bluuebunny/crossref_metadata_2025_split huggingface dataset:
Flow and Heat Transfer in Rotating Compressor Cavities With Inverted Shroud-Throughflow Temperature Differences
Authors: Pernak Mikolaj J. , Nicholas Tom E. W. , Carnevale Mauro , Lock Gary D. , Tang Hui , Scobie James A. 
Published: November 2024

Abstract
In an aero-engine compressor, co-rotating discs form cavities that interact with an axial throughflow of secondary air at low radius. In the high-pressure (HP) compressor the shroud is hotter than the throughflow (directed downstream to the turbine) and the radial temperature gradient creates buoyancy-induced flow at Grashof numbers ∼1013. Such flows can be unstable and typically take the form of counter-rotating vortex pairs separated by radial hot and cold plumes. However, in low pressure (LP) and intermediate pressure (IP) compressors the secondary air is directed upstream. In this inverse scenario, the axial throughflow is hotter than the compressor discs, reversing the disc temperature gradient and eliminating the fundamental driver for buoyancy. Despite its practical application and importance, this inverse scenario has not been previously investigated. The University of Bath Compressor Cavity Rig has been uniquely designed to simulate such flows, measuring temperature, and unsteady pressure in the frame of reference of the rotating discs. Bayesian and spectral analysis have determined the radial distribution of disc heat flux, as well as the asymmetry of the rotating vortex structures and their slip relative to the discs. Unexpectedly, the new data reveal the flow structure in cavities with positive and inverted temperature differences are fundamentally similar (albeit with reversed radial-temperature profiles). Isothermal cases identified a critical Rossby number (Ro), above which the flow structure in the cavity was dominated by a toroidal vortex. At subcritical Ro, the flow structure for the inverted temperature gradient continued to be governed by buoyancy due to disc heat transfer. Momentum exchange with the axial throughflow and the gradient of circumferential pressure combine to vary the slip and vortex symmetry. This paper provides the first data and analysis of flow and heat transfer during inverse throughflow conditions in LP and IP compressors. The new insights are of importance for the determination of the thermal stresses in discs, engine life, compressor blade clearance and efficiency.
Association Between 24-Hour Movement Behaviors and Adiposity in Malaysian Schoolchildren: A Compositional Isotemporal Substitution Analysis
Authors: Wong Jyh Eiin , Palarea-Albaladejo Javier , Lee Shoo Thien , Koh Denise , Khouw Ilse , Poh Bee Koon , _ _ 
Published: November 2024

Background: Physical activity (PA), sedentary behavior (SB), and sleep are interrelated 24-hour movement behaviors that are important for the growth and well-being of children. This cross-sectional study examined the relationship between 24-hour movement behaviors and adiposity, and predicted changes in adiposity following compositional time reallocations in 7- to 12.9-year-old Malaysian children from the South East Asian Nutrition Surveys II Malaysia. Methods: A total of 381 children (mean age 9.7 [1.6] y, 57% girls) provided 24-hour wrist-worn GENEActiv accelerometry data which captured time spent for sleep, SB, light PA and moderate to vigorous PA (MVPA). Indicators of adiposity were derived from anthropometry and bioelectrical impedance analysis: body-mass-index-for-age, waist circumference, waist-to-height ratio, percent body fat, and body mass index. The composition of 4-part movement behaviors was expressed as isometric log-ratio coordinates which were entered into regression models. Isotemporal substitution analysis was used to assess changes in adiposity indicators when reallocating time between movement behaviors. Results: Relative to other movement behaviors, time spent on MVPA was significantly associated with waist circumference, waist-to-height ratio, percent body fat, and fat mass index. A 15-minute one-to-one reallocation from other movement behaviors to MVPA predicted lower body-mass-index-for-age (−0.03 to −0.11), smaller waist circumference (−0.67 to −1.28 cm), lower waist-to-height ratio (−0.004 to −0.008), percent body fat (−0.87% to −1.47%), and fat mass index (−0.23 to −0.42). Replacing SB and light PA with sleep or MVPA was associated with lower adiposity. Conclusions: The overall composition of movement behavior was significantly associated with the adiposity of Malaysian schoolchildren. Promoting MVPA and sleep and reducing SB and light PA are important for prevention of childhood obesity.
Insights into the regulatory mechanisms and application prospects of the transcription factor Cra
Authors: Huang Ying , Jia Kai-Zhi , Zhao Wei , Zhu Li-Wen 
Published: November 2024

ABSTRACT

Cra (catabolite repressor/activator) is a global transcription factor (TF) that plays a pleiotropic role in controlling the transcription of several genes involved in carbon utilization and energy metabolism. Multiple studies have investigated the regulatory mechanism of Cra and its rational use for metabolic regulation, but due to the complexity of its regulation, there remain challenges in the efficient use of Cra. Here, the structure, mechanism of action, and regulatory function of Cra in carbon and nitrogen flow are reviewed. In addition, this paper highlights the application of Cra in metabolic engineering, including the promotion of metabolite biosynthesis, the regulation of stress tolerance and virulence, the use of a Cra-based biosensor, and its coupling with other transcription factors. Finally, the prospects of Cra-related regulatory strategies are discussed. This review provides guidance for the rational design and construction of Cra-based metabolic regulation systems.
Potential health risk assessment of cyanobacteria across global lakes
Authors: Hu Hang , Zhang Zhenyan , Chen Bingfeng , Zhang Qi , Xu Nuohan , Paerl Hans W. , Wang Tingzhang , Hong Wenjie , Penuelas Josep , Qian Haifeng 
Published: November 2024

ABSTRACT

Cyanobacterial blooms pose environmental and health risks due to their production of toxic secondary metabolites. While current methods for assessing these risks have focused primarily on bloom frequency and intensity, the lack of comprehensive and comparable data on cyanotoxins makes it challenging to rigorously evaluate these health risks. In this study, we examined 750 metagenomic data sets collected from 103 lakes worldwide. Our analysis unveiled the diverse distributions of cyanobacterial communities and the genes responsible for cyanotoxin production across the globe. Our approach involved the integration of cyanobacterial biomass, the biosynthetic potential of cyanotoxin, and the potential effects of these toxins to establish potential cyanobacterial health risks. Our findings revealed that nearly half of the lakes assessed posed medium to high health risks associated with cyanobacteria. The regions of greatest concern were East Asia and South Asia, particularly in developing countries experiencing rapid industrialization and urbanization. Using machine learning techniques, we mapped potential cyanobacterial health risks in lakes worldwide. The model results revealed a positive correlation between potential cyanobacterial health risks and factors such as temperature, N
2
O emissions, and the human influence index. These findings underscore the influence of these variables on the proliferation of cyanobacterial blooms and associated risks. By introducing a novel quantitative method for monitoring potential cyanobacterial health risks on a global scale, our study contributes to the assessment and management of one of the most pressing threats to both aquatic ecosystems and human health.

IMPORTANCE
Our research introduces a novel and comprehensive approach to potential cyanobacterial health risk assessment, offering insights into risk from a toxicity perspective. The distinct geographical variations in cyanobacterial communities coupled with the intricate interplay of environmental factors underscore the complexity of managing cyanobacterial blooms at a global scale. Our systematic and targeted cyanobacterial surveillance enables a worldwide assessment of cyanobacteria-based potential health risks, providing an early warning system.
Lyme borreliosis in Brazil: a critical review on the Baggio–Yoshinari syndrome (Brazilian Lyme-like disease)
Authors: Labruna Marcelo B. , Faccini-Martínez Álvaro A. , Muñoz-Leal Sebastián , Szabó Matias P. J. , Angerami Rodrigo N. 
Published: November 2024

SUMMARY

Lyme borreliosis or Lyme disease is the most frequently reported tick-borne disease in the Northern Hemisphere. In countries of the Southern Hemisphere, such as Brazil, since the early 1990s, some researchers have argued for the existence of an autochthonous Lyme-like borreliosis, known locally as the Baggio–Yoshinari syndrome (BYS), an alleged “Brazilian borreliosis” supposedly caused by a different strain of
Borrelia burgdorferi
and transmitted by hard ticks. Currently, the existence of BYS in Brazil is still accepted by a large part of the human health care workers, scientists, medical societies, and patients. In fact, this alleged “Brazilian borreliosis” has been the tick-borne zoonotic disease with the greatest number of reported cases and published studies in Brazil during this century, second only to Brazilian spotted fever. In this manuscript, we reviewed all manuscripts directly related to BYS that have been published in Brazil during the last 35 years. This analysis included 199 individual human cases that have been reported in Brazil since 1989, plus multiple studies on ticks, domestic, and wild animals. Our revision aimed to provide a critical opinion on whether the current published works allow healthcare workers, public health agencies, and patients to accept the existence of Lyme disease, BYS, or other Lyme borreliosis-related disease in Brazil. For this purpose, we evaluated the strengths and weaknesses of each published study, considering the diagnostic methods used, such as serological, microbiological, and molecular analyses. Based on these evaluations, we conclude that there is not enough evidence to support the occurrence of Lyme borreliosis in Brazil or that BYS (Brazilian Lyme-like disease) is caused by a bacterium of the genus
Borrelia
. This assumption is based on the inaccuracy, unreliability, and misinterpretation of the different diagnostic methods that have been used in Brazil. Recognizing the lack of technical evidence for the occurrence of Lyme borreliosis in Brazil has highly relevant implications. For example, it becomes imperative to raise awareness among the country’s medical profession, as they have adopted unnecessary and extreme therapies recommended for patients with a supposed borrelial infection, including BYS, in Brazil. Finally, the technical analyses carried out in this study could be applied to other countries in the Southern Hemisphere (
e.g.
, Argentina, South Africa, Australia), where cases classified and alleged as Lyme disease have been reported.
Dissecting the role of the HA1-226 leucine residue in the fitness and airborne transmission of an A(H9N2) avian influenza virus
Authors: Sun Xiangjie , Belser Jessica A. , Pulit-Penaloza Joanna A. , Brock Nicole , Kieran Troy J. , Pappas Claudia , Zeng Hui , Tumpey Terrence M. , Maines Taronna R. 
Published: November 2024

ABSTRACT

A better understanding of viral factors that contribute to influenza A virus (IAV) airborne transmission is crucial for pandemic preparedness. A limited capacity for airborne transmission was recently observed in a human A(H9N2) virus isolate (A/Anhui-Lujiang/39/2018, AL/39) that possesses a leucine (L) residue at position HA1-226 (H3 numbering), indicative of human-like receptor binding potential. To evaluate the roles of the residue at this position in virus fitness and airborne transmission, a wild-type AL/39 (AL/39-wt) and a mutant virus (AL/39-HA1-L226Q) with a single substitution at position HA1-226 from leucine to glutamine (Q), a consensus residue in avian influenza viruses, were rescued and assessed in the ferret model. The AL/39-HA1-L226Q virus lost the ability to transmit by air, although the virus had a comparable capacity for replication, induced similar levels of host innate immune responses, and was detected at comparable levels in the air surrounding the inoculated ferrets relative to AL/39-wt virus. However, ferrets showed a lower susceptibility to AL/39-HA1-L226Q virus infection compared to the AL/39-wt virus. Furthermore, the AL/39-wt and AL/39-HA1-L226Q viruses each gained dominance in different anatomic sites in the respiratory tract in a co-infection competition model in ferrets. Taken together, our findings demonstrate that the increasing dominance of HA1-L226 residue in an avian A(H9N2) virus plays multifaceted roles in virus infection and transmission in the ferret model, including improved virus fitness and infectivity.

IMPORTANCE
Although the capacity for human-like receptor binding is a key prerequisite for non-human origin influenza A virus (IAV) to become airborne transmissible in mammalian hosts, the underlying molecular basis is not well understood. In this study, we investigated a naturally occurring substitution (leucine to glutamine) at residue 226 in the HA of an avian-origin A(H9N2) virus and assessed the impact on virus replication and airborne transmission in the ferret model. We demonstrate that the enhanced airborne transmission associated with the HA1-L226 virus was mainly due to the increased infectivity of the virus. Interestingly, we found that, unlike most sites in the ferret respiratory tract, ferret ethmoid turbinate lined with olfactory epithelium favors replication of the AL/39-HA1-L226Q virus, suggesting that this site may serve as a unique niche for IAV with avian-like receptor binding specificity to potentially allow the virus to spread to extrapulmonary tissues and to facilitate adaptation of the virus to human hosts.
Rapid production of recombinant rotaviruses by overexpression of NSP2 and NSP5 genes with modified nucleotide sequences
Authors: Kanai Yuta , Kotaki Tomohiro , Sakai Satoko , Ishisaka Toshie , Matsuo Kayoko , Yoshida Yukino , Hirai Katsuhisa , Minami Shohei , Kobayashi Takeshi 
Published: November 2024

ABSTRACT

Reverse genetics systems for rotaviruses (RV) facilitate the generation of genetically engineered RVs by transfection of 11 plasmids encoding 11 genomic viral RNA segments. In addition to viral genome expression, overexpression of NSP2 and NSP5 has been used to increase the rescue efficiency of recombinant RVs. Here, we showed that the overexpression of nucleotide sequence-modified NSP2 and NSP5 enabled the rapid and efficient production of recombinant RVs. Using improved reverse genetics, we established a reverse genetics system for human and bovine RV clinical isolates, as well as laboratory strains of bovine RV (NCDV and UK) and porcine RV (Gottfried). In addition, we rescued low-replicating recombinant RVs carrying a mutant NSP4 lacking the double-layered particle-binding domain, which was deficient in the efficient production of mature virions. These advancements in reverse genetics enabled the generation of molecular clones of RV clinical isolates and recombinant RVs harboring critical amino acid mutations, offering a versatile platform for investigating RV biology and pathogenesis.

IMPORTANCE
Recombinant rotavirus (RV) synthesis via reverse genetics relies on both the viral propagation capacity and the efficiency of the experimental system. Since the establishment of our reverse genetics system, several enhancements have been implemented to augment the rescue efficiency. Nevertheless, challenges persist in generating RV clinical strains and recombinant viruses with low replication capacities. Notably, this improved reverse genetics system successfully facilitated the establishment of molecular clones of human and bovine RV clinical isolates. Fecal samples from patients with RV typically harbor quasi-species or, occasionally, multiple genotypes of RV. In the present study, we performed the genetic sequencing of clinical viral strains during the early propagation stages in cultured cells. Subsequently, infectious viruses were synthesized, allowing the characterization of circulating viruses in nature. This approach provides valuable insights into the genetic diversity and dynamics of RV populations and contributes to a more comprehensive understanding of viral pathogenesis and evolution.
No evidence that mutations in SARS-CoV-2 variants of concern derive from homologous fragments in gut microbiota
Authors: Parry Rhys H. , Lytras Spyros , Petrone Mary E. , Wille Michelle , Crits-Christoph Alexander , Gifford Robert J. , Saito Akatsuki , Smura Teemu , Peacock Thomas P. 
Published: November 2024

ABSTRACT

Understanding the origin and evolution of mutations in SARS-CoV-2 variants of concern (VOCs) is a critical area of research. B. Cao, X. Wang, W. Yin, Z. Gao, and B. Xia (mBio 15:e03187-23, 2024,
https://doi.org/10.1128/mbio.03187-23
) proposed that these mutations originated from bacterial sequences incorporated into the viral genome through stochastic template-switching by the viral RNA-dependent RNA polymerase (RdRp). Their analysis suggested that 62% of the viral mutation fragments (VMFs) in key SARS-CoV-2 proteins were identical to bacterial protein sequences. Given the implications of this finding, we re-examined the methods employed and argue that they resulted in false-positive findings. Specifically, the short query length of VMFs, seven amino acids, leads to spurious matches in large protein databases, as indicated by high BLAST Expect values. Furthermore, we analyzed the nucleotide sequence of VMFs, revealing no unique homology between SARS-CoV-2 and bacterial sequences. Consequently, the evidence does not support the hypothesis that bacterial sequences contribute to the evolution of SARS-CoV-2 VOCs. Instead, the emergence of these variants is more plausibly attributed to factors intrinsic to viral replication and evolution, such as the error-prone nature of RdRp, intrahost diversity, and recombination of related viral sublineages.
Limit of detection of
Salmonella
ser. Enteritidis using culture-based versus culture-independent diagnostic approaches
Authors: Bradford L. M. , Yao L. , Anastasiadis C. , Cooper A. L. , Blais B. , Deckert A. , Reid-Smith R. , Lau C. , Diarra M. S. , Carrillo C. , Wong A. 
Published: November 2024

ABSTRACT

To prevent the spread of foodborne illnesses, the presence of pathogens in the food chain is monitored by government agencies and food producers. The culture-based methods currently employed are sensitive but time- and labor-intensive, leading to increasing interest in exploring culture-independent diagnostic tests (CIDTs) for pathogen detection. However, few studies quantify the relative sensitivity and reliability of these CIDTs compared to current approaches. To address this issue, we conducted a comparison of the limit of detection (LOD
50
) for
Salmonella
between a culture-based method and three CIDTs: qPCR (targeting
invA
and
stn
), metabarcode (16S) sequencing, and shotgun metagenomic sequencing. Samples of chicken feed and chicken caecal contents were spiked with
S
. serovar Enteritidis and subjected to culture- and DNA-based detection methods. To explore the impact of non-selective enrichment on LOD
50
, all samples underwent both immediate DNA extraction and overnight enrichment prior to gDNA extraction. In addition to this spike-in experiment, feed and caecal samples acquired from the field were tested with culturing, qPCR, and metabarcoding. In general, LOD
50
was comparable between qPCR and shotgun sequencing methods. Overnight microbiological enrichment resulted in an improvement in LOD
50
with up to a three-log decrease. However,
Salmonella
reads were detected in some unspiked feed samples, suggesting false-positive detection of
Salmonella
. In addition, the LOD
50
in feeds was three logs lower than in caecal contents, underscoring the impact of background microbiota on
Salmonella
detection using all methods.

IMPORTANCE
The appeal of culture-independent diagnostic tests (CIDTs) is increased speed with lowered cost, as well as the potential to detect multiple pathogen species in a single analysis and to monitor other areas of concern such as antimicrobial resistance genes or virulence factors. This study provides quantitative data on the sensitivity of CIDTs relative to current approaches, which is essential for determining the feasibility of implementing these methods in pathogen surveillance programs.
Biofilm matrix regulation by
Candida glabrata
Zap1 under acidic conditions: transcriptomic and proteomic analyses
Authors: Gonçalves Bruna , Pires Diana Priscila , Fernandes Liliana , Pacheco Miguel , Ferreira Tiago , Osório Hugo , Soares Ana Raquel , Henriques Mariana , Silva Sónia 
Published: November 2024

ABSTRACT

The vaginal acidic environment potentiates the formation of
Candida glabrata
biofilms, leading to complicated and recurrent infections. Importantly, the production of matrix is known to contribute to the recalcitrant features of
Candida
biofilms. In this study, we reveal that Zap1 regulates the matrix of
C. glabrata
acidic biofilms and analyzed the modulation of their transcriptome (by microarrays) and matrix proteome (by LC-MS/MS) by Zap1. For that, the deletion mutant
zap1
Δ and its complemented strain
zap1
Δ::
ZAP1
were constructed, and their biofilms were developed at pH 4 (adjusted with lactic acid). The results revealed that Zap1 is a negative regulator of the total amount of protein and carbohydrate in the biofilm matrix. Accordingly, various genes and matrix proteins with predicted functions in the regulation of carbohydrate metabolism, sugar binding, sugar transport, and adhesion (including Epa family) were repressed by Zap1. Nevertheless, the results also suggested that Zap1 is essential to the delivery and organization of some matrix components. Indeed, Zap1 was required for the secretion of 122 proteins to the matrix and induced the expression of 557 genes, including various targets involved in glucan metabolism. Additionally, Zap1 induced targets with roles in virulence, resistance to antifungals, and host immunity evasion, including yapsins,
ERG
family, and moonlighting proteins. Zap1 was also required for the secretion of acidic-specific matrix proteins, indicating a contribution to the response to the acidic environment. Overall, this study demonstrates that Zap1 is a relevant regulator of the biofilm matrix, contributing to a better understanding of
C. glabrata
acidic biofilms.

IMPORTANCE

The rising prevalence of vulvovaginal candidiasis (VVC) and the increasing presence of
Candida
spp. with aggressive virulence features and low susceptibility to common antifungals, particularly
Candida glabrata
, have resulted in more severe, prolonged, and recurrent cases of VVC, with significant implications for patients. This research offers valuable insights into the molecular changes that contribute to the formation of
C. glabrata
biofilms in the acidic vaginal environment, representing a significant advancement in the understanding of
C. glabrata
’s virulence. Notably, this study identified Zap1 as a critical regulator of
C. glabrata
biofilm matrix, with additional potential roles in adhesion, antifungal resistance, evasion of host immunity, and response to acidic conditions, making it a promising target for new therapeutic approaches. Importantly, Zap1 is the first regulator of the biofilm matrix to be identified in
C. glabrata
, and the elucidation of its targets (including genes and matrix proteins) lays a strong foundation for future research.