bluuebunny/crossref_metadata_2025_split huggingface dataset:
Revealing hidden viruses inducing similar yellowing symptoms or remaining asymptomatic in cucurbit crops
Authors: de Moya‐Ruiz Celia , Juárez Miguel , Gómez Pedro 
Published: October 2024

AbstractMixed viral infections occur frequently in plants, leading to diseases that can be difficult to diagnose, especially when an unknown virus is hidden behind expression of symptoms common to other viruses. We monitored aphid‐ and whitefly‐transmitted viruses in two cucurbit crops (melon and watermelon) for three consecutive seasons (2021–2023) across three production regions in Spain, focusing on the common yellowing and mosaic symptoms. A total of 984 symptomatic leaf samples from 246 field plots were tested for 10 frequently found cucurbit viruses. Cucurbit aphid‐borne yellows virus (CABYV) was the most prevalent virus infecting both cucurbit crops over the three seasons. Additionally, occurrence of watermelon mosaic virus (WMV) in samples with mosaic symptoms was significant. However, an important proportion of yellowing symptomatic samples tested negative for known viruses. Using a sequence‐independent approach, we identified a novel polerovirus, Pepo aphid‐borne yellows virus (PABYV), which was widespread, infecting both crops. Analysis of our long‐term cucurbit frozen‐sample collection revealed that PABYV had emerged in Spain in 2018, possibly unnoticed as its yellowing symptoms were similar to CABYV, with which it was frequently associated. Additionally, we found the cryptic Cucumis melo endornavirus (CmEV) in all tested melon samples from 2011 and, for the first time, in pumpkin. Genetic characterization of CABYV, PABYV and CmEV populations revealed a replacement of ancient CABYV isolates by contemporary ones, while PABYV and CmEV isolates were genetically homogenous among their populations. This study underlines the need for continuous surveillance and further investigation into common symptoms of mixed viral infections.
Respublica Noumenon: Kant, Rousseau, and Plato's Republic
Authors: Kryluk Michael 
Published: October 2024

AbstractThis article examines the philosophical sources for Kant's interpretation of Plato's Republic and its impact on his conception of the ideal state. I argue that Kant's knowledge of Plato was not derived from Plato's writings, but from secondary accounts. More specifically, I focus on four authors whose discussions of Plato influenced Kant's understanding of the perfect republic: Brucker, Cicero, Wolff, and Rousseau. Two main claims emerge. First, I show that Kant's appeal to the Republic intervenes in a longstanding debate about the irrational and “enthusiastic” character of Platonic idealism. Second, I emphasize Rousseau's role in instigating Kant's interest in Plato and shaping his conception of the perfect, fully self‐legislating republic that serves as the regulative norm of the state which existing regimes can and should strive to emulate. The result of my analysis is a better understanding of Kant's relationship to Plato and Rousseau, as well as the philosophical motivations behind his version of the ideal republic.
A Multi-Scale Thermal-Mechanical Numerical Method for Mini-Channel Heat Exchanger Subjected to Fluid Pressure Loads
Authors: Xu Zirui , Zhang Xiaoxu , Tan Yin , Bi Jiyuan , Li Ri , Yang Xiongwei , Wang Qiuwang , Ma Ting 
Published: October 2024

Abstract
This study proposes a novel multi-scale numerical method for thermal-mechanical analysis of mini-channel heat exchangers (MCHEs) under internal fluid pressure and temperature loads. The method comprises a macro-scale model for global analysis and a meso-scale model for detailed submodel analysis, specifically focusing on the internal fluid pressure effects within the MCHEs. The macroscopic model divides the MCHE into cover plate and homogenized regions subjected to pressure and temperature loads. To incorporate internal pressures into the homogenized MCHE model, mathematical equations are formulated to convert internal fluid pressures into equivalent strain loads. Additionally, a novel equivalent thermal expansion method is introduced, integrating internal fluid pressure loads by prescribing equivalent thermal expansion coefficients alongside spatially-varying nodal temperature fields within the MCHE. The meso-scale models with detailed channel patterns are assigned to specific portions of the homogenized region. The integration of the mesoscale model into the macroscopic framework is achieved through the application of the submodel method. Comparisons between the equivalent and actual MCHE models show that the proposed equivalent method can provide accurate predictions for thermal-mechanical deformations and stresses, and significantly reduce the computational expenses.
Study on Dynamic Postbuckling Stability of Fast Reactor Vessels Subjected to Vertical Vibration
Authors: Ye Yiji , Ichimiya Masakazu , Kasahara Naoto 
Published: October 2024

Abstract
As a lesson learned from the Fukushima nuclear accident, the importance of accident mitigation for beyond-design basis events (BDBEs) is recognized. Excessive earthquake is a typical BDBE. During such events, the fast reactor vessel (FRV) is vulnerable to buckling. The safety goal of FRV under excessive earthquake is to achieve a stable post-buckling state. Our previous study on bending buckling confirmed a global response stability under horizontal vibration. As a parallel study, this paper focuses on axial compression buckling under vertical vibration. Shaking table experiments using thin-walled cylindrical models (R/t = 260) are carried out. Similar methodology is applied to investigate the buckling and post-buckling behavior. It is found that axial compression buckling shares an extensive similarity with bending buckling in both buckling mode and post-buckling behavior. Similar global response stability is confirmed due to phase-inverse phenomenon. After buckling, buckling failure becomes stable and does not progress further even when an intense input amplitude is continuously applied. The vibrational load acts as a displacement-controlled load in the out-of-phase domain such that immediate collapse is prevented. Most input energy is dissipated in hysteresis loops rather than being carried by the mass. These mechanisms are independent of input waveform and can be applied to an arbitrary seismic input. In addition, a conservative limit displacement for global response stability is identified. Moreover, the effect of the input frequency ratio, the initial geometrical imperfection, and the gravitational force on the post-buckling behavior are clarified.
Layer segmented filamentous bacteria colonize and impact gut health of broiler chickens
Authors: Meinen-Jochum Jared , Skow Caleb J. , Mellata Melha 
Published: October 2024

ABSTRACT

In commercial poultry farms, chicks hatch away from their progenitors from which they acquire key host-specific microbiota, like segmented filamentous bacteria (SFB) involved in gut maturation in early life. This study investigated whether providing chicken SFB to newly hatched broilers would increase their gut maturation and resistance to bacteria relevant to broiler and human health. One-day-old Ross308 broilers were orally treated with either phosphate-buffered saline (CON) or layer-derived SFB (D-SFB). On days 5, 10, 17, and 24, feces were collected to detect and enumerate SFB and
Enterobacteriaceae
. On days 8, 15, 22, and 29, birds were euthanized, intestinal samples were collected to detect and enumerate SFB through quantitative PCR (qPCR) and microscopy and expression of genes associated with gut immune function through reverse transcription-qPCR. This study showed that, despite their host specificity, layer SFB can colonize their genetically distinct relative broilers. Ileal SFB colonization was accelerated by a week with the SFB treatment and covered the proximal, medial, and distal sections of the ileum. Colonization of the ileum by SFB in early life highly activated gene expression of intestinal barrier proteins and cytokines, e.g., IL-10 and IFNγ but not IL-17. SFB treatment reduced the level of
Enterobacteriaceae
in the gut and provided superior resistance to intestinal and extraintestinal pathogens as tested
in vitro
. Overall, early gut colonization of SFB is imperative for the maturation of the gut immune system and the establishment of a homeostatic gut environment. Improving our understanding of gut immune maturation in food-producing animals is crucial for both human and animal health.

IMPORTANCE
In commercial farms, newly hatched chicks may lack host-specific microbiota that help mature their gut immune system for lifelong health benefits. Here, introducing an avian segmented filamentous bacteria (SFB) to commercially sourced chickens orally at hatch accelerated SFB colonization of the ileum. Remarkably, SFB from layers were able to colonize broilers and enhance gut immune maturation, and this immunomodulation impacted the ability to increase intestinal and extraintestinal resistance to bacteria relevant to poultry and human health. With the antibiotic restrictions in animal production, strategies that will help mitigate infections are urgently needed. In summary, we developed a live prophylactic for newly hatched chicks to improve animal health and food safety. Due to the host specificity of SFB, our data highlight the importance of investigating the molecular mechanism of SFB interaction in their own host.
E.PathDash, pathway activation analysis of publicly available pathogen gene expression data
Authors: Taub Lily , Hampton Thomas H. , Sarkar Sharanya , Doing Georgia , Neff Samuel L. , Finger Carson E. , Ferreira Fukutani Kiyoshi , Stanton Bruce A. 
Published: October 2024

ABSTRACT

E.PathDash facilitates re-analysis of gene expression data from pathogens clinically relevant to chronic respiratory diseases, including a total of 48 studies, 548 samples, and 404 unique treatment comparisons. The application enables users to assess broad biological stress responses at the KEGG pathway or gene ontology level and also provides data for individual genes. E.PathDash reduces the time required to gain access to data from multiple hours per data set to seconds. Users can download high-quality images such as volcano plots and boxplots, differential gene expression results, and raw count data, making it fully interoperable with other tools. Importantly, users can rapidly toggle between experimental comparisons and different studies of the same phenomenon, enabling them to judge the extent to which observed responses are reproducible. As a proof of principle, we invited two cystic fibrosis scientists to use the application to explore scientific questions relevant to their specific research areas. Reassuringly, pathway activation analysis recapitulated results reported in original publications, but it also yielded new insights into pathogen responses to changes in their environments, validating the utility of the application. All software and data are freely accessible, and the application is available at
scangeo.dartmouth.edu/EPathDash
.

IMPORTANCE

Chronic respiratory illnesses impose a high disease burden on our communities and people with respiratory diseases are susceptible to robust bacterial infections from pathogens, including
Pseudomonas aeruginosa
and
Staphylococcus aureus
, that contribute to morbidity and mortality. Public gene expression datasets generated from these and other pathogens are abundantly available and an important resource for synthesizing existing pathogenic research, leading to interventions that improve patient outcomes. However, it can take many hours or weeks to render publicly available datasets usable; significant time and skills are needed to clean, standardize, and apply reproducible and robust bioinformatic pipelines to the data. Through collaboration with two microbiologists, we have shown that E.PathDash addresses this problem, enabling them to elucidate pathogen responses to a variety of over 400 experimental conditions and generate mechanistic hypotheses for cell-level behavior in response to disease-relevant exposures, all in a fraction of the time.
Depletion of m
6
A-RNA in
Escherichia coli
reduces the infectious potential of T5 bacteriophage
Authors: Saikia Bibakhya , Riquelme-Barrios Sebastian , Carell Thomas , Brameyer Sophie , Jung Kirsten 
Published: October 2024

ABSTRACT

N
6
-Methyladenosine (m
6
A) is the most abundant internal modification of mRNA in eukaryotes that plays, among other mechanisms, an essential role in virus replication. However, the understanding of m
6
A-RNA modification in prokaryotes, especially in relation to phage replication, is limited. To address this knowledge gap, we investigated the effects of m
6
A-RNA modifications on phage replication in two model organisms:
Vibrio campbellii
BAA-1116 (previously
Vibrio harveyi
BB120) and
Escherichia coli
MG1655. An m
6
A-RNA-depleted
V. campbellii
mutant (Δ
rlmF
Δ
rlmJ
) did not differ from the wild type in the induction of lysogenic phages or in susceptibility to the lytic Virtus phage. In contrast, the infection potential of the T5 phage, but not that of other T phages or the lambda phage, was reduced in an m
6
A-RNA-depleted
E. coli
mutant (Δ
rlmF
Δ
rlmJ
) compared to the wild type. This was shown by a lower plaquing efficiency and a higher percentage of surviving cells. There were no differences in the T5 phage adsorption rate, but the mutant exhibited a 5-min delay in the rise period during the one-step growth curve. This is the first report demonstrating that
E. coli
cells with lower m
6
A-RNA levels have a higher chance of surviving T5 phage infection.

IMPORTANCE

The importance of RNA modifications has been thoroughly studied in the context of eukaryotic viral infections. However, their role in bacterial hosts during phage infections is largely unexplored. Our research delves into this gap by investigating the effect of host
N
6
-methyladenosine (m
6
A)-RNA modifications during phage infection. We found that an
Escherichia coli
mutant depleted of m
6
A-RNA is less susceptible to T5 infection than the wild type. This finding emphasizes the need to further investigate how RNA modifications affect the fine-tuned regulation of individual bacterial survival in the presence of phages to ensure population survival.
Emerging
bla
NDM
-positive
Salmonella enterica
in Chinese pediatric infections
Authors: Ke Yefang , Zhu Zhe , Lu Wenbo , Liu Wenyuan , Ye Lina , Jia Chenghao , Yue Min 
Published: October 2024

ABSTRACT

Non-typhoidal
Salmonella
(NTS) is a common zoonotic foodborne pathogen, whose rising antimicrobial resistance has been an urgent threat to global public health. Here, we reported two carbapenem-resistant
Salmonella enterica
(CRSE) strains (NBFE-049 and NBFE-164) carrying the
bla
NDM
genes, which were recovered from two Chinese children, belonged to
Salmonella enterica
serovar Typhimurium (
S
. Typhimurium) monophasic variant (
S
. 1,4,[5],12:i:-) ST34 (a sequence type) and
S
. Typhimurium ST19, respectively. Genes
bla
NDM-5
and
bla
NDM-13
were detected in NBFE-049 and NBFE-164, respectively. The
bla
NDM-5
in NBFE-049 was located in an IncHI2-type plasmid, named pNBFE-049. In NBFE-164, the
bla
NDM-13
was located in an IncI1-type plasmid, named pNBFE-164. The plasmid pNBFE-164 successfully transferred its resistance phenotype into the recipient strain
Escherichia coli
J53 with a high efficiency of 1.1 × 10
−2
, while no transconjugants were obtained in pNBFE-049 conjugation assays. We further elucidated the genetic relationships of globally occurring New Delhi Metallo-β-lactamase (NDM)-positive strains and locally distributed clinical strains within the same serovar. The closest relative of NBFE-049 was clinical
Salmonella
strain 1722, which was recovered in 2020 and differed by only three Single Nucleotide Polymorphisms (SNPs). No NDM-positive ST19 could be found in the National Center for Biotechnology Information (NCBI) database, and NBFE-164 showed a close genetic relationship with the other ST19 in this area. To sum up, we suggested the potential contributions of clonal spread and plasmid-mediated
bla
NDM
transfer in CRSE dissemination. This study reported the complete genome of two
bla
NDM
-carrying
S
. Typhimurium isolates, shedding new insights into the antimicrobial resistance mechanisms and dissemination patterns of the emerging CRSE.

IMPORTANCE

NTS is one of the most common zoonotic pathogens that causes foodborne illnesses, while
S
. Typhimurium is one of the most common serovars. With the rising prevalence of multi-resistant
Salmonella
worldwide, carbapenems have emerged as the last-line antibiotics for treating severe bacterial infections. In this study, we reported the genomic characteristics of two carbapenem-resistant
S
. Typhimurium strains, which were recovered from two pediatric patients, carrying
bla
NDM-5
and
bla
NDM-13
, providing new insights into the antimicrobial resistance deteriminants and transmission risk of
bla
NDM
-positive NTS in China. We suggested the potential contributions of clonal spread and plasmid-mediated
bla
NDM
transfer in CRSE dissemination. Future enhanced surveillance policy should mitigate CRSE spreading, and more importantly, clinical antimicrobial therapeutic regimens should be adjusted accordingly.
Development of a new
Acinetobacter baumannii
pneumonia rabbit model for the preclinical evaluation of future anti-infective strategies
Authors: Albac S. , Anzala N. , Bonnot D. , Djama C. , Chavanet P. , Croisier D. 
Published: October 2024

ABSTRACT

Carbapenem-resistant
Acinetobacter baumannii
(CRAB) is an emerging cause of hospital-acquired pneumonia (HAP). Preclinical large models are warranted to predict the efficacy and the resistance profile of anti-infectives and mimic how they will be used in the human treatment of CRAB-HAP. Here we reported on the development of an
Acinetobacter baumannii
experimental pneumonia model in immunocompromised rabbits, receiving a 48-h human-simulated regimen. The efficacy of meropenem (2 g/q8h i.v. over prolonged 3-h perfusion), rifampin (25 mg/kg/q8h, i.v.), or the combination of meropenem and rifampin was assessed in rabbits infected with the carbapenem-susceptible
ATCC 17978
reference strain or the CRAB
Turc 2
clinical strain. The emergence of rifampin mutants was also investigated. Meropenem demonstrated a strong pulmonary bacterial reduction in animals infected with the
ATCC 17978
strain (unlike the CRAB strain). The high rifampin dosage was associated with a 1.3 Log
10
bacterial killing on average but induced the emergence of high-level resistant mutants in 80%–100% of animals, depending on the strain. The adjunction of rifampin to meropenem did not improve the bioburden in the lungs but partially reduced the number of animals exhibiting resistant mutants, whatever the tested strain. However, this adjunctive treatment was insufficient to overcome the emergence of resistance since mutation prevention concentration-related pharmacodynamic indices were unattainable at this dose. This CRAB pneumonia rabbit model represents an innovative tool to evaluate the efficacy of new or existing therapies and will provide informative data on how they can meet the resistance pharmacodynamic targets, which now need to be investigated before deciding on clinical therapeutic regimens.

IMPORTANCE

Within intensive care unit settings, carbapenem-resistant
Acinetobacter baumannii
(CRAB) has emerged as a frequent cause of hospital-acquired pneumonia (HAP) with poor clinical outcomes. This multidrug-resistant pathogen remains very challenging to study in clinical trials, and the U.S. Food and Drug Administration highlighted the limitations of existing small animal models for evaluating antibacterial or prophylactic strategies against such critical infections. These limitations include the difficulty in anticipating the risk of the emergence of resistance during treatment. Here we developed a new
Acinetobacter baumannii
pneumonia rabbit model using high inoculum. We demonstrated the emergence of resistance with rifampin, an existing antibiotic debated as a rescuing option to treat CRAB infections; and even intensified rifampin doses failed to close the mutant selection window. This CRAB pneumonia rabbit model represents a valuable tool to evaluate the efficacy of new or existing therapies and provides supportive data in antimicrobial resistance pharmacodynamics.
Sirtuin-dependent reversible lysine acetylation of the
o
-succinylbenzoyl-coenzyme A synthetase of
Bacillus subtilis
Authors: Burckhardt Rachel M. , Escalante-Semerena Jorge C. 
Published: October 2024

ABSTRACT

Reversible lysine acylation (RLA) is a conserved posttranslational modification that cells of all domains of life use to regulate the biological function of proteins, some of which have enzymatic activity. Many AMP-forming organic acid:CoA ligases are regulated
via
acylation in prokaryotes and eukaryotes. Here, we report the acetylation of the
o
-succinylbenzoyl-CoA synthetase (EC 6.2.1.26) of
Bacillus subtilis
(
Bs
MenE) by the GCN5-related acetyltransferase (GNAT) AcuA enzyme of this bacterium.
Bs
MenE is part of the metabolic pathway that assembles menaquinone (MK), an essential component of the electron transport chain in
B. subtilis
. We demonstrate that the active-site lysine 471 (K471) of
Bs
MenE is acetylated specifically by
Bs
AcuA, and that acetylated
Bs
MenE (
Bs
MenE
Ac
) is deacetylated by the NAD
+
-dependent sirtuin (
Bs
SrtN) of this bacterium. The
in vivo
analyses performed in this study were done in an
Escherichia coli
Δ
menE
strain because the enzymatic activity of MenE is essential in
B. subtilis
, but not in
E. coli
. The use of a heterologous system allowed us to assess the effect of acetylation on
Bs
MenE function under MK-dependent growth conditions. Based on our
in vivo
data, we suggest that regulation of
Bs
MenE by RLA reduces MK production, negatively affecting the growth rate and yield of the culture.

IMPORTANCE

Reversible lysine acylation (RLA) is a posttranslational modification used by all cells to rapidly control the biological function of proteins. Herein, we identify an acetyltransferase and deacetylase in the soil bacterium
Bacillus subtilis
that can modify/demodify an enzyme required for the synthesis of menaquinone (MK), an essential electron carrier involved in respiration in cells of all domains of life. Based on our data, we suggest that under some as-yet-undefined physiological conditions,
B. subtilis
modulates MK biosynthesis, which changes the flux of electrons through the electron transport chain of this bacterium. To our knowledge, this is the first example of control of respiration by RLA.