49 research outputs found
Convolutional Sparse Support Estimator Based Covid-19 Recognition from X-ray Images
Coronavirus disease (Covid-19) has been the main agenda of the whole world
since it came in sight in December 2019. It has already caused thousands of
causalities and infected several millions worldwide. Any technological tool
that can be provided to healthcare practitioners to save time, effort, and
possibly lives has crucial importance. The main tools practitioners currently
use to diagnose Covid-19 are Reverse Transcription-Polymerase Chain reaction
(RT-PCR) and Computed Tomography (CT), which require significant time,
resources and acknowledged experts. X-ray imaging is a common and easily
accessible tool that has great potential for Covid-19 diagnosis. In this study,
we propose a novel approach for Covid-19 recognition from chest X-ray images.
Despite the importance of the problem, recent studies in this domain produced
not so satisfactory results due to the limited datasets available for training.
Recall that Deep Learning techniques can generally provide state-of-the-art
performance in many classification tasks when trained properly over large
datasets, such data scarcity can be a crucial obstacle when using them for
Covid-19 detection. Alternative approaches such as representation-based
classification (collaborative or sparse representation) might provide
satisfactory performance with limited size datasets, but they generally fall
short in performance or speed compared to Machine Learning methods. To address
this deficiency, Convolution Support Estimation Network (CSEN) has recently
been proposed as a bridge between model-based and Deep Learning approaches by
providing a non-iterative real-time mapping from query sample to ideally sparse
representation coefficient' support, which is critical information for class
decision in representation based techniques.Comment: 10 page
COVID-19 Infection Map Generation and Detection from Chest X-Ray Images
Computer-aided diagnosis has become a necessity for accurate and immediate
coronavirus disease 2019 (COVID-19) detection to aid treatment and prevent the
spread of the virus. Numerous studies have proposed to use Deep Learning
techniques for COVID-19 diagnosis. However, they have used very limited chest
X-ray (CXR) image repositories for evaluation with a small number, a few
hundreds, of COVID-19 samples. Moreover, these methods can neither localize nor
grade the severity of COVID-19 infection. For this purpose, recent studies
proposed to explore the activation maps of deep networks. However, they remain
inaccurate for localizing the actual infestation making them unreliable for
clinical use. This study proposes a novel method for the joint localization,
severity grading, and detection of COVID-19 from CXR images by generating the
so-called infection maps. To accomplish this, we have compiled the largest
dataset with 119,316 CXR images including 2951 COVID-19 samples, where the
annotation of the ground-truth segmentation masks is performed on CXRs by a
novel collaborative human-machine approach. Furthermore, we publicly release
the first CXR dataset with the ground-truth segmentation masks of the COVID-19
infected regions. A detailed set of experiments show that state-of-the-art
segmentation networks can learn to localize COVID-19 infection with an F1-score
of 83.20%, which is significantly superior to the activation maps created by
the previous methods. Finally, the proposed approach achieved a COVID-19
detection performance with 94.96% sensitivity and 99.88% specificity
Advance Warning Methodologies for COVID-19 using Chest X-Ray Images
Coronavirus disease 2019 (COVID-19) has rapidly become a global health
concern after its first known detection in December 2019. As a result, accurate
and reliable advance warning system for the early diagnosis of COVID-19 has now
become a priority. The detection of COVID-19 in early stages is not a
straightforward task from chest X-ray images according to expert medical
doctors because the traces of the infection are visible only when the disease
has progressed to a moderate or severe stage. In this study, our first aim is
to evaluate the ability of recent \textit{state-of-the-art} Machine Learning
techniques for the early detection of COVID-19 from chest X-ray images. Both
compact classifiers and deep learning approaches are considered in this study.
Furthermore, we propose a recent compact classifier, Convolutional Support
Estimator Network (CSEN) approach for this purpose since it is well-suited for
a scarce-data classification task. Finally, this study introduces a new
benchmark dataset called Early-QaTa-COV19, which consists of 1065 early-stage
COVID-19 pneumonia samples (very limited or no infection signs) labelled by the
medical doctors and 12 544 samples for control (normal) class. A detailed set
of experiments shows that the CSEN achieves the top (over 97%) sensitivity with
over 95.5% specificity. Moreover, DenseNet-121 network produces the leading
performance among other deep networks with 95% sensitivity and 99.74%
specificity.Comment: 12 page
YKL-40 tissue expression and plasma levels in patients with ovarian cancer
<p>Abstract</p> <p>Background</p> <p>YKL-40 (chitinase-3-like-1) is a member of "mammalian chitinase-like proteins". The protein is expressed in many types of cancer cells and the highest plasma YKL-40 levels have been found in patients with metastatic disease, short recurrence/progression-free intervals, and short overall survival. The aim of the study was to determine the expression of YKL-40 in tumor tissue and plasma in patients with borderline ovarian tumor or epithelial ovarian cancer (OC), and investigate prognostic value of this marker.</p> <p>Methods</p> <p>YKL-40 protein expression was determined by immunohistochemistry in tissue arrays from 181 borderline tumors and 473 OC. Plasma YKL-40 was determined by ELISA in preoperative samples from 19 patients with borderline tumor and 76 OC patients.</p> <p>Results</p> <p>YKL-40 protein expression was found in cancer cells, tumor associated macrophages, neutrophils and mast cells. The tumor cell expression was higher in OC than in borderline tumors (p = 0.001), and associated with FIGO stage (p < 0.0001) and histological subtype (p = 0.0009). Positive YKL-40 expression (≥ 5% staining) was not associated with reduced survival. Plasma YKL-40 was also higher in patients with OC than in patients with borderline tumors (p < 0.0001), and it was positively correlated to serum CA-125 (p < 0.0001) and FIGO stage (p = 0.0001). Univariate Cox analysis of plasma YKL-40 showed association with overall survival (p < 0.0001). Multivariate Cox analysis, including plasma YKL-40, serum CA125, FIGO stage, age and radicality after primary surgery as variables, showed that elevated plasma YKL-40 was associated with a shorter survival (HR = 2.13, 95% CI: 1.40–3.25, p = 0.0004).</p> <p>Conclusion</p> <p>YKL-40 in OC tissue and plasma are related to stage and histology, but only plasma YKL-40 is a prognostic biomarker in patients with OC.</p
Fungal infection-related mortality versus total mortality as an outcome in trials of antifungal agents
BACKGROUND: Disease specific mortality is often used as outcome rather than total mortality in clinical trials. This approach assumes that the classification of cause of death is unbiased. We explored whether use of fungal infection-related mortality as outcome rather than total mortality leads to bias in trials of antifungal agents in cancer patients. METHODS: As an estimate of bias we used relative risk of death in those patients the authors considered had not died from fungal infection. Our sample consisted of 69 trials included in four systematic reviews of prophylactic or empirical antifungal treatment in patients with cancer and neutropenia we have published previously. RESULTS: Thirty trials met the inclusion criteria. The trials comprised 6130 patients and 869 deaths, 220 (25%) of which were ascribed to fungal infection. The relative risk of death was 0.85 (95% CI 0.75–0.96) for total mortality, 0.57 (95% CI 0.44–0.74) for fungal mortality, and 0.95 (95% CI 0.82–1.09) for mortality among those who did not die from fungal infection. CONCLUSION: We could not support the hypothesis that use of disease specific mortality introduces bias in antifungal trials on cancer patients as our estimate of the relative risk for mortality in those who survived the fungal infection was not increased. We conclude that it seems to be reliable to use fungal mortality as the primary outcome in trials of antifungal agents. Data on total mortality should be reported as well, however, to guard against the possible introduction of harmful treatments
Impact of chronic obstructive pulmonary disease on short-term outcome in patients with ST-elevation myocardial infarction during COVID-19 pandemic: insights from the international multicenter ISACS-STEMI registry
Background: Chronic obstructive pulmonary disease (COPD) is projected to become the third cause of mortality worldwide. COPD shares several pathophysiological mechanisms with cardiovascular disease, especially atherosclerosis. However, no definite answers are available on the prognostic role of COPD in the setting of ST elevation myocardial infarction (STEMI), especially during COVID-19 pandemic, among patients undergoing primary angioplasty, that is therefore the aim of the current study. Methods: In the ISACS-STEMI COVID-19 registry we included retrospectively patients with STEMI treated with primary percutaneous coronary intervention (PCI) between March and June of 2019 and 2020 from 109 high-volume primary PCI centers in 4 continents. Results: A total of 15,686 patients were included in this analysis. Of them, 810 (5.2%) subjects had a COPD diagnosis. They were more often elderly and with a more pronounced cardiovascular risk profile. No preminent procedural dissimilarities were noticed except for a lower proportion of dual antiplatelet therapy at discharge among COPD patients (98.9% vs. 98.1%, P = 0.038). With regards to short-term fatal outcomes, both in-hospital and 30-days mortality occurred more frequently among COPD patients, similarly in pre-COVID-19 and COVID-19 era. However, after adjustment for main baseline differences, COPD did not result as independent predictor for in-hospital death (adjusted OR [95% CI] = 0.913[0.658–1.266], P = 0.585) nor for 30-days mortality (adjusted OR [95% CI] = 0.850 [0.620–1.164], P = 0.310). No significant differences were detected in terms of SARS-CoV-2 positivity between the two groups. Conclusion: This is one of the largest studies investigating characteristics and outcome of COPD patients with STEMI undergoing primary angioplasty, especially during COVID pandemic. COPD was associated with significantly higher rates of in-hospital and 30-days mortality. However, this association disappeared after adjustment for baseline characteristics. Furthermore, COPD did not significantly affect SARS-CoV-2 positivity. Trial registration number: NCT 04412655 (2nd June 2020)
Gender Difference in the Effects of COVID-19 Pandemic on Mechanical Reperfusion and 30-Day Mortality for STEMI: Results of the ISACS-STEMI COVID-19 Registry
Background. Several reports have demonstrated the impact of the COVID-19 pandemic on the management and outcome of patients with ST-segment elevation myocardial infarction (STEMI). The aim of the current analysis is to investigate the potential gender difference in the effects of the COVID-19 pandemic on mechanical reperfusion and 30-day mortality for STEMI patients within the ISACS-STEMI COVID-19 Registry. Methods. This retrospective multicenter registry was performed in high-volume primary percutaneous coronary intervention (PPCI) centers on four continents and included STEMI patients undergoing PPCIs in March–June 2019 and 2020. Patients were divided according to gender. The main outcomes were the incidence and timing of the PPCI, (ischemia time ≥ 12 h and door-to-balloon ≥ 30 min) and in-hospital or 30-day mortality. Results. We included 16683 STEMI patients undergoing PPCIs in 109 centers. In 2020 during the pandemic, there was a significant reduction in PPCIs compared to 2019 (IRR 0.843 (95% CI: 0.825–0.861, p < 0.0001). We did not find a significant gender difference in the effects of the COVID-19 pandemic on the numbers of STEMI patients, which were similarly reduced from 2019 to 2020 in both groups, or in the mortality rates. Compared to prepandemia, 30-day mortality was significantly higher during the pandemic period among female (12.1% vs. 8.7%; adjusted HR [95% CI] = 1.66 [1.31–2.11], p < 0.001) but not male patients (5.8% vs. 6.7%; adjusted HR [95% CI] = 1.14 [0.96–1.34], p = 0.12). Conclusions. The COVID-19 pandemic had a significant impact on the treatment of patients with STEMI, with a 16% reduction in PPCI procedures similarly observed in both genders. Furthermore, we observed significantly increased in-hospital and 30-day mortality rates during the pandemic only among females. Trial registration number: NCT 04412655