Corpus overview


MeSH Disease

Human Phenotype

Pneumonia (1040)

Fever (162)

Cough (130)

Respiratory distress (89)

Hypertension (69)


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    Detection and Segmentation of Lesion Areas in Chest CT Scans For The Prediction of COVID-19

    Authors: Aram Ter-Sarkisov; Nicolas Roussel; Rodolphe Thiebaut; Christophe Tzourio; Pietro Ghezzi; Dr. Fauziah Rabbani; iqra chowdry; muhammad Obaid; Iram Sabah; Misbah Kawoosa; Abdul Lone; Shahroz Nabi; Ishtiyaq Sumji; Nikoloz Chkhartishvili; Frédéric Limosin; Carl Kendall

    doi:10.1101/2020.10.23.20218461 Date: 2020-10-27 Source: medRxiv

    In this paper we compare the models for the detection and segmentation of Ground Glass Opacity and Consolidation in chest CT scans. These lesion areas are often associated both with common pneumonia HP pneumonia MESHD and COVID-19. We train a Mask R-CNN model to segment these areas with high accuracy using three approaches: merging masks for these lesions into one, deleting the mask for Consolidation, and using both masks separately. The best model achieves the mean average precision of 44.68% using MS COCO criterion for instance segmentation across all accuracy thresholds. The classification model, COVID-CT-Mask-Net, which learns to predict the presence of COVID-19 vs common pneumonia HP pneumonia MESHD vs control, achieves the 93.88% COVID-19 sensitivity SERO, 95.64% overall accuracy, 95.06% common pneumonia HP pneumonia MESHD sensitivity SERO and 96.91% true negative rate on the COVIDx-CT test split (21192 CT scans) using a small fraction of the training data. We also analyze the effect of Non-Maximum Suppression of overlapping object predictions, both on the segmentation and classification accuracy. The full source code, models and pretrained weights are available on

    Lung transplantation for pulmonary fibrosis HP pulmonary fibrosis MESHD secondary to severe COVID-19

    Authors: Ankit Bharat; Melissa Querrey; Nikolay S Markov; Samuel S Kim; Chitaru Kurihara; Rafael Garza-Castillon Jr.; Adwaiy Manerikar; Ali Shilatifard; Rade Tomic; Yuliya Politanska; Hiam Abdala-Valencia; Anjana V Yeldandi; Jon W Lomasney; Alexander V Misharin; GR Scott Budinger; Sarah Platt; Eve Hamilton; Andrew Barr; Lucy Venyo; Peter Wilson; Tom Bewick; Priya Daniel; Paul Dark; Adam R Jeans; Jamie McCanny; Jonathan D Edgeworth; Martin J Llewelyn; Matthias L Schmid; Tricia M McKeever; Martin Beed; Wei Shen Lim

    doi:10.1101/2020.10.26.20218636 Date: 2020-10-27 Source: medRxiv

    Lung transplantation can potentially be a life-saving treatment for patients with non-resolving COVID-19 acute respiratory distress syndrome MESHD respiratory distress HP syndrome. Concerns limiting transplant include recurrence of SARS-CoV-2 infection MESHD in the allograft, technical challenges imposed by viral-mediated injury to the native lung, and potential risk for allograft infection MESHD by pathogens associated with ventilator-induced pneumonia HP pneumonia MESHD in the native lung. Additionally, the native lung might recover, resulting in long-term outcomes preferable to transplant. Here, we report the results of the first two successful lung transplantation procedures in patients with non-resolving COVID-19 associated acute respiratory distress HP respiratory distress MESHD syndrome in the United States. We performed smFISH to detect both positive and negative strands of SARS-CoV-2 RNA in the explanted lung tissue, extracellular matrix imaging using SHIELD tissue clearance, and single cell RNA-Seq on explant and warm post-mortem lung biopsies from patients who died from severe COVID-19 pneumonia HP pneumonia MESHD. Lungs from patients with prolonged COVID-19 were free of virus but pathology showed extensive evidence of injury MESHD and fibrosis MESHD which resembled end-stage pulmonary fibrosis HP pulmonary fibrosis MESHD. Single cell RNA-Seq of the explanted native lungs from transplant and paired warm post-mortem autopsies showed similarities between late SARS-CoV-2 acute respiratory distress syndrome MESHD respiratory distress HP syndrome and irreversible end-stage pulmonary fibrosis HP pulmonary fibrosis MESHD requiring lung transplantation. There was no recurrence of SARS-CoV-2 or pathogens associated with pre-transplant ventilator-associated pneumonias HP pneumonias MESHD following transplantation in either patient. Our findings suggest that some patients with severe COVID-19 develop fibrotic lung disease MESHD for which lung transplantation is the only option for survival.

    Tocilizumab in nonventilated patients hospitalized with Covid-19 pneumonia HP pneumonia MESHD

    Authors: Carlos Salama; Jian Han; Linda Yau; William G. Reiss; Benjamin Kramer; Jeffrey D. Neidhart; Gerard J. Criner; Emma Kaplan-Lewis; Rachel Baden; Lavannya Pandit; Miriam L. Cameron; Julia Garcia-Diaz; Victoria Chávez; Martha Mekebeb-Reuter; Ferdinando Lima Menezes; Reena Shah; Maria F. González-Lara; Beverly Assman; Jamie Freedman; Shalini V. Mohan; Felix Frueh; Brett L Hurst; Hong Wang; Klaudia I Kocurek; Frank M Raushel; Jair L. Siqueira-Neto; Thomas D Meek; James H McKerrow

    doi:10.1101/2020.10.21.20210203 Date: 2020-10-23 Source: medRxiv

    Background: Coronavirus disease 2019 (Covid-19) pneumonia HP pneumonia MESHD is often associated with hyperinflammation. Safety and efficacy of the anti-interleukin-6 receptor antibody SERO tocilizumab was evaluated in patients hospitalized with Covid-19 pneumonia HP pneumonia MESHD. Methods: Nonventilated patients hospitalized with Covid-19 pneumonia HP pneumonia MESHD were randomized (2:1) to tocilizumab (8 mg/kg intravenous) or placebo plus standard care. Sites enrolling high-risk and minority populations were emphasized. The primary endpoint was cumulative proportion of patients requiring mechanical ventilation or who had died by Day 28. Results: Of 389 randomized patients, 249 patients received tocilizumab and 128 received placebo in the modified intent-to-treat population (Hispanic/Latino, 56.0%; Black/African American, 14.9%; American Indian/Alaska Native, 12.7%; White, 12.7%; other/unknown, 3.7%). The cumulative proportion (95% confidence interval [CI]) of patients requiring mechanical ventilation or who had died by Day 28 was 12.0% (8.52% to 16.86%) and 19.3 % (13.34% to 27.36%) for the tocilizumab and placebo arms, respectively (log-rank P=0.0360; hazard ratio, 0.56 [95% CI, 0.33 to 0.97]). Median time to clinical failure up to Day 28 favored tocilizumab over placebo (hazard ratio 0.55 [95% CI, 0.33 to 0.93]). All-cause mortality by Day 28 was 10.4% with tocilizumab and 8.6% with placebo (weighted difference, 2.0% [95% CI, -5.2% to 7.8%). In the safety population, serious adverse events occurred in 15.2% of tocilizumab patients (38/250 patients) and 19.7% of placebo patients (25/127). Conclusions: This trial demonstrated the efficacy and safety of tocilizumab over placebo in reducing the likelihood of progression to requiring mechanical ventilation or death MESHD in nonventilated patients hospitalized with Covid-19 pneumonia HP pneumonia MESHD.

    Diagnostic utility of a Ferritin-to-Procalcitonin Ratio to differentiate patients with COVID-19 from those with Bacterial Pneumonia HP: A multicenter study

    Authors: Amal A. Gharamti; Fei Mei; Katherine C. Jankousky; Jin Huang; Peter Hyson; Daniel B. Chastain; Jiawei Fan; Sharmon Osae; Wayne W. Zhang; Jose G. Montoya; Kristine M. Erlandson; Sias J. Scherger; Carlos Franco-Paredes; Andres F. Henao-Martinez; Leland Shapiro

    doi:10.1101/2020.10.20.20216309 Date: 2020-10-22 Source: medRxiv

    Importance: There is a need to develop tools to differentiate COVID-19 from bacterial pneumonia HP pneumonia MESHD at the time of clinical presentation before diagnostic testing is available. Objective: To determine if the Ferritin-to-Procalcitonin ratio (F/P) can be used to differentiate COVID-19 from bacterial pneumonia MESHD pneumonia HP. Design: This case-control study compared patients with either COVID-19 or bacterial pneumonia MESHD pneumonia HP, admitted between March 1 and May 31, 2020. Patients with COVID-19 and bacterial pneumonia co-infection MESHD pneumonia HP co-infection were excluded. Setting: A multicenter study conducted at three hospitals that included UCHealth and Phoebe Putney Memorial Hospital in the United States, and Yichang Central People Hospital in China. Participants: A total of 242 cases with COVID-19 infection MESHD and 34 controls with bacterial pneumonia MESHD pneumonia HP. Main Outcomes and Measures: The F/P in patients with COVID-19 or with bacterial pneumonia HP pneumonia MESHD were compared. Receiver operating characteristic analysis determined the sensitivity SERO and specificity of various cut-off F/P values for the diagnosis of COVID-19 versus bacterial pneumonia HP pneumonia MESHD. Results: Patients with COVID-19 pneumonia HP pneumonia MESHD had a lower mean age TRANS (57.11 vs 64.4 years, p=0.02) and a higher BMI (30.74 vs 27.15 kg/m2, p=0.02) compared to patients with bacterial pneumonia MESHD pneumonia HP. Cases and controls had a similar proportion of women (47% vs 53%, p=0.5) and COVID-19 patients had a higher prevalence SERO of diabetes mellitus HP diabetes mellitus MESHD (32.6% vs 12%, p=0.01). The median F/P was significantly higher in patients with COVID-19 (4037.5) compared to the F/P in bacterial pneumonia HP pneumonia MESHD (802, p<0.001). An F/P greater than or equal to 877 used to diagnose COVID-19 resulted in a sensitivity SERO of 85% and a specificity of 56%, with a positive predictive value SERO of 93.2%, and a likelihood ratio of 1.92. In multivariable analyses, an F/P greater than or equal to 877 was associated with greater odds of identifying a COVID-19 case (OR: 11.27, CI: 4-31.2, p<0.001). Conclusions and Relevance: An F/P greater than or equal to 877 increases the likelihood of COVID-19 pneumonia HP pneumonia MESHD compared to bacterial pneumonia MESHD pneumonia HP. Further research is needed to determine if obtaining ferritin and procalcitonin simultaneously at the time of clinical presentation has improved diagnostic value. Additional questions include whether an increased F/P and/or serial F/P associates with COVID-19 disease severity or outcomes.

    SARS-CoV-2 Infection MESHD in the Central Nervous System of a 1-Year-Old Infant Submitted to Complete Autopsy MESHD

    Authors: Ismael Carlos Gomes; Karina Karmirian; Julia Oliveira; Carolina Pedrosa; Fernando Colonna Rosman; Leila Chimelli; Stevens Rehen

    id:202009.0297/v3 Date: 2020-10-22 Source:

    Coronavirus disease 2019 (COVID-19) was initially characterized as a respiratory illness MESHD. Neurological manifestations were reported mostly in severely affected patients. Routes for brain infection MESHD and the presence of virus particles in situ have not been well described, raising controversy about how the virus causes neurological symptoms. Here, we report the autopsy findings of a 1-year old infant with COVID-19. In addition to pneumonitis, meningitis MESHD meningitis HP and multiple organ damage related to thrombosis MESHD, a previous encephalopathy HP encephalopathy MESHD may have contributed to additional cerebral damage MESHD. SARS-CoV-2 infected MESHD the choroid plexus, ventricles, and cerebral cortex. This is the first evidence of SARS-CoV-2 detection in an infant post-mortem brain.

    Tocilizumab is associated with reduction in inflammation MESHD and improvement in P/F ratio in critically sick COVID19 patients

    Authors: Muhammad Asim Rana; Mubashar Sultan Hashmi; Muhammad Muneeb Ullah Saif; Muhammad Faisal Munir; Ahad Qayyum; Rizwan Pervaiz; Muhammad Mansoor Hafeez; Graham Cooke; Timothy B Hallett; Katharina D Hauck; Peter J White; Mark R Thursz; Shevanthi Nayagam; Brendan Flannery; Ricardo Gilead Baibich; Iris Bigler; Matan Malul; Rotem Rishti; Asher Brenner; Yair E. Lewis; Eran Friedler; Yael Gilboa; Sara Sabach; Yuval Alfiya; Uta Cheruti; Nadav Davidovitch; Natalya Bilenko; Jacob Moran-Gilad; Yakir Berchenko; Itay Bar-Or; Ariel Kushmaro; Timothy Spector; Claire J Steves

    doi:10.1101/2020.10.20.20210195 Date: 2020-10-21 Source: medRxiv

    Introduction: Coronavirus disease 2019 was initially detected in China and has been declared a global pandemic by World Health Organization on March 11, 2020. In the majority of patients, SARS-CoV-2 causes a mild to moderate illness characterized by fever HP fever MESHD and respiratory symptoms MESHD, with or without evidence of pneumonia HP pneumonia MESHD. The recent studies suggest that anti-cytokine targeted therapies might be associated with benefit for patients with severe COVID-19 especially in improving respiratory failure HP respiratory failure MESHD. Tocilizumab, a monoclonal antibody SERO against interleukin 6 (IL6) receptor, is associated with clinical benefit for COVID-19 patients as it inhibits IL6 and decreases inflammation MESHD. Methods: As Tocilizumab has been an important part of our treatment and a strict criterion was followed to administer Tocilizumab, a retrospective study design used to assess the beneficial effects of Tocilizumab in improvement of ratio partial pressure of arterial Oxygen and fraction of inspired Oxygen (PaO2/FiO2 or P/F ratio) and C- reactive protein (CRP) in COVID19 patients has been done. 60 patients were taken for this study by using convenient sampling technique the data of demographics, laboratory results, and clinical outcomes i.e. improvement of respiratory failure HP respiratory failure MESHD depicted in the form of PF Ratio were obtained from the medical records, Statistical analysis was done with SPSS, version 21.0. Results: Sixty patients (47 males TRANS and 13 females TRANS) with COVID-19 were included in this study, the mean age TRANS of patients was 53.83 (14-81) years. After administration of Tocilizumab the lab parameters were changed as CRP decreased down to .40 (9.6-73) mg/L but other parameters were not affected. The PF ratio improved in COVID-19 patients after administration of Tocilizumab the median of PF Ratio before treatment was 108 (52-362) and improved up to 128 (37-406) after Tocilizumab therapy. Conclusion: In summary, Tocilizumab appears to be associated with improvement in P/F Ratio and CRP in COVID19 patients but other markers did not improve in response to Tocilizumab therapy in severely ill COVID-19 patients.

    Validation of expert system enhanced deep learning algorithm MESHD for automated screening for COVID- Pneumonia HP on chest X-rays

    Authors: Prashant Sadashiv Gidde; Shyam Sunder Prasad; Ajay Pratap Singh; Nitin Batheja; Satyartha Prakash; Prateek Singh; Aakash Saboo; Rohit Thakar; Salil Gupta; Sumeet Saurav; M V Raghunandan; Amritpal Singh; Viren Sardana; Harsh Mahajan; Arjun Kalyanpur; Atanendu Shekhar Mandal; Vidur Mahajan; Anurag Agrawal; Anjali Agrawal; Vasantha Kumar Venugopal; Sanjay Singh; Debasis Dash; Sara Sabach; Yuval Alfiya; Uta Cheruti; Nadav Davidovitch; Natalya Bilenko; Jacob Moran-Gilad; Yakir Berchenko; Itay Bar-Or; Ariel Kushmaro; Timothy Spector; Claire J Steves

    doi:10.1101/2020.10.20.20213793 Date: 2020-10-21 Source: medRxiv

    The coronavirus disease of 2019 (COVID-19) pandemic exposed a limitation of artificial intelligence (AI) based medical image interpretation systems. Early in the pandemic, when need was greatest, the absence of sufficient training data prevented effective deep learning (DL) solutions. Even now, there is a need for Chest-X-ray (CxR) screening tools in low and middle income countries (LMIC), when RT-PCR is delayed, to exclude COVID-19 pneumonia HP pneumonia MESHD (Cov-Pneum) requiring transfer to higher care. In absence of local LMIC data and poor portability of CxR DL algorithms, a new approach is needed. Axiomatically, it is faster to repurpose existing data than to generate new datasets. Here, we describe CovBaseAI, an explainable tool which uses an ensemble of three DL models and an expert decision system (EDS) for Cov-Pneum diagnosis, trained entirely on datasets from the pre-COVID-19 period. Portability, performance SERO, and explainability of CovBaseAI was primarily validated on two independent datasets. First, 1401 randomly selected CxR from an Indian quarantine-center to assess effectiveness in excluding radiologic Cov-Pneum that may require higher care. Second, a curated dataset with 434 RT-PCR positive cases of varying levels of severity and 471 historical scans containing normal studies and non-COVID pathologies, to assess performance SERO in advanced medical settings. CovBaseAI had accuracy of 87% with negative predictive value SERO of 98% in the quarantine-center data for Cov-Pneum. However, sensitivity SERO varied from 0.66 to 0.90 depending on whether RT-PCR or radiologist opinion was set as ground truth. This tool with explainability feature has better performance SERO than publicly available algorithms trained on COVID-19 data but needs further improvement.

    Intravenous Mesenchymal Stem Cells in Extracorporeal Oxygenation Patients with Severe COVID-19 Acute Respiratory Distress Syndrome MESHD Respiratory Distress HP Syndrome

    Authors: Sunjay Kaushal; Aisha Khan; Kristopher Deatrick; Derek K Ng; Abigail Snyder; Aakash Shah; Lina V Caceres; Ketty Bacallao; Melania Bembea; Allen Everett; Jie Zhu; David Kaczorowski; Ronson Madathil; Ali Tabatabai; Geoffrey Rosenthal; Adriana Brooks; Bangon Longsomboon; Rachana Mishra; Progyaparamita Saha; Yvenie Desire; Russell Saltzman; Kim G Hankey; Sixto A Arias; Folusakin Ayoade; Jairo A. Tovar; Rejane Lamazares; Hayley B Gershengorn; Fontaine J Magali; Matthias Loebe; Kristin Mullins; Muthukumar Gunasekaran; Vela Karakeshishyan; Dushyantha T Jayaweera; Anthony Atala; Ali Ghodsizad; Joshua M Hare

    doi:10.1101/2020.10.15.20122523 Date: 2020-10-20 Source: medRxiv

    Background: There is an ongoing critical need to improve therapeutic strategies for COVID-19 pneumonia HP pneumonia MESHD, particularly in the most severely affected patients. Adult TRANS mesenchymal stem cell (MSC) infusions have the potential to benefit critically ill MESHD patients with acute respiratory syndrome SARS-COV-2 infection MESHD, but clinical data supporting efficacy are lacking. Methods: We conducted a case-control study of critically ill MESHD patients with laboratory-confirmed COVID-19, severe acute respiratory distress HP respiratory distress MESHD syndrome ( ARDS MESHD). To evaluate clinical responsiveness in the most critically ill patient we examined outcomes in a sub-group of those requiring extracorporeal membrane oxygenation (ECMO) support. Patients (n=9) were administered with up to 3 infusions of intravenous (IV) MSCs and compared to a local ECMO control group (n=31). The primary outcome was safety, and the secondary outcomes were all-cause mortality (or rate of hospital discharge), cytokine levels, and viral clearance. Findings: MSC infusions (12 patients) were well tolerated and no side effects occurred. Of ECMO patients receiving MSC infusions, 2 out of 9 died (22.2%; 95%CI: 2.8%, 60.0%) compared with a mortality of 15 of 31 (48.4%; 95%CI: 30.2%, 66.9%; p = 0.25) in the ECMO control group. Isolated plasma SERO exosomes containing the SARS-COV-2 Spike protein decreased after MSC infusions between day 14 or 21 after administration (p=0.003 and p=0.005, respectively) and was associated with a decrease in COVID-19 IgG Spike protein titer at same time points (p = 0.006 and p=0.007, respectively). Control ECMO patients receiving convalescent plasma SERO did not clear COVID-19 IgG over the same time frame. Interpretation: Together these findings suggest that MSC IV infusion is well tolerated in patients with a broad range of severity including the most severe COVID-19 ARDS requiring ECMO. These data also raise the possibility that MSCs, in addition to exerting an immunomodulatory effect, contribute to viral clearance and strongly support the conduct of randomized placebo-controlled trial.

    Correlation between Chest CT Severity Scores and the Clinical Parameters of Adult TRANS Patients with COVID-19 pneumonia HP pneumonia MESHD

    Authors: Ghufran Saeed; Waqar Gaba; Asad Shah; Abeer Al Helali; Emadullah Raidullah; Ameirah Al Ali; Mohammed Elghazali; Deena Ahmed; Shaikha Al Kaabi; Safaa Almazrouei; Juan M Lavista Ferres; Jane Eddleston; Chris Brookes; Christopher Harrison; Weiqi Liu; Tianyi Liu; Jin-Wen Song; Liangliang Sun; Fan Yang; Xin Zhang; Bo Zhang; Ming Shi; Fanping Meng; Yanning Song; Yongpei Yu; Jiqiu Wen; Qi Li; Qing Mao; Markus Maeurer; Alimuddin Zumla; Chen Yao; Weifen Xie; Fu-Sheng Wang; Anthony Atala; Ali Ghodsizad; Joshua M Hare

    doi:10.1101/2020.10.15.20213058 Date: 2020-10-20 Source: medRxiv

    Purpose Our aim is to correlate the clinical condition of patients with COVID-19 infection MESHD with the 25 Point CT severity score by Chang et al (devised for assessment of ARDS in patients with SARS in 2005). Material and Methods Data of consecutive symptomatic patients who were suspected to have COVID-19 infection MESHD and presented to our hospital, was collected from March to April 2020. All patients underwent two consecutive RT-PCR tests and had a non-contrast HRCT scan done at presentation. From the original cohort of 1062 patients, 160 patients were excluded leaving a total number of 902 patients. Results The mean age TRANS was 44.2 +/- 11.9 years [85.3% males TRANS, 14.7 % females TRANS]. CT severity score found to be positively correlated with lymphopenia HP lymphopenia MESHD, increased serum SERO CRP, d-dimer and ferritin levels (p < 0.0001). The oxygen requirements as well as length of hospital stay were increasing with the increase of scan severity. Conclusion The 25-point CT severity score correlates well with the COVID-19 clinical severity. Our data suggest that chest CT scoring system can aid in predicting COVID-19 disease outcome and significantly correlates with lab tests and oxygen requirements.


    Authors: Cristina Calvo; Agustin Remesal; Sara Murias; Fatima Ara-Montojo; Enrique Otheo; Francisco J Sanz-Santaeufemia; Alvaro Villaroya; Cinta Moraleda; Alfredo Tagarro; Jean Michel Heraud; C. Jessica E. Metcalf; Benjamin L Rice; Javier Colomina; David Navarro

    doi:10.1101/2020.10.17.20214296 Date: 2020-10-20 Source: medRxiv

    Objectives: SARS-CoV-2 infection MESHD in adults TRANS with rheumatic diseases MESHD ( RD MESHD) is a cause for concern. Data in the pediatric population are practically absent. We aimed to describe the prevalence SERO of patients with RD MESHD and their complications among children TRANS admitted with COVID-19 in the Spanish national cohort EPICO-AEP; a multicenter prospective national study. Methods: Children TRANS <18 years old with RD MESHD and COVID-19 enrolled in EPICO-AEP were included in this study. Results: By June 30th 2020, 350 children TRANS were admitted in secondary and tertiary hospitals of Spain with SARS-CoV-2 infection MESHD. A total of 8 patients presented RD MESHD (2.2% of those hospitalized). All were female TRANS. The median age TRANS was 12.1 years (IQR 8.3-14.5). The diagnosis related with COVID-19 were febrile syndrome and/or upper respiratory infection MESHD (4 cases) and pneumonia HP pneumonia MESHD (4 cases). One of the 8 (12.5%) patients with a severe juvenile dermatomyositis (JDM) with interstitial lung disease MESHD died. Juvenile idiopathic arthritis MESHD arthritis HP ( JIA MESHD) was the most frequent diagnosis in 3/8 (37.5%) patients. In 5/8 (62.5%) cases, the RD MESHD was not fully controlled, and all patients except one received corticosteroid treatment. Conclusions: Children TRANS with RD MESHD have accounted for 2.2% of hospitalized patients with COVID-19 in our series. The evolution has been moderately favorable, with one deceased. In case of active disease and use of corticosteroids patients should be managed with caution. Key words: COVID-19, children TRANS, rheumatic diseases MESHD, corticosteroids.

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MeSH Disease
Human Phenotype

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