bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bacterial Growth Temperature as a Horizontally Acquired Polygenic Trait
Authors: Farrell Anne A , Nesbø Camilla L , Zhaxybayeva Olga 
Published: December 2024

Abstract
Evolutionary events leading to organismal preference for a specific growth temperature, as well as genes whose products are needed for a proper function at that temperature, are poorly understood. Using 64 bacteria from phylum Thermotogota as a model system, we examined how optimal growth temperature changed throughout Thermotogota history. We inferred that Thermotogota's last common ancestor was a thermophile and that some Thermotogota evolved the mesophilic and hyperthermophilic lifestyles secondarily. By modeling gain and loss of genes throughout Thermotogota history and by reconstructing their phylogenies, we demonstrated that adaptations to lower and higher growth temperature involve both the acquisition of necessary genes and loss of unnecessary genes. Via a pangenome-wide association study, we correlated presence/absence of 68 genes with specific optimal growth temperature intervals. While some of these genes are poorly characterized, most are involved in metabolism of amino acids, nucleotides, carbohydrates, and lipids, as well as in signal transduction and regulation of transcription. Most of the 68 genes have a history of horizontal gene transfer with other bacteria and archaea that often grow at similar temperatures, suggesting that parallel acquisitions of genes likely promote independent adaptations of different Thermotogota species to specific growth temperatures.
Arterial thoracic outlet syndrome caused by a cervical rib: a combined thoracoscopic and supraclavicular approach for ‘en bloc’-resection
Authors: Lutz Jon Andri , Psathas Emmanouil , Rouiller Benoît , Azenha Luis Filipe 
Published: December 2024

Abstract
A cervical rib is the cause of ∼5% of thoracic outlet syndromes (TOS). We report the case of a patient with arterial TOS due to the presence of a cervical rib, managed by combined thoracoscopic and supraclavicular approach. An 18-year-old female patient presented with symptoms of arterial TOS. Magnetic resonance imaging and computed tomography angiography scans showed a tortuous subclavian artery due to a fused cervical and 1st rib. Three-port thoracoscopy was performed, which allowed to mobilize the ventral part of the 1st rib. Supraclavicular access allowed mobilization as well as central division of the ribs. After removal of the ribs, the subclavian artery presented a normal calibre and aspect. In recent years, there has been a trend towards minimally invasive approach to TOS, either by thoracoscopy or by robotic-assisted surgery. The advantages of this approach are the ‘enbloc’-resection of both ribs and the possibility to evaluate the subclavian artery during the same procedure and perform repair if necessary.
The BnamiR827–BnaA09.NLA1–BnaPHT1 module regulates phosphate homeostasis, pollen viability, and seed yield in Brassica napus
Authors: Wu Tao , Han Bei , Wang Yajie , Zhang Bingbing , Wang Chuang , Wang Sheliang , Cai Hongmei , Liu Zhu , Hammond John P , Kant Surya , Ding Guangda , Xu Fangsen , Shi Lei 
Published: December 2024

Abstract
Phosphorus (P) is an essential macronutrient for the growth and yield of crops. However, there is limited understanding of the regulatory mechanisms of phosphate (Pi) homeostasis, and its impact on growth, development, and yield-related traits in Brassica napus. Here, we identified four NITROGEN LIMITATION ADAPTATION1 (BnaNLA1) genes in B. napus; their expression was predominant in roots and suppressed by Pi starvation-induced BnamiR827. All the BnaNLA1 proteins have similar sequences, subcellular localizations, and abilities to rescue the growth defects of the atnla1 mutant. One of the genes, BnaA09.NLA1, is expressed abundantly in roots, and also in old leaves, anthers, and pollen. Knocking out BnaNLA1 genes or overexpressing BnamiR827 resulted in increased concentrations of Pi in leaves and stamens and reduced pollen viability, thereby negatively impacting seed yield. Bimolecular fluorescence complementation (BiFC) and split-ubiquitin yeast two-hybrid (Y2H) analyses demonstrated that BnaA09.NLA1 interacted with seven Pi transporters highly expressed in roots and/or anthers (i.e. BnaPT8/10/11/27/35/37/42) to regulate Pi uptake and Pi allocation in anthers. Taken together, this study demonstrates that the BnamiR827–BnaA09.NLA1–BnaPHT1 module is involved in the regulation of Pi uptake and Pi allocation in floral organs, which is vital for the growth, pollen viability, and seed yield of B. napus.
Receptor kinase LecRK-I.9 regulates cell wall remodelling during lateral root formation in Arabidopsis
Authors: Bellande Kevin , Roujol David , Chourré Josiane , Le Gall Sophie , Martinez Yves , Jauneau Alain , Arico Denise , Mithöfer Axel , Burlat Vincent , Jamet Elisabeth , Canut Hervé 
Published: December 2024

Abstract
Assembling and remodelling the cell wall is essential for plant development. Cell wall dynamics are controlled by cell wall proteins, polysaccharide biosynthesis, and a variety of sensor and receptor systems. LecRK-I.9, an Arabidopsis thaliana plasma membrane-localized lectin receptor kinase, was previously shown to be involved in cell wall–plasma membrane contacts and to play roles in plant–pathogen interactions, but until now its role in development was not known. LecRK-I.9 is transcribed at a high level in root tissues including the pericycle. Comparative transcript profiling of a loss-of-function mutant versus the wild type identified LecRK-I.9 as a regulator of cell wall metabolism. Consistently, lecrk-I.9 mutants displayed an increased pectin methylesterification level correlated with decreased pectin methylesterase and increased polygalacturonase activities. Also, LecRK-I.9 negatively impacted lateral root development through the direct or indirect regulation of genes encoding (i) cell wall remodelling proteins during early events of lateral root initiation, and (ii) cell wall signalling peptides (CLE2 and CLE4) repressing lateral root emergence and growth. Furthermore, low nitrate reduced LecRK-I.9 expression in roots, particularly in the lateral root emergence zone: even in these conditions, the control of CLE2 and CLE4 expression is maintained. Altogether, the results show that LecRK-I.9 is a key player in negatively regulating both pre-branch site formation and lateral root emergence.
Harnessing deliberative regulation to address inequities in accessing healthcare services in England
Authors: Germain Sabrina , Veronesi Gianluca 
Published: December 2024

Abstract
System-level decisions around the commissioning and provision of healthcare services in England have contributed to barriers in accessing the National Health Service. In this article, we ask how to better regulate resource allocation to ensure greater equity in access to healthcare services. First, we focus on the Health and Care Act 2022, which, drawing on principles of deliberative regulation to address health inequalities, initiates a shift away from previous regulatory approaches towards a collaborative decision-making model. We then shed light on the systemic factors creating and maintaining access barriers by considering shortcomings in previous regulatory approaches. With these in mind, we consider whether deliberative regulation—providing communities with resources to create normative solutions to intrinsic issues—could help address these systemic challenges. To assess the potential of laws or policies to achieve greater equity in healthcare, we also introduce an evaluative framework based on deliberative principles. We apply this framework to a case study of an Integrated Care System to gauge the extent to which the Health and Care Act 2022 has indeed been effectively adopting a deliberative approach by intentionally engaging marginalized communities in decision-making and devising accountability mechanisms for the allocation of healthcare resources.
Tunable piezoelectric PLLA nanofiber membranes for enhanced mandibular repair with optimal self-powering stimulation
Authors: Chen Shuo , Wang Xinqing , Zhang Dong , Huang Zhenhua , Xie Yina , Chen Fangping , Liu Changsheng 
Published: December 2024

Abstract
Poly (l-lactic acid) (PLLA) is a biocompatible, biodegradable material with piezoelectric properties, making it a promising candidate for providing self-powered stimulation to accelerate tissue repair. Repairs to various tissues, such as bone, cartilage and nerve, necessitate distinct piezoelectric characteristics even from the same material. However, the extensive utilization of PLLA piezoelectric scaffolds in various tissue is hindered by their low and single piezoelectric constants. In this study, PLLA nanofiber membranes with enhanced and adjustable piezoelectric constants (d33) were fabricated through oriented electrospinning. By carefully controlling the parameters of the spinning solution, a steady increase in d33 values from 0 to 30 pC/N was achieved. This advancement allows tailoring of PLLA nanofiber membranes to meet various piezoelectric requirements of different tissues. As an example of tailoring the optimal piezoelectric constants, we developed PLLA-2-0, PLLA-2-10, PLLA-2-15 and PLLA-2-20 nanofiber membranes with d33 values of 0, 5, 10 and 15 pC/N, respectively. The impact of varying piezoelectric constants of PLLA nanofiber membranes on cellular behavior and repair efficacy were validated through in vitro cellular experiments and in vivo mandibular critical defect repair. The results indicated that PLLA-2-20 demonstrated superior cell proliferation rate up to 130% and an osteogenic differentiation level approximately twice of the control. In addition, PLLA-2-20 significantly promoted cell adhesion and migration, and the cell aspect ratio was about five times higher than that of the control group. In vivo, PLLA-2-20 optimal restorative effects on rat mandibles via endogenous mechanical force-mediated piezoelectric stimulation, leading to complete histological restoration within 8 weeks. These findings highlight the potential of the PLLA membranes with high and adjustable d33 by a straightforward process. This study provides a novel approach for the development of highly electroactive membranes tailored to specific tissue repair needs.
Early Life Stress, DNA Methylation of NR3C1 and HSD11B2, and Oral Feeding Skill Development in Preterm Infants
Authors: Griffith Thao , Tell Dina , Green Stefan J. , Ford Ashley , Bohan Adam , Grunwaldt Jennifer , Amin Sachin , White-Traut Rosemary , Janusek Linda 
Published: December 2024

Background:
Early life stress exposure in preterm infants may alter DNA methylation of NR3C1 and HSD11B2, disrupting neurobehaviors needed for oral feeding (PO) skill development.

Purpose:
To (1) examine the feasibility of the study protocol; (2) describe early life stress, DNA methylation of NR3C1 and HSD11B2, and PO skill development; and (3) explore the association between DNA methylation of NR3C1 and HSD11B2 and infant characteristics, early life stress, and PO skill development.

Method:
We employed a longitudinal descriptive pilot study (N = 10). Infant characteristics were collected from the infant’s electronic medical record. Early life stress was assessed via the modified Neonatal Infant Stressor Scale. DNA methylation of NR3C1 exon 1F and HSD11B2 promoter regions was analyzed from the infant’s buccal samples. PO skill development was evaluated using the Early Feeding Skills Assessment.

Results:
Infants who experienced more acute and chronic stress during their neonatal intensive care unit hospitalization demonstrated higher DNA methylation at CpG 17 and 31 of the NR3C1 exon 1F and at CpG 4 and 28 of the HSD11B2 promoter regions. Infants with higher DNA methylation at these CpG sites also exhibited less optimal PO skill development and experienced longer transition from first to full PO.

Implications for Practice and Research:
Our findings revealed relationships among early life stress, DNA methylation of NR3C1 and HSD11B2, and PO skill development in preterm infants. Future research is warranted to examine the multiomics pathways whereby early life stress influences the phenotypes of infant outcomes.
Resuscitation in Paediatric Septic Shock Using Vitamin C and Hydrocortisone (RESPOND): The RESPOND Randomized Controlled Trial Protocol
Authors: Raman Sainath , Gibbons Kristen S. , Jayashree Muralidharan , Lalitha AV , Bellomo Rinaldo , Blythe Robin , Buckley David , Butt Warwick , Cho Hwa Jin , Cree Michele , de Souza Daniela C. , Erickson Simon , Festa Marino , Ganu Subodh , George Shane , James Ebor Jacob , Johnson Kerry , Le Marsney Renate , Lister Paula , Pham Trang M. T. , Singh Puneet , Venkatesh Balasubramanian , Wall Renee , Long Debbie A. , Schlapbach Luregn J. ,   on behalf of the Resuscitation in Paediatric Septic Shock using Vitamin C and Hydrocortisone (RESPOND) Study Group and the Australian and New Zealand Intensive Care Society Paediatric Study Group (ANZICS PSG)
Published: December 2024

Objectives:
Pediatric sepsis results in significant morbidity and mortality worldwide. There is an urgent need to investigate adjunctive therapies that can be administered early. We hypothesize that using vitamin C combined with hydrocortisone increases survival free of inotropes/vasopressors support until day 7 compared with standard care. Here we describe the Resuscitation in Paediatric Septic Shock using Vitamin C and Hydrocortisone (RESPOND) trial protocol, which aims to address this hypothesis.

Design:
Randomized, open label, controlled, parallel-group, three-arm trial with integrated economic evaluation.

Setting:
Nine Australia and New Zealand PICUs, with interest from additional international sites.

Patients:
Children between 7 days and younger than 18 years old who are treated for suspected or confirmed sepsis and receiving inotropes/vasopressors for greater than 1 hour.

Interventions:
IV vitamin C (100 mg/kg [maximum 5 g] every 6 hr) and hydrocortisone (1 mg/kg [maximum 50 mg] every 6 hr), or IV hydrocortisone alone (1 mg/kg [maximum 50 mg] every 6 hr) or standard care.

Measurements and Main Results:
Three hundred eighty-four children will be randomly assigned to receive the interventions, or standard care in a 1:1:1 ratio with stratification by steroid administration pre-randomization and hospital site. The primary outcome is time alive and free of inotropes/vasopressors, censored at 7 days. Secondary outcomes include 28-day mortality, survival free of organ support, PICU length of stay, quality of life, functional status and neurodevelopmental vulnerability at 6 months post-enrollment, and hospitalization-related costs. Statistical analysis will be based on an intention-to-treat principle. The study has ethical approval (HREC/20/QCHQ/69922, dated December 21, 2020), is registered in the Australian New Zealand Clinical Trials Registry (ACTRN12621000247875), commenced recruitment on December 8, 2021, and is expected to finish recruitment by mid-2026.

Conclusions:
Dissemination of the results will occur through publication in peer-reviewed journals, presentations at international conferences, and additional consumer-informed pathways.
Hemostatic Outcome Definitions in Pediatric Extracorporeal Membrane Oxygenation: Challenges in Cohorts From Rotterdam (2019–2023) and Melbourne (2016–2022)
Authors: Drop Joppe , Van Den Helm Suelyn , Letunica Natasha , Wildschut Enno , de Hoog Matthijs , de Boode Willem , Barton Rebecca , Yaw Hui Ping , Newall Fiona , Horton Stephen , Chiletti Roberto , Johansen Amy , Best Derek , McKittrick Joanne , Butt Warwick , d’Udekem Yves , MacLaren Graeme , Ignjatovic Vera , Attard Chantal , van Ommen C. Heleen , Monagle Paul 
Published: December 2024

Objectives:
To determine if a priori standardization of outcome hemostatic definitions alone was adequate to enable useful comparison between two cohorts of pediatric extracorporeal membrane oxygenation (ECMO) patients, managed according to local practice and protocol.

Design:
Comparison of two separate prospective cohort studies performed at different centers with standardized outcome definitions agreed upon a priori.

Setting:
General and cardiac PICUs at the Royal Children’s Hospital (RCH) in Melbourne, Australia, and the Sophia Children’s Hospital (SCH) in Rotterdam, The Netherlands.

Patients:
Children (0–18 yr old) undergoing ECMO.

Interventions:
None.

Measurements and Main Results:
Although outcome definitions were standardized a priori, the interpretation of surgical interventions varied. The SCH study included 47 ECMO runs (September 2019 to April 2023), and the RCH study included 97 ECMO runs (September 2016 to Jan 2022). Significant differences in patient populations were noted. RCH patients biased toward frequent cardiac ECMO indications, central cannulation, and cardiopulmonary bypass before ECMO. The frequency of outcome ascertainment was not standardized.

Conclusions:
This international comparison shows that standardizing hemostatic outcome definitions alone is insufficient for sensible comparison. Uniform interpretation of definitions, consistent frequency of outcome ascertainment, and stratification based on patient populations and ECMO practices are required. Our results highlight the granularity of detail needed for cross-center comparison of hemostatic outcomes in pediatric ECMO. Further work is needed as we move toward potential multicenter trials of pediatric ECMO.
Enhancing Clinical Trial Efficiency: The Impact of a Dual Digital Alert System on Quantitative Imaging Report Turnaround Time
Authors: Bhalde Rucha , Taslicay Ceylan Altintas , Virarkar Mayur , Sun Jia , Burke Sean Michael , Nayak Anish , Rao Sujaya , Mayuresh Sadhale , Morani Ajaykumar , Bhosale Priya 
Published: December 2024

Objective
This study aimed to assess the effectiveness of a dual digital alert system and automatic radiologist reassignment in improving the efficiency of quantitative imaging report delivery for clinical trials.

Materials and Methods
Assessing tumor metrics is critical to oncologic disease management, informed treatment planning, and for monitoring therapeutic response and even more so in cancer clinical research trials. A collaborative effort with the Institutional Research Information Systems division led to developing a web-based system with a Java backend, tested using Agile methodology to improve patient care with improved turnaround time (TAT) of quantitative reports. The system sent dual digital alerts including a page and an email notification to the radiologist based on the last submitted date and time for each QIAC report and autoreassigned radiologists till report finalization. Data was extracted from the Quantitative Imaging Analysis Core database for comparing the TAT, calculated as time difference between the submission of preliminary reports by Imaging Research Specialists and the finalization by radiologists before and after the digital alert system implementation.

Results
Implementing the dual digital alert system significantly increased the number of cases finalized within 6 hours to 50%. For nonexpedited cases, the mean TAT decreased by 57.2% from 85.9 hours to 36.8 hours (P < 0.001). Expedited cases saw a reduction in mean TAT by 63.7% from 44.9 hours to 16.3 hours (P = 0.022). Baseline and follow-up cases also showed significantly reduced mean and median TAT after deployment (P < 0.001).

Conclusions
The dual digital alert system and automatic radiologist reassignment significantly improved the TAT for quantitative imaging reports in clinical trials. This enhancement in report delivery efficiency led to better therapeutic decision making and increased patient satisfaction in clinical settings.
A Spatiotemporal Atlas of Mouse Gastrulation and Early Organogenesis to Explore Axial Patterning and ProjectIn VitroModels ontoIn VivoSpace
Authors: Harland Luke TG , Lohoff Tim , Koulena Noushin , Pierson Nico , Pape Constantin , Ameen Farhan , Griffiths Jonathan , Theeuwes Bart , Wilson Nicola K , Kreshuk Anna , Reik Wolf , Nichols Jennifer , Cai Long , Marioni John C , Gottgens Berthold , Ghazanfar Shila 
Published: December 2024

SUMMARYAt the onset of murine gastrulation, pluripotent epiblast cells migrate through the primitive streak, generating mesodermal and endodermal precursors, while the ectoderm arises from the remaining epiblast. Together, these germ layers establish the body plan, defining major body axes and initiating organogenesis. Although comprehensive single cell transcriptional atlases of dissociated mouse embryos across embryonic stages have provided valuable insights during gastrulation, the spatial context for cell differentiation and tissue patterning remain underexplored. In this study, we employed spatial transcriptomics to measure gene expression in mouse embryos at E6.5 and E7.5 and integrated these datasets with previously published E8.5 spatial transcriptomics1and a scRNA-seq2atlas spanning E6.5 to E9.5. This approach resulted in a comprehensive spatiotemporal atlas, comprising over 150,000 cells with 88 refined cell type annotations as well as genome-wide transcriptional imputation during mouse gastrulation and early organogenesis. The atlas facilitates exploration of gene expression dynamics along anterior-posterior and dorsal-ventral axes at cell type, tissue, and organismal scales, revealing insights into mesodermal fate decisions within the primitive streak. Moreover, we developed a bioinformatics pipeline to project additional scRNA-seq datasets into a spatiotemporal framework and demonstrate its utility by analysing cardiovascular models of gastrulation3. To maximise impact, the atlas is publicly accessible via a user-friendly web portal empowering the wider developmental and stem cell biology communities to explore mechanisms of early mouse development in a spatiotemporal context.
Who said that? Deciphering Complex Coral Reef Soundscapes with Spatial Audio and 360° Video
Authors: Dantzker Marc S. , Duggan Matthew T. , Berlik Erika , Delikaris-Manias Symeon , Bountourakis Vasileios , Pulkki Ville , Rice Aaron N. 
Published: December 2024

AbstractCoral reef soundscapes hold an untapped wealth of biodiversity information. While they are easy to record, they are nearly impossible to decipher because we know very little about which sound is made by which species. With identified fish sounds, acoustic monitoring can directly measure biodiversity, detect key or invasive species, identify behavioral events and frequencies, and estimate abundance, all at temporal and spatial scales not possible with methods like eDNA or visual surveys. Using a novel approach to visualize underwater sound, we present the most extensive collection of identified natural sounds from reef-associated Atlantic fishes. These sounds were all ascribed to speciesin situon a crowded Caribbean coral reef. The soundfield analysis technique combines visualizations of spatial audio with 360° video recordings, a method not previously accomplished underwater. We used these species identifications to decipher a representative section of a soundscape recording from a separate recording device. We have collected our identified recordings into a growing open-access resource to catalyze passive acoustic monitoring research, enabling a species-specific resolution of coral reef soundscape dynamics and providing critical validated information for developing machine learning models required to analyze an ever-expanding collection of long-term recordings.