Deep residual networks for automatic segmentation of laparoscopic videos of the liver

MOTIVATION: For primary and metastatic liver cancer patients undergoing liver resection, a laparoscopic approach can reduce recovery times and morbidity while offering equivalent curative results; however, only about 10% of tumours reside in anatomical locations that are currently accessible for laparoscopic resection. Augmenting laparoscopic video with registered vascular anatomical models from pre-procedure imaging could support using laparoscopy in a wider population. Segmentation of liver tissue on laparoscopic video supports the robust registration of anatomical liver models by filtering out false anatomical correspondences between pre-procedure and intra-procedure images. In this paper, we present a convolutional neural network (CNN) approach to liver segmentation in laparoscopic liver procedure videos. METHOD: We defined a CNN architecture comprising fully-convolutional deep residual networks with multi-resolution loss functions. The CNN was trained in a leave-one-patient-out cross-validation on 2050 video frames from 6 liver resections and 7 laparoscopic staging procedures, and evaluated using the Dice score. RESULTS: The CNN yielded segmentations with Dice scores ≥0.95 for the majority of images; however, the inter-patient variability in median Dice score was substantial. Four failure modes were identified from low scoring segmentations: minimal visible liver tissue, inter-patient variability in liver appearance, automatic exposure correction, and pathological liver tissue that mimics non-liver tissue appearance. CONCLUSION: CNNs offer a feasible approach for accurately segmenting liver from other anatomy on laparoscopic video, but additional data or computational advances are necessary to address challenges due to the high inter-patient variability in liver appearance

p53 Activation by Knockdown Technologies

Morpholino phosphorodiamidate antisense oligonucleotides (MOs) and short interfering RNAs (siRNAs) are commonly used platforms to study gene function by sequence-specific knockdown. Both technologies, however, can elicit undesirable off-target effects. We have used several model genes to study these effects in detail in the zebrafish, Danio rerio. Using the zebrafish embryo as a template, correct and mistargeting effects are readily discernible through direct comparison of MO-injected animals with well-studied mutants. We show here indistinguishable off-targeting effects for both maternal and zygotic mRNAs and for both translational and splice-site targeting MOs. The major off-targeting effect is mediated through p53 activation, as detected through the transferase-mediated dUTP nick end labeling assay, acridine orange, and p21 transcriptional activation assays. Concurrent knockdown of p53 specifically ameliorates the cell death induced by MO off-targeting. Importantly, reversal of p53-dependent cell death by p53 knockdown does not affect specific loss of gene function, such as the cell death caused by loss of function of chordin. Interestingly, quantitative reverse-transcriptase PCR, microarrays and whole-mount in situ hybridization assays show that MO off-targeting effects are accompanied by diagnostic transcription of an N-terminal truncated p53 isoform that uses a recently recognized internal p53 promoter. We show here that MO off-targeting results in induction of a p53-dependent cell death pathway. p53 activation has also recently been shown to be an unspecified off-target effect of siRNAs. Both commonly used knockdown technologies can thus induce secondary but sequence-specific p53 activation. p53 inhibition could potentially be applicable to other systems to suppress off-target effects caused by other knockdown technologies

Anaplastic Lymphoma Kinase Is Required for Neurogenesis in the Developing Central Nervous System of Zebrafish

10.1371/journal.pone.0063757PLoS ONE85

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

p53 Activation by Knockdown Technologies

Morpholino phosphorodiamidate antisense oligonucleotides (MOs) and short interfering RNAs (siRNAs) are commonly used platforms to study gene function by sequence-specific knockdown. Both technologies, however, can elicit undesirable off-target effects. We have used several model genes to study these effects in detail in the zebrafish, Danio rerio. Using the zebrafish embryo as a template, correct and mistargeting effects are readily discernible through direct comparison of MO-injected animals with well-studied mutants. We show here indistinguishable off-targeting effects for both maternal and zygotic mRNAs and for both translational and splice-site targeting MOs. The major off-targeting effect is mediated through p53 activation, as detected through the transferase-mediated dUTP nick end labeling assay, acridine orange, and p21 transcriptional activation assays. Concurrent knockdown of p53 specifically ameliorates the cell death induced by MO off-targeting. Importantly, reversal of p53-dependent cell death by p53 knockdown does not affect specific loss of gene function, such as the cell death caused by loss of function of chordin. Interestingly, quantitative reverse-transcriptase PCR, microarrays and whole-mount in situ hybridization assays show that MO off-targeting effects are accompanied by diagnostic transcription of an N-terminal truncated p53 isoform that uses a recently recognized internal p53 promoter. We show here that MO off-targeting results in induction of a p53-dependent cell death pathway. p53 activation has also recently been shown to be an unspecified off-target effect of siRNAs. Both commonly used knockdown technologies can thus induce secondary but sequence-specific p53 activation. p53 inhibition could potentially be applicable to other systems to suppress off-target effects caused by other knockdown technologies

Intraoperative Liver Surface Completion with Graph Convolutional VAE

In this work we propose a method based on geometric deep learning to predict the complete surface of the liver, given a partial point cloud of the organ obtained during the surgical laparoscopic procedure. We introduce a new data augmentation technique that randomly perturbs shapes in their frequency domain to compensate the limited size of our dataset. The core of our method is a variational autoencoder (VAE) that is trained to learn a latent space for complete shapes of the liver. At inference time, the generative part of the model is embedded in an optimisation procedure where the latent representation is iteratively updated to generate a model that matches the intraoperative partial point cloud. The effect of this optimisation is a progressive non-rigid deformation of the initially generated shape. Our method is qualitatively evaluated on real data and quantitatively evaluated on synthetic data. We compared with a state-of-the-art rigid registration algorithm, that our method outperformed in visible areas

Synthesis, thin film deposition and optical characterization of epithiopropylcarbazole polymer

Carbazolic copolymer namely epithiopropylcarbazole with glycidyl butyrate have been developed to be used in holographic recording. This paper describes an analysis, from synthesis of the material to its applications, together with the corresponding characterizations. The investigated materials were photosensitive copolymers obtained from epithiopropylcarbazole (ETPC) with glycidyl butyrate (GB). A detailed investigation was undertaken involving infrared spectroscopy in order to establish the chemical structure and the composition of the copolymer. Each step of chemical synthesis was carefully controlled by IR analysis. Spin coating procedure using programmable spin-coater was used to obtain the thin films. The thickness of the polymer film was varied by changing the concentration of polymer solution. It was shown the linear thickness dependence on polymer concentration. Photoinduced phenomena were investigated by UV-VIS and IR spectroscopy. In comparison with other carbazole-containing polymers, copolymer epithiopropylcarbazole with glycidyl butyrate have no changes in UV-VIS transmission spectra after irradiation. And only IR spectroscopy could be applied to distinguish such changes. Holographic recording were applied for recording characteristics investigation. It was shown that via a holographic recording process, it is possible to hide record of holograms and read it only after chemical etching. The surface of etched diffraction gratings were characterized by atomic force microscopy analysis

Yield Assessment of Off-grid PV Systems in Nigeria

Off-grid PV systems are providing critical access to energy services for millions of people throughout the globe. However, optimum sizing of these PV systems still poses a challenge, as inadequate system sizing could result in low system reliability and/or high cost of electricity generated. This paper presents a hybrid method of sizing off-grid PV systems for undefined electricity consumption. It then compares this sizing with off-grid PV systems installed in Nigeria - ranked the most populous electricity-deficit country in the world. The yields of the installed off-grid PV systems are also simulated for four major cities in Nigeria. Results show that for the over 1.5MWp of off-grid PV systems installed in the country, there is a potential 1.11 – 3.04 MWh of unutilised surplus electricity, which can supply 2hours of green electricity to at least 2,000 Tier-2 households during peak demand in the dry hot season. Thus, our hybrid model provides design and operational insight to off-grid PV system optimizatio

CARNIVORA FROM THE EARLY PLEISTOCENE OF GRĂUNCEANU (OLTEŢ RIVER VALLEY, DACIAN BASIN, ROMANIA)

The Grăunceanu site in the Olteţ River Valley has yielded a rich carnivoran assemblage including at least 10, possibly 11 species: Vulpes alopecoides, Nyctereutes megamastoides, Ursus etruscus, Meles thorali, Lutraeximia sp., Pliocrocuta perrieri, Lynx issiodorensis, Puma pardoides, Megantereon cultridens, Homotherium latidens and possibly Pachycrocuta brevirostris. The faunal assemblage is compared with approximately coeval sites Europe and western Asia. This comparative analysis shows that the Grăunceanu assemblage shows the greatest similarities with sites to the west such as Senèze and, particularly, Saint-Vallier, rather than more easternly ones such as Liventsovka and Dmanisi. The relative abundance of the taxa at Grăunceanu was compared to that of Saint-Vallier and broad similarities were found, except for the absence of some cursorially adapted taxa present at Saint-Vallier but absent from Grăunceanu. The absence at Grăunceanu of taxa with a reconstructed cursorial hunting strategy, such as Chasmaporthetes and Acinonyx, may suggest less open habitat at Grăunceanu than indicated in previous paleoenvironmental reconstructions

Semantic Web Tools and Decision-Making

Semantic Web technologies are intertwined with decision-making processes. In this paper the general objectives of the semantic web tools are reviewed and characterized, as well as the categories of decision support tools, in order to establish an intersection of utility and use. We also elaborate on actual and foreseen possibilities for a deeper integration, considering the actual implementation, opportunities and constraints in the decision-making context.info:eu-repo/semantics/publishedVersio