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An efficient and safe strategy for germ cell-specific automatic excision of foreign DNA in F1 hybrid transgenic silkworms

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Insect Science 2024年第1期31卷 28-46页

作者： Dingpei Long Rongpeng Liu Yang Huang Anyao Fu Yuli Zhang Zhanzhang Hao Qiang Li Hanfu Xu Zhonghuai Xiang Aichun Zhao state Key Laboratory of Resource Insects Institute of Sericulture and Systems BiologySouthwest UniversityChongqingChina Department of Biology Georgia State UniversityAtlantaGeorgiaUSA Guangxi Institute of Sericulture Science NanningGuangxiChina Department of Mathematics and Statistics Georgia State UniversityAtlantaGeorgiaUSA

The safety of transgenic technology is a major obstacle in the popularization and use of transgenic silkworms and their *** sericulture,only the first filial generation(F1)hybrid eggs produced by cross-breeding Japanese and Chinese original strains are usually used for the large-scale breeding of silkworms,but this may result in uncontrolled transgene dispersal during the popularization and application of the F1 hybrid transgenic *** address this issue,we developed a safe and efficient strategy using the GAL4/Upstream activating sequence(UAS)system,the FLP/flippase recognition target(FRT)system,and the gonad-specific expression gene promoters(RSHP1p and Nanosp)for the germ cell-specific automatic excision of foreign DNA in the F1 hybrid transgenic *** established 2 types of activator strains,R1p::GAL4-Gr and Nsp::GAL4-Gr,containing the testis-specific GAL4 gene expression cassettes driven by RSHP1p or Nanosp,respectively,and 1 type of effector strain,UAS::FLP-Rg,containing the UAS-linked FLP gene expression *** FLP recombinase-mediated sperm-specific complete excision of FRT-flanked target DNA in the F1 double-transgenic silkworms resulting from the hybridization of R1p::GAL4-Gr and UAS::FLP-Rg was 100%,whereas the complete excision efficiency resulting from the hybridization of Nsp::GAL4-Gr and UAS::FLP-Rg ranged from 13.73%to 80.3%.Additionally,we identified a gene,sw11114,that is expressed in both testis and ovary of Bombyx mori,and can be used to establish novel gonad-specific expression systems in transgenic *** strategy has the potential to fundamentally solve the safety issue in the production of F1 transgenic silkworm eggs and provides an important reference for the safety of transgenic technology in other insect species.

关键词： Bombyx mori FLP/FRT system GAL4/UAS system germ cell-specific excision safety of transgenic technology transgenic silkworm

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Molecular regulation of calcium-sensing receptor(CaSR)-mediated signaling

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Chronic Diseases and Translational Medicine 2024年第3期10卷 167-194页

作者： Li Tian Corey Andrews Qiuyun Yan Jenny J.Yang Department of Chemistry Center for Diagnostics and TherapeuticsAdvanced Translational Imaging FacilityGeorgia State UniversityAtlantaGeorgiaUSA

Calcium-sensing receptor(CaSR),a family C G-protein-coupled receptor,plays a crucial role in regulating calcium homeostasis by sensing small concentration changes of extracellular Ca^(2+),Mg^(2+),amino acids(e.g.,L-Trp and L-Phe),small peptides,anions(e.g.,HCO_(3)^(-)and PO_(4)^(3-)),and ***-mediated intracellular Ca^(2+)signaling regulates a diverse set of cellular processes including gene transcription,cell proliferation,differentiation,apoptosis,muscle contraction,and neuronal *** of CaSR with mutations results in diseases such as autosomal dominant hypocalcemia,familial hypocalciuric hypercalcemia,and neonatal severe *** also influences calciotropic disorders,such as osteoporosis,and noncalciotropic disorders,such as cancer,Alzheimer's disease,and pulmonary arterial *** study first reviews recent advances in biochemical and structural determination of the framework of CaSR and its interaction sites with natural ligands,as well as exogenous positive allosteric modulators and negative allosteric *** establishment of the first CaSR protein-protein interactome network revealed 94 novel players involved in protein processing in endoplasmic reticulum,trafficking,cell surface expression,endocytosis,degradation,and signaling *** roles of these proteins in Ca^(2+)-dependent cellular physiological processes and in CaSR-dependent cellular signaling provide new insights into the molecular basis of diseases caused by CaSR mutations and dysregulated CaSR activity caused by its protein interactors and facilitate the design of therapeutic agents that target CaSR and other family C G-protein-coupled receptors.

关键词： calcium signaling calcium-sensing receptor G-protein-coupled receptors structure trafficking

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An Encoding-Decoding Framework Based on CNN for circ RNA-RBP Binding Sites Prediction

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Chinese Journal of Electronics 2024年第1期33卷 256-263页

作者： Yajing GUO Xiujuan LEI Yi PAN School of Computer Science Shaanxi Normal University Faculty of Computer Science and Control Engineering Shenzhen Institute of Advanced TechnologyChinese Academy of Sciences Department of Computer Science Georgia State University

Predicting RNA binding protein(RBP) binding sites on circular RNAs(circ RNAs) is a fundamental step to understand their interaction mechanism. Numerous computational methods are developed to solve this problem, but they cannot fully learn the features. Therefore, we propose circ-CNNED, a convolutional neural network(CNN)-based encoding and decoding framework. We first adopt two encoding methods to obtain two original matrices. We preprocess them using CNN before fusion. To capture the feature dependencies, we utilize temporal convolutional network(TCN) and CNN to construct encoding and decoding blocks, respectively. Then we introduce global expectation pooling to learn latent information and enhance the robustness of circ-CNNED. We perform circ-CNNED across 37 datasets to evaluate its effect. The comparison and ablation experiments demonstrate that our method is superior. In addition, motif enrichment analysis on four datasets helps us to explore the reason for performance improvement of circ-CNNED.

关键词： Proteins RNA Neural networks Encoding Robustness Decoding Convolutional neural networks

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A Study of EM Algorithm as an Imputation Method: A Model-Based Simulation Study with Application to a Synthetic Compositional Data

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Open Journal of Modelling and Simulation 2024年第2期12卷 33-42页

作者： Yisa Adeniyi Abolade Yichuan Zhao Department of Mathematics and Statistics Georgia State University Atlanta Georgia USA

Compositional data, such as relative information, is a crucial aspect of machine learning and other related fields. It is typically recorded as closed data or sums to a constant, like 100%. The statistical linear model is the most used technique for identifying hidden relationships between underlying random variables of interest. However, data quality is a significant challenge in machine learning, especially when missing data is present. The linear regression model is a commonly used statistical modeling technique used in various applications to find relationships between variables of interest. When estimating linear regression parameters which are useful for things like future prediction and partial effects analysis of independent variables, maximum likelihood estimation (MLE) is the method of choice. However, many datasets contain missing observations, which can lead to costly and time-consuming data recovery. To address this issue, the expectation-maximization (EM) algorithm has been suggested as a solution for situations including missing data. The EM algorithm repeatedly finds the best estimates of parameters in statistical models that depend on variables or data that have not been observed. This is called maximum likelihood or maximum a posteriori (MAP). Using the present estimate as input, the expectation (E) step constructs a log-likelihood function. Finding the parameters that maximize the anticipated log-likelihood, as determined in the E step, is the job of the maximization (M) phase. This study looked at how well the EM algorithm worked on a made-up compositional dataset with missing observations. It used both the robust least square version and ordinary least square regression techniques. The efficacy of the EM algorithm was compared with two alternative imputation techniques, k-Nearest Neighbor (k-NN) and mean imputation (), in terms of Aitchison distances and covariance.

关键词： Compositional Data Linear Regression Model Least Square Method Robust Least Square Method Synthetic Data Aitchison Distance Maximum Likelihood Estimation Expectation-Maximization Algorithm k-Nearest Neighbor and Mean imputation

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Few-Shot Graph Classification with Structural-Enhanced Contrastive Learning for Graph Data Copyright Protection

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Tsinghua Science and Technology 2024年第2期29卷 605-616页

作者： Kainan Zhang DongMyung Shin Daehee Seo Zhipeng Cai Department of Computer Science Georgia State UniversityAtlantaGA 30303USA LSWare Inc. Seoul 08504Republic of Korea College of Intelligence Information Engineering Sangmyung UniversitySeoul 03016Republic of Korea

Open-source licenses can promote the development of machine learning by allowing others to access,modify,and redistribute the training ***,not all open-source licenses may be appropriate for data sharing,as some may not provide adequate protections for sensitive or personal information such as social network ***,some data may be subject to legal or regulatory restrictions that limit its sharing,regardless of the licensing model ***,obtaining large amounts of labeled data can be difficult,time-consuming,or expensive in many real-world ***-shot graph classification,as one application of meta-learning in supervised graph learning,aims to classify unseen graph types by only using a small amount of labeled ***,the current graph neural network methods lack full usage of graph structures on molecular graphs and social network *** structural features are known to correlate with molecular properties in chemistry,structure information tends to be ignored with sufficient property information ***,the common binary classification task of chemical compounds is unsuitable in the few-shot setting requiring novel ***,this paper focuses on the graph classification tasks of a social network,whose complex topology has an uncertain relationship with its nodes'*** two multi-class graph datasets with large node-attribute dimensions constructed to facilitate the research,we propose a novel learning framework that integrates both meta-learning and contrastive learning to enhance the utilization of graph topological *** experiments demonstrate the competitive performance of our framework respective to other state-of-the-art methods.

关键词： few-shot learning contrastive learning data copyright protection

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The impact of the Rural Minimum Living Standard Guarantee(Rural Dibao)Program on child nutrition outcomes

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Journal of Integrative Agriculture 2024年第2期23卷 444-456页

作者： Dian Chen Xiangming Fang Yu Chen Xiaodong Zheng Zhuo Chen Rodney B.W.Smith Academy of Global Food Economics and Policy China Agricultural UniversityBeijing 100083China School of Public Health Georgia State UniversityAtlanta 30303USA School of Economics Zhejiang Gongshang UniversityHangzhou 310018China College of Public Health University of GeorgiaAthens 30602USA Department of Applied Economics University of MinnesotaSaint Paul 55108USA

The Rural Minimum Living Standard Guarantee(Rural Dibao)is an important unconditional cash transfer program to alleviate poverty in rural *** the importance of children’s nutrition in breaking poverty cycles,little is known about the impact of Rural Dibao on child nutrition *** China Family Panel Studies(CFPS),this paper examines the effects of Rural Dibao on child nutrition outcomes and investigates potential pathways and heterogeneous *** exploit propensity score matching and difference-in-differences techniques to evaluate the effects of the Rural Dibao program on child nutrition *** results suggest that Rural Dibao significantly impacts the nutrition outcomes of children up to 15 years of ***,our results suggest that Rural Dibao improves child height-to-age z-scores by 1.05 standard deviations and lowers the probability of stunting by 11.9 percentage *** analyses suggest that increased protein intake is the main pathway through which Rural Dibao participation contributes to better nutrition *** also find that the effect of the program is more pronounced among girls,children who are non-left-behind or live with highly educated mothers,and those from low-income families and poor *** findings suggest that Rural Dibao participation helps improve child nutrition outcomes through improving diet quality.

关键词： Rural Minimum Living Standard Guarantee nutrition height-to-age z-scores stunting rural China

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Uncertainty Comparison Between Value-at-Risk and Expected Shortfall

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Communications in Mathematical Research 2024年第1期40卷 102-124页

作者： Qing Liu Weimin Liu Liang Peng Gengsheng Qin School of Statistics Jjiangxi University of Finance and EconomicsNanchangJiangxi 330013China Department of Mathematics and Statistics Georgia State UniversityAtlantaGA 30303USA Maurice R.Greenberg School of Risk Science Georgia State UniversityAtlantaGA 20303USA

Value-at-Risk(VaR)and expected shortfall(ES)are two key risk measures in financial risk *** these two measures has been a hot debate,and most discussions focus on risk measure *** paper uses independent data and autoregressive models with normal or t-distribution to examine the effect of the heavy tail and dependence on comparing the nonparametric inference uncertainty of these two risk *** and numerical analyses suggest that VaR at 99%level is better than ES at 97.5%level for distributions with heavier tails.

关键词： α-mixing asymptotic variance expected shortfall Value-at-Risk

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Time Complexity of the Oracle Phase in Grover’s Algorithm

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American Journal of Computational Mathematics 2024年第1期14卷 1-10页

作者： Ying Liu Department of Engineering Technology Savannah State University Savannah Georgia

Since Grover’s algorithm was first introduced, it has become a category of quantum algorithms that can be applied to many problems through the exploitation of quantum parallelism. The original application was the unstructured search problems with the time complexity of O(). In Grover’s algorithm, the key is Oracle and Amplitude Amplification. In this paper, our purpose is to show through examples that, in general, the time complexity of the Oracle Phase is O(N), not O(1). As a result, the time complexity of Grover’s algorithm is O(N), not O(). As a secondary purpose, we also attempt to restore the time complexity of Grover’s algorithm to its original form, O(), by introducing an O(1) parallel algorithm for unstructured search without repeated items, which will work for most cases. In the worst-case scenarios where the number of repeated items is O(N), the time complexity of the Oracle Phase is still O(N) even after additional preprocessing.

关键词： Quantum Computing Oracle Amplitude Amplification Grover’s Algorithm

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O(logN) Algorithm for Amplitude Amplification and O(logN) Algorithms for Amplitude Transfer in Grover’s Algorithm

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American Journal of Computational Mathematics 2024年第2期14卷 169-188页

作者： Ying Liu Department of Engineering Technology Savannah State University Savannah Georgia USA

Grovers algorithm is a category of quantum algorithms that can be applied to many problems through the exploitation of quantum parallelism. The Amplitude Amplification in Grovers algorithm is T = O(N). This paper introduces two new algorithms for Amplitude Amplification in Grovers algorithm with a time complexity of T = O(logN), aiming to improve efficiency in quantum computing. The difference between Grovers algorithm and our first algorithm is that the Amplitude Amplification ratio in Grovers algorithm is an arithmetic series and ours, a geometric one. Because our Amplitude Amplification ratios converge much faster, the time complexity is improved significantly. In our second algorithm, we introduced a new concept, Amplitude Transfer where the marked state is transferred to a new set of qubits such that the new qubit state is an eigenstate of measurable variables. When the new qubit quantum state is measured, with high probability, the correct solution will be obtained.

关键词： Quantum Computing Oracle Amplitude Amplification Grover’s Algorithm

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Neurobiology of Supporting Syntactic Chains of Self-Grooming in Rodents and Its Biochecmical Characteristics

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Journal of Biosciences and Medicines 2024年第4期12卷 330-352页

作者： Giorgi Andronikashvili Tea Gurashvili Khatuna Dondoladze Marina Nikolaishvili Malkhaz Makashvili Beritashvili Center for Experimental Biomedicine Laboratory of Neurology Tbilisi Georgia Department of Neuro Physiology Grigor Robakidze University Tbilisi Georgia Department of Physiology Ilia State University Tbilisi Georgia

Grooming is an innate behavior that serves multiple purposes and has a dual nature, reflecting both comfort and stress. Auto-grooming, in particular, is highly sensitive to stressors and can be influenced by natural and synthetic anxiolytics. Researchers believe that rodent grooming can be a valuable tool in translational neurobiological studies, specifically focusing on aberrant grooming, such as the syntactic chain of grooming, which can serve as an experimental model for certain human psycho-nervous disorders.

关键词： Grooming Microstructure Translational Medicine Clinical Medicine Stress

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