bluuebunny/crossref_metadata_2025_split huggingface dataset:
Biotransformation of eicosapentaenoic acid into the dihydroxyeicosapentaenoic acids resolvin E4 and its enantiomer by 15S- and 15R-lipoxygenases expressed in Escherichia coli
Authors: Lee Jin , Park Hyun-Ah , Shin Kyung-Chul , Oh Deok-Kun 
Published: April 2024

Abstract

Objectives
To enhance the production of resolvin E4 (RvE4) or its enantiomer from eicosapentaenoic acid (EPA), Archangium violaceum 15S-lipoxygenase (15S-LOX) or Sorangium cellulosum 15R-LOX was expressed in Escherichia coli with solvent, polymer, and adsorbent resin, respectively.
Results
The concentrations of cells and substrate and the types and concentrations of solvent, polymer, and resin were optimized for the biotransformation of EPA into RvE4 (5S,15S-dihydroxyeicosapentaenoic acid) and its enantiomer (5R,15R-dihydroxyeicosapentaenoic acid). Under optimized conditions, A. violaceum 15S-LOX and S. cellulosum 15R-LOX expressed in E. coli converted 6.0 mM (1.8 g L−1) EPA into 4.3 mM (1.4 g L−1) RvE4 and 5.8 mM (1.9 g L−1) RvE4 enantiomer in 60 min, with productivities of 4.3 and 5.8 mM h−1 and molar conversions of 72 and 97%, respectively. The concentrations of RvE4 and its enantiomer resulting from the conversion of EPA with solvent, polymer, and resin were 3.1- and 5.3-fold higher than those without additives, respectively.
Conclusions
The concentrations, productivities, and conversions of RvE4 and its enantiomer were increased by optimizing the concentrations of cells and substrate and the types and concentrations of solvent, polymer, and adsorbent resin.
Developing and Testing a Framework for Coding General Practitioners' Free-Text Diagnoses in Electronic Medical Records - A Reliability Study for Generating Training Data in Natural Language Processing
Authors: Wallnöfer Audrey , Burgstaller Jakob M. , Weiss Katja , Rosemann Thomas , Senn Oliver , Markun Stefan 
Published: April 2024

Abstract

Background
Diagnoses entered by general practitioners into electronic medical records have great potential for research and practice, but unfortunately, diagnoses are often in uncoded format, making them of little use. Natural language processing (NLP) could assist in coding free-text diagnoses, but NLP models require local training data to unlock their potential. The aim of this study was to develop a framework of research-relevant diagnostic codes, to test the framework using free-text diagnoses from a Swiss primary care database and to generate training data for NLP modelling.
Methods
The framework of diagnostic codes was developed based on input from local stakeholders and consideration of epidemiological data. After pre-testing, the framework contained 105 diagnostic codes, which were then applied by two raters who independently coded randomly drawn lines of free text (LoFT) from diagnosis lists extracted from the electronic medical records of 3000 patients of 27 general practitioners. Coding frequency and mean occurrence rates (n and %) and inter-rater reliability (IRR) of coding were calculated using Cohen's kappa (Κ).
Results
The sample consisted of 26,980 LoFTs and in 56.3% no code could be assigned because it was not a specific diagnosis. The most common diagnostic codes were, 'dorsopathies' (3.9%) and 'other diseases of the circulatory system' (3.1%). Raters were in almost perfect agreement (Κ ≥0.81) for 69 of the 105 diagnostic codes, and 28 codes showed a substantial agreement (K between 0.61 and 0.80). Both high coding frequency and almost perfect agreement was found in 37 codes, including codes that are particularly difficult to identify from components of the electronic medical record, such as musculoskeletal conditions, cancer or tobacco use.
Conclusion
The coding framework was characterised by a subset of very frequent and highly reliable diagnostic codes, which will be the most valuable targets for training NLP models for automated disease classification based on free-text diagnoses from Swiss general practice.
Discovery of intestinal mRNA expression profiles correlated with mucosal healing of ustekinumab patients with Crohn’s disease: bioinformatics analysis and prospective cohort validation
Authors: Li Qing , Huang Zicheng , Yang Hongsheng , Tang Jian , Zuo Tao , Yang Qingfan , Huang Zhaopeng , Guo Qin , Li Miao , Gao Xiang , Chao Kang 
Published: April 2024

Abstract
Background:
Variations existed in responses to ustekinumab (UST) treatment in patients with Crohn's disease (CD), but the underlying cause remains unknown. Our objective was to investigate the involvement of immune cells and identify potential biomarkers that can predict the response to IL 12/23 inhibitors in patients with CD.
Methods:
GSE207022 dataset was analyzed, which consisted of 54 non-responders and 9 responders to UST in CD cohort. Differentially expressed genes (DEGs) were identified,followed by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses. LASSO (Least absolute shrinkage and selection operator) regression was used to further screen the most powerful hub genes. ROC curve analysis was employed to evaluate the predictive performances of these genes. ssGSEA was used to estimate the proportion of immune cell types. These significantly altered genes were further subjected to clustering analysis into immune cell-related infiltration. To validate the reliability of the candidates, patients prescribed with UST as the first line biologics in a prospective cohort were included as an independent validation dataset.
Results:
A total of 99 DEGs were obtained from the integrated dataset. Analyses of GO and KEGG revealed a significant enrichment of immune response pathways in CD patients. Thirteen genes (SOCS3, CD55, KDM5D, IGFBP5, LCN2, SLC15A1, XPNPEP2, HLA-DQA2, HMGCS2, DDX3Y, ITGB2, CDKN2B and HLA-DQA1) which were primarily associated with the response versus non-response patients were identified and included to conduct the LASSO model. These genes accurately predicted treatment response with an area under the curve (AUC) of 0.938. Non-response individuals exhibited a relatively high Th1 cell polarization. Both LCN2 and KDM5D genes showed positive correlations with Th1 cells. Furthermore, we validated LCN2 and KDM5D genes as effective predictive markers using independent validation datasets and preliminary experimental verification.
Conclusions:
Th1 cell polarization was an important cause of non-response to UST therapy in CD patients. LCN2 and KDM5D could be used as predictive markers to identify non-response patients effectively.
Trial registration:
Trial registration number: NCT05542459; Date of registration: 2022-09-14; URL: https://www.clinicaltrials.gov.
The Lusinde late-post-tectonic Variscan granite (Central Iberian Zone): pluton emplacement at the termination of the Juzbado-Penalva shear zone
Authors: Portela Luís Pedro de Castro Figueiredo , Azevedo Maria do Rosário , Medina Jorge , Aguado Beatriz Valle 
Published: April 2024

Abstract

The Lusinde biotite granite constitutes a small late-post-tectonic Variscan massif, emplaced along the western termination of the Juzbado-Penalva Shear Zone (JPCSZ). The main objective of this work is to constrain the time of crystallisation of the Lusinde massif and to apply the technique of anisotropy of magnetic susceptibility to better understand pluton emplacement and internal structure. New LA–ICP–MS U–Pb zircon geochronological data for this intrusion yielded an emplacement age of 295 ± 1 Ma. The Lusinde granite shows relatively low values of magnetic susceptibility (Km = 152 × 10-6 to 271 × 10-6 SI), typical of granites of the ilmenite series in which biotite is the main carrier of magnetic signal. A pyroxene- and amphibole-bearing mafic microgranular enclave exhibits higher Km magnitudes (536 × 10-6 SI). Magnetic foliations are steeply plunging and strike subparallel to the pluton irregular margins. Magnetic lineations show rather variable directions and steep plunges, suggesting that the whole massif may correspond to a feeder zone. The studied pluton seems to belong to an E-W band of steep lineations traced along the northern border of the main mass of the Cota-Viseu late-post-tectonic granite and associated mafic and intermediate rocks, which has been interpreted as an alignment of feeder zones related to the extensional termination of the Juzbado-Penalva Shear Zone (JPCSZ). As a result, it is concluded that the emplacement of the Lusinde granite was tectonically controlled by the JPCSZ.
Intact functional brain networks in the isolated hemisphere of people after hemispherotomy
Authors: Bauer Tobias , Gauvry Charlotte , Markett Sebastian , Kreter-Schönleber Thomas , Hoppe Christian , Borger Valeri , Vatter Hartmut , Sander Josemir , Gabriel Markus , Mormann Florian , Radbruch Alexander , Surges Rainer , Rüber Theodor 
Published: April 2024

Abstract

Cognition and behaviour are thought to be underpinned by seven segregated brain networks, whose tasks range from the sensory role of the visual network to intrinsic mental processes such as consciousness carried out by the default-mode network. However, it is unclear whether functional integrity of these networks is retained when the brain is devoid of external inputs. Here we investigate the functional organisation of individual brain hemispheres in individuals having undergone hemispherotomy (HT) due to pharmacoresistant epilepsy. Although this procedure results in one hemisphere being isolated from the rest of the nervous system, we find that the functional organisation of the seven macroscale networks is retained in the isolated hemisphere, including the default-mode network. However, both isolated and connected hemispheres have a lower degree of network segregation after HT, compared to healthy brains. Our results indicate that isolated hemispheres preserve functional integrity, thereby instigating inquiries into their cognitive capacities and their potential to be “islands of awareness”.
A novel ultrasound image denoising algorithm based on Neighbor2Neighbor unsupervised learning model
Authors: Wei Peiyang , Gan Jianhong , Wang Liping , Shi Xiaoyu , Shang Mingsheng 
Published: April 2024

Abstract

Ultrasound images are widely adopted in medical diagnosis, thus whose the quality and accuracy are crucial. The mainstream supervised deep learning denoisation methods generally require noise-clean image pairs of samples, which is not feasible in real ultrasound scenarios. Due to these limitations of independent noise, current unsupervised denoizing methods like Neighbor2Neighbor cannot address correlated noise in ultrasound images. Meanwhile, due to the random neighborhood downsampler, this method results in pixel loss. This work proposes an effective Neighbor2Neighbor algorithm to deal with the pixel loss problem by reconstructing the image through a refined downsampling strategy. Moreover, the structural similarity function and the regularization term are introduced into the loss function, which can suppress the independent and correlated noises more effectively. After experimental comparison with the state-of-the-art baseline algorithms including BM3D, Noise2Noise, Noise2Void, Neighbor2Neighbor, the proposed algorithm has excellent performance in PSNR, MSSIM, PSLM and EPI.
Endophytic interaction of the filamentous fungus Neurospora crassa with the grass Brachypodium distachyon roots
Authors: Kollath-Leiß Krisztina , Repnik Urska , Winter Hannes , Winkelmann Heinrich , Freund Anna Sophie , Kempken Frank 
Published: April 2024

Abstract

Fungi, beyond their role as saprophytes, engage in intricate relationships with plants, showcasing diverse connections ranging from mutualistic to pathogenic. We describe here an endophytic interaction employing two well-established model organisms, the grass Brachypodium distachyon and the ascomycete Neurospora crassa. Although N. crassa has been extensively investigated under laboratory conditions, its ecological characteristics remain largely unknown. In contrast, B. distachyon, a sweet grass closely related to significant crops, demonstrates remarkable ecological flexibility and participates in a variety of fungal interactions, encompassing both mutualistic and harmful associations. Through comprehensive microscopic analysis using electron, fluorescence, and confocal laser scanning microscopy, we discovered a novel endophytic interaction between N. crassa and B. distachyon roots, where fungal hyphae not only thrive in the apoplastic space and vascular bundle, but also may colonize plant root cells. This consistent connection between the fungus and B. distachyon suggests a natural association of the fungus with Poaceae. This discovery opens new perspectives for understanding the fungal life cycle in nature. Moreover, we present a tool for studying plant-fungus interspecies communication, combining well-established model systems.
A Study on the Knowledge, Attitude, and Practice of Research Integrity among Medical Professionals in Ningxia, China
Authors: Jin Yiran , Wei Jie , Zhang Jingyi , Luo Sang , Yuan Liwei , Zou Xiaojie , Liu Dan 
Published: April 2024

Abstract

This study utilizes a Knowledge, Attitude, and Practice (KAP) questionnaire to investigate the awareness of medical professionals in the Ningxia region regarding research integrity and their attitudes towards academic misconduct. A comprehensive analysis of the factors contributing to academic misconduct is performed, with the aim of providing insights for the formulation of policies to enhance research integrity. The research employs a self-designed KAP survey questionnaire distributed online for clinical doctors and nurses in hospitals, faculty members in medical higher education institutions, and undergraduates enrolled in medical schools in the Ningxia region. A total of 1013 valid questionnaires were collected, with a majority of participants (76.2%) having received training in research integrity. Most respondents demonstrated a basic understanding of research integrity and maintained a resistant attitude towards academic misconduct. However, there exists an insufficient awareness of certain forms of academic misconduct, indicating the need for further reinforcement of the stance against such behaviors. The study recommends implementing multifaceted measures to enhance the ethical awareness and attitudes of researchers.
Field Releases of Neoseiulus barkeri: Effects on Megalurothrips usitatus Abundance and Arthropod Diversity
Authors: Chi Yuanming , Yu Chen , Feng MingYue , Shu Kai , Zhu Yilin , Shi WangPeng 
Published: April 2024

Abstract

Megalurothrips usitatus (Bagnall) (Thysanoptera: Thripidae) is an important pest in Vigna unguiculata (L.) Walp. Neoseiulus barkeri (Hughes) (Acari: Phytoseiidae) is widely used for control of pest mites and insects worldwide. We evaluated its effect on M. usitatus when predators (N. barkeri) or insecticides (Spinetoram) were applied in the fields. Neoseiulus barkeri Hughes consumed 80% of M. usitatus prey offered within 6 hours, and predation showed Type III functional response with prey density. The maximum consumption of N. barkeri was 27.29 ± 1.02 individuals·per d per arena (1.5 cm diameter), while the optimal prey density for the predatory mite was 10.35 ± 0.68 individuals per·d per arena (1.5 cm diameter). The developmental duration of N. barkeri fed with M. usitatus was significantly shorter than those fed with the dried fruit mite, Carpoglyphus lactis (L.) (Acari: Astigmata) . In field trials, the efficiency of N. barkeri against M. usitatus was not significantly different from that of applications of the insecticide spinetoram. Biodiversity of other insects in treated fields was assessed, and there were 21 insect species in garden plots treated with N. barkeri releases. The total abundance (N), Shannon’s diversity index (H), Pielou’s evenness index (J) and Simpson’s diversity index (D) of the garden plots treated with predatory mites were all significantly higher than that in the garden plots treated with spinetoram, where we found no species of predators or parasitoids and 7 herbivores. Our results show that N. barkeri is a potential means to control M. usitatus while preserving arthropod diversity at the level of treated gardens.
Comparing the performance of machine learning models for predicting the compressive strength of concrete
Authors: Loureiro Arthur Afonso Bitencourt , Stefani Ricardo 
Published: April 2024

Abstract

This study aimed to investigate and compare the performance of different machine learning models in predicting the compressive strength of concrete using a data set of 1234 compressive strength values. The predictive variables were selected based on their relevance using the SelectKBest method, resulting in an analysis of eight and six predictive variables. The evaluation was conducted through linear correlation studies via simple linear regression and non-linear correlation studies using support vector regression (SVR), gradient boosting (GB), and artificial neural networks (ANN). The results showed a coefficient of determination (R²) = 0.85 and a root mean square error (RMSE) = 30.9051 MPa for SVR, R² = 0.90 and RMSE = 25.5979 MPa for GB, and R² = 0.87 and RMSE = 5.781 MPa for ANN. The comparison between the machine learning methods revealed significant differences. For instance, GB stood out with a higher R² value, demonstrating its remarkable ability to explain the variability in the data. Conversely, ANN showed the lowest RMSE value, indicating notable accuracy in the predictions. The choice between these approaches depends on considerations regarding the balance between explainability and accuracy. While GB provides a more in-depth understanding of the relationship between variables, ANN stands out for the accuracy of its predictions.
Development and validation of a dynamic nomogram for individualized prediction of survival in patients with colon cancer
Authors: Sun Yuting , Huang Longchang , Shen Xiaoming , Yang Zenghui , Xu Binghua , Bao Chuanqing , Shi Yifan 
Published: April 2024

Abstract

Current tools for predicting survival outcomes in colon cancer patients depend predominantly on clinical and pathologic characteristics, but accumulating evidence demonstrates that nutritional status is closely related to patient outcomes. We aimed to establish a new dynamic nomogram for individualized prediction of postoperative overall survival (OS). The clinicopathological and nutritional data of colon cancer patients undergoing radical resection were retrospectively collected and randomly divided into the primary and validation cohorts. Risk factors on OS rates were investigated by Cox analyses and the nomogram was constructed using significant predictors. Among 1,024 patients, 341 deaths were observed after median follow-up of 54 months. Five independent prognostic factors including nutritional status assessments, were incorporated into the nomogram. The C-index regarding 1-, 3-, and 5-year OS were 0.830, 0.859, and 0.757 in the primary cohort and 0.843, 0.870, and 0.773 in the validation cohort, respectively. Calibration curves for the probability of OS exhibited an optimal agreement. The decision curve analyses demonstrated the greater application value of the nomogram than the TNM staging system. Based on the nomogram, these patients could be divided into three scenarios with significant prognostic classification (P < 0.0001). We developed and validated an easy-to-use dynamic nomogram to predict postoperative OS for patients with colon cancer.
Study Protocol: The Use of Rituximab in Nephrotic Glomerulonephritis (TURING)
Authors: Willcocks Lisa , Qian Wendi , Cader Ruzaika , Gatley Katrina , Siddiqui Hira , Tabebisong Endurance , Champion Karlena , Kronbichler Andreas , Lightstone Liz , Jayne David , Wilson Edward , Griffith Megan 
Published: April 2024

Abstract

Background: Minimal Change Disease (MCD) and Focal Segmental Glomerulosclerosis (FSGS) are a spectrum of disease causing the nephrotic syndrome (NS), characterised by proteinuria with debilitating oedema, as well as a high risk of venous thromboembolic disease and infection. Untreated, 50-60% patients with FSGS progress to end stage kidney disease after 5 years. These diseases respond to immunosuppression with high dose glucocorticoids, but 75% will relapse as the glucocorticoids are withdrawn, leading to significant morbidity associated with prolonged use. In children, the B cell depleting monoclonal antibody rituximab reduces relapse risk, but this drug has not been tested in randomised controlled trial in adults.
Methods: 130-150 adults with new or relapsing MCD/FSGS, from UK Renal Units, are being randomised to receive either rituximab (two 1g infusions two weeks apart) or placebo. Partipicipants are recruited when they present with nephrosis, and all are treated with glucocorticoids as per KDIGO guidelines. Once in remission, prednisolone is withdrawn according to a pre-specified regimen. If in remission at 6 months, participants receive a further dose of trial drug. If they relapse, they are unblinded, and if they have received placebo, they are offered open label rituximab with protocolised prednisolone as in the main phase of the trial. The primary end point is time from remission to relapse. A number of secondary endpoints will be assessed including the effect of rituximab on: (1) NHS and societal resource use and hence cost: (2) safety: (3) other measures of efficacy, such as achievement of partial and complete remission of NS and the preservation of renal function: (4) health status of participant.
Trial Registration: TURING received ethical approval on 14 Jun 2019 - REC reference: 19/LO/0738. It is registered on EudraCT, with ID number: 2018-004611-50, with a start date of 2019-06-14.
Alleviating Asthma-Induced Mitochondrial Dysfunction and Oxidative Stress: Lactobacillus rhamnosus Intervention via Notch1 Signaling Pathway
Authors: Liu Si , Chen Shao-Tian , Jiang Xin-Yan , Shang Xiao-Yun , Nan Yang 
Published: April 2024

Abstract
Immune system disorders play a crucial role in asthma. Probiotics can be beneficial in maintaining a healthy balance of gut bacteria and improving metabolism. Lactobacillus rhamnosus (L. rhamnosus) is a gram-positive probiotic found primarily in the intestines of humans and animals. However, the mechanism by which L. rhamnosus treats asthma is unknown. Here, we confirmed that L. rhamnosus had a protective effect on the lung tissues of asthmatic mice. In addition, L. rhamnosus significantly modulated the balance of T cell subpopulations and promoted the expression of Treg cells, increasing the proportion of inhibited Th17 and restoring immune function. Mechanistically, L. rhamnosus inhibited the activation of NOD-like receptor heat protein domain-related protein 3 (NLRP3) inflammatory vesicles caused by asthma-induced oxidative stress and mitochondrial dysfunction. In conclusion, L. rhamnosus ameliorated asthma by mediating Notch1 signaling pathway-induced NLRP3 inflammasome activation and Dynamin-related protein 1 (Drp1) translational activation. In words, our study provides a theoretical basis for the use of probiotics, represented by L. rhamnosus, as effective agents for the prevention and treatment of asthma.