The use of microscopy and three-dimensional visualization to evaluate the structure of microbial biofilms cultivated in the Calgary Biofilm Device

Microbes frequently live within multicellular, solid surface-attached assemblages termed biofilms. These microbial communities have architectural features that contribute to population heterogeneity and consequently to emergent cell functions. Therefore, three-dimensional (3D) features of biofilm structure are important for understanding the physiology and ecology of these microbial systems. This paper details several protocols for scanning electron microscopy and confocal laser scanning microscopy (CLSM) of biofilms grown on polystyrene pegs in the Calgary Biofilm Device (CBD). Furthermore, a procedure is described for image processing of CLSM data stacks using amira(™), a virtual reality tool, to create surface and/or volume rendered 3D visualizations of biofilm microorganisms. The combination of microscopy with microbial cultivation in the CBD – an apparatus that was designed for high-throughput susceptibility testing – allows for structure-function analysis of biofilms under multivariate growth and exposure conditions

Deep learning-based left ventricular segmentation demonstrates improved performance on respiratory motion-resolved whole-heart reconstructions

IntroductionDeep learning (DL)-based segmentation has gained popularity for routine cardiac magnetic resonance (CMR) image analysis and in particular, delineation of left ventricular (LV) borders for LV volume determination. Free-breathing, self-navigated, whole-heart CMR exams provide high-resolution, isotropic coverage of the heart for assessment of cardiac anatomy including LV volume. The combination of whole-heart free-breathing CMR and DL-based LV segmentation has the potential to streamline the acquisition and analysis of clinical CMR exams. The purpose of this study was to compare the performance of a DL-based automatic LV segmentation network trained primarily on computed tomography (CT) images in two whole-heart CMR reconstruction methods: (1) an in-line respiratory motion-corrected (Mcorr) reconstruction and (2) an off-line, compressed sensing-based, multi-volume respiratory motion-resolved (Mres) reconstruction. Given that Mres images were shown to have greater image quality in previous studies than Mcorr images, we hypothesized that the LV volumes segmented from Mres images are closer to the manual expert-traced left ventricular endocardial border than the Mcorr images.MethodThis retrospective study used 15 patients who underwent clinically indicated 1.5 T CMR exams with a prototype ECG-gated 3D radial phyllotaxis balanced steady state free precession (bSSFP) sequence. For each reconstruction method, the absolute volume difference (AVD) of the automatically and manually segmented LV volumes was used as the primary quantity to investigate whether 3D DL-based LV segmentation generalized better on Mcorr or Mres 3D whole-heart images. Additionally, we assessed the 3D Dice similarity coefficient between the manual and automatic LV masks of each reconstructed 3D whole-heart image and the sharpness of the LV myocardium-blood pool interface. A two-tail paired Student’s t-test (alpha = 0.05) was used to test the significance in this study.Results & DiscussionThe AVD in the respiratory Mres reconstruction was lower than the AVD in the respiratory Mcorr reconstruction: 7.73 ± 6.54 ml vs. 20.0 ± 22.4 ml, respectively (n = 15, p-value = 0.03). The 3D Dice coefficient between the DL-segmented masks and the manually segmented masks was higher for Mres images than for Mcorr images: 0.90 ± 0.02 vs. 0.87 ± 0.03 respectively, with a p-value = 0.02. Sharpness on Mres images was higher than on Mcorr images: 0.15 ± 0.05 vs. 0.12 ± 0.04, respectively, with a p-value of 0.014 (n = 15).ConclusionWe conclude that the DL-based 3D automatic LV segmentation network trained on CT images and fine-tuned on MR images generalized better on Mres images than on Mcorr images for quantifying LV volumes

Geographic and temporal trends in the molecular epidemiology and genetic mechanisms of transmitted HIV-1 drug resistance:an individual-patient- and sequence-level meta-analysis

Regional and subtype-specific mutational patterns of HIV-1 transmitted drug resistance (TDR) are essential for informing first-line antiretroviral (ARV) therapy guidelines and designing diagnostic assays for use in regions where standard genotypic resistance testing is not affordable. We sought to understand the molecular epidemiology of TDR and to identify the HIV-1 drug-resistance mutations responsible for TDR in different regions and virus subtypes.status: publishe

Time to Switch to Second-line Antiretroviral Therapy in Children With Human Immunodeficiency Virus in Europe and Thailand.

Background: Data on durability of first-line antiretroviral therapy (ART) in children with human immunodeficiency virus (HIV) are limited. We assessed time to switch to second-line therapy in 16 European countries and Thailand. Methods: Children aged <18 years initiating combination ART (≥2 nucleoside reverse transcriptase inhibitors [NRTIs] plus nonnucleoside reverse transcriptase inhibitor [NNRTI] or boosted protease inhibitor [PI]) were included. Switch to second-line was defined as (i) change across drug class (PI to NNRTI or vice versa) or within PI class plus change of ≥1 NRTI; (ii) change from single to dual PI; or (iii) addition of a new drug class. Cumulative incidence of switch was calculated with death and loss to follow-up as competing risks. Results: Of 3668 children included, median age at ART initiation was 6.1 (interquartile range (IQR), 1.7-10.5) years. Initial regimens were 32% PI based, 34% nevirapine (NVP) based, and 33% efavirenz based. Median duration of follow-up was 5.4 (IQR, 2.9-8.3) years. Cumulative incidence of switch at 5 years was 21% (95% confidence interval, 20%-23%), with significant regional variations. Median time to switch was 30 (IQR, 16-58) months; two-thirds of switches were related to treatment failure. In multivariable analysis, older age, severe immunosuppression and higher viral load (VL) at ART start, and NVP-based initial regimens were associated with increased risk of switch. Conclusions: One in 5 children switched to a second-line regimen by 5 years of ART, with two-thirds failure related. Advanced HIV, older age, and NVP-based regimens were associated with increased risk of switch

Segmentation and differentiation of biofilm structures

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Accelerating MR Neuroimaging of Stroke Using Sparse Acquisition Coupled with Nonlinear Reconstruction Techniques

The guiding theme of my research is to accelerate and improve magnetic resonance (MR) imaging such that it becomes the clinical modality of choice in diagnosing, treating, and hopefully preventing stroke. Stroke, be it ischemic or haemorrhagic, is a leading cause of death and permanent disability worldwide: it is a medical emergency that requires rapid diagnosis to initiate early patient treatment and prevent irreversible brain injury. Computed tomography (CT) is currently the preferred imaging modality due to its high spatial and temporal resolution. MR imaging is a slower technique than CT, but it offers a significantly broader and more varied set of image contrasts and functional information than CT. Simply stated, the goal of my research is to accelerate the MR acquisition and/or increase resolution without sacrificing image quality in order to provide high quality diagnostic information. The most obvious way to scan faster is to acquire fewer data points, although this can often yield undesired reductions in image quality such as blurring, aliasing, or ghosting artefacts. Fortunately, numerous recent developments using multiple channel receiver coils and advanced reconstruction techniques are overcoming these drawbacks. This doctoral thesis investigates many of these advanced signal acquisition and processing techniques as they apply to stroke. In terms of diagnosis, I compare several state-of-the-art paradigms to accelerate key sequences of an acute MR stroke protocol. For treatment, I describe an enhanced passive MR catheter tracking approach that enables continuous monitoring of the catheter during endovascular procedures. And finally, with regards to stroke prevention, I present a novel imaging technique for assessing atherosclerosis in carotid arteries. In all cases, numerical and experimental verifications provided diagnostic images of very high quality (and comparable to conventional MR scans), albeit acquired 2 to 6 times faster. This work and continued efforts worldwide are inching us closer to making MR imaging the modality of choice in the comprehensive management of acute stroke patients

Improvement in RCA Vessel Sharpness using the 2D-T2-Prep for R = 1,3, and 6.

<p>Improvement in RCA Vessel Sharpness using the 2D-T2-Prep for R = 1,3, and 6.</p

Improvement in the mean vessel sharpness, as measured in a coronary-mimicking phantom, when using a 2D-T₂-Prep instead of a conventional T₂-Prep, for GRAPPA accelerations of R = 1,2,3,4,5, and 6.

<p>Results are shown for a "vessel" section <b>a)</b> parallel to the accelerated direction (gray triangles) and <b>b)</b> perpendicular to the accelerated direction (black squares). As artefacts propagate along the accelerated direction, the parallel case acts as a vessel sharpness control, whereas the perpendicular case may be used to determine the relative benefit of the 2D-T₂-Prep.</p