bluuebunny/crossref_metadata_2025 huggingface dataset:
Myths and methodologies: Assessment of dynamic cerebral autoregulation by the mean flow index
Authors: Olsen Markus Harboe , Riberholt Christian Gunge , Berg Ronan M. G. , Møller Kirsten
Published: February 2024

The mean flow index—usually referred to as Mx—has been used for assessing dynamic cerebral autoregulation (dCA) for almost 30 years. However, concerns have arisen regarding methodological consistency, construct and criterion validity, and test–retest reliability. Methodological nuances, such as choice of input (cerebral perfusion pressure, invasive or non‐invasive arterial pressure), pre‐processing approach and artefact handling, significantly influence mean flow index values, and previous studies correlating mean flow index with other established dCA metrics are confounded by inherent methodological flaws like heteroscedasticity, while the mean flow index also fails to discriminate individuals with presumed intact versus impaired dCA (discriminatory validity), and its prognostic performance (predictive validity) across various conditions remains inconsistent. The test–retest reliability, both within and between days, is generally poor. At present, no single approach for data collection or pre‐processing has proven superior for obtaining the mean flow index, and caution is advised in the further use of mean flow index‐based measures for assessing dCA, as current evidence does not support their clinical application.
Inertial Parameter Identification for Closed-Loop Mechanisms: Adaptation of Linear Regression for Coordinate Partitioning
Authors: Pyrhönen Lauri , Willems Thijs , Mikkola Aki , Naets Frank
Published: February 2024

This study investigates the use of linear-regression-based identification in rigid multibody system applications. A multibody system model, originally described with differential-algebraic equations (DAE), is transformed into a set of ordinary differential equations using coordinate partitioning. This allows the identification framework (where the system is described with ordinary differential equations) to be applied to rigid multibody systems described with nonminimal coordinates. The methodology is demonstrated via numerical and experimental validation on a slider–crank mechanism. The results show that the presented methodology is capable of accurately identifying the system's inertial parameters even with a short motion trajectory used for training. The presented linear-regression-based identification approach opens new opportunities to develop more accurate multibody models. The resulting updated multibody models can be considered especially useful for state-estimation and the control of multibody systems.
A Decoupling Algorithm for Efficient Estimation of Failure Probability Function Based on Statistical Moment Functions
Authors: Li Hengchao , Lu Zhenzhou , Feng Kaixuan
Published: February 2024

Failure probability function (FPF) is an important index that reflects the influence of designable distribution parameters on the safety degree of a structure, and it can be used for decoupling reliability optimization models. Thus, its efficient solution is expected. A decoupling algorithm based on statistical moment functions (SMFs) of performance function is proposed to solve the FPF efficiently in this paper. The proposed algorithm first constructs an extended density weight function (EDWF), which can cover the interested region of the distribution parameters and is independent of the distribution parameters so that the statistical moment integrals corresponding to different realizations of the distribution parameters can share the same EDWF. Then, using the same EDWF, a strategy is dexterously designed to estimate the SMFs by sharing a set of integral characteristic nodes. Finally, the FPF is approximated by the SMFs, which varies with the distribution parameters in the interested design region. In addition, the proposed algorithm introduces the Box–Cox transformation of the performance function to guide the high accuracy of FPF approximated by the SMFs. The main contribution of the proposed algorithm is constructing the EDWF to decouple the dependence of solving SMFs on the realizations of the distribution parameters over the interested region and designing the strategy of estimating the SMFs by sharing the same integral characteristic nodes. Since the proposed algorithm employs a point estimation method to evaluate the FPF, it has higher efficiency than the competitive methods. Numerical and engineering examples demonstrate the superiority of the proposed algorithm.
A reduced-order-model-based equivalent circuit for piezoelectric micro-electro-mechanical-system loudspeakers modeling
Authors: Gazzola C. , Zega V. , Corigliano A. , Lotton P. , Melon M.
Published: February 2024

Piezoelectric micro-electro-mechanical-system (MEMS) speakers are emerging as promising implementations of loudspeakers at the microscale, as they are able to meet the ever-increasing requirements for modern audio devices to become smaller, lighter, and integrable into digital systems. In this work, we propose a finite element model (FEM)–assisted lumped-parameters equivalent circuit for a fast and accurate modeling of these types of devices. The electro-mechanical parameters are derived from a pre-stressed FEM eigenfrequency analysis, to account for arbitrarily complex geometries and for the shift of the speaker resonance frequency due to an initial non-null pre-deflected configuration. The parameters of the acoustical circuit are instead computed through analytical formulas. The acoustic short-circuit between the speaker front and rear sides is taken into account through a proper air-gaps modeling. The very good matching in terms of radiated sound pressure level among the equivalent circuit predictions, FEM simulations, and experimental data proves the ability of the proposed method to accurately simulate the speaker performance. Moreover, due to its generality, it represents a versatile tool for designing piezoelectric MEMS speakers.
Ecological sound loudness in environmental sound representations
Authors: Oszczapinska Urszula , Heller Laurie M. , Jang Seojun , Nance Bridget
Published: February 2024

Listeners recognizing environmental sounds must contend with variations in level due to the source level and the environment. Nonetheless, variations in level disrupt short-term sound recognition [Susini, Houix, Seropian, and Lemaitre (2019). J. Acoust. Soc. Am. 146(2), EL172–EL176] suggesting that loudness is encoded. We asked whether the experimental custom of setting sounds to equal levels disrupts long-term recognition, especially if it creates a mismatch with ecological loudness. Environmental sounds were played at equalized or ecological levels. Although recognition improved with increased loudness and familiarity, this relationship was unaffected by equalization or real-life experience with the source. However, sound pleasantness was altered by deviations from the ecological level.
Interparticle friction in sheared dense suspensions: Comparison of the viscous and frictional rheology descriptions
Authors: Peerbooms Wouter , Nadorp Tim , van der Heijden Antoine , Breugem Wim-Paul
Published: February 2024

In the literature, two different frameworks exist for describing the rheology of solid/liquid suspensions: (1) the “viscous” framework in terms of the relative suspension viscosity, ηr, as a function of the reduced solid volume fraction, ϕ/ϕm, with ϕm the maximum flowable packing fraction, and (2) the “frictional” framework in terms of a macroscopic friction coefficient, μ, as a function of the viscous number, Iv, defined as the ratio of the viscous shear to the wall-normal particle stress. Our goal is to compare the two different frameworks, focusing on the effect of friction between particles. We have conducted a particle-resolved direct numerical simulation study of a dense non-Brownian suspension of neutrally buoyant spheres in slow plane Couette flow. We varied the bulk solid volume fraction from ϕb=0.1 to 0.6 and considered three different Coulomb friction coefficients: μc=0, 0.2, and 0.39. We find that ηr scales well with ϕ/ϕm, with ϕm obtained from fitting the Maron–Pierce correlation. We also find that μ scales well with Iv. Furthermore, we find a monotonic relation between ϕ/ϕm and Iv, which depends only weakly on μc. Since ηr=μ/Iv, we thus find that the two frameworks are largely equivalent and that both account implicitly for Coulomb friction. However, we find that the normal particle stress differences, N1 and N2, when normalized with the total shear stress and plotted against either ϕ/ϕm or Iv, remain explicitly dependent on μc in a manner that is not yet fully understood.
The Efficiency of Respiratory Exercises in Rehabilitation of Low Back Pain: A Systematic Review and Meta-Analysis
Authors: Zhai Haiting , Zhang Liqing , Xia JiXiang , Li Cheng
Published: February 2024

Background: Low back pain (LBP) is a common musculoskeletal disorder, and respiratory exercise is considered a nonsurgical management method. Therefore, this systematic review and meta-analysis aims to estimate the results of randomized controlled trials on the effect of respiratory training in reducing LBP and its dose relationship. Methods: The present study was conducted from January 2020 to January 2022, following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines (2020). Relevant studies were searched in multiple databases including PubMed, Web of Science, the Cochrane Library, EBSCO, Scopus, ScienceDirect, Wan Fang and China Knowledge Network, ClinicalTrials.gov, and Google Scholar, using a combination of MeSH/Emtree terms and free-text words. The heterogeneity of the studies was assessed using the I2 statistic. Results: A total of 14 publications were included in the meta-analysis, with a total sample size of 698 individuals, aged 60–80 years. Respiratory exercise was effective in relieving LBP (standardized mean difference = −0.87, P < .00001) and improving physical disability (standardized mean difference = −0.79, P < .00001). The type of breathing and the total duration of breathing exercises were found to be the source of heterogeneity in this study by subgroup analysis. Subgroup analysis revealed that the most significant effect sizes of breathing resistance exercise to reduce LBP and the most significant effect sizes of breathing relaxation techniques to alleviate physical disability were performed 3 to 5 times per week and period >4 weeks. Respiratory exercise reducing LBP and improving functional disability was most effective when the total duration of the intervention was >500 minutes. Funnel plots showed that the results of the 2 overall studies were reliable without publication bias. Conclusions: Respiratory exercise can effectively reduce LBP and improve physical disability. Therefore, these exercises can be regarded as a part of a LBP management plan. We recommend an exercise program with 30 to 50 minutes, 3 to 5 times per week, and >4 weeks of breathing resistance exercise program as the most effective for treating LBP.
A multi-species outbreak of VIM-producing carbapenem-resistant bacteria in a burn unit and subsequent investigation of rapid development of cefiderocol resistance
Authors: Freiberg Jeffrey A. , Tao Lili , Manuel Carmila , Mike Laura A. , Nelson George E. , Harris Bryan D. , Mathers Amy J. , Talbot Thomas R. , Skaar Eric P. , Humphries Romney M.
Published: February 2024

Carbapenem resistance due to metallo-β-lactamases (MBLs) such as the Verona integron-encoded metallo-β-lactamase (VIM) is particularly problematic due to the limited treatment options. We describe a case series of bacterial infections in a tertiary care hospital due to multi-species acquisition of a VIM gene along with our experience using novel β-lactam antibiotics and antibiotic combinations to treat these infections. Four patients were treated with the combination of ceftazidime-avibactam and aztreonam, with no resistance to the combination detected. However, cefiderocol-resistant
Klebsiella pneumoniae
isolates were detected in two out of the five patients who received cefiderocol within 3 weeks of having started the antibiotic. Strain pairs of sequential susceptible and resistant isolates from both patients were analyzed using whole-genome sequencing. This analysis revealed that the pairs of isolates independently acquired point mutations in both the
cirA
and
fiu
genes, which encode siderophore receptors. These point mutations were remade in a laboratory strain of
K. pneumoniae
and resulted in a significant increase in the MIC of cefiderocol, even in the absence of a beta-lactamase enzyme or a penicillin-binding protein 3 (PBP3) mutation. While newer β-lactam antibiotics remain an exciting addition to the antibiotic armamentarium, their use must be accompanied by diligent monitoring for the rapid development of resistance.
Interspecies variability in protein binding of antibiotics basis for translational PK/PD studies—a case study using cefazolin
Authors: Ahmed Hifza , Böhmdorfer Michaela , Eberl Sabine , Jäger Walter , Zeitlinger Markus
Published: February 2024

For antimicrobial agents in particular, plasma protein binding (PPB) plays a pivotal role in deciphering key properties of drug candidates. Animal models are generally used in the preclinical development of new drugs to predict their effects in humans using translational pharmacokinetics/pharmacodynamics (PK/PD). Thus, we compared the protein binding (PB) of cefazolin as well as bacterial growth under various conditions
in vitro
. The PB extent of cefazolin was studied in human, bovine, and rat plasmas at different antibiotic concentrations in buffer and media containing 20–70% plasma or pure plasma using ultrafiltration (UF) and equilibrium dialysis (ED). Moreover, bacterial growth and time–kill assays were performed in Mueller Hinton Broth (MHB) containing various plasma percentages. The pattern for cefazolin binding to plasma proteins was found to be similar for both UF and ED. There was a significant decrease in cefazolin binding to bovine plasma compared to human plasma, whereas the pattern in rat plasma was more consistent with that in human plasma. Our growth curve analysis revealed considerable growth inhibition of
Escherichia coli
at 70% bovine or rat plasma compared with 70% human plasma or pure MHB. As expected, our experiments with cefazolin at low concentrations showed that
E. coli
grew slightly better in 20% human and rat plasma compared to MHB, most probably due to cefazolin binding to proteins in the plasma. Based on the example of cefazolin, our study highlights the interspecies differences of PB with potential impact on PK/PD. These findings should be considered before preclinical PK/PD data can be extrapolated to human patients.
Methionine oxidation of carbohydrate-active enzymes during white-rot wood decay
Authors: Molinelli Lise , Drula Elodie , Gaillard Jean-Charles , Navarro David , Armengaud Jean , Berrin Jean-Guy , Tron Thierry , Tarrago Lionel
Published: February 2024

White-rot fungi employ secreted carbohydrate-active enzymes (CAZymes) along with reactive oxygen species (ROS), like hydrogen peroxide (H
2
O
2
), to degrade lignocellulose in wood. H
2
O
2
serves as a co-substrate for key oxidoreductases during the initial decay phase. While the degradation of lignocellulose by CAZymes is well documented, the impact of ROS on the oxidation of the secreted proteins remains unclear, and the identity of the oxidized proteins is unknown. Methionine (Met) can be oxidized to Met sulfoxide (MetO) or Met sulfone (MetO
2
) with potential deleterious, antioxidant, or regulatory effects. Other residues, like proline (Pro), can undergo carbonylation. Using the white-rot
Pycnoporus cinnabarinus
grown on aspen wood, we analyzed the Met content of the secreted proteins and their susceptibility to oxidation combining H
2
18
O
2
with deep shotgun proteomics. Strikingly, their overall Met content was significantly lower (1.4%) compared to intracellular proteins (2.1%), a feature conserved in fungi but not in metazoans or plants. We evidenced that a catalase, widespread in white-rot fungi, protects the secreted proteins from oxidation. Our redox proteomics approach allowed the identification of 49 oxidizable Met and 40 oxidizable Pro residues within few secreted proteins, mostly CAZymes. Interestingly, many of them had several oxidized residues localized in hotspots. Some Met, including those in GH7 cellobiohydrolases, were oxidized up to 47%, with a substantial percentage of sulfone (13%). These Met are conserved in fungal homologs, suggesting important functional roles. Our findings reveal that white-rot fungi safeguard their secreted proteins by minimizing their Met content and by scavenging ROS and pinpoint redox-active residues in CAZymes.

IMPORTANCE

The study of lignocellulose degradation by fungi is critical for understanding the ecological and industrial implications of wood decay. While carbohydrate-active enzymes (CAZymes) play a well-established role in lignocellulose degradation, the impact of hydrogen peroxide (H
2
O
2
) on secreted proteins remains unclear. This study aims at evaluating the effect of H
2
O
2
on secreted proteins, focusing on the oxidation of methionine (Met). Using the model white-rot fungi
Pycnoporus cinnabarinus
grown on aspen wood, we showed that fungi protect their secreted proteins from oxidation by reducing their Met content and utilizing a secreted catalase to scavenge exogenous H
2
O
2
. The research identified key oxidizable Met within secreted CAZymes. Importantly, some Met, like those of GH7 cellobiohydrolases, undergone substantial oxidation levels suggesting important roles in lignocellulose degradation. These findings highlight the adaptive mechanisms employed by white-rot fungi to safeguard their secreted proteins during wood decay and emphasize the importance of these processes in lignocellulose breakdown.
Deciphering the metabolism of
Lactobacillus delbrueckii
subsp.
delbrueckii
during soy juice fermentation using phenotypic and transcriptional analysis
Authors: Harlé Olivier , Niay Jérôme , Parayre Sandrine , Nicolas Aurélie , Henry Gwenaële , Maillard Marie-Bernadette , Valence Florence , Thierry Anne , Guédon Éric , Falentin Hélène , Deutsch Stéphanie-Marie
Published: February 2024

In the context of sustainable diet, the development of soy-based yogurt fermented with lactic acid bacteria is an attractive alternative to dairy yogurts. To decipher the metabolism of
Lactobacillus delbrueckii
subsp.
delbrueckii
during soy juice (SJ) fermentation, the whole genome of the strain CIRM-BIA865 (
Ld
865) was sequenced and annotated. Then
Ld
865 was used to ferment SJ. Samples were analyzed throughout fermentation for their cell number, carbohydrate, organic acid, free amino acid, and volatile compound contents. Despite acidification, the number of
Ld
865 cells did not rise, and microscopic observations revealed the elongation of cells from 3.6 µm (inoculation) to 36.9 µm (end of fermentation). This elongation was observed in SJ but not in laboratory-rich medium MRS. Using transcriptomic analysis, we showed that the biosynthesis genes of peptidoglycan and membrane lipids were stably expressed, in line with the cell elongation observed, whereas no genes implicated in cell division were upregulated. Among the main sugars available in SJ (sucrose, raffinose, and stachyose),
Ld
865 only used sucrose. The transcriptomic analysis showed that
Ld
865 implemented the two transport systems that it contains to import sucrose: a PTS system and an ABC transporter. To fulfill its nitrogen needs,
Ld
865 probably first consumed the free amino acids of the SJ and then implemented different oligopeptide transporters and proteolytic/peptidase enzymes. In conclusion, this study showed that
Ld
865 enables fast acidification of SJ, despite the absence of cell division, leads to a product rich in free amino acids, and also leads to the production of aromatic compounds of interest.

IMPORTANCE

To reduce the environmental and health concerns related to food, an alternative diet is recommended, containing 50% of plant-based proteins. Soy juice, which is protein rich, is a relevant alternative to animal milk, for the production of yogurt-like products. However, soy “beany” and “green” off-flavors limit the consumption of such products. The lactic acid bacteria (LAB) used for fermentation can help to improve the organoleptic properties of soy products. But metabolic data concerning LAB adapted to soy juice are lacking. The aim of this study was, thus, to decipher the metabolism of
Lactobacillus delbrueckii
subsp.
delbrueckii
during fermentation of a soy juice, based on a multidisciplinary approach. This result will contribute to give tracks for a relevant selection of starter. Indeed, the improvement of the organoleptic properties of these types of products could help to promote plant-based proteins in our diet.
Proceedings of the Clinical Microbiology Open 2022—assessing clinical laboratory and industry responses to COVID-19 pandemic testing capacity challenges (part 1)
Authors: Peaper David R. , Doern Christopher D. , Sharp Susan ,   On behalf of the ASM Clinical and Public Health Microbiology Committee and the ASM Corporate Council
Published: February 2024

As the COVID-19 pandemic winds down, clinical and public health laboratories, along with industry partners, reflect on the successes and failures of the pandemic response. To capture the lessons learned and better prepare for the next pandemic, the Clinical Microbiology Open (CMO) assembled key stakeholders including directors of clinical laboratories, industry partners, and state and federal agencies such as the Centers for Disease Control and Prevention and the Food and Drug Administration. Participants were asked to provide their perspectives on the initial pandemic response, supply chain constraints especially during surges, staffing challenges, test triage and communication strategies, clinical informatics needs, laboratory financial impacts of SARS-CoV-2 testing, and the emergency use authorization process. This manuscript summarizes the diagnostic laboratory and industry perspectives on these issues that were presented and discussed at CMO and proposes some steps that could be taken to improve future pandemic responses.
Influenza D virus utilizes both 9-
O
-acetylated
N
-acetylneuraminic and 9-
O
-acetylated
N
-glycolylneuraminic acids as functional entry receptors
Authors: Uprety Tirth , Yu Jieshi , Nogales Aitor , Naveed Ahsan , Yu Hai , Chen Xi , Liu Yunpeng , Bowman Andrew S. , Martinez-Sobrido Luis , Parrish Colin R. , Melikyan Gregory B. , Wang Dan , Li Feng
Published: February 2024

Influenza D virus (IDV) utilizes bovines as a primary reservoir with periodical spillover to other hosts. We have previously demonstrated that IDV binds both 9-
O
-acetylated
N
-acetylneuraminic acid (Neu5,9Ac
2
) and 9-
O
-acetylated
N
-glycolylneuraminic acid (Neu5Gc9Ac). Bovines produce both Neu5,9Ac
2
and Neu5Gc9Ac, while humans are genetically unable to synthesize Neu5Gc9Ac. 9-
O
-Acetylation of sialic acids is catalyzed by CASD1 via a covalent acetyl-enzyme intermediate. To characterize the role of Neu5,9Ac
2
and Neu5Gc9Ac in IDV infection and determine which form of 9-
O
-acetylated sialic acids drives IDV entry, we took advantage of a CASD1 knockout (KO) MDCK cell line and carried out feeding experiments using synthetic 9-
O
-acetyl sialic acids in combination with the single-round and multi-round IDV infection assays. The data from our studies show that (i) CASD1 KO cells are resistant to IDV infection and lack of IDV binding to the cell surface is responsible for the failure of IDV replication; (ii) feeding CASD1 KO cells with Neu5,9Ac
2
or Neu5Gc9Ac resulted in a dose-dependent rescue of IDV infectivity; and (iii) diverse IDVs replicated robustly in CASD1 KO cells fed with either Neu5,9Ac
2
or Neu5Gc9Ac at a level similar to that in wild-type cells with a functional CASD1. These data demonstrate that IDV can utilize Neu5,9Ac
2
- or non-human Neu5Gc9Ac-containing glycan receptor for infection. Our findings provide evidence that IDV has acquired the ability to infect and transmit among agricultural animals that are enriched in Neu5Gc9Ac, in addition to posing a zoonotic risk to humans expressing only Neu5,9Ac
2
.

IMPORTANCE

Influenza D virus (IDV) has emerged as a multiple-species-infecting pathogen with bovines as a primary reservoir. Little is known about the functional receptor that drives IDV entry and promotes its cross-species spillover potential among different hosts. Here, we demonstrated that IDV binds exclusively to 9-
O
-acetylated
N
-acetylneuraminic acid (Neu5,9Ac
2
) and non-human 9-
O
-acetylated
N
-glycolylneuraminic acid (Neu5Gc9Ac) and utilizes both for entry and infection. This ability in effective engagement of both 9-
O-
acetylated sialic acids as functional receptors for infection provides an evolutionary advantage to IDV for expanding its host range. This finding also indicates that IDV has the potential to emerge in humans because Neu5,9Ac
2
is ubiquitously expressed in human tissues, including lung. Thus, results of our study highlight a need for continued surveillance of IDV in humans, as well as for further investigation of its biology and cross-species transmission mechanism.
Ubiquitin-specific proteinase 1 stabilizes PRRSV nonstructural protein Nsp1β to promote viral replication by regulating K48 ubiquitination
Authors: Zhai Yunyun , Du Yongkun , Yuan Hang , Fan Shuai , Chen Xing , Wang Jiang , He Wenrui , Han Shichong , Zhang Yuhang , Hu Man , Zhang Gaiping , Kong Zhengjie , Wan Bo
Published: February 2024

The porcine reproductive and respiratory syndrome virus (PRRSV) can lead to severe reproductive problems in sows, pneumonia in weaned piglets, and increased mortality, significantly negatively impacting the economy. Post-translational changes are essential for the host-dependent replication and long-term infection of PRRSV. Uncertainty surrounds the function of the ubiquitin network in PRRSV infection. Here, we screened 10 deubiquitinating enzyme inhibitors and found that the ubiquitin-specific proteinase 1 (USP1) inhibitor ML323 significantly inhibited PRRSV replication
in vitro
. Importantly, we found that USP1 interacts with nonstructural protein 1β (Nsp1β) and deubiquitinates its K48 to increase protein stability, thereby improving PRRSV replication and viral titer. Among them, lysine at position 45 is essential for Nsp1β protein stability. In addition, deficiency of USP1 significantly reduced viral replication. Moreover, ML323 loses antagonism to PRRSV rSD16-K45R. This study reveals the mechanism by which PRRSV recruits the host factor USP1 to promote viral replication, providing a new target for PRRSV defense.

IMPORTANCE

Deubiquitinating enzymes are critical factors in regulating host innate immunity. The porcine reproductive and respiratory syndrome virus (PRRSV) nonstructural protein 1β (Nsp1β) is essential for producing viral subgenomic mRNA and controlling the host immune system. The host inhibits PRRSV proliferation by ubiquitinating Nsp1β, and conversely, PRRSV recruits the host protein ubiquitin-specific proteinase 1 (USP1) to remove this restriction. Our results demonstrate the binding of USP1 to Nsp1β, revealing a balance of antagonism between PRRSV and the host. Our research identifies a brand-new PRRSV escape mechanism from the immune response.
Absence of CD80 reduces HSV-1 replication in the eye and delays reactivation but not latency levels
Authors: Jaggi Ujjaldeep , Matundan Harry H. , Oh Jay J. , Ghiasi Homayon
Published: February 2024

Herpes simplex virus-1 (HSV-1) infections are among the most frequent serious viral eye infections in the U.S. and are a major cause of viral-induced blindness. HSV-1 infection is known to induce T cell activation, proliferation, and differentiation that play crucial roles in the development of virus-induced inflammatory lesions, leading to eye disease and causing chronic corneal damage. CD80 is a co-stimulatory molecule and plays a leading role in T cell differentiation. Previous efforts to limit lesion severity by controlling inflammation at the cellular level led us to ask whether mice knocked out for CD80 would show attenuated virus replication following reactivation. By evaluating the effects of CD80 activity on primary and latent infection, we found that in the absence of CD80, virus replication in the eyes and virus reactivation in latent trigeminal ganglia were both significantly reduced. However, latency in latently infected CD80
−/−
mice did not differ significantly from that in wild-type (WT) control mice. Reduced virus replication in the eyes of CD80
−/−
mice correlated with significantly expanded CD11c gene expression as compared to WT mice. Taken together, our results indicate that suppression of CD80 could offer significant beneficial therapeutic effects in the treatment of Herpes Stromal Keratitis (HSK).

IMPORTANCE

Of the many problems associated with recurrent ocular infection, reducing virus reactivation should be a major goal of controlling ocular herpes simplex virus-1 (HSV-1) infection. In this study, we have shown that the absence of CD80 reduces HSV-1 reactivation, which marks the establishment of a previously undescribed mechanism underlying viral immune evasion that could be exploited to better manage HSV infection.
Two distinct ferredoxins are essential for nitrogen fixation by the iron nitrogenase in
Rhodobacter capsulatus
Authors: Addison Holly , Glatter Timo , K. A. Hochberg Georg , Rebelein Johannes G.
Published: February 2024

Nitrogenases are the only enzymes able to fix gaseous nitrogen into bioavailable ammonia and hence are essential for sustaining life. Catalysis by nitrogenases requires both a large amount of ATP and electrons donated by strongly reducing ferredoxins or flavodoxins. Our knowledge about the mechanisms of electron transfer to nitrogenase enzymes is limited: The electron transport to the iron (Fe)-nitrogenase has hardly been investigated. Here, we characterized the electron transfer pathway to the Fe-nitrogenase in
Rhodobacter capsulatus via
proteome analyses, genetic deletions, complementation studies, and phylogenetics. Proteome analyses revealed an upregulation of four ferredoxins under nitrogen-fixing conditions reliant on the Fe-nitrogenase in a molybdenum nitrogenase knockout strain, compared to non-nitrogen-fixing conditions. Based on these findings,
R. capsulatus
strains with deletions of ferredoxin (
fdx
) and flavodoxin (
fld, nifF
) genes were constructed to investigate their roles in nitrogen fixation by the Fe-nitrogenase.
R. capsulatus
deletion strains were characterized by monitoring diazotrophic growth and Fe-nitrogenase activity
in vivo
. Only deletions of
fdxC
or
fdxN
resulted in slower growth and reduced Fe-nitrogenase activity, whereas the double deletion of both
fdxC
and
fdxN
abolished diazotrophic growth. Differences in the proteomes of ∆
fdxC
and ∆
fdxN
strains, in conjunction with differing plasmid complementation behaviors of
fdxC
and
fdxN,
indicate that the two Fds likely possess different roles and functions. These findings will guide future engineering of the electron transport systems to nitrogenase enzymes, with the aim of increased electron flux and product formation.

IMPORTANCE

Nitrogenases are essential for biological nitrogen fixation, converting atmospheric nitrogen gas to bioavailable ammonia. The production of ammonia by diazotrophic organisms, harboring nitrogenases, is essential for sustaining plant growth. Hence, there is a large scientific interest in understanding the cellular mechanisms for nitrogen fixation
via
nitrogenases. Nitrogenases rely on highly reduced electrons to power catalysis, although we lack knowledge as to which proteins shuttle the electrons to nitrogenases within cells. Here, we characterized the electron transport to the iron (Fe)-nitrogenase in the model diazotroph
Rhodobacter capsulatus
, showing that two distinct ferredoxins are very important for nitrogen fixation despite having different redox centers. In addition, our research expands upon the debate on whether ferredoxins have functional redundancy or perform distinct roles within cells. Here, we observe that both essential ferredoxins likely have distinct roles based on differential proteome shifts of deletion strains and different complementation behaviors.
Complete genome sequences of two
Klebsiella pneumoniae
phages from Dakar, Senegal
Authors: Ndiaye Issa , Debarbieux Laurent , Diagne Moussa Moise , Sow Ousmane , Cissé Abdoulaye , Ba Bissoume Sambe , Fall Cheikh , Dieye Yakhya , Dia Ndongo , Seck Abdoulaye , de Magny Guillaume Constantin
Published: February 2024

Two bacteriophages (phages) of
Klebsiella pneumoniae
were isolated from sewage water collected from Dakar, Senegal. Phage vKpIN17 belongs to the
Przondovirus
genus within the
Autographiviridae
family, with double-stranded DNA genomes, whereas vKpIN18 belongs to the
Webervirus
genus of the
Drexlerviridae
family.
Draft genome sequence of potentially dikaryotic black fungus
Aureobasidium melanogenum
isolated from aircraft
Authors: Wagner Dominique N. , Varaljay Vanessa A. , Lyon Wanda J. , Crouch Audra L. , Allex-Buckner Clayton , Biffinger Justin C. , Crookes-Goodson Wendy J. , Kelley-Loughnane Nancy , Stamps Blake W.
Published: February 2024

The
Ascomycota
yeast
Aureobasidium melanogenum
strain W12 was isolated from an aircraft polymer-coated surface. The genome size is 53,160,883 bp with a G + C content of 50.13%. The genome contains fatty acid transporters, cutinases, hydroxylases, and lipases potentially used for survival on polymer coatings on aircraft.
Draft genome sequences of
Escherichia
spp. isolates from New Zealand environmental sources
Authors: Biggs Patrick J. , Moinet Marie , Rogers Lynn E. , Devane Megan , Muirhead Richard , Stott Rebecca , Marshall Jonathann C. , Cookson Adrian L.
Published: February 2024

Escherichia coli
is often used as a fecal indicator bacterium for water quality monitoring. We report the draft genome sequences of 500
Escherichia
isolates including newly described
Escherichia
species, namely
Escherichia marmotae
,
Escherichia ruysiae,
and
Escherichia whittamii
, obtained from diverse environmental sources to assist with improved public health risk assessments.
Draft genome sequence of
Xylaria bambusicola
isolate GMP-LS, the root and basal stem rot pathogen of sugarcane in Indonesia
Authors: Selvaraj Poonguzhali , Muralishankar Vayutha , Muruganantham Sahanna , Tham Jeremy H. F. , Saeroji Saefudin , Susiyanti Endah , Lau Kenny J. X. , Naqvi Naweed I.
Published: February 2024

The first draft genome of
X. bambusicola
GMP-LS, the causal pathogen of the Root, and Basal Stem Rot disease in Sugarcane is presented based on single-molecule real-time PacBio sequencing. Xylaria genome (72.43 Mb) is predicted to encode 13,430 proteins and will contribute to molecular understanding of fungal pathogenesis.
A photoheterotrophic bacterium from Iceland has adapted its photosynthetic machinery to the long days of polar summer
Authors: Tomasch Jürgen , Kopejtka Karel , Bílý Tomáš , Gardiner Alastair T. , Gardian Zdenko , Shivaramu Sahana , Koblížek Michal , Kaftan David
Published: February 2024

During their long evolution, anoxygenic phototrophic bacteria have inhabited a wide variety of natural habitats and developed specific strategies to cope with the challenges of any particular environment. Expression, assembly, and safe operation of the photosynthetic apparatus must be regulated to prevent reactive oxygen species generation under illumination in the presence of oxygen. Here, we report on the photoheterotrophic
Sediminicoccus
sp. strain KRV36, which was isolated from a cold stream in north-western Iceland, 30 km south of the Arctic Circle. In contrast to most aerobic anoxygenic phototrophs, which stop pigment synthesis when illuminated, strain KRV36 maintained its bacteriochlorophyll synthesis even under continuous light. Its cells also contained between 100 and 180 chromatophores, each accommodating photosynthetic complexes that exhibit an unusually large carotenoid absorption spectrum. The expression of photosynthesis genes in dark-adapted cells was transiently downregulated in the first 2 hours exposed to light but recovered to the initial level within 24 hours. An excess of membrane-bound carotenoids as well as high, constitutive expression of oxidative stress response genes provided the required potential for scavenging reactive oxygen species, safeguarding bacteriochlorophyll synthesis and photosystem assembly. The unique cellular architecture and an unusual gene expression pattern represent a specific adaptation that allows the maintenance of anoxygenic phototrophy under arctic conditions characterized by long summer days with relatively low irradiance.

IMPORTANCE

The photoheterotrophic bacterium
Sediminicoccus
sp. KRV36 was isolated from a cold stream in Iceland. It expresses its photosynthesis genes, synthesizes bacteriochlorophyll, and assembles functional photosynthetic complexes under continuous light in the presence of oxygen. Unraveling the molecular basis of this ability, which is exceptional among aerobic anoxygenic phototrophic species, will help to understand the evolution of bacterial photosynthesis in response to changing environmental conditions. It might also open new possibilities for genetic engineering of biotechnologically relevant phototrophs, with the aim of increasing photosynthetic activity and their tolerance to reactive oxygen species.
Extreme environments simplify reassembly of communities of arbuscular mycorrhizal fungi
Authors: Šibanc Nataša , Clark Dave R. , Helgason Thorunn , Dumbrell Alex J. , Maček Irena
Published: February 2024

The ecological impacts of long-term (press) disturbance on mechanisms regulating the relative abundance (i.e., commonness or rarity) and temporal dynamics of species within a community remain largely unknown. This is particularly true for the functionally important arbuscular mycorrhizal (AM) fungi; obligate plant-root endosymbionts that colonize more than two-thirds of terrestrial plant species. Here, we use high-resolution amplicon sequencing to examine how AM fungal communities in a specific extreme ecosystem—mofettes or natural CO
2
springs caused by geological CO
2
exhalations—are affected by long-term stress. We found that in mofettes, specific and temporally stable communities form as a subset of the local metacommunity. These communities are less diverse and dominated by adapted, “stress tolerant” taxa. Those taxa are rare in control locations and more benign environments worldwide, but show a stable temporal pattern in the extreme sites, consistently dominating the communities in grassland mofettes. This pattern of lower diversity and high dominance of specific taxa has been confirmed as relatively stable over several sampling years and is independently observed across multiple geographic locations (mofettes in different countries). This study implies that the response of soil microbial community composition to long-term stress is relatively predictable, which can also reflect the community response to other anthropogenic stressors (e.g., heavy metal pollution or land use change). Moreover, as AM fungi are functionally differentiated, with different taxa providing different benefits to host plants, changes in community structure in response to long-term environmental change have the potential to impact terrestrial plant communities and their productivity.

IMPORTANCE

Arbuscular mycorrhizal (AM) fungi form symbiotic relationships with more than two-thirds of plant species. In return for using plant carbon as their sole energy source, AM fungi improve plant mineral supply, water balance, and protection against pathogens. This work demonstrates the importance of long-term experiments to understand the effects of long-term environmental change and long-term disturbance on terrestrial ecosystems. We demonstrated a consistent response of the AM fungal community to a long-term stress, with lower diversity and a less variable AM fungal community over time under stress conditions compared to the surrounding controls. We have also identified, for the first time, a suite of AM fungal taxa that are consistently observed across broad geographic scales in stressed and anthropogenically heavily influenced ecosystems. This is critical because global environmental change in terrestrial ecosystems requires an integrative approach that considers both above- and below-ground changes and examines patterns over a longer geographic and temporal scale, rather than just single sampling events.
(Pan)genomic analysis of two
Rhodococcus
isolates and their role in phenolic compound degradation
Authors: Benning Sarah , Pritsch Karin , Radl Viviane , Siani Roberto , Wang Zhongjie , Schloter Michael
Published: February 2024

The genus
Rhodococcus
is recognized for its potential to degrade a large range of aromatic substances, including plant-derived phenolic compounds. We used comparative genomics in the context of the broader
Rhodococcus
pan-genome to study genomic traits of two newly described
Rhodococcus
strains (type-strain
Rhodococcus pseudokoreensis
R79
T
and
Rhodococcus koreensis
R85) isolated from apple rhizosphere. Of particular interest was their ability to degrade phenolic compounds as part of an integrated approach to treat apple replant disease (ARD) syndrome. The pan-genome of the genus
Rhodococcus
based on 109 high-quality genomes was open with a small core (1.3%) consisting of genes assigned to basic cell functioning. The range of genome sizes in
Rhodococcus
was high, from 3.7 to 10.9 Mbp. Genomes from host-associated strains were generally smaller compared to environmental isolates which were characterized by exceptionally large genome sizes. Due to large genomic differences, we propose the reclassification of distinct groups of rhodococci like the
Rhodococcus equi
cluster to new genera. Taxonomic species affiliation was the most important factor in predicting genetic content and clustering of the genomes. Additionally, we found genes that discriminated between the strains based on habitat. All members of the genus
Rhodococcus
had at least one gene involved in the pathway for the degradation of benzoate, while biphenyl degradation was mainly restricted to strains in close phylogenetic relationships with our isolates. The ~40% of genes still unclassified in larger
Rhodococcus
genomes, particularly those of environmental isolates, need more research to explore the metabolic potential of this genus.

IMPORTANCE

Rhodococcus
is a diverse, metabolically powerful genus, with high potential to adapt to different habitats due to the linear plasmids and large genome sizes. The analysis of its pan-genome allowed us to separate host-associated from environmental strains, supporting taxonomic reclassification. It was shown which genes contribute to the differentiation of the genomes based on habitat, which can possibly be used for targeted isolation and screening for desired traits. With respect to apple replant disease (ARD), our isolates showed genome traits that suggest potential for application in reducing plant-derived phenolic substances in soil, which makes them good candidates for further testing against ARD.
‘Considering the reality, I am very lucky’: how professional players and staff perceive injury prevention and performance protection in women’s football
Authors: Bolling Caroline , Tomás Rita , Verhagen Evert
Published: February 2024

Objective

To explore the beliefs and perceptions of professional female footballers and staff regarding injury prevention and performance protection in professional women’s football.

Methods

This qualitative study applied semistructured interviews with 18 participants from 3 top-tier teams from 2 countries (Portugal and England) and 4 nationalities, including 2 physiotherapists, 5 players, 3 team doctors, 2 head coaches, 3 strength and conditioning coaches, 2 managers, and 1 head of performance. Data analysis applied constant comparison analysis, using principles of grounded theory. There were no major differences in the perspectives of players and staff, and the findings are presented together.

Results

Identifying and reporting injuries and recognising potential injury risk factors were mentioned to influence the prevention of injury. Participants stated that the growth and evolution of women’s football could influence injury risk. Before reaching the professional level, exposure to potential risk factors, such as lack of recovery, limited awareness and opportunities for prevention (eg, preventive exercises and load management strategies), was believed to impact players’ injury risk. Players further described their experiences and the ‘bumpy road’ to becoming a professional player, their current context and potential future improvements for women’s football regarding injury prevention and performance protection.

Conclusion

Professional female football players face different injury risks during different moments of their careers. According to elite players and staff, amateur and semiprofessionals have limited resources and lack injury prevention strategies. Professional players and staff perceived the current preventive measures as good and relied on the value of individualised care and a multidisciplinary approach. In the future, more resources and structured injury prevention strategies are needed in youth and non-professional levels of women’s football to reduce injury risk and allow more players to reach their maximal performance.
Understanding the educational inequalities in suicide attempts and their mediators: a Mendelian randomisation study
Authors: Zhu Jiahao , Liu Houpu , Gao Rui , Ding Lilu , Wang Jing , Yang Ye , Zhou Dan , Li Yingjun
Published: February 2024

Background

Educational inequalities in suicide have become increasingly prominent over the past decade. Elucidating modifiable risk factors that serve as intermediaries in the impact of low educational attainment on suicide has the potential to reduce health disparities.

Aims

To examine the risk factors that mediate the relationship between educational attainment and suicide attempts and quantify their contributions to the mediation effect.

Methods

We conducted a two-sample Mendelian randomisation (MR) analysis to estimate the causal effect of educational attainment on suicide attempts, utilising genome-wide association study summary statistics from the Integrative Psychiatric Research (iPSYCH; 6024 cases and 44 240 controls) and FinnGen (8978 cases and 368 299 controls). We systematically evaluated 42 putative mediators within the causal pathway connecting reduced educational attainment to suicide attempts and employed two-step and multivariable MR to quantify the proportion of the mediated effect.

Results

In the combined analysis of iPSYCH and FinnGen, each standard deviation (SD) decrease in genetically predicted educational attainment (equating to 3.4 years of education) was associated with a 105% higher risk of suicide attempts (odds ratio (OR): 2.05; 95% confidence interval (CI): 1.81 to 2.31). Of the 42 risk factors analysed, the two-step MR identified five factors that mediated the association between educational attainment and suicide attempts. The respective proportions of mediation were 47% (95% CI: 29% to 66%) for smoking behaviour, 36% (95% CI: 0% to 84%) for chronic pain, 49% (95% CI: 36% to 61%) for depression, 35% (95% CI: 12% to 59%) for anxiety and 26% (95% CI: 18% to 34%) for insomnia. Multivariable MR implicated these five mediators collectively, accounting for 68% (95% CI: 40% to 96%) of the total effect.

Conclusions

This study identified smoking, chronic pain and mental disorders as primary intervention targets for attenuating suicide risk attributable to lower educational levels in the European population.