An XAI approach for COVID-19 detection using transfer learning with X-ray images.

The coronavirus disease (COVID-19) has continued to cause severe challenges during this unprecedented time, affecting every part of daily life in terms of health, economics, and social development. There is an increasing demand for chest X-ray (CXR) scans, as pneumonia is the primary and vital complication of COVID-19. CXR is widely used as a screening tool for lung-related diseases due to its simple and relatively inexpensive application. However, these scans require expert radiologists to interpret the results for clinical decisions, i.e., diagnosis, treatment, and prognosis. The digitalization of various sectors, including healthcare, has accelerated during the pandemic, with the use and importance of Artificial Intelligence (AI) dramatically increasing. This paper proposes a model using an Explainable Artificial Intelligence (XAI) technique to detect and interpret COVID-19 positive CXR images. We further analyze the impact of COVID-19 positive CXR images using heatmaps. The proposed model leverages transfer learning and data augmentation techniques for faster and more adequate model training. Lung segmentation is applied to enhance the model performance further. We conducted a pre-trained network comparison with the highest classification performance (F1-Score: 98%) using the ResNet model.

COVID-19: vaccination vs. hospitalization.

OBJECTIVE: Vaccination is the most efficient way to control the coronavirus disease 2019 (COVID-19) pandemic, but vaccination rates remain below the target level in most countries. This multicenter study aimed to evaluate the vaccination status of hospitalized patients and compare two different booster vaccine protocols. SETTING: Inoculation in Turkey began in mid-January 2021. Sinovac was the only available vaccine until April 2021, when BioNTech was added. At the beginning of July 2021, the government offered a third booster dose to healthcare workers and people aged > 50 years who had received the two doses of Sinovac. Of the participants who received a booster, most chose BioNTech as the third dose. METHODS: We collected data from 25 hospitals in 16 cities. Patients hospitalized between August 1 and 10, 2021, were included and categorized into eight groups according to their vaccination status. RESULTS: We identified 1401 patients, of which 529 (37.7%) were admitted to intensive care units. Nearly half (47.8%) of the patients were not vaccinated, and those with two doses of Sinovac formed the second largest group (32.9%). Hospitalizations were lower in the group which received 2 doses of Sinovac and a booster dose of BioNTech than in the group which received 3 doses of Sinovac. CONCLUSION: Effective vaccinations decreased COVID-19-related hospitalizations. The efficacy after two doses of Sinovac may decrease over time; however, it may be enhanced by adding a booster dose. Moreover, unvaccinated patients may be persuaded to undergo vaccination.

COVID-19 Pandemic and the Global Perspective of Turkish Thoracic Society.

It has been more than 3 months now since the first case of COVID-19 was reported in Turkey. Globally, the number of confirmed cases and deaths reached 9,653,048 and 491,128 respectively, as reported by 216 countries by June 27, 2020. Turkey had 1,396 new cases, 194,511 total cases, and 5,065 deaths by the same date. From the first case until today, the Turkish Thoracic Society (TTS) has been very proactive in educating doctors, increasing public awareness, undertaking academic studies, and assisting with public health policies. In the present report, social, academic, and management perspectives of the pandemic are presented under appropriate subtitles. During this critical public health crisis, TTS has once again demonstrated its readiness and constructive stance by supporting public health, healthcare workers, and the environment. This review summarizes the perspective of TTS on each aspect of the COVID-19 pandemic and casts light on its contributions.

The role of mediastinoscopy in the diagnosis of non-lung cancer diseases.

BACKGROUND: Mediastinoscopy is a good method to evaluate mediastinal lesions. We sought to determine the current role of mediastinoscopy in the investigation of non-lung cancer patients with mediastinal lymphadenopathy. MATERIALS AND METHODS: We retrospectively reviewed clinical parameters (age, gender, histological diagnosis, morbidity, mortality) of all patients without lung cancer who consecutively underwent mediastinoscopy in Hospital of Faculty of Medicine of Dicle University between June 2003 and December 2016. RESULTS: Two-hundred twenty nine patients without lung cancer who underwent mediastinoscopy for the pathological evaluation of mediastinum during the study period were included. There were 156 female (68%) and 73 male (32%) patients. Mean age was 52.6 years (range, 16 to 85 years). Mean operative time was 41 minutes (range, 25 to 90 minutes). Mean number of biopsies was 9.3 (range, 5 to 24). Totally, 45 patients (19.6%) had previously undergone a nondiagnostic bronchoscopic biopsy such as transbronchial needle aspiration or endobronchial ultrasound-guided transbronchial needle aspiration. Mediastinoscopy was diagnostic for all patients. Diagnosis included sarcoidosis (n=100), tuberculous lymphadenitis (n=66), anthracosis lymphadenitis (n=44), lymphoma (n=11) metastatic carcinoma (n=5), and Castleman's disease (n=1); there was a diagnosis of silicosis in one patient and tymoma in one patient. Neither operative mortality nor major complication developed. The only minor complication was wound infection which was detected in three patients. CONCLUSION: Although newer diagnostic modalities are being increasingly used to diagnose mediastinal diseases, mediastinoscopy continues to be a reliable method for the investigation of mediastinal lesions.

Urgent thoracotomy for penetrating chest trauma: analysis of 158 patients of a single center.

BACKGROUND: Penetrating injuries to the chest present a frequent and challenging problem, but the majority of these injuries can be managed non-\operatively. The aim of this study was to describe the incidence of penetrating chest trauma and the ultimate techniques used for operative management, as well as the diagnosis, complications, morbidity and mortality. METHODS: A retrospective 9-year review of patients who underwent an operative procedure following penetrating chest trauma was performed. The mechanism of injury, gender, age, physiological and outcome parameters, including injury severity score (ISS), chest abbreviated injury scale (AIS) score, lung injury scale score, concomitant injuries, time from admission to operating room, transfusion requirement, indications for thoracotomy, intra-operative findings, operative procedures, length of hospital stay (LOS) and rate of mortality were recorded. RESULTS: A total of 1123 patients who were admitted with penetrating thoracic trauma were investigated. Of these, 158 patients (93 stabbings, 65 gunshots) underwent a thoracotomy within 24 h after the penetrating trauma. There were 146 (92.4%) male and 12 (7.6%) female patients, and their mean age was 25.72 9.33 (range, 15­54) years. The mean LOS was 10.65 8.30 (range, 5­65) days. Patients admitted after a gunshot had a significantly longer LOS than those admitted with a stab wound (gunshot, 13.53 9.92 days; stab wound, 8.76 6.42 days, p < 0.001). Patients who died had a significantly lower systolic blood pressure (SBP) on presentation in the emergency room (42.94 36.702 mm Hg) compared with those who survived (83.96 27.842 mm Hg, p = 0.001). The overall mortality rate was 10.8% (n = 17). Mortality for patients with stab wounds was 8/93 (8.6%) compared with 9/65 (13.8%) for patients with gunshot wounds (p = 0.29). Concomitant abdominal injuries (p = 0.01), diaphragmatic injury (p = 0.01), ISS (p = 0.001), chest AIS score (p < 0.05), ongoing output (p = 0.001), blood transfusion volume (p < 0.01) and SBP (p = 0.001) were associated with mortality. CONCLUSION: Penetrating injuries to the chest requiring a thoracotomy are uncommon, and lung-sparing techniques have become the most frequently used procedures for lung injuries. The presence of associated abdominal injuries increased the mortality five-fold. Factors that affected mortality were ISS, chest AIS score, SBP, ongoing chest output, blood transfusion volume, diaphragmatic injury and associated abdominal injury.

Quality of life, depression and anxiety in young male patients with silicosis due to denim sandblasting.

The aim of this study was to estimate the quality of life, depression and anxiety in patients with silicosis due to denim sandblasting. This study was conducted on 50 young male patients with silicosis and 30 controls. A socio-demographic data form, Short Form-36 (SF-36), the Beck depression inventory (BDI) and the Beck anxiety inventory (BAI) were used to determine quality of life, depression and anxiety. The mean scores of SF-36, BDI and BAI were higher in the patients than in the controls. Correlation analysis revealed a strong negative correlation between all scales of SF-36 and BDI scores. Additionally, there was strong negative correlation between five scales of SF-36 and BAI scores. We suggest that silicosis might be detrimental to the quality of life and increase depression and anxiety in patients with silicosis due to denim sandblasting.

Adapted T cell interferon-gamma release assay for the diagnosis of pleural tuberculosis.

BACKGROUND: Better and more rapid tests are needed for the diagnosis of tuberculous pleural effusion (TPE), given the known limitations of conventional diagnostic tests. OBJECTIVES: To estimate diagnostic accuracy of the QuantiFERON-TB Gold In-Tube (QFT-GIT) test (and its components) using data-derived cutoffs in pleural fluid. METHODS: The QFT-GIT test was performed on whole blood and pleural fluid from 43 patients with TPE and 29 control subjects (non-TPE). To achieve the objective, QFT-GIT test, estimating likelihood ratios and receiver operating curve analysis were performed. RESULTS: The sensitivity and specificity using the QFT-GIT for the diagnosis of TPE were 48.8% and 79.3%, respectively, in pleural fluid. The best cutoff points for tuberculosis (TB) antigen, nil and TB antigen minus nil results were estimated at 0.70, 0.90 and 0.30 IU/ml, respectively. Area under the curve of TB antigen IFN-γ response was 0.86 (CI: 0.76-0.93), nil tube was 0.80 (CI: 0.69-0.89) and TB antigen minus nil tube was 0.82 (CI: 0.72-0.90). When the best cutoff scores of the nil tubes were set at this value, the results of a likelihood ratio of a positive and a negative test were 9.44 (7.4-12.0) and 0.37 (0.09-1.5), respectively. The percentages of indeterminate results in pleural fluid among the TPE cases were 42% (most of them caused by high nil IFN-γ values) using the QFT-GIT test. CONCLUSION: QFT-GIT test or its components have poor accuracy in the diagnosis of TPE, largely because of a high number of indeterminate results due to high background IFN-γ production in the TPE.

MDCT findings of denim-sandblasting-induced silicosis: a cross-sectional study.

BACKGROUND: Denim sandblasting is as a novel cause of silicosis in Turkey, with reports of a recent increase in cases and fatal outcomes. We aimed to describe the radiological features of patients exposed to silica during denim sandblasting and define factors related to the development of silicosis. METHODS: Sixty consecutive men with a history of exposure to silica during denim sandblasting were recruited. All CT examinations were performed using a 64-row multi-detector CT (MDCT). The nodules were qualitatively and semi-quantitatively analyzed by grading nodular profusion (NP) on CT images. RESULTS: Silicosis was diagnosed radiologically in 73.3% of patients (44 of 60). The latency period (the time between initial exposure and radiological imaging) and duration of silica exposure was longer in patients diagnosed with silicosis than in those without silicosis (p < 0.05). Nodules were present in all cases with centrilobular type as the commonest (63.6%). All cases of silicosis were clinically classified as accelerated and 11.4% had progressive massive fibrosis (PMF). Mild NP lesions were the most prevalent in all six zones of the lung. The NP score was significantly correlated with the duration of silica exposure, the latency period, presence of PMF, and pleural thickening. Enlarged lymphadenopathy was present in 45.5% of patients. CONCLUSIONS: The duration of exposure and the latency period are important for development of silicosis in denim sandblasters. MDCT is a useful tool in detecting findings of silicosis in workers who has silica exposure.

Incidence of tuberculosis disease and latent tuberculosis infection in patients with end stage renal disease in an endemic region.

AIM: Patients in chronic renal failure suffer impaired cellular immunity and have an increased risk of tuberculosis (TB). Our aim in this multicenter study was to determine the incidence of TB and to evaluate latent tuberculosis infection (LTBI) in hemodialysis patients. METHODS: We retrospectively evaluated the frequency of TB in 779 dialysis patients at 13 hemodialysis centers in five different cities in Southeast Turkey. The tuberculin skin test (TST) was conducted in 733 patients to detect LTBI. RESULTS: The mean age of the patients was 51.2 +/- 15.9 years; 398 (51.1%) of the patients were female, and 53.9% of patients had a BCG scar. The mean dialysis duration time was 35.1 +/- 33.4 months. TB was diagnosed in 34 cases. The incidence rate of TB in patients undergoing hemodialysis was 3.1%. Ten patients had a history of TB before beginning hemodialysis, and 24 patients had a history of TB after beginning hemodialysis. A diagnosis of TB was made based on clinical data in eight patients and microbiologically or pathologically in 26 patients. The median time between the initiation of dialysis to the diagnosis of TB was 11 months. Extrapulmonary TB occurred in 45.8% of cases, and the most common site of involvement was the lymph nodes. The TST was positive in 61.8% of TB patients and in 37.5% of those with no history of TB. CONCLUSIONS: The incidence of TB is high in hemodialysis patients, and they should be evaluated periodically to exclude insidious infection and reduce morbidity and mortality.

Environmental asbestos-related pleural plaque in southeast of Turkey.

It is known that many malignant and benign pleural diseases occur due to environmental exposure to mineral fibers. Calcified pleural plaque (CPP) is an important sign of asbestos exposure on chest radiographic examination. To study the possible change in the prevalence of CPP and diffuse pleural thickening 3 decades after cessation of asbestos exposure. CPP were detected in 29.9% of the villagers; 4.7% had diffuse pleural thickening and 0.7% had asbestosis. The significant variable for CPP and diffuse pleural thickening was age. The youngest villager with CPP was 33 years of age and the prevalence of CPP increased with an increase in age. The reason for our cases with CPP being of advanced age is the discontinuation of asbestos exposure. This finding enables us to suggest that environmental asbestos-related disease will gradually decrease in future decades.

Effects of atorvastatin on smoking-induced alveolar injury in rat lungs.

BACKGROUND: Smoking is one of the most serious health care issues worldwide, as one third to one half of all people who smoke eventually use tobacco habitually. Chronic smoke exposure causes airway and lung parenchymal inflammation and the destruction of alveolar cell walls. Statins may have anti-inflammatory effects that would play a role in preventing the cellular damage associated with smoking. OBJECTIVE: The aim of this study was to investigate whether atorvastatin protects against smoking-induced inflammation in alveolar epithelial type I (ATI) and type II (ATII) cells in the lungs of rats. METHODS: Adult male albino Wistar rats (200-250 g) were randomly divided into 3 groups and exposed to cigarette smoke 8 hours per day for 15 days. During that 15-day period, the 2 treatment groups received atorvastatin 0.5 or 1.0 mg/kg/d in 2 mL of methyl cellulose solution and the control group received 2 mL of methyl cellulose solution alone, all via nasogastric catheter. After the 15 days, the lungs were excised and the tissues were examined by transmission electron microscopy. RESULTS: Thirty rats were divided into 3 groups of 10 rats each. All rats survived the 15 days. In the atorvastatin 0.5-mg group, no changes were found in the ATI cells or in the blood-air barrier. In the atorvastatin 1.0-mg group, we observed hyperplasia in the common basal membranes. Hypertrophy, mitochondrial crystolysis (MC), and intracytoplasmic edema (ICE) were detected in the ATI cells in the 1.0-mg group, while chromatin condensation, atrophic appearance, cell shrinkage, and cyto-plasmic vacuolization were observed in the ATII cells. The rough endoplasmic reticulum (rER) tubules of the ATII cells appeared spiral-shaped. In the control group, minimal ICE was detected in the ATI cells. However, microvillus deformation, pseu-dopod formation, edema, mitochondrial swelling, and MC were observed in the ATII cells. We also observed MC, several pinocytic vesicles, and normal rER tubules in the endothelial cells of the control group. CONCLUSIONS: The administration of atorvastatin 0.5 mg/kg/d was associated with some attenuation of lung injury caused by smoke inhalation in these rat lungs. However, atorvastatin 1.0 mg/kg/d was associated with lung damage. Future studies are needed to evaluate the dose-response relationship of atorvastatin to smoking-induced alveolar damage.