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Article ; Online: sOCP: a framework predicting smORF coding potential based on TIS and in-frame features and effectively applied in the human genome.

Peng, Zhao / Li, Jiaqiang / Jiang, Xingpeng / Wan, Cuihong

2024 Volume 25, Issue 3

Abstract: Small open reading frames (smORFs) have been acknowledged to play various roles on essential biological pathways and affect human beings from diabetes to tumorigenesis. Predicting smORFs in silico is quite a prerequisite for processing the omics data. ... ...

Abstract	Small open reading frames (smORFs) have been acknowledged to play various roles on essential biological pathways and affect human beings from diabetes to tumorigenesis. Predicting smORFs in silico is quite a prerequisite for processing the omics data. Here, we proposed the smORF-coding-potential-predicting framework, sOCP, which provides functions to construct a model for predicting novel smORFs in some species. The sOCP model constructed in human was based on in-frame features and the nucleotide bias around the start codon, and the small feature subset was proved to be competent enough and avoid overfitting problems for complicated models. It showed more advanced prediction metrics than previous methods and could correlate closely with experimental evidence in a heterogeneous dataset. The model was applied to Rattus norvegicus and exhibited satisfactory performance. We then scanned smORFs with ATG and non-ATG start codons from the human genome and generated a database containing about a million novel smORFs with coding potential. Around 72 000 smORFs are located on the lncRNA regions of the genome. The smORF-encoded peptides may be involved in biological pathways rare for canonical proteins, including glucocorticoid catabolic process and the prokaryotic defense system. Our work provides a model and database for human smORF investigation and a convenient tool for further smORF prediction in other species.
MeSH term(s)	Animals ; Humans ; Rats ; Genome, Human ; Open Reading Frames ; Peptides/genetics ; Proteins/genetics
Chemical Substances	Peptides ; Proteins
Language	English
Publishing date	2024-04-10
Publishing country	England
Document type	Journal Article
ZDB-ID	2068142-2
ISSN	1477-4054 ; 1467-5463
ISSN (online)	1477-4054
ISSN	1467-5463
DOI	10.1093/bib/bbae147
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Article ; Online: A First Evaluation of ERA5-Land Reanalysis Temperature Product Over the Chinese Qilian Mountains

Peng Zhao / Zhibin He

Frontiers in Earth Science, Vol

2022 Volume 10

Abstract: Reanalysis temperature products are important datasets for temperature estimates over high-elevation areas with few meteorological stations. In this study, surface 2 m air temperature data from 17 meteorological stations from 1979 to 2017 in the Qilian ... ...

Abstract	Reanalysis temperature products are important datasets for temperature estimates over high-elevation areas with few meteorological stations. In this study, surface 2 m air temperature data from 17 meteorological stations from 1979 to 2017 in the Qilian Mountains (QLM) are used for comparison with the newest reanalysis product: ERA5-Land derived from the European Centre for Medium-Range Weather Forecasts (ECMWF). In general, the ERA5-Land temperature product can reproduce the observation variation at different time scales very well. A high monthly correlation coefficient that ranges from 0.978 to 0.998 suggests that ERA5-Land reanalysis temperature could capture the observations very well. However, attention should be paid before using ERA5-Land at individual sites because of the average root-mean-square-error (RMSE) of 2.2°C of all stations. The biases between ERA5-Land temperature and observations are mainly caused by the elevation differences between ERA5-Land grid points and meteorological sites. The annual mean temperature shows a significant warming trend (0.488°C/decade) from 1979 to 2017 based on the observations. ERA5-Land reanalysis temperature captures the increasing trend very well (0.379°C/decade). The biggest positive warming trends of observations and ERA5-Land are both found in summer with values of 0.574°C/decade and 0.496°C/decade, respectively. We suggest that ERA5-Land generally reproduces the temperature trend very well for observations and is reliable for scientific research over the QLM.
Keywords	reanalysis ; air temperature ; ERA5-Land ; Qilian Mountains ; warming trend ; Science ; Q
Subject code	910
Language	English
Publishing date	2022-08-01T00:00:00Z
Publisher	Frontiers Media S.A.
Document type	Article ; Online
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Article ; Online: Implications of elevation-dependent warming to water resources over the Chinese Qilian Mountains

Peng Zhao / Zhibin He / Jun Du

Journal of Water and Climate Change, Vol 14, Iss 1, Pp 239-

2023 Volume 252

Abstract: Warming in mountainous regions has experienced obvious elevation dependence (the warming rate of air temperature is amplified with elevation), which accelerates the melting of ice and snow, affecting glacier size and mass, and water resources in ... ...

Abstract	Warming in mountainous regions has experienced obvious elevation dependence (the warming rate of air temperature is amplified with elevation), which accelerates the melting of ice and snow, affecting glacier size and mass, and water resources in mountainous regions. Here, we used ERA5-Land monthly averaged datasets from 1979 to 2019 to analyze the elevation-dependent warming (EDW) variability, driving factor, and its implications to water resources in the Qilian Mountains (QLM). Results showed that: (1) Annual mean temperature shows a significant increasing trend in the QLM from 1979 to 2019 (0.31 °C/10a; p < 0.01), and the warming rate of annual mean temperature increased with elevation in the QLM in general. For seasonal scales, the most obvious EDW was found in summer. In the past 41 years, snow cover and snow depth showed a slight decreasing trend. There was a significant negative correlation between temperature and snow cover, which can explain that enhanced regional warming has caused decreases in snow cover and snow depth, largely controlling the pattern of EDW on the QLM. EDW has significant implications for water resources over QLM, especially above 5,000 m. Our study can provide a reference in understanding the importance of EDW to water resources in mountainous areas. HIGHLIGHTS ERA5-Land reanalysis 2 m temperature data are reliable in Qilian Mountains.; There is an obvious elevation-dependent warming (EDW) of annual mean temperature, especially above 5,000 m.; Snow cover in Qilian Mountain showed a decreasing trend.; Snow cover is an important mechanism driving EDW.; EDW has an important implication for water resources (especially above 5,000 m).;
Keywords	elevation-dependent warming ; era5-land reanalysis ; qilian mountains ; snow cover ; water sources ; Environmental technology. Sanitary engineering ; TD1-1066 ; Environmental sciences ; GE1-350
Language	English
Publishing date	2023-01-01T00:00:00Z
Publisher	IWA Publishing
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Response to a Comment on “Scar‐Degrading Endothelial Cells as a Treatment for Advanced Liver Fibrosis”

Peng Zhao / Tian Sun / Cheng Lyu / Yanan Du

Advanced Science, Vol 10, Iss 17, Pp n/a-n/a (2023)

2023

Keywords	Science ; Q
Language	English
Publishing date	2023-06-01T00:00:00Z
Publisher	Wiley
Document type	Article ; Online
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Article ; Online: Field Measurement Study on Dynamic Characteristics of the Shanghai World Financial Center

Xu Wang / Hu Kong / Guoliang Zhang / Peng Zhao

Applied Sciences, Vol 13, Iss 7973, p

2023 Volume 7973

Abstract: It is of great practical importance to study the vibration response characteristics of super high-rise buildings under an earthquake action to provide a basis for seismic design and later maintenance of structures in coastal areas. During this study, the ...

Abstract	It is of great practical importance to study the vibration response characteristics of super high-rise buildings under an earthquake action to provide a basis for seismic design and later maintenance of structures in coastal areas. During this study, the Shanghai World Financial Center (SWFC)’s health monitoring system was utilized to monitor earthquakes of magnitude 6.4 in Taiwan, 6.0 in Japan, 7.2 in the East China Sea, and 4.4 in Jiangsu, in real-time. Through the improved Envelope Random Decrement Technique (E-RDT), the dynamic properties of super high-rise buildings were examined under different earthquake effects in terms of the acceleration power spectrum, natural frequency, damping ratio, and mode shape. The results demonstrated that (1) the vibration responses of the structure in X (East–West) and Y (North–South) directions under four earthquakes were consistent, and with increasing floor height, the discreteness of the amplitude and acceleration signals of vibration responses increased. (2) The first two natural frequencies of the structure in X and Y directions decreased with the increase in amplitude, but the damping ratio increased with the increase in amplitude. The minimum values of the first two natural frequencies are 0.1498 Hz and 0.4312 Hz, respectively, and the maximum values of the first two damping ratios are 0.0086 and 0.0068, respectively. (3) Under different earthquake excitations, the SWFC’s mode shape’s estimates were similar, and their change trends in the X and Y directions were nonlinear as the number of floors increased. The structure was not seriously damaged by the four earthquakes. This study can provide helpful information for the seismic design of super high-rise buildings based on its findings.
Keywords	field measurement ; seismic response ; dynamic characteristics ; super high-rise building ; Technology ; T ; Engineering (General). Civil engineering (General) ; TA1-2040 ; Biology (General) ; QH301-705.5 ; Physics ; QC1-999 ; Chemistry ; QD1-999
Subject code	621
Language	English
Publishing date	2023-07-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
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Article ; Online: Genome-Wide Identification of the CBF Gene Family and ICE Transcription Factors in Walnuts and Expression Profiles under Cold Conditions

Huijuan Zhou / Jiayu Ma / Hengzhao Liu / Peng Zhao

International Journal of Molecular Sciences, Vol 25, Iss 1, p

2023 Volume 25

Abstract: Cold stress impacts woody tree growth and perennial production, especially when the temperature rapidly changes in late spring. To address this issue, we conducted the genome-wide identification of two important transcription factors (TFs), CBF (C-repeat ...

Abstract	Cold stress impacts woody tree growth and perennial production, especially when the temperature rapidly changes in late spring. To address this issue, we conducted the genome-wide identification of two important transcription factors (TFs), CBF (C-repeat binding factors) and ICE (inducers of CBF expression), in three walnut ( Juglans ) genomes. Although the CBF and ICE gene families have been identified in many crops, very little systematic analysis of these genes has been carried out in J. regia and J. sigillata . In this study, we identified a total of 16 CBF and 12 ICE genes in three Juglans genomes using bioinformatics analysis. Both CBF and ICE had conserved domains, motifs, and gene structures, which suggests that these two TFs were evolutionarily conserved. Most ICE genes are located at both ends of the chromosomes. The promoter cis -regulatory elements of CBF and ICE genes are largely involved in light and phytohormone responses. Based on 36 RNA sequencing of leaves from four walnut cultivars (‘Zijing’, ‘Lvling’, ‘Hongren’, and ‘Liao1’) under three temperature conditions (8 °C, 22 °C, and 5 °C) conditions in late spring, we found that the ICE genes were expressed more highly than CBFs . Both CBF and ICE proteins interacted with cold-related proteins, and many putative miRNAs had interactions with these two TFs. These results determined that CBF1 and ICE1 play important roles in the tolerance of walnut leaves to rapid temperature changes. Our results provide a useful resource on the function of the CBF and ICE genes related to cold tolerance in walnuts.
Keywords	walnut ; CBF ; ICE1 ; low temperature ; gene family ; Biology (General) ; QH301-705.5 ; Chemistry ; QD1-999
Subject code	572
Language	English
Publishing date	2023-12-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Unraveling air–water two-phase flow patterns in water pipelines based on multiple signals and convolutional neural networks

Peng Zhao / Ziyang Xu / Haixing Liu / Bing Yu

Aqua, Vol 72, Iss 12, Pp 2472-

2023 Volume 2486

Abstract: Flow pattern identification (FPI) is crucial for evaluating air entrapment in water pipelines and ensuring the safety of pipeline operations. The presence of two-phase flow in water pipelines not only leads to pressure fluctuations but also induces ... ...

Abstract	Flow pattern identification (FPI) is crucial for evaluating air entrapment in water pipelines and ensuring the safety of pipeline operations. The presence of two-phase flow in water pipelines not only leads to pressure fluctuations but also induces pipeline vibration. However, current research has primarily focused on using pressure-related signals for FPI, and the analysis of vibration signals in FPI is rare. In this study, FPI in water pipelines is investigated based on convolutional neural networks (CNNs) using high-frequency vibration signals. The information fusion of vibration signals in FPI is newly proposed via the stacked generalization technique. The proposed method is compared with pressure signal-based FPI methods and the effect of signal sampling parameters on FPI accuracy is discussed. The results show that the performance of vibration signals (including axial or radial acceleration signals) outperforms pressure signals in both time and frequency domains. Moreover, the fusion of vibration signals shows the superior results compared to any univariate signals. The duration of sampling has a more significant impact on the results of FPI than the sampling frequency. This study provides a new way that FPI theory is applied to solve air entrapment evaluation in water pipelines. HIGHLIGHTS The high-frequency vibration signal was proposed for flow pattern identification.; Vibration signals outperform pressure signals for flow pattern recognition.; The vibration signals fused by stacked generalization have better performance than single signals.; For vibration signals, sampling duration has a greater impact on the flow pattern identification performance than sampling frequency.;
Keywords	accelerometer sensor ; convolutional neural networks ; flow pattern identification ; stacked generalization ; vibration signals ; water pipelines ; Environmental technology. Sanitary engineering ; TD1-1066 ; Environmental sciences ; GE1-350
Subject code	621 ; 690
Language	English
Publishing date	2023-12-01T00:00:00Z
Publisher	IWA Publishing
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Identification of novel smORFs and microprotein acting in response to rehydration of Nostoc flagelliforme.

Peng, Zhao / Huwanixi, Aishuake / Wan, Cuihong

Proteomics

2023 Volume 23, Issue 12, Page(s) e2200473

Abstract: Nostoc flagelliforme, a terrestrial cyanobacterium spread throughout arid and semi-arid areas, has been long known for its outstanding adaptability to extremely dry conditions. This microorganism is able to recover biological activities within hours ... ...

Abstract	Nostoc flagelliforme, a terrestrial cyanobacterium spread throughout arid and semi-arid areas, has been long known for its outstanding adaptability to extremely dry conditions. This microorganism is able to recover biological activities within hours after months of anhydrobiosis state, attracting investigation through proteomic analysis. Except for canonical proteome, microproteins encoded by small ORFs (smORFs) have recently been regarded as indispensable participants in metabolic processes. However, the involvement of smORFs in N. flagelliforme remains unknown. Here we first constructed a smORF database in N. flagelliforme using bioinformatic prediction, resulting in 6072 novel smORFs. Then LS-MS/MS analysis was applied to identify expression patterns of microproteins and seek smORFs and their encoded microprotein playing a role during rehydration. In total, 18 novel microproteins were mined based on a smORF searching strategy combined with three proteomic assays, of which five were annotated as ribosomal proteins, one as RNA polymerase subunit, and one as acetohydroxy acid isomeroreductase. We also suggested the possible functions of smORFs according to their expression pattern and discovered two neighboring and homologous smORFs. All these results will expand our knowledge of smORFs-encoded microproteins and their relation to the stress response of extremophilic microorganisms.
MeSH term(s)	Humans ; Proteomics ; Open Reading Frames ; Tandem Mass Spectrometry ; Nostoc/genetics ; Nostoc/metabolism ; Fluid Therapy ; Micropeptides
Language	English
Publishing date	2023-04-03
Publishing country	Germany
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2032093-0
ISSN	1615-9861 ; 1615-9853
ISSN (online)	1615-9861
ISSN	1615-9853
DOI	10.1002/pmic.202200473
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Article ; Online: The Effects of Energy on the Relationship between the Acoustic Focal Region and Biological Focal Region during Low-Power Cumulative HIFU Ablation

Peng Zhao / Yuebing Wang / Shiqi Tong / Jie Tao / Yongjie Sheng

Applied Sciences, Vol 13, Iss 4492, p

2023 Volume 4492

Abstract: The biological focal region (BFR) induced by a single high-intensity focused ultrasound (HIFU) exposure is considered to be the foundation of the ultrasound ablation of tumor lesions. The purpose of this study was to explore the relationship between the ... ...

Abstract	The biological focal region (BFR) induced by a single high-intensity focused ultrasound (HIFU) exposure is considered to be the foundation of the ultrasound ablation of tumor lesions. The purpose of this study was to explore the relationship between the acoustic focal region (AFR) and the BFRs with different combinations of power and time in low-power cumulative HIFU treatment. The finite-difference time-domain (FDTD) method was used to simulate AFR and BFR during HIFU ablation. The acoustic fields, the temperature profiles, and the shapes of BFRs were calculated by the Westervelt equation, Pennes’ equation, and the equivalent thermal dose model. In order to verify the simulation rules, phantom and ex vivo bovine livers were exposed by HIFU with a different power and time. The results demonstrated that in the low-power cumulative HIFU treatment, when the lengths of BFRs and the length of AFR were approximately equal, the shape of the BFR induced by ‘high power × short time’ exposure was closer to that of AFR than the shape of the BFR induced by ‘low power × long time’ exposure, and the exposure energy required was significantly reduced. The analysis revealed the relationship between the BFR and the AFR with different acoustic power. This study provides a reference for doctors to determine power, time, and movement distance in clinical treatment.
Keywords	high intensity focused ultrasound ; low power cumulative HIFU ; acoustic focal region ; biological focal region ; Technology ; T ; Engineering (General). Civil engineering (General) ; TA1-2040 ; Biology (General) ; QH301-705.5 ; Physics ; QC1-999 ; Chemistry ; QD1-999
Language	English
Publishing date	2023-04-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Heat stress inhibits the proliferation and differentiation of myoblasts and is associated with damage to mitochondria

Jiawei Lu / Huixia Li / Debing Yu / Peng Zhao / Yuan Liu

Frontiers in Cell and Developmental Biology, Vol

2023 Volume 11

Abstract: Introduction: Heat stress is harmful to the health of humans and animals, more and more common, as a consequence of global warming, while the mechanism that heat stress modulates skeletal development remains unknown. Hence, we conducted a model of heat ... ...

Abstract	Introduction: Heat stress is harmful to the health of humans and animals, more and more common, as a consequence of global warming, while the mechanism that heat stress modulates skeletal development remains unknown. Hence, we conducted a model of heat stress in vitro.Methods: We used Hu sheep myoblasts as the research object, real-time quantitative PCR (RT-qPCR) and western blot (WB) were conducted to detect the expression of mRNA and protein in heat-stressed myoblasts. The would-healing assay was used to detect the migration of myoblasts. The mitochondria were observed by a transmission electron microscope.Results: mRNA and protein expression of HSP60 was significantly enriched in the heat-stressed myoblasts during proliferation and differentiation (p < 0.05). In our study, we indicated that heat stress enriched the intracellular ROS of the myoblasts (p < 0.001), leading to an increase in autophagy in the myoblasts to induce apoptosis. The results demonstrated that the protein expression of LC3B-1 and BCL-2 was significantly increased in myoblasts under heat stress during proliferation and differentiation (p < 0.05). Additionally, heat stress inhibited mitochondrial biogenesis and function and reduced the mitochondrial membrane potential and downregulated the expression of mtCo2, mtNd1 and DNM1L (p < 0.05) in myoblasts during proliferation and differentiation. Consequently, heat stress inhibited the proliferation and differentiation of the myoblasts, in accordance with the downregulation of the expression of PAX7, MYOD, MYF5, MYOG and MYHC (p < 0.05). Moreover, heat stress also inhibited the cell migration of the myoblasts.Discussion: This work demonstrates that heat stress inhibits proliferation and differentiation, and accelerates apoptosis by impairing mitochondrial function and promoting autophagy, which provides a mechanism to understand heat stress affects the development of the skeletal muscle.
Keywords	heat stress ; myoblasts ; mitochondria ; proliferation ; differentiation ; Biology (General) ; QH301-705.5
Language	English
Publishing date	2023-04-01T00:00:00Z
Publisher	Frontiers Media S.A.
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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