bluuebunny/crossref_metadata_2025 huggingface dataset:
Experimental Investigation of New Electro-Active Polymers-Based Plasma Actuators for Flow Control and Ice Mitigation Applications
Authors: Rodrigues Frederico , Mbanguine Leonardo , Páscoa José
Published: September 2024

The current work introduces a new device for effective flow control and ice removal applications based on the combination of a non-thermal plasma discharge with the excitation of an electroactive polymer membrane. This new device designated electroactive polymer (EAP) plasma actuator is particularly interesting for aeronautic and wind power applications since it allows to perform simultaneous flow control and ice removal operations. To prove the concept, in the current work, electroactive polymers-based plasma actuator devices are fabricated and experimentally tested. For the initial tests a “VHB 4910” from 3M was used as dielectric layer and electrically conductive grease was utilized to fabricate the flexible electrodes. Initial tests demonstrate that the electro active polymer selected is able to sustain the levels of voltages needed to generate the plasma discharge. The new EAP device is tested and compared with conventional Kapton plasma actuators with conventional copper tape electrodes and flexible electrodes. The preliminary results demonstrate that this new concept is feasible, and the EAP plasma actuator is able to generate induced flow velocities similar to the conventional Kapton actuator however needs to be implemented with higher thicknesses Finally, it is worth mentioning that this new EAP actuator brings several other advantages, mainly for deicing purposes since the electro-active polymer movement will difficult the ice adhesion and help to expel the ice from the surface.
Effect of Swelling Behavior of Rubber Rings on the Sealing Performance for 70MPA Hydrogen Pressure Reducing Valves
Authors: Hua Ting-feng , Yang Xue-hua , Long Yun-fei , Jin Zhi-jiang , Qian Jin-yuan
Published: September 2024

The sealing structures of 70MPa hydrogen pressure reducing valves (HPRV) are important for avoiding leakage. A novel constitutive model considering rubber hyperelasticity and hydrogen-induced strain was built. The model describes the mechanisms of how hydrogen swelling influences sealing performance. Utilizing the finite element software (ABAQUS), in tandem with the user material subroutine (UMAT), a numerical model of the rubber O-ring sealing apparatus under high-pressure hydrogen is developed. The model emphasizes the swelling behavior. Contact stress and Von Mises stress of rubber rings are analyzed to characterize the sealing performance. The influence of various parameters on the sealing performance are discussed respectively, including the hydrogen pressure and the seal gap. The results show that the optimal pre-compression ratio for the structure analyzed is approximated at 5%. Compared to traditional design, this design not only enhances the seal length, but also attenuates the Von Mises stress at the stress concentration point.
A Data-Based One-Layer Formulation of the Two-Equation RANS Models
Authors: Hu Xiaohan , Huang George , Kunz Robert , Yang Xiang
Published: September 2024

The conventional k-ε model accurately predicts the slope of the logarithmic law but falls short in estimating its intercept as well as the buffer layer. This limitation can be addressed either through a two-layer formulation or by introducing additional terms. However, both strategies necessitate extra adjustable constants and ad-hoc functions. In contrast, this paper introduces a novel one-layer k-ε model, which seamlessly integrates the law of the wall while preserving the essential structure of the k-ε framework. Our approach modifies the unclosed dissipation terms in the k and ε equations specifically within the wall layer. We invoke no other assumption than the general law of the wall and the assumptions that led to the k-ε model. Neither do we resort to ad hoc source terms. The revised model yields the following physical scalings in the viscous sublayer: k ∼ y2, ε ∼ y0. In addition, we demonstrate analytically the in-feasibility of sustaining the vt ∼ y3 scaling. Beyond the sublayer scalings, our model effectively captures the mean flow characteristics in both the buffer layer and the logarithmic layer, resulting in robust predictions of skin friction for zero-pressure-gradient flat-plate boundary layers and plane channels. To further validate our one-layer formulation, we apply our model to boundary layers under varying pressure gradients and channels experiencing sudden deceleration. Our model’s results closely align with the reference direct numerical simulation and experimental datasets.
Experiments and Mechanistic Modeling of Sand Erosion of 90° Elbows in Liquid-Dominated Multiphase Flows
Authors: Vieira Ronald , Biglari Farshad , Shirazi Siamack , Duplat Simona , Gao Haijing
Published: September 2024

Pipeline erosion is a common phenomenon in various industries dealing with the transportation of fluids, especially those containing solid particles. Identifying wall thickness loss of pipes and fittings due to solid particle erosion becomes very challenging under multiphase gas-liquid flow conditions which are very common in the oil and gas industry. For instance, it is of utmost importance for operators in the oil and gas industry to make accurate predictions about the internal erosion of elbows within their systems. In this study, erosion measurements were carried out on a standard 50.8 mm (2-inch) stainless steel 316 elbow to assess mechanistic models for predicting erosion rates for elbows in vertical slug-churn flow with sand, a common occurrence in liquid-dominated production systems. Erosion experiments were performed in a large-scale multiphase flow loop, adjusting the velocities of gas (air) and liquid (water), and using particles of 75, 150 and 300 μm in size. In the experiments, superficial liquid and gas velocities ranged from 2 to 5.9 m/s and from 5.8 to 17.5 m/s, respectively. These tests were conducted in an upward vertical direction. Paint removal experiments were conducted to determine the erosion patterns and hot spots of erosion using acrylic elbows. Erosion data was collected using a non-intrusive ultrasonic technique. It was observed that the location of maximum erosion changes as the superficial velocities change. Finally, a semi-mechanistic model based on a drift-flux approach was able to predict the observed maximum erosion rates with an acceptable degree of accuracy. Comparisons with existing models in the literature are also presented.
Vortex Flow Structure Generated by an Inclined Sweeping Jet in Cross Flow
Authors: Fuchiwaki Masaki , Raghu Surya
Published: September 2024

A sweeping jet from the fluidic oscillator has attracted attention as an active flow control device in recent years. However, the flow field generated by the sweeping jet ejected into a main flow is not only the complex behaviors of the sweeping jet but also the interaction between the sweeping jet and the main flow, it is easy to consider that it will be a very complex phenomenon. However, the detailed of the vortex structure has not understood sufficiently. Three dimensional vortex structure generated by the interaction between the sweeping jet and the main flow quantitatively was investigated by the stereo PIV measurement. For Vj/V∞ = 6.0, the interaction between the sweeping jet and the main flow is not very large, and the decay of the sweeping jet causes the decay of the entire vortex structure. However, for Vj/V∞ = 2.0, the sweeping jet and the main flow strongly interact, and form a vortex flow with a main rotation component in the direction perpendicular to the main flow, instead of a linear flow in the main flow direction. From the viewpoint of separation control, the vortex structure generated for Vj/V∞ = 2.0 may be extremely effective for separation control since the sweeping jet strongly interacts with the main flow, and not only induces a vortex flow perpendicular to the main flow, but also maintains this structure continuously down the wake.
Numerical Modeling and Validation of Microbubble Enhanced HIFU for Noninvasive Tumor Ablation
Authors: Ma Jingsen , Hsiao Chao-Tsung , Deng Xiaolong
Published: September 2024

High Intensity Focused Ultrasound (HIFU) is applied in therapeutic and surgical medical interventions such as for tissue ablation in cancer treatment and in benign prostatic hyperplasia. Its application frontier has moved towards the treatment of deep-seated tumors such as in the liver and brain, but is discouraged by acoustic energy loss on the path deep into body. One promising solution is to inject microbubbles, such as ultrasonic contrast agents, in the target region to enhance target tissue heating via bubble dynamics. To accelerate the clinical transition of this noninvasive and target therapy, further understanding of microbubble-enhanced HIFU acoustic and thermal fields is essential to predict the bio-effects of the HIFU on the target tissue and its surroundings and for the development of standards to ensure the safety and efficacy of the treatments. For this purpose, a two-way coupled Euler-Lagrange computational tool, 3DYNAFSHIFU, has been developed to enable accurate characterization of acoustic and thermal fields for microbubble-enhanced HIFU. This paper summarizes the main features of its numerical algorithms for accuracy and HPC schemes for speedup, followed by its preliminary validation against in-vitro experiments and further evaluation under ex-vivo settings. This contribution spotlights the future of seeking mechanical solutions as a powerful and safe alternative to the existing chemical and/or ionizing therapies to treat tumors.
Effect of Pipe Size on Solid Particle Erosion of Elbow in Liquid-Solid Flow: Experimental and CFD Analysis
Authors: Biglari Farshad , Nadeem Asad , Hasan Mubashir , Parsi Mazdak , Karimi Soroor , Vieira Ronald , Shirazi Siamack
Published: September 2024

Solid particle erosion prediction in liquid-solid flow is inherently more complex than in gas-solid systems due to the large interactions between fluids and solids and the low Stokes number of particles. In pipelines and pipe fittings, especially in industries such as oil and gas and mining, where sand particles are commonly found in transported fluids, solid particle erosion poses a significant challenge. These abrasive particles can cause wear and damage to the walls of pipes and fittings, with elbows being particularly susceptible due to their abrupt change in flow direction.

The influence of pipe size on solid particle erosion in liquid-solid flow has been examined for elbows in series. Experiments were conducted using 50.8-mm (2-inch) and 76.2-mm (3-inch) stainless steel 316 standard elbows in a liquid-solid flow with a liquid velocity of approximately 6 m/s and volume sand concentration of around 2 percent with 300 particle size. The outcomes of this research provide valuable insights into the relationship between pipe size, comparing erosion rates and profiles, and determining the location of maximum erosion in both first and second elbows.

Notably, the study reveals that the 3-inch elbow experiences a considerably lower maximum erosion rate compared to the 2-inch elbow. Furthermore, the CFD simulations offer a deeper understanding of the underlying fluid dynamics and erosion mechanisms. This study not only investigates the specific case of pipe size but also contributes to a standardized method for more accurate CFD simulation of solid particle erosion in liquid-solid flow for elbows.
Uncertainty Analysis in Solid Particle Erosion Through Validation and Refinement of Experimental Data and Comparison With CFD
Authors: Hasan Mubashir , Biglari Farshad , Nadeem Asad , Othayq Mazen M. , Shirazi Siamack A. , Karimi Soroor
Published: September 2024

In the present work, gas-sand erosion experiments selected from the literature are repeated to study data validation. A standard 3-inch (76.2 mm) stainless steel elbow with a bend radius to pipe diameter ratio (r/D) equal to 1.5 is used. Wall thickness loss is measured using fixed-mounted Ultrasonic Transducers (UT) at 6 different locations on the outer wall of the investigated elbow. The flow conditions are gas-sand with 15, 23, and 31 m/s gas velocities and 75 and 300-μm sand particle sizes. A statistical approach of 99 percent confidence interval is utilized to find and remove the outliers in the data sets. Upper and lower bounds of erosion are presented to visualize the confidence of erosion data around the average profile. Moreover, additional experimental cases are studied to expand the range of data. These experimental conditions include 39 and 47 m/s gas velocities with 75 and 300-μm sand particle sizes. In the next step, the erosion data variance is calculated at different angles on the outer wall of the elbows before and after applying the uncertainty analysis. It is seen that by applying the uncertainty analysis, the variance of the experimental erosion values is reduced by a range of 20 to 99 %. The experimental erosion profiles along the outer wall of the elbow are compared with erosion profiles obtained from CFD (Computational Fluid Dynamics) performed for similar conditions. CFD contours of erosion are in agreement with the average erosion profile obtained from the experimental data.
Investigating the Influence of Mutual Orientation Between Heat Flux and Gravity on the Melting Dynamics of Phase Change Material
Authors: Kansara Keyur , Singh Shobhana , Dwivedi Navin K. , Khodachenko Maxim L.
Published: September 2024

The present work employs numerical simulations, using Rayleigh-Bénard (RB) convection as a platform, to investigate the influence of different orientations of the gravity vector and heat flux on the melting dynamics of a Phase Change Material (PCM). A paraffin-based PCM with Prandtl number Pr ≈ 71 and Stefan number Ste ≈ 0.33 is utilized to analyze the melting process over a wide range of Rayleigh numbers (102 ≤ Ra ≤ 107). The simulations are conducted in a differentially heated square enclosure, employing the control volume-based enthalpy porosity approach to examine the melting process at various angles between the gravity vector and the incoming heat flux. The results demonstrate that the mutual orientation of the incoming heat flux and gravity significantly affects features of convective motion in the liquid phase and the overall thermally driven heat transfer within the PCM. Specifically, when gravity and heat flux are oppositely directed, the melted fluid exhibits characteristics resembling RB convection, including flow instabilities, bifurcations, structured flow patterns, and chaotic flow behavior. However, a critical orientation angle exists above which melting occurs with a rotational convective motion of the liquid PCM, and the flow remains laminar throughout. In the case of co-directed gravity and heat flux, melting occurs solely through diffusion without the formation of convection currents. This work aims to explore potential changes in flow phenomena, establish criteria for the onset of instabilities, map changes in interface topology, elucidate complexities of nonlinear flow dynamics, and draw comparisons with classical RB systems. In summary, the present study provides comprehensive insights into the dynamics and stability criteria of a phase-change RB system across a broad range of Rayleigh numbers at different mutual orientations between heat flux direction and gravity vector.
Design and Development of Test-Rig for Experimental Study of Flow Field Associated With Supersonic Retro Propulsion
Authors: May Melissa , Thorman Conrad , Ruud Jace , Carolan Mitchell , Wollman Annaliese , Lemmon Braydon , McNeil Carsten , Thalakkottor Joseph
Published: September 2024

Propelling future human landings on Mars involves a groundbreaking powered descent phase from supersonic conditions, a novel approach in Martian missions. The challenges arising from interactions among retrorocket engine plumes, freestream flow, and the descending vehicle present significant hurdles, impacting aerodynamic behavior during descent. While full-scale flow field simulations have been conducted computationally, existing ground and flight data lack adequacy for calibrating uncertainties in aerodynamic interference for proposed Mars descent vehicles. To address this, a wind tunnel test apparatus is designed to assess powered descent aerodynamics for large-scale human Mars entry concepts, aiming to identify gaps in computational predictive capabilities. Conducted in the South Dakota Mines’s Unsteady Supersonic Wind Tunnel, the test apparatus utilizes a sub-scale model with a 70-degree spherical cone resembling the heat shield of a low lift-to-drag vehicle. The blunt model allows exploration of nozzle plume direction, number, location, size, and area ratio effects. The study will be conducted for varying degrees of pitch, yaw, and roll. Key measurements include heatshield aerodynamic forces, discrete, and distributed pressure, and high-speed flow field visualization using Schlieren imaging. This paper comprehensively addresses the design and development of the test apparatus.
PIV and High-Speed Imaging Investigation of Falling Liquid Droplet Properties
Authors: Azimy Noushin , Lichty Emmelia , Anderson Keldon , Karimi Soroor
Published: September 2024

Liquid droplet impact is a subject that has been investigated in both engineering and non-engineering applications to understand and to control this phenomenon. Spray cooling, inkjet printing, spray coating and painting, soil erosion prevention, pesticide application, and impact erosion are merely a few examples in which droplet impact is involved. Erosion caused by droplet impact on a solid surface is important in numerous elements of industrial equipment, such as pipelines, steam turbines, and wind turbine blades. Though experimental and modeling studies have been performed on this topic, most failed to perform quantitative investigation especially when it came to the erosion of wind turbine blades. Moreover, most approaches assume that the impacting droplets are completely spherical and unaffected by any local turbulence or vortex shedding. As the droplet erosion process could be affected by several parameters, such as the impact velocity, shape and size of the droplets, this study focuses on investigating droplet properties and movement in a controlled lab environment. High speed imaging and Particle Image Velocimetry (PIV) methods are used for this purpose. PIV is used to measure the velocity, circularity, and size of the falling droplets in both disturbed and un-disturbed flow conditions. High-speed camera imaging provides additional insight to the path of the droplets’ movement in the presence of any turbulence. Experiments are performed at a variety of flow rates utilizing a range of blunt needle gauge sizes to create different droplet sizes. It is observed that the blunt needles produce a train of droplets that are different in size following each leading droplet. This is a crucial observation as it will have a direct impact on the magnitude of erosion and should be considered in the future modeling efforts.
Partial Jet Cutting and Torque Evaluation on Cut-In Jet Deflector for Pelton Turbine
Authors: Khan Firoz , Kumar Arun , Staubli Thomas
Published: September 2024

Deflectors of Pelton turbine divert the jet completely and prevent the turbine from going to run away speed in case of load rejection. Moreover, partial cutting of the jet using cut-in jet deflector plays a role in fast controlling of power and the associated positive effect on the stabilization of the electrical grid. During this control operation cut-in jet deflectors are subjected to forces and torques which must be handled by the servomotor. Therefore, experimental measurements at different angular positions of the cut deflector are required to determine the torque for the design of the deflector and its servomotor. During the partial jet cutting the jet quality is also important as the remaining jet has to impact the Pelton runner for active power generation. In this study, an experimental investigation was carried out using a torque transducer. In addition, CFD simulations were conducted to observe the flow behavior of the jet during cutting. It is observed that the torque acting on the cut-in jet deflector increases with increasing the jet cutting angle but shows a decreasing tendency after reaching the maximum value. At lower jet cutting angles of 3° and 6°, the jet remains nearly straight, indicating minimal deviation.
Athlete Sleep Screening Questionnaire in Japanese: Adaptation and Validation Study
Authors: Tsukahara Yuka , Kodama Satoshi , Kikuchi Saaya , Day Carly
Published: September 2024

Context: General screening methods for athletes are limited. This study aims to analyze the reliability and validity of the Japanese version of the athlete sleep screening questionnaire. Methods: In total, 111 female collegiate athletes completed the initial test and retest. The independent variables included the kind of sports of the participants and their athletic level, grade (freshman, sophomore, junior, and senior), and age. The reliability of the questionnaire was assessed using Cronbach’s alpha and intraclass correlation coefficients. Athletes competing in team sports and individual sports were compared to evaluate for differences. Results: A total of 38.7% of athletes had moderate to severe sleep difficulty score. Their Cronbach’s alpha for test and retest were .34 and .44, respectively. The intraclass correlation coefficient indicated sufficient internal consistency and test–retest validity. The mean sleep difficulty scores were 7.0 (2.3) and 6.5 (2.1) for test and retest, but no significant difference was observed between the individual and team sport athletes. Results of multivariable regression analysis revealed that having sleep and performance issues during travel was related to sleep difficulty scores (Coef 1.44, P < .01). Conclusions: Athletes of all levels have sleep disorders. The Japanese version of athlete sleep screening questionnaire has been validated with sufficient test–retest validity but has poor internal consistency. Thus, although Japanese version of the athlete sleep screening questionnaire is an appropriate questionnaire for assessing sleep disorders in athletes whose primary language is Japanese, future research is needed to optimize the questionnaire accounting for cultural variation.
A high content imaging assay for identification of specific inhibitors of native
Plasmodium
liver stage protein synthesis
Authors: McLellan James L. , Morales-Hernandez Beatriz , Saeger Sarah , Hanson Kirsten K.
Published: September 2024

Plasmodium
parasite resistance to antimalarial drugs is a serious threat to public health in malaria-endemic areas. Compounds that target core cellular processes like translation are highly desirable, as they should be capable of killing parasites in their liver and blood stage forms, regardless of molecular target or mechanism. Assays that can identify these compounds are thus needed. Recently, specific quantification of native
Plasmodium berghei
liver stage protein synthesis, as well as that of the hepatoma cells supporting parasite growth, was achieved via automated confocal feedback microscopy of the o-propargyl puromycin (OPP)-labeled nascent proteome, but this imaging modality is limited in throughput. Here, we developed and validated a miniaturized high content imaging (HCI) version of the OPP assay that increases throughput, before deploying this approach to screen the Pathogen Box. We identified only two hits; both of which are parasite-specific quinoline-4-carboxamides, and analogs of the clinical candidate and known inhibitor of blood and liver stage protein synthesis, DDD107498/cabamiquine. We further show that these compounds have strikingly distinct relationships between their antiplasmodial and translation inhibition efficacies. These results demonstrate the utility and reliability of the
P. berghei
liver stage OPP HCI assay for the specific, single-well quantification of
Plasmodium
and human protein synthesis in the native cellular context, allowing the identification of selective
Plasmodium
translation inhibitors with the highest potential for multistage activity.
The increase of particle size shifts the biogeochemical cycle functions of mineral-associated microorganisms and weakens the mineral-associated organic carbon sink in mangrove soils
Authors: Zhang Yixuan , Xia Ziqin , Zuo Yaqiang , Ding Junjie , Wang Jianxin , Qu Wu
Published: September 2024

Mineral-organic matter–microbe interactions greatly impact the biogeochemical processes and biodiversity in soils. An increasing trend of particle size (PS) in mangrove soils has been observed because of the relative sea level rise. However, the impacts of PS increase on the microbial biogeochemical functions and carbon sink in the mineral-associated microcosms are exceedingly nebulous. This work showed a remarkable difference in the communities of mineral-associated microorganisms (MMOs) in various PS fractions. Heavy metal contents and urease activity were the factors that mostly driven the MMO community variation in different PS fractions. Large PS fraction attenuated the stability of MMO communities according to the co-occurrence network characteristics. The PS increase significantly (
P
< 0.05) lowered the gene abundances for carbon input (e.g., carbon fixation) and raised the gene abundances for carbon loss (e.g., aerobic respiration). Combined with the significant decrease of mineral-associated organic carbon (MOC) in large PS fraction (
P
< 0.05), this work inferred that the PS increase could weaken the MOC sink partially due to the MMO function shift for carbon cycle. The current work indicated unhealthy changes of MMO communities and MOC storage in mangrove soils, and PS was of significance as an indicator for predicting the carbon sink function, especially for the stable form, such as MOC, in the soils of mangroves under the ecological background of climate migration.

IMPORTANCE

Carbon with stable forms, such as mineral-associated organic carbon (MOC), is crucial for the sink capabilities in mangrove soils, and mineral-associated microorganisms (MMOs) are important players for the formation and metabolism of MOC. Therefore, the future successions of the MMO functions and MOC contents under the background of climate change are of value for a deeper understanding of mangrove ecology. The relative sea level rise caused by the global warming results in the increase of mangrove soil particle size (PS), which provides distinct microcosms for MMOs and MOC. However, the responses of MMO functions and MOC content to the PS increase of mangrove soils are unknown. The current study aims to reveal the succession regulations of MMO functions and their potential ecological impacts for the storages of MOC in different PS fractions, therefore widening our knowledge of future function migration and promoting the research development of mangrove.
PROPEL: a scalable model for postbaccalaureate training to promote diversity in the biomedical workforce
Authors: Allen Jessica , Abdiwahab Ekland , Morris Meghan D. , Le Saux Claude Jourdan , Betancur Paola , Ansel K. Mark , Hernandez Ryan D. , Nystul Todd G.
Published: September 2024

Promoting diversity in the scientific workforce is crucial for harnessing the potential of available talent and ensuring equitable access to Science, Technology, Engineering, Mathematics, and Medicine (STEM-M) careers. We have developed an innovative program called Postbaccalaureate Research Opportunity to Promote Equity in Learning (PROPEL) that provides scientific and career development training for postbaccalaureate scholars from historically excluded backgrounds in STEM-M fields with an interest in pursuing a PhD or MD/PhD degree. Our program is distinct from other postbaccalaureate programs in that scholars are hired by individual labs rather than funded centrally by the program. This funding mechanism removes the idea that central funding is necessary to encourage faculty to train diverse scholars and allows the program to scale dynamically according to the needs of the scientific community. The PROPEL program started in 2020 with six scholars and has since grown to an enrollment of over 100, making it the largest postbaccalaureate program for biomedical research in the country. Here, we describe the program structure and curriculum, our strategy for recruitment, the enrollment trends, the program demographics, metrics of scholar engagement, and outcomes for scholars who completed the program in 2023. Our experience demonstrates the strong demand from both scholars and faculty for programming of this type and describes the feasibility of implementation.
Batf3-cDC1 control Th1 and fungicidal responses during cryptococcal meningitis: is this enough to control meningitis?
Authors: Coelho Carolina
Published: September 2024

Dendritic cells are crucial for bridging innate and adaptive immunity. Cryptococcosis, caused by
Cryptococcus neoformans
and
Cryptococcus gattii
, is responsible for >15% of AIDS-related deaths. A recent study by Xu et al. showed that
Batf3
-dependent conventional type 1 dendritic (cDC1) cells are key players in generating IFNγ
+
CD4
+
T cell and fungicidal lung and brain tissue-resident responses during murine cryptococcosis, contributing to fungal clearance in the lungs and brain of mice (J. Xu, R. Hissong, R. Bareis, A. Creech, et al., mBio 15:e02853-23, 2024,
https://doi.org/10.1128/mbio.02853-23
). However, despite their critical role, the depletion of
Batf3
-dependent cDC1 cells did not significantly alter overall mouse survival or disease progression, highlighting the complex immune regulation required to survive cryptococcal infection and the need for further research in medical mycology.
Posttranslational modifications: an emerging functional layer of diet-host-microbe interactions
Authors: Duchovni Lirit , Shmunis Genrieta , Lobel Lior
Published: September 2024

The microbiome plays a vital role in human health, with changes in its composition impacting various aspects of the body. Posttranslational modification (PTM) regulates protein activity by attaching chemical groups to amino acids in an enzymatic or non-enzymatic manner. PTMs offer fast and dynamic regulation of protein expression and can be influenced by specific dietary components that induce PTM events in gut microbiomes and their hosts. PTMs on microbiome proteins have been found to contribute to host-microbe interactions. For example, in
Escherichia coli
, S-sulfhydration of tryptophanase regulates uremic toxin production and chronic kidney disease in mice. On a broader microbial scale, the microbiomes of patients with inflammatory bowel disease exhibit distinct PTM patterns in their metaproteomes. Moreover, pathogens and commensals can alter host PTM profiles through protein secretion and diet-regulated metabolic shifts. The emerging field of metaPTMomics focuses on understanding PTM profiles in the microbiota, their association with lifestyle factors like diet, and their functional effects on host-microbe interactions.
Taxonomy of
Pseudomonas
spp. determines interactions with
Bacillus subtilis
Authors: Lyng Mark , Þórisdóttir Birta , Sveinsdóttir Sigrún H. , Hansen Morten L. , Jelsbak Lars , Maróti Gergely , Kovács Ákos T.
Published: September 2024

Bacilli and pseudomonads are among the most well-studied microorganisms commonly found in soil and frequently co-isolated. Isolates from these two genera are frequently used as plant beneficial microorganisms; therefore, their interaction in the plant rhizosphere is relevant for agricultural applications. Despite this, no systematic approach has been employed to assess the coexistence of members from these genera. Here, we screened 720 fluorescent soil isolates for their effects on
Bacillus subtilis
pellicle formation in two types of media and found a predictor for interaction outcome in
Pseudomonas
taxonomy. Interactions were context-dependent, and both medium composition and culture conditions strongly influenced interactions. Negative interactions were associated with
Pseudomonas capeferrum
,
Pseudomonas entomophila
, and
Pseudomonas protegens
, and 2,4-diacetylphloroglucinol was confirmed as a strong (but not exclusive) inhibitor of
B. subtilis
. Non-inhibiting strains were closely related to
Pseudomonas trivialis
and
Pseudomonas lini
. Using such a non-inhibiting isolate,
Pseudomonas
P9_31, which increased
B. subtilis
pellicle formation demonstrated that the two species were spatially segregated in cocultures. Our study is the first one to propose an overall negative outcome from pairwise interactions between
B. subtilis
and fluorescent pseudomonads; hence, cocultures comprising members from these groups are likely to require additional microorganisms for coexistence.

IMPORTANCE

There is a strong interest in the microbial ecology field to predict interaction among microorganisms, whether two microbial isolates will promote each other’s growth or compete for resources. Numerous studies have been performed based on surveying the available literature or testing phylogenetically diverse sets of species in synthetic communities. Here, a high throughput screening has been performed using 720
Pseudomonas
isolates, and their impact on the biofilm formation of
Bacillus subtilis
was tested. The aim was to determine whether a majority of
Pseudomonas
will promote or inhibit the biofilms of
B. subtilis
in the co-cultures. This study reports that
Pseudomonas
taxonomy is a good predictor of interaction outcome, and only a minority of
Pseudomonas
isolates promote
Bacillus
biofilm establishment.
A specific and ultrasensitive Cas12a/crRNA assay with recombinase polymerase amplification and lateral flow biosensor technology for the rapid detection of
Streptococcus pyogenes
Authors: Cheng Yu , Lyu Jiawen , Han Jiangfeng , Feng Long , Li Xiangmei , Li Pei , Zhang Shanfeng , Zang Wenqiao
Published: September 2024

The potential of CRISPR/Cas systems for nucleic acid detection in novel biosensing applications is remarkable. The current clinical diagnostic detection of
Streptococcus pyogenes
(
S. pyogenes
) is based on serological identification, culture, and PCR. We report a rapid, simple, and sensitive method for detecting and screening for
S. pyogenes
. This novel method is a promising supplemental test. After 10 min of the sample processing and 10 min of recombinase polymerase amplification, followed by 10 min of Cas12 reaction and 3 min of lateral flow biosensor (LFB) readout, a visible outcome can be observed without the need for magnification within 33 min. This platform is robust, inexpensive, and appropriate for on-site testing. A new technique for detection was created using CRISPR-Cas12a technology, which includes two measurements: a fluorescent-CRISPR-
S. pyogenes
test and a LFB-CRISPR-
S. pyogenes
test. An approach utilizing CRISPR Cas12a was developed, and the accuracy and precision of this technique were assessed. The LoD for the fluorescence-CRISPR-
S. pyogenes
assay was 1 copy/μL, and the technique effectively differentiated
S. pyogenes
from other microorganisms. Moreover, the detection outcomes were presented in a user-friendly manner using lateral flow biosensor strips. Conclusion: A rapid and sensitive Cas12a/crRNA assay using recombinase RPA and LFB was developed to detect
S. pyogenes
. The Cas12a/crRNA-based assay exhibited high specificity among different bacteria strains and extremely high sensitivity. The accuracy and rapidity of this method make it a promising tool for
S. pyogenes
detection and screening.

IMPORTANCE

Patients may experience a range of symptoms due to
Streptococcus pyogenes
infections, including superficial skin infections, pharyngitis, and invasive diseases in subcutaneous tissues like streptococcal toxic shock syndrome. At present, the clinical diagnostic detection of
S. pyogenes
is based on serological identification, culture, and PCR. These detection methods are time-consuming and require sophisticated equipment, making these methods challenging for routine laboratories. Thus, there is a need for a detection platform that is capable of quickly and accurately identifying
S. pyogenes
. In this study, a rapid and sensitive Cas12a/crRNA assay using recombinase RPA and LFB was developed to detect
S. pyogenes
. The Cas12a/crRNA-based assay exhibited high specificity among different bacteria strains and extremely high sensitivity. This method probably plays an important role for
S. pyogenes
detection and screening.
Phenotypic and genomic comparison of three human outbreak and one cattle-associated Shiga toxin-producing
Escherichia coli
O157:H7
Authors: Peroutka-Bigus Nathan , Nielsen Daniel W. , Trachsel Julian , Mou Kathy T. , Sharma Vijay K. , Kudva Indira T. , Loving Crystal L.
Published: September 2024

Escherichia coli
O157:H7-adulterated food products are associated with disease outbreaks in humans. Although cattle feces are a source for
E. coli
O157:H7 contamination, it is unclear if human-associated outbreak isolates differentially colonize and shed in the feces of cattle from that of non-outbreak isolates. It is also unclear if phenotypes, such as biofilm formation, cell attachment, or toxin production, differentiate environmental
E. coli
O157:H7 isolates from those associated with human illness. The objective of this study was to compare the genotypes and phenotypes of a diverse set of
E. coli
O157:H7 isolates, with the intent of identifying differences that could inform cattle colonization and fecal shedding, along with virulence potential in humans. Isolates differed in attachment phenotypes on human Caco-2 cells and bovine-derived recto-anal junction squamous epithelial cells, with curli having a strong impact on attachment to the human-derived cell line. The prototypical
E. coli
O157 isolate EDL933 had the greatest expression of the adhesin gene
iha
, yet it had decreased expression of the virulence genes
stx2
,
eae
, and
ehxA
compared the lineage I/II isolates RM6067W and/or FRIK1989. Strong or weak biofilm production was not associated with significant differences in cattle colonization or shedding, suggesting biofilms may not play a major role in cattle colonization. No significant differences in cattle colonization and fecal shedding were detected, despite genomic and
in vitro
phenotypic differences. The outbreak isolate associated with the greatest incidence of hemolytic uremic syndrome, RM6067W, induced the greatest Vero cell cytotoxicity and had the greatest
stx2
gene expression.

IMPORTANCE

Foodborne illness has major impacts on global health and imposes financial hardships on food industries.
Escherichia coli
serotype O157:H7 is associated with foodborne illness. Cattle feces are a source of
E. coli
O157:H7, and routine surveillance has led to an abundance of
E. coli
O157:H7 genomic data. The relationship between
E. coli
O157:H7 genome and phenotype is not clearly discerned for cattle colonization/shedding and improved understanding could lead to additional strategies to limit
E. coli
O157:H7 in the food chain. The goal of the research was to evaluate genomic and phenotypic attributes of
E. coli
O157:H7 associated with cattle colonization and shedding, environmental persistence, and human illness. Our results indicate variations in biofilm formation and
in vitro
cellular adherence was not associated with differences in cattle colonization or shedding. Overall, processes involved in cattle colonization and various phenotypes in relation to genotype are complex and remain not well understood.
The timing and duration of large-scale carbon release in the Early Jurassic
Authors: Kemp David B. , Ramezani Jahandar , Izumi Kentaro , Al-Suwaidi Aisha , Huang Chunju , Chen Wenhan , Zhu Yuqing
Published: September 2024

The Toarcian oceanic anoxic event (T-OAE, ca. 183 Ma) in the Early Jurassic was one of the most significant warming events of the Phanerozoic, associated with large-scale carbon emissions, mass extinction, and perturbations to hydrology and ocean chemistry. However, the age and duration of this hyperthermal have long been uncertain, hindering our understanding of the timing and pace of carbon release and the associated environmental and biotic changes. We present high-precision radioisotopic dates bracketing a biostratigraphically constrained record of the T-OAE in Japan. Our geochronology reveals an unexpectedly short T-OAE duration of ∼300 k.y. and a temporal coincidence with Ferrar large igneous province (LIP) magmatism. Our dates refute previous work linking the T-OAE to the earlier Karoo LIP, which was coincident with an earlier carbon cycle perturbation at the Pliensbachian–Toarcian boundary. Our results suggest both events were driven by extremely rapid (perhaps sub-millennial scale) thermogenic carbon degassing during LIP sill intrusion.
Comparative efficacy of pharmacological and non-pharmacological interventions for mitigating pain and anxiety associated with venipuncture: a randomised controlled trial
Authors: Suleman Sherzad Khudeida , Yahya Nizer , Nilsson Stefan , Enskär Karin
Published: September 2024

Background

Venipuncture is one of the most commonly performed medical procedures in paediatric care, but it can also be one of the most painful and distressing experiences for patients. Finding effective strategies to manage pain and fear associated with venipuncture is crucial for improving the paediatric patient experience and promoting positive health outcomes. This study aimed to evaluate the efficacy of a combined approach using a topical analgesic cream (TKTX cream) and a distraction technique (Trace Image and Colouring for Kids-Book, TICK-B) in reducing pain intensity and fear levels in children undergoing venipuncture procedures.

Methods

We conducted this randomised controlled trial among 176 children aged 6–12 years undergoing venipuncture. Participants were randomly assigned to four groups: TICK-B, TKTX cream, TICK-B+TKTX cream and a control group. Pain and fear were measured using the Wong-Baker FACES Pain Rating Scale and Children’s Fear Scale. The study was carried out from 20 February 2024 to 1 June 2024 at the emergency unit of Heevi paediatric teaching hospital in the Kurdistan region of Iraq. In the intervention groups, TICK-B was applied for 2–3 min before needle insertion, and TKTX cream was applied 20 min before the venipuncture procedure. All outcome measures were evaluated 2–3 min after the completion of the venipuncture procedure.

Results

The combined TICK-B (colouring book) and TKTX cream (topical anaesthetic) intervention was the most effective in reducing both pain intensity (mean score 2.80 vs 7.24 in the control, p<0.001) and fear levels (mean score 0.93 vs 2.83 in the control, p<0.001) during and after venipuncture procedures compared with individual interventions and control.

Conclusions

The combined TICK-B distraction and TKTX cream topical anaesthetic intervention was the most effective in reducing pain intensity and fear during and after venipuncture in children, providing a practical strategy for healthcare providers to optimise needle procedure management.

Trial registration number

NCT06326125.
Pancreatic incidentaloma: incidental findings from history towards the era of liquid biopsy
Authors: Löhr J-Matthias , Vujasinovic Miroslav , Kartalis Nikolaos , Osten Philipp
Published: September 2024

This report provides an overview of the most common diagnostic methods that bring to light incidental findings of pancreatic cancer. It reviews the impact of medical imaging and genetic assessment on the definitions of incidental findings and incidentaloma of the pancreas. For different diagnostic approaches (eg, MRI and CT) and for different affections (cysts/intraductal papillary mucinous neoplasia, solid lesions), specific guidelines have been proposed and some are established. Based on this, we summarise the differences between the traditional methods with those applied in the PANCAID project. Biomarkers, genetic predispositions, mutations and circulating tumour cells give rise to different levels of concern. The final part of the report discusses the risks and the opportunities associated with further diagnostic procedures and surgical interventions. From the ethical perspective, the most urging question is, can a screening based on liquid biopsy and blood samples open a gateway for the prevention of pancreatic cancer—even if morbidity and lethality of today’s surgical interventions is still very high?
Genome-wide association studies for growth and feed efficiency traits in American mink
Authors: Davoudi Pourya , Do Duy Ngoc , Rathgeber Bruce , Colombo Stefanie , Sargolzaei Mehdi , Plastow Graham , Wang Zhiquan , Miar Younes
Published: September 2024

The objective of this study was to identify potential genetic variants and positional candidate genes associated with growth and feed efficiency traits in American mink. Genome-wide association studies (GWAS) were performed using deregressed estimated breeding values of 1037–1872 individuals (as pseudophenotypes), genotyped with the Affymetrix Mink 70K single nucleotide polymorphism (SNP) array. A total of 42 SNPs located on 11 different chromosomes were significantly (false discovery rate < 0.01) associated with six growth and feed efficiency traits. Furthermore, 153 genes were identified within 1-Mb windows flanking these significant SNPs. Several positional candidate genes such as TUBB, CDKN1A, SRSF3, GPRC6A, RFX6, and KPNA5 were previously associated with feed efficiency and growth traits in other livestock species. The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses revealed that these genes were involved in lipid metabolism, hormone signaling and regulation, and muscle development. To our knowledge, this is the first GWAS to identify genetic variants and biological mechanisms associated with growth and feed efficiency traits in American mink. These findings provide a biological foundation for improving these traits using genomic selection programs to select more efficient mink.
Tracking the trajectory of frankia research through bibliometrics: trends and future directions
Authors: Mhamdi Ridha , Gtari Maher
Published: September 2024

Frankia represent a unique group of filamentous, sporangia-forming bacteria, renowned for their exceptional capacity to establish symbiotic partnerships with actinorhizal plants. The objective of this paper is to offer quantitative insights into the current state of frankia research and its future potential. A comprehensive bibliometric analysis covering the years 2000–2022 was conducted using Scopus and SciVal. A steady increase in both annual publication and international collaboration has been observed, particularly since 2013. Research performance metrics for the last 5 years (2018–2022) indicate China and India as leaders with high Field-Weighted Citation Impact scores. This analysis highlighted prominent authors, research groups, and the evolving research landscape, suggesting an increasing focus on molecular and genomic aspects. The genomic era has transformed our understanding of frankia biology, highlighting their significance in diverse ecological and agricultural contexts. This study comprehensively maps the evolving landscape of frankia research, emphasizing key milestones that have catalysed international interest in frankia–actinorhizal research, expanding our perception of frankia’s capabilities beyond its traditional symbiotic role. As research in this field progresses, a deeper comprehension of frankia–plant interactions, symbiotic signalling, and the intricacies of metabolic pathways holds the promise of revealing innovative techniques for optimizing nitrogen fixation and broadening the spectrum of host plants.