bluuebunny/crossref_metadata_2025 huggingface dataset:
Modeling Microwave-Enhanced Chemical Vapor Infiltration Process for Preventing Premature Pore Closure
Authors: Ge Wenjun , Ramanuj Vimal , Li Mengnan , Sankaran Ramanan , She Ying , Dardas Zissis
Published: September 2024

The chemical vapor infiltration (CVI) process involves infiltrating a porous preform with reacting gases that undergo chemical transformation at high temperatures to deposit the ceramic phase within the pores, ultimately leading to a dense composite. The conventional CVI process in composite manufacturing needs to follow an isothermal approach to minimize temperature differences between the external and internal surfaces of the preform, ensuring that reactive gases infiltrate internal pores before external surfaces seal. This study addresses the challenge of premature pore closure in CVI processes through microwave heating. A frequency-domain microwave solver is developed in Open-FOAM to investigate volumetric heating mechanisms within the preform. Through numerical studies, we demonstrate the capability of microwave heating of creating an inside-out temperature inversion. This inversion accelerates reactions proximal to the preform center, effectively mitigating the risk of premature external pore closure and ensuring uniform densification. The results reveal a significant enhancement in temperature inversion when high-permittivity reflectors are incorporated to generate resonant waves. This microwave heating strategy is then coupled with high-fidelity direct numerical simulation (DNS) of reacting flow, enabling the analysis of resulting densification processes. The DNS simulation includes detailed chemistry and realistic diffusion coefficients. The numerical results can be used to estimate the impact of microwave-induced temperature inversion on densification in productions.
Analytical and Numerical Modeling of Thermal Transport in Liquid Hydrogen Tanks
Authors: Owens Charles Abdol-Hamid , Park Hoyeon , Flores Robert Joseph , Wentlent Luke , Brouwer Jack , Lee Jaeho
Published: September 2024

Hydrogen is an element that can be stored via phase change through compression or liquification by varying temperature and pressure, or through physical or chemical bonding. This study provides a closed-form transient temperature model of a spherical liquid hydrogen storage tank heated over time with validation provided by a numerical model. The analytical temperature model couples the lumped capacitance approach with the transient heat equation, and the analytical thermal diffusivity model for the hollow glass bubble (HGB) insulation uses a combination of the effective medium theory (EMT), Parallel, and Series models. In the numerical model, the Newton-Raphson method is used to solve the transient energy and Navier-stokes equations to assess the effectiveness of the insulation. For the thermal conductivity model, as the wall thickness of the individual HGBs increases from 0.5μm to 50μm, the effective thermal conductivity of the insulation increases from 0.01W · m−1K−1 to 0.41W · m−1K−1. For a constant surface temperature from 280K to 320K, the numerical model illustrates that the time to critical point τ decreases from τ ≈ 60days to τ ≈ 41days. When the analytical model is iterated to the same τ at each surface temperature, the critical temperature TC is located radially at approximately 7.88m, rather than 7.85m, illustrating the limitations of the analytical model. An insulation design space relates the different thermal conductivity k and volumetric heat capacity ρCp values for the insulation at the critical pressure to find the corresponding τ. A power series relationship is found from the insulation design space for the critical time τ as a function of k and ρCp.
Flow Measurement Through Machine Learning: A Novel Non-Intrusive Volumetric Flow Meter
Authors: da Silva Ramon Peruchi Pacheco , Samadi Forooza , Woodbury Keith , Carpenter Joseph
Published: September 2024

An innovative non-intrusive flow meter was designed for the water flow measurement at ambient temperature under steady-state conditions [1]. This paper aims to possibly expand the designed flow meter to cover a wider range of flow rates. In this regard, the most accurate machine learning model for predicting volumetric flow rates using the previously designed flow meter will is identified, and the achieved resolution, degree of uncertainty, cost considerations, and flow range capabilities of this novel flow meter will be benchmarked against an existing non-intrusive flow meter currently available in the market. The device features a band heater positioned outside of the pipe, complemented by two thermocouples that monitor the outer wall’s temperature. The procedure involves activating the band heater for 60 seconds, followed by deactivation and the recording of temperatures over the subsequent 120 seconds. Multiple tests are conducted for each mass flow rate, ranging from 8.5 GPM to 40 GPM. Arduino-based data collection is employed to record the temperature response for the system. Statistically, three temperature parameters are evaluated: maximum temperature, average temperature differences during heating, and average temperature differences during cooling. Regression learner methods are utilized to establish correlations between volumetric flow rates and temperature parameters.
Fast Cooling Technology for Sample Stick in Top Loading Cryostats
Authors: Zou An , Davis Reese , Winters Dennis , Carlson David , Adhikari Daksh , Radyjowski Patryk , Chen Chien-Hua
Published: September 2024

Cryostats are essentially important sample environments for low-temperature neutron scattering experiments. They are primarily used to investigate materials of interest, i.e., samples of crystalline solids or powders, at temperatures below 100K. Dry cryostats, where the samples are cooled by helium exchange gas, are favored due to their simple operation, low maintenance, and, most importantly, moderate usage of progressively more expensive helium. However, samples in dry cryostats usually take almost two hours to cool from room temperature to ∼80 K, causing time-consuming changeover delays. Since neutron scattering experiments are usually conducted under strict time restraints at large-scale user facilities, maximizing instrument time utilization is of great significance. A novel sample stick with an embedded liquid nitrogen transport line is presented and shown to achieve improved cooling performance by involving the boiling of liquid nitrogen. The preliminary experiments demonstrate a cooling time of < 2 min, compared to ∼2 hr for a typical dry cryostat.
Recent Advancements in the Pressure Sensitive Paint (PSP) Technique for Film Cooling Effectiveness Measurements
Authors: Wright Lesley M. , Han Je-Chin
Published: September 2024

Over the past several decades, researchers from around the world have embraced the use of Pressure Sensitive Paint (PSP) to obtain detailed film cooling effectiveness distributions. Utilizing the mass transfer analogy along with the luminescence characteristics of PSP, the mixing behavior of the coolant and mainstream flows is easily quantified. As the method relies on tracking the concentration of various gases in contact with the paint, the measurements are not affected by thermal diffusion through the test surface. Therefore, researchers provide film cooling effectiveness distributions that are spatially, highly resolved, even in the near-hole regions. Such distributions are not only needed to visualize the three-dimensional mixing occurring near the holes, but the measurements can also be used to validate numerical simulations. When PSP was first introduced to the gas turbine and film cooling communities, steady, film cooling effectiveness distributions were primarily obtained in low-speed flows with simple geometries and coolant-to-mainstream density ratios of unity. However, as more researchers have integrated this measurement tool into their labs, the use of the paint has expanded to include flow conditions and cooling configurations relevant to advanced gas turbine engines. In this review, the mass transfer analogy for film cooling effectiveness measurements will be explained, and the recent, widespread deployment of the method will be discussed. Within the past decade, laboratories have successfully utilized traditional PSP for full coverage airfoil cooling over a range of coolant-to-mainstream density ratios simulating engine conditions. In addition, “binary” and “fast response” paints have gained popularity. The binary PSP is most often used in high speed flows, where viscous heating may affect the response of traditional PSP. A second luminophore in the binary paint allows for correction of the local temperature variation and improves the accuracy of the mass transfer analogy. Finally, fast response PSPs now allow researchers to visualize the unsteady interaction of the coolant and mainstream flows, yielding time-resolved film cooling effectiveness distributions. This review will discuss these developments and provide opportunities for further advancement into the future.
Infrared Assisted Convective Drying of Moist Paper Handsheet: A Numerical Study
Authors: Yu Hanshen , Yagoobi Jamal
Published: September 2024

The motivation of this study is to understand the combined effects of electrical infrared (IR) emitters, dielectrophoretic (DEP) mechanism, and hot air drying with slot jet reattachment (SJR) nozzles altogether on drying of moist paper handsheets. Experiments and simulations are conducted to physically understand heat transfer characteristics on a uniquely designed, fully electrified smart dryer without gas burners, aiming to reduce carbon footprint. In this work, a simulation for the smart dryer that allows infrared-assisted convection drying is developed. The finite difference method is implemented in the drying process simulation of combined technologies under different operating conditions, including dryer temperatures, air flow rate, and IR surface temperature, to provide physical insight numerically. Experiments are carried out on paper handsheets to verify IR energy penetration and combine its effect into the governing equation, not just as a boundary condition but also as an internal heat source by an absorption coefficient for paper pulp. Varying view factors on infrared drying are also assessed for continuous drying. The experiment-fused simulation gives us an in-depth understanding of infrared-assisted convection drying, showing the effectiveness of combining SJR and DEP drying and enabling future optimization to reduce energy costs without losing quality.
Simulation of Supercritical Fluids With Reduced Domains In Horizontal Flows
Authors: Hardy Devon , Ricklick Marc , Boetcher Sandra
Published: September 2024

The ability to use supercritical fluids as a heat transfer medium has benefits near the critical point as the specific heat and thermal conductivity approach infinity. However, because of these large thermodynamic property variations estimates for the heat transfer coefficients and wall temperatures can be difficult. With large changes in thermodynamic properties, threedimensional simulations have been used for heat transfer predictions, which can be time-consuming and computationally expensive. To reduce computational expenses, a comparison is made between 2D-axisymmetric and 3D horizontal round tubes using STAR CCM+ 2206. 2D and 3D cases are investigated at various inlet temperatures, mass fluxes, heat-flux to mass-flux ratios, pipe diameters, and pressures to investigate the impact on axisymmetric simulation approximations. A comparison between 3D and 2D-axisymmetric simulations for the circumferentially averaged heat transfer coefficients, Richardson number, and expected pressure drop is made. Across all cases, the maximum percent difference in heat transfer coefficient was 9.4% for an inlet temperature of 295 K, mass flux of 400 kg · m−2 · s−1, operating pressure of 7.5 MPa, applied heat flux of 32 kW · m−2, through a 6 mm pipe. At an inlet temperature of 295 K, a mass flux of 200 kg · m−2 · s−1, an operating pressure of 8 MPa and an applied heat flux of 12 kW · m−2 through a 2 mm pipe, the maximum percent difference in Richardson number was 40.87%. With an inlet temperature of 307 K, mass flux of 600 kg · m−2 · s−1, an operating pressure of 8 MPa, and applied heat flux of 36 kW · m−2, through a 12 mm pipe, the maximum percent difference in pressure drop was 16.87%. The utilization of 2D-axisymmetric domains for supercritical fluids can reduce computational expenses while producing similar results to their 3D counterparts within 40% depending on parameter.
Machine Learning Algorithms for Predicting Condensation Pressure Drop in Mini/Micro Channels
Authors: Barghi Golezani Farshad , Li Jiayuan , Pirnstill Logan , Kharangate Chirag
Published: September 2024

Recent years have seen a big increase in the amount of heat that needs to be dissipated within small systems. This means that single-phase heat transfer is no longer good enough. Because of this, two-phase heat transfer, which can get rid of more heat since liquid changing to vapor takes up latent heat, has become crucial. However, two-phase systems have higher pressure drops than single-phase ones, which decreases overall efficiency. So being able to accurately predict the pressure drop is really important for efficiency and reliability. Currently available models for two-phase flow pressure drop prediction are not very accurate or helpful. Our research uses machine learning techniques, including Polynomial Linear regression, Random Forest algorithms, and Neural Networks, to tackle this problem. We looked at a dataset of 4337 data points with 45 features from 25 studies and used feature selection methods like Kendall correlation and techniques like Lasso and RFE to select features. Our findings show nonlinear machine learning ways, especially Neural Networks, are better at predicting pressure drops than traditional models. The Neural Network model performed great, with a Mean Absolute Percentage Error of 13.89% and an adjusted R2 of 0.9941. This shows state-of-the-art neural nets can be highly effective in thermal system analysis.
Optimization of a Hybrid Thermal Protection System for Space Vehicles
Authors: Nabi Syed Arafun , Najafi Hamidreza
Published: September 2024

Thermal protection system (TPS) plays a pivotal role in safeguarding space vehicles from extreme aerothermal heating during atmospheric entry. To ensure effective thermal management, Hybrid Thermal Protection seamlessly integrating both active and passive TPS is an innovative solution. The passive TPS consists of an insulative layer on vehicle skin to counteract the aerothermal heat. Although a thicker layer enhances insulation, a trade-off arises between the thickness of the passive layer and the spacecraft’s weight. Beneath the passive TPS layer lies the active TPS functioning as a heat exchanger where the vehicle fuel liquid is considered as coolant. The effectiveness of the active TPS is influenced by parameters such as the coolant flowrate and the design of the flow channel. In this paper, two potential designs for the active TPS are considered and the resulting hybrid systems are studied through parametric analysis and optimization using multi-objective optimization through genetic algorithm. Two objective functions including the total weight of the system as well as the required pumping power are considered and parameters including coolant velocity, thickness of passive TPS layer and thickness of gyroid are used as the optimization variables. The methodology used and results produced from this study provide insights regarding the design and optimization of hybrid TPS and the potentials for using triply periodic minimal surfaces to achieve enhanced heat transfer performance.
Optimization of Thermal Management in Power Electronics by the Design of Split Channel Cooling Systems Through Numerical Simulations
Authors: Taghavi Hooman , Raghu Sowmya , Khan Jamil A.
Published: September 2024

Managing high thermal loads efficiently in power electronics is crucial to ensure reliable operation and enhance the operational lifecycle and efficiency. This study presents a numerical analysis of advanced cooling techniques using split microchannel cooling systems incorporating crossflow, specifically tailored for power electronics. Using ANSYS CFX, a three-dimensional numerical investigation of fluid flow and heat transfer performance of the power converters’ primary and secondary sides with the novel split channel configurations is studied.

Various channel designs, ranging from single to multiple split configurations (dual, quadruple, and hexa-split), in addition to channel size (3mm–6mm), coolant inlet velocity (0.5 m/s to 6 m/s), channel shape (circular, rectangular, semicircular, and half-hexagon) and the incorporation of transverse flow to optimize heat dissipation are examined. Compared to a traditional straight channel, a mixed channel with the same hydraulic diameter configuration exhibited an average 40% lower pressure drop. Optimized parallel channel designs achieve a ∼10% reduction in temperature at the highest power loss configuration. This reduction is primarily attributed to the targeted surface area increase for heat dissipation at the hot spot regions and the induced turbulence in the coolant water flow, which collectively enhances the convective heat transfer coefficient.

Our findings underscore the superiority of split and parallel channel configurations, especially when integrated with crossflow, in addressing the critical cooling requirements of power electronics systems. Thus, the insights gained from this research are expected to significantly influence future design considerations and operational strategies in high thermal load power electronics cooling.
Centrifugal Compressor Design Optimization for S R-30 Small Scale Gas Turbine Engine Using Numerical Simulations and Machine Learning Approach
Authors: Raghu Sowmya , Khan Jamil A.
Published: September 2024

In this paper, a case-study of SR-30 small scale straight turbojet engine with centrifugal compressor, reverse annular combustion chamber and axial turbine is conducted and serves as a pre-cursor for the development of Compressor Design tool.

The first stage involves conducting experiments using SR-30 gas turbine engine to obtain operational characteristics from 45000–80000 RPM. The centrifugal compressor consists of 9 primary and 9 secondary blades with temperature and pressure probes at the inlet and exhaust locations of the compressor. A 1D thermodynamic analysis is conducted and an analytical framework is developed to obtain the compressor map at various mass flow rates and at various ambient pressure and temperature conditions.

The second stage involves conducting numerical analysis and simulations using Bladegen and ANSYS CFX to obtain the obtain the efficiency parameters of the existing design. Using Bladegen, 12 different parameters such as blade angles, incidence angles, loss factors etc. are identified to refine design parameters, optimize performance at various design, off-design, steady-state and transient conditions.

The final stage involves a development of machine learning methodology to create a physics-based data-driven model for predicting operational efficiency using the experimental data and an explicit inverse aerodynamic design methodology is developed to obtain the centrifugal compressor design parameters.

A first-of-its-kind python based Graphical User Interface (GUI) is created as a plug-and-play software to obtain the design and performance parameters of the centrifugal compressor based on numerical simulations and machine learning methodologies.
Local Variation of Heat Transfer for Laminar Flow Over a Finite Width Flat Plate
Authors: Taliaferro Matthew E.
Published: September 2024

Lateral variation of wall heat transfer in laminar boundary layer flow is investigated for geometries where both the heated and cooled/adiabatic surfaces are finite in lateral extent. Two dimensional conduction models are compared to three dimensional thermal numerical simulations for a variety of Prandtl numbers, boundary conditions, unheated starting lengths, and widths. It is found that the conduction model works remarkably well at predicting wall heat transfer and the most relevant length scale for describing the problem is the conduction thickness. Three dimensionless spanwise variables that fully characterize the heat transfer are defined using the conduction thickness: the lateral location and the widths of the heated and cooled/adiabatic region normalized by the conduction thickness. The lateral variation of the Nusselt number is described for various widths and boundary conditions, with only the isoflux-adiabatic set of boundary conditions not resulting power law behavior for the Nusselt number near the lateral edge. Furthermore, it is found the spanwise extent of the region affected by the lateral edge is of the same order of magnitude as the conduction thickness. Effects of the finite lateral width and various boundary conditions on the heat flux at the center of a finite strip, convection from infinitesimally small strips, and lateral spacing of heated components are explored and presented. Finally, the accuracy and computational simplicity of the conduction model allows for impressive savings in numerical modeling of conjugate heat transfer where lateral variation in heat transfer is important.
Choked Gas and Liquid Carbon Dioxide Flow Through Microchannels With Parallel Multi Orifices
Authors: Niazi Soroush , Peles Yoav
Published: September 2024

Carbon dioxide (CO2) has potential usage for cooling applications due to its exceptional thermophysical properties near the pseudocritical condition. However, literature pertinent to these conditions is scarce, and as a result, predicting the fluid flow in equipment and flow restriction elements near the critical condition is challenging. In this study, the depressurization effect on the mass flow rate through channels with multiple micro constriction elements is investigated with silicon-based microfluidic devices consisting of arrays of microchannels (micro-orifices). A close-loop experimental setup was built to provide control and measurement of pressure and temperature at the inlet and outlet. Inlet pressure was set to 5.8 and 6.6 MPa (corresponding to liquid and gas states respectively), and outlet pressure ranged from 1.2 to 6.4 MPa. Mass flow rate and density are controlled and measured by a Coriolis flow controller at the inlet. The mass flow rate vs. pressure drops plot exhibits initial increase followed by a smooth convergence as the outlet pressure decreased. The choking phenomenon was observed for both gas and liquid inlet conditions that led to significant temperature drop along the channel with multi parallel micro-orifices.
Effect of Triton X-100 surfactant and agitation on tetramethylammonium hydroxide wet etching for microneedle fabrication
Authors: He Yu , Hu Wenhan , Cui Bo
Published: September 2024

Solid silicon (Si) microneedles have many applications such as skin pretreatment to form micrometer-sized holes in the skin surface in transdermal drug delivery systems. Wet etching based on tetramethylammonium hydroxide (TMAH) is an efficient method to fabricate solid microneedles. However, it is challenging to increase the density of microneedle arrays due to the faster lateral etching than the vertical etching that requires a large initial mask size. In this work, we used wet etching based on TMAH to fabricate solid Si microneedles. One kind of nonionic surfactant, Triton X-100, was introduced into the TMAH solution to suppress the lateral etching. When Triton X-100 was added into TMAH for a given etching condition, the maximum height (attained right before the mask fell off) of microneedles could reach ∼230 μm for 600 μm square-shaped mask size and 700 μm array period, compared to microneedles of maximum 152 μm height for the same mask size and period without surfactant addition. Correspondingly, when the target heights of microneedles were the same as ∼230 μm, denser (down to 700 μm period, 600 μm mask size) microneedle arrays were achieved with the help of Triton X-100, in comparison to arrays down to 900 μm period (800 μm mask size) without surfactant addition. Furthermore, agitation by a magnetic stirring bar is important for the fabrication of dense solid Si microneedle arrays based on TMAH. The microneedle structures were rhombic pyramid in shape with Triton X-100 and agitation. But microneedle structures obtained with Triton X-100 yet without agitation were octagonal pyramid in shape with a much less steep side surface.
Automated detection of Bornean white-bearded gibbon (Hylobates albibarbis) vocalizations using an open-source framework for deep learning
Authors: Owens A. F. , Hockings Kimberley J. , Imron Muhammed Ali , Madhusudhana Shyam , Mariaty  , Setia Tatang Mitra , Sharma Manmohan , Maimunah Siti , Van Veen F. J. F. , Erb Wendy M.
Published: September 2024

Passive acoustic monitoring is a promising tool for monitoring at-risk populations of vocal species, yet, extracting relevant information from large acoustic datasets can be time-consuming, creating a bottleneck at the point of analysis. To address this, an open-source framework for deep learning in bioacoustics to automatically detect Bornean white-bearded gibbon (Hylobates albibarbis) “great call” vocalizations in a long-term acoustic dataset from a rainforest location in Borneo is adapted. The steps involved in developing this solution are described, including collecting audio recordings, developing training and testing datasets, training neural network models, and evaluating model performance. The best model performed at a satisfactory level (F score = 0.87), identifying 98% of the highest-quality calls from 90 h of manually annotated audio recordings and greatly reduced analysis times when compared to a human observer. No significant difference was found in the temporal distribution of great call detections between the manual annotations and the model's output. Future work should seek to apply this model to long-term acoustic datasets to understand spatiotemporal variations in H. albibarbis' calling activity. Overall, a roadmap is presented for applying deep learning to identify the vocalizations of species of interest, which can be adapted for monitoring other endangered vocalizing species.
HPV18 E7 inhibits LATS1 kinase and activates YAP1 by degrading PTPN14
Authors: Blakely William J. , Hatterschide Joshua , White Elizabeth A.
Published: September 2024

High-risk human papillomavirus (HPV) oncoproteins inactivate cellular tumor suppressors to reprogram host cell signaling pathways. HPV E7 proteins bind and degrade the tumor suppressor PTPN14, thereby promoting the nuclear localization of the YAP1 oncoprotein and inhibiting keratinocyte differentiation. YAP1 is a transcriptional coactivator that drives epithelial cell stemness and self-renewal. YAP1 activity is inhibited by the highly conserved Hippo pathway, which is frequently inactivated in human cancers. MST1/2 and LATS1/2 kinases form the core of the Hippo kinase cascade. Active LATS1 kinase is phosphorylated on threonine 1079 and inhibits YAP1 by phosphorylating it on amino acids including serine 127. Here, we tested the effect of high-risk (carcinogenic) HPV18 E7 on Hippo pathway activity. We found that either PTPN14 knockout or PTPN14 degradation by HPV18 E7 decreased the phosphorylation of LATS1 T1079 and YAP1 S127 in human keratinocytes and inhibited keratinocyte differentiation. Conversely, PTPN14-dependent differentiation required LATS kinases and certain PPxY motifs in PTPN14. Neither MST1/2 kinases nor the putative PTPN14 phosphatase active sites were required for PTPN14 to promote differentiation. Together, these data support that PTPN14 inactivation or degradation of PTPN14 by HPV18 E7 reduce LATS1 activity, promoting active YAP1 and inhibiting keratinocyte differentiation.

IMPORTANCE

The Hippo kinase cascade inhibits YAP1, an oncoprotein and driver of cell stemness and self-renewal. There is mounting evidence that the Hippo pathway is targeted by tumor viruses including human papillomavirus. The high-risk HPV E7 oncoprotein promotes YAP1 nuclear localization and the carcinogenic activity of high-risk HPV E7 requires YAP1 activity. Blocking HPV E7-dependent YAP1 activation could inhibit HPV-mediated carcinogenesis, but the mechanism by which HPV E7 activates YAP1 has not been elucidated. Here we report that by degrading the tumor suppressor PTPN14, HPV18 E7 inhibits LATS1 kinase, reducing inhibitory phosphorylation on YAP1. These data support that an HPV oncoprotein can inhibit Hippo signaling to activate YAP1 and strengthen the link between PTPN14 and Hippo signaling in human epithelial cells.
Genome sequence of
Colletotrichum karsti
isolated from rose leaves exhibiting anthracnose symptoms in Potchefstroom, South Africa
Authors: Maguvu Tawanda E. , Raimi Adekunle , Trouillas Florent P. , Adeleke Rasheed , Bezuidenhout Cornelius C.
Published: September 2024

We present the genome sequence of
Colletotrichum karsti
isolated from rose leaves exhibiting anthracnose symptoms. The genome was assembled to 53.2 Mbp organized into 753 scaffolds having an N50 of 582,313 kbp and a GC content of 52.5%. The genome had an estimated 99.4% of the core Ascomycota genes.
Draft genome sequences of
Epichloë bromicola
strains isolated from
Elymus ciliaris
Authors: Miura Atsushi , Imano Sayaka , Ashida Akira , Sato Ikuo , Chiba Sotaro , Tanaka Aiko , Camagna Maurizio , Takemoto Daigo
Published: September 2024

Epichloë
species are endophytic fungi that systemically colonize grass species. Here, we report the genome sequences of
Epichloë bromicola
strains HS and DP isolated for the first time from
Elymus ciliaris
in Nagoya, Japan.
Draft genome sequence of 16
Aspergillus flavus
isolated from cashew nuts from coastal Kenya
Authors: Gachanja Pauline Wambui , Onyango Manase Aloo , Musangi Colletah Rhoda , Juma Bicko Steve , Mukhebi Dennis Wamalabe , Muzami Eugene Mwanza , Katua Kyalo , Mbinda Wilton Mwema
Published: September 2024

Aspergillus flavus
is a soil-borne fungus known for its aflatoxin contamination of agricultural products. Here, we report the draft genome sequences of 16 predicted aflatoxin-producing
A. flavus
isolated from cashew nuts from coastal Kenya.
Complete genome sequence of bacterium
Peribacillus simplex
strain IMGN11 from soil
Authors: Lee Sangmin , Kim Yeongjun , Han Jeong A. , Lee Ho-Seok , Kim Eun Yu
Published: September 2024

We report the complete genome sequence of
Peribacillus simplex
, a spore-forming bacterium originally classified within the
Bacillus
genus.
Peribacillus simplex
exhibits antibiotic, plant growth-promoting, and xenobiotic-degrading activities and resistance to environmental contamination. The genome sequence of
Peribacillus simplex
will provide insights into its capabilities and potential as a biocontrol agent.
Genome-based model for differentiating between infection and carriage
Staphylococcus aureus
Authors: Chen Jianyu , Du Wenyin , Li Yuehe , Zhou Huiliu , Ouyang Dejia , Yao Zhenjiang , Fu Jinjian , Ye Xiaohua
Published: September 2024

Staphylococcus aureus
(
S. aureus
) is a clinically significant opportunistic pathogen, which can colonize multiple body sites in healthy individuals and cause various life-threatening diseases in both children and adults worldwide. The genetic backgrounds of
S. aureus
that cause infection versus asymptomatic carriage vary widely, but the potential genetic elements (k-mers) associated with
S. aureus
infection remain unknown, which leads to difficulties in differentiating infection isolates from harmless colonizers. Here, we address the disease-associated k-mers by using a comprehensive genome-wide association study (GWAS) to compare the genetic variation of
S. aureus
isolates from clinical infection sites (272 isolates) with nasal carriage (240 isolates). This study uncovers consensus evidence that certain k-mers are overrepresented in infection isolates compared with carriage isolates, indicating the presence of specific genetic elements associated with
S. aureus
infection. Moreover, the random forest (RF) model achieved a classification accuracy of 77% for predicting disease status (infection vs carriage), with 68% accuracy for a single highest-ranked k-mer, providing a simple target for identifying high-risk genotypes. Our findings suggest that the disease-causing
S. aureus
is a pathogenic subpopulation harboring unique genomic variation that promotes invasion and infection, providing novel targets for clinical interventions.

IMPORTANCE

Defining the disease-causing isolates is the first step toward disease control. However, the disease-associated genetic elements of
Staphylococcus aureus
remain unknown, which leads to difficulties in differentiating infection isolates from harmless carriage isolates. Our comprehensive genome-wide association study (GWAS) found consensus evidence that certain genetic elements are overrepresented among infection isolates than carriage isolates, suggesting that the enrichment of disease-associated elements may promote infection. Notably, a single k-mer predictor achieved a high classification accuracy, which forms the basis for early diagnostics and interventions.
Analysis of the utility of a rapid vesicle isolation method for clinical strains of
Pseudomonas aeruginosa
Authors: Henriquez Tania , Santoro Francesco , Medaglini Donata , Pallecchi Lucia , Clemente Ilaria , Bonechi Claudia , Magnani Agnese , Paccagnini Eugenio , Gentile Mariangela , Lupetti Pietro , Marvasi Massimiliano , Pini Alessandro , Bracci Luisa , Falciani Chiara
Published: September 2024

Pseudomonas aeruginosa
, a pathogen capable of causing diseases ranging from mild to life-threatening, has a large arsenal of virulence factors. Notably, extracellular vesicles have emerged as significant players in the pathogenesis of this organism. However, the full range of their functions is still being studied, and difficulties related to vesicle purification (long protocols, low yields, and specialized instruments) have become a major obstacle for their characterization. In this context, the utility of rapid new methods of vesicle isolation from clinical strains is still unknown. Here, we analyze the utility of the ExoBacteria OMV isolation kit for a collection of clinical strains of
P. aeruginosa
. We first phenotypically characterized 15
P
.
aeruginosa
strains to ensure that our samples were heterogeneous. We then determined the best conditions for purifying vesicles from
P. aeruginosa
PAO1 reference strain by the rapid method and used them to isolate vesicles from clinical strains. Our results indicated that M9 minimal medium is the best for obtaining high purity with the rapid isolation kit. Although we were able to isolate vesicles from at least four strains, the low yield and the large number of strains with unpurifiable vesicles showed that the kit was not practical or convenient for clinical strains. Our findings suggest that although fast procedures for vesicle purification can be of great utility for
Escherichia coli
, the more complex phenotypes of clinical isolates of
P. aeruginosa
are a challenge for these protocols and new alternatives/optimizations need to be developed.

IMPORTANCE

Pseudomonas aeruginosa
is recognized as an opportunistic pathogen in humans and animals. It can effectively colonize various environments thanks to a large set of virulence factors that include extracellular vesicles. Different methods were recently developed to reduce the time and effort associated with vesicle purification. However, the utility of rapid vesicle isolation methods for clinical strains of
P. aeruginosa
(which are recognized as being highly diverse) is not yet known. In this context, we analyzed the utility of the ExoBacteria OMV Isolation kit for vesicle purification in
P. aeruginosa
clinical strains. Our findings showed that the kit does not seem to be convenient for research on clinical strains due to low vesicle recovery. Our results underscore the importance of developing new rapid vesicle purification protocols/techniques for specific clinical phenotypes.
Characterization of acquired β-lactamases in
Pseudomonas aeruginosa
and quantification of their contributions to resistance
Authors: Glen Karl A. , Lamont Iain L.
Published: September 2024

Pseudomonas aeruginosa
is a highly problematic opportunistic pathogen that causes a range of different infections. Infections are commonly treated with β-lactam antibiotics, including cephalosporins, monobactams, penicillins, and carbapenems, with carbapenems regarded as antibiotics of last resort. Isolates of
P. aeruginosa
can contain horizontally acquired
bla
genes encoding β-lactamase enzymes, but the extent to which these contribute to β-lactam resistance in this species has not been systematically quantified. The overall aim of this research was to address this knowledge gap by quantifying the frequency of β-lactamase-encoding genes in
P. aeruginosa
and by determining the effects of β-lactamases on susceptibility of
P. aeruginosa
to β-lactams. Genome analysis showed that β-lactamase-encoding genes are present in 3% of
P. aeruginosa
but are enriched in carbapenem-resistant isolates (35%). To determine the substrate antibiotics, 10 β-lactamases were expressed from an integrative plasmid in the chromosome of
P. aeruginosa
reference strain PAO1. The β-lactamases reduced susceptibility to a variety of clinically used antibiotics, including carbapenems (meropenem, imipenem), penicillins (ticarcillin, piperacillin), cephalosporins (ceftazidime, cefepime), and a monobactam (aztreonam). Different enzymes acted on different β-lactams. β-lactamases encoded by the genomes of
P. aeruginosa
clinical isolates had similar effects to the enzymes expressed in strain PAO1. Genome engineering was used to delete β-lactamase-encoding genes from three carbapenem-resistant clinical isolates and increased susceptibility to substrate β-lactams. Our findings demonstrate that acquired β-lactamases play an important role in β-lactam resistance in
P. aeruginosa
, identifying substrate antibiotics for a range of enzymes and quantifying their contributions to resistance.

IMPORTANCE

Pseudomonas aeruginosa
is an extremely problematic pathogen, with isolates that are resistant to the carbapenem class of β-lactam antibiotics being in critical need of new therapies. Genes encoding β-lactamase enzymes that degrade β-lactam antibiotics can be present in
P. aeruginosa
, including carbapenem-resistant isolates. Here, we show that β-lactamase genes are over-represented in carbapenem-resistant isolates, indicating their key role in resistance. We also show that different β-lactamases alter susceptibility of
P. aeruginosa
to different β-lactam antibiotics and quantify the effects of selected enzymes on β-lactam susceptibility. This research significantly advances the understanding of the contributions of acquired β-lactamases to antibiotic resistance, including carbapenem resistance, in
P. aeruginosa
and by implication in other species. It has potential to expedite development of methods that use whole genome sequencing of infecting bacteria to inform antibiotic treatment, allowing more effective use of antibiotics, and facilitate the development of new antibiotics.
Changes in the pharyngeal and nasal microbiota in pediatric patients with adenotonsillar hypertrophy
Authors: Del Chierico Federica , Piazzesi Antonia , Fiscarelli Ersilia Vita , Ristori Maria Vittoria , Pirona Ilaria , Russo Alessandra , Citerà Nicoletta , Macari Gabriele , Santarsiero Sara , Bianco Fabrizio , Antenucci Valeria , Damiani Valerio , Mercuri Luigi , De Vincentis Giovanni Carlo , Putignani Lorenza
Published: September 2024

The present study aimed to investigate the pharyngeal and nasal microbiota composition in children with adenotonsillar hypertrophy (AH) and assess longitudinal alterations in both microbiota after a probiotic oral spray treatment. A cohort of 57 AH patients were enrolled and randomly assigned to the probiotic and placebo groups for a 5-month treatment course. Pharyngeal and nasal swabs were collected before and after treatment and analyzed by 16S rRNA-based metataxonomics and axenic cultures for pathobiont identification. 16S rRNA sequences from pharyngeal and nasal swabs of 65 healthy children (HC) were used as microbiota reference profiles. We found that the pharyngeal and nasal microbiota of AH children were similar. When compared to HC, we observed an increase of the genera
Rothia
,
Granulicatella
,
Streptococcus
,
Neisseria
, and
Haemophilus
, as well as a reduction of
Corynebacterium
,
Pseudomonas, Acinetobacter,
and
Moraxella
in both microbiota of AH patients. After probiotic treatment, we confirmed the absence of adverse effects and a reduction of upper respiratory tract infections (URTI). Moreover, the composition of pharyngeal microbiota was positively influenced by the reduction of potential pathobionts, like
Haemophilus
spp., with an increase of beneficial microbial metabolic pathways. Finally, the probiotic reduced the abundance of the pathobionts
Streptococcus mitis
and
Gemella haemolysans
in relation to AH severity. In conclusion, our results highlight the alterations of the pharyngeal and nasal microbiota associated with AH. Moreover, probiotic administration conferred protection against URTI and reduced the presence of potential pathobionts in patients with AH.

IMPORTANCE

Adenotonsillar hypertrophy (AH) is considered the main cause of breathing disorders during sleep in children. AH patients, after significant morbidity and often multiple courses of antibiotics, often proceed to tonsillectomy and/or adenoidectomy. Given the potential risks associated with these procedures, there is a growing interest in the use of nonsurgical adjuvant therapies, such as probiotics, that could potentially reduce their need for surgical intervention. In this study, we investigated the pharyngeal and nasal microbiota in patients with AH compared with healthy children. Furthermore, we tested the effects of probiotic spray administration on both disease symptoms and microbiota profiles, to evaluate the possible use of this microbial therapy as an adjuvant for AH patients.
Dynamic response of the intestinal microbiome to
Eimeria maxima-
induced coccidiosis in chickens
Authors: Liu Jing , Guo Jiaqing , Whitmore Melanie A. , Tobin Isabel , Kim Dohyung M. , Zhao Zijun , Zhang Guolong
Published: September 2024

Eimeria maxima
is a major cause of coccidiosis in chickens and a key predisposing factor for other economically significant diseases such as necrotic enteritis. However, a detailed understanding of the intestinal microbiome response to
E. maxima
infection is still lacking. This study aimed to comprehensively investigate the dynamic changes of the intestinal microbiome for 14 days post-infection (dpi) with
E. maxima
. Bacterial 16S rRNA gene sequencing was performed with the ileal and cecal digesta collected from mock and
E. maxima-
infected chickens at the prepatent (3 dpi), acute (5 and 7 dpi), and recovery phases (10 and 14 dpi) of infection. Although no notable changes were observed at 3 dpi, significant alterations of the microbiota occurred in both the ileum and cecum at 5 and 7 dpi. By 14 dpi, the intestinal microbiota tended to return to a healthy state. Notably,
Lactobacillus
was enriched in response to
E. maxima
infection in both the ileum and cecum, although individual
Lactobacillus
,
Ligilactobacillus
, and
Limosilactobacillus
species varied in the temporal pattern of response. Concurrently, major short-chain fatty acid-producing bacteria, such as
Faecalibacterium
, were progressively suppressed by
E. maxima
in the cecum. On the other hand, opportunistic pathogens such as
Escherichia
,
Enterococcus
, and
Staphylococcus
were significantly enriched in the ileum during acute infection.

IMPORTANCE

We have observed for the first time the dynamic response of the intestinal microbiota to
Eimeria maxima
infection, synchronized with its life cycle. Minimal changes occur in both the ileal and cecal microbiota during early infection, while significant alterations coincide with acute infection and disruption of the intestinal mucosal lining. As animals recover from coccidiosis, the intestinal microbiota largely returns to normal.
E. maxima
-induced intestinal inflammation likely creates an environment conducive to the growth of aerotolerant anaerobes such as
Lactobacillus
, as well as facultative anaerobes such as
Escherichia
,
Enterococcus
, and
Staphylococcus
, while suppressing the growth of obligate anaerobes such as short-chain fatty acid-producing bacteria. These findings expand our understanding of the temporal dynamics of the microbiota structure during
Eimeria
infection and offer insights into the pathogenesis of coccidiosis, supporting the rationale for microbiome-based strategies in the control and prevention of this condition.
Hepatitis B surface antigen impairs TLR4 signaling by upregulating A20 expression in monocytes
Authors: Wang Cong , Huang Chenlu , Li Yaming , Bai Jinjin , Zhao Kuangjie , Fang Zhong , Chen Jieliang
Published: September 2024

Toll-like receptors (TLRs) play a crucial role in eliminating viral infection. Conversely, viruses have evolved various strategies to disrupt TLR signaling during chronic infection. In the case of hepatitis B virus (HBV), we previously reported that plasma hepatitis B surface antigen (HBsAg) is closely associated with impaired TLR responses in peripheral blood mononuclear cells from chronic hepatitis B (CHB) patients, but the reasons remain unclear. In this study, we investigated the mechanism by which HBsAg suppresses TLR4 signaling in monocyte cell lines. The monocyte cell line THP-1 was pretreated with HBsAg, followed by lipopolysaccharide (LPS) stimulation. Levels of proinflammatory cytokines and the activation of NF-κB, c-JNK, and ERK were examined. We found that HBsAg did not influence the LPS-induced activation of p65, but it disrupted NF-κB promoter activity through the ectopic expression of myeloid differentiation factor 88 (MyD88) and TAK1, suggesting that HBsAg can block downstream TLR4 signaling. Furthermore, we proved that LPS-induced polyubiquitination of tumor necrosis factor receptor-associated factor 6 (TRAF6) and the formation of the TRAF6-TAB2 complex were inhibited in HBsAg-pretreated cells. Interestingly, HBsAg led to a significant upregulation of A20, a ubiquitin-editing enzyme. Correspondingly, downregulation of A20 using siRNA restored LPS-mediated cytokines production, reflecting its crucial role in HBsAg-mediated inhibition of TLR4 signaling. These results demonstrated a novel mechanism by which HBsAg disrupts TLR4 signaling through the upregulation of A20, suggesting that targeting A20 may be a potential strategy to help restore monocyte functions.

IMPORTANCE

Clearance HBsAg indicates a functional cure of HBV infection, but in chronic hepatitis B (CHB), it is hard to achieve. HBsAg has been found to regulate anti-viral immune responses, such as the activation of TLR. Our previous jobs proved that HBsAg negatively correlates with TLR2/4 activation in monocytes from CHB patients and blocks TLR2 ligand-indcuced IL-12 production in monocytes. However, how TLR4 signaling is affected by HBsAg remains unknown. In this study, we not only observed impaired TLR4 activation after pretreated monocytes with HBsAg but also identified HBsAg-induced A20 play a role in this impairment, which suggests that targeting A20 may be a viable strategy to restore monocyte functions in CHB.