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Article ; Online: Temperature and the maturation of fish: a simple sine-wave model for predicting accelerated spring spawning

Pauly, D. / Liang, Cui

Environ Biol Fish. 2022 Oct., v. 105, no. 10 p.1481-1487

2022

Abstract: Global warming affects the phenology of the Earth’s flora and fauna, notably by advancing the date at which many plants and animals tend to reproduce. We use fish, where this reproductive acceleration is well-documented, to present a simple approach ... ...

Abstract	Global warming affects the phenology of the Earth’s flora and fauna, notably by advancing the date at which many plants and animals tend to reproduce. We use fish, where this reproductive acceleration is well-documented, to present a simple approach based on sine curves to predict, in spring spawning fish, the minimum number of days (Δdₘᵢₙ) that spawning is advanced as the result of a given increase in water temperature (Δ°C). We show, via comparison with field estimates, that our simple model’s robust predictions correspond to observed values of Δdₘᵢₙ/Δ°C, and discuss both the potential uses and the limitations of the model.
Keywords	fauna ; fish ; flora ; models ; phenology ; spring ; water temperature
Language	English
Dates of publication	2022-10
Size	p. 1481-1487.
Publishing place	Springer Netherlands
Document type	Article ; Online
ZDB-ID	196790-3
ISSN	1573-5133 ; 0378-1909
ISSN (online)	1573-5133
ISSN	0378-1909
DOI	10.1007/s10641-022-01212-0
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Spatial and Temporal Variations in Autumn Fish Assemblages in the Offshore Waters of the Yangtze Estuary

Chen, Zhaomin / Liang, Cui / Xian, Weiwei

Diversity. 2023 May 15, v. 15, no. 5

2023

Abstract: The offshore waters of the Yangtze Estuary are an important fish habitat, and the large gradient of environmental conditions leads to different fish assemblages. We studied the spatial and temporal variations in fish assemblages and their relationships ... ...

Abstract	The offshore waters of the Yangtze Estuary are an important fish habitat, and the large gradient of environmental conditions leads to different fish assemblages. We studied the spatial and temporal variations in fish assemblages and their relationships with environmental factors in the offshore waters of the Yangtze Estuary during the autumns of 2012–2016. The fish assemblage consisted of 64 fish species from 39 families, of which 6 species were dominant. There were significant interannual differences in fish abundance, biomass, and species composition, with the highest abundance and biomass in 2013, the lowest abundance in 2016, and the lowest biomass in 2015. Redundancy analysis revealed that total suspended particles and dissolved oxygen drove interannual variation in fish abundance, biomass, and species composition, and depth drove spatial variation in the fish assemblage. According to the depth, the fish were classified as shallow assemblage and deep assemblage. Understanding the spatial and temporal patterns of fish assemblage in the offshore waters of the Yangtze Estuary is beneficial to the conservation of fish and the sustainable use of fishery resources in the offshore waters of the Yangtze Estuary.
Keywords	biomass ; dissolved oxygen ; estuaries ; fish ; fisheries ; habitats ; species diversity
Language	English
Dates of publication	2023-0515
Publishing place	Multidisciplinary Digital Publishing Institute
Document type	Article ; Online
ZDB-ID	2518137-3
ISSN	1424-2818
ISSN	1424-2818
DOI	10.3390/d15050669
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Using dual stable isotopes method for nitrate sources identification in Cao-E River Basin, Eastern China

Jiangnan Li / Qianhang Sun / Kun Lei / Liang Cui / Xubo Lv

Frontiers in Environmental Science, Vol

2023 Volume 11

Abstract: Excess nitrate (NO3−) of water is a worldwide environmental problem. Therefore, identifying the sources and analyzing respective contribution rates are of great importance for improving water quality. The current study was carried out to identify the ... ...

Abstract	Excess nitrate (NO3−) of water is a worldwide environmental problem. Therefore, identifying the sources and analyzing respective contribution rates are of great importance for improving water quality. The current study was carried out to identify the potential sources of NO3− pollution in Cao-E River basin, in Eastern China. Surface water samples were collected during the dry season and wet season. Multiple hydrochemical indices, dual NO3− isotopes (δ15N–NO3− and δ18O–NO3−) and a Bayesian model (stable isotope analysis in R, MixSIAR) were applied to identify NO3− sources and estimate the proportional contributions of multiple NO3− sources. During the sampling period, nitrification was a dominant nitrogen transformation process in the study area. The results of the NO3− isotopes suggested that manure and sewage (M&S), soil nitrogen (SN) and nitrogen fertilizer (NF) were the major contributors to NO3−. Moreover, the results obtained from the MixSIAR model showed that the proportional contributions of atmospheric deposition (AD), NF, M&S and SN to NO3− were 2.82, 15.45, 44.25, 37.47% and 3.14, 23.39, 31.78, 41.69% in the dry and wet season, respectively. This study provided evidence to further understand the sources, transport, and transformation of N in Cao-E River basin, which deepens the understanding of the management of N contaminant.
Keywords	Nitrogen ; isotopes sources ; transformation ; MixSIAR model ; source trace atmospheric deposition ; soil N reservoir ; Environmental sciences ; GE1-350
Subject code	550
Language	English
Publishing date	2023-06-01T00:00:00Z
Publisher	Frontiers Media S.A.
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Somatic Mutation of FAT Family Genes Implicated Superior Prognosis in Patients With Stomach Adenocarcinoma

Qingjun Wang / Liang Cui / Pansong Li / Yuanyuan Wang

Frontiers in Medicine, Vol

2022 Volume 9

Abstract: FAT family genes encode protocadherin, which regulates tumor cell proliferation and migration. Although transcriptional levels of FAT family members had been reported in multiple malignant tumors, the association between mutation and prognosis of the FAT ...

Abstract	FAT family genes encode protocadherin, which regulates tumor cell proliferation and migration. Although transcriptional levels of FAT family members had been reported in multiple malignant tumors, the association between mutation and prognosis of the FAT family in stomach adenocarcinoma (STAD) has not been investigated. Herein, we performed a multi-omics integrative bioinformatics analysis using genomic and mRNA expression data to explore the role of gene mutations across the FAT family on clinical outcomes of STAD. The results showed that FAT mutations occurred in 174 of 435 (40%) of the samples. Patients with FAT mutations possessed significantly better progression-free survival (P = 0.019) and overall survival (P = 0.034) than those with non-FAT mutations, and FAT mutations exhibited significantly higher tumor mutational burden (TMB) and microsatellite instability. Notably, FAT mutations had a greater effect on somatic single-nucleotide variation than copy number variation and resulted in more abundant DNA damage repair (DDR) mutations. Further investigation demonstrated that FAT mutations contributed to an inflammatory tumor microenvironment (TME), as indicated by significantly increased numbers of activated CD4 and CD8 T cells, and significantly decreased numbers of mast cell, plasmacytoid dendritic cell, type 2 T helper cell, and high expression of immune-promoting genes. Moreover, biological process antigen processing and presentation, DNA replication, and DDR-related pathways were significantly upregulated in patients with FAT mutations. Collectively, FAT mutations significantly improved the survival of patients with STAD by enhancing tumor immunogenicity (e.g., TMB and DDR mutations) and an inflamed TME, indicating that the FAT family might be a potential prognostic and therapeutic biomarker for STAD.
Keywords	stomach adenocarcinomas ; FAT family ; DNA damage repair ; prognosis ; somatic mutation ; tumor microenvironment ; Medicine (General) ; R5-920
Language	English
Publishing date	2022-06-01T00:00:00Z
Publisher	Frontiers Media S.A.
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Defining Bacterial RNA-RNA Interactomes Using CLASH.

Esteban-Serna, Sofia / Chu, Liang-Cui / Chauhan, Mehak / Raja, Pujitha / Granneman, Sander

Methods in molecular biology (Clifton, N.J.)

2024 Volume 2741, Page(s) 307–345

Abstract: Methicillin-resistant Staphylococcus aureus (MRSA) is a bacterial pathogen accounting for high mortality rates among infected patients. Transcriptomic regulation by small RNAs (sRNAs) has been shown to regulate networks promoting antibiotic resistance ... ...

Abstract	Methicillin-resistant Staphylococcus aureus (MRSA) is a bacterial pathogen accounting for high mortality rates among infected patients. Transcriptomic regulation by small RNAs (sRNAs) has been shown to regulate networks promoting antibiotic resistance and virulence in S. aureus. Yet, the biological role of most sRNAs during MRSA host infection remains unknown. To fill this gap, in collaboration with the lab of Jai Tree, we performed comprehensive RNA-RNA interactome analyses in MRSA using CLASH under conditions that mimic the host environment. Here we present a detailed version of this optimized CLASH (cross-linking, ligation, and sequencing of hybrids) protocol we recently developed, which has been tailored to explore the RNA interactome in S. aureus as well as other Gram-positive bacteria. Alongside, we introduce a compilation of helpful Python functions for analyzing folding energies of putative RNA-RNA interactions and streamlining sRNA and mRNA seed discovery in CLASH data. In the accompanying computational demonstration, we aim to establish a standardized strategy to evaluate the likelihood that observed chimeras arise from true RNA-RNA interactions.
MeSH term(s)	Humans ; RNA, Bacterial/genetics ; Staphylococcus aureus/genetics ; Methicillin-Resistant Staphylococcus aureus/genetics ; Computational Biology/methods ; RNA, Messenger/genetics ; Gene Expression Regulation, Bacterial ; RNA, Small Untranslated/genetics
Chemical Substances	RNA, Bacterial ; RNA, Messenger ; RNA, Small Untranslated
Language	English
Publishing date	2024-01-13
Publishing country	United States
Document type	Journal Article
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-0716-3565-0_17
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Iron(III) and BF

Li, Xue / Liao, Lin-Fen / Ding, Li-Yao / Chen, Chun-Hua / Liang, Cui / Mo, Dong-Liang

Organic letters

2024 Volume 26, Issue 15, Page(s) 3060–3064

Abstract: We described an iron(III) and ... ...

Abstract	We described an iron(III) and BF
Language	English
Publishing date	2024-03-29
Publishing country	United States
Document type	Journal Article
ISSN	1523-7052
ISSN (online)	1523-7052
DOI	10.1021/acs.orglett.4c00693
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Effect of optical fiber end face scratches on laser-induced damage threshold.

Wu, Xiao / Lin, Lin / Zhang, Zhihang / Liang, Cui / Zhang, Dengwei

Applied optics

2023 Volume 62, Issue 31, Page(s) 8235–8241

Abstract: The scratches on the fiber end face can enhance the local electrical field, which lowers the damage threshold. The damage mechanism of a high-energy laser is investigated. The effect of scratches on the electric field is simulated by the finite ... ...

Abstract	The scratches on the fiber end face can enhance the local electrical field, which lowers the damage threshold. The damage mechanism of a high-energy laser is investigated. The effect of scratches on the electric field is simulated by the finite difference time domain (FDTD) solution. The results show that the depth of the scratch has a greater ability to influence the electric field than the width, and multiple scratches have a stronger modulation than a single scratch. In calculation, the damage threshold of the scratch-free end face is 0.456
Language	English
Publishing date	2023-11-21
Publishing country	United States
Document type	Journal Article
ISSN	1539-4522
ISSN (online)	1539-4522
DOI	10.1364/AO.502869
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Associative memory neurons of encoding multi-modal signals are recruited by neuroligin-3-mediated new synapse formation

Yang Xu / Tian-liang Cui / Jia-yi Li / Bingchen Chen / Jin-Hui Wang

eLife, Vol

2023 Volume 12

Abstract: The joint storage and reciprocal retrieval of learnt associated signals are presumably encoded by associative memory cells. In the accumulation and enrichment of memory contents in lifespan, a signal often becomes a core signal associatively shared for ... ...

Abstract	The joint storage and reciprocal retrieval of learnt associated signals are presumably encoded by associative memory cells. In the accumulation and enrichment of memory contents in lifespan, a signal often becomes a core signal associatively shared for other signals. One specific group of associative memory neurons that encode this core signal likely interconnects multiple groups of associative memory neurons that encode these other signals for their joint storage and reciprocal retrieval. We have examined this hypothesis in a mouse model of associative learning by pairing the whisker tactile signal sequentially with the olfactory signal, the gustatory signal, and the tail-heating signal. Mice experienced this associative learning show the whisker fluctuation induced by olfactory, gustatory, and tail-heating signals, or the other way around, that is, memories to multi-modal associated signals featured by their reciprocal retrievals. Barrel cortical neurons in these mice become able to encode olfactory, gustatory, and tail-heating signals alongside the whisker signal. Barrel cortical neurons interconnect piriform, S1-Tr, and gustatory cortical neurons. With the barrel cortex as the hub, the indirect activation occurs among piriform, gustatory, and S1-Tr cortices for the second-order associative memory. These associative memory neurons recruited to encode multi-modal signals in the barrel cortex for associative memory are downregulated by neuroligin-3 knockdown. Thus, associative memory neurons can be recruited as the core cellular substrate to memorize multiple associated signals for the first-order and the second-order of associative memories by neuroligin-3-mediated synapse formation, which constitutes neuronal substrates of cognitive activities in the field of memoriology.
Keywords	associative learning ; associative memory neuron ; barrel cortex ; synapses ; neurons ; Medicine ; R ; Science ; Q ; Biology (General) ; QH301-705.5
Subject code	612
Language	English
Publishing date	2023-12-01T00:00:00Z
Publisher	eLife Sciences Publications Ltd
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Identification of bladder cancer subtypes and predictive model for prognosis, immune features, and immunotherapy based on neutrophil extracellular trap-related genes

Changhong Guo / Peiying Li / Xingkui Guo / Xinfen Wang / Bo Liu / Liang Cui

Scientific Reports, Vol 13, Iss 1, Pp 1-

2023 Volume 18

Abstract: Abstract Bladder cancer is the most common malignant tumor of urinary system, and its morbidity and mortality are increasing rapidly. Although great advances have been made in medical technology in recent years, there is still a lack of effective ... ...

Abstract	Abstract Bladder cancer is the most common malignant tumor of urinary system, and its morbidity and mortality are increasing rapidly. Although great advances have been made in medical technology in recent years, there is still a lack of effective prognostic and therapeutic methods for bladder cancer. NETs are reticulated DNA structures decorated with various protein substances released extracellularly by neutrophils stimulated by strong signals. Recently, it has been found that NETs are closely related to the growth, metastasis and drug resistance of many types of cancers. However, up to now, the research on the relationship between NETs and bladder cancer is still not enough. In this study, we aimed to conduct a comprehensive analysis of NRGs in bladder cancer tissues to evaluate the relationship between NRGs and prognosis prediction and sensitivity to therapy in patients with bladder cancer. We scored NRGs in each tissue by using ssGSEA, and selected gene sets that were significantly associated with NRGs scores by using the WCGNA algorithm. Based on the expression profiles of NRGs-related genes, NMF clustering analysis was performed to identify different BLCA molecular subtypes. For the differentially expressed genes between subtypes, we used univariate COX regression, LASSO regression and multivariate COX regression to further construct a hierarchical model of BLCA patients containing 10 genes. This model and the nomogram based on this model can accurately predict the prognosis of BLCA patients in multiple datasets. Besides, BLCA patients classified based on this model differ greatly in their sensitivity to immunotherapy and targeted therapies, which providing a reference for individualized treatment of patients with bladder cancer.
Keywords	Medicine ; R ; Science ; Q
Subject code	616
Language	English
Publishing date	2023-11-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Masking and unmasking fishing down effects: The Bohai Sea (China) as a case study

Liang, Cui / Pauly, Daniel

Ocean & coastal management. 2020 Feb. 01, v. 184

2020

Abstract: The Bohai Sea, in Northeastern China, which has been severely overexploited since the 1950s, is not only an exemplary case of the ‘fishing down’ phenomenon (where large, high-trophic level fish are replaced by smaller fish and invertebrates as the ... ...

Abstract	The Bohai Sea, in Northeastern China, which has been severely overexploited since the 1950s, is not only an exemplary case of the ‘fishing down’ phenomenon (where large, high-trophic level fish are replaced by smaller fish and invertebrates as the overall biomass is reduced), but also can be used to illustrate one of the masking effects for fishing down. Thus, the decadal decline in the mean trophic level of the biomass in the Bohai Sea is more pronounced than the decline of the mean trophic level of the catch extracted from that sea. This effect is similar to what occurred in the Celtic Sea, where previous authors called this difference ‘skipper effect’ (because skippers try to maintain catches of larger fish), and in the Gulf of Thailand. The skipper effect appears to be a powerful masking factor for the fishing down phenomenon, i.e., biomass tend to be more affected than suggested by time series of the mean trophic of catches.
Keywords	biomass ; case studies ; coastal zone management ; fish ; invertebrates ; time series analysis ; trophic levels ; China ; Thailand ; Yellow Sea
Language	English
Dates of publication	2020-0201
Publishing place	Elsevier Ltd
Document type	Article
ISSN	0964-5691
DOI	10.1016/j.ocecoaman.2019.105033
Database	NAL-Catalogue (AGRICOLA)

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