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NASA-LaRc Flight-Critical Digital Systems Technology Workshop

The outcome is documented of a Flight-Critical Digital Systems Technology Workshop held at NASA-Langley December 13 to 15 1988. The purpose of the workshop was to elicit the aerospace industry's view of the issues which must be addressed for the practical realization of flight-critical digital systems. The workshop was divided into three parts: an overview session; three half-day meetings of seven working groups addressing aeronautical and space requirements, system design for validation, failure modes, system modeling, reliable software, and flight test; and a half-day summary of the research issues presented by the working group chairmen. Issues that generated the most consensus across the workshop were: (1) the lack of effective design and validation methods with support tools to enable engineering of highly-integrated, flight-critical digital systems, and (2) the lack of high quality laboratory and field data on system failures especially due to electromagnetic environment (EME).

Meissner, C. W., Jr.↗

FOREWORD: Satellite Remote Sensing Beyond 2015

Satellite remote sensing has progressed tremendously since the first Landsat was launched on June 23, 1972. Since the 1970s, satellite remote sensing and associated airborne and in situ measurements have resulted in vital and indispensable observations for understanding our planet through time. These observations have also led to dramatic improvements in numerical simulation models of the coupled atmosphere-land-ocean systems at increasing accuracies and predictive capability. The same observations document the Earth's climate and are driving the consensus that Homo sapiens is changing our climate through greenhouse gas emissions. These accomplishments are the combined work of many scientists from many countries and a dedicated cadre of engineers who build the instruments and satellites that collect Earth observation data from satellites, all working toward the goal of improving our understanding of the Earth. This edition of the Remote Sensing Handbook (Vol. I, II, and III) is a compendium of information for many research areas of our Planet that have contributed to our substantial progress since the 1970s. Remote sensing community is now using multiple sources of satellite and in situ data to advance our studies, what ever they might be. In the following paragraphs, I will illustrate how valuable and pivotal role satellite remote sensing has played in climate system study over last five decades, The Chapters in the Remote Sensing Handbook (Vol. I, II, and III) provides many other specific studies on land, water, and other applications using EO data of last five decades, The Landsat system of Earth-observing satellites has led the way in pioneering sustained observations of our planet. From 1972 to the present, at least one and sometimes two Landsat satellites have been in operation. Starting with the launch of the first NOAA-NASA Polar Orbiting Environmental Satellites NOAA-6 in 1978, improved imaging of land, clouds, and oceans and atmospheric soundings of temperature were accomplished. The NOAA system of polar-orbiting meteorological satellites has continued uninterrupted since that time, providing vital observations for numerical weather prediction. These same satellites are also responsible for the remarkable records of sea surface temperature and land vegetation index from the Advanced Very High Resolution Radiometers (AVHRR) that now span more than 33 years, although no one anticipated these valuable climate records from this instrument before the launch of NOAA-7 in 1981. The success of data from the AVHRR led to the design of the MODIS instruments on NASA's Earth Observing System of satellite platforms that improved substantially upon the AVHRR. The first of the EOS platforms, Terra, was launched in 2000 and the second of these platforms, Aqua, was launched in 2002.

Tucker, Compton J.↗

The seventh blind test of crystal structure prediction: structure ranking methods

A seventh blind test of crystal structure prediction has been organized by the Cambridge Crystallographic Data Centre. The results are presented in two parts, with this second part focusing on methods for ranking crystal structures in order of stability. The exercise involved standardized sets of structures seeded from a range of structure generation methods. Participants from 22 groups applied several periodic DFT-D methods, machine learned potentials, force fields derived from empirical data or quantum chemical calculations, and various combinations of the above. In addition, one non-energy-based scoring function was used. Results showed that periodic DFT-D methods overall agreed with experimental data within expected error margins, while one machine learned model, applying system-specific AIMnet potentials, agreed with experiment in many cases demonstrating promise as an efficient alternative to DFT-based methods. For target XXXII, a consensus was reached across periodic DFT methods, with consistently high predicted energies of experimental forms relative to the global minimum (above 4 kJ mol −1 at both low and ambient temperatures) suggesting a more stable polymorph is likely not yet observed. The calculation of free energies at ambient temperatures offered improvement of predictions only in some cases (for targets XXVII and XXXI). Several avenues for future research have been suggested, highlighting the need for greater efficiency considering the vast amounts of resources utilized in many cases.

Chemistry↗

RCEMIP-II: mock-Walker simulations as phase II of the radiative–convective equilibrium model intercomparison project

Abstract. The radiative–convective equilibrium (RCE) model intercomparison project (RCEMIP) leveraged the simplicity of RCE to focus attention on moist convective processes and their interactions with radiation and circulation across a wide range of model types including cloud-resolving models (CRMs), general circulation models (GCMs), single-column models, global cloud-resolving models, and large-eddy simulations. While several robust results emerged across the spectrum of models that participated in the first phase of RCEMIP (RCEMIP-I), two points that stand out are (1) the strikingly large diversity in simulated climate states and (2) the strong imprint of convective self-aggregation on the climate state. However, the lack of consensus in the structure of self-aggregation and its response to warming is a barrier to understanding. Gaining a deeper understanding of convective aggregation and tropical climate will require reducing the degrees of freedom with which convection can vary. Therefore, we propose phase II of RCEMIP (RCEMIP-II) that utilizes a prescribed sinusoidal sea surface temperature (SST) pattern to provide a constraint on the structure of convection and move one critical step up the model hierarchy. This so-called “mock-Walker” configuration generates features that resemble observed tropical circulations. The specification of the mock-Walker protocol for RCEMIP-II is described, along with example results from one CRM and one GCM. RCEMIP-II will consist of five required simulations: three simulations with the same three mean SSTs as in RCEMIP-I but with an SST gradient and two additional simulations at one of the mean SSTs with different values of the SST gradients. We also test the sensitivity to the imposed SST gradient and the domain size. Under weak SST gradients, unforced self-aggregation emerges across the entire domain, similar to what was found in RCEMIP. As the SST gradient increases, the convective region narrows and is more confined to the warmest SSTs. At warmer mean SSTs and stronger SST gradients, low-frequency variability in the convective aggregation emerges, suggesting that simulations of at least 200 d may be needed to achieve robust equilibrium statistics in this configuration. Simulations with different domain sizes generally have similar mean statistics and convective structures, depending on the value of the SST gradient. The prescribed SST boundary condition is the only difference in the set-up between RCEMIP-II and RCEMIP-I, which enables comparison between the two; however, we also welcome participation in RCEMIP-II from models that did not participate in RCEMIP-I.

Geology↗

The Completed SDSS-IV Extended Baryon Oscillation Spectroscopic Survey: N-body Mock Challenge for Galaxy Clustering Measurements

We develop a series of N-body data challenges, functional to the final analysis of the extended Baryon Oscillation Spectroscopic Survey (eBOSS) Data Release 16 (DR16) galaxy sample. The challenges are primarily based on high-fidelity catalogues constructed from the Outer Rim simulation - a large box size realization (3h(-1) Gpc) characterized by an unprecedented combination of volume and mass resolution, down to 1.85 x 10(9) h(-1)M(circle dot). We generate synthetic galaxy mocks by populating Outer Rim haloes with a variety of halo occupation distribution (HOD) schemes of increasing complexity, spanning different redshift intervals. We then assess the performance of three complementary redshift space distortion (RSD) models in configuration and Fourier space, adopted for the analysis of the complete DR16 eBOSS sample of Luminous Red Galaxies (LRG5). We find all the methods mutually consistent, with comparable systematic errors on the Alcock-Paczynski parameters and the growth of structure, and robust to different HOD prescriptions - thus validating the robustness of the models and the pipelines used for the baryon acoustic oscillation (BAO) and full shape clustering analysis. In particular, all the techniques are able to recover and alpha(11) to within 0.9 per cent, and f sigma(8) to within 1.5 per cent. As a by-product of our work, we are also able to gain interesting insights on the galaxy-halo connection. Our study is relevant for the final eBOSS DR16 'consensus cosmology', as the systematic error budget is informed by testing the results of analyses against these high-resolution mocks. In addition, it is also useful for future large-volume surveys, since similar mock-making techniques and systematic corrections can be readily extended to model for instance the Dark Energy Spectroscopic Instrument (DESI) galaxy sample.

cosmology: theory, large-scale structure of Univer↗

A Model for Turbulence Spectra in the Equilibrium Range of the Stable Atmospheric Boundary Layer

Stratification can cause turbulence spectra to deviate from Kolmogorov's isotropic -5/3 power law scaling in the universal equilibrium range at high Reynolds numbers. However, a consensus has not been reached with regard to the exact shape of the spectra. Here we propose a shape of the turbulent kinetic energy and temperature spectra in horizontal wavenumber for the equilibrium range that consists of three regimes at small Froude number: the buoyancy subrange, a transition region, and the isotropic inertial subrange through dimensional analysis and substantial revision of previous theoretical approximation. These spectral regimes are confirmed by various observations in the atmospheric boundary layer. The representation of the transition region in direct numerical simulations will require large-scale separation between the Dougherty-Ozmidov scale and the Kolmogorov scale for strongly stratified turbulence at high Reynolds numbers, which is still challenging computationally. In addition, we suggest that the failure of Monin-Obukhov similarity theory in the very stable atmospheric boundary layer is due to the fact that it does not consider the buoyancy scale that characterizes the transition region.

54 ENVIRONMENTAL SCIENCES↗

Icehouse Effect: A Selective Arctic Cooling Trend Current Models are Missing

The icehouse effect is a hypothesized climate feedback mechanism which could result in human-caused surface cooling trends in polar regions. Once understood in detail, it becomes apparent that these trends, which are discernable in the literature, but have been largely dismissed, do not conflict with the consensus assessment of the evidence, which infers century-scale Arctic warming. In fact, confirmation of the hypothesis would substantially strengthen the argument that there is a detectable human influence on today's climate. This apparent enigma is resolved only through careful attention to the detail of the hypothesis and the data supporting it. The posited surface cooling is entirely dependent on the existence of climate warming in layers capping the stable boundary layer. Also, the cooling is not pandemic, but is selective. It is readily revealed in properly sorted data by making use of the principles of micrometeorological similarity. Specifically, the cooling is manifest under a range of favorable turbulence conditions which can develop and disappear locally on time scales of minutes to hours because of the intrinsically intermittent nature of stable boundary layer turbulence. Because of the fine-scale nature of the processes which produce the cooling, modeling it is a difficult proposition. Vertical resolution on the order of 1 meter is required. Adequate models of intermittent surface fluxes coupled with radiation exchange do not currently exist, not as parameterizations for aggregated systems, nor in large eddy simulation (LES) models. This presentation will introduce the theory. An important testable null hypothesis emerges: the icehouse effect produces a unique signature or "fingerprint" which could not be produced by any other known process. The presence of this signature will be demonstrated using nearly all available Arctic temperature observations. Its aggregate effect is clearly found in Arctic monthly surface temperature trends when sorted by climatological stability. Using all available Arctic rawinsonde ascents - about 1.1 million profiles, "frozen moments" of the icehouse processes are captured in various states. Because turbulent time scales are so short in the stable boundary layer. each of these snapshots can be treated as independent -- their chronology is irrelevant. Micrometeorological similarity is invoked to reassemble the soundings into bins of similar stability and it is in a wide, coherent range of these stability bins where the cooling effect is revealed.

Wetzel, Peter J.↗

Evaluating Probabilistic Deep Learning Methods for Uncertainty Quantification of Precipitation Bias Correction

Climate models often exhibit biases in their precipitation predictions, particularly underestimating high-intensity events and overestimating low precipitation. Deep learning approaches offer promising solutions, but their epistemic uncertainty associated with a deep learning–based bias correction method has not previously been quantified for reliable downstream climate impact studies. While methods for capturing the epistemic uncertainty in deep learning frameworks exist, there is currently no consensus on the best method. In this work, we compare three uncertainty quantification (UQ) methods—Deep Ensembles (DEns), Monte Carlo Dropout (MCD), and Flipout—by assessing the reliability of their uncertainty estimates using standard measures such as sharpness and calibration. These UQ methods are applied to an existing deep learning precipitation bias correction model known as UFNet: a coupled U-Net and fully connected neural network. The methods utilized to assess the models’ uncertainties are 1) calibration, which ensures that the expected probabilities of the model align with reality and 2) sharpness, which is a measure of the precision of the model’s probabilistic predictions. Of the three UQ methods evaluated, the DEns and MCD methods demonstrated the best-calibrated performance (expected calibration error of 0.36 and 0.35, respectively), compared to Flipout (0.58). In contrast, Flipout had the sharpest predictions and the highest metric performance in bias correcting precipitation—especially for higher-order moments such as kurtosis with a spatial correlation of 72% compared to 32% and 55% spatial correlation for DEns and MCD, respectively. Of the three UQ methods, MCD was found to be the most suitable method for UQ purposes based on its calibration, sharpness, and computational requirements.

Bayesian methods↗

The DESI DR1 peculiar velocity survey: Growth rate measurements from the galaxy power spectrum

The large-scale structure of the Universe and its evolution encapsulate a wealth of cosmological information. A powerful means of unlocking this knowledge lies in measuring the auto-power spectrum and/or the cross-power spectrum of the galaxy density and momentum fields, followed by the estimation of cosmological parameters based on these spectrum measurements. In this study, we generalize the cross-power spectrum model to accommodate scenarios in which the density and momentum fields are derived from distinct galaxy surveys. The growth rate of the large-scale structures of the Universe, commonly represented as fσ 8 , was extracted by jointly fitting the monopole and quadrupole moments of the auto-density power spectrum, the monopole of the auto-momentum power spectrum, and the dipole of the cross-power spectrum. Our estimators, theoretical models, and parameter-fitting framework were tested using mocks, confirming their robustness and accuracy in retrieving the fiducial growth rate from simulation. These techniques were then applied to analyse the power spectrum of the DESI Bright Galaxy Survey and Peculiar Velocity Survey. The fit result of the growth rate is fσ8 = 0.440$^{+0.080}_{−0.096}$ at effective redshift zeff = 0.07. By synthesizing the fitting outcomes from correlation functions, maximum likelihood estimation, and the power spectrum, a consensus value is yielded of fσ 8 (z eff = 0.07) = 0.450$^{+0.055}_{−0.055}$, and correspondingly we obtain γ = 0.580$^{+0.110}_{−0.110}$, Ω m = 0.301$^{+0.011}_{−0.011}$, and σ 8 = 0.834$^{+0.032}_{−0.032}$. The measured fσ8 and γ are consistent with the prediction of the Λ cold dark matter model and general relativity.

79 ASTRONOMY AND ASTROPHYSICS↗

Thermal neutral format based on the step technology

The exchange of models is one of the most serious problems currently encountered in the practice of spacecraft thermal analysis. Essentially, the problem originates in the diversity of computing environments that are used across different sites, and the consequent proliferation of native tool formats. Furthermore, increasing pressure to reduce the development's life cycle time has originated a growing interest in the so-called spacecraft concurrent engineering. In this context, the realization of the interdependencies between different disciplines and the proper communication between them become critical issues. The use of a neutral format represents a step forward in addressing these problems. Such a means of communication is adopted by consensus. A neutral format is not directly tied to any specific tool and it is kept under stringent change control. Currently, most of the groups promoting exchange formats are contributing with their experience to STEP, the Standard for Exchange of Product Model Data, which is being developed under the auspices of the International Standards Organization (ISO 10303). This paper presents the different efforts made in Europe to provide the spacecraft thermal analysis community with a Thermal Neutral Format (TNF) based on STEP. Following an introduction with some background information, the paper presents the characteristics of the STEP standard. Later, the first efforts to produce a STEP Spacecraft Thermal Application Protocol are described. Finally, the paper presents the currently harmonized European activities that follow up and extend earlier work on the area.

Almazan, P. Planas↗

The Second Phase of the Global Land-Atmosphere Coupling Experiment (GLACE-2)

A major motivation for the study of the coupled land-atmosphere system is the idea that soil moisture anomalies may affect future meteorological variables through their effects on future surface energy and water budgets. If true, the accurate initialization of soil moisture in a subseasonal or seasonal forecast system may improve forecast skill, making the forecast products more valuable to society. The GLACE-2 project is examining, through a coordinated experiment using a wide variety of models, the degree to which subseasonal (out to two months) precipitation and air temperature forecasts improve through the realistic initialization of soil moisture. For the first time ever, a global consensus should emerge regarding the value of land initialization for forecasts, perhaps motivating national forecast centers to make full use of land moisture initialization in their operations

Koster, Randal D.↗

The DESI DR1 Peculiar Velocity Survey: Growth Rate Measurements from the Galaxy Power Spectrum

The large-scale structure of the Universe and its evolution encapsulate a wealth of cosmological information. A powerful means of unlocking this knowledge lies in measuring the auto-power spectrum and/or the cross-power spectrum of the galaxy density and momentum fields, followed by the estimation of cosmological parameters based on these spectrum measurements. In this study, we generalize the cross-power spectrum model to accommodate scenarios where the density and momentum fields are derived from distinct galaxy surveys. The growth rate of the large-scale structures of the Universe, commonly represented as $fσ_8$, is extracted by jointly fitting the monopole and quadrupole moments of the auto-density power spectrum, the monopole of the auto-momentum power spectrum, and the dipole of the cross-power spectrum. Our estimators, theoretical models and parameter-fitting framework have been tested using mocks, confirming their robustness and accuracy in retrieving the fiducial growth rate from simulation. These techniques are then applied to analyze the power spectrum of the DESI Bright Galaxy Survey and Peculiar Velocity Survey, and the fit result of the growth rate is $fσ_8=0.440^{+0.080}_{-0.096}$ at effective redshift $z_{\rm eff}=0.07$. By synthesizing the fitting outcomes from correlation functions, maximum likelihood estimation and power spectrum, yields a consensus value of $fσ_8(z_{\rm eff}=0.07) = 0.450 ^{+0.055}_{-0.055}$, and correspondingly we obtain $γ=0.580^{+0.110}_{-0.110}$, $Ω_\mathrm{m}=0.301^{+0.011}_{-0.011}$ and $σ_8=0.834^{+0.032}_{-0.032}$. The measured $fσ_8$ and $γ$ are consistent with the prediction of the $Λ$ Cold Dark Matter Model and General Relativity.

Qin, F. [Marseille, CPPM] (ORCID:0000000179507864)↗

Accounting for Training Data Error in Machine Learning Applied to Earth Observations

Remote sensing, or Earth Observation (EO), is increasingly used to understand Earth system dynamics and create continuous and categorical maps of biophysical properties and land cover, especially based on recent advances in machine learning (ML). ML models typically require large, spatially explicit training datasets to make accurate predictions. Training data (TD) are typically generated by digitizing polygons on high spatial-resolution imagery, by collecting in situ data, or by using pre-existing datasets. TD are often assumed to accurately represent the truth, but in practice almost always have error, stemming from (1) sample design, and (2) sample collection errors. The latter is particularly relevant for image-interpreted TD, an increasingly commonly used method due to its practicality and the increasing training sample size requirements of modern ML algorithms. TD errors can cause substantial errors in the maps created using ML algorithms, which may impact map use and interpretation. Despite these potential errors and their real-world consequences for map-based decisions, TD error is often not accounted for or reported in EO research. Here we review the current practices for collecting and handling TD. We identify the sources of TD error, and illustrate their impacts using several case studies representing different EO applications (infrastructure mapping, global surface flux estimates, and agricultural monitoring), and provide guidelines for minimizing and accounting for TD errors. To harmonize terminology, we distinguish TD from three other classes of data that should be used to create and assess ML models: training reference data, used to assess the quality of TD during data generation; validation data, used to iteratively improve models; and map reference data, used only for final accuracy assessment. We focus primarily on TD, but our advice is generally applicable to all four classes, and we ground our review in established best practices for map accuracy assessment literature. EO researchers should start by determining the tolerable levels of map error and appropriate error metrics. Next, TD error should be minimized during sample design by choosing a representative spatio-temporal collection strategy, by using spatially and temporally relevant imagery and ancillary data sources during TD creation, and by selecting a set of legend definitions supported by the data. Furthermore, TD error can be minimized during the collection of individual samples by using consensus-based collection strategies, by directly comparing interpreted training observations against expert-generated training reference data to derive TD error metrics, and by providing image interpreters with thorough application-specific training. We strongly advise that TD error is incorporated in model outputs, either directly in bias and variance estimates or, at a minimum, by documenting the sources and implications of error. TD should be fully documented and made available via an open TD repository, allowing others to replicate and assess its use. To guide researchers in this process, we propose three tiers of TD error accounting standards. Finally, we advise researchers to clearly communicate the magnitude and impacts of TD error on map outputs, with specific consideration given to the likely map audience.

58 GEOSCIENCES↗

Intestinal single-cell atlas reveals novel lymphocytes in pigs with similarities to human cells

Lymphocytes can heavily influence intestinal health, but resolving intestinal lymphocyte function is challenging as the intestine contains a vastly heterogeneous mixture of cells. Pigs are an advantageous biomedical model, but deeper understanding of intestinal lymphocytes is warranted to improve model utility. Twenty-six cell types were identified in the porcine ileum by single-cell RNA sequencing and further compared with cells in human and murine ileum. Though general consensus of cell subsets across species was revealed, some porcine-specific lymphocyte subsets were identified. Differential tissue dissection and in situ analyses conferred spatial context, revealing similar locations of lymphocyte subsets in Peyer’s patches and epithelium in pig-to-human comparisons. Like humans, activated and effector lymphocytes were abundant in the ileum but not periphery of pigs, suggesting tissue-specific and/or activation-associated gene expression. Gene signatures for peripheral and ileal innate lymphoid cells newly discovered in pigs were defined and highlighted similarities to human innate lymphoid cells. Overall, we reveal novel lymphocyte subsets in pigs and highlight utility of pigs for intestinal research applications.

Life Sciences & Biomedicine - Other Topics↗

Final STS-35 Columbia descent BET products and results for LaRC OEX investigations

Final STS-35 'Columbia' descent Best Estimate Trajectory (BET) products have been developed for Langley Research Center (LaRC) Orbiter Experiments (OEX) investigations. Included are the reconstructed inertial trajectory profile; the Extended BET, which combines the inertial data and, in this instance, the National Weather Service atmospheric information obtained via Johnson Space Center; and the Aerodynamic BET. The inertial BET utilized Inertial Measurement Unit 1 (IMU1) dynamic measurements for deterministic propagation during the ENTREE estimation process. The final estimate was based on the considerable ground based C-band tracking coverage available as well as Tracking Data and Relay Satellite System (TDRSS) Doppler data, a unique use of the latter for endo-atmospheric flight determinations. The actual estimate required simultaneous solutions for the spacecraft position and velocity, spacecraft attitude, and six IMU parameters - three gyro biases and three accelerometer scale factor correction terms. The anchor epoch for this analysis was 19,200 Greenwich Mean Time (GMT) seconds which corresponds to an initial Shuttle altitude of approximately 513 kft. The atmospheric data incorporated were evaluated based on Shuttle derived considerations as well as comparisons with other models. The AEROBET was developed based on the Extended BET, the measured spacecraft configuration information, final mass properties, and the final Orbiter preoperation databook. The latter was updated based on aerodynamic consensus incrementals derived by the latest published FAD. The rectified predictions were compared versus the flight computed values and the resultant differences were correlated versus ensemble results for twenty-two previous STS entry flights.

Oakes, Kevin F.↗

Final Plenary Session Transcript

Let s start with the report - as you know - when we are talking about flow control it is a multi-disciplinary type of work. So it involves many people and disciplines. This group first discussed the important issues associated with flow control. As you start doing flow control what are the issues to which you really have to start paying attention? That is the first part I am going to present. Then in the second part I will present some challenges - problems that we should really be looking at. So as far as the issues - if you want to control a flow, you really need to understand the flow physics, because anything that you do comes from the flow physics. The design of the controllers, your decisions on the actuators, sensors, reduced order modeling and all of that, would be helped if you understand flow physics. And you have to have a specific objective - what exactly are you controlling? Are you trying to reduce drag, eliminate separation, reduce noise, enhance mixing? So you have to have very specific control objectives. From all the talks we have seen here actuation is extremely important and it is very problem specific. It depends on what problem you are dealing with so you have to design and build actuators for that specific problem. Sensors obviously are very important, especially when you are dealing with feedback control. Consensus was that when you dealing with flow control, you must take an integrated approach; from the beginning you have to take into account every aspect of it and even maybe to modify your experiment, your geometry, to go along with the actuation, sensors and control models. Development of tools is very important in this multi-disciplinary problem. The tools include CFD, reduced order modeling, controller design, understanding and utilizing the instabilities of the flow, etc. So, in order to have success in flow control, we really need to develop these tools.

Gostelow, Paul↗

A Proposed Clock Synchronization Method for the Solar System Internet

Networked communications in space are necessary to achieve scalability in terms of the number of communicating nodes but also in terms of the overall system complexity. A key component to such a system is the ability to synchronize clocks, which is the focus of this paper. The so-called Solar System Internet (SSI) will be built upon Delay Tolerant Networking (DTN), which, in analogy to the Internet Protocol (IP), can be considered a suite of protocols necessary for networking in the space domain. Therefore, our goal is to extend this suite to include a DTN clock synchronization capability, analogous to the Network Time Protocol (NTP) used in the Internet. A motivating example of a network in space is NASA’s LunaNet, a vision for a multi-hop multi-path network extending to the moon wherein not all nodes will have direct connections to an authoritative reference clock. In this paper, we propose a general clock synchronization methodology and algorithm that could be used for LunaNet as well as more elaborate time-varying networks. In recent years, DTN has benefited from modeling efforts founded on the mathematical tool of sheaves. Here we continue this work to provide an approach to clock synchronization. Due to the time-varying nature of space networks, absolute consensus is not possible. However, the sheaf Laplacian provides a practical, distributed approach to approximating consensus by allowing data to diffuse through the network. In particular, the sheaf Laplacian is readily computable, lending our approach to implementation. Our approach is well suited to handle the difficulties of space networks. For instance, differences in clock accuracy mean certain nodes are more authoritative than others; we can account for these differences through hierarchies in the network, generalizing the strata in NTP. Furthermore, just as error estimation is an integral part of NTP, we are able to give concrete error bounds for our approach. Indeed, different applications (e.g., communications schedules, pointing, navigation, distributed science) will have different requirements, hence it is necessary to maintain clocks within a given tolerance. We outline some of the necessary steps to turn our approach into a practical network protocol that could be used in DTN, and we conclude the paper with suggestions for future research.

Michael Moy↗

A consensus-based ensemble approach to improve transcriptome assembly

Systems-level analyses, such as differential gene expression analysis, co-expression analysis, and metabolic pathway reconstruction, depend on the accuracy of the transcriptome. Multiple tools exist to perform transcriptome assembly from RNAseq data. However, assembling high quality transcriptomes is still not a trivial problem. This is especially the case for non-model organisms where adequate reference genomes are often not available. Different methods produce different transcriptome models and there is no easy way to determine which are more accurate. Furthermore, having alternative-splicing events exacerbates such difficult assembly problems. While benchmarking transcriptome assemblies is critical, this is also not trivial due to the general lack of true reference transcriptomes. In this study, we first provide a pipeline to generate a set of the simulated benchmark transcriptome and corresponding RNAseq data. Using the simulated benchmarking datasets, we compared the performance of various transcriptome assembly approaches including both de novo and genome-guided methods. The results showed that the assembly performance deteriorates significantly when alternative transcripts (isoforms) exist or for genome-guided methods when the reference is not available from the same genome. To improve the transcriptome assembly performance, leveraging the overlapping predictions between different assemblies, we present a new consensus-based ensemble transcriptome assembly approach, ConSemble. Without using a reference genome, ConSemble using four de novo assemblers achieved an accuracy up to twice as high as any de novo assemblers we compared. When a reference genome is available, ConSemble using four genome-guided assemblies removed many incorrectly assembled contigs with minimal impact on correctly assembled contigs, achieving higher precision and accuracy than individual genome-guided methods. Furthermore, ConSemble using de novo assemblers matched or exceeded the best performing genome-guided assemblers even when the transcriptomes included isoforms. We thus demonstrated that the ConSemble consensus strategy both for de novo and genome-guided assemblers can improve transcriptome assembly. The RNAseq simulation pipeline, the benchmark transcriptome datasets, and the script to perform the ConSemble assembly are all freely available from: http://bioinfolab.unl.edu/emlab/consemble/.

59 BASIC BIOLOGICAL SCIENCES↗