bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genome mining to elucidate antimicrobial and plant growth promoting potentials in Lactic acid bacteria
Authors: Vargas Christian , Botero Lina , Rodriguez Edwin , Dávila Lorena , Racedo Camilo , Barrera Claudia , Bernal Adriana J. , Jiménez Hugo , Zuluaga Paola , González Carolina 
Published: February 2025

Abstract
The pangenome of lactic acid bacteria (LAB) was constructed with five bacterial strains isolated from oat silage produced by smallholder farmers from a region in the highlands of the Colombian Andes. The goal of this work was to use genome mining to elucidate some potential mechanisms of action associated with plant growth promotion and biocontrol in LAB. Multiple genes were uncovered, including those associated with antibiosis and antimicrobial compound production, genes that induce plant defense and phytohormone activation. Additionally, genome sequencing suggested mechanisms for LAB to protect against abiotic and biotic stress. Furthermore, genes that may improve phosphorus availability and those that might stimulate root growth were present. We then tested some of these findings in vitro. For instance, the biocontrol activity of these strains was evaluated against the fungal pathogens Fusarium oxsyporum f. sp. cubense (Foc R1 and Foc TR4) and the bacterial pathogen Ralstonia solanacearum (Rs). All tested strains showed the ability to significantly inhibit pathogen growth in vitro. The capability of LAB to grow at high concentrations of fusaric acid was demonstrated, suggesting that LAB might have detoxification mechanisms to compete with other microorganisms. Also, the ability of LAB to solubilize phosphate and produce IAA was demonstrated. These two properties might be involved in plant-growth promotion. Here we show that genomic sequencing can be an efficient tool to identify putative biocontrol or plant-growth promoting related sequences for genome mining.
Metabolic reprogramming in malignant A375 cells treated with a ruthenium (II) complex: insights from GCxGC-TOF/MS metabolomics
Authors: Adu-Amankwaah Francis , Hussan Ayesha , Amenuvor Gershon , Mavumengwana Vuyo , Sitole Lungile 
Published: February 2025

Abstract

Introduction
Melanoma is an aggressive form of cancer characterised by its high metabolic adaptability that contributes to drug resistance. To this end, ruthenium complexes have emerged as a promising class of compounds in the discovery of cancer drugs due to their unique chemical properties and potential to overcome some of the limitations of conventional chemotherapy. In our previous study, we synthesised, characterised, and performed cytotoxicity tests of a ruthenium (II) complex (GA113) against the malignant A375 melanoma cell line. Our previous findings revealed favourable cytotoxicity, with an IC50 value of 8.76 µM which formed the basis current study.

Objective
Elucidate the metabolic mechanism of GA113 in malignant A753 melanoma cells.

Method
A two-dimensional gas chromatography time-of-flight mass spectrometry (GCxGC-TOF/MS) cellular metabolomics approach was used, and univariate and multivariate statistical methods were applied to the metabolomics data.

Results
33 metabolites were identified as significant discriminators between GA113-treated and untreated A375 melanoma cells. Changes in 19 of these 33 metabolites were mapped to pantothenate and coenzyme A biosynthesis, citrate cycle, cysteine and methionine metabolism, arginine and proline metabolism, and alanine, aspartate, and glutamate metabolism.

Conclusion
These findings suggest that GA113 exerts its anticancer effects by disrupting essential metabolic pathways in melanoma cells, which presents a promising therapeutic avenue to target melanoma metabolism.
Observation of the Orientation of Snow Hydrometeors at Sheltered and Unsheltered Sites
Authors: Grazioli J. , Condolf M. , Roulet Y.‐A. , Coletti F. , Berne A. 
Published: February 2025

AbstractKnowledge about orientation of falling snow is still poorly documented with field measurements despite its importance, for example, in the interpretation of remote sensing data. This study investigates the orientation of snow hydrometeors using data from a Multi‐Angle Snowflake Camera. We explore the impact of different observational setups (sheltered vs. unsheltered), wind speed, hydrometeor type, and axis ratio on the orientation distributions. Numerical simulations are used to select the best orientation estimator and to understand the reason behind contrasting results reported in past literature. We find that previously reported non‐zero median orientations are likely artifacts due to averaging absolute values of orientations from the three individual cameras. Observed orientations generally follow a symmetrical distribution around 0, with broader distributions observed at unsheltered sites and/or high wind conditions. Observed distributions may vary significantly from those assumed in previous studies, highlighting the need for further research on hydrometeor orientations under varying environmental conditions.
Scaling High‐Resolution Soil Organic Matter Composition to Improve Predictions of Potential Soil Respiration Across the Continental United States
Authors: Shi Cheng , Mudunuru Maruti , Bowman Maggie , Zhao Qian , Toyoda Jason , Kew Will , Corilo Yuri , Qafoku Odeta , Bargar John R. , Karra Satish , Graham Emily B. 
Published: February 2025

AbstractDespite the importance of microbial soil organic matter (SOM) respiration in regulating the flux of carbon between soils and the atmosphere, soil carbon cycling models remain primarily based on climate and soil properties, leading to large uncertainty in predictions. To address this knowledge gap, we analyzed high‐resolution water‐extractable SOM profiles from soil cores collected across the United States by the 1,000 Soils Pilot of the Molecular Observation Network. Our innovation lies in using machine learning to distill thousands of SOM formula into tractable units; and it enables integrating data from molecular measurements into soil respiration models. In surface soils, SOM chemistry provided better estimates of potential soil respiration than soil physicochemistry, and using them combined yielded the best prediction. Overall, we identify specific subsets of organic molecules that may improve predictions of global soil respiration and create a strong basis for developing new representations in process‐based models.
Assessment, detection, and validation of clinical associations of thirdhand smoke exposure (ADVOCATE) study protocol
Authors: Melinda Mahabee-Gittens E. , Matt Georg E. , Lopez-Galvez Nicolas , Hoh Eunha , Quintana Penelope J. E. , Dodder Nathan G. , Jandarov Roman A. , Stone Lara , Wullenweber Chase A. , Ahluwalia Jasjit S. , Merianos Ashley L. 
Published: February 2025

Abstract

Background
Thirdhand smoke (THS) pollution is the residue of secondhand smoke (SHS) remaining in homes long after active smoking has ceased. This study is the first to characterize the clinical correlates of THS exposure (THSe) in children independent of secondhand smoke exposure (SHSe). The prevalence, sociodemographic characteristics, tobacco smoke exposure patterns, sources, clinical, and biomarker effects associated with THSe will be examined.

Method
Smoking and nonsmoking parents and their 0–11-year-olds (N = 1013) were recruited. Children were categorized into tobacco smoke exposure (TSE) groups via biochemical validation with salivary cotinine and hand nicotine: (1) no exposure group (NEG); (2) THSe-only group (TEG); and (3) Mixed SHSe and THSe group (MEG). At enrollment, 6-weeks, and 6-months, parental assessments and children’s biological and home samples were obtained and analyzed for SHSe, THSe, THS pollution, inflammatory and oxidative stress markers.

Results
The mean (SD) child age was 5.8 (3.4) years; 50.7% were female; and 97% were non-Hispanic (97.0%); 67.5% were White, 25.7% were Black, 6.8% were Other/unknown race. In total, 57.9%, 18.2%, and 21.9% were classified in the NEG, TEG, and MEG, respectively. Sample and data analyses are ongoing.

Conclusion
This project will provide unique insights into how THSe in the absence of SHSe affects the clinical, inflammatory, and oxidative responses in children.

Impact

This is the first prospective longitudinal study to examine the prevalence of thirdhand smoke exposure in children of nonsmokers.

Unlike prior tobacco smoke exposure research, this study will examine the contribution of thirdhand smoke exposure to pediatric health outcomes.

Results will provide unique insights into how thirdhand smoke exposure in the absence of secondhand smoke exposure affects the clinical, inflammatory, and oxidative responses in children of nonsmokers.
Impact of dietary Biocide clay on growth, physiological status, and histological indicators of the liver and digestive tract in Nile tilapia (Oreochromis niloticus)
Authors: El-Naby Asmaa S. Abd , El Asely Amel M. , Hussein Mona N. , Khattaby Abd El-Rahman A. , Abo-Al-Ela Haitham G. 
Published: February 2025

Abstract
This study evaluated the effects of Biocide, containing silicon tetrahedrons and organic acids, on growth performance, feed utilization, immune response, and oxidative status in Nile tilapia (Oreochromis niloticus). A total of 300 Nile tilapia fingerlings (initial weight: 3.55 ± 0.01 g) were distributed across 15 tanks and fed diets containing 0.0 (control), 0.25, 0.5, 1, and 2 g kg⁻¹ Biocide for 90 days, with three replicate tanks per treatment. Biocide is enriched with organic acids (fumaric acid and citric acid) and amino acids (glutamine, tyrosine, methionine, serine, and threonine). Fish fed Biocide-supplemented diets demonstrated significantly improved growth performance, with the highest weight gain, feed conversion ratio, and protein efficiency ratio observed in the 1 g kg⁻¹ group. Survival rates did not differ significantly among treatments. Whole-body crude protein content peaked in the 1 g kg⁻¹ group, while moisture, lipid, and ash contents remained unchanged. Hematological parameters, including red blood cell count, hemoglobin concentration, and packed cell volume, improved significantly. Serum lipid profiles showed reduced cholesterol, triglycerides, low-density lipoprotein, and very-low-density lipoprotein levels, alongside increased high-density lipoprotein levels, particularly in the 1 g kg⁻¹ group. Antioxidant enzyme activities (catalase, glutathione peroxidase) and total antioxidant capacity were significantly elevated in the liver and intestine, while malondialdehyde levels decreased. Digestive enzyme activities (amylase, lipase, and protease) were markedly enhanced. Histopathological analysis revealed improved liver, stomach, and intestinal morphology, including increased mucous secretion and enhanced intestinal villi structure, in fish fed 1 g kg⁻¹ Biocide. In conclusion, Biocide supplementation, particularly at 1 g kg⁻¹, significantly improved growth performance, feed utilization, immune function, and antioxidant capacity in Nile tilapia. Notably, the findings highlight Biocide’s primary mode of action on gut health, underscoring its potential as a dietary additive for improving aquaculture productivity.
Magnetic resonance imaging signatures of neuroinflammation in major depressive disorder with religious and spiritual problems
Authors: Kaszás Alexandra , Kelemen Oguz , Kéri Szabolcs 
Published: February 2025

Abstract
Religious and spiritual (R/S) struggles, such as questioning of faith, existential and ethical concerns, and interpersonal conflicts, are associated with depressive symptoms. Neuroinflammation is critical in major depressive disorder (MDD) and is linked to stress associated with R/S problems. This study aimed to investigate whether the presence of DSM-5 R/S problems contributes to neuroinflammation. We recruited 93 MDD patients and 93 healthy controls with and without R/S problems. MRI-based restricted fraction (RF) values, an index of neuroinflammation, were measured in the hippocampus, amygdala, and neocortex. Depression and anxiety were assessed using the Hamilton Depression and Anxiety Rating Scales (HAM-D, HAM-A), while R/S problems were quantified using the Religious and Spiritual Struggles Scale (RSS-14). Results revealed elevated RF values in the amygdala and hippocampus of healthy individuals and MDD patients with R/S problems relative to those without R/S problems, with the highest values in MDD patients with R/S problems. Importantly, R/S problems and depressive symptoms were independent predictors of RF values in the amygdala and hippocampus but not in the cortex. Elevated cortical RF values were associated with MDD. These findings indicate that R/S struggles are not secondary manifestations of depression but may independently contribute to neurobiological changes.
ZnO-nanoparticles and stage-based drought tolerance in wheat (Triticum aestivum L.): effect on morpho-physiology, nutrients uptake, grain yield and quality
Authors: Raza Muhammad Aown Sammar , Muhammad Faqeer , Farooq Muhammad , Aslam Muhammad Usman , Akhter Naseem , Toleikienė Monika , Binobead Manal Abdulaziz , Ali M Ajmal , Rizwan Muhammad , Iqbal Rashid 
Published: February 2025

Abstract
Drought-stressed and zinc-deficient soils are major contributors to reduced wheat yields and low-quality grains, especially in semi-arid regions of the world. Zinc-oxide nanoparticles (ZnO-NPs) are adept enough to avoid these losses if applied under the right dose at the right growth stage of many crops including wheat (Triticum aestivum L.). Therefore, a pot experiment was conducted with four levels of ZnO-NPs (0, 50, 100 and 150 ppm), and drought imposed at tillering (D1) and grain filling (D2) stages, considering normal irrigation as control (D0), to explore interactive effects of ZnO-NPs and drought episodes on growth, eco-physiology, yield, and grain quality of wheat. The results depicted dose and growth stage-dependent variations in all recorded parameters. ZnO-NPs (150 ppm) significantly increased the number of grains (12.5%), grain weight (12.4%), total yield (25.5%), and zinc contents (58.6%) when the crop was exposed to drought stress at tillering stage, compared to the control treatment. Likewise, drought at grain filling stage with ZnO-NPs (150 ppm) significantly enhanced plant height, spike length, biomass, zinc contents, and grain protein by 15.5%, 3.2%, 16.7%, 100.0%, and 53.8%, respectively, when compared with control treatment. Thus, ZnO-NPs emerged as a potential drought alleviator and yield-oriented safe nano-fertilizer for wheat in semi-arid regions facing irrigation challenges.
Detecting rice (Oryza sativa) panicle using an improved YOLOv5 model
Authors: Seng Xiaoyue , Yang Xue , Liu Tonghai , Zhang Rui , Yuan Chuangchuang , Guo TianTian , Liu Wenzheng 
Published: February 2025

Context Rice (Oryza sativa) panicle provides important information to improve production efficiency, optimise resources, and aid in successful breeding of high-performing rice varieties. Aims In order to efficiently count rice panicles, a rice panicle recognition model based on YOLOv5s-Slim Neck-GhostNet was evaluated. Methods We used the developmental stages from heading to maturity as the time period to collect data for testing and validating the model. The GSConv convolution module from the YOLOv5 (You Only Look Once) model was compared with the original Conv convolution. We improved the original C3 module and replaced it with VoVGSCSP module, which further enhanced the detection ability of the model for small targets, such as rice panicles. To further optimise the performance of the model and reduce the computational complexity, we replaced the original backbone network of the model with a lightweight and efficient GhostNet structure. Key results Our results showed that the precision of the test set was 96.5%, the recall was 94.6%, the F1-score was 95.5%, and the mAP@0.5 was 97.2%. Compared with the original YOLOv5s model, mAP@0.5 increased by 1.8%, and the model size is reduced by 5.7M. Conclusions The improved YOLOv5 model had increased capability to detect and count rice panicles in real time. Our method reduced the size of the model while maintaining an acceptable level of accuracy. Implications The technology provides an intelligent and automated solution to better monitor rice panicle development, and has the potential for practical application in agricultural settings.
Toba Batak manang
Authors: Erlewine Michael Yoshitaka 
Published: February 2025

Abstract
This paper offers a description of the multifunctional morpheme manang in Toba Batak (Austronesian; Sumatra) — as the disjunctor, the interrogative complementizer, and a particle forming wh-based polarity items — contextualized within the broader semantic and typological literatures on such meaning expressions. I also observe a puzzle regarding its form: the form manang diverges substantially from its functional equivalent, barang, as described in H. N. Van der Tuuk’s pioneering grammar of Toba Batak (Van der Tuuk 1864–1867). I argue that consideration of this historical change supports the analysis of these various uses of manang as a case of functional polysemy, reflecting a common conceptual core.
Construction of ZnO/oxygen-deficient Bi2WO6 photocatalyst for highly efficient degradation of TCH
Authors: Xiaojiao Wang , Chen Lili , Zhang Jiao , Xing Baolin , Xu Bing , Mi Guofa , Liu Baozhong , Wu Yuanfeng , Chen Lunjian 
Published: February 2025

Abstract
More and more attention has been paid to the photocatalytic degradation of tetracycline hydrochloride (TCH). Constructing heterojunctions and designing defect structures are important means to improve the separation efficiency of photogenerated carriers and catalytic activity. ZnO/BWO-x composite photocatalyst with n-n heterojunction and oxygen vacancy was synthesized through the solvothermal method. Compared with ZnO and BWO-x, ZnO/BWO-x has a wider visible light absorption range, higher photogenerated charge migration rate, and lower photogenerated electron-hole pair recombination rate. When the molar ratio of ZnO and BWO-O3 is 1:1, the prepared composite photocatalyst (ZnO/BWO-5) has the highest photocatalytic activity, and under visible light irradiation for 180 min, the degradation rate of TCH reaches 85.53% significantly higher than that before compounding. After further exploration, it is found that the photocatalytic effect of ZnO/BWO-5 is the best under the conditions of pH=9, photocatalyst dosage of 40 mg, and tetracycline concentration of 20 mg/L. The reasons for the enhanced photocatalytic activity of ZnO/BWO-x composites are summarized as follows: (1)Oxygen vacancies reduce the band gap and improve the utilization of visible light; (2)The lower conduction band potential of ZnO can complement with Bi2WO6, and the staggered composite energy levels form an n-n heterojunction, which is conducive to the rapid separation of photogenerated carriers.&#xD;
Automated hallucination detection for synthetic CT images used in MR-only radiotherapy workflows
Authors: Parchur Abdul K , Zarenia Mohammad , Gage Colette , Paulson Eric S , Ahunbay Ergun 
Published: February 2025

Abstract

Objective. Artificial intelligence (AI)-generated synthetic CT (sCT) images have become commercially available to provide electron densities and reference anatomies in MR-only radiotherapy workflows. However, hallucinations (false regions of bone or air) introduced in AI-generated sCT images may affect the accuracy of dose calculation and patient setup verification. We developed a tool to detect bone hallucinations and/or inaccuracies in AI-generated pelvic sCT images used in MR-only workflows. Approach. A deep learning auto segmentation (DLAS) model was trained to auto-segment bone on MR images. The model was implemented with a 3D SegResNet network architecture using the MONAI framework with a training dataset of 86 Dixon MR image sets paired with their corresponding ground truth contours derived from planning CT images deformed to the MR images. The model performance was then assessed on an independent testing dataset (n = 10). Main results. The DLAS model-based hallucination screener identified hallucinations in bone structures using daily MR images and accurately flagged these regions on sCT images. The sensitivity of the screener is adjustable based on the distance of discrepancies between bone regions derived from sCT to bone contours generated by the DLAS. The average specificity of the DLAS model was 0.78, 0.93 and 0.98 for distance parameters of 0.8, 1.0 and 1.2 cm, respectively. The screener identified false high-density hallucination regions in the abdomen of AI-generated sCT images for all testing patients, highlighting potential issues with the training data used for the AI sCT model. Significance. A hallucination screener for AI-generated pelvic sCT images was developed and implemented for routine clinical use. The screener serves as an important quality assurance tool for MR-only radiotherapy workflows. By identifying potential AI-generated errors, the hallucination screener may improve the safety and accuracy of sCT images used for dose calculation and image guidance.
Highly birefringent photonic crystal fiber with all elliptical air holes for supercontinuum laser source of OPCPA
Authors: Li Yinan , Qiu Liyun , Yang Lei , Zhou Kainan , Deng Ying , Li Wei , Zou Yu 
Published: February 2025

Abstract
In this paper, we propose a highly birefringent photonic crystal fiber (HB-PCF) with all orthogonally arranged elliptical air holes, to generate supercontinuum (SC) including a specific wavelength in the near-infrared range. A tellurite material TeO2–ZnO–Al2O3–La2O3 is used as the background material of the photonic crystal fiber (PCF). The simulation results indicate that the proposed PCF can realize high birefringence (up to 10−2), high nonlinearity (5000 W−1·km−1 and 6000

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in x and y polarizations, respectively) at 800 nm. SC spanning from 650 to 1120 nm is generated when pump pulses with a central wavelength of 800 nm, peak power of 2500 W, and width of 20 fs are launched into the 15 mm-long HB-PCF. Our numerical results meet the requirements of an optical parametric chirped-pulse amplification facility to generate a polarized SC covering 1053 nm with 800 nm-pulse pumping.
Impact of impurity seeding on shattered pellet injection mitigations on the Joint European Torus
Authors: Sheikh U. , Jachmich S. , Kong M. , Bodner G. , Eidietis N. , Ficker O. , Lehnen M. , Reux C. , Stein-Lubrano B. , Svoboda J. , Contributors JET ,   the EUROfusion Tokamak Exploitation Team
Published: February 2025

Abstract
Plasma disruptions present a significant challenge to the viability of fusion energy production in tokamak reactors. Among disruption mitigation techniques, shattered pellet injection (SPI) has emerged as a promising approach. The results presented in this paper show novel findings of the impact of nitrogen and neon seeding on the disruption mitigation sequence following SPI on the Joint European Torus (JET). This study exposes an order of magnitude reduction in pre-thermal quench duration for highly seeded plasmas and pure deuterium SPI, a result with significant implications for staggered SPI schemes currently under development. Conversely, no reduction in disruption thermal load mitigation efficacy was observed for single neon and hydrogen mixed SPI across a range of seeding levels, indicating the robustness of this approach. A novel pathway for thermal load mitigation and enhanced runaway electron avoidance with pure deuterium SPI into strongly seeded plasmas is also presented.