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Article ; Online: All who wander are not lost: the search for homology during homologous recombination.

Hu, Jingyi / Crickard, J Brooks

2024 Volume 52, Issue 1, Page(s) 367–377

Abstract: Homologous recombination (HR) is a template-based DNA double-strand break repair pathway that functions to maintain genomic integrity. A vital component of the HR reaction is the identification of template DNA to be used during repair. This occurs ... ...

Abstract	Homologous recombination (HR) is a template-based DNA double-strand break repair pathway that functions to maintain genomic integrity. A vital component of the HR reaction is the identification of template DNA to be used during repair. This occurs through a mechanism known as the homology search. The homology search occurs in two steps: a collision step in which two pieces of DNA are forced to collide and a selection step that results in homologous pairing between matching DNA sequences. Selection of a homologous template is facilitated by recombinases of the RecA/Rad51 family of proteins in cooperation with helicases, translocases, and topoisomerases that determine the overall fidelity of the match. This menagerie of molecular machines acts to regulate critical intermediates during the homology search. These intermediates include recombinase filaments that probe for short stretches of homology and early strand invasion intermediates in the form of displacement loops (D-loops) that stabilize paired DNA. Here, we will discuss recent advances in understanding how these specific intermediates are regulated on the molecular level during the HR reaction. We will also discuss how the stability of these intermediates influences the ultimate outcomes of the HR reaction. Finally, we will discuss recent physiological models developed to explain how the homology search protects the genome.
MeSH term(s)	Homologous Recombination ; DNA/metabolism ; DNA Repair ; DNA Helicases/metabolism ; DNA Breaks, Double-Stranded ; Proteins/genetics
Chemical Substances	DNA (9007-49-2) ; DNA Helicases (EC 3.6.4.-) ; Proteins
Language	English
Publishing date	2024-02-07
Publishing country	England
Document type	Journal Article
ZDB-ID	184237-7
ISSN	1470-8752 ; 0300-5127
ISSN (online)	1470-8752
ISSN	0300-5127
DOI	10.1042/BST20230705
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Article: An attention-based approach for assessing the effectiveness of emotion-evoking in immersive environment.

Liu, Feng / Zhou, Yihao / Hu, Jingyi

Heliyon

2024 Volume 10, Issue 3, Page(s) e25017

Abstract: Visual stimuli within an immersive virtual environment impact human perception and behavior in notably different ways compared to the real world. Previous studies have presented evidence indicating that individuals in various emotional states exhibit an ... ...

Abstract	Visual stimuli within an immersive virtual environment impact human perception and behavior in notably different ways compared to the real world. Previous studies have presented evidence indicating that individuals in various emotional states exhibit an unconscious attentional bias toward either positive or negative stimuli. However, whether these findings can be replicated within an immersive virtual environment remains uncertain. In this study, we devised an attention-based experiment to explore whether the correlation between participants' emotional states and the valence of visual stimuli influences their attentional bias. Participants (n=28) viewed 360-degree videos with varying valence levels (positive and negative) to evoke emotions. Subsequently, we utilized standard emotional human faces as stimuli to assess how the consistency in video valence and emotional faces affects reaction time (RT) in Go tasks and error rates in No-go tasks. We employed the Ex-Gaussian approach to analyze the RT data. The parameters-mu (
Language	English
Publishing date	2024-01-22
Publishing country	England
Document type	Journal Article
ZDB-ID	2835763-2
ISSN	2405-8440
ISSN	2405-8440
DOI	10.1016/j.heliyon.2024.e25017
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Article ; Online: Chemical vapor deposition growth of graphene and other nanomaterials with 3D architectures towards electrocatalysis and secondary battery-related applications.

Peng, You / Hu, Jingyi / Huan, Yahuan / Zhang, Yanfeng

Nanoscale

2024 Volume 16, Issue 16, Page(s) 7734–7751

Abstract: Recently, two-dimensional (2D) layered materials, such as graphene and transition metal dichalcogenides (TMDCs), have garnered a lot of attention in energy storage/conversion-related fields due to their novel physical and chemical properties. ... ...

Abstract	Recently, two-dimensional (2D) layered materials, such as graphene and transition metal dichalcogenides (TMDCs), have garnered a lot of attention in energy storage/conversion-related fields due to their novel physical and chemical properties. Constructing flat graphene and TMDCs nanosheets into 3D architectures can significantly increase their exposed surface area and prevent the restacking of adjacent 2D layers, thus dramatically promoting their applications in various energy-related fields. Chemical Vapor Deposition (CVD) is a low-cost, facile, and scalable method, which has been widely employed to produce high-quality graphene and TMDCs nanosheets with 3D architectures. During the CVD process, the morphologies and properties of the 3D architectures of such 2D materials can be designed by selecting substrates with different compositions, stacking geometries, and micro-structures. In this review, we focus on the recent advances in the CVD synthesis of graphene, TMDCs, and their hybrids with 3D architectures on different 3D-structured substrates, as well as their applications in the electrocatalytic hydrogen evolution reaction (HER) and various secondary batteries. In addition, the challenges and future prospects for the CVD synthesis and energy-related applications of these unique layered materials will also be discussed.
Language	English
Publishing date	2024-04-25
Publishing country	England
Document type	Journal Article ; Review
ZDB-ID	2515664-0
ISSN	2040-3372 ; 2040-3364
ISSN (online)	2040-3372
ISSN	2040-3364
DOI	10.1039/d3nr06143d
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Article: Reduced interocular suppression after inverse patching in anisometropic amblyopia.

Hu, Jingyi / Chen, Jing / Ku, Yixuan / Yu, Minbin

Frontiers in neuroscience

2023 Volume 17, Page(s) 1280436

Abstract: Purpose: Recent investigations observed substantial enhancements in binocular balance, visual acuity, and stereovision among older children and adults with amblyopia by patching the amblyopic eye (i.e., inverse patching) for 2 h daily over 2 months. ... ...

Abstract	Purpose: Recent investigations observed substantial enhancements in binocular balance, visual acuity, and stereovision among older children and adults with amblyopia by patching the amblyopic eye (i.e., inverse patching) for 2 h daily over 2 months. Despite these promising findings, the precise neural mechanisms underlying inverse patching remain elusive. This study endeavors to delve deeper into the neural alterations induced by inverse patching, focusing on steady-state visual evoked potentials (SSVEPs). We specifically investigate the changes in SSVEPs following monocular deprivation of either the fellow eye or the amblyopic eye in older amblyopic children and adults. Method: Ten participants (17.60 ± 2.03 years old; mean ± SEM), clinically diagnosed with anisometropic amblyopia, were recruited for this study. Each participant underwent a 120 min patching session on their fellow eye on the first day, followed by a similar session on their amblyopic eye on the second day. Baseline steady-state visual evoked potentials (SSVEPs) measurements were collected each day prior to patching, with post-patching SSVEPs measurements obtained immediately after the patching session. The experimental design incorporated a binocular rivalry paradigm, utilizing SSVEPs measurements. Results: The results revealed that inverse patching induced a heightened influence on neural plasticity, manifesting in a reduction of interocular suppression from the fellow eye to the amblyopic eye. In contrast, patching the fellow eye demonstrated negligible effects on the visual cortex. Furthermore, alterations in interocular suppression subsequent to inverse patching exhibited a correlation with the visual acuity of the amblyopic eye. Conclusion: Inverse patching emerges as a promising therapeutic avenue for adolescents and adults grappling with severe anisometropic amblyopia that proves refractory to conventional interventions. This innovative approach exhibits the potential to induce more robust neural plasticity within the visual cortex, thereby modulating neural interactions more effectively than traditional amblyopia treatments.
Language	English
Publishing date	2023-12-11
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2411902-7
ISSN	1662-453X ; 1662-4548
ISSN (online)	1662-453X
ISSN	1662-4548
DOI	10.3389/fnins.2023.1280436
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Article ; Online: Association between antihypertensive drugs and hepatocellular carcinoma: A trans-ancestry and drug-target Mendelian randomization study.

Wang, Zhenqian / Lu, Jiawen / Hu, Jingyi

Liver international : official journal of the International Association for the Study of the Liver

2023 Volume 43, Issue 6, Page(s) 1320–1331

Abstract: Background and aims: Antihypertensive drugs were recently reported to have an oncogenic role in common cancer, however, whether these drugs would affect the risk of hepatocellular carcinoma (HCC) remains unclear.: Methods: A drug-target Mendelian ... ...

Abstract	Background and aims: Antihypertensive drugs were recently reported to have an oncogenic role in common cancer, however, whether these drugs would affect the risk of hepatocellular carcinoma (HCC) remains unclear. Methods: A drug-target Mendelian randomization method was adopted to examine the long-term effect of 12 antihypertensive drugs classes on the risk of HCC in Europeans and East Asians. To proxy antihypertensive drugs, we leveraged genetic variants located near or within drug target genes that were associated with systolic blood pressure (SBP). Genetically proxied drugs associated with reduced risk of coronary artery disease were included in primary analysis. Genetic summary statistics of SBP and HCC were derived from publicly available large-scale genome-wide association studies in Europeans and East Asians respectively. Expression quantitative trait loci (eQTLs) of drugs target genes were used to proxy drugs in a sensitivity analysis. Results: Genetically proxied thiazides and related diuretics were associated with decreased risk of HCC in both Europeans (OR [95% CI]: 0.79 [0.73, 0.86] per 1 mmHg reduction in SBP; p < 0.001) and East Asians (0.60 [0.45, 0.82]; p = 0.001). Genetically proxied beta-adrenoceptor blockers (BBs) were strongly associated with increased risk of HCC in Europeans (1.46 [1.12, 1.91]; p = 0.004). These findings were replicated in deCODE genetics study and remained consistent when using eQTLs to proxy antihypertensive drugs. Conclusions: Our findings suggested that thiazides diuretics may lower the risk of HCC in both Europeans and East Asians, while BBs may increase the risk of HCC specifically in Europeans. Further studies are warranted to explore the potential of repurposing or retargeting antihypertensive drugs for HCC prevention.
MeSH term(s)	Humans ; Antihypertensive Agents/therapeutic use ; Carcinoma, Hepatocellular/drug therapy ; Mendelian Randomization Analysis ; Genome-Wide Association Study ; Liver Neoplasms/drug therapy ; Diuretics ; Adrenergic beta-Antagonists ; Thiazides ; Polymorphism, Single Nucleotide
Chemical Substances	Antihypertensive Agents ; Diuretics ; Adrenergic beta-Antagonists ; Thiazides
Language	English
Publishing date	2023-04-08
Publishing country	United States
Document type	Journal Article
ZDB-ID	2102783-3
ISSN	1478-3231 ; 1478-3223
ISSN (online)	1478-3231
ISSN	1478-3223
DOI	10.1111/liv.15566
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Zs.A 1632: Show issues

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Article ; Online: Mechanism of growth inhibition mediated by disorder of chlorophyll metabolism in rice (Oryza sativa) under the stress of three polycyclic aromatic hydrocarbons.

Hu, Jingyi / Chen, Jie / Wang, Wei / Zhu, Lizhong

Chemosphere

2023 Volume 329, Page(s) 138554

Abstract: Photosynthesis mediated by chlorophyll metabolism is the basis for plant growth, and also the important regulatory mechanism of carbon pool in cropland ecosystems. Soil organic pollutants induced growth inhibition in crop plants, herein, we conducted an ... ...

Abstract	Photosynthesis mediated by chlorophyll metabolism is the basis for plant growth, and also the important regulatory mechanism of carbon pool in cropland ecosystems. Soil organic pollutants induced growth inhibition in crop plants, herein, we conducted an in-depth investigation on the effects of three representative polycyclic aromatic hydrocarbons (PAHs), including phenanthrene (PHE), pyrene (PYR), and benzo[a]pyrene (BaP) on rice (Oryza sativa) growth and photosynthesis. PAHs were absorbed via root uptake and accumulated in leaves, causing the swelling of thylakoids and the increase of osmiophilic granules in chloroplasts. The actual quantum efficiency of PSII was significantly decreased under the stress of PHE, PYR, and BaP by 29.9%, 11.9%, and 24.1% respectively, indicating the inhibition in photon absorption and transfer, which was consistent with the decrease of chlorophyll a (22.3%-32.2% compared to the control) in rice leaves. Twenty-two encoding genes involved in chlorophyll metabolism were determined and the results indicated that the expression of chlorophyll synthetases was downregulated by over 50% whereas the degradation process was promoted. Consequently, the production of carbohydrates and the carbon fixation were inhibited, which revealed by the downregulation of intermediate metabolites in Calvin cycle and the declined carboxylation rate. The disturbed photosynthesis resulted in the decrease of the biomasses of both roots (21.0%-42.7%) and leaves (6.4%-22.1%) under the tested PAH stresses. The findings of this study implied that the photosynthetic inhibition was possibly attributed to the disorder of chlorophyll metabolism, thus providing novel insights into the mechanism of growth inhibition induced by organic pollutants and theoretical basis for the estimation of cropland carbon sequestration potential.
MeSH term(s)	Polycyclic Aromatic Hydrocarbons/metabolism ; Oryza/metabolism ; Chlorophyll A/metabolism ; Ecosystem ; Photosynthesis ; Environmental Pollutants/metabolism ; Chlorophyll/metabolism
Chemical Substances	Polycyclic Aromatic Hydrocarbons ; Chlorophyll A (YF5Q9EJC8Y) ; phenanthrene (448J8E5BST) ; pyrene (9E0T7WFW93) ; Environmental Pollutants ; Chlorophyll (1406-65-1)
Language	English
Publishing date	2023-04-08
Publishing country	England
Document type	Journal Article
ZDB-ID	120089-6
ISSN	1879-1298 ; 0045-6535 ; 0366-7111
ISSN (online)	1879-1298
ISSN	0045-6535 ; 0366-7111
DOI	10.1016/j.chemosphere.2023.138554
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Article ; Online: The impact of carbon finance on energy consumption structure: evidence from China

Geng, Limin / Hu, Jingyi / Shen, Wenxing

Environ Sci Pollut Res. 2023 Mar., v. 30, no. 11 p.30107-30121

2023

Abstract: As a financial innovation model to promote sustainable economic development, carbon finance promotes green and inclusive economic development by reshaping the financial system. As a big energy consumer, China has been committed to the green ... ...

Abstract	As a financial innovation model to promote sustainable economic development, carbon finance promotes green and inclusive economic development by reshaping the financial system. As a big energy consumer, China has been committed to the green transformation of energy structure, and carbon finance has been regarded as an important tool to support carbon emission reduction. This paper divides carbon finance from three levels, financial macro, environmental governance, and technological development, and selects 17 indexes to measure the development level of carbon finance in China. Time series regression model and the entropy weight method (EWM) are used to analyze the impact of carbon finance on China’s energy consumption structure. The empirical results show that carbon finance plays a positive role in promoting China’s energy consumption structure, and developing carbon finance is conducive to the use of clean energy and the optimization of energy consumption structure in China; carbon finance can further optimize China’s energy consumption structure by investing capital, resources, and technology in industries related to promoting clean energy consumption. Therefore, China should continue to develop carbon finance and promote the establishment of a unified national carbon trading market; at the same time, China should use the CCER trading mechanism to promote the development of renewable energy and enhance the endogenous driving force of energy transformation by promoting technological progress.
Keywords	capital ; carbon ; clean energy ; economic development ; energy conversion ; entropy ; environmental governance ; finance ; markets ; models ; regression analysis ; renewable energy sources ; time series analysis ; China
Language	English
Dates of publication	2023-03
Size	p. 30107-30121.
Publishing place	Springer Berlin Heidelberg
Document type	Article ; Online
ZDB-ID	1178791-0
ISSN	1614-7499 ; 0944-1344
ISSN (online)	1614-7499
ISSN	0944-1344
DOI	10.1007/s11356-022-24303-y
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Mechanism of growth inhibition mediated by disorder of chlorophyll metabolism in rice (Oryza sativa) under the stress of three polycyclic aromatic hydrocarbons

Hu, Jingyi / Chen, Jie / Wang, Wei / Zhu, Lizhong

Chemosphere. 2023 July, v. 329 p.138554-

2023

Abstract	Photosynthesis mediated by chlorophyll metabolism is the basis for plant growth, and also the important regulatory mechanism of carbon pool in cropland ecosystems. Soil organic pollutants induced growth inhibition in crop plants, herein, we conducted an in-depth investigation on the effects of three representative polycyclic aromatic hydrocarbons (PAHs), including phenanthrene (PHE), pyrene (PYR), and benzo[a]pyrene (BaP) on rice (Oryza sativa) growth and photosynthesis. PAHs were absorbed via root uptake and accumulated in leaves, causing the swelling of thylakoids and the increase of osmiophilic granules in chloroplasts. The actual quantum efficiency of PSII was significantly decreased under the stress of PHE, PYR, and BaP by 29.9%, 11.9%, and 24.1% respectively, indicating the inhibition in photon absorption and transfer, which was consistent with the decrease of chlorophyll a (22.3%–32.2% compared to the control) in rice leaves. Twenty-two encoding genes involved in chlorophyll metabolism were determined and the results indicated that the expression of chlorophyll synthetases was downregulated by over 50% whereas the degradation process was promoted. Consequently, the production of carbohydrates and the carbon fixation were inhibited, which revealed by the downregulation of intermediate metabolites in Calvin cycle and the declined carboxylation rate. The disturbed photosynthesis resulted in the decrease of the biomasses of both roots (21.0%–42.7%) and leaves (6.4%–22.1%) under the tested PAH stresses. The findings of this study implied that the photosynthetic inhibition was possibly attributed to the disorder of chlorophyll metabolism, thus providing novel insights into the mechanism of growth inhibition induced by organic pollutants and theoretical basis for the estimation of cropland carbon sequestration potential.
Keywords	Calvin cycle ; Oryza sativa ; absorption ; carbon dioxide fixation ; carbon sequestration ; carbon sinks ; carboxylation ; chlorophyll ; cropland ; growth retardation ; ligases ; metabolites ; phenanthrenes ; photons ; photosystem II ; plant growth ; rice ; soil ; thylakoids ; Polycyclic aromatic hydrocarbons ; Chlorophyll metabolism ; Photosynthesis
Language	English
Dates of publication	2023-07
Publishing place	Elsevier Ltd
Document type	Article ; Online
ZDB-ID	120089-6
ISSN	1879-1298 ; 0045-6535 ; 0366-7111
ISSN (online)	1879-1298
ISSN	0045-6535 ; 0366-7111
DOI	10.1016/j.chemosphere.2023.138554
Database	NAL-Catalogue (AGRICOLA)

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Article: A systematic review and meta-analysis comparing the diagnostic capability of automated breast ultrasound and contrast-enhanced ultrasound in breast cancer.

Zhang, Haoyu / Hu, Jingyi / Meng, Rong / Liu, Fangfang / Xu, Fan / Huang, Min

Frontiers in oncology

2024 Volume 13, Page(s) 1305545

Abstract: Objective: To compare the diagnostic performance of automated breast ultrasound (ABUS) and contrast-enhanced ultrasound (CEUS) in breast cancer.: Methods: Published studies were collected by systematically searching the databases PubMed, Embase, ... ...

Abstract	Objective: To compare the diagnostic performance of automated breast ultrasound (ABUS) and contrast-enhanced ultrasound (CEUS) in breast cancer. Methods: Published studies were collected by systematically searching the databases PubMed, Embase, Cochrane Library and Web of Science. The sensitivities, specificities, likelihood ratios and diagnostic odds ratio (DOR) were confirmed. The symmetric receiver operator characteristic curve (SROC) was used to assess the threshold of ABUS and CEUS. Fagan's nomogram was drawn. Meta-regression and subgroup analyses were applied to search for sources of heterogeneity among the included studies. Results: A total of 16 studies were included, comprising 4115 participants. The combined sensitivity of ABUS was 0.88 [95% CI (0.73-0.95)], specificity was 0.93 [95% CI (0.82-0.97)], area under the SROC curve (AUC) was 0.96 [95% CI (0.94-0.96)] and DOR was 89. The combined sensitivity of CEUS was 0.88 [95% CI (0.84-0.91)], specificity was 0.76 [95% CI (0.66-0.84)], AUC was 0.89 [95% CI (0.86-0.92)] and DOR was 24. The Deeks' funnel plot showed no existing publication bias. The prospective design, partial verification bias and blinding contributed to the heterogeneity in specificity, while no sources contributed to the heterogeneity in sensitivity. The post-test probability of ABUS in BC was 75%, and the post-test probability of CEUS in breast cancer was 48%. Conclusion: Compared with CEUS, ABUS showed higher specificity and DOR for detecting breast cancer. ABUS is expected to further improve the accuracy of BC diagnosis.
Language	English
Publishing date	2024-01-09
Publishing country	Switzerland
Document type	Systematic Review
ZDB-ID	2649216-7
ISSN	2234-943X
ISSN	2234-943X
DOI	10.3389/fonc.2023.1305545
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Article: Clinical value of lymphocyte count in autoimmune diabetic nephropathy.

Xiang, Zhongyuan / Liu, Wen'en / Fu, Sangya / Hu, Jingyi / Yang, Yanyi

Zhong nan da xue xue bao. Yi xue ban = Journal of Central South University. Medical sciences

2024 Volume 48, Issue 11, Page(s) 1639–1649

Abstract: Objectives: In recent years, the prevalence of diabetic nephropathy (DN) has increased significantly. An increasing number of studies have shown that lymphocyte-associated inflammatory responses play a role in DN. This study aims to investigate the ... ...

Title translation	淋巴细胞计数在自身免疫性糖尿病肾病中的临床价值（英文）.
Abstract	Objectives: In recent years, the prevalence of diabetic nephropathy (DN) has increased significantly. An increasing number of studies have shown that lymphocyte-associated inflammatory responses play a role in DN. This study aims to investigate the relationship between lymphocytes and DN in patients with autoimmune diabetes. Methods: The clinical data of 226 patients with Type 1 diabetes (T1D) and 79 patients with latent autoimmune diabetes in adults (LADA) were retrospectively studied and stratified according to the urinary albumin to creatinine ratio (ACR). Risk factors associated with DN were analyzed using correlation analysis and logistic regression. Results: In T1D and LADA patients, systolic blood pressure (SBP), uric acid duration, and diabetes duration in patients with normoalbuminuria were lower or shorter than those in patients with macroalbuminuria ( Conclusions: Lymphocyte counts in autoimmune diabetic patients are closely associated with DN, suggesting that lymphocyte-mediated inflammation may be involved in the pathogenesis of DN in autoimmune diabetic patients. This study provides a possible perspective for using lymphocytes as a potential biomarker for the early identification of individuals at risk for DN and potential therapeutic targets for DN.
MeSH term(s)	Adult ; Humans ; Diabetic Nephropathies ; Diabetes Mellitus, Type 1/complications ; Retrospective Studies ; Lymphocyte Count ; Risk Factors ; Albuminuria
Language	Chinese
Publishing date	2024-03-01
Publishing country	China
Document type	Journal Article
ZDB-ID	2168533-2
ISSN	1672-7347
ISSN	1672-7347
DOI	10.11817/j.issn.1672-7347.2023.230110
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