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At least 1,549 records · Page 86
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Functional and genetic markers of niche partitioning among enigmatic members of the human oral microbiome

Abstract Introduction Microbial residents of the human oral cavity have long been a major focus of microbiology due to their influence on host health and intriguing patterns of site specificity amidst the lack of dispersal limitation. However, the determinants of niche partitioning in this habitat are yet to be fully understood, especially among taxa that belong to recently discovered branches of microbial life. Results Here, we assemble metagenomes from tongue and dental plaque samples from multiple individuals and reconstruct 790 non-redundant genomes, 43 of which resolve to TM7, a member of the Candidate Phyla Radiation, forming six monophyletic clades that distinctly associate with either plaque or tongue. Both pangenomic and phylogenomic analyses group tongue-specific clades with other host-associated TM7 genomes. In contrast, plaque-specific TM7 group with environmental TM7 genomes. Besides offering deeper insights into the ecology, evolution, and mobilome of cryptic members of the oral microbiome, our study reveals an intriguing resemblance between dental plaque and non-host environments indicated by the TM7 evolution, suggesting that plaque may have served as a stepping stone for environmental microbes to adapt to host environments for some clades of microbes. Additionally, we report that prophages are widespread among oral-associated TM7, while absent from environmental TM7, suggesting that prophages may have played a role in adaptation of TM7 to the host environment. Conclusions Our data illuminate niche partitioning of enigmatic members of the oral cavity, including TM7, SR1, and GN02, and provide genomes for poorly characterized yet prevalent members of this biome, such as uncultivated Flavobacteriaceae.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

A field guide for aging passerine nestlings using growth data and predictive modeling

Abstract Background Accurate nestling age is valuable for studies on nesting strategies, productivity, and impacts on reproductive success. Most aging guides consist of descriptions and photographs that are time consuming to read and subjective to interpret. The Western Bluebird ( Sialia mexicana ) is a secondary cavity-nesting passerine that nests in coniferous and open deciduous forests. Nest box programs for cavity-nesting species have provided suitable nesting locations and opportunities for data collection on nestling growth and development. Methods We developed models for predicting the age of Western Bluebird nestlings from morphometric measurements using model training and validation. These were developed for mass, tarsus, and two different culmen measurements. Results Our models were accurate to within less than a day, and each model worked best for a specific age range. The mass and tarsus models can be used to estimate the ages of Western Bluebird nestlings 0–10 days old and were accurate to within 0.5 days for mass and 0.7 days for tarsus. The culmen models can be used to estimate ages of nestlings 0–15 days old and were also accurate to within less than a day. The daily mean, minimum, and maximum values of each morphometric measurement are provided and can be used in the field for accurate nestling age estimations in real time. Conclusions The model training and validation procedures used here demonstrate that this method can create aging models that are highly accurate. The methods can be applied to any passerine species provided sufficient nestling morphometric data are available.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

High Force Spring Clamp System

This is the Final Technical Report for the work by Hyperboloid LLC using SBIR Grant # DE-SC0019579. The work responded to US DOE SBIR Topics FY2019, Phase 1, Release 1, August 13 2018, Topic: 30. a. (2) SRF cavity joining techniques that create vacuum seals without resorting to the use of bolted flanges in order to minimize particulates. Hyperboloid LLC designed, developed and tested the High Force Spring Clamp System characterized in Patent US 9756715 that is aimed at solving this topic. The patent is held by Thomas Jefferson National Accelerator Facility. The flange bolts are substituted with exceptionally high force, binder-clip-like “C” Clamps. The clamps are opened and applied by hydraulic based tooling called “Clamp Openers” using particle minimization methods. Model 1 Clamp reached the goal of sealing the SRF industry standard hexagonal section, aluminum alloy gasket, leak-free on a research cavity as determined by a superfluid helium challenge, at 2 K for 2 assembly cycles. Descriptions include the ANSYS calculations that determine the size and shape of the clamp, the details of the Clamp Opener construction, particle counts from sealing flanges using both bolts and clamps. Model 2 Clamp, at half the size, needing a softer metallic gasket to be successful, is more readily adaptable to Cryomodule designs. It was tested, but a needs soft gasket development to be successful.

43 PARTICLE ACCELERATORS↗
DOE OSTI2024

Contactless Position Measurement System for Remote Alignment of Highly Reflective Objects

The Contactless Position Measurement System (CPMS) permits automatic alignment of highly-reflecting components that cannot or should not be touched by human hands, such as those used in SRF cavities. CPMS also has application during maintenance of fusion reactors, when the components in the reactor are radioactive. The length of time for which humans can handle the components in order to carry out maintenance or repairs is limited. We would like to measure the relative positions of such objects so we can bring them into alignment with motorized stages, thus eliminating the need for human contact. The CPMS is a computer vision system that measures the location of highly reflective components to within a fraction of a millimeter by finding the edges of silhouette images. This is done by placing a uniform, infrared backlight behind the components, and viewing each component with two low-aberration, infrared cameras. Each of these stereoscopic cameras are located within a coordinate system we set up with reference platforms, light sources, and survey cameras distributed around the perimeter of the string assembly room, or fusion reactor. We obtain stereoscopic silhouette images of each component, and we use these to determine the position of the component within our string assembly coordinate system. The CPMS combines the silhouette images with knowledge of the dimensions of the objects to obtain the relative positions of components in its field of view. These position measurements then allow us to mechanically maneuver the components into contact. Once we know where they are, we can move the components to where they are supposed to be with motorized stages or other mechanical means, check they are in the right place, and bolt them together. In Phase I, we built a prototype infrared backlights and cameras, tested it, wrote an analysis program to fit the images. At a range of 50 cm, we are able to measure the relative positions of two stainless steel flanges with an accuracy of 150 μm rms. The next steps are to test the analysis program with motorized stages, build a full-size prototype, and implement it in an cleanroom with SRF cavity assembly. This can be done in a cost effective way given the materials with which the system is designed. As Open Source Instruments achieved more in Phase I than anticipated, despite not receiving a Phase II SBIR grant, we hope to move forward with product development and sales with a testing partner.

43 PARTICLE ACCELERATORS↗
DOE OSTI2020

COMBLE-ISLAS water isotopes in precipitation (COMBLEISLASISO)

During the measurement period, precipitation was sampled on daily to sub-daily basis with a sampling kit consiting of a clear plastic box (60x40x40 cm) mounted to a ground structure. Daily sampling lasted from 22 Feb to 24 Mar 2020. At a fixed time of day (10 UTC), samples were collected and the sampling box cleaned for the next sample. Additionally, during intense observations periods (IOPs) announced by ISLAS, ARMS scientists increased sampling frequency to sub-daily sampling. During the campaign period, 2 IOPs were conducted, with in total 12 samples taken. IOP1 lasted from 27 Feb 10 to 02 Mar 2020, and IOP2 lasted from 12 Mar to 14 Mar 2020. Solid precipitation in the box was then melted, transferred to an 8 ml glass vial, sealed and shipped to FARLAB (University of Bergen, Norway) for stable water isotope analysis. Measured stable isotope composition of precipitation samples will be related to conditions at other sampling locations, and at the evaporation site to inform about conservation of water isotope quantities. In the period from 22 Feb to 24 Mar, 23 daily samples were collected at 10 UTC for stable water isotope analysis. During the entire sampling period, a high variability of precipitation phase was encountered. Most samples were recovered in the form of graupel/snow (12 samples), as rain (7 samples), and the remaining samples fell as graupel, snow, rain or frozen rain. Precipitation amounts varied between <1 mm (26 Feb) and 140 mm (25 Feb) within the sampling box. Furthermore, higher-resolution sampling was conducted during 2 intense observation periods (IOPs). During IOP1, lasting from 27 Feb 10 UTC to 02 Mar 10 UTC, 7 samples were collected, all of them as solid phase precipitation. IOP2 lasted from 12 Mar 10 UTC to 14 Mar 09 UTC, and 5 samples (all as graupel/snow) were collected. Samples were processed according to FARLAB standard measurement procedures. In short, samples were transferred to 1.5 ml glass vials with rubber/PTFE septa (part #548-0907, VWR, USA). An autosampler (A0325, Picarro Inc) transferred ca. 2&micro;l per injection into a high-precision vapourizer (A0211, Picarro Inc, USA) heated to 110&deg;C. After blending with dry N2 (< 5 ppm H2O) the gas mixture was directed into the measurement cavity of a Cavity-Ring Down Spectrometer (L2140-i, Picarro Inc) for about 7 min with a typical water concentration of 20 000 ppm. Memory effects were reduced by two times measuring a vapour mixture at a mixing ratio of 50 000 ppm, obtained from 2 injections of 2 &micro;l for 5 min at the beginning of each new sample vial. Thereafter, another 6 injections of 2 &micro;l per sample were measured individually as described above, and averages of the last 5 injections were used for further processing. Three standards were measured at the beginning and end of each batch, including a drift standard DI2 (&delta;D: -50.72&plusmn;0.73 permil, &delta;18O: -7.63&plusmn;0.10 permil), and for calibration the laboratory standards GLW (&delta;D: -307.79&plusmn;0.75 permil, &delta;18O: -40.02&plusmn;0.07 permil) and EVAP2 (&delta;D: 9.52&plusmn;0.65 permil, &delta;18O: 1.81&plusmn;0.13 permil). A detailed calibration report is included with the final uploaded data set.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Exploration of Wire Array Metamaterials for the Plasma Axion Haloscope

A plasma haloscope has recently been proposed as a feasible approach to extend the search for dark matter axions above 10 GHz (≈40 μeV), whereby the microwave cavity in a conventional axion haloscope is supplanted by a wire array metamaterial. Since the plasma frequency of a metamaterial is determined by its unit cell, and is thus a bulk property, a metamaterial resonator of any frequency can be made arbitrarily large, in contrast to a microwave cavity which incurs a steep penalty in volume with increasing frequency. To assess the actual potential of this concept as a practical dark matter haloscope, the basic properties of wire array metamaterials have been investigated through an extensive series of S 21 measurements in the 10 GHz range. This report presents some new systematics of wire array metamaterials themselves including the approach to full plasmonic behavior, the applicability of the semianalytic theory of Belov, and estimates of the loss term which bode favorably for the plasmonic haloscope application. This present work constitutes the first precision test of the semianalytic theory of Belov et al., for which the predicted plasma frequency agrees with the experimental value at the 0.1% level.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2021

Characterization of a Molecule Partially Confined at the Pore Mouth of a Zeotype

Abstract We investigate the interaction between a molecule and a pore mouth—a critical step in adsorption processes—by characterizing the conformation of a macrocyclic calix[4]arene‐Ti IV complex, which is grafted on the external surface of a zeotype (*‐SVY). X‐ray absorption and 13 C{ 1 H} CPMAS NMR spectroscopies independently detect a unique conformation of this complex when it is grafted at crystallographically equivalent locations that lie at the interface of 7 Å hemispherical microporous cavities and the external surface. Electronic structure calculations support the presence of this unique conformation, and suggest that it is brought about by a specific orientation of the macrocycle that maximizes non‐covalent interactions between calix[4]arene upper‐rim tert ‐butyl substituents and the microporous‐cavity walls. Our comparative study provides a rare “snapshot” of a molecule partially confined at a pore mouth, an essential intermediate for adsorption into micropores, and demonstrates how surrounding environment controls this confinement in a sensitive fashion.

Grosso‐Giordano, Nicolás A.↗
DOE OSTI2023

Highly Coupled Heterobicycle‐Fused Porphyrin Dimers: Excitonic Coupling and Charge Separation with Coordinated Fullerene, C 60

Abstract Porphyrin dimers have been widely explored and studied owing to their importance in photosynthetic systems. A vast variety of dimers linked by different groups and at different angles have been synthesized and studied; however, the means by which to synthesize rigidly fused porphyrins with direct conjugation of the chromophores remains limited. Such a class of porphyrins may possess interesting properties that unconjugated or stacked dimers may not exhibit. In this study, bisbenzimidazole‐fused porphyrin dimers and their mono‐ and bis−zinc derivatives are synthesized and characterized. As a consequence of excitonic coupling, these dimers exhibit a split Soret band irrespective of the metal ion in the porphyrin cavity. Steady‐state fluorescence and excitation spectra followed by femtosecond transient absorption spectral studies of the heterometallated dimer, (free‐base and zinc porphyrin) reveals the occurrence of efficient singlet‐singlet energy transfer (>95 % efficiency and rate constant >10 12 s −1 ) within the dyad. Further, donor‐acceptor conjugates were formed by metal‐ligand axial coordination of phenyl imidazole functionalized C 60 and were characterized by a variety of physicochemical techniques. Excited state charge separation from both singlet and triplet excited states of ZnP in the conjugates has been established. The lifetime of the final charge‐separated state was in the 30–40 μs range revealing charge stabilization. Interestingly, no charge separation in the conjugate derived from the heterometallated dimer was observed wherein excitation transfer dominated the process. The present study brings out the importance of the rigid π‐spacer connecting porphyrin dimers in governing the energy and electron transfer events when coupled with an electron acceptor.

Chemistry↗
DOE OSTI2022

Analysis of the Spontaneous Emission Limited Linewidth of an Integrated III–V/SiN Laser

Abstract This article describes a calculation of the spontaneous emission limited linewidth of a semiconductor laser consisting of hybrid or heterogeneously integrated, silicon and III–V intracavity components. Central to the approach are a) description of the multi‐element laser cavity in terms of composite laser/free‐space eigenmodes, b) use of multimode laser theory to treat mode competition and multiwave mixing, and c) incorporation of quantum‐optical contributions to account for spontaneous emission effects. Application of the model is illustrated for the case of linewidth narrowing in an InAs quantum‐dot laser coupled to a high‐ SiN cavity.

42 ENGINEERING↗
DOE OSTI2023

Coherent Random Lasing in Subwavelength Quasi‐2D Perovskites

Abstract Quasi‐2D lead halide perovskites have garnered increasing interest as lasing gain media. Relatively simple fabrication, high refractive index, and unique quantum well structure encourage their use in traditional cavity lasers and cavity‐free systems called random lasers (RLs). Despite tremendous advances reported thus far, coherent random lasing in quasi‐2D perovskite subwavelength films has not been reported. Consequently, coherent optical feedback mechanisms in quasi‐2D perovskite systems are still unexplored. Here, this work reports the observation of coherent random lasing in subwavelength quasi‐2D perovskite films. Statistical analysis of spectral measurements reveals Lévy‐like intensity fluctuations, replica symmetry breaking confirms random lasing, and the coherent modes are studied with spectral and spatial correlation techniques. The observed coherent lasing modes are found to be extended states that arise from the random crystal grain structure during fabrication and span the entire pump volume. These modes out‐compete diffusive lasing due to their coherence.

47 OTHER INSTRUMENTATION↗
DOE OSTI2024

Ligand‐induced CaMKIIα hub Trp403 flip, hub domain stacking, and modulation of kinase activity

Abstract γ‐Hydroxybutyric acid (GHB) analogs are small molecules that bind competitively to a specific cavity in the oligomeric CaMKIIα hub domain. Binding affects conformation and stability of the hub domain, which may explain the neuroprotective action of some of these compounds. Here, we describe molecular details of interaction of the larger‐type GHB analog 2‐(6‐(4‐chlorophenyl)imidazo[1,2‐b]pyridazine‐2‐yl)acetic acid (PIPA). Like smaller‐type analogs, PIPA binding to the CaMKIIα hub domain promoted thermal stability. PIPA additionally modulated CaMKIIα activity under sub‐maximal CaM concentrations and ultimately led to reduced substrate phosphorylation. A high‐resolution X‐ray crystal structure of a stabilized CaMKIIα (6x mutant) hub construct revealed details of the binding mode of PIPA, which involved outward placement of tryptophan 403 (Trp403), a central residue in a flexible loop close to the upper hub cavity. Small‐angle X‐ray scattering (SAXS) solution structures and mass photometry of the CaMKIIα wild‐type hub domain in the presence of PIPA revealed a high degree of ordered self‐association (stacks of CaMKIIα hub domains). This stacking neither occurred with the smaller compound 3‐hydroxycyclopent‐1‐enecarboxylic acid (HOCPCA), nor when Trp403 was replaced with leucine (W403L). Additionally, CaMKIIα W403L hub was stabilized to a larger extent by PIPA compared to CaMKIIα hub wild type, indicating that loop flexibility is important for holoenzyme stability. Thus, we propose that ligand‐induced outward placement of Trp403 by PIPA, which promotes an unforeseen mechanism of hub domain stacking, may be involved in the observed reduction in CaMKIIα kinase activity. Altogether, this sheds new light on allosteric regulation of CaMKIIα activity via the hub domain.

Biochemistry & Molecular Biology↗
DOE OSTI2020

Using transparent fish to observe barotrauma associated with downstream passage through hydropower turbines

During downstream passage of hydroelectric facilities, fish can be injured by rapid decompression; this is especially noted during hydroturbine passage. The rapid decrease in pressure can cause barotrauma as undissolved gas expands according to Boyle’s law. However, it is difficult to see barotrauma occurring within the body of the fish in real time. In order to determine if transparent fish could provide greater insight into barotrauma, five species of transparent tropical fish were exposed to rapid decompressions so internal injuries could be viewed noninvasively. Before and after photos were taken to review the injuries and high speed video allowed observations of barotrauma pathways in vivo. High speed video recordings show the expansion of the swim bladder and subsequent release of gas through the mouth and gills, and into the body cavity when the swim bladder ruptured. Post-decompression photographs show that many internal injuries were visible and included hemorrhaging and the presence of emphysema within the body cavity and tissues. These observations provide new opportunities to understand the pathways and effects of barotrauma.

13 HYDRO ENERGY↗
DOE OSTI2019

Inferior Vena Cava Rupture Caused by Balloon Angioplasty During the Treatment of Budd–Chiari Syndrome

Objective: Percutaneous transluminal balloon angioplasty (PTA) is the main treatment option for Budd–Chiari syndrome (BCS) with inferior vena cava (IVC) obstruction. However, IVC rupture caused by PTA has never been reported. Materials and Methods: Between August 2004 and December 2016, a consecutive cohort of 617 BCS patients with obstructed IVC who underwent PTA with or without stent placement were reviewed retrospectively to identify IVC rupture. Pre- and post-procedural imaging data, clinical and procedural technical data were analyzed. Results: Of the 617 BCS patients, five patients had IVC rupture caused by PTA (0.81%). Four of these patients had retroperitoneal, intra-hepatic IVC rupture without extravasation into abdominal cavity which was successfully managed conservatively. One patient had supra-hepatic IVC rupture into the pericardial cavity which was surgically treated. Conclusion: IVC rupture is a rare complication of PTA treatment of BCS and most commonly located at the intra-hepatic IVC caused by oversized balloons which does not require additional treatment.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2021

Submonolayer Quantum-Dot Based Saturable Absorber for Femtosecond Pulse Generation

Semiconductor saturable absorber mirrors (SESAMs) enable passive modelocking of several ultrafast solid-state lasers. Conventionally, SESAMs in the 1-µm wavelength range have employed InGaAs quantum wells (QWs) as absorbers. Here we demonstrate a SESAM based on InAs/GaAs submonolayer quantum dots (SML QDs) capable of generating femtosecond pulses by passively modelocking a vertical-external-cavity surface-emitting laser (VECSEL). Structural measurements are carried out to verify the quality and composition of the QDs. Modelocking experiments with a VECSEL and the QD SESAM in a ring cavity configuration yield pulses as short as 185 fs at 1025 nm. Compared to a traditional QW absorber, SML QD SESAMs exhibit ~ 25% faster recovery times. This also translates to slower power degradation rates or higher damage thresholds in SML QD SESAMs.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Toolpath considerations for hybrid additive manufacturing

Hybrid additive manufacturing combines both additive and subtractive manufacturing processes to fabricate geometrically complex, dimensionally accurate parts that are difficult to make using either additive or subtractive manufacturing alone. Industrial applications for hybrid additive manufacturing include direct manufacturing (building whole parts), feature addition (adding onto existing parts), and remanufacturing or repair operations. To coordinate the additive and subtractive processes, computer-aided manufacturing (CAM) software must generate distinct toolpaths for each process. Each application requires different considerations and inputs when generating the toolpaths. For example, when building a part with an internal cavity that would otherwise be unmanufacturable due to reach or access limitations, a CAM must determine which layer(s) of deposition are appropriate to machine to create the internal cavity. This chapter explores the area of toolpath generation for hybrid manufacturing by discussing the necessary considerations that are unique to a hybrid process.

Feldhausen, Thomas↗