scholarly journals Per-Covid-19: A Benchmark Database For Covid-19 Percentage Prediction From CT-scans

2021 ◽  
Author(s):  
Fares Bougourzi ◽  
Cosimo Distante ◽  
Ouafi Abdelkrim ◽  
Fadi Dornaika ◽  
Abdenour Hadid ◽  
...  
Keyword(s):  
Neural Network ◽  
Polymerase Chain Reaction ◽  
Intensive Care ◽  
Loss Functions ◽  
Ct Scans ◽  
Rt Pcr ◽  
Chain Reaction ◽  
X Ray ◽  
Benchmark Database ◽  
Polymerase Chain

Abstract Covid-19 infection recognition is very important step in the fighting against the new pandemic Covid-19. In fact, many methods have been used to recognize the Covid-19 infection including Reverse transcription polymerase chain reaction (RT-PCR), X-ray scan and CT-scan. In addition to the recognition of the Covid-19 infection, CT-scans can provide more important information about the evolution of this disease and its severity. With the extensive number of Covid-19 infections, estimating the Covid-19 percentage can help the intensive care to free up the resuscitation beds for the critical cases and follow other protocol for less severity cases. In this paper, we propose Covid-19 percentage estimation database. Moreover, we evaluate the performance of three Covolutional Neural Network (CNN) architectures which are ResneXt-50, Densenet-161 and Inception-v3. For the three CNN architectures, we use two loss functions which are MSE and Dynamic Huber. In addition, two pretrained scenarios are investigated (ImageNet pretrained models and X-ray pretrained models). The evaluated approaches achieved promising results, where Inception-v3 with using Dynamic Huber loss function and X-ray pretrained model achieved the best performance.

scholarly journals Is the Portable Chest Radiographic More Reliable to Reveal Covid19 in Highly Suspicion Patient before Real-Time Reverse Transcription Polymerase Chain Reaction (RT-PCR) Test?

2021 ◽  
Vol 6 (03) ◽  
pp. 228-236
Author(s):  
Bushra A. A. Albazi ◽  
Dr Noof. Albaz ◽  
Dr Nayef. Alqahtani ◽  
Dr. Angham Salih ◽  
Dr Rafat Mohtasab
Keyword(s):  
Polymerase Chain Reaction ◽  
Retrospective Study ◽  
Predictive Value ◽  
Rt Pcr ◽  
Chain Reaction ◽  
X Ray ◽  
Polymerase Chain ◽  
Rate Type ◽  
Test Result ◽  
Pcr Test

A large number of patients with coronavirus disease 2019 (COVID-19) present at hospitals. There are a limited number of isolation rooms open, and patients must often wait a long time to get a reverse transcription-polymerase chain reaction (RT-PCR) test done. This necessitates the introduction of effective triage plans. A patient with suspicions is referred to an emergency room (ED) depending on their medical record for a simple physical assessment, blood test findings, and chest imaging.A retrospective study design was conduct at Prince Sultan Medical Military City (PSMMC). Ethical approval was obtained from the institutional board to wave the consent forms since it is a retrospective study. Only the primary investigator has had the data access to the patients’ medical records. The collected patient records were under specific categories, including symptoms score starts from 5 and above, RT-PCR test result done after CXRP imaging, the patient admitted to the emergency department (ED). Excluding all CXRP done after RT-PCR TEST, positive Covid 19 admitted to the intensive care unit (ICU), pediatric patients, and patients with score symptoms were less than five. Two experienced radiologists reviewed the images blindly, and the inter-observer reliability of observations noted by the radiologists was calculated. As for the relationship between the x-ray reading and the RT-PCR test result, our results showed a high correlation between the variables (chi-square χ² = 12.44, with df =1, and p<0.001). The sensitivity of x-ray diagnosing covid19 was 65.52 %, while the specificity was 54.51 %, and the accuracy of radiologists reading was 58.17 %. Furthermore, the positive predictive value (PPV) was 41.76 %, and the negative predictive value (NPV) was 76.05%. Finally, the false positive rate (type-i error (alpha) was 45.49%, and the false-negative rate (type-ii error (beta) was 34.48% Our research findings show that CXRP imaging can detect COVID-19 infection in symptomatic patients and can be a valuable addition to RT-PCR testing. In an inpatient ED environment where availability of test kits, laboratory equipment, and laboratory personnel is compromised and risks delaying patient treatment and hospital workflow, serial CXRP could theoretically be used as an adjunct diagnostic function and monitoring in patients suspected of having COVID-19.

scholarly journals Gambaran Klinis dan Karakteristik Neonatus dari Ibu Terkonfimasi Covid-2019 di Rumah Sakit Dr. Soetomo

Sari Pediatri ◽  
2021 ◽  
Vol 22 (5) ◽  
pp. 285
Author(s):  
Risa Etika ◽  
Kartika Darma Handayani ◽  
Setya Mithra Hartiastuti ◽  
Virani Diana ◽  
Aminuddin Harahap ◽  
...  
Keyword(s):  
Intensive Care Unit ◽  
Polymerase Chain Reaction ◽  
Intensive Care ◽  
Severe Acute Respiratory Syndrome ◽  
Neonatal Intensive Care Unit ◽  
Reverse Transcription ◽  
Neonatal Intensive Care ◽  
Rt Pcr ◽  
Chain Reaction ◽  
Polymerase Chain

Latar belakang. Penyakit Coronavirus 2019 (COVID-19) merupakan penyakit yang pertama kali dilaporkan di Wuhan, China dan telah menyebar ke seluruh dunia. Data ibu hamil dan bayi baru lahir belum banyak dipublikasikan.Tujuan. Untuk mendeskripsikan gambaran dan karakteristik klinis neonatus yang lahir dari ibu dengan infeksi severe acute respiratory syndrome-coronavirus (SARS-CoV-2) perinatal.Metode. Penelitian ini merupakan penelitian retrospektif yang dilaksanakan di ruang perawatan neonatal intensive care unit (NICU) Rumah Sakit Umum Daerah Dr.Soetomo Surabaya pada tanggal April - Oktober 2020. Populasi adalah neonatus yang lahir dari ibu terkonfimasi COVID-19 di di Rumah Sakit Dr. Soetomo Surabaya. Data diperoleh dari rekam medik.Hasil. Total terdapat 109 ibu dengan hasil pemeriksaan positif reverse transcription - polymerase chain reaction (RT PCR) COVID-19, dan hanya 2 bayi dengan hasil RT-PCR COVID-19 positif. Usia rata-rata ibu hamil 28±5,9 tahun. Duapuluh sembilan bayi (26,61%) lahir kurang bulan. Cara persalinan didominasi oleh sectio caesaria sebanyak 64 ibu hamil (58,72%). Terdapat 23 bayi (21,11%) lahir dengan berat badan lahir <2500 gram dan 3 bayi dengan hasil negatif RT-PCR COVID-19 meninggal.Kesimpulan. Saat ini belum terbukti adanya penularan secara vertikal COVID 19, sementara itu transmisi horizontal diperkirakan sebagai sumber infeksi pada neonatus. Penerapan protokol kesehatan terbukti efektif mencegah infeksi terhadap neonatus. 

scholarly journals Contamination inside CT gantry in the SARS-CoV-2 era

2020 ◽  
Vol 4 (1) ◽  
Author(s):  
João Matos ◽  
Francesco Paparo ◽  
Marco Mori ◽  
Alessio Veneziano ◽  
Marina Sartini ◽  
...  
Keyword(s):  
Computed Tomography ◽  
Polymerase Chain Reaction ◽  
Severe Acute Respiratory Syndrome ◽  
Ribonucleic Acid ◽  
Ct Scanner ◽  
Rt Pcr ◽  
Chain Reaction ◽  
X Ray ◽  
Detection And Counting ◽  
Polymerase Chain

Abstract We investigated whether the internal gantry components of our computed tomography (CT) scanner contain severe acute respiratory syndrome 2 (SARS-CoV-2) ribonucleic acid (RNA), bacterial or fungal agents. From 1 to 27 March 2020, we performed 180 examinations of patients with confirmed SARS-CoV-2 infection using a dedicated CT scanner. On 27 March 2020, this CT gantry was opened and sampled in each of the following components: (a) gantry case; (b) inward airflow filter; (c) gantry motor; (d) x-ray tube; (e) outflow fan; (f) fan grid; (g) detectors; and (h) x-ray tube filter. To detect SARS-CoV-2 RNA, samples were analysed using reverse transcriptase-polymerase chain reaction (RT-PCR). To detect bacterial or fungal agents, samples have been collected using “replicate organism detection and counting” contact plates of 24 cm2, containing tryptic soy agar, and subsequently cultured. RT-PCR detected SARS-CoV-2 RNA in the inward airflow filter sample. RT-PCR of remaining gantry samples did not reveal the presence of SARS-CoV-2 RNA. Neither bacterial nor fungal agents grew in the agar-based growth medium after the incubation period. Our data showed that SARS-Cov-2 RNA can be found inside the CT gantry only in the inward airflow filter. All remaining CT gantry components were devoid of SARS-CoV-2 RNA.

1504: Molecular Diagnosis and Staging of Prostate Cancer Using Clusterin in Real Time Reverse Transcription Polymerase Chain Reaction (RT-PCR)

2006 ◽  
Vol 175 (4S) ◽  
pp. 485-486
Author(s):  
Sabarinath B. Nair ◽  
Christodoulos Pipinikas ◽  
Roger Kirby ◽  
Nick Carter ◽  
Christiane Fenske
Keyword(s):  
Prostate Cancer ◽  
Polymerase Chain Reaction ◽  
Real Time ◽  
Molecular Diagnosis ◽  
Reverse Transcription ◽  
Rt Pcr ◽  
Chain Reaction ◽  
Polymerase Chain

Polymerase chain reaction amplification and typing of rotavirus in environmental samples

1995 ◽  
Vol 31 (5-6) ◽  
pp. 371-374 ◽  
Author(s):  
R. Gajardo ◽  
R. M. Pintó ◽  
A. Bosch
Keyword(s):  
Polymerase Chain Reaction ◽  
Environmental Samples ◽  
Polymerase Chain Reaction Amplification ◽  
Rt Pcr ◽  
Chain Reaction ◽  
Pcr Assay ◽  
Group A ◽  
Reaction Amplification ◽  
Stool Specimens ◽  
Polymerase Chain

A reverse transcription polymerase chain reaction (RT-PCR) assay is described that has been developed for the detection and serotyping of group A rotavirus in stool specimens and concentrated and non-concentrated sewage specimens.

scholarly journals Machine Learning Prediction of SARS-CoV-2 Polymerase Chain Reaction Results with Routine Blood Tests

2020 ◽  
Author(s):  
Thomas Tschoellitsch ◽  
Martin Dünser ◽  
Carl Böck ◽  
Karin Schwarzbauer ◽  
Jens Meier
Keyword(s):  
Machine Learning ◽  
Polymerase Chain Reaction ◽  
Characteristic Curve ◽  
Cohort Analysis ◽  
Rt Pcr ◽  
Chain Reaction ◽  
Blood Tests ◽  
Routine Blood ◽  
Machine Learning Model ◽  
Polymerase Chain

Abstract Objective The diagnosis of COVID-19 is based on the detection of SARS-CoV-2 in respiratory secretions, blood, or stool. Currently, reverse transcription polymerase chain reaction (RT-PCR) is the most commonly used method to test for SARS-CoV-2. Methods In this retrospective cohort analysis, we evaluated whether machine learning could exclude SARS-CoV-2 infection using routinely available laboratory values. A Random Forests algorithm with 1353 unique features was trained to predict the RT-PCR results. Results Out of 12,848 patients undergoing SARS-CoV-2 testing, routine blood tests were simultaneously performed in 1528 patients. The machine learning model could predict SARS-CoV-2 test results with an accuracy of 86% and an area under the receiver operating characteristic curve of 0.90. Conclusion Machine learning methods can reliably predict a negative SARS-CoV-2 RT-PCR test result using standard blood tests.

scholarly journals A meta-analysis of accuracy and sensitivity of chest CT and RT-PCR in COVID-19 diagnosis

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Fatemeh Khatami ◽  
Mohammad Saatchi ◽  
Seyed Saeed Tamehri Zadeh ◽  
Zahra Sadat Aghamir ◽  
Alireza Namazi Shabestari ◽  
...  
Keyword(s):  
Polymerase Chain Reaction ◽  
Reverse Transcriptase ◽  
Ct Scan ◽  
Predictive Value ◽  
Meta Analysis ◽  
Chest Ct ◽  
Rt Pcr ◽  
Chain Reaction ◽  
Polymerase Chain ◽  
Chest Ct Scan

AbstractNowadays there is an ongoing acute respiratory outbreak caused by the novel highly contagious coronavirus (COVID-19). The diagnostic protocol is based on quantitative reverse-transcription polymerase chain reaction (RT-PCR) and chests CT scan, with uncertain accuracy. This meta-analysis study determines the diagnostic value of an initial chest CT scan in patients with COVID-19 infection in comparison with RT-PCR. Three main databases; PubMed (MEDLINE), Scopus, and EMBASE were systematically searched for all published literature from January 1st, 2019, to the 21st May 2020 with the keywords "COVID19 virus", "2019 novel coronavirus", "Wuhan coronavirus", "2019-nCoV", "X-Ray Computed Tomography", "Polymerase Chain Reaction", "Reverse Transcriptase PCR", and "PCR Reverse Transcriptase". All relevant case-series, cross-sectional, and cohort studies were selected. Data extraction and analysis were performed using STATA v.14.0SE (College Station, TX, USA) and RevMan 5. Among 1022 articles, 60 studies were eligible for totalizing 5744 patients. The overall sensitivity, specificity, positive predictive value, and negative predictive value of chest CT scan compared to RT-PCR were 87% (95% CI 85–90%), 46% (95% CI 29–63%), 69% (95% CI 56–72%), and 89% (95% CI 82–96%), respectively. It is important to rely on the repeated RT-PCR three times to give 99% accuracy, especially in negative samples. Regarding the overall diagnostic sensitivity of 87% for chest CT, the RT-PCR testing is essential and should be repeated to escape misdiagnosis.

scholarly journals Evaluation of Sandwich Enzyme-Linked Immunosorbent Assay and Reverse Transcription Polymerase Chain Reaction for the Diagnosis of Foot-and-Mouth Disease

Intervirology ◽  
2021 ◽  
pp. 1-6
Author(s):  
Salman Khan ◽  
Syed Asad Ali Shah ◽  
Syed Muhammad Jamal
Keyword(s):  
Polymerase Chain Reaction ◽  
Viral Genome ◽  
Foot And Mouth Disease ◽  
Enzyme Linked Immunosorbent Assay ◽  
Rt Pcr ◽  
Chain Reaction ◽  
Kappa Value ◽  
Polymerase Chain ◽  
Pcr Assays ◽  
Level Of Agreement

<b><i>Background:</i></b> Foot-and-mouth disease (FMD) is an infectious and highly contagious disease of cloven-hoofed domestic and wild animals, causing heavy economic losses to the livestock industry. Rapid and reliable diagnosis of the disease is essential for the implementation of effective control measures. This study compared sandwich enzyme-linked immunosorbent assay (S-ELISA) and conventional reverse transcription polymerase chain reaction (RT-PCR) for the diagnosis of FMD. <b><i>Methods:</i></b> A total of 60 epithelial samples from suspected cases of FMD were tested using both S-ELISA and RT-PCR assays. The level of agreement between the assays was assessed by calculating the Kappa value. <b><i>Results:</i></b> S-ELISA detected 38 (63%) samples positive for FMD virus (FMDV). Being predominant, serotype O was detected in 22 (57.9%) of the total samples tested positive, whereas 9 (23.7%) and 7 (18.4%) samples were found positive for serotypes A and Asia-1, respectively. RT-PCR detected viral genome in 51 (85%) of the samples using pan-FMDV primers set, 1F/1R. Thirty-six samples were found positive and 7 negative by both the tests. The level of agreement between the tests was assessed by calculating the Kappa value, which was found to be fair (Kappa value = 0.303 and 95% CI = 0.089; 0.517) and significant (<i>p</i> = 0.009). However, 2 samples, which were found positive on S-ELISA tested negative on RT-PCR. This may be attributed to the presence of nucleotide mismatch(es) in the primer-binding sites that may have resulted in failure of amplification of the viral genome. The serotype-specific RT-PCR assays not only confirmed serotyping results of S-ELISA but were also able to establish serotype in 9 S-ELISA-negative but pan-FMDV RT-PCR-positive samples. <b><i>Conclusions:</i></b> The RT-PCR assay contributes significantly to establishing a quick, sensitive, and definitive diagnosis of FMD in resource-constrained countries. Samples giving negative results in S-ELISA should be tested in RT-PCR for the disease detection and virus typing.

Detection of specific mRNAs in single nephron segments by use of the polymerase chain reaction

1990 ◽  
Vol 258 (5) ◽  
pp. F1470-F1474 ◽  
Author(s):  
T. Moriyama ◽  
H. R. Murphy ◽  
B. M. Martin ◽  
A. Garcia-Perez
Keyword(s):  
Polymerase Chain Reaction ◽  
Aldose Reductase ◽  
Collecting Duct ◽  
Specific Gene ◽  
Rt Pcr ◽  
Chain Reaction ◽  
Nephron Segments ◽  
Single Nephron ◽  
Specific Mrnas ◽  
Polymerase Chain

We have developed a procedure to detect specific mRNAs in single renal nephron segments. This approach combines microdissection, reverse transcription (RT) of the target mRNA, and amplification of the resulting cDNA using the polymerase chain reaction (PCR). After microdissection, the sample is placed in a tube where it is permeabilized and where all reactions are performed directly without the need for isolation of the RNA. Our model target was the mRNA for aldose reductase. This enzyme catalyzes the conversion of glucose to sorbitol. Its expression is modulated by changes in extracellular osmolality in the renal medulla. RT-PCR of inner medullary collecting duct (1 mm) and glomeruli (6-10) yielded a product of the predicted length (670 base pairs) defined by the PCR primers. Its identity was confirmed by a specific oligonucleotide probe that differed from the primers. RT-PCR of proximal tubules (1 mm) resulted in no aldose reductase-specific amplification product. RT-PCR is generally applicable for measuring specific gene expression in single nephron segments or small numbers of cultured cells. Utility, limitations, and refinements of this approach are discussed.

Expression of hyaluronan synthase-3 in porcine oviducal epithelium during oestrus

2003 ◽  
Vol 15 (2) ◽  
pp. 99 ◽  
Author(s):  
Paisan Tienthai ◽  
Naoko Kimura ◽  
Paraskevi Heldin ◽  
Eimei Sato ◽  
Heriberto Rodriguez-Martinez
Keyword(s):  
Polymerase Chain Reaction ◽  
Reverse Transcription ◽  
Hyaluronan Synthase ◽  
Critical Periods ◽  
Rt Pcr ◽  
Chain Reaction ◽  
Mean Values ◽  
Polymerase Chain ◽  
Sperm Reservoir ◽  
Oviduct Fluid

Hyaluronan (HA) has been related to fertilization and embryo development in the pig. Furthermore, HA is present in pig oviduct fluid and the lining epithelium, particularly of the pre-ovulatory sperm reservoir. Because the mechanisms that regulate HA synthesis have not yet been clarified, semiquantitative reverse transcription-polymerase chain reaction (RT-PCR) was conducted to assess the expression of mRNAs of two HA-synthesizing enzymes (has2 and has3) in the oviduct epithelium (uterotubal junction, isthmus, ampullary–isthmic junction and ampulla segments) of non-inseminated (control) and inseminated (treatment) sows at pre-, peri- and post-ovulatory oestrus. Only has3 mRNA was detected; it was present in all tubal segments of both control and treatment samples. The level of has3 expression did not vary significantly between non-inseminated and inseminated specimens, but there was a tendency (NS) for increased mean values during the peri- and post-ovulatory stages compared with pre-ovulation. It is concluded that has3 is expressed by the porcine endosalpinx epithelium and the levels of expression do not vary during the critical periods of sperm transport and fertilization, despite fluctuating levels of HA in the tubal fluid at corresponding periods.

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