bluuebunny/crossref_metadata_2025_split huggingface dataset:
Assessing vulnerability to embolism and hydraulic safety margins in reed‐like Restionaceae
Authors: West A. G. , Atkins K. , van Blerk J. J. , Skelton R. P. 
Published: April 2024

Abstract

The African Restionaceae (Poales), the dominant graminoid layer in the megadiverse Cape Floristic Region of South Africa, are distributed across a wide range of moisture availability, yet currently there is very little known about the underlying hydraulics of this group.

We tested two methods for measuring culm vulnerability to embolism, the optical and pneumatic methods, in three species of Cannomois ranging in habitat from semi‐riparian (Cannomois virgata) to dryland (Cannomois parviflora and C. congesta). Estimates of culm xylem vulnerability were coupled with measures of turgor loss point (ΨTLP) and minimum field water potential (ΨMD) to assess hydraulic safety margins.

The optical and pneumatic methods produced similar estimates of P50, but differed for P12 and P88. All three species were quite vulnerable to embolism, with P50 of –1.9 MPa (C. virgata), −2.3 MPa (C. congesta), and −2.4 MPa (C. parviflora). Estimates of P50, ΨTLP and ΨMD aligned with habitat moisture stress, with highest values found in the semi‐riparian C. virgata. Consistent differences in P50, ΨMD and ΨTLP between species resulted in consistent hydraulic safety margins across species of 0.96 ± 0.1 MPa between ΨMD and P50, with onset of embolism occurring 0.43 ± 0.04 MPa after ΨTLP for all three species.

Our study demonstrates that restio occupancy of dry environments involves more than the evolution of highly resistant xylem, suggesting that other aspects of water relations are key to understanding trait–environment relationships in this group.
An agrogeophysical modelling framework for the detection of soil compaction spatial variability due to grazing using field‐scale electromagnetic induction data
Authors: Romero‐Ruiz Alejandro , O'Leary Dave , Daly Eve , Tuohy Patrick , Milne Alice , Coleman Kevin , Whitmore Andrew P. 
Published: April 2024

AbstractSoil compaction is a regarded as a major environmental and economical hazard, degrading soils across the world. Changes in soil properties due to compaction are known to lead to decrease in biomass and increase in greenhouse gas emissions, nutrient leaching and soil erosion. Quantifying adverse impacts of soil compaction and developing strategies for amelioration relies on an understanding of soil compaction extent and temporal variability. The main indicators of soil compaction (i.e., reduction of pore space, increase in bulk density and decrease in soil transport properties) are relatively easy to quantify in laboratory conditions but such traditional point‐based methods offer little information on soil compaction extent at the field scale. Recently, geophysical methods have been proposed to provide non‐invasive information about soil compaction. In this work, we developed an agrogeophysical modelling framework to help address the challenges of characterizing soil compaction across grazing paddocks using electromagnetic induction (EMI) data. By integrative modelling of grazing, soil compaction, soil processes and EMI resistivity anomalies, we demonstrate how spatial patterns of EMI observations can be linked to management leading to soil compaction and concurrent modifications of soil functions. The model was tested in a dairy farm in the midlands of Ireland that has been grazed for decades and shows clear signatures of grazing‐induced compaction. EMI data were collected in the summer of 2021 and autumn of 2022 under dry and wet soil moisture conditions, respectively. For both years, we observed decreases of apparent electrical resistivity at locations that with visible signatures of compaction such as decreased vegetation and water ponding (e.g., near the water troughs and gates). A machine learning algorithm was used to cluster EMI data with three unique cluster signatures assumed to be representative of heavy, moderately, and non‐compacted field zones. We conducted 1D process‐based simulations corresponding to non‐compacted and compacted soils. The modelled EMI signatures agree qualitatively and quantitatively with the measured EMI data, linking decreased electrical resistivities to zones that were visibly compacted. By providing a theoretical framework based on mechanistic modelling of soil management and compaction, our work may provide a strategy for utilizing EMI data for detection of soil degradation due to compaction.
A scoping review of the role of policy in mitigating childhood obesity in underserved populations using the RE‐AIM framework
Authors: Gance‐Cleveland Bonnie , Frenn Marilyn , Browne Nancy , Greenberg Cindy Smith , Snethen Julia A. , Hodges Eric A. , Fial Alissa V. , Small Leigh , Irving Sharon Y. 
Published: April 2024

AbstractBackgroundChildhood obesity is an escalating crisis in the United States. Health policy may impact this epidemic which disproportionally affects underserved populations.AimThe aim was to use the reach, effectiveness, adoption, implementation, and maintenance (RE‐AIM) framework to assess health policy impact on preventing or treating school‐aged children (5 > 18 years) with obesity in underserved populations.MethodsA scoping review of 842 articles was conducted. Twenty‐four articles met the inclusion criteria and underwent data extraction.ResultsTwelve studies included subgroup analysis, with four suggesting an impact of policy on at‐risk groups. None of the 24 studies fully applied the RE‐AIM framework. Policies positively impacted childhood obesity in 12 studies across the sample.Linking Evidence to ActionOur review revealed inconsistent evidence for the effectiveness of policy on childhood obesity, perhaps due to the lack of focus on the social determinants of health. In addition, many studies did not evaluate the outcomes for underserved populations. Therefore, we propose more attention to social determinants in future legislation and evaluation of policy effectiveness on underserved populations. Findings identify an urgent need for the design, implementation, and evaluation of policies specifically directed to address the inequities of racism, social injustices, and social determinants of health that impact childhood obesity in the United States. Future work needs to identify who was reached by the policy, who benefitted from the policy, and how policies were implemented to address obesity‐related health disparities. Nurses should advocate for the evaluation of childhood obesity policies, particularly in underserved populations, to determine effectiveness. Nurses, particularly those trained in population and community health and research, should advocate for policy research that considers inequities rather than controls for these variables. Multi‐layered interventions can then be tailored to sub‐populations and evaluated more effectively.
Closed 3‐forms in five dimensions and embedding problems
Authors: Donaldson Simon , Lehmann Fabian 
Published: April 2024

AbstractWe consider the question if a five‐dimensional manifold can be embedded into a Calabi–Yau manifold of complex dimension 3 such that the real part of the holomorphic volume form induces a given closed 3‐form on the 5‐manifold. We define an open set of 3‐forms in dimension five which we call strongly pseudoconvex, and show that for closed strongly pseudoconvex 3‐forms, the perturbative version of this embedding problem can be solved if a finite‐dimensional vector space of obstructions vanishes.
Transcriptomic responses to antibiotic exposure in
Mycobacterium tuberculosis
Authors: Poonawala Husain , Zhang Yu , Kuchibhotla Sravya , Green Anna G. , Cirillo Daniela Maria , Di Marco Federico , Spitlaeri Andrea , Miotto Paolo , Farhat Maha R. 
Published: April 2024

ABSTRACT

Transcriptional responses in bacteria following antibiotic exposure offer insights into antibiotic mechanism of action, bacterial responses, and characterization of antimicrobial resistance. We aimed to define the transcriptional antibiotic response (TAR) in
Mycobacterium tuberculosis
(Mtb) isolates for clinically relevant drugs by pooling and analyzing Mtb microarray and RNA-seq data sets. We generated 99 antibiotic transcription profiles across 17 antibiotics, with 76% of profiles generated using 3–24 hours of antibiotic exposure and 49% within one doubling of the WHO antibiotic critical concentration. TAR genes were time-dependent, and largely specific to the antibiotic mechanism of action. TAR signatures performed well at predicting antibiotic exposure, with the area under the receiver operating curve (AUC) ranging from 0.84-1.00 (TAR <6 hours of antibiotic exposure) and 0.76–1.00 (>6 hours of antibiotic exposure) for upregulated genes and 0.57–0.90 and 0.87–1.00, respectfully, for downregulated genes. This work desmonstrates that transcriptomics allows for the assessment of antibiotic activity in Mtb within 6 hours of exposure.
Complete genome sequence of invasive
Streptococcus pneumoniae
serotype 11A causing meningitis in an adult patient, Italy 2022
Authors: Amadesi Stefano , Vocale Caterina , Guariglia Davide , Cricca Monica , Lazzarotto Tiziana , Sambri Vittorio , Gaibani Paolo 
Published: April 2024

ABSTRACT

Streptococcus pneumoniae
is a major global health concern, being a common cause of meningitis in both children and adults. Here, we report the complete genome sequence of P10_PNE_LCR, a
S. pneumoniae
11A strain isolated in Northern Italy from an adult patient diagnosed with meningitis.
Metagenome-assembled bacterial genomes from benthic microbial mats in ice-covered Lake Vanda, Antarctica
Authors: Powell Tyler , Sumner Dawn Y. , Jungblut Anne D. , Hawes Ian , Mackey Tyler , Grettenberger Christen 
Published: April 2024

ABSTRACT

We recovered 57 bacterial metagenome-assembled genomes (MAGs) from benthic microbial mat pinnacles from Lake Vanda, Antarctica. These MAGs provide access to genomes from polar environments and can assist in culturing and utilizing these Antarctic bacteria.
Supplemental Material: A little mica goes a long way: Impact of phyllosilicates on quartz deformation fabrics in naturally deformed rocks
Authors: Gottardi Raphaël , al. et 
Published: April 2024

<p>Figure S1: Simplified geological map and cross section of the Raft River Mountains. Table S1: Quartz textural results from electron backscatter diffraction analysis. File S1: Analytical procedure. </p>
Association of empiric antibiotic selection and clinical outcomes in hospitalised children with severe orbital infections: a retrospective cohort study
Authors: Krueger Carsten , Nguyen Emily Lan-Vy , Mahant Sanjay , Borkhoff Cornelia M , Cichon Jessica , Drouin Olivier , Pound Catherine , Quet Julie , Wahi Gita , Bayliss Ann , Vomiero Gemma , Foulds Jessica , Kanani Ronik , Sakran Mahmoud , Sehgal Anupam , Pullenayegum Eleanor , Widjaja Elysa , Reginald Arun , Wolter Nikolaus , Parkin Patricia , Gill Peter J 
Published: April 2024

ObjectiveTo determine the association of initial empiric antibiotic regimens with clinical outcomes in hospitalised children with severe orbital infections.DesignMulti-centre observational cohort study using data from 2009 to 2018 clinical records.SettingCanadian children’s hospitals (7) and community hospitals (3).PatientsChildren between 2 months and 18 years hospitalised for >24 hours with severe orbital infections.InterventionsEmpiric intravenous antibiotic regimen in the first 24 hours of hospitalisation.Main outcome measuresLength of hospital stay and surgical intervention using multivariable median regression and multivariate logistic regression, with adjustment for covariates.ResultsOf 1421 patients, 60.0% were male and the median age was 5.5 years (IQR 2.4–9.9). Median length of stay was 86.4 hours (IQR 56.9–137.5) and 180 (12.7%) received surgical intervention. Patients receiving broad-spectrum empiric antibiotics had an increased median length of stay, ranging from an additional 13.8 hours (third generation cephalosporin and anaerobic coverage) to 19.5 hours (third generation cephalosporin, staphylococcal and anaerobic coverage). No antibiotic regimen was associated with a change in the odds of surgical intervention. These findings remained unchanged in sensitivity analyses restricted to more severely ill patients. There was a twofold increase in the percentage of patients receiving the broadest empiric antibiotic regimens containing both staphylococcal and anaerobic coverage from 17.8% in 2009 to 40.3% in 2018.ConclusionsEmpiric use of broad-spectrum antibiotics with staphylococci and anaerobic coverage was associated with longer length of stay and similar rates of surgery in children with orbital infections. There is an urgent need for comparative effectiveness studies of various antibiotic regimes.
Definitions of digital biomarkers: a systematic mapping of the biomedical literature
Authors: Macias Alonso Ana Karen , Hirt Julian , Woelfle Tim , Janiaud Perrine , Hemkens Lars G 
Published: April 2024

BackgroundTechnological devices such as smartphones, wearables and virtual assistants enable health data collection, serving as digital alternatives to conventional biomarkers. We aimed to provide a systematic overview of emerging literature on ‘digital biomarkers,’ covering definitions, features and citations in biomedical research.MethodsWe analysed all articles in PubMed that used ‘digital biomarker(s)’ in title or abstract, considering any study involving humans and any review, editorial, perspective or opinion-based articles up to 8 March 2023. We systematically extracted characteristics of publications and research studies, and any definitions and features of ‘digital biomarkers’ mentioned. We described the most influential literature on digital biomarkers and their definitions using thematic categorisations of definitions considering the Food and Drug Administration Biomarkers, EndpointS and other Tools framework (ie, data type, data collection method, purpose of biomarker), analysing structural similarity of definitions by performing text and citation analyses.ResultsWe identified 415 articles using ‘digital biomarker’ between 2014 and 2023 (median 2021). The majority (283 articles; 68%) were primary research. Notably, 287 articles (69%) did not provide a definition of digital biomarkers. Among the 128 articles with definitions, there were 127 different ones. Of these, 78 considered data collection, 56 data type, 50 purpose and 23 included all three components. Those 128 articles with a definition had a median of 6 citations, with the top 10 each presenting distinct definitions.ConclusionsThe definitions of digital biomarkers vary significantly, indicating a lack of consensus in this emerging field. Our overview highlights key defining characteristics, which could guide the development of a more harmonised accepted definition.
Multimodal modeling with low-dose CT and clinical information for diagnostic artificial intelligence on mediastinal tumors: a preliminary study
Authors: Yamada Daisuke , Kojima Fumitsugu , Otsuka Yujiro , Kawakami Kouhei , Koishi Naoki , Oba Ken , Bando Toru , Matsusako Masaki , Kurihara Yasuyuki 
Published: April 2024

BackgroundDiagnosing mediastinal tumours, including incidental lesions, using low-dose CT (LDCT) performed for lung cancer screening, is challenging. It often requires additional invasive and costly tests for proper characterisation and surgical planning. This indicates the need for a more efficient and patient-centred approach, suggesting a gap in the existing diagnostic methods and the potential for artificial intelligence technologies to address this gap. This study aimed to create a multimodal hybrid transformer model using the Vision Transformer that leverages LDCT features and clinical data to improve surgical decision-making for patients with incidentally detected mediastinal tumours.MethodsThis retrospective study analysed patients with mediastinal tumours between 2010 and 2021. Patients eligible for surgery (n=30) were considered ‘positive,’ whereas those without tumour enlargement (n=32) were considered ‘negative.’ We developed a hybrid model combining a convolutional neural network with a transformer to integrate imaging and clinical data. The dataset was split in a 5:3:2 ratio for training, validation and testing. The model’s efficacy was evaluated using a receiver operating characteristic (ROC) analysis across 25 iterations of random assignments and compared against conventional radiomics models and models excluding clinical data.ResultsThe multimodal hybrid model demonstrated a mean area under the curve (AUC) of 0.90, significantly outperforming the non-clinical data model (AUC=0.86, p=0.04) and radiomics models (random forest AUC=0.81, p=0.008; logistic regression AUC=0.77, p=0.004).ConclusionIntegrating clinical and LDCT data using a hybrid transformer model can improve surgical decision-making for mediastinal tumours, showing superiority over models lacking clinical data integration.
School performance and educational achievement in children exposed to maternal cancer in utero
Authors: Greiber Iben Katinka , Viuff Jakob Hansen , Karlsen Mona Aarenstrup , Lidegaard Øjvind , Mikkelsen Anders Preztmann , Hjortshøj Cristel Sørensen , Storgaard Lone , Mellemkjær Lene 
Published: April 2024

BackgroundIn utero exposure to maternal cancer and cancer treatment might influence the child’s cognitive development. This study investigated if exposure to maternal cancer during fetal life impacted school performance and educational achievement as adults.MethodsThis nationwide retrospective cohort study identified all live-born children in Denmark between January 1978 and December 2013. Exposure was defined as maternal cancer diagnosis during pregnancy. Four partly overlapping birth cohorts were constructed depending on the outcome of interest: (1) receiving special educational support for birth years 2001–2013; (2) grade point average (GPA) at the final exams after 10th grade for 1986–2003; (3) educational achievement at 20 years for 1978–1998; and (4) education at 30 years for 1978–1988. Logistic and linear models were adjusted for birth year, maternal age, maternal education and maternal death.ResultsThe estimated probability of receiving special educational support was similar in the exposed group and the reference (adjusted OR 0.96; 95% CI 0.46 to 1.77, non-significant). The GPA did not statistically differ (0.13 grade points; 95% CI −0.18 to 0.45, non-significant). The achieved educational levels were similar for the exposed group and the reference at 20 years, with an adjusted OR of 1.07 (95% CI 0.82 to 1.40) for low versus medium educational level, and at 30 years with an adjusted OR of 0.73 (95% CI 0.35 to 1.50) for low versus high educational level and of 1.07 (95% CI 0.66 to 1.72) for medium versus high educational level.ConclusionOur findings did not indicate poorer performance in compulsory school nor impairment of adult educational achievement after exposure to maternal cancer in utero.
Microscopic state of BHs and an exact one body method for binary dynamics in general relativity
Authors: Zeng Ding-fang 
Published: April 2024

AbstractIn gravitational collapses, the horizon and singularity’s realisation in the finite future of the proper time used co-moving observer happens in the future of infinitely far away future of the normal time used outside probe. To the latter the horizon and singularity defined in the singularity theorem are physical realities only in the sense of uncertainty principle and ensemble interpretation. We provide two exact time dependent solution families to the Einstein equation and show that they form a pair of complementary description for the microscopic state of black holes by showing that the Bekenstein–Hawking entropy formula follows properly from their canonical wave function’s degeneracy. We also develop an eXact One Body method for general relativity two-body dynamics whose conservative part calls no post newtonian approximation as input and applies to the full three stages of black hole binary merger events. By this method, we analytically calculate the gravitational wave forms following from such merger processes. In the case black holes carry exact and apriori horizon and singularity our wave forms agree with those following from conventional effective one body method but exhibit more consistent late time behaviour. In the case black holes carry only asymptotic horizon and extended inner structure thus experiencing banana shape deformation as the merger occurs, our wave forms exhibit all features especially the late time quasi-normal mode type oscillation seen in real observations.
Integrin αvβ3 Upregulation in Response to Nutrient Stress Promotes Lung Cancer Cell Metabolic Plasticity
Authors: Nam Arin , Jain Shashi , Wu Chengsheng , Campos Alejandro , Shepard Ryan M. , Yu Ziqi , Reddy Joshua P. , Von Schalscha Tami , Weis Sara M. , Onaitis Mark , Wettersten Hiromi I. , Cheresh David A. 
Published: April 2024

Abstract

Cancer stem/tumor-initiating cells display stress tolerance and metabolic flexibility to survive in a harsh environment with limited nutrient and oxygen availability. The molecular mechanisms underlying this phenomenon could provide targets to prevent metabolic adaptation and halt cancer progression. Here, we showed in cultured cells and live human surgical biopsies of non–small cell lung cancer that nutrient stress drives the expression of the epithelial cancer stem cell marker integrin αvβ3 via upregulation of the β3 subunit, resulting in a metabolic reprogramming cascade that allows tumor cells to thrive despite a nutrient-limiting environment. Although nutrient deprivation is known to promote acute, yet transient, activation of the stress sensor AMP-activated protein kinase (AMPK), stress-induced αvβ3 expression via Src activation unexpectedly led to secondary and sustained AMPK activation. This resulted in the nuclear localization of peroxisome proliferator-activated receptor-gamma coactivator 1α (PGC1α) and upregulation of glutamine metabolism, the tricarboxylic acid cycle, and oxidative phosphorylation. Pharmacological or genetic targeting of this axis prevented lung cancer cells from evading the effects of nutrient stress, thereby blocking tumor initiation in mice following orthotopic implantation of lung cancer cells. These findings reveal a molecular pathway driven by nutrient stress that results in cancer stem cell reprogramming to promote metabolic flexibility and tumor initiation.

Significance:
Upregulation of integrin αvβ3, a cancer stem cell marker, in response to nutrient stress activates sustained AMPK/PGC1α signaling that induces metabolic reprogramming in lung cancer cells to support their survival.
See related commentary by Rainero, p. 1543