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A novel essential domain perspective for exploring gene essentiality

Yao Lu, Yulan Lu, Jingyuan Deng, Hai Peng, Hui Lu, Long Jason Lu
2015 Bioinformatics  
Motivation: Genes with indispensable functions are identified as essential; however, the traditional gene-level studies of essentiality have several limitations. In this study, we characterized gene essentiality from a new perspective of protein domains, the independent structural or functional units of a polypeptide chain. Results: To identify such essential domains, we have developed an Expectation-Maximization (EM) algorithm-based Essential Domain Prediction (EDP) Model. With simulated
more » ... ts, the model provided convergent results given different initial values and offered accurate predictions even with noise. We then applied the EDP model to six microbial species and predicted 1879 domains to be essential in at least one species, ranging 10-23% in each species. The predicted essential domains were more conserved than either non-essential domains or essential genes. Comparing essential domains in prokaryotes and eukaryotes revealed an evolutionary distance consistent with that inferred from ribosomal RNA. When utilizing these essential domains to reproduce the annotation of essential genes, we received accurate results that suggest protein domains are more basic units for the essentiality of genes. Furthermore, we presented several examples to illustrate how the combination of essential and non-essential domains can lead to genes with divergent essentiality. In summary, we have described the first systematic analysis on gene essentiality on the level of domains.
doi:10.1093/bioinformatics/btv312 pmid:26002906 fatcat:zigrtdrmwrcapercwwtfm2svwm

Synthesis of two titanosilicates with distinct interlayer connections from similar gels

Peng Ji, Kun Lu, Xinqing Lu, Hao Xu, Peng Wu
2017 Dalton Transactions  
Ti-SSZ-70 and Ti-ECNU-6, with identical intralayer structure but distinct interlayer connections, were prepared from similar synthetic gels. These two titanosilicate catalysts exhibited outstanding catalytic activities in the liquid-phase epoxidation of alkenes.
doi:10.1039/c7dt00640c pmid:28401221 fatcat:ho7yvhc4wna67l42cyity4d3d4

Conformal Bach flow [article]

Jiaqi Chen, Peng Lu, Jie Qing
2021 arXiv   pre-print
Then for every f ∈ C α,0 (M × [0, T ]) there is a unique solution u ∈ C 2m+α,1 (M × [0, T ]) of ∂ t u = Lu + f, u(0, ·) = 0.  ... 
arXiv:2104.08968v1 fatcat:gzekwthv6bbgng62lq6wn6p7le

Structure Learning with Similarity Preserving [article]

Zhao Kang and Xiao Lu and Yiwei Lu and Chong Peng and Zenglin Xu
2019 arXiv   pre-print
Leveraging on the underlying low-dimensional structure of data, low-rank and sparse modeling approaches have achieved great success in a wide range of applications. However, in many applications the data can display structures beyond simply being low-rank or sparse. Fully extracting and exploiting hidden structure information in the data is always desirable and favorable. To reveal more underlying effective manifold structure, in this paper, we explicitly model the data relation. Specifically,
more » ... e propose a structure learning framework that retains the pairwise similarities between the data points. Rather than just trying to reconstruct the original data based on self-expression, we also manage to reconstruct the kernel matrix, which functions as similarity preserving. Consequently, this technique is particularly suitable for the class of learning problems that are sensitive to sample similarity, e.g., clustering and semisupervised classification. To take advantage of representation power of deep neural network, a deep auto-encoder architecture is further designed to implement our model. Extensive experiments on benchmark data sets demonstrate that our proposed framework can consistently and significantly improve performance on both evaluation tasks. We conclude that the quality of structure learning can be enhanced if similarity information is incorporated.
arXiv:1912.01197v1 fatcat:rrgraoj4hfdbboa66qx5rbfcgu

Boosting Image Recognition with Non-differentiable Constraints [article]

Xuan Li, Yuchen Lu, Peng Xu, Jizong Peng, Christian Desrosiers, Xue Liu
2019 arXiv   pre-print
In this paper, we study the problem of image recognition with non-differentiable constraints. A lot of real-life recognition applications require a rich output structure with deterministic constraints that are discrete or modeled by a non-differentiable function. A prime example is recognizing digit sequences, which are restricted by such rules (e.g., container code detection, social insurance number recognition, etc.). We investigate the usefulness of adding non-differentiable constraints in
more » ... arning for the task of digit sequence recognition. Toward this goal, we synthesize six different datasets from MNIST and Cropped SVHN, with three discrete rules inspired by real-life protocols. To deal with the non-differentiability of these rules, we propose a reinforcement learning approach based on the policy gradient method. We find that incorporating this rule-based reinforcement can effectively increase the accuracy for all datasets and provide a good inductive bias which improves the model even with limited data. On one of the datasets, MNIST_Rule2, models trained with rule-based reinforcement increase the accuracy by 4.7% for 2000 samples and 23.6% for 500 samples. We further test our model against synthesized adversarial examples, e.g., blocking out digits, and observe that adding our rule-based reinforcement increases the model robustness with a relatively smaller performance drop.
arXiv:1910.00736v1 fatcat:dik2zmnsjjdtjaoebqtbbpygce

SIRT7 activates p53 by enhancing PCAF-mediated MDM2 degradation to arrest the cell cycle

Ya-Fei Lu, Xiao-Peng Xu, Xiao-Peng Lu, Qian Zhu, Ge Liu, Yan-Tao Bao, He Wen, Ying-Lu Li, Wei Gu, Wei-Guo Zhu
2020 Oncogene  
Whole cell lysates were analyzed by immunoblotting. b Quantitation of MDM2 G lu c o s e d e p r iv a ti Cells were harvested and then lysed in lysis buffer [1% Nonidet P-40, 20 mM Tris-HCl (pH 8.0)  ... 
doi:10.1038/s41388-020-1305-5 pmid:32404984 fatcat:52j42ewjbjc7dfhkl2wemvn2fm

CLCN2-related leukoencephalopathy: a case report and review of the literature

Zhuoxin Guo, Tingting Lu, Lisheng Peng, Huanhuan Cheng, Fuhua Peng, Jin Li, Zhengqi Lu, Shaoqiong Chen, Wei Qiu
2019 BMC Neurology  
Loss-of-function mutations in the CLCN2 gene were recently discovered to be a cause of a type of leukodystrophy named CLCN2-related leukoencephalopathy (CC2L), which is characterized by intramyelinic edema. Herein, we report a novel mutation in CLCN2 in an individual with leukodystrophy. Case presentation: A 38-year-old woman presented with mild hand tremor, scanning speech, nystagmus, cerebellar ataxia in the upper limbs, memory decline, tinnitus, and dizziness. An ophthalmologic examination
more » ... dicated macular atrophy, pigment epithelium atrophy and choroidal capillary atrophy. Brain magnetic resonance imaging (MRI) showed the diffuse white matter involvement of specific white matter tracts. Decreased diffusion anisotropy was detected in various brain regions of the patient. Diffusion tensor tractography (DTT) showed obviously thinner tracts of interest than in the controls, with a decreased fiber number (FN), increased radial diffusivity (RD) and unchanged axial diffusivity (AD). A novel homozygous c.2257C > T (p.Arg753Ter) mutation in exon 20 of the CLCN2 gene was identified. Conclusion: CC2L is a rare condition characterized by diffuse edema involving specific fiber tracts that pass through the brainstem. The distinct MRI patterns could be a strong indication for CLCN2 gene analysis. The findings of our study may facilitate the understanding of the pathophysiology and clinical symptoms of this disease.
doi:10.1186/s12883-019-1390-7 fatcat:6ii3r4mpxvb4nlyuy7slle2fsq

Ruthenium atomically dispersed in carbon outperforms platinum toward hydrogen evolution in alkaline media

Bingzhang Lu, Lin Guo, Feng Wu, Yi Peng, Jia En Lu, Tyler J. Smart, Nan Wang, Y. Zou Finfrock, David Morris, Peng Zhang, Ning Li, Peng Gao (+2 others)
2019 Nature Communications  
Hydrogen evolution reaction is an important process in electrochemical energy technologies. Herein, ruthenium and nitrogen codoped carbon nanowires are prepared as effective hydrogen evolution catalysts. The catalytic performance is markedly better than that of commercial platinum catalyst, with an overpotential of only -12 mV to reach the current density of 10 mV cm-2 in 1 M KOH and -47 mV in 0.1 M KOH. Comparisons with control experiments suggest that the remarkable activity is mainly
more » ... to individual ruthenium atoms embedded within the carbon matrix, with minimal contributions from ruthenium nanoparticles. Consistent results are obtained in first-principles calculations, where RuCxNy moieties are found to show a much lower hydrogen binding energy than ruthenium nanoparticles, and a lower kinetic barrier for water dissociation than platinum. Among these, RuC2N2 stands out as the most active catalytic center, where both ruthenium and adjacent carbon atoms are the possible active sites.
doi:10.1038/s41467-019-08419-3 pmid:30733437 pmcid:PMC6367462 fatcat:gnek7bc56ra7bowhhbkmlo7bzu

Cobalt-Catalyzed Dehydrogenative Silylation of Vinylarenes

Biao Cheng, Peng Lu, Jiajin Zhao, Zhan Lu
2019 Youji huaxue  
A highly chemo-, regio-, and stereo-selective cobalt-catalyzed dehydrogenative silylation of vinylarenes was described. The imidazoline iminopyridine cobalt complex could promote this reaction effectively and improve the chemoselectivity dramatically. This protocol used earth-abundant transition metal, readily available alkenes and hydrosilanes to construct valuable vinylsilanes. The reaction could be carried out in gramscale and the proposed mechanism was also described.
doi:10.6023/cjoc201903018 fatcat:lopnkgrd2zarfpy54k63b2dxmu

Ancient Ricci Flow Solutions on Bundles [article]

Peng Lu, Y.K. Wang
2016 arXiv   pre-print
We generalize the circle bundle examples of ancient solutions of the Ricci flow discovered by Bakas, Kong, and Ni to a class of principal torus bundles over an arbitrary finite product of Fano Kähler-Einstein manifolds studied by Wang and Ziller in the context of Einstein geometry. As a result, continuous families of κ-collapsed and κ-noncollapsed ancient solutions of type I are obtained on circle bundles for all odd dimensions ≥ 7. In dimension 7 such examples moreover exist on pairs of
more » ... rphic but not diffeomorphic manifolds. Continuous families of κ-collapsed ancient solutions of type I are also obtained on torus bundles for all dimensions ≥ 8.
arXiv:1606.01112v1 fatcat:247cf2mjvjevtgb3h563p76sci

Principal stratification analysis using principal scores [article]

Peng Ding, Jiannan Lu
2016 arXiv   pre-print
Acknowledgments Peng Ding's work is partially supported by grant R305D150040 from Institute of Education Sciences, USA.  ... 
arXiv:1602.01196v1 fatcat:p5ybcsulgnfd7cdocp2qvcjsqi

Spectra of edge-independent random graphs [article]

Linyuan Lu, Xing Peng
2012 arXiv   pre-print
Chung, Lu, and Vu [4, 5] studied spectra of adjacency matrices of random power law graphs and spectra of Laplacian matrices of random graphs with given expected degree sequences.  ...  Chung-Lu-Vu [5] proved if δ ≫ √w ln 3 n then for each non-trivial eigenvalue λ i (L), we have |1 − λ i (L)| ≤ 4 + o(1) √ δ . (1) Note that in this case I −L = T −1/2Ā T −1/2 ; its (i, j)-entry is given  ... 
arXiv:1204.6207v1 fatcat:t6fcfu4o5rczzpoeyxm7wzdb2q

Ancient solutions for Andrews' hypersurface flow [article]

Peng Lu, Jiuru Zhou
2018 arXiv   pre-print
We construct the ancient solutions of the hypersurface flows in Euclidean spaces studied by B. Andrews in 1994. As time t → 0^- the solutions collapse to a round point where 0 is the singular time. But as t→-∞ the solutions become more and more oval. Near the center the appropriately-rescaled pointed Cheeger-Gromov limits are round cylinder solutions S^J ×R^n-J, 1 ≤ J ≤ n-1. These results are the analog of the corresponding results in Ricci flow (J=n-1) and mean curvature flow.
arXiv:1812.04926v1 fatcat:v7l4ijey3bcy5cnnfzyrcgjtgy

Synthesis of ultra-small mordenite zeolite nanoparticles

Yi Xu, Xuefeng Shen, Cheng Peng, Yue Ma, Lu Han, Peng Wu, Honggen Peng, Shunai Che
2018 Science China Materials  
Shen X performed the TEM measurement, Ma Y and Peng C measured the catalytic properties of materials. Xu Y wrote the paper with support from Che S, Peng H, Wu P and Han L.  ... 
doi:10.1007/s40843-018-9257-3 fatcat:qcy6tdxidzc2fl65fnkhqsheui

EZH2 promotes angiogenesis through inhibition of miR-1/Endothelin-1 axis in nasopharyngeal carcinoma

Juan Lu, Fei-Peng Zhao, Zengliu Peng, Meng-Wen Zhang, Shao-Xiong Lin, Bi-Jun Liang, Bao Zhang, Xiong Liu, Lu Wang, Gang Li, Wen-Dong Tian, Ying Peng (+2 others)
2014 OncoTarget  
Lu et al. showed that VEGF stimulation led to upregulated E2F expression, which directly modulated EZH2 levels.  ... 
doi:10.18632/oncotarget.2435 pmid:25237831 pmcid:PMC4294357 fatcat:hbdl5s5iwjbyne5iwmxvji574u
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