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Genetic stability and DNA fingerprinting of the Hemarthria compressa cultivar "Guangyi"

Linkai Huang, Yu Zhang, Jing Zhang, Xinquan Zhang, Wengang Xie, Xiaomei Jiang, Fei Peng, Yanhong Yan, Xiao Ma, Wei Liu, Yan Peng, Guohua Yin (+1 others)
2014 Biochemical Systematics and Ecology  
The author suggested that genetic variation may have been the result of somatic mutation (Zhang et al., 2008) .  ...  Primers Total number of bands Polymorphic bands Percentage of polymorphic bands Guangyi Species of whip grass Guangyi Species of whip grass UBC810 10 1 7 0.10 0.70 UBC811 11 0 6 0.00  ... 
doi:10.1016/j.bse.2014.03.027 fatcat:ba5zhte4orgvtgketuu6x6u7vi

Distilling EEG Representations via Capsules for Affective Computing [article]

Guangyi Zhang, Ali Etemad
2021 arXiv   pre-print
Very Recently, Zhang and Etemad proposed a Riemannian Fusion Network (RFNet) to learn the temporal information through an LSTM-attention network [4] .  ... 
arXiv:2105.00104v1 fatcat:awz343arcrajxb3epfi2llkxny

Ranking with submodular functions on a budget [article]

Guangyi Zhang, Nikolaj Tatti, Aristides Gionis
2022 arXiv   pre-print
Table 1 : 1 Datasets statistics Dataset n = |V | m = |F | Songs 1872 100 Movies 3669 100 Books 3753 1000 20 Newsgroups 172 5 Handwritten Digits 1347 3 https://github.com/Guangyi-Zhang/max-submodular-ranking  ...  Streeter and Golovin (2008) and Zhang et al. (2012) introduce a notion of string submodularity, which restricts the diminishing returns to only the prefix subsequence relation.  ... 
arXiv:2204.04168v1 fatcat:g2gjcq3qvbhhhcs6fcpfie5kja

Long-chain alcohols derived from the microalga Monoraphidium

Xuewei Yang, Xin Dai, Rui Zhang, Cong Shao, Shu Geng, Guangyi Chen, Xianhua Liu, Guangyi Wang
2013 Advances in Energy Research  
This study was to investigate the composition and characteristics of long-chained alcohols extracted from the algal strain Monoraphidium 3s35. The production of biomass was optimized using different cultivation methods. Under the aerated growth condition, this strain yielded up to 37.26% extracts of dry weight and 576 mgL -1 biomass. The major compounds of the extracts are mainly long-chained alcohols (89.24%), with carbon chain length ranging from 12 to 20. Interestingly, or the long-chained
more » ... cohols, 3-(2-Methoxyethyl)-1-nonanol, 3,7,11, 15-Tetramethyl-2-hexadecen-1-ol and oleyl alcohol accounted for 53.68%, 23.45%, and 12.11%, respectively. Because of their amphipathic nature, these long-chained alcohols have been widely used in bioenergy production and cosmetics industry. Furthermore, Monoraphidium 3s35 produced 9.73% of C 17 and C 20 alkanes, which can be used as an important supplement for the petrodiesel-like fuel.
doi:10.12989/eri.2013.1.2.107 fatcat:pph5um2fuvdzzli4wfjgflqx3y

Draft genome of a porcupinefish, Diodon Holocanthus [article]

Mengyang Xu, Xiaoshan Su, Mengqi Zhang, Ming Li, Xiaoyun Huang, Guangyi Fan, Xin Liu, He Zhang
2019 bioRxiv   pre-print
The long-spine porcupinefish, Diodon holocanthus (Diodontidae, Tetraodontiformes, Actinopterygii), also known as the freckled porcupinefish, attracts great interest of ecology and economy. Its distinct characteristics including inflation reaction, spiny skin and tetradotoxin, however, have not been fully studied without a complete genome assembly. In this study, the whole genome of a single individual was sequenced using single tube-Long Fragment Read co-barcode reads, generating 154.3 Gb of
more » ... red-end data (219.8× depth). The gap was further filled using small amount of Oxford Nanopore MinION long read dataset (11.4Gb, 15.9× depth). Taking full use of long, medium, short-range of genome assembly information, the final assembled sequences with a total length of 650.02 Mb obtained contig and scaffold N50 sizes of 2.15 Mb and 8.13 Mb, respectively, despite of high repetitive content. Benchmarking Universal Single-Copy Orthologs captured 95.7% (2,474) of core genes to assess the completeness. In addition, 206.5 Mb (32.10%) of repetitive sequences were identified, and 20,840 protein-coding genes were annotated, among which 18,281 (87.72%) proteins were assigned with possible functions. This is the first demonstration of de novo genome of the porcupinefish, which will benefit downstream analysis of ontogeny, phylogeny, and evolution, and improve the exploration of its unique defensive mechanism.
doi:10.1101/775387 fatcat:dfvuvghdtjhzriibydvv6nm2wu

Compositional Variability and Mutation Spectra of Monophyletic SARS-CoV-2 Clades [article]

Xufei Teng, Qianpeng Li, Zhao Li, Yuansheng Zhang, Guangyi Niu, Meng Zhang, Jingfa Xiao, Jun Yu, Zhang Zhang, Shuhui Song
2020 bioRxiv   pre-print
COVID-19 and its causative pathogen SARS-CoV-2 have rushed the world into a staggering pandemic in a few months and a global fight against both is still going on. Here, we describe an analysis procedure where genome composition and its variables are related, through the genetic code, to molecular mechanisms based on understanding of RNA replication and its feedback loop from mutation to viral proteome sequence fraternity including effective sites on replicase-transcriptase complex. Our analysis
more » ... starts with primary sequence information and identity-based phylogeny based on 22,051 SARS-CoV-2 genome sequences and evaluation of sequence variation patterns as mutation spectrum and its 12 permutations among organized clades tailored to two key mechanisms: strand-biased and function-associated mutations. Our findings include: (1) The most dominant mutation is C-to-U permutation whose abundant second-codon-position counts alter amino acid composition toward higher molecular weight and lower hydrophobicity albeit assumed most slightly deleterious. (2) The second abundance group includes: three negative-strand mutations U-to-C, A-to-G, G-to-A and a positive-strand mutation G-to-U generated through an identical mechanism as C-to-U. (3) A clade-associated and biased mutation trend is found attributable to elevated level of the negative-sense strand synthesis. (4) Within-clade permutation variation is very informative for associating non-synonymous mutations and viral proteome changes. These findings demand a bioinformatics platform where emerging mutations are mapped on to mostly subtle but fast-adjusting viral proteomes and transcriptomes to provide biological and clinical information after logical convergence for effective pharmaceutical and diagnostic applications. Such thoughts and actions are in desperate need, especially in the middle of the War against COVID-19.
doi:10.1101/2020.08.26.267781 fatcat:qkpnkirttfd7ljgbh67uhdzhcq

Deep Recurrent Semi-Supervised EEG Representation Learning for Emotion Recognition [article]

Guangyi Zhang, Ali Etemad
2021 arXiv   pre-print
EEG-based emotion recognition often requires sufficient labeled training samples to build an effective computational model. Labeling EEG data, on the other hand, is often expensive and time-consuming. To tackle this problem and reduce the need for output labels in the context of EEG-based emotion recognition, we propose a semi-supervised pipeline to jointly exploit both unlabeled and labeled data for learning EEG representations. Our semi-supervised framework consists of both unsupervised and
more » ... pervised components. The unsupervised part maximizes the consistency between original and reconstructed input data using an autoencoder, while simultaneously the supervised part minimizes the cross-entropy between the input and output labels. We evaluate our framework using both a stacked autoencoder and an attention-based recurrent autoencoder. We test our framework on the large-scale SEED EEG dataset and compare our results with several other popular semi-supervised methods. Our semi-supervised framework with a deep attention-based recurrent autoencoder consistently outperforms the benchmark methods, even when small sub-sets (3\%, 5\% and 10\%) of the output labels are available during training, achieving a new state-of-the-art semi-supervised performance.
arXiv:2107.13505v1 fatcat:67qlewtmvff3njpjepj2nlea5e

Chromosome-level genome assembly of the African pike, Hepsetus odoe [article]

Xiao Du, Xiaoning Hong, Guangyi Fan, Xiaoyun Huang, Shuai Sun, Bingjie Ouyang, He Zhang, Mengqi Zhang, Shanshan Liu, Xin Liu, Wenwei Zhang
2020 bioRxiv   pre-print
The order Characiformes is one of the largest components of the freshwater teleost fauna inhabiting exclusively in South America and Africa with great ecological and economical significance. Yet, quite limited genomic resources are available to study this group and their transatlantic vicariance. In this study we present a chromosome-level genome assembly of the African pike (Hepsetus odoe), a representative member of the African Characiformes. To this end, we generated 119, 11, and 67 Gb reads
more » ... using the single tube long fragment read (stLFR), Oxford Nanopore, and Hi-C sequencing technologies, respectively. We obtained an 862.1 Mb genome assembly with the contig and scaffold N50 of 347.4 kb and 25.8 Mb, respectively. Hi-C sequencing produced 29 chromosomes with 742.5 Mb, representing 86.1% of the genome. 24,314 protein-coding genes were predicted and 23,999 (98.7%) genes were functionally annotated. The chromosomal-scale genome assembly will be useful for functional and evolutionary studies of the African pike and promote the study of Characiformes speciation and evolution.
doi:10.1101/2020.05.13.094987 fatcat:qzw4ma5cjfadnb6hsteudhx4s4

Using Terminal Circuit for Power System Electromagnetic Transient Simulation [article]

Yijing Liu, Xiang Zhang, Renchang Dai, Guangyi Liu
2021 arXiv   pre-print
The modern power system is evolving with increasing penetration of power electronics introducing complicated electromagnetic phenomenon. Electromagnetic transient (EMT) simulation is essential to understand power system behavior under disturbance which however is one of the most sophisticated and time-consuming applications in power system. To improve the electromagnetic transient simulation efficiency while keeping the simulation accuracy, this paper proposes to model and simulate power system
more » ... electromagnetic transients by very large-scale integrated circuit (VLSI) as a preliminary exploration to eventually represent power system by VLSI circuit chip avoiding numerical calculation. To proof the concept, a simple 5 bus system is modeled and simulated to verify the feasibility of the proposed approach.
arXiv:2107.00540v1 fatcat:js3hwcpktnhzdm3rxydcehhgxy

The mechanisms of histone modification in post-traumatic stress disorder

Yingqian ZHANG, Guangyi ZHAO, Yuwei HAN, Jingyi ZHANG, Chengqi CAO, Li WANG, Kunlin ZHANG
2022 Advances in Psychological Science  
Post-traumatic stress disorder (PTSD) is a mental disorder with complex etiology, which mostly occurs after severe traumatic events. The genesis and development of PTSD involves complex interactions between environmental triggers and genetic susceptibility, resulting in great individual differences. As a discipline investigating the changes in gene expression regulated by environment factors, the role of epigenetics in PTSD is attracting more and more attention in recent years. Histone
more » ... ion, as one of the epigenetic mechanisms, plays an important role in the biological pathways for PTSD. Since histone modification can regulated by a variety of enzymes, its flexible reversibility and elaborate regulation provides the possibility and convenience for the corresponding drug development. Therefore, in-depth exploration of the histone modification for the clinical treatment and drug development of PTSD is of great significance. Current studies on histone modification in PTSD mainly use animal models, with few clinical studies, focusing on histone H3 and H4 acetylation. In addition, consistent with previous findings, the changes in histone modification mostly occurred in prefrontal cortex, hippocampus, and amygdala, involved in the regulation of related pathways including the immune system, serotonin system, and the neuropeptide Y system. Current findings about histone modification in PTSD showed great heterogeneity, future studies should adopt more consistent and practical methods of analysis and reporting, to maximize study impact.
doi:10.3724/sp.j.1042.2022.00098 fatcat:fqueocxptfbo3agfbpkqeruzjy

Chromosome-level genome assembly of a butterflyfish, Chelmon rostratus [article]

Xiaoyun Huang, Yue Song, Suyu Zhang, Yunga A, Yue Chang, He Zhang, Chang Li, Yong Zhao, Meiru Liu, Xin Liu, Guangyi Fan
2019 bioRxiv   pre-print
Chelmon rostratus (Teleostei, Perciformes, Chaetodontidae) is a copperband butterflyfish, living in tropical areas. Just as other coral reef fish, it can be cultivated as an ornamental fish, thus providing genome information for this species might help understanding the genome evolution of Chaetodontidae (without previous genomes available) and adaptation/evolution of coral reef fish. In this study, we sequenced and assembled a draft genome of Chelmon rostratus. Using the stLFR linked-read
more » ... we assembled a genome of 638.88 Mb in size with contig and scaffold N50 sizes of 294.41 kb and 2,62 Mb, respectively. Up to 21.47 % of the genome was found to be repetitive sequences and 21,375 protein-coding genes were annotated. Among these annotated protein-coding genes, 20,163 (94.33%) proteins were assigned with possible functions. As the first genome for Chaetodontidae family, the information of these data helpfully to improve the essential to the further understanding and exploration of marine ecological environment symbiosis with coral and the genomic innovations and molecular mechanisms contributing to its unique morphology and physiological features.
doi:10.1101/719187 fatcat:6hfgsqhpbfgv5f6bdugmxpqwzy

Optimal deletion-robust coreset for submodular maximization [article]

Guangyi Zhang, Nikolaj Tatti, Aristides Gionis
2022 arXiv   pre-print
In recent years we have witnessed an increase on the development of methods for submodular optimization, which have been motivated by the wide applicability of submodular functions in real-world data-science problems. In this paper, we contribute to this line of work by considering the problem of robust submodular maximization against unexpected deletions, which may occur due to privacy issues or user preferences. Specifically, we study and derive bounds for the minimum number of items a
more » ... ng algorithm has to remember, in order to achieve a non-trivial approximation guarantee against adversarial deletions up to d items. We call the set of items that are kept by the algorithm before adversarial deletions a deletion-robust coreset. We propose a single-pass streaming algorithm that yields a (1-2ϵ)/(4p)-approximation for maximizing a non-decreasing submodular function under a general p-matroid constraint and requires a coreset size k + d/ϵ, where k is the maximum size of a feasible solution. To the best of our knowledge, this is the first work to achieve an (asymptotically) optimal coreset size, as no constant approximation is possible with a coreset of size sublinear in d.
arXiv:2203.01241v2 fatcat:bksm34qnovb2bepn4tkkx6fgbm

Graph Computing based Distributed State Estimation with PMUs [article]

Yi Lu, Chen Yuan, Xiang Zhang, Hua Huang, Guangyi Liu, Renchang Dai, Zhiwei Wang
2020 arXiv   pre-print
Power system state estimation plays a fundamental and critical role in the energy management system (EMS). To achieve a high performance and accurate system states estimation, a graph computing based distributed state estimation approach is proposed in this paper. Firstly, a power system network is divided into multiple areas. Reference buses are selected with PMUs being installed at these buses for each area. Then, the system network is converted into multiple independent areas. In this way,
more » ... e power system state estimation could be conducted in parallel for each area and the estimated system states are obtained without compromise of accuracy. IEEE 118-bus system and MP 10790-bus system are employed to verify the results accuracy and present the promising computation performance.
arXiv:2002.09477v1 fatcat:qx7bggdesbb4pawilhnc7elkru

Holistic Semi-Supervised Approaches for EEG Representation Learning [article]

Guangyi Zhang, Ali Etemad
2022 arXiv   pre-print
Recently, supervised methods, which often require substantial amounts of class labels, have achieved promising results for EEG representation learning. However, labeling EEG data is a challenging task. More recently, holistic semi-supervised learning approaches, which only require few output labels, have shown promising results in the field of computer vision. These methods, however, have not yet been adapted for EEG learning. In this paper, we adapt three state-of-the-art holistic
more » ... ed approaches, namely MixMatch, FixMatch, and AdaMatch, as well as five classical semi-supervised methods for EEG learning. We perform rigorous experiments with all 8 methods on two public EEG-based emotion recognition datasets, namely SEED and SEED-IV. The experiments with different amounts of limited labeled samples show that the holistic approaches achieve strong results even when only 1 labeled sample is used per class. Further experiments show that in most cases, AdaMatch is the most effective method, followed by MixMatch and FixMatch.
arXiv:2109.11732v2 fatcat:pfua3rgkzvemfmdqoqm6hnwx3e

Chromosome-level genome assembly of the humpback puffer, Tetraodon palembangensis

Rui Zhang, Chang Li, Mengjun Yu, Xiaoyun Huang, Mengqi Zhang, Shanshan Liu, Shanshan Pan, Weizhen Xue, Congyan Wang, Chunyan Mao, He Zhang, Guangyi Fan
2021 Gigabyte  
The humpback puffer, Tetraodon palembangensis, is a poisonous freshwater pufferfish species mainly distributed in Southeast Asia (Thailand, Laos, Malaysia and Indonesia). The humpback puffer has many interesting biological features, such as inactivity, tetrodotoxin production and body expansion. Here, we report the first chromosome-level genome assembly of the humpback puffer. The genome size is 362 Mb, with a contig N50 value of ∼1.78 Mb and a scaffold N50 value of ∼15.8 Mb. Based on this
more » ... e assembly, ∼61.5 Mb (18.11%) repeat sequences were identified, 19,925 genes were annotated, and the function of 90.01% of these genes could be predicted. Finally, a phylogenetic tree of ten teleost fish species was constructed. This analysis suggests that the humpback puffer and T. nigroviridis share a common ancestor 18.1 million years ago (MYA), and diverged from T. rubripes 45.8 MYA. The humpback puffer genome will be a valuable genomic resource to illustrate possible mechanisms of tetrodotoxin synthesis and tolerance.
doi:10.46471/gigabyte.17 fatcat:6mvaufsc75e7fanlxaq7i3wp7u
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