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At least 1,423 records · Page 79

IslandViewer 4: expanded prediction of genomic islands for larger-scale datasets

IslandViewer is a widely-used webserver for the prediction and interactive visualization of genomic islands (GIs, regions of probable horizontal origin) in bacterial and archaeal genomes. GIs disproportionately encode factors that enhance the adaptability and competitiveness of the microbe within a niche, including virulence factors and other medically or environmentally important adaptations. We report here the release of IslandViewer 4, with novel features to accommodate the needs of larger-scale microbial genomics analysis, while expanding GI predictions and improving its flexible visualization interface. A user management web interface as well as an HTTP API for batch analyses are now provided with a secured authentication to facilitate the submission of larger numbers of genomes and the retrieval of results. In addition, IslandViewer’s integrated GI predictions from multiple methods have been improved and expanded by integrating the precise Islander method for pre-computed genomes, as well as an updated IslandPath-DIMOB for both pre-computed and user-supplied custom genome analysis. Finally, pre-computed predictions including virulence factors and antimicrobial resistance are now available for 6193 complete bacterial and archaeal strains publicly available in RefSeq. IslandViewer 4 provides key enhancements to facilitate the analysis of GIs and better understand their role in the evolution of successful environmental microbes and pathogens.

59 BASIC BIOLOGICAL SCIENCES↗

Large Contribution of Meteorological Factors to Inter-Decadal Changes in Regional Aerosol Optical Depth

Aerosol optical depth (AOD) has become a crucial metric for assessing global climate change. Although global and regional AOD trends have been studied extensively, it remains unclear what factors are driving the inter-decadal variations in regional AOD and how to quantify the relative contribution of each dominant factor. This study used a long-term (1980–2016) aerosol dataset from the Modern-Era Retrospective Analysis for Research and Applications, version 2 (MERRA-2) reanalysis, along with two satellite-based AOD datasets (MODIS/Terra and MISR) from 2001 to 2016, to investigate the long-term trends in global and regional aerosol loading. Statistical models based on emission factors and meteorological parameters were developed to identify the main factors driving the inter-decadal changes of regional AOD and to quantify their contribution. Evaluation of the MERRA-2 AOD with the ground-based measurements of AERONET indicated significant spatial agreement on the global scale (r= 0.85, root-mean-square error = 0.12, mean fractional error = 38.7 %, fractional gross error = 9.86 % and index of agreement = 0.94). However, when AOD observations from the China Aerosol Remote Sensing Network (CARSNET) were employed for independent verification, the results showed that MERRA-2 AODs generally underestimated CARSNET AODs in China (relative mean bias = 0.72 and fractional gross error =−34.3 %). In general, MERRA-2 was able to quantitatively reproduce the annual and seasonal AOD trends on both regional and global scales, as observed by MODIS/Terra, although some differences were found when compared to MISR. Over the 37-year period in this study, significant decreasing trends were observed over Europe and the eastern United States. In contrast, eastern China and southern Asia showed AOD increases, but the increasing trend of the former reversed sharply in the most recent decade. The statistical analyses suggested that the meteorological parameters explained a larger proportion of the AOD variability (20.4 %–72.8 %) over almost all regions of interest (ROIs) during 1980–2014 when compared with emission factors (0 %–56 %). Further analysis also showed that SO2 was the dominant emission factor, explaining 12.7 %–32.6 % of the variation in AOD over anthropogenic-aerosol-dominant regions, while black carbon or organic carbon was the leading factor over the biomass-burning-dominant (BBD) regions, contributing 24.0 %–27.7 % of the variation. Additionally, wind speed was found to be the leading meteorological parameter, explaining 11.8 %–30.3 % of the variance over the mineral-dust-dominant regions, while ambient humidity (including soil moisture and relative humidity) was the top meteorological parameter over the BBD regions, accounting for 11.7 %–35.5 % of the variation. The results of this study indicate that the variation in meteorological parameters is a key factor in determining the inter-decadal change in regional AOD.

Huizheng Che↗

Genome-wide profiling of histone (H3) lysine 4 (K4) tri-methylation (me3) under drought, heat, and combined stresses in switchgrass

Background: Switchgrass (Panicum virgatum L.) is a warm-season perennial (C4) grass identified as an important biofuel crop in the United States. It is well adapted to the marginal environment where heat and moisture stresses predominantly affect crop growth. However, the underlying molecular mechanisms associated with heat and drought stress tolerance still need to be fully understood in switchgrass. The methylation of H3K4 is often associated with transcriptional activation of genes, including stress-responsive. Therefore, this study aimed to analyze genome-wide histone H3K4-tri-methylation in switchgrass under heat, drought, and combined stress. Results: In total, ~ 1.3 million H3K4me3 peaks were identified in this study using SICER. Among them, 7,342; 6,510; and 8,536 peaks responded under drought (DT), drought and heat (DTHT), and heat (HT) stresses, respectively. Most DT and DTHT peaks spanned 0 to + 2000 bases from the transcription start site [TSS]. By comparing differentially marked peaks with RNA-Seq data, we identified peaks associated with genes: 155 DT-responsive peaks with 118 DT-responsive genes, 121 DTHT-responsive peaks with 110 DTHT-responsive genes, and 175 HT-responsive peaks with 136 HT-responsive genes. We have identified various transcription factors involved in DT, DTHT, and HT stresses. Gene Ontology analysis using the AgriGO revealed that most genes belonged to biological processes. Most annotated peaks belonged to metabolite interconversion, RNA metabolism, transporter, protein modifying, defense/immunity, membrane traffic protein, transmembrane signal receptor, and transcriptional regulator protein families. Further, we identified significant peaks associated with TFs, hormones, signaling, fatty acid and carbohydrate metabolism, and secondary metabolites. qRT-PCR analysis revealed the relative expressions of six abiotic stress-responsive genes (transketolase, chromatin remodeling factor-CDH3, fatty-acid desaturase A, transmembrane protein 14C, beta-amylase 1, and integrase-type DNA binding protein genes) that were significantly (P < 0.05) marked during drought, heat, and combined stresses by comparing stress-induced against un-stressed and input controls. Conclusion: Our study provides a comprehensive and reproducible epigenomic analysis of drought, heat, and combined stress responses in switchgrass. Significant enrichment of H3K4me3 peaks downstream of the TSS of protein-coding genes was observed. In addition, the cost-effective experimental design, modified ChIP-Seq approach, and analyses presented here can serve as a prototype for other non-model plant species for conducting stress studies.

59 BASIC BIOLOGICAL SCIENCES↗

NECAP: NASA's Energy-Cost Analysis Program. Part 1: User's manual

The NECAP is a sophisticated building design and energy analysis tool which has embodied within it all of the latest ASHRAE state-of-the-art techniques for performing thermal load calculation and energy usage predictions. It is a set of six individual computer programs which include: response factor program, data verification program, thermal load analysis program, variable temperature program, system and equipment simulation program, and owning and operating cost program. Each segment of NECAP is described, and instructions are set forth for preparing the required input data and for interpreting the resulting reports.

Henninger, R. H.↗

Radiative heat transfer in rocket thrust chambers and nozzles

Numerical models based on the discrete exchange factor (DEF) and the zonal methods for radiative analysis of rocket engines containing a radiatively participating medium have been developed. These models implement a new technique for calculating the direct exchange factors to account for possible blockage by the nozzle throat. Given the gas and surface temperature distributions, engine geometry, and radiative properties, the models compute the wall radiative heat fluxes at different axial positions. The results of sample calculations for a typical rocket engine (engine 700 at NASA), which uses RP-1 (a kerosene-type propellant), are presented for a wide range of surface and gas properties. It is found that the heat transfer by radiation can reach up to 50 percent of that due to convection. The maximum radiative heat flux is at the inner side of the engine, where the gas temperature is the highest. While the results of both models are in excellent agreement, the computation time of the DEF method is found to be much smaller.

Hammad, K. J.↗

Synopsis of aeronautic radiator investigations for years 1917 and 1918

Extensive series of experiments have been conducted at the Bureau of Standards to determine the properties of cooling radiator cores manufactured for airplanes and to develop improvements in design. The analysis of the problem on which this work was based, and consequently the experimental method employed, is different from that commonly used. Instead of attempting to test complete radiators, either full size or in model, uniform sections representing different types of core construction have been tested and an analysis of the results made with a view to determining independently the various factors which influence its performance. This report describes referenced method of analysis in predicting the performance of radiators designed for aeronautic use.

Dickinson, H C↗

Targeting CCL2/CCR2 Signaling Overcomes MEK Inhibitor Resistance in Acute Myeloid Leukemia

Emerging evidence underscores the critical role of extrinsic factors within the microenvironment in protecting leukemia cells from therapeutic interventions, driving disease progression, and promoting drug resistance in acute myeloid leukemia (AML). This finding emphasizes the need for the identification of targeted therapies that inhibit intrinsic and extrinsic signaling to overcome drug resistance in AML. We performed a comprehensive analysis utilizing a cohort of ~300 AML patient samples. This analysis encompassed the evaluation of secreted cytokines/growth factors, gene expression, and ex vivo drug sensitivity to small molecules. Our investigation pinpointed a notable association between elevated levels of CCL2 and diminished sensitivity to the MEK inhibitors (MEKi). We validated this association through loss-of-function and pharmacologic inhibition studies. Further, we deployed global phosphoproteomics and CRISPR/Cas9 screening to identify the mechanism of CCR2-mediated MEKi resistance in AML. Our multifaceted analysis unveiled that CCL2 activates multiple prosurvival pathways, including MAPK and cell-cycle regulation in MEKi-resistant cells. Employing combination strategies to simultaneously target these pathways heightened growth inhibition in AML cells. Both genetic and pharmacologic inhibition of CCR2 sensitized AML cells to trametinib, suppressing proliferation while enhancing apoptosis. These findings underscore a new role for CCL2 in MEKi resistance, offering combination therapies as an avenue to circumvent this resistance. Our study demonstrates a compelling rationale for translating CCL2/CCR2 axis inhibitors in combination with MEK pathway-targeting therapies, as a potent strategy for combating drug resistance in AML. This approach has the potential to enhance the efficacy of treatments to improve AML patient outcomes.

60 APPLIED LIFE SCIENCES↗

Technoeconomic assessment of distillation heat transfer intensification using aeroelastically fluttering reeds

Dry cooling, where forced air is the heat transfer medium, is a preferable cooling method in arid locations lacking readily available process water. However, such locations often experience high ambient temperatures that limit the effectiveness of air cooling. The objective of this study is to quantify the economic and energetic benefits of heat transfer intensification via the implementation of aeroelastically fluttering reeds to the air-cooled condenser of a methanol distillation column. Condenser size and performance, regarding recovered methanol and required fan power, is evaluated across condenser operating temperatures (T cond ) from 60 to 62°C and heat transfer coefficients (U) U base –2U base for a range of inlet air temperatures based on ambient temperature data from Yuma, Arizona. Under typical design sizing, condenser capital cost was reduced by 6%–35% (1.3U base –2U base ) and nominal methanol recovery was increased from 0.26% to 0.38% (T cond = 62–60°C). At optimized condenser size, all enhanced U and T cond pairs increase methanol recovery and reduce fan power costs compared to the optimal Ubase reference. Overall, using enhanced heat transfer to maintain condenser temperature under a wider range of inlet conditions, rather than to reduce operation temperature, produces more favorable performance. Methanol price is not a determining factor in which pairs are profitable. Analysis was repeated for a global warming scenario, revealing more valuable improvements under elevated temperatures. Energy savings from condenser improvement to a methanol production system are not significant with respect to an optimized conventional system. Furthermore, unit economic and energetic incentives suggest implementation of fluttering reeds may be justified in other applications.

42 ENGINEERING↗

Moments of axial-vector GPD from lattice QCD: quark helicity, orbital angular momentum, and spin-orbit correlation

In this work, we present a lattice QCD calculation of the Mellin moments of the twist-2 axial-vector generalized parton distribution (GPD), $\overset{\sim }{H}\left(x,\xi, t\right)$ , at zero skewness, ξ, with multiple values of the momentum transfer, t. Our analysis employs the short-distance factorization framework on ratio-scheme renormalized quasi-GPD matrix elements. The calculations are based on an N f = 2 + 1 + 1 twisted mass fermions ensemble with clover improvement, a lattice spacing of a = 0.093 fm, and a pion mass of m π = 260 MeV. We consider both the iso-vector and iso-scalar cases, utilizing next-to-leading-order perturbative matching while omitting the disconnected contributions and gluon mixing in the iso-scalar case. For the first time, we determine the Mellin moments of $\overset{\sim }{H}$ up to the fifth order. From these moments, we discuss the quark helicity and orbital angular momentum contributions to the nucleon spin, as well as the spin-orbit correlations of the quarks. Additionally, we perform a Fourier transform over the momentum transfer, which allows us to explore the spin structure in the impact-parameter space.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Patient Compliance with Surveillance Following Elective Endovascular Aneurysm Repair

PurposeIntegral to maintaining good outcomes post-endovascular aneurysm repair (EVAR) is a robust surveillance protocol. A significant proportion of patients fail to comply with surveillance, exposing themselves to complications. We examine EVAR surveillance in Wessex (UK), exploring factors that may predict poor compliance.MethodsRetrospective analysis of 179 consecutive elective EVAR cases [2008–2013] was performed. 167 patients were male, with the age range of 50–95. Surveillance was conducted centrally (tertiary referral trauma centre) and at four spoke units. Surveillance compliance and predictors of non-compliance including age, gender, co-morbid status, residential location and socioeconomic status were analysed for univariate significance.ResultsFifty patients (27.9 %) were non-compliant with surveillance; 14 (8.1 %) had no imaging post-EVAR. At 1 year, 56.1 % (of 123 patients) were compliant. At years 2 and 3, 41.5 and 41.2 % (of 65 and 34 patients, respectively) were compliant. Four years post-EVAR, only one of eight attended surveillance (12.5 %). There were no statistically significant differences in age (p = 0.77), co-morbid status or gender (p = 0.64). Distance to central unit (p = 0.67) and surveillance site (p = 0.56) was non-significant. While there was a trend towards compliance in upper-middle-class socioeconomic groups (ABC1 vs. C1C2D), correlating with >50 % of non-compliant patients living within <10 mile radius of the central unit, overall predictive value was not significant (p = 0.82).ConclusionsCompliance with surveillance post-EVAR is poor. No independent predictor of non-compliance has been confirmed, but socioeconomic status appears to be relevant. There is a worrying drop-off in attendance beyond the first year. This study highlights a problem that needs to be addressed urgently, if we are to maintain good outcomes post-EVAR.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

Modeling of the Process of Electrostatic Sorption on Suspended Particles of Solid-Phase Powders in Air Space

In the present work, the authors have made a literature analysis of the influence of various factors on the adsorbability of harmful substances in air space. A physicomathematical substantiation of the improvement of the sorption capacity due to the presence of a charge on particles of nanostructured sorption compositions has been proposed. The kinetics of sorption as a function of the interaction time and the dispersity of particles of the charged sorbent and neutral particles of the solute has been determined. Experimental and theoretical assessment of the process of coagulation of liquid-phase particles of glycerin with electrostatically charged solid-phase powders of various kinds in a closed volume have been made. The proposed physicomathematical model of electrostatic sorption was tested for adequacy to experimental data on variation in the average volume-surface diameter of electrostatically charged aerosol formations with time.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

Process Parameter Optimization in Refill Friction Spot Welding of 6061 Aluminum Alloys Using Response Surface Methodology

6061-T6 aluminum alloy joint was fabricated by refill friction stir spot welding (RFSSW) on which three process parameters of tool rotation speed, sleeve moving rate, and plunge depth make an important effect. The response surface methodology (RSM) was applied to establish a mathematical model to study the effect of process parameters on lap shear fracture load (LSFL) of the RFSSWed joints which were performed in Box–Behnken designs with three factors, three levels and 15 runs. Analysis of variance used to check the adequacy of the developed model indicates that the mathematical model is significant. LSFL increases with the increase in tool rotation speed, sleeve plunge depth, and sleeve moving rate to maximum and then decreases. Sleeve plunge depth makes the most effect on LSFL in all process parameters. The RFSSW process parameters were also optimized using RSM to predict maximize LSFL. The joint produced using a tool rotational speed of 1506 rpm, sleeve moving rate of 1.01 mm/s and sleeve plunge depth of 2.46 mm displays higher LSFL.

36 MATERIALS SCIENCE↗

LncRNA MALAT1 regulates oxLDL-induced CD36 expression via activating β-catenin

Highlights: • The role of MALAT1 in lipid uptake was explored. • The regulatory mechanism of oxLDL-induced CD36 was also involved. • We first found oxLDL induces MALAT1 transcription by activating the NF-κB pathway. • MALAT1 promotes lipid uptake by promoting CD36 expression via activating β-catenin. The expression of scavenger receptors in macrophages regulating lipid uptake plays an important role in foam cell formation and the subsequent atherosclerotic plaque formation. Long non-coding RNA MALAT1 is abundantly expressed in THP-1-derived macrophages, and oxidized low-density lipoprotein promotes its transcription by qRT-PCR and RNA FISH detection. Through chemical inhibitor treatments and by performing a dual luciferase reporter analysis, we found that oxLDL induces MALAT1 transcription through the NF-κB pathway. The knockdown of MALAT1 using siRNA transfection affects lipid uptake in macrophages. To understand the details, we checked the scavenger receptors, which mainly control lipid uptake, and found that MALAT1 knockdown decreased CD36 expression. Additionally, we also incubated macrophages with actinomycin D, combined with a dual luciferase reporter analysis, and we found that MALAT1 influenced CD36 expression at the transcription level. We aim to investigate the detailed mechanism by which MALAT1 promotes CD36 transcription, and thus, we designed and synthesized biotin-TEG labeled oligonucleotides to precipitate the MALAT1 RNA-DNA-protein complex in vivo. Combined with SDS-PAGE electrophoresis and a subsequent mass spectra analysis, β-catenin, a transcription factor that promotes CD36 transcription, was found in the complex. By performing R-IPs, we validated that β-catenin was bound to MALAT1 under the oxLDL treatment. In addition, using VAX939, a chemical inhibitor of β-catenin, MALAT1 was demonstrated to promote CD36 transcription partly via β-catenin. We also performed chips to detect whether MALAT1 affects β-catenin accumulation in the binding sites of the CD36 promoter and found that MALAT1 knockdown decreases β-catenin binding to the CD36 promoter and vice versa. In conclusion, oxLDL induced MALAT1 transcription and MALAT1 recruits β-catenin to binding sites on the CD36 promoter to induce CD36 expression, which enhances lipid uptake in macrophages.

60 APPLIED LIFE SCIENCES↗

Biomass pretreatment with distillable ionic liquids for an effective recycling and recovery approach

Ionic liquid (IL) pretreatment methods show incredible promise for the efficient conversion of lignocellulosic feedstocks to fuels and chemicals. Given their low vapor pressures, distillation-based methods of extracting ionic liquids out of biomass post-pretreatment have historically been ignored in favor of alternative methods. We demonstrate a process to distill four acetate-based ionic liquids ([EthA][OAc], [PropA][OAc], [MAEthA][OAc], and [DMAEthA][OAc]) at low pressure and high purity that overcome some disadvantages of “water washing” and “one pot” recovery methods. Out of four tested ILs, ethanolamine acetate ([EthA][OAc]) is shown to have the most agreeable conversion metrics for commercial bioconversion processes achieving 73.6% and 51.4% of theoretical glucose and xylose yields respectively and >85 % recovery rates. Our process metrics are factored into a techno-economic analysis where [EthA][OAc] distillation is compared to other recovery methods as well as ethanolamine pretreatment at both milliliter and liter scales. In conclusion, although our TEA shows [EthA][OAc] distillation underperforming against other processes, we show a step-by-step avenue to reduce sugar production cost below the wholesale dextrose price at scale.

09 BIOMASS FUELS↗

Hydrological analysis in watersheds with a variable-resolution global climate model (VR-CESM)

Traditionally, watershed-scale hydrology is simulated by distributed hydrological models with offline meteorological forcing data, or by regional regional climate models that link atmospheric and land hydrology interactions. Global climate models (GCMs) are rarely used to study watershed-scale hydrology due to the relatively coarse grid resolution, computationally expensive downscaling, and simplified physical processes. Recently, however, watershed-scale hydrology analysis has become possible in GCMs due to the development of variable-resolution GCMs that dynamically couple the hydrological processes between atmosphere and land systems at fine resolutions in selected regions and coarse resolution elsewhere. In this study, we used the variable-resolution Community Earth System Model (VR-CESM) with refined-resolution (14 km) in the western U.S. and eastern China to evaluate watershed-scale hydrology. Furthermore, we compared the historical VR-CESM outputs with gauge measurements and other hydrological models (e.g., National Water Model in the U.S.) and calibrated the subsurface runoff capacities in four mountainous watersheds. An RCP8.5 projection from 2007 to 2050 is used to estimate the impact of changing precipitation and snow climatology on watershed hydrology. We also analyzed the long-term runoff variability and the possibility of extreme runoff events as simulated by the VR-CESM. Although calibration is not possible in larger-scale watersheds, VR-CESM simulates the long-term annual variability of watersheds and provides insights on climate change impacts on hydrology. We conclude that refined-resolution VR-CESM can be used for watershed-scale hydrology analysis to understand water resources and water balance, in addition to traditional watershed-scale hydrological models. It enables hydrological analysis at multiple watersheds in one simulation and can help understand the two-way dynamics between land surface hydrology and atmospheric processes, and is especially practical for projecting climate change impacts. However, it is challenging to apply VR-CESM for hydrologic analysis in regulated watersheds as human factors (e.g., pumping, irrigation, water diversion) have not been fully addressed in VR-CESM.

54 ENVIRONMENTAL SCIENCES↗

Molecular Structure of Sphingomyelin in Fluid Phase Bilayers Determined by the Joint Analysis of Small-Angle Neutron and X-ray Scattering Data

In this work, we have determined the fluid bilayer structure of palmitoyl sphingomyelin (PSM) and stearoyl sphingomyelin (SSM) by simultaneously analyzing small-angle neutron and X-ray scattering data. Using a newly developed scattering density profile (SDP) model for sphingomyelin lipids, we report structural parameters including the area per lipid, total bilayer thickness, and hydrocarbon thickness, in addition to lipid volumes determined by densitometry. Unconstrained all-atom simulations of PSM bilayers at 55 °C using the C36 CHARMM force field produced a lipid area of 56 Å 2 , a value that is 10% lower than the one determined experimentally by SDP analysis (61.9 Å2). Furthermore, scattering form factors calculated from the unconstrained simulations were in poor agreement with experimental form factors, even though segmental order parameter (S CD ) profiles calculated from the simulations were in relatively good agreement with S CD profiles obtained from NMR experiments. Conversely, constrained area simulations at 61.9 Å 2 resulted in good agreement between the simulation and experimental scattering form factors, but not with S CD profiles from NMR. We discuss possible reasons for the discrepancies between these two types of data that are frequently used as validation metrics for molecular dynamics force fields.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Polymer, Additives, and Processing Effects on N95 Filter Performance

The current severe acute respiratory syndrome coronavirus 2 (SARS-COV-2) pandemic has highlighted the need for personal protective equipment, specifically filtering facepiece respirators like N95 masks. While it is common knowledge that polypropylene (PP) is the industry standard material for filtration media, trial and error is often required to identify suitable commercial precursors for filtration media production. This work aims to identify differences between several commercial grades of PP and demonstrate the development of N95 filtration media with the intent that the industry partners can pivot and help address N95 shortages. Three commercial grades of high melt flow index PP were melt blown at Oak Ridge National Laboratory and broadly characterized by several methods including differential scanning calorimetry (DSC), X-ray diffraction (XRD), and neutron scattering. Despite the apparent similarities (high melt flow and isotacticity) between PP feedstocks, the application of corona charging and charge enhancing additives improve each material to widely varying degrees. From the analysis performed here, the most differentiating factor appears to be related to crystallization of the polymer and the resulting electret formation. Materials with higher crystallization onset temperatures, slower crystallization rates, and larger number of crystallites form a stronger electret and are more effective at filtration.

36 MATERIALS SCIENCE↗