Deciphering hierarchical organization of topologically associated domains through change-point testing.

BACKGROUND: The nucleus of eukaryotic cells spatially packages chromosomes into a hierarchical and distinct segregation that plays critical roles in maintaining transcription regulation. High-throughput methods of chromosome conformation capture, such as Hi-C, have revealed topologically associating domains (TADs) that are defined by biased chromatin interactions within them. RESULTS: We introduce a novel method, HiCKey, to decipher hierarchical TAD structures in Hi-C data and compare them across samples. We first derive a generalized likelihood-ratio (GLR) test for detecting change-points in an interaction matrix that follows a negative binomial distribution or general mixture distribution. We then employ several optimal search strategies to decipher hierarchical TADs with p values calculated by the GLR test. Large-scale validations of simulation data show that HiCKey has good precision in recalling known TADs and is robust against random collisions of chromatin interactions. By applying HiCKey to Hi-C data of seven human cell lines, we identified multiple layers of TAD organization among them, but the vast majority had no more than four layers. In particular, we found that TAD boundaries are significantly enriched in active chromosomal regions compared to repressed regions. CONCLUSIONS: HiCKey is optimized for processing large matrices constructed from high-resolution Hi-C experiments. The method and theoretical result of the GLR test provide a general framework for significance testing of similar experimental chromatin interaction data that may not fully follow negative binomial distributions but rather more general mixture distributions

Planning urban energy systems adapting to extreme weather

In the context of increasing urbanization and climate change globally, urban energy systems (UES) planning needs adequate consideration of climate change, particularly to ensure energy supply during extreme weather events (EWE) such as heatwaves, floods, and typhoons. Here we propose a two-layer modeling framework for UES planning considering the impact of EWE. An application of the framework to a typical coastal city of Xiamen, China reveals that deploying energy storage (i.e., pumped hydro and battery) offers significant flexibility to ensure the critical demand is met during typhoon as a typical EWE and avoids over investment in supply technologies. This requires an extra 2.8% total cost on investment and operation of UES for 20 years. Planning energy systems with proper consideration of EWE can ensure robust urban energy services even with increasing penetration of fluctuating renewables, and we offer a flexible and computationally efficient paradigm for UES planning considering the impact of EWE

Cost-efficient decarbonization of local energy systems by whole-system based design optimization

On the way toward Net Zero 2050, the UK government set the 2035 target by slashing 78 % emissions compared to the 1990-level. To help understand how an electrified local energy system could contribute to this target and the associated cost, we develop a whole-system based local energy optimization (LEO) model. The model captures a series of state-of-the-art technologies including building fabric retrofit, battery storage, electro-mobility, electro-heating, demand response, distributed renewable, and Peer-to-Peer (P2P) energy trading. And the model enables trade-off assessment between cost and emissions minimization, compares two system operating modes, i.e., cost-oriented and grid-impact-oriented, and evaluates the impacts from weather risks and capital cost assumptions. A case study in Wales reveals (1) capital cost assumptions can lead up to 30.8 % overall cost difference of the local energy system; (2) operating the system in cost-oriented mode can save up to 5 % cost than in the grid-impact-oriented mode; (3) electro-heating by heat pumps has the highest priority among all investigated technologies. Overall, this study demonstrates how to design and operate a cost-efficient and electrified UK local energy system by the whole-system incorporation of near-term technical and business model advances towards a decarbonized future

Novi VP2/VP3 rekombinantni senekavirus A izoliran u sjevernoj Kini

Senecavirus A (SVA), previously called the Seneca Valley virus, is the only member of the genus Senecavirus within the family Picornaviridae. This virus was discovered as a serendipitous finding in 2002 and named Seneca Valley virus 001 (SVV-001). SVA is an emerging pathogen that can cause vesicular lesions and epidemic transient neonatal a sharp decline in swine. In this study, an SVA strain was isolated from a pig herd in Shandong Province in China and identified as SVA-CH-SDFX-2022. The full-length genome was 7282 nucleotides (nt) in length and contained a single open reading frame (ORF), excluding the poly (A) tails of the SVA isolates. Phylogenetic analysis showed that the isolate shares its genomic organization, resembling and sharing high nucleotide identities of 90.5% to 99.6%, with other previously reported SVA isolates. The strain was proved by in vitro characterization and the results demonstrate that the virus has robust growth ability in vitro. The recombination event of the SVA-CH-SDFX-2022 isolate was found and occurred between nts 1836 and 2710, which included the region of the VP2 (partial), and VP3 (partial) genes. It shows the importance of faster vaccine development and a better understanding of virus infection and spread because of increased infection rates and huge economic losses. This novel incursion has substantial implications for the regional control of vesicular transboundary diseases, and will be available for further study of the epidemiology of porcine SVA. Our findings provide useful data for studying SVA in pigs.Senekavirus A (SVA), prije nazivan virusom doline Seneca Valley, jedini je pripadnik roda senekavirusa u porodici Picornaviridae. Virus je slučajno otkriven 2002. i nazvan virusom doline Seneca 001 (SVV-001). SVA je novi patogen koji može uzrokovati vezikularne lezije i prolaznu epidemiju novorođene prasadi s naglim gubicima u proizvodnji. U ovom je istraživanju soj SVA izoliran u populaciji svinja iz provincije Shandong u Kini i identificiran kao SVA-CHSDFX-2022. Kompletni genom izolata SVA imao je 7282 nukleotida (nt) u dužini i sadržavao je jedan otvoreni okvir za očitavanje (ORF), bez poli-A repova. Filogenetska je analiza pokazala da izolat u velikoj mjeri sadržava genomsku organizaciju i nukleotidne identitete, od 90,5 % do 99,6 %, s drugim poznatim SVA izolatima. Karakterizacija virusa je pokazala da ima veliku sposobnost rasta in vitro. Pronađena je rekombinacija izolata SVA-CH-SDFX-između nukleotida 1836 i 2710 što je uključilo regiju gena VP2 (parcijalno) i gena VP3 (parcijalno). Zbog visoke stope infektivnosti i golemih ekonomskih gubitaka važan je brži razvoj cjepiva i bolje razumijevanje zaraze. Rezultati ovog istraživanja pružaju korisne podatke za proučavanje SVA virusa, posebno s obzirom na njegovu epidemiologiju u svinja i regionalnu prekograničnu kontrolu vezikularnih bolesti

A review on modelling methods, tools and service of integrated energy systems in China

An integrated energy system (IES) is responsible for aggregating various energy carriers, such as electricity, gas, heating, and cooling, with a focus on integrating these components to provide an efficient, low-carbon, and reliable energy supply. This paper aims to review the modeling methods, tools, and service modes of IES in China to evaluate opportunities for improving current practices. The models reviewed in this paper are classified as demand forecasting or energy system optimization models based on their modeling progress. Additionally, the main components involved in the IES modeling process are presented, and typical domestic tools utilized in the modeling processes are discussed. Finally, based on a review of several demonstration projects of IES, future development directions of IES are summarized as the integration of data-driven and engineering models, improvements in policies and mechanisms, the establishment of regional energy management centers, and the promotion of new energy equipment

Muscle Quality of Sword Prawn (Parapenaeopsis hardwickii) during Cold Storage Based on Changes of Endogenous Enzyme Activity

Objective: To investigate the changes of endogenous enzyme activity and muscle quality characteristics of Sword prawn (Parapenaeopsis hardwickii) under cold storage. Methods: Sword prawn (Parapenaeopsis hardwickii) was taken as the research object. The muscle texture, TCA-soluble peptide, myofibril protein content and myofibril fragmentation index, as well as the activities of endogenous enzymes in the head and muscle of intact and headless shrimp were compared and analyzed at 0°C for 0, 2, 4 and 6 d. Results: With the extension of cold storage time, the content of TCA-soluble peptide and myofibril fragmentation index in muscle of both groups showed an increasing trend. The myofibril protein content gradually decreased, their content in muscle of whole shrimp group and headless shrimp group reduced by 56.65% and 44.63%, respectively, after 6 d of cold storage. While the hardness and elasticity of shrimp in both groups always decreased. During cold storage, the trypsin activity in the head of whole shrimp group decreased gradually, while the activity in the muscle of whole shrimp group increased continuously. The trypsin activity in the muscle of decapitated shrimp group reduced slowly, and the trypsin activity in the head and muscle of whole shrimp group and the muscle of decapitated shrimp group changed by 16.9%, 68.8%, and 15.2%, respectively. In shrimp muscle, the calpain activity decreased with the extension of cold storage time, and the decrease rate was higher in whole shrimp group. The changes of the activities of cathepsin B, D, H and L were different during cold storage. The cathepsin activities in decapitated shrimp were higher than those in whole shrimp. The activities of cathepsins in each muscle subcellular structure of the two groups decreased gradually during cold storage. And the activities in whole shrimp group were higher than those in decapitated shrimp group. Conclusion: The muscle quality characteristics of the headless shrimp group were better than those of the whole shrimp group, and the endogenous enzyme activities in whole shrimp group were relatively higher than those in decapitated shrimp group during cold storage. Therefore, decapitated shrimp storage is more conducive to protect shrimp meat quality

Phenotyping cotton ovule fibre initiation with spatial statistics

Yield in cultivated cotton (Gossypium spp.) is affected by the number and distribution of fibres initiated on the seed surface but, apart from simple statistical summaries, little has been done to assess this phenotype quantitatively. Here we use two types of spatial statistics to describe and quantify differences in patterning of cotton ovule fibre initials (FI). The following five different species of Gossypium were analysed: G. hirsutum L., G. barbadense L., G. arboreum, G. raimondii Ulbrich. and G. trilobum (DC.) Skovsted. Scanning electron micrographs of FIs were taken on the day of anthesis. Cell centres for fibre and epidermal cells were digitised and analysed by spatial statistics methods appropriate for marked point processes and tessellations. Results were consistent with previously published reports of fibre number and spacing. However, it was shown that the spatial distributions of FIs in all of species examined exhibit regularity, and are not completely random as previously implied. The regular arrangement indicates FIs do not appear independently of each other and we surmise there may be some form of mutual inhibition specifying fibre-initial development. It is concluded that genetic control of FIs differs from that of stomata, another well studied plant idioblast. Since spatial statistics show clear species differences in the distribution of FIs within this genus, they provide a useful method for phenotyping cotton. © CSIRO 2007

Influences of pH Values’ Changes on the Oxide Film of U-0.79 wt.% Ti Alloy in Aqueous Solution—A Combined Study of Traditional Electrochemical Tests and Scanning Reference Electrode Technique

By combining traditional electrochemical tests including Tafel extension method and Mott-Schottky fitting, spectroscopic ellipsometry (SE) and a micro-region analysis technique, which is an integrated system of a scanning reference electrode technique and scanning tunneling microscope (SRET/STM), the changes in properties of the oxide film that formed on the surface of the U-0.79 wt.% Ti alloy (U-Ti alloy in short) in 0.1 M NaNO3 were carefully investigated as the pH value changed. The results show that the properties of the oxide film are strongly pH-dependent. The corrosion potential and corrosion current density decrease with the increasing pH value. The oxide film appears to be a p-type semiconductor at pH = 2.43. However, the transition from n-type to p-type for the oxide film as a semiconductor is observed with the increasing applied potential when the solution pH value varies from 2.43 to 7.0. The oxide film presents as an n-type semiconductor when the pH value varies from 7.0 to 11.44. In addition, during the transition of the pH, the roughness and the number of active points of the alloy surface decreases while the oxide film is thicker. It can be concluded that the corrosion resistance of the oxide film formed on the U-Ti alloy surface is enhanced in neutral or alkaline solutions

A Low-Altitude Remote Sensing Inspection Method on Rural Living Environments Based on a Modified YOLOv5s-ViT

The governance of rural living environments is one of the important tasks in the implementation of a rural revitalization strategy. At present, the illegal behaviors of random construction and random storage in public spaces have seriously affected the effectiveness of the governance of rural living environments. The current supervision on such problems mainly relies on manual inspection. Due to the large number and wide distribution of rural areas to be inspected, this method is limited by obvious disadvantages, such as low detection efficiency, long-time spending, and huge consumption of human resources, so it is difficult to meet the requirements of efficient and accurate inspection. In response to the difficulties encountered, a low-altitude remote sensing inspection method on rural living environments was proposed based on a modified YOLOv5s-ViT (YOLOv5s-Vision Transformer) in this paper. First, the BottleNeck structure was modified to enhance the multi-scale feature capture capability of the model. Then, the SimAM attention mechanism module was embedded to intensify the model’s attention to key features without increasing the number of parameters. Finally, the Vision Transformer component was incorporated to improve the model’s ability to perceive global features in the image. The testing results of the established model showed that, compared with the original YOLOv5 network, the Precision, Recall, and mAP of the modified YOLOv5s-ViT model improved by 2.2%, 11.5%, and 6.5%, respectively; the total number of parameters was reduced by 68.4%; and the computation volume was reduced by 83.3%. Relative to other mainstream detection models, YOLOv5s-ViT achieved a good balance between detection performance and model complexity. This study provides new ideas for improving the digital capability of the governance of rural living environments