# bib

id: cord-346846-yle3z5z2
author: Murnain, Kaila L
title: Evaluation of the Slit Lamp Shield to reduce droplet exposure
date: 2020-05-25
extension: .txt
mime: text/plain
words: 486
sentence: 23
flesch: 45
cache: cache/cord-346846-yle3z5z2.txt
txt: txt/cord-346846-yle3z5z2.txt
summary:
  It is important to remember to continue to use other personal protective equipment as guided by local protocols, and that frequent disinfection of the shield, equipment and surfaces is still required. In our simulation (Video S1), a clinician attired in personal protective equipment including surgical mask and face shield was positioned in the examination position.


id: cord-322238-8iwljdoi
author: Chen, Qin
date: 2010-08-29
extension: .txt
mime: text/plain
words: 1714
sentence: 69
flesch: 44
cache: cache/cord-322238-8iwljdoi.txt
txt: txt/cord-322238-8iwljdoi.txt
title:
  Detection of swine transmissible gastroenteritis coronavirus using loop-mediated isothermal amplification

summary:
  The sensitivity of LAMP was demonstrated by comparing with PCR tests using serial dilutions (10 -1 to 10 -7 ) of TGEV RNA samples as template. Five other pig viruses were used to confirm the specificity of the LAMP for TGEV detection.


id: cord-316816-yjbcvf3o
author: Cardoso, Tereza C.
date: 2010-08-21
extension: .txt
mime: text/plain
words: 2089
sentence: 89
flesch: 48
cache: cache/cord-316816-yjbcvf3o.txt
txt: txt/cord-316816-yjbcvf3o.txt
title:
  Visual detection of turkey coronavirus RNA in tissues and feces by reverse-transcription loop-mediated isothermal amplification (RT-LAMP) with hydroxynaphthol blue dye

summary:
  In conclusion, RT-LAMP with HNB dye was shown to be a sensitive, simple assay for the rapid diagnosis of TCoV infection, either directly from feces or in association with virus isolation methods. A number of 25 ileumecaecal junction samples from the 25 infected embryos 13 were scored as negative for TCoV infection with IFA (Table 2 ).


id: cord-343632-cv3qgno3
author: Zhang, Yinhua
title: Rapid Molecular Detection of SARS-CoV-2 (COVID-19) Virus RNA Using Colorimetric LAMP
date: 2020-02-29
extension: .txt
mime: text/plain
words: 2347
sentence: 100
flesch: 42
cache: cache/cord-343632-cv3qgno3.txt
txt: txt/cord-343632-cv3qgno3.txt
summary:
  This test was additionally verified using RNA samples purified from respiratory swabs collected from COVID-19 patients in Wuhan, China with equivalent performance to a commercial RT-qPCR test while requiring only heating and visual inspection. This study describes testing and validation of 5 sets LAMP primers targeting two fragments of the SARS-CoV-2 genome using short (~300bp) RNA fragments made with in vitro transcription and RNA samples from patients.


id: cord-265172-rn9pkk52
author: Michiwaki, Yuhei
date: 2020-10-09
extension: .txt
mime: text/plain
words: 2435
sentence: 99
flesch: 40
cache: cache/cord-265172-rn9pkk52.txt
txt: txt/cord-265172-rn9pkk52.txt
title:
  Emergent carotid artery stenting following intravenous alteplase infusion after rapid negative diagnosis for COVID-19 by loop-mediated isothermal amplification assay: A case report

summary:
  During the COVID-19 pandemic, the LAMP assay for COVID-19 detection might be a suitable diagnostic strategy preceding stroke treatment because of the rapid turnaround time. During the COVID-19 pandemic, the LAMP assay for COVID-19 detection might be a suitable diagnostic strategy preceding stroke treatment because of the rapid turnaround time.


id: cord-256845-5pjam7em
author: Stranieri, Angelica
date: 2017-01-18
extension: .txt
mime: text/plain
words: 2352
sentence: 72
flesch: 38
cache: cache/cord-256845-5pjam7em.txt
txt: txt/cord-256845-5pjam7em.txt
title:
  Reverse transcriptase loop-mediated isothermal amplification for the detection of feline coronavirus

summary:
  RT-nPCR positive FCoV RNA from a cat with FIP was used as positive control and RNase-free water as negative control. In the case the sensitivity of the test might be ameliorated through further studies, the RT-LAMP could be extremely useful, due to its low costs and rapidity, in those situations where the Table 2 Results obtained on the samples tested with RT-nPCR (PCR) and LAMP and evaluated with agarose gel electrophoresis (LAMP GEL) and hydroxynaphtol blue dye (LAMP HNB detection of FCoV must be repeated over time and on a high number of cats (e.g. breeding catteries).


id: cord-302663-gb2vgs97
author: Mekata, Tohru
title: Detection of yellow head virus in shrimp by loop-mediated isothermal amplification (LAMP)
date: 2006-04-04
extension: .txt
mime: text/plain
words: 2545
sentence: 104
flesch: 55
cache: cache/cord-302663-gb2vgs97.txt
txt: txt/cord-302663-gb2vgs97.txt
summary:
  This suggests RT-LAMP is a more rapid method for the detection of shrimp virus, compared to the RT-PCR method which takes 30-60 min for RT reaction and at least 2-3 h for conventional PCR method. In this paper, the RT-LAMP assay for detection of YHV RNA in shrimp is described.


id: cord-271735-gprd79di
author: Shirato, Kazuya
title: Detecting amplicons of loop‐mediated isothermal amplification
date: 2019-08-13
extension: .txt
mime: text/plain
words: 2520
sentence: 96
flesch: 29
cache: cache/cord-271735-gprd79di.txt
txt: txt/cord-271735-gprd79di.txt
summary:
  Loop-mediated isothermal amplification of DNA Accelerated reaction by loopmediated isothermal amplification using loop primers Real-time reversetranscription loop-mediated isothermal amplification for rapid detection of rift valley Fever virus Effect of internal primer-template mismatches on loop-mediated isothermal amplification Detection of Middle East respiratory syndrome coronavirus using reverse transcription loop-mediated isothermal amplification (RT-LAMP) Development of fluorescent reverse transcription loop-mediated isothermal amplification (RT-LAMP) using quenching probes for the detection of the Middle East respiratory syndrome coronavirus Loop-mediated isothermal amplification (LAMP) for the direct detection of human pulmonary infections with environmental (nontuberculosis) mycobacteria The rapid detection of salmonella from food samples by loop-mediated isothermal amplification (LAMP) Efficacy of loop mediated isothermal amplification (LAMP) assay for the laboratory identification of Mycobacterium tuberculosis isolates in a resource limited setting Detection of Mycoplasma pneumoniae by loop-mediated isothermal amplification (LAMP) assay and serology in pediatric communityacquired pneumonia Development and evaluation of a loop-mediated isothermal amplification method for rapid diagnosis of Bordetella pertussis infection Molecular diagnostic tools in mycobacteriology Examination of the rapid detection of legionella from bathwater samples by the loopmediated isothermal amplification and polymerase chain reaction methods Loop-mediated isothermal amplification (LAMP) assay for detection of Theileria Onepot reverse transcriptional loop-mediated isothermal amplification (RT-LAMP) for detecting MERS-CoV False-positive results and the polymerase chain reaction Avoidance of PCR false positives Detection of loopmediated isothermal amplification reaction by turbidity derived from magnesium pyrophosphate formation Avoiding false positives with PCR Enzymatic amplification of beta-globin genomic sequences and restriction site analysis for diagnosis of sickle cell anemia Nucleic acid sequence-based amplification Real-time turbidimetry of LAMP reaction for quantifying template DNA Loop-mediated isothermal amplification (LAMP) of gene sequences and simple visual detection of products Fluorescent quenchingbased quantitative detection of specific DNA/RNA using a BODIPY (R) FL-labeled probe or primer Development of real-time fluorescent reverse transcription loop-mediated isothermal amplification assay with quenching primer for influenza virus and respiratory syncytial virus Development of real-time fluorescent reverse transcription loop-mediated isothermal amplification assays for rhinovirus detection How to cite this article: Shirato K. Detecting amplicons of loop-mediated isothermal amplification


id: cord-321886-0b3ocoh9
author: Zhang, Chao-fan
date: 2010-08-04
extension: .txt
mime: text/plain
words: 2774
sentence: 103
flesch: 54
cache: cache/cord-321886-0b3ocoh9.txt
txt: txt/cord-321886-0b3ocoh9.txt
title:
  Loop-mediated isothermal amplification for rapid detection and differentiation of wild-type pseudorabies and gene-deleted virus vaccines

summary:
  En et al. (2008) described a LAMP system for PRV detection but that LAMP system could not differentiate between swine infected with wild-type PRV and swine vaccinated with PRV gE-deleted. The use of LAMP is described for determining whether swine are infected with wild-type PRV or have been vaccinated with PRV gE-and remain uninfected by wild-type strains.


id: cord-343136-kftffes0
author: Mohon, Abu Naser
title: Optimization and clinical validation of dual-target RT-LAMP for SARS-CoV-2
date: 2020-09-15
extension: .txt
mime: text/plain
words: 2595
sentence: 99
flesch: 44
cache: cache/cord-343136-kftffes0.txt
txt: txt/cord-343136-kftffes0.txt
summary:
  The RT-LAMP assay described is unique in that it offers the most thorough clinical validation to date meeting regulatory standards which include precision studies on several instruments, reproducibility studies over 20 days, a robust clinical validation sample set, and a limit of detection equal or superior to other LAMP studies (50 copies per reaction). LAMP primer sets were designed targeting unique regions of the Spike (S) protein gene and RNA-dependent RNA Polymerase gene (RdRP) were ultimately used (Table 1) .


id: cord-305399-98sqovwb
author: Li, Hao
date: 2019-04-22
extension: .txt
mime: text/plain
words: 2859
sentence: 96
flesch: 47
cache: cache/cord-305399-98sqovwb.txt
txt: txt/cord-305399-98sqovwb.txt
title:
  Development of a reverse transcription-loop-mediated isothermal amplification (RT-LAMP) assay for the detection of porcine pegivirus

summary:
  In the past decade, loop-mediated isothermal amplification (LAMP) has become an effective technique, which exhibits high sensitivity and specificity for diagnosing important pathogens in medicine and veterinary medicine (Notomi et al., 2015) . LAMP is a nucleic acid amplification-based method that generally requires a group of four specific external and internal primers (Notomi et al., 2000) .


id: cord-307068-360qs3ov
author: Hagiwara, Masanori
date: 2007-03-26
extension: .txt
mime: text/plain
words: 3334
sentence: 162
flesch: 52
cache: cache/cord-307068-360qs3ov.txt
txt: txt/cord-307068-360qs3ov.txt
title:
  Loop‐mediated isothermal amplification method for detection of human papillomavirus type 6, 11, 16, and 18

summary:
  In order to evaluate the reliability of HPV type‐specific LAMP detecting HPV DNA from clinical samples, tissue specimens were obtained from 27 patients with external genital polypoid lesions. HPV DNA was not detected in the seborrheic keratoses, epidermolytic acanthoma, and hairy nymphae.


id: cord-002081-vi6rth9o
author: Zhang, Chao
date: 2016-06-01
extension: .txt
mime: text/plain
words: 3400
sentence: 110
flesch: 35
cache: cache/cord-002081-vi6rth9o.txt
txt: txt/cord-002081-vi6rth9o.txt
title:
  Establishment and application of a real-time loop-mediated isothermal amplification system for the detection of CYP2C19 polymorphisms

summary:
  Plavix (clopidogrel bisulfate) Genetic polymorphism of cytochrome P450 2C19 in Mexican Americans: A cross-ethnic comparative study Effects of CYP2C19 genotype on outcomes of clopidogrel treatment ACCF/AHA clopidogrel clinical alert: approaches to the FDA boxed warning: a report of the American College of Cardiology Foundation Task Force on clinical expert consensus documents and the American Heart Association endorsed by the Society for Cardiovascular Angiography and Interventions and the Society of Thoracic Surgeons Loop-mediated isothermal amplification targeting insect resistant and herbicide tolerant transgenes: Monitoring for GM contamination in supply chain Circulating tumor DNA as a liquid biopsy for cancer Genetic polymorphism analysis of CYP2C19 in Chinese Han populations from different geographic areas of mainland China Real-time loop-mediated isothermal amplification (RealAmp) for the species-specific identification of Plasmodium vivax Real-time fluorescence loop mediated isothermal amplification for the diagnosis of malaria Real-time loop-mediated isothermal amplification (LAMP) assay for group specific detection of important trichothecene producing Fusarium species in wheat Detection of Middle East respiratory syndrome coronavirus using reverse transcription loop-mediated isothermal amplification (RT-LAMP) Development of an electrochemical method for Ochratoxin A detection based on aptamer and loop-mediated isothermal amplification Clinical evaluation of a loop-mediated isothermal amplification (LAMP) assay for rapid detection of neisseria meningitidis in Cerebrospinal Fluid Loop-mediated isothermal amplification of DNA (LAMP): Thus, the wide application of this simple, rapid and low-cost genotyping LAMP method in SNP detection is imperative.


id: cord-338899-qt17jhg0
author: Lakshmi, Vemu
title: Clinical Features and Molecular Diagnosis of Chikungunya Fever from South India
date: 2008-05-01
extension: .txt
mime: text/plain
words: 3630
sentence: 152
flesch: 45
cache: cache/cord-338899-qt17jhg0.txt
txt: txt/cord-338899-qt17jhg0.txt
summary:
  In the present study, the detection of CHIK virus RNA in 48.6% of samples by RT-PCR and in 55.4% of samples by RT-LAMP, as well as the detection of IgM antibodies in 21.5% of samples, confi med that the causative agent of this epidemic was CHIK virus. As is the case for most alphaviruses, detection of CHIK virus depends on isolation of the virus in blood specimens obtained from viremic patients or in infected tissue specimens obtained from blood-feeding arthropods, which are time-consuming.


id: cord-331641-u27ohm5p
author: Liu, Xiaonan
date: 2018-09-15
extension: .txt
mime: text/plain
words: 3853
sentence: 146
flesch: 45
cache: cache/cord-331641-u27ohm5p.txt
txt: txt/cord-331641-u27ohm5p.txt
title:
  A direct isothermal amplification system adapted for rapid SNP genotyping of multifarious sample types

summary:
  1C illustrates that the Direct-LAMP could accurately detect all possible homozygotes and heterozygotes of MTHFR C677T with whole blood sample. Whole blood sample was collected using EDTA-coated tubes.


id: cord-332961-ebr623rm
author: Zhang, Qingli
date: 2017-11-30
extension: .txt
mime: text/plain
words: 3921
sentence: 127
flesch: 39
cache: cache/cord-332961-ebr623rm.txt
txt: txt/cord-332961-ebr623rm.txt
title:
  Reverse transcription loop-mediated isothermal amplification for rapid and quantitative assay of covert mortality nodavirus in shrimp

summary:
  Early Mortality Syndrome (EMS)/Acute Hepatopancreatic Necrosis Syndrome (AHPNS) Development of reverse transcription loop-mediated isothermal amplification assay for rapid detection of an emerging potyvirus: tomato necrotic stunt virus Development of loop-mediated isothermal amplification assay for detection of Entamoeba histolytica Real-time turbidimetry of LAMP reaction for quantifying template DNA Development of a new method for diagnosis of rubella virus infection by reverse transcription-loop-mediated isothermal amplification Detection of loop-mediated isothermal amplification reaction by turbidity derived from magnesium pyrophosphate formation Loop-mediated isothermal amplification reaction using a nondenatured template Accelerated reaction by loop-mediated isothermal amplification using loop primers Loop-mediated isothermal amplification of DNA Real-time reverse transcription loop-mediated isothermal amplification for rapid detection of West Nile virus Comparison of real-time reverse transcription loopmediated isothermal amplification and real-time reverse transcription polymerase chain reaction for detection of noroviruses in municipal wastewater Loop-mediated isothermal amplification (LAMP) of gene sequences and simple visual detection of products Loop-mediated isothermal amplification method for rapid detection of the toxic dinoflagellate Alexandrium, which causes algal blooms and poisoning of shellfish A novel method of real-time reverse transcription loop-mediated isothermal amplification developed for rapid and quantitative detection of human astrovirus Principles and methods of validation of diagnostic assays for infectious diseases Discussion of the control measures for the ''bottom death (covert mortality disease) of Pacific white shrimp Comprehensive control of the covert mortality disease of Pacific white shrimp Development and evaluation of a loop-mediated isothermal amplification assay for the rapid detection of porcine cytomegalovirus under field conditions To be cautious of ''bottom death in the intensive farming of Pacific white shrimp A new nodavirus is associated with covert mortality disease of shrimp Development of a reverse transcription loop-mediated isothermal amplification assay for rapid detection of grass carp reovirus In summary, this report describes a rapid, highly sensitive, highly specific, financially economical, quantitative RT-LAMP method for CMNV detection.


id: cord-310657-04pp0o74
author: Lu, Renfei
date: 2020-04-18
extension: .txt
mime: text/plain
words: 4074
sentence: 152
flesch: 44
cache: cache/cord-310657-04pp0o74.txt
txt: txt/cord-310657-04pp0o74.txt
title:
  A Novel Reverse Transcription Loop-Mediated Isothermal Amplification Method for Rapid Detection of SARS-CoV-2

summary:
  In the real-time monitoring system, SYTO9 is used as a fluorescent dye which has a minimal inhibitory effect on LAMP amplification Nucleic acids of another 15 viruses (including: influenza A, B, and C viruses; parainfluenza viruses type 1-3; enterovirus; RSV A and B groups; HCoV-HKU-1; HCoV-NL63; human rhinovirus; human metapneumovirus; adenovirus; and bocavirus) were obtained from positive clinical samples from children with acute respiratory tract infections.


id: cord-312222-aw5849rc
author: Österdahl, Marc F.
date: 2020-10-20
extension: .txt
mime: text/plain
words: 3959
sentence: 160
flesch: 48
cache: cache/cord-312222-aw5849rc.txt
txt: txt/cord-312222-aw5849rc.txt
title:
  Detecting SARS-CoV-2 at point of care: preliminary data comparing loop-mediated isothermal amplification (LAMP) to polymerase chain reaction (PCR)

summary:
  However, as the pandemic has progressed, it has become apparent that there is no true gold standard for COVID-19 testing with highly-anticipated antibody testing not always proving helpful; even in mild disease, antibodies in PCR positive patients may not be detected [22] . Low temperatures (< 36°C were detected in a minority of COVID PCR positive patients ( Table 3 ).


id: cord-279229-2226jnfl
author: Savan, R
date: 2005-11-22
extension: .txt
mime: text/plain
words: 4191
sentence: 170
flesch: 38
cache: cache/cord-279229-2226jnfl.txt
txt: txt/cord-279229-2226jnfl.txt
title:
  Loop‐mediated isothermal amplification: an emerging technology for detection of fish and shellfish pathogens

summary:
  Furthermore, LAMP detection was superior to PCR when spleen DNA extracted from infected fish was used as template. Recently, PCR detection has been possible for nocardiosis (Kono, Ooyama, Chen & Sakai 2001; Miyoshi & Suzuki 2002) .


id: cord-284644-9k2oox64
author: Sharma, Vikrant
date: 2017-12-15
extension: .txt
mime: text/plain
words: 4491
sentence: 145
flesch: 38
cache: cache/cord-284644-9k2oox64.txt
txt: txt/cord-284644-9k2oox64.txt
title:
  Evaluation of clinical applicability of reverse transcription-loop-mediated isothermal amplification assay for detection and subtyping of Influenza A viruses

summary:
  Virus isolation using egg embryo culture or cell culture is considered as 'gold standard' for influenza virus detection but the whole process is labour intensive and lengthy taking 3-7 days for obtaining results (Ellis and Zambon, 2002) . Influenza viruses belong to the family Orthomyxoviridae, characterized by segmented, negative-sense, single stranded RNA genome (Shaw and Palese, 2013) .


id: cord-333220-tcvs4beg
author: Lee, Szu-Yuan
title: Compact optical diagnostic device for isothermal nucleic acids amplification
date: 2008-08-12
extension: .txt
mime: text/plain
words: 4854
sentence: 204
flesch: 44
cache: cache/cord-333220-tcvs4beg.txt
txt: txt/cord-333220-tcvs4beg.txt
summary:
  This system can provide appropriate reaction conditions for HBV LAMP DNA amplification. After the performance of micro-reactor system is confirmed, HBV LAMP reactions can be transplanted into this system.


id: cord-297974-sduz0j35
author: Bokelmann, L.
date: 2020-08-06
extension: .txt
mime: text/plain
words: 4771
sentence: 200
flesch: 47
cache: cache/cord-297974-sduz0j35.txt
txt: txt/cord-297974-sduz0j35.txt
title:
  Rapid, reliable, and cheap point-of-care bulk testing for SARS-CoV-2 by combining hybridization capture with improved colorimetric LAMP (Cap-iLAMP)

summary:
  Amplification in LAMP reactions is often detected colorimetrically by a pH sensitive dye that changes color when extensive DNA synthesis lowers the pH of the reaction (Tanner et al. 2015) . Evaluation of different amounts of Tte UvrD helicase in LAMP reactions.


id: cord-252686-viz05uam
author: Dong, Qing
date: 2019-11-04
extension: .txt
mime: text/plain
words: 5066
sentence: 190
flesch: 45
cache: cache/cord-252686-viz05uam.txt
txt: txt/cord-252686-viz05uam.txt
title:
  A signal-flexible gene diagnostic strategy coupling loop-mediated isothermal amplification with hybridization chain reaction

summary:
  In this paper, through designing partial of LAMP amplicon sequence as the input sequence to trigger HCR reaction, we for the first time couple the LAMP and HCR together to achieve both ultra-sensitivity and significant signal change for general gene targets. The 8% native PAGE gel (without or with GelRed stain) results show that HCR reaction took place with the Mimic-T introduced ( Fig. 2A and B, lane 4e6) .


id: cord-334518-mjr6u7ak
author: Hu, X.
date: 2020-05-23
extension: .txt
mime: text/plain
words: 5165
sentence: 213
flesch: 44
cache: cache/cord-334518-mjr6u7ak.txt
txt: txt/cord-334518-mjr6u7ak.txt
title:
  Development and clinical application of a rapid and sensitive loop-mediated isothermalamplification test for SARS-CoV-2 infection

summary:
  Additionally, nasopharyngeal swabs from COVID-19 patients had a higher positive rate than sputum specimens in both the RT-qPCR and LAMP assays. Respiratory samples were collected and tested with LAMP and the results were compared with those obtained by RT-qPCR.


id: cord-280442-jtvez46y
author: Wu, Xuan
date: 2019-11-01
extension: .txt
mime: text/plain
words: 5316
sentence: 194
flesch: 47
cache: cache/cord-280442-jtvez46y.txt
txt: txt/cord-280442-jtvez46y.txt
title:
  Simultaneous and visual detection of infectious bronchitis virus and Newcastle disease virus by multiple LAMP and lateral flow dipstick

summary:
  NDV detection assays were specific to the NDV templates ( Figure 4B ). As for NDV detection assays, positive results were observed only when NDV templates existed.


id: cord-318120-vfznyyz6
author: Dauner, Allison L.
date: 2015-05-15
extension: .txt
mime: text/plain
words: 5272
sentence: 193
flesch: 39
cache: cache/cord-318120-vfznyyz6.txt
txt: txt/cord-318120-vfznyyz6.txt
title:
  Development of a pan-serotype reverse transcription loop-mediated isothermal amplification assay for the detection of dengue virus

summary:
  Wallingford: CAB International Dengue and dengue hemorrhagic fever Development of simple and rapid assay to detect viral RNA of tick-borne encephalitis virus by reverse transcription-loop-mediated isothermal amplification Rapid identification of dengue virus isolates by using monoclonal antibodies in an indirect immunofluorescence assay Development and evaluation of a novel loop-mediated isothermal amplification method for rapid detection of severe acute respiratory syndrome coronavirus Highly sensitive detection of malaria parasitemia in a malaria-endemic setting: performance of a new loop-mediated isothermal amplification kit in a remote clinic in Uganda Loop-mediated isothermal amplification for direct detection of Mycobacterium tuberculosis complex, M. avium, and M. intracellulare in sputum samples Rapid detection of dengue viral RNA in mosquitoes by nucleic acid-sequence based amplification (NASBA) Tolerance of loop-mediated isothermal amplification to a culture medium and biological substances Laboratory diagnosis of dengue virus infection: current and future perspectives in clinical diagnosis and public health Comparison of methods for extraction of nucleic acid from hemolytic serum for PCR amplification of hepatitis B virus DNA sequences A real-time reverse transcription loop-mediated isothermal amplification assay for the rapid detection of yellow fever virus A simple, inexpensive device for nucleic acid amplification without electricity-toward instrument-free molecular diagnostics in low-resource settings Simultaneous detection and differentiation of dengue virus serotypes 1-4, Japanese encephalitis virus, and West Nile virus by a combined reverse-transcription loop-mediated isothermal amplification assay Rapid identification of dengue virus by reverse transcription-polymerase chain reaction using field-deployable instrumentation The Direct Boil-LAMP method: a simple and rapid diagnostic method for cutaneous leishmaniasis Detection of loop-mediated isothermal amplification reaction by turbidity derived from magnesium pyrophosphate formation Real-time turbidimetry of LAMP reaction for quantifying template DNA Loop-mediated isothermal amplification reaction using a nondenatured template Accelerated reaction by loop-mediated isothermal amplification using loop primers Rapid detection and differentiation of dengue virus serotypes by NS1 specific reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay in patients presenting to a tertiary care hospital in Loopmediated isothermal amplification of DNA Real-time reverse transcription loopmediated isothermal amplification for rapid detection of West Nile virus Rapid detection and differentiation of dengue virus serotypes by a real-time reverse transcription-loopmediated isothermal amplification assay Development and evaluation of reverse transcription-loop-mediated isothermal amplification assay for rapid and real-time detection of Japanese encephalitis virus Rapid and sensitive detection of Macrobrachium rosenbergii nodavirus in giant freshwater prawns by reverse transcription loop-mediated isothermal amplification combined with a lateral flow dipstick Microevolution and virulence of dengue viruses Loop-mediated isothermal amplification assay for rapid diagnosis of malaria infections in an area of endemicity in Thailand Current advances in dengue diagnosis Simultaneous multiple target detection in real-time loop-mediated isothermal amplification Trends in dengue diagnosis Detection of dengue viruses using reverse transcription-loop-mediated isothermal amplification Rapid detection and quantification of Japanese encephalitis virus by real-time reverse transcription loop-mediated isothermal amplification The molecular epidemiology of Dengue viruses, genetic variation and microevolution The molecular epidemiology of dengue viruses, genetic variation and microevolution Dengue viremia titer, antibody response pattern, and virus serotype correlate with disease severity This work would not have been possible without the generous support of the Ministry of Health Peru, Direccion General de Epidemiologia and DIRESA Piura, Tumbes, Madre de Dios, and Iquitos. In conclusion, this work adds to the growing body of isothermal amplification assays available to detect DENV.


id: cord-005377-36io7zsm
author: Sidoti, Francesca
title: Alternative Molecular Tests for Virological Diagnosis
date: 2012-04-09
extension: .txt
mime: text/plain
words: 5999
sentence: 235
flesch: 30
cache: cache/cord-005377-36io7zsm.txt
txt: txt/cord-005377-36io7zsm.txt
summary:
  A virus (H1N1) by real-time nucleic acid sequence-based amplification Development and validation of a commercial real time NASBA assay for the rapid confirmation of influenza AH5N1 virus in clinical samples Clinical evaluation of NucliSens magnetic extraction and Nu-cliSens analytical specific reagents for the real-time detection of respiratory syncytial virus (RSV) in pediatric respiratory specimens A one-tube quantitative HIV-1 RNA NASBA nucleic acid amplification assay using electrochemiluminiscent (ECL) labelled probes Quantitation of human immunodeficiency virus type 1 RNA in different biological compartments Single rapid realtime monitored isothermal RNA amplification assay for quantification of human immunodeficiency virus type 1 isolates from groups M, N, and O Evaluation of the persistence of infectious human norovirus on food surfaces by using real time nucleic acid sequence-based amplification Diagnosis of human metapneumovirus infection in immunosuppressed lung transplant recipients and children evaluated for pertussis Real time NASBA detection of SARSassociated coronavirus and comparison with real-time reverse transcription-PCR Evaluation of real time nucleic acid based amplification for detection of Chikungunya virus in clinical sample Nucleic acid sequencebased amplification assays for rapid detection of West Nile and St. Louis encephalitis viruses Real time nucleic acid sequence-based amplification assay for detection of hepatitis A virus Characterization of the quantitative HCV NASBA assay Evaluation of a new NASBA assay for the detection of hepatitis C virus based on the NucliSens basic kit reagents Detection of rhinoviruses by tissue culture and two independent amplification techniques, nucleic acid sequence-based amplification and reverse transcription-PCR, in children with acute respiratory infections during a winter season A sensitive and robust method for measles RNA detection Comparative detection of rabies RNA by NASBA, real-time PCR and conventional PCR Rapid and simple method for the purification of nucleic acids Comparison of five methods for extraction of Legionella pneumophila from respiratory specimens Evaluation of NucliSens easyMAG for automated nucleic acid extraction from various clinical specimens Development and evaluation of nucleic acid sequence based amplification (NASBA) for diagnosis of enterovirus infections using the NucliSens Ò Basic Kit Development of a novel one-tube isothermal reverse transcription thermophilic helicase-dependent amplification platform for rapid RNA detection Helicase dependent OnChip-amplification and its use in multiplex pathogen detection Bacteriophage T4 gene 32 protein: modulation of protein-nucleic acid and protein-protein association by structural domains Snapshot of the genome of the pseudo-T-even bacteriophage RB49 Escherichia coli helicase II (uvrD) protein can completely unwind fully duplex linear and nicked circular DNA Characterization of a thermostable UvrD helicase and its participation in helicase-dependent amplification Colorimetric detection of Helicobacter pylori DNA using isothermal helicase-dependent amplification and gold nanoparticle probes Improving isothermal DNA amplification speed for the rapid detection of Mycobacterium tuberculosis An oligomeric form of E. coli UvrD is required for optimal helicase activity Helicase-dependent isothermal DNA amplification Complete nucleotide sequence of bacteriophage T7 DNA and the locations of T7 genetic elements Bacteriophage T7: minimal requirements for the replication of a duplex DNA molecule Characterization of the helicase and primase activities of the 63-kDa component of the bacteriophage T7 gene 4 protein Cloning and expression of gene 4 of bacteriophage T7 and creation and analysis of T7 mutants lacking the 4A primase/ helicase or the 4B helicase DNA replication DNA-dependent nucleoside 5 0 -triphosphatase activity of the gene 4 protein of bacteriophage T7 Escherichia coli thioredoxin confers processivity on the DNA polymerase activity of the gene 5 protein of bacteriophage T7 Isothermal DNA amplification in vitro: the helicase-dependent amplification system Nucleic acid assay system for tier II labs and moderately complex clinics to detect HIV in low-resource settings A rapid and simple isothermal nucleic acid amplification test for detection of herpes simplex virus types 1 and 2 Detection of Helicobacter pylori by enzyme-linked immunosorbent assay of thermophilic helicase-dependent isothermal DNA amplification Helicase-dependent amplification: use in OnChip amplification and potential for point-of-care diagnostics Real-time PCR array chip with capillary-driven sample loading and reactor sealing for point-ofcare applications An integrated disposable device for DNA extraction and helicase dependent amplification Real-time electrochemical monitoring of isothermal helicase-dependent amplification of nucleic acids The first HDA system for isothermal DNA amplification was developed by using E. coli UvrD DNA helicase (*82 kDa) along with a DNA polymerase, and two accessory proteins (SSBs): T4 gene 32 or RB 49 gene 32 proteins [78, 79] .


id: cord-328042-e1is656g
author: Klein, Steffen
title: SARS-CoV-2 RNA Extraction Using Magnetic Beads for Rapid Large-Scale Testing by RT-qPCR and RT-LAMP
date: 2020-08-07
extension: .txt
mime: text/plain
words: 6357
sentence: 224
flesch: 47
cache: cache/cord-328042-e1is656g.txt
txt: txt/cord-328042-e1is656g.txt
summary:
  Magnetic bead RNA extraction was benchmarked against the commercial QIAcube extraction platform. Magnetic bead RNA extraction was performed in 96-well plates in combination with a magnet plate optimized for 96 deep-well plates.


id: cord-276718-3lujp0oy
author: Neeraja, M.
date: 2014-10-24
extension: .txt
mime: text/plain
words: 6153
sentence: 206
flesch: 45
cache: cache/cord-276718-3lujp0oy.txt
txt: txt/cord-276718-3lujp0oy.txt
title:
  Rapid detection and differentiation of dengue virus serotypes by NS1 specific reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay in patients presenting to a tertiary care hospital in Hyderabad, India

summary:
  b RT-LAMP and CDC real time RT-PCR assay detected 8 samples which were negative for NS1 Ag by ELISA and NS1 RT PCR assay. All the primers were assessed for specificity before use in LAMP assays with a BLAST search with sequences in the Gen Bank (Table 1) .


id: cord-332820-6qx6svs5
author: Buck, M. D.
title: Standard operating procedures for SARS-CoV-2 detection by a clinical diagnostic RT-LAMP assay
date: 2020-07-01
extension: .txt
mime: text/plain
words: 4099
sentence: 183
flesch: 46
cache: cache/cord-332820-6qx6svs5.txt
txt: txt/cord-332820-6qx6svs5.txt
summary:
  https://doi.org/10.1101/2020.06.29.20142430 doi: medRxiv preprint A Novel Coronavirus from Patients with Pneumonia in China A new coronavirus associated with human respiratory disease in China A pneumonia outbreak associated with a new coronavirus of probable bat origin Laboratory testing of SARS-CoV, MERS-CoV, and SARS-CoV-2 (2019-nCoV): Current status, challenges, and countermeasures Scalable and Resilient SARS-CoV-2 testing in an Academic Centre Loop-mediated isothermal amplification of DNA Loop-mediated isothermal amplification (LAMP): a rapid, accurate, and cost-effective diagnostic method for infectious diseases Rapid and simple colorimetric detection of multiple influenza viruses infecting humans using a reverse transcriptional loop-mediated isothermal amplification (RT-LAMP) diagnostic platform Rapid Detection of Zika Virus in Urine Samples and Infected Mosquitos by Reverse Transcription-Loop-Mediated Isothermal Amplification SARS-CoV-2 Detection Using an Isothermal Amplification Reaction and a Rapid, Inexpensive Protocol for Sample Inactivation and Purification Shotgun Transcriptome and Isothermal Profiling of SARS-CoV-2 Infection Reveals Unique Host Responses, Viral Diversification, and Drug Interactions Development of Reverse Transcription Loop-Mediated Isothermal Amplification Assays Targeting Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Methods of inactivation of SARS-CoV-2 for downstream biological assays Enhancing Colorimetric LAMP Amplification Speed and Sensitivity with Guanidine Chloride No reuse allowed without permission. As such, the standard operating procedure (SOP) developed here is ready to be deployed for diagnostic testing of SARS-CoV-2.


id: cord-282126-gmjnbnx5
author: Yang, Limin
date: 2012-08-07
extension: .txt
mime: text/plain
words: 2140
sentence: 94
flesch: 55
cache: cache/cord-282126-gmjnbnx5.txt
txt: txt/cord-282126-gmjnbnx5.txt
title:
  Development and application of a reverse transcription loop-mediated isothermal amplification method for rapid detection of Duck hepatitis A virus type 1

summary:
  After a comparison of different DHAV-1 subgroup genomes, the conserved domain 2C of the genome was selected as the domain for LAMP primer design and was used for screening a group of primers with good amplification efficiency. DHAV-1 total RNA concentration was measured spectrophotometrically at A260 and A280.


id: cord-302829-1o1jo8uk
author: Chen, Hao-tai
title: Rapid detection of porcine circovirus type 2 by loop-mediated isothermal amplification
date: 2008-03-19
extension: .txt
mime: text/plain
words: 2822
sentence: 86
flesch: 38
cache: cache/cord-302829-1o1jo8uk.txt
txt: txt/cord-302829-1o1jo8uk.txt
summary:
  The detection rate of PCV2 LAMP for 86 clinical samples was 96.5% and appeared greater than that of the PCR method. Overall, the detection rate of PCV2 LAMP for 86 clinical tissue samples was 96.5% and appeared better than that for the PCR method.


id: cord-003342-wmmbkmrg
author: Wang, De-Guo
title: Two Methods for Increased Specificity and Sensitivity in Loop-Mediated Isothermal Amplification
date: 2015-04-07
extension: .txt
mime: text/plain
words: 2870
sentence: 97
flesch: 35
cache: cache/cord-003342-wmmbkmrg.txt
txt: txt/cord-003342-wmmbkmrg.txt
summary:
  However, there is still no report studying non-specific amplification and cause of false positive results in LAMP reactions at present. For practical application of LAMP as well as reduction of the rate of false positive results in LAMP reactions, most researches currently focus on development of closed-tube detection to reduce aerosol pollution and cross pollution, which include the use of turbidity [12] , SYBR Green


id: cord-004307-4sltubqk
author: Horiuchi, Sho
date: 2020-01-14
extension: .txt
mime: text/plain
words: 2953
sentence: 100
flesch: 38
cache: cache/cord-004307-4sltubqk.txt
txt: txt/cord-004307-4sltubqk.txt
title:
  A novel loop-mediated isothermal amplification method for efficient and robust detection of EGFR mutations

summary:
  Cancer statics Introduction to the 2015 world health organization classification of tumors of the lung, pleura, thymus, and heart Five-year survival in EGFR-mutant metastatic lung adenocarcinoma treated with EGFR-TKIs Activating mutations in the epidermal growth factor receptor underlying responsiveness of non-small-cell lung cancer to gefitinib RET fusion gene: Translation to personalized lung cancer therapy Chipping away at the lung cancer genome Genotyping and genomic profiling of non-small-cell lung cancer: Implications for current and future therapies EGFR mutations in lung cancer: Correlation with clinical response to gefitinib therapy Activity of epidermal growth factor receptor-tyrosine kinase inhibitors in patients with non-small cell lung cancer harboring rare epidermal growth factor receptor mutations First-line erlotinib versus gemcitabine/cisplatin in patients with advanced EGFR mutation-positive non-small-cell lung cancer: Analyses from the phase III, randomized, open-label, ENSURE study Afatinib versus cisplatin-based chemotherapy for EGFR mutation-positive lung adenocarcinoma (LUX-Lung 3 and LUX-Lung 6): Analysis of overall survival data from two randomised, phase 3 trials Current and future molecular testing in NSCLC, what can we expect from new sequencing technologies? Cost of cancer diagnosis using next-generation sequencing targeted gene panels in routine practice: A nationwide French study Loop-mediated isothermal amplification of DNA Sensitive and rapid detection of mycoplasma pneumoniae by loop-mediated isothermal amplification Rapid detection of the severe acute respiratory syndrome (SARS) coronavirus by a loop-mediated isothermal amplification assay Rapid diagnosis of H5N1 avian influenza virus infection by newly developed influenza H5 hemagglutinin gene-specific loop-mediated isothermal amplification method The IASLC lung cancer staging project: Proposals for revision of the TNM stage groupings in the forthcoming (eighth) edition of the TNM Classification for lung cancer A commercial real-time PCR kit provides greater sensitivity than direct sequencing to detect KRAS mutations: A morphology-based approach in colorectal carcinoma Efficiency of the Therascreen® RGQ PCR kit for the detection of EGFR mutations in non-small cell lung carcinomas Detection of epidermal growth factor receptor mutations in serum as a predictor of the response to gefitinib in patients with non-small-cell lung cancer Sensitive detection of DNA polymorphisms by the serial invasive signal amplification reaction Genetic heterogeneity of the epidermal growth factor receptor in non-small cell lung cancer cell lines revealed by a rapid and sensitive detection system, the peptide nucleic acid-locked nucleic acid PCR clamp A rapid, sensitive assay to detect EGFR mutation in small biopsy specimens from lung cancer Reliability of the peptide nucleic acid-locked nucleic acid polymerase chain reaction clamp-based test for epidermal growth factor receptor mutations integrated into the clinical practice for non-small cell lung cancers Accuracy of the cobas EGFR mutation assay in non-small-cell lung cancer compared with three laboratory-developed tests Mycoplasma pneumoniae from the respiratory tract and beyond An updated loop-mediated isothermal amplification method for rapid diagnosis of H5N1 avian influenza viruses Detection of gene point mutation in paraffin sections using in situ loop-mediated isothermal amplification Non-isotopic silver-stained SSCP is more sensitive than automated direct sequencing for the detection of PTEN mutations in a mixture of DNA extracted from normal and tumor cells Epidermal growth factor receptor gene mutation in non-small cell lung cancer using highly sensitive and fast TaqMan PCR assay The authors would like to thank Mr Satoru Michiyuki, employee of Eiken Chemical Co., Ltd., Otawara, Japan, for his valuable comments and suggestions concerning the LAMP SH analyzed the data and wrote the initial draft of the manuscript. LAMP EGFR mutation analysis.


id: cord-001762-dtvzwin8
author: Jeong, Joojin
date: 2015-09-30
extension: .txt
mime: text/plain
words: 2859
sentence: 96
flesch: 45
cache: cache/cord-001762-dtvzwin8.txt
txt: txt/cord-001762-dtvzwin8.txt
title:
  Development of a Rapid Detection Method for Potato virus X by Reverse Transcription Loop-Mediated Isothermal Amplification

summary:
  RT-LAMP PCR, one of the variants of LAMP PCR, has been used for the diagnosis of plant RNA viruses (Ju, 2011; Nie, 2005) . Diagnosis and control of cereal viruses in the Middle East A sensitive and reliable RT-nested PCR assay for detection of Citrus tristeza Virus from naturally infected Citrus plants Simultaneous detection of potato viruses, PLRV, PVA, PVX and PVY from dormant potato tubers by TaqMan real-time RT-PCR Emerging infectious diseases of plants: pathogen pollution, climate change and agrotechnological drivers Sensitive and rapid detection of peach latent mosaic viroid by the reverse transcription loop-mediated isothermal amplification Visual detection of turkey coronavirus RNA in tissues and feces by reverse-transcription loop-mediated isothermal amplification (RT-LAMP) with hydroxynaphthol blue dye Characteristics of the microplate method of enzyme linked immunosorbent assay for the detection of plant viruses Biological, Serological and molecular diagnosis of three major potato viruses in Egypt Requirement of sense transcription for homology-dependent virus resistance and trans-inactivation Development of immunocapture reverse transcription loop-mediated isothermal amplification for the detection of Tomato spotted wilt virus from chrysanthemum Climate change effects on plant disease: genomes and ecosystems Immunocapture reverse transcription-polymerase chain reaction combined with nested PCR greatly increases the detection of Prunus necrotic ring spot virus in the peach Enhanced detection of Prune dwarf virus in peach leaves by immunocapture-reverse transcription-polymerase chain reaction with nested polymerase chain Reaction (IC-RT-PCR Nested PCR) Simple and rapid detection of Potato leafroll virus (PLRV) by reverse transcription loop-mediated isothermal amplification (RT-LAMP) Further studies on resistance -breaking strains of Potato virus X Detection of important plant viruses in In vitro regenerated potato plants by Double antibody sandwich method of ELISA Rapid detection of squash leaf curl virus by loop-mediated isothermal amplification Molecular diagnosis of plant viruses Estimation of vector propensity for Lettuce mosaic virus based on viral detection in single aphids A single tube, quantitative real-time RT-PCR assay that detects four potato viruses simultaneously Accelerated reaction by loop-mediated isothermal amplification using loop primers Reverse transcription loop-mediated isothermal amplification of DNA for detection of Potato virus Y Loop-mediated isothermal amplification of DNA New device and method for capture, reverse transcription, and nested PCR in a single closed-tube Rapid detection and differentiation of Dengue virus serotypes by a real-time reverse transcription-loop-mediated isothermal amplification assay a new generation of innovative gene amplification technique perspectives in clinical diagnosis of infectious diseases Agroinfiltration-based Potato virus X replicons to dissect the requirements of viral infection Primerdirected enzymatic amplification of DNA with a thermostable DNA polymerase Reverse transcription loo-mediated isothermal amplification (RT-LAMP) for rapid detection of viral hemorrhagic septicaemia virus (VHS) Loop-mediated isothermal amplification (LAMP) of gene sequences and simple visual detection of product Development of loop-mediated isothermal amplification assay for specific and rapid detection of camelpox virus in clinical samples Development of a Rapid Detection Method for PVX by RT Potato viruses in China Detection of Roundup ready soybean by loop-mediated isothermal amplification combined with a lateral-flow dipstick Detection of mix-infected potato viruses with multiplex RT-PCR Diagnosis of plant viral pathogens One-step detection of Bean pod mottle virus in soybean seed by the reverse-transcription loop-mediated isothermal amplification


id: cord-333524-a6p6ma8r
author: Khan, Pavana
date: 2020-09-23
extension: .txt
mime: text/plain
words: 8847
sentence: 389
flesch: 42
cache: cache/cord-333524-a6p6ma8r.txt
txt: txt/cord-333524-a6p6ma8r.txt
title:
  Isothermal SARS-CoV-2 Diagnostics: Tools for Enabling Distributed Pandemic Testing as a Means of Supporting Safe Reopenings

summary:
  Assay: A Case for Rapid, Ultrasensitive and Visual Detection of Novel Coronavirus SARS-CoV-2 and HIV Virus An Ultrasensitive, Rapid, and Portable Coronavirus SARS-CoV SARS-CoV-2 Detection with CRISPR Diagnostics CDetection: CRISPR-Cas12b-Based DNA Detection with Sub-Attomolar Sensitivity and Single-Base Specificity Development and Evaluation of Recombinase-Aided Amplification Assays Incorporating Competitive Internal Controls for Detection of Human Adenovirus Serotypes 3 and 7 Direct Observation of DNA Target Searching and Cleavage by CRISPR-Cas12a SHERLOCK: Nucleic Acid Detection with CRISPR Nucleases Pointof-Care Testing for COVID-19 Using SHERLOCK. CRISPR-based detection uses both primer-specific amplification and guide RNA directed detection, thus increasing sequence specificity in two different ways.


id: cord-285088-krim73zt
author: Wang, Deguo
date: 2020-04-21
extension: .txt
mime: text/plain
words: 1807
sentence: 44
flesch: 38
cache: cache/cord-285088-krim73zt.txt
txt: txt/cord-285088-krim73zt.txt
title:
  One-pot Detection of COVID-19 with Real-time Reverse-transcription Loop-mediated Isothermal Amplification (RT-LAMP) Assay and Visual RT-LAMP Assay

summary:
  NO external funding The COVID-19 epidemic Chest Imaging Appearance of COVID-19 Infection Detection of 2019 novel coronavirus (2019-nCoV) by real-time RT-PCR Loop-mediated isothermal amplification of DNA Accelerated reaction by loop-mediated isothermal amplification using loop primers Development and evaluation of a loop-mediated isothermal amplification (LAMP) method for detecting Listeria monocytogenes in raw milk Rapid Detection of Listeria monocytogenes in raw milk with loop-mediated isothermal amplification and chemosensor Evaluation and improvement of LAMP assays for detection of Escherichia coli serogroups O26, O45, O103, O111, O121, O145, and O157. Methods Six specific LAMP primers targeting the N gene of COVID-19 were designed, the RT-LAMP reaction system was optimized with plasmid pUC57 containing N gene sequence, the detection limit was determined with a serial dilution of the plasmid pUC57 containing N gene sequence, and the one-pot real-time RT-LAMP assay and one-pot visual RT-LAMP assay for the detection of COVID-19 were established.


id: cord-348243-e5tdb08v
author: Schermer, Bernhard
title: Rapid SARS-CoV-2 testing in primary material based on a novel multiplex RT-LAMP assay
date: 2020-11-02
extension: .txt
mime: text/plain
words: 3962
sentence: 159
flesch: 48
cache: cache/cord-348243-e5tdb08v.txt
txt: txt/cord-348243-e5tdb08v.txt
summary:
  Next, the reaction was diluted with 80 μl of HybriDetect Buffer (Milenia), mixed, and then a HybriDetect dipstick (Milenia) was placed in the reaction tube and incubated at RT. Transferring such assays to automated microfluidic formats [11] can become an important tool to support disease control strategies.


id: cord-323845-s78t5qxj
author: Soliman, H.
date: 2006-05-31
extension: .txt
mime: text/plain
words: 3912
sentence: 136
flesch: 43
cache: cache/cord-323845-s78t5qxj.txt
txt: txt/cord-323845-s78t5qxj.txt
title:
  Reverse transcription loop-mediated isothermal amplification (RT-LAMP) for rapid detection of viral hemorrhagic septicaemia virus (VHS)

summary:
  The specificity of the VHS-LAMP primers and conditions to VHS virus was confirmed by its aptitude to amplify only RNA from VHS virus serotypes, with no amplification of IHNVor non-infected fish (Fig. 5) . Agarose gel highlighting the specificity of the RT-LAMP primers to VHS virus RNA.


id: cord-287104-4k8pqbc0
author: Lee, J. Y.
date: 2019-04-04
extension: .txt
mime: text/plain
words: 2019
sentence: 73
flesch: 44
cache: cache/cord-287104-4k8pqbc0.txt
txt: txt/cord-287104-4k8pqbc0.txt
title:
  Development of Rapid and Specific Detection for the Human Aichivirus A Using the Loop-Mediated Isothermal Amplification from Water Samples

summary:
  Virus taxonomy at the XIth international congress of virology Aichi virus strains in children with gastroenteritis Isolation of cytopathic small round virus (Aichi virus) from Pakistani children and Japanese travelers from Southeast Asia Isolation of cytopathic small round viruses with BS-C-1 cells from patients with gastroenteritis Epidemiology of human parechovirus, Aichi virus and salivirus in fecal samples from hospitalized children with gastroenteritis in Hong Kong Aichi virus shedding in high concentrations in patients with acute diarrhea Molecular characterization of the first Aichi viruses isolated in Europe and in South America Detection and genomic characterization of Aichi viruses in stool samples from children in Monastir, Tunisia Etiological role of viruses in outbreaks of acute gastroenteritis in The Netherlands from 1994 through Aichi virus, norovirus, astrovirus, enterovirus, and rotavirus involved in clinical cases from a french oysterrelated gastroenteritis outbreak Isolation and molecular characterization of Aichi viruses from fecal specimens collected in Japan, Bangladesh, Thailand, and Vietnam Molecular detection and nucleotide sequence analysis of a new Aichi virus closely related to canine kobuvirus in sewage samples Aichi virus in sewage and surface water, the Netherlands Molecular detection and characterization of Aichi viruses in sewage-polluted waters of venezuela Prevalance and genetic diversity of Aichi viruses in wastewater and river water in japan Aichi virus 1: Enviromental Occurrence and Behavior. In addition, confirm system of positive LAMP reaction was developed by using the restriction enzyme Aci I and Hae III.


id: cord-268993-2sjh17mw
author: Rödel, Jürgen
date: 2020-08-31
extension: .txt
mime: text/plain
words: 2456
sentence: 108
flesch: 51
cache: cache/cord-268993-2sjh17mw.txt
txt: txt/cord-268993-2sjh17mw.txt
title:
  Use of the variplex(TM) SARS-CoV-2 RT-LAMP as a rapid molecular assay to complement RT-PCR for COVID-19 diagnosis

summary:
  For a single test 15 l of RT master mix and 8 l of eluted RNA were pipetted into two wells of a Genie test strip (Amplex Diagnostics). The combination of RT with Bst polymerase possessing a DNA strand displacement activity allows amplification of target genes at a constant temperature in less than one hour.


id: cord-268627-nnx46nwf
author: Ren, Xiaofeng
date: 2011-02-01
extension: .txt
mime: text/plain
words: 2777
sentence: 137
flesch: 55
cache: cache/cord-268627-nnx46nwf.txt
txt: txt/cord-268627-nnx46nwf.txt
title:
  Development of reverse transcription loop-mediated isothermal amplification for rapid detection of porcine epidemic diarrhea virus

summary:
  To the knowledge, this is the first report regarding the establishment and optimization of a RT-LAMP for PEDV N gene. Using PEDV RNA and six primers targeting the PEDV N gene, an RT-LAMP was done at 65°C in a water bath for 1 h.


id: cord-344636-go5cw92q
author: Huang, Wei E.
title: RT‐LAMP for rapid diagnosis of coronavirus SARS‐CoV‐2
date: 2020-04-25
extension: .txt
mime: text/plain
words: 4780
sentence: 202
flesch: 56
cache: cache/cord-344636-go5cw92q.txt
txt: txt/cord-344636-go5cw92q.txt
summary:
  However, this extreme sensitivity is also a double-edged sword: carry-over contamination was common in LAMP reactions, which usually cause false positive results (Hsieh et al., 2014; Ma et al., 2017) . Primers were designed using LAMP primer designing software, PrimerExplorer (http:// primerexplorer.jp/e/; Tomita et al., 2008) .


id: cord-258057-ti0rpt0q
author: Zhao, Kai
title: Establishment of a Porcine Parvovirus (PPV) LAMP Visual Rapid Detection Method
date: 2020-07-01
extension: .txt
mime: text/plain
words: 3736
sentence: 151
flesch: 51
cache: cache/cord-258057-ti0rpt0q.txt
txt: txt/cord-258057-ti0rpt0q.txt
summary:
  Green I and realized the visual detection for PPV LAMP instead of by the conventional gel electrophoresis analysis or fluorescent detection . J o u r n a l P r e -p r o o f To verify the specificity of PPV detection by LAMP, the DNA (PPV, PCV2, PRV) and cDNA samples (PRRSV, CSFV) were amplified as sample templates by the LAMP reaction at 59.0℃ for 50 min and terminated at 80℃ for 3 min, respectively.


id: cord-271434-30nh2gc7
author: Tian, Fei
title: A fully automated centrifugal microfluidic system for sample-to-answer viral nucleic acid testing
date: 2020-07-27
extension: .txt
mime: text/plain
words: 4324
sentence: 169
flesch: 44
cache: cache/cord-271434-30nh2gc7.txt
txt: txt/cord-271434-30nh2gc7.txt
summary:
  We envisioned that this microfluidic system free of aerosol contamination may facilitate viral nucleic acid detection outside the diagnostic laboratory, promoting diagnosis efficiency of infectious diseases and preventing onward transmission. In another work, a multifunctional microfluidic device pre-loaded with wax-sealed reagents was designed for extraction and amplification of viral nucleic acids in a point-of-care format [33] .


id: cord-338942-q4neat3x
author: Zhang, Haoqing
title: LAMP-on-a-chip: Revising microfluidic platforms for loop-mediated DNA amplification
date: 2019-01-31
extension: .txt
mime: text/plain
words: 5759
sentence: 270
flesch: 38
cache: cache/cord-338942-q4neat3x.txt
txt: txt/cord-338942-q4neat3x.txt
summary:
  A modified visual loop-mediated isothermal amplification method for diagnosis and differentiation of main pathogens from Mycobacterium tuberculosis complex Colorimetric LAMP microfluidic chip for detecting three allergens: peanut, sesame and soybean Development of mitochondrial loop-mediated isothermal amplification for detection of the small liver fluke Opisthorchis viverrini (Opisthorchiidae; Trematoda Rapid detection of food-borne Listeria monocytogenes by real-time quantitative loop-mediated isothermal amplification Real time loop-mediated isothermal amplification using a portable fluorescence scanner for rapid and simple detection of Vibrio parahaemolyticus A CCD-based fluorescence imaging system for real-time loopmediated isothermal amplification-based rapid and sensitive detection of waterborne pathogens on microchips Microfluidic electrochemical assay for rapid detection and quantification of Escherichia coli Detection of roundup ready soybean by loop-mediated isothermal amplification combined with a lateral-flow dipstick Evaluation of reverse transcription loopmediated isothermal amplification in conjunction with ELISA-hybridization assay for molecular detection of Mycobacterium tuberculosis Loop-mediated isothermal amplification combined with colorimetric nanogold for detection of the microsporidian Enterocytozoon hepatopenaei in penaeid shrimp Ion sensing (EIS) real-time quantitative monitorization of isothermal DNA amplification A polycarbonate based surface plasmon resonance sensing cartridge for high sensitivity HBV loop-mediated isothermal amplification GMO detection using a bioluminescent real time reporter (BART) of loop mediated isothermal amplification (LAMP) suitable for field use On-chip LAMP-BART reaction for viral DNA real-time bioluminescence detection A novel HBV genotypes detecting system combined with microfluidic chip, loop-mediated isothermal amplification and GMR sensors Loop-mediated isothermal amplification (LAMP): recent progress in research and development A device for point-ofcare genetic testing using a smartphone Rapid isolation and detection of aquaculture pathogens in an integrated microfluidic system using loop-mediated isothermal amplification A microfluidic lab-on-a-disc integrated loop mediated isothermal amplification for foodborne pathogen detection Development of a high-throughput centrifugal loop-mediated isothermal amplification microdevice for multiplex foodborne pathogenic bacteria detection Identifying multiple bacterial pathogens by loop-mediated isothermal amplification on a rotate & react slipchip Development and evaluation of a loop-mediated isothermal amplification assay for the rapid detection of Staphylococcus aureus in food Development and application of a rapid and simple loopmediated isothermal amplification method for food-borne Salmonella detection Handheld device for real-time, quantitative, LAMP-based detection of Salmonella enterica using assimilating probes Loop-mediated isothermal amplification for Salmonella detection in food and feed: current applications and future directions A facile cascade signal amplification strategy using DNAzyme loop-mediated isothermal amplification for the ultrasensitive colorimetric detection of Salmonella Development and application of a loop-mediated isothermal amplification method on rapid detection Escherichia coli O157 strains from food samples Centrifugal loop-mediated isothermal amplification microdevice for rapid, multiplex and colorimetric foodborne pathogen detection Integrated glass microdevice for nucleic acid purification, loop-mediated isothermal amplification, and online detection Monte Carlo modelingbased digital loop-mediated isothermal amplification on a spiral chip for absolute quantification of nucleic acids This work was supported by the Foreign Experts Program of P.R. China (W099109). Isothermal amplification techniques require simple hardware and they are rather insensitive to polymerase inhibitors, making the amplification process robust.


id: cord-104321-fpoztmcl
author: Almasi, Mohammad Amin
date: 2017
extension: .txt
mime: text/plain
words: 3455
sentence: 108
flesch: 36
cache: cache/cord-104321-fpoztmcl.txt
txt: txt/cord-104321-fpoztmcl.txt
title:
  Loop Mediated Isothermal Amplification (LAMP) for Embryo Sex Determination in Pregnant Women at Eight Weeks of Pregnancy

summary:
  This robust assay is quick, sensitive and specific enough to be applied for gene detection. In conclusion, sex determination using detection of SRY gene by LAMP method in fresh human blood shows the smear and/or ladder band only in male blood samples, but not in female samples.


id: cord-283415-1nu399lz
author: Jiang, Kuiyu
date: 2012-08-14
extension: .txt
mime: text/plain
words: 2790
sentence: 114
flesch: 49
cache: cache/cord-283415-1nu399lz.txt
txt: txt/cord-283415-1nu399lz.txt
title:
  Development of A Loop-Mediated Isothermal Amplification (LAMP) for the Detection of F5 Fimbriae Gene in Enterotoxigenic Escherichia coli (ETEC)

summary:
  key: cord-283415-1nu399lz authors: Jiang, Kuiyu; Zhu, Ying; Liu, Wenxin; Feng, Yufei; He, Lili; Guan, Weikun; Hu, Wenxia; Shi, Dongfang title: Development of A Loop-Mediated Isothermal Amplification (LAMP) for the Detection of F5 Fimbriae Gene in Enterotoxigenic Escherichia coli (ETEC) date: 2012-08-14 journal: Curr Microbiol DOI: 10.1007/s00284-012-0204-6 sha: doc_id: 283415 cord_uid: 1nu399lz The objective of this study was to establish a loop-mediated isothermal amplification (LAMP) method for the detection of F5 fimbriae gene in Enterotoxigenic Escherichia coli. Thus, the LAMP assay may be a new method for rapid detection of F5 fimbriae gene of ETEC.


id: cord-000625-cpjlzutk
author: Ablordey, Anthony
title: Detection of Mycobacterium ulcerans by the Loop Mediated Isothermal Amplification Method
date: 2012-04-03
extension: .txt
mime: text/plain
words: 3678
sentence: 161
flesch: 44
cache: cache/cord-000625-cpjlzutk.txt
txt: txt/cord-000625-cpjlzutk.txt
summary:
  None of the IS2404 PCR negative samples were positive in both types of LAMP assays. Thirty clinical specimens from suspected Buruli ulcer patients were investigated by the modified LAMP (or pocket warmer LAMP) and the conventional LAMP, as well as IS2404 PCR, a reference method for the detection of Mycobacterium ulcerans.


id: cord-002720-lrkscs71
author: Kurosaki, Yohei
date: 2017-10-18
extension: .txt
mime: text/plain
words: 4956
sentence: 177
flesch: 46
cache: cache/cord-002720-lrkscs71.txt
txt: txt/cord-002720-lrkscs71.txt
title:
  Development and evaluation of a rapid molecular diagnostic test for Zika virus infection by reverse transcription loop-mediated isothermal amplification

summary:
  Zika virus: history of a newly emerging arbovirus Zika Virus Outbreak, Bahia, Brazil Zika Virus Associated with Microcephaly Possible Association Between Zika Virus Infection and Microcephaly -Brazil Association between Zika virus infection and microcephaly in Brazil Congenital Zika virus syndrome in Brazil: a case series of the first 1501 livebirths with complete investigation Probable transfusion-transmitted Zika virus in Brazil Transmission of Zika Virus Through Sexual Contact with Travelers to Areas of Ongoing Transmission -Continental United States Sexually acquired Zika virus: a systematic review Molecular evolution of Zika virus during its emergence in the 20(th) century Zika Virus Transmission from French Polynesia to Brazil Zika virus in the Americas: Early epidemiological and genetic findings Detection of Zika virus in urine Detection of Zika virus in saliva Comparison of Test Results for Zika Virus RNA in Urine, Serum, and Saliva Specimens from Persons with Travel-Associated Zika Virus Disease -Florida Persistence of Zika Virus in Body Fluids -Preliminary Report Zika Virus Testing Considerations: Lessons Learned from the First 80 Real-Time Reverse Transcription-PCR-Positive Cases Diagnosed in New York State Viral load kinetics of Zika virus in plasma, urine and saliva in a couple returning from Martinique, French West Indies Quantitative real-time PCR detection of Zika virus and evaluation with field-caught mosquitoes Genetic and serologic properties of Zika virus associated with an epidemic, Yap State, Micronesia Zika Virus: Diagnostics for an Emerging Pandemic Threat Prolonged detection of Zika virus RNA in urine samples during the ongoing Zika virus epidemic in Brazil Rapid Molecular Detection of Zika Virus in Acute-Phase Urine Samples Using the Recombinase Polymerase Amplification Assay First case of laboratory-confirmed Zika virus infection imported into Europe Cross reactivity of commercial anti-dengue immunoassays in patients with acute Zika virus infection Loop-mediated isothermal amplification of DNA Development and evaluation of a novel loop-mediated isothermal amplification method for rapid detection of severe acute respiratory syndrome coronavirus Loop-mediated isothermal amplification (LAMP): principle, features, and future prospects Deployment of a Reverse Transcription Loop-Mediated Isothermal Amplification Test for Ebola Virus Surveillance in Remote Areas in Guinea Development and Evaluation of Reverse Transcription-Loop-Mediated Isothermal Amplification (RT-LAMP) key: cord-002720-lrkscs71 authors: Kurosaki, Yohei; Martins, Danyelly Bruneska Gondim; Kimura, Mayuko; Catena, Andriu dos Santos; Borba, Maria Amélia Carlos Souto Maior; Mattos, Sandra da Silva; Abe, Haruka; Yoshikawa, Rokusuke; de Lima Filho, José Luiz; Yasuda, Jiro title: Development and evaluation of a rapid molecular diagnostic test for Zika virus infection by reverse transcription loop-mediated isothermal amplification date: 2017-10-18 journal: Sci Rep DOI: 10.1038/s41598-017-13836-9 sha: doc_id: 2720 cord_uid: lrkscs71 The recent outbreak of Zika virus (ZIKV) disease caused an enormous number of infections in Central and South America, and the unusual increase in the number of infants born with microcephaly associated with ZIKV infection aroused global concern.


id: cord-295491-zlah6u5s
author: Günther, Sonja
date: 2018-03-11
extension: .txt
mime: text/plain
words: 3796
sentence: 137
flesch: 45
cache: cache/cord-295491-zlah6u5s.txt
txt: txt/cord-295491-zlah6u5s.txt
title:
  Detection of feline Coronavirus in effusions of cats with and without feline infectious peritonitis using loop-mediated isothermal amplification

summary:
  RNA was extracted from body cavity effusion samples of 71 cats, including 34 samples from cats with a definitive diagnosis of FIP, and 37 samples of control cats with similar clinical signs but other confirmed diseases. Body cavity effusion samples of all cats were obtained ante mortem with ultrasound guidance for diagnostic purposes.


id: cord-296977-yzhsdz9c
author: Soares, R. R. G.
date: 2020-11-06
extension: .txt
mime: text/plain
words: 6546
sentence: 214
flesch: 41
cache: cache/cord-296977-yzhsdz9c.txt
txt: txt/cord-296977-yzhsdz9c.txt
title:
  Point-of-care detection of SARS-CoV-2 in nasopharyngeal swab samples using an integrated smartphone-based centrifugal microfluidic platform

summary:
  We introduce a novel portable bead-based centrifugal microfluidic platform and demonstrate LAMP based viral RNA detection directly from heat-inactivated nasopharyngeal swab samples. These features can potentially pave the way to bring routine and scalable diagnostics to RLS, as well as expanding the current diagnostic capacities in high-income countries by bringing viral RNA detection directly to the field.


id: cord-000049-rl7sdzd7
author: Lee, David
date: 2009-02-02
extension: .txt
mime: text/plain
words: 2901
sentence: 114
flesch: 50
cache: cache/cord-000049-rl7sdzd7.txt
txt: txt/cord-000049-rl7sdzd7.txt
title:
  Detection of genetically modified organisms (GMOs) using isothermal amplification of target DNA sequences

summary:
  This work shows that GMO detection can be carried out using LAMP for routine screening as well as for specific events detection. We have tested the upper limits of DNA that LAMP reactions can tolerate and found that up to 200 ng DNA in a 20 μl reaction, positive detection is reproducible.


id: cord-288887-lshsgex3
author: Yoda, Tomoko
date: 2007-01-23
extension: .txt
mime: text/plain
words: 4932
sentence: 199
flesch: 52
cache: cache/cord-288887-lshsgex3.txt
txt: txt/cord-288887-lshsgex3.txt
title:
  Evaluation and application of reverse transcription loop‐mediated isothermal amplification for detection of noroviruses

summary:
  The reactivity of the RT-LAMP assay developed in this study was compared with that of EC NV GI and EC NV GII detection kits (Eiken Chemical Co., Ltd.); the results are listed in Table II . The advantages of using OPIPH RT-LAMP systems compared with conventional NV detection kits are: (1) sensitivity is higher in some NV genotypes (GI.3 and GII.3); (2) specific GI genotypes (GI.3, 11, and 12) that cannot be detected by a conventional GI kit can be detected by the GI primer set developed in this study; and (3) additional treatment, that is, heating at 958C for 5 min and being kept on ice for 5 min, is not required in the OPIPH system.


id: cord-333331-ddcz7zck
author: Yang, Jin
title: Detection of hepatitis C virus by an improved loop-mediated isothermal amplification assay
date: 2011-05-12
extension: .txt
mime: text/plain
words: 5212
sentence: 220
flesch: 51
cache: cache/cord-333331-ddcz7zck.txt
txt: txt/cord-333331-ddcz7zck.txt
summary:
  Adding AP to the Principle of AP in LAMP amplification. When comparing the electrophoresis bands of the products of the AP-LAMP, AP-B3 LAMP and Pre-LAMP assays, the first two showed a similar pattern.


id: cord-324094-23kzr8rq
author: Parida, M. M.
title: Rapid and real-time detection technologies for emerging viruses of biomedical importance
date: 2008-11-01
extension: .txt
mime: text/plain
words: 5710
sentence: 188
flesch: 39
cache: cache/cord-324094-23kzr8rq.txt
txt: txt/cord-324094-23kzr8rq.txt
summary:
  LAMP amplifi cation can also be accomplished with the two outer (F3 and B3) and two internal primers (FIP and BIP) but by using the two loop primers (FLP and BLP), the amplifi cation is accelerated and thereby shortens amplifi cation time by one third to one half ( (Notomi et al 2000) . Designing of a highly sensitive and specifi c primer set is crucial for performing LAMP amplifi cation.


id: cord-276957-pk33dl8q
author: Hu, Xuejiao
date: 2020-08-26
extension: .txt
mime: text/plain
words: 5659
sentence: 201
flesch: 39
cache: cache/cord-276957-pk33dl8q.txt
txt: txt/cord-276957-pk33dl8q.txt
title:
  Development and Clinical Application of a Rapid and Sensitive Loop-Mediated Isothermal Amplification Test for SARS-CoV-2 Infection

summary:
  RT-LAMP primers for COVID-19 were specific and had a 9.14% to 37.56% nucleotide mismatching with SARS, MERS, and other coronavirus sequences (see Table S2 ). Application of RT-LAMP for SARS-CoV-2 (ii) Cohort II.


id: cord-002982-zwvesrct
author: Thiessen, Lindsey D.
date: 2018-04-20
extension: .txt
mime: text/plain
words: 5667
sentence: 194
flesch: 37
cache: cache/cord-002982-zwvesrct.txt
txt: txt/cord-002982-zwvesrct.txt
title:
  Development of a quantitative loop-mediated isothermal amplification assay for the field detection of Erysiphe necator

summary:
  These traits make LAMP useful in field detection assays (Harper, Ward & Clover, 2010; Kubota et al., 2008; Temple & Johnson, 2011; Tomlinson, Barker & Boonham, 2007; Tomlinson, Dickinson & Boonham, 2010) . In addition to inhibitors from the rods, the variability of inhibitors from field collections may have caused inconsistencies in qLAMP assay detection results compared to the qPCR assay detection results.


id: cord-264676-k531q3ir
author: Liu, Yi
date: 2009-07-09
extension: .txt
mime: text/plain
words: 3930
sentence: 146
flesch: 42
cache: cache/cord-264676-k531q3ir.txt
txt: txt/cord-264676-k531q3ir.txt
title:
  In situ reverse-transcription loop-mediated isothermal amplification (in situ RT-LAMP) for detection of Japanese encephalitis viral RNA in host cells

summary:
  Fields virology Japanese encephalitis: current worldwide status New initiatives for the control of Japanese encephalitis by vaccination Viral infections of humans An intranasal challenge model for testing Japanese encephalitis vaccines in rhesus monkeys Rapid diagnosis of Japanese encephalitis by using an immunoglobulin M dot enzyme immunoassay Identification of dengue sequences by genomic amplification: rapid diagnosis of dengue virus serotypes in peripheral blood Rapid identification of flavivirus using the polymerase chain reaction Detection of Japanese encephalitis virus in mouse peripheral blood mononuclear cells using an in situ reverse transcriptase polymerase chain reaction Accelerated reaction by loop mediated isothermal amplification using loop primers Loop-mediated isothermal amplification of DNA Rapid detection and quantification of Japanese encephalitis virus by real-time reverse transcription loop-mediated isothermal amplification Potential role of Armigeres subalbatus (Diptera: Culcidae) in the transmission of Japanese encephalitis virus in the absence of rice culture on Liu-Chiu islet A model to study neurotropism and persistency of Japanese encephalitis virus infection in human neuroblastoma cells and leukocytes Analysis of Japanese encephalitis epidemic in western Nepal in 1997 A survey of the clinical sequelae of Japanese encephalitis A hospital-based surveillance for Japanese encephalitis in Bali Sensitive and specific detection of strains of Japanese encephalitis using a one-step TaqMan RT-PCR technique Development and evaluation of SYBR Green I-based one-step real-time RT-PCR assay for detection and quantization of Japanese encephalitis virus Detection of West Nile and Japanese encephalitis viral genome sequences in cerebrospinal fluid from acute encephalitis cases in Karachi NASBA and other transcription-based amplification methods for research and diagnostic microbiology TaqMan reverse transcription polymerase chain reaction for the detection of Japanese encephalitis virus Detection of loop-mediated isothermal amplification reaction by turbidity derived from magnesium pyrophosphate formation Development and evaluation of a novel loop-mediated isothermal amplification method for rapid detection of severe acute respiratory syndrome coronavirus Development of H5-RT-LAMP (loop-mediated isothermal amplification) system for rapid diagnosis of H5 avian influenza virus infection Rapid detection and differentiation of Dengue virus serotypes by real-time reverse transcription loop-mediated isothermal amplification assay Rapid and real-time detection of hepatitis A virus by reverse transcription loop-mediated isothermal amplification assay Evaluation of loop-mediated isothermal amplification (LAMP) to rapidly detect arbuscular mycorrhizal fungi Specific and rapid detection of food-borne Salmonella by loop-mediated isothermal amplification method Development of a multiplex loop-mediated isothermal amplification (mLAMP) method for the simultaneous detection of bovine Babesia parasites Species-specific loop-mediated isothermal amplification (LAMP) for diagnosis of trypanosomosis Evaluation of loop-mediated isothermal amplification (LAMP), PCR and parasitological tests for detection of Trypanosoma evansi in experimentally infected pigs Rapid sexing of water buffalo (Bubalus bubalis) embryos using loop-mediated isothermal amplification Real-time reverse transcription loop-mediated isothermal amplification for rapid detection of West Nile virus Development and evaluation of reverse transcription-loop-mediated isothermal amplification assay for rapid and real-time detection of Japanese encephalitis virus Rapid and real-time detection of Chikungunya virus by reverse transcription loop-mediated isothermal amplification assay Persistence, latency and reactivation of Japanese encephalitis virus infection in mice Persistence of Japanese encephalitis virus in the human nervous system Japanese encephalitis virus latency in peripheral blood lymphocytes and recurrence of infection in children Detection and isolation of Japanese encephalitis virus from blood clots collected during the acute phase of infection The blood-brain barrier in the cerebrum is the initial site for the Japanese encephalitis virus entering the central nervous system Funding: This work was financially supported by grants from Chang Gung Memorial Hospital (CMRPD160162 and EMREPD180191). 27 Application of RT-LAMP to JE virus detection has been shown to be relatively rapid and allows for virus quantification.


id: cord-271504-t3y1w9ef
author: Luo, Zichao
date: 2020-06-16
extension: .txt
mime: text/plain
words: 14501
sentence: 633
flesch: 38
cache: cache/cord-271504-t3y1w9ef.txt
txt: txt/cord-271504-t3y1w9ef.txt
title:
  Combating the Coronavirus Pandemic: Early Detection, Medical Treatment, and a Concerted Effort by the Global Community

summary:
  Structural basis of influenza virus fusion inhibition by the antiviral drug Arbidol New small-molecule drug design strategies for fighting resistant influenza A Characteristics of arbidol-resistant mutants of influenza virus: implications for the mechanism of anti-influenza action of arbidol Mechanism of inhibition of enveloped virus membrane fusion by the antiviral drug arbidol Membranotropic effects of arbidol, a broad antiviral molecule, on phospholipid model membranes Clinical characteristics and therapeutic procedure for four cases with 2019 novel coronavirus pneumonia receiving combined Chinese and Western medicine treatment Discovering drugs to treat coronavirus disease 2019 (COVID-19) Effects of chloroquine on viral infections: an old drug against today's diseases Effect of weak bases on the intralysosomal pH in mouse peritoneal macrophages Mechanisms of action of hydroxychloroquine and chloroquine: implications for rheumatology Chloroquine inhibits autophagic flux by decreasing autophagosomelysosome fusion New insights into the antiviral effects of chloroquine Anti-HIV effects of chloroquine: inhibition of viral particle glycosylation and synergism with protease inhibitors Hydroxychloroquine, a less toxic derivative of chloroquine, is effective in inhibiting SARS-CoV-2 infection in vitro Chloroquine is a potent inhibitor of SARS coronavirus infection and spread In vitro inhibition of severe acute respiratory syndrome coronavirus by chloroquine Remdesivir and chloroquine effectively inhibit the recently emerged novel coronavirus (2019-nCoV) in vitro Breakthrough: chloroquine phosphate has shown apparent efficacy in treatment of COVID-19 associated pneumonia in clinical studies Chloroquine and hydroxychloroquine as available weapons to fight COVID-19 In vitro antiviral activity and projection of optimized dosing design of hydroxychloroquine for the treatment of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Effects of chronic exposure to hydroxychloroquine or chloroquine on inner retinal structures Animal toxicity and pharmacokinetics of hydroxychloroquine sulfate Retroviral proteases and their roles in virion maturation Host cell proteases: critical determinants of coronavirus tropism and pathogenesis Influenza and SARS-coronavirus activating proteases TMPRSS2 and HAT are expressed at multiple sites in human respiratory and gastrointestinal tracts Research and development on therapeutic agents and vaccines for COVID-19 and related human coronavirus diseases Virusencoded proteinases and proteolytic processing in the Nidovirales The SARS-coronavirus papain-like protease: structure, function and inhibition by designed antiviral compounds Crystal Structures of the Main Peptidase from the SARS Coronavirus Inhibited by a Substrate-like Aza-peptide Epoxide Simultaneous treatment of human bronchial epithelial cells with serine and cysteine protease inhibitors prevents severe acute respiratory syndrome coronavirus entry Protease inhibitors targeting coronavirus and filovirus entry Efficacy of camostat mesilate compared with famotidine for treatment of functional dyspepsia: is camostat mesilate effective? Camostat mesilate attenuates pancreatic fibrosis via inhibition of monocytes and pancreatic stellate cells activity Recent research by Hoffmann et al. showed a promising in vitro inhibitory effect of this serine protease inhibitor in SARS-CoV and 2019-nCoV on human lung cells, showing potential as a viable option for COVID-19 treatment [113] .


id: cord-342145-cq6xe5r7
author: Dao Thi, Viet Loan
title: A colorimetric RT-LAMP assay and LAMP-sequencing for detecting SARS-CoV-2 RNA in clinical samples
date: 2020-08-12
extension: .txt
mime: text/plain
words: 9345
sentence: 376
flesch: 52
cache: cache/cord-342145-cq6xe5r7.txt
txt: txt/cord-342145-cq6xe5r7.txt
summary:
  Therefore, it appeared that the N-A primer set used for the RT-LAMP assay performed equally well with either IVT RNA or RNA samples isolated from the pharyngeal swab specimens. For samples with a CT ≤ 30 as measured by RT-qPCR with E-Sarbeco primers, we found overall satisfactory sensitivity and specificity values for SARS-CoV-2 RNA detection by the RT-LAMP assay using RNA samples isolated from pharyngeal swab specimens ( Fig. 3 and Table 1 ).


id: cord-304343-m7tbdfri
author: Khandia, Rekha
date: 2019-07-03
extension: .txt
mime: text/plain
words: 20405
sentence: 788
flesch: 25
cache: cache/cord-304343-m7tbdfri.txt
txt: txt/cord-304343-m7tbdfri.txt
title:
  A Comprehensive Review of Autophagy and Its Various Roles in Infectious, Non-Infectious, and Lifestyle Diseases: Current Knowledge and Prospects for Disease Prevention, Novel Drug Design, and Therapy

summary:
  Autophagic degradation of inhibitor of apoptosis dBruce controls DNA fragmentation during late oogenesis in Drosophila Suppression of T cell autophagy results in decreased viability and function of T cells through accelerated apoptosis in a murine sepsis model Combination of TRAIL and Chal-24 synergistically induces autophagy-mediated apoptosis in lung cancer cells Induction of autophagy-dependent necroptosis is required for childhood acute lymphoblastic leukemia cells to overcome glucocorticoid resistance FADD and caspase-8 control the outcome of autophagic signaling in proliferating T cells Identification of small molecule inhibitors of phosphatidylinositol 3-kinase and autophagy Fas-associated death domain (FADD) is a negative regulator of T-cell receptor-mediated necroptosis Caspase inhibition prevents tumor necrosis factor-α-induced apoptosis and promotes necrotic cell death in mouse hepatocytes in vivo and in vitro An ursolic acid derived small molecule triggers cancer cell death through hyperstimulation of macropinocytosis L929 cells depends on autocrine production of TNFα mediated by the PKC-MAPKs-AP-1 pathway The sirtuin family, therapeutic targets to treat diseases of aging Antineoplastic activity of the cytosolic FoxO1 results from autophagic cell death RIP3, a molecular switch for necrosis and inflammation Knockout of Atg5 inhibits proliferation and promotes apoptosis of DF-1 cells The autophagy machinery controls cell death switching between apoptosis and necroptosis Sorafenib-induced defective autophagy promotes cell death by necroptosis NAD+ depletion triggers macrophage necroptosis, a cell death pathway exploited by Mycobacterium tuberculosis ADP-ribose) polymerase 1, PARP1, modifies EZH2 and inhibits EZH2 histone methyltransferase activity after DNA damage Receptor interacting protein kinase-3 determines cellular necrotic response to TNF-alpha AMP-activated protein kinase, an emerging drug target to regulate imbalances in lipid and carbohydrate metabolism to treat cardio-metabolic diseases Role of AMPK-mTOR-Ulk1/2 in the regulation of autophagy: Cross talk, shortcuts, and feedbacks ATM signals to TSC2 in the cytoplasm to regulate mTORC1 in response to ROS Autophagy recognizes intracellular Salmonella enterica serovar Typhimurium in damaged vacuoles Listeria monocytogenes ActA is a key player in evading autophagic recognition Interactions between Shigella flexneri and the autophagy machinery NOD proteins: Regulators of inflammation in health and disease Similarly, components were found to be degraded by autophagy during developmental apoptosis [185] , whilst it was recently shown that inhibiting autophagy increased apoptosis and accelerated mortality in murine sepsis models with inadequate autophagy pathways in CD4 + T cells, indicating that autophagy has a functional role against apoptosis and immunosuppression in T cells in sepsis [186] .


id: cord-004133-32w6g7qk
author: Walker, Faye M.
title: Advances in Directly Amplifying Nucleic Acids from Complex Samples
date: 2019-09-30
extension: .txt
mime: text/plain
words: 13589
sentence: 583
flesch: 39
cache: cache/cord-004133-32w6g7qk.txt
txt: txt/cord-004133-32w6g7qk.txt
summary:
  A Useful Tool for the Surveillance of blaOXA-23-Positive Carbapenem-Resistant Acinetobacter baumannii Flinders technology associates (FTA) filter paper-based DNA extraction with polymerase chain reaction (PCR) for detection of Pneumocystis jirovecii from respiratory specimens of immunocompromised patients Operational feasibility of using loop-mediated isothermal amplification for diagnosis of pulmonary tuberculosis in microscopy centers of developing countries Successful use of saliva without DNA extraction for detection of macrolide-resistant Mycoplasma pneumoniae DNA in children using LNA probe-based real-time PCR Rapid typing of STRs in the human genome by HyBeacon melting Ultra-rapid DNA analysis using HyBeacon probes and direct PCR amplification from saliva Comparison of boiling and robotics automation method in DNA extraction for metagenomic sequencing of human oral microbes Comparison of DNA Extraction Methods in Analysis of Salivary Bacterial Communities Study of inter-and intra-individual variations in the salivary microbiota Microbiological diversity of generalized aggressive periodontitis by 16S rRNA clonal analysis A Sweet Spot for Molecular Diagnostics: Coupling Isothermal Amplification and Strand Exchange Circuits to Diagnosis of mycobacterial infections by nucleic acid amplification: 18-month prospective study Pilot study of a rapid and minimally instrumented sputum sample preparation method for molecular diagnosis of tuberculosis Efficacy of loop mediated isothermal amplification (LAMP) assay for the laboratory identification of Mycobacterium tuberculosis isolates in a resource limited setting A novel and more sensitive loop-mediated isothermal amplification assay targeting IS6110 for detection of Mycobacterium tuberculosis complex Development of an in-house loop-mediated isothermal amplification (LAMP) assay for detection of Mycobacterium tuberculosis and evaluation in sputum samples of Nepalese patients Rapid detection of Mycobacterium tuberculosis by recombinase polymerase amplification Polymerase chain reaction for diagnosis of M. tuberculosis: Comparison of simple boiling and a conventional method for DNA extraction Detection of Mycobacterium tuberculosis in sputum samples by polymerase chain reaction using a simplified procedure Detection of Mycobacterium tuberculosis in clinical samples by two-step polymerase chain reaction and nonisotopic hybridization methods Rapid, simple method for treating clinical specimens containing Mycobacterium tuberculosis to remove DNA for polymerase chain reaction An extremely rapid and simple DNA-release method for detection of M. tuberculosis from clinical specimens Evaluation of a simple loop-mediated isothermal amplification test kit for the diagnosis of tuberculosis Evaluation of the efficacy of five DNA extraction methods for the detection of Mycobacterium tuberculosis DNA in direct and processed sputum by an in-house PCR method Clinical usefulness of multiplex PCR lateral flow in MRSA detection: A novel, rapid genetic testing method Development and evaluation of a rapid multiplex-PCR based system for Mycobacterium tuberculosis diagnosis using sputum samples Polymerase chain reaction for detection of Mycobacterium tuberculosis A simple method for diagnosing M. tuberculosis infection in clinical samples using PCR Self-Collected versus Clinician-Collected Sampling for Chlamydia and Gonorrhea Screening: A Systemic Review and Meta-Analysis Validation of real-time PCR for laboratory diagnosis of Acanthamoeba keratitis Effects of topical anaesthetics and fluorescein on the real-time PCR used for the diagnosis of Herpesviruses and Acanthamoeba keratitis Inhibition of PCR by Aqueous and Vitreous Fluids Use of the polymerase chain reaction to detect Bordetella pertussis in patients with mild or atypical symptoms of infection Diagnostic accuracy of a prototype point-of-care test for ocular chlamydia trachomatis under field conditions in the Gambia and Senegal High-throughput STR analysis for DNA database using direct PCR Multicenter clinical evaluation of the novel Amongst the collection of approaches for direct PCR amplification on saliva samples, those that begin with dried saliva swabs fully circumvent DNA extraction, purification, and quantification [93] .


# url

id: cord-343632-cv3qgno3
domain: www.bgi.com
url:
  https://www.bgi.com/global/company/news/bgi-develops-realtime-dna-based-kit-for-detecting-the-2019-novel-coronavirus/


id: cord-328042-e1is656g
domain: www.the-scientist.com
url:
  www.the-scientist.com/news-opinion/rna-extraction-kits-for-covid-19-tests-are-in-short-supplyin-us-67250


