### Recent Submissions

• #### Analysis of Fuel Properties on Combustion Characteristics in a Narrow-throat Pre-chamber Engine

(The Society of Automotive Engineers, 2021-04-14) [Conference Paper]
In this study, the authors investigated the effect of fuel properties on the combustion characteristics by employing methane, methanol, ethanol, and primary reference fuels (PRFs) as the main chamber fuel while using methane for the pre-chamber. Global excess air ratios (λ) from 1.6 to lean limit were tested, while 13% of total fuel energy supplied to the engine was delivered via the pre-chamber. The gaseous methane was injected into the pre-chamber at the gas exchange top-dead-center (TDC). Port fuel injection was tested with both open and closed inlet valves. The pre-chamber assembly was designed to fit into the diesel injector pocket of the base engine, which resulted in a narrow throat diameter of 3.3 mm. The combustion stability limit was set at 5% of the coefficient of variation of gross IMEP, and the knock intensity limit was set at 10 bar. GT-Power software was used to estimate the composition of pre-chamber species and was used in heat release analysis of the two chambers. It was found that the rich limit was controlled by engine knock. Hence a higher reactivity fuel (lower octane) had to be operated leaner. However, with the increasing reactivity, the lean limit was also extended, while the peak efficiency was also obtained with a leaner mixture. With PRF 90, the lean limit was at global-λ = 3.0, while the limit was 2.3 with methane. The alcohol fuels exhibited a different behavior from the methane and the PRFs. Ethanol has the same lean limit as PRF100, but methanol could be operated up to global-λ = 3.2. The pre-chamber combustion did not change much with the different fuels in the main chamber, so the combustion stability trends must be related to the transition from burning jets to ignition of the main chamber charge and its subsequent combustion.
• #### Characterization of microbiologically influenced corrosion by comprehensive metagenomic analysis of an inland oil field.

(Gene, Elsevier BV, 2021-01-15) [Article]
Corrosion in pipelines and reservoir tanks in oil plants is a serious problem in the global energy industry because it causes substantial economic losses associated with frequent part replacement and can lead to potential damage to entire crude oil fields. Previous studies revealed that corrosion is mainly caused by microbial activities in a process currently termed microbiologically influenced corrosion (MIC) or biocorrosion. Identifying the bacteria responsible for biocorrosion is crucial for its suppression. In this study, we analyzed the microbial communities present at corrosion sites in oil plant pipelines using comparative metagenomic analysis along with bioinformatics and statistics. We analyzed the microbial communities in pipelines in an oil field in which groundwater is used as injection water. We collected samples from four different facilities in the oil field. Metagenomic analysis revealed that the microbial community structures greatly differed even among samples from the same facility. Treatments such as biocide administration and demineralization at each location in the pipeline may have independently affected the microbial community structure. The results indicated that microbial inspection throughout the pipeline network is essential to prevent biocorrosion at industrial plants. By identifying the bacterial species responsible for biocorrosion, this study provides bacterial indicators to detect and classify biocorrosion. Furthermore, these species may serve as biomarkers to detect biocorrosion at an early stage. Then, appropriate management such as treatment with suitable biocides can be performed immediately and appropriately. Thus, our study will serve as a platform for obtaining microbial information related to biocorrosion to enable the development of a practical approach to prevent its occurrence.
• #### Development of a simplified n-heptane/methane model for high-pressure direct-injection natural gas marine engines

(Frontiers in Energy, Springer Science and Business Media LLC, 2021-01-15) [Article]
High-pressure direct-injection (HPDI) of natural gas is one of the most promising solutions for future ship engines, in which the combustion process is mainly controlled by the chemical kinetics. However, the employment of detailed chemical models for the multi-dimensional combustion simulation is significantly expensive due to the large scale of the marine engine. In the present paper, a reduced n-heptane/methane model consisting of 35-step reactions was constructed using multiple reduction approaches. Then this model was further reduced to include only 27 reactions by utilizing the HyChem (Hybrid Chemistry) method. An overall good agreement with the experimentally measured ignition delay data of both n-heptane and methane for these two reduced models was achieved and reasonable predictions for the measured laminar flame speeds were obtained for the 35-step model. But the 27-step model cannot predict the laminar flame speed very well. In addition, these two reduced models were both able to reproduce the experimentally measured in-cylinder pressure and heat release rate profiles for a HPDI natural gas marine engine, the highest error of predicted combustion phase being 6.5%. However, the engine-out CO emission was over-predicted and the highest error of predicted NOx emission was less than 12.9%. The predicted distributions of temperature and equivalence ratio by the 35-step and 27-step models are similar to those of the 334-step model. However, the predicted distributions of OH and CH2O are significantly different from those of the 334-step model. In short, the reduced chemical kinetic models developed provide a high-efficient and dependable method to simulate the characteristics of combustion and emissions in HPDI natural gas marine engines.
• #### Characterization of microbiologically influenced corrosion by comprehensive metagenomic analysis of an inland oil field.

(Gene, Elsevier BV, 2021-01-15) [Article]
Corrosion in pipelines and reservoir tanks in oil plants is a serious problem in the global energy industry because it causes substantial economic losses associated with frequent part replacement and can lead to potential damage to entire crude oil fields. Previous studies revealed that corrosion is mainly caused by microbial activities in a process currently termed microbiologically influenced corrosion (MIC) or biocorrosion. Identifying the bacteria responsible for biocorrosion is crucial for its suppression. In this study, we analyzed the microbial communities present at corrosion sites in oil plant pipelines using comparative metagenomic analysis along with bioinformatics and statistics. We analyzed the microbial communities in pipelines in an oil field in which groundwater is used as injection water. We collected samples from four different facilities in the oil field. Metagenomic analysis revealed that the microbial community structures greatly differed even among samples from the same facility. Treatments such as biocide administration and demineralization at each location in the pipeline may have independently affected the microbial community structure. The results indicated that microbial inspection throughout the pipeline network is essential to prevent biocorrosion at industrial plants. By identifying the bacterial species responsible for biocorrosion, this study provides bacterial indicators to detect and classify biocorrosion. Furthermore, these species may serve as biomarkers to detect biocorrosion at an early stage. Then, appropriate management such as treatment with suitable biocides can be performed immediately and appropriately. Thus, our study will serve as a platform for obtaining microbial information related to biocorrosion to enable the development of a practical approach to prevent its occurrence.
• #### A first-principles approach for treating wastewaters

(International Journal of Quantum Chemistry, Wiley, 2021-01-15) [Article]
Numerous materials are employed for the removal of contaminants from wastewaters. However, the regeneration/reuse of these materials is still seldom practiced. Quantitative insights into intermolecular forces between the contaminants and the functional surfaces might aid the rational design of reusable materials. Here, we compare the efficacies of aliphatic (C8H18), aromatic (C6H6), and aromatic perfluorinated (C6F6) moieties at removing methylene blue (MB+) as a surrogate cationic dye from water. We employed density functional theory with an implicit polarizable continuum model for water to accurately determine the contributions of the solvent's electrostatics in the adsorption process. Our calculations pinpointed the relative contributions of ππ stacking, van der Waals complexation, hydrogen bonding, and cationπ interactions, predicting that MB+ would bind the strongest with C6F6 due to hydrogen bonding and the weakest with C8H18. Complementary laboratory experiments revealed that, despite the similar hydrophobicity of silica beads functionalized with SiC8H17, SiC6H5, and SiC6F5 groups, as characterized by their water contact angles, the relative uptake of aqueous MB+ varied as SiC6F5 (95%) > SiC6H5 (35%) > SiC8H17 (3%). This first principles-led experimental approach can be easily extended to other classes of dyes, thereby advancing the rational design of adsorbents.
• #### A zero liquid discharge system integrating multi-effect distillation and evaporative crystallization for desalination brine treatment

(Desalination, Elsevier BV, 2021-01-13) [Article]
• #### Chromatin phosphoproteomics unravels a function for AT-hook motif nuclear localized protein AHL13 in PAMP-triggered immunity

(Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, 2021-01-08) [Article]
In many eukaryotic systems during immune responses, mitogen-activated protein kinases (MAPKs) link cytoplasmic signaling to chromatin events by targeting transcription factors, chromatin remodeling complexes, and the RNA polymerase machinery. So far, knowledge on these events is scarce in plants and no attempts have been made to focus on phosphorylation events of chromatin-associated proteins. Here we carried out chromatin phosphoproteomics upon elicitor-induced activation of Arabidopsis. The events in WT were compared with those in mpk3, mpk4, and mpk6 mutant plants to decipher specific MAPK targets. Our study highlights distinct signaling networks involving MPK3, MPK4, and MPK6 in chromatin organization and modification, as well as in RNA transcription and processing. Among the chromatin targets, we characterized the AT-hook motif containing nuclear localized (AHL) DNA-binding protein AHL13 as a substrate of immune MAPKs. AHL13 knockout mutant plants are compromised in pathogen-associated molecular pattern (PAMP)-induced reactive oxygen species production, expression of defense genes, and PAMP-triggered immunity. Transcriptome analysis revealed that AHL13 regulates key factors of jasmonic acid biosynthesis and signaling and affects immunity toward Pseudomonas syringae and Botrytis cinerea pathogens. Mutational analysis of the phosphorylation sites of AHL13 demonstrated that phosphorylation regulates AHL13 protein stability and thereby its immune functions.
• #### Transcriptomic analysis identifies organ-specific metastasis genes and pathways across different primary sites.

(Journal of translational medicine, Springer Science and Business Media LLC, 2021-01-08) [Article]
BackgroundMetastasis is the most devastating stage of cancer progression and often shows a preference for specific organs.MethodsTo reveal the mechanisms underlying organ-specific metastasis, we systematically analyzed gene expression profiles for three common metastasis sites across all available primary origins. A rank-based method was used to detect differentially expressed genes between metastatic tumor tissues and corresponding control tissues. For each metastasis site, the common differentially expressed genes across all primary origins were identified as organ-specific metastasis genes.ResultsPathways enriched by these genes reveal an interplay between the molecular characteristics of the cancer cells and those of the target organ. Specifically, the neuroactive ligand-receptor interaction pathway and HIF-1 signaling pathway were found to have prominent roles in adapting to the target organ environment in brain and liver metastases, respectively. Finally, the identified organ-specific metastasis genes and pathways were validated using a primary breast tumor dataset. Survival and cluster analysis showed that organ-specific metastasis genes and pathways tended to be expressed uniquely by a subgroup of patients having metastasis to the target organ, and were associated with the clinical outcome.ConclusionsElucidating the genes and pathways underlying organ-specific metastasis may help to identify drug targets and develop treatment strategies to benefit patients.
• #### Elucidating the Role of Virulence Traits in the Survival of Pathogenic E. coli PI-7 Following Disinfection

(Frontiers in bioengineering and biotechnology, Frontiers Media SA, 2021-01-08) [Article]
Reuse and discharge of treated wastewater can result in dissemination of microorganisms into the environment. Deployment of disinfection strategies is typically proposed as a last stage remediation effort to further inactivate viable microorganisms. In this study, we hypothesize that virulence traits, including biofilm formation, motility, siderophore, and curli production along with the capability to internalize into mammalian cells play a role in survival against disinfectants. Pathogenic E. coli PI-7 strain was used as a model bacterium that was exposed to diverse disinfection strategies such as chlorination, UV and solar irradiation. To this end, we used a random transposon mutagenesis library screening approach to generate 14 mutants that exhibited varying levels of virulence traits. In these 14 isolated mutants, we observed that an increase in virulence traits such as biofilm formation, motility, curli production, and internalization capability, increased the inactivation half-lives of mutants compared to wild-type E. coli PI-7. In addition, oxidative stress response and EPS production contributed to lengthening the lag phase duration (defined as the time required for exposure to disinfectant prior to decay). However, traits related to siderophore production did not help with survival against the tested disinfection strategies. Taken together, the findings suggested that selected virulence traits facilitate survival of pathogenic E. coli PI-7, which in turn could account for the selective enrichment of pathogens over the nonpathogenic ones after wastewater treatment. Further, the study also reflected on the effectiveness of UV as a more viable disinfection strategy for inactivation of pathogens.