Review
Engineering, Environmental
Emily Garner, Benjamin C. Davis, Erin Milligan, Matthew Forrest Blair, Ishi Keenum, Ayella Maile-Moskowitz, Jin Pan, Mariah Gnegy, Krista Liguori, Suraj Gupta, Aaron J. Prussin, Linsey C. Marr, Lenwood S. Heath, Peter J. Vikesland, Liqing Zhang, Amy Pruden
Summary: The emergence of NGS technologies has revolutionized the water industry's ability to address complex microbiological challenges, although faced with barriers like cost and expertise. Research has focused on the applications of NGS in water, wastewater, and recycled water, highlighting key contributions and future directions for advancement.
Article
Multidisciplinary Sciences
Zhenli Diao, Dongsheng Han, Rui Zhang, Jinming Li
Summary: This review summarizes the potential applications and challenges of metagenomic next-generation sequencing (mNGS) in the diagnosis of lower respiratory tract infections (LRIs), aiming to promote the integration of mNGS into the management of patients with respiratory tract infections in a clinical setting.
JOURNAL OF ADVANCED RESEARCH
(2022)
Review
Biochemistry & Molecular Biology
Pei Yee Tiew, Oliver W. Meldrum, Sanjay H. Chotirmall
Summary: Microbiomics has made significant advancements in the past decade due to the availability of next-generation sequencing (NGS) and multi-omic technologies. Integration of NGS and multi-omic datasets allows for comprehensive assessment of endophenotypes in chronic respiratory diseases like chronic obstructive pulmonary disease (COPD). Valuable insights have been gained into the role of microbial communities in COPD onset, progression, prognosis, and treatment response. Identifying specific microbes and metabolic signatures associated with COPD can lead to new therapeutic interventions and prognosis-related biomarkers. However, the analysis and interpretation of the large amount of data generated by these technologies remain challenging, and standardized methods are lacking.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Immunology
Ravina Kullar, Emanuele Chisari, James Snyder, Christopher Cooper, Javad Parvizi, Jason Sniffen
Summary: This article discusses the gaps in traditional culture and introduces the utility of next-generation sequencing (NGS) in diagnosing and treating peri-prosthetic joint infections. It highlights the clinical benefits of using NGS compared to culture alone and emphasizes the potential of NGS in improving the yield of identifying infective organisms in challenging cases.
CLINICAL INFECTIOUS DISEASES
(2023)
Article
Immunology
Denver T. Niles, Paula A. Revell, Daniel Ruderfer, Lucila Marquez, J. Chase McNeil, Debra L. Palazzi
Summary: Plasma metagenomic next-generation sequencing (mNGS) has the potential to detect multiple organisms with a single test. The study found that mNGS testing had the highest clinical impact in immunocompromised patients with well-defined deep-seated infections. Further research is needed to evaluate the full range of clinical scenarios for which mNGS testing is beneficial.
PEDIATRIC INFECTIOUS DISEASE JOURNAL
(2022)
Article
Mathematics, Applied
Ashaq Hussain Bhat, Tu N. Nguyen, Korhan Cengiz, Puniethaa Prabhu
Summary: The HBEA clustering algorithm uses exact pairwise global alignment algorithm to improve cluster quality and extract cluster representatives. Experimental investigation showed that HBEA produces better operational taxonomic unit (OTU) clusters and computational complexity than other algorithms.
MATHEMATICAL METHODS IN THE APPLIED SCIENCES
(2021)
Review
Fisheries
Tina Kollannoor Johny, Rinu Madhu Puthusseri, Sarita Ganapathy Bhat
Summary: The fish gut is a complex ecosystem influenced by various factors, and the gut microbiota plays important roles in the physiological functions of the host. With technological advancements, the application of culture-independent techniques in studying fish gut microbiota is promising for a better understanding.
AQUACULTURE RESEARCH
(2021)
Article
Immunology
Rachel K. To, Nanda Ramchandar, Aamisha Gupta, Alice Pong, Christopher Cannavino, Jennifer Foley, Lauge Farnaes, Nicole G. Coufal
Summary: Pediatric infective endocarditis is associated with underlying heart disease, and accurate identification of pathogens is crucial for treatment. Plasma next-generation sequencing showed a high detection rate in this case series.
PEDIATRIC INFECTIOUS DISEASE JOURNAL
(2021)
Article
Medicine, General & Internal
Junyan Qu, Zhiyong Zong
Summary: This case report presents a case of strongyloidiasis in a Chinese male patient diagnosed using metagenomic next-generation sequencing (mNGS). The study highlights the potential of mNGS in detecting uncommon infectious diseases and emphasizes the importance of raising awareness of strongyloidiasis in non-endemic areas.
FRONTIERS IN MEDICINE
(2022)
Article
Immunology
Mengjia Qian, Bijun Zhu, Yanxia Zhan, Lingyan Wang, Qi Shen, Miaomiao Zhang, Lei Yue, Duojiao Wu, Hao Chen, Xiangdong Wang, Yunfeng Cheng
Summary: The negative prediction accuracy rate of the original specimen is significant when the mNGS test is negative. However, other laboratory assays results and clinical presentations should always be carefully considered prior to drawing a diagnosis.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2022)
Letter
Medicine, General & Internal
Peng Song, Xia Li
Summary: The symptoms of disseminated strongyloidiasis are atypical, making it difficult to diagnose in non-endemic areas. The use of mNGS technology in clinical practice is becoming increasingly common and plays an important role in detecting Strongyloides in non-endemic areas.
WORLD JOURNAL OF CLINICAL CASES
(2022)
Article
Chemistry, Multidisciplinary
Vasilka Chopkova, Mariana Petkova, Stefan Shilev
Summary: This study investigated the bacterial diversity of mesophilic and thermophilic phases of composting in two different sites using Illumina HiSeq sequencing and phylogenetic analysis. The results showed that the mesophilic phase had a higher number of bacterial species compared to the thermophilic phase, and there were differences in bacterial diversity between the two composting sites.
APPLIED SCIENCES-BASEL
(2023)
Article
Multidisciplinary Sciences
Deepanshi Mishra, Gita Satpathy, Rohan Chawla, Daizy Paliwal, Subrat Kumar Panda
Summary: The feasibility of 16S rRNA metagenomics using next generation sequencing in microbial diagnosis of culture negative endophthalmitis was studied. Metagenomics could detect and identify bacterial pathogens in up to species level in most culture negative vitreous specimens, showing potential for widespread use in endophthalmitis diagnosis where culture negativity is high.
Article
Medicine, General & Internal
Charlotte Michel, Michela Raimo, Vladimir Lazarevic, Nadia Gaia, Nina Leduc, Christiane Knoop, Marie Hallin, Olivier Vandenberg, Jacques Schrenzel, David Grimaldi, Maya Hites
Summary: NGS offers added diagnostic and quantitative values compared to PCR tests in diagnosing respiratory infections in immune-compromised patients, providing more accurate and comprehensive information that can potentially lead to better clinical outcomes.
FRONTIERS IN MEDICINE
(2021)
Article
Medicine, General & Internal
Hongli Li, Luqing Wei, Fenge Li
Summary: This article reports a case of lung nodules caused by MAC infection. The use of mNGS ensured a rapid and accurate diagnosis, demonstrating the potential role of mNGS in diagnosing MAC infection.
FRONTIERS IN MEDICINE
(2023)
Article
Multidisciplinary Sciences
Sinara Carla da Silva Araujo, Rita C. B. Silva-Portela, Daniel Chaves de Lima, Marbella Maria Bernardes da Fonseca, Wydemberg J. Araujo, Uaska Bezerra da Silva, Amanda P. Napp, Evandro Pereira, Marilene H. Vainstein, Lucymara Fassarella Agnez-Lima
SCIENTIFIC REPORTS
(2020)
Article
Biochemistry & Molecular Biology
Aquiles Sales Craveiro Sarmento, Josivan Gomes Lima, Ana Rafaela de Souza Timoteo, Marcela Abbott Galvao Ururahy, Aurigena Antunes de Araujo, Roseane Carvalho Vasconcelos, Veronica Kristina Candido Dantas, Lucymara Fassarella Agnez-Lima, Julliane Tamara AraiIjo de Melo Campos
BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR AND CELL BIOLOGY OF LIPIDS
(2020)
Article
Biotechnology & Applied Microbiology
W. J. Araujo, J. S. Oliveira, S. C. S. Araujo, C. F. Minnicelli, R. C. B. Silva-Portela, M. M. B. Fonseca, J. F. Freitas, K. K. Silva-Barbalho, A. P. Napp, J. E. S. Pereira, M. C. R. Peralba, L. M. P. Passaglia, M. H. Vainstein, L. F. Agnez-Lima
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2020)
Article
Parasitology
Debora de Almeida Aloise, Wendel Coura-Vital, Mariangela Carneiro, Marlus Venancio Rodrigues, Gislani Acasia da Silva Toscano, Ramiza Bernardino da Silva, Rita de Cassia Barreto Silva-Portela, Fabrica Lima Fontes-Dantas, Lucymara Fassarella Agnez-Lima, Ricardo Wagner Almeida Vitor, Valter Ferreira de Andrade-Neto
Summary: This study found a significant association between ocular toxoplasmosis and APEX1 gene polymorphism, but not with MYD88 gene polymorphism. This suggests that APEX1 (rs1130409) polymorphism is a risk factor for the occurrence of ocular toxoplasmosis in the studied population.
Article
Multidisciplinary Sciences
Paulo Eduardo T. Soares, Marcia Danielle A. Dantas, Rita de Cassia B. Silva-Portela, Lucymara F. Agnez-Lima, Daniel Carlos F. Lanza
Summary: The study characterized the diversity of the Penaeus vannamei mitochondrial genome, identified inter-individual variability and heteroplasmy, and highlighted the importance of cautious design of mitochondrial markers for this species. The results will contribute to enhancing the efficiency of mitochondrial markers for population or individual studies.
Article
Cell Biology
Thais Teixeira Oliveira, Fabricia Lima Fontes-Dantas, Rayssa Karla de Medeiros Oliveira, Daniele Maria Lopes Pinheiro, Leonam Gomes Coutinho, Vandeclecio Lira da Silva, Sandro Jose de Souza, Lucymara Fassarella Agnez-Lima
Summary: Chemical inhibition of APE1/Ref-1 affects gene expression in an inflammatory cellular model, reducing the expression of certain cytokines and chemokines. It also impacts transcriptional factors such as NRF1 and ETS family regulators, suggesting partial overlap between APE1 redox and DNA repair functions.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Daniel Chaves de Lima, Inacio Gomes Medeiros, Rita De Cassia Silva-Portela, Francisco Carlos da Silva Junior, Lucymara Fassarela Agnez-Lima, Jorge Estefano Santana de Souza, Silvia R. Batistuzzo de Medeiros
Summary: This study aimed to detect and compare new plasmids in Brazilian strains of Chromobacterium violaceum using next-generation sequencing techniques. Several plasmids were found to be similar to the previously discovered pChV1, while others had a common origin but had diverged. Genes related to plasmid segregation/maintenance, viral structural proteins, and proteins with unknown functions were also detected. These findings may enhance our ability to exploit C. violaceum in industrial and clinical applications through better genetic manipulation.
CANADIAN JOURNAL OF MICROBIOLOGY
(2022)
Article
Infectious Diseases
Alessandra P. Lamarca, Luiz G. P. de Almeida, Ronaldo da Silva Francisco Jr, Lucymara Fassarella Agnez Lima, Katia Castanho Scortecci, Vinicius Pietta Perez, Otavio J. Brustolini, Eduardo Sergio Soares Sousa, Danielle Angst Secco, Angela Maria Guimaraes Santos, George Rego Albuquerque, Ana Paula Melo Mariano, Bianca Mendes Maciel, Alexandra L. Gerber, Ana Paula de C. Guimaraes, Paulo Ricardo Nascimento, Francisco Paulo Freire Neto, Sandra Rocha Gadelha, Luis Cristovao Porto, Eloiza Helena Campana, Selma Maria Bezerra Jeronimo, Ana Tereza R. Vasconcelos
Summary: The sharp increase of COVID-19 cases in late 2020 has made Brazil the new epicenter of the ongoing SARS-CoV-2 pandemic. The study identified the widespread dispersal of P.1 and P.2 lineages across Brazil, with P.2 being the predominant lineage in most states. The presence of new lineages descending from B.1.1.33, including those carrying the E484K mutation, highlights the importance of continuous sequencing to monitor vaccine effectiveness and identify novel variants of interest.
PLOS NEGLECTED TROPICAL DISEASES
(2021)
Article
Energy & Fuels
Marbella Maria Bernardes da Fonseca, Julia Firme Freitas, Rita de Cassia Barreto Silva-Portela, Carolina Fonseca Minnicelli, Kamilla Karla Da Silva-Barbalho, Lucymara Fassarella Agnez-Lima
Summary: The microbiome of ultra-deep pre-salt oil reservoirs, characterized by high pressure and high carbon dioxide content, has been poorly explored. This study revealed a higher biodiversity in pre-salt oil samples compared to other oil field samples, with a high occurrence of uncultivated or poorly classified taxa. The microbial communities in pre-salt oil samples showed distinct differentiation from contaminated, non-contaminated, and oil reservoir samples worldwide.
Review
Immunology
Thais Teixeira Oliveira, Leonam Gomes Coutinho, Laysa Ohana Alves de Oliveira, Ana Rafaela de Souza Timoteo, Guilherme Cavalcanti Farias, Lucymara Fassarella Agnez-Lima
Summary: APE1 is a multifunctional enzyme that is essential for maintaining cellular homeostasis and regulating immune response. It plays important roles in cell signaling, senescence, and inflammatory pathways, and is involved in the pathogenesis of various diseases, including cancer and neurological disorders. APE1 inhibitors have potential therapeutic uses, particularly in infectious and immune diseases.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Cardiac & Cardiovascular Systems
Jorge Luiz Dantas de Medeiros, Bruno Carneiro Bezerra, Helen Rainara Araujo Cruz, Katarina Azevedo de Medeiros, Maria Eduarda Cardoso de Melo, Aquiles Sales Craveiro Sarmento, Marcela Abbott Galvao Ururahy, Lucymara Fassarella Agnez Lima, Alcebiades Jose dos Santos Neto, Josivan Gomes Lima, Vanessa Resqueti, Lucien Peroni Gualdi, Guilherme Fregonezi, Julliane Tamara Araujo de Melo Campos
Summary: This study evaluated the differences in functional exercise capacity, cardiovascular response, and peripheral arterial disease (PAD) between patients with Congenital Generalized Lipodystrophy (CGL) and healthy individuals. It was found that CGL patients had lower functional exercise capacity and higher cardiovascular effort. Better physical performance was associated with higher ankle-brachial index (ABI) in CGL patients.
BMC CARDIOVASCULAR DISORDERS
(2022)
Meeting Abstract
Respiratory System
Julliane Tamara Araujo de Melo Campos, Aquiles Sales Craveiro Sarmento, Jorge Luiz Dantas De Medeiros, Bruno Carneiro Bezerra, Lucien Peroni Gualdi, Josivan Gomes Lima, Lucymara Fassarella Agnez-Lima
EUROPEAN RESPIRATORY JOURNAL
(2020)
Article
Energy & Fuels
Yingna Du, Chen Huang, Wei Jiang, Qiangwei Yan, Yongfei Li, Gang Chen
Summary: In this study, anionic surfactants modified hydrotalcite was used as a flow improver for crude oil under low-temperature conditions. The modified hydrotalcite showed a significant viscosity reduction effect on crude oil. The mechanism of the modified hydrotalcite on viscosity and pour point of crude oil was explored through characterization and analysis of the modified hydrotalcite and oil samples.
Article
Energy & Fuels
Mohammad Saeid Rostami, Mohammad Mehdi Khodaei
Summary: In this study, a hybrid structure, MIL-53(Al)@MWCNT, was synthesized by combining MIL-53(Al) particles and -COOH functionalized multi-walled carbon nanotube (MWCNT). The hybrid structure was then embedded in a polyethersulfone (PES) polymer matrix to prepare a mixed matrix membrane (MMM) for CO2/CH4 and CO2/N2 separation. The addition of MWCNTs prevented MIL-53(Al) aggregation, improved membrane mechanical properties, and enhanced gas separation efficiency.
Article
Energy & Fuels
Yunlong Li, Desheng Huang, Xiaomeng Dong, Daoyong Yang
Summary: This study develops theoretical and experimental techniques to determine the phase behavior and physical properties of DME/flue gas/water/heavy oil systems. Eight constant composition expansion (CCE) tests are conducted to obtain new experimental data. A thermodynamic model is used to accurately predict saturation pressure and swelling factors, as well as the phase boundaries of N2/heavy oil systems and DME/CO2/heavy oil systems, with high accuracy.
Article
Energy & Fuels
Morteza Afkhamipour, Ebad Seifi, Arash Esmaeili, Mohammad Shamsi, Tohid N. Borhani
Summary: Non-conventional amines are being researched worldwide to overcome the limitations of traditional amines like MEA and MDEA. Adequate process and thermodynamic models are crucial for understanding the applicability and performance of these amines in CO2 absorption, but studies on process modeling for these amines are limited. This study used rate-based modeling and Deshmukh-Mather method to model CO2 absorption by DETA solution in a packed column, validated the model with experimental data, and conducted a sensitivity analysis of mass transfer correlations. The study also compared the CO2 absorption efficiency of DETA solution with an ionic solvent [bmim]-[PF6] and highlighted the importance of finding optimum operational parameters for maximum absorption efficiency.
Article
Energy & Fuels
Arastoo Abdi, Mohamad Awarke, M. Reza Malayeri, Masoud Riazi
Summary: The utilization of smart water in EOR operations has gained attention, but more research is needed to understand the complex mechanisms involved. This study investigated the interfacial tension between smart water and crude oil, considering factors such as salt, pH, asphaltene type, and aged smart water. The results revealed that the hydration of ions in smart water plays a key role in its efficacy, with acidic and basic asphaltene acting as intrinsic surfactants. The pH also influenced the interfacial tension, and the aged smart water's interaction with crude oil depended on asphaltene type, salt, and salinity.
Article
Energy & Fuels
Dongao Zhu, Kun Zhu, Lixian Xu, Haiyan Huang, Jing He, Wenshuai Zhu, Huaming Li, Wei Jiang
Summary: In this study, cobalt-based metal-organic frameworks (Co-based MOFs) were used as supports and co-catalysts to confine the NHPI catalyst, solving the leaching issue. The NHPI@Co-MOF with carboxyl groups exhibited stronger acidity and facilitated the generation of active oxygen radicals O2•, resulting in enhanced catalytic activity. This research provides valuable insights into the selection of suitable organic linkers and broadens the research horizon of MOF hybrids in efficient oxidative desulfurization (ODS) applications.
Article
Energy & Fuels
Edwin G. Hoyos, Gloria Amo-Duodu, U. Gulsum Kiral, Laura Vargas-Estrada, Raquel Lebrero, Rail Munoz
Summary: This study investigated the impact of carbon-coated zero-valent nanoparticle concentration on photosynthetic biogas upgrading. The addition of nanoparticles significantly increased microalgae productivity and enhanced nitrogen and phosphorus assimilation. The presence of nanoparticles also improved the quality of biomethane produced.
Article
Energy & Fuels
Yao Xiao, Asma Leghari, Linfeng Liu, Fangchao Yu, Ming Gao, Lu Ding, Yu Yang, Xueli Chen, Xiaoyu Yan, Fuchen Wang
Summary: Iron is added as a flocculant in wastewater treatment and the hydrothermal carbonization (HTC) of sludge produces wastewater containing Fe. This study investigates the effect of aqueous phase (AP) recycling on hydrochar properties, iron evolution and environmental assessment during HTC of sludge. The results show that AP recycling process improves the dewatering performance of hydrochar and facilitates the recovery of Fe from the liquid phase.
Article
Energy & Fuels
He Liang, Tao Wang, Zhenmin Luo, Jianliang Yu, Weizhai Yi, Fangming Cheng, Jingyu Zhao, Xingqing Yan, Jun Deng, Jihao Shi
Summary: This study investigated the influence of inhibitors (carbon dioxide, nitrogen, and heptafluoropropane) on the lower flammability limit of hydrogen and determined the critical inhibitory concentration needed for complete suppression. The impact of inhibitors on explosive characteristics was evaluated, and the inhibitory mechanism was analyzed with chemical kinetics. The results showed that with the increase of inhibitor quantity, the lower flammability limit of hydrogen also increased. The research findings can contribute to the safe utilization of hydrogen energy.
Article
Energy & Fuels
Zonghui Liu, Zhongze Zhang, Yali Zhou, Ziling Wang, Mingyang Du, Zhe Wen, Bing Yan, Qingxiang Ma, Na Liu, Bing Xue
Summary: In this study, high-performance solid catalysts based on phosphotungstic acid (HPW) supported on Zr-SBA-15 were synthesized and evaluated for the one-pot conversion of furfural (FUR) to γ-valerolactone (GVL). The catalysts were characterized using various techniques, and the ratio of HPW and Zr was found to significantly affect the selectivity of GVL. The HPW/Zr-SBA-15 (2-4-15) catalyst exhibited the highest GVL yield (83%) under optimized reaction conditions, and it was determined that a balance between Bronsted acid sites (BAS) and Lewis acid sites (LAS) was crucial for achieving higher catalytic performance. The reaction parameters and catalyst stability were also investigated.
Article
Energy & Fuels
Michael Stoehr, Stephan Ruoff, Bastian Rauch, Wolfgang Meier, Patrick Le Clercq
Summary: As part of the global energy transition, an experimental study was conducted to understand the effects of different fuel properties on droplet vaporization for various conventional and alternative fuels. The study utilized a flow channel to measure the evolution of droplet diameters over time and distance. The results revealed the temperature-dependent effects of physical properties, such as boiling point, liquid density, and enthalpy of vaporization, and showed the complex interactions of preferential vaporization and temperature-dependent influences of physical properties for multi-component fuels.
Article
Energy & Fuels
Yuan Zhuang, Ruikang Wu, Xinyan Wang, Rui Zhai, Changyong Gao
Summary: Through experimental validation and optimization of the chemical kinetic model, it was found that methanol can accelerate the oxidation reaction of ammonia, and methanol can be rapidly oxidized at high concentration. HO2 was found to generate a significant amount of OH radicals, facilitating the oxidation of methanol and ammonia. Rating: 7.5/10.
Article
Energy & Fuels
Radwan M. EL-Zohairy, Ahmed S. Attia, A. S. Huzayyin, Ahmed I. EL-Seesy
Summary: This paper presents a lab-scale experimental study on the impact of diethyl ether (DEE) as an additive to waste cooking oil biodiesel with Jet A-1 on combustion and emission features of a swirl-stabilized premixed flame. The addition of DEE to biodiesel significantly affects the flame temperature distribution and emissions. The W20D20 blend of DEE, biodiesel, and Jet A-1 shows similar flame temperature distribution to Jet A-1 and significantly reduces UHC, CO, and NOx emissions compared to Jet A-1.
Article
Energy & Fuels
Jiang Bian, Ziyuan Zhao, Yang Liu, Ran Cheng, Xuerui Zang, Xuewen Cao
Summary: This study presents a novel method for ammonia separation using supersonic flow and develops a mathematical model to investigate the condensation phenomenon. The results demonstrate that the L-P nucleation model accurately characterizes the nucleation process of ammonia at low temperatures. Numerical simulations also show that increasing pressure and concentration can enhance ammonia condensation efficiency.
Article
Energy & Fuels
Shiyuan Pan, Xiaodan Shi, Beibei Dong, Jan Skvaril, Haoran Zhang, Yongtu Liang, Hailong Li
Summary: Integrating CO2 capture with biomass-fired combined heat and power (bio-CHP) plants is a promising method for achieving negative emissions. This study develops a reliable data-driven model based on the Transformer architecture to predict the flowrate and CO2 concentration of flue gas in real time. The model validation shows high prediction accuracy, and the potential impact of meteorological parameters on model accuracy is assessed. The results demonstrate that the Transformer model outperforms other models and using near-infrared spectral data as input features improves the prediction accuracy.
