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The success of embolisation, a minimally invasive treatment of liver cancer, could be evaluated in the operational room with cone-beam CT by acquiring a dynamic perfusion scan. The reconstruction algorithm must address the issues of low temporal sampling and higher noise levels inherent in cone-beam CT systems, compared to conventional CT. Therefore, a model-based perfusion reconstruction based on the time separation technique (TST) was applied. TST uses basis functions to model time attenuation curves. These functions are either analytical or based on prior knowledge, extracted using singular value decomposition from CT perfusion data. To explore how well the prior knowledge can model perfusion dynamics and what the potential limitations are, the dynamic CBCT perfusion scan was simulated under different noise levels. The TST method was compared to static reconstruction. It was demonstrated that a set consisting of only four basis functions results in perfusion maps that preserve relevant information, denoises the data, and outperforms static reconstruction under higher noise levels. TST with prior knowledge would not only outperform static reconstruction, but also the TST with analytical basis functions. Furthermore, it has been shown that only eight CBCT rotations, unlike previously assumed ten, are sufficient to obtain the perfusion maps comparable to the reference CT perfusion maps. This contributes to saving dose and reconstruction time. The real dynamic CBCT perfusion scan, reconstructed under the same conditions as the simulated scan, shows potential for maintaining the accuracy of the perfusion maps. By visual inspection, the embolised region was matching to that in corresponding CT perfusion maps. Further analysis of a larger cohort of patient data is needed to draw final conclusions regarding the expected advantages of the time separation technique., Comment: 28 pages, 11 figures

We introduce a novel lattice-gas cellular automaton (LGCA) for compressible vectorial active matter with polar and nematic velocity alignment. Interactions are, by construction, zero-range. For polar alignment, we show the system undergoes a phase transition that promotes aggregation with strong resemblance to the classic zero-range process. We find that above a critical point, the states of a macroscopic fraction of the particles in the system coalesce into the same state, sharing the same position and momentum (polar condensate). For nematic alignment, the system also exhibits condensation, but there exist fundamental differences: a macroscopic fraction of the particles in the system collapses into a filament, where particles possess only two possible momenta. Furthermore, we derive hydrodynamic equations for the active LGCA model to understand the phase transitions and condensation that undergoes the system. We also show that generically the discrete lattice symmetries -- e.g. of a square or hexagonal lattice -- affect drastically the emergent large-scale properties of on-lattice active systems. The study puts in evidence that aligning active matter on the lattice displays new behavior, including phase transitions to states that share similarities to condensation models.

Approximate Bayesian Computation (ABC) is a widely applicable and popular approach to estimating unknown parameters of mechanistic models. As ABC analyses are computationally expensive, parallelization on high-performance infrastructure is often necessary. However, the existing parallelization strategies leave resources unused at times and thus do not optimally leverage them yet. We present look-ahead scheduling, a wall-time minimizing parallelization strategy for ABC Sequential Monte Carlo algorithms, which utilizes all available resources at practically all times by proactive sampling for prospective tasks. Our strategy can be integrated in e.g. adaptive distance function and summary statistic selection schemes, which is essential in practice. Evaluation of the strategy on different problems and numbers of parallel cores reveals speed-ups of typically 10-20% and up to 50% compared to the best established approach. Thus, the proposed strategy allows to substantially improve the cost and run-time efficiency of ABC methods on high-performance infrastructure.

Lead time data is compositional data found frequently in the hospitality industry. Hospitality businesses earn fees each day, however these fees cannot be recognized until later. For business purposes, it is important to understand and forecast the distribution of future fees for the allocation of resources, for business planning, and for staffing. Motivated by 5 years of daily fees data, we propose a new class of Bayesian time series models, a Bayesian Dirichlet Auto-Regressive Moving Average (B-DARMA) model for compositional time series, modeling the proportion of future fees that will be recognized in 11 consecutive 30 day windows and 1 last consecutive 35 day window. Each day's compositional datum is modeled as Dirichlet distributed given the mean and a scale parameter. The mean is modeled with a Vector Autoregressive Moving Average process after transforming with an additive log ratio link function and depends on previous compositional data, previous compositional parameters and daily covariates. The B-DARMA model offers solutions to data analyses of large compositional vectors and short or long time series, offers efficiency gains through choice of priors, provides interpretable parameters for inference, and makes reasonable forecasts.

The Covid-19 pandemic led to several challenges in everybody working life. Many companies worldwide enabled comprehensive remote work settings for their employees. Agile Software Development Teams are affected by the switch to remote work as agile methods setting communication and collaboration in focus. The well-being and motivation of software engineers and developers, which impacting their performance, are influenced by specific context factors. This paper aims to analyze identify specific context factors for a good remote work setting. We designed a single case study at a German ecommerce company and conducted an experiment using a gamification approach including eight semi-structured interviews. Our results show, that the agile software development team members to their health. Furthermore, most the team members value the gamification approach to put more focus on physical activities and the health well-being. We discuss several practical implications and provide recommendations for other teams and companies.

Computational models have great potential to accelerate bioscience, bioengineering, and medicine. However, it remains challenging to reproduce and reuse simulations, in part, because the numerous formats and methods for simulating various subsystems and scales remain siloed by different software tools. For example, each tool must be executed through a distinct interface. To help investigators find and use simulation tools, we developed BioSimulators (https://biosimulators.org), a central registry of the capabilities of simulation tools and consistent Python, command-line, and containerized interfaces to each version of each tool. The foundation of BioSimulators is standards, such as CellML, SBML, SED-ML, and the COMBINE archive format, and validation tools for simulation projects and simulation tools that ensure these standards are used consistently. To help modelers find tools for particular projects, we have also used the registry to develop recommendation services. We anticipate that BioSimulators will help modelers exchange, reproduce, and combine simulations., Comment: 6 pages, 2 figures

Bile, the central metabolic product of the liver, is secreted by hepatocytes into bile canaliculi (BC), tubular subcellular structures of 0.5-2 $\mu$m diameter which are formed by the apical membranes of juxtaposed hepatocytes. BC interconnect to build a highly ramified 3D network that collects and transports bile towards larger interlobular bile ducts (IBD). The transport mechanism of bile is of fundamental interest and the current text-book model of "osmotic canalicular bile flow", i.e. enforced by osmotic water influx, has recently been quantitatively verified based on flux measurements and BC contractility (Meyer et al., 2017) but challenged in the article entitled "Intravital dynamic and correlative imaging reveals diffusion-dominated canalicular and flow-augmented ductular bile flux" (Vartak et al., 2020). We feel compelled to share a series of arguments that question the key conclusions of this study (Vartak et al., 2020), particularly because it risks to be misinterpreted and misleading for the field in view of potential clinical applications. We summarized the arguments in the following 8 points., Comment: 8 pages, 4 figures

Research software has become a central asset in academic research. It optimizes existing and enables new research methods, implements and embeds research knowledge, and constitutes an essential research product in itself. Research software must be sustainable in order to understand, replicate, reproduce, and build upon existing research or conduct new research effectively. In other words, software must be available, discoverable, usable, and adaptable to new needs, both now and in the future. Research software therefore requires an environment that supports sustainability. Hence, a change is needed in the way research software development and maintenance are currently motivated, incentivized, funded, structurally and infrastructurally supported, and legally treated. Failing to do so will threaten the quality and validity of research. In this paper, we identify challenges for research software sustainability in Germany and beyond, in terms of motivation, selection, research software engineering personnel, funding, infrastructure, and legal aspects. Besides researchers, we specifically address political and academic decision-makers to increase awareness of the importance and needs of sustainable research software practices. In particular, we recommend strategies and measures to create an environment for sustainable research software, with the ultimate goal to ensure that software-driven research is valid, reproducible and sustainable, and that software is recognized as a first class citizen in research. This paper is the outcome of two workshops run in Germany in 2019, at deRSE19 - the first International Conference of Research Software Engineers in Germany - and a dedicated DFG-supported follow-up workshop in Berlin., Comment: Official position paper 001 of de-RSE e.V. - Society for Research Software (https://de-rse.org) --- 16 pages, 1 figure + 1 page supplementary material, 4 figures --- Submitted to the F1000 Research Science Policy Research Gateway on 2020-04-03

How epithelial cells coordinate their polarity to form functional tissues is an open question in cell biology. Here, we characterize a unique type of polarity found in liver tissue, nematic cell polarity, which is different from vectorial cell polarity in simple, sheet-like epithelia. We propose a conceptual and algorithmic framework to characterize complex patterns of polarity proteins on the surface of a cell in terms of a multipole expansion. To rigorously quantify previously observed tissue-level patterns of nematic cell polarity (Morales-Navarette et al., eLife 8:e44860, 2019), we introduce the concept of co-orientational order parameters, which generalize the known biaxial order parameters of the theory of liquid crystals. Applying these concepts to three-dimensional reconstructions of single cells from high-resolution imaging data of mouse liver tissue, we show that the axes of nematic cell polarity of hepatocytes exhibit local coordination and are aligned with the biaxially anisotropic sinusoidal network for blood transport. Our study characterizes liver tissue as a biological example of a biaxial liquid crystal. The general methodology developed here could be applied to other tissues or in-vitro organoids., Comment: 27 pages, 9 color figures

A photoacoustic (PA) sensor for fast and real-time gas sensing is demonstrated. The PA sensor is a standalone system controlled by a Field-Programmable Gate Array (FPGA). The PA cell has been designed for flow noise immunity using computational fluid dynamics (CFD) analysis. The aim of the CFD analysis was to investigate and minimize the influence of the gas distribution and the flow noise on the PA signal. PA measurements were conducted at different flow rates by exciting molecular C-H stretch vibrational bands of hexane (C$_6$H$_{14}$) and decane (C$_{10}$H$_{22}$) molecules in clean air at 2950 cm$^{-1}$ (3.38 $\mu$m) with a custom made mid-infrared interband cascade laser (ICL). We observe a (1$\sigma$, standard deviation) sensitivity of 0.4 $\pm0.1$ ppb (nmol/mol) for hexane in clean air at flow rates up to 1.7 L/min, corresponding to a normalized noise equivalent absorption (NNEA) coefficient of 2.5$\times 10^{-9}$ W cm$^{-1}$ Hz$^{-1/2}$, demonstrating high sensitivity and fast real-time gas analysis. An Allan deviation analysis for decane shows that the detection limit at optimum integration time is 0.25 ppbV (nmol/mol)., Comment: 6 pages, 5 figures

The polarisation of cells and tissues is fundamental for tissue morphogenesis during biological development and regeneration. A deeper understanding of biological polarity pattern formation can be gained from the consideration of pattern reorganisation in response to an opposing instructive cue, which we here consider by example of experimentally inducible body axis inversions in planarian flatworms. Our dynamically diluted alignment model represents three processes: entrainment of cell polarity by a global signal, local cell-cell coupling aligning polarity among neighbours and cell turnover inserting initially unpolarised cells. We show that a persistent global orienting signal determines the final mean polarity orientation in this stochastic model. Combining numerical and analytical approaches, we find that neighbour coupling retards polarity pattern reorganisation, whereas cell turnover accelerates it. We derive a formula for an effective neighbour coupling strength integrating both effects and find that the time of polarity reorganisation depends linearly on this effective parameter and no abrupt transitions are observed. This allows to determine neighbour coupling strengths from experimental observations. Our model is related to a dynamic $8$-Potts model with annealed site-dilution and makes testable predictions regarding the polarisation of dynamic systems, such as the planarian epithelium., Comment: Preprint as prior to first submission to Journal of the Royal Society Interface. 25 pages, 6 figures, plus supplement (18 pages, contains 1 table and 7 figures). A supplementary movie is available from https://dx.doi.org/10.6084/m9.figshare.c3887818

We demonstrate an online (in-situ) sensor for continuous detection of oil contamination in compressed air systems complying with the ISO-8573 standard. The sensor is based on the photo-acoustic (PA) effect. The online and real-time PA sensor system has the potential to benefit a wide range of users that require high purity compressed air. Among these are hospitals, pharmaceutical industries, electronics manufacturers, and clean room facilities. The sensor was tested for sensitivity, repeatability, robustness to molecular cross-interference, and stability of calibration. Explicit measurements of hexane (C${_6}$H$_{14}$) and decane (C${_{10}}$H$_{22}$) vapors via excitation of molecular C-H vibrations at approx. 2950 cm$^{-1}$ (3.38 $\mu$m) were conducted with a custom made interband cascade laser (ICL). For the decane measurements a (1 $\sigma$) standard deviation (STD) of 0.3 ppb was demonstrated, which corresponds to a normalized noise equivalent absorption (NNEA) coefficient for the prototype PA sensor of 2.8$\times 10^{-9}$ W cm$^{-1}$ Hz$^{1/2}$., Comment: 6 pages, 7 figures

Endocytosis underlies many cellular functions including signaling and nutrient uptake. The endocytosed cargo gets redistributed across a dynamic network of endosomes undergoing fusion and fission. Here, a theoretical approach is reviewed which can explain how the microscopic properties of endosome interactions cause the emergent macroscopic properties of cargo trafficking in the endosomal network. Predictions by the theory have been tested experimentally and include the inference of dependencies and parameter values of the microscopic processes. This theory could also be used to infer mechanisms of signal-trafficking crosstalk. It is applicable to in vivo systems since fixed samples at few time points suffice as input data., Comment: review, 11 pages, 3 figures

A photoacoustic (PA) sensor based on higher order acoustic modes is demonstrated. The PA sensor is designed to enhance the gas-detection performance and simultaneously suppress ambient noise sources (e.g. flow noise, electrical noise and external acoustic noise). Two microphones are used and positioned such that the PA signals are ($\pi$) out of phase. Ambient acoustic noise are approximately in the same phase and will be subtracted and thus improve the SNR. In addition, by placing the gas in- and outlets so that the gas flows through the node of the first higher order membrane mode the coupling of flow noise is approximately 20 dB lower compared with flow through the fundamental mode at 5 L/min. The noise reduction and thus the increase in sensitivity is demonstrated by measuring vibrational lines of methanol and methane using a broadband interband cascade laser emitting radiation at 3.38 $\mu$m. A signal-to-noise improvement of 20 (26 dB) using higher order modes are demonstrated compared with the fundamental mode. The maximum normalized noise equivalent absorption coefficient is 1.1 $\times 10^{-6}$ W cm$^{-1}$ Hz$^{1/2}$ for a flow of 5 L/min. It is anticipated that the noise cancelation strategy may find use in many practical industrial and environmental PA sensors, where ambient noise sources plays a crucial role for the absolute sensitive., Comment: 5 pages, 5 figures

A compact versatile photoacoustic (PA) sensor for trace gas detection is reported. The sensor is based on an integrating sphere as the PA absorption cell with an organ pipe tube attached to increase the sensitivity of the PA sensor. The versatility and enhancement of the sensitivity of the PA signal is investigated by monitoring specific ro-vibrational lines of CO2 in the 2 mm wavelength region and of NO2 in the 405 nm region. The measured enhancement factor of the PA signal exceeds 1200, which is due to the acoustic resonance of the tube and the absorption enhancement of the integrating sphere relatively to a non-resonant single pass cell. It is observed that the background absorption signals are highly attenuated due to the thermal conduction and diffusion effects in the polytetrafluoroethylene cell walls. This demonstrates that careful choice of cell wall materials can be highly beneficial to the sensitivity of the PA sensor. These properties makes the sensor suitable for various practical sensor applications in the ultraviolet to the near infrared wavelength region, including climate, environmental and industrial monitoring., Comment: Accepted for publication in optics express

We report measurements of the isotope shifts of the (3s3p)$^3$P$_{0,1,2}$ - (3s4s)$^3$S$_1$ Mg I transitions for the stable isotopes $^{24}$Mg (I=0), $^{25}$Mg (I=5/2) and $^{26}$Mg (I=0). Furthermore the $^{25}$Mg $^3$S$_1$ hyperfine coefficient A($^3$S$_1$) = (-321.6 $\pm$ 1.5) MHz is extracted and found to be in excellent agreement with state-of-the-art theoretical predictions giving A($^3$S$_1$) = -325 MHz and B($^3$S$_1$) $\simeq 10^{-5}$ MHz. Compared to previous measurements, the data presented in this work is improved up to a factor of ten., Comment: 4 pages, 4 figures submitted to PRA