bluuebunny/crossref_metadata_2025_split huggingface dataset:
Lower fecal microbiota transplantation ameliorates ulcerative colitis by eliminating oral-derived Fusobacterium nucleatum and virulence factor
Authors: Li Dong-Hao , Li Zong-Wei , Sun Qi , Wang Lei , Ning Shou-Bin 
Published: August 2024

Abstract
Background
Recently, the oral oncobacterium Fusobacterium nucleatum (F. nucleatum), has been linked with ulcerative colitis (UC). Here, we aim to investigate whether Fecal Microbiota Transplantation (FMT) can alleviate UC by restoring gut microbiota and eliminating oral-derived F. nucleatum and virulence factor fadA.

Method
C57BL/6J mice were randomly divided into a healthy control group (HC), Dextran Sulfate Sodium group (DSS), oral inoculation group (OR), upper FMT group (UFMT), and lower FMT group (LFMT). Disease activity index, body weight, survival rate, and histopathological scores were used to measure the severity of colitis. The function of the intestinal mucosal barrier was evaluated by performing immunohistochemical staining of the tight junction protein Occludin. Real-time PCR was used to assess the relative abundance of the nusG gene and the virulence gene fadA. Cytokine levels were detected by ELISA. Full-length sequencing of 16S rRNA was used to analyze the changes and composition of gut microbiota.

Findings
Oral incubation of F. nucleatum further exacerbated the severity of colitis and gut dysbiosis. Peptostreptococcaceae, Enterococcaceae, and Escherichia coli were significantly enriched in OR mice. However, LFMT mice showed an obvious decrease in disease activity and were more effective in restoring gut microbiota and eliminating F. nucleatum than UFMT mice. Bacteroidota, Lachnospiraceae, and Prevotellaceae were mainly enriched bacteria in LFMT mice. In addition, Genera such as Lactobacillus, Allobaculum, and Bacteroidales were found negative correlation with TNF-α, IL-1β, and IL-6. Genera like Romboutsia, Escherichia Shigella, Enterococcus, and Clostridium were found positively correlated with TNF-α, IL-1β, and IL-6.

Conclusions
Oral incubation of F. nucleatum further exacerbates the severity and dysbiosis in DSS-induced colitis mice. Besides, lower tract FMT can ameliorate colitis by restoring the gut microbiota diversity and eliminating F. nucleatum and virulence factor fadA.
An automated calculation pipeline for differential pair interaction energies with molecular force fields using the Tinker Molecular Modeling Package
Authors: Bänsch Felix , Daniel Mirco , Lanig Harald , Steinbeck Christoph , Zielesny Achim 
Published: August 2024

AbstractAn automated pipeline for comprehensive calculation of intermolecular interaction energies based on molecular force-fields using the Tinker molecular modelling package is presented. Starting with non-optimized chemically intuitive monomer structures, the pipeline allows the approximation of global minimum energy monomers and dimers, configuration sampling for various monomer–monomer distances, estimation of coordination numbers by molecular dynamics simulations, and the evaluation of differential pair interaction energies. The latter are used to derive Flory–Huggins parameters and isotropic particle–particle repulsions for Dissipative Particle Dynamics (DPD). The computational results for force fields MM3, MMFF94, OPLS-AA and AMOEBA09 are analyzed with Density Functional Theory (DFT) calculations and DPD simulations for a mixture of the non-ionic polyoxyethylene alkyl ether surfactant C10E4 with water to demonstrate the usefulness of the approach.Scientific ContributionTo our knowledge, there is currently no open computational pipeline for differential pair interaction energies at all. This work aims to contribute an (at least academically available, open) approach based on molecular force fields that provides a robust and efficient computational scheme for their automated calculation for small to medium-sized (organic) molecular dimers. The usefulness of the proposed new calculation scheme is demonstrated for the generation of mesoscopic particles with their mutual repulsive interactions.
Genetic structure of the European white elm (Ulmus laevis Pall., Ulmaceae) in Switzerland
Authors: Dermelj Lena , Fragnière Yann , Jacob Gwenaël , Küffer Nicolas , Sciboz Jacques , Parisod Christian , Kozlowski Gregor 
Published: August 2024

Abstract
Key message
Populations of the European white elm (Ulmus laevis Pall.) in Switzerland can be considered natural. They show no evidence of genetic differentiation from other European populations. In the past, the U. laevis populations were probably more widespread and continuous in Switzerland with a larger gene flow.

Context
In Switzerland, at the margin of its distribution range, U. laevis is rare and considered endangered. Whether the species is native to Switzerland has been disputed, and it is often surmised to be solely cultivated, without any natural population in the country.

Aims
The structure of genetic diversity among Swiss populations of U. laevis and comparison to European populations are expected to shed light on the origin of local populations and support their management.

Methods
We analyzed 19 populations (194 individuals) in Switzerland and 15 populations (158 individuals) from other European countries, using a set of five microsatellite loci.

Results
(1) 90% of the genetic variation in European and Swiss populations occurs within populations. (2) We did not detect isolation by distance at the regional or continental scale. (3) Clustering analysis did not reveal any spatial pattern in the level of admixture of individuals within Swiss or other European populations.

Conclusion
Moderate levels of genetic diversity and evidence for recent gene flow between populations indicate that habitat deterioration, loss, and fragmentation are the main threats to the persistence of U. laevis populations in Switzerland.
Superior mesenteric artery syndrome following spine surgery in idiopathic adolescent scoliosis: a systematic review
Authors: Pappalardo Gaetano , Pola Enrico , Bertini Fracesca Alzira , Nasto Luigi Aurelio , Eschweiler Jörg , Schäfer Luise , Migliorini Filippo 
Published: August 2024

AbstractSuperior mesenteric artery syndrome (SMAS) is a rare and unpredictable complication after correction spine surgery for adolescent idiopathic scoliosis (AIS). The management of this condition is poorly investigated, with controversial outcomes. This investigation systematically reviewed current evidence on pathogenesis, risk factors, management, and outcomes of SMAS following correction spine surgery for AIS. The present systematic review was conducted according to the 2020 PRISMA statement. All the included investigations reported SMAS presentation following scoliosis correction surgery in AIS. 29 articles with 61 eligible patients were included in this review. The mean age of the patients was 15.8 ± 7.2 years. The mean weight was 45.3 ± 8.0 kg, the mean height 159.6 ± 13.6 cm, and the mean BMI 16.5 ± 2.9 kg/m2. The mean duration of the treatment for SMAS was 21.6 ± 10.3 days. The mean interval between spine surgery and symptoms of SAMS was 69 days, with high between-studies variability (3 days to 4 years). Prompt identification of risk factors and an early diagnosis are necessary to manage SMAS and reduce the risk of complications. Additional investigations are required to establish risk factors and diagnostic criteria.Level of evidence Level IV, systematic review.
An insight into the origin of elemental chromium in the lacquer of Qin terracotta warriors
Authors: Chenchen Yang , Bo Rong , Jing Huang , Xutong Chen , Desheng Lan , Fengyi He , Shaojun Yan , Ling He , Lingjie Meng , Junyan Liang , Wenxian Lu 
Published: August 2024

Abstract
The origin of elemental chromium for the archaeological weapons from the pits of Qin terracotta warriors in China has been highly controversial. Although previous studies have highlighted that the chromium on the surface of weapon originated from the contamination of surrounding lacquer, the exact origin of chromium in the lacquer remains unclear. In this work, the measurement by inductively coupled plasma-mass spectrometer (ICP-MS) firstly confirmed that the elemental chromium was indeed contained in the archaeological Qin original lacquer. Nevertheless, the amount of elemental chromium in the Qin lacquer was as low as 0.0759 μg/mg, disclosing that it was impossible to artificially add extra refined chromium-containing substance to the lacquer in the preparation of the terracotta warriors. The soil from the archaeological site of Qin lacquer was found to have a chromium amount of 0.0660 μg/mg by ICP-MS. After the hygrothermal and soil-buried aging cycles for the lab-prepared lacquer, the surface and depth elemental analyses by time of flight-secondary ion mass spectrometer (TOF–SIMS) showed a gradient distribution of elemental chromium from the surface to interior of aged lacquer, indicating the migration and enrichment behavior of elemental chromium from the burial soil towards the lacquer. To explore the migration mechanism of elemental chromium, fluorescence imaging technique was employed in combination with Fourier transform infrared spectrometry (FT-IR) and X-ray photoelectron spectroscopy (XPS) characterizations. The results revealed that catechol-containing fragments were formed during hygrothermal and soil-buried aging of lacquer and consequently coordinated with chromium ions, inducing the migration of elemental chromium towards the lacquer.
Development of preoperative nomograms to predict the risk of overall and multifocal positive surgical margin after radical prostatectomy
Authors: Xu Lili , Peng Qianyu , Zhang Gumuyang , Zhang Daming , Zhang Jiahui , Zhang Xiaoxiao , Bai Xin , Chen Li , Guo Erjia , Xiao Yu , Jin Zhengyu , Sun Hao 
Published: August 2024

Abstract
Objective
To develop preoperative nomograms using risk factors based on clinicopathological and MRI for predicting the risk of positive surgical margin (PSM) after radical prostatectomy (RP).

Patients and methods
This study retrospectively enrolled patients who underwent prostate MRI before RP at our center between January 2015 and November 2022. Preoperative clinicopathological factors and MRI-based features were recorded for analysis. The presence of PSM (overall PSM [oPSM]) at pathology and the multifocality of PSM (mPSM) were evaluated. LASSO regression was employed for variable selection. For the final model construction, logistic regression was applied combined with the bootstrap method for internal verification. The risk probability of individual patients was visualized using a nomogram.

Results
In all, 259 patients were included in this study, and 76 (29.3%) patients had PSM, including 40 patients with mPSM. Final multivariate logistic regression revealed that the independent risk factors for oPSM were tumor diameter, frank extraprostatic extension, and annual surgery volume (all p < 0.05), and the nomogram for oPSM reached an area under the curve (AUC) of 0.717 in development and 0.716 in internal verification. The independent risk factors for mPSM included the percentage of positive cores, tumor diameter, apex depth, and annual surgery volume (all p < 0.05), and the AUC of the nomogram for mPSM was 0.790 in both development and internal verification. The calibration curve analysis showed that these nomograms were well-calibrated for both oPSM and mPSM.

Conclusions
The proposed nomograms showed good performance and were feasible in predicting oPSM and mPSM, which might facilitate more individualized management of prostate cancer patients who are candidates for surgery.
Advances in the mechanism of small nucleolar RNA and its role in DNA damage response
Authors: Shen Li-Ping , Zhang Wen-Cheng , Deng Jia-Rong , Qi Zhen-Hua , Lin Zhong-Wu , Wang Zhi-Dong 
Published: August 2024

AbstractSmall nucleolar RNAs (snoRNAs) were previously regarded as a class of functionally conserved housekeeping genes, primarily involved in the regulation of ribosome biogenesis by ribosomal RNA (rRNA) modification. However, some of them are involved in several biological processes via complex molecular mechanisms. DNA damage response (DDR) is a conserved mechanism for maintaining genomic stability to prevent the occurrence of various human diseases. It has recently been revealed that snoRNAs are involved in DDR at multiple levels, indicating their relevant theoretical and clinical significance in this field. The present review systematically addresses four main points, including the biosynthesis and classification of snoRNAs, the mechanisms through which snoRNAs regulate target molecules, snoRNAs in the process of DDR, and the significance of snoRNA in disease diagnosis and treatment. It focuses on the potential functions of snoRNAs in DDR to help in the discovery of the roles of snoRNAs in maintaining genome stability and pathological processes.
Collaborative inquiry in action: a case study of lesson study for intercultural education
Authors: Qin Xiaolei 
Published: August 2024

AbstractThe evolving nature of intercultural education necessitates a shift from static to reflective pedagogies among teachers. This case study investigates the efficacy of a collaborative lesson study (LS) approach in enhancing Chinese university instructors' proficiency in participatory, non-essentialist intercultural teaching. Six English as a Foreign Language instructors at a Chinese university engaged in three iterative LS cycles over one month, integrating new intercultural communication materials into their classes. Data were collected through lesson documents, observations, discussions, and interviews. The immersive LS process significantly expanded instructors' understanding of key intercultural communication concepts, encouraged the adoption of more student-centered methodologies, and prompted critical reflection on prior cultural assumptions. The collaborative engagement facilitated a deeper theoretical grasp and practical application of non-essentialist principles. Challenges included time constraints due to teaching workloads, discomfort in peer feedback exchange, and a broader lack of coordinated intercultural teacher training. Despite these challenges, this study underscores the potential of LS as a robust model for advancing intercultural teaching capacity through collaborative inquiry. It hints at the promise of LS in bridging the theory–practice divide in intercultural education, paving the way for more nuanced, non-essentialist instruction.
Real-world analysis of brain atrophy in multiple sclerosis patients with an artificial intelligence based software tool
Authors: Reinhardt Caroline , Angstwurm Klemens , Freudenstein David , Lee De-Hyung , Wendl Christina , Linker Ralf A. 
Published: August 2024

Abstract
Background
Atrophy of white and grey matter volumes occurs early in the brains of people with multiple sclerosis (pwMS) and has great clinical relevance. In clinical trials, brain atrophy can be quantified by magnetic resonance imaging (MRI) with automated software tools.

Methods
In this study, we analyze volumes of various brain regions with the software “md brain” based on routine MRI scans of 53 pwMS in a real-world setting. We compare brain volumes of pwMS with an EDSS ≥ 3.5 and a disease duration ≥ 10 years to the brain volumes of pwMS with an EDSS < 3.5 and a disease duration < 10 years as well as with or without immunotherapy.

Results
pwMS with an EDSS ≥ 3.5 and a disease duration ≥ 10 years had significantly lower volumes of the total brain, the grey matter and of the frontal, temporal, parietal and occipital lobe regions as compared to pwMS with an EDSS < 3.5 and a disease duration < 10 years. Regional brain volumes were significantly lower in pwMS without immunotherapy.

Conclusions
The study showed that higher EDSS, longer disease duration and absence of immunotherapy was associated with lower volumes in a number of brain regions. Further real-world studies may include larger patient cohorts in longitudinal analyses.
Efficacy of nano-silicon extracted from rice husk to modulate the physio-biochemical constituents of wheat for ameliorating drought tolerance without causing cytotoxicity
Authors: Abdo Rahma Ahmed , Hazem Mahmoud M. , El-Assar Abd El-Monaem , Saudy Hani Saber , El-Sayed Salwa M. 
Published: August 2024

Abstract
Background
Abiotic stresses, like drought, are the major cause of shrinking plant, growth crop yields and quality. Nanotechnology has provided a significant improvement in increasing plant growth and yield of crops under stress conditions. This work assessed the potential of silicon for mitigating the negative effects of drought against wheat. In completely randomized design with three replicates, wheat seedlings grown under three watering levels (100, 60 and 40% of water holding capacity) were treated by silicon dioxide (SiO2) as a normal or bulk form (Si) and SiO2 nanoparticles (SiNPs) with concentrations of 100 and 200 mg L−1. SiNPs was extracted from rice husk.

Results
Si and SiNPs treatments are shown to improve the growth of plants and increase the shoots and root weight, relative water content, photosynthetic pigments, and proline in wheat. SiO2 either normal or nanoparticles at 100 mg L−1 decreased lipid peroxidation as malondialdehyde was reduced. Also, nano-silicon increased free amino acids, antioxidant enzymes while decreased soluble sugars. Cytotoxicity assay proved the safety of nano-silicon usage.

Conclusions
In conclusion, the present study documented the significance of rice husk-extracted nano-silicon at rate of 100 mg L−1 for improving growth and increasing tolerance to drought in wheat grown under water deficit.
L-arginine: its role in human physiology, in some diseases and mainly in viral multiplication as a narrative literature review
Authors: Pedrazini Maria Cristina , Martinez Elizabeth Ferreira , dos Santos Victor Augusto Benedicto , Groppo Francisco Carlos 
Published: August 2024

Abstract
Background
L-arginine (Arg) is an amino acid that contributes to several aspects of human biochemistry. Individuals with malnutrition and certain physical conditions could benefit from arginine intake. However, as Arg is required by certain viruses, it is advised to avoid it in one's diet and supplementation during viral illnesses. New studies have emerged during the COVID-19 pandemic, and pioneering research has been reviewed.

Main body of the abstract
The purpose of this review is to determine when and why Arg depletion, supplementation, or avoidance is advisable, considering the divergent results. A narrative review was conducted by surveying scientific publications indexed in electronic databases. Studies published from 1960 up to 2024, with no language restrictions, were included. Arg comes from proteins in the human diet. The kidney is the main site of endogenous Arg synthesis and also responsible for the overall metabolism of this amino acid, participating in synthesis, degradation and reabsorption. The liver can synthesize Arg, but since this is completely recycled in the urea cycle, it contributes little or no to the Arg plasma flux. Arg present in diet is passively absorbed in the small intestine and also transformed into urea and ornithine via urea cycle in hepatocytes. It is associated with macrophage metabolism, vasomotor control, intracellular signaling, memory formation, immune response, and an important messenger of the bronchopulmonary, cardiovascular and neural systems. Thus, excessive or decreased Arg concentration could impair health condition. High Arg concentrations stimulated rapid reactivation and resumption of protein synthesis in some viruses.

Conclusion
According to research, caution should be exercised when supplementing or depleting the amino acid arginine. Individuals who are carriers of latent viruses, such as herpesviruses, and/or who have been exposed to other viruses studied, should avoid arginine supplements and the consumption of foods rich in arginine. However, as prophylaxis or antiviral therapy, control of arginine intake as well as the use of lysine supplements, its antagonist, is recommended for short periods starting after a possible viral exposure, or in face of stimuli that can remove viruses from their latent state and/or at the very beginning of the viral manifestation, in order to avoid a large viral multiplication and consequently control the infection. Long-term arginine depletion can significantly affect cellular metabolism and its use as supplemental therapy needs case-by-case evaluation.

Graphical abstract
Revisiting diabetes risk of olanzapine versus aripiprazole in serious mental illness care
Authors: Agniel Denis , Normand Sharon-Lise T. , Newcomer John W. , Zelevinsky Katya , Poulos Jason , Tsuei Jeannette , Horvitz-Lennon Marcela 
Published: August 2024

Background
Exposure to second-generation antipsychotics (SGAs) carries a risk of type 2 diabetes, but questions remain about the diabetogenic effects of SGAs.

Aims
To assess the diabetes risk associated with two frequently used SGAs.

Method
This was a retrospective cohort study of adults with schizophrenia, bipolar I disorder or severe major depressive disorder (MDD) exposed during 2008–2013 to continuous monotherapy with aripiprazole or olanzapine for up to 24 months, with no pre-period exposure to other antipsychotics. Newly diagnosed type 2 diabetes was quantified with targeted minimum loss-based estimation; risk was summarised as the restricted mean survival time (RMST), the average number of diabetes-free months. Sensitivity analyses were used to evaluate potential confounding by indication.

Results
Aripiprazole-treated patients had fewer diabetes-free months compared with olanzapine-treated patients. RMSTs were longer in olanzapine-treated patients, by 0.25 months [95% CI: 0.14, 0.36], 0.16 months [0.02, 0.31] and 0.22 months [0.01, 0.44] among patients with schizophrenia, bipolar I disorder and severe MDD, respectively. Although some sensitivity analyses suggest a risk of unobserved confounding, E-values indicate that this risk is not severe.

Conclusions
Using robust methods and accounting for exposure duration effects, we found a slightly higher risk of type 2 diabetes associated with aripiprazole compared with olanzapine monotherapy regardless of diagnosis. If this result was subject to unmeasured selection despite our methods, it would suggest clinician success in identifying olanzapine candidates with low diabetes risk. Confirmatory research is needed, but this insight suggests a potentially larger role for olanzapine in the treatment of well-selected patients, particularly for those with schizophrenia, given the drug's effectiveness advantage among them.