Analysis of the Asymmetry between Both Eyes in Early Diagnosis of Glaucoma Combining Features Extracted from Retinal Images and OCTs into Classification Models.

This study aims to analyze the asymmetry between both eyes of the same patient for the early diagnosis of glaucoma. Two imaging modalities, retinal fundus images and optical coherence tomographies (OCTs), have been considered in order to compare their different capabilities for glaucoma detection. From retinal fundus images, the difference between cup/disc ratio and the width of the optic rim has been extracted. Analogously, the thickness of the retinal nerve fiber layer has been measured in spectral-domain optical coherence tomographies. These measurements have been considered as asymmetry characteristics between eyes in the modeling of decision trees and support vector machines for the classification of healthy and glaucoma patients. The main contribution of this work is indeed the use of different classification models with both imaging modalities to jointly exploit the strengths of each of these modalities for the same diagnostic purpose based on the asymmetry characteristics between the eyes of the patient. The results show that the optimized classification models provide better performance with OCT asymmetry features between both eyes (sensitivity 80.9%, specificity 88.2%, precision 66.7%, accuracy 86.5%) than with those extracted from retinographies, although a linear relationship has been found between certain asymmetry features extracted from both imaging modalities. Therefore, the resulting performance of the models based on asymmetry features proves their ability to differentiate healthy from glaucoma patients using those metrics. Models trained from fundus characteristics are a useful option as a glaucoma screening method in the healthy population, although with lower performance than those trained from the thickness of the peripapillary retinal nerve fiber layer. In both imaging modalities, the asymmetry of morphological characteristics can be used as a glaucoma indicator, as detailed in this work.

Decision Trees for Glaucoma Screening Based on the Asymmetry of the Retinal Nerve Fiber Layer in Optical Coherence Tomography.

Purpose: The aim of this study was to analyze the relevance of asymmetry features between both eyes of the same patient for glaucoma screening using optical coherence tomography. Methods: Spectral-domain optical coherence tomography was used to estimate the thickness of the peripapillary retinal nerve fiber layer in both eyes of the patients in the study. These measurements were collected in a dataset from healthy and glaucoma patients. Several metrics for asymmetry in the retinal nerve fiber layer thickness between the two eyes were then proposed. These metrics were evaluated using the dataset by performing a statistical analysis to assess their significance as relevant features in the diagnosis of glaucoma. Finally, the usefulness of these asymmetry features was demonstrated by designing supervised machine learning models that can be used for the early diagnosis of glaucoma. Results: Machine learning models were designed and optimized, specifically decision trees, based on the values of proposed asymmetry metrics. The use of these models on the dataset provided good classification of the patients (accuracy 88%, sensitivity 70%, specificity 93% and precision 75%). Conclusions: The obtained machine learning models based on retinal nerve fiber layer asymmetry are simple but effective methods which offer a good trade-off in classification of patients and simplicity. The fast binary classification relies on a few asymmetry values of the retinal nerve fiber layer thickness, allowing their use in the daily clinical practice for glaucoma screening.

B-SCAN ULTRASONOGRAPHY OF VITREOUS DYNAMICS DURING INTRAVITREAL ADMINISTRATION OF ANTIANGIOGENICS.

PURPOSE: To study the distribution of angiogenesis inhibitors (anti-Vascular Endothelial Growth Factor) injected into the vitreous cavity by means of simultaneous ultrasonography. METHODS: Three hundred and thirty-two B-scan ultrasound sequences of 121 eyes from 95 patients were recorded simultaneously to the intravitreal anti-Vascular Endothelial Growth Factor administration. The dynamics of the injected substance and the presence of reflux were studied, associating them with the presence/absence of total posterior vitreous detachment. RESULTS: Three well-defined patterns were distinguished. Pattern A: the medication penetrates the vitreous in a linear manner until reaching the retina (3.6%, n = 12). Pattern B: the medication adopts a globular shape and then moves down reaching the retrohyaloid space (37%, n = 123). Pattern C: the medication remains in a globular form (54%, n = 180). The pattern was not identified in 17 (5.1%) injections. Pattern A was only observed in vitrectomized eyes. The reflux (7.8%) was exclusive in eyes showing a C pattern. A relationship (P < 0.001) was observed between the presence/absence of total posterior vitreous detachment, the patterns, and the presence of reflux. CONCLUSION: This study document for the first time the behavior of antiangiogenic medication injected into the vitreous cavity and how its distribution and the presence of reflux is conditioned by the previous state of the vitreous body.

First report of bacterial leaf blight caused by Xanthomonas hortorum pv. carotae on carrots in Spain.

In September 2019, symptoms resembling those of bacterial leaf blight were observed on carrot plants (Daucus carota L. subsp. sativus Hoffm.) cv. Romance cultivated in commercial plots in Chañe (Segovia), Spain. Symptoms were observed in two plots surveyed representing three hectares, with an incidence greater than 90%, and also in some plots in other nearby municipalities sown with the same batch of seeds. The lesions observed at the ends of the leaves were initially yellow that develop dark brown to black with chlorotic halos on leaflets that turned necrotic. Yellow, Xanthomonas-like colonies were isolated onto YPGA medium (Ridé 1969) from leaf lesions. Two bacterial isolates were selected and confirmed by real-time PCR using a specific primer set for Xanthomonas hortorum pv. carotae (Temple et al. 2013). All isolates were gram-negative, aerobic rods positive for catalase, able of hydrolyzing casein and aesculin and growing at 2% NaCl, while were negative for oxidase and urease tests. Sequences of 16S rRNA gene showed 100% similarity with Xanthomonas campestris, X. arboricola, X. gardneri, X. cynarae strains (GenBank accession numbers: MW077507.1 and MW077508.1 for the isolates CRD19-206.3 and CRD19-206.4, respectively). However, the resulting phylogeny of multilocus sequence analysis (MLSA) of a concatenation of the housekeeping genes atpD, dnaK, and efp (Bui Thi Ngoc et al. 2010), by using neighbour-joining trees generated with 500 bootstrap replicates, grouped the two isolates with the X. hortorum pv. carotae M081 strain (Kimbrel et al. 2011) (GenBank accession numbers: MW161270 and MW161271 for atpD for the two isolates, respectively; MW161268 and MW161269 for dnaK; MW161272 and MW161273 for efp). A pairwise identity analysis revealed a 100% identity between all three isolates. Pathogenicity of the isolates was tested by spray inoculation (Christianson et al. 2015) with a bacterial suspension (108 CFU/ml) prepared in sterile distilled water at 3 to 4 true-leaf stage (six plants per isolate). Sterile distilled water was used as negative control. The inoculated plants were incubated in a growth chamber (25°C and 95% relative humidity [RH]) for 72 h, and then transferred to a greenhouse at 24 to 28°C and 65% RH. Characteristic leaf blight symptoms developed on inoculated carrot plants, while no symptoms were observed on the negative control plants 20 days after inoculation. The bacterium was re-isolated from symptomatic tissue and the identity confirmed through PCR analysis. Based on PCR, morphological and phenotypic tests, sequence analysis, and pathogenicity assays, the isolates were identified as X. hortorum pv. carotae. To our knowledge, this is the first report of bacterial leaf blight of carrot caused by X. hortorum pv. carotae in Spain, and the first molecular and pathological characterization. It is important to early detect this pathogen and take suitable measures to prevent its spread, since it could cause yield losses for a locally important crop such as carrot.

Automatic Segmentation of the Retinal Nerve Fiber Layer by Means of Mathematical Morphology and Deformable Models in 2D Optical Coherence Tomography Imaging.

Glaucoma is a neurodegenerative disease process that leads to progressive damage of the optic nerve to produce visual impairment and blindness. Spectral-domain OCT technology enables peripapillary circular scans of the retina and the measurement of the thickness of the retinal nerve fiber layer (RNFL) for the assessment of the disease status or progression in glaucoma patients. This paper describes a new approach to segment and measure the retinal nerve fiber layer in peripapillary OCT images. The proposed method consists of two stages. In the first one, morphological operators robustly detect the coarse location of the layer boundaries, despite the speckle noise and diverse artifacts in the OCT image. In the second stage, deformable models are initialized with the results of the previous stage to perform a fine segmentation of the boundaries, providing an accurate measurement of the entire RNFL. The results of the RNFL segmentation were qualitatively assessed by ophthalmologists, and the measurements of the thickness of the RNFL were quantitatively compared with those provided by the OCT inbuilt software as well as the state-of-the-art methods.

Serum Phospholipid Fatty Acids and Mammographic Density in Premenopausal Women.

BACKGROUND: The role of fatty acids (FAs) on mammographic density (MD) is unclear, and available studies are based on self-reported dietary intake. OBJECTIVES: This study assessed the association between specific serum phospholipid fatty acids (PLFAs) and MD in premenopausal women. METHODS: The cross-sectional study DDM-Madrid recruited 1392 Spanish premenopausal women, aged 39-50 y, who attended a screening in a breast radiodiagnosis unit of Madrid City Council. Women completed lifestyle questionnaires and FFQs. Percentage MD was estimated using a validated computer tool (DM-Scan), and serum PLFA percentages were measured by GC-MS. Multivariable linear regression models were used to quantify the association of FA tertiles with MD. Models were adjusted for age, education, BMI, waist circumference, parity, oral contraceptive use, previous breast biopsies, and energy intake, and they were corrected for multiple testing. RESULTS: Women in the third tertile of SFAs showed significantly higher MD compared with those in the first tertile (ßT3vsT1 = 7.53; 95% CI: 5.44, 9.61). Elevated relative concentrations of palmitoleic (ßT3vsT1 = 3.12; 95% CI: 0.99, 5.25) and gondoic (ßT3vsT1 = 2.67; 95% CI: 0.57, 4.77) MUFAs, as well as high relative concentrations of palmitelaidic (ßT3vsT1 = 5.22; 95% CI: 3.15, 7.29) and elaidic (ßT3vsT1 = 2.69; 95% CI: 0.59, 4.79) trans FAs, were also associated with higher MD. On the contrary, women with elevated relative concentrations of n-6 (ω-6) linoleic (ßT3vsT1 = -5.49; 95% CI; -7.62, -3.35) and arachidonic (ßT3vsT1 = -4.68; 95% CI: -6.79, -2.58) PUFAs showed lower MD. Regarding desaturation indices, an elevated palmitoleic to palmitic ratio and a low ratio of oleic to steric and arachidonic to dihomo-γ-linolenic acids were associated with higher MD. CONCLUSIONS: Spanish premenopausal women with high relative concentrations of most SFAs and some MUFAs and trans FAs showed an increased MD, whereas those with high relative concentrations of some n-6 PUFAs presented lower density. These results, which should be confirmed in further studies, underscore the importance of analyzing serum FAs individually.

Draft Genome Resources of Two Strains ("ESVL" and "IVIA5901") of Xylella fastidiosa Associated with Almond Leaf Scorch Disease in Alicante, Spain.

An outbreak of Xylella fastidiosa subsp. multiplex sequence type ST6 was discovered in 2017 in mainland Spain affecting almond trees. Two cultured almond strains, "ESVL" and "IVIA5901," were subjected to high throughput sequencing and the draft genomes assembled. Phylogenetic analysis conclusively indicated they belong to the subspecies multiplex, and pairwise comparisons of the chromosomal genomes showed an average nucleotide identity higher than 99%. Interestingly, the two strains differ for the presence of the plasmids pXF64-Hb_ESVL and pUCLA-ESVL detected only in the ESVL strain. The availability of these draft genomes contribute to extend the European genomic sequence dataset, a first step toward setting new research to elucidate the pathway of introduction and spread of the numerous strains of this subspecies so far detected in Europe.

Criteria of adequacy for vitamin D testing and prevalence of deficiency in clinical practice.

BACKGROUND: Vitamin D deficiency is an important concern in clinical settings although there is no consensus on who should undergo 25-OH-vitamin D testing. We studied the prevalence of vitamin D deficiency before and after introducing adequacy (clinical and biochemical) criteria for testing. METHODS: A total of 32,363 tests for 25-OH-vitamin D were retrospectively evaluated. Requests were unrestricted until December 2010 and justification criteria were applied from January 2011. During 6 years, 25,656 samples were analyzed (UHPLC) of which 12,315 were considered the first visit. The prevalence of deficiency was assessed for all the samples and according to the year, sex, season, age, origin of the requests, inclusion of adequacy criteria and consecutive visits. RESULTS: A significant proportion of the requests (25%) were unjustified and less than half of the clinically or biochemically-justified tests displayed serum concentrations indicative of deficiency. Application of adequacy criteria resulted in a non-significant increase in the prevalence of deficiency, both at the first visit (36.5 vs. 41.7, p=0.17) and for all the samples analyzed (32.0 vs. 35.5, p=0.14). The percentage of deficiency decreased in consecutive visits although 2/3 and 41% of the patients remained deficient on the second and third visit, respectively. Moreover, at least 1/5 of sufficient patients at the first test became deficient in subsequent evaluations. CONCLUSIONS: A significant proportion of the requests was unjustified by clinical or biochemical criteria. Our data also indicate that clinical and biochemical criteria may be necessary (to be present) to justify vitamin D testing but not sufficient (predictive) to indicate the presence of vitamin D deficiency.

Survival Estimation Using Multistate Cormack-Jolly-Seber Models-The Case of the Bearded Vulture Gypaetus barbatus in Spain.

The bearded vulture (Gypaetus barbatus) is an endangered species with a specialist osteophagous (bone) diet. We estimated the survival and productivity of this vulture in the Aragonese Pyrenees, where the main population of the species in Europe is found. We used a database covering a period of 33 years (1987-2020). To estimate the probability of survival, we used Cormack-Jolly-Seber models with a Bayesian approach. Our models estimated a survival rate of 0.90 ± 0.08 in juveniles, 0.95 ± 0.04 in subadults and 0.92 ± 0.05 in adults. The survival probability increased over the study period in adults and subadults but not in juveniles. By contrast, productivity decreased over the same period. Our study provides updated information on the status of two demographic parameters of great importance to the species and allows us to identify the most vulnerable age classes and to plan conservation actions to improve the situation of the species in a territory that is a donor of specimens for reintroduction projects. The estimated survival values suggest that more caution should be exercised when planning these feeding points according to the use the species makes of them.

Bioavailability of Lutein from Marigold Flowers (Free vs. Ester Forms): A Randomised Cross-Over Study to Assess Serum Response and Visual Contrast Threshold in Adults.

Lutein (Lut) and zeaxanthin (Zeax) are found in the blood and are deposited in the retina (macular pigment). Both are found in the diet in free form and esterified with fatty acids. A high intake and/or status is associated with a lower risk of chronic diseases, especially eye diseases. There is a large global demand for Lut in the dietary supplement market, with marigold flowers being the main source, mainly as lutein esters. As the bioavailability of Lut from free or ester forms is controversial, our aim was to assess the bioavailability of Lut (free vs. ester) and visual contrast threshold (CT). Twenty-four healthy subjects (twelve women, twelve men), aged 20-35 and 50-65 years, were enrolled in a cross-sectional study to consume 6 mg lutein/day from marigold extract (free vs. ester) for two months. Blood samples were taken at baseline and after 15, 40, and 60 days in each period. Serum Lut and Zeax were analysed using HPLC, and dietary intake was determined with a 7-day food record at the beginning of each period. CT, with and without glare, was at 0 and 60 days at three levels of visual angle. Lut + Zeax intake at baseline was 1.9 mg/day, and serum lutein was 0.36 µmol/L. Serum lutein increased 2.4-fold on day 15 (up to 0.81 and 0.90 µmol/L with free and ester lutein, respectively) and was maintained until the end of the study. Serum Zeax increased 1.7-fold. There were no differences in serum Lut responses to free or ester lutein at any time point. CT responses to lutein supplementation (free vs. ester) were not different at any time point. CT correlated with Lut under glare conditions, and better correlations were obtained at low frequencies in the whole group due to the older group. The highest correlations occurred between CT at high frequency and with glare with serum Lut and Lut + Zeax. Only in the older group were inverse correlations found at baseline at a high frequency with L + Z and with Lut/cholesterol and at a low frequency with Lut/cholesterol. In conclusion, daily supplementation with Lut for 15 days significantly increases serum Lut in normolipemic adults to levels associated with a reduced risk of age-related eye disease regardless of the chemical form of lutein supplied. Longer supplementation, up to two months, does not significantly alter the concentration achieved but may contribute to an increase in macular pigment (a long-term marker of lutein status) and thus improve the effect on visual outcomes.

Critical evaluation of assays for vitamin D status.

PURPOSE OF REVIEW: The objective is to highlight new aspects and methodological developments in the assessment of vitamin D status in clinical settings. RECENT FINDINGS: Recent advances in the assessment of vitamin D status mostly concern two areas: the emerging clinical and analytical interest in other circulating vitamin D metabolites [i.e. 3-epimer and 24,25-(OH)2 D] that opens a new perspective for the vitamin D metabolite profiling in health and disease and methodological improvements including the development of reference measurement procedures, the certification of Standard Reference Materials, the development and application of Standardization protocols and the change of the Vitamin D External Quality Assurance Survey (DEQAS) to an accuracy-based proficiency testing scheme. SUMMARY: Despite the improvement in the analytical imprecision between methods and laboratories over the last years, the reported prevalence of vitamin D deficiency in a given population still depends on the method used. Improvements in quality control procedures, however, will improve the standardization, accuracy and comparability of methods. At present, the analytical evaluation of other circulating vitamin D metabolites (vitamin D profiling) and their clinical utility is, however, limited to liquid chromatography users.

Phytochemical Analysis and Anti-Inflammatory Potential of Acanthus mollis L. Rhizome Hexane Extract.

The rhizomes of Acanthus mollis have traditionally been used for the treatment of several ailments involving inflammation. However, to the best of our knowledge, their chemical composition and pharmacological properties have not been studied until now. As a first approach, this study analyses the A. mollis rhizome hexane extract phytochemistry and its anti-inflammatory and antioxidant capacities in HepG2 and RAW 264.7 cell culture assays. Chemical profiling was performed with gas chromatography mass spectrometry without the modification of native molecules. Free phytosterols (such as ß-sitosterol) account for 70% of detected compounds. The anti-inflammatory capacity of the rhizome extract of A. mollis is mediated by the decrease in the NO production in RAW 264.7 that has previously been stimulated with lipopolysaccharide in a dose-dependent manner. Furthermore, HepG2 pre-treatment with the rhizome extract prevents any damage being caused by oxidative stress, both through ROS scavenge and through the antioxidant cellular enzyme system. In this respect, the extract reduced the activity of glutathione peroxidase and reductase, which were stimulated under oxidative stress conditions. Our results suggest that the extract from the rhizomes of A. mollis may constitute a potential source of natural products with anti-inflammatory activity and could validate the traditional use of A. mollis.

Primary-Sjögren's-Syndrome-Related Interstitial Lung Disease: A Clinical Review Discussing Current Controversies.

Lung involvement, especially interstitial lung disease, is a potentially severe extra-glandular manifestation of Primary Sjogren's Syndrome (pSS-ILD). ILD can manifest either as a late complication of pSS or anticipate sicca symptoms, likely reflecting two different patho-physiological entities. Presence of lung involvement in pSS subjects can remain subclinical for a long time; therefore, patients should be actively screened, and lung ultrasound is currently being investigated as a potential low cost, radiation-free, easily repeatable screening tool for detection of ILD. In contrast, rheumatologic evaluation, serology testing, and minor salivary gland biopsy are crucial for the recognition of pSS in apparently idiopathic ILD patients. Whether the HRCT pattern influences prognosis and treatment response in pSS-ILD is not clear; a UIP pattern associated with a worse prognosis in some studies, but not in others. Many aspects of pSS-ILD, including its actual prevalence, association with specific clinical-serological characteristics, and prognosis, are still debated by the current literature, likely due to poor phenotypic stratification of patients in clinical studies. In the present review, we critically discuss these and other clinically relevant "hot topics" in pSS-ILD. More specifically, after a focused discussion, we compiled a list of questions regarding pSS-ILD that, in our opinion, are not easily answered by the available literature. We subsequently tried to formulate adequate answers on the basis of an extensive literature search and our clinical experience. At the same, we highlighted different issues that require further investigation.

Application of an integrated catchment-lake model approach for simulating effects of climate change on lake inputs and biogeochemistry.

Climate change is simultaneously affecting lakes and their catchments, resulting in altered runoff patterns in the catchment and modified mixing and biogeochemical dynamics in lakes. The effects of climate change in a catchment will eventually have an impact on the dynamics of a downstream water body as well. An integrated model would allow considering how changes in the watershed affect the lake, but coupled modelling studies are rare. In this study we integrate a catchment model (SWAT+) and a lake model (GOTM-WET) to obtain holistic predictions for Lake Erken, Sweden. Using five different global climate models, projections of climate, catchment loads and lake water quality for the mid and end of the 21st century have been obtained under two future scenarios (SSP 2-45 and SSP 5-85). Temperature, precipitation and evapotranspiration will increase in the future, overall resulting in an increase in water inflow to the lake. An increasing importance of surface runoff will also have consequences on the catchment soil, hydrologic flow paths, and the input of nutrients to the lake. In the lake, water temperatures will rise, leading to increased stratification and a drop in oxygen levels. Nitrate levels are predicted to remain unchanged, while phosphate and ammonium levels increase. A coupled catchment-lake configuration such as that illustrated here allows prediction of future biogeochemical conditions of a lake, including linking land use changes to changing lake conditions, as well as eutrophication and browning studies. Since climate affects both the lake and the catchment, simulations of climate change should ideally take into account both systems.

Practice-based training strategy for therapist-driven prostate MR-Linac adaptive radiotherapy.

Purpose: To develop a practice-based training strategy to transition from radiation oncologist to therapist-driven prostate MR-Linac adaptive radiotherapy. Methods and materials: In phase 1, 7 therapists independently contoured the prostate and organs-at-risk on T2-weighted MR images from 11 previously treated MR-Linac prostate patients. Contours were evaluated quantitatively (i.e. Dice similarity coefficient [DSC] calculated against oncologist generated online contours) and qualitatively (i.e. oncologist using a 5-point Likert scale; a score ≥ 4 was deemed a pass, a 90% pass rate was required to proceed to the next phase). Phase 2 consisted of supervised online workflow with therapists required no intervention from the oncologist on 10 total cases to advance. Phase 3 involved unsupervised therapist-driven workflow, with offline support from oncologists prior to the next fraction. Results: In phase 1, the mean DSC was 0.92 (range 0.85-0.97), and mean Likert score was 3.7 for the prostate. Five therapists did not attain a pass rate (3-5 cases with prostate contour score < 4), underwent follow-up one-on-one review, and performed contours on a further training set (n = 5). Each participant completed a median of 12 (range 10-13) cases in phase 2; of 82 cases, minor direction were required from the oncologist on 5 regarding target contouring. Radiation oncologists reviewed 179 treatment fractions in phase 3, and deemed 5 cases acceptable but with suggestions for next fraction; all other cases were accepted without suggestions. Conclusion: A training stepwise program was developed and successfully implemented to enable a therapist-driven workflow for online prostate MR-Linac adaptive radiotherapy.

Oxidative Stress Mediates Epigenetic Modifications and the Expression of miRNAs and Genes Related to Apoptosis in Diabetic Retinopathy Patients.

Knowledge on the underlying mechanisms and molecular targets for managing the ocular complications of type 2 diabetes mellitus (T2DM) remains incomplete. Diabetic retinopathy (DR) is a major cause of irreversible visual disability worldwide. By using ophthalmological and molecular-genetic approaches, we gathered specific information to build a data network for deciphering the crosslink of oxidative stress (OS) and apoptosis (AP) processes, as well as to identify potential epigenetic modifications related to noncoding RNAs in the eyes of patients with T2DM. A total of 120 participants were recruited, being classified into two groups: individuals with T2MD (T2MDG, n = 67), divided into a group of individuals with (+DR, n = 49) and without (-DR, n = 18) DR, and a control group (CG, n = 53). Analyses of compiled data reflected significantly higher plasma levels of malondialdehyde (MDA), superoxide dismutase (SOD), and glutathione peroxidase (GPx) and significantly lower total antioxidant capacity (TAC) in the +DR patients compared with the -DR and the CG groups. Furthermore, the plasma caspase-3 (CAS3), highly involved in apoptosis (AP), showed significantly higher values in the +DR group than in the -DR patients. The microRNAs (miR) hsa-miR 10a-5p and hsa-miR 15b-5p, as well as the genes BCL2L2 and TP53 involved in these pathways, were identified in relation to DR clinical changes. Our data suggest an interaction between OS and the above players in DR pathogenesis. Furthermore, potential miRNA-regulated target genes were identified in relation to DR. In this concern, we may raise new diagnostic and therapeutic challenges that hold the potential to significantly improve managing the diabetic eye.

Tracking SARS-CoV-2 introductions in Mozambique using pandemic-scale phylogenies: a retrospective observational study.

BACKGROUND: From the start of the SARS-CoV-2 outbreak, global sequencing efforts have generated an unprecedented amount of genomic data. Nonetheless, unequal sampling between high-income and low-income countries hinders the implementation of genomic surveillance systems at the global and local level. Filling the knowledge gaps of genomic information and understanding pandemic dynamics in low-income countries is essential for public health decision making and to prepare for future pandemics. In this context, we aimed to discover the timing and origin of SARS-CoV-2 variant introductions in Mozambique, taking advantage of pandemic-scale phylogenies. METHODS: We did a retrospective, observational study in southern Mozambique. Patients from Manhiça presenting with respiratory symptoms were recruited, and those enrolled in clinical trials were excluded. Data were included from three sources: (1) a prospective hospital-based surveillance study (MozCOVID), recruiting patients living in Manhiça, attending the Manhiça district hospital, and fulfilling the criteria of suspected COVID-19 case according to WHO; (2) symptomatic and asymptomatic individuals with SARS-CoV-2 infection recruited by the National Surveillance system; and (3) sequences from SARS-CoV-2-infected Mozambican cases deposited on the Global Initiative on Sharing Avian Influenza Data database. Positive samples amenable for sequencing were analysed. We used Ultrafast Sample placement on Existing tRees to understand the dynamics of beta and delta waves, using available genomic data. This tool can reconstruct a phylogeny with millions of sequences by efficient sample placement in a tree. We reconstructed a phylogeny (~7·6 million sequences) adding new and publicly available beta and delta sequences. FINDINGS: A total of 5793 patients were recruited between Nov 1, 2020, and Aug 31, 2021. During this time, 133 328 COVID-19 cases were reported in Mozambique. 280 good quality new SARS-CoV-2 sequences were obtained after the inclusion criteria were applied and an additional 652 beta (B.1.351) and delta (B.1.617.2) public sequences were included from Mozambique. We evaluated 373 beta and 559 delta sequences. We identified 187 beta introductions (including 295 sequences), divided in 42 transmission groups and 145 unique introductions, mostly from South Africa, between August, 2020 and July, 2021. For delta, we identified 220 introductions (including 494 sequences), with 49 transmission groups and 171 unique introductions, mostly from the UK, India, and South Africa, between April and November, 2021. INTERPRETATION: The timing and origin of introductions suggests that movement restrictions effectively avoided introductions from non-African countries, but not from surrounding countries. Our results raise questions about the imbalance between the consequences of restrictions and health benefits. This new understanding of pandemic dynamics in Mozambique can be used to inform public health interventions to control the spread of new variants. FUNDING: European and Developing Countries Clinical Trials, European Research Council, Bill & Melinda Gates Foundation, and Agència de Gestió d'Ajuts Universitaris i de Recerca.

Domain adaptation of automated treatment planning from computed tomography to magnetic resonance.

Objective.Machine learning (ML) based radiation treatment planning addresses the iterative and time-consuming nature of conventional inverse planning. Given the rising importance of magnetic resonance (MR) only treatment planning workflows, we sought to determine if an ML based treatment planning model, trained on computed tomography (CT) imaging, could be applied to MR through domain adaptation.Methods.In this study, MR and CT imaging was collected from 55 prostate cancer patients treated on an MR linear accelerator. ML based plans were generated for each patient on both CT and MR imaging using a commercially available model in RayStation 8B. The dose distributions and acceptance rates of MR and CT based plans were compared using institutional dose-volume evaluation criteria. The dosimetric differences between MR and CT plans were further decomposed into setup, cohort, and imaging domain components.Results.MR plans were highly acceptable, meeting 93.1% of all evaluation criteria compared to 96.3% of CT plans, with dose equivalence for all evaluation criteria except for the bladder wall, penile bulb, small and large bowel, and one rectum wall criteria (p< 0.05). Changing the input imaging modality (domain component) only accounted for about half of the dosimetric differences observed between MR and CT plans. Anatomical differences between the ML training set and the MR linac cohort (cohort component) were also a significant contributor.Significance.We were able to create highly acceptable MR based treatment plans using a CT-trained ML model for treatment planning, although clinically significant dose deviations from the CT based plans were observed. Future work should focus on combining this framework with atlas selection metrics to create an interpretable quality assurance QA framework for ML based treatment planning.

Impact of intrafraction changes in delivered dose of the day for prostate cancer patients treated with stereotactic body radiotherapy via MR-Linac.

Purpose: The purpose of this study is to evaluate the impact of intrafraction pelvic motion by comparing the adapted plan dose (APD) and the computed delivered dose of the day (DDOTD) for patients with prostate cancer (PCa) treated with SBRT on the MR-Linac. Methods: Twenty patients with PCa treated with MR-guided adaptive SBRT were included. A 9-field IMRT distribution was adapted based on the anatomy of the day to deliver a total prescription dose of 3000 cGy in 5 fractions to the prostate plus a 5 mm isotropic margin. Prostate, bladder, and rectum were re-contoured on the MR-image acquired during treatment delivery (MRBO). DDOTD was computed by propagating the dose from the daily adapted plan generated during treatment onto the MRBO. Results: Target coverage was met for all fractions, however, computed DDOTD was significantly less than the APD (p < 0.05). During an average treatment of 53 min, mean bladder volume increased by 116%, which led to a significant decrease in the DDOTD bladder D40% (p < 0.001). However, DDOTD to bladder 5 cc was significantly higher (p < 0.001) than APD. Rectum intrafraction changes were observed based on a volume change of -20% to 83% and presence of significant dose changes from APD to DDOTD for rectum D20% (p < 0.05) and D1cc (p < 0.0001). Conclusions: Intrafraction motion observed during prostate SBRT treatment on the MR-Linac have dosimetric impacts on both the target and organs at risk. Post-treatment computation using DDOTD may inform adaptation beyond anatomic changes in subsequent treatment fractions to best capitalize on MR-Linac technology and widen the therapeutic index of SBRT for PCa.