NeXtQSM -- A complete deep learning pipeline for data-consistent quantitative susceptibility mapping trained with hybrid data

Deep learning based Quantitative Susceptibility Mapping (QSM) has shown great potential in recent years, obtaining similar results to established non-learning approaches. Many current deep learning approaches are not data consistent, require in vivo training data or solve the QSM problem in consecutive steps resulting in the propagation of errors. Here we aim to overcome these limitations and developed a framework to solve the QSM processing steps jointly. We developed a new hybrid training data generation method that enables the end-to-end training for solving background field correction and dipole inversion in a data-consistent fashion using a variational network that combines the QSM model term and a learned regularizer. We demonstrate that NeXtQSM overcomes the limitations of previous deep learning methods. NeXtQSM offers a new deep learning based pipeline for computing quantitative susceptibility maps that integrates each processing step into the training and provides results that are robust and fast

Collaborative multi-scale 3D city and infrastructure modeling and simulation

Computer-aided collaborative and multi-scale 3D planning are challenges for complex railway and subway track infrastructure projects in the built environment. Many legal, economic, environmental, and structural requirements have to be taken into account. The stringent use of 3D models in the different phases of the planning process facilitates communication and collaboration between the stake holders such as civil engineers, geological engineers, and decision makers. This paper presents concepts, developments, and experiences gained by an interdisciplinary research group coming from civil engineering informatics and geo-informatics banding together skills of both, the Building Information Modeling and the 3D GIS world. New approaches including the development of a collaborative platform and 3D multi-scale modelling are proposed for collaborative planning and simulation to improve the digital 3D planning of subway tracks and other infrastructures. Experiences during this research and lessons learned are presented as well as an outlook on future research focusing on Building Information Modeling and 3D GIS applications for cities of the future

Robust estimation of bacterial cell count from optical density

Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data

A software tool to automatically evaluate and quantify diffusion weighted images

Diffusion weighted imaging (DWI) derived apparent diffusion coefficient (ADC) is currently used in identifying and post-therapy followup of several types of tumours. In brain tumours in particular ADC values are known to correlate inversely to tumour cellularity and high and low malignant areas can be distinguished based on ADC values. The average ADC value increases after successful chemotherapy, radiotherapy or a combination of both and is used as a surrogate marker for treatment response. More recently DWI derived ADC has been used to differentiate pancreatic cancer from healthy pancreatic tissue although with some limitations. A second DWI derived parameter, the perfusion fraction f has also shown promise in classifying pancreatic lesions. This parameter is estimated using special multiple b-value prototypes and the IVIM model. The main purpose of our project was to develop a software platform to assist radiologists in studying cancerous lesions by quantifying and mapping these two DWI derived parameters: ADC and perfusion fraction f. The platform we developed automatically calculates and maps the ADC and IVIM-model perfusion fraction f values from raw diffusion data. Furthermore, the software enables the automated delineation and ADC quantification of tissue sections in a fast, objective, user independent manner and has so far been applied to successfully delineating brain tumours. The perfusion fraction f mapping capabilities have so far been successfully applied to delineate pancreatic cancer lesions from healthy tissue. Further studies are in preparation to apply this software tool to study both ADC and perfusion fraction f in other types of cancerous lesions

Enhancing pancreatic adenocarcinoma delineation in diffusion derived intravoxel incoherent motion f-maps through automatic vessel and duct segmentation

Diffusion-based intravoxel incoherent motion imaging has recently gained interest as a method to detect and characterize pancreatic lesions, especially as it could provide a radiation- and contrast agent-free alternative to existing diagnostic methods. However, tumor delineation on intravoxel incoherent motion-derived parameter maps is impeded by poor lesion-to-pancreatic duct contrast in the f-maps and poor lesion-to-vessel contrast in the D-maps. The distribution of the diffusion and perfusion parameters within vessels, ducts, and tumors were extracted from a group of 42 patients with pancreatic adenocarcinoma. Clearly separable combinations of f and D were observed, and receiver operating characteristic analysis was used to determine the optimal cutoff values for an automated segmentation of vessels and ducts to improve lesion detection and delineation on the individual intravoxel incoherent motion-derived maps. Receiver operating characteristic analysis identified f = 0.28 as the cutoff for vessels (Area under the curve (AUC) = 0.901) versus tumor/duct and D = 1.85 \u3bcm(2) /ms for separating duct from tumor tissue (AUC = 0.988). These values were incorporated in an automatic segmentation algorithm and then applied to 42 patients. This yielded clearly improved tumor delineation compared to individual intravoxel incoherent motion-derived maps. Furthermore, previous findings that indicated that the f value in pancreatic cancer is strongly reduced compared to healthy pancreatic tissue were reconfirmed. Magn Reson Med, 2011. \ua9 2011 Wiley-Liss, Inc

The mitochondrial ribosomal of the large subunit, afo1p, determines cellular longevity through mitochondrial back-signaling via TOR1

Abstract: Yeast mother cell‐specific aging constitutes a model of replicative aging as it occurs in stem cell populations ofhigher eukaryotes. Here, we present a new long‐lived yeast deletion mutation, afo1 (for aging factor one), that confers a60% increase in replicative lifespan. AFO1/MRPL25 codes for a protein that is contained in the large subunit of themitochondrial ribosome. Double mutant experiments indicate that the longevity‐increasing action of the afo1 mutation isindependent of mitochondrial translation, yet involves the cytoplasmic Tor1p as well as the growth‐controllingtranscription factor Sfp1p. In their final cell cycle, the long‐lived mutant cells do show the phenotypes of yeast apoptosisindicating that the longevity of the mutant is not caused by an inaility to undergo programmed cell death. Furthermore,the afo1 mutation displays high resistance against oxidants. Despite the respiratory deficiency the mutant has paradoxicalincrease in growth rate compared to generic petite mutants. A comparison of the single and double mutant strains for afo1and fob1 shows that the longevity phenotype of afo1 is independen of the formation of ERCs (ribosomal DNA minicircles).AFO1/MRPL25 function establishes a new connection between mitochondria, metabolism and aging

The mitochondrial ribosomal of the large subunit, afo1p, determines cellular longevity through mitochondrial back-signaling via TOR1

Abstract: Yeast mother cell‐specific aging constitutes a model of replicative aging as it occurs in stem cell populations ofhigher eukaryotes. Here, we present a new long‐lived yeast deletion mutation, afo1 (for aging factor one), that confers a60% increase in replicative lifespan. AFO1/MRPL25 codes for a protein that is contained in the large subunit of themitochondrial ribosome. Double mutant experiments indicate that the longevity‐increasing action of the afo1 mutation isindependent of mitochondrial translation, yet involves the cytoplasmic Tor1p as well as the growth‐controllingtranscription factor Sfp1p. In their final cell cycle, the long‐lived mutant cells do show the phenotypes of yeast apoptosisindicating that the longevity of the mutant is not caused by an inaility to undergo programmed cell death. Furthermore,the afo1 mutation displays high resistance against oxidants. Despite the respiratory deficiency the mutant has paradoxicalincrease in growth rate compared to generic petite mutants. A comparison of the single and double mutant strains for afo1and fob1 shows that the longevity phenotype of afo1 is independen of the formation of ERCs (ribosomal DNA minicircles).AFO1/MRPL25 function establishes a new connection between mitochondria, metabolism and aging

Characterising highly active nuclear waste simulants

Reprocessing of spent nuclear fuel produces a highly active liquor (HAL) waste stream, which is typically stored over extended periods of many years in waste tanks equipped with extensive heat exchange capability. Over time, particulates are known to precipitate from the HAL within these tanks. Particle simulants provide a route for understanding the physical behaviour of these HAL solids under different agitation and transfer conditions. Particle and dispersion characterisation techniques are used here to understand the behaviour of two types of simulant HAL solids, viz. caesium phosphomolybdate (CPM) and zirconium molybdate (ZM), in dispersion. Distinct properties are established for CPM and ZM and compared to a common oxide particle material titanium dioxide (TiO). The results of this study highlight the influence of key aspects of the HAL particulates, such as size and shape, on relevant solid-liquid properties such as sedimentation and rheology. The influence of bulk liquid properties such as electrolyte concentration and pH is also investigated. The results indicate various possible behaviours within the tanks which may impact the storage, remobilisation and pipeline transport of this class of nuclear waste

The Traveling Heads 2.0: Multicenter Reproducibility of Quantitative Imaging Methods at 7 Tesla

ObjectThis study evaluates inter-site and intra-site reproducibility at ten different 7 T sites for quantitative brain imaging.Material and MethodsTwo subjects – termed the “traveling heads” – were imaged at ten different 7 T sites with a harmonized quantitative brain MR imaging protocol. In conjunction with the system calibration, MP2RAGE, QSM, CEST and multi-parametric mapping/relaxometry were examined.ResultsQuantitative measurements with MP2RAGE showed very high reproducibility across sites and subjects, and errors were in concordance with previous results and other field strengths. QSM had high inter-site reproducibility for relevant subcortical volumes. CEST imaging revealed systematic differences between the sites, but reproducibility was comparable to results in the literature. Relaxometry had also very high agreement between sites, but due to the high sensitivity, differences caused by different applications of the B1 calibration of the two RF coil types used were observed.ConclusionOur results show that quantitative brain imaging can be performed with high reproducibility at 7 T and with similar reliability as found at 3 T for multicenter studies of the supratentorial brain