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All sourcesNASA NTRSDOE OSTI
DOE OSTI2014

Interactive prostate segmentation using atlas-guided semi-supervised learning and adaptive feature selection

Purpose: Accurate prostate segmentation is necessary for maximizing the effectiveness of radiation therapy of prostate cancer. However, manual segmentation from 3D CT images is very time-consuming and often causes large intra- and interobserver variations across clinicians. Many segmentation methods have been proposed to automate this labor-intensive process, but tedious manual editing is still required due to the limited performance. In this paper, the authors propose a new interactive segmentation method that can (1) flexibly generate the editing result with a few scribbles or dots provided by a clinician, (2) fast deliver intermediate results to the clinician, and (3) sequentially correct the segmentations from any type of automatic or interactive segmentation methods. Methods: The authors formulate the editing problem as a semisupervised learning problem which can utilize a priori knowledge of training data and also the valuable information from user interactions. Specifically, from a region of interest near the given user interactions, the appropriate training labels, which are well matched with the user interactions, can be locally searched from a training set. With voting from the selected training labels, both confident prostate and background voxels, as well as unconfident voxels can be estimated. To reflect informative relationship between voxels, location-adaptive features are selected from the confident voxels by using regression forest and Fisher separation criterion. Then, the manifold configuration computed in the derived feature space is enforced into the semisupervised learning algorithm. The labels of unconfident voxels are then predicted by regularizing semisupervised learning algorithm. Results: The proposed interactive segmentation method was applied to correct automatic segmentation results of 30 challenging CT images. The correction was conducted three times with different user interactions performed at different time periods, in order to evaluate both the efficiency and the robustness. The automatic segmentation results with the original average Dice similarity coefficient of 0.78 were improved to 0.865–0.872 after conducting 55–59 interactions by using the proposed method, where each editing procedure took less than 3 s. In addition, the proposed method obtained the most consistent editing results with respect to different user interactions, compared to other methods. Conclusions: The proposed method obtains robust editing results with few interactions for various wrong segmentation cases, by selecting the location-adaptive features and further imposing the manifold regularization. The authors expect the proposed method to largely reduce the laborious burdens of manual editing, as well as both the intra- and interobserver variability across clinicians.

07 ISOTOPE AND RADIATION SOURCES↗
DOE OSTI2016

SU-C-209-05: Monte Carlo Model of a Prototype Backscatter X-Ray (BSX) Imager for Projective and Selective Object-Plane Imaging

Purpose: To develop a Monte Carlo N-Particle (MCNP) model for the validation of a prototype backscatter x-ray (BSX) imager, and optimization of BSX technology for medical applications, including selective object-plane imaging. Methods: BSX is an emerging technology that represents an alternative to conventional computed tomography (CT) and projective digital radiography (DR). It employs detectors located on the same side as the incident x-ray source, making use of backscatter and avoiding ring geometry to enclose the imaging object. Current BSX imagers suffer from low spatial resolution. A MCNP model was designed to replicate a BSX prototype used for flaw detection in industrial materials. This prototype consisted of a 1.5mm diameter 60kVp pencil beam surrounded by a ring of four 5.0cm diameter NaI scintillation detectors. The imaging phantom consisted of a 2.9cm thick aluminum plate with five 0.6cm diameter holes drilled halfway. The experimental image was created using a raster scanning motion (in 1.5mm increments). Results: A qualitative comparison between the physical and simulated images showed very good agreement with 1.5mm spatial resolution in plane perpendicular to incident x-ray beam. The MCNP model developed the concept of radiography by selective plane detection (RSPD) for BSX, whereby specific object planes can be imaged by varying kVp. 10keV increments in mean x-ray energy yielded 4mm thick slice resolution in the phantom. Image resolution in the MCNP model can be further increased by increasing the number of detectors, and decreasing raster step size. Conclusion: MCNP modelling was used to validate a prototype BSX imager and introduce the RSPD concept, allowing for selective object-plane imaging. There was very good visual agreement between the experimental and MCNP imaging. Beyond optimizing system parameters for the existing prototype, new geometries can be investigated for volumetric image acquisition in medical applications. This material is based upon work supported under an Integrated University Program Graduate Fellowship sponsored by the Department of Energy Office of Nuclear Energy.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

SU-G-BRC-13: Model Based Classification for Optimal Position Selection for Left-Sided Breast Radiotherapy: Free Breathing, DIBH, Or Prone

Purpose: There are clinical decision challenges to select optimal treatment positions for left-sided breast cancer patients—supine free breathing (FB), supine Deep Inspiration Breath Hold (DIBH) and prone free breathing (prone). Physicians often make the decision based on experiences and trials, which might not always result optimal OAR doses. We herein propose a mathematical model to predict the lowest OAR doses among these three positions, providing a quantitative tool for corresponding clinical decision. Methods: Patients were scanned in FB, DIBH, and prone positions under an IRB approved protocol. Tangential beam plans were generated for each position, and OAR doses were calculated. The position with least OAR doses is defined as the optimal position. The following features were extracted from each scan to build the model: heart, ipsilateral lung, breast volume, in-field heart, ipsilateral lung volume, distance between heart and target, laterality of heart, and dose to heart and ipsilateral lung. Principal Components Analysis (PCA) was applied to remove the co-linearity of the input data and also to lower the data dimensionality. Feature selection, another method to reduce dimensionality, was applied as a comparison. Support Vector Machine (SVM) was then used for classification. Thirtyseven patient data were acquired; up to now, five patient plans were available. K-fold cross validation was used to validate the accuracy of the classifier model with small training size. Results: The classification results and K-fold cross validation demonstrated the model is capable of predicting the optimal position for patients. The accuracy of K-fold cross validations has reached 80%. Compared to PCA, feature selection allows causal features of dose to be determined. This provides more clinical insights. Conclusion: The proposed classification system appeared to be feasible. We are generating plans for the rest of the 37 patient images, and more statistically significant results are to be presented.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2019

Catalyst-free, highly selective synthesis of ammonia from nitrogen and water by a plasma electrolytic system

There is a growing need for scalable ammonia synthesis at ambient conditions that relies on renewable sources of energy and feedstocks to replace the Haber-Bosch process. Electrically driven approaches are an ideal strategy for the reduction of nitrogen to ammonia but, to date, have suffered from low selectivity associated with the catalyst. Here, we present a hybrid electrolytic system characterized by a gaseous plasma electrode that facilitates the study of ammonia formation in the absence of any material surface. We find record-high faradaic efficiency (up to 100%) for ammonia from nitrogen and water at atmospheric pressure and temperature with this system. Ammonia measurements under varying reaction conditions in combination with scavengers reveal that the unprecedented selectivity is achieved by solvated electrons produced at the plasma-water interface, which react favorably with protons to produce the key hydrogen radical intermediate. Our results demonstrate that limitations in selectivity can be circumvented by using catalyst-free solvated electron chemistry. In the absence of adsorption steps, the importance of controlling proton concentration and transport is also revealed.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

High-loading single Pt atom sites [Pt-O(OH) x ] catalyze the CO PROX reaction with high activity and selectivity at mild conditions

The preferential oxidation of CO (PROX) in hydrogen-rich fuel gas streams is an attractive option to remove CO while effectively conserving energy and H 2 . However, high CO conversion with concomitant high selectivity to CO 2 but not H 2 O is challenging. Here, we report the synthesis of high-loading single Pt atom (2.0 weight %) catalysts with oxygen-bonded alkaline ions that stabilize the cationic Pt. The synthesis is performed in aqueous solution and achieves high Pt atom loadings in a single-step incipient wetness impregnation of alumina or silica. Promisingly, these catalysts have high CO PROX selectivity even at high CO conversion (~99.8% conversion, 70% selectivity at 110°C) and good stability under reaction conditions. These findings pave the way for the design of highly efficient single-atom catalysts, elucidate the role of –OH species in CO oxidation, and confirm the absence of a support effect for our case.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Selective chemical looping combustion of acetylene in ethylene-rich streams

Here, the requirement for C 2 H 2 concentrations below 2 parts per million (ppm) in gas streams for C 2 H 4 polymerization necessitates its semihydrogenation to C 2 H 4 . Here, we demonstrate selective chemical looping combustion of C 2 H 2 in C 2 H 4 -rich streams by Bi 2 O 3 as an alternative catalytic pathway to reduce C 2 H 2 concentration below 2 ppm. Bi 2 O 3 combusts C 2 H 2 with a first-order rate constant that is 3000 times greater than the rate constant for C 2 H 4 combustion. In successive redox cycles, the lattice O of Bi 2 O 3 can be fully replenished without discernible changes in local Bi coordination or C 2 H 2 combustion selectivity. Heterolytic activation of C–H bonds across Bi–O sites and the higher acidity of C 2 H 2 results in lower barriers for C 2 H 2 activation than C 2 H 4 , enabling selective catalytic hydrocarbon combustion leveraging differences in molecular deprotonation energies.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Formation of hydrided Pt-Ce-H sites in efficient, selective oxidation catalysts

Single-atom site catalysts can improve the rates and selectivity of many catalytic reactions. For this work, we have modified Pt 1 /CeO 2 single sites by combining them with molecular groups and with oxygen vacancies of the support. The new sites include hydrided (Pt 2+ -Ce 3+ Hδ) and hydroxylated (Pt 2+ -Ce 3+ OH) sites that exhibit higher reactivity and selectivity to previous single sites for several reactions, including a ninefold increase in the reaction rate for carbon monoxide (CO) oxidation, and a 2.3-fold improvement of propylene selectivity for oxidative dehydrogenation of propane. The atomic structure and reaction steps of these sites were determined with in situ and ex situ spectroscopy techniques and theoretical methods.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2019

Experimental Evolution of Extreme Resistance to Ionizing Radiation in Escherichia coli after 50 Cycles of Selection

In prior work (D. R. Harris et al., J Bacteriol 191:5240–5252, 2009, https://doi.org/10.1128/JB.00502-09; B. T. Byrne et al., Elife 3:e01322, 2014, https://doi.org/10.7554/eLife.01322), we demonstrated that Escherichia coli could acquire substantial levels of resistance to ionizing radiation (IR) via directed evolution. Major phenotypic contributions involved adaptation of organic systems for DNA repair. We have currently undertaken an extended effort to generate E. coli populations that are as resistant to IR as Deinococcus radiodurans . After an initial 50 cycles of selection using high-energy electron beam IR, four replicate populations exhibit major increases in IR resistance but have not yet reached IR resistance equivalent to D. radiodurans . Regular deep sequencing reveals complex evolutionary patterns with abundant clonal interference. Prominent IR resistance mechanisms involve novel adaptations to DNA repair systems and alterations in RNA polymerase. Adaptation is highly specialized to resist IR exposure, since isolates from the evolved populations exhibit highly variable patterns of resistance to other forms of DNA damage. Sequenced isolates from the populations possess between 184 and 280 mutations. IR resistance in one isolate, IR9-50-1, is derived largely from four novel mutations affecting DNA and RNA metabolism: RecD A90E, RecN K429Q, and RpoB S72N/RpoC K1172I. Additional mechanisms of IR resistance are evident. IMPORTANCE Some bacterial species exhibit astonishing resistance to ionizing radiation, with Deinococcus radiodurans being the archetype. As natural IR sources rarely exceed mGy levels, the capacity of Deinococcus to survive 5,000 Gy has been attributed to desiccation resistance. To understand the molecular basis of true extreme IR resistance, we are using experimental evolution to generate strains of Escherichia coli with IR resistance levels comparable to Deinococcus . Experimental evolution has previously generated moderate radioresistance for multiple bacterial species. Yet, these efforts could not take advantage of modern genomic sequencing technologies. In this report, we examine four replicate bacterial populations after 50 selection cycles. Genomic sequencing allows us to follow the genesis of mutations in populations throughout selection. Novel mutations affecting genes encoding DNA repair proteins and RNA polymerase enhance radioresistance. However, more contributors are apparent.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Potential–Dependent BDAC Adsorption on Zinc Enabling Selective Suppression of Zinc Corrosion for Energy Storage Applications

Utility-scale zinc (Zn) batteries are a promising solution to address the problem of intermittency of renewable energy sources; however, Zn-metal anodes in these batteries suffer from capacity loss due to spontaneous corrosion of the Zn especially when high-surface area anode configurations are employed. Additionally, Zn dendrites are known to form during battery charging limiting the cycle-life of these batteries. Electrolyte additives have been explored that prevent aforementioned issues, but these too come at a cost, i.e., surface-blocking additives polarize the electrode surface leading to loss in the voltaic and energy efficiencies of the battery. In this contribution, a novel electrolyte additive, benzyldimethylhexadecylammonium chloride (BDAC), is investigated for its ability to suppresses corrosion of Zn in an acidic (pH = 3) electrolyte. An attribute of BDAC distinct from previously studied additives is that it selectively suppresses electrochemical activity when the Zn electrode is at its corrosion potential; however, during high-rate Zn deposition (charging) or stripping (discharging), BDAC is essentially deactivated and thus it does not appreciably polarize the electrode surface, thus minimizing voltaic efficiency losses. This selective corrosion suppression behavior is explored using slow-scan voltammetry, which reveals hysteresis implying a potential- or current-dependent BDAC adsorption mechanism in which BDAC reaches higher surface coverages when the partial currents at the Zn surface are low (e.g., at or near the corrosion potential), but BDAC coverage is reduced considerably when the Zn deposition or stripping rates are increased. Numerical simulations of the BDAC diffusion-adsorption process corroborate this mechanism. Ramifications of our approach to the selective suppression of Zn dendrites are discussed.

25 ENERGY STORAGE↗
DOE OSTI2021

Optimal dimensionality selection for independent component analysis of transcriptomic data

Independent component analysis is an unsupervised machine learning algorithm that separates a set of mixed signals into a set of statistically independent source signals. Applied to high-quality gene expression datasets, independent component analysis effectively reveals both the source signals of the transcriptome as co-regulated gene sets, and the activity levels of the underlying regulators across diverse experimental conditions. Two major variables that affect the final gene sets are the diversity of the expression profiles contained in the underlying data, and the user-defined number of independent components, or dimensionality, to compute. Availability of high-quality transcriptomic datasets has grown exponentially as high-throughput technologies have advanced; however, optimal dimensionality selection remains an open question. We computed independent components across a range of dimensionalities for four gene expression datasets with varying dimensions (both in terms of number of genes and number of samples). We computed the correlation between independent components across different dimensionalities to understand how the overall structure evolves as the number of user-defined components increases. We then measured how well the resulting gene clusters reflected known regulatory mechanisms, and developed a set of metrics to assess the accuracy of the decomposition at a given dimension. We found that over-decomposition results in many independent components dominated by a single gene, whereas under-decomposition results in independent components that poorly capture the known regulatory structure. From these results, we developed a new method, called OptICA, for finding the optimal dimensionality that controls for both over- and under-decomposition. Specifically, OptICA selects the highest dimension that produces a low number of components that are dominated by a single gene. We show that OptICA outperforms two previously proposed methods for selecting the number of independent components across four transcriptomic databases of varying sizes. OptICA avoids both over-decomposition and under-decomposition of transcriptomic datasets resulting in the best representation of the organism’s underlying transcriptional regulatory network.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Performing k eff Validation of As-Loaded Criticality Safety Calculations Using UNF-ST&DARDS: Applicable Experiment Selection

The general method for performing validation of as loaded criticality safety calculations using UNF ST&DARDS is presented in a paper by Clarity, which includes a description of the UNF-ST&DARDS system. Proof-of-principle analyses were performed in the summer of 2019 for MPC-32 dual purpose canisters (DPCs) containing pressurized water reactor (PWR) fuel assemblies. Summaries of these results are presented in this and a companion paper for this conference. The current paper describes the TSUNAMI-IP calculations performed to select applicable experiments for validation of 11 MPC-32 DPCs. The companion paper discusses the TSUNAMI-3D calculations used to generate sensitivity data to support the experiment selections discussed here. Experiment selection is based on the sensitivity/uncertainty (S/U) methods used to validate criticality safety calculations of as-loaded DPCs containing pressurized water reactor (PWR) spent nuclear fuel (SNF). This process has been demonstrated and is summarized in this paper. The approach is similar to that used in NUREG/CR-7109, which provides an approach for validation of PWR burnup credit (BUC), including major and minor actinides and major fission products. The premise of S/U-based validation is that applicable experiments—those having a similar bias to a given application system—will have similar sensitivities for each isotope and reaction in the two systems. It is assumed that cross sections with larger uncertainties are more likely to contain data errors which contribute to the bias. The integral index c k thus propagates the system sensitivities with the nuclear covariance data to calculate a correlation coefficient representing the similarity of the two systems. In this work, a c k value of 0.8 or higher is interpreted as identifying an experiment with sufficient similarity for use in validation. This paper presents a brief summary of the characteristics of the 11 MPC-32 DPCs used in the proof of-principle analysis for as-loaded criticality safety calculation validation and an overview of the critical experiment suite with which each of these DPC models was compared. A summary and discussion of c k results is also presented, followed by conclusions and a discussion of future work to be performed for validation of UNF ST&DARDS as-loaded criticality safety calculations.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2022

Dual-band selective circular dichroism in mid-infrared chiral metasurfaces

Most chiral metamaterials and metasurfaces are designed to operate in a single wavelength band and with a certain circular dichroism (CD) value. Here, mid-infrared chiral metasurface absorbers with selective CD in dual-wavelength bands are designed and demonstrated. The dual-band CD selectivity and tunability in the chiral metasurface absorbers are enabled by the unique design of a unit cell with two coupled rectangular bars. It is shown that the sign of CD in each wavelength band can be independently controlled and flipped by simply adjusting the geometric parameters, the width and the length, of the vertical rectangular bars. The mechanism of the dual-band CD selection in the chiral metasurface absorber is further revealed by studying the electric field and magnetic field distributions of the antibonding and bonding modes supported in the coupled bars under circularly polarized incident light. Furthermore, the chiral resonance wavelength can be continuously increased by scaling up the geometric parameters of the metasurface unit cell. The demonstrated results will contribute to the advance of future mid-infrared applications such as chiral molecular sensing, thermophotovoltaics, and optical communication.

36 MATERIALS SCIENCE↗
DOE OSTI2019

High-temperature, spectrally-selective, scalable, and flexible thin-film Si absorber and emitter

Solar thermal technologies have great potential to provide low-cost storage for solar energy. However, their efficiencies are limited by a lack of scalable, mechanically flexible, durable, yet highly-efficient spectrally-selective solar absorbers suitable for high temperatures at low solar concentrations. Here, we overcome these challenges by fabricating a scalable free-standing spectrally-selective thin-film Si absorber and emitter (SSTFS) composite. Its high-temperature emittance shows strong spectral selectivity, even at 595 °C. Thermal stability is proven by measuring optical properties before and after thermal cycling equivalent to one day of concentrated sunlight. Despite the use of crystalline Si, the fabricated SSTFS composite exhibits exceptional mechanical flexibility to cover most surface geometries. The SSTFS composite demonstrates the potential of high-temperature, efficient and flexible solar absorbers and thermal emitters to advance renewable solar energy with storage.

36 MATERIALS SCIENCE↗
DOE OSTI2014

Mutations in global regulators lead to metabolic selection during adaptation to complex environments

Adaptation to ecologically complex environments can provide insights into the evolutionary dynamics and functional constraints encountered by organisms during natural selection. Unlike adaptation to a single limiting resource, adaptation to a new environment with abundant and varied resources can be difficult to achieve by small incremental changes since many mutations are required to achieve even modest gains in fitness. Since changing complex environments are quite common in nature, we investigated how such an epistatic bottleneck can be avoided to allow rapid adaptation. We show that adaptive mutations arise repeatedly in independently evolved populations in the context of greatly increased genetic and phenotypic diversity. We go on to show that weak selection requiring substantial metabolic reprogramming can be readily achieved by mutations in the global response regulator arcA and the stress response regulator rpoS . We identified 46 unique single-nucleotide variants of arcA and 18 mutations in rpoS , nine of which resulted in stop codons or large deletions, suggesting that a subtle modulation of ArcA function and knockouts of rpoS are largely responsible for the metabolic shifts leading to adaptation. These mutations allow a higher order “metabolic selection” that eliminates epistatic bottlenecks, which could occur when many changes would be required. Proteomic and carbohydrate analysis of adapting E. coli populations revealed an up-regulation of enzymes associated with the TCA cycle and amino acid metabolism and an increase in the secretion of putrescine. The overall effect of adaptation across populations is to redirect and efficiently utilize uptake and catabolism of abundant amino acids. Concomitantly, there is a pronounced spread of more ecologically limited strains that results from specialization through metabolic erosion. Remarkably, the global regulators arcA and rpoS can provide a “one-step” mechanism of adaptation to a novel environment, which highlights the importance of global resource management as a powerful strategy to adaptation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

The role of density-dependent and –independent processes in spawning habitat selection by salmon in an Arctic riverscape

Density-dependent (DD) and density-independent (DI) habitat selection is strongly linked to a species’ evolutionary history. Determining the relative importance of each is necessary because declining populations are not always the result of altered DI mechanisms but can often be the result of DD via a reduced carrying capacity. Here, we developed spatially and temporally explicit models throughout the Chena River, Alaska to predict important DI mechanisms that influence Chinook salmon spawning success. We used resource-selection functions to predict suitable spawning habitat based on geomorphic characteristics, a semi-distributed water-and-energy balance hydrologic model to generate stream flow metrics, and modeled stream temperature as a function of climatic variables. Spawner counts were predicted throughout the core and periphery spawning sections of the Chena River from escapement estimates (DD) and DI variables. In addition, we used isodar analysis to identify whether spawners actively defend spawning habitat or follow an ideal free distribution along the riverscape. Aerial counts were best explained by escapement and reference to the core or periphery, while no models with DI variables were supported in the candidate set. Moreover, isodar plots indicated habitat selection was best explained by ideal free distributions, although there was strong evidence for active defense of core spawning habitat. These results are surprising, given salmon commonly defend spawning resources, and are likely due to competition occurring at finer spatial scales than addressed in this study.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2018

Insights into DNA substrate selection by APOBEC3G from structural, biochemical, and functional studies

Human apolipoprotein B mRNA-editing enzyme-catalytic polypeptide-like 3 (A3) proteins are a family of cytidine deaminases that catalyze the conversion of deoxycytidine (dC) to deoxyuridine (dU) in single-stranded DNA (ssDNA). A3 proteins act in the innate immune response to viral infection by mutating the viral ssDNA. One of the most well-studied human A3 family members is A3G, which is a potent inhibitor of HIV-1. Each A3 protein prefers a specific substrate sequence for catalysis—for example, A3G deaminates the third dC in the CCCA sequence motif. However, the interaction between A3G and ssDNA is difficult to characterize due to poor solution behavior of the full-length protein and loss of DNA affinity of the truncated protein. Here, we present a novel DNA-anchoring fusion strategy using the protection of telomeres protein 1 (Pot1) which has nanomolar affinity for ssDNA, with which we captured an A3G-ssDNA interaction. We crystallized a non-preferred adenine in the -1 nucleotide-binding pocket of A3G. The structure reveals a unique conformation of the catalytic site loops that sheds light onto how the enzyme scans substrate in the -1 pocket. Furthermore, our biochemistry and virology studies provide evidence that the nucleotide-binding pockets on A3G influence each other in selecting the preferred DNA substrate. Together, the results provide insights into the mechanism by which A3G selects and deaminates its preferred substrates and help define how A3 proteins are tailored to recognize specific DNA sequences. This knowledge contributes to a better understanding of the mechanism of DNA substrate selection by A3G, as well as A3G antiviral activity against HIV-1.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Direct selection of functional fluorescent-protein antibody fusions by yeast display

Antibodies are important reagents for research, diagnostics, and therapeutics. Many examples of chimeric proteins combining the specific target recognition of antibodies with complementing functionalities such as fluorescence, toxicity or enzymatic activity have been described. However, antibodies selected solely on the basis of their binding specificities are not necessarily ideal candidates for the construction of chimeras. Here, we describe a high throughput method based on yeast display to directly select antibodies most suitable for conversion to fluorescent chimera. A library of scFv binders was converted to a fluorescent chimeric form, by cloning thermal green protein into the linker between VH and VL, and directly selecting for both binding and fluorescent functionality. This allowed us to directly identify antibodies functional in the single chain TGP format, that manifest higher protein expression, easier protein purification, and one-step binding assays.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Forward variable selection enables fast and accurate dynamic system identification with Karhunen-Loève decomposed Gaussian processes

A promising approach for scalable Gaussian processes (GPs) is the Karhunen-Loève (KL) decomposition, in which the GP kernel is represented by a set of basis functions which are the eigenfunctions of the kernel operator. Such decomposed kernels have the potential to be very fast, and do not depend on the selection of a reduced set of inducing points. However KL decompositions lead to high dimensionality, and variable selection thus becomes paramount. This paper reports a new method of forward variable selection, enabled by the ordered nature of the basis functions in the KL expansion of the Bayesian Smoothing Spline ANOVA kernel (BSS-ANOVA), coupled with fast Gibbs sampling in a fully Bayesian approach. It quickly and effectively limits the number of terms, yielding a method with competitive accuracies, training and inference times for tabular datasets of low feature set dimensionality. Theoretical computational complexities are O ( N P 2 ) in training and O ( P ) per point in inference, where N is the number of instances and P the number of expansion terms. The inference speed and accuracy makes the method especially useful for dynamic systems identification, by modeling the dynamics in the tangent space as a static problem, then integrating the learned dynamics using a high-order scheme. The methods are demonstrated on two dynamic datasets: a ‘Susceptible, Infected, Recovered’ (SIR) toy problem, along with the experimental ‘Cascaded Tanks’ benchmark dataset. Comparisons on the static prediction of time derivatives are made with a random forest (RF), a residual neural network (ResNet), and the Orthogonal Additive Kernel (OAK) inducing points scalable GP, while for the timeseries prediction comparisons are made with LSTM and GRU recurrent neural networks (RNNs) along with the SINDy package.

Hayes, Kyle↗