61 Works

A novel role for nucleolin in splice site selection

Kinneret Shefer, Ayub Boulos, Valer Gotea, Maram Arafat, Yair Ben Chaim, Aya Muharram, Sara Isaac, Amir Eden, Joseph Sperling, Laura Elnitski & Ruth Sperling
Latent 5ʹ splice sites, not normally used, are highly abundant in human introns, but are activated under stress and in cancer, generating thousands of nonsense mRNAs. A previously proposed mechanism to suppress latent splicing was shown to be independent of NMD, with a pivotal role for initiator-tRNA independent of protein translation. To further elucidate this mechanism, we searched for nuclear proteins directly bound to initiator-tRNA. Starting with UV-crosslinking, we identified nucleolin (NCL) interacting directly and...

Research on infrared dim and small target detection algorithm based on local contrast and gradient

Weihong Lin, Leihong Zhang, Zimin Shen, Dawei Zhang, Jian Chen, Jie Zhou, Wei Peng & Fengshou Wu
The rapid development of infrared technology makes it widely applicable in such fields as military, medical, testing and communications.This paper proposes an algorithm based on local contrast and gradient (LCG). Specifically, the algorithm uses the difference of gaussian and threshold segmentation to preprocess to obtain the position of possible target points. Then, local contrast processing is conducted for the possible target points. Finally, the global is processed using an improved directional gradient. According to the...

Research on infrared dim and small target detection algorithm based on local contrast and gradient

Weihong Lin, Leihong Zhang, Zimin Shen, Dawei Zhang, Jian Chen, Jie Zhou, Wei Peng & Fengshou Wu
The rapid development of infrared technology makes it widely applicable in such fields as military, medical, testing and communications.This paper proposes an algorithm based on local contrast and gradient (LCG). Specifically, the algorithm uses the difference of gaussian and threshold segmentation to preprocess to obtain the position of possible target points. Then, local contrast processing is conducted for the possible target points. Finally, the global is processed using an improved directional gradient. According to the...

Expansion of a vertical effective field-of-view for an optical 360° holographic display

Jun Wang, Jie Zhou, yang wu, XiangLi Lei & Yuqi Zhang
Cylindrical holography, as a promising 360° display technology, has already attracted a lot of attention. In a previous study, an optical 360° cylindrical holography has been achieved in the visible spectrum using a planar spatial light modulator (SLM) and a 45° conical mirror. Although 360° field-of-view (FOV) is successfully achieved in the horizontal direction, in the previous study, the vertical FOV remains as small as the planar holography, and its expansion is not only necessary...

Additional file 4 of Different color regulation mechanism in willow barks determined using integrated metabolomics and transcriptomics analyses

Jie Zhou, Jiahui Guo, Qingsheng Chen, Baosong Wang, Xudong He, Qiang Zhuge & Pu Wang
Additional file 4: Table S8. The differential expressed genes identified inwillow barks.

Additional file 2 of A haplotype-resolved genome assembly of the Nile rat facilitates exploration of the genetic basis of diabetes

Huishi Toh, Chentao Yang, Giulio Formenti, Kalpana Raja, Lily Yan, Alan Tracey, William Chow, Kerstin Howe, Lucie A. Bergeron, Guojie Zhang, Bettina Haase, Jacquelyn Mountcastle, Olivier Fedrigo, John Fogg, Bogdan Kirilenko, Chetan Munegowda, Michael Hiller, Aashish Jain, Daisuke Kihara, Arang Rhie, Adam M. Phillippy, Scott A. Swanson, Peng Jiang, Dennis O. Clegg, Erich D. Jarvis … & Yury V. Bukhman
Additional file 2: Supplementary Table 1. TOGA status of 18430 ancestral placental mammal genes in muroid rodent genome assemblies. Supplementary Table 2. Positively selected genes and their mutation tolerance in humans according to gnomAD.

Four ionones and ionone glycosides from the whole plant of Rehmannia piasezkii

Jie Zhou, Guo-Ru Shi, Wan-Qi Zhang, Ruo-Yun Chen, Yan-Fei Liu & De-Quan Yu
Four new ionones and ionone glycosides (1–4) were isolated from the whole plant of Rehmannia piasezkii Maxim. Their planar structures as well as absolute configuration were confirmed via spectroscopic analysis, ECD calculation, and X-ray crystallography. Compounds 1–4 were tested for their cytotoxicity against five human tumor cell lines and ability to inhibit LPS-activated NO production in the BV2 cell line.

Additional file 2 of A comprehensive update on CIDO: the community-based coronavirus infectious disease ontology

Yongqun He, Hong Yu, Anthony Huffman, Asiyah Yu Lin, Darren A. Natale, John Beverley, Ling Zheng, Yehoshua Perl, Zhigang Wang, Yingtong Liu, Edison Ong, Yang Wang, Philip Huang, Long Tran, Jinyang Du, Zalan Shah, Easheta Shah, Roshan Desai, Hsin-hui Huang, Yujia Tian, Eric Merrell, William D. Duncan, Sivaram Arabandi, Lynn M. Schriml, Jie Zheng … & Barry Smith
Additional file 2: Supplemental Table 1. Resources used for our coronavirus disease-related data collection.

Additional file 2 of A comprehensive update on CIDO: the community-based coronavirus infectious disease ontology

Yongqun He, Hong Yu, Anthony Huffman, Asiyah Yu Lin, Darren A. Natale, John Beverley, Ling Zheng, Yehoshua Perl, Zhigang Wang, Yingtong Liu, Edison Ong, Yang Wang, Philip Huang, Long Tran, Jinyang Du, Zalan Shah, Easheta Shah, Roshan Desai, Hsin-hui Huang, Yujia Tian, Eric Merrell, William D. Duncan, Sivaram Arabandi, Lynn M. Schriml, Jie Zheng … & Barry Smith
Additional file 2: Supplemental Table 1. Resources used for our coronavirus disease-related data collection.

A comprehensive update on CIDO: the community-based coronavirus infectious disease ontology

Yongqun He, Hong Yu, Anthony Huffman, Asiyah Yu Lin, Darren A. Natale, John Beverley, Ling Zheng, Yehoshua Perl, Zhigang Wang, Yingtong Liu, Edison Ong, Yang Wang, Philip Huang, Long Tran, Jinyang Du, Zalan Shah, Easheta Shah, Roshan Desai, Hsin-hui Huang, Yujia Tian, Eric Merrell, William D. Duncan, Sivaram Arabandi, Lynn M. Schriml, Jie Zheng … & Barry Smith
Abstract Background The current COVID-19 pandemic and the previous SARS/MERS outbreaks of 2003 and 2012 have resulted in a series of major global public health crises. We argue that in the interest of developing effective and safe vaccines and drugs and to better understand coronaviruses and associated disease mechenisms it is necessary to integrate the large and exponentially growing body of heterogeneous coronavirus data. Ontologies play an important role in standard-based knowledge and data representation,...

Comparison of intestinal flora between patients with chronic and advanced Schistosoma japonicum infection

Chen Zhou, Junhui Li, Chen Guo, Zhaoqin Zhou, Zhen Yang, Yu Zhang, Jie Jiang, Yu Cai, Jie Zhou & Yingzi Ming
Abstract Background Schistosoma japonicum infection is an important public health problem, imposing heavy social and economic burdens in 78 countries worldwide. However, the mechanism of transition from chronic to advanced S. japonicum infection remains largely unknown. Evidences suggested that gut microbiota plays a role in the pathogenesis of S. japonicum infection. However, the composition of the gut microbiota in patients with chronic and advanced S. japonicum infection is not well defined. In this study, we...

Additional file 1 of A haplotype-resolved genome assembly of the Nile rat facilitates exploration of the genetic basis of diabetes

Huishi Toh, Chentao Yang, Giulio Formenti, Kalpana Raja, Lily Yan, Alan Tracey, William Chow, Kerstin Howe, Lucie A. Bergeron, Guojie Zhang, Bettina Haase, Jacquelyn Mountcastle, Olivier Fedrigo, John Fogg, Bogdan Kirilenko, Chetan Munegowda, Michael Hiller, Aashish Jain, Daisuke Kihara, Arang Rhie, Adam M. Phillippy, Scott A. Swanson, Peng Jiang, Dennis O. Clegg, Erich D. Jarvis … & Yury V. Bukhman
Additional file 1: Figure S1. Venn diagram of gene lists linked to type 2 diabetes by different types of evidence. Figure S2. Heterozygosity inferred by comparing the paternal and maternal scaffolded contigs, shown on the paternal scaffolds. Figure S3. Length distributions of structural variants. Figure S4. Functional classification of duplicated genes. Figure S5. Sequence alignment of Nile rat Gckr proteins to 113 mammalian orthologs. Figure S6. Missing Nile rat Hadh gene present in alternate haplotype...

Supplementary document for Quantitative tumor depth determination using dual wavelength excitation fluorescence - 5997611.pdf

Christine OBrien, Kevin Bishop, Haini Zhang, Xiao Xu, Leonid Shmuylovich, Elizabeth Conley, Karen Nwosu, Katie Duncan, Suman Mondal & Gail Sudlow
Supplemental figures

Scheduling method for pairing night-shift and morning-shift duties on metro lines with complex structure

Zixuan Zhu, Ruihua Xu, Fangsheng Wang & Pieter Vansteenwegen
Scheduling the night-shift and morning-shift duties pairing plan (NMDPP) is a common process in Chinese metro crew management. Since metro crews work in a special working environment, sufficient rest is essential for them. NMDPP will affect the rest time of crews on metro lines with multiple depots and handover points. To improve the rest time of crews, this paper proposes a binary programming model to optimise the NMDPP. Moreover, a hybrid algorithm combining General Variable...

A novel role for nucleolin in splice site selection

Kinneret Shefer, Ayub Boulos, Valer Gotea, Maram Arafat, Yair Ben Chaim, Aya Muharram, Sara Isaac, Amir Eden, Joseph Sperling, Laura Elnitski & Ruth Sperling
Latent 5ʹ splice sites, not normally used, are highly abundant in human introns, but are activated under stress and in cancer, generating thousands of nonsense mRNAs. A previously proposed mechanism to suppress latent splicing was shown to be independent of NMD, with a pivotal role for initiator-tRNA independent of protein translation. To further elucidate this mechanism, we searched for nuclear proteins directly bound to initiator-tRNA. Starting with UV-crosslinking, we identified nucleolin (NCL) interacting directly and...

A novel role for nucleolin in splice site selection

Kinneret Shefer, Ayub Boulos, Valer Gotea, Maram Arafat, Yair Ben Chaim, Aya Muharram, Sara Isaac, Amir Eden, Joseph Sperling, Laura Elnitski & Ruth Sperling
Latent 5ʹ splice sites, not normally used, are highly abundant in human introns, but are activated under stress and in cancer, generating thousands of nonsense mRNAs. A previously proposed mechanism to suppress latent splicing was shown to be independent of NMD, with a pivotal role for initiator-tRNA independent of protein translation. To further elucidate this mechanism, we searched for nuclear proteins directly bound to initiator-tRNA. Starting with UV-crosslinking, we identified nucleolin (NCL) interacting directly and...

The effects of age, sex, weight, and breed on canid methylomes

Liudmilla Rubbi, Haoxuan Zhang, Junxi Feng, Christopher He, Patrick Kurnia, Prashansa Ratan, Aakash Tammana, Sabina House, Michael Thompson, Colin Farrell, Sagi Snir, Daniel Stahler, Elaine A. Ostrander, Bridgett M. vonHoldt & Matteo Pellegrini
Unlike genomes, which are static throughout the lifespan of an organism, DNA methylomes are dynamic. To study these dynamics, we developed quantitative models that measure the effect of multiple factors on DNA methylomes including, age, sex, weight, and genetics. We conducted our study in canids, which prove to be an ideal species to assess epigenetic moderators due to their extreme variability in size and well-characterized genetic structure. We collected buccal swabs from 217 canids (207...

Quantitative tumor depth determination using dual wavelength excitation fluorescence

Christine OBrien, Kevin Bishop, Haini Zhang, Xiao Xu, Leonid Shmuylovich, Elizabeth Conley, Karen Nwosu, Katie Duncan, Suman Mondal & Gail Sudlow
Quantifying solid tumor margins with fluorescence-guided surgery approaches is a challenge, particularly when using near infrared (NIR) wavelengths due to increased penetration depths. An NIR dual wavelength excitation fluorescence (DWEF) approach was developed that capitalizes on the wavelength-dependent attenuation of light in tissue to determine fluorophore depth. A portable dual wavelength excitation fluorescence imaging system was built and tested in parallel with an NIR tumor-targeting fluorophore in tissue mimicking phantoms, chicken tissue, and in vivo...

Three new pyridine alkaloids and one new iridoid analogue from the leaves of Rehmannia glutinosa

Guo-Ru Shi, Jie Zhou, Xin Wang, Ruo-Yun Chen, Yan-Fei Liu & De-Quan Yu
As part of an ongoing project on Rehmannia species, three new pyridine alkaloides (glutinosines A − C), and one new iridoid analogue (rehmaglutin E), were isolated from the leaves of Rehmannia glutinosa. The structures of the new compounds were established by extensive spectroscopic analysis and electronic circular dichroism calculations.

Expansion of a vertical effective field-of-view for an optical 360° holographic display

Jun Wang, Jie Zhou, yang wu, XiangLi Lei & Yuqi Zhang
Cylindrical holography, as a promising 360° display technology, has already attracted a lot of attention. In a previous study, an optical 360° cylindrical holography has been achieved in the visible spectrum using a planar spatial light modulator (SLM) and a 45° conical mirror. Although 360° field-of-view (FOV) is successfully achieved in the horizontal direction, in the previous study, the vertical FOV remains as small as the planar holography, and its expansion is not only necessary...

Links of daily shared appraisal and collaboration to support, mood, and self-care in type 2 diabetes

Melissa Zajdel, Jeanean B Naqvi, Nynke MD Niezink & Vicki S Helgeson
Research has increasingly recognized the links of communal coping—a shared appraisal of a stressor and collaborative action to manage it—to positive adjustment outcomes in chronic illness. However, past literature rarely examines if these two components have unique links to relationship and health outcomes, if one component is more strongly linked than the other component to these outcomes, or if the two components interact to influence outcomes. Additionally, the impact of shared appraisal and collaboration may...

Additional file 4 of A comprehensive update on CIDO: the community-based coronavirus infectious disease ontology

Yongqun He, Hong Yu, Anthony Huffman, Asiyah Yu Lin, Darren A. Natale, John Beverley, Ling Zheng, Yehoshua Perl, Zhigang Wang, Yingtong Liu, Edison Ong, Yang Wang, Philip Huang, Long Tran, Jinyang Du, Zalan Shah, Easheta Shah, Roshan Desai, Hsin-hui Huang, Yujia Tian, Eric Merrell, William D. Duncan, Sivaram Arabandi, Lynn M. Schriml, Jie Zheng … & Barry Smith
Additional file 4: Supplemental Table 3. Protein Ontology representation of SARS-CoV-2 proteins. Comparative information in RefSeq and UniProtKB is also provided.

A comprehensive update on CIDO: the community-based coronavirus infectious disease ontology

Yongqun He, Hong Yu, Anthony Huffman, Asiyah Yu Lin, Darren A. Natale, John Beverley, Ling Zheng, Yehoshua Perl, Zhigang Wang, Yingtong Liu, Edison Ong, Yang Wang, Philip Huang, Long Tran, Jinyang Du, Zalan Shah, Easheta Shah, Roshan Desai, Hsin-hui Huang, Yujia Tian, Eric Merrell, William D. Duncan, Sivaram Arabandi, Lynn M. Schriml, Jie Zheng … & Barry Smith
Abstract Background The current COVID-19 pandemic and the previous SARS/MERS outbreaks of 2003 and 2012 have resulted in a series of major global public health crises. We argue that in the interest of developing effective and safe vaccines and drugs and to better understand coronaviruses and associated disease mechenisms it is necessary to integrate the large and exponentially growing body of heterogeneous coronavirus data. Ontologies play an important role in standard-based knowledge and data representation,...

Different color regulation mechanism in willow barks determined using integrated metabolomics and transcriptomics analyses

Jie Zhou, Jiahui Guo, Qingsheng Chen, Baosong Wang, Xudong He, Qiang Zhuge & Pu Wang
Abstract Background The rich yellow-orange to vividly deep red bark of willow (Salix spp.) branches have high ornamental and economic value. However, the mechanism underlying the regulation of willow branch color remains unknown. Therefore, we performed metabolomics and transcriptomics analyses of purple, green, and red willow barks to elucidating the mechanisms regulating color development. Results Seven anthocyanins were isolated; pelargonidin, petunidin 3-O-rutinoside, and cyanin chloride were the most abundant in red bark, whereas pelargonin chloride...

Additional file 2 of Different color regulation mechanism in willow barks determined using integrated metabolomics and transcriptomics analyses

Jie Zhou, Jiahui Guo, Qingsheng Chen, Baosong Wang, Xudong He, Qiang Zhuge & Pu Wang
Additional file 2: TableS6. The metabolites identified in positive ion mode.

Registration Year

  • 2022
    61

Resource Types

  • Text
    23
  • Dataset
    19
  • Collection
    17
  • Image
    2

Affiliations

  • National Human Genome Research Institute
    61
  • Southern Medical University
    44
  • Chinese Academy of Sciences
    44
  • Shanghai Jiao Tong University
    38
  • Nantong University
    38
  • Wuhan University
    38
  • Sichuan Agricultural University
    38
  • Tongji University
    38
  • Nanjing Tech University
    38
  • Yunnan University
    26