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Artificial Intelligence-Assisted Loop Mediated Isothermal Amplification (ai-LAMP) for Rapid and Reliable Detection of SARS-CoV-2 [article]

Mohammed A Rohaim, Emily Clayton, Irem Sahin, Julianne Vilela, Manar Khalifa, Mohammed Al-Natour, Mahmoud Bayoumi, Aurore Poirier, Manoharanehru Branavan, Mukunthan Tharmakulasingam, Nouman S Chaudhry, Ravinder Sodi (+12 others)
2020 medRxiv   pre-print
However, this requires a reliable and clinically validated diagnostic platform for the sensitive and specific identification of SARS-CoV-2.  ...  To further enhance the assay performance and to remove any subjectivity associated with operator interpretation of result, we engineered a novel hand-held smart diagnostic device.  ...  (B) Corresponding PCR products were run on gel to demonstrate 329 specificity.  ... 
doi:10.1101/2020.07.08.20148999 fatcat:gkrsvqilvndq5ba6powurl5jyu

Artificial Intelligence-Assisted Loop Mediated Isothermal Amplification (AI-LAMP) for Rapid Detection of SARS-CoV-2

Mohammed A. Rohaim, Emily Clayton, Irem Sahin, Julianne Vilela, Manar E. Khalifa, Mohammad Q. Al-Natour, Mahmoud Bayoumi, Aurore C. Poirier, Manoharanehru Branavan, Mukunthan Tharmakulasingam, Nouman S. Chaudhry, Ravinder Sodi (+16 others)
2020 Viruses  
However, this requires a reliable and clinically validated diagnostic platform for the sensitive and specific identification of SARS-CoV-2.  ...  To further enhance the assay performance and to remove any subjectivity associated with operator interpretation of results, we engineered a novel hand-held smart diagnostic device.  ...  The funders had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript, or in the decision to publish the results.  ... 
doi:10.3390/v12090972 pmid:32883050 fatcat:5nef5scurfeb7dn37cqpthswpq

Narrowing the Genetic Causes of Language Dysfunction in the 1q21.1 Microduplication Syndrome

Antonio Benítez-Burraco, Montserrat Barcos-Martínez, Isabel Espejo-Portero, Maite Fernández-Urquiza, Raúl Torres-Ruiz, Sandra Rodríguez-Perales, Ma Salud Jiménez-Romero
2018 Frontiers in Pediatrics  
ROBO1, a candidate for dyslexia, is also highly upregulated, whereas, TLE3, a target of FOXP2, is significantly downregulated.  ...  Among the genes found duplicated in the child, CDH1L is upregulated in the blood of the proband.  ...  ACKNOWLEDGMENTS We would like to thank the proband and his family for their participation in this research.  ... 
doi:10.3389/fped.2018.00163 pmid:29922639 pmcid:PMC5996825 fatcat:q4r5vri6zjcoxdtfiatzyfxyzq

Data, reagents, assays and merits of proteomics for SARS-CoV-2 research and testing

Jana Zecha, Chien-Yun Lee, Florian P. Bayer, Chen Meng, Vincent Grass, Johannes Zerweck, Karsten Schnatbaum, Thomas Michler, Andreas Pichlmair, Christina Ludwig, Bernhard Kuster
2020 Molecular & Cellular Proteomics  
In light of the results obtained and including recent publications or manuscripts on preprint servers, we critically discuss the merits of mass spectrometry-based proteomics for SARS-CoV-2 research and  ...  We assessed the merits of these PRM assays using supernatants of virus-infected Vero E6 cells and challenged the assays by analyzing two diagnostic cohorts of 24 (+30) SARS-CoV-2 positive and 28 (+9) negative  ...  Two cohorts (C1 and C2) of in total 54 PCR-positive and 37 PCR-negative diagnostic samples were analyzed.  ... 
doi:10.1074/mcp.ra120.002164 pmid:32591346 pmcid:PMC7780043 fatcat:bgn6s3s7dvemfoi73feszlsvzm

Web-based LinRegPCR: application for the visualization and analysis of (RT)-qPCR amplification and melting data

Andreas Untergasser, Jan M. Ruijter, Vladimir Benes, Maurice J. B. van den Hoff
2021 BMC Bioinformatics  
Background The analyses of amplification and melting curves have been shown to provide valuable information on the quality of the individual reactions in quantitative PCR (qPCR) experiments and to result  ...  series of qPCR experiments by splitting its functionality into a stand-alone back-end RDML (Real-time PCR Data Markup Language) Python library and several companion applications for data visualization  ...  They also thank Jaco Hagoort for his help in enabling AU to access the source code of the Windows version of LinRegPCR.  ... 
doi:10.1186/s12859-021-04306-1 fatcat:lvcq55r25fddzfpa2i6izhw4ri

A Novel Loss-of-Function SEMA3E Mutation in a Patient with Severe Intellectual Disability and Cognitive Regression

Alyssa J. J. Paganoni, Federica Amoruso, Javier Porta Pelayo, Beatriz Calleja-Pérez, Valeria Vezzoli, Paolo Duminuco, Alessia Caramello, Roberto Oleari, Alberto Fernández-Jaén, Anna Cariboni
2022 International Journal of Molecular Sciences  
The underlying genetic and molecular mechanisms are complex, but are thought to involve, among others, alterations in genes implicated in axon guidance and/or neural circuit formation as demonstrated by  ...  ) gene, which encodes for a key secreted cue that controls mouse brain development.  ...  The funders had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript, or in the decision to publish the results.  ... 
doi:10.3390/ijms23105632 pmid:35628442 pmcid:PMC9143429 fatcat:oiuj2ieghjhe7mnd7nfjlbdvsm

A Multiplex Fluidic Chip for Rapid Phenotypic Antibiotic Susceptibility Testing

Pikkei Wistrand-Yuen, Christer Malmberg, Nikos Fatsis-Kavalopoulos, Moritz Lübke, Thomas Tängdén, Johan Kreuger, Jennifer M. Bomberger
2020 mBio  
MIC values were automatically obtained by tracking the growth rates of individual microcolonies in different regions of antibiotic gradients.  ...  The multiplex fluidic chip for phenotypic AST described in the present study may enable data on antimicrobial resistance within 2 to 4 h, allowing for an early initiation of appropriate antibiotic therapy  ...  ACKNOWLEDGMENTS We thank Gunnar Kahlmeter and Erika Matuschek at the EUCAST Development Laboratory for fruitful discussions, test strains, and BMD susceptibility data.  ... 
doi:10.1128/mbio.03109-19 pmid:32098819 pmcid:PMC7042698 fatcat:cdaw6bosnng7ncgevtt43wsd7u

Informatics

2015 Laboratory Investigation  
It is currently being used as part of an NGS-based molecular diagnostic assay that detects actionable mutations in solid tumors in a CLIA-certified laboratory.  ...  Results: CGA includes capabilities for automatic scheduling of jobs, monitoring analysis runs, and automatically saving information about each run (including command line options, versions and standard  ...  Results: A total of 1251 cases were submitted for telepathology consultations, including 144 cases in 2012, 614 in 2013, and 493 in the first 8 months of 2014.  ... 
doi:10.1038/labinvest.2015.17 fatcat:74eygyy7o5gkrhizoootoyfol4

Segmental uniparental isodisomy (UPD) for 2p16 without clinical symptoms: implications for UPD and other genetic studies of chromosome 2

C. A STRATAKIS
2001 Journal of Medical Genetics  
This research was supported in part by the Association Française contre les Myopathies and by grants from the MDA and March of Dimes (EAS).  ...  JKvKR is recipient of a grant from INSERM, JWT is a recipient of a grant from the Wellcome Trust. EAS is an MNI Killam Scholar.  ...  Figure 3 ( 3 A) 5% polyacrylamide gel of RT-PCR products from the proband and three control RNAs.  ... 
doi:10.1136/jmg.38.2.106 pmid:11288708 pmcid:PMC1734803 fatcat:ov6xzrjp6nbvrhbpvmo5qkaemu

Genomic monitoring of SARS-CoV-2 uncovers an Nsp1 deletion variant that modulates type I interferon response

Jing-wen Lin, Chao Tang, Han-cheng Wei, Baowen Du, Chuan Chen, Minjin Wang, Yongzhao Zhou, Ming-xia Yu, Lu Cheng, Suvi Kuivanen, Natacha S. Ogando, Lev Levanov (+62 others)
2021 Cell Host and Microbe  
Taken together, our virologic surveillance characterizes recurrent genetic diversity and identified mutations in Nsp1 of biological and clinical importance, which collectively may aid molecular diagnostics  ...  One variant, containing a deletion in the Nsp1-coding region (Δ500-532), was found in more than 20% of our sequenced samples and associates with higher RT-PCR cycle thresholds and lower serum IFN-β levels  ...  The PCR products were visualized using Qsep1 (BiOptic, China) capillary gel electrophoresis (CGE) with an S2 DNA cartridge.  ... 
doi:10.1016/j.chom.2021.01.015 pmid:33548198 pmcid:PMC7846228 fatcat:twkvg5iuybanhoi55yvzbbmz6y

Language impairment with a partial duplication of DOCK8 [article]

Antonio Benitez-Burraco, Maite Fernandez-Urquiza, M Salud Jimenez-Romero
2020 bioRxiv   pre-print
Regarding the molecular causes of the observed symptoms, they might result from the altered expression of selected genes involved in procedural learning, particularly, some of components of the SLIT/ROBO  ...  We report in detail on the cognitive and language features of a child with a duplication in the 9p24.3 region (arr[hg19] 9p24.3(266,045-459,076)x3).  ...  products were analyzed by capillary electrophoresis in an automatic 329 sequencer Hitachi 3500 and further analyzed with the Coffalyser V 1.0 software from 330 MRC-Holland. 331 332 Microarrays for whole-genome  ... 
doi:10.1101/2020.06.16.155523 fatcat:nptkalq2mjehdfwv75xuhsbk3m

Defective glucose metabolism in polycystic kidney disease identifies a new therapeutic strategy

Isaline Rowe, Marco Chiaravalli, Valeria Mannella, Valeria Ulisse, Giacomo Quilici, Monika Pema, Xuewen W Song, Hangxue Xu, Silvia Mari, Feng Qian, York Pei, Giovanna Musco (+1 others)
2013 Nature Medicine  
We show that mutation in PKD1 results in enhanced glycolysis in cells, in a murine model of PKD, and in human-derived ADPKD kidneys.  ...  of use: Authors' Contributions IR designed and performed the experiments, interpreted them, wrote the manuscript.  ...  The lab Boletta is especially indebted to Bramani S. for her continuous, intelligent and motivating support.  ... 
doi:10.1038/nm.3092 pmid:23524344 pmcid:PMC4944011 fatcat:xau4tlsoubbehdxof5fmnen7dm

Special Issue(S1): Proceedings of World Congress & Expo on Biotechnology and Bioengineering

Biotechnology and Bioengineering
2017 International Journal of Biotechnology and Bioengineering  
D-cell hypothesis of schizophrenia: A breakthrough for novel therapeutic strategies of neuropsychiatric disorders D ue to complexity of the human central nervous system (CNS), there is an urgent necessity  ...  to elucidate pathophysiology of disorders in the human CNS.  ...  At the moment, I am working in my doctoral thesis in the center of plant molecular biology of the University of Chile, framed in the PhD in molecular biotechnology from the same university.  ... 
doi:10.25141/2475-3432-2017-2.001 fatcat:k5hnrnuuzzhynmezvbn367d7sy

Resveratrol enhances HBV replication through activating Sirt1-PGC-1α-PPARα pathway

Yixian Shi, Yongjun Li, Chenjie Huang, Lixiong Ying, Jihua Xue, Haicong Wu, Zhi Chen, Zhenggang Yang
2016 Scientific Reports  
In addition, we found that this pathway is also required for fastinginduced HBV transcription.  ...  Surprisingly, we found that RSV administration dramatically up-regulated HBV DNA production in HBV-expressing cells and the mouse model via activating the Sirt1-PGC-1α -PPARα pathway.  ...  Serum HBsAg and HBeAg levels were detected automatically by Abbott i2000SR using the Architect HBsAg and HBeAg Reagent kits (Abbott Diagnostics, Abbott Park, IL, USA).  ... 
doi:10.1038/srep24744 pmid:27098390 pmcid:PMC4838842 fatcat:ifyup3a7ijbjtobiztejpbzdzm

Abstract

2021 Vox Sanguinis  
cDNA sequences to human reference genome coordinates; and (4) development of software capable of automatically interpreting the large amount of data.  ...  The use of automated molecular testing platforms, has led to identification of not only high prevalence antigen negative types found primarily in African descent populations, like U-, Js(b-), and Hy-but  ...  Genomic DNA was isolated from whole blood and molecular investi- The molecular laboratory performs RHD genotyping for screening, diagnostic and for emergency cases.  ... 
doi:10.1111/vox.13117 pmid:34060100 fatcat:eff3ps633nhrhdvpr4tlxtzg4q
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