bluuebunny/crossref_metadata_2025_split huggingface dataset:
Regulation of lignin biosynthesis by GhCAD37 affects fiber quality and anther vitality in upland cotton
Authors: Li Haipeng , Guo Jinggong , Li Kun , Gao Yuwen , Li Hang , Long Lu , Chu Zongyan , Du Yubei , Zhao Xulong , Zhao Bing , Lan Chen , Botella José Ramón , Zhang Xuebin , Jia Kun‐Peng , Miao Yuchen 
Published: November 2024

SUMMARYCotton stands as a pillar in the textile industry due to its superior natural fibers. Lignin, a complex polymer synthesized from phenylalanine and deposited in mature cotton fibers, is believed to be essential for fiber quality, although the precise effects remain largely unclear. In this study, we characterized two ubiquitously expressed cinnamyl alcohol dehydrogenases (CAD), GhCAD37A and GhCAD37D (GhCAD37A/D), in Gossypium hirsutum. GhCAD37A/D possess CAD enzymatic activities, to catalyze the generation of monolignol products during lignin biosynthesis. Analysis of transgenic cotton knockout and overexpressing plants revealed that GhCAD37A/D are important regulators of fiber quality, positively impacting breaking strength but negatively affecting fiber length and elongation percentage by modulating lignin biosynthesis in fiber cells. Moreover, GhCAD37A/D are shown to modulate anther vitality and affect stem lodging trait in cotton by influencing lignin biosynthesis in the vascular bundles of anther and stem, respectively. Additionally, our study revealed that Ghcad37A/D knockout plants displayed red stem xylem, likely due to the overaccumulation of aldehyde intermediates in the phenylpropanoid metabolism pathway, as indicated by metabolomics analysis. Thus, our work illustrates that GhCAD37A/D are two important enzymes of lignin biosynthesis in different cotton organs, influencing fiber quality, anther vitality, and stem lodging.
Evaluation of a rapid test for point‐of‐care detection of cardiac troponin I in serum of healthy and diseased dogs and cats
Authors: Santarelli G. , Sebastián Marcos P. , Talavera J. , Aznar‐Cervantes S. D. , Fernández del Palacio J. 
Published: November 2024

AbstractObjectives(1) To compare the results of a rapid test for qualitative detection of cardiac troponin I (cTnI) values >1 ng/mL with those obtained using a reference quantitative method and (2) to perform a semiquantitative assessment of rapid test results using this point‐of‐care (POC) assay.DesignProspective cross‐sectional study from April 2015 to November 2020.SettingSecondary referral hospital.AnimalsEighty dogs and 20 cats, with and without cardiovascular disease.InterventionsNone.Measurements and Main ResultsSerum samples were obtained, and cTnI rapid test was conducted in parallel with chemiluminescence assay (reference standard). Positive results from the rapid test were further classified as mild and strong positives, based on subjective assessment of the color intensity of the test line. Rapid test was deemed valid in all patients. There was agreement for positive samples between the qualitative and quantitative techniques in 31 dogs and 5 cats, and for negative samples in 43 dogs and 13 cats, resulting in a strong and moderate agreement, respectively. There was a significant difference between color scale groups.ConclusionsThe rapid test assessed provides a feasible POC option to determine concentrations of cTnI >1 ng/mL in dogs and cats and shows a moderate to strong agreement with a validated conventional quantitative assay. Furthermore, semiquantitative assessment allows estimation of the magnitude of the elevation.
Validation of Exercise and Postexercise Energy Expenditure Estimates Using Hip and Wrist Accelerometer Algorithms
Authors: Remillard Nicholas M. , Hoogkamer Wouter , Layec Gwenael , Sirard John 
Published: November 2024

To estimate physical activity intensity, accelerometer-based devices are often calibrated to energy expenditure (EE) measures using indirect calorimetry (IC). Most EE estimation algorithms are based on steady-state data and do not consider excess postexercise oxygen consumption (EPOC). Purpose: The purpose of this study is to determine the effect of incorporating EPOC into linear and nonlinear accelerometer methods for estimating EE after high-intensity running. Methods: Nine adult males participated in three visits using IC to measure EE while wearing wrist and hip ActiGraph accelerometers. Each visit is described as follows: (a) Visit 1: a treadmill VO2peak test determined treadmill speed for subsequent visits; (b) Visit 2: 20-min seated baseline and three vigorous treadmill running bouts (30, 60, and 120 s) with 20-min seated rest between; and (c) Visit 3: 60-min supine baseline and a 30-min treadmill run followed by 3-hr supine rest. Fifteen EE estimation algorithms were compared with IC-measured EE. The bias (ActiGraph accelerometers − IC) and 95% confidence interval of the bias were used to determine significance. Results: Linear regression EE algorithms tended to overestimate EE after each exercise bout (mean bias kilocalories [95% confidence intervals]; 30 s: 12.5 [3.3, 21.6], 60 s: 9.6 [0.4, 18.9], 120 s: 6.5 [−2.7, 15.7], and 30 min: 177.5 [84.6, 262.1]). The nonlinear algorithms underestimated EE after the short bouts and, due to the wide confidence interval, demonstrated no bias after the 30-min bout (30 s: −7.9 [−10.2, −5.6], 60 s: −10.9 [−14.0, −7.9], 120 s: −15.4 [−15.9, −14.8], 30 min: 14.8[−39.5, 69.2]). Adding EPOC did not improve EE estimates. Conclusions: Generally, the addition of measured EPOC did not improve device-based EE estimates. Nonlinear methods demonstrated less bias in estimating postexercise EE than linear methods.
A Treadmill-Based Evaluation of the Validity of the ActivPAL4 for Detecting Steps in Walking and Running in Healthy Adults
Authors: Choi Jordan , Hon Sereen , Redpath Louise , Wu Chi Chian , Stansfield Ben 
Published: November 2024

Objective: To accurately characterize people’s physical activity validated measurement devices must be used. The activPAL4 physical activity monitor allows measurement of stepping. A systematic approach was taken to validate the monitor for walking and running, across the walk to run transition. Methods: A cross-sectional sample of healthy young adults completed an incremental treadmill-based protocol (speeds 3.0–11.8 km/hr in 0.4 km/hr increments; 0.83–3.28 m/s). A video-based reference standard was used to evaluate the accuracy of the activPAL4 (thigh-mounted activity monitor) in detecting steps with mean percentage error, mean absolute percentage error, and agreement calculated. A linear regression modeled mean percentage error using sex, body mass index, height, cadence, and step length. Results: Thirty-six participants (25.6 ± 3.7 years, 18 M/18 F) transitioned from walking to running between 1.61 and 2.28 m/s. Mean percentage error between activPAL4 and video-based step count within speeds ranged from 1.6% to 4.3% for walking and 1.1% to 20.5% for running. Overall, walking step detection was good (mean absolute percentage error 3.1%), but steps were undercounted by the activPAL4 during running (mean absolute percentage error 14.5%). Regression modeling indicated that in walking for males activPAL4 undercounted by 2.85%, for females 1.79%. In running, for males activPAL4 undercounted steps by 13.3%, for females 15.6%. Sex and body mass index explained only a small amount of variance(). Cadence was the most important predictor of percentage error in running () contributing to an adjusted R2 of .391. Conclusion: The activPAL4 measures walking steps well across the range of walking speeds from 0.83 to 1.94 m/s. Running steps were undercounted by the activPAL4 in relation to video-based observation between 10% and 20% between 1.83 and 3.28 m/s.
Assessing the Efficacy of Sport-Based Physical Education on Children’s Activity Behaviors: A Randomized Controlled Trial
Authors: Cepni Aliye B. , Walsh David W. , Kim Hanjoe , Yoon Cynthia Y. , Hughes Sheryl O. , Ledoux Tracey A. , Johnston Craig A. 
Published: November 2024

Background: Children from low-income and racial/ethnic minority backgrounds are more prone to insufficient physical activity and heightened sedentary behaviors. This study aims to increase moderate to vigorous physical activity and decrease sedentary behaviors among high-risk children through an inclusive and transformative sport skill development physical education (PE) intervention. Methods: Elementary school-aged children were recruited from 3 public schools located in underserved communities in Houston, TX. Classrooms were randomly assigned to a sport-based PE class (intervention, 12 classrooms, n = 124) or a standard PE class (control, 13 classrooms, n = 133). The intervention was implemented at school by teachers over 10 weeks, whereas at home, the intervention group received equipment, virtual classes, and parent trainings. Activity behaviors were assessed using accelerometry (ActiGraph GT3X+) at baseline and post intervention. Multilevel linear mixed-effects models were conducted to examine changes in activity behaviors between the study conditions. Results: Participants were 9.33 (0.68) years old, and 46% were females, who identified as either Hispanic/Latino (48%) and/or Black (38%). The difference in minutes of weekend sedentary behavior change was 32 minutes between study conditions (P = .012). Specifically, intervention girls decreased weekend sedentary behavior by 37 minutes, whereas girls in the control condition increased by 8 minutes (P < .01). Despite the direction of change in overall, weekday, or weekend moderate to vigorous physical activity and overall or weekday sedentary behaviors in favor of the intervention, these effects did not reach the statistically significant level compared to the control condition. Conclusions: Sport-based PE intervention can be an important strategy to decrease child sedentary behaviors during out-of-school periods, particularly among girls.
Recombination across distant coronavirid species and genera is a rare event with distinct genomic features
Authors: Patiño-Galindo Juan , García-Sastre Adolfo , Kuhn Jens H. , Rabadan Raul , Palacios Gustavo 
Published: November 2024

ABSTRACT

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2; family
Coronaviridae
, genus
Betacoronavirus
, subgenus
Sarbecovirus
) has caused millions of deaths, prompting a need for better understanding of coronavirid emergence and spillover to humans. As an evaluation of how some features of SARS-CoV-2, unique among sarbecoviruses, may have been acquired from related viruses, we conducted phylogenetic and recombination analyses to compare the frequency of recombination among coronavirids across vs within genera, subgenera, and species. Among known betacoronaviruses, we identified 199 (183 intraspecies, 16 interspecies, but no intersubgenera) recombination events. Phylogenetic analyses revealed that the ancestry of interspecies events was limited and less prone to affect 5′ regions of coronavirid genome open reading frame 1 (ORF1) than intraspecies events. On the contrary, interspecies events were significantly more prone to impact the 3′ end (ORF6–ORF8 and the nucleocapsid protein [
N
] ORF), suggesting the existence of region-specific constraints on recombination. This work substantiated that recombination among betacoronaviruses is limited by the genome similarity between their parental viruses. We conclude that SARS-CoV-2 likely acquired unique features through recombination with closely related circulating sarbecoviruses (most likely from the same species) that co-existed geographically.

IMPORTANCE
Understanding the evolutionary events that led to SARS-CoV-2 emergence, spillover, and spread is crucial to prevent, or at least be prepared for, the same type of occurrence in the future. Given that SARS-CoV-2 has some characteristics not found in other closely related viruses, we aimed to systematically assess how likely these unique features may have been acquired through recombination. We found that, although recombination is a frequent phenomenon among betacoronaviruses, it is mostly limited to closely related members of the same species. Therefore, we conclude that the most likely scenario involved feature acquisition from recombination with a closely related virus that was circulating in a geographically overlapping area or through a different biological process, but not recombination from a virus of a different species, genus, or subgenus.
Metabolomic profiles of stony coral species from the Dry Tortugas National Park display inter- and intraspecies variation
Authors: Deutsch Jessica M. , Demko Alyssa M. , Jaiyesimi Olakunle A. , Foster Gabriel , Kindler Adelaide , Pitts Kelly A. , Vekich Tessa , Williams Gareth J. , Walker Brian K. , Paul Valerie J. , Garg Neha 
Published: November 2024

ABSTRACT

Coral reefs are experiencing unprecedented loss in coral cover due to increased incidence of disease and bleaching events. Thus, understanding mechanisms of disease susceptibility and resilience, which vary by species, is important. In this regard, untargeted metabolomics serves as an important hypothesis-building tool enabling the delineation of molecular factors underlying disease susceptibility or resilience. In this study, we characterize metabolomes of four species of visually healthy stony corals, including
Meandrina meandrites
,
Orbicella faveolata
,
Colpophyllia natans
, and
Montastraea cavernosa
, collected at least a year before stony coral tissue loss disease reached the Dry Tortugas, Florida, and demonstrate that both symbiont and host-derived biochemical pathways vary by species. Metabolomes of
Meandrina meandrites
displayed minimal intraspecies variability and the highest biological activity against coral pathogens when compared to other species in this study. The application of advanced metabolite annotation methods enabled the delineation of several pathways underlying interspecies variability. Specifically, endosymbiont-derived vitamin E family compounds, betaine lipids, and host-derived acylcarnitines were among the top predictors of interspecies variability. Since several metabolite features that contributed to inter- and intraspecies variation are synthesized by the endosymbiotic Symbiodiniaceae, which could be a major source of these compounds in corals, our data will guide further investigations into these Symbiodiniaceae-derived pathways.

IMPORTANCE
Previous research profiling gene expression, proteins, and metabolites produced during thermal stress have reported the importance of endosymbiont-derived pathways in coral bleaching resistance. However, our understanding of interspecies variation in these pathways among healthy corals and their role in diseases is limited. We surveyed the metabolomes of four species of healthy corals with differing susceptibilities to the devastating stony coral tissue loss disease and applied advanced annotation approaches in untargeted metabolomics to determine the interspecies variation in host and endosymbiont-derived pathways. Using this approach, we propose the survey of immune markers such as vitamin E family compounds, acylcarnitines, and other metabolites to infer their role in resilience to coral diseases. As time-resolved multi-omics datasets are generated for disease-impacted corals, our approach and findings will be valuable in providing insight into the mechanisms of disease resistance.
Clinical laboratory evaluation of the Hologic Panther Aptima BV and CV/TV assays for the diagnosis of vaginitis in Dunedin, Aotearoa New Zealand
Authors: Elvy Juliet , Carter Katelyn , Paterson Jenna , Smith Megan , Parslow Gayleen , Ussher James E. 
Published: November 2024

ABSTRACT

Vaginitis presentations are common, but traditional diagnostic methods are imperfect. Molecular methods for bacterial vaginosis (BV) and vulvovaginal candidiasis (CV) are increasingly available but not commonly utilized in Aotearoa New Zealand. We evaluated the Hologic Aptima BV and CV/
Trichomonas vaginalis
(TV) assays against our current methods (Gram stain, yeast culture, and Hologic Aptima TV assay) and performed a retrospective BV clinical audit. The BV Aptima assay performed well with high sensitivity (97.5%) and specificity (96.3%) when the indeterminate BV category was excluded. BV indeterminate samples were almost evenly split between positive and negative results when tested on the Aptima BV assay. BV Gram stain interpretation was error prone, with 20% of samples discordant on duplicate examination. Although the Aptima CV assay was highly sensitive, it lacked specificity compared with Gram stain (83.5%) but was similar to culture (91.2%). Our BV clinical audit showed that patients with a BV indeterminate result were less likely to be treated for BV than those with a positive result, meaning more women may be treated for BV if this assay were implemented. Overall, implementation may improve laboratory workflow and consistency of reporting, but cost may be a barrier. The clinical impact of changing methods needs to be considered.

IMPORTANCE
In this paper, we evaluate the performance of the Aptima molecular assays against current Gram stain and culture methods, as well as a clinical audit to determine the potential clinical impact of implementation. Although molecular methods are increasingly used in other countries, New Zealand has not yet adopted this approach. Importantly, we found Gram stain for bacterial vaginosis (BV) to be error prone, with 20% of Gram stain results discordant on repeat examination. We show the potential for molecular methods to increase BV diagnoses and improve reproducibility and consistency of reporting which, according to our clinical audit results, would lead to more women being treated for this dysbiosis condition overall.
Liquid biopsy to identify Barrett’s oesophagus, dysplasia and oesophageal adenocarcinoma: theEMERALDmulticentre study
Authors: Miyoshi Jinsei , Mannucci Alessandro , Scarpa Marco , Gao Feng , Toden Shusuke , Whitsett Timothy , Inge Landon J , Bremner Ross M , Takayama Tetsuji , Cheng Yulan , Bottiglieri Teodoro , Nagetaal Iris D , Shrubsole Martha J , Zaidi Ali H , Wang Xin , Coleman Helen G , Anderson Lesley A , Meltzer Stephen J , Goel Ajay 
Published: November 2024

BackgroundThere is no clinically relevant serological marker for the early detection of oesophageal adenocarcinoma (EAC) and its precursor lesion, Barrett’s oesophagus (BE).ObjectiveTo develop and test a blood-based assay for EAC and BE.DesignOesophageal MicroRNAs of BaRRett, Adenocarcinoma and Dysplasia (EMERALD) was a large, international, multicentre biomarker cohort study involving 792 patient samples from 4 countries (NCT06381583) to develop and validate a circulating miRNA signature for the early detection of EAC and high-risk BE. Tissue-based miRNA sequencing and microarray datasets (n=134) were used to identify candidate miRNAs of diagnostic potential, followed by validation using 42 pairs of matched cancer and normal tissues. The usefulness of the candidate miRNAs was initially assessed using 108 sera (44 EAC, 34 EAC precursors and 30 non-disease controls). We finally trained a machine learning model (XGBoost+AdaBoost) on RT-qPCR results from circulating miRNAs from a training cohort (n=160) and independently tested it in an external cohort (n=295).ResultsAfter a strict process of biomarker discovery and selection, we identified six miRNAs that were overexpressed in all sera of patients compared with non-disease controls from three independent cohorts of different nationalities (miR-106b, miR-146a, miR-15a, miR-18a, miR-21 and miR-93). We established a six-miRNA diagnostic signature using the training cohort (area under the receiver operating characteristic curve (AUROC): 97.6%) and tested it in an independent cohort (AUROC: 91.9%). This assay could also identify patients with BE among patients with gastro-oesophageal reflux disease (AUROC: 94.8%, sensitivity: 92.8%, specificity: 85.1%).ConclusionUsing a comprehensive approach integrating unbiased genome-wide biomarker discovery and several independent experimental validations, we have developed and validated a novel blood test that might complement screening options for BE/EAC.Trial registration numberNCT06381583.
Searching for the vector-like X-quark at the future electron–proton colliders
Authors: Zhang Yan-Ju , Zhu Yong-Tao , Han Lin , Bi Yan-Ping , Liu Tai-Gang 
Published: November 2024

AbstractIn a simplified model including an exotic vector-like X-quark (VLQ-X) with electric charge 5/3, we investigate the process $$e^{+}p \rightarrow \bar{\nu }_{e}X+\bar{\nu }_{e}X\bar{t}$$

e
+

p
→

ν

¯

e

X
+

ν

¯

e

X

t

¯

induced by the couplings between the VLQ-X and the first- and third-generation quarks at the future ep colliders. We further explore the prospects of discovering the VLQ-X via the $$X\rightarrow tW$$

X
→
t
W

decay model at the electron–hadron Future Circular Collider (FCC-eh) with its proposed 60 GeV electron beam and 50 TeV proton beam. We focus our analysis on the final states, including two same-sign lepton (electrons or muons) or $$\mu \mu $$

μ
μ

pairs, at least one b-tagged jet, and large missing transverse momentum. By performing a detailed signal-to-background analysis and detector simulations, the 95% confidence level exclusion limits and $$5\sigma $$

5
σ

discovery reaches are presented in terms of parameter space regions.
Black hole solutions in double field theory
Authors: Ying Shuxuan 
Published: November 2024

AbstractIn this paper, we study black hole solutions in double field theory. In the first part, we introduce a solution-generating method and classify black hole solutions into three categories in standard double field theory. To solve the problem of double time, we utilize space/time split double field theory in the second part to derive black hole solutions. By introducing a cosmological constant and imposing the strong constraint, our findings indicate that when considering the entire doubled spacetime, the curvature signifies a generalized AdS vacuum. However, in the subspace of the entire spacetime, black holes and curvature singularities emerge.
Signatures from the observed jet power and the radiative efficiency for rotating black holes in loop quantum gravity
Authors: Cheng Zhengwei , Chen Songbai , Jing Jiliang 
Published: November 2024

AbstractWe investigate the radiative efficiency and jet power in the spacetime of a rotating black hole within the framework of loop quantum gravity (LQG), which includes an additional LQG parameter. The results show that as the LQG parameter increases, the radiative efficiency decreases for slowly rotating black holes while it increases for rapidly rotating black holes. Furthermore, the jet power is found to increase for different black hole spins. With the observed data from the well-known sources A0620-00, H1743-322, XTE J1550-564, GRS1124-683, GRO J1655-40, and GRS1915+105, we make some constraints on the black hole spin parameter and the LQG parameter. The presence of the LQG parameter broadens the allowed range of the black hole spin parameter for sources A0620-00, H1743-322, XTE J1550-564 and GRO J1655-40. However, for the source GRS 1915+105, there is no overlap between the allowed parameter regions, which implies that the rotating LQG black hole cannot simultaneously account for the observed jet power and the radiative efficiency as in other black hole spacetimes
Planar vortices in a Lorentz symmetry breaking environment
Authors: Mavigno E. , Belich H. , Luchini G. 
Published: November 2024

AbstractWe revisit planar vortex solutions within a model derived from the dimensional reduction of scalar electromagnetism, with a quartic potential incorporating the Carroll–Field–Jackiw term. We explore analytically and numerically the influence of a Lorentz symmetry-breaking constant field on these configurations and our analysis shows how this constant field can produce a new asymptotic behaviour characterised by damped oscillations of the electric and magnetic fields on the edge of the vortices.