bluuebunny/crossref_metadata_2025 huggingface dataset:
Modeling the molecular fingerprint of protein-lipid interactions of MLKL on complex bilayers
Authors: Ramirez Ricardo X. , Campbell Oluwatoyin , Pradhan Apoorva J. , Atilla-Gokcumen G. Ekin , Monje-Galvan Viviana
Published: January 2023

Lipids, the structural part of membranes, play important roles in biological functions. However, our understanding of their implication in key cellular processes such as cell division and protein-lipid interaction is just emerging. This is the case for molecular interactions in mechanisms of cell death, where the role of lipids for protein localization and subsequent membrane permeabilization is key. For example, during the last stage of necroptosis, the mixed lineage kinase domain-like (MLKL) protein translocates and, eventually, permeabilizes the plasma membrane (PM). This process results in the leakage of cellular content, inducing an inflammatory response in the microenvironment that is conducive to oncogenesis and metastasis, among other pathologies that exhibit inflammatory activity. This work presents insights from long all-atom molecular dynamics (MD) simulations of complex membrane models for the PM of mammalian cells with an MLKL protein monomer. Our results show that the binding of the protein is initially driven by the electrostatic interactions of positively charged residues. The protein bound conformation modulates lipid recruitment to the binding site, which changes the local lipid environment recruiting PIP lipids and cholesterol, generating a unique fingerprint. These results increase our knowledge of protein-lipid interactions at the membrane interface in the context of molecular mechanisms of the necroptotic pathway, currently under investigation as a potential treatment target in cancer and inflamatory diseases.
A biocatalytic peptidobiosensing molecular bridge for detecting osteosarcoma marker protein
Authors: Jing Pengwei , Wang Ying , Sun Weixue , Li Guishi , Zhang Zuofu , Xu Qiang , Li Hao
Published: January 2023

A biosensing scheme requiring only one-step sample incubation before signal collection, and using a compact “three-in-one” probe of target-binding, signal conversion, and amplification, may greatly simplify the design of biosensors. Therefore, sparing the multi-step addition of enzymes, protein, and nanomaterial, as well as the associated complexity and non-specific interactions. In this work, a peptide probe aimed at such compact features has been designed, based on protein-triggered, conformation-driven, and Cu (II) facilitated side-chain di-tyrosine cyclization. This design can use target-probe recognition to induce discriminated cross-linking and self-cleavage of the probe, resulting in retention or dissociation of a signal amplification motif from the search and consequently quantitative detection performance. The method has also been tested preliminarily in fractioned osteosarcoma clinical samples, showing an acceptable coherence between signal readout and clinical diagnosis. On the basis of these early findings, it is reasonable to assume that the proposed probe will be beneficial for the next development of tumor screening and prognosis sensors.
Development of an analytical method for accurate and precise determination of rare earth element concentrations in geological materials using an MC-ICP-MS and group separation
Authors: Lee Seung-Gu , Ko Kyung-Seok
Published: January 2023

The concentration of rare earth elements (REEs) in geological materials including SLRS-6 (natural water certified reference material) and JB1b, JA1, and JG2 (Standard Rock Materials of Geological Survey of Japan) can be used as a tracer to characterize various geochemical processes in earth systems. Particularly, accurate and precise determination of rare earth element concentration in natural waters is difficult due to their extremely low concentration and the interference of polyatomic oxides. In this study, we developed a method for accurate and precise determination of the REE (particularly heavy rare earth elements) concentrations in geological materials including natural waters using a multi-collector inductively coupled plasma mass spectrometer (MC-ICP-MS) and group separation by 2-hydroxyisobutyric acid (HIBA). The REEs were separated into light rare earth elements (LREEs, La–Ce–Pr–Nd), middle rare earth elements (MREEs, Sm–Eu–Gd–Tb), and heavy rare earth elements (HREEs, Dy–Ho–Er–Tm–Yb–Lu) by a cation-exchange column (AG50W-X8 200–400 mesh) using HIBA. The recovery rates of each REE in the natural water sample exceeded 98%, whereas the recovery rates of each REE in rock materials exceeded 95% except for HREEs. The method developed in this study can accurately measure the REE concentrations (particularly HREE) in geological materials without polyatomic oxide interference during the REE analysis by using the MC-ICP-MS and, thus, can correctly interpret the geochemical implications of REEs in geological systems. The determination of the Sr concentrations and Sr isotopic ratios of SLRS-6 CRM and JB1b, JA1, and JG2 SRMs is also reported, and they are shown to be in good agreement with the recommended values.
The probiotic and immunomodulation effects of Limosilactobacillus reuteri RGW1 isolated from calf feces
Authors: Huang Kailang , Shi Weibing , Yang Bin , Wang Jiakun
Published: January 2023

Introduction

Limosilactobacillus reuteri is a gut symbiont with multiple remarkable beneficial effects on host health, and members of L. reuteri are valuable probiotic agents. However, L. reuteri showed obvious host specificity.

Methods

In our study, a novel L. reuteri RGW1 was isolated from feces of healthy calves, and its potential as a probiotic candidate were assessed, by combining in vitro, in vivo experiments and genomic analysis.

Results and discussion

RGW1 was sensitive to all the antibiotics tested, and it did not contain any virulence factor-coding genes. This isolate showed good tolerance to acid (pH 3.0), 0.3% bile salt, and simulated gastric fluid. Moreover, this isolate showed a high hydrophobicity index (73.7 ± 4.6%) and was able to adhere to Caco-2 cells, and antagonize Escherichia coli F5. Treatment of LPS-induced mice with RGW1 elevated TGF-β and IL-10 levels, while RGW1 cell-free supernatant (RCS) decreased TNF-α levels in the sera. Both RGW1 and RCS increased the villus height and villus height/crypt depth ratio of colon. Genomic analysis revealed the mechanism of the probiotic properties described above, and identified the capacity of RGW1 to biosynthesize L-lysine, folate, cobalamin and reuterin de novo. Our study demonstrated the novel bovine origin L. reuteri RGW1 had multiple probiotic characteristics and immunomodulation effects, and provided a deeper understanding of the relationship between these probiotic properties and genetic features.
Climate change, natural disasters, and international migration: A country-level analysis considering climatic zones
Authors: Martínez-Zarzoso Inma , Nowak-Lehmann Felicitas , Paschoaleto Rafael Duarte Lisboa
Published: January 2023

Climate change and natural disasters might increase the vulnerability of populations in affected regions. This article investigates the link between climatic events and bilateral migration from countries in the Global South to OECD countries. A gravity model is estimated using panel data techniques and bearing in mind potential sources of heterogeneity across subsamples. The main novelty is to distinguish by climatic zones, while also considering commonly used social and economic stresses, such as income levels and incidence of conflict. The analysis is based on bilateral emigration flows from 76 developing countries to OECD countries in the last decades. The results show that increasing extreme temperatures and storms in arid and semi-arid zones act as triggers of bilateral migration from South to North and that the estimated effects are non-negligible. The results are robust to a battery of tests, including dividing the sample according to the levels of conflict and poverty.
Comparative analyses of the effects of divergent winds on the kinetic energy budget with the adoptions of two methods during the extratropical transition of Typhoon Rumbia (1818)
Authors: Zhou Guanbo , Du Jia , Cao Jie , Liu Lu , Li Xingyu
Published: January 2023

Modification of the divergent wind components and domain of interests can result in obvious changes in the kinetic energy (KE) budget of typhoons and other synoptic systems. Before analyzing the effects of divergent winds on the KE budget of Typhoon Rumbia (2018) during its entire life cycle, especially in its extratropical transition (ET) process, a hybrid integral method to partition the horizontal wind fields in a limited domain with high accuracy is adopted, in comparison with the commonly used iterative method under two sets of domains, that is, the typhoon following domain and the outermost domain that covers the entire typhoon track. The relative importance of the divergent and non-divergent winds in the KE budget is investigated in the three stages of the ET process, namely, the pre-development, re-intensification, and dissipation stages. It is found that the divergent winds computed by the iterative method with a lower accuracy result in sizable errors in spatiotemporal variations of the KE of the typhoon during its ET process, which thus leads to obvious forecasting errors.
Study on triaxial test and constitutive prediction model of frozen silty clay
Authors: Teng Zhen-Chao , Teng Yun-Chao , Liu Jia-Lin , Zhou Ya-Dong , Liu Xiao-Yan , Li Zheng-Wei , Tao Cheng-Yun
Published: January 2023

With the increasing demand for engineering construction in the seasonal frozen area and the background of the Belt and Road Initiative, the frozen soil constitutive model should be studied in depth. At present, the constitutive prediction model of frozen silty clay has many problems, such as complex formula, single model application and poor prediction ability. Random forest optimal model hyperparameter input was very difficult. Particle Swarm Optimization (PSO) was used to optimize the parameters of the number of neurons, dropout and batch_size in the Long-term and Short-Term Memory network (LSTM) structure. The optimization results were 61, 0.09 and 95 respectively. The results showed that the strength tended to be stable after 6,9,6,9 and 9 freeze-thaw cycles under initial moisture content = 25, 22.5, 20, 17.5, and 15%, respectively. After 18 freeze-thaw cycles, the strength decreased by 2.66%, 11.85%, 18.83%, 16.79, and 29.02%, respectively. The predicted values of frozen soil binary medium model (BM), random forest model (RF) and PSO-LSTM model were compared with the measured values under different working conditions, and good accuracy was obtained. The R2 of the PSO-LSTM model test set was trained to more than 98%, and RMSE, MAE and MAPE were also trained to the lowest under the same working conditions. The influencing factors of deviator stress of frozen silty clay were given in order from strong to weak: initial moisture content>strain>confining pressure>number of freeze-thaw cycles. The LSTM optimal combination input parameters were searched by PSO, and the parameter adjustment speed of the model for the data learning process of frozen silty clay was greatly increased, which was conducive to the promotion of other soil constitutive prediction models. A new constitutive prediction model of frozen silty clay was developed using PSO-LSTM algorithm. 15 working conditions had been verified, and the optimal model had high accuracy in the constitutive prediction of frozen silty clay, which provided a good reference for the application of frozen soil engineering in cold regions.
Characteristics of in situ stress field of coalbed methane reservoir and its influence on permeability in western Guizhou coalfield, China
Authors: Lv Fang , Yang Ruidong , Yi Tongsheng , Gao Wei , Wang Xu , Cheng Wei , Zhang Yan , Li Ronglei , Yan Zhihua , Liu Yaohui , Li Geng
Published: January 2023

In-situ stress is an important indicator for the preferential selection of coalbed methane (CBM) exploration dessert zones, and is a key factor affecting the production capacity of coalbed methane wells. Coal reservoir permeability is one of the key parameters to evaluate the recoverability and modifiability of coalbed methane and reflects the seepage capacity of coal reservoirs. In this study, in situ stress data were collected from multiple injection/fall-off tests of multiple parameter wells in western Guizhou province, China The relationships among parameters such as pore pressure (Pp), closure pressure (Pc), breakdown pressure (Pb), in situ stress, coal permeability, and depth were explore. Using Anderson’s classification method, the distribution of three different in situ stress states was counted. A new simplified model diagram of triaxial principal stress and depth in the study area is proposed by linearly fitting the triaxial principal stress and burial depth. The envelope equation and median equation of the lateral pressure coefficient k-value stress ratio with depth of burial obtained by Brown and Hoek method were calculated using hyperbolic regression algorithm. The k-values were found to be discrete at shallower depths and converge at deeper depths, gradually converging to .65. The control of in situ stress on the permeability of coal reservoirs was explored, and a strong positive correlation was found between the permeability and the Z-shaped variation of the lateral pressure coefficient k-values at shallow depths of 1,000 m. Also, the distribution pattern of vertical permeability basically corresponds to the stress transition zone from the strike-slip fault mode to the normal fault mode. The coal seam permeability has a strong sensitivity to effective in situ stress (EIS). In this study, the least squares method with multiple fitting of power exponents is applied to analyze the control mechanism of EIS on permeability in depth and reveal a new relationship between permeability and EIS that is different from that considered by previous authors. Summarizing the above research results, the vertical CBM in western Guizhou is divided into three development potential zones, and 400–1,000 m burial depth is the most favorable vertical development zone.
Crater effects of shallow burial explosions in soil based on SPH-FEM analysis
Authors: Cui Ying , Li Zhangjian , Fang Jun , Zhao Ben
Published: January 2023

This study analyzed the effects and influencing factors of shallowly-buried explosions in soil based on the design and implementation of static explosion experiments and numerical simulations. Based on the static explosion test data, a numerical analysis model of SPH-FEM was established and the explosion process and pit parameters in explosions shallowly buried in soil were analyzed. The results of numerical calculations and comparisons verified the effectiveness of the SPH-FEM method in simulating shallowly-buried explosions in soil. Furthermore, the similarities and differences between the SPH-FEM and ALE methods in the numerical simulation of the same explosion in the soil were assessed. The relationships between the blasting pit radius and explosive depth, and between the explosives weight and pit volume were analyzed. The empirical curve formula of the explosive depth and the crater radius with 9.35 kg of TNT explosive were obtained by mathematical fitting. The results showed that the SPH-FEM method was more refined and more computationally efficient than the ALE method to simulate shallow burial explosions in soil. The established empirical curve formula, which expressed the relationship between the explosive burial depth and the pit radius, effectively predicted the pit radius of the shallow burial explosion. With increasing explosive burial depth, the pit radius increased to the peak value and then decreased rapidly.
Seismic architecture of Yongle isolated carbonate platform in Xisha Archipelago, South China Sea
Authors: Liu Gang , Wu Shiguo , Gao Jinwei , Zhang Hanyu , Han Xiaohui , Qin Yongpeng , Tian Liyan , Chen Wanli , Huang Xiaoxia
Published: January 2023

This study presented recently reprocessed multi-channel seismic data and multi-beam bathymetric map to reveal the geomorphology and stratigraphic architecture of the Yongle isolated carbonate platform in the Xisha Archipelago, northwestern South China Sea. Our results show that the upper slope angles of Yongle carbonate platform exceed 10° and even reach to ∼32.5° whereas the lower slope angles vary from .5° to 5.3°. The variations of slope angles show that margins of Yongle Atoll belong to escarpment (bypass) margins to erosional (escarpment) margins. The interior of carbonate platform is characterized by sub-parallel to parallel, semi-continuous to continuous reflectors with medium-to high-amplitude and low-to medium-frequency. The platform shows a sub-flat to flat-topped shape in its geometry with aggradation and backstepping occurring on the platform margins. According to our seismic-well correlation, the isolated carbonate platform started forming in Early Miocene, grew during Early to Middle Miocene, and subsequently underwent drowning in Late Miocene, Pliocene and Quaternary. Large-scale submarine mass transport deposits are observed in the southeastern and southern slopes of Yongle Atoll to reshape the slopes since Late Miocene. The magmatism and hydrothermal fluid flow pipes around the Yongle Atoll have been active during 10.5–2.6 Ma. Their activity might intensify dolomitization of the Xisha isolated carbonate platforms during Late Miocene to Pliocene. Our results further suggest that the Yongle carbonate platform is situated upon a pre-existing fault-bounded block with a flat pre-Cenozoic basement rather than a large scale volcano as previously known and the depth of the basement likely reached to 1400 m, which is deeper than the well CK-2 suggested.
CoFHE: Software and hardware Co-design for FHE-based machine learning as a service
Authors: Zheng Mengxin , Ju Lei , Jiang Lei
Published: January 2023

Introduction: Privacy concerns arise whenever sensitive data is outsourced to untrusted Machine Learning as a Service (MLaaS) platforms. Fully Homomorphic Encryption (FHE) emerges one of the most promising solutions to implementing privacy-preserving MLaaS. But prior FHE-based MLaaS faces challenges from both software and hardware perspectives. First, FHE can be implemented by various schemes including BGV, BFV, and CKKS, which are good at different FHE operations, e.g., additions, multiplications, and rotations. Different neural network architectures require different numbers of FHE operations, thereby preferring different FHE schemes. However, state-of-the-art MLaaS just naïvely chooses one FHE scheme to build FHE-based neural networks without considering other FHE schemes. Second, state-of-the-art MLaaS uses power-hungry hardware accelerators to process FHE-based inferences. Typically, prior high-performance FHE accelerators consume >160 Watt, due to their huge capacity (e.g., 512 MB) on-chip SRAM scratchpad memories.

Methods: In this paper, we propose a software and hardware co-designed FHE-based MLaaS framework, CoFHE. From the software perspective, we propose an FHE compiler to select the best FHE scheme for a network architecture. We also build a low-power and high-density NAND-SPIN and SRAM hybrid scratchpad memory system for FHE hardware accelerators.

Results: On average, under the same security and accuracy constraints, on average, CoFHE accelerates various FHE-based inferences by 18%, and reduces the energy consumption of various FHE-based inferences by 26%.

Discussion: CoFHE greatly improves the latency and energy efficiency of FHE-based MLaaS.
Glycaemic control and novel technology management strategies in pregestational diabetes mellitus
Authors: Newman Christine , Ero Adesuwa , Dunne Fidelma P.
Published: January 2023

Introduction

Pregestational diabetes (PGDM) is an increasingly common and complex condition that infers risk to both mother and infant. To prevent serious morbidity, strict glycaemic control is essential. The aim of this review is to review the glucose sensing and insulin delivering technologies currently available for women with PGDM.

Methods

We reviewed online databases for articles relating to technology use in pregnancy using a combination of keywords and MeSH headings. Relevant articles are included below.

Results

A number of technological advancements have improved care and outcomes for women with PGDM. Real time continuous glucose monitoring (rtCGM) offers clear advantages in terms of infants size and neonatal intensive care unit admissions; and further benefits are seen when combined with continuous subcutaneous insulin delivery (insulin pump) and algorithms which continuously adjust insulin levels to glucose targets (hybrid closed loop). Other advancements including flash or intermittent scanning CGM (isCGM) and stand-alone insulin pumps do not confer as many advantages for women and their infants, however they are increasingly used outside of pregnancy and many women enter pregnancy already using these devices.

Discussion

This article offers a discussion of the most commonly used technologies in pregnancy and evaluates their current and future roles.
A Monte Carlo tree search-based method for decision making of generator serial restoration sequence
Authors: Xu Wenwen , Chen Shuting , Han Guangxin , Yu Nan , Xu Han
Published: January 2023

Reasonable generator serial restoration sequence is a key issue to the system restoration following blackouts. This paper proposed an optimization method for the decision making of generator serial restoration sequence based on Monte Carlo tree search algorithm. First, the generator serial restoration sequence mechanism during the restoration process is analyzed. Considering the maximization of the total power generation capacity as the objective function, this paper also consider generator’s hot start. Second, the Monte Carlo tree search algorithm (MCTS) is applied to decide the generator serial restoration sequence. In the simulation stage of MCTS, the Dijkstra’s algorithm is utilized to determine the shortest path between the selected generator and the recovered power system. Finally, the IEEE 39 bus system and Hebei power grid system are used to validate the proposed algorithm. Simulation results show that the proposed method is efficiency and it can provide an reasonable generator serial restoration sequence to maximizing power generation during the restoration process.
Offense and defence against adversarial sample: A reinforcement learning method in energy trading market
Authors: Li Donghe , Yang Qingyu , Ma Linyue , Peng Zhenhua , Liao Xiao
Published: January 2023

The energy trading market that can support free bidding among electricity users is currently the key method in smart grid demand response. Reinforcement learning is used to formulate optimal strategies for them to obtain optimal strategies. Non-etheless, the security problem raised by artificial intelligence technology has been paid more and more attention. For example, the neural network has been proved to be able to resist adversarial example attacks, thus affecting its training results. Considering that reinforcement learning is also widely used for training by neural networks, the security problem can not be ignored, especially in scenarios with high security requirements such as smart grids. To this end, we study the security issues in reinforcement learning-based bidding strategy method facing by the adversarial example. First of all, regarding to the electric vehicle double auction market, we formalize the bidding decision problem of EVs into a Markov Decision Process, so that reinforcement learning is used to solve this problem. Secondly, from the perspective of attackers, we have designed a local Fast Gradient Sign Method which affects the environment and the results of reinforcement learning by changing its own bidding. Then, from the perspective of the defender, we designed a reinforcement learning training network containing an attack identifier based on the deep neural network, so as to identify malicious injection attacks to resist against adversarial attacks. Finally, comprehensive simulations are conducted to verify our proposed method. The results shows that, our proposed attack method will reduce the auction profit by influencing reinforcement learning algorithm, and the protect method will be able to completely resist such attacks.
The influence mechanism of effective stress, adsorption effect and Klinkenberg effect on coal seam permeability
Authors: Wang Mian , Yang Yongliang , Zhou Yinbo , Shi Hanfeng , Huang Jilei
Published: January 2023

Permeability is an important parameter in the process of coalbed methane exploitation. To improve the production efficiency of coalbed methane and explore the control mechanism of the gas flow law in coal, the permeability of helium and nitrogen in the same coal sample was tested under different effective stress (the difference between external stress and pore pressure of coal mass) and pressure by using the seepage device. Based on the gas flow theory, the interaction mechanism of effective stress, adsorption effect and Klinkenberg effect in controlling the permeability has been analyzed. Increasing the gas pressure will enhance the adsorption and deformation ability of coal, causing the reduction of pore size, while it will also cause the reduction of effective stress and stress deformation. There is a certain competition between them under the same external stress condition, which will lead to the change of pore and then affect the permeability of coal seam. The Klinkenberg effect will lead to more complex change factors of permeability, especially in laboratory experiments. Both adsorption deformation and stress deformation will affect the pore structure of coal body, which will also lead to changes in the influence degree of Klinkenberg effect on apparent permeability. Under the influence of adsorption effect, the Klinkenberg effect may be a variable. The experimental results in this work elaborate the microscopic control mechanism of gas permeability change in coal. It can not only provide important guidance for gas injection technology, but also enrich the theory of coal seam gas flow.
Dynamic relationship between green bonds and major financial asset markets from the perspective of climate change
Authors: Gao Lijun , Guo Kun , Wei Xianhua
Published: January 2023

After the signing of the Paris Agreement, countries around the world paid more attention to climate change and made more efforts to enact policies. Under the dual pressure of policy and environment, each market is affected to different degrees. At the same time, as a new environmental protection tool, the green bond rose to prominence, causing a shock to various markets, but also has a certain hedging role. However, there are few studies on the dynamic co-movement and risk spillover effect between green bonds and stock markets, crude oil and gold in the existing literature. Therefore, it is necessary to explore the changes in the relationship between various markets for the reasonable avoidance of climate risks. Based on the relationship between the three green investment instruments (S&P green Bond, China Green Bond and climate bond) and the three markets, this paper adds the impact analysis on climate risk and policy risk. The conclusions obtained not only have guiding significance for investors interested in environmental protection in asset allocation and hedge selection, but also have reference significance for policymakers who want to realize green investment, which helps smooth the transition to a low-carbon economy.
Application of stable index and transport index for regional air pollution over Twain-Hu Basin
Authors: Yue Yanyu , Bai Yongqing , He Huan , Xu Lin , Chen Xuan , Zhou Yue , Tang Zijun , Zhan Tian
Published: January 2023

Affected by stagnant and transmission air pollution, Regional pollution day (RPD) frequently occurs in Twain-Hu Basin. In the winter halfaear of 2015–2021 (November to March of following year), the Regional pollution days reached 331 days. A variety of weather systems together lead to regional air pollution. Based on the observation data of PM2.5 concentration and multi-source meteorological elements during the study period, the weather types of Regional pollution days in Twain-Hu Basin can be divided into four types by using the T-model (T-PCA) classification method, namely, uniform pressure field (42 days), front of cold high-pressure bottom (180 days), back of high-pressure (81 days), and low pressure with an inverted trough field (28 days). Under the influence of uniform pressure field and front of cold high-pressure bottom, it shows the meteorological characteristics of static pollution and transmission pollution, respectively. A stable index (STI) is constructed to describe the PM2.5 pollution caused by the stagnant weather, and a transport index (TRI) is constructed to describe the PM2.5 pollution caused by the transport weather. They have a satisfactory evaluation effect on PM2.5 pollution under the influence of uniform pressure field and front of cold high-pressure bottom, respectively. Interestingly, the correlation coefficients between the pollution index (A stable index + transport index) and PM2.5 concentration could increase obviously to 0.48–0.71 when A stable index and transport index are considered comprehensively. Furthermore, the validation in the winter halfaear of 2021/2022 show that the correlation coefficient of most stations is above 0.70. Therefore, satisfactory performance in validation suggests that this index construction method can be well applied to regional pollution assessment in Twain-Hu Basin.
Whole-genome resequencing and bisulfite sequencing provide new insights into the feeding habit domestication in mandarin fish (Siniperca chuatsi)
Authors: Li Ling , He Shan , Lin Ming-Hui , Zhang Yan-Peng , Kuhl Heiner , Liang Xu-Fang
Published: January 2023

Mandarin fish (Siniperca chuatsi) is one of the most economically important fish in China. However, it has the peculiar feeding habit that it feeds solely on live prey fish since first-feeding, while refuses dead prey fish or artificial diets. After the specific training procedure, partial individuals could accept dead prey fish and artificial diets. The genetic basis of individual difference in artificial diet feeding habit is still unknown. In the present study, the resequencing was performed between 10 individuals which could be domesticated to accept artificial diets and 10 individuals which could not. Through the selective sweep analysis based on heterozygosity (Hp) and population differentiation coefficient (Fst), 57 candidate windows were identified as the putative selected regions for feeding habit domestication of mandarin fish, involved in 149 genes. These genes were related to memory, vision and olfaction function, which could be potential targets of molecular marker assistant breeding of artificial diet feeding trait. Beside of the DNA sequence, we also explored the potential role of DNA methylation in feeding habit domestication in mandarin fish. Whole-genome bisulfite sequencing was performed between the individuals which could be domesticated to accept artificial diets and those could not. 5,976 differentially methylated regions were identified, referring to 3,522 genes, such as the genes involved in cAMP signaling pathway. The DNA methylation changes of these genes might contribute to the adaption of artificial diets in mandarin fish. In conclusion, the putative selected regions and the differentially methylated regions were identified in the whole genome, providing new insights into the feeding habit domestication from live prey fish to artificial diets in mandarin fish. And the involved genes were identified as the candidate genes for molecular breeding of artificial diet utilization in mandarin fish.
ACKR3 promotes CXCL12/CXCR4-mediated cell-to-cell-induced lymphoma migration through LTB4 production
Authors: Antonello Paola , Pizzagalli Diego U. , Foglierini Mathilde , Melgrati Serena , Radice Egle , Thelen Sylvia , Thelen Marcus
Published: January 2023

Chemotaxis is an essential physiological process, often harnessed by tumors for metastasis. CXCR4, its ligand CXCL12 and the atypical receptor ACKR3 are overexpressed in many human cancers. Interfering with this axis by ACKR3 deletion impairs lymphoma cell migration towards CXCL12. Here, we propose a model of how ACKR3 controls the migration of the diffused large B-cell lymphoma VAL cells in vitro and in vivo in response to CXCL12. VAL cells expressing full-length ACKR3, but not a truncated version missing the C-terminus, can support the migration of VAL cells lacking ACKR3 (VAL-ko) when allowed to migrate together. This migration of VAL-ko cells is pertussis toxin-sensitive suggesting the involvement of a Gi-protein coupled receptor. RNAseq analysis indicate the expression of chemotaxis-mediating LTB4 receptors in VAL cells. We found that LTB4 acts synergistically with CXCL12 in stimulating the migration of VAL cells. Pharmacologic or genetic inhibition of BLT1R markedly reduces chemotaxis towards CXCL12 suggesting that LTB4 enhances in a contact-independent manner the migration of lymphoma cells. The results unveil a novel mechanism of cell-to-cell-induced migration of lymphoma.
Recombinant full-length Bacillus Anthracis protective antigen and its 63 kDa form elicits protective response in formulation with addavax
Authors: Sharma Shikhar , Bahl Vanndita , Srivastava Gaurav , Shamim Risha , Bhatnagar Rakesh , Gaur Deepak
Published: January 2023

Introduction

Bacillus anthracis is the causative agent for the lethal disease anthrax, primarily affecting animals and humans in close contact with an infected host. The pathogenicity of B. anthracis is attributed to the secreted exotoxins and their outer capsule. The host cell-binding exotoxin component “protective antigen” (PA) is reported to be a potent vaccine candidate. The aim of our study is to produce several PA constructs and analyze their vaccine potential.

Methods

We have designed the various subunit, PA-based recombinant proteins, i.e., full-length Protective antigen (PA-FL), C-terminal 63 kDa fragment (PA63), Protective antigen domain 1-domain 4 chimeras (PA-D1-4) and protective antigen domain 4 (PA-D4) and analyzed their vaccine potential with different human-compatible adjuvants in the mouse model. We have optimized the process and successfully expressed our recombinant antigens as soluble proteins, except full-length PA. All the recombinant antigen formulations with three different adjuvants i.e., Addavax, Alhydrogel, and Montanide ISA 720, were immunized in different mouse groups. The vaccine efficacy of the formulations was analyzed by mouse serum antigen-specific antibody titer, toxin neutralization assay, and survival analysis of mouse groups challenged with a lethal dose of B. anthracis virulent spores.

Results

We have demonstrated that the PA-FL addavax and PA63 addavax formulations were most effective in protecting spore-challenged mice and serum from the mice immunized with PAFL addavax, PA-FL alhydrogel, PA63 addavax, and PA63 alhydrogel formulations were equivalently efficient in neutralizing the anthrax lethal toxin. The higher levels of serum Th1, Th2, and Th17 cytokines in PA-FL addavax immunized mice correspond to the enhanced protection provided by the formulation in challenged mice.

Discussion

We have demonstrated that the PA-FL addavax and PA63 addavax formulations exhibit equivalent efficiency as vaccine formulation both in a mouse model of anthrax and mammalian cell lines. However, PA63 is a smaller antigen than PA-FL and more importantly, PA63 is expressed as a soluble protein in E. coli, which imparts a translational advantage to PA63-based formulation. Thus, the outcome of our study has significant implications for the development of protective antigen-based vaccine formulations for human use against the lethal disease anthrax.
Low circulatory Fe and Se levels with a higher IL-6/IL-10 ratio provide nutritional immunity in tuberculosis
Authors: Kaushik Sandeep R. , Sahu Sukanya , Guha Hritusree , Saha Sourav , Das Ranjit , Kupa Rukuwe-u , Kapfo Wetetsho , Deka Trinayan , Basumatary Rumi , Thong Asunu , Dasgupta Arunabha , Goswami Bidhan , Pandey Amit Kumar , Saikia Lahari , Khamo Vinotsole , Das Anjan , Nanda Ranjan Kumar
Published: January 2023

Tuberculosis (TB) patients show dysregulated immunity, iron metabolism, and anemia. In this study, circulatory cytokines, trace metals, and iron-related proteins (hepcidin, ferroportin, transferrin, Dmt1, Nramp1, ferritin, ceruloplasmin, hemojuvelin, aconitase, and transferrin receptor) were monitored in case (active tuberculosis patients: ATB) and control (non-tuberculosis: NTB and healthy) study populations (n = 72, male: 100%, mean age, 42.94 years; range, 17–83 years). Using serum elemental and cytokine levels, a partial least square discriminate analysis model (PLS-DA) was built, which clustered ATB patients away from NTB and healthy controls. Based on the PLS-DA variable importance in projection (VIP) score and analysis of variance (ANOVA), 13 variables were selected as important biosignatures [IL-18, IL-10, IL-13, IFN-γ, TNF-α, IL-5, IL-12 (p70), IL-1β, copper, zinc, selenium, iron, and aluminum]. Interestingly, low iron and selenium levels and high copper and aluminum levels were observed in ATB subjects. Low circulatory levels of transferrin, ferroportin, and hemojuvelin with higher ferritin and ceruloplasmin levels observed in ATB subjects demonstrate an altered iron metabolism, which partially resolved upon 6 months of anti-TB therapy. The identified biosignature in TB patients demonstrated perturbed iron homeostasis with anemia of inflammation, which could be useful targets for the development of host-directed adjunct therapeutics.
Three-phase extraction of polysaccharide from Stropharia rugosoannulata: Process optimization, structural characterization and bioactivities
Authors: Li Xinxin , Zhang Zhiqiang , Wang Li , Zhao Haoqiang , Jia Yahui , Ma Xia , Li Jinzhan , Wang Yi , Ma Bingji
Published: January 2023

The isolation of Stropharia rugosoannulata polysaccharide (SRP) by three-phase extraction was optimized, and its structure and biological activities were identified. The optimal extraction conditions were: mass fraction of ammonium sulfate, 20%; volume ratio of sample solution to t-butanol, 1:1.5; extraction temperature, 35°C. Under these conditions, the yield of SRP was 6.85% ± 0.13%. SRP was found to be composed of glucose (35.79%), galactose (26.80%), glucuronic acid (9.92%), fructose (8.65%), xylose (7.92%), fucose (4.19%), arabinose (3.46%) and rhamnose (3.26%), with the molecular weight of 27.52 kDa. The results of DPPH, hydroxyl, ABTS+ radical scavenging and reducing power tests showed that SRP had good antioxidant capacities. SRP had no cytotoxic effect on RAW264.7 macrophages at the concentrations of 25-200 μg/mL, and could significantly promote phagocytosis activity and cell migration according to CCK-8 assay, phagocytosis assay and cell scratch experiment. SRP can significantly stimulate the transcript expression levels of TNF-α, IL-1β and IL-6, as determined by RT-PCR and Western blot assays. SRP activated the TLR4/NF-κB signaling pathway, and autophagy also occurred. These results suggest that SRP is a safe antioxidant and immunomodulator, and that it can be used in the development of functional foods and/or pharmaceuticals.
Biophysical modelling and graph theory identify key connectivity hubs in the Mediterranean marine reserve network
Authors: Abecasis David , Fragkopoulou Eliza , Claro Bruno , Assis Jorge
Published: January 2023

Connectivity plays a key role in the effectiveness of MPA networks ensuring metapopulation resilience through gene flow and recruitment effect. Yet, despite its recognized importance for proper MPA network functioning, connectivity is not often assessed and is very seldomly used in marine spatial planning. Here, we combined biophysical modelling with graph theory to identify Mediterranean marine reserves that support connectivity between different ecoregions through stepping-stone processes, thus preventing network fragmentation, and those that have an important role as propagule source areas contributing to the recruitment and rescue effects. We identified 19 reserves that play a key role towards the functioning of the network, serving either as stepping-stones or as propagule sources, yet with distinct patterns between ecological groups with contrasting propagule duration (PD). The Côte D’Azur marine reserves are important both as stepping-stones and propagule sources for several ecological groups. Also, key is the Capo Rizzuto and Plemmirio marine reserves due to their role as stepping stones between different marine ecoregions, particularly for species with longer PD (Pisces, Crustacea and Echinodermata). These results provide stakeholders and managers with crucial information for the implementation and management of an efficient marine reserve network in the Mediterranean.
Biogeography and potential ecological functions of prokaryotes in the hydrothermal and non-hydrothermal field sediments of the Indian Ocean Ridges
Authors: Huang Jing , Chen Ping , Zhu Yaxin , Wang Jian , Song Lei , Han Xiqiu , Huang Ying
Published: January 2023

A consensus is emerging on marine microbial biogeography. However, knowledge of the biodiversity and biogeographic patterns of deep-sea microbes and the drivers is far from adequate. In this study, we investigated the diversity and biogeography of prokaryotes at the Indian Ocean Ridges (IOR) using 16S rRNA gene and dsrB sequencing combined with bioinformatics analyses. A total of 39 hydrothermal field sediment (HFS) and non-hydrothermal field sediment (NHFS) samples were collected from the Carlsberg Ridge (CR) and Southwest Indian Ridge (SWIR). Seventy-four prokaryotic phyla were detected in the samples, of which 13 phyla were distributed across all samples. The composition of prokaryotic communities diverged between HFSs and NHFSs, but not between the CR and SWIR. Sixteen phyla were differentially enriched between HFSs and NHFSs. The community structure was significantly correlated to calcium, sulfur, total phosphorus, and total nitrogen, the first three of which were the main distinguishing factors of HFSs and NHFSs. Moreover, a weak distance–decay pattern was observed among the NHFS communities. PICRUSt predictions revealed functional discrepancies in carbon and nitrogen metabolism between the HFS and NHFS communities, and dsrB sequencing analysis indicated higher diversity of sulfate reduction genes and taxa in HFSs than in NHFSs. The diversity and relative abundance of corresponding functional taxa and genes suggested that the nitrogen cycle might be centralized in an energy-generating manner to support the microbial community in NHFSs while the sulfur cycle is more important for the HFS community. These findings provide new insights into microbial biogeography and metabolic differentiation along the IOR that are influenced by hydrothermal activity.
The relationship between inorganic nutrients and diversity of dinoflagellate cysts: An evaluation from the perspective of species abundance distribution
Authors: Gao Junfeng , Su Qiang
Published: January 2023

The relationships between the inorganic nutrients and diversity of dinoflagellate cysts (the N-Dc relationships) are one of the most central issues in coastal ecology. It is not only an important pathway to explore the ecological processes of plankton, but also a key element for assessing eutrophication in marine ecosystems. Although the N-Dc relationships have been studied for many years, they have remained controversial, which may be attributed to (1) using samples collected from a single source (2) considering an insufficient range of nutrient concentrations (3) rarely taking into account species abundance distributions (SAD) that could better represent diversity. In this study, the N-Dc relationships are evaluated according to a compiled dataset, which cover the wide range of nutrient concentrations. Species diversity of cysts are estimated by four common diversity metrics and a new SAD parameter. Results show that all diversity metrics are negative with nutrients, which supports that low diversity of cysts could be considered as a signal of eutrophication. Additionally, this study finds a new pattern that SAD of cysts (Nr/N1, Nr and N1 is the abundance of the r-th and the first species in descending order) with decreasing nutrients appears to gradually approach 1: 1/2: 1/3…. In the future, if this pattern can be verified by more investigations, understanding the negative N-Dc relationships is more likely to provide new direction for assessing and managing eutrophication in coastal ecosystem, and even for exploring the general mechanisms determining diversity.
Exploring the research landscape of the past, present, and future of thyroid nodules
Authors: Chen Pei , Feng Chenzhe , Huang Leyi , Chen Haolin , Feng Yeqian , Chang Shi
Published: January 2023

Introduction

The purpose of this study was to assess the landscape of thyroid nodules research during the last 22 years using machine learning and text analysis.

Methods

In November 2021, we obtained from PubMed all works indexed under the Medical Subject Headings (MeSH) subject line “thyroid nodules.” The entire set of search results was retrieved in XML format, and metadata such as title, abstract, keywords, MeSH words, and year of publication were extracted for bibliometric evaluation from the original XML files. To increase the specificity of the investigation, the Latent Dirichlet allocation (LDA) topic modeling method was applied.

Results

Our study included 5,770 research papers. By using frequency analysis of MeSH terms, research on thyroid nodules was divided into two categories: clinical and basic. The proportion of clinical research is nearing 89% and is dominated by the differential diagnosis of thyroid nodules. In contrast, the proportion of MeSH terms relating to basic research was just 11%, with DNA mutation analysis being the most common topic. Following this, LDA analysis revealed the thyroid nodule study had three clusters: Imaging Studies, Biopsy and Diagnosis, and Epidemiology and Screening of Thyroid Cancer. The result suggests that current thyroid nodule research appears to have focused on ultrasonography and histological diagnosis, which are tightly correlated. Molecular biomarker research has increased, therefore enhancing the diagnostic precision of thyroid nodules. However, inflammation, anxiety, and mental health disorders related to thyroid nodules have received little attention.

Conclusion

Basic research on thyroid nodules has unmet research requirements. Future research could focus on developing strategies to more efficiently identify malignant nodules, exploring the mechanism of thyroid nodule development, and enhancing the quality of life of thyroid patients.