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At least 163 records · Page 9

Focus enhancement in long schlieren imaging systems using corrector lenses

Long schlieren imaging systems, where the parallel light test section is longer than the focal length of the focusing schlieren optics, have a limited region in the test section in which any occluding object, such as a wind tunnel model, is in focus in the schlieren image. Corrector lenses are introduced here to alter the location in the test section where image focus is achieved. Corrector lenses with focal lengths varying from −1000 to −100mm were studied. Lens-type inline and z -type mirror schlieren systems were experimentally tested with multiple collecting optic focal lengths to characterize the changes in focal position. An automated image processing method was used to determine the plane of best focus from image sequences. The introduction of the corrector lens was observed to move the location of best focus within the schlieren system test section while also causing a decrease in the focal sharpness of the images and altering the magnification. The thin lens equation was found to provide a good estimate of the focal location change in the schlieren imaging systems with the addition of the corrector lens.

Torres, Sivana M.↗

Method of making a distributed optical fiber sensor having enhanced Rayleigh scattering and enhanced temperature stability, and monitoring systems employing same

A method of making an optical fiber sensor device for distributed sensing includes generating a laser beam comprising a plurality of ultrafast pulses, and focusing the laser beam into a core of an optical fiber to form a nanograting structure within the core, wherein the nanograting structure includes a plurality of spaced nanograting elements each extending substantially parallel to a longitudinal axis of optical fiber. Also, an optical fiber sensor device for distributed sensing includes an optical fiber having a longitudinal axis, a core, and a nanograting structure within the core, wherein the nanograting structure includes a plurality of spaced nanograting elements each extending substantially parallel to the longitudinal axis of the optical fiber. Also, a distributed sensing method and system and an energy production system that employs such an optical fiber sensor device.

42 ENGINEERING↗

Method of making a distributed optical fiber sensor having enhanced Rayleigh scattering and enhanced temperature stability, and monitoring systems employing same

A method of making an optical fiber sensor device for distributed sensing includes generating a laser beam comprising a plurality of ultrafast pulses, and focusing the laser beam into a core of an optical fiber to form a nanograting structure within the core, wherein the nanograting structure includes a plurality of spaced nanograting elements each extending substantially parallel to a longitudinal axis of optical fiber. Also, an optical fiber sensor device for distributed sensing includes an optical fiber having a longitudinal axis, a core, and a nanograting structure within the core, wherein the nanograting structure includes a plurality of spaced nanograting elements each extending substantially parallel to the longitudinal axis of the optical fiber. Also, a distributed sensing method and system and an energy production system that employs such an optical fiber sensor device.

Chen, Peng Kevin↗

Range extender mediates long-distance enhancer activity

Although most mammalian transcriptional enhancers regulate their cognate promoters over distances of tens of kilobases, some enhancers act over distances in the megabase range1. The sequence features that enable such long-distance enhancer–promoter interactions remain unclear. Here we used in vivo enhancer-replacement experiments at the mouse Shh locus to show that short- and medium-range limb enhancers cannot initiate gene expression at long-distance range. We identify a cis-acting element, range extender (REX), that confers long-distance regulatory activity and is located next to a long-range limb enhancer of Sall1. The REX element has no endogenous enhancer activity. However, addition of the REX to other short- and mid-range limb enhancers substantially increases their genomic interaction range. In the most extreme example observed, addition of REX increased the range of an enhancer by an order of magnitude from its native 73 kb to 848 kb. The REX element contains highly conserved [C/T]AATTA homeodomain motifs that are critical for its activity. These motifs are enriched in long-range limb enhancers genome-wide, including the ZRS (zone of polarizing activity (ZPA) regulatory sequence), a benchmark long-range limb enhancer of Shh2. The ZRS enhancer with mutated [C/T]AATTA motifs maintains limb activity at short range, but loses its long-range activity, resulting in severe limb reduction in knock-in mice. In summary, we identify a sequence signature associated with long-range enhancer–promoter interactions and describe a prototypical REX element that is necessary and sufficient to confer long-distance activation by remote enhancers.

Bower, Grace↗

Characterization of Mammalian In Vivo Enhancers Using Mouse Transgenesis and CRISPR Genome Editing [Book Chapter]

Embryonic morphogenesis is strictly dependent on tight spatiotemporal control of developmental gene expression, which is typically achieved through the concerted activity of multiple enhancers driving cell type-specific expression of a target gene. Mammalian genomes are organized in topologically associated domains, providing a preferred environment and framework for interactions between transcriptional enhancers and gene promoters. While epigenomic profiling and three-dimensional chromatin conformation capture have significantly increased the accuracy of identifying enhancers, assessment of subregional enhancer activities via transgenic reporter assays in mice remains the gold standard for assigning enhancer activity in vivo. Once this activity is defined, the ideal method to explore the functional necessity of a transcriptional enhancer and its contribution to target gene dosage and morphological or physiological processes is deletion of the enhancer sequence from the mouse genome. Here we present detailed protocols for efficient introduction of enhancer-reporter transgenes and CRISPR-mediated genomic deletions into the mouse genome, including a step-by-step guide for pronuclear microinjection of fertilized mouse eggs. We provide instructions for the assembly and genomic integration of enhancer-reporter cassettes that have been used for validation of thousands of putative enhancer sequences accessible through the VISTA enhancer browser, including a recently published method for robust site-directed transgenesis at the H11 safe-harbor locus. Together, these methods enable rapid and large-scale assessment of enhancer activities and sequence variants in mice, which is essential to understand mammalian genome function and genetic diseases.

cis-regulatory elements↗

Uncovering hidden enhancers through unbiased in vivo testing

Chromatin signatures are widely used to identify tissue-specific in vivo enhancers, but their sensitivity and specificity remains unclear. Here we show that many developmental enhancers remain undetectable using currently available chromatin data. In an initial comparison of over 1200 developmental enhancers with tissue-matched chromatin data, 14% (n = 285) lacked canonical enhancer-associated chromatin signatures. To further assess the prevalence of enhancers missed by chromatin profiling approaches, we used a high-throughput transgenic enhancer assay to screen the regulatory landscapes of two key developmental genes at 5 kb resolution, spanning 1.3 Mb of mouse sequence in total. We observed that 23 of 88 (26%) in vivo enhancers discovered by this approach lacked enhancer-associated chromatin signatures in the respective tissue. Our findings suggest the existence of tens of thousands of enhancers that remain undiscovered by currently available chromatin data, underscoring the continued need for expanding resources for enhancer discovery.

Epigenomics↗

New Perspective on Phase Space Density Analysis for Outer Radiation Belt Enhancements: The Influence of MeV Electron Injections

Observation of growing phase space density (PSD) peak in the outer electron radiation belt has been considered evidence for local wave-driven acceleration as a primary cause of radiation belt enhancement. However, recent studies showed that strong substorm-associated MeV electron injections can also cause significant radiation belt enhancements on fast timescales (~10s min). Such rapid enhancements pose challenges for determining true spatial PSD profiles. To address this, we conduct a detailed spatiotemporal analysis of electron flux and PSD during an enhancement event, using Van Allen Probes data. Our analysis reveals rapid and intermittent flux enhancements. During these rapid enhancements, inbound spacecraft observed false PSD peaks, due to spacecraft's relatively slow movement. However, we identify time intervals of stable fluxes between enhancements, enabling us to determine quasi-stationary PSD profiles with no noticeable peaks. This study provides new insights into accurate PSD analysis, critical for understanding the mechanisms underlying radiation belt enhancements.

79 ASTRONOMY AND ASTROPHYSICS↗

Evaluating Heat Extraction Performance of Closed-Loop Geothermal Systems with Thermally Conductive Enhancements in Conduction-Only Reservoirs: Preprint

We investigated the impact of disc-shaped and linear thermal enhancements on performance of closed-loop geothermal systems using steady-state and transient COMSOL numerical simulations. Thermal enhancements refer to thermally conductive material introduced in the rocks surrounding a wellbore to compensate for the relatively low rock thermal conductivity and increase heat extraction. Materials proposed include composite cements with thermally conductive additives such as metals or graphite to obtain overall cement thermal conductivities of 10 to 100x the rock thermal conductivity. Our simulation approach was modeling a subsegment (e.g., 100 m long) of a wellbore with idealized (e.g., perfect disc-shaped) thermal enhancements, and we report results as relative increase in heat extraction with respect to systems without thermal enhancements. We did not evaluate technical feasibility or cost of installing thermal enhancements. Simulations indicate that for 5-mm thick disc-shaped thermal enhancements with 5-m radius, repeated every 1 m along the wellbore and with thermal conductivity of 100x the rock thermal conductivity, the thermal output increases roughly 20% with respect to a closed-loop system without thermal enhancements. For fishbone structure thermal enhancements, we estimate a roughly 7% increase in thermal output for 5-m long radially outward pipes with half the radius of the main wellbore, repeated every 2.5 m, with thermal conductivity of 100x the rock thermal conductivity.

advanced geothermal systems↗

In vivo mapping of mutagenesis sensitivity of human enhancers

Distant-acting enhancers are central to human development1. However, our limited understanding of their functional sequence features prevents the interpretation of enhancer mutations in disease2. Here we determined the functional sensitivity to mutagenesis of human developmental enhancers in vivo. Focusing on seven enhancers that are active in the developing brain, heart, limb and face, we created over 1,700 transgenic mice for over 260 mutagenized enhancer alleles. Systematic mutation of 12-base-pair blocks collectively altered each sequence feature in each enhancer at least once. We show that 69% of all blocks are required for normal in vivo activity, with mutations more commonly resulting in loss (60%) than in gain (9%) of function. Using predictive modelling, we annotated critical nucleotides at the base-pair resolution. The vast majority of motifs predicted by these machine learning models (88%) coincided with changes in in vivo function, and the models showed considerable sensitivity, identifying 59% of all functional blocks. Taken together, our results reveal that human enhancers contain a high density of sequence features that are required for their normal in vivo function and provide a rich resource for further exploration of human enhancer logic.

Kosicki, Michael↗

Ultraconserved enhancer function does not require perfect sequence conservation

Ultraconserved enhancer sequences show perfect conservation between human and rodent genomes, suggesting that their functions are highly sensitive to mutation. However, current models of enhancer function do not sufficiently explain this extreme evolutionary constraint. We subjected 23 ultraconserved enhancers to different levels of mutagenesis, collectively introducing 1,547 mutations, and examined their activities in transgenic mouse reporter assays. Overall, we find that the regulatory properties of ultraconserved enhancers are robust to mutation. Upon mutagenesis, nearly all (19/23, 83%) still functioned as enhancers at one developmental stage, as did most of those tested again later in development (5/9, 56%). Replacement of endogenous enhancers with mutated alleles in mice corroborated results of transgenic assays, including the functional resilience of ultraconserved enhancers to mutation. Furthermore, our findings show that the currently known activities of ultraconserved enhancers do not necessarily require the perfect conservation observed in evolution and suggest that additional regulatory or other functions contribute to their sequence constraint.

59 BASIC BIOLOGICAL SCIENCES↗

Supervised enhancer prediction with epigenetic pattern recognition and targeted validation

Enhancers are important non-coding elements, but they have traditionally been hard to characterize experimentally. The development of massively parallel assays allows the characterization of large numbers of enhancers for the first time. Here, we developed a framework using Drosophila STARR-seq to create shape-matching filters based on meta-profiles of epigenetic features. We integrated these features with supervised machine-learning algorithms to predict enhancers. We further demonstrated that our model could be transferred to predict enhancers in mammals. We comprehensively validated the predictions using a combination of in vivo and in vitro approaches, involving transgenic assays in mice and transduction-based reporter assays in human cell lines (153 enhancers in total). The results confirmed that our model can accurately predict enhancers in different species without re-parameterization. Finally, we examined the transcription factor binding patterns at predicted enhancers versus promoters. Here, we demonstrated that these patterns enable the construction of a secondary model that effectively distinguishes enhancers and promoters.

59 BASIC BIOLOGICAL SCIENCES↗

Identification of conserved skeletal enhancers associated with craniosynostosis risk genes

Abstract Craniosynostosis, defined by premature fusion of one or multiple cranial sutures, is a common congenital defect affecting more than 1/2000 infants and results in restricted brain expansion. Single gene mutations account for 15%–20% of cases, largely as part of a syndrome, but the majority are nonsyndromic with complex underlying genetics. We hypothesized that the two noncoding genomic regions identified by a GWAS for craniosynostosis contain distal regulatory elements for the risk genes BMPER and BMP2. To identify such regulatory elements, we surveyed conserved noncoding sequences from both risk loci for enhancer activity in transgenic Danio rerio. We identified enhancers from both regions that direct expression to skeletal tissues, consistent with the endogenous expression of bmper and bmp2. For each locus, we also found a skeletal enhancer that also contains a sequence variant associated with craniosynostosis risk. We examined the activity of each enhancer during craniofacial development and found that the BMPER-associated enhancer is active in the restricted region of cartilage closely associated with frontal bone initiation. The same enhancer is active in mouse skeletal tissues, demonstrating evolutionarily conserved activity. Using enhanced yeast one-hybrid assays, we identified transcription factors that bind each enhancer and observed differential binding between alleles, implicating multiple signaling pathways. Our findings help unveil the genetic mechanism of the two craniosynostosis risk loci. More broadly, our combined in vivo approach is applicable to many complex genetic diseases to build a link between association studies and specific genetic mechanisms.

He(何璇), Xuan Anita (ORCID:0000000313221972)↗

Mass enhancement in 3 d and s - p perovskites from symmetry breaking

In some d-electron oxides, the measured effective mass m* exptl has long been known to be significantly larger than the model effective mass m* model deduced from mean-field band theory, i.e., m* exptl =βm* model , where β>1 is the “mass-enhancement” or “mass-renormalization” factor. Previous applications of density functional theory (DFT), based on a symmetry-restricted structure with the smallest number of possible magnetic, orbital, and structural degrees of freedom, missed such mass enhancement. This fact has been taken as evidence of strong electronic correlation, often described via the symmetry-restricted dynamic mean-field approach of the many-body theory, being the exclusive enabling physics. This paper uses instead a static density functional approach that does not restrict positional or spin degrees of freedom (symmetry-broken structures). This approach analyzes the contributions of different symmetry-broken modalities to mass enhancement for a few nominally highly correlated d-electron perovskites as well as the nominally uncorrelated, closed-shell s-p bonding perovskites. It shows that the energy-lowering symmetry-broken spin effects (e.g., nonzero local moment in the paramagnetic phase) and structural effects (e.g., atomic displacement) as described in mean-field DFT already manifest mass enhancement for both electrons and holes in a range of d-electron perovskites SrVO 3 , SrTiO 3 , BaTiO 3 , and LaMnO 3 , as well as p-electron perovskites CsPbI 3 and SrBiO 3 , including both metals (SrVO 3 ) and insulators (the rest). This is revealed only when enlarged unit cells of the same parent global symmetry, which are large enough to allow for symmetry-breaking distortions and concomitant variations in spin order, are explored for their ability to lower the total energy. Positional symmetry breaking that leads to mass enhancement includes octahedral rotation in halide perovskites such as CsPbI 3 , Jahn-Teller-like Q${+}\atop{2}$ distortion in LaMnO 3 , and bond disproportionation in SrBiO 3 , while magnetic symmetry breaking resulting in mass enhancement includes the formation of a distribution of local moments in SrVO3 that averages to zero in the paramagnetic phase. Not all symmetry breaking leads to significant mass enhancement, e.g., the rather small octahedral rotations in the nearly perfectly cubic SrTiO 3 cause negligible mass enhancement, as do the paraelectric displacements in BaTiO 3 . In principle, by ergodicity, the two descriptions, i.e., the symmetry-restricted dynamic approach with a single time-fluctuating magnetic moment and the symmetry-broken mean-field approach with a static distribution of spatially fluctuated local moments, are not mutually exclusive but are a choice of representation and consequently, a choice of computational efficiency. In approximate implementations, the symmetry-broken mean-field approach appears to remove much of what was strong correlation in dynamically correlated symmetry-restricted solutions, leaving smaller (“weak”) residual correlation with respect to the exact solution.

36 MATERIALS SCIENCE↗

Understanding the dynamics of vacuole trafficking and secretion for enhanced plant storage reserves

Vacuoles are essential in plants and serve roles in both protein and organelle degradation for reutilization and storage of high energy molecules such as storage proteins which are critical for seed germination under normal and stress conditions and impact biomass production and nutrition. In addition, plants secrete many different molecules such as cell wall components, lipids, waxes and others that are important for plant protection, structure and biomass. Vacuole accumulation and secretion are closely linked and highly regulated pathways within the endomembrane trafficking network. We have discovered many drug-like synthetic small molecules that can suppress vacuole trafficking and enhance secretion; other chemicals can enhance vacuole trafficking and suppress secretion. The ability of our compounds to modulate these pathways indicates that these pathways are tightly coupled and highly regulated. Thus, to achieve the goals of enhanced energy reserves or enhanced secretion it is essential to understand how this dynamic is controlled. Bioactive chemicals have provided us unique insight into natural mechanisms controlling the dynamics of vacuole trafficking and secretion that was not possible previously. One such compound, ES2, negatively modulates secretion while enhancing vacuole trafficking. This is the first compound discovered that targets an essential secretory complex known as the exocyst and will reveal important regulatory domains controlling secretion and vacuole trafficking. During the current funding period, we determined the structure of the EXO70A1 in plants and identifying its binding site. To understand the dynamics of vacuole trafficking it is key to have compounds that inhibit vacuole trafficking as well as enhancing it (ES2). We have used sophisticated image analysis to identify another novel compound ES17 that enhances secretion while negatively modulating vacuole trafficking (opposite of ES2). We have already made rapid progress. Our preliminary data indicates that ES17 very specifically targets a late stage of vesicle fusion with the tonoplast which is highly regulated. Thus, ES17 is an ideal compound to dissect the regulation of vacuole targeting dynamics. In addition, we have now synthesized a biotinylated version of ES17 that is fully functional, permitting the use of chemical proteomics to identify the cognate target with a high probability of success. We propose to investigate the ES17 target which can negatively modulate vacuole trafficking and combine this with knowledge of the ES2 target which can promote vacuole trafficking. Dissecting the mechanisms controlling the dynamics of secretion vs vacuole accumulation and the use of synthetic modulators will permit us to understand and regulate trafficking to enhance secretion to the plasma membrane and cell wall or the accumulation of biological energy reserves for increased biomass, nutritional value, stress resistance, and the secretion of specialized plant products.

59 BASIC BIOLOGICAL SCIENCES↗

Close Major-merger Pairs at z = 0: Bulge-to-total Ratio and Star Formation Enhancement

We present a study of the bulge-to-total ratio (B/T) of a Ks-band-selected sample of 88 close major-merger pairs of galaxies (H-KPAIR), based on two-dimensional decompositions of SDSS r-band images with galfit. We investigate the dependence of the interaction-induced specific star formation rate enhancement (sSFR enh ) on the B/T ratio, and the effects of this dependence on the differences between star-forming galaxies (SFGs) in spiral+spiral (S+S) and spiral+elliptical (S+E) pairs. Of all the 132 spiral galaxies in H-KPAIR, the 44 in S+E pairs show higher B/T than those in the 44 S+S pairs, with means of B/T = 0.35 ± 0.05 and B/T = 0.26 ± 0.03, respectively. Furthermore, there is a strong negative dependence of sSFR enh on the B/T ratio, and only paired SFGs with B/T < 0.3 show significant (>5σ) enhancement. Paired SFGs in S+S pairs show a similar trend, and many disky SFGs (B/T < 0.1) in S+S pairs have strong sSFR enhancements (sSFR enh > 0.7 dex). For SFGs in S+E pairs, the sSFR has no clear B/T dependence, nor any significant enhancement in any B/T bin. Disky SFGs in S+S pairs show significant (>4σ) enhancement in molecular gas content (${M}_{{{\rm{H}}}_{2}}/{M}_{\mathrm{star}}$), while SFGs in S+E pairs have no such enhancement in any B/T bin. No significant enhancement of the total gas content (Mgas/Mstar) is found in any B/T bin for paired galaxies. The star formation efficiency of either the total gas (SFE gas = SFR/M gas ) or molecular gas (${\mathrm{SFE}}_{{{\rm{H}}}_{2}}=\mathrm{SFR}/{M}_{{{\rm{H}}}_{2}}$) does not depend on the B/T ratio. The only significant (> 4σ) SFE enhancement found for paired SFGs is the SFE gas for disky SFGs in S+S pairs.

79 ASTRONOMY AND ASTROPHYSICS↗

A global study of hygroscopicity-driven light-scattering enhancement in the context of other in situ aerosol optical properties

The scattering and backscattering enhancement factors (ƒ(RH) and ƒ b (RH)) describe how aerosol particle light scattering and backscattering, respectively, change with relative humidity (RH). They are important parameters in estimating direct aerosol radiative forcing (DARF). In this study we use the dataset presented in Burgos et al. (2019) that compiles ƒ(RH) and ƒ b (RH) measurements at three wavelengths (i.e., 450, 550 and 700 nm) performed with tandem nephelometer systems at multiple sites around the world. We present an overview of ƒ(RH) and ƒ b (RH) based on both long-term and campaign observations from 23 sites representing a range of aerosol types. The scattering enhancement shows a strong variability from site to site, with no clear pattern with respect to the total scattering coefficient. In general, higher ƒ(RH) is observed at Arctic and marine sites, while lower values are found at urban and desert sites, although a consistent pattern as a function of site type is not observed. The backscattering enhancement ƒ b (RH) is consistently lower than ƒ(RH) at all sites, with the difference between ƒ(RH) and ƒ b (RH) increasing for aerosol with higher ƒ(RH). This is consistent with Mie theory, which predicts higher enhancement of the light scattering in the forward than in the backward direction as the particle takes up water. Our results show that the scattering enhancement is higher for PM 1 than PM 10 at most sites, which is also supported by theory due to the change in scattering efficiency with the size parameter that relates particle size and the wavelength of incident light. At marine-influenced sites this difference is enhanced when coarse particles (likely sea salt) predominate. For most sites, ƒ(RH) is observed to increase with increasing wavelength, except at sites with a known dust influence where the spectral dependence of ƒ(RH) is found to be low or even exhibit the opposite pattern. The impact of RH on aerosol properties used to calculate radiative forcing (e.g., single-scattering albedo, ω 0 , and backscattered fraction, b) is evaluated. The single-scattering albedo generally increases with RH, while b decreases. The net effect of aerosol hygroscopicity on radiative forcing efficiency (RFE) is an increase in the absolute forcing effect (negative sign) by a factor of up to 4 at RH = 90 % compared to dry conditions (RH < 40 %). Because of the scarcity of scattering enhancement measurements, an attempt was made to use other more commonly available aerosol parameters (i.e., ω 0 and scattering Ångström exponent, α sp ) to parameterize ƒ(RH). The majority of sites (75 %) showed a consistent trend with ω 0 (higher ƒ(RH = 85 %) for higher ω 0 ), while no clear pattern was observed between ƒ(RH = 85 %) and αsp. This suggests that aerosol ω 0 is more promising than α sp as a surrogate for the scattering enhancement factor, although neither parameter is ideal. Nonetheless, the qualitative relationship observed between ω 0 and ƒ(RH) could serve as a constraint on global model simulations.

54 ENVIRONMENTAL SCIENCES↗

Nanoparticle-Enhanced Plasma Discharge Using Nanosecond High-Voltage Pulses

By discharging nanosecond high-voltage (5 kV) pulses across an insulating substrate containing Au, Pt, or Cu nanoparticles, a 3 order of magnitude (1000×) enhancement in the generation of plasma can be achieved through local field enhancement on the surface of the nanoparticles. The low-temperature nature of this transient plasma is crucial to maintaining the structural integrity of these delicate nanoparticles. These nanoparticles provide up to a 1000-fold enhancement in the generation of the plasma, which is localized to the surface of the nanoparticles where it is potentially useful (e.g., for catalysis). Additionally, we performed both time-domain and frequency-domain calculations of the electromagnetic response of the nanoparticles based on high-resolution transmission electron microscope (HRTEM) images, which show local field enhancement of the nanosecond high-voltage pulse on the order of 3×. Since the plasma initiation depends exponentially on the peak electric field strength, this 3-fold increase in the local electric field can result in a several orders of magnitude increases in the generation of plasma at a given applied external field strength. In order to rule out plasmon-resonance enhancement, which is often associated with small metal nanoparticles, we performed finite difference time domain (FDTD) simulations in the optical frequency domain, which show that the effect of plasmon resonance is negligible for Pt nanoparticles. We therefore attribute the nanoparticle-based enhancement to the generation of plasma (an electrostatic effect) rather than enhanced coupling of light from the near field to the far field via the plasmon resonance phenomenon (an optical effect).

36 MATERIALS SCIENCE↗