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At least 1,081 records · Page 60

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DOE OSTI2010

Evidence for alternative quaternary structure in a bacterial Type III secretion system chaperone

Type III secretion systems are a common virulence mechanism in many Gram-negative bacterial pathogens. These systems use a nanomachine resembling a molecular needle and syringe to provide an energized conduit for the translocation of effector proteins from the bacterial cytoplasm to the host cell cytoplasm for the benefit of the pathogen. Prior to translocation specialized chaperones maintain proper effector protein conformation. The class II chaperone, Invasion plasmid gene (Ipg) C, stabilizes two pore forming translocator proteins. IpgC exists as a functional dimer to facilitate the mutually exclusive binding of both translocators. In this study, we present the 3.3 {angstrom} crystal structure of an amino-terminally truncated form (residues 10-155, denoted IpgC10-155) of the class II chaperone IpgC from Shigella flexneri. Our structure demonstrates an alternative quaternary arrangement to that previously described for a carboxy-terminally truncated variant of IpgC (IpgC{sup 1-151}). Specifically, we observe a rotationally-symmetric 'head-to-head' dimerization interface that is far more similar to that previously described for SycD from Yersinia enterocolitica than to IpgC1-151. The IpgC structure presented here displays major differences in the amino terminal region, where extended coil-like structures are seen, as opposed to the short, ordered alpha helices and asymmetric dimerization interface seen within IpgC{sup 1-151}. Despite these differences, however, both modes of dimerization support chaperone activity, as judged by a copurification assay with a recombinant form of the translocator protein, IpaB. Conclusions: From primary to quaternary structure, these results presented here suggest that a symmetric dimerization interface is conserved across bacterial class II chaperones. In light of previous data which have described the structure and function of asymmetric dimerization, our results raise the possibility that class II chaperones may transition between asymmetric and symmetric dimers in response to changes in either biochemical modifications (e.g. proteolytic cleavage) or other biological cues. Such transitions may contribute to the broad range of protein-protein interactions and functions attributed to class II chaperones.

36 MATERIALS SCIENCE↗

DOE OSTI2011

β1 integrin mediates an alternative survival pathway in breast cancer cells resistant to lapatinib

The overexpression of human epidermal growth factor receptor (HER)-2 in 20% of human breast cancers and its association with aggressive growth has led to widespread use of HER2-targeted therapies, such as trastuzumab (T) and lapatinib (L). Despite the success of these drugs, their efficacy is limited in patients whose tumors demonstrate de novo or acquired resistance to treatment. The b1 integrin resides on the membrane of the breast cancer cell, activating several elements of breast tumor progression including proliferation and survival. We developed a panel of HER2-overexpressing cell lines resistant to L, T, and the potent LT combination through long-term exposure and validated these models in 3D culture. Parental and L/T/LT-resistant cells were subject to HER2 and b1 integrin inhibitors in 3D and monitored for 12 days, followed by quantification of colony number. Parallel experiments were conducted where cells were either stained for Ki-67 and Terminal deoxynucleotidyl transferase dUTP nick end labeling (TUNEL) or harvested for protein and analyzed by immunoblot. Results were subjected to statistical testing using analysis of variance and linear contrasts, followed by adjustment with the Sidak method. Using multiple cell lines including BT474 and HCC1954, we reveal that in L and LT resistance, where phosphorylation of EGFR/HER1, HER2, and HER3 are strongly inhibited, kinases downstream of b1 integrin– including focal adhesion kinase (FAK) and Src–are up-regulated. Blockade of b1 by the antibody AIIB2 abrogates this up-regulation and functionally achieves significant growth inhibition of L and LT resistant cells in 3D, without dramatically affecting the parental cells. SiRNA against b1 as well as pharmacologic inhibition of FAK achieve the same growth inhibitory effect. In contrast, trastuzumab-resistant cells, which retain high levels of phosphorylated EGFR/HER1, HER2, and HER3, are only modestly growth-inhibited by AIIB2. Our data suggest that HER2 activity, which is suppressed in resistance involving L but not T alone, dictates whether b1 mediates an alternative pathway driving resistance. Our findings justify clinical studies investigating the inhibition of b1 or its downstream signaling moieties as strategies to overcome acquired L and LT resistance.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2013

Single site-specific integration targeting coupled with embryonic stem cell differentiation provides a high-throughput alternative to in vivo enhancer analyses

Comprehensive analysis of cis-regulatory elements is key to understanding the dynamic gene regulatory networks that control embryonic development. While transgenic animals represent the gold standard assay, their generation is costly, entails significant animal usage, and in utero development complicates time-course studies. As an alternative, embryonic stem (ES) cells can readily be differentiated in a process that correlates well with developing embryos. Here, we describe a highly effective platform for enhancer assays using an Hsp68/ Venus reporter cassette that targets to the Hprt locus in mouse ES cells. This platform combines the flexibility of Gateway H cloning, live cell trackability of a fluorescent reporter, low background and the advantages of single copy insertion into a defined genomic locus. We demonstrate the successful recapitulation of tissue-specific enhancer activity for two cardiac and two haematopoietic enhancers. In addition, we used this assay to dissect the functionality of the highly conserved Ets/Ets/Gata motif in the Scl+19 enhancer, which revealed that the Gata motif is not required for initiation of enhancer activity. We further confirmed that Gata2 is not required for endothelial activity of the Scl+19 enhancer using Gata2 -/- Scl+19 transgenic embryos. We have therefore established a valuable toolbox to study gene regulatory networks with broad applicability.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Constellation's best estimate alternate source term methodology overview

Safety analyses for a nuclear power plants need to consider postulated accidents that results in at risk of accidental release of radiation. The regulations require plant specific safety analysis reports to include an evaluation of the requirements of 10CFR50.67. Such a safety analysis report mandates limits such that calculated radiological consequences relative to certain dose locations do not exceed a total effective dose equivalent (TEDE) limits following a postulated release of radioactivity. Calculations are performed to estimate the radiological consequences, in terms of dose, to people and equipment to ensure the estimated doses are within the prescribed limits. Analysis should demonstrate, with reasonable assurance, that these prescribed limits are complied with. Conventional methodologies utilize conservative approaches to address lack of uncertainty quantification in the utilized approaches, methods, and/or inputs. These built-in excess conservatisms often result in compounding effects and hence overly conservative results in the estimated radiological consequences, which leads to inaccurate margin evaluation for operation and accident mitigation. Therefore, evaluating accurate dose consequences is needed for both operational and safety reasons. The research documented in this paper provides an overview of Constellation's Best Estimate Alternate Source Term (BEAST) Methodology. BEAST methodology relies upon the use of realistic yet bounding input distributions for key analysis parameters, which replaces use of conservative deterministic singular inputs that bound overall analysis domain. This approach enables evaluating a more accurate accident analysis response, while enabling a bounding licensing basis envelope via more accurate quantification of uncertainty in the application. Therefore, built-in margin for a given scenario is more accurately evaluated.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

DOE OSTI2022

Alternative analysis of the MINERVE ZPR oscillation experiments

Delayed neutrons are of fundamental importance in the field of nuclear reactor dynamics and control. However, the precursor yield fraction for a given nuclear reactor are dependent on the properties of the reactor. Thus, in-pile experiments, such as oscillation experiments are conducted in order to measure those values. In this work, an alternative analysis of the piston oscillation experiments that have been conducted in the MINERVE reactor in 2013 is performed. A new method which evolves effective terms that cancel out undesired drifts of the flux during the experiments is presented. The evaluation of the uncertainty on the values of the response function is also presented. Moreover, the effective delayed neutron fraction β{sub eff} is evaluated and is compared to results in previous works. As the analysis has led to an estimation of β{sub eff} with a large uncertainty, it has been deduced that the oscillation experiments that have been conducted in MINERVE are not a reliable method of experimentation to determine the value of β{sub eff} in the reactor and that the noise experiments are better suited for that purpose.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

DOE OSTI2016

Systems-Wide Prediction of Enzyme Promiscuity Reveals a New Underground Alternative Route for Pyridoxal 5’-Phosphate Production in E. coli

Recent insights suggest that non-specific and/or promiscuous enzymes are common and active across life. Understanding the role of such enzymes is an important open question in biology. Here we develop a genome-wide method, PROPER, that uses a permissive PSI-BLAST approach to predict promiscuous activities of metabolic genes. Enzyme promiscuity is typically studied experimentally using multicopy suppression, in which over-expression of a promiscuous ‘replacer’ gene rescues lethality caused by inactivation of a ‘target’ gene. We use PROPER to predict multicopy suppression in Escherichia coli, achieving highly significant overlap with published cases (hypergeometric p = 4.4e-13). We then validate three novel predicted target-replacer gene pairs in new multicopy suppression experiments. We next go beyond PROPER and develop a network-based approach, GEM-PROPER, that integrates PROPER with genome-scale metabolic modeling to predict promiscuous replacements via alternative metabolic pathways. GEM-PROPER predicts a new indirect replacer (thiG) for an essential enzyme (pdxB) in production of pyridoxal 5’-phosphate (the active form of Vitamin B 6 ), which we validate experimentally via multicopy suppression. Here, we perform a structural analysis of thiG to determine its potential promiscuous active site, which we validate experimentally by inactivating the pertaining residues and showing a loss of replacer activity. Thus, this study is a successful example where a computational investigation leads to a network-based identification of an indirect promiscuous replacement of a key metabolic enzyme, which would have been extremely difficult to identify directly.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2012

Multiple Novel Alternative Splicing Forms of FBXW7α Have a Translational Modulatory Function and Show Specific Alteration in Human Cancer

BXW7 acts as a tumor suppressor through ubiquitination and degradation of multiple oncoproteins. Loss of FBXW7 expression, which could be partially attributed by the genomic deletion or mutation of FBXW7 locus, is frequently observed in various human cancers. However, the mechanisms regulating FBXW7 expression still remain poorly understood. Here we examined the 59 region of FBXW7 gene to investigate the regulation of FBXW7 expression. We identified seven alternative splicing (AS) 59-UTR forms of FBXW7a that are composed of multiple novel non-coding exons. A significant difference in translational efficiency among these 59-UTRs variants was observed by in vivo Luciferase reporter assay and Western blot. Furthermore, we found that the mRNA level of the AS form with high translational efficiency was specifically reduced in more than 80% of breast cancer cell lines and in more than 50% of human primary cancers from various tissues. In addition, we also identified mutations of FBXW7 in prostate cancers (5.6%), kidney cancers (16.7%), and bladder cancers (18.8%). Our results suggest that in addition to mutation, differential expression of FBXW7a AS forms with different translational properties may serve as a novel mechanism for inactivation of FBXW7 in human cancer.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2017

Functional vs. Traditional Analysis in Biomechanical Gait Data: An Alternative Statistical Approach

In human motion studies, discrete points such as peak or average kinematic values are commonly selected to test hypotheses. The purpose of this study was to describe a functional data analysis and describe the advantages of using functional data analyses when compared with a traditional analysis of variance (ANOVA) approach. Nineteen healthy participants (age: 22 ± 2 yrs, body height: 1.7 ± 0.1 m, body mass: 73 ± 16 kg) walked under two different conditions: control and pain+effusion. Pain+effusion was induced by injection of sterile saline into the joint capsule and hypertonic saline into the infrapatellar fat pad. Sagittal-plane ankle, knee, and hip joint kinematics were recorded and compared following injections using 2×2 mixed model ANOVAs and FANOVAs. The results of ANOVAs detected a condition × time interaction for the peak ankle (F1,18 = 8.56, p = 0.01) and hip joint angle (F1,18 = 5.77, p = 0.03), but did not for the knee joint angle (F1,18 = 0.36, p = 0.56). The functional data analysis, however, found several differences at initial contact (ankle and knee joint), in the mid-stance (each joint) and at toe off (ankle). Although a traditional ANOVA is often appropriate for discrete or summary data, in biomechanical applications, the functional data analysis could be a beneficial alternative. Thus when using the functional data analysis approach, a researcher can (1) evaluate the entire data as a function, and (2) detect the location and magnitude of differences within the evaluated function.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2017

Donor-Recipient Identification in Para- and Poly-phyletic Trees Under Alternative HIV-1 Transmission Hypotheses Using Approximate Bayesian Computation

Diversity of the founding population of Human Immunodeficiency Virus Type 1 (HIV-1) transmissions raises many important biological, clinical, and epidemiological issues. In up to 40% of sexual infections, there is clear evidence for multiple founding variants, which can influence the efficacy of putative prevention methods, and the reconstruction of epidemiologic histories. To infer who-infected-whom, and to compute the probability of alternative transmission scenarios while explicitly taking phylogenetic uncertainty into account, we created an approximate Bayesian computation (ABC) method based on a set of statistics measuring phylogenetic topology, branch lengths, and genetic diversity. We applied our method to a suspected heterosexual transmission case involving three individuals, showing a complex monophyletic-paraphyletic-polyphyletic phylogenetic topology. We detected that seven phylogenetic lineages had been transmitted between two of the individuals based on the available samples, implying that many more unsampled lineages had also been transmitted. Testing whether the lineages had been transmitted at one time or over some length of time suggested that an ongoing superinfection process over several years was most likely. While one individual was found unlinked to the other two, surprisingly, when evaluating two competing epidemiological priors, the donor of the two that did infect each other was not identified by the host root-label, and was also not the primary suspect in that transmission. This highlights that it is important to take epidemiological information into account when analyzing support for one transmission hypothesis over another, as results may be nonintuitive and sensitive to details about sampling dates relative to possible infection dates. Here, our study provides a formal inference framework to include information on infection and sampling times, and to investigate ancestral node-label states, transmission direction, transmitted genetic diversity, and frequency of transmission.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

TEAMER: Results of Investigating Structural Design Concepts and Alternative Materials for a Wave Power System

Included here are materials from a study on the design of a three-body Wave Energy Converter (WEC) utilizing a heave plate, dual Power Take Offs (PTOs), and single point mooring. A material trade study has been conducted to evaluate the effects of introducing various metallic and fiber-reinforced polymer (FRP) elements to the design. The baseline design is C-Power's patented k2 Wave Power System (WPS). This Testing Expertise and Access for Marine Energy Research (TEAMER) Request for Technical Support (RFTS) 9 effort resulted in alternative designs of the WPS center member, the nacelle. The analysis resulting from this study will inform the design of a lightweight structure with lower manufacturing and operating costs that increases energy conversion and power-to-weight ratio of the device. The dataset contains several components: finite element analysis (FEA) data, hand calculations, and CAD models. FEA files includes those used for and generated by finite element simulations. Calculations include hand calculations performed using Microsoft Excel, which assess core laminate properties, buckling, and other structural aspects in accordance with risk management DNV-RP-C201 standards. CAD materials include Solidworks files for parts, assemblies, and drawings of the evaluated models.

16 TIDAL AND WAVE POWER↗

DOE OSTI2026

Data for Rod et al., "Alternating salt and freshwater floods of coastal soils impact soil structure, hydraulic properties, and oxygen dynamics"

This dataset includes laboratory experiment data on soil structure, hydraulic properties, and oxygen dynamics associated with Rod et al. 2026 https://doi.org/10.1002/vzj2.70073. There are six data files from a lab-based flood simulation of either freshwater (FW) or alternating brackish saltwater (SW) and FW using soil cores from a coastal forest at the Smithsonian Environmental Research Center. For soil information please see the Location section of the metadata. Files include: CO2, surface chemistry, water retention, dissolved oxygen, and soil specific surface area. Each file is in CSV format and can be opened/read with any plain text tabular file reader (Microsoft Excel, R, etc.). Purpose of Experiment: To investigate how hydrologic intensification affects soil structure and oxygen dynamics, we conducted a series of laboratory-based flood simulations. After three SW-FW floods (6 floods total) there were significant changes in pore size distribution, significant redistribution of colloids, and the A-horizon became sodic. We concluded that a small number of SW flooding events can induce a measurable change in soil physical properties that directly impacts the biogeochemical dynamics.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2024

Reinforcement Learning as a Parsimonious Alternative to Prediction Cascades: A Case Study on Image Segmentation

Deep learning architectures have achieved state-of-the-art (SOTA) performance on computer vision tasks such as object detection and image segmentation. This may be attributed to the use of over-parameterized, monolithic deep learning architectures executed on large datasets. Although such large architectures lead to increased accuracy, this is usually accompanied by a larger increase in computation and memory requirements during inference. While this is a non-issue in traditional machine learning (ML) pipelines, the recent confluence of machine learning and fields like the Internet of Things (IoT) has rendered such large architectures infeasible for execution in low-resource settings. For some datasets, large monolithic pipelines may be overkill for simpler inputs. To address this problem, previous efforts have proposed decision cascades where inputs are passed through models of increasing complexity until the desired performance is achieved. However, we argue that cascaded prediction leads to sub-optimal throughput and increased computational cost due to wasteful intermediate computations. To address this, we propose PaSeR (Parsimonious Segmentation with Reinforcement Learning) a non-cascading, cost-aware learning pipeline as an efficient alternative to cascaded decision architectures. Through experimental evaluation on both real-world and standard datasets, we demonstrate that PaSeR achieves better accuracy while minimizing computational cost relative to cascaded models. Further, we introduce a new metric IoU/GigaFlop to evaluate the balance between cost and performance. On the real-world task of battery material phase segmentation, PaSeR yields 179% improvement over SOTA MatPhase model and a 196% improvement over IDK Cascades under the IoU/GigaFlop metric. We also demonstrate PaSeR’s adaptability to complementary models trained on a noisy MNIST dataset, where it outperforms all baselines on IoU/GigaFlop by an average of 44%.

Srikshan, Bharat↗

DOE OSTI2018

Alternate Null Hypothesis Correlation: A New Approach to Automatic Seismic Event Detection

This paper describes a new method of seismic signal detection that improves upon the conventional waveform correlation method. Recent studies suggested that a significant limiting factor in the application of waveform correlation to regional and global scale monitoring is the false alarm rate. The false alarms do not originate from detections on noise but rather from seismic arrivals with unrelated source locations. This article presents results from an approach to waveform correlation that exploits techniques from signal processing and machine learning to improve the accuracy of detecting seismic arrivals. We modify the detection model for waveform correlation such that transient signals from noncollocated seismicity are considered when designing the detectors. The new approach uses waveform templates from known catalog events to train a supervised machine learning algorithm that derives a new set of detectors to represent the unique characteristics of the template waveforms; these new detectors maximize the likelihood of detecting only the desired events, thereby minimizing false alarms. We train a waveform correlation template library for a single three-component seismic monitoring station. We then review results from applying the new detectors, known as alternate null hypothesis correlation (ANCorr) templates, to a test set of seismic waveforms. Finally, we compare ANCorr results with those from application of the conventional waveform correlation matched filter technique.

58 GEOSCIENCES↗

DOE OSTI2015

Overview of Alternative Bunching and Current-shaping Techniques for Low-Energy Electron Beams

Techniques to bunch or shape an electron beam at low energies (E <15 MeV) have important implications toward the realization of table-top radiation sources [1] or to the design of compact multi-user free-electron lasers[2]. This paper provides an overview of alternative methods recently developed including techniques such as wakefield-based bunching, space-charge-driven microbunching via wave-breaking [3], ab-initio shaping of the electron-emission process [4], and phase space exchangers. Practical applications of some of these methods to foreseen free-electron-laser configurations are also briefly discussed [5].

43 PARTICLE ACCELERATORS↗

DOE OSTI2018

Beam formation in the alternative JLEIC ion complex

The proposed alternative design approach for the JLab-EIC (JLEIC) ion complex uses a more compact linac and pre-booster, and consolidates the electron storage ring (ering) as a large booster for the ions. Following a parameter study showing the feasibility of this design approach, we have adapted the e-ring lattice by adding RF sections to accelerate ion beams. In this study, we focus on the transverse beam formation for protons and lead ions from the ion source to collision point including the linac, pre-booster, e-ring and collider ring. Effects such as stripping injection, space charge, intra-beam scattering and beam cooling determine the total charge accumulated in each ring and the final luminosity of the collider.

Mustapha, Brahim↗

DOE OSTI2022

Transverse Stability in an Alternating Symmetry Planar Dielectric Wakefield Structure

Dielectric Wakefield Acceleration (DWA) is a promising technique for realizing the next generation of linear colliders. It provides access to significantly higher accelerating gradients than traditional radio-frequency cavities. One impediment to realizing a DWA-powered accelerator is the issue of the transverse stability of the beams within the dielectric structure due to short-range wakefields. These short-range wakefields have a tendency to induce a phenomenon known as single-bunch beam breakup, which acts as its name implies and destroys the relevant beam. We attempt to solve this issue by leveraging the quadrupole mode excited in a planar dielectric structure and then alternating the orientation of said structure to turn an unstable system into a stable one. We examine this issue computationally to determine the limits of stability and based on those simulations describe a future experimental realization of this strategy.

43 PARTICLE ACCELERATORS↗

DOE OSTI2023

Demonstration of Magnetron as an Alternative RF Source for SRF Accelerators

Magnetron has been considered as alternate high-efficiency, low-cost RF sources for linacs and storage rings [1] for national labs and industrial applications. After the demonstration of magnetrons power to drive and combine for a radio frequency cavity at 2450 MHz in CW mode, we have used trim coils adding to a water-cooled magnetron and amplitude modulation feedback to further suppress the side-band noise to -46.7 dBc level. We also demonstrated the phase-locking to an industrial grade cooking magnetron transmitter at 915 MHz with a 75 kW CW power delivered to a water load by using a -26.6 dBc injection signal [2]. The sideband noise from the 3-Phase SCRs DC power supply can be reduced to -16.2 dBc level. Further noise reduction and their power combining scheme using magic-tee and cavity type combiners for higher power application (2x75kW) are to be presented. We intent to use one power station to drive the normal conducting and superconducting RF cavities for the inductrial linac. We also going to demonstarte a vertical SRF cavity test with a high input coupling Q using a 2.45GHz magnetron and comparing with a baseline test result using a solid state amplifier.

Wang, H.↗

DOE OSTI2014

Alternative spawning strategy and temperature for larval emergence of longfin dace ( Agosia chrysogaster ) in stream mesocosms

To determine if the strategy of spawning in saucer-like depressions is obligate or facultative for longfin dace ( Agosia chrysogaster ), we collected adults from four sites in the upper Gila River (southwestern New Mexico), stocked them in separate outdoor stream-mesocosms lined with cobble substrate, and made daily observations for the presence of saucer-nests and hatched larvae. Larvae were observed from three of the four mesocosms and emerged at temperatures ranging from 19.2 24.0 °C. Here, the absence of saucer-nests in all mesocosms throughout the study indicates that longfin dace can spawn over cobble substrate and have larvae hatch successfully, suggesting that longfin dace can use an alternate spawning strategy when sand substrate is not available for construction of saucer-nests.

59 BASIC BIOLOGICAL SCIENCES↗