Pub Date : 2022-12-26DOI: 10.1101/2022.12.23.22283921
B. Tanriover, Abdulmecit Gungor, M. Al‐Obaidi, B. Thajudeen, R. Wong, I. Mansour, T. Zangeneh, K. Johnson, N. Low, Roshan Alam, Erik Alonso González, B. Sandikçi, S. Muruganpandian, G. Gupta, E. Bedrick, T. Saridogan, K. Mendoza
BACKGROUND: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can evade neutralizing antibodies, raising concerns about the effectiveness of anti-spike monoclonal antibodies (mAb). METHODS: This study reports a retrospective data analysis in Banner Health Care System. Out of 109,788 adult patients who tested positive for COVID-19, the study cohort was split into patients who received Casirivimab-Imdevimab (Cas-Imd) (N=10,836; Delta-predominant period 6/2021-11/2021) and Sotrovimab (N=998; Omicron-predominant period 12/2021-1/2022) mAb compared to propensity-matched control groups (N=10,836 and N=998), respectively. Index date was the date of mAb administration or the date of positive COVID-19 testing. The primary and secondary outcomes were the incidence of composite outcome (all-cause hospitalization and/or mortality) and ICU admission at 30-days following index date, respectively. RESULTS: Compared to the propensity-matched untreated control cohort, the Cas-Imd mAb reduced the composite outcome (from 7.5% to 3.7%; difference: -3.8% [95% CI: (-4.4%, -3.2%)], p <0.01) regardless of their vaccination status, while Sotrovimab mAb did not (5.0% vs. 3.8%; difference: -1.2% [95% CI: (-3.1%, 0.7%)], p =0.22). In terms of the secondary outcome, similarly Cas-Imd mAb decreased ICU admission during the first hospitalization (from 1.5% to 0.5%; difference: -1.0% [95% CI: (-1.3%, -0.7%)], p <0.01) compared to the control group, whereas Sotrovimab mAb did not (0.9% vs. 0.6%; difference: -0.3% [95% CI: (-1.2%, 0.6%)], p =0.61). Comparing the periods, the Omicron-predominant period was associated with lower composite outcome than that during the Delta-predominant period. CONCLUSIONS: Cas-Imd mAb was effective against the SARS-CoV-2 Delta variant, however sotrovimab lacked efficacy in patients with SARS-CoV-2 Omicron-predominant period.
{"title":"EFFECTIVENESS OF CASIRIVIMAB-IMDEVIMAB AND SOTROVIMAB MONOCLONAL ANTIBODY TREATMENT AMONG HIGH-RISK PATIENTS WITH SARS-CoV-2 INFECTION: A REAL-WORLD EXPERIENCE","authors":"B. Tanriover, Abdulmecit Gungor, M. Al‐Obaidi, B. Thajudeen, R. Wong, I. Mansour, T. Zangeneh, K. Johnson, N. Low, Roshan Alam, Erik Alonso González, B. Sandikçi, S. Muruganpandian, G. Gupta, E. Bedrick, T. Saridogan, K. Mendoza","doi":"10.1101/2022.12.23.22283921","DOIUrl":"https://doi.org/10.1101/2022.12.23.22283921","url":null,"abstract":"BACKGROUND: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can evade neutralizing antibodies, raising concerns about the effectiveness of anti-spike monoclonal antibodies (mAb). METHODS: This study reports a retrospective data analysis in Banner Health Care System. Out of 109,788 adult patients who tested positive for COVID-19, the study cohort was split into patients who received Casirivimab-Imdevimab (Cas-Imd) (N=10,836; Delta-predominant period 6/2021-11/2021) and Sotrovimab (N=998; Omicron-predominant period 12/2021-1/2022) mAb compared to propensity-matched control groups (N=10,836 and N=998), respectively. Index date was the date of mAb administration or the date of positive COVID-19 testing. The primary and secondary outcomes were the incidence of composite outcome (all-cause hospitalization and/or mortality) and ICU admission at 30-days following index date, respectively. RESULTS: Compared to the propensity-matched untreated control cohort, the Cas-Imd mAb reduced the composite outcome (from 7.5% to 3.7%; difference: -3.8% [95% CI: (-4.4%, -3.2%)], p <0.01) regardless of their vaccination status, while Sotrovimab mAb did not (5.0% vs. 3.8%; difference: -1.2% [95% CI: (-3.1%, 0.7%)], p =0.22). In terms of the secondary outcome, similarly Cas-Imd mAb decreased ICU admission during the first hospitalization (from 1.5% to 0.5%; difference: -1.0% [95% CI: (-1.3%, -0.7%)], p <0.01) compared to the control group, whereas Sotrovimab mAb did not (0.9% vs. 0.6%; difference: -0.3% [95% CI: (-1.2%, 0.6%)], p =0.61). Comparing the periods, the Omicron-predominant period was associated with lower composite outcome than that during the Delta-predominant period. CONCLUSIONS: Cas-Imd mAb was effective against the SARS-CoV-2 Delta variant, however sotrovimab lacked efficacy in patients with SARS-CoV-2 Omicron-predominant period.","PeriodicalId":72279,"journal":{"name":"Archives of clinical and biomedical research","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-12-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43573733","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2022-11-14DOI: 10.1101/2022.11.11.22282032
R. E. Carpenter, V. Tamrakar, E. Brown, S. Almas, R. Sharma
Rapid classification and detection of SARS-CoV-2 variants have been critical in comprehending the virus's transmission dynamics. Clinical manifestation of the infection is influenced by comorbidities such as age, immune status, diabetes, and the infecting variant. Thus, clinical management may differ for new variants. For example, some monoclonal antibody treatments are variant-specific. Yet, an FDA-approved test for detecting the SARS-CoV-2 variant is unavailable. A laboratory-developed test (LDT) remains a viable option for reporting the infecting variant for clinical intervention or epidemiological purposes. Accordingly, we have validated the Illumina COVID-Seq assay as an LDT according to the guidelines prescribed by the College of American Pathologists (CAP) and Clinical Laboratory Improvement Amendments (CLIA). The limit of detection (LOD) of this test is Ct<30 (~15 viral copies) and >200X genomic coverage, and the test is 100% specific in the detection of existing variants. The test demonstrated 100% precision in inter-day, intra-day, and intra-laboratory reproducibility studies. It is also 100% accurate, defined by reference strain testing and split sample testing with other CLIA laboratories. Advanta Genetics LDT COVID Seq has been reviewed by CAP inspectors and is under review by FDA for Emergency Use Authorization.
{"title":"COVID Seq as Laboratory Developed Test (LDT) for diagnosis of SARS-CoV-2 Variants of Concern (VOC)","authors":"R. E. Carpenter, V. Tamrakar, E. Brown, S. Almas, R. Sharma","doi":"10.1101/2022.11.11.22282032","DOIUrl":"https://doi.org/10.1101/2022.11.11.22282032","url":null,"abstract":"Rapid classification and detection of SARS-CoV-2 variants have been critical in comprehending the virus's transmission dynamics. Clinical manifestation of the infection is influenced by comorbidities such as age, immune status, diabetes, and the infecting variant. Thus, clinical management may differ for new variants. For example, some monoclonal antibody treatments are variant-specific. Yet, an FDA-approved test for detecting the SARS-CoV-2 variant is unavailable. A laboratory-developed test (LDT) remains a viable option for reporting the infecting variant for clinical intervention or epidemiological purposes. Accordingly, we have validated the Illumina COVID-Seq assay as an LDT according to the guidelines prescribed by the College of American Pathologists (CAP) and Clinical Laboratory Improvement Amendments (CLIA). The limit of detection (LOD) of this test is Ct<30 (~15 viral copies) and >200X genomic coverage, and the test is 100% specific in the detection of existing variants. The test demonstrated 100% precision in inter-day, intra-day, and intra-laboratory reproducibility studies. It is also 100% accurate, defined by reference strain testing and split sample testing with other CLIA laboratories. Advanta Genetics LDT COVID Seq has been reviewed by CAP inspectors and is under review by FDA for Emergency Use Authorization.","PeriodicalId":72279,"journal":{"name":"Archives of clinical and biomedical research","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"44228465","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2022-10-06DOI: 10.1101/2022.10.03.22280657
Li-Yu Daisy Liu, V. Prabhakar
Data obtained from clinical trials for a given disease often capture reliable empirical features of the highest quality which are limited to few studies/experiments. In contrast, knowledge data extracted from biomedical literature captures a wide range of clinical information relevant to a given disease that may not be as reliable as the experimental data. Therefore, we propose a novel method of training that co-optimizes two AI algorithms on experimental data and knowledge-based information from literature respectively to supplement the learning of one algorithm with that of the other and apply this method to prioritize/rank causal genes for Alzheimer's Disease (AD). One algorithm generates unsupervised embeddings for gene nodes in a protein-protein interaction network associated with experimental data. The other algorithm generates embeddings for the nodes/entities in a knowledge graph constructed from biomedical literature. Both these algorithms are co-optimized to leverage information from each other's domain. Therefore; a downstream inferencing task to rank causal genes for AD ensures the consideration of experimental and literature data available to implicate any given gene in the geneset. Rank-based evaluation metrics computed to validate the gene rankings prioritized by our algorithm showed that the top ranked positions were highly enriched with genes from a ground truth set that were experimentally verified to be causal for the progression of AD. Keywords : Alzheimer's Disease, Causal gene prioritization, Co-optimization, Protein-Protein interaction network, Knowledge Graph
{"title":"Unsupervised co-optimization of a graph neural network and a knowledge graph embedding model to prioritize causal genes for Alzheimers Disease","authors":"Li-Yu Daisy Liu, V. Prabhakar","doi":"10.1101/2022.10.03.22280657","DOIUrl":"https://doi.org/10.1101/2022.10.03.22280657","url":null,"abstract":"Data obtained from clinical trials for a given disease often capture reliable empirical features of the highest quality which are limited to few studies/experiments. In contrast, knowledge data extracted from biomedical literature captures a wide range of clinical information relevant to a given disease that may not be as reliable as the experimental data. Therefore, we propose a novel method of training that co-optimizes two AI algorithms on experimental data and knowledge-based information from literature respectively to supplement the learning of one algorithm with that of the other and apply this method to prioritize/rank causal genes for Alzheimer's Disease (AD). One algorithm generates unsupervised embeddings for gene nodes in a protein-protein interaction network associated with experimental data. The other algorithm generates embeddings for the nodes/entities in a knowledge graph constructed from biomedical literature. Both these algorithms are co-optimized to leverage information from each other's domain. Therefore; a downstream inferencing task to rank causal genes for AD ensures the consideration of experimental and literature data available to implicate any given gene in the geneset. Rank-based evaluation metrics computed to validate the gene rankings prioritized by our algorithm showed that the top ranked positions were highly enriched with genes from a ground truth set that were experimentally verified to be causal for the progression of AD. Keywords : Alzheimer's Disease, Causal gene prioritization, Co-optimization, Protein-Protein interaction network, Knowledge Graph","PeriodicalId":72279,"journal":{"name":"Archives of clinical and biomedical research","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-10-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"44237689","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2022-08-30DOI: 10.1101/2022.08.29.22279161
J. Nguyen Van, Benoit Pilmis, Amir Khaterchi, Olivier Billuart, Gauthier Péan De Ponfill, Alban Le Monnier, Elie Azria, A. Mizrahi
Background SARS-CoV-2 has been responsible for more than 550 million cases of COVID-19 worldwide. RT-PCR is considered the gold standard for the diagnosis of patients suspected of having COVID-19. During the heightened waves of the pandemic, more rapid tests have been required. Point-of-care tests (POCT) for COVID-19 include antigen tests, serological tests, and other molecular-based platforms. The ID NOW COVID-19 assay (Abbott) performs an isothermal gene amplification of a target encoding the RNA-dependent RNA polymerase of SARSCoV-2. The main objective of this study was to evaluate the organizational impact following the implementation of a POC testing platform ID NOW in a maternity ward. Materials and Methods This retrospective study included pregnant women admitted for Groupe Hospitalier Paris Saint- Joseph Paris. The study was conducted over 2 periods lasting 6 months each. The first period (P1) corresponded to the 2nd wave in France (July to December 2020) whereas the second (P2) period focused on the 3rd wave (February to July 2021). During P1, viral detection was performed by RT-PCR at the laboratory. During P2, it was performed with the ID NOW COVID-19 test directly in the delivery room by nursing staff after training and certification. Our primary endpoint was the length of time in the birth room from admission to discharge in the postpartum period. Results 2447 pregnant women were included, 1053 during P1 and 1394 during P2. The median age, percentage of singleton pregnancies, mean gestational age, percentage of nulliparous individuals, percentage of vaginal deliveries, and COVID19 positivity rate were comparable between the two periods. During P2, the length of stay in the delivery room was significantly shorter than during P1 (17.9 vs 14.7 hours, p<0.001). Conclusion Analysis of the data from this study following the implementation of the ID NOW POCT in the maternity ward indicates a significant decrease in the length of stay in the birth room. This outcome needs to be confirmed in a multicenter cohort, in particular to precise the specific impact of COVID-19 care on delays.
背景SARS-CoV-2已导致全球超过5.5亿例新冠肺炎病例。RT-PCR被认为是诊断疑似患有新冠肺炎患者的金标准。在疫情加剧期间，需要进行更快速的检测。新冠肺炎的点对点检测（POCT）包括抗原检测、血清学检测和其他基于分子的平台。ID NOW新冠肺炎测定（Abbott）对编码SARSCoV-2的RNA依赖性RNA聚合酶的靶点进行等温基因扩增。本研究的主要目的是评估在产科病房实施POC测试平台ID NOW后的组织影响。材料和方法这项回顾性研究包括巴黎圣约瑟夫医院的孕妇。该研究分两个阶段进行，每个阶段持续6个月。第一个时期（P1）对应于法国的第二波（2020年7月至12月），而第二个时期（P2）集中于第三波（2021年2月至7月）。在P1期间，在实验室通过RT-PCR进行病毒检测。在P2期间，由护理人员在培训和认证后直接在产房进行ID NOW新冠肺炎检测。我们的主要终点是产后从入院到出院在产房的时间长度。结果包括2447名孕妇，其中1053名在P1期，1394名在P2期。两个时期的中位年龄、单胎妊娠百分比、平均胎龄、未产妇百分比、阴道分娩百分比和COVID19阳性率具有可比性。在P2期间，产房的停留时间明显短于P1期间（17.9小时vs 14.7小时，p＜0.001）。结论在产科病房实施ID NOW POCT后，对本研究数据的分析表明，产房停留时间显著缩短。这一结果需要在多中心队列中得到证实，特别是为了精确新冠肺炎护理对延迟的具体影响。
{"title":"Organizational impact of an ID NOW COVID-19 point-of-care testing for SARS-CoV2 detection in a maternity ward","authors":"J. Nguyen Van, Benoit Pilmis, Amir Khaterchi, Olivier Billuart, Gauthier Péan De Ponfill, Alban Le Monnier, Elie Azria, A. Mizrahi","doi":"10.1101/2022.08.29.22279161","DOIUrl":"https://doi.org/10.1101/2022.08.29.22279161","url":null,"abstract":"Background SARS-CoV-2 has been responsible for more than 550 million cases of COVID-19 worldwide. RT-PCR is considered the gold standard for the diagnosis of patients suspected of having COVID-19. During the heightened waves of the pandemic, more rapid tests have been required. Point-of-care tests (POCT) for COVID-19 include antigen tests, serological tests, and other molecular-based platforms. The ID NOW COVID-19 assay (Abbott) performs an isothermal gene amplification of a target encoding the RNA-dependent RNA polymerase of SARSCoV-2. The main objective of this study was to evaluate the organizational impact following the implementation of a POC testing platform ID NOW in a maternity ward. Materials and Methods This retrospective study included pregnant women admitted for Groupe Hospitalier Paris Saint- Joseph Paris. The study was conducted over 2 periods lasting 6 months each. The first period (P1) corresponded to the 2nd wave in France (July to December 2020) whereas the second (P2) period focused on the 3rd wave (February to July 2021). During P1, viral detection was performed by RT-PCR at the laboratory. During P2, it was performed with the ID NOW COVID-19 test directly in the delivery room by nursing staff after training and certification. Our primary endpoint was the length of time in the birth room from admission to discharge in the postpartum period. Results 2447 pregnant women were included, 1053 during P1 and 1394 during P2. The median age, percentage of singleton pregnancies, mean gestational age, percentage of nulliparous individuals, percentage of vaginal deliveries, and COVID19 positivity rate were comparable between the two periods. During P2, the length of stay in the delivery room was significantly shorter than during P1 (17.9 vs 14.7 hours, p<0.001). Conclusion Analysis of the data from this study following the implementation of the ID NOW POCT in the maternity ward indicates a significant decrease in the length of stay in the birth room. This outcome needs to be confirmed in a multicenter cohort, in particular to precise the specific impact of COVID-19 care on delays.","PeriodicalId":72279,"journal":{"name":"Archives of clinical and biomedical research","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-08-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43775745","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2022-07-12DOI: 10.1101/2022.07.10.22277467
C. Troup, D. Mukhopadhyay, T. Chakrabarty, A. Madan, S. Satyanarayana, S. Mehta, S. Dwarakanath
The global outbreak of COVID-19 highlighted the need for rapid and accurate diagnostic testing to control the spread of this highly contagious disease (1-5). Here, we describe the nCoVega COVID-19 antigen rapid test (~ 15min) that can detect the presence of the SARS-COV-2 virus particles from saliva sample on a portable device. The portable reader instrument, the Vega-200, has a small footprint and is designed for use at point of care settings. The test detects the fluorescence signal using wide-field illumination from antigen-antibody complexes captured on a special filter matrix (6). Results of this clinical evaluation of 183 subjects demonstrates that the nCoVega COVID-19 test performs at par with qRT-PCR tests (7) (gold standard) for both symptomatic and asymptomatic patients with a strong inverse correlation between RFU (relative fluorescence units) and Ct counts (from RT-PCR). Based on a recently-filed EUA application with the FDA, the test has an analytical performance of 15.3 TCID50/mL, and 100% specificity for COVID-19 as compared to other human respiratory viruses, including other human coronaviruses. The test has recently been CE-approved. The working principle of this assay and test system can be used for developing other rapid, inexpensive antigen assays and it can offer an end-to-end, point-of-care solution to meet the continuous demand in tackling existing and emerging infectious diseases across the globe.
{"title":"Development of an Accurate and Rapid Antigen Assay for COVID-19 Diagnostics Using Saliva","authors":"C. Troup, D. Mukhopadhyay, T. Chakrabarty, A. Madan, S. Satyanarayana, S. Mehta, S. Dwarakanath","doi":"10.1101/2022.07.10.22277467","DOIUrl":"https://doi.org/10.1101/2022.07.10.22277467","url":null,"abstract":"The global outbreak of COVID-19 highlighted the need for rapid and accurate diagnostic testing to control the spread of this highly contagious disease (1-5). Here, we describe the nCoVega COVID-19 antigen rapid test (~ 15min) that can detect the presence of the SARS-COV-2 virus particles from saliva sample on a portable device. The portable reader instrument, the Vega-200, has a small footprint and is designed for use at point of care settings. The test detects the fluorescence signal using wide-field illumination from antigen-antibody complexes captured on a special filter matrix (6). Results of this clinical evaluation of 183 subjects demonstrates that the nCoVega COVID-19 test performs at par with qRT-PCR tests (7) (gold standard) for both symptomatic and asymptomatic patients with a strong inverse correlation between RFU (relative fluorescence units) and Ct counts (from RT-PCR). Based on a recently-filed EUA application with the FDA, the test has an analytical performance of 15.3 TCID50/mL, and 100% specificity for COVID-19 as compared to other human respiratory viruses, including other human coronaviruses. The test has recently been CE-approved. The working principle of this assay and test system can be used for developing other rapid, inexpensive antigen assays and it can offer an end-to-end, point-of-care solution to meet the continuous demand in tackling existing and emerging infectious diseases across the globe.","PeriodicalId":72279,"journal":{"name":"Archives of clinical and biomedical research","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-07-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48599196","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2022-07-06DOI: 10.1101/2022.07.04.22277205
L. Edenbrandt, E. Tragardh, J. Ulén
Medical imaging, especially computed tomography (CT), is becoming increasingly important in research studies and clinical trials and adequate image quality is essential for reliable results. The aim of this study was to develop an artificial intelligence (AI)-based method for quality assessment of CT studies, both regarding the parts of the body included (i.e. head, chest, abdomen, pelvis), and other image features (i.e. presence of hip prosthesis, intravenous contrast and oral contrast). Approach: 1,000 CT studies from eight different publicly available CT databases were retrospectively in- cluded. The full dataset was randomly divided into a training (n = 500), a validation/tuning (n = 250), and a testing set (n = 250). All studies were manually classified by an imaging specialist. A deep neural network network was then trained to directly classify the 7 different properties of the image. Results: The classification results on the 250 test CT studies showed accuracy for the anatomical regions and presence of hip prosthesis in the interval 98.4% to 100.0%. The accuracy for intravenous contrast was 89.6% and for oral contrast 82.4%. Conclusions: We have shown that it is feasible to develop an AI-based method to automatically perform a quality assessment regarding if correct body parts are included in CT scans, with a very high accuracy.
{"title":"AI-based image quality assessment in CT","authors":"L. Edenbrandt, E. Tragardh, J. Ulén","doi":"10.1101/2022.07.04.22277205","DOIUrl":"https://doi.org/10.1101/2022.07.04.22277205","url":null,"abstract":"Medical imaging, especially computed tomography (CT), is becoming increasingly important in research studies and clinical trials and adequate image quality is essential for reliable results. The aim of this study was to develop an artificial intelligence (AI)-based method for quality assessment of CT studies, both regarding the parts of the body included (i.e. head, chest, abdomen, pelvis), and other image features (i.e. presence of hip prosthesis, intravenous contrast and oral contrast). Approach: 1,000 CT studies from eight different publicly available CT databases were retrospectively in- cluded. The full dataset was randomly divided into a training (n = 500), a validation/tuning (n = 250), and a testing set (n = 250). All studies were manually classified by an imaging specialist. A deep neural network network was then trained to directly classify the 7 different properties of the image. Results: The classification results on the 250 test CT studies showed accuracy for the anatomical regions and presence of hip prosthesis in the interval 98.4% to 100.0%. The accuracy for intravenous contrast was 89.6% and for oral contrast 82.4%. Conclusions: We have shown that it is feasible to develop an AI-based method to automatically perform a quality assessment regarding if correct body parts are included in CT scans, with a very high accuracy.","PeriodicalId":72279,"journal":{"name":"Archives of clinical and biomedical research","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-07-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47499714","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2022-04-16DOI: 10.1101/2022.04.13.22273855
Danelle Wright, Carmen Chan, Wirawit Chaochaisit, Mio Ogawa, J. Tanaka, Satoshi Nozaki, Shinji Narita, Eisuke Shimizu, H. Aoshima, I. Baran
Background: The rapid spread of SARS-CoV-2 worldwide has led to the emergence of new variants due to the presence of mutations that alter viral characteristics, but there have been few studies on trends in viral lineages in Japan, an island country. We hypothesized that changes in cycle threshold (Ct) values on reverse transcription polymerase chain reaction (RT-PCR) reflect the prevalent variants during a given period. Methods: We performed next-generation sequencing of positive samples to identify the viral lineages in Japan in 2021 and compared variant prevalence with the average Ct values on routine RT-PCR using 4 primer sets. Results: Based on 3 sequencing runs, the highly transmissible Alpha variant, which prevailed over other lineages, such as R.1, from April 2021, was dominated by the even stronger Delta variant between July and August 2021 in Japan. The decrease in our routine RT-PCR Ct values with 4 primer sets correlated with these fluctuations in lineage prevalence over time. Conclusions: We confirmed that our RT-PCR protocol reflects the trends in SARS-CoV-2 variant prevalence over time regardless of sequence mutation. This may aid in the tracking of new variants in the population.
{"title":"Rapid displacement of SARS-CoV-2 variants within Japan correlates with cycle threshold values on routine RT-PCR testing","authors":"Danelle Wright, Carmen Chan, Wirawit Chaochaisit, Mio Ogawa, J. Tanaka, Satoshi Nozaki, Shinji Narita, Eisuke Shimizu, H. Aoshima, I. Baran","doi":"10.1101/2022.04.13.22273855","DOIUrl":"https://doi.org/10.1101/2022.04.13.22273855","url":null,"abstract":"Background: The rapid spread of SARS-CoV-2 worldwide has led to the emergence of new variants due to the presence of mutations that alter viral characteristics, but there have been few studies on trends in viral lineages in Japan, an island country. We hypothesized that changes in cycle threshold (Ct) values on reverse transcription polymerase chain reaction (RT-PCR) reflect the prevalent variants during a given period. Methods: We performed next-generation sequencing of positive samples to identify the viral lineages in Japan in 2021 and compared variant prevalence with the average Ct values on routine RT-PCR using 4 primer sets. Results: Based on 3 sequencing runs, the highly transmissible Alpha variant, which prevailed over other lineages, such as R.1, from April 2021, was dominated by the even stronger Delta variant between July and August 2021 in Japan. The decrease in our routine RT-PCR Ct values with 4 primer sets correlated with these fluctuations in lineage prevalence over time. Conclusions: We confirmed that our RT-PCR protocol reflects the trends in SARS-CoV-2 variant prevalence over time regardless of sequence mutation. This may aid in the tracking of new variants in the population.","PeriodicalId":72279,"journal":{"name":"Archives of clinical and biomedical research","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-04-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48034408","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2022-02-23DOI: 10.1101/2022.02.21.22271311
Muhammad Nausherwan Khan, Erum Azhar, Areeba Zain, Meredith Root Bowman, Natasha Tahir Ahmed, Muhammad Arslan Khan, Leigh Caswell, Abdul Waheed
Introduction: Social Determinants of Health (SDOH) play a key role in impacting the health outcomes of any population. Community Health Workers (CHWs) play an important role in health promotion, disease prevention, and management of chronic illnesses. This study aims at exploring the knowledge, attitude, and practices of health care professionals towards CHWs to fully integrate in them for mitigation of SDOH. Materials and Methods: A cross-sectional study utilizing an anonymous survey questionnaire across 4 clinical sites was carried out from June 2016 to November 2017 in a major healthcare system (Presbyterian) in Albuquerque, New Mexico. Descriptive statistics (means, standard deviations, and proportions) were collected. Categorical variables were analyzed using Chi-squared and Fishers exact test; a p-value of <0.05 was considered statistically significant, using SAS 9.4 statistical software. Results: Almost half of the health professionals had no knowledge about the social determinants of health. Almost a quarter of the health professionals did not know the role of CHWs in healthcare, however, 100% of the respondents across all clinic and practice locations and regardless of their role or scope of the practice believed that greater involvement of CHWs would improve patient outcomes. Conclusion: There is a knowledge deficit among health care providers about the social determinants of health (SDOH).More educational and teaching opportunities on SDOH and CHWs to all health professionals should be provided to all health professionals so the clinical team can help manage SDOH in addition to providing clinical care.
{"title":"Knowledge, Attitude, and Practices of Health Professionals Working in A Major Health Care System Regarding Social Determinants of Health (SDOH) and Community Health Workers (CHWs)","authors":"Muhammad Nausherwan Khan, Erum Azhar, Areeba Zain, Meredith Root Bowman, Natasha Tahir Ahmed, Muhammad Arslan Khan, Leigh Caswell, Abdul Waheed","doi":"10.1101/2022.02.21.22271311","DOIUrl":"https://doi.org/10.1101/2022.02.21.22271311","url":null,"abstract":"Introduction: Social Determinants of Health (SDOH) play a key role in impacting the health outcomes of any population. Community Health Workers (CHWs) play an important role in health promotion, disease prevention, and management of chronic illnesses. This study aims at exploring the knowledge, attitude, and practices of health care professionals towards CHWs to fully integrate in them for mitigation of SDOH. Materials and Methods: A cross-sectional study utilizing an anonymous survey questionnaire across 4 clinical sites was carried out from June 2016 to November 2017 in a major healthcare system (Presbyterian) in Albuquerque, New Mexico. Descriptive statistics (means, standard deviations, and proportions) were collected. Categorical variables were analyzed using Chi-squared and Fishers exact test; a p-value of <0.05 was considered statistically significant, using SAS 9.4 statistical software. Results: Almost half of the health professionals had no knowledge about the social determinants of health. Almost a quarter of the health professionals did not know the role of CHWs in healthcare, however, 100% of the respondents across all clinic and practice locations and regardless of their role or scope of the practice believed that greater involvement of CHWs would improve patient outcomes. Conclusion: There is a knowledge deficit among health care providers about the social determinants of health (SDOH).More educational and teaching opportunities on SDOH and CHWs to all health professionals should be provided to all health professionals so the clinical team can help manage SDOH in addition to providing clinical care.","PeriodicalId":72279,"journal":{"name":"Archives of clinical and biomedical research","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-02-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41478539","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2022-02-22DOI: 10.21203/rs.3.rs-1274428/v1
R. Rakotosaona, S. A. Mioramalala, M. Rakotoarisoa, Antsa Rakotondrandriana, Emmanuel Randrianarivo, F. Rabetokotany, F. Rakoto, D. Razafimandimby, A. Ravélo, Fridolin Maminiaina, R. Rapelanoro, Z. Randriamanantany, R. Rakotoarivelo, O. R. Alson, A. Ratsimbasoa
Background There is currently no validated, effective, safe treatment for severe illness caused by SARS-CoV-2. CVO PLUS CURATIF (CVO+C) is a capsule formulation of two compounds of plant origin with anti-inflammatory and antiviral activities in vitro: artemisinin and 1,8-cineole. These compounds have been repurposed for possible use as an oral treatment against COVID-19. Methods We performed a phase 3 randomized clinical trials on patients over the age of 18 years with SARS-CoV-2 infection confirmed by RT-PCR and mild-to-moderate symptoms. Patients were randomly assigned to receive CVO+C (3 capsules per day) or placebo for 15 days. The primary outcome was the proportion of patients testing negative for SARS-CoV-2 by RT-PCR on day 28 and an absence of severe and serious adverse events. Recovery time, and biological parameters on days 7, 14, 21 and 28 of the trial were considered as secondary outcomes. The safety outcomes considered were adverse events on treatment. Results In total, 1,576 individuals underwent RT-PCR screening for SARS-CoV-2 infection during the study period. Positive test results were obtained for 591 subjects, 339 of whom met the inclusion criteria for this study. The final analysis included 339 subjects: 132 from the CVO+C arm and 144 from the placebo arm. Treatment efficacy differed significantly (p=0.011) between the CVO+C arm (87.1%, 95% CI: 81.3%-92.9%, with 70.45% of patients cured by day 14) and the placebo arm (75.0%, 95% CI: 67.8% - 82.1%), with an OR of 2.25. The median time to recovery was 14 days for the CVO+C group and 21 days for the placebo group. A total of 72 incidences of mild and moderate adverse events, 14 severe adverse events and no serious adverse events were observed in both groups. ConclusionCVO+C was effective for the treatment of mild-to-moderate COVID-19. None of the patients in the CVO+C arm displayed progression to the severe form of COVID-19. Liver kidney and metabolic functions were preserved in all patients.Trial registration: Registered at Pan African Clinical Trials Registry: (No. PACTR202103601407640, date of approval: 24/03/2021) and approved by the ethics committee of the Ministry of Public Health of Madagascar (approval No. 216 MINSANP/SG/AGMED/CERBM, 17/12/2020)
{"title":"Efficacy and safety of CVO PLUS CURATIF capsules, Malagasy improved traditional medication for treating COVID-19 a randomized, double-blind, placebo-controlled trial","authors":"R. Rakotosaona, S. A. Mioramalala, M. Rakotoarisoa, Antsa Rakotondrandriana, Emmanuel Randrianarivo, F. Rabetokotany, F. Rakoto, D. Razafimandimby, A. Ravélo, Fridolin Maminiaina, R. Rapelanoro, Z. Randriamanantany, R. Rakotoarivelo, O. R. Alson, A. Ratsimbasoa","doi":"10.21203/rs.3.rs-1274428/v1","DOIUrl":"https://doi.org/10.21203/rs.3.rs-1274428/v1","url":null,"abstract":"\u0000 Background There is currently no validated, effective, safe treatment for severe illness caused by SARS-CoV-2. CVO PLUS CURATIF (CVO+C) is a capsule formulation of two compounds of plant origin with anti-inflammatory and antiviral activities in vitro: artemisinin and 1,8-cineole. These compounds have been repurposed for possible use as an oral treatment against COVID-19. Methods We performed a phase 3 randomized clinical trials on patients over the age of 18 years with SARS-CoV-2 infection confirmed by RT-PCR and mild-to-moderate symptoms. Patients were randomly assigned to receive CVO+C (3 capsules per day) or placebo for 15 days. The primary outcome was the proportion of patients testing negative for SARS-CoV-2 by RT-PCR on day 28 and an absence of severe and serious adverse events. Recovery time, and biological parameters on days 7, 14, 21 and 28 of the trial were considered as secondary outcomes. The safety outcomes considered were adverse events on treatment. Results In total, 1,576 individuals underwent RT-PCR screening for SARS-CoV-2 infection during the study period. Positive test results were obtained for 591 subjects, 339 of whom met the inclusion criteria for this study. The final analysis included 339 subjects: 132 from the CVO+C arm and 144 from the placebo arm. Treatment efficacy differed significantly (p=0.011) between the CVO+C arm (87.1%, 95% CI: 81.3%-92.9%, with 70.45% of patients cured by day 14) and the placebo arm (75.0%, 95% CI: 67.8% - 82.1%), with an OR of 2.25. The median time to recovery was 14 days for the CVO+C group and 21 days for the placebo group. A total of 72 incidences of mild and moderate adverse events, 14 severe adverse events and no serious adverse events were observed in both groups. ConclusionCVO+C was effective for the treatment of mild-to-moderate COVID-19. None of the patients in the CVO+C arm displayed progression to the severe form of COVID-19. Liver kidney and metabolic functions were preserved in all patients.Trial registration: Registered at Pan African Clinical Trials Registry: (No. PACTR202103601407640, date of approval: 24/03/2021) and approved by the ethics committee of the Ministry of Public Health of Madagascar (approval No. 216 MINSANP/SG/AGMED/CERBM, 17/12/2020)","PeriodicalId":72279,"journal":{"name":"Archives of clinical and biomedical research","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-02-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48394515","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
N. Hajela, Mercedes Dobson-Brazier, Jenna Sawdon Bea
Background: Each year 1.1 million people report having a burn injury, with 45,000 people requiring hospitalization. Patients suffering from a burn, experience one of the most excruciating types of pain, that is most commonly unsuccessfully treated though analgesics. Physical therapy increases a patient’s pain thus decreasing a patient’s compliance with treatment and willingness to move. Virtual reality has been proven to decrease burn pain, but there is limited information on the effects it has on range of motion and treatment enjoyment. The purpose of this study is to determine the effectiveness of VR as a treatment tool to increase ROM and enjoyment as part of cognitive distraction while decreasing reported pain when compared to standard physical therapy in patients with acute burns. Methods: The search between Science Direct, Cinahl and PubMed yielded a total of 242 articles in total which were reviewed based on relevance of titles and abstracts. Prior to reviewing abstracts there were 77s. Prior to reviewing abstracts there were 77 Arch Clin Biomed Res 2022; 6 (1): 94-118 DOI: 10.26502/acbr.50170229 Archives of Clinical and Biomedical Research Vol. 6 No. 1 – February 2022. [ISSN 2572-9292]. 95 duplicates removed, leaving 165 non-duplicate articles. There were 131 articles removed after reading the abstract and finding the articles did not fit within the meta-analysis leaving 34 articles left to review for inclusion/exclusion criteria. After reviewing the articles, 8 studies eligible for this metaanalysis based on the inclusion and exclusion criteria were analyzed though Microsoft Excel. The studies were used for the following three outcome measures: range of motion, pain and enjoyment. Results: Range of motion presented with homogenous results with a grand effect size of 0.19. Pain was found to have homogeneity with grand effect size of -0.45. Enjoyment was the only outcome measure that presented with heterogeneity and a grand effect size of 1.30. Virtual reality was proven to be an effective way to decrease pain and improving enjoyment. Range of motion had a trend to favoring virtual reality; therefore, virtual reality is a feasible treatment tool for patient’s suffering from an acute burn injury. Future research is needed to determine the effects of each joint on range of motion, and the correlation between enjoyment and movement. Conclusion: Based on these findings, physical therapists can use VR as a treatment tool to help their patients recover faster with less pain compared to traditional physical therapy. One of the most common complications of a burn injury is contracture formation. This is typically due to decreased movement from the patient during the healing stage, but VR can help improve movement as mentioned above. Having a decrease in pain and an increase in enjoyment can lead to a decrease in anxiety to physical therapy and movement in general thereby leading to better patient outcomes and improve their quality of life.
{"title":"Effectiveness of Virtual Reality Vs Standard Physical Therapy on Range of Motion, Pain and Enjoyment in Patients with Acute Burns: A Meta-Analysis and Evidence Based Review","authors":"N. Hajela, Mercedes Dobson-Brazier, Jenna Sawdon Bea","doi":"10.26502/acbr.50170229","DOIUrl":"https://doi.org/10.26502/acbr.50170229","url":null,"abstract":"Background: Each year 1.1 million people report having a burn injury, with 45,000 people requiring hospitalization. Patients suffering from a burn, experience one of the most excruciating types of pain, that is most commonly unsuccessfully treated though analgesics. Physical therapy increases a patient’s pain thus decreasing a patient’s compliance with treatment and willingness to move. Virtual reality has been proven to decrease burn pain, but there is limited information on the effects it has on range of motion and treatment enjoyment. The purpose of this study is to determine the effectiveness of VR as a treatment tool to increase ROM and enjoyment as part of cognitive distraction while decreasing reported pain when compared to standard physical therapy in patients with acute burns. Methods: The search between Science Direct, Cinahl and PubMed yielded a total of 242 articles in total which were reviewed based on relevance of titles and abstracts. Prior to reviewing abstracts there were 77s. Prior to reviewing abstracts there were 77 Arch Clin Biomed Res 2022; 6 (1): 94-118 DOI: 10.26502/acbr.50170229 Archives of Clinical and Biomedical Research Vol. 6 No. 1 – February 2022. [ISSN 2572-9292]. 95 duplicates removed, leaving 165 non-duplicate articles. There were 131 articles removed after reading the abstract and finding the articles did not fit within the meta-analysis leaving 34 articles left to review for inclusion/exclusion criteria. After reviewing the articles, 8 studies eligible for this metaanalysis based on the inclusion and exclusion criteria were analyzed though Microsoft Excel. The studies were used for the following three outcome measures: range of motion, pain and enjoyment. Results: Range of motion presented with homogenous results with a grand effect size of 0.19. Pain was found to have homogeneity with grand effect size of -0.45. Enjoyment was the only outcome measure that presented with heterogeneity and a grand effect size of 1.30. Virtual reality was proven to be an effective way to decrease pain and improving enjoyment. Range of motion had a trend to favoring virtual reality; therefore, virtual reality is a feasible treatment tool for patient’s suffering from an acute burn injury. Future research is needed to determine the effects of each joint on range of motion, and the correlation between enjoyment and movement. Conclusion: Based on these findings, physical therapists can use VR as a treatment tool to help their patients recover faster with less pain compared to traditional physical therapy. One of the most common complications of a burn injury is contracture formation. This is typically due to decreased movement from the patient during the healing stage, but VR can help improve movement as mentioned above. Having a decrease in pain and an increase in enjoyment can lead to a decrease in anxiety to physical therapy and movement in general thereby leading to better patient outcomes and improve their quality of life.","PeriodicalId":72279,"journal":{"name":"Archives of clinical and biomedical research","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"69340103","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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