bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Polarizable CASSCF/MM Approach Using the Interface Between OpenMMPol Library and Cfour
Authors: Nottoli Tommaso , Bondanza Mattia , Lipparini Filippo , Mennucci Benedetta 
Published: December 2024

ABSTRACTWe present a polarizable embedding quantum mechanics/molecular mechanics (QM/MM) framework for ground‐ and excited‐state Complete Active Space Self‐Consistent Field (CASSCF) calculations on molecules within complex environments, such as biological systems. These environments are modeled using the AMOEBA polarizable force field. This approach is implemented by integrating the OpenMMPol library with the CFour quantum chemistry software suite. The implementation supports both single‐point energy evaluations and geometry optimizations, facilitated by the availability of analytical gradients. We demonstrate the methodology by applying it to two distinct photoreceptors, exploring the impact of the protein environment on the structural and photophysical properties of their embedded chromophores.
PFAS in agroecosystems: Sources, impacts, and opportunities for mitigating risks to human and ecosystem health
Authors: Preisendanz Heather E. , Li Hui , Mashtare Michael , Mina Odette 
Published: December 2024

AbstractConcerns regarding per‐ and polyfluoroalkyl substances (PFAS) and their precursors have driven increased research into their sources, impacts, and mitigation strategies, aiming to reduce their prevalence in the environment. While much of this research has centered on known large sources of PFAS (e.g., military bases, airports, fire training sites, and some manufacturing facilities), there has been increased interest in evaluating the inadvertent introduction of PFAS into agroecosystems from beneficial reuse of treated domestic wastewater for irrigation and land application of biosolids and composts derived from food waste. Additional sources to agricultural fields include the use of PFAS‐containing pesticides. These activities raise questions regarding the potential impacts of PFAS introduced to agricultural systems on rural water supplies, soil health, and food safety. This special section contains papers that fall into three categories: (i) source assessment of PFAS in water and wastewater residuals destined for beneficial reuse in agroecosystems, (ii) improved understanding of PFAS fate and transport in agroecosystems following land application of PFAS‐containing materials, and (iii) small‐scale assessment of techniques that demonstrate promise for mitigating PFAS mobilization in agroecosystems. The work contained in this special section can be used to help guide future decisions related to PFAS guidelines, policies, and regulations in agroecosystems intended to protect human and ecological health.
Regulation of Branchial Anoctamin 1 Expression in Freshwater‐ and Seawater‐Acclimated Japanese Medaka, Oryzias latipes
Authors: Konno Norifumi , Togashi Ayane , Miyanishi Hiroshi , Azuma Morio , Nakamachi Tomoya , Matsuda Kouhei 
Published: December 2024

ABSTRACTIn euryhaline teleosts, the cystic fibrosis transmembrane conductance regulator (CFTR) in seawater (SW)‐type chloride cells facilitates apical Cl− secretion for SW adaptation, while alternative Cl− excretion pathways remain understudied. This study investigates the role of the calcium‐activated chloride channel, Anoctamin 1 (ANO1), in the gills of the euryhaline Japanese medaka (Oryzias latipes) under hyperosmolality and cortisol (CORT) influence. Acclimation to artificial SW, NaCl, mannitol, or glucose significantly upregulated ANO1 and CFTR mRNA expression in gills, unlike urea treatment. In situ hybridization revealed ANO1 mRNA in chloride cells co‐expressing CFTR and Na+, K+‐ATPase under hyperosmotic conditions. ANO1 inhibition elevated plasma Cl− concentration, indicating impaired Cl− excretion. CORT or dexamethasone administration in freshwater (FW) fish significantly increased branchial ANO1 and CFTR mRNA expression, an effect attenuated by the glucocorticoid receptor (GR) antagonist RU486. Hyperosmotic treatment of isolated gill tissues rapidly induced ANO1 mRNA expression independent of CFTR mRNA changes, and this induction was unaffected by RU486. These findings highlight the dual regulation of ANO1 expression via hyperosmolality‐induced cellular response and the CORT–GR system. Thus, branchial ANO1 may likely complement CFTR in Cl⁻ excretion, playing a key role in the hyperosmotic adaptation of euryhaline teleosts.
Investigation of Response Aggregation Methods in Divergent Thinking Assessments
Authors: Saretzki Janika , Andrae Rosalie , Forthmann Boris , Benedek Mathias 
Published: December 2024

ABSTRACTDivergent thinking (DT) ability is widely regarded as a central cognitive capacity underlying creativity, but its assessment is challenged by the fact that DT tasks yield a variable number of responses. Various approaches for the scoring of DT tasks have been proposed, which differ in how responses are evaluated and aggregated within a task. The present study aimed to identify methods that maximize psychometric quality while also reducing the confounding effect of DT fluency. We compared traditional scoring approaches (summative and average scoring) to more recent methods such as snapshot as well as top‐ and max‐scoring. We further explored the moderating role of task complexity as well as metacognitive abilities. A sample of 300 participants was recruited via Prolific. Reliability evidence was assessed in terms of internal consistency, concurrent criterion validity in terms of correlations with real‐life creative behavior, creative self‐beliefs, and openness. Findings confirm that alternative aggregation methods reduce the confounding effect of DT fluency. Reliability tends to increase as a function of the number of included responses with three responses as a minimal requirement for decent reliability evidence. Convergent validity was highest for snapshot as well as max‐scoring when using a medium number of three ideas.
Examining the Idea Density and Semantic Distance of Responses Given by AI to Tests of Divergent Thinking
Authors: Runco Mark A. , Turkman Burak , Acar Selcuk , Abdulla Alabbasi Ahmed M. 
Published: December 2024

ABSTRACTResearch suggests that generative AI (GAI) responds to divergent thinking (DT) prompts with multiple ideas, some of which seem to be original. The present investigation administered 55 DT tasks to three GAI services (Bard, GPT 3.5, and GPT 4.0). Instead of examining individual responses, an Idea Density algorithm was used to assess the output. This algorithm quantifies the ideas within responses, controlling for the number of words. A subset of the DT tests administered to the GAI were also scored for Semantic Distance, which estimates originality. Results indicated that the three GAI models differed in the Idea Density of the output. There were also significant differences between Realistic and Nonrealistic DT tasks. As has been the case in human samples, directions given when the GAI received the prompts also had a significant impact, with more Idea Density following directions that explicitly prompted original responses. Adjusted scores removed all verbiage in the output, which did not actually address the questions conveyed by the prompts. These corrected scores shared approximately 50% of the variance with the uncorrected “raw” responses, implying that the typical output of GAI is not always relevant. This was interpreted in the context of the standard definition of creativity, which emphasizes effectiveness, as well as originality.
Intercepting more radiation or higher use efficiency: pathways to enhancing biomass and yield in two wheat cultivars with distinct spike types under wide‐belt sowing
Authors: Tong Jin , Lu Yu , Xiong Yulei , Li Wen , Lin Wen , Xue Jianfu , Sun Min , Wang Yuechao , Gao Zhiqiang 
Published: December 2024

AbstractBACKGROUNDIn north China, wide‐belt sowing (WBS) is widely used in wheat production because it increases the yield by improving the plant distribution and reducing the competition for resources compared with conventional narrow‐drill sowing (NDS). Yield formation is also different for wheat varieties with distinct spike types. Therefore, it is important to explore the effects of WBS on the yields of wheat varieties with different spike types.RESULTSWe conducted a field experiment using Shannong20 (SN20, a multi‐spike variety) and Shannong30 (SN30, a heavy‐spike variety) for three seasons under WBS and NDS. WBS increased yields of both varieties by 9.3–11.1% than NDS. The yield increase for SN20 came from improvement in pre‐anthesis biomass, whereas the post‐anthesis biomass improved for SN30. Before anthesis, the increased biomass for SN20 by WBS was due to higher radiation interception because of the increased population size and leaf area index. After anthesis, WBS increased the biomass via improving radiation use efficiency (RUE) for SN30. WBS improved the radiation intensity in the sub‐top and middle canopy layers which was beneficial for increasing RUE. In addition, the higher maximum leaf net photosynthesis rate (Amax) also contributed to the increase in RUE for SN30. The increased Amax for SN30 was due to the increased specific leaf nitrogen and leaf antioxidant capacity.CONCLUSIONIn short, the radiation interception before anthesis was mainly responsible for the yield increase for the multi‐spike variety, whereas for the heavy‐spike variety, the yield improvement only came from the increased RUE after anthesis under WBS. © 2024 Society of Chemical Industry.
Simultaneous Determination of 12 Disinfection By‐Products in Fish Muscles by Solvent Extraction Coupled With Gas Chromatography Equipped With an Electron Capture Detector
Authors: Ding Miao‐miao , Zhamaerding Ai‐ke‐yi‐dan‐mu , Hu Xia‐lin , Liu Mei‐chuan , Yin Da‐qiang 
Published: December 2024

ABSTRACTDisinfection by‐products (DBPs) have received considerable focus due to potential teratogenic, carcinogenic, and mutagenic effects; however, there is an evident gap in the availability of analytical methodologies for the simultaneous determination of DBPs in fish, especially iodinated DBPs. This paper developed an innovative analytical method for the simultaneous determination of 12 DBPs, including four trihalomethanes (THMs), three haloacetonitriles, and five iodinated THMs (I‐THMs), in fish muscle, utilizing solvent extraction followed by gas chromatography with electron capture detection. The method incorporates tert‐butyl methyl ether as an extraction solvent, performing efficient vortex mixing, extraction, and centrifugation under reduced temperature conditions to facilitate the processing of physically disrupted fish tissues. It demonstrates sensitivity with detection limits from 0.21 to 4.02 ng/g, with recoveries from 58.7% to 129.7%. Applied to real fish samples, including bass (n = 7) and carp (n = 7), all contained detectable DBPs, with concentrations between 8.2 and 275.25 ng/g. Significantly, bass from aquaculture facility exhibited the highest contamination, particularly with chlorodiiodomethane at 194.57 ng/g. I‐THMs present in all fish samples. Notably, this is the first paper about the analytical protocol of I‐THMs in biological matrices. This developed method will facilitate further research on human exposure assessment of DBPs through consumption of fish.
Effects of (Assisted) Natural Regeneration on Infiltrability and Preferential Flow Pathways in the Khasi Hills (Meghalaya, NE India)
Authors: Zwartendijk Bob W. , Bruijnzeel L. Adrian , Ghimire Chandra P. , Pde Felix , Mulligan Mark , Zhang Jun 
Published: December 2024

ABSTRACTIntensified slash‐and‐burn cultivation and forest clearing have caused severe land degradation in the Khasi Hills (Meghalaya plateau, NE India). Despite very high annual rainfall, the region faces severe water scarcity during the dry season. Local initiatives aim to restore forests through assisted natural regeneration (ANR) in this hydrologically poorly known area. As a first step towards assessing the potential hydrological impact of forest regrowth and ANR, we measured infiltrability at sites representing Imperata‐dominated grassland (n = 2, degraded baseline); < 20‐year‐old fallows with ANR (n = 3); semi‐mature to old‐growth forests (n = 4, near‐natural baseline); and a bench‐terraced Cryptomeria plantation. Group‐median infiltrability was highest in forests (425 mm h−1), followed by young fallows with ANR, and grasslands (145 and 68 mm h−1, respectively), and the terraced plantation (50 mm h−1). Infiltrability increased with regrowth age at an average rate of 3.0 mm h−1 y−1. Dye infiltration experiments were used to identify dominant percolation pathways per main land‐cover type. Infiltration in the least‐disturbed forest was dominated by flow along roots, stones and other preferential pathways, while matrix flow dominated in the grassland; the ANR site showed intermediate behaviour (macropore flow with high matrix interaction). Comparing median infiltrabilities with (maximum) hourly rainfall intensities suggested infiltration‐excess overland flow may occur occasionally in the grasslands. Despite improved infiltrability during regrowth (with or without ANR), the extreme monsoon rainfall and often shallow and stony soils pose serious limitations to rebuilding soil water storage capacity and favour frequent saturation‐excess overland flow.
The recent development, application, and future prospects of muscle atrophy animal models
Authors: Zhang Gongchang , Hu Fengjuan , Huang Tingting , Ma Xiaoqing , Cheng Ying , Liu Xiaolei , Jiang Wenzhou , Dong Birong , Fu Chenying 
Published: December 2024

AbstractMuscle atrophy, characterized by the loss of muscle mass and function, is a hallmark of sarcopenia and cachexia, frequently associated with aging, malignant tumors, chronic heart failure, and malnutrition. Moreover, it poses significant challenges to human health, leading to increased frailty, reduced quality of life, and heightened mortality risks. Despite extensive research on sarcopenia and cachexia, consensus in their assessment remains elusive, with inconsistent conclusions regarding their molecular mechanisms. Muscle atrophy models are crucial tools for advancing research in this field. Currently, animal models of muscle atrophy used for clinical and basic scientific studies are induced through various methods, including aging, genetic editing, nutritional modification, exercise, chronic wasting diseases, and drug administration. Muscle atrophy models also include in vitro and small organism models. Despite their value, each of these models has certain limitations. This review focuses on the limitations and diverse applications of muscle atrophy models to understand sarcopenia and cachexia, and encourage their rational use in future research, therefore deepening the understanding of underlying pathophysiological mechanisms, and ultimately advancing the exploration of therapeutic strategies for sarcopenia and cachexia.
Bacterial abundance and diversity in 64–74 Ma subseafloor igneous basement from the Louisville Seamount Chain
Authors: Sylvan Jason B. , Tully Benjamin J. , Morono Yuki , Alt Jeffrey C. , Grim Sharon L. , Inagaki Fumio , Koppers Anthony A. P. , Edwards Katrina J. 
Published: December 2024

Impact statementThe aquifer in the subseafloor igneous basement is a massive, continuous microbial substrate, yet sparingly little is known about life in this habitat. The work to date has focused largely on describing microbial diversity in the young basement (<10 Ma), where the basaltic crust is still porous and fluid flow through it is active. Here, we test the hypothesis that microbial life exists in subseafloor basement >65 Ma using samples collected from the Louisville Seamount Chain via seafloor drilling. Cell biomass was heterogeneous in nature, ranging from below detection to ~104 cells cm−3. Bacterial 16S rRNA genes from core samples and enrichment incubations are dominated by lineages putatively carrying out nitrogen, sulfur, and metal redox processes and hydrocarbon oxidation. Taken together, the data indicate that microbial life is indeed present in subseafloor igneous basement >65 Ma, which significantly expands the range of the subseafloor biosphere where microbial life is known to exist.
Genotype–microbiome–metabolome associations in early childhood and their link to BMI
Authors: Aparicio Andrea , Sun Zheng , Gold Diane R. , Lasky‐Su Jessica A. , Litonjua Augusto A. , Weiss Scott T. , Lee‐Sarwar Kathleen , Liu Yang‐Yu 
Published: December 2024

Impact statementThrough the analysis of data from children aged 6 months to 8 years enrolled in the Vitamin D Antenatal Asthma Reduction Trial (VDAART), significant simultaneous associations were identified between variants in the fragile histidine triad (FHIT) gene, children's body mass index, microbiome features related to obesity, and key lipids and amino acids. These patterns represent evidence of the genotype influence in shaping the host microbiome in developing stages and new potential biomarkers for childhood obesity, insulin resistance, and type 2 diabetes.
Longitudinal Efficacy of Nusinersen Treatment on Health‐Related Quality of Life and Independence in Children With Later‐Onset Spinal Muscular Atrophy
Authors: Huang Siyi , Jiang Liya , Zhou Dongming , Yan Yue , Feng Yijie , Yu Yicheng , Yao Mei , Gao Feng , Mao Shanshan 
Published: December 2024

ABSTRACTIntroduction/AimsThe rising use of disease‐modifying therapy is progressively impacting the health‐related quality of life (HRQoL) of patients with spinal muscular atrophy (SMA) in their daily lives. This study aimed to evaluate the changes in HRQoL and independence in children with later‐onset SMA receiving longitudinal treatment with nusinersen.MethodsForty‐nine pediatric patients with later‐onset SMA (symptom onset after 6 months of age) and their caregivers were enrolled. The HRQoL of patients evaluated by the proxy‐reported Pediatric Quality of Life Inventory 3.0 Neuromuscular Module (PedsQL NMM) and the independence level determined by the SMA Independence Scale–Upper Limb Module (SMAIS–ULM) were assessed. Caregiver HRQoL was assessed using the Pediatric Quality of Life Inventory Family Impact Module (PedsQL FIM). Motor function was recorded using the Hammersmith Functional Motor Scale Expanded (HFMSE) and the Revised Upper Limb Module (RULM), with subsequent analysis of the correlation between motor function, HRQoL, and independence scores.ResultsA significant difference was observed across all domains of the proxy‐reported PedsQL NMM and in the independence assessment over the 18‐month follow‐up period (p < 0.001). A positive correlation was identified between RULM and total PedsQL NMM scores (Pearson‐r = 0.539, p < 0.001), as well as SMAIS‐ULM scores (Spearman‐rho = 0.507, p < 0.001). Scores in all modules of the PedsQL FIM improved over time (p < 0.001).DiscussionThis study demonstrates the longitudinal effects of nusinersen treatment on multifaceted aspects of SMA patients, as captured by patient‐reported outcome measures (PROMs). The inclusion of PROMs should be considered as part of the SMA multidisciplinary assessment.
Automated White Matter Fiber Tract Segmentation for the Brainstem
Authors: Li Mingchu , Zeng Qingrun , Zhang Jiawei , Huang Ying , Wang Xu , Ribas Eduardo Carvalhal , Wu Xiaolong , Liu Xiaohai , Liang Jiantao , Chen Ge , Feng Yuanjing , Li Mengjun 
Published: December 2024

ABSTRACTThis study aimed to develop an automatic segmentation method for brainstem fiber bundles. We utilized the brainstem as a seed region for probabilistic tractography based on multishell, multitissue constrained spherical deconvolution in 40 subjects from the Human Connectome Project (HCP). All tractography data were registered into a common space to construct a brainstem fiber cluster atlas. A total of 100 fiber clusters were identified and annotated. Cortical parcellation–based fiber selection was then performed to extract fibers within the annotated clusters that projected to their corresponding cortical regions. This atlas was applied for automatic brainstem fiber bundle segmentation in 10 HCP subjects and 8 patients with brainstem cavernous malformations. The spatial overlap between automatic and manual reconstruction was assessed. Ultimately, eight fiber bundles were identified in the brainstem atlas on the basis of their trajectories: the corticospinal tract (CST), corticobulbar tract, frontopontine tract, parieto‐occipital‐pontine tract, medial lemniscus, and superior, middle, and inferior cerebellar peduncles. The mean and standard deviation of the weighted dice (wDice) scores between the automatic and manual reconstructions were 0.9076 ± 0.0950 for the affected CST, 0.9388 ± 0.0439 for the contralateral CST, 0.9130 ± 0.0588 for the affected medial lemniscus, and 0.9600 ± 0.0243 for the contralateral medial lemniscus. This proposed method effectively distinguishes major brainstem fiber bundles across subjects while reducing labor costs and interoperator variability inherent to manual reconstruction. Additionally, this method is robust in that it allows for the visualization and identification of fiber tracts surrounding brainstem cavernous malformations.
Time‐Domain Spectral BFS Plate Element With Lobatto Basis for Wave Propagation Analysis
Authors: Ambati Hela , Eisenträger Sascha , Kapuria Santosh 
Published: December 2024

ABSTRACTA computationally efficient spectral Kirchhoff plate element is presented for time‐domain analysis of wave propagation at high frequencies in thin isotropic plates. It employs a ‐continuous spectral interpolation based on the modified bi‐Hermite polynomials using the Gauss–Lobatto–Legendre (GLL) points as a basis with selective collocation of rotational and twisting degrees of freedom (DOFs) at element edge and corner nodes. The lowest order version of the proposed element reduces to the classical Bogner–Fox–Schmit (BFS) element for Kirchhoff plates. The GLL basis allows diagonalisation of the mass matrix using the nodal quadrature technique, which enhances the computational efficiency. The numerical properties of the proposed element are comprehensively evaluated, including the conditioning of the system matrices. Moreover, the effect of employing different numerical integration schemes and nodal sets is examined in both static and free vibration analyses. The effectiveness of the proposed element in wave propagation problems is evaluated by comparing its performance to the converged solutions achieved using the BFS element with a very fine mesh. Results demonstrate that the current element, without and even with mass matrix diagonalisation delivers exceptional accuracy while also exhibiting faster convergence and enhanced computational efficiency than the existing Kirchhoff plate elements.