A surgical activity model of laparoscopic cholecystectomy for co-operation with collaborative robots.

BACKGROUND: Laparoscopic cholecystectomy is a very frequent surgical procedure. However, in an ageing society, less surgical staff will need to perform surgery on patients. Collaborative surgical robots (cobots) could address surgical staff shortages and workload. To achieve context-awareness for surgeon-robot collaboration, the intraoperative action workflow recognition is a key challenge. METHODS: A surgical process model was developed for intraoperative surgical activities including actor, instrument, action and target in laparoscopic cholecystectomy (excluding camera guidance). These activities, as well as instrument presence and surgical phases were annotated in videos of laparoscopic cholecystectomy performed on human patients (n = 10) and on explanted porcine livers (n = 10). The machine learning algorithm Distilled-Swin was trained on our own annotated dataset and the CholecT45 dataset. The validation of the model was conducted using a fivefold cross-validation approach. RESULTS: In total, 22,351 activities were annotated with a cumulative duration of 24.9 h of video segments. The machine learning algorithm trained and validated on our own dataset scored a mean average precision (mAP) of 25.7% and a top K = 5 accuracy of 85.3%. With training and validation on our dataset and CholecT45, the algorithm scored a mAP of 37.9%. CONCLUSIONS: An activity model was developed and applied for the fine-granular annotation of laparoscopic cholecystectomies in two surgical settings. A machine recognition algorithm trained on our own annotated dataset and CholecT45 achieved a higher performance than training only on CholecT45 and can recognize frequently occurring activities well, but not infrequent activities. The analysis of an annotated dataset allowed for the quantification of the potential of collaborative surgical robots to address the workload of surgical staff. If collaborative surgical robots could grasp and hold tissue, up to 83.5% of the assistant's tissue interacting tasks (i.e. excluding camera guidance) could be performed by robots.

A large 'Active Magnetic Shield' for a high-precision experiment: nEDM collaboration.

We present a novel Active Magnetic Shield (AMS), designed and implemented for the n2EDM experiment at the Paul Scherrer Institute. The experiment will perform a high-sensitivity search for the electric dipole moment of the neutron. Magnetic-field stability and control is of key importance for n2EDM. A large, cubic, 5 m side length, magnetically shielded room (MSR) provides a passive, quasi-static shielding-factor of about 105 for its inner sensitive volume. The AMS consists of a system of eight complex, feedback-controlled compensation coils constructed on an irregular grid spanned on a volume of less than 1000 m3 around the MSR. The AMS is designed to provide a stable and uniform magnetic-field environment around the MSR, while being reasonably compact. The system can compensate static and variable magnetic fields up to ±50µT (homogeneous components) and ±5µT/m (first-order gradients), suppressing them to a few µT in the sub-Hertz frequency range. The presented design concept and implementation of the AMS fulfills the requirements of the n2EDM experiment and can be useful for other applications, where magnetically silent environments are important and spatial constraints inhibit simpler geometrical solutions.

Ensuring privacy protection in the era of big laparoscopic video data: development and validation of an inside outside discrimination algorithm (IODA).

BACKGROUND: Laparoscopic videos are increasingly being used for surgical artificial intelligence (AI) and big data analysis. The purpose of this study was to ensure data privacy in video recordings of laparoscopic surgery by censoring extraabdominal parts. An inside-outside-discrimination algorithm (IODA) was developed to ensure privacy protection while maximizing the remaining video data. METHODS: IODAs neural network architecture was based on a pretrained AlexNet augmented with a long-short-term-memory. The data set for algorithm training and testing contained a total of 100 laparoscopic surgery videos of 23 different operations with a total video length of 207 h (124 min ± 100 min per video) resulting in 18,507,217 frames (185,965 ± 149,718 frames per video). Each video frame was tagged either as abdominal cavity, trocar, operation site, outside for cleaning, or translucent trocar. For algorithm testing, a stratified fivefold cross-validation was used. RESULTS: The distribution of annotated classes were abdominal cavity 81.39%, trocar 1.39%, outside operation site 16.07%, outside for cleaning 1.08%, and translucent trocar 0.07%. Algorithm training on binary or all five classes showed similar excellent results for classifying outside frames with a mean F1-score of 0.96 ± 0.01 and 0.97 ± 0.01, sensitivity of 0.97 ± 0.02 and 0.0.97 ± 0.01, and a false positive rate of 0.99 ± 0.01 and 0.99 ± 0.01, respectively. CONCLUSION: IODA is able to discriminate between inside and outside with a high certainty. In particular, only a few outside frames are misclassified as inside and therefore at risk for privacy breach. The anonymized videos can be used for multi-centric development of surgical AI, quality management or educational purposes. In contrast to expensive commercial solutions, IODA is made open source and can be improved by the scientific community.

The very large n2EDM magnetically shielded room with an exceptional performance for fundamental physics measurements.

We present the magnetically shielded room (MSR) for the n2EDM experiment at the Paul Scherrer Institute, which features an interior cubic volume with each side of length 2.92 m, thus providing an accessible space of 25 m3. The MSR has 87 openings of diameter up to 220 mm for operating the experimental apparatus inside and an intermediate space between the layers for housing sensitive signal processing electronics. The characterization measurements show a remanent magnetic field in the central 1 m3 below 100 pT and a field below 600 pT in the entire inner volume, up to 4 cm to the walls. The quasi-static shielding factor at 0.01 Hz measured with a sinusoidal 2 µT peak-to-peak signal is about 100 000 in all three spatial directions and increases rapidly with frequency to reach 108 above 1 Hz.

Ultracold neutron storage and transport at the PSI UCN source.

Efficient neutron transport is a key ingredient to the performance of ultracold neutron (UCN) sources, important to meeting the challenges placed by high precision fundamental physics experiments. At the Paul Scherrer Institute's UCN source we have been continuously improving our understanding of the UCN source parameters by performing a series of studies to characterize neutron production and moderation, and UCN production, extraction, and transport efficiency to the beamport. The present study on the absolute UCN transport efficiency completes our previous publications. We report on complementary measurements, namely one on the height-dependent UCN density and a second on the transmission of a calibrated quantity of UCN over a ∼ 16  m long UCN guide section connecting one beamport via the source storage vessel to another beamport. These allow us quantifying and optimizing the performance of the guide system based on extensive Monte Carlo simulations.

The design of the n2EDM experiment: nEDM Collaboration.

We present the design of a next-generation experiment, n2EDM, currently under construction at the ultracold neutron source at the Paul Scherrer Institute (PSI) with the aim of carrying out a high-precision search for an electric dipole moment of the neutron. The project builds on experience gained with the previous apparatus operated at PSI until 2017, and is expected to deliver an order of magnitude better sensitivity with provision for further substantial improvements. An overview is of the experimental method and setup is given, the sensitivity requirements for the apparatus are derived, and its technical design is described.

Data blinding for the nEDM experiment at PSI.

Psychological bias towards, or away from, prior measurements or theory predictions is an intrinsic threat to any data analysis. While various methods can be used to try to avoid such a bias, e.g. actively avoiding looking at the result, only data blinding is a traceable and trustworthy method that can circumvent the bias and convince a public audience that there is not even an accidental psychological bias. Data blinding is nowadays a standard practice in particle physics, but it is particularly difficult for experiments searching for the neutron electric dipole moment (nEDM), as several cross measurements, in particular of the magnetic field, create a self-consistent network into which it is hard to inject a false signal. We present an algorithm that modifies the data without influencing the experiment. Results of an automated analysis of the data are used to change the recorded spin state of a few neutrons within each measurement cycle. The flexible algorithm may be applied twice (or more) to the data, thus providing the option of sequentially applying various blinding offsets for separate analysis steps with independent teams. The subtle manner in which the data are modified allows one subsequently to adjust the algorithm and to produce a re-blinded data set without revealing the initial blinding offset. The method was designed for the 2015/2016 measurement campaign of the nEDM experiment at the Paul Scherrer Institute. However, it can be re-used with minor modification for the follow-up experiment n2EDM, and may be suitable for comparable projects elsewhere.

Measurement of the Permanent Electric Dipole Moment of the Neutron.

We present the result of an experiment to measure the electric dipole moment (EDM) of the neutron at the Paul Scherrer Institute using Ramsey's method of separated oscillating magnetic fields with ultracold neutrons. Our measurement stands in the long history of EDM experiments probing physics violating time-reversal invariance. The salient features of this experiment were the use of a ^{199}Hg comagnetometer and an array of optically pumped cesium vapor magnetometers to cancel and correct for magnetic-field changes. The statistical analysis was performed on blinded datasets by two separate groups, while the estimation of systematic effects profited from an unprecedented knowledge of the magnetic field. The measured value of the neutron EDM is d_{n}=(0.0±1.1_{stat}±0.2_{sys})×10^{-26} e.cm.

Nisin incorporation enhances the inactivation of lactic acid bacteria during the acid wash step of bioethanol production from sugarcane juice.

Bioethanol fermentation is continuously exposed to contamination by Lactic Acid Bacteria (LAB). In this study, the effect of adding nisin (250 mg l-1 ) to the acid wash on the viability of five bacterial contaminants were evaluated both alone and in co-incubation with Saccharomyces cerevisiae. Additionally, fed-batch fermentation was performed using an acid or acid/nisin wash for S. cerevisiae alone and cocultured with the LAB strains. Parameters such as ethanol production, sugar consumption and lactic acid production were monitored. Four model LAB were more susceptible to the acid/nisin wash than the acid wash, and were most susceptible when incubated with yeast. A fifth model LAB was very sensitive to both treatments regardless of the presence of yeast. The addition of nisin to the acid wash lowered the required time for adequate washing and resulted in a higher ethanol production (54·5 ± 0·1 g l-1 ) than the acid wash alone (52·6 ± 0·1 g l-1 ) in a subsequent fermentation. These results indicate the potential benefits of supplementing with nisin to improve the acid wash step of bioethanol fermentations. SIGNIFICANCE AND IMPACT OF THE STUDY: Acid washing by the bioethanol fermentation industry reduces yeast efficiency and selects for contaminant bacteria that are resistant to acid treatments. This study demonstrates that the incorporation of nisin into the acid wash step results in a more potent removal of lactic acid bacteria while significantly shortening the length of time needed for the acid wash.

Yeast Derived LysA2 Can Control Bacterial Contamination in Ethanol Fermentation.

Contamination of fuel-ethanol fermentations continues to be a significant problem for the corn and sugarcane-based ethanol industries. In particular, members of the Lactobacillaceae family are the primary bacteria of concern. Currently, antibiotics and acid washing are two major means of controlling contaminants. However, antibiotic use could lead to increased antibiotic resistance, and the acid wash step stresses the fermenting yeast and has limited effectiveness. Bacteriophage endolysins such as LysA2 are lytic enzymes with the potential to contribute as antimicrobials to the fuel ethanol industries. Our goal was to evaluate the potential of yeast-derived LysA2 as a means of controlling Lactobacillaceae contamination. LysA2 intracellularly produced by Pichia pastoris showed activity comparable to Escherichia coli produced LysA2. Lactic Acid Bacteria (LAB) with the A4α peptidoglycan chemotype (L-Lys-D-Asp crosslinkage) were the most sensitive to LysA2, though a few from that chemotype were insensitive. Pichia-expressed LysA2, both secreted and intracellularly produced, successfully improved ethanol productivity and yields in glucose (YPD60) and sucrose-based (sugarcane juice) ethanol fermentations in the presence of a LysA2 susceptible LAB contaminant. LysA2 secreting Sacharomyces cerevisiae did not notably improve production in sugarcane juice, but it did control bacterial contamination during fermentation in YPD60. Secretion of LysA2 by the fermenting yeast, or adding it in purified form, are promising alternative tools to control LAB contamination during ethanol fermentation. Endolysins with much broader lytic spectrums than LysA2 could supplement or replace the currently used antibiotics or the acidic wash.

Creative lysins: Listeria and the engineering of antimicrobial enzymes.

Cell wall lytic enzymes have been of increasing interest as antimicrobials for targeting Gram-positive spoilage and pathogenic bacteria, largely due to the development of strains resistant to antibiotics and bacteriophage therapy. Such lysins show considerable promise against Listeria monocytogenes, a primary concern in food-processing environments, but there is room for improvement via protein engineering. Advances in antilisterial applications could benefit from recent developments in lysin biotechnology that have largely targeted other organisms. Herein we present various considerations for the future development of lysins, including environmental factors, cell physiology concerns, and dynamics of protein architecture. Our goal is to review key developments in lysin biotechnology to provide a contextual framework for the current models of lysin-cell interactions and highlight key considerations for the characterization and design of novel lytic enzymes.

Observation of Gravitationally Induced Vertical Striation of Polarized Ultracold Neutrons by Spin-Echo Spectroscopy.

We describe a spin-echo method for ultracold neutrons (UCNs) confined in a precession chamber and exposed to a |B0|=1 µT magnetic field. We have demonstrated that the analysis of UCN spin-echo resonance signals in combination with knowledge of the ambient magnetic field provides an excellent method by which to reconstruct the energy spectrum of a confined ensemble of neutrons. The method takes advantage of the relative dephasing of spins arising from a gravitationally induced striation of stored UCNs of different energies, and also permits an improved determination of the vertical magnetic-field gradient with an exceptional accuracy of 1.1 pT/cm. This novel combination of a well-known nuclear resonance method and gravitationally induced vertical striation is unique in the realm of nuclear and particle physics and should prove to be invaluable for the assessment of systematic effects in precision experiments such as searches for an electric dipole moment of the neutron or the measurement of the neutron lifetime.

Test of Lorentz invariance with spin precession of ultracold neutrons.

A clock comparison experiment, analyzing the ratio of spin precession frequencies of stored ultracold neutrons and 199Hg atoms, is reported. No daily variation of this ratio could be found, from which is set an upper limit on the Lorentz invariance violating cosmic anisotropy field b perpendicular < 2 x 10(-20) eV (95% C.L.). This is the first limit for the free neutron. This result is also interpreted as a direct limit on the gravitational dipole moment of the neutron |gn| < 0.3 eV/c2 m from a spin-dependent interaction with the Sun. Analyzing the gravitational interaction with the Earth, based on previous data, yields a more stringent limit |gn| < 3 x 10(-4) eV/c2 m.

Direct experimental verification of neutron acceleration by the material optical potential of solid 2H2.

We have measured the acceleration of neutrons by the material optical potential of solid 2H2. Using a gravitational spectrometer, we find a minimal kinetic energy Ec = (99+/-7) neV of neutrons from a superthermal ultracold neutron (UCN) source with solid 2H2 as an UCN converter. The result is in excellent agreement with theoretical predictions, Ec = 106 neV.

Direct experimental limit on neutron-mirror-neutron oscillations.

In case a mirror world with a copy of our ordinary particle spectrum would exist, the neutron n and its degenerate partner, the mirror neutron n', could potentially mix and undergo nn' oscillations. The interaction of an ordinary magnetic field with the ordinary neutron would lift the degeneracy between the mirror partners, diminish the n' amplitude in the n wave function and, thus, suppress its observability. We report an experimental comparison of ultracold neutron storage in a trap with and without superimposed magnetic field. No influence of the magnetic field is found and, assuming negligible mirror magnetic fields, a limit on the oscillation time taunn' > 103 s (95% C.L.) is derived.

Cold neutron energy dependent production of ultracold neutrons in solid deuterium.

A measurement of the production of ultracold neutrons from velocity-selected cold neutrons on gaseous and solid deuterium targets is reported. The expected energy dependence for two-particle collisions with well defined neutron and Maxwell-Boltzmann distributed molecular velocities is found for the gas target. The solid target data agree in shape with the phonon density-of-states curve and provide strong evidence for the phonon model including multiphonon excitations.

Measured total cross sections of slow neutrons scattered by solid deuterium and implications for ultracold neutron sources.

The total scattering cross sections for slow neutrons with energies in the range 100 neV to 3 meV for solid ortho-2H2 at 18 and 5 K, frozen from the liquid, have been measured. The 18 K cross sections are found to be in excellent agreement with theoretical expectations and for ultracold neutrons dominated by thermal up scattering. At 5 K the total scattering cross sections are found to be dominated by the crystal defects originating in temperature induced stress but not deteriorated by temperature cycles between 5 and 10 K.

Measured total cross sections of slow neutrons scattered by gaseous and liquid 2H(2).

The total scattering cross sections for slow neutrons with energies E in the range 300 neV to 3 meV for gaseous and liquid ortho-2H2 have been measured. The cross sections for 2H2 gas are found to be in excellent agreement with both the Hamermesh and Schwinger and the Young and Koppel models. For liquid 2H(2), we confirm the existing experimental data in the cold neutron range and the discrepancy with the gas models. We find a clear 1 / square root[E'] dependence at low energies for both states. A simple explanation for the liquid 2H2 cross section is offered.

Magnetic Field Stabilization for Magnetically Shielded Volumes by External Field Coils.

For highly sensitive magnetic measurements, e.g., a measurement of the neutron electric dipole moment (EDM), the magnetic field has to be stable in time on a level below picoTesla. One of several measures we employ to achieve this uses an external field coil system which can stabilize the ambient external field at a predefined value. Here we report on the construction and characterization of such a system in the magnetic test facility at PSI. The system actively stabilizes the field along the axis of the EDM experiment by means of four coils in a Helmholtz-like configuration. Additional coils serve to compensate for transverse ambient field components. Because of the long integration times in the EDM experiment (about 100 s or more) only slow disturbances have to be corrected for. The performance of the system has been measured using static and moving magnetic sources and suppression factors in excess of 200 have been observed.