An Open Source Motion Planning Framework for Autonomous Minimally Invasive Surgical Robots

Planning and execution of autonomous tasks in minimally invasive surgical robotic are significantly more complex with respect to generic manipulators. Narrow abdominal cavities and limited entry points restrain the use of external vision systems and specialized kinematics prevent the straightforward use of standard planning algorithms. In this work, we present a novel implementation of a motion planning framework for minimally invasive surgical robots, composed of two subsystems: An arm-camera registration method only requiring the endoscopic camera and a graspable device, compatible with a 12mm trocar port, and a specialized trajectory planning algorithm, designed to generate smooth, non straight trajectories. The approach is tested on a DaVinci Research Kit obtaining an accuracy of 2.71±0.89 cm in the arm-camera registration and of 1.30±0.39 cm during trajectory execution. The code is organised into STORM Motion Library (STOR-MoLib), an open source library, publicly available for the research community

Renal replacement therapy-requiring acute kidney injury due to tubulointerstitial nephritis and uveitis syndrome: case report

Background Acute kidney injury is a major challenge for today’s healthcare systems around the globe. Renal replacement therapy has been shown to be beneficial in acute kidney injury, but treatment highly depends on the cause of the acute kidney injury. One less common cause is tubulointerstitial nephritis, which comes in different entities. A very rare type of tubulointerstitial nephritis is tubulointerstitial nephritis and uveitis syndrome, in which the patient presents with additional uveitis. Case presentation A 19-year-old caucasian male presented with mild dyspnea, lack of appetite, weight loss, and moderate itchiness. Lab results showed an acute kidney injury with marked increase of serum creatinine. The patient was started on prednisolone immediately after admission. As the patient in this case showed symptoms of uremia on admission, we decided to establish renal replacement therapy, which is unusual in tubulointerstitial nephritis and uveitis syndrome. During his course of dialysis, the patient developed symptoms of sepsis probably due to a catheter-related infection requiring intensive care and antibiotic treatment, which had to be terminated early as the patient developed a rash. Intensified immunosuppression, combined with antibiotics, significantly resolved excretory kidney dysfunction. Conclusions Since both the primary inflammatory process and the secondary infectious complication significantly impaired excretory kidney function, kidney function of younger individuals with new-onset anterior uveitis should be monitored over time and during follow-up

Towards Autonomous Robotic Minimally Invasive Ultrasound Scanning and Vessel Reconstruction on Non-Planar Surfaces

Autonomous robotic Ultrasound (US) scanning has been the subject of research for more than 2 decades. However, little work has been done to apply this concept into a minimally invasive setting, in which accurate force sensing is generally not available and robot kinematics are unreliable due to the tendon-driven, compliant robot structure. As a result, the adequate orientation of the probe towards the tissue surface remains unknown and the anatomy reconstructed from scan may become highly inaccurate. In this work we present solutions to both of these challenges: an attitude sensor fusion scheme for improved kinematic sensing and a visual, deep learning based algorithm to establish and maintain contact between the organ surface and the US probe. We further introduce a novel scheme to estimate and orient the probe perpendicular to the center line of a vascular structure. Our approach enables, for the first time, to autonomously scan across a non-planar surface and navigate along an anatomical structure with a robotically guided minimally invasive US probe. Our experiments on a vessel phantom with a convex surface confirm a significant improvement of the reconstructed curved vessel geometry, with our approach strongly reducing the mean positional error and variance. In the future, our approach could help identify vascular structures more effectively and help pave the way towards semi-autonomous assistance during partial hepatectomy and the potential to reduce procedure length and complication rates

The Role of Millimeter-Waves in the Distance Measurement Accuracy of an FMCW Radar Sensor

High-accuracy, short-range distance measurement is required in a variety of industrial applications e.g., positioning of robots in a fully automated production process, level measurement of liquids in small containers. An FMCW radar sensor is suitable for this purpose, since many of these applications involve harsh environments. Due to the progress in the field of semiconductor technology, FMCW radar sensors operating in different millimeter-wave frequency bands are available today. An important question in this context, which has not been investigated so far is how does a millimeter-wave frequency band influence the sensor accuracy, when thousands of distance measurements are performed with a sensor. This topic has been dealt with for the first time in this paper. The method used for analyzing the FMCW radar signal combines a frequency- and phase-estimation algorithm. The frequency-estimation algorithm based on the fast Fourier transform and the chirp-z transform provides a coarse estimate of the target distance. Subsequently, the phase-estimation algorithm based on a cross-correlation function provides a fine estimate of the target distance. The novel aspects of this paper are as follows. First, the estimation theory concept of Cramér-Rao lower bound (CRLB) has been used to compare the accuracy of two millimeter-wave FMCW radars operating at 60 GHz and 122 GHz. In this comparison, the measurement parameters (e.g., bandwidth, signal-to-noise ratio) as well as the signal-processing algorithm used for both the radars are the same, thus ensuring an unbiased comparison of the FMCW radars, solely based on the choice of millimeter-wave frequency band. Second, the improvement in distance measurement accuracy obtained after each step of the combined frequency- and phase-estimation algorithm has been experimentally demonstrated for both the radars. A total of 5100 short-range distance measurements are made using the 60 GHz and 122 GHz FMCW radar. The measurement results are analyzed at various stages of the frequency- and phase-estimation algorithm and the measurement error is calculated using a nanometer-precision linear motor. At every stage, the mean error values measured with the 60 GHz and 122 GHz FMCW radars are compared. The final accuracy achieved using both radars is of the order of a few micrometers. The measured standard deviation values of the 60 GHz and 122 GHz FMCW radar have been compared against the CRLB. As predicted by the CRLB, this paper experimentally validates for the first time that the 122 GHz FMCW radar provides a higher repeatability of micrometer-accuracy distance measurements than the 60 GHz FMCW radar. View Full-Tex

A Comparative Study of Spatio-Temporal U-Nets for Tissue Segmentation in Surgical Robotics

In surgical robotics, the ability to achieve high levels of autonomy is often limited by the complexity of the surgical scene. Autonomous interaction with soft tissues requires machines able to examine and understand the endoscopic video streams in real-time and identify the features of interest. In this work, we show the first example of spatio-temporal neural networks, based on the U-Net, aimed at segmenting soft tissues in endoscopic images. The networks, equipped with Long Short-Term Memory and Attention Gate cells, can extract the correlation between consecutive frames in an endoscopic video stream, thus enhancing the segmentation’s accuracy with respect to the standard U-Net. Initially, three configurations of the spatiotemporal layers are compared to select the best architecture. Afterwards, the parameters of the network are optimised and finally the results are compared with the standard U-Net. An accuracy of 83:77%±2:18% and a precision of 78:42%±7:38% are achieved by implementing both Long Short Term Memory (LSTM) convolutional layers and Attention Gate blocks. The results, although originated in the context of surgical tissue retraction, could benefit many autonomous tasks such as ablation, suturing and debridement

Diversity of Eukaryotic DNA Replication Origins Revealed by Genome-Wide Analysis of Chromatin Structure

Eukaryotic DNA replication origins differ both in their efficiency and in the characteristic time during S phase when they become active. The biological basis for these differences remains unknown, but they could be a consequence of chromatin structure. The availability of genome-wide maps of nucleosome positions has led to an explosion of information about how nucleosomes are assembled at transcription start sites, but no similar maps exist for DNA replication origins. Here we combine high-resolution genome-wide nucleosome maps with comprehensive annotations of DNA replication origins to identify patterns of nucleosome occupancy at eukaryotic replication origins. On average, replication origins contain a nucleosome depleted region centered next to the ACS element, flanked on both sides by arrays of well-positioned nucleosomes. Our analysis identified DNA sequence properties that correlate with nucleosome occupancy at replication origins genome-wide and that are correlated with the nucleosome-depleted region. Clustering analysis of all annotated replication origins revealed a surprising diversity of nucleosome occupancy patterns. We provide evidence that the origin recognition complex, which binds to the origin, acts as a barrier element to position and phase nucleosomes on both sides of the origin. Finally, analysis of chromatin reconstituted in vitro reveals that origins are inherently nucleosome depleted. Together our data provide a comprehensive, genome-wide view of chromatin structure at replication origins and suggest a model of nucleosome positioning at replication origins in which the underlying sequence occludes nucleosomes to permit binding of the origin recognition complex, which then (likely in concert with nucleosome modifiers and remodelers) positions nucleosomes adjacent to the origin to promote replication origin function

Cell Lineage Specific Distribution of H3K27 Trimethylation Accumulation in an In Vitro Model for Human Implantation

Female mammals inactivate one of their two X-chromosomes to compensate for the difference in gene-dosage with males that have just one X-chromosome. X-chromosome inactivation is initiated by the expression of the non-coding RNA Xist, which coats the X-chromosome in cis and triggers gene silencing. In early mouse development the paternal X-chromosome is initially inactivated in all cells of cleavage stage embryos (imprinted X-inactivation) followed by reactivation of the inactivated paternal X-chromosome exclusively in the epiblast precursors of blastocysts, resulting temporarily in the presence of two active X-chromosomes in this specific lineage. Shortly thereafter, epiblast cells randomly inactivate either the maternal or the paternal X-chromosome. XCI is accompanied by the accumulation of histone 3 lysine 27 trimethylation (H3K27me3) marks on the condensed X-chromosome. It is still poorly understood how XCI is regulated during early human development. Here we have investigated lineage development and the distribution of H3K27me3 foci in human embryos derived from an in-vitro model for human implantation. In this system, embryos are co-cultured on decidualized endometrial stromal cells up to day 8, which allows the culture period to be extended for an additional two days. We demonstrate that after the co-culture period, the inner cell masses have relatively high cell numbers and that the GATA4-positive hypoblast lineage and OCT4-positive epiblast cell lineage in these embryos have segregated. H3K27me3 foci were observed in ∼25% of the trophectoderm cells and in ∼7.5% of the hypoblast cells, but not in epiblast cells. In contrast with day 8 embryos derived from the co-cultures, foci of H3K27me3 were not observed in embryos at day 5 of development derived from regular IVF-cultures. These findings indicate that the dynamics of H3K27me3 accumulation on the X-chromosome in human development is regulated in a lineage specific fashion

Variability of Sequence Surrounding the Xist Gene in Rodents Suggests Taxon-Specific Regulation of X Chromosome Inactivation

One of the two X chromosomes in female mammalian cells is subject to inactivation (XCI) initiated by the Xist gene. In this study, we examined in rodents (voles and rat) the conservation of the microsatellite region DXPas34, the Tsix gene (antisense counterpart of Xist), and enhancer Xite that have been shown to flank Xist and regulate XCI in mouse. We have found that mouse regions of the Tsix gene major promoter and minisatellite repeat DXPas34 are conserved among rodents. We have also shown that in voles and rat the region homologous to the mouse Tsix major promoter, initiates antisense to Xist transcription and terminates around the Xist gene start site as is observed with mouse Tsix. A conservation of Tsix expression pattern in voles, rat and mice suggests a crucial role of the antisense transcription in regulation of Xist and XIC in rodents. Most surprisingly, we have found that voles lack the regions homologous to the regulatory element Xite, which is instead replaced with the Slc7a3 gene that is unassociated with the X-inactivation centre in any other eutherians studied. Furthermore, we have not identified any transcription that could have the same functions as murine Xite in voles. Overall, our data show that not all the functional elements surrounding Xist in mice are well conserved even within rodents, thereby suggesting that the regulation of XCI may be at least partially taxon-specific

Nuclear Mitochondrial DNA Activates Replication in Saccharomyces cerevisiae

The nuclear genome of eukaryotes is colonized by DNA fragments of mitochondrial origin, called NUMTs. These insertions have been associated with a variety of germ-line diseases in humans. The significance of this uptake of potentially dangerous sequences into the nuclear genome is unclear. Here we provide functional evidence that sequences of mitochondrial origin promote nuclear DNA replication in Saccharomyces cerevisiae. We show that NUMTs are rich in key autonomously replicating sequence (ARS) consensus motifs, whose mutation results in the reduction or loss of DNA replication activity. Furthermore, 2D-gel analysis of the mrc1 mutant exposed to hydroxyurea shows that several NUMTs function as late chromosomal origins. We also show that NUMTs located close to or within ARS provide key sequence elements for replication. Thus NUMTs can act as independent origins, when inserted in an appropriate genomic context or affect the efficiency of pre-existing origins. These findings show that migratory mitochondrial DNAs can impact on the replication of the nuclear region they are inserted in