174 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...

Feasibility and preliminary efficacy for morning bright light therapy to improve sleep and plasma biomarkers in US Veterans with TBI. A prospective, open-label, single-arm trial

Jonathan Elliott, Alisha McBride, Nadir Balba, Stanley Thomas, Cassandra Pattinson, Benjamin Morasco, Andrea Wilkerson, Jessica Gill & Miranda Lim
Mild traumatic brain injury (TBI) is associated with persistent sleep-wake dysfunction, including insomnia and circadian rhythm disruption, which can exacerbate functional outcomes including mood, pain, and quality of life. Present therapies to treat sleep-wake disturbances in those with TBI (e.g., cognitive behavioral therapy for insomnia) are limited by marginal efficacy, poor patient acceptability, and/or high patient/provider burden. Thus, this study aimed to assess the feasibility and preliminary efficacy of morning bright light therapy, to improve...

Supplementary document for Optical-field-induced surface nanobumps in near infrared laser direct cleaning of nanoparticles on silicon - 5938365.pdf

Shuowen Zhang, Ling Wu, Jiyong Tang, Volodymyr S Kovalenko, Lisha Fan & Jianhua Yao
Figures S1, S2, S3, S4 used in the manuscript.

Estimating vaccine effectiveness against SARS-CoV-2 infection, hospitalization and death from ecologic data in Costa Rica

Romain Fantin, Rolando Herrero, Allan Hildesheim, Cristina Barboza-Solís, Amada Aparicio, D. Rebecca Prevots, Ruth M. Pfeiffer & Mitchell H. Gail
Abstract Background Clinical trials and individual-level observational data in Israel demonstrated approximately 95% effectiveness of mRNA-based vaccines against symptomatic SARS-CoV-2 infection. Individual-level data are not available in many countries, particularly low- and middle- income countries. Using a novel Poisson regression model, we analyzed ecologic data in Costa Rica to estimate vaccine effectiveness and assess the usefulness of this approach. Methods We used national data from December 1, 2020 to May 13, 2021 to ascertain incidence,...

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...

Additional file 1 of The NORMAN Suspect List Exchange (NORMAN-SLE): facilitating European and worldwide collaboration on suspect screening in high resolution mass spectrometry

Hiba Mohammed Taha, Reza Aalizadeh, Nikiforos Alygizakis, Jean-Philippe Antignac, Hans Peter H. Arp, Richard Bade, Nancy Baker, Lidia Belova, Lubertus Bijlsma, Evan E. Bolton, Werner Brack, Alberto Celma, Wen-Ling Chen, Tiejun Cheng, Parviel Chirsir, Ľuboš Čirka, Lisa A. D’Agostino, Yannick Djoumbou Feunang, Valeria Dulio, Stellan Fischer, Pablo Gago-Ferrero, Aikaterini Galani, Birgit Geueke, Natalia Głowacka, Juliane Glüge … & Emma L. Schymanski
Additional file 1: Summary of the NORMAN-SLE datasets (CSV format) as of 4 May 2022 [81].

CC16 polymorphisms in asthma, asthma subtypes, and asthma control in adults from the Agricultural Lung Health Study

KC Gribben, AB Wyss, JA Poole, PA Farazi, C Wichman, M Richards-Barber, LE Beane Freeman, PK Henneberger, DM Umbach, SJ London, TD LeVan & Kelli C. Gribben
Abstract Background The club cell secretory protein (CC16) has anti-inflammatory and antioxidant effects and is a potential early biomarker of lung damage. The CC16 single nucleotide polymorphism (SNP) rs3741240 risk allele (A) has been inconsistently linked to asthma; other tagging SNPs in the gene have not been explored. The aim was to determine whether CC16 tagging polymorphisms are associated with adult asthma, asthma subtypes or asthma control in the Agricultural Lung Health Study (ALHS). Methods...

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 3 of Genome-wide profiling of retroviral DNA integration and its effect on clinical pre-infusion CAR T-cell products

Lipei Shao, Rongye Shi, Yingdong Zhao, Hui Liu, Alexander Lu, Jinxia Ma, Yihua Cai, Tatyana Fuksenko, Alejandra Pelayo, Nirali N. Shah, James N. Kochenderfer, Scott M. Norberg, Christian Hinrichs, Steven L. Highfill, Robert P Somerville, Sandhya R. Panch, Ping Jin & David F. Stroncek
Additional file 3: Figure S3. Annotation of shared differentially expressed genes between lentiviral and γ-retroviral CAR T-cell products. Related to Figure 4.

Additional file 8 of Genome-wide profiling of retroviral DNA integration and its effect on clinical pre-infusion CAR T-cell products

Lipei Shao, Rongye Shi, Yingdong Zhao, Hui Liu, Alexander Lu, Jinxia Ma, Yihua Cai, Tatyana Fuksenko, Alejandra Pelayo, Nirali N. Shah, James N. Kochenderfer, Scott M. Norberg, Christian Hinrichs, Steven L. Highfill, Robert P Somerville, Sandhya R. Panch, Ping Jin & David F. Stroncek
Additional file 8: Table S3. Differential alternative splicing transcripts with viral integration.

Additional file 9 of Genome-wide profiling of retroviral DNA integration and its effect on clinical pre-infusion CAR T-cell products

Lipei Shao, Rongye Shi, Yingdong Zhao, Hui Liu, Alexander Lu, Jinxia Ma, Yihua Cai, Tatyana Fuksenko, Alejandra Pelayo, Nirali N. Shah, James N. Kochenderfer, Scott M. Norberg, Christian Hinrichs, Steven L. Highfill, Robert P Somerville, Sandhya R. Panch, Ping Jin & David F. Stroncek
Additional file 9: Table S4. Differential integration sites at gene locus based on clinical outcomes.

Genome-wide profiling of retroviral DNA integration and its effect on clinical pre-infusion CAR T-cell products

Lipei Shao, Rongye Shi, Yingdong Zhao, Hui Liu, Alexander Lu, Jinxia Ma, Yihua Cai, Tatyana Fuksenko, Alejandra Pelayo, Nirali N. Shah, James N. Kochenderfer, Scott M. Norberg, Christian Hinrichs, Steven L. Highfill, Robert P Somerville, Sandhya R. Panch, Ping Jin & David F. Stroncek
Abstract Background Clinical CAR T-cell therapy using integrating vector systems represents a promising approach for the treatment of hematological malignancies. Lentiviral and γ-retroviral vectors are the most commonly used vectors in the manufacturing process. However, the integration pattern of these viral vectors and subsequent effect on CAR T-cell products is still unclear. Methods We used a modified viral integration sites analysis (VISA) pipeline to evaluate viral integration events around the whole genome in pre-infusion CAR...

Autoantibody discovery across monogenic, acquired, and COVID19-associated autoimmunity with scalable PhIP-Seq

Sara Vazquez, Sabrina Mann, Aaron Bodansky, Andrew Kung, Zoe Quandt, Elise Ferré, Nils Landegren, Daniel Eriksson, Paul Bastard, Shen-Ying Zhang, Jamin Liu, Anthea Mitchell, Caleigh Mandel-Brehm, Brenda Miao, Gavin Sowa, Kelsey Zorn, Alice Chan, Chisato Shimizu, Adriana Tremoulet, Kara Lynch, Michael Wilson, Olle Kämpe, Kerry Dobbs, Ottavia Delmonte, Luigi Notarangelo … & Joseph DeRisi
Phage Immunoprecipitation-Sequencing (PhIP-Seq) allows for unbiased, proteome-wide autoantibody discovery across a variety of disease settings, with identification of disease-specific autoantigens providing new insight into previously poorly understood forms of immune dysregulation. Despite several successful implementations of PhIP-Seq for autoantigen discovery, including our previous work (Vazquez et al. 2020), current protocols are inherently difficult to scale to accommodate large cohorts of cases and importantly, healthy controls. Here, we develop and validate a high throughput extension of...

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 6 of Multicohort transcriptome analysis of whole blood identifies robust human response signatures in Plasmodium falciparum infections

Yan-hui Zhang, Xin-zhuan Su, Jian Li, Jia-jian Shi & Li-hua Xie
Additional file 6: FigureS6. Immunophenotyping of whole-blood samples in malaria-infected and uninfected groups in GSE1124 datasets based on ssGSEA. The ssGSEA scores (enrichment level) were compared between noninfected and malaria-infected groups in each dataset. The statistical analyses were performed using the unpaired t-test. * p<0.05, ** p<0.01, *** p<0.001, **** p<0.0001.

Additional file 6 of Multicohort transcriptome analysis of whole blood identifies robust human response signatures in Plasmodium falciparum infections

Yan-hui Zhang, Xin-zhuan Su, Jian Li, Jia-jian Shi & Li-hua Xie
Additional file 6: FigureS6. Immunophenotyping of whole-blood samples in malaria-infected and uninfected groups in GSE1124 datasets based on ssGSEA. The ssGSEA scores (enrichment level) were compared between noninfected and malaria-infected groups in each dataset. The statistical analyses were performed using the unpaired t-test. * p<0.05, ** p<0.01, *** p<0.001, **** p<0.0001.

Additional file 7 of Multicohort transcriptome analysis of whole blood identifies robust human response signatures in Plasmodium falciparum infections

Yan-hui Zhang, Xin-zhuan Su, Jian Li, Jia-jian Shi & Li-hua Xie
Additional file 7: Figure S7. Immunophenotyping of whole-blood samples in malaria-infected and uninfected groups in GSE117613 datasets based on ssGSEA. The ssGSEA scores (enrichment level) were compared between noninfected and malaria-infected groups in each dataset. The statistical analyses were performed using the unpaired t-test. * p<0.05, ** p<0.01, *** p<0.001, **** p<0.0001.

Additional file 1 of Assessing the feasibility of sustaining SARS-CoV-2 local containment in China in the era of highly transmissible variants

Yan Wang, Kaiyuan Sun, Zhaomin Feng, Lan Yi, Yanpeng Wu, Hengcong Liu, Quanyi Wang, Marco Ajelli, Cécile Viboud & Hongjie Yu
Additional file 1: Figure S1. Epidemic trajectory, vaccine uptake, and clinical severity of Hong Kong SAR’s Omicron wave. Figure S2. Vaccinations uptake by age in Hong Kong SAR, China, mainland China and New Zealand. Figure S3. Population immunity levels in the baseline immunization scenario and the enhanced immunization scenarios. Figure S4. The observed epidemic growth rate and effective reproduction numbers with baseline interventions in the early stage of the two recent outbreaks in mainland China....

Additional file 1 of Personalized genome assembly for accurate cancer somatic mutation discovery using tumor-normal paired reference samples

Chunlin Xiao, Zhong Chen, Wanqiu Chen, Cory Padilla, Michael Colgan, Wenjun Wu, Li-Tai Fang, Tiantian Liu, Yibin Yang, Valerie Schneider, Charles Wang & Wenming Xiao
Additional file 1. Included all the supplementary tables for this manuscript.

Personalized genome assembly for accurate cancer somatic mutation discovery using tumor-normal paired reference samples

Chunlin Xiao, Zhong Chen, Wanqiu Chen, Cory Padilla, Michael Colgan, Wenjun Wu, Li-Tai Fang, Tiantian Liu, Yibin Yang, Valerie Schneider, Charles Wang & Wenming Xiao
Abstract Background The use of a personalized haplotype-specific genome assembly, rather than an unrelated, mosaic genome like GRCh38, as a reference for detecting the full spectrum of somatic events from cancers has long been advocated but has never been explored in tumor-normal paired samples. Here, we provide the first demonstrated use of de novo assembled personalized genome as a reference for cancer mutation detection and quantifying the effects of the reference genomes on the accuracy...

Additional file 10 of Multicohort transcriptome analysis of whole blood identifies robust human response signatures in Plasmodium falciparum infections

Yan-hui Zhang, Xin-zhuan Su, Jian Li, Jia-jian Shi & Li-hua Xie
Additional file 10: Table S1. The subsets of genes and immune cell types identified from the ImmPort database.

Additional file 11 of Multicohort transcriptome analysis of whole blood identifies robust human response signatures in Plasmodium falciparum infections

Yan-hui Zhang, Xin-zhuan Su, Jian Li, Jia-jian Shi & Li-hua Xie
Additional file 11: Table S2. The upregulated genes in malaria-infected relative to noninfected individuals in the discovery datasets.

Additional file 1 of Multicohort transcriptome analysis of whole blood identifies robust human response signatures in Plasmodium falciparum infections

Yan-hui Zhang, Xin-zhuan Su, Jian Li, Jia-jian Shi & Li-hua Xie
Additional file 1: FigureS1. The receiver operating characteristic (ROC) curves of DEG expression in differentiating the malaria-infected group from the noninfected group in discovery cohorts GSE117613, GSE1124-GPL96, and GSE34404 and validation cohort GSE35858.

Additional file 1 of Management of Multisystem Inflammatory Syndrome in Children (MIS-C) in resource limited settings: The Kenyan Experience

Angela Migowa, Pauline Samia, Sean del Rossi, Oliver Ombeva Malande, Jasmit Shah, Chemutai Kenei, Joy Ayaya, Daisy Jeruto, Laura Oyiengo & Laura Lewandowski
Additional file 1.

Registration Year

  • 2022
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Affiliations

  • National Institutes of Health
    174
  • Shanghai Jiao Tong University
    76
  • Guangzhou Medical University
    68
  • Southern Medical University
    64
  • Huazhong University of Science and Technology
    62
  • Chinese Academy of Sciences
    60
  • Nanjing Agricultural University
    60
  • Sichuan Agricultural University
    58
  • Tongji Hospital
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  • Chinese Academy of Medical Sciences & Peking Union Medical College
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