bluuebunny/crossref_metadata_2025_split huggingface dataset:
Reshaped DNA methylation cooperating with homoeolog‐divergent expression promotes improved root traits in synthesized tetraploid wheat
Authors: Miao Lingfeng , Xu Weiya , Liu Yanhong , Huang Xiangyi , Chen Zhe , Wang Huifang , Wang Zihao , Chen Yongming , Song Qingxin , Zhang Jing , Han Fangpu , Peng Huiru , Yao Yingyin , Xin Mingming , Hu Zhaorong , Ni Zhongfu , Sun Qixin , Xing Jiewen , Guo Weilong 
Published: February 2024

Summary
Polyploidization is a major event driving plant evolution and domestication. However, how reshaped epigenetic modifications coordinate gene transcription to generate phenotypic variations during wheat polyploidization is currently elusive.
Here, we profiled transcriptomes and DNA methylomes of two diploid wheat accessions (SlSl and AA) and their synthetic allotetraploid wheat line (SlSlAA), which displayed elongated root hair and improved root capability for nitrate uptake and assimilation after tetraploidization.
Globally decreased DNA methylation levels with a reduced difference between subgenomes were observed in the roots of SlSlAA. DNA methylation changes in first exon showed strong connections with altered transcription during tetraploidization. Homoeolog‐specific transcription was associated with biased DNA methylation as shaped by homoeologous sequence variation. The hypomethylated promoters showed significantly enriched binding sites for MYB, which may affect gene transcription in response to root hair growth. Two master regulators in root hair elongation pathway, AlCPC and TuRSL4, exhibited upregulated transcription levels accompanied by hypomethylation in promoter, which may contribute to the elongated root hair. The upregulated nitrate transporter genes, including NPFs and NRTs, also are significantly associated with hypomethylation, indicating an epigenetic‐incorporated regulation manner in improving nitrogen use efficiency.
Collectively, these results provided new insights into epigenetic changes in response to crop polyploidization and underscored the importance of epigenetic regulation in improving crop traits.
Comparison of the immune response and protection against the experimental Toxoplasma gondii infection elicited by immunization with the recombinant proteins BAG1, ROP8, and BAG1‐ROP8
Authors: Xing Yien , Yang Jun , Yao Pengjing , Xie Linding , Liu Min , Cai Yihong 
Published: February 2024

AbstractToxoplasmosis is one of the most dangerous zoonotic diseases, causing serious economic losses worldwide due to abortion and reproductive problems. Vaccination is the best way to prevent disease; thus, it is imperative to develop a candidate vaccine for toxoplasmosis. BAG1 and ROP8 have the potential to become vaccine candidates. In this study, rTgBAG1, rTgROP8, and rTgBAG1‐rTgROP8 were used to evaluate the immune effect of vaccines in each group by detecting the humoral and cellular immune response levels of BABL/c mice after immunization and the ability to resist acute and chronic infection with Toxoplasma gondii (T. gondii). We divided the mice into vaccine groups with different proteins, and the mice were immunized on days 0, 14, and 28. The protective effects of different proteins against T. gondii were analysed by measuring the cytokines, serum antibodies, splenocyte proliferation assay results, survival time, and number and diameter of brain cysts of mice after infection. The vaccine groups exhibited substantially higher IgG, IgG1, and IgG2a levels and effectively stimulated lymphocyte proliferation. The levels of IFN‐γ and IL‐2 in the vaccine group were significantly increased. The survival time of the mice in each vaccine group was prolonged and the diameter of the cysts in the vaccine group was smaller; rTgBAG1‐rTgROP8 had a better protection. Our study showed that the rTgBAG1, rTgROP8, and rTgBAG1‐rTgROP8 recombinant protein vaccines are partial but effective approaches against acute or chronic T. gondii infection. They are potential candidates for a toxoplasmosis vaccine.
APCs in sinus floor augmentation
Authors: Valentini Pascal , Calciolari Elena , Monlezun Sebastien , Akcalı Aliye , Donos Nikos , Quirynen Marc 
Published: February 2024

AbstractAfter tooth loss in the posterior area of the maxilla, sinus floor elevation is often required to compensate the vertical bone loss due to sinus pneumatization. This narrative review reports on the potential benefits of autologous platelet concentrates (APCs) during this procedure. As for transcrestal approach, APCs have been used as “sole” substitute/graft. However, because of the low number of clinical trials available with PRGF, and even none for PRP, no definitive conclusions can be made regarding their efficacy. The number of studies on the use of L‐PRF were outnumbered indicating good feasibility for vertical bone gain, with a high implant survival rate and a low degree of complications. PRP and PRGF have not been studied as a “single/sole” substitute for a one‐stage lateral window approach, probably because of the weak physical characteristics of the membranes. L‐PRF alone appears to be a predictable grafting material for lateral maxillary sinus grafting and a reduced RBH should not be considered as a risk factor. Compared to a “standard” bone substitute L‐PRF shows slightly less vertical bone gain (consider enough membrane application and use of bony window as new sinus floor roof over the implant apices), enhanced early resorption (first 6 months after application), but a similar stable bone gain afterward. For a two‐stage lateral window approach, APCs “alone” cannot be recommended, due to their weak withstand to the sinus pneumatization forces. APCs combined with bone substitutes seem to accelerate bone formation, without any additional benefits on the long‐term new bone gain. The use of L‐PRF membranes for the treatment of perforations appears to be an effective treatment option, but further clinical studies are needed to confirm this. Even though the abovementioned statements are based on large numbers of studies, additional RCTs comparing APCs with different types of grafting procedures for sinus elevation are needed.
Microbial education for marine invertebrate disease prevention in aquaculture
Authors: Dantan Luc , Toulza Eve , Petton Bruno , Montagnani Caroline , Degremont Lionel , Morga Benjamin , Fleury Yannick , Mitta Guillaume , Gueguen Yannick , Vidal‐Dupiol Jeremie , Cosseau Céline 
Published: February 2024

AbstractThe holobiont theory expands the notion of individual multicellular organisms as a community composed of a host and all its associated microorganisms. This concept has been extensively studied in the field of aquaculture, where increasing evidence has highlighted the importance of the host associated microorganisms in species fitness. Here, we focus our review on mollusc and crustacean species in which microbiota dysbiosis has recently been described in the context of various diseases, resulting in significant economic losses. Influencing the holobiont structure through the use of probiotics is a potential strategy that could improve the fitness or the robustness of cultivated species. We discuss here the possibility of developing microbiome targeted prophylactic approaches by promoting (1) methods to identify host microbial community that fosters good health status and (2) early life microbial education to favour long‐term resistance to stress or disease. This review aims to inform the aquaculture industry about potential strategies in rearing practices to mitigate diseases and economic losses.
Public health nurses' experiences with mental health promotion for adolescent immigrants in schools: A qualitative study
Authors: Bringaker Annette Owusu , Dahl Berit Misund 
Published: February 2024

AbstractAims and ObjectivesThis study aimed to explore public health nurses' experiences with mental health promotion for adolescent immigrants in lower secondary and high school, aiming to enhance knowledge and insights for effective mental health promotion.Methodological Design and JustificationA qualitative design employing a hermeneutic approach was chosen. Thirteen public health nurses were selected using purposive criterion sampling and snowballing. Thematic analysis was applied, adhering to COREQ guidelines for transparency.Ethical Issues and ApprovalThe research was approved by the Norwegian Centre for Research Data. The guidelines of the National Committee for Research Ethics in the Social Sciences and the Humanities were followed.Research Methods, Instruments, and/or InterventionsData were collected through three focus‐group interviews (n = 13), using semi‐structured interview guides to explore the experiences of public health nurses in promoting mental health among adolescent immigrants.Outcome MeasuresThis study identified three key themes: (i) Striving to understand adolescent immigrants' mental health aspects, including both positive and negative aspects; (ii) Different strategies for promoting mental health, viewing adolescents as both recipients and contributors to their well‐being; and (iii) Barriers to public health nurses' promotion of mental health, including language, cultural, and knowledge‐related obstacles and trust issues.ResultsPublic health nurses noted that language barriers and trust issues often delayed adolescent immigrants from seeking help for mental health concerns. Cultural competence and empathy were deemed crucial. To meet these needs, public health nurses must build rapport with parents, collaborate with professionals, implement follow‐up programmes, and advocate for policy changes.Study LimitationsLimitations of this qualitative study include potential bias from the authors' background and non‐generalizability of results to other contexts.ConclusionsIn conclusion, public health nurses' experiences reveal the need for enhanced cultural competence, language proficiency, and trust‐building to better serve adolescent immigrants. Collaborative efforts, follow‐up programmes, and policy advocacy are essential to improve mental health promotion in school settings.
Interactions between calcium‐induced arrhythmia triggers and the electrophysiological–anatomical substrate underlying the induction of atrial fibrillation
Authors: Colman Michael A. , Varela Marta , MacLeod Rob S. , Hancox Jules C. , Aslanidi Oleg V. 
Published: February 2024

AbstractAtrial fibrillation (AF) is the most common cardiac arrhythmia and is sustained by spontaneous focal excitations and re‐entry. Spontaneous electrical firing in the pulmonary vein (PV) sleeves is implicated in AF generation. The aim of this simulation study was to identify the mechanisms determining the localisation of AF triggers in the PVs and their contribution to the genesis of AF. A novel biophysical model of the canine atria was used that integrates stochastic, spontaneous subcellular Ca2+ release events (SCRE) with regional electrophysiological heterogeneity in ionic properties and a detailed three‐dimensional model of atrial anatomy, microarchitecture and patchy fibrosis. Simulations highlighted the importance of the smaller inward rectifier potassium current (IK1) in PV cells compared to the surrounding atria, which enabled SCRE more readily to result in delayed‐afterdepolarisations that induced triggered activity. There was a leftward shift in the dependence of the probability of triggered activity on sarcoplasmic reticulum Ca2+ load. This feature was accentuated in 3D tissue compared to single cells (Δ half‐maximal [Ca2+]SR = 58 μM vs. 22 μM). In 3D atria incorporating electrical heterogeneity, excitations preferentially emerged from the PV region. These triggered focal excitations resulted in transient re‐entry in the left atrium. Addition of fibrotic patches promoted localised emergence of focal excitations and wavebreaks that had a more substantial impact on generating AF‐like patterns than the PVs. Thus, a reduced IK1, less negative resting membrane potential, and fibrosis‐induced changes of the electrotonic load all contribute to the emergence of complex excitation patterns from spontaneous focal triggers.
imageKey points
Focal excitations in the atria are most commonly associated with the pulmonary veins, but the mechanisms for this localisation are yet to be elucidated.
We applied a multi‐scale computational modelling approach to elucidate the mechanisms underlying such localisations.
Myocytes in the pulmonary vein region of the atria have a less negative resting membrane potential and reduced time‐independent potassium current; we demonstrate that both of these factors promote triggered activity in single cells and tissues.
The less negative resting membrane potential also contributes to heterogeneous inactivation of the fast sodium current, which can enable re‐entrant‐like excitation patterns to emerge without traditional conduction block.
Uncertainty Quantification of a Machine Learning Model for Identification of Isolated Nonlinearities With Conformal Prediction
Authors: Najera-Flores David A. , Jacobs Justin , Dane Quinn D. , Garland Anthony , Todd Michael D. 
Published: February 2024

Abstract
Structural nonlinearities are often spatially localized, such joints and interfaces, localized damage, or isolated connections, in an otherwise linearly behaving system. Quinn and Brink (2021, “Global System Reduction Order Modeling for Localized Feature Inclusion,” ASME J. Vib. Acoust., 143(4), p. 041006.) modeled this localized nonlinearity as a deviatoric force component. In other previous work (Najera-Flores, D. A., Quinn, D. D., Garland, A., Vlachas, K., Chatzi, E., and Todd, M. D., 2023, “A Structure-Preserving Machine Learning Framework for Accurate Prediction of Structural Dynamics for Systems With Isolated Nonlinearities,”), the authors proposed a physics-informed machine learning framework to determine the deviatoric force from measurements obtained only at the boundary of the nonlinear region, assuming a noise-free environment. However, in real experimental applications, the data are expected to contain noise from a variety of sources. In this work, we explore the sensitivity of the trained network by comparing the network responses when trained on deterministic (“noise-free”) model data and model data with additive noise (“noisy”). As the neural network does not yield a closed-form transformation from the input distribution to the response distribution, we leverage the use of conformal sets to build an illustration of sensitivity. Through the conformal set assumption of exchangeability, we may build a distribution-free prediction interval for both network responses of the clean and noisy training sets. This work will explore the application of conformal sets for uncertainty quantification of a deterministic structure-preserving neural network and its deployment in a structural health monitoring framework to detect deviations from a baseline state based on noisy measurements.
Process Optimization of Robotic Grinding to Guarantee Material Removal Accuracy and Surface Quality Simultaneously
Authors: Li Dingwei , Yang Jixiang , Ding Han 
Published: February 2024

Abstract
Simultaneously guaranteeing material removal accuracy and surface quality of robotic grinding is crucial. However, existing studies of robotic grinding process optimization have mainly focused on a single indicator that solely considers contour error or surface roughness, while studies that simultaneously investigate the impact of contact force, spindle speed, feed rate, inclination angle, and path space on the material removal profile (MRP) and the surface roughness are lacking. This paper proposes a hybrid optimization method that considers dimensional accuracy and surface quality constraints. First, an MRP model that considers the coupling influence of the contact force, spindle speed, feed rate, and inclination angle is presented. Then, a surface roughness model that considers the inclination angle is established. Finally, the contact force, feed rate, inclination angle, and path space are simultaneously optimized to satisfy the hybrid constraints of MRP accuracy and surface roughness. The proposed method ensures maximum grinding efficiency while satisfying dimensional accuracy and surface quality constraints. The proposed method is verified on an industrial robotics grinding system with a pneumatic force-controlled actuator. The results show that the proposed method has higher profile accuracy and lower surface roughness than traditional methods.
Genetic synergy between
Acinetobacter baumannii
undecaprenyl phosphate biosynthesis and the Mla system impacts cell envelope and antimicrobial resistance
Authors: Noel Hannah R. , Keerthi Sowmya , Ren Xiaomei , Winkelman Jonathan D. , Troutman Jerry M. , Palmer Lauren D. 
Published: February 2024

ABSTRACT

Acinetobacter baumannii
is a Gram-negative bacterial pathogen that poses a major health concern due to increasing multidrug resistance. The Gram-negative cell envelope is a key barrier to antimicrobial entry and includes an inner and outer membrane. The maintenance of lipid asymmetry (Mla) system is the main homeostatic mechanism by which Gram-negative bacteria maintain outer membrane asymmetry. Loss of the Mla system in
A. baumannii
results in attenuated virulence and increased susceptibility to membrane stressors and some antibiotics. We recently reported two strain variants of the
A. baumannii
type strain ATCC 17978: 17978VU and 17978UN. Here, ∆
mlaF
mutants in the two ATCC 17978 strains display different phenotypes for membrane stress resistance, antibiotic resistance, and pathogenicity in a murine pneumonia model. Although allele differences in
obgE
were previously reported to synergize with ∆
mlaF
to affect growth and stringent response,
obgE
alleles do not affect membrane stress resistance. Instead, a single-nucleotide polymorphism (SNP) in the essential gene encoding undecaprenyl pyrophosphate (Und-PP) synthase,
uppS
, results in decreased enzymatic rate and decrease in total Und-P levels in 17978UN compared to 17978VU. The UppS
UN
variant synergizes with ∆
mlaF
to reduce capsule and lipooligosaccharide (LOS) levels, increase susceptibility to membrane stress and antibiotics, and reduce persistence in a mouse lung infection. Und-P is a lipid glycan carrier required for the biosynthesis of
A. baumannii
capsule, cell wall, and glycoproteins. These findings uncover synergy between Und-P and the Mla system in maintaining the
A. baumannii
cell envelope and antibiotic resistance.

IMPORTANCE

Acinetobacter baumannii
is a critical threat to global public health due to its multidrug resistance and persistence in hospital settings. Therefore, novel therapeutic approaches are urgently needed. We report that a defective undecaprenyl pyrophosphate synthase (UppS) paired with a perturbed Mla system leads to synthetically sick cells that are more susceptible to clinically relevant antibiotics and show reduced virulence in a lung infection model. These results suggest that targeting UppS or undecaprenyl species and the Mla system may resensitize
A. baumannii
to antibiotics in combination therapies. This work uncovers a previously unknown synergistic relationship in cellular envelope homeostasis that could be leveraged for use in combination therapy against
A. baumannii
.
Interpretation of vaginal metagenomic characteristics in different types of vaginitis
Authors: Song Jiarong , Dong Xue , Lan Yue , Lu Yunwei , Liu Xu , Kang Xuena , Huang Zhonglu , Yue Bisong , Liu Yu , Ma Wenjin , Zhang Libo , Yan Haijun , He Miao , Fan Zhenxin , Guo Tao 
Published: February 2024

ABSTRACT

Although vaginitis is closely related to vaginal microecology in females, the precise composition and functional potential of different types of vaginitis remain unclear. Here, metagenomic sequencing was applied to analyze the vaginal flora in patients with various forms of vaginitis, including cases with a clue cell proportion ranging from 1% to 20% (Clue1_20), bacterial vaginitis (BV), vulvovaginal candidiasis (VVC), and BV combined with VVC (VVC_BV). Our results identified
Prevotella
as an important biomarker between BV and Clue1_20. Moreover, a gradual decrease was observed in the relative abundance of shikimic acid metabolism associated with bacteria producing indole as well as a decline in the abundance of
Gardnerella vaginalis
in patients with BV, Clue1_20, and healthy women. Interestingly, the vaginal flora of patients in the VVC_BV group exhibited structural similarities to that of the VVC group, and its potentially functional characteristics resembled those of the BV and VVC groups. Finally,
Lactobacillus crispatus
was found in high abundance in healthy samples, greatly contributing to the stability of the vaginal environment. For the further study of
L. crispatus
, we isolated five strains of
L. crispatus
from healthy samples and evaluated their capacity to inhibit
G. vaginalis
biofilms and produce lactic acid
in vitro
to select the potential probiotic candidate for improving vaginitis in future clinical studies. Overall, we successfully identified bacterial biomarkers of different vaginitis and characterized the dynamic shifts in vaginal flora between patients with BV and healthy females. This research advances our understanding and holds great promise in enhancing clinical approaches for the treatment of vaginitis.

IMPORTANCE

Vaginitis is one of the most common gynecological diseases, mostly caused by infections of pathogens such as
Candida albicans
and
Gardnerella vaginalis
. In recent years, it has been found that the stability of the vaginal flora plays an important role in vaginitis. Furthermore, the abundant
Lactobacillus
-producing rich lactic acid in the vagina provides a healthy acidic environment such as
Lactobacillus crispatus
. The metabolites of
Lactobacillus
can inhibit the colonization of pathogens. Here, we collected the vaginal samples of patients with bacterial vaginitis (BV), vulvovaginal candidiasis (VVC), and BV combined with VVC to discover the differences and relationships among the different kinds of vaginitis by metagenomic sequencing. Furthermore, because of the importance of
L. crispatus
in promoting vaginal health, we isolated multiple strains from vaginal samples of healthy females and chose the most promising strain with potential probiotic benefits to provide clinical implications for treatment strategies.