bluuebunny/crossref_metadata_2025 huggingface dataset:
Efficacy and safety of digital therapeutic application of Sleep Index‐Based Treatment for Insomnia (dSIBT‐I): a pilot study
Authors: Chung Seockhoon , Cho Inn‐Kyu , Kim Jiyoung , Lee Dongin , Cho Eulah , Choi Jung Mun , Ha Tae Kyoung , Lee Young Jun , Kim Ji Hyun , Choi Ji Ho
Published: September 2023

The aim of this study was to evaluate the safety and efficacy of digital therapeutic application of Sleep Index‐Based Treatment for Insomnia (dSIBT‐I) and compare them with those of digital application of Cognitive Behavioural Therapy for Insomnia (dCBT‐I). This randomised prospective pilot study was conducted at the Asan Medical Center. A total of 50 patients with insomnia were recruited between December 2022 and January 2023 and randomly allocated to the dSIBT‐I or dCBT‐I group. The study was carried out for one month. The primary outcome was the significant reduction in Insomnia Severity Index score at Week 4 compared to baseline, while the secondary outcome was proportion of participants whose Insomnia Severity Index scores were reduced to <15 at Week 4. We performed linear mixed model and generalised estimating equation analyses. Both dSIBT‐I and dCBT‐I groups showed significant improvements in Insomnia Severity Index scores at Week 4. There was no significant difference between two groups in terms of Insomnia Severity Index scores at Week 4 (group × time effect, F = 1.07, p = 0.382) and proportion of participants whose Insomnia Severity Index scores were reduced to <15 at Week 4 (group × time effects, F = 1.80, p = 0.615). However, at Week 2, the dSIBT‐I group showed better results than the dCBT‐I group in terms of both Insomnia Severity Index scores (p = 0.044) and proportion of participants whose Insomnia Severity Index scores were reduced to <15 (82.6% vs. 48.0%, p = 0.017). No treatment‐emergent adverse events were reported in either group. The dSIBT‐I is a safe and effective therapy for insomnia, with rapid treatment effects.
Give me a U, give me a V, give me an L!: How effective are countercyclical policies in shaping the output dynamic during recessions
Authors: Castañeda Gonzalo , Castro Peñarrieta Luis
Published: September 2023

In this paper, we argue that studying recession events through the shapes observed in sequences of GDP data can help to avoid methodological complications and offer new insights to traditional inquiries. With a set of 147 recession events from 77 countries, we analyze whether the shape of the output dynamic might be affected by the application of countercyclical policies. Firstly, we apply a machine learning technique to discover and cluster the shapes (or ‘shapelets’) that prevail in empirical spells. Secondly, we use a multinomial model to study fiscal and monetary interventions, in which we specify the categorical variable with a set of statistically different shapelets. Not only do we find strong empirical evidence that it is possible to overcome a recession through countercyclical policies, but also that there are non‐linear effects that make it more likely when the strength of these policies crosses certain thresholds.
ABA is required for differential cell wall acidification associated with root hydrotropic bending in tomato
Authors: Li Ying , Chen Yadi , Jiang Shuqiu , Dai Hui , Xu Weifeng , Zhang Qian , Zhang Jianhua , Dodd Ian C. , Yuan Wei
Published: September 2023

Hydrotropism is an important adaptation of plant roots to the uneven distribution of water, with current research mainly focused on Arabidopsis thaliana. To examine hydrotropism in tomato (Solanum lycopersicum) primary roots, we used RNA sequencing to determine gene expression of root tips (apical 5 mm) on dry and wet sides of hydrostimulated roots grown on agar plates. Hydrostimulation enhances cell division and expansion on the dry side compared with the wet side of the root tip. In hydrostimulated roots, the abscisic acid (ABA) biosynthesis gene ABA4 was induced more on the dry than the wet side of root tips. The ABA biosynthesis inhibitor Fluridone and the ABA‐deficient mutant notabilis (not) significantly decreased hydrotropic curvature. Wild‐type, but not the ABA biosynthesis mutant not, root tips showed asymmetric H+ efflux, with greater efflux on the dry than on the wet side of root tips. Thus, ABA mediates asymmetric H+ efflux, allowing the root to bend towards the wet side to take up more water.
Immune response, phenotyping and molecular graft surveillance in kidney transplant recipients following severe acute respiratory syndrome coronavirus 2 vaccination
Authors: Ali Nicole M , Herati Ramin S , Mehta Sapna A , Leonard Jeanette , Miles Jake , Lonze Bonnie E , DiMaggio Charles , Tatapudi Vasishta S , Stewart Zoe A , Alnazari Nasser , Neumann Henry J , Thomas Jeffrey , Cartiera Katarzyna , Weldon Elaina , Michael Jennifer , Hickson Christopher , Whiteson Harris , Khalil Karen , Stern Jeffrey M , Allen Joseph R , Tuen Michael , Gray‐Gaillard Sophie L , Solis Sabrina M , Samanovic Marie I , Mulligan Mark J , Montgomery Robert A
Published: September 2023

Background

Understanding immunogenicity and alloimmune risk following severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) vaccination in kidney transplant recipients is imperative to understanding the correlates of protection and to inform clinical guidelines.

Methods

We studied 50 kidney transplant recipients following SARS‐CoV‐2 vaccination and quantified their anti‐spike protein antibody, donor‐derived cell‐free DNA (dd‐cfDNA), gene expression profiling (GEP), and alloantibody formation.

Results

Participants were stratified using nucleocapsid testing as either SARS‐CoV‐2‐naïve or experienced prior to vaccination. One of 34 (3%) SARS‐CoV‐2 naïve participants developed anti‐spike protein antibodies. In contrast, the odds ratio for the association of a prior history of SARS‐CoV‐2 infection with vaccine response was 18.3 (95% confidence interval 3.2, 105.0, p < 0.01). Pre‐ and post‐vaccination levels did not change for median dd‐cfDNA (0.23% vs. 0.21% respectively, p = 0.13), GEP scores (9.85 vs. 10.4 respectively, p = 0.45), calculated panel reactive antibody, de‐novo donor specific antibody status, or estimated glomerular filtration rate.

Conclusions

SARS‐CoV‐2 vaccines do not appear to trigger alloimmunity in kidney transplant recipients. The degree of vaccine immunogenicity was associated most strongly with a prior history of SARS‐CoV‐2 infection.

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A Multivariate Method for Dynamic System Analysis: Multivariate Detrended Fluctuation Analysis Using Generalized Variance
Authors: Wallot Sebastian , Irmer Julien Patrick , Tschense Monika , Kuznetsov Nikita , Højlund Andreas , Dietz Martin
Published: September 2023

Fractal fluctuations are a core concept for inquiries into human behavior and cognition from a dynamic systems perspective. Here, we present a generalized variance method for multivariate detrended fluctuation analysis (mvDFA). The advantage of this extension is that it can be applied to multivariate time series and considers intercorrelation between these time series when estimating fractal properties. First, we briefly describe how fractal fluctuations have advanced a dynamic system understanding of cognition. Then, we describe mvDFA in detail and highlight some of the advantages of the approach for simulated data. Furthermore, we show how mvDFA can be used to investigate empirical multivariate data using electroencephalographic recordings during a time‐estimation task. We discuss this methodological development within the framework of interaction‐dominant dynamics. Moreover, we outline how the availability of multivariate analyses can inform theoretical developments in the area of dynamic systems in human behavior.
Biogeographic influences on the evolution and historical dispersal of the Australo‐Pacific Dacini fruit flies (Tephritidae: Dacinae)
Authors: Starkie Melissa L. , Cameron Stephen L. , Krosch Matt N. , Sweet Andrew D. , Clarke Anthony R.
Published: September 2023

Fruit flies (Tephritidae: Dacini) are a frugivorous insect group that exhibit high endemic diversity in the rainforests of Australia and the western Pacific. In this region, biogeography has been influenced by tectonic plate movements and cycles of isolation and re‐connection of landmasses and rainforest habitats during glacial periods. However, how such factors have influenced the speciation and historical dispersal of the regional Dacini is largely unknown. To address this, we use a dated phylogeny to reconstruct the biogeographical history of the tribe. We found the Dacini radiated eastward into the Pacific islands largely from sources in New Guinea. We also found evidence for historical dispersal from both Australia and New Guinea into New Caledonia, a pathway unique to this island compared with neighbouring islands. There was also evidence for multiple, bidirectional dispersal events between Papua New Guinea and Australia, likely facilitated by the cyclically exposed Torres Strait land bridge. Cape York in far northern Australia was likely the only entry point for species dispersing into Australia; there was no evidence for entry of flies into Australia directly from West Papua or Wallacea. Several lineages radiated after entering Australia, such as members of the Bactrocera dorsalis species group. Within Australia, speciation was not associated with the biogeographic barriers known to have impacted other rainforest fauna in eastern Australia. Overall, we demonstrate that isolation between islands and large landmasses is important in the evolution of the Australo‐Pacific Dacini, but the reason for their extensive radiation within Australia and Papua New Guinea remains unclear.
A Preliminary Report on Students’ Reflections about Their Learning in an Active Learning Classroom
Authors: Liang Su , Vega Tina
Published: September 2023

In the past decades, College Algebra has become a big hurdle for students to graduate or further pursue STEM or related careers. For most of the student population, College Algebra is a terminal course and only a small portion of students take it for further mathematics courses. The traditional content of College Algebra does not serve either group of students well (Mathematical Association of America, 2004; Mathematical Association of America & National Council of Teachers of Mathematics, 2012). In recent years, at a large Hispanic-serving university, the course design for liberal arts students has been changed. An active-learning curriculum has been implemented, namely Quantitative Reasoning. This curriculum engages students with opportunities to learn math concepts from relevant everyday sources and even their own personally collected data. Students build their own understanding of mathematics by relevant data-based situations experienced through preview activities designed to prepare students for class, collaboration in class discussion and discovery through relevant problem situations, and practice activities extending learning after each lesson. The purpose of this study was to investigate student perceptions of their learning outcomes from an active-learning structured course. That is, what impact does a course design with pre-assignment tasks, authentic problem solving through collaboration in class, and practice assignments after lessons have on diverse student populations in a quantitative reasoning course?
A functor for constructing R$R$‐matrices in the category O$\mathcal {O}$ of Borel quantum loop algebras
Authors: Pinet Théo
Published: September 2023

We tackle the problem of constructing ‐matrices for the category associated to the Borel subalgebra of an arbitrary untwisted quantum loop algebra . For this, we define an invertible exact functor from the category linked to to the one linked to . This functor is compatible with tensor products, preserves irreducibility, and interchanges the subcategories and of Hernandez and Leclerc (Algebra Number Theory 10 (2016) 2015–2052). We construct ‐matrices for by applying on the braidings already found for by Hernandez (Represent. Theory 26 (2022) 179–210). We also use the factorization of the latter intertwiners in terms of stable maps to deduce an analogous factorization for our new braidings. We finally obtain as byproducts new relations for the Grothendieck ring as well as a functorial interpretation of a remarkable ring isomorphism of Hernandez–Leclerc.
Parametric Reduced Order Model of a Gas Bearings Supported Rotor
Authors: Goutaudier Dimitri , Schiffmann Jüurg , Nobile Fabio
Published: September 2023

Gas bearings use pressurized gas as a lubricant to support and guide rotating machinery. These bearings have a number of advantages over traditional lubricated bearings, including higher efficiency in a variety of applications and reduced maintenance requirements. However, they are more complex to operate and exhibit nonlinear behaviors. This paper presents a parametric hyper reduced order model (h-ROM) of a gas bearings supported rotor enabling to speed up the computations up to a factor 100 while preserving satisfactory accuracy. A Galerkin projection setting is employed to reduce the dimension of the governing equations and the nonlinear terms are efficiently tackled with a sparse sampling technique. The performances of the h-ROM are compared to a high fidelity model both in terms of accuracy and computation time, demonstrating the potential for future anomaly detection applications.
Innovative Air Bypass System for Low-Emission Multi-Can Combustors
Authors: Ćosić Bernhard , Wassmer Dominik , Reiß Frank , Kluss David , Pähr Judith , Reumschüssel Johann Moritz , Beuth Jan Paul , Szeponik Martin , Reichel Thoralf , Paschereit Christian Oliver
Published: September 2023

Gas turbines that are used as compressor drives are often operated in the part load regime because compressor stations are usually designed for operation with full power at extreme weather conditions. Consequently, these gas turbines must comply with strict emission regulations at unfavorably low turbine inlet temperatures. To extend the low-emission operation range of the premixed combustion systems, many gas turbines bypass a part of the compressed air upstream of the combustor and either blow it off into the exhaust stack or reinject it into the secondary combustion zone. This study presents a new approach that overcomes shortcomings by injecting the compressed air in the burner head in the vicinity of the primary combustion zone. This is particularly attractive for multi-can combustors. Atmospheric combustion tests are conducted for two different air injection designs. The first design features lower air injection velocity and the second features higher injection velocities. Both injection strategies are tested with the industrial MGT gas turbine can combustor. The full size burner is tested at atmospheric conditions in a burner test rig with a quartz flame tube and natural gas as fuel. The performance of the air bypass system is assessed by means of CO and NOx emission measurements for different air bypass ratios. Additionally, OH* chemiluminescence camera pictures are presented and compared to numerical calculations. It is found that the air injection in the annular vicinity of the swirl flame does not cause increased CO emissions by quenching or other effects.
Failure Analysis of Urban Rail Transit Networks Incorporating Ridership Patterns
Authors: Saadat Yalda , Ayyub Bilal M. , Zhang Yanjie , Zhang Dongming , Huang Hongwei
Published: September 2023

In any nonlinear system as complex as an urban rail transit network or metrorail network, some incidence of perturbations of its state is inevitable. These perturbations, such as natural hazards, can highly affect the networks' resilience. Increasing the ability of metrorail networks to withstand such perturbations requires robustness and vulnerability assessments as key attributes of resilience and necessary steps toward developing reliable networks. Most models developed for this purpose associate a network's failures to binary representations of the failure of its components without incorporating weight factors. Since ridership is a primary factor to define the metrorail network performance, this paper proposes a general ridership pattern, considers different failure cases, and uses a novel methodology to quantitatively measure the weighted-network resilience attributes incorporating ridership throughout the Washington, DC Metrorail as a case study. The proposed methodology has clear relationships to adjacency and link-weight matrices and defines a new expression for the weighted global network efficiency based on the sum of weights on each geodesic path. Results show that the most vulnerable stations and links hold critical positions in the network topological structure and/or bear larger amounts of ridership. For the case study, the most vulnerable components include transfer stations located in the city center as well as stations and links on the northwest section of the Red Line. The methodology presented herein provides insights for enhancing critical components during the planning and operation of a metrorail by mitigating the risks associated with failure events.
Assessment of Bulk Oxygen Capacity and Transient Redox Behavior of Foamed Lanthanum Strontium Manganese Perovskites
Authors: McCord Dylan C. , Gager Elizabeth J. , Lee Kangjae , McDaniel Anthony H. , Nino Juan C. , Scheffe Jonathan R.
Published: September 2023

Synthesis of solar thermochemical hydrogen (STCH) production redox materials with engineered structures, for example, replica foams, can enable efficient heat and mass transport and are critical for scaled-up systems. Prior work has motivated the use of lanthanum strontium manganese (LSM)-type perovskites as foamed STCH materials, but the effect of their morphology on bulk and kinetic behavior has not been reported. In this work, replica and direct foamed samples of La0.65Sr0.35MnO3-δ (LSM35) were fabricated and compared to synthesized powders and dense monoliths, and similarly synthesized CeO2-δ (ceria) foams, regarding their specific reaction rates and bulk oxygen capacity/H2 yields. Changes in oxygen capacity (Δδ) and reaction rates were measured between 1200 °C and 1400 °C by using fixed ratios of steam and hydrogen during both reduction and oxidation steps, allowing for analysis under practical high conversion conditions. Results suggest bulk behavior and reaction rates of the foamed LSM materials are comparable to their powder analogues. Differences in reaction rates were observed only when replica foamed samples were subjected to rapid laser heating (emulating conditions expected in solar furnaces), which is expected but has not been demonstrated at such a small scale. Foamed samples were further subjected to 50 redox cycles at 1400 °C to evaluate their stability. Results show no statistically significant decrease in hydrogen production for any of the foamed samples, but the direct foamed samples became brittle with time. Together, these results demonstrate the viability of replica foamed LSM perovskites for integration in scaled-up STCH systems.
Modified Finite Difference Methods for Reynold Equation With Film Thickness Discontinuity
Authors: He Qiang , Hu Fengming , Huang Weifeng , Hu Yang , Cong Guohui , Zhang Yixun
Published: September 2023

In hydrodynamic lubrication problems, the presence of step structures on the surface can cause discontinuities in the film thickness. This article proposes two models for solving the two-dimensional Reynolds equation with film thickness discontinuity using the finite difference method (FDM). In model I, the film thickness variable is defined at the center of the mesh grids, allowing the Reynolds equation to be reformulated in a weak form that eliminates the singularity of film thickness discontinuity and satisfies the flow continuity condition at the film thickness discontinuity region. By considering the step boundary on the surface as the interface, model II is constructed based on the immersed interface method, turning the hydrodynamic lubrication problem into a classical interface problem. The jump conditions across the interface are derived in accordance with the continuous flow requirement. A phase-field function is adopted to describe the interface on the uniform rectangular mesh grids. Numerical experiments are conducted to assess the accuracy and capabilities of the two proposed models for analyzing a step-dimple-textured sealing. The results demonstrate that both modified FDM models can effectively address the thickness discontinuity issue. Model II achieves second-order accuracy for the pressure distribution when dealing with curved interfaces based on Cartesian grids, whereas model I demonstrates first-order accuracy. Both the proposed models exhibit superior accuracy compared to the traditional second-order central FDM when dealing with curved interfaces. Moreover, the performance of model II is further assessed by simulating lubrication problems with complex groove shapes, and the results indicate its flexibility in addressing thickness discontinuity problems with complex curve interface.
The Weekly Periodization of Top 5 Tour de France General Classification Finishers: A Multiple Case Study
Authors: Gallo Gabriele , Mateo-March Manuel , Gotti Daniel , Maunder Ed , Codella Roberto , Ruggeri Piero , Faelli Emanuela , Filipas Luca
Published: September 2023

Purpose: The aim of this study was to describe individual training characteristics, racing strategies, and periodization in preparation for the Tour de France in 2 world-class road cyclists finishing in the top 5 of the general classification. Methods: Week‐by‐week power meter training and racing data of 2 (A and B) road cyclists (age: 29 and 23 y; maximum oxygen consumption: 83 and 81 mL·min−1·kg−1; and relative 20‐min record power output: 6.9 and 6.5 W·kg−1) in the preparation phase (December–July/August) leading up to the Tour de France were retrospectively analyzed. Weekly volume and intensity distribution in power zones were considered. Results: Cyclists A and B completed 46 and 19 races, 22.5 (6.3) and 18.2 (5.1) h·wk−1, with a pyramidal intensity distribution of 81.0%–13.3%–5.7%, and 88.8%–7.9%–3.3% in zone 1–zone 2–zone 3. Cyclist B spent 14 days at altitude. Increased high-intensity volume and polarization index occurred during race weeks. During periods without racing, training intensity progressively increased. Strength training was performed during November and December but not during the following months. During tapering, total exercise volume and time at high intensity decreased. Conclusion: These data provide novel insights into the periodization of world-class road cyclists in advance of a top 5 placing in the Tour de France general classification.
Neuromedin U programs eosinophils to promote mucosal immunity of the small intestine
Authors: Li Yu , Liu Shaorui , Zhou Kewen , Wang Yinsheng , Chen Yan , Hu Wen , Li Shuyan , Li Hui , Wang Yan , Wang Qiuying , He Danyang , Xu Heping
Published: September 2023

Eosinophils are granulocytes that play an essential role in type 2 immunity and regulate multiple homeostatic processes in the small intestine (SI). However, the signals that regulate eosinophil activity in the SI at steady state remain poorly understood. Through transcriptome profiling of eosinophils from various mouse tissues, we found that a subset of SI eosinophils expressed neuromedin U (NMU) receptor 1 (NMUR1). Fate-mapping analyses showed that NMUR1 expression in SI eosinophils was programmed by the local microenvironment and further enhanced by inflammation. Genetic perturbation and eosinophil-organoid coculture experiments revealed that NMU-mediated eosinophil activation promotes goblet cell differentiation. Thus, NMU regulates epithelial cell differentiation and barrier immunity by stimulating NMUR1-expressing eosinophils in the SI, which highlights the importance of neuroimmune-epithelial cross-talk in maintaining tissue homeostasis.
Integrative conjugative elements mediate the high prevalence of
tmexCD3-toprJ1b
in
Proteus
spp. of animal source
Authors: Peng Kai , Li Yangfan , Wang Qiaojun , Yang Pengbin , Wang Zhiqiang , Li Ruichao
Published: September 2023

Integrative conjugative elements (ICEs) are important mobile elements that are associated with the dissemination of antibiotic resistance genes (ARGs) in
Proteus
. Recent studies demonstrated that the tigecycline resistance gene cluster
tmexCD-toprJ
has emerged in ICEs of
Proteus
. However, the prevalence of
tmexCD-toprJ
positive
Proteus
from animal sources is unclear. To cover the gap, a total of 762
Proteus
spp. were isolated from animal source from six provinces of China to identify the
tmexCD-toprJ
positive isolates. Eight
tmexCD-toprJ
positive isolates were identified, with the
tmexCD-toprJ
positive rate of 1.05% against all
Proteus
spp. and 2.79% against ICE-bearing
Proteus
spp. The
tmexCD-toprJ
gene cluster in these
Proteus
spp. were
tmexCD3-toprJ1b
and all of them were carried by ICEs. Genetic structure analysis showed that
tmexCD3-toprJ1b
-bearing ICEs were complicated and plastic, but the
tmexCD3-toprJ1b
was specifically integrated into variable region III (VRIII) of ICEs with the help of integrases. Furthermore, we found that the
umuC
gene, which is presented in VRIII of ICEs and other genetic structures of many other bacterial genomes, was a hotspot for the integration of
tmexCD-toprJ
-bearing potential mobile elements. In summary, our results suggested that
Proteus
were important reservoirs for
tmexCD-toprJ
due to the high prevalence of ICEs. Therefore, continuous surveillance of ICEs-associated ARGs in
Proteus
is necessary and significant for controlling their future transmission.

IMPORTANCE

The emergence and spread of
tmexCD-toprJ
have greatly weakened the function of tigecycline. Although studies have demonstrated the significance of
Proteus
as carriers for
tmexCD-toprJ
, the epidemic mechanism and characteristics of
tmexCD-toprJ
in
Proteus
remain unclear. Herein, we deciphered that the
umuC
gene in VRIII of SXT/R391 ICEs was a hotspot for the integration of
tmexCD3-toprJ1b
-bearing mobile genetic elements by genomic analysis. The mobilization and dissemination of
tmexCD3-toprJ1b
in
Proteus
were mediated by highly prevalent ICEs. Furthermore, the co-occurrence of
tmexCD3-toprJ1b
-bearing ICEs with other chromosomally encoded multidrug resistance gene islands warned that the chromosomes of
Proteus
are significant reservoirs of ARGs. Overall, our results provide significant insights for the prevention and control of
tmexCD3-toprJ1b
in
Proteus
.
Interplay between bacterial 5′-NAD-RNA decapping hydrolase NudC and DEAD-box RNA helicase CsdA in stress responses
Authors: Mickutė Milda , Krasauskas Renatas , Kvederavičiūtė Kotryna , Tupikaitė Gytė , Osipenko Aleksandr , Kaupinis Algirdas , Jazdauskaitė Monika , Mineikaitė Raminta , Valius Mindaugas , Masevičius Viktoras , Vilkaitis Giedrius
Published: September 2023

Both prokaryotic and eukaryotic RNAs can be 5′-capped by the metabolite nicotinamide adenine dinucleotide (NAD). Nudix hydrolases, such as bacterial NudC, specifically remove NAD-caps; however, the molecular and cellular functions of these epitranscriptomic modulators remain elusive. Here, we discuss the roles of NudC under stress conditions and the effects of extracellular cues on the NAD epitranscriptome. Our proteome-wide analysis detected the proteins associated with the RNA degradosome as well as ribosomes and stress-responsive proteins in a NudC interactome. Moreover, we confirmed the physical association of NudC with the cold shock DEAD-box RNA helicase CsdA and the RNA chaperone Hfq. Interestingly, knocking out
csdA
similar to ∆
nudC
leads to an increased number of identified 5′-NAD-RNA species compared to wild type, exposing CsdA as a new player in a potentially unexplored layer of NAD-epitranscriptomic landscape. Mass spectrometry analysis also revealed the drastic up-regulation of 5′-NAD-RNA in response to cold. Furthermore, the inactivation of NudC in bacteria changes the levels of sRNA and protein-coding transcripts associated with bacterial chemotaxis and flagellar assembly pathways. We experimentally demonstrate that the decapping hydrolase NudC suppresses the flagellar movement, while CsdA stimulates it. Thus, the interplay between NudC and CsdA regulates bacterial mobility and coordinates stress-avoidance behavior.

IMPORTANCE

Non-canonical 5′-caps removing RNA hydrolase NudC, along with stress-responsive RNA helicase CsdA, is crucial for 5′-NAD-RNA decapping and bacterial movement.
Antimicrobial resistance, pathogenic potential, and genomic features of carbapenem-resistant
Klebsiella pneumoniae
isolated in Chile: high-risk ST25 clones and novel mobile elements
Authors: Veloso Marcelo , Arros Patricio , Acosta Joaquin , Rojas Roberto , Berríos-Pastén Camilo , Varas Macarena , Araya Pamela , Hormazábal Juan Carlos , Allende Miguel L. , Chávez Francisco P. , Lagos Rosalba , Marcoleta Andrés E.
Published: September 2023

Multidrug- and carbapenem-resistant
Klebsiella pneumoniae
(CR-
Kp
) are critical threats to global health and key traffickers of resistance genes to other pathogens. Despite the sustained increase in CR-
Kp
infections in Chile, few strains have been described at the genomic level, lacking details of their resistance and virulence determinants and the mobile elements mediating their dissemination. In this work, we studied the antimicrobial susceptibility and performed a comparative genomic analysis of 10 CR-
Kp
isolates from the Chilean surveillance of carbapenem-resistant
Enterobacteriaceae
. High resistance was observed among the isolates (five ST25, three ST11, one ST45, and one ST505), which harbored 44 plasmids, most carrying genes for conjugation and resistance to several antibiotics and biocides. Ten plasmids encoding carbapenemases were characterized, including novel plasmids or variants with additional resistance genes, a novel genetic environment for
bla
KPC-2
, and plasmids widely disseminated in South America. ST25 K2 isolates belonging to CG10224, a clone traced back to 2012 in Chile, which recently acquired
bla
NDM-1
,
bla
NDM-7
, or
bla
KPC-2
plasmids stood out as high-risk clones. Moreover, this corresponds to the first report of ST25 and ST45
Kp
producing NDM-7 in South America and ST505 CR-
Kp
producing both NDM-7 and KPC-2 worldwide. Also, we characterized a variety of genomic islands carrying virulence and fitness factors. These results provide baseline knowledge for a detailed understanding of molecular and genetic determinants behind antibiotic resistance and virulence of CR
-Kp
in Chile and South America.

IMPORTANCE

In the ongoing antimicrobial resistance crisis, carbapenem-resistant strains of
Klebsiella pneumoniae
are critical threats to public health. Besides globally disseminated clones, the burden of local problem clones remains substantial. Although genomic analysis is a powerful tool for improving pathogen and antimicrobial resistance surveillance, it is still restricted in low- to middle-income countries, including Chile, causing them to be underrepresented in genomic databases and epidemiology surveys. This study provided the first 10 complete genomes of the Chilean surveillance for carbapenem-resistant
K. pneumoniae
in healthcare settings, unveiling their resistance and virulence determinants and the mobile genetic elements mediating their dissemination, placed in the South American and global
K. pneumoniae
epidemiological context. We found ST25 with K2 capsule as an emerging high-risk clone, along with other lineages producing two carbapenemases and several other resistance and virulence genes encoded in novel plasmids and genomic islands.
In vivo
gene expression profile of
Haemophilus influenzae
during human pneumonia
Authors: Polland Linnea , Rydén Hanna , Su Yi , Paulsson Magnus
Published: September 2023

Haemophilus influenzae
is a major cause of community-acquired pneumonia. While studied extensively in various laboratory models, less is known about the cell function while inside the human lung. We present the first analysis of the global gene expression of
H. influenzae
while the bacteria are in the lung during pneumonia (
in vivo
conditions) and contrast it with bacterial isolates that have been cultured under standard laboratory conditions (
in vitro
conditions). Patients with pneumonia were recruited from emergency departments and intensive care units during 2018–2020 (
n
= 102). Lower respiratory samples were collected for bacterial culture and RNA extraction. Patient samples with
H. influenzae
(
n
= 8) and colonies from bacterial cultures (
n
= 6) underwent RNA sequencing. The reads were then pseudo-aligned to core and pan genomes created from 15 reference strains. While bacteria cultured
in vitro
clustered tightly by principal component analysis of core genome (
n
= 1067) gene expression, bacteria in the patient samples had more diverse transcriptomic signatures and did not group with their lab-cultured counterparts. In total, 328 core genes were significantly differentially expressed between
in vitro
and
in vivo
conditions. The most highly upregulated genes
in vivo
included
tbpA
and
fbpA
, which are involved in the acquisition of iron from transferrin, and the stress response gene
msrAB
. The biosynthesis of nucleotides/purines and molybdopterin-scavenging processes were also significantly enriched
in vivo
. In contrast, major metabolic pathways and iron-sequestering genes were downregulated under this condition. In conclusion, extensive transcriptomic differences were found between bacteria while in the human lung and bacteria that were cultured
in vitro
.

IMPORTANCE

The human-specific pathogen
Haemophilus influenzae
is generally not well suited for studying in animal models, and most laboratory models are unlikely to approximate the diverse environments encountered by bacteria in the human airways accurately. Thus, we have examined the global gene expression of
H. influenzae
during pneumonia. Extensive differences in the global gene expression profiles were found in
H. influenzae
while in the human lung compared to bacteria that were grown in the laboratory. In contrast, the gene expression profiles of isolates collected from different patients were found to cluster together when grown under the same laboratory conditions. Interesting observations were made of how
H. influenzae
acquires and uses iron and molybdate, endures oxidative stress, and regulates central metabolism while in the lung. Our results indicate important processes during infection and can guide future research on genes and pathways that are relevant in the pathogenesis of
H. influenzae
pneumonia.
Temporal approach to identifying ectomycorrhizal community associated with Mongolian pine in a desert environment, northern China
Authors: Ren Yue , Gao Guanglei , Ding Guodong , Zhang Ying , Zhao Peishan , Wang Jiayuan
Published: September 2023

To date, the ectomycorrhizal (EM) fungi community has been widely investigated with aging plantations affected by the pedologic factors. However, knowledge on the effects of phenology induced by climatic factors across the age range remains poorly understood on an intra-annual scale. Here, we sampled the fine roots of Mongolian pine (
Pinus sylvestris
var.
mongolica
) plantations at different stages of the growing season (from April to September) across three stand ages (27, 34, and 44 yr) in the Mu Us Desert, Northwest China. We aim to disentangle the community composition and structure of EM fungi, as well as the impact of climate on EM fungi. We observed that the 173 distinct EM fungal operational taxonomic units (OTUs) were identified.
Geopora
,
Inocybe
,
Tomentella,
and
Tuber
were the most frequent, and their dominance was maintained as stand aging. The richness and community composition were not significantly different with stand aging (
P
> 0.05). Host phenology and stand age are two important factors that have shaped the EM fungal community. The growing stage affected the beta diversity of the EM fungal community more than stand age, and this variation of the EM fungal community was closely related to seasonal climate, particularly precipitation. This improved information will provide a theoretical basis for the reforestation and rehabilitation of the Mongolian pine plantations using mycorrhizal techniques.

IMPORTANCE

Ectomycorrhizal (EM) fungi are particularly important for host plants in a desert ecosystem. With a high degree of plasticity, EM fungi are largely influenced by host plant and environmental variables and fundamentally contribute to the ability of individuals to adapt to environmental changes. Therefore, the EM fungi are important for Mongolian pine (
Pinus sylvestris
var.
mongolica
) plantation in a desert ecosystem. Although previous studies have concluded that multiple endogenous and exogenous processes ultimately lead to species-specific temporal patterns in EM fungal populations. We still neglect the effect of host phenology on EM fungal activity. The significance of our study is the interplay between climate-driven EM fungi and plant phenology.
Canine respiratory coronavirus in Thailand undergoes mutation and evidences a potential putative parent for genetic recombination
Authors: Poonsin Panida , Wiwatvisawakorn Vorapun , Chansaenroj Jira , Poovorawan Yong , Piewbang Chutchai , Techangamsuwan Somporn
Published: September 2023

Canine respiratory coronavirus (CRCoV) is associated with canine infectious respiratory disease complex. Although its detection has been reported worldwide, the genomic characteristics and evolutionary patterns of this virus remain poorly defined. In this study, 21 CRCoV sequences obtained from dogs in Thailand during two episodes (2013–2015, group A; 2021–2022, group B) were characterized and analyzed. The genomic characteristics of Thai CRCoVs changed from 2013 to 2022 and showed a distinct phylogenetic cluster. Phylogenetic analysis of the spike (S) genes divided the analyzed CRCoV strains into five clades. The full-length genome characterization revealed that all Thai CRCoVs possessed a nonsense mutation within the nonstructural gene located between the S and envelope genes, leading to a truncated putative nonstructural protein. Group B Thai CRCoV strains represented the signature nonsynonymous mutations in the S gene that was not identified in group A Thai CRCoVs, suggesting the ongoing evolutionary process of Thai CRCoVs. Although no evidence of recombination of Thai CRCoV strains was found, our analysis identified one Thai CRCoV strain as a potential parent virus for a CRCoV strain found in the United States. Selective pressure analysis of the hypervariable S region indicated that the CRCoV had undergone purifying selection during evolution. Evolutionary analysis suggested that the CRCoV was emerged in 1992 and was first introduced in Thailand in 2004, sharing a common ancestor with Korean CRCoV strains. These findings regarding the genetic characterization and evolutionary analysis of CRCoVs add to the understanding of CRCoVs.

IMPORTANCE

Knowledge of genomic characterization of the CRCoV is still limited and its evolution remains poorly investigated. We, therefore, investigated the full-length genome of CRCoV in Thailand for the first time and analyzed the evolutionary dynamic of CRCoV. Genomic characterization of Thai CRCoV strains revealed that they possess unique genome structures and have undergone nonsynonymous mutations, which have not been reported in previously described CRCoV strains. Our work suggests that the Thai CRCoVs were not undergone mutation through genetic recombination for their evolution. However, one Thai CRCoV strain PP158_THA_2015 was found to be a potential parent virus for the CRCoV strains found in the United States. This study provides an understanding of the genomic characterization and highlights the signature mutations and ongoing evolutionary process of CRCoV that could be crucial for monitoring in the future.
Host-specific adaptation drove the coevolution of leek yellow stripe virus and
Allium
plants
Authors: Kawakubo Shusuke , Kim Hangil , Takeshita Minoru , Masuta Chikara
Published: September 2023

Host adaptation plays a crucial role in virus evolution and is a consequence of long-term interactions between virus and host in a complex arms race between host RNA silencing and viral RNA silencing suppressor (RSS) as counterdefense. Leek yellow stripe virus (LYSV), a potyvirus causing yield loss of garlic, infects several species of
Allium
plants. The unexpected discovery of an interspecific hybrid of garlic, leek, and great-headed (GH) garlic motivated us to explore the host-adaptive evolution of LYSV. Here, using Bayesian phylogenetic comparative methods and a functional assay of viral RSS activity, we show that the evolutionary context of LYSV has been shaped by the host adaptation of the virus during its coevolution with
Allium
plants. Our phylogenetic analysis revealed that LYSV isolates from leek and their taxonomic relatives (
Allium ampeloprasum
complex; AAC) formed a distinct monophyletic clade separate from garlic isolates and are likely to be uniquely adapted to AAC. Our comparative studies on viral accumulation indicated that LYSV accumulated at a low level in leek, whereas LYSVs were abundant in other
Allium
species such as garlic and its relatives. When RSS activity of the viral P1 and HC-Pro of leek LYSV isolate was analyzed, significant synergism in RSS activity between the two proteins was observed in leek but not in other species, suggesting that viral RSS activity may be important for the viral host-specific adaptation. We thus consider that LYSV may have undergone host-specific evolution at least in leek, which must be driven by speciation of its
Allium
hosts.

IMPORTANCE

Potyviruses are the most abundant plant RNA viruses and are extremely diversified in terms of their wide host range. Due to frequent host switching during their evolution, host-specific adaptation of potyviruses may have been shaped by numerous host factors. However, any critical determinants for viral host range remain largely unknown, possibly because of the repeated gain and loss of virus infectivity of plants. Leek yellow stripe virus (LYSV) is a species of the genus
Potyvirus
, which has a relatively narrow host range, generally limited to hosts in the genus
Allium
. Our investigations on leek and leek relatives (
Allium ampeloprasum
complex), which must have been generated through interspecies hybridization, revealed that LYSV accumulation remained low in leek as a result of viral host adaptation in competition with host resistance such as RNA silencing. This study presents LYSV as an ideal model to study the process of host-adaptive evolution and virus-host coevolution.
Eugenol works synergistically with colistin against colistin-resistant
Pseudomonas aeruginosa
and
Klebsiella pneumoniae
isolates by enhancing membrane permeability
Authors: Kong Jingchun , Wang Yue , Yao Zhuocheng , Lin Yishuai , Zhang Yi , Han Yijia , Zhou Tieli , Ye Jianzhong , Cao Jianming
Published: September 2023

Colistin is a potent antibiotic for the treatment of carbapenem-resistant Gram-negative bacteria and is considered a last-resort drug. Unfortunately, the incidence of colistin-resistant bacteria isolated from patients is continuously growing due to clinical reuse of colistin. In this study, we found that the combination of colistin and eugenol has a significant synergistic antibacterial effect and reverses the sensitivity of colistin-resistant
Pseudomonas aeruginosa
and
Klebsiella pneumoniae
against colistin, as confirmed by checkerboard and time-kill assays. Crystal violet staining and scanning electron microscopy revealed colistin and eugenol’s synergistic antibiofilm action. Concerning the synergy mechanism, the results revealed that the combination of eugenol and colistin increases membrane permeability and causes considerable membrane damage, further inhibiting bacteria synergistically. Meanwhile, up to 500 µg/mL of eugenol is non-toxic to RAW 264.7 cells, and the colistin/eugenol combination is also efficacious
in vivo
, as demonstrated by the
Galleria mellonella
infection model. Our findings indicate that the colistin/eugenol combination is a viable treatment option for colistin-resistant
P. aeruginosa
and
K. pneumoniae
clinical infections.

IMPORTANCE

Colistin is used as a last resort for severe infections caused by multidrug-resistant Gram-negative bacteria, however, colistin resistance is increasing. As a result, we investigated the synergistic effect of eugenol/colistin combination, and the results revealed significant antibacterial and antibiofilm action. Eugenol may help clinical colistin-resistant
Pseudomonas aeruginosa
and
Klebsiella pneumoniae
recover their susceptibility. These findings suggest that combining eugenol and colistin may be a viable treatment option for colistin-resistant pathogen clinical infections.
Normative value of hyperopia reserve and myopic shift in Chinese children and adolescents aged 3–16 years
Authors: Wang Jingjing , Qi Ziyi , Feng Yanqing , Chen Jun , Du Linlin , Yang Jinliuxing , Xie Hui , Zhu Jianfeng , Zou Haidong , He Xiangui , Xu Xun
Published: September 2023

Background

This research aims to generate normative values of hyperopia reserve and refractive progression as effective tools to estimate the risk of myopia.

Methods

A 1-year follow-up study was conducted among Chinese children and adolescents aged 3–16 years selected from schools and kinder gardens using cluster sampling. All participants underwent examinations including visual acuity, axial length and cycloplegic autorefraction (1% cyclopentolate). Percentiles of spherical equivalent (SE) were calculated using Lambda-Mu-Sigma (LMS) method. Age-specific refractive progression and hyperopia reserve were determined by backward calculation.

Results

Of 3118 participants, 1702 (54.6%) were boys with a mean baseline age of 7.30 years. The 50th percentile of SE estimated by LMS decreased from 1.04 D at 3 years to −2.04 D at 16 years in boys, while from 1.29 D to −2.81 D in girls. The 1-year refractive progression of myopes (0.81 D) was greater than that of non-myopes (0.51 D). The normative value of hyperopia reserve was 2.64 (range: 2.40 D–2.88 D) at 3 years and −0.35 (range: −0.50 to −0.17) D at 16 years, with the maximum progression of 0.35 D at the age of 6 years.

Conclusion

Age-specific normative values of hyperopia reserve and yearly myopic shift in children and adolescents aged 3–16 years were provided, helping identify and monitor myopia and giving prevention in advance.