Automatic, global registration in laparoscopic liver surgery

PURPOSE: The initial registration of a 3D pre-operative CT model to a 2D laparoscopic video image in augmented reality systems for liver surgery needs to be fast, intuitive to perform and with minimal interruptions to the surgical intervention. Several recent methods have focussed on using easily recognisable landmarks across modalities. However, these methods still need manual annotation or manual alignment. We propose a novel, fully automatic pipeline for 3D-2D global registration in laparoscopic liver interventions. METHODS: Firstly, we train a fully convolutional network for the semantic detection of liver contours in laparoscopic images. Secondly, we propose a novel contour-based global registration algorithm to estimate the camera pose without any manual input during surgery. The contours used are the anterior ridge and the silhouette of the liver. RESULTS: We show excellent generalisation of the semantic contour detection on test data from 8 clinical cases. In quantitative experiments, the proposed contour-based registration can successfully estimate a global alignment with as little as 30% of the liver surface, a visibility ratio which is characteristic of laparoscopic interventions. Moreover, the proposed pipeline showed very promising results in clinical data from 5 laparoscopic interventions. CONCLUSIONS: Our proposed automatic global registration could make augmented reality systems more intuitive and usable for surgeons and easier to translate to operating rooms. Yet, as the liver is deformed significantly during surgery, it will be very beneficial to incorporate deformation into our method for more accurate registration

ABCD Neurocognitive Prediction Challenge 2019: Predicting Individual Residual Fluid Intelligence Scores from Cortical Grey Matter Morphology

We predicted fluid intelligence from T1-weighted MRI data available as part of the ABCD NP Challenge 2019, using morphological similarity of grey-matter regions across the cortex. Individual structural covariance networks (SCN) were abstracted into graph-theory metrics averaged over nodes across the brain and in data-driven communities/modules. Metrics included degree, path length, clustering coefficient, centrality, rich club coefficient, and small-worldness. These features derived from the training set were used to build various regression models for predicting residual fluid intelligence scores, with performance evaluated both using cross-validation within the training set and using the held-out validation set. Our predictions on the test set were generated with a support vector regression model trained on the training set. We found minimal improvement over predicting a zero residual fluid intelligence score across the sample population, implying that structural covariance networks calculated from T1-weighted MR imaging data provide little information about residual fluid intelligence

Real-time control of distributed batteries with blockchain-enabled market export commitments

Recent years have seen a surge of interest in distributed residential batteries for households with renewable generation. Yet, assuring battery assets are profitable for their owners requires a complex optimisation of the battery asset and additional revenue sources, such as novel ways to access wholesale energy markets. In this paper, we propose a framework in which wholesale market bids are placed on forward energy markets by an aggregator of distributed residential batteries that are controlled in real time by a novel Home Energy Management System (HEMS) control algorithm to meet the market commitments, while maximising local self-consumption. The proposed framework consists of three stages. In the first stage, an optimal day-ahead or intra-day scheduling of the aggregated storage assets is computed centrally. For the second stage, a bidding strategy is developed for wholesale energy markets. Finally, in the third stage, a novel HEMS real-time control algorithm based on a smart contract allows coordination of residential batteries to meet the market commitments and maximise self-consumption of local production. Using a case study provided by a large UK-based energy demonstrator, we apply the framework to an aggregator with 70 residential batteries. Experimental analysis is done using real per minute data for demand and production. Results indicate that the proposed approach increases the aggregator’s revenues by 35% compared to a case without residential flexibility, and increases the self-consumption rate of the households by a factor of two. The robustness of the results to uncertainty, forecast errors and to communication latency is also demonstrated

ruvA Mutants that resolve Holliday junctions but do not reverse replication forks

RuvAB and RuvABC complexes catalyze branch migration and resolution of Holliday junctions (HJs) respectively. In addition to their action in the last steps of homologous recombination, they process HJs made by replication fork reversal, a reaction which occurs at inactivated replication forks by the annealing of blocked leading and lagging strand ends. RuvAB was recently proposed to bind replication forks and directly catalyze their conversion into HJs. We report here the isolation and characterization of two separation-of-function ruvA mutants that resolve HJs, based on their capacity to promote conjugational recombination and recombinational repair of UV and mitomycin C lesions, but have lost the capacity to reverse forks. In vivo and in vitro evidence indicate that the ruvA mutations affect DNA binding and the stimulation of RuvB helicase activity. This work shows that RuvA's actions at forks and at HJs can be genetically separated, and that RuvA mutants compromised for fork reversal remain fully capable of homologous recombination

Breathing motion compensated registration of laparoscopic liver ultrasound to CT

Laparoscopic Ultrasound (LUS) is regularly used during laparoscopic liver resection to locate critical vascular structures. Many tumours are iso-echoic, and registration to pre-operative CT or MR has been proposed as a method of image guidance. However, factors such as abdominal insufflation, LUS probe compression and breathing motion cause deformation of the liver, making this task far from trivial. Fortunately, within a smaller local region of interest a rigid solution can suffice. Also, the respiratory cycle can be expected to be consistent. Therefore, in this paper we propose a feature-based local rigid registration method to align tracked LUS data with CT while compensating for breathing motion. The method employs the Levenberg-Marquardt Iterative Closest Point (LMICP) algorithm, registers both on liver surface and vessels and requires two LUS datasets, one for registration and another for breathing estimation. Breathing compensation is achieved by fitting a 1D breathing model to the vessel points. We evaluate the algorithm by measuring the Target Registration Error (TRE) of three manually selected landmarks of a single porcine subject. Breathing compensation improves accuracy in 77% of the measurements. In the best case, TRE values below 3mm are obtained. We conclude that our method can potentially correct for breathing motion without gated acquisition of LUS and be integrated in the surgical workflow with an appropriate segmentation

A simplified multi-criteria evaluation model for landfill site ranking and selection based on AHP and GIS

This study used GIS based Multi-criteria Decision Analysis (MCDA) approach for evaluating the most environmentally suitable landfill sites in the study area. The weights of relative importance of the factors guiding landfill siting were estimated using pair-wise comparisons in AHP. The maps showing suitable landfill sites were generated applying a weighted linear combination (WLC) in GIS using a comparison matrix to aggregate different significant scenarios associated with environmental and economic objectives. To determine the appropriate areas where landfill sites can be located, thematic maps for all the criteria were generated using GIS. A final map was produced showing suitability for the location of the landfill sites. The suitable sites having an area equal to or above 4 ha at one place and 90% of which is barren land were considered suitable for landfill. The selected candidate sites were ranked to get the most desirable sites for landfill

Heavy reliance on plants for Romanian cave bears evidenced by amino acid nitrogen isotope analysis

Heavy reliance on plants is rare in Carnivora and mostly limited to relatively small species in subtropical settings. The feeding behaviors of extinct cave bears living during Pleistocene cold periods at middle latitudes have been intensely studied using various approaches including isotopic analyses of fossil collagen. In contrast to cave bears from all other regions in Europe, some individuals from Romania show exceptionally high δ15N values that might be indicative of meat consumption. Herbivory on plants with high δ15N values cannot be ruled out based on this method, however. Here we apply an approach using the δ15N values of individual amino acids from collagen that offsets the baseline δ15N variation among environments. The analysis yielded strong signals of reliance on plants for Romanian cave bears based on the δ15N values of glutamate and phenylalanine. These results could suggest that the high variability in bulk collagen δ15N values observed among cave bears in Romania reflects niche partitioning but in a general trophic context of herbivory

CSAP localizes to polyglutamylated microtubules and promotes proper cilia function and zebrafish development

The diverse populations of microtubule polymers in cells are functionally distinguished by different posttranslational modifications, including polyglutamylation. Polyglutamylation is enriched on subsets of microtubules including those found in the centrioles, mitotic spindle, and cilia. However, whether this modification alters intrinsic microtubule dynamics or affects extrinsic associations with specific interacting partners remains to be determined. Here we identify the microtubule-binding protein centriole and spindle–associated protein (CSAP), which colocalizes with polyglutamylated tubulin to centrioles, spindle microtubules, and cilia in human tissue culture cells. Reducing tubulin polyglutamylation prevents CSAP localization to both spindle and cilia microtubules. In zebrafish, CSAP is required for normal brain development and proper left–right asymmetry, defects that are qualitatively similar to those reported previously for depletion of polyglutamylation-conjugating enzymes. We also find that CSAP is required for proper cilia beating. Our work supports a model in which polyglutamylation can target selected microtubule-associated proteins, such as CSAP, to microtubule subpopulations, providing specific functional capabilities to these populations.National Institutes of Health (U.S.) (Grant no. GM074746)American Cancer Society. Research Scholar Grant (121776)National Institute of General Medical Sciences (U.S.) (GM088313

Critical Early Roles for col27a1a and col27a1b in Zebrafish Notochord Morphogenesis, Vertebral Mineralization and Post-embryonic Axial Growth

Fibrillar collagens are well known for their links to human diseases, with which all have been associated except for the two most recently identified fibrillar collagens, type XXIV collagen and type XXVII collagen. To assess functions and potential disease phenotypes of type XXVII collagen, we examined its roles in zebrafish embryonic and post-embryonic development.We identified two type XXVII collagen genes in zebrafish, col27a1a and col27a1b. Both col27a1a and col27a1b were expressed in notochord and cartilage in the embryo and early larva. To determine sites of type XXVII collagen function, col27a1a and col27a1b were knocked down using morpholino antisense oligonucleotides. Knockdown of col27a1a singly or in conjunction with col27a1b resulted in curvature of the notochord at early stages and formation of scoliotic curves as well as dysmorphic vertebrae at later stages. These defects were accompanied by abnormal distributions of cells and protein localization in the notochord, as visualized by transmission electron microscopy, as well as delayed vertebral mineralization as detected histologically.Together, our findings indicate a key role for type XXVII collagen in notochord morphogenesis and axial skeletogenesis and suggest a possible human disease phenotype

Fishing the Molecular Bases of Treacher Collins Syndrome

Treacher Collins syndrome (TCS) is an autosomal dominant disorder of craniofacial development, and mutations in the TCOF1 gene are responsible for over 90% of TCS cases. The knowledge about the molecular mechanisms responsible for this syndrome is relatively scant, probably due to the difficulty of reproducing the pathology in experimental animals. Zebrafish is an emerging model for human disease studies, and we therefore assessed it as a model for studying TCS. We identified in silico the putative zebrafish TCOF1 ortholog and cloned the corresponding cDNA. The derived polypeptide shares the main structural domains found in mammals and amphibians. Tcof1 expression is restricted to the anterior-most regions of zebrafish developing embryos, similar to what happens in mouse embryos. Tcof1 loss-of-function resulted in fish showing phenotypes similar to those observed in TCS patients, and enabled a further characterization of the mechanisms underlying craniofacial malformation. Besides, we initiated the identification of potential molecular targets of treacle in zebrafish. We found that Tcof1 loss-of-function led to a decrease in the expression of cellular proliferation and craniofacial development. Together, results presented here strongly suggest that it is possible to achieve fish with TCS-like phenotype by knocking down the expression of the TCOF1 ortholog in zebrafish. This experimental condition may facilitate the study of the disease etiology during embryonic development