bluuebunny/crossref_metadata_2025_split huggingface dataset:
Syntrichia ruralis: emerging model moss genome reveals a conserved and previously unknown regulator of desiccation in flowering plants
Authors: Zhang Xiaodan , Ekwealor Jenna T. B. , Mishler Brent D. , Silva Anderson T. , Yu Li'ang , Jones Andrea K. , Nelson Andrew D. L. , Oliver Melvin J. 
Published: February 2024

Summary

Water scarcity, resulting from climate change, poses a significant threat to ecosystems. Syntrichia ruralis, a dryland desiccation‐tolerant moss, provides valuable insights into survival of water‐limited conditions.

We sequenced the genome of S. ruralis, conducted transcriptomic analyses, and performed comparative genomic and transcriptomic analyses with existing genomes and transcriptomes, including with the close relative S. caninervis. We took a genetic approach to characterize the role of an S. ruralis transcription factor, identified in transcriptomic analyses, in Arabidopsis thaliana.

The genome was assembled into 12 chromosomes encompassing 21 169 protein‐coding genes. Comparative analysis revealed copy number and transcript abundance differences in known desiccation‐associated gene families, and highlighted genome‐level variation among species that may reflect adaptation to different habitats. A significant number of abscisic acid (ABA)‐responsive genes were found to be negatively regulated by a MYB transcription factor (MYB55) that was upstream of the S. ruralis ortholog of ABA‐insensitive 3 (ABI3). We determined that this conserved MYB transcription factor, uncharacterized in Arabidopsis, acts as a negative regulator of an ABA‐dependent stress response in Arabidopsis.

The new genomic resources from this emerging model moss offer novel insights into how plants regulate their responses to water deprivation.
Blocking of awn development‐related gene OsGAD1 coordinately boosts yield and quality of Kam Sweet Rice
Authors: Luo Jun , Amin Bakht , Wu Bilong , Wu Bowen , Huang Weiting , Salmen Saleh H. , Fang Zhongming 
Published: February 2024

AbstractKam Sweet Rice is a high‐quality local variety of Guizhou province in China, but most varieties have awns on lemma. In this study, we aimed to obtain awnless varieties of Kam Sweet Rice by blocking the awn development‐related gene OsGAD1 using CRISPR/Cas9 technology. We determined that natural variations of the OsGAD1 triggered different lengths of awns of Kam Sweet Rice. We found that the awning rate of the CRISPR lines of OsGAD1 in Guxiangnuo, Goujingao and Gouhuanggang decreased by over 65%, and the number of grains per panicle and yield per plant increased by more than 17% and 20% compared to the wild‐types. Furthermore, we indicated that blocking OsGAD1 resulted in an increase of over 2% in the brown rice rate and milled rice rate in these varieties. In addition, the analysis of the transcriptome revealed that the regulation of awn development and yield formation in CRISPR lines of OsGAD1 may involve genes associated with phytohormone and nitrogen pathways. These results suggest that blocking OsGAD1 in Kam Sweet Rice using CRISPR/Cas9 technology can be used for breeding programs seeking high yield and grain quality of Kam Sweet Rice.
Modelling the impact of replacing fish oil with plant oils: A meta‐analysis to match the optimal plant oil for major cultured fish
Authors: Qian Yi‐Fan , Wang Jun‐Xian , Qiao Fang , Luo Yuan , Chen Li‐Qiao , Zhang Mei‐Ling , Du Zhen‐Yu 
Published: February 2024

AbstractThe replacement of fish oil with plant oils is a common practice in aquaculture to compensate for the shortage of fish oil supply and has been thoroughly studied. However, because the experimental conditions vary in many aspects, the results are usually inconsistent quantitatively. Therefore, a meta‐analysis was conducted based on a dataset containing 328 articles to systematically model the influence of plant oils on the main aquaculture fish. In addition to demonstrating the species‐specific dose‐dependent impact of plant oils on fish growth, feed utilization efficiency, lipid deposition and health parameters, we have also investigated the role of other factors in this process. We found that the adverse effects caused by plant oils worsen as the experimental duration extends for Atlantic salmon, while Gilthead seabream and European seabass gradually adapt to the change. Further, water temperature could be a decisive factor for Rainbow trout, and early adaptation to plant oils would be helpful for Gilthead seabream. Moreover, sufficient fishmeal supply could alleviate the adverse effects caused by plant oils for most species, but for Gilthead seabream and European seabass, the growth suppression effect of plant oil was larger when fed high‐fishmeal diets. Besides, by comprehensively considering the effects of plant oils, we matched the potential optimal plant oil for each fish species. Our article quantitatively modelled the adverse effects of replacing fish oil with plant oils, investigated the influences of assistant factors and offered a panorama of the research status with emphasis on potential breakthrough orientations.
Efficient drift parameter estimation for ergodic solutions of backward SDEs
Authors: Ogihara Teppei , Stadje Mitja 
Published: February 2024

AbstractWe derive consistency and asymptotic normality results for quasi‐maximum likelihood methods for drift parameters of ergodic stochastic processes observed in discrete time in an underlying continuous‐time setting. The special feature of our analysis is that the stochastic integral part is unobserved and nonparametric. Additionally, the drift may depend on the (unknown and unobserved) stochastic integrand. Our results hold for ergodic semi‐parametric diffusions and backward SDEs. Simulation studies confirm that the methods proposed yield good convergence results.
Are trunk stability and endurance determinant factors for whole‐body dynamic balance in physically active young males? A multidimensional analysis
Authors: De Los Ríos‐Calonge J. , Barbado D. , Prat‐Luri A. , Juan‐Recio C. , Heredia‐Elvar J. R. , Elvira J. L. L. , Vera‐Garcia F. J. 
Published: February 2024

AbstractObjectivesDetermine if (a) a better trunk stability and endurance are associated with an improved whole‐body dynamic balance, and if (b) the assessment tests can be interchanged within each capability.MethodsSixty‐three physically active young males performed three trunk stability (i.e., the lumbopelvic stability, the unstable sitting and the sudden loading sitting tests), three trunk muscle endurance (i.e., the Biering–Sørensen, the side bridge and the front bridge tests) and four whole‐body dynamic balance (i.e., the tandem and the single‐leg stance, the Y‐Balance, and the single‐leg triple hop tests) tests two times. After assessing the reliability of the variables, a Pearson correlation analysis was performed.ResultsThe correlations between trunk stability and endurance tests with dynamic balance tests were non‐significant except for the unstable sitting test with both the tandem (r = 0.502) and the single‐leg stance (r = 0.522) tests. Moreover, no relationships were observed between the trunk stability and the trunk muscle endurance tests. Interestingly, no relationships were found between most tests within each capability (i.e., trunk stability, trunk endurance, and dynamic balance) except: (i) the front bridge stability test and the back (r = 0.461) and the side (r = 0.499) bridge stability tests; (ii) the two side bridge endurance tests (r = 0.786); (iii) the tandem and the single‐leg stance tests (0.439 ≤ r ≤ 0.463); (iv) the Y‐Balance and the single‐leg triple hop tests (0.446 ≤ r ≤ 0.477).ConclusionBetter trunk function does not seem to be a relevant factor for dynamic balance in young active males. In this population, specific measures are needed as the test interchangeability is questioned.
Bicistronic expression of nuclear transgenes in Chlamydomonas reinhardtii
Authors: Jacobebbinghaus Nick , Lauersen Kyle J. , Kruse Olaf , Baier Thomas 
Published: February 2024

SUMMARYIn eukaryotic organisms, proteins are typically translated from monocistronic messenger RNAs containing a single coding sequence (CDS). However, recent long transcript sequencing identified 87 nuclear polycistronic mRNAs in Chlamydomonas reinhardtii natively carrying multiple co‐expressed CDSs. In this study, we investigated the dynamics of 22 short intergenic sequences derived from these native polycistronic loci by their application in genetic constructs for synthetic transgene expression. A promising candidate sequence was identified based on the quantification of transformation efficiency and expression strength of a fluorescence reporter protein. Subsequently, the expression of independent proteins from one mRNA was verified by cDNA amplification and protein molecular mass characterization. We demonstrated engineered bicistronic expression in vivo to drive successful co‐expression of several terpene synthases with the selection marker aphVIII. Bicistronic transgene design resulted in significantly increased (E)‐α‐bisabolene production of 7.95 mg L−1 from a single open reading frame, 18.1× fold higher than previous reports. Use of this strategy simplifies screening procedures for identification of high‐level expressing transformants, does not require the application of additional fluorescence reporters, and reduces the nucleotide footprint compared to classical monocistronic expression cassettes. Although clear advantages for bicistronic transgene expression were observed, this strategy was found to be limited to the aphVIII marker, and further studies are necessary to gain insights into the underlying mechanism that uniquely permits this co‐expression from the algal nuclear genome.
Tympanic membrane perforations cannot be reliably detected using computed tomography based on 15 cadaver dogs
Authors: Stokowski Scott , Hespel Adrien‐Maxence , Drake Elizabeth , de Swarte Marie , Cole Robert , Johnson Kryssa , Morandi Federica , Zhu Xiaojuan 
Published: February 2024

AbstractThe integrity of the tympanic membrane is an important factor when deciding treatment and therapeutic recommendations for dogs with ear disease; however, otoscopic examination may be difficult to perform due to features of external ear canal disease or patient compliance. CT is useful for the evaluation of middle ear disease, including cases in which middle ear disease is detected incidentally. The tympanic membrane is detectable using CT, but anecdotally, apparent focal defects or discontinuities of the tympanic membrane are often seen in patients with and without ear disease. The purpose of this prospective, observer agreement study was to determine if perforations of the tympanic membrane are reliably detectable on CT. Fifteen cadaver dogs underwent CT and video otoscopy to verify the integrity of each tympanic membrane. Cadavers were randomly assigned to have the tympanic membranes left intact or to undergo a myringotomy on either the left, the right, or both sides. CT was performed immediately following the myringotomies. Four blinded evaluators evaluated the pre‐ and post‐myringotomy scans for a total of 30 scans (60 tympanic membranes). Average accuracy was low (44%), and interobserver agreement for all four evaluators was fair. Although the tympanic membrane is visible on CT, perforations of the tympanic membrane are unlikely to be accurately detected or excluded. The appearance of an intact tympanic membrane or defect in the membrane on CT should not be used as criteria to guide clinical treatment recommendations based on this cadaver model.
Validation of a RANS Turbulence Model for a S833 Wind Turbine Airfoil With a Trailing Edge Flap Using Oil Visualization and Pressure Taps
Authors: Jami Rafat , Johnson David A. 
Published: February 2024

Abstract
The aerodynamics of a small wind turbine blade was captured using a γ–Reθ k–ω shear stress transport transitional turbulence model tuned with production limiter coefficients at a Reynolds number of 1.70×105. The computational fluid dynamics simulations were validated against wind tunnel experiments that included airfoil pressure tap measurements and surface oil flow visualization (SOFV) to capture the flow field. The uniqueness of this blade included a trailing edge flap that was 20% of the chord controlled using a servomotor. The test matrix included angles of attack (AOA) between 1 deg and 7 deg with flap angles of 10 deg in the upward and downward position. Two locations were always observed on the airfoil: a leading edge region of high shear and a midsection of flow separation. Within the flow separation section, two distinct regions existed: a complete detachment of flow from the airfoil surface creating a stagnation region which was followed by a reverse flow region. A third location of flow reattachment near the trailing edge was observed for all cases excluding a downward angled trailing edge flap. The utilization of the flap resulted in changes to the size of the separation zone and the movement of the separation zone along the chord. The numerical skin friction coefficient, oil residue profiles from the SOFV, and pressure tap measurements all showed onset of separation locations on the chord within 10%. The computational fluid dynamics model also predicted the coefficient of pressure across the chord of the airfoil within 10% in comparison to the experimental measurements.
Post-Buckling Analysis of Arch and Serpentine Structures Under End-to-End Compression
Authors: Zhang Zheng , Ye Fuhua , Dong Yuhang , Zhang Fan , Fan Zhichao 
Published: February 2024

Abstract
Arch and serpentine structures are two fundamental structural forms with significant applications in various fields. When subjected to compressive loading at both ends, these structures undergo flexural-torsional post-buckling, resulting in complex deformation modes that are challenging to describe using basic functions (e.g., trigonometric functions and polynomial functions), posing significant challenges in finding analytical solutions. In this study, we propose a novel approach to address this issue. By representing the lateral displacement with a trigonometric series expansion and utilizing the equilibrium equation, the angular displacement is expressed in terms of special functions known as Mathieu functions. Furthermore, the energy method is employed to obtain analytical solutions for the flexural-torsional post-buckling deformation components. The theoretical findings are validated through experiments and finite element analysis. Based on the theoretical results, explicit analytical expressions for the maximum principal strain and the bending-torsion ratio of the structures are derived, offering valuable insights for the design of arch and serpentine structures in practical applications.
Population pharmacokinetic rationale for intravenous contezolid acefosamil followed by oral contezolid dosage regimens
Authors: Bulitta Jürgen B. , Fang Edward , Stryjewski Martin E. , Wang Wen , Atiee George J. , Stark Jeffrey G. , Hafkin Barry 
Published: February 2024

ABSTRACT

Contezolid is a novel oxazolidinone antibiotic with a promising safety profile. Oral contezolid and its intravenous (IV) prodrug contezolid acefosamil (CZA) are in development for treatment of diabetic foot and acute bacterial skin and skin structure infections (ABSSSI). The prodrug CZA is converted to active contezolid via intermediate MRX-1352. This study aimed to provide the pharmacokinetic rationale for safe, effective, and flexible dosage regimens with initial IV CZA followed by oral contezolid. We simultaneously modeled plasma concentrations from 110 healthy volunteers and 74 phase 2 patients with ABSSSI via population pharmacokinetics (using the importance sampling estimation algorithm), and optimized dosage regimens by Monte Carlo simulations. This included data on MRX-1352, contezolid, and its metabolite MRX-1320 from 66 healthy volunteers receiving intravenous CZA (150–2400 mg) for up to 28 days, and 74 patients receiving oral contezolid [800 mg every 12 h (q12h)] for 10 days. The apparent total clearance for 800 mg oral contezolid with food was 16.0 L/h (23.4% coefficient of variation) in healthy volunteers and 17.7 L/h (53.8%) in patients. CZA was rapidly converted to MRX-1352, which subsequently transformed to contezolid. The proposed dosage regimen used an IV CZA 2000 mg loading dose with 1000 mg IV CZA q12h as maintenance dose(s), followed by 800 mg oral contezolid q12h (with food). During each 24-h period, Monte Carlo simulations predicted this regimen to achieve consistent areas under the curve of 91.9 mg·h/L (range: 76.3–106 mg·h/L) under all scenarios. Thus, this regimen was predicted to reliably achieve efficacious contezolid exposures independent of timing of switch from IV CZA to oral contezolid.

IMPORTANCE
This study provides the population pharmacokinetic rationale for the dosage regimen of the intravenous (IV) prodrug contezolid acefosamil (CZA) followed by oral contezolid. We developed the first integrated population model for the pharmacokinetics of the MRX-1352 intermediate prodrug, active contezolid, and its main metabolite MRX-1320 based on data from three clinical studies in healthy volunteers and phase 2 patients. The proposed regimen was predicted to reliably achieve efficacious contezolid exposures independent of timing of switch from IV CZA to oral contezolid.
Progress on network modeling and analysis of gut microecology: a review
Authors: Luo Meng , Zhu Jinlin , Jia Jiajia , Zhang Hao , Zhao Jianxin 
Published: February 2024

ABSTRACT

The gut microecological network is a complex microbial community within the human body that plays a key role in linking dietary nutrition and host physiology. To understand the complex relationships among microbes and their functions within this community, network analysis has emerged as a powerful tool. By representing the interactions between microbes and their associated omics data as a network, we can gain a comprehensive understanding of the ecological mechanisms that drive the human gut microbiota. In addition, the network-based approach provides a more intuitive analysis of the gut microbiota, simplifying the study of its complex dynamics and interdependencies. This review provides a comprehensive overview of the methods used to construct and analyze networks in the context of gut microecological background. We discuss various types of network modeling approaches, including co-occurrence networks, causal networks, dynamic networks, and multi-omics networks, and describe the analytical techniques used to identify important network properties. We also highlight the challenges and limitations of network modeling in this area, such as data scarcity and heterogeneity, and provide future research directions to overcome these limitations. By exploring these network-based methods, researchers can gain valuable insights into the intricate relationships and functional roles of microbial communities within the gut, ultimately advancing our understanding of the gut microbiota’s impact on human health.
Supplemental Material: Comprehensive seismic evidence for the inducing mechanism of extremely shallow 2019 Changning M<sub>s</sub> 6.0 earthquake by solution salt mining, Sichuan Basin, China
Authors: Anyiam Uzonna Okenna , Qian Jiawei , Tan Yuyang , Zhang Haijiang 
Published: February 2024

<div>Details on seismic tomography, model resolution tests, in-situ V<sub>p</sub>/V<sub>s</sub> ratio estimation, focal mechanism determination, stress parameters inversion, excess pore fluid pressures estimation, and Coulomb failure stress analysis, as well as additional figures and tables supporting main text and supplementary material. </div>
Development and evaluation of a manualised mental health awareness and stigma reduction intervention for Black faith communities: study protocol for the ON TRAC feasibility study
Authors: Codjoe Louisa Natalie , Henderson Claire , N'Danga-Koroma Joelyn , Lempp Heidi , Romeo Renee , Bakolis Ioannis , Thornicroft Graham 
Published: February 2024

IntroductionThis paper presents the study protocol for a feasibility study of a manualised mental health awareness and stigma reduction intervention for Black faith communities, as part of the Outcomes and Needs of Traditional Religious And Complementary practitioners (ON TRAC) project. The primary objective is to assess the feasibility and acceptability of the intervention and the secondary objectives include assessment of the feasibility of: recruiting participants to take part in the intervention, delivering the intervention, and conducting qualitative assessments, and use of the selected scales. The findings from this study will be used to inform the development of a subsequent trial which will focus on exploring the potential impact of the intervention on stigma-related knowledge, attitudes, and behaviour.Methods and analysisThe study uses a mixed-methods approach. A total of 80 participants from four Black Majority Churches in South London will be recruited. Randomisation of the participants will be at an individual level to either the intervention group (who will participate in the 10 week Mental Health Awareness Course intervention) or to the waiting list control group (who will receive the same intervention, 8 weeks after the intervention group). Outcomes for both arms will be collected at baseline, postintervention, and at 4 week follow-up. In addition, focus group discussions will be conducted with participants in the intervention group, a week following the end of the 10 week session course, to investigate the feasibility and acceptability of the mental health awareness course.Ethics and disseminationThe results of this research will be disseminated at local, national, and international levels.Trial registration numberISRCTN12253092.
Health economic evaluations of preventative care for perinatal anxiety and associated disorders: a rapid review
Authors: Pisavadia Kalpa , Spencer Llinos Haf , Tuersley Lorna , Coates Rose , Ayers Susan , Edwards Rhiannon Tudor 
Published: February 2024

ObjectivesPerinatal mental health problems affect one in five women and cost the UK £8.1 billion for every year of births, with 72% of this cost due to the long-term impact on the child. We conducted a rapid review of health economic evaluations of preventative care for perinatal anxiety and associated disorders.DesignThis study adopted a rapid review approach, using principles of the standard systematic review process to generate quality evidence. This methodology features a systematic database search, Preferred Reporting Items for Systematic Reviews and Meta-Analyses diagram, screening of evidence, data extraction, critical appraisal and narrative synthesis.Data sourcesPubMed, Cumulative Index to Nursing and Allied Health Literature, Cochrane Library, Applied Social Sciences Index and Abstracts, PsycINFO and MEDLINE.Eligibility criteria for selecting studiesStudies that evaluated the costs and cost-effectiveness of preventative care for perinatal anxiety and associated disorders carried out within the National Health Service and similar healthcare systems.Data extraction and synthesisA minimum of two independent reviewers used standardised methods to search, screen, critically appraise and synthesise included studies.ResultsThe results indicate a lack of economic evaluation specifically for perinatal anxiety, with most studies focusing on postnatal depression (PND). Interventions to prevent postnatal mental health problems are cost-effective. Modelling studies have also been conducted, which suggest that treating PND with counselling would be cost-effective.ConclusionThe costs of not intervening in maternal mental health outweigh the costs of preventative interventions. Preventative measures such as screening and counselling for maternal mental health are shown to be cost-effective interventions to improve outcomes for women and children.PROSPERO registration numberCRD42022347859.