bluuebunny/crossref_metadata_2025_split huggingface dataset:
Associations of corticosteroid therapy and tonsillectomy with kidney survival in a multicenter prospective study for IgA nephropathy
Authors: Kawamura Tetsuya , Hirano Keita , Koike Kentaro , Nishikawa Masako , Shimizu Akira , Joh Kensuke , Katafuchi Ritsuko , Hashiguchi Akinori , Matsuzaki Keiichi , Maruyama Shoichi , Tsuboi Nobuo , Narita Ichiei , Yano Yuichiro , Yokoo Takashi , Suzuki Yusuke 
Published: October 2023

AbstractEfficacy of systemic corticosteroid therapy (CS) for long-term kidney survival in patients with IgA nephropathy (IgAN) is controversial. Therefore, prospective studies evaluating targeted therapies to lymphatic tissues in mucosal immune system responsible for production of nephritogenic IgA have been desired worldwide. Here, we aimed to evaluate the associations of CS and combination therapy of CS and tonsillectomy (CS + Tx) with kidney survival, using database from a nationwide multicenter prospective cohort study on IgAN. Primary outcome was a 50% increase in serum creatinine from baseline or dialysis induction. The analysis included 941 patients (CS/CS + Tx/non-CS 239/364/338), 85 (9.0%) of whom reached outcomes during median follow-up of 5.5 (interquartile range 2.0–8.0) years. On overlap weighting analysis with balanced baseline characteristics, CS and CS + Tx were associated with lower risk of kidney events when compared with non-CS (hazard ratio [HR] 0.51, 95% confidence interval [CI] 0.29–0.88 and HR 0.20, 95%CI 0.09–0.44, respectively). Notably, when compared with the CS, CS + Tx was associated with a lower risk of kidney events (HR 0.40, 95%CI 0.18–0.91). Present study demonstrated, keeping with favorable association of systemic CS with kidney survival, concurrent tonsillectomy as one of targeted interventions to lymphatic tissues may provide additional improvement to kidney survival in patients with IgAN.
Mucosal expression of PI3, ANXA1, and VDR discriminates Crohn’s disease from ulcerative colitis
Authors: James Jaslin Pallikkunnath , Nielsen Boye Schnack , Christensen Ib Jarle , Langholz Ebbe , Malham Mikkel , Poulsen Tim Svenstrup , Holmstrøm Kim , Riis Lene Buhl , Høgdall Estrid 
Published: October 2023

AbstractDifferential diagnosis of inflammatory bowel disease (IBD) to Crohn’s disease (CD) or ulcerative colitis (UC) is crucial for treatment decision making. With the aim of generating a clinically applicable molecular-based tool to classify IBD patients, we assessed whole transcriptome analysis on endoscopy samples. A total of 408 patient samples were included covering both internal and external samples cohorts. Whole transcriptome analysis was performed on an internal cohort of FFPE IBD samples (CD,n = 16 and UC,n = 17). The 100 most significantly differentially expressed genes (DEG) were tested in two external cohorts. Ten of the DEG were further processed by functional enrichment analysis from which seven were found to show consistent significant performance in discriminating CD from UC:PI3, ANXA1, VDR, MTCL1, SH3PXD2A-AS1, CLCF1, and CD180. Differential expression ofPI3,ANXA1, andVDRwas reproduced by RT-qPCR, which was performed on an independent sample cohort of 97 patient samples (CD,n = 44 and UC,n = 53). Gene expression levels of the three-gene profile, resulted in an area under the curve of 0.84 (P = 0.02) in discriminating CD from UC, and therefore appear as an attractive molecular-based diagnostic tool for clinicians to distinguish CD from UC.
Starvation induces changes in abundance and small RNA cargo of extracellular vesicles released from Plasmodium falciparum infected red blood cells
Authors: Vetter Leonie , Bajalan Amanj , Ahamed Mohammad Tanvir , Scasso Caterina , Shafeeq Sulman , Andersson Björn , Ribacke Ulf 
Published: October 2023

AbstractThe lethal malaria parasite Plasmodium falciparum needs to constantly respond and adapt to changes within the human host in order to survive and transmit. One such change is composed of nutritional limitation, which is augmented with increased parasite loads and intimately linked to severe disease development. Extracellular vesicles released from infected red blood cells have been proposed as important mediators of disease pathogenesis and intercellular communication but whether important for the parasite response to nutritional availability is unknown. Therefore, we investigated the abundance and small RNA cargo of extracellular vesicles released upon short-term nutritional starvation of P. falciparum in vitro cultures. We show that primarily ring-stage parasite cultures respond to glucose and amino acid deprivation with an increased release of extracellular vesicles. Small RNA sequencing of these extracellular vesicles further revealed human miRNAs and parasitic tRNA fragments as the main constituent biotypes. Short-term starvations led to alterations in the transcriptomic profile, most notably in terms of the over-represented biotypes. These data suggest a potential role for extracellular vesicles released from P. falciparum infected red blood cells in the response to nutritional perturbations, their potential as prognostic biomarkers and point towards an evolutionary conserved role among protozoan parasites.
Ketogenic diet influence on the elemental homeostasis of internal organs is gender dependent
Authors: Kawon Kamil , Rugiel Marzena , Setkowicz Zuzanna , Matusiak Katarzyna , Kubala-Kukus Aldona , Stabrawa Ilona , Szary Karol , Rauk Zuzanna , Chwiej Joanna 
Published: October 2023

AbstractThe ketogenic diet (KD) is a low-carbohydrate and high-fat diet that gains increasing popularity in the treatment of numerous diseases, including epilepsy, brain cancers, type 2 diabetes and various metabolic syndromes. Although KD is effective in the treatment of mentioned medical conditions, it is unfortunately not without side effects. The most frequently occurring undesired outcomes of this diet are nutrient deficiencies, the formation of kidney stones, loss of bone mineral density, increased LDL (low-density lipoprotein) cholesterol levels and hormonal disturbances. Both the diet itself and the mentioned adverse effects can influence the elemental composition and homeostasis of internal organs. Therefore, the objective of this study was to determine the elemental abnormalities that appear in the liver, kidney, and spleen of rats subjected to long-term KD treatment. The investigation was conducted separately on males and females to determine if observed changes in the elemental composition of organs are gender-dependent. To measure the concentration of P, S, K, Ca, Fe, Cu, Zn and Se in the tissues the method of the total reflection X-ray fluorescence (TXRF) was utilized. The obtained results revealed numerous elemental abnormalities in the organs of animals fed a high-fat diet. Only some of them can be explained by the differences in the composition and intake of the ketogenic and standard diets. Furthermore, in many cases, the observed anomalies differed between male and female rats.
Spatial genetic structure and seed quality of a southernmost Abies nephrolepis population
Authors: Kim Sunjeong , Lee Hye-Jin , Kim Yang-Gil , Kang Kyu-Suk 
Published: October 2023

AbstractAbies nephrolepis (Trautv. ex Maxim.) Maxim. has its southernmost populations in South Korea and they are expected to decline under climate change. To establish a strategic conservation plan, this study aimed to investigate the spatial genetic structure and seed characteristics of A. nephrolepis. We used nine microsatellite markers on 165 individuals of A. nephrolepis and sampled seeds in a southernmost population at Mt. Hambaeksan, South Korea. We observed a high level of heterozygosity, and a simulation study found that sampling 20 individuals was enough to secure sufficient genetic diversity on average. Spatial autocorrelation analysis revealed that individuals had a positive genetic relationship until 30 m. Bayesian clustering models, STRUCTURE and GENELAND, failed to achieve a consensus in the optimal number of population (K), estimating K = 1 and K = 2, respectively. Principal coordinate analysis supported the absence of genetic substructure within the study population. There was a large variance in seed production among mother trees. On average, seeds of A. nephrolepis from Mt. Hambaeksan had a purity of 70.4% and a germination percentage of 32.2%. We found that seed weight was the most effective indicator of seed quality. Mother trees at higher altitudes had poorer purity which is threatening to A. nephrolepis considering the upslope retreat of subalpine species under climate change. Our results provide insights into the interactions among spatial processes, genetic structure, and seed quality within a population of A. nephrolepis.
Lignosus rhinocerotis extract ameliorates airway inflammation and remodelling via attenuation of TGF-β1 and Activin A in a prolonged induced allergic asthma model
Authors: Muhamad Siti-Aminah , Safuan Sabreena , Stanslas Johnson , Wan Ahmad Wan Amir Nizam , Bushra Solehah-Mohd-Rosdan , Nurul Asma Abdullah 
Published: October 2023

AbstractAllergic asthma is associated with chronic airway inflammation and progressive airway remodelling. The sclerotium of Lignosus rhinocerotis (Cooke) Ryvarden (Tiger Milk mushroom) is used traditionally to treat various illnesses, including asthma in Southeast Asia. This study was carried out to evaluate the effect of L. rhinocerotis extract (LRE) on airway inflammation and remodelling in a chronic model of asthma. The present study investigated the therapeutic effects of LRE on airway inflammation and remodelling in prolonged allergen challenged model in allergic asthma. Female Balb/C mice were sensitised using ovalbumin (OVA) on day 0 and 7, followed by OVA-challenged (3 times/week) for 2, 6 and 10 weeks. LRE (125, 250, 500 mg/kg) were administered by oral gavage one hour after every challenge. One group of mice were left untreated after the final challenge for two weeks. LRE suppressed inflammatory cells and Th2 cytokines (IL-4, IL-5 and IL-13) in BALF and reduced IgE level in the serum. LRE also attenuated eosinophils infiltration and goblet cell hyperplasia in the lung tissues; as well as ameliorated airway remodelling by reducing smooth muscle thickness and reducing the expressions of TGF-β1 and Activin A positive cell in the lung tissues. LRE attenuated airway inflammation and remodelling in the prolonged allergen challenge of allergic asthma model. These findings suggest the therapeutic potential of LRE as an alternative for the management of allergic asthma.
Development of novel parameters for characterising scale morphology of wool fibre and its correlation with dye diffusion coefficient of acid dye
Authors: Paul Subhadeep , Hewitt Andrew , Rana Sohel , Goswami Parikshit 
Published: October 2023

AbstractThis paper reports the development of novel surface parameters which can be used to characterise the scale structure of wool fibres obtained from different breeds. Scanning electron microscopy and subsequent image analysis technique were used to study wool fibres from Leicester, Dartmoor, Ryeland and Herdwick breeds of sheep. Novel scale parameters related to wool fibre’s effective chemical diffusion pathway were developed. Namely, the total scale perimeter per 100 µm fibre length and scale perimeter index, which is the total scale perimeter per 100 µm length divided by the fibre diameter. Wool fibres obtained from different breeds showed significant differences in their scale pattern with the change in fibre diameter. The scale perimeter per 100 µm length increased with the fibre diameter and showed a polynomial correlation. It was also demonstrated that an increase in the diameter of the wool fibre resulted in an increase in the apparent dye diffusion coefficient, which contrasts the established theory that finer fibres are associated with a higher dyeing rate. The increase in effective diffusion pathway (total scale perimeter per 100 µm) for the wool fibres (among different breeds) resulted in a higher dye diffusion rate at the initial phase of dyeing (liquor to surface).
Notable improvements on LWFA through precise laser wavefront tuning
Authors: Oumbarek Espinos Driss , Rondepierre Alexandre , Zhidkov Alexei , Pathak Naveen , Jin Zhan , Huang Kai , Nakanii Nobuhiko , Daito Izuru , Kando Masaki , Hosokai Tomonao 
Published: October 2023

AbstractLaser wakefield acceleration (LWFA) continues to grow and awaken interest worldwide, especially as in various applications it approaches performance comparable to classical accelerators. However, numerous challenges still exist until this can be a reality. The complex non-linear nature of the process of interaction between the laser and the induced plasma remains an obstacle to the widespread LWFA use as stable and reliable particle sources. It is commonly accepted that the best wavefront is a perfect Gaussian distribution. However, experimentally, this is not correct and more complicated ones can potentially give better results. in this work, the effects of tuning the laser wavefront via the controlled introduction of aberrations are explored for an LWFA accelerator using the shock injection configuration. Our experiments show the clear unique correlation between the generated beam transverse characteristics and the different input wavefronts. The electron beams stability, acceleration and injection are also significantly different. We found that in our case, the best beams were generated with a specific complex wavefront. A greater understanding of electron generation as function of the laser input is achieved thanks to this method and hopes towards a higher level of control on the electrons beams by LWFA is foreseen.
The preliminary in vitro study and application of deep learning algorithm in cone beam computed tomography image implant recognition
Authors: Ou-yang Shaobo , Han Shuqin , Sun Dan , Wu Hongping , Chen Jianping , Cai Ying , Yin Dongmei , Ou-yang Huidan , Liao Lan 
Published: October 2023

AbstractTo properly repair and maintain implants, which are bone tissue implants that replace natural tooth roots, it is crucial to accurately identify their brand and specification. Deep learning has demonstrated outstanding capabilities in analysis, such as image identification and classification, by learning the inherent rules and degrees of representation of data models. The purpose of this study is to evaluate deep learning algorithms and their supporting application software for their ability to recognize and categorize three dimensional (3D) Cone Beam Computed Tomography (CBCT) images of dental implants. By using CBCT technology, the 3D imaging data of 27 implants of various sizes and brands were obtained. Following manual processing, the data were transformed into a data set that had 13,500 two-dimensional data. Nine deep learning algorithms including GoogleNet, InceptionResNetV2, InceptionV3, ResNet50, ResNet50V2, ResNet101, ResNet101V2, ResNet152 and ResNet152V2 were used to perform the data. Accuracy rates, confusion matrix, ROC curve, AUC, number of model parameters and training times were used to assess the efficacy of these algorithms. These 9 deep learning algorithms achieved training accuracy rates of 100%, 99.3%, 89.3%, 99.2%, 99.1%, 99.5%, 99.4%, 99.5%, 98.9%, test accuracy rates of 98.3%, 97.5%, 94.8%, 85.4%, 92.5%, 80.7%, 93.6%, 93.2%, 99.3%, area under the curve (AUC) values of 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00. When used to identify implants, all nine algorithms perform satisfactorily, with ResNet152V2 achieving the highest test accuracy, classification accuracy, confusion matrix area under the curve, and receiver operating characteristic curve area under the curve area. The results showed that the ResNet152V2 has the best classification effect on identifying implants. The artificial intelligence identification system and application software based on this algorithm can efficiently and accurately identify the brands and specifications of 27 classified implants through processed 3D CBCT images in vitro, with high stability and low recognition cost.
Identification of cuproptosis-related gene SLC31A1 and upstream LncRNA-miRNA regulatory axis in breast cancer
Authors: Wu Jia-hao , Cheng Tian-cheng , Zhu Bei , Gao Hai-yan , Zheng Lin , Chen Wei-xian 
Published: October 2023

AbstractMounting evidence indicate that cuproptosis, a novel form of programmed cell death, contributes to cancer development and progression. However, a comprehensive analysis regarding the expressions, functions, and regulatory network of cuproptosis-related genes is still lacking. In the present work, cuproptosis-related genes, upstream miRNAs and lncRNAs, and clinical data of breast cancer from TCGA database were analyzed by R language including Cox regression analysis, correlation calculation, ROC curve construction, and survival evaluation, and were further verified by public-available databases. Chemosensitivity and immune infiltration were also evaluated by online tools. SLC31A1 was significantly increased in breast cancer samples than those in normal tissues. SLC31A1 was negatively related to a favorable outcome in breast cancer, and the AUC value increased with the prolongation of follow-up time. LINC01614 and miR-204-5p were potential upstream regulators of SLC31A1. Moreover, SLC31A1 was significantly positively correlated with different immune cells infiltration, immune cell biomarkers, and immune checkpoints in breast cancer. SLC31A1 was a potential cuproptosis-related gene in breast cancer, which was significantly upregulated and was able to predict diagnosis, prognosis, chemosensitivity, and immune infiltration. LINC01640/miR-204-5p/SLC31A1 might be a significant and promising axis during cuproptosis in breast cancer.
Mindfulness-based randomized controlled trials led to brain structural changes: an anatomical likelihood meta-analysis
Authors: Siew Savannah , Yu Junhong 
Published: October 2023

AbstractMindfulness has become increasingly popular and the practice presents in many different forms. Research has been growing extensively with benefits shown across various outcomes. However, there is a lack of consensus over the efficacy of randomized controlled mindfulness interventions, both traditional and mind–body formats. This study aimed to investigate the structural brain changes in mindfulness-based interventions through a meta-analysis. Scopus, PubMed, Web of Science, and PsycINFO were searched up to April 2023. 11 studies (n = 581) assessing whole-brain voxel-based grey matter or cortical thickness changes after a mindfulness RCT were included. Anatomical likelihood estimation was used to carry out voxel-based meta-analysis with leave-one-out sensitivity analysis and behavioural analysis as follow-ups. One significant cluster (p < 0.001, Z = 4.76, cluster size = 632 mm3) emerged in the right insula and precentral gyrus region (MNI = 48, 10, 4) for structural volume increases in intervention group compared to controls. Behavioural analysis revealed that the cluster was associated with mental processes of attention and somesthesis (pain). Mindfulness interventions have the ability to affect neural plasticity in areas associated with better pain modulation and increased sustained attention. This further cements the long-term benefits and neuropsychological basis of mindfulness-based interventions.
Serum 25-hydroxyvitamin D level is associated with short-term glycemic variability metrics derived from continuous glucose monitoring in T2DM
Authors: Zhao Guohong , Yu Xinwen , Wang Lin , Jin Yuxin , Yang Aili , Sun Fei , Wang Xin , Jing Xiaorui , Gao Bin 
Published: October 2023

AbstractThis study aims to investigate the association between 25-hydroxyvitamin D (25OHD) and continuous glucose monitoring-assessed short-term glycemic variability (GV) and HbA1c among patients with type 2 diabetes mellitus (T2DM). We conducted a cross-sectional study recruiting 325 patients. The association between 25OHD and GV metrics (mean amplitude of glycemic excursions [MAGE], coefficient of variation [CV], standard deviation of sensor glucose [SD], and TIR) and HbA1c were analyzed using multivariable linear and logistic regression analyses. The 25OHD level and GV metrics showed significant differences among HbA1c groups (P < 0.01). CV, MAGE, SD and HbA1c decreased, and TIR increased with ascending 25OHD tertiles (P < 0.05). Serum 25OHD was inversely associated with CV (β = − 0.211 [− 0.350 to − 0.071], P < 0.01) and HbA1c (β = − 0.061 [− 0.114 to − 0.031], P < 0.01), and further multivariable analyses confirmed these results (P < 0.05). However, no association of HbA1c and 25OHD was found with the highest tertile of CV. These findings revealed that increased GV and HbA1c were both associated with lower 25OHD, and the relationship between HbA1c and 25OHD was attenuated with higher glucose CV in T2DM. Taken together, the analyses suggest that increasing vitamin D status has effects on improvements in long-term glycemic control and low glycemic variability.
Quantification of human mature frataxin protein expression in nonhuman primate hearts after gene therapy
Authors: Rojsajjakul Teerapat , Hordeaux Juliette J. , Choudhury Gourav R. , Hinderer Christian J. , Mesaros Clementina , Wilson James M. , Blair Ian A. 
Published: October 2023

AbstractDeficiency in human mature frataxin (hFXN-M) protein is responsible for the devastating neurodegenerative and cardiodegenerative disease of Friedreich’s ataxia (FRDA). It results primarily through epigenetic silencing of the FXN gene by GAA triplet repeats on intron 1 of both alleles. GAA repeat lengths are most commonly between 600 and 1200 but can reach 1700. A subset of approximately 3% of FRDA patients have GAA repeats on one allele and a mutation on the other. FRDA patients die most commonly in their 30s from heart disease. Therefore, increasing expression of heart hFXN-M using gene therapy offers a way to prevent early mortality in FRDA. We used rhesus macaque monkeys to test the pharmacology of an adeno-associated virus (AAV)hu68.CB7.hFXN therapy. The advantage of using non-human primates for hFXN-M gene therapy studies is that hFXN-M and monkey FXN-M (mFXN-M) are 98.5% identical, which limits potential immunologic side-effects. However, this presented a formidable bioanalytical challenge in quantification of proteins with almost identical sequences. This could be overcome by the development of a species-specific quantitative mass spectrometry-based method, which has revealed for the first time, robust transgene-specific human protein expression in monkey heart tissue. The dose response is non-linear resulting in a ten-fold increase in monkey heart hFXN-M protein expression with only a three-fold increase in dose of the vector.
International maritime regulation decreases sulfur dioxide but increases nitrogen oxide emissions in the North and Baltic Sea
Authors: Van Roy Ward , Van Roozendael Benjamin , Vigin Laurence , Van Nieuwenhove Annelore , Scheldeman Kobe , Merveille Jean-Baptiste , Weigelt Andreas , Mellqvist Johan , Van Vliet Jasper , van Dinther Danielle , Beecken Jorg , Tack Frederik , Theys Nicolas , Maes Frank 
Published: October 2023

AbstractSulfur dioxide and nitrogen oxide emissions from shipping have been regulated internationally for more than fifteen years. Emissions reduction from shipping provides benefits for human health and the environment, but the effectiveness of regulations in reducing ship emissions is less well understood. Here, we examine how the establishment of European Emission Control Areas and other international maritime regulations in the North and Baltic Seas affect sulfur dioxide and nitrogen oxide emissions in the region. We combine and analyze more than 110,000 ship plume measurements, inspection results, and satellite data from 2018 to 2022. We find that compliance rates for sulfur emissions are higher near ports than in open waters. However, the regulations did not affect the concentration of nitrogen oxide emissions, which increased in the past three years. These findings highlight the need for enhanced emission regulations that improve air quality.