphatase activity (30 µg NPP g-1 FW min-1). With the increase of SMS proportion in the substrate, the medium pH and electrical conductance (EC) increased with the decrease of foliar size. The available N and P contents in the substrates showed contrasting relationship with N and P contents in pepper plants. Therefore, fresh SMS cannot be directly used as the substrate for the culture of pepper plants. According to our findings fresh SMS was recommended to be mixed in the proportion of 25% with commercial peat for the culture of horticultural plants