Chest X-ray imaging technology used for the early detection and screening of COVID-19 pneumonia is both accessible worldwide and affordable compared to other non-invasive technologies. Additionally, ...deep learning methods have recently shown remarkable results in detecting COVID-19 on chest X-rays, making it a promising screening technology for COVID-19. Deep learning relies on a large amount of data to avoid overfitting. While overfitting can result in perfect modeling on the original training dataset, on a new testing dataset it can fail to achieve high accuracy. In the image processing field, an image augmentation step (i.e., adding more training data) is often used to reduce overfitting on the training dataset, and improve prediction accuracy on the testing dataset. In this paper, we examined the impact of geometric augmentations as implemented in several recent publications for detecting COVID-19. We compared the performance of 17 deep learning algorithms with and without different geometric augmentations. We empirically examined the influence of augmentation with respect to detection accuracy, dataset diversity, augmentation methodology, and network size. Contrary to expectation, our results show that the removal of recently used geometrical augmentation steps actually improved the Matthews correlation coefficient (MCC) of 17 models. The MCC without augmentation (MCC = 0.51) outperformed four recent geometrical augmentations (MCC = 0.47 for Data Augmentation 1, MCC = 0.44 for Data Augmentation 2, MCC = 0.48 for Data Augmentation 3, and MCC = 0.49 for Data Augmentation 4). When we retrained a recently published deep learning without augmentation on the same dataset, the detection accuracy significantly increased, with a
and a
-value of 2.23 × 10
. This is an interesting finding that may improve current deep learning algorithms using geometrical augmentations for detecting COVID-19. We also provide clinical perspectives on geometric augmentation to consider regarding the development of a robust COVID-19 X-ray-based detector.
The vertebrate respiratory system is challenging to study. The complex relationship between the lungs and adjacent tissues, the vast structural diversity of the respiratory system both within ...individuals and between taxa, its mobility (or immobility) and distensibility, and the difficulty of quantifying and visualizing functionally important internal negative spaces have all impeded descriptive, functional, and comparative research. As a result, there is a relative paucity of three-dimensional anatomical information on this organ system in all vertebrate groups (including humans) relative to other regions of the body. We present some of the challenges associated with evaluating and visualizing the vertebrate respiratory system using computed and micro-computed tomography and its subsequent digital segmentation. We discuss common mistakes to avoid when imaging deceased and live specimens and various methods for merging manual and threshold-based segmentation approaches to visualize pulmonary tissues across a broad range of vertebrate taxa, with a particular focus on sauropsids (reptiles and birds). We also address some of the recent work in comparative evolutionary morphology and medicine that have used these techniques to visualize respiratory tissues. Finally, we provide a clinical study on COVID-19 in humans in which we apply modeling methods to visualize and quantify pulmonary infection in the lungs of human patients.
Renal hyperparathyroidism (RHPT), seen in the setting of end stage renal disease (ESRD) is associated with four gland hyperplasia. If refractory to medical management, patients are referred for ...surgical evaluation for parathyroidectomy. Ectopic parathyroid glands are more common in patients with RHPT and can be found in 26%–46% of patients, sometimes representing a diagnostic imaging challenge. If not accurately distinguished on imaging, they may not be found during neck exploration, which could result in recurrent disease or failure to obtain surgical cure. Different imaging modalities such as ultrasound, 99m-technetium sestamibi scan, or dynamic contrast-enhanced parathyroid computed tomography scan are available to attempt localization of parathyroid glands prior to surgery to help direct surgical exploration. More recently, dynamic, contrast-enhanced parathyroid magnetic resonance imaging (4D-MRI) has been shown to be a useful alternative imaging modality, particularly in patients with ESRD avoiding the use of iodinated contrast. Here we report two cases of ectopic parathyroid glands detected using 4D-MRI in the setting of parathyroidectomy for RHPT.
Patient A is a 35-year-old female with a history of ESRD secondary to nephrotic syndrome whose 4th parathyroid gland was identified on 4D-MRI in the right inferior pole of the thyroid.
Patient B is a 42-year-old male with a history of ESRD secondary to membranous nephropathy who had a parathyroid lesion identified on 4D-MRI near the left common carotid artery. In both cases, 4D-MRI proved to be a useful tool for localization of the missing parathyroid gland. KCI Citation Count: 0
Gait disorders, a highly prevalent condition in older adults, are associated with several adverse health consequences. Gait analysis allows qualitative and quantitative assessments of gait that ...improves the understanding of mechanisms of gait disorders and the choice of interventions. This manuscript aims (1) to give consensus guidance for clinical and spatiotemporal gait analysis based on the recorded footfalls in older adults aged 65 years and over, and (2) to provide reference values for spatiotemporal gait parameters based on the recorded footfalls in healthy older adults free of cognitive impairment and multi-morbidities.
International experts working in a network of two different consortiums (i.e., Biomathics and Canadian Gait Consortium) participated in this initiative. First, they identified items of standardized information following the usual procedure of formulation of consensus findings. Second, they merged databases including spatiotemporal gait assessments with GAITRite® system and clinical information from the "Gait, cOgnitiOn & Decline" (GOOD) initiative and the Generation 100 (Gen 100) study. Only healthy-free of cognitive impairment and multi-morbidities (i.e., ≤ 3 therapeutics taken daily)-participants aged 65 and older were selected. Age, sex, body mass index, mean values, and coefficients of variation (CoV) of gait parameters were used for the analyses.
Standardized systematic assessment of three categories of items, which were demographics and clinical information, and gait characteristics (clinical and spatiotemporal gait analysis based on the recorded footfalls), were selected for the proposed guidelines. Two complementary sets of items were distinguished: a minimal data set and a full data set. In addition, a total of 954 participants (mean age 72.8 ± 4.8 years, 45.8% women) were recruited to establish the reference values. Performance of spatiotemporal gait parameters based on the recorded footfalls declined with increasing age (mean values and CoV) and demonstrated sex differences (mean values).
Based on an international multicenter collaboration, we propose consensus guidelines for gait assessment and spatiotemporal gait analysis based on the recorded footfalls, and reference values for healthy older adults.
Purpose: The purpose of this work was to evaluate the ability of a treatment delivery verification system to detect clinically significant mechanical errors in VMAT delivery utilizing data contained ...within a commercial record and verify (RV) system, and to test whether the system can be used to reconstruct dose distributions that agree more closely with measured dose distributions than do the original treatment plans.Methods: VMAT treatment plans from five prostate patients, five head and neck patients, and five post-mastectomy chest wall patients treated at our clinic were selected for this study. Known mechanical errors were introduced into each plan, and the dosimetric effect of each error was evaluated by a radiation oncologist to determine mechanical error thresholds for clinical acceptability. Next, shifted plans were delivered on an Elekta linear accelerator, and the resulting dose distribution was measured with a two-dimensional diode array. During delivery, positions of the gantry, multi-leaf collimator (MLC), and jaws were captured in both the RV system and the linac verification interface (LVI). Following plan delivery, recorded delivery data were analyzed to characterize the ability of the recording systems to recognize true mechanical error. Finally, delivery parameters from both recording systems were imported to the treatment planning system and used to recalculate the dose delivered to the measurement phantom to test whether the system can be used to reconstruct dose distributions that agree more closely with measured dose distributions than do the original treatment plans.Results: Minimum mechanical error thresholds over all fifteen cases were found to be 1 mm for systematic MLC error, 2 mm for Gaussian-random MLC error, 3 mm for uniform-random MLC error, 3 mm for central leaf pair error and 2° for gantry error. Analyzing delivery data yielded p-values less than 0.05 for both RV and LVI systems for all central leaf pair and gantry shifts (1, 2, and 3 mm central leaf pair shifts and 1, 2, 3, and 5° rotations), which means that each system could reliably detect errors at threshold values. Reconstruction of delivery data by both RV and LVI systems failed to yield p-values less than 0.05 for prostate, head and neck, and chest wall cases.Conclusion: Both delivery verification systems examined were capable of detecting mechanical errors of 1 mm of the MLC and 2° of the gantry that produce clinically unacceptable changes in the planned dose distribution. However, dose reconstructed using the recorded delivery parameters showed no significant improvement in agreement with measured values. Thus, while the delivery verification system can detect mechanical errors, it cannot more accurately estimate the daily delivered dose than the original plans do.
The Asp358Ala variant (rs2228145; A>C) in the IL (interleukin)-6 receptor ( IL6R) gene has been implicated in the development of abdominal aortic aneurysms (AAAs), but its effect on AAA growth over ...time is not known. We aimed to investigate the clinical association between the IL6R-Asp358Ala variant and AAA growth and to assess the effect of blocking the IL-6 signaling pathway in mouse models of aortic aneurysm rupture or dissection.
Using data from 2863 participants with AAA from 9 prospective cohorts, age- and sex-adjusted mixed-effects linear regression models were used to estimate the association between the IL6R-Asp358Ala variant and annual change in AAA diameter (mm/y). In a series of complementary randomized trials in mice, the effect of blocking the IL-6 signaling pathways was assessed on plasma biomarkers, systolic blood pressure, aneurysm diameter, and time to aortic rupture and death.
After adjusting for age and sex, baseline aneurysm size was 0.55 mm (95% CI, 0.13-0.98 mm) smaller per copy of the minor allele C of the Asp358Ala variant. Change in AAA growth was -0.06 mm per year (-0.18 to 0.06) per copy of the minor allele; a result that was not statistically significant. Although all available worldwide data were used, the genetic analyses were not powered for an effect size as small as that observed. In 2 mouse models of AAA, selective blockage of the IL-6 trans-signaling pathway, but not combined blockage of both, the classical and trans-signaling pathways, was associated with improved survival ( P<0.05).
Our proof-of-principle data are compatible with the concept that IL-6 trans-signaling is relevant to AAA growth, encouraging larger-scale evaluation of this hypothesis.
Hepatorenal tyrosinemia (HT1, fumarylacetoacetate hydrolase deficiency, MIM 276700) can cause severe hepatic, renal and peripheral nerve damage. In Québec, HT1 is frequent and neonatal HT1 screening ...is practiced. Nitisinone (NTBC, Orfadin ®) inhibits tyrosine degradation prior to the formation of toxic metabolites like succinylacetone and has been offered to HT1 patients in Québec since 1994.
We recorded the clinical course of 78 Québec HT1 patients born between 1984 and 2004. There were three groups: those who never received nitisinone (28 patients), those who were first treated after 1month of age (26 patients) and those treated before 1month (24 patients). Retrospective chart review was performed for events before 1994, when nitisinone treatment began, and prospective data collection thereafter.
No hospitalizations for acute complications of HT1 occurred during 5731months of nitisinone treatment, versus 184 during 1312months without treatment (p<0.001). Liver transplantation was performed in 20 non-nitisinone-treated patients (71%) at a median age of 26months, versus 7 late-treated patients (26%, p<0.001), and no early-treated patient (p<0.001). No early-treated patient has developed detectable liver disease after more than 5years. Ten deaths occurred in non-nitisinone treated patients versus two in treated patients (p<0.01). Both of the latter deaths were from complications of transplantation unrelated to HT1. One probable nitisinone-related event occurred, transient corneal crystals with photophobia.
Nitisinone treatment abolishes the acute complications of HT1. Some patients with established liver disease before nitisinone treatment eventually require hepatic transplantation. Patients who receive nitisinone treatment before 1month had no detectable liver disease after more than 5years.
► A 25-year record of hepatorenal tyrosinemia (HT1) in Québec is presented. ► 71% of non-nitisinone treated HT1 patients required liver transplantation (median age, 26m). ► Nitisinone treatment abolished the acute complications of HT1 and reduced HT1-related deaths. ► Some late-treated patients, who had liver findings before treatment, required transplantation. ► Screened newborns with early nitisinone treatment had no detectable liver disease after≥5y.
Plant-parasitic nematodes are major agricultural pests worldwide and novel approaches to control them are sorely needed. We report the draft genome sequence of the root-knot nematode Meloidogyne ...incognita, a biotrophic parasite of many crops, including tomato, cotton and coffee. Most of the assembled sequence of this asexually reproducing nematode, totaling 86 Mb, exists in pairs of homologous but divergent segments. This suggests that ancient allelic regions in M. incognita are evolving toward effective haploidy, permitting new mechanisms of adaptation. The number and diversity of plant cell wall-degrading enzymes in M. incognita is unprecedented in any animal for which a genome sequence is available, and may derive from multiple horizontal gene transfers from bacterial sources. Our results provide insights into the adaptations required by metazoans to successfully parasitize immunocompetent plants, and open the way for discovering new antiparasitic strategies.
Celotno besedilo
Dostopno za:
DOBA, IJS, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
The eco-evolutionary interactions among members of the vertebrate gut microbiota that ultimately result in host-specific communities are poorly understood. Here we show that Lactobacillus reuteri ...coexists with species that belong to the Lactobacillus johnsonii cluster (L. johnsonii, L. gasseri, and L taiwanensis) in a taxonomically wide range of rodents, suggesting cohabitation over evolutionary times. The two dominant Lactobacillus species found in wild mice establish a commensalistic relationship in gastric biofilms when introduced together into germ-free mice in which L. reuteri facilitates colonization of L. taiwanensis. Genomic analysis revealed allopatric diversification in strains of both species that originated from geographically separated locations (Scotland and France). Allopatry of the strains resulted in reduced formation of mixed biofilms in vitro, indicating that interspecies interactions in gastric Lactobacillus-biofilms are the result of an adaptive evolutionary process that occurred in a biogeographical context. In summary, these findings suggest that members within the vertebrate gut microbiota can evolve inter-dependencies through ecological facilitation, which could represent one mechanism by which host-specific bacterial communities assemble across vertebrate species and an explanation for their spatial and biogeographic patterns.
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