scholarly journals DW-UNet: Loss Balance under Local-Patch for 3D Infection Segmentation from COVID-19 CT Images

Diagnostics ◽  
2021 ◽  
Vol 11 (11) ◽  
pp. 1942
Author(s):  
Cheng Chen ◽  
Jiancang Zhou ◽  
Kangneng Zhou ◽  
Zhiliang Wang ◽  
Ruoxiu Xiao

(1) Background: COVID-19 has been global epidemic. This work aims to extract 3D infection from COVID-19 CT images; (2) Methods: Firstly, COVID-19 CT images are processed with lung region extraction and data enhancement. In this strategy, gradient changes of voxels in different directions respond to geometric characteristics. Due to the complexity of tubular tissues in lung region, they are clustered to the lung parenchyma center based on their filtered possibility. Thus, infection is improved after data enhancement. Then, deep weighted UNet is established to refining 3D infection texture, and weighted loss function is introduced. It changes cost calculation of different samples, causing target samples to dominate convergence direction. Finally, the trained network effectively extracts 3D infection from CT images by adjusting driving strategy of different samples. (3) Results: Using Accuracy, Precision, Recall and Coincidence rate, 20 subjects from a private dataset and eight subjects from Kaggle Competition COVID-19 CT dataset tested this method in hold-out validation framework. This work achieved good performance both in the private dataset (99.94–00.02%, 60.42–11.25%, 70.79–09.35% and 63.15–08.35%) and public dataset (99.73–00.12%, 77.02–06.06%, 41.23–08.61% and 52.50–08.18%). We also applied some extra indicators to test data augmentation and different models. The statistical tests have verified the significant difference of different models. (4) Conclusions: This study provides a COVID-19 infection segmentation technology, which provides an important prerequisite for the quantitative analysis of COVID-19 CT images.

2016 ◽  
Vol 5 (11) ◽  
pp. 5041
Author(s):  
Farkhondeh Jamshidi ◽  
Ahmad Ghorbani ◽  
Sina Darvishi*

The abuse of some pesticides especially to suicide is one of the current problems of pesticides. Aluminum phosphide induced poisoning usually happens to suicide and sometimes it is due to accidental occupational exposure and in a few cases it has some criminal intensions. This study is conducted to evaluate patients poisoned with aluminum phosphide. In the present study the medical records of cases of poisoning with rice tablets (aluminum phosphide) hospitalized in Ahvaz Razi hospital is studied. Accordingly, a checklist is prepared that included demographic information of patients (age, gender) and information on patient records (information on poisoning) are completed using the patients’ medical records. The analysis of data is done by SPSS V22. 18 patients poisoned with rice tablet (aluminum phosphide) are studied. Results of the study show that 11 patients are male and seven are female. The mean patient age is 27.06 ±8.04 years that is 28 ±9 and 25 ±6.02 in men and women respectively. Statistical tests show no statistically significant difference in mean age in both genders (P> 0.05). Among patients, 11 subjects took aluminum phosphide to attempt suicide and 3 cases took it unintentionally and of course the reason is not mentioned in four cases. Among the patients who tried to commit suicide by taking aluminum phosphide, 6 cases are male and 5 cases are female that no statistically significant difference is observed between the genders in this respect (P> 0.05). In addition to the study of the complications caused by this poisoning and its mortality, it is recommended to responsible authorities to provide the necessary educations and treatments to prevent this type of poisoning.


2019 ◽  
Vol 2019 ◽  
pp. 1-9 ◽  
Author(s):  
Michał Klimont ◽  
Mateusz Flieger ◽  
Jacek Rzeszutek ◽  
Joanna Stachera ◽  
Aleksandra Zakrzewska ◽  
...  

Hydrocephalus is a common neurological condition that can have traumatic ramifications and can be lethal without treatment. Nowadays, during therapy radiologists have to spend a vast amount of time assessing the volume of cerebrospinal fluid (CSF) by manual segmentation on Computed Tomography (CT) images. Further, some of the segmentations are prone to radiologist bias and high intraobserver variability. To improve this, researchers are exploring methods to automate the process, which would enable faster and more unbiased results. In this study, we propose the application of U-Net convolutional neural network in order to automatically segment CT brain scans for location of CSF. U-Net is a neural network that has proven to be successful for various interdisciplinary segmentation tasks. We optimised training using state of the art methods, including “1cycle” learning rate policy, transfer learning, generalized dice loss function, mixed float precision, self-attention, and data augmentation. Even though the study was performed using a limited amount of data (80 CT images), our experiment has shown near human-level performance. We managed to achieve a 0.917 mean dice score with 0.0352 standard deviation on cross validation across the training data and a 0.9506 mean dice score on a separate test set. To our knowledge, these results are better than any known method for CSF segmentation in hydrocephalic patients, and thus, it is promising for potential practical applications.


2021 ◽  
Vol 80 (Suppl 1) ◽  
pp. 1360.1-1360
Author(s):  
M. Jordhani ◽  
D. Ruci ◽  
F. Skana ◽  
E. Memlika

Background:The COVID-19 global pandemic has had a great impact on world population due to morbidity, mortality and restriction measures in order to stop the progression of COVID-19.Patients with rheumatic and musculoskeletic diseases, and especially rheumatoid arthritis (RA) patients, being one of the vulnerable classes of chronic patients, were recommended to follow the government’s rules1.Objectives:The aim of this study was to evaluate DAS-28-ESR in patients with rheumatoid arthritis before and after lockdown period.Methods:This is a multi-center observational study including 85 patients which were evaluated before and after lockdown for their disease activity score according to DAS-28-ESR score. They had been diagnosed with rheumatoid arthritis more than 5 years ago. A thorough physical examination was performed before and after the lockdown period. It included examination of tender and swollen joints and patient’s global health. They were completed with all required laboratory data, including erythrosedimentation rate. For a more accurate calculation, DAS-28-ESR was used in an electronic version. Patients with other inflammatory or infective diseases were excluded from the study. All data were statistically evaluated using statistical tests such as t-student test.Results:The first group (the one before lockdown) had an average DAS-28-ESR of 4.7 while after the lockdown period, the average DAS-28-ESR was 5.16.After statistically evaluating all data, it was found that there exists a significant difference between DAS-28-ESR score before and after COVID-19 lockdown (p=0.0011).Conclusion:Our study showed that lockdown period due to COVID-19 pandemic, has aggravated disease activity in patients with Rheumatoid Arthritis. This may be consequence of various causes such as physical inactivity and difficulty to follow-up or to take the medication properly.References:[1]Landewé RB, Machado PM, Kroon F, et al, EULAR provisional recommendations for the management of rheumatic and musculoskeletal diseases in the context of SARS-CoV-2, Annals of the Rheumatic Diseases 2020;79:851-858.Disclosure of Interests:None declared.


2021 ◽  
Vol 9 ◽  
pp. 205031212110202
Author(s):  
Rgda Mohamed Osman ◽  
Mounkaila Noma ◽  
Abdallah Elssir Ahmed ◽  
Hanadi Abdelbagi ◽  
Rihab Ali Omer ◽  
...  

Objectives: Rheumatoid arthritis is a chronic inflammatory autoimmune disease. This study aimed to determine the association of interleukin-17A-197G/A polymorphism with rheumatoid arthritis in Sudanese patients. Methods: A case–control study was conducted between March and December 2018. Clinical and demographic data of the study participants were collected and analyzed. Polymerase chain reaction restriction fragment length polymorphism molecular technique was done to investigate interleukin-17A-197G/A polymorphisms. All statistical tests were considered statistically significant when p < 0.05. Results: The study population included 266 participants aged between 1 and 85 years, with an average of 40 years, classified into 85 (31.2%) cases (mean age 48.5 ± 11.3 years), and 181 (68.8%) controls (mean age 35.3 ± 15.9 years). The interleukin-17A homozygote AA genotype was more frequent among the control group compared to the case group; 95 (52.5%) and 7 (8.2%), respectively. The homozygote GG and the heterozygote AG genotypes were proportionally not different among the cases and control groups; 13 (54.2%) and 11 (45.8%), and 65 (46.4%) and 75 (53.6%), respectively. According to the distribution of interleukin-17A genotypes, a statistically significant difference was observed among cases with the interleukin-17A AA and AG genotypes, p values 0.001 and 0.004, respectively. For the association interleukin-17A genotypes and family history a negatively significant association was reported (95% confidence interval, –0.219, p value = 0.001). There was also a negatively significant association of interleukin-17A genotypes and anti-cyclic citrullinated peptide (95% confidence interval, −0.141, p value = 0.002). Conclusion: This study is the first study in Sudan established the association between interleukin-17A-197G/A (rs2275913) polymorphisms and susceptibly to rheumatoid arthritis. These findings appeal for further research in Sudan to investigate the exact role of IL-17A in immunopathology and disease severity among Sudanese rheumatoid arthritis


2020 ◽  
Vol 79 (Suppl 1) ◽  
pp. 497.2-497
Author(s):  
J. Arroyo Palomo ◽  
M. Arce Benavente ◽  
C. Pijoan Moratalla ◽  
B. A. Blanco Cáceres ◽  
A. Rodriguez

Background:Musculoeskeletal ultrasound (MSUS) is frequently used in several rheumatology units to detect subclinical inflammation in patients with joint symptoms suspected for progression to inflammatory arthritis (IA). Synovitis grade I (EULAR-OMERACT combined score) is known to be a casual finding in healthy individuals, but studies headed to unravel its possible role on rheumatic diseases are sparse.Objectives:To investigate the correlation between synovitis grade I, and the diagnosis of IA made after a year follow-up period since MSUS findings, in patients of an MSUS-specialized unit of a Rheumatology Department.Methods:We conducted a descriptive, retrospective and unicentric study. 30 patients were selected from the MSUS-specialized unit of our Rheumatology Department from July-18 to January-19. Patients presenting synovitis grade 0 (exclusively), 2 and/or 3 on combined score were excluded. Data collection at baseline included age, sex, immunological profile and previous physical examination to the MSUS findings, as well as the diagnosis made by the rheumatologist in 1-year visit follow-up: dividing the patient sample into two groups: those who were diagnosed with IA and those not. Non-parametric statistical tests for comparing means were used.Results:The mean age was 51,6 years and 70% were females. 6 (20%) patients were diagnosed with inflammatory arthritis after a year follow-up: 2 (4,8%) psoriatic arthritis, 1 (3,3%) undifferentiated arthritis, 1 (3,3%) rheumatoid arthritis, 1 (3,3%) Sjögren’s syndrome. Non-inflammatory arthropathies were also found 24 (80%), of which, 12 (40%) were non-specific arthralgias and 8 (19%) osteoarthritis.In the group of patients who did not developed an IA the mean C-reactive protein (CPR) value was 3,12 mg/L and erythrocyte sedimentation rate (ESR) was 8,2 mm; all of them were rheumatoid factor (RF) positive and ACPA-negative except one patient. 5 (31,3%) patients presented low antinuclear antibodies (ANAs) levels. In those who HLA B-27 and Cw6 were tested (4,25%); both were negative except for one that was HLA B-27 positive. The median number of swollen and painful joint count was 0, and the mean of joints with MSUS involvement was 3,5; the mean involved metacarpophalangeal (MCP) joints was 1,83; proximal interphalangeal (PIP) joints was 1,48 and distal interphalangeal (DIP) joints 0,21.Among the group of patients that developed an IA the mean of CPR and ESR was 9,27 mg/L and 14,17 mm respectively; 2 (33%) patients were RF- positive, and 1 ACPA-positive. ANAs were positive in 3 cases (50%). The median of swollen joint count was 2 and for painful joint count was 0, the median of joints with MSUS involvement was 4,5. The mean of MSUS involvement was for MCP, PIP and DIP joints: 1,67, 2 and 0. Comparing the means of CPR values in the two groups with Student’s t-test we obtained a statistically significant difference (p=0,023). No other significant differences were found.Conclusion:Despite the limitations and possible statistical bias, the presence of MSUS-defined synovitis grade I and elevated CRP levels could be related to further diagnoses of inflammatory arthropathy. Besides, the absence of synovitis in DIP joints might have a diagnostic role. Normal physical exploration and normal levels of CRP might suggest low MSUS value. However, further research is needed to clarify the role of MSUS-defined synovitis grade I.References:[1]D’Agostino MA et al. Scoring ultrasound synovitis in rheumatoid arthritis: a EULAR-OMERACT ultrasound taskforce-Part 1: definition and development of a standardized, consensus-based scoring system. RMD Open. 2017;3(1):e000428.[2]Van den Berg R et al. What is the value of musculoskeletal ultrasound in patients presenting with arthralgia to predict inflammatory arthritis development? A systematic literature review. Arthritis Research & Therapy (2018) 20:228.Disclosure of Interests:None declared


2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Dongdong Gu ◽  
Liyun Chen ◽  
Fei Shan ◽  
Liming Xia ◽  
Jun Liu ◽  
...  

Abstract Background Spatial and temporal lung infection distributions of coronavirus disease 2019 (COVID-19) and their changes could reveal important patterns to better understand the disease and its time course. This paper presents a pipeline to analyze statistically these patterns by automatically segmenting the infection regions and registering them onto a common template. Methods A VB-Net is designed to automatically segment infection regions in CT images. After training and validating the model, we segmented all the CT images in the study. The segmentation results are then warped onto a pre-defined template CT image using deformable registration based on lung fields. Then, the spatial distributions of infection regions and those during the course of the disease are calculated at the voxel level. Visualization and quantitative comparison can be performed between different groups. We compared the distribution maps between COVID-19 and community acquired pneumonia (CAP), between severe and critical COVID-19, and across the time course of the disease. Results For the performance of infection segmentation, comparing the segmentation results with manually annotated ground-truth, the average Dice is 91.6% ± 10.0%, which is close to the inter-rater difference between two radiologists (the Dice is 96.1% ± 3.5%). The distribution map of infection regions shows that high probability regions are in the peripheral subpleural (up to 35.1% in probability). COVID-19 GGO lesions are more widely spread than consolidations, and the latter are located more peripherally. Onset images of severe COVID-19 (inpatients) show similar lesion distributions but with smaller areas of significant difference in the right lower lobe compared to critical COVID-19 (intensive care unit patients). About the disease course, critical COVID-19 patients showed four subsequent patterns (progression, absorption, enlargement, and further absorption) in our collected dataset, with remarkable concurrent HU patterns for GGO and consolidations. Conclusions By segmenting the infection regions with a VB-Net and registering all the CT images and the segmentation results onto a template, spatial distribution patterns of infections can be computed automatically. The algorithm provides an effective tool to visualize and quantify the spatial patterns of lung infection diseases and their changes during the disease course. Our results demonstrate different patterns between COVID-19 and CAP, between severe and critical COVID-19, as well as four subsequent disease course patterns of the severe COVID-19 patients studied, with remarkable concurrent HU patterns for GGO and consolidations.


2021 ◽  
Author(s):  
Jonathan P Scoville ◽  
Evan Joyce ◽  
Joshua Hunsaker ◽  
Jared Reese ◽  
Herschel Wilde ◽  
...  

Abstract BACKGROUND Minimally invasive surgery (MIS) has been shown to decrease length of hospital stay and opioid use. OBJECTIVE To identify whether surgery for epilepsy mapping via MIS stereotactically placed electroencephalography (SEEG) electrodes decreased overall opioid use when compared with craniotomy for EEG grid placement (ECoG). METHODS Patients who underwent surgery for epilepsy mapping, either SEEG or ECoG, were identified through retrospective chart review from 2015 through 2018. The hospital stay was separated into specific time periods to distinguish opioid use immediately postoperatively, throughout the rest of the stay and at discharge. The total amount of opioids consumed during each period was calculated by transforming all types of opioids into their morphine equivalents (ME). Pain scores were also collected using a modification of the Clinically Aligned Pain Assessment (CAPA) scale. The 2 surgical groups were compared using appropriate statistical tests. RESULTS The study identified 43 patients who met the inclusion criteria: 36 underwent SEEG placement and 17 underwent craniotomy grid placement. There was a statistically significant difference in median opioid consumption per hospital stay between the ECoG and the SEEG placement groups, 307.8 vs 71.5 ME, respectively (P = .0011). There was also a significant difference in CAPA scales between the 2 groups (P = .0117). CONCLUSION Opioid use is significantly lower in patients who undergo MIS epilepsy mapping via SEEG compared with those who undergo the more invasive ECoG procedure. As part of efforts to decrease the overall opioid burden, these results should be considered by patients and surgeons when deciding on surgical methods.


2021 ◽  
Vol 11 (1) ◽  
Author(s):  
S. Mojdeh Mirmomen ◽  
Andrew E. Arai ◽  
Evrim B. Turkbey ◽  
Andrew J. Bradley ◽  
Julie C. Sapp ◽  
...  

AbstractIn this work, we sought to delineate the prevalence of cardiothoracic imaging findings of Proteus syndrome in a large cohort at our institution. Of 53 individuals with a confirmed diagnosis of Proteus syndrome at our institution from 10/2001 to 10/2019, 38 individuals (men, n = 23; average age = 24 years) underwent cardiothoracic imaging (routine chest CT, CT pulmonary angiography and/or cardiac MRI). All studies were retrospectively and independently reviewed by two fellowship-trained cardiothoracic readers. Disagreements were resolved by consensus. Differences between variables were analyzed via parametric and nonparametric tests based on the normality of the distribution. The cardiothoracic findings of Proteus syndrome were diverse, but several were much more common and included: scoliosis from bony overgrowth (94%), pulmonary venous dilation (62%), band-like areas of lung scarring (56%), and hyperlucent lung parenchyma (50%). In addition, of 20 individuals who underwent cardiac MRI, 9/20 (45%) had intramyocardial fat, mostly involving the endocardial surface of the left ventricular septal wall. There was no statistically significant difference among the functional cardiac parameters between individuals with and without intramyocardial fat. Only one individual with intramyocardial fat had mildly decreased function (LVEF = 53%), while all others had normal ejection fraction.


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