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Book ; Online: Golden Ratio Information for Neural Spike Code

Deng, Bo

2023

Abstract: Spike bursting is a ubiquitous feature of all neuronal systems. Assuming the spiking states form an alphabet for a communication system, what is the optimal information processing rate? and what is the channel capacity? Here we demonstrate that the ... ...

Abstract	Spike bursting is a ubiquitous feature of all neuronal systems. Assuming the spiking states form an alphabet for a communication system, what is the optimal information processing rate? and what is the channel capacity? Here we demonstrate that the quaternary alphabet of spike number code gives the maximal processing rate, and that a binary source in Golden Ratio distribution gives rise to the channel capacity. A multi-time scaled neural circuit is shown to satisfy the hypotheses of this neural communication system.
Keywords	Quantitative Biology - Neurons and Cognition
Publishing date	2023-11-14
Publishing country	us
Document type	Book ; Online
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Article ; Online: Backward bifurcation of a plant virus dynamics model with nonlinear continuous and impulsive control.

Qiu, Guangming / Yang, Zhizhong / Deng, Bo

Mathematical biosciences and engineering : MBE

2024 Volume 21, Issue 3, Page(s) 4056–4084

Abstract: Roguing and elimination of vectors are the most commonly seen biological control strategies regarding the spread of plant viruses. It is practically significant to establish the mathematical models of plant virus transmission and regard the effect of ... ...

Abstract	Roguing and elimination of vectors are the most commonly seen biological control strategies regarding the spread of plant viruses. It is practically significant to establish the mathematical models of plant virus transmission and regard the effect of removing infected plants as well as eliminating vector strategies on plant virus eradication. We proposed the mathematical models of plant virus transmission with nonlinear continuous and pulse removal of infected plants and vectors. In terms of the nonlinear continuous control strategy, the threshold values of the existence and stability of multiple equilibria have been provided. Moreover, the conditions for the occurrence of backward bifurcation were also provided. Regarding the nonlinear impulsive control strategy, the stability of the disease-free periodic solution and the threshold of the persistence of the disease were given. With the application of the fixed point theory, the conditions for the existence of forward and backward bifurcations of the model were presented. Our results demonstrated that there was a backward bifurcation phenomenon in continuous systems, and there was also a backward bifurcation phenomenon in impulsive control systems. Moreover, we found that removing healthy plants increased the threshold $ R_{1}. $ Finally, numerical simulation was employed to verify our conclusions.
MeSH term(s)	Models, Biological ; Models, Theoretical ; Computer Simulation ; Plants ; Plant Viruses ; Nonlinear Dynamics
Language	English
Publishing date	2024-03-28
Publishing country	United States
Document type	Journal Article
ZDB-ID	2265126-3
ISSN	1551-0018 ; 1551-0018
ISSN (online)	1551-0018
ISSN	1551-0018
DOI	10.3934/mbe.2024179
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Advancements of 3D bioprinting in regenerative medicine: Exploring cell sources for organ fabrication.

Ma, Yue / Deng, Bo / He, Runbang / Huang, Pengyu

Heliyon

2024 Volume 10, Issue 3, Page(s) e24593

Abstract: 3D bioprinting has unlocked new possibilities for generating complex and functional tissues and organs. However, one of the greatest challenges lies in selecting the appropriate seed cells for constructing fully functional 3D artificial organs. Currently, ...

Abstract	3D bioprinting has unlocked new possibilities for generating complex and functional tissues and organs. However, one of the greatest challenges lies in selecting the appropriate seed cells for constructing fully functional 3D artificial organs. Currently, there are no cell sources available that can fulfill all requirements of 3D bioprinting technologies, and each cell source possesses unique characteristics suitable for specific applications. In this review, we explore the impact of different 3D bioprinting technologies and bioink materials on seed cells, providing a comprehensive overview of the current landscape of cell sources that have been used or hold potential in 3D bioprinting. We also summarized key points to guide the selection of seed cells for 3D bioprinting. Moreover, we offer insights into the prospects of seed cell sources in 3D bioprinted organs, highlighting their potential to revolutionize the fields of tissue engineering and regenerative medicine.
Language	English
Publishing date	2024-01-17
Publishing country	England
Document type	Journal Article ; Review
ZDB-ID	2835763-2
ISSN	2405-8440
ISSN	2405-8440
DOI	10.1016/j.heliyon.2024.e24593
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Article ; Online: Evaluation and optimization of FTIR spectroscopy to quantify PHA production by municipal wastewater sludge.

Deng, Bo / Rao, Lingfen / Rodriguez-Freire, Lucia

Spectrochimica acta. Part A, Molecular and biomolecular spectroscopy

2024 Volume 312, Page(s) 124012

Abstract: Polyhydroxyalkanoate (PHA) is a family of naturally-occurring biopolymers synthesized by more than 300 microorganisms in the environment. These biopolymers have been investigated as a source material to substitute fossil fuel-based polymers; hence the ... ...

Abstract	Polyhydroxyalkanoate (PHA) is a family of naturally-occurring biopolymers synthesized by more than 300 microorganisms in the environment. These biopolymers have been investigated as a source material to substitute fossil fuel-based polymers; hence the synthesis of biopolymers and their characterization is a critical step in optimizing the process. Because of this, the biological production of PHA using PHA-producing microorganisms is currently the dominating process; however, the use of microbial mixed culture (MMC), such as wastewater sludge, is gaining attention. Different than pure cultures, MMC has higher culturing condition tolerance since the complex species composition and is easily obtained from wastewater treatment plants, which shortens the culturing time, lowers the cost, and promotes the application. The main constraint in MMC-based PHA is the extraction and quantification of PHA from the more complex matrix. In this paper, Fourier-transform infrared (FTIR) spectroscopy is evaluated to be used as a quantification method of PHA in MMC systems. Firstly, commercially available analytical standards, which consist of PHA/PHB, and two different solvents (chloroform and dichloromethane), were used and tested by this method, with KBr card and liquid cell methods, and the results are validated by gas chromatography mass spectrometry (GC/MS). The method was then tested using 12 samples from wastewater treatment plants. The PHA content in biomass varied from 3.42 w/w% to 1.22 w/w% following extraction with chloroform as solvent as determined by this method. In the four different combination standards, the best one is consisted of PHB and chloroform, and FTIR-liquid cell showed higher promise for PHA quantification in complex matrices.
MeSH term(s)	Wastewater ; Sewage/chemistry ; Polyhydroxyalkanoates/analysis ; Spectroscopy, Fourier Transform Infrared/methods ; Chloroform ; Bioreactors ; Biopolymers
Chemical Substances	Wastewater ; Sewage ; Polyhydroxyalkanoates ; Chloroform (7V31YC746X) ; Biopolymers
Language	English
Publishing date	2024-02-10
Publishing country	England
Document type	Journal Article
ZDB-ID	210413-1
ISSN	1873-3557 ; 0370-8322 ; 0584-8539 ; 1386-1425
ISSN (online)	1873-3557
ISSN	0370-8322 ; 0584-8539 ; 1386-1425
DOI	10.1016/j.saa.2024.124012
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Article: Application and progress of advanced eye movement examinations in cognitive impairment.

Leng, Qi / Deng, Bo / Ju, Yi

Frontiers in aging neuroscience

2024 Volume 16, Page(s) 1377406

Abstract: The worldwide incidence of cognitive impairment is escalating, yet no effective solutions for these afflictions have been discovered. Consequently, the importance of early identification and immediate intervention is heightened. Advanced eye movements-a ... ...

Abstract	The worldwide incidence of cognitive impairment is escalating, yet no effective solutions for these afflictions have been discovered. Consequently, the importance of early identification and immediate intervention is heightened. Advanced eye movements-a form of voluntary eye movements that includes anti-saccades, memory-guided saccades, predictive saccades, pro-saccades and gap/overlap saccades, mediated by the cerebral cortex and subcortical pathways reflect cognitive levels and functions across different domains. In view of their objectivity, reproducibility, and non-invasive characteristics, advanced eye movement examination possesses significant prospective utility across a wide range of cognitive impairment. This paper extensively reviews various models associated with advanced eye movement examinations and their current applications in cognitive impairment such as Alzheimer's disease, Lewy body dementia and frontotemporal dementia. Advanced eye movement examination can serve as a biomarker for early screening diagnosis and research on cognitive impairment. In the future, combining advanced eye movement examination with neuropsychological scale assessment and other diagnostic methods may contribute to further early identification of these types of diseases.
Language	English
Publishing date	2024-04-17
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2558898-9
ISSN	1663-4365
ISSN	1663-4365
DOI	10.3389/fnagi.2024.1377406
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Article ; Online: A Swin transformer encoder-based StyleGAN for unbalanced endoscopic image enhancement.

Deng, Bo / Zheng, Xiangwei / Chen, Xuanchi / Zhang, Mingzhe

Computers in biology and medicine

2024 Volume 175, Page(s) 108472

Abstract: With the rapid development of artificial intelligence, automated endoscopy-assisted diagnostic systems have become an effective tool for reducing the diagnostic costs and shortening the treatment cycle of patients. Typically, the performance of these ... ...

Abstract	With the rapid development of artificial intelligence, automated endoscopy-assisted diagnostic systems have become an effective tool for reducing the diagnostic costs and shortening the treatment cycle of patients. Typically, the performance of these systems depends on deep learning models which are pre-trained with large-scale labeled data, for example, early gastric cancer based on endoscopic images. However, the expensive annotation and the subjectivity of the annotators lead to an insufficient and class-imbalanced endoscopic image dataset, and these datasets are detrimental to the training of deep learning models. Therefore, we proposed a Swin Transformer encoder-based StyleGAN (STE-StyleGAN) for unbalanced endoscopic image enhancement, which is composed of an adversarial learning encoder and generator. Firstly, a pre-trained Swin Transformer is introduced into the encoder to extract multi-scale features layer by layer from endoscopic images. The features are subsequently fed into a mapping block for aggregation and recombination. Secondly, a self-attention mechanism is applied to the generator, which adds detailed information of the image layer by layer through recoded features, enabling the generator to autonomously learn the coupling between different image regions. Finally, we conducted extensive experiments on a private intestinal metaplasia grading dataset from a Grade-A tertiary hospital. The experimental results show that the images generated by STE-StyleGAN are closer to the initial image distribution, achieving a Fréchet Inception Distance (FID) value of 100.4. Then, these generated images are used to enhance the initial dataset to improve the robustness of the classification model, and achieved a top accuracy of 86 %.
Language	English
Publishing date	2024-04-16
Publishing country	United States
Document type	Journal Article
ZDB-ID	127557-4
ISSN	1879-0534 ; 0010-4825
ISSN (online)	1879-0534
ISSN	0010-4825
DOI	10.1016/j.compbiomed.2024.108472
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Article ; Online: Research progress in the role and mechanism of acyloxyacyl hydrolase in diseases

WU Zhenkai / DENG Bo / PAN Yu / DING Feng

Shanghai Jiaotong Daxue xuebao. Yixue ban, Vol 43, Iss 1, Pp 101-

2023 Volume 107

Abstract: Lipopolysaccharide (LPS) is an essential component of the outer wall of gram-negative bacteria and can induce a strong inflammatory response in the body. Acyloxyacyl hydrolase (AOAH) is a highly conserved host lipase expressed in a variety of cells, ... ...

Abstract	Lipopolysaccharide (LPS) is an essential component of the outer wall of gram-negative bacteria and can induce a strong inflammatory response in the body. Acyloxyacyl hydrolase (AOAH) is a highly conserved host lipase expressed in a variety of cells, including neutrophils, macrophages and proximal tubular epithelial cells. AOAH can inactivate LPS by selectively removing the secondary acyl chains from the lipid A moiety of gram-negative bacterial LPS, which alleviates inflammation and tissue damage, promotes the recovery from the immune tolerance and regains normal responsiveness. It plays an essential role in host defenses against infection. Moreover, AOAH has been shown in vivo and in vitro for a variety of enzymatic activities including phospholipase, lysophospholipase and diacylglycerol lipase. Researches increasingly show that AOAH plays a critical role in various noninfectious diseases such as allergic asthma, psoriasis, chronic pelvic pain and other autoimmune diseases and chronic inflammatory diseases in addition to infections. Besides, DING Feng Research Group, Department of Nephrology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine found that AOAH was capable of attenuating renal fibrosis via proximal renal tubular epithelial cells CD74 signaling pathway. Given the increasingly diverse role of AOAH in diseases, this article reviews its sources, structure, effects and possible mechanisms in diseases in order to provide reference for future research on its roles in diseases and new lines of investigation into disease pathogenesis and novel therapeutic targets.
Keywords	lipopolysaccharide ; acyloxyacyl hydrolase (aoah) ; inflammation ; fibrosis ; Medicine ; R
Subject code	610
Language	Chinese
Publishing date	2023-01-01T00:00:00Z
Publisher	Editorial Office of Journal of Shanghai Jiao Tong University (Medical Science)
Document type	Article ; Online
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Article ; Online: An Inverse Problem: Trappers Drove Hares to Eat Lynx.

Deng, Bo

Acta biotheoretica

2018 Volume 66, Issue 3, Page(s) 213–242

Abstract: The Canadian lynx and snowshoe hare pelt data by the Hudson Bay Company did not fit the classical predator-prey theory. Rather than following the peak density of the hare, that of the lynx leads it, creating the hares-eat-lynx (HEL) paradox. Although ... ...

Abstract	The Canadian lynx and snowshoe hare pelt data by the Hudson Bay Company did not fit the classical predator-prey theory. Rather than following the peak density of the hare, that of the lynx leads it, creating the hares-eat-lynx (HEL) paradox. Although trappers were suspected to play a role, no mathematical model has ever demonstrated the HEL effect. Here we show that the long-held assumption that the pelt number is a proxy of the wild populations is false and that when the data are modeled by the harvest rates by the trappers, the problem is finally resolved: both the HEL paradox and the classical theory are unified in our mechanistic hare-lynx-competitor-trapper (HLCT) model where competitor stands for all predators of the hares other than the lynx. The result is obtained by systematically fitting the data to various models using Newton's inverse problem method. Main findings of this study include: the prey-eats-predator paradox in kills by an intraguild top-predator can occur if the top-predator prefers the predator to the prey; the benchmark HLCT model is more sensitive to all lynx-trapper interactions than to the respective hare-trapper interactions; the Hudson Bay Company's hare pelt number maybe under-reported; and, the most intriguing of all, the trappers did not interfere in each other's trapping activities.
MeSH term(s)	Algorithms ; Animals ; Canada ; Ecology ; Ecosystem ; Female ; Hares/physiology ; Lynx/physiology ; Male ; Models, Biological ; Models, Statistical ; Population Dynamics ; Predatory Behavior ; Reproducibility of Results
Language	English
Publishing date	2018-05-30
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	63-2
ISSN	1572-8358 ; 0001-5342
ISSN (online)	1572-8358
ISSN	0001-5342
DOI	10.1007/s10441-018-9333-z
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Article ; Online: Analytical solution of overlying pipe deformation caused by tunnel excavation based on Pasternak foundation model.

Fu, Daxi / Deng, Bo / Yang, Minghui / Zhen, Binbin

Scientific reports

2023 Volume 13, Issue 1, Page(s) 921

Abstract: The existing tunnel construction causes stratum deformation, which in turn leads to additional deformation and internal force of the overlying pipeline, thus increasing the risk of pipeline accidents. Then, how to correctly calculate the deformation and ... ...

Abstract	The existing tunnel construction causes stratum deformation, which in turn leads to additional deformation and internal force of the overlying pipeline, thus increasing the risk of pipeline accidents. Then, how to correctly calculate the deformation and internal force of pipeline is the key to pipeline safety evaluation. To this end, this study firstly used the Pasternak foundation beam model to simulate the interaction of pipeline and soil, and divided the pipeline into the void area (i.e., pipeline-soil detachment) and the coordination area (i.e., pipeline-soil is always deformed together) between pipeline and soil. The differential equation of pipeline deflection for the void area and the coordination area were established respectively, and the solutions of pipeline deflection, the internal force of pipeline and the width of pipeline-soil void area were presented. Subsequently, the accuracy of the proposed method was verified by comparing with the available model and field test data, and it is found that the calculation results are too conservative without considering the pipeline-soil voiding phenomenon. Finally, the detailed parametric analysis was conducted. The results show that the pipeline deflection decreases with the increase of the pipeline-tunnel spacing between pipeline and tunnel, the pipeline bending stiffness and the soil elastic modulus, but increases with the increase of the formation loss rate, and the width of pipeline-soil void area increases with the increase of the pipeline-tunnel spacing, the pipeline bending stiffness and the soil elastic modulus.
Language	English
Publishing date	2023-01-17
Publishing country	England
Document type	Journal Article
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-022-26635-8
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Article ; Online: Association between brachial-ankle pulse wave velocity and microvascular complications in type 2 diabetes mellitus.

Pei, Yifei / Shu, Yuan / Deng, Bo / Liu, Yuting

BMC endocrine disorders

2023 Volume 23, Issue 1, Page(s) 98

Abstract: Purpose/aim: To investigate the relationship between brachial-ankle pulse wave velocity (baPWV) and microvascular complications in type 2 diabetes mellitus (T2DM).: Materials and methods: From 2019 to 2021, our hospital enrolled 322 patients with ... ...

Abstract	Purpose/aim: To investigate the relationship between brachial-ankle pulse wave velocity (baPWV) and microvascular complications in type 2 diabetes mellitus (T2DM). Materials and methods: From 2019 to 2021, our hospital enrolled 322 patients with T2DM. Clinical information and biochemical indicators of patients were collected from the inpatient electronic medical record system and analyzed retrospectively. Fundus photography, nerve conduction testing, and sensory threshold measurement were all conducted on the subjects. We measured the pulse wave velocity on both sides of the arm and ankle, then averaged the results. The enrolled cases were divided into two groups based on the baPWV: Group 1 (<the reference cutoff value, n = 160) and Group 2 (≥ the reference cutoff value, n = 162). The association between associated factors and baPWV abnormalities was investigated using a logistic regression model.<br />Results: Group 2 had higher Systolic Blood Pressure(SBP), Diastolic Blood Pressure (DBP), duration of diabetes, Fasting Plasma Glucose (FPG), Blood Urea Nitrogen (BUN) and Serum Uric Acid (SUA) than group 1 (all p < 0.05). The prevalence of diabetic retinopathy, peripheral neuropathy and nephropathy in group 2 was higher compared to group 1 (p < 0.05). After classifying subjects according to the presence or absence of diabetic complications, we found that the baPWV of the Diabetic Peripheral Neuropathy (DPN) group and Diabetic Nephropathy (DN) group was noticeably higher than that of non-DPN group and non-DN group, respectively (both p < 0.05). The baPWV increased with the aggravation of Diabetic Retinopathy (DR) (p < 0.05). Multivariate logistic regression analysis showed that DBP (OR 1.039, 95%CI 1.010-1.068 p = 0.008), duration of diabetes (OR 1.059, 95%CI 1.017-1.103 p = 0.006), FPG (OR 1.104, 95%CI 1.025-1.188 p = 0.009) and BUN (OR 1.128, 95%CI 1.001-1.270 p = 0.048) were all independently and positively associated with baPWV. Conclusions: The baPWV is strongly associated with microvascular complications of T2DM. The DBP, duration of diabetes, FPG, and BUN were all independent associated factors of baPWV.
MeSH term(s)	Humans ; Diabetes Mellitus, Type 2/complications ; Diabetes Mellitus, Type 2/epidemiology ; Ankle Brachial Index ; Diabetic Retinopathy/diagnosis ; Diabetic Retinopathy/epidemiology ; Diabetic Retinopathy/etiology ; Ankle ; Retrospective Studies ; Pulse Wave Analysis ; Uric Acid ; Blood Pressure ; Diabetic Nephropathies/complications ; Risk Factors
Chemical Substances	Uric Acid (268B43MJ25)
Language	English
Publishing date	2023-05-04
Publishing country	England
Document type	Journal Article
ZDB-ID	2091323-0
ISSN	1472-6823 ; 1472-6823
ISSN (online)	1472-6823
ISSN	1472-6823
DOI	10.1186/s12902-023-01355-w
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