bluuebunny/crossref_metadata_2025_split huggingface dataset:
Numerical Simulation of Phase Change Dual-Phase-Lag Bioheat Model With Nanocryosurgery Using Radial Basis Function Meshfree Approach
Authors: Verma Rohit , Kalita Jiten C. 
Published: January 2025

Abstract
The current study is concerned with the numerical simulation of the phase change process in a two-dimensional (2D) dual-phase-lag (DPL) bioheat model applied to nanocryosurgery. A Gaussian radial basis function (RBF) meshfree approach coupled with a Crank–Nicolson type of time discretization is employed on an irregular soft tissue domain. The simulation considers the introduction of three types of nanoparticles (NPs)—gold, alumina oxide, and iron oxide into the cryosurgical process. Temperature profiles were computed for situations both with and without the incorporation of nanoparticles, and the freezing interface was analyzed under different conditions. The results demonstrate the significant influence of nanoparticles on enhancing the freezing process, leading to a more controlled and effective cryoablation. The inclusion of nanoparticles not only accelerates the freezing front but also provides a more uniform temperature distribution within the target tissue. This study highlights the advantages of using a meshfree RBF approach in handling complex geometries, alongside the potential of nanoparticle-enhanced cryosurgery to improve clinical outcomes. These findings contribute valuable insights into the optimization of cryosurgical techniques and the development of more effective cancer treatments.
Effect of Variable Angular Piping Bends Geometry on Turbulent Flow of Supercritical Water in an SCWR Plant Piping Network: A Three-Dimensional Computational Fluid Dynamics Investigation
Authors: Khan Mohammad , Haque Jehad , Islam Saad , Putul Lubon , Hasan Mehedi 
Published: January 2025

Abstract
One of the most critical components of super critical water reactor (SCWR) plant is pipe bend, carrying massive volume of supercritical water. Because of its intense fluctuation of velocity and pressure, it can exhibit unusual flow pattern in pipe bends conveying fluid. This unusual flow pattern may destroy the integrity of the piping network. Alternatively, because of unique chemical and physical properties, transportation of SCW can adversely effect on the integrity of the pipe bends, indicating probable failure of piping network. Therefore, intensive studies of SCW flow in bends are a must as a part of designing an efficient plant piping network. This article presents CFD analysis, carried out to examine the effect of variable pipe bend angle (90 deg, 120 deg, and 135 deg) on turbulent flow of SCW. The analysis indicates that the portion of the straight inlet pipe with fully developed flow shows no variation of results in all bend configurations. The study also reveals that secondary currents strengthen at lower bend angles and culminate the formation of vertices at the outlet of the right-angled elbow. It is found from the study that a greater part of the cross-sectional area is covered by the vortices at the bend midplanes compared to the bend outlets, where mixing of stream wise flow occurs as well. It is revealed that the radial positions of each vortex center are closer to the circumference of the pipe, and appear to be insensitive to bend angle. The study is ended with the comparison between supercritical water and normal water at standard conditions.
Temporal dynamics of airborne fungi in Swedish forest nurseries
Authors: Larsson Rebecca , Menkis Audrius , Olson Åke 
Published: January 2025

ABSTRACT

In Sweden, reforestation of managed forests relies predominantly on planting nursery-produced tree seedlings. However, the intense production using containerized cultivation systems (e.g., high seedling density, irrigation from above, regular fertilization) creates favorable conditions for fungal infections. Despite the harmful role of diseases in forest nurseries, the origin and dispersal factors of fungal pathogens remain largely unknown. A better understanding of the airborne spread of pathogens could improve the prediction of fungal infection, ultimately optimizing preventative methods and decreasing the use of fungicides. This study investigated the temporal dynamics of airborne fungi in forest nurseries, with a focus on fungal pathogens. Airborne fungi were monitored in four Swedish forest nurseries over two growing seasons using spore traps and high-throughput sequencing. Fungal pathogens were identified using bioinformatics and quantified with quantitative PCR. Results showed strong temporal shifts of airborne fungal diversity and community composition following the growing seasons. The airborne spread included high abundances of important fungal pathogens (e.g.,
Cladosporium
sp.,
Botrytis cinerea
,
Alternaria
sp.,
Sydowia polyspora
, and
Melampsora populnea
) with individual temporal and spatial variations. In general, the deposited spore loads of nursery pathogens correlated positively with increased temperature and negatively with higher precipitation. This was expressed the strongest for
Cladosporium
sp.,
Alternaria
sp., and
M. populnea
, which suggests a higher availability of fungal inoculum in warm and dry periods. This study highlights the influence of seasonality on the temporal dynamics of economically important fungal pathogens in Swedish forest nurseries, which should be considered in the development of a local decision support system.

IMPORTANCE
Fungal diseases in forest nurseries have significant environmental and economic impacts on the tree seedling production. This study highlights the role of seasonality in the airborne spread of fungal pathogens in Swedish forest nurseries. By analyzing airborne fungal spores using advanced sequencing and monitoring techniques, key fungal pathogens and their dispersal patterns over two growing seasons were identified. The findings indicate that warmer, drier periods may increase the spread of fungal pathogens, emphasizing the need for targeted preventative measures. Understanding these temporal dynamics can help optimize the use of fungicides in forest nurseries, thereby promoting more sustainable and environmentally friendly management practices. This research provides valuable insights for improving disease management in forest nurseries, ultimately supporting sustainable tree seedling production.
Shewanella
is a putative producer of polyunsaturated fatty acids in the gut soil of the composting earthworm
Eisenia fetida
Authors: Wittlinger Jan-Philpp , Castejón Natalia , Hausmann Bela , Berry David , Schnorr Stephanie L. 
Published: January 2025

ABSTRACT

Polyunsaturated fatty acids (PUFAs) play a crucial role in aiding bacteria to adapt to extreme and stressful environments. While there is a well-established understanding of their production, accrual, and transfer within marine ecosystems, knowledge about terrestrial environments remains limited. Investigation of the intestinal microbiome of earthworms has illuminated the presence of PUFAs presumably of microbial origin, which contrasts with the surrounding soil. To comprehensively study this phenomenon, a multi-faceted approach was employed, combining fatty acid analysis with amplicon sequencing of the PfaA-KS domain of the anaerobic fatty acid synthase gene (
pfa
), as well as the 16S rRNA and 18S rRNA genes. This methodology was applied to scrutinize the gut microbiome of
Eisenia fetida
, its compost-based dietary source, and the resultant castings. This study unveiled a distinct gut soil ecosystem from input compost and output castings in fatty acid profile as well as type and abundance of organisms. 16S sequencing provided insights into the microbial composition, showing increased relative abundance of certain Pseudomonadota, including
Shewanellaceae
, and Planctomycetota, including
Gemmataceae
within the gut microbiome compared to input bulk soil compost, while Actinomycetota and Bacillota were relatively enriched compared to the casted feces. Sequencing of the PfaA-KS domain revealed amplicon sequence variants (ASVs) belonging primarily to
Shewanella
. Intriguingly, the 20C PUFAs were identified only in gut soil samples, though PfaA-KS sequence abundance was highest in output castings, indicating a unique metabolism occurring only in the gut. Overall, the results indicate that
Shewanella
can explain PUFA enrichment in the gut environment because of the
pfa
gene presence detected
via
PfaA-KS sequence data.

IMPORTANCE

Prior research has demonstrated that earthworm microbiomes can potentially harbor polyunsaturated fatty acids (PUFAs) that are not found within their residing soil environment. Moreover, distinct indicator species have been pinpointed for various microbial genera in earthworm microbiomes. Nevertheless, none of these studies have integrated metataxonomic and fatty acid analyses to explore the origin of PUFA synthesis in any earthworm species, with the objective of identifying the specific organisms and locations responsible for this production. This study suggests that earthworms accumulate PUFAs produced from bacteria, especially
Shewanella,
activated through the gut ecosystem.
Adaptation of clinical bacteriology techniques for remote polar research
Authors: Pallett Scott J. C. , Kwok Bill K. , Wong Stephanie M. Y. , Moore Luke S. P. 
Published: January 2025

ABSTRACT

Remote polar regions offer unique opportunities and significant challenges for antimicrobial resistance research in a near-pristine environment. While core microbiology techniques continue to have an important role in supporting environmental research, the severe cold climate presents considerable challenges to laboratory research. We explore adaptations required for core bacteriology investigations in polar regions on an unsupported remote expedition c. 600 km north of the Arctic Circle utilizing the National Collection of Type Culture bacterial strains. Methods of culture, microscopy, biochemical and phenotypic testing, vortex, and centrifuge techniques are explored. Across −21.5 to −41.0°C, culture was satisfactorily enabled using a solar-powered USB incubator and an electricity-free water-bath option utilizing white gas for a variety of standard culture media. Microscopy and biochemical tests supported organism identification. Phenotypic testing for carbapenemase-producing genes using lateral flow devices showed good performance without modification (Carba-5, 20/20 carbapenemase-producing organism tests, 100% sensitivity; 100/100 negative targets, 100% specificity). The modified centrifuge was enabled with a 3D printed disk and Dremel drill and microbial DNA extraction (ZymoBIOMICS) kits were able to extract DNA of suitable quality for analysis. With suitable adaptations, conducting core microbiology techniques (with potential relevance for more advanced techniques) is possible in the remote extreme cold environment.

IMPORTANCE
Antimicrobial resistance (AMR) represents one of the key global public health threats currently facing humanity. The recent UN High-Level Meeting on AMR highlighted the need for greater knowledge generation on its environmental aspects while also considering the potential adverse effects of climate change. The polar regions of the world offer a unique opportunity for AMR research in a near-pristine environment while also holding the potential for novel resistance mechanisms and/or antimicrobial peptide discovery within melting permafrost or glacial ice. Despite considerable technological advances in microbiology, operating in severe cold environments continues to present significant operational challenges. Our report here offers a basis for adaptations to enable both environmental and clinical antimicrobial resistance, microbiome, and discovery research for operating in the harshest of remote environments.
Rapid visual detection of hepatitis E virus combining reverse transcription recombinase-aided amplification with lateral flow dipstick and real-time fluorescence
Authors: Wei Bingyan , Wang Wenlong , Guo Zixuan , Yin Wenjiao , Cheng Minheng , Yang Yifei , Tian Yuewei , Sun Yaxin , Liu Tianlong , Hu Yanxin , She Ruiping , Tian Jijing 
Published: January 2025

ABSTRACT

Hepatitis E virus (HEV) is a globally prevalent zoonotic pathogen that is primarily spread through the fecal-oral route, such as by consuming undercooked or contaminated pork. HEV infection leads to an estimated 3.3 million symptomatic cases of viral hepatitis and 70,000 deaths in human populations each year. Therefore, a rapid and accurate method for detecting HEV in serum or stool samples is essential. In this study, we aimed to develop and evaluate two methods for the rapid and convenient detection of HEV RNA: reverse transcription recombinase-aided amplification with lateral flow dipstick (RT-RAA-LFD) and quantitative real-time reverse transcription recombinase-aided amplification (qRT-RAA). We optimized the reaction conditions and assessed their sensitivity and specificity. The RT-RAA-LFD assay completed its reaction at 39°C within 15 minutes, achieving a 95% limit of detection (LOD) of 247 copies/μL. The qRT-RAA assay, completed at 42°C within 20 minutes, had a 95% LOD of 25 copies/μL. Both assays demonstrated no cross-reactivity with other porcine pathogens and exhibited strong specificity. In testing 245 porcine bile and fecal samples, the RT-RAA-LFD assay showed a kappa value of 0.943 (
P
< 0.001) with a 97.14% (238/245) coincidence rate compared with quantitative reverse transcription PCR. Similarly, the qRT-RAA assay achieved a kappa value of 0.976 (
P
< 0.001) with a 98.78% (242/245) coincidence rate. In conclusion, these two RT-RAA assays show promising potential as effective diagnostic tools for broad and efficient screening of swine HEV in veterinary clinics.

IMPORTANCE
Hepatitis E virus (HEV) is a globally widespread zoonotic pathogen that poses a significant public health risk. Swine serve as the primary natural host for zoonotic HEV. This study introduces a rapid and precise method for detecting swine HEV RNA, showcasing its potential as an effective diagnostic tool for comprehensive and efficient screening of swine HEV in veterinary clinics.
Prolonged incubation time unwarranted for acute periprosthetic joint infections
Authors: Morreel E. R. L. , van Dessel H. A. , Geurts J. , Savelkoul P. H. M. , van Loo I. H. M. 
Published: January 2025

ABSTRACT

Current laboratory protocols for periprosthetic joint infections (PJIs) involve a standard 10- to 14-day incubation period. However, recent evidence indicates considerable variability in the time to diagnosis (TTD) between acute and chronic PJIs. TTD is also influenced by the employed culture media and sample types. Enriched liquid media, such as broths and blood culture bottles, along with sonication fluid culture, are commonly used, though their incremental benefit for PJI diagnosis remains debated. We retrospectively analyzed 187 confirmed hip and knee PJIs, each with at least three intraoperative samples. Comparison of TTD among early acute (
n
= 68), late acute (
n
= 52), and late chronic (
n
= 67) PJIs revealed a significant difference, particularly between late acute and late chronic infections (
P
< 0.004). Early acute and late acute PJIs were diagnosed within 5 days in 97.1% and 98.1% of cases, respectively, contrasting with 14 days required for 97.1% of late chronic PJIs. Enriched liquid media significantly improved species detection, especially in polymicrobial and anaerobic infections. Pediatric and anaerobic blood culture bottles demonstrated superior efficacy over thioglycolate broths for diagnostic confirmation. Sonication fluid culture was essential for confirming diagnoses in 17.6% of cases. Our findings highlight that clinical presentation, rather than time since primary arthroplasty, should guide incubation duration: both early acute and late acute PJIs can be diagnosed within 5 days. Medical microbiology laboratories should consider shorter incubation times for acute PJIs to optimize diagnostic efficiency. The use of blood culture bottles and sonication fluid culture proves invaluable for accurate PJI diagnosis.

IMPORTANCE
While molecular techniques are becoming increasingly employed, culture remains the gold standard for diagnosing periprosthetic joint infections. However, guidance for laboratory protocols is limited and highly variable. This article aims to increase diagnostic efficiency by providing concrete recommendations for medical microbiology laboratories.
Structure of the T=13 capsid of infectious pancreatic necrosis virus (IPNV)—a salmonid birnavirus
Authors: Munke Anna , Ahmed Abdelrahim Gamil Amr , Mikalsen Aase B. , Wang Han , Evensen Øystein , Okamoto Kenta 
Published: January 2025

ABSTRACT

Birnaviruses infect a broad range of vertebrate hosts, including fish and birds, and cause substantial economic losses in the fishery and livestock industries. The infectious pancreatic necrosis virus (IPNV), an aquabirnavirus, specifically infects salmonids. While structures on T=1 subviral particles of the birnaviruses, including IPNV, have been studied, structural insights into the infectious T=13 particles have been limited to the infectious bursal disease virus (IBDV), an avibirnavirus. Determining the capsid structure of the T=13 particle of IPNV is crucial for advancing knowledge of its antigenicity, capsid assembly, and possible functional structures. Here, the capsid structure of the IPNV L5 strain has been determined at a resolution of 2.75 Å. The overall structure resembles the T=13 IBDV structure, with notable differences in the surface loops on the P domain of the VP2 capsid protein essential for antigenicity and virulence. Additionally, previously undescribed structural features have been identified, including the C-terminal regions of the VP2 subunits within the pentagonal assembly unit at each 5-fold axis, which interlock with adjacent VP2 subunits. This interlocking, together with class-averaged projections of triangular and pentagonal units, suggests that the pentagonal unit formation could be important for a correct T=13 particle assembly, preventing the formation of T=1 subviral particles. Furthermore, positively charged residues in obstructed capsid pores at each 5-fold axis are speculated to facilitate intraparticle genome synthesis of IPNV.

IMPORTANCE
Aquabirnaviruses cause deadly infectious diseases in salmonid fish, posing significant challenges for both wild and farmed fish populations. The most prevalent aquabirnavirus worldwide is the infectious pancreatic necrosis virus, whose multifunctional capsid is critical to its infection, replication, and maturation. Previously, research has focused on the structure of the virus’ non-infectious subviral capsid. In this study, however, the first structure of the large, infectious, and functional form of the capsid has been determined. This new capsid structure reveals functional motifs that were previously unclear in the non-infectious capsid. These motifs are believed to be essential for the virus’ replication and particle assembly, making them promising targets for developing strategies to control virus proliferation.
Autoinducer-2 enhances the defense of
Vibrio furnissii
against oxidative stress and DNA damage by modulation of c-di-GMP signaling via a two-component system
Authors: Zhang Heng , Zhao Wenjin , Yang Wenguang , Zhang Huimin , Qian Xinyu , Sun Kai , Yang Qiao , Shen Xihui , Zhang Lei 
Published: January 2025

ABSTRACT

As a universal language across the bacterial kingdom, the quorum sensing signal autoinducer-2 (AI-2) can coordinate many bacterial group behaviors. However, unknown AI-2 receptors in bacteria may be more than what has been discovered so far, and there are still many unknown functions for this signal waiting to be explored. Here, we have identified a membrane-bound histidine kinase of the pathogenic bacterium
Vibrio furnissii
, AsrK, as a receptor that specifically detects AI-2 under low boron conditions. In contrast with another well-known AI-2 receptor LuxP that recognizes the borated form of AI-2, AsrK is found to show higher affinity with AI-2 under borate-depleted conditions, and thus boron has a negative effect on AI-2 sensing by AsrK in regulation of the biofilm and motility phenotypes. AI-2 binds to the extracytoplasmic dCache_1 domain of AsrK to inhibit its autokinase activity, thus decreasing the phosphorylation level of its cognate response regulator AsrR and activating the phosphodiesterase activity of AsrR to degrade the cellular second messenger cyclic di-GMP (c-di-GMP). AI-2 perception by the AsrK-AsrR system remarkably reduces intracellular c-di-GMP levels and enhances tolerance of
V. furnissii
to oxidative stress and DNA damage by upregulating the transcription of universal stress proteins including UspA1, UspA2, and UspE. Our study reveals a previously unrecognized mechanism for AI-2 detection in bacteria and also provides new insights into the important role of AI-2 in bacterial defense against oxidative stress and DNA damage.

IMPORTANCE

The QS signal AI-2 is widely synthesized in bacteria and has been implicated in the regulation of numerous bacterial group behaviors. However, in contrast to the wide distribution of this signal, its receptors have only been found in a small number of bacterial species, and the underlying mechanisms for the detection of and response to AI-2 remain elusive in most bacteria. It is worth noting that the periplasmic protein LuxP is the uniquely identified receptor for AI-2 in
Vibrio
spp. Here, we identify a second type of AI-2 receptor, a membrane-bound histidine kinase with a periplasmic dCache_1 sensory domain, in a member of the genus
Vibrio
, and thus show that AI-2 enhances the defense of
V. furnissii
against oxidative stress and DNA damage by modulation of c-di-GMP signaling via the AsrK-AsrR two-component system. Our results reveal a previously unrecognized AI-2 sensing mechanism and expand our understanding of the physiological roles of AI-2 in bacteria.