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SnpReady for Rice (SR4R) Database
[article]
2020
bioRxiv
pre-print
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The information commons for rice (IC4R) database is a collection of ~18 million SNPs (single nucleotide polymorphisms) identified by the resequencing of 5,152 rice accessions. Although IC4R offers ultra-high density rice variation map, these raw SNPs are not readily usable for the public. To satisfy different research utilizations of SNPs for population genetics, evolutionary analysis, association studies and genomic breeding in rice, the raw genotypic data of the 18 million SNPs were processed
doi:10.1101/2020.01.11.902999
fatcat:bxe2k2gj6jetbo3fugfbn4luvm
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... by unified bioinformatics pipelines. The outcomes were used to develop a daughter database of IC4R - SnpReady for Rice (SR4R). The SR4R presents four reference SNP panels, including 2,097,405 hapmapSNPs after data filtration and genotype imputation, 156,502 tagSNPs selected from linkage disequilibrium (LD)-based redundancy removal, 1,180 fixedSNPs selected from genes exhibiting selective sweep signatures, and 38 barcodeSNPs selected from DNA fingerprinting simulation. SR4R thus offers a highly efficient rice variation map that combines reduced SNP redundancy with extensive data describing the genetic diversity of rice populations. In addition, SR4R provides rice researchers with a web-interface that enables them to browse all four SNP panels, use online toolkits, and retrieve the original data and scripts for a variety of population genetics analyses on local computers. The SR4R is freely available to academic users at http://sr4r.ic4r.org/.
The Elements of Data Sharing
2020
Genomics, Proteomics & Bioinformatics
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Compositional Variability and Mutation Spectra of Monophyletic SARS-CoV-2 Clades
[article]
2020
bioRxiv
pre-print
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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
doi:10.1101/2020.08.26.267781
fatcat:qkpnkirttfd7ljgbh67uhdzhcq
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... 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.
ABIOTIC STRESS GENE 1 mediates aroma volatiles accumulation by activating MdLOX1a in apple
[article]
2022
bioRxiv
pre-print
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., 2004; Zhang et al., 2006; Zhang et al., 2009; Contreras et al., 2017) . ...
Similarly, in kiwifruit, AdLox5 participates in fruity aroma ester synthesis in the cytoplasm (Zhang et al., 2006; Zhang et al., 2009) . ...
doi:10.1101/2022.02.24.481825
fatcat:cu47i7znkrhrbplzslqtekb2xq
SoyOmics: A deeply integrated database on soybean multi-omics
[article]
2023
bioRxiv
pre-print
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Zhang, M., Liu, S., Wang, Z., Yuan, Y., Zhang, Z., Liang, Q., Yang, X., Duan, Z., Liu, Y., Kong, F., et al. (2022) . Progress in soybean functional genomics over the past decade. Plant Biotechnol. ...
., Zhang, J., Wu, Y., Li, J., Sirohi, M.H., and Wang, F. (2021) . Applications of multi-omics technologies for crop improvement. Front Plant Sci. 12:563953. ...
doi:10.1101/2023.02.05.527102
fatcat:aoyutsyed5czbdku3pwqocmvly
Clinical application of the 2011 IFCPC colposcope terminology
2021
BMC Women's Health
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Background Colposcopy offers an accurate way to the diagnose of cervical precancerous lesions. However, the diagnostic accuracy of colposcopy is unsatisfied. This study was to evaluate colposcopic accuracy according to the 2011 International Federation of Cervical Pathology and Colposcopy (IFCPC) terminology. Methods A retrospective cohort study was performed in 1,838 patients who underwent colposcopy in Shandong Qianfoshan Hospital, Cheeloo College of Medicine, Shandong University from October
doi:10.1186/s12905-021-01395-1
pmid:34167543
fatcat:f4m5kp37gfccbmpmlcfcca4qhe
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... 2013 to April 2018. Using conization or cervical biopsy pathology as the gold standard, the agreement between colposcopic diagnosis and pathologic diagnosis was calculated, and correlations between variables were analyzed. Results As an authoritative and widely used terminology for colposcopy diagnosis, the 2011 IFCPC terminology has certain clinical practicality and diagnostic accuracy. However, some signs such as mosaic, punctation, sharp border, inner border sign and ridge sign had high specificity but unsatisfactory sensitivity, which limited the diagnostic value. Therefore, we discussed the Lugol's staining, a very common sign in colposcopy, and analyzed the diagnostic significance of bright yellow staining in low-grade squamous intraepithelial lesion (LSIL) and mustard yellow staining in high-grade squamous intraepithelial lesion (HSIL). The results showed that mustard yellow may be a valuable indicator in the diagnosis of HSIL. Conclusion The 2011 IFCPC colposcope terminology has standardized interpretations of the colposcopic findings and improved the accuracy of colposcopy diagnosis. The aceto-white epithelium still has important diagnostic value; however, the value of a few signs is needed to be discussed and new signs are expected to be discovered. Although the significance of Lugol's staining was diminishing, mustard yellow might be a valuable indicator for the diagnosis of HSIL.
Less Is More: Picking Informative Frames for Video Captioning
[article]
2018
arXiv
pre-print
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In video captioning task, the best practice has been achieved by attention-based models which associate salient visual components with sentences in the video. However, existing study follows a common procedure which includes a frame-level appearance modeling and motion modeling on equal interval frame sampling, which may bring about redundant visual information, sensitivity to content noise and unnecessary computation cost. We propose a plug-and-play PickNet to perform informative frame picking
arXiv:1803.01457v1
fatcat:jbtslrr4ljd37o5i3izyuovqpe
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... in video captioning. Based on a standard Encoder-Decoder framework, we develop a reinforcement-learning-based procedure to train the network sequentially, where the reward of each frame picking action is designed by maximizing visual diversity and minimizing textual discrepancy. If the candidate is rewarded, it will be selected and the corresponding latent representation of Encoder-Decoder will be updated for future trials. This procedure goes on until the end of the video sequence. Consequently, a compact frame subset can be selected to represent the visual information and perform video captioning without performance degradation. Experiment results shows that our model can use 6-8 frames to achieve competitive performance across popular benchmarks.
Efficient Synthesis of Allolactose
2014
Youji huaxue
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Allolactose (β-D-galactopyranosyl-(1→6)-α,β-D-glucopyranose) is a reducing disaccharide playing important biological role in bacterial metabolism. Two synthetic methods of allolactose including regioselective glycosylation and stepwise synthesis were investigated using D-glucose and D-galactose as the starting materials. The later approach involved a five-spot strategy, 44% overall yields and all the intermediates were easily to be purified, making the route suitable for large scale preparation
doi:10.6023/cjoc201312028
fatcat:ndgckge3sbbbvew2kvwbabd5si
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... of the target compound. All the compounds were characterized by NMR and HRMS spectra.
McAN: an ultrafast haplotype network construction algorithm
[article]
2022
bioRxiv
pre-print
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AbstractSummaryHaplotype network is becoming popular due to its increasing use in analyzing genealogical relationships of closely related genomes. We newly proposed McAN, a minimum-cost arborescence based haplotype network construction algorithm, by considering mutation spectrum history (mutations in ancestry haplotype should be contained in descendant haplotype), node size (corresponding to sample count for a given node) and sampling time. McAN is two orders of magnitude faster than the
doi:10.1101/2022.07.23.501111
fatcat:mz7rigtm5fajtiyaoemgydx23y
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... f-the-art algorithms, making it suitable for analyzation of massive sequences.AvailabilitySource code is written in C/C++ and available at https://github.com/Theory-Lun/McAN and https://ngdc.cncb.ac.cn/biocode/tools/BT007301 under the MIT license. The online web service of McAN is available at https://ngdc.cncb.ac.cn/ncov/online/tool/haplotype. SARS-CoV-2 dataset are available at https://ngdc.cncb.ac.cn/ncov/.
Efficient Synthesis of Epilactose
2017
Youji huaxue
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Epilactose (4-O-β-D-galactopyranosyl-D-mannose) is a reducing disaccharide with satisfactory prebiotic properties. A superior synthetic methods were confirmed by screening different coupled donors and acceptors which were synthesized from D-mannose and D-galactose, respectively. This route gets 50% overall yields and all the intermediates are easily to be purified, making the route suitable for large scale preparation of the target compound. All the compounds were characterized by NMR and HRMS spectra.
doi:10.6023/cjoc201608010
fatcat:mnhfizfku5hqtjs7jblya4ltu4
New evaluation metrics for mesh segmentation
2013
Computers & graphics
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[14] CD, HD, RI, CE Zhang et al. (2012) [15] RI, CE results. ...
doi:10.1016/j.cag.2013.05.021
fatcat:p6utrcntvvdfbguv5hitkrkgrq
Synthesis and insecticidal activities of 5-deoxyavermectin B2a oxime ester derivatives
2018
RSC Advances
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Three series of avermectin B2a oxime ester derivatives were synthesized and evaluated for their insecticidal activity.
doi:10.1039/c7ra13258a
pmid:35542930
pmcid:PMC9078043
fatcat:km6fmalsxfcpdneszjmohporxi
Synthesis and Insecticidal Activity of 4"-Avermectin Triazole Derivatives Containing Amide Unit
2018
Youji huaxue
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Live Memory Acquisition through FireWire
[chapter]
2011
Lecture Notes of the Institute for Computer Sciences, Social Informatics and Telecommunications Engineering
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Although FireWire-based memory acquisition method has been introduced for several years, the methodologies are not discussed in detail and still lack of practical tools. Besides, the existing method is not working stably when dealing with different versions of Windows. In this paper, we try to compare different memory acquisition methods and discuss their virtues and disadvantages. Then, the methodologies of FireWire-based memory acquisition are discussed. Finally, we give a practical
doi:10.1007/978-3-642-23602-0_14
fatcat:e3sxnw35avb4bobyw5kuzfezwy
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... tion of FireWire-based acquisition tool that can work well with different versions of Windows without causing BSoD problems.
Well‐Defined Nanostructures for Electrochemical Energy Conversion and Storage
2020
Advanced Energy Materials
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[276] Zhang et al. also reported the confinement of red phosphorus in N-doped carbon (P@NMC) for SIBs. ...
Shuhui Sun is a full professor at the Institut National de la Recherche Scientifique (INRS), Center for Energy, Materials, and Telecommunications, Canada. ...
doi:10.1002/aenm.202001537
fatcat:cfvfliv235bbhliimzsic2f4u4
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