bluuebunny/crossref_metadata_2025_split huggingface dataset:
PredCMB: predicting changes in microbial metabolites based on the gene–metabolite network analysis of shotgun metagenome data
Authors: Ji Jungyong , Jung Sungwon 
Published: January 2025

Abstract

Motivation
Microbiota-derived metabolites significantly impact host biology, prompting extensive research on metabolic shifts linked to the microbiota. Recent studies have explored both direct metabolite analyses and computational tools for inferring metabolic functions from microbial shotgun metagenome data. However, no existing tool specifically focuses on predicting changes in individual metabolite levels, as opposed to metabolic pathway activities, based on shotgun metagenome data. Understanding these changes is crucial for directly estimating the metabolic potential associated with microbial genomic content.

Results
We introduce Predicting Changes in Microbial metaBolites (PredCMB), a novel method designed to predict alterations in individual metabolites between conditions using shotgun metagenome data and enzymatic gene–metabolite networks. PredCMB evaluates differential enzymatic gene abundance between conditions and estimates its influence on metabolite changes. To validate this approach, we applied it to two publicly available datasets comprising paired shotgun metagenomics and metabolomics data from inflammatory bowel disease cohorts and the cohort of gastrectomy for gastric cancer. Benchmark evaluations revealed that PredCMB outperformed a previous method by demonstrating higher correlations between predicted metabolite changes and experimentally measured changes. Notably, it identified metabolite classes exhibiting major alterations between conditions. By enabling the prediction of metabolite changes directly from shotgun metagenome data, PredCMB provides deeper insights into microbial metabolic dynamics than existing methods focused on pathway activity evaluation. Its potential applications include refining target metabolite selection in microbial metabolomic studies and assessing the contributions of microbial metabolites to disease pathogenesis.

Availability and implementation
Freely available to non-commercial users at https://www.sysbiolab.org/predcmb.
Development of a scoring system to predict endovascular crossing of femoropopliteal artery chronic total occlusions: the Endo VAscular CROSsing Score for Chronic Total Occlusions (EVACROSS-CTO)
Authors: Matthaiou Nikolas , Klontzas Michail E , Kasioumi Konstantina , Kakkos George A , Kehagias Elias , Tsetis Dimitrios 
Published: January 2025

Abstract

Objectives
To develop a predictive score for the prediction of successful endovascular crossing in femoropopliteal artery chronic total occlusions (CTOs).

Methods
In this retrospective study, 84 patients were divided 70%:30% into a training and a testing cohort. Parameters such as cap morphology, side branches, bridging collaterals, flush occlusion, and length were derived from pre-procedural CT angiography. Lesions were segmented and calcification burden was assessed by thresholding. A score (EndoVAscular CROSsing Score for Chronic Total Occlusion [EVACROSS-CTO]) was built based on multivariate logistic regression. Receiver operating characteristics (ROC) curve analysis determined the optimal score threshold, with reported accuracy, sensitivity, specificity, and area under the curve (AUC).

Results
Factors including age &gt; 50 years (P = .036, odds ratio (OR) = 53.7), calcification percentage &gt;10% (P = .011, OR = 16.63), the presence of a flush occlusion (P = .02, OR = 15.564), the presence of a distal side branch (P = .018, OR = 9.879), and the presence of a proximal side branch (P = 0.064, OR = 23.369) were identified as suitable for inclusion in the score. Score values were assigned based on the relative odds ratio for each factor with a maximum score of 22. EVACROSS-CTO was able to predict the success of endovascular recanalization with an AUC-ROC of 79.8% (95% CI, 58.5%-100%). A score &gt;16 yielded a sensitivity of 75% with a specificity of 70.6% for the prediction of treatment failure.

Conclusions
A score was developed by incorporating variables derived from pre-procedural CT angiography, demonstrating promising predictive capacity in determining the success of endovascular recanalization of CTOs.

Advances in knowledge
EVACROSS-CTO incorporates imaging variables for the prediction of endovascular recanalization success. This score will allow improved pre-procedural planning for femoropopliteal CTO management.
Assessing chronic effects of chemical pollution on biodiversity using mean species abundance relationships
Authors: Schoenke Venja S A M , Wang Jiaqi , Van den Brink Paul J , Hendriks A Jan 
Published: January 2025

Abstract
Because chemical pollution poses a persistent threat to freshwater ecosystems and biodiversity, innovative methodologies are required to address the ecological risks associated with such pollutants. This study predicts the long-term impacts of chemicals based on an equation that describes the time dependency of the median lethal and effect concentration (L(E)C50) with the critical body residue concept. This way, the methodology can predict species sensitivity distributions for any given time point. The methodology was extended to predict the mean species abundance relationships (MSAR) as an indicator of biodiversity. To test and validate the methodology, data from a case study with six freshwater arthropods exposed short- and long-term to imidacloprid were used. The potentially affected fraction of species (PAF) and its opposite (1-PAF) were used to validate the MSAR framework itself. The accuracy of the predicted chronic LC50 values was species-dependent. However, except for one species, all predicted chronic LC50 values were within the 95% confidence intervals (CIs) of the fits based on only acute data. The mean differences between the predicted and calculated MSARs were between 2% and 6%. The predicted MSARs generally underestimated the impact of imidacloprid. However, all predicted MSARs were either similar or lower than the calculated 1-PAF, and their CIs covered the calculated MSARs. Thus, the study found that the presented methodology is useful for predicting the long-term effects of chemical pollutants.
Comparison of in vitro transcriptomic points of departure with fish acute and chronic toxicity values: a case study of rainbow trout cells exposed to pesticides
Authors: Emberley-Korkmaz Sophie , Mittal Krittika , Xu Ke , Head Jessica , Basu Niladri 
Published: January 2025

Abstract
There is growing interest in transcriptomic points of departure (tPOD) values from in vitro experiments as an alternative to animal test method. The study objective was to calculate tPODs in rainbow trout gill cells (RTgill-W1 following Organisation for Economic Co-operaon and Development [OECD] 249) exposed to pesticides, and to evaluate how these values compare to fish acute and chronic toxicity data. Cells were exposed to one fungicide (chlorothalonil), 10 herbicides (atrazine, glyphosate, imazethapyr, metolachlor, diquat, s-metolachlor, aminomethylphosphonic acid, dicamba, dimethenamid-P, metribuzin), eight insecticides (chlorpyrifos, diazinon, permethrin, carbaryl, clothianidin, imidacloprid, thiamethoxam, chlorantraniliprole), and OECD 249 positive control 3,4-dichloroaniline. Pesticide concentrations in wells were modeled with IV-MBM EQP Ver. 2.1. Sequencing libraries were prepared with UPXome, and tPODs calculated with ExpressAnalyst. The method identified 14,449 unique genes, with 1,115 genes having &gt;5 counts in the 576 samples sequenced. For all chemicals, tPODs were derived, and tPOD mode values ranged from 0.0004 to 125 µM with an average of 36 µM. There were significant correlations between tPOD mode values (x-value) and median effect concentrations from RTgill-W1 cells (y = 0.92x + 1.2, R2 = 0.9, p &lt; 0.00001; n = 11), rainbow trout acute toxicity median lethal concentrations (y = 0.81x + 0.8, R2 = 0.63, p &lt; 0.0001; n = 20), fish chronic sublethal effect concentrations (y = 0.53x − 0.2, R2 = 0.4, p = 0.009; n = 16), and fish chronic lethal effect concentrations (y = 0.64x − 0.023, R2 = 0.59, p = 0.0013; n = 14). Bland–Altman plot analyses of these comparisons also showed good agreement. Pathway-level benchmark doses were calculated when statistical requirements were met, and only possible for four pesticides. These findings support the notion that tPODs from short-term in vitro studies may be comparable to effect concentration data from in vivo studies of fish exposed for chronic durations.
Determination of bacteriocin genes and antimicrobial activity of Lactiplantibacillus plantarum isolated from feta cheese samples
Authors: Akbulut Sumeyye , Dasdemir Elanur , Ozkan Hakan , Adiguzel Ahmet 
Published: January 2025

Abstract
In this study designed to isolate lactic acid bacteria (LAB) with bacteriocin production potential, white cheese samples were collected from different provinces of Turkey and isolation was carried out. A series of experiments were carried out for the main purpose and the actual bacteriocin producers were identified by detecting the genes encoding this bacteriocin. The experiments carried out in this direction were initially carried out with 20 isolates and as a result of various experiments, the number of isolates was reduced to 8 and the study was continued with 8 isolates. In order to determine that the eight isolates identified as a result of a phenotypic and biochemical characterization study were true bacteriocin-producing strains, their antibacterial activity was investigated and then the presence of bacteriocin genes was examined by specific polymerase chain reaction (PCR) using gene-specific primers. As a result, MS16 coded Lactiplantibacillus plantarum OR922652 was found to have strong antibacterial activity against Escherichia coli, Klebsiella pneumonia, Yersinia enterocolitica, Listeria monocytogenes, Bacillus cereus, and Staphylococcus aureus; the isolate was susceptible to clinically important antibiotics (ciprofloxacin, gentamicin, penicillin G, ampicillin, chloramphenicol, and vancomycin) and resistant to erythromycin, had no hemolytic activity and possessed plnA and plnD genes encoding bacteriocin production. In conclusion, the MS16 coded L. plantarum isolate has emerged as a promising strain that can be used especially in the health field and in the food industry related to LAB.
Challenges in Geographic Access to Specialized Pediatric Burn Care in the United States
Authors: Dougherty Jacob M , Blake Eva S , Rittle Christopher J , Fan Zhaohui , Hunter Mary A , Hemmila Mark R , Sangji Naveen F 
Published: January 2025

Abstract

Background
Geographical access to pediatric burn centers in the US is not well described. Patients may receive care at American Burn Association (ABA)-verified burn centers, unverified burn centers, or non-burn centers. A recent study indicated that most US counties do not have an ABA-verified pediatric burn center within 100 miles. However, access to unverified burn centers that provide care to pediatric burn patients was not considered. We studied access to all pediatric burn centers across different US regions, using American College of Surgeons (ACS) Committee on Trauma-verified pediatric trauma centers as a benchmark.

Study Design
An observational cohort study was conducted using 2022 US Census data. Individuals aged ≤14 years were included. Geographical location was determined by residence ZIP code. Pediatric burn centers were identified from the ABA directory. Pediatric trauma centers were identified by ACS verification status using the ACS Hospitals and Facilities directory. Population access to pediatric burn and trauma centers within 50, 100, and 300 miles of the home ZIP code was assessed.

Results
Of US children, 62.1%, 83.5%, and 98.6% live within 50, 100, and 300 miles of a pediatric burn center. Access to ABA-verified pediatric burn centers is lower compared to access to ACS-verified pediatric trauma centers.

Conclusions
Overall, the US population has limited access to pediatric burn centers compared to pediatric trauma centers. The services offered and outcomes should be studied to better understand differences in the quality of care provided by verified and unverified centers.
A Pilot Study on the Impact of Smoking on Adipose Derived Stem Cell Function in Burn Patients
Authors: Deville Paige , Dennis Jenna , Warren Olivia , Fontenot Cameron , Messa Genevieve , Carter Jeffrey E , Phelan Herb A , Schoen Jonathan , Hobden Jeffery A , Siggins Robert W , McTernan Patrick M , Molina Patricia E , Smith Alison A 
Published: January 2025

Abstract
Adipose-derived stem cells (ADSCs) have an important role in the modulation of burned tissue repair through the release of paracrine factors that stimulate the wound healing response. In this study, we tested the hypothesis that smoking status alters the profile of paracrine factors secreted from ADSCs isolated from damaged adipose tissue.
Adipose tissue was collected from adult patients (N=8) with severe burn injuries (&gt;20% total body surface area) at the index operation. ADSCs were extracted and cultured in vitro. Supernatants were harvested 30 hours after plating and used for cytokine determinations by Multiplex assay. Fluorescence activated single cell sorting (FACS) confirmed their phenotype with markers CD 90, CD 166, and CD 73. Univariate analyses were performed to compare the two cohorts (Smokers vs non smokers).
Higher amounts of anti-inflammatory cytokines IL-4 (p=0.03) and IL-10 (p=0.04) and pro-inflammatory cytokines TNF-alpha (p=0.03), IL-8, and IFN-gamma (p=0.03) were detected in burn patients who were current everyday smokers when compared to nonsmokers, or former smokers. No significant differences in supernatant concentrations of IL-17, IL-1 beta, TGF-alpha, IL-6, and IL-13 were observed (p&gt;0.05). Mortality was higher in the smoker group when compared to non-smokers.
The results from this study suggest that smoking status in patients with a major burn injury may alter the paracrine factors secreted from ADSCs, and on-going studies will increase sample size and refine experimental approach. Furthermore, these results support the need for studies examining the systemic effects of smoking status of patients suffering burn injuries impacts the wound healing.
Coordination and Incumbency Advantage in Multi-Party Systems—Evidence from French Elections
Authors: Dano Kevin , Ferlenga Francesco , Galasso Vincenzo , Le Pennec Caroline , Pons Vincent 
Published: January 2025

Abstract
Free and fair elections should incentivize elected officials to exert effort and enable citizens to select representative politicians and occasionally replace incumbents. However, incumbency advantage and coordination failures possible in multi-party systems may jeopardize this process. We ask whether these two forces compound each other. Using a regression discontinuity design (RDD) in French two-round local and parliamentary elections, we find that close winners are more likely to run again and to win the next election by 33 and 25 percentage points, respectively. Incumbents who run again personalize their campaign communication more and face fewer ideologically close competitors, revealing that parties from the incumbent’s orientation coordinate more effectively than parties on the losing side. A complementary RDD shows that candidates who marginally qualify for the runoff also rally new voters. We conclude that party coordination on the incumbent and voter coordination on candidates who won or gained visibility in a previous election both contribute to incumbents’ future success.
Historicizing the Nineteenth-Century Entrepreneurial Theatrical Artisan: The Case of Henry Hamilton
Authors: Bradley Hayley 
Published: January 2025

Abstract
This paper sets out to establish the historiographical significance of a theatrical artisan and his body of work, in order to question the roots and routes of our methodologies for mapping the period. Henry Hamilton’s career as dramatist spanned 45 years (1873–1918), during which time he consistently and prolifically created works that were commercially successful and popular with audiences: from autumn dramas at Drury Lane to musical comedies for the Gaiety theatre. Whilst in his own lifetime Hamilton’s repertoire sat centrally in the theatrical marketplace he opted to live privately on the periphery of the developing celebrity culture. Over time, both Hamilton’s identity and his creative practice have been overlooked; therefore, my consideration of Hamilton here is a response to an imperative for democratizing nineteenth- and early twentieth-century theatre history through recovery, inclusivity, and revision. Hamilton represents a synecdochal figure, a methodological case study for similar ‘hidden’ practitioners who, like Hamilton, worked as part of a growing, vibrant but economically precarious industry and who, in a rapidly changing and increasingly industrialized culture, adapted to shifting working practices and public taste. While acknowledging existing scholarship of nineteenth- to early twentieth-century theatre, this paper argues for new narrative routes in our historiographical practice. It proposes approaches that examine the theatre industry through its economic and production-based dynamics, recovering similar theatrical artisan figures to map a different network of practitioners to be embedded in our overall understanding of the many ways in which theatre functioned as a cultural practice and enterprise during the era.
Measuring the matter fluctuations in the Local Universe with the ALFALFA catalogue
Authors: Franco Camila , Oliveira Jezebel , Lopes Maria , Avila Felipe , Bernui Armando 
Published: January 2025

ABSTRACT
The standard model of cosmology describes the matter fluctuations through the matter power spectrum, where $\sigma _{8} \equiv \sigma _{8,0} \equiv \sigma _{8}(z = 0)$, defined at the scale of $8\, h^{-1}$ Mpc, acts as a normalization parameter. Currently, the literature reports measurements of $\sigma _{8}$ analysing different cosmic tracers, where some of these results were obtained assuming a fiducial cosmology. In this study, we measure, in a model-independent approach, the matter fluctuations in the Local Universe using H i extragalactic sources mapped by the ALFALFA survey. Our analyses allow us to test the standard cosmological model under extreme conditions in the highly non-linear Local Universe, quantifying the amplitude of the matter fluctuations there. Our work directly measures $\sigma _{8}$ using the three-dimensional distances of the H i sources determined by the ALFALFA survey without assuming a fiducial cosmology, resulting in a robust model-independent measurement of $\sigma _{8}$. Our methodology involves the construction of suitable mock catalogues to simulate the large-scale structure features observed in the data, applying the two-point correlation function, and making use of Markov chain Monte Carlo methods to estimate the parameters. Analysing these data, we measure $\sigma _8 = 0.78 \pm 0.04$ for $h = 0.6727$, $\sigma _8 = 0.80 \pm 0.05$ for $h = 0.698$, and $\sigma _8 = 0.83 \pm 0.05$ for $h = 0.7304$. Considering the data pairs $(\sigma _8, H_0)$ from the Planck cosmic microwave background (CMB) and Atacama Cosmology Telescope (ACT) CMB-lensing analyses, our measurement agrees with them within $1\, \sigma$ confidence level. From a model-independent perspective, we find that the scale where the matter fluctuation is 1 is $R = 7.2 \pm 1.5~\text{Mpc}$.
Synthetic photorespiratory bypass improves rice productivity by enhancing photosynthesis and nitrogen uptake
Authors: Chen Guoxin , Li Yanni , Jin Kaining , Gao Jiabei , Wu Suting , Cui Xuean , Mao Chuanzao , Yin Xinyou , Lu Tiegang , Zhang Zhiguo 
Published: January 2025

Abstract
Photorespiration, often considered as a wasteful process, is a key target for bioengineering to improve crop yields. Several photorespiratory bypasses have been designed to efficiently metabolize 2-phosphoglycolate and increase the CO2 concentration in chloroplasts, thereby reducing photorespiration. However, the suppression of primary nitrate assimilation remains an issue when photorespiration is inhibited. In this study, we designed a carbon and nitrogen metabolism–coupled photorespiratory bypass, termed the GCBG bypass, in rice (Oryza sativa) chloroplasts. Our results demonstrated efficient assembly and expression of the GCBG bypass in rice chloroplasts, which affected the levels of typical metabolites and their derivatives of natural photorespiration and enhanced the photosynthetic efficiency. Metabolomic analyses revealed that oxaloacetate, produced from glycolate in chloroplasts, positively impacted amino acid synthesis, energy metabolism, and sugar synthesis. The engineered GCBG plants showed an average yield increase of 19.0% (17.8% to 20.2%) compared with wild-type plants under natural growth conditions, alongside improved nitrogen uptake, which compensated for 44.1% of yield losses under nitrogen-limited conditions. In summary, the GCBG bypass substantially improved the photosynthetic efficiency, biomass, and yield in rice by integrating carbon and nitrogen metabolism. This study introduces a strategy for engineering high-yielding rice or other crops with improved photosynthetic efficiency and nitrogen uptake.
Anakinra improves retention rate of targeted treatments in Erdheim–Chester disease
Authors: Campochiaro Corrado , Tomelleri Alessandro , Catamerò Francesco , Pegoraro Francesco , Vaglio Augusto , Dagna Lorenzo 
Published: January 2025

Abstract

Objective
Erdheim–Chester disease (ECD) is a rare non-Langerhans cell histiocytosis that exhibits a wide spectrum of clinical manifestations. The recent identification of activating mutations in the MAPK–ERK pathway in patients with ECD has led to the introduction of targeted therapies. The most commonly used targeted therapies are BRAF and MEK inhibitors, which are highly effective but also carry significant toxicity. The aim of our study was to assess drug retention of targeted therapies in ECD patients from two Italian referral centres and to investigate the influence of a combined anakinra plus targeted therapy approach.

Methods
We retrospectively analysed drug retention rate (DRR) in a cohort of ECD patients who received targeted therapies, alone or combined with anakinra.

Results
Among 52 patients undergoing 60 treatment courses, vemurafenib (72%) was the most used drug, followed by cobimetinib (23%), trametinib (3%) and dabrafenib (2%). The overall 18-month DRR for all the treatment courses was 72%, with no significant differences between agents. Adverse reactions were the leading cause (76%) of discontinuation. Sixteen patients (27%) received a combined treatment with anakinra. This combination therapy was associated with a significantly higher 18-month DRR (94% vs 65%, P = 0.0251). Survival analysis also showed that drug retention was better in the anakinra group (log-rank test P = 0.040).

Conclusions
ECD patients on targeted therapies showed an overall 18-month DRR of 72%, with no significant differences between specific molecules. The combination of anakinra and targeted therapies was associated with a significantly improved drug retention.