On directed information theory and Granger causality graphs

Directed information theory deals with communication channels with feedback. When applied to networks, a natural extension based on causal conditioning is needed. We show here that measures built from directed information theory in networks can be used to assess Granger causality graphs of stochastic processes. We show that directed information theory includes measures such as the transfer entropy, and that it is the adequate information theoretic framework needed for neuroscience applications, such as connectivity inference problems.Comment: accepted for publications, Journal of Computational Neuroscienc

Compressed representation of brain genetic transcription

The architecture of the brain is too complex to be intuitively surveyable without the use of compressed representations that project its variation into a compact, navigable space. The task is especially challenging with high-dimensional data, such as gene expression, where the joint complexity of anatomical and transcriptional patterns demands maximum compression. Established practice is to use standard principal component analysis (PCA), whose computational felicity is offset by limited expressivity, especially at great compression ratios. Employing whole-brain, voxel-wise Allen Brain Atlas transcription data, here we systematically compare compressed representations based on the most widely supported linear and non-linear methods-PCA, kernel PCA, non-negative matrix factorization (NMF), t-stochastic neighbour embedding (t-SNE), uniform manifold approximation and projection (UMAP), and deep auto-encoding-quantifying reconstruction fidelity, anatomical coherence, and predictive utility with respect to signalling, microstructural, and metabolic targets. We show that deep auto-encoders yield superior representations across all metrics of performance and target domains, supporting their use as the reference standard for representing transcription patterns in the human brain.Comment: 21 pages, 5 main figures, 1 supplementary figur

Long-Term Testing of Rhodium-Based Catalysts for Mixed Alcohol Synthesis ? 2013 Progress Report

The U.S. Department of Energy’s Pacific Northwest National Laboratory has been conducting research since 2005 to develop a catalyst for the conversion of synthesis gas (carbon monoxide and hydrogen) into mixed alcohols for use in liquid transportation fuels. Initially, research involved screening possible catalysts based on a review of the literature, because at that time, there were no commercial catalysts available. The screening effort resulted in a decision to focus on catalysts containing rhodium and manganese. Subsequent research identified iridium as a key promoter for this catalyst system. Since then, research has continued to improve rhodium/manganese/iridium-based catalysts, optimizing the relative and total concentrations of the three metals, examining baseline catalysts on alternative supports, and examining effects of additional promoters. Testing was continued in FY 2013 to evaluate the performance and long-term stability of the best catalysts tested to date. Three tests were conducted. A long-term test of over 2300 hr duration at a single set of operating conditions was conducted with the best carbon-supported catalyst. A second test of about 650 hr duration at a single set of operating conditions was performed for comparison using the same catalyst formulation on an alternative carbon support. A third test of about 680 hr duration at a single set of operating conditions was performed using the best silica-supported catalyst tested to date

Mixed Alcohol Synthesis Catalyst Screening 2007 Progress Report

Pacific Northwest National Laboratory (PNNL) and National Renewable Energy Laboratory (NREL) are researching the feasibility of producing mixed alcohols from biomass-derived synthesis gas (syngas). PNNL is obtaining commercially available mixed alcohol or preparing promising mixed-alcohol catalysts and screening them in a laboratory-scale reactor system. The most promising catalysts are provided to NREL for testing using a slipstream from a pilot-scale biomass gasifier. After a review of the literature in 2006 and conversations with companies that produce catalysts, it was determined that no commercial mixed-alcohol synthesis catalysts were available. One manufacturer supplied a modified methanol catalyst that was tested in the PNNL laboratory-scale system and provided to NREL for further testing. PNNL also prepared and tested the behavior of 10 other catalysts representing the distinct catalyst classes for mixed alcohol syntheses. Based on those results,testing in 2007 focused on the performance of the rhodium-based catalysts. The effects of adding promoters to the rhodium catalysts in addition to the manganese already being used were examined. The iron and rhenium promoters both stood out as achieving higher carbon selectivities , followed by Cu. Iridium and Li, on the other hand, had low carbon selectivity ratios of 0.27 and 0.22, respectively. Although testing of candidate promoters is not complete, it appears that Ir and Li promoters warrant further optimization and possibly combination to further improve STYs and carbon selectivities to C2+ oxygenates. However, using these promoters, it will be necessary to incorporate a separate hydrogenation catalyst to improve the yield of C2+ alcohols with respect to the other oxygenates. Fe, Re, and Cu stand out as possible candidates in this respect, but additional research is needed to examine whether they can be combined with the other promoters on the Rh-based catalyst or need to be optimized on a separate catalyst support that is either physically mixed or used in series with the promoted Rh-based catalyst

Evaluation of Promoters for Rhodium-Based Catalysts for Mixed Alcohol Synthesis

Pacific Northwest National Laboratory (PNNL) and National Renewable Energy Laboratory (NREL) are conducting research to investigate the feasibility of producing mixed alcohols from biomass-derived synthesis gas (syngas). PNNL is tasked with obtaining commercially-available catalysts or preparing promising mixed-alcohol catalysts and screening them in a laboratory-scale reactor system. Commercially-available catalysts and the most promising experimental catalysts are provided to NREL for testing using a slipstream from a pilot-scale biomass gasifier. A total of 28 tests were conducted to evaluate 22 different promoters as well as an unpromoted catalyst. The following general trends were observed for the test results: • The highest carbon selectivity to C2+ oxygenates occurred at the lowest reaction temperatures and accompanying lowest space time yields (STYs). • The lowest carbon selectivity to C2+ oxygenates occurred at the highest reaction temperatures because of high carbon conversion to hydrocarbons. • The highest C2+-oxygenate STYs occurred between 300°C and 325°C, with the gas hourly space velocity (GHSV) adjusted when necessary to maintain carbon conversion ranges between ~ 30 and 40 percent. Higher carbon selectivity to hydrocarbons at higher temperatures resulted in lower C2+-oxygenate STYs. • When catalysts were heated to between 300°C and 325°C the catalysts showed evidence of some deactivation with respect to C2+ oxygenate productivity, accompanied by reduced chain growth for the hydrocarbon products. The degree of deactivation and the temperature at which it occurred varied between the different catalysts tested. Of all of the catalysts evaluated, the Li-promoted catalysts had the highest carbon selectivity to C2+ oxygenates (47 percent) under the conditions at which the maximum C2+-oxygenate STYs were obtained

Interoperability and FAIRness through a novel combination of Web technologies

Data in the life sciences are extremely diverse and are stored in a broad spectrum of repositories ranging from those designed for particular data types (such as KEGG for pathway data or UniProt for protein data) to those that are general-purpose (such as FigShare, Zenodo, Dataverse or EUDAT). These data have widely different levels of sensitivity and security considerations. For example, clinical observations about genetic mutations in patients are highly sensitive, while observations of species diversity are generally not. The lack of uniformity in data models from one repository to another, and in the richness and availability of metadata descriptions, makes integration and analysis of these data a manual, time-consuming task with no scalability. Here we explore a set of resource-oriented Web design patterns for data discovery, accessibility, transformation, and integration that can be implemented by any general- or special-purpose repository as a means to assist users in finding and reusing their data holdings. We show that by using off-the-shelf technologies, interoperability can be achieved atthe level of an individual spreadsheet cell. We note that the behaviours of this architecture compare favourably to the desiderata defined by the FAIR Data Principles, and can therefore represent an exemplar implementation of those principles. The proposed interoperability design patterns may be used to improve discovery and integration of both new and legacy data, maximizing the utility of all scholarly outputs

Optimization of Rhodium-Based Catalysts for Mixed Alcohol Synthesis -- 2009 Progress Report

Pacific Northwest National Laboratory (PNNL) has been conducting research for the United States Department of Energy, Energy Efficiency Renewable Energy, Biomass Program to investigate the feasibility of producing mixed alcohols from biomass-derived synthesis gas (syngas). This research has involved the screening of potential catalysts, and optimization of the more promising ones, using laboratory scale reactors. During 2009, the main goal of the testing program focused on optimizing selected supported catalysts containing rhodium (Rh) and manganese (Mn). Optimization involved examining different total concentrations and atomic ratios of Rh and Mn as well as that of the more promising promoters (Ir and Li) identified in the earlier screening studies. Evaluation of catalyst performance focused on attaining improvements with respect to the space-time-yield and converted carbon selectivity to C2+ oxygenates, with additional consideration given to the fraction of the oxygenates that were C2+ alcohols

Optimization of Rhodium-Based Catalysts for Mixed Alcohol Synthesis ? 2012 Progress Report

Pacific Northwest National Laboratory has been conducting research to investigate the feasibility of producing mixed alcohols from biomass-derived synthesis gas (syngas). In recent years, this research has primarily involved the further development of catalysts containing rhodium and manganese based on the results of earlier catalyst screening tests. Testing continued in FY 2012 to further improve the Ir-promoted RhMn catalysts on both silica and carbon supports for producing mixed oxygenates from synthesis gas. This testing re-examined selected alternative silica and carbon supports to follow up on some uncertainties in the results with previous test results. Additional tests were conducted to further optimize the total and relative concentrations of Rh, Mn, and Ir, and to examine selected promoters and promoter combinations based on earlier results. To establish optimum operating conditions, the effects of the process pressure and the feed gas composition also were evaluated

High-dispersion absorption-line spectroscopy of AE Aqr

High-dispersion time-resolved spectroscopy of the unique magnetic cataclysmic variable AE Aqr is presented. A radial velocity analysis of the absorption lines yields K2= 168.7 ± 1 km s−1. Substantial deviations of the radial velocity curve from a sinusoid are interpreted in terms of intensity variations over the secondary star's surface. A complex rotational velocity curve as a function of orbital phase is detected which has a modulation frequency of twice the orbital frequency, leading to an estimate of the binary inclination angle that is close to 70°. The minimum and maximum rotational velocities are used to indirectly derive a mass ratio of q= 0.6 and a radial velocity semi-amplitude of the white dwarf of K1= 101 ± 3 km s−1. We present an atmospheric temperature indicator, based on the absorption-line ratio of Fe I and Cr I lines, whose variation indicates that the secondary star varies from K0 to K4 as a function of orbital phase. The ephemeris of the system has been revised, using more than 1000 radial velocity measurements, published over nearly five decades. From the derived radial velocity semi-amplitudes and the estimated inclination angle, we calculate that the masses of the stars are M1= 0.63 ± 0.05 M⊙; M2= 0.37 ± 0.04 M⊙, and their separation is a= 2.33 ± 0.02 R⊙. Our analysis indicates the presence of a late-type star whose radius is larger, by a factor of nearly 2, than the radius of a normal main-sequence star of the same mass. Finally, we discuss the possibility that the measured variations in the rotational velocity, temperature and spectral type of the secondary star as functions of orbital phase may, like the radial velocity variations, be attributable to regions of enhanced absorption on the star's surface

Optimization of Rhodium-Based Catalysts for Mixed Alcohol Synthesis -- 2010 Progress Report

Pacific Northwest National Laboratory has been conducting research for the U.S. Department of Energy, Energy Efficiency Renewable Energy, Biomass Program to investigate the feasibility of producing mixed alcohols from biomass-derived synthesis gas. In recent years this research has primarily involved the further development of a silica-supported catalyst containing rhodium and manganese that was selected from earlier catalyst screening tests. A major effort during 2010 was to examine alternative catalyst supports to determine whether other supports, besides the Davisil 645 silica, would improve performance. Optimization of the Davisil 645 silica-supported catalyst also was continued with respect to candidate promoters iridium, platinum, and gallium, and examination of selected catalyst preparation and activation alternatives for the baseline RhMn/SiO2 catalyst