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Atomic force microscopy (AFM) measurements have revealed hardening of intact fibroblasts after treatment with colchicine. The reliability of AFM measurements was confirmed by the identification of cells the lateral response of which to indentation did not disturb the normal force contribution. AFM data on the mechanical characteristics of such cells admit an unambiguous interpretation.
The plasticization of a polymer electrolyte usually promotes its ionic conductivity but decreases its storage modulus due to the increased polymer chain flexibility. Herein, we show that such a tradeoff between the ionic conductivity and the mechanical robustness of the polymer electrolyte can be alleviated by selective plasticization of the ion-conductive block, such as poly(ethylene oxide) (PEO) in a polystyrene (PS)– PEO–PS block copolymer (SEO) electrolyte using an ether type plasticizer, tetraethylene glycol dimethyl ether (TEGDME). In this work, at maximum plasticizer loading, the room temperature ionic conductivity increases by up to 3 orders, whereas the storage modulus, G' reduces to half, is still on the order of 10 2 MPa. At above the melting temperature of the PEO block, the dynamic storage modulus, G' of the plasticized membrane surpasses its dry PS-PEO-PS counterpart. Such a phenomenon results from that, a) TEGDME co-crystallizes with PEO to promote its crystallinity and hence the storage modulus, b) TEGDME swells the amorphous PEO phase to enhance the polymer chain segmental mobility and hence ionic conductivity, and c) the PS phase remains intact from TEGDME to keep the SEO elastic.
Lithium metal is an ideal anode for high energy density batteries, however the implementation of lithium metal anodes remains challenging. Beyond the development of highly efficient electrolytes, degradation processes restrict cycle life and reduce practical energy density. Herein lithium volumetric expansion and degradation pathways are studied in half cells through coupling electrochemical analysis with cross-sectional imaging of the intact electrode stack using a cryogenic laser plasma focused ion beam and scanning electron microscope. Here, we find that the volumetric capacity is compromised as early as the first cycle, at best reaching values only half the theoretical capacity (1033 vs 2045 mAh cm -3 ). By the 101st electrodeposition, the practical volumetric capacity decreases to values ranging from 143 to 343 mAh cm -3 .
In solid oxide cells (SOCs), the choice between galvanostatic (constant current) and potentiostatic (constant voltage) modes does not significantly affect the performance of SOCs as long as the cell components remain unchanged and intact. However, the degradation of cell components, which leads to changes in electrochemical and physical properties of the cell, elevates the importance of the selected operating mode. This paper aims to investigate the effects of galvanostatic and potentiostatic operating modes on the evolving properties of SOCs and their subsequent influence on performance durability. Employing non-equilibrium thermodynamic analysis, a crucial approach for understanding the degradation phenomena within an active electrochemical system, this study aims to provide in-depth insights into how these operating modes affect the longevity and efficacy of SOCs. Key findings include: In cases where oxygen electrode (OE) degradation is accelerated by higher partial pressure of oxygen ( p O 2 ), operating under constant voltage electrolysis can mitigate the high p O 2 at the OE|electrolyte (OE|EL) interface. Conversely, if OE degradation occurs more rapidly under a lower p O 2 , constant current electrolysis is more effective in suppressing degradation by achieving a high p O 2 at the OE|EL interface. For degradation of the fuel electrode (FE) due to higher p O 2 , constant current electrolysis is beneficial for more stable performance, which helps maintain low p O 2 at the FE|EL interface. When FE degradation is accelerated by lower p O 2 , constant voltage electrolysis can avert low p O 2 at the FE|EL interface. In practical scenarios, more complex degradation mechanisms come into play, especially when p O 2 significantly deviates from initial conditions. Degradation in one electrode can influence p O 2 in the other electrode, a phenomenon more pronounced in potentiostatic than in galvanostatic electrolysis.
Here, lithium-rich layered oxides (LRLO) x Li 2 MnO 3 • (1- x )Li M O 2 continue to attract attention owing to their promise of high capacity and energy density as lithium-ion battery cathodes, despite the degradation of atomic structure and energy density (voltage fade) with cycling. First-principles DFT calculations for the model systems M = Co and M = Mn 0.5 Ni 0.5 provide insights into the atomic-scale transformations in the bulk during the first charge and discharge of LRLO. The simulations were performed with the VASP code at the GGA+ U level. Molecular dynamics simulations were conducted at T = 1000 K (charge) and 2000 K (discharge) to accelerate the dynamics. Considerable Co migration to the Li layer occurs during the first charge for the system with M = Co, but the Li M O 2 component remains substantially intact for the system with M = Mn 0.5 Ni 0.5 . First-charge oxygen dimerization in the M = Co system occurs in both the Li M O 2 and the Li 2 MnO 3 components of the material, and exceeds than for M = Mn 0.5 Ni 0.5 , where dimerization is essentially confined to the Li 2 MnO 3 component. About half of the oxygen dimers created during the voltage plateau dissociate during the first discharge. Analysis of the redox suggests that some Mn 3+ is generated during the first charge for the system M = Co.
Proteomics R package for matching peptide fragments for both digested and intact proteomics
TP53 is the most frequently mutated gene in cancer, yet key target genes for p53-mediated tumor suppression remain unidentified. Here, we characterize a rare, African-specific germline variant of TP53 in the DNA-binding domain Tyr107His (Y107H). Nuclear magnetic resonance and crystal structures reveal that Y107H is structurally similar to wild-type p53. Consistent with this, we find that Y107H can suppress tumor colony formation and is impaired for the transactivation of only a small subset of p53 target genes; this includes the epigenetic modifier PADI4, which deiminates arginine to the nonnatural amino acid citrulline. Surprisingly, we show that Y107H mice develop spontaneous cancers and metastases and that Y107H shows impaired tumor suppression in two other models. We show that PADI4 is itself tumor suppressive and that it requires an intact immune system for tumor suppression. We identify a p53–PADI4 gene signature that is predictive of survival and the efficacy of immune-checkpoint inhibitors.
Obesity can increase the risk of bone fragility, even when bone mass is intact. This fragility stems from poor bone quality, potentially caused by deficiencies in bone matrix material properties. However, cellular and molecular mechanisms leading to obesity-related bone fragility are not fully understood. Using male mouse models of obesity, we discovered TGF-β signaling plays a critical role in mediating the effects of obesity on bone. High-carbohydrate and high-fat diets increase TGF-β signaling in osteocytes, which impairs their mitochondrial function, increases cellular senescence, and compromises perilacunar/canalicular remodeling and bone quality. By specifically inhibiting TGF-β signaling in mouse osteocytes, some of the negative effects of high-fat and high-carbohydrate diets on bones, including the lacunocanalicular network, perilacunar/canalicular remodeling, senescence, and mechanical properties such as yield stress, were mitigated. DMP1-Cre–mediated deletion of TGF-β receptor II also blunted adverse effects of high-fat and high-carbohydrate diets on energy balance and metabolism. These findings suggest osteocytes are key in controlling bone quality in response to high-fat and high-carbohydrate diets. Calibrating osteocyte function could mitigate bone fragility associated with metabolic diseases while reestablishing energy balance.
Ensuring robustness and resilience in intermodal transportation systems is essential for the continuity and reliability of global logistics. These systems are vulnerable to various disruptions, including natural disasters and technical failures. Despite significant research on freight transportation resilience, investigating the robustness of the system after targeted and climate-change-driven disruption remains a crucial challenge. Drawing on network science methodologies, this study models the interdependencies within the rail and water transport networks and simulates different disruption scenarios to evaluate system responses. Here, we use the data from the U.S. Department of Energy Volpe Center for network topology and tonnage projections. The proposed framework quantifies deliberate, stochastic, and climate-driven infrastructure failure, using higher resolution downscaled multiple Earth System Models’ simulations from Coupled Model Intercomparison Project Phase version 6. We show that the disruptions of a few nodes could have a larger impact on the total tonnage of freight transport than on network topology. For example, the removal of targeted 20 nodes can bring the total tonnage carrying capacity to 30% with about 75% of the rail freight network intact. This research advances the theoretical understanding of transportation resilience and provides practical applications for infrastructure managers and policymakers. By implementing these strategies, stakeholders and policymakers can better prepare for and respond to unexpected disruptions, ensuring sustained operational efficiency in transportation networks.
The co-optimization of in-cylinder combustion and after-treatment technology has become a major aspect in engine design and development, with the goal of meeting the increasingly restrictive emission regulations in the transportation industry. Selective Catalytic Reduction is a robust technology to control the emission of NO x , and the injection of urea in water solution is the exhaust tailpipe is a key aspect of its operation. The proposed work uses high-fidelity Computational Fluid Dynamics to characterize the atomization dynamics of the liquid jet in relevant cross-flow conditions. The study focuses on a commercial low-pressure (9 bar) pressure-swirl injector which is characterized in its internal geometry through high-resolution X-ray micro-computational tomography. The internal two-phase flow has been modeled according to the volume-of-fluid approach in a large eddy simulation framework and validated against near-nozzle X-ray radiography measurement. Moreover, characterizing the breakup dynamics for the swirling hollow cone formation, and assessing the influence of the cross-flow in the breakup dynamics was completed. The results have been reported proposing Re-Oh maps and probability density functions of the spray kinematics. Higher cross-flow momentum generates an increase in the jet intact length and a reduction of the liquid droplet diameters. The axial momentum of the jet is affected by the cross-flow already in the near-nozzle region, determining a relevant deviation of the spray velocities. In conclusion, this work aims to inform the initialization of Eulerian-Lagrangian spray models through the assignment of droplet kinematics and static one-way coupling between volume-of-fluid results and Lagrangian spray parcels, to be used for system-size domain simulations.
Tropical forests are critical for the global carbon budget, yet they have been threatened by deforestation and forest degradation by fire, selective logging, and fragmentation. Existing uncertainties on land cover classification and in biomass estimates hinder accurate attribution of carbon emissions to specific forest classes. In this study, we used textural metrics derived from PlanetScope images to implement a probabilistic classification framework to identify intact, logged and burned forests in three Amazonian sites. We also estimated biomass for these forest classes using airborne lidar and compared biomass uncertainties using the lidar-derived estimates only to biomass uncertainties considering the forest degradation classification as well. Our classification approach reached overall accuracy of 0.86, with accuracy at individual sites varying from 0.69 to 0.93. Logged forests showed variable biomass changes, while burned forests showed an average carbon loss of 35%. We found that including uncertainty in forest degradation classification significantly increased uncertainty and decreased estimates of mean carbon density in two of the three test sites. Our findings indicate that the attribution of biomass changes to forest degradation classes needs to account for the uncertainty in forest degradation classification. By combining very high-resolution images with lidar data, we could attribute carbon stock changes to specific pathways of forest degradation. This approach also allows quantifying uncertainties of carbon emissions associated with forest degradation through logging and fire. Both the attribution and uncertainty quantification provide critical information for national greenhouse gas inventories.
Background: Conventional aqueous dilute sulfuric acid (DSA) pretreatment of lignocellulosic biomass facilitates hemicellulose solubilization and can improve subsequent enzymatic digestibility of cellulose to fermentable glucose. However, much of the lignin after DSA pretreatment either remains intact within the cell wall or readily redeposits back onto the biomass surface. This redeposited lignin has been shown to reduce enzyme activity and contribute to rapid enzyme deactivation, thus, necessitating significantly higher enzyme loadings than deemed economical for biofuel production from biomass. Results: In this study, we demonstrate how detrimental lignin redeposition on biomass surface after pretreatment can be prevented by employing Co-solvent Enhanced Lignocellulosic Fractionation (CELF) pretreatment that uses THF–water co-solvents with dilute sulfuric acid to solubilize lignin and overcome limitations of DSA pretreatment. We first find that enzymatic hydrolysis of CELF-pretreated switchgrass can sustain a high enzyme activity over incubation periods as long as 5 weeks with enzyme doses as low as 2 mg protein/g glucan to achieve 90% yield to glucose. A modified Ninhydrin-based protein assay revealed that the free-enzyme concentration in the hydrolysate liquor, related to enzyme activity, remained unchanged over long hydrolysis times. DSA-pretreated switchgrass, by contrast, had a 40% drop in free enzymes in solution during incubation, providing evidence of enzyme deactivation. Furthermore, measurements of enzyme adsorption per gram of lignin suggested that CELF prevented lignin redeposition onto the biomass surface, and the little lignin left in the solids was mostly integral to the original lignin–carbohydrate complex (LCC). Scanning electron micrographs and NMR characterization of lignin supported this observation. Conclusions: Enzymatic hydrolysis of solids from CELF pretreatment of switchgrass at low enzyme loadings was sustained for considerably longer times and reached higher conversions than for DSA solids. Analysis of solids following pretreatment and enzymatic hydrolysis showed that prolonged cellulase activity could be attributed to the limited lignin redeposition on the biomass surface making more enzymes available for hydrolysis of more accessible glucan.
Transposable elements (TEs) can be key drivers of evolution, but the mechanisms and scope of how they impact gene and genome function are largely unknown. Previous analyses revealed that TE-mediated gene amplifications can have variable effects on fungal genomes, from inactivation of function to production of multiple active copies. For example, a DNA methyltransferase gene in the wheat pathogen Zymoseptoria tritici (synonym Mycosphaerella graminicola) was amplified to tens of copies, all of which were inactivated by Repeat-Induced Point mutation (RIP) including the original, resulting in loss of cytosine methylation. In another wheat pathogen, Pyrenophora tritici-repentis, a histone H3 gene was amplified to tens of copies with little evidence of RIP, leading to many potentially active copies. To further test the effects of transposon-aided gene amplifications on genome evolution and architecture, the repetitive fraction of the significantly expanded genome of the banana pathogen, Pseudocercospora fijiensis, was analyzed in greater detail. These analyses identified a housekeeping gene, histone H3, which was captured and amplified to hundreds of copies by a hAT DNA transposon, all of which were inactivated by RIP, except for the original. In P. fijiensis the original H3 gene probably was not protected from RIP, but most likely was maintained intact due to strong purifying selection. Comparative analyses revealed that a similar event occurred in five additional genomes representing the fungal genera Cercospora, Pseudocercospora and Sphaerulina. These results indicate that the interplay of TEs and RIP can result in different and unpredictable fates of amplified genes, with variable effects on gene and genome evolution.
The murine CBA/J mouse model widely supports immunology and enteric pathogen research. This model has illuminated Salmonella interactions with the gut microbiome since pathogen proliferation does not require disruptive pretreatment of the native microbiota, nor does it become systemic, thereby representing an analog to gastroenteritis disease progression in humans. Despite the value to broad research communities, microbiota in CBA/J mice are not represented in current murine microbiome genome catalogs. Here we present the first microbial and viral genomic catalog of the CBA/J murine gut microbiome. Using fecal microbial communities from untreated and Salmonella-infected, highly inflamed mice, we performed genomic reconstruction to determine the impacts on gut microbiome membership and functional potential. From high depth whole community sequencing (~ 42.4 Gbps/sample), we reconstructed 2281 bacterial and 4516 viral draft genomes. Salmonella challenge significantly altered gut membership in CBA/J mice, revealing 30 genera and 98 species that were conditionally rare and unsampled in non-inflamed mice. Additionally, inflamed communities were depleted in microbial genes that modulate host anti-inflammatory pathways and enriched in genes for respiratory energy generation. Our findings suggest decreases in butyrate concentrations during Salmonella infection corresponded to reductions in the relative abundance in members of the Alistipes. Strain-level comparison of CBA/J microbial genomes to prominent murine gut microbiome databases identified newly sampled lineages in this resource, while comparisons to human gut microbiomes extended the host relevance of dominant CBA/J inflammation-resistant strains. This CBA/J microbiome database provides the first genomic sampling of relevant, uncultivated microorganisms within the gut from this widely used laboratory model. Using this resource, we curated a functional, strain-resolved view on how Salmonella remodels intact murine gut communities, advancing pathobiome understanding beyond inferences from prior amplicon-based approaches. Salmonella-induced inflammation suppressed Alistipes and other dominant members, while rarer commensals like Lactobacillus and Enterococcus endure. The rare and novel species sampled across this inflammation gradient advance the utility of this microbiome resource to benefit the broad research needs of the CBA/J scientific community, and those using murine models for understanding the impact of inflammation on the gut microbiome more generally.
Abstract Background Previous research in autism and other neurodevelopmental disorders (NDDs) has indicated an important contribution of protein-coding (coding) de novo variants (DNVs) within specific genes. The role of de novo noncoding variation has been observable as a general increase in genetic burden but has yet to be resolved to individual functional elements. In this study, we assessed whole-genome sequencing data in 2671 families with autism (discovery cohort of 516 families, replication cohort of 2155 families). We focused on DNVs in enhancers with characterized in vivo activity in the brain and identified an excess of DNVs in an enhancer named hs737. Results We adapted the fitDNM statistical model to work in noncoding regions and tested enhancers for excess of DNVs in families with autism. We found only one enhancer (hs737) with nominal significance in the discovery (p = 0.0172), replication (p = 2.5 × 10 −3 ), and combined dataset (p = 1.1 × 10 −4 ). Each individual with a DNV in hs737 had shared phenotypes including being male, intact cognitive function, and hypotonia or motor delay. Our in vitro assessment of the DNVs showed they all reduce enhancer activity in a neuronal cell line. By epigenomic analyses, we found that hs737 is brain-specific and targets the transcription factor gene EBF3 in human fetal brain. EBF3 is genome-wide significant for coding DNVs in NDDs (missense p = 8.12 × 10 −35 , loss-of-function p = 2.26 × 10 −13 ) and is widely expressed in the body. Through characterization of promoters bound by EBF3 in neuronal cells, we saw enrichment for binding to NDD genes (p = 7.43 × 10 −6 , OR = 1.87) involved in gene regulation. Individuals with coding DNVs have greater phenotypic severity (hypotonia, ataxia, and delayed development syndrome [HADDS]) in comparison to individuals with noncoding DNVs that have autism and hypotonia. Conclusions In this study, we identify DNVs in the hs737 enhancer in individuals with autism. Through multiple approaches, we find hs737 targets the gene EBF3 that is genome-wide significant in NDDs. By assessment of noncoding variation and the genes they affect, we are beginning to understand their impact on gene regulatory networks in NDDs.
Generally wastewater such agricultural runoff is considered a nuisance; however, it could be harnessed as a potential source of nutrients like nitrates and phosphates in integrated biorefinery context. In the current study, microalgae Chlorella sp. S5 was used for bioremediation of agricultural runoff and the leftover algal biomass was used as a potential source for production of biofuels in an integrated biorefinery context. The microalgae Chlorella sp. S5 was cultivated on Blue Green (BG 11) medium and a comprehensive optimization of different parameters including phosphates, nitrates, and pH was carried out to acquire maximum algal biomass enriched with high lipids content. Dry biomass was quantified using the solvent extraction technique, while the identification of nitrates and phosphates in agricultural runoff was carried out using commercial kits. The algal extracted lipids (oils) were employed in enzymatic trans-esterification for biodiesel production using whole-cell biomass of Bacillus subtilis Q4 MZ841642. The resultant fatty acid methyl esters (FAMEs) were analyzed using Fourier transform infrared (FTIR) spectroscopy and gas chromatography coupled with mass spectrometry (GC–MS). Subsequently, both the intact algal biomass and its lipid-depleted algal biomass were used for biogas production within a batch anaerobic digestion setup. Interestingly, Chlorella sp. S5 demonstrated a substantial reduction of 95% in nitrate and 91% in phosphate from agricultural runoff. The biodiesel derived from algal biomass exhibited a noteworthy total FAME content of 98.2%, meeting the quality standards set by American Society for Testing and Materials (ASTM) and European union (EU) standards. Furthermore, the biomethane yields obtained from whole biomass and lipid-depleted biomass were 330.34 NmL/g VS added and 364.34 NmL/g VS added , respectively. In conclusion, the findings underscore the potent utility of Chlorella sp. S5 as a multi-faceted resource, proficiently employed in a sequential cascade for treating agricultural runoff, producing biodiesel, and generating biogas within the integrated biorefinery concept.
Locating undocumented (or poorly documented) oil and gas wells for environmental assessment is often difficult. Remnant features that confirm the presence of a well (intact casing/wellhead, well bore, etc.) are typically less than a meter in size and often are obscured from direct observation on the ground or from the air (by dense vegetation, for example). To efficiently find such features, it is useful to first systematically compile publicly available digital data at progressively smaller scales prior to embarking on field campaigns. Further, the information presented here describes the procedure developed and used by the U.S. Department of Energy's National Energy Technology Laboratory to locate potential oil and gas well sites for follow-up field verification and characterization. Digital data are first compiled from national and state resources such as well location/production databases, historical topographic maps, historical aerial photographs, and LiDAR data. Although each data set is likely to be incomplete or inaccurate to some extent, combining the data resources using geographic information system technology can generate potential well site targets with a higher degree of confidence, which improves the efficiency of fieldwork activities. This workflow was developed in the Appalachian Basin region, and although certain aspects may be unique, the general process would be applicable to locating undocumented wells in other regions.
Context The optimal measure of vitamin D status is unknown. Objective To directly measure circulating free 25-hydroxyvitamin D [25(OH)D] concentrations and relationships to total 25(OH)D in a clinically diverse sample of humans. Design Cross-sectional analysis. Setting Seven academic sites. Patients A total of 1661 adults: healthy (n = 279), prediabetic (n = 479), outpatients (n = 714), cirrhotic (n = 90), pregnant (n = 20), nursing home resident (n = 79). Interventions Merge research data on circulating free 25(OH)D (directly-measured immunoassay), total 25(OH)D (liquid chromatography/tandem mass spectrometry), D-binding protein [DBP; by radial (polyclonal) immunodiffusion assay], albumin, creatinine, intact parathyroid hormone, and DBP haplotype. Main outcome measures Distribution of free 25(OH)D (ANOVA with Bonferroni correction for post hoc comparisons) and relationships between free and total 25(OH)D (mixed-effects modeling incorporating clinical condition, DBP haplotype with sex, race, estimated glomerular filtration rate (eGFR), body mass index (BMI), and other covariates). Results Free 25(OH)D was 4.7 ± 1.8 pg/mL (mean ± SD) in healthy persons and 4.3 ± 1.9 pg/mL in outpatients, with levels of 0.5 to 8.1 pg/mL and 0.9 to 8.1 pg/mL encompassing 95% of healthy persons and outpatients, respectively. Free 25(OH)D was higher in patients with cirrhosis (7.1 ± 3.0 pg/mL; P < 0.0033) and nursing home residents (7.9 ± 2.1 pg/mL; P < 0.0033) than in other groups and differed between whites and blacks (P < 0.0033) and between DBP haplotypes (P < 0.0001). Mixed-effects modeling of relationships between free and total 25(OH)D identified clinical conditions (patients with cirrhosis > nursing home residents > patients with prediabetes > outpatients > pregnant women) and BMI (lesser effect) as covariates affecting relationships but not eGFR, sex, race, or DBP haplotype. Conclusions Total 25(OH)D, health condition, race, and DBP haplotype affected free 25(OH)D, but only health conditions and BMI affected relationships between total and free 25(OH)D. Clinical importance of free 25(OH)D needs to be established in studies assessing outcomes.