A convolutional neural network for segmentation of yeast cells without manual training annotations

MOTIVATION: Single-cell time-lapse microscopy is a ubiquitous tool for studying the dynamics of complex cellular processes. While imaging can be automated to generate very large volumes of data, the processing of the resulting movies to extract high-quality single-cell information remains a challenging task. The development of software tools that automatically identify and track cells is essential for realizing the full potential of time-lapse microscopy data. Convolutional neural networks (CNNs) are ideally suited for such applications, but require great amounts of manually annotated data for training, a time-consuming and tedious process. RESULTS: We developed a new approach to CNN training for yeast cell segmentation based on synthetic data and present (i) a software tool for the generation of synthetic images mimicking brightfield images of budding yeast cells and (ii) a convolutional neural network (Mask R-CNN) for yeast segmentation that was trained on a fully synthetic dataset. The Mask R-CNN performed excellently on segmenting actual microscopy images of budding yeast cells, and a density-based spatial clustering algorithm (DBSCAN) was able to track the detected cells across the frames of microscopy movies. Our synthetic data creation tool completely bypassed the laborious generation of manually annotated training datasets, and can be easily adjusted to produce images with many different features. The incorporation of synthetic data creation into the development pipeline of CNN-based tools for budding yeast microscopy is a critical step toward the generation of more powerful, widely applicable and user-friendly image processing tools for this microorganism. AVAILABILITY AND IMPLEMENTATION: The synthetic data generation code can be found at https://github.com/prhbrt/synthetic-yeast-cells. The Mask R-CNN as well as the tuning and benchmarking scripts can be found at https://github.com/ymzayek/yeastcells-detection-maskrcnn. We also provide Google Colab scripts that reproduce all the results of this work. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online

Predictors of waterpipe smoking progression among youth in Irbid, Jordan: A Longitudinal Study (2008-2011)

BACKGROUND: The predictors of waterpipe smoking progression are yet to be examined using a longitudinal study that is guided by a theoretical model of behavioral change. This study identifies the gender-specific predictors of waterpipe smoking progression among adolescents in Irbid, Jordan. METHODS: This study uses data from a school longitudinal study of smoking behavior in Irbid, Jordan. A random sample of 19 schools was selected by probability proportionate to size. A total of 1781 seventh graders were enrolled at baseline, and completed a questionnaire annually from 2008 through 2011. Students who reported ever smoking waterpipe (N = 864) at any time point were assessed for progression (escalation in the frequency of waterpipe smoking) in the subsequent follow-up. Grouped-time survival analysis was used to identify the risk of progression. RESULTS: During the three years of follow-up, 29.6% of students progressed in waterpipe smoking. Predictors of waterpipe smoking progression were higher mother's education, enrollment in public school, frequent physical activity, and low refusal self-efficacy among boys, having ever smoked cigarettes, and having friends and siblings who smoke waterpipe among girls. Awareness of harms of waterpipe was protective among boys and seeing warning labels on the tobacco packs was protective among girls. CONCLUSIONS: Even at this early stage, about a third of waterpipe smokers progressed in their habit during the 3 year follow up. Factors predicting progression of use differed by gender, which calls for gender-specific approaches to waterpipe interventions among Jordanian youth

Predictors of Cigarette Smoking Progression Among a School-Based Sample of Adolescents in Irbid, Jordan: A Longitudinal Study (2008–2011)

INTRODUCTION: Little evidence regarding longitudinal predictors of cigarette smoking progression is available from developing countries. This study aimed to identify gender-specific individual and social predictors of cigarette smoking progression among a school-based sample of adolescents in Irbid, Jordan. METHODS: A total of 1781 seventh graders (participation rate 95%) were enrolled and completed an annual self-administered questionnaire from 2008 through 2011. Students who reported ever-smoking a cigarette at baseline or in the subsequent follow-up but not being heavy daily smokers (\u3e10 cigarettes per day) were eligible for this analysis (N = 669). Grouped-time survival analyses were used to identify predictors of cigarette smoking progression in boys and girls. RESULTS: Among the study sample, 38.3% of students increased the frequency and /or amount of cigarette smoking during the 3 years of follow-up. Among individual factors, the urge to smoke in the morning predicted smoking progression for boys and girls. The independent predictors of cigarette smoking progression were friends\u27 smoking and attending public schools in boys, and siblings\u27 smoking in girls. Discussing the dangers of smoking with family members was protective for girls. CONCLUSION: Boys and girls progressed similarly in cigarette smoking once they initiated the habit. Progression among girls was solely family-related, while it was peer-related for boys

Measuring decline in white matter integrity after systemic treatment for breast cancer:Omitting skeletonization enhances sensitivity

Chemotherapy for non-central nervous system cancers is associated with abnormalities in brain structure and function. Diffusion tensor imaging (DTI) allows for studying in vivo microstructural changes in brain white matter. Tract-based spatial statistics (TBSS) is a widely used processing pipeline in which DTI data are typically normalized to a generic DTI template and then ‘skeletonized’ to compensate for misregistration effects. However, this approach greatly reduces the overall white matter volume that is subjected to statistical analysis, leading to information loss. Here, we present a re-analysis of longitudinal data previously analyzed with standard TBSS (Menning et al., BIB 2018, 324–334). For our current approach, we constructed a pipeline with an optimized registration method in Advanced Normalization Tools (ANTs) where DTI data are registered to a study-specific, high-resolution T1 template and the skeletonization step is omitted. In a head to head comparison, we show that with our novel approach breast cancer survivors who had received chemotherapy plus or minus endocrine therapy (BC + SYST, n = 26) showed a global decline in overall FA that was not present in breast cancer survivors who did not receive systemic therapy (BC-SYST, n = 23) or women without a cancer diagnosis (no cancer controls, NC, n = 30). With the standard TBSS approach we did not find any group differences. Moreover, voxel-based analysis for our novel pipeline showed a widespread decline in FA in the BC + SYST compared to the NC group. Interestingly, the BC-SYST group also showed a decline in FA compared to the NC group, although in much less voxels. These results were not found with the standard TBSS approach. We demonstrate that a modified processing pipeline makes DTI data more sensitive to detecting changes in white matter integrity in non-CNS cancer patients after treatment, particularly chemotherapy

Waterpipe a gateway to cigarette smoking initiation among adolescents in Irbid, Jordan: a longitudinal study

SETTING: According to anecdotal evidence, waterpipe smoking may lead to the initiation of cigarette smoking among young people. This hypothesis is yet to be examined using an appropriate study design and a theoretical model for behavioral change. OBJECTIVE: To compare the risk of cigarette smoking initiation among waterpipe-only smokers and never smokers in a school-based sample of adolescents from Irbid, Jordan. METHODS: A total of 1454 cigarette-naïve participants were drawn from a longitudinal study on smoking behavior conducted in Irbid among 1781 seventh graders who were enrolled at baseline (2008) and completed the study questionnaire on smoking behavior annually until 2011. Grouped time-survival analysis was used to compare the risk of subsequent initiation of cigarette smoking between waterpipe smokers (n = 298) and never smokers (n = 1156) using adjusted hazard ratios (aHRs) and 95% confidence intervals (95%CI). RESULTS: Risk of initiation of cigarette smoking among waterpipe smokers was significantly higher than among never smokers after adjusting for potential confounders (aHR 1.67, 95%CI 1.46–1.92). The association between waterpipe and cigarette smoking initiation was dose-dependent. The risk of initiating cigarette smoking increased with increase in the frequency of waterpipe smoking (P for linear trend < 0.001). CONCLUSIONS: Waterpipe smoking led to the initiation of cigarette smoking among this cohort of Jordanian adolescents; the effect was dose-dependent

Time trends of cigarette and waterpipe smoking among a cohort of school children in Irbid, Jordan, 2008–11

Background: Coordinated high-impact interventions and community-level changes in smoking behaviour norms effectively reduced prevalence of smoking among youth in many developed countries. Smoking trends among Jordanian adolescents are likely different than their Western counterparts and must be understood in the context of their daily lives to tailor interventions specifically for adolescents in this setting. Methods: Between 2008 and 2011, a school-based longitudinal study was conducted in Irbid, Jordan. All seventh-grade students in 19 randomly selected schools (of 60) were surveyed annually for 4 years. Outcomes of interest were time trends in smoking behaviour, age at initiation and change in frequency of smoking. Results: Among 1781 participants, baseline prevalence of current smoking (cigarettes or waterpipe) for boys was 22.9% and 8.7% for girls. Prevalence of ever-smoking and current any smoking, cigarette smoking, waterpipe smoking and dual cigarette/waterpipe smoking was significantly higher in boys than girls each year (P \u3c 0.001). Smoking prevalence increased every year after year 2 for current smoking (P \u3c 0.05) across all methods (any, cigarette, waterpipe and dual). At all time points for both boys and girls, prevalence of waterpipe smoking was higher than that of cigarette smoking (P \u3c 0.001). Conclusion: This study shows intensive smoking patterns at early ages among Jordanian youth in Irbid, characterized by a predominance of waterpipe smoking and steeper age-related increase in cigarette smoking. It also points to the possibility of waterpipe being the favourite method for introducing youth to tobacco, as well as being a vehicle for tobacco dependence and cigarette smoking

Forecasting future prevalence of type 2 diabetes mellitus in Syria

Background Type 2 diabetes mellitus (T2DM) is increasingly becoming a major public health problem worldwide. Estimating the future burden of diabetes is instrumental to guide the public health response to the epidemic. This study aims to project the prevalence of T2DM among adults in Syria over the period 2003?2022 by applying a modelling approach to the country?s own data. Methods Future prevalence of T2DM in Syria was estimated among adults aged 25æyears and older for the period 2003?2022 using the IMPACT Diabetes Model (a discrete-state Markov model). Results According to our model, the prevalence of T2DM in Syria is projected to double in the period between 2003 and 2022 (from 10% to 21%). The projected increase in T2DM prevalence is higher in men (148%) than in women (93%). The increase in prevalence of T2DM is expected to be most marked in people younger than 55æyears especially the 25?34æyears age group. Conclusions The future projections of T2DM in Syria put it amongst countries with the highest levels of T2DM worldwide. It is estimated that by 2022 approximately a fifth of the Syrian population aged 25æyears and older will have T2DM

The effect of strict state measures on the epidemiologic curve of COVID-19 infection in the context of a developing country : a simulation from Jordan

COVID-19 has posed an unprecedented global public health threat and caused a significant number of severe cases that necessitated long hospitalization and overwhelmed health services in the most affected countries. In response, governments initiated a series of non-pharmaceutical interventions (NPIs) that led to severe economic and social impacts. The effect of these intervention measures on the spread of the COVID-19 pandemic are not well investigated within developing country settings. This study simulated the trajectories of the COVID-19 pandemic curve in Jordan between February and May and assessed the effect of Jordan’s strict NPI measures on the spread of COVID-19. A modified susceptible, exposed, infected, and recovered (SEIR) epidemic model was utilized. The compartments in the proposed model categorized the Jordanian population into six deterministic compartments: suspected, exposed, infectious pre-symptomatic, infectious with mild symptoms, infectious with moderate to severe symptoms, and recovered. The GLEAMviz client simulator was used to run the simulation model. Epidemic curves were plotted for estimated COVID-19 cases in the simulation model, and compared against the reported cases. The simulation model estimated the highest number of total daily new COVID-19 cases, in the pre-symptomatic compartmental state, to be 65 cases, with an epidemic curve growing to its peak in 49 days and terminating in a duration of 83 days, and a total simulated cumulative case count of 1048 cases. The curve representing the number of actual reported cases in Jordan showed a good pattern compatibility to that in the mild and moderate to severe compartmental states. The reproduction number under the NPIs was reduced from 5.6 to less than one. NPIs in Jordan seem to be effective in controlling the COVID-19 epidemic and reducing the reproduction rate. Early strict intervention measures showed evidence of containing and suppressing the disease