bluuebunny/crossref_metadata_2025_split huggingface dataset:
Defining the threshold: triglyceride to high-density lipoprotein cholesterol (TG/HDL-C) ratio’s non-linear impact on tubular atrophy in primary membranous nephropathy
Authors: Guan Mijie , Wu Liling , Cheng Yuan , Qi Dongli , Chen Jia , Song Haiying , Hu Haofei , Wan Qijun 
Published: January 2024

BackgroundHyperlipidemia is common in primary membranous nephropathy (PMN) patients, and tubular atrophy (TA) is an unfavorable prognostic factor. However, the correlation between the triglyceride to high-density lipoprotein cholesterol (TG/HDL-C) ratio and TA is controversial. Therefore, our study aimed to investigate the association between the TG/HDL-C ratio and TA in PMN patients.MethodsWe conducted a cross-sectional study and collected data from 363 PMN patients at Shenzhen Second People’s Hospital from January 2008 to April 2023. The primary objective was to evaluate the independent correlation between the TG/HDL-C ratio and TA using binary logistic regression model. We used a generalized additive model along with smooth curve fitting and multiple sensitivity analyses to explore the relationship between these variables. Additionally, subgroup analyses were conducted to delve deeper into the results.ResultsOf the 363 PMN patients, 75 had TA (20.66%). The study population had a mean age of 46.598 ± 14.462 years, with 217 (59.78%) being male. After adjusting for sex, age, BMI, hypertension, history of diabetes, smoking, alcohol consumption, UPRO, eGFR, HB, FPG, and ALB, we found that the TG/HDL-C ratio was an independent risk factor for TA in PMN patients (OR=1.29, 95% CI: 1.04, 1.61, P=0.0213). A non-linear correlation was observed between the TG/HDL-C ratio and TA, with an inflection point at 4.25. The odds ratios (OR) on the left and right sides of this inflection point were 1.56 (95% CI: 1.17, 2.07) and 0.25 (95% CI: 0.04, 1.54), respectively. Sensitivity analysis confirmed these results. Subgroup analysis showed a consistent association between the TG/HDL-C ratio and TA, implying that factors such as gender, BMI, age, UPRO, ALB, hypertension and severe nephrotic syndrome had negligible effects on the link between the TG/HDL-C ratio and TA.ConclusionOur study demonstrates a non-linear positive correlation between the TG/HDL-C ratio and the risk of TA in PMN patients, independent of other factors. Specifically, the association is more pronounced when the ratio falls below 4.25. Based on our findings, it would be advisable to decrease the TG/HDL-C ratio below the inflection point in PMN patients as part of treatment strategies.
More complex than expected—mapping activities and youths’ experiences at BioBlitz events to the rosette model of science communication
Authors: Lorke Julia , Ballard Heidi L. , Robinson Lucy D. 
Published: January 2024

Deficit, dialogue, or participation—which of these three main models of science communications is the best fit to describe activities and experiences of citizen science? One might assume that participation is the best match, but the reality of citizen science events is more complex. The rosette model of science communication offers a more detailed set of subcategories, e.g., educate, entertain, or do, in addition to the three main models—deficit, dialogue and participation. To systematically describe citizen science activities and experiences, we apply data on what activities are offered and what young people (5–19 years old) experience when participating in a citizen science event format called BioBlitzes across the rosette model. The mapping results illustrate how the rosette model can help to make citizen science project designers and practitioners more aware of the various modes of science communications that they may encounter at BioBlitz events and inform their design decisions regarding how settings can shape participants’ experiences.
Endometrial DNA methylation signatures during the time of breeding in relation to the pregnancy outcome in postpartum dairy cows fed a control diet or supplemented with rumen-protected methionine
Authors: Salilew-Wondim Dessie , Tholen Ernst , Held-Hoelker Eva , Shellander Karl , Blaschka Carina , Drillich Marc , Iwersen Michael , Suess David , Gebremedhn Samuel , Tesfaye Dawit , Parys Claudia , Helmbrecht Ariane , Guyader Jessie , Miskel Dennis , Trakooljul Nares , Wimmers Klaus , Hoelker Michael 
Published: January 2024

Post calving metabolic stress reduces the fertility of high producing dairy cows possibly by altering the expression of genes in the maternal environment via epigenetic modifications. Therefore, this study was conducted to identify endometrial DNA methylation marks that can be associated with pregnancy outcomes in postpartum cows at the time of breeding. For this, twelve days post-calving, cows were either offered a control diet or supplemented daily with rumen-protected methionine. Cows showing heat 50–64 days postpartum were artificially inseminated. Endometrial cytobrush samples were collected 4–8 h after artificial insemination and classified based on the pregnancy out comes as those derived from cows that resulted in pregnancy or resulted in no pregnancy. The DNAs isolated from endometrial samples were then subject to reduced representative bisulfite sequencing for DNA methylation analysis. Results showed that in the control diet group, 1,958 differentially methylated CpG sites (DMCGs) were identified between cows that resulted in pregnancy and those that resulted in no pregnancy of which 890 DMCGs were located on chr 27: 6217254–6225600 bp. A total of 537 DMCGs were overlapped with 313 annotated genes that were involved in various pathways including signal transduction, signalling by GPCR, aldosterone synthesis and secretion. Likewise, in methionine supplemented group, 3,430 CpG sites were differentially methylated between the two cow groups of which 18.7% were located on Chr27: 6217254–6225600 bp. A total of 1,781 DMCGS were overlapped with 890 genes which involved in developmental and signalling related pathways including WNT-signalling, focal adhesion and ECM receptor interaction. Interestingly, 149 genes involved in signal transduction, axon guidance and non-integrin membrane-ECM interactions were differentially methylated between the two cow groups irrespective of their feeding regime, while 453 genes involved in axon guidance, notch signalling and collagen formation were differentially methylated between cows that received rumen protected methionine and control diet irrespective of their fertility status. Overall, this study indicated that postpartum cows that could potentially become pregnant could be distinguishable based on their endometrial DNA methylation patterns at the time of breeding.
Topical antifungal keratitis therapeutic potential of Clitoria ternatea Linn. flower extract: phytochemical profiling, in silico modelling, and in vitro biological activity assessment
Authors: Yolin Angel Poomany Arul Soundara Rajan , Jeyakumar Palanisamy , Jasmin Suriya Arul Raj , Sheena Aliyas , Karuppiah Ponmurugan , Periyasami Govindasami , Stalin Antony , Murugan Kasi 
Published: January 2024

IntroductionFungal keratitis (FK) poses a severe threat to vision, potentially leading to blindness if not promptly addressed. Clitoria ternatea flower extracts have a history of use in Ayurvedic and Indian traditional medicines, particularly for treating eye ailments. This study investigates the antifungal and antibiofilm effects of Clitoria ternatea flower extracts on the FK clinical isolate Coniochaeta hoffmannii. Structural details and key compound identification were analysed through FTIR and GC-MS.MethodsThe minimum inhibitory concentration (MIC) and minimum fungicidal concentration (MFC) of Clitoria ternatea flower extracts were determined using broth dilution and well plate techniques. Biofilm inhibitory activity was assessed through microscopic evaluation, while anti-irritant and cytotoxic properties were evaluated using CAE-EI and MTT assays. Through GC-MS and FT-IR analysis the compounds dissolved in the extract and their functional group were studied, and their toxicity screening and pharmacokinetic prediction were conducted in silico. Subsequently, compounds with high corneal permeability were further identified, and molecular docking and simulation studies at 150 ns were used to investigate their interactions with fungal virulence factors and human inflammatory proteins.Results and DiscussionAt a concentration of 250 µg/mL, the Clitoria ternatea flower extract displayed effective biofilm inhibition. MIC and MFC values were determined as 500 and 1000 µg/mL, respectively. CAE-EI and MTT assays indicated no significant irritant and cytotoxic effects up to a concentration of 3 mg/mL. Compounds like 9,9-dimethoxybicyclo[3.3.1]nonane-2,4-dione showed high corneal permeability with strong and stable interactions with fungal virulence cellobiose dehydrogenase, endo β 1,4 xylanase, and glucanase, as well as corneal inflammation-associated human TNF-α and Interleukin IL-1b protein targets. The findings indicate that extracts from C. ternatea flowers could be formulated for an effective and safe alternative for developing new topical FK therapeutics.
Identification of L11L and L7L as virulence-related genes in the African swine fever virus genome
Authors: Fan Jiaqi , Zhang Jingyuan , Wang Fengjie , Miao Faming , Zhang Han , Jiang Yiqian , Qi Yu , Zhang Yanyan , Hui Lili , Zhang Dan , Yue Huixian , Zhou Xintao , Li Qixuan , Wang Yu , Chen Teng , Hu Rongliang 
Published: January 2024

IntroductionAfrican swine fever (ASF) is an infectious disease that causes considerable economic losses in pig farming. The agent of this disease, African swine fever virus (ASFV), is a double-stranded DNA virus with a capsid membrane and a genome that is 170-194 kb in length encoding over 150 proteins. In recent years, several live attenuated strains of ASFV have been studied as vaccine candidates, including the SY18ΔL7-11. This strain features deletion of L7L, L8L, L9R, L10L and L11L genes and was found to exhibit significantly reduced pathogenicity in pigs, suggesting that these five genes play key roles in virulence.MethodsHere, we constructed and evaluated the virulence of ASFV mutations with SY18ΔL7, SY18ΔL8, SY18ΔL9, SY18ΔL10, and SY18ΔL11L.ResultsOur findings did not reveal any significant differences in replication efficiency between the single-gene deletion strains and the parental strains. Pigs inoculated with SY18ΔL8L, SY18ΔL9R and SY18ΔL10L exhibited clinical signs similar to those inoculated with the parental strains. Survival rate of pigs inoculated with 103.0TCID50 of SY18ΔL7L was 25%, while all pigs inoculated with 103.0TCID50 of SY18ΔL11L survived, and 50% inoculated with 106.0TCID50 SY18ΔL11L survived.DiscussionThe results indicate that L8L, L9R and L10L do not affect ASFV SY18 virulence, while the L7L and L11L are associated with virulence.
Predictors for unfavorable prognosis after stroke with perforator artery disease
Authors: Song Linghua , Lou Xiaoli , Han Wenhao , Yang Lihui , Guo Siping , Jiang Yasi , Peng Hao , Hao Yonggang 
Published: January 2024

Background and purposePerforator artery disease (PAD) is an important subtype of ischemic stroke. The risk factors affecting the prognosis of patients with PAD are unclear. This study aimed to investigate the risk factors affecting the unfavorable prognosis of PAD.MethodsPatients with PAD were enrolled from Dushu Lake Hospital Affiliated to Soochow University and diagnosed as stroke with PAD during the period from September 2021 to July 2023 and followed up with a modified Rankin Scale (mRS) after 90 days, defining the mRS of 0–2 as a group with favorable prognosis, and 3–6 as a group with unfavorable functional outcome. Logistic regression was used to identify predictors for PAD. Multiple logistic regression analysis and receiver operating characteristics (ROC) were used to identify predictors of unfavorable prognosis.ResultsOf the 181 enrolled patients, 48 (26.5%) were identified with unfavorable prognosis. On multivariate analysis, increased age (OR = 1.076, 95% CI: 1.012 ~ 1.144, p = 0.019), higher National Institutes of Health Stroke Scale (NIHSS) score at admission (OR = 2.930, 95% CI: 1. 905 ~ 4.508, p &lt; 0.001), and increased neutrophil-to-lymphocyte ratio (NLR) (OR = 3.028, 95% CI: 1.615 ~ 5.675, p = 0.001) were independent risk factors for unfavorable prognosis in patients with PAD, and the area under the receiver operating characteristic curve was 0.590, 0.905, and 0.798, and the multi-factor diagnostic model (Model 2) showed reliable diagnostic specificity and sensitivity (area under the curve = 0.956, p &lt; 0.001, specificity 0.805, sensitivity 0.958, accuracy 0.845).ConclusionIncreased baseline NLR and NIHSS score and aging may be independent risk factors for unfavorable prognosis of patients with PAD. NLR can be used as a potential biological indicator to predict the prognosis of stroke with PAD.
Case report: Beneficial effects of visual cortex tDCS stimulation combined with visual training in patients with visual field defects
Authors: Lian Yanhua , Cheng Xiaoping , Chen Qunlin , Huang Libin , Xie Lili , Wang Wenzong , Ni Jun , Chen Xinyuan 
Published: January 2024

BackgroundVisual field defect (VFD) refers to the phenomenon that the eye is unable to see a certain area within the normal range of vision, which may be caused by eye diseases, neurological diseases and other reasons. Transcranial direct current stimulation (tDCS) is expected to be an effective treatment for the recovery or partial recovery of VFD. This paper describes the potential for tDCS in combination with visual retraining strategies to have a positive impact on vision recovery, and the potential for neuroplasticity to play a key role in vision recovery.MethodsThis case report includes two patients. Patient 1 was diagnosed with a right occipital hemorrhage and homonymous hemianopia. Patient 2 had multiple facial fractures, a contusion of the right eye, and damage to the optic nerve of the right eye, which was diagnosed as a peripheral nerve injury (optic nerve injury). We administered a series of treatments to two patients, including transcranial direct current stimulation; visual field restoration rehabilitation: paracentric gaze training, upper and lower visual field training, VR rehabilitation, and perceptual training. One time per day, 5 days per week, total 6 weeks.ResultsAfter 6 weeks of visual rehabilitation and tDCS treatment, Patient 1 Humphrey visual field examination showed a significant improvement compared to the initial visit, with a reduction in the extent of visual field defects, increased visual acuity, and improvement in most visual functions. Patient 2 had an expanded visual field, improved visual sensitivity, and substantial improvement in visual function.ConclusionOur case reports support the feasibility and effectiveness of tDCS combined with visual rehabilitation training in the treatment of occipital stroke and optic nerve injury settings.
The supplementation of a high dose of fish oil during pregnancy and lactation led to an elevation in Mfsd2a expression without any changes in docosahexaenoic acid levels in the retina of healthy 2-month-old mouse offspring
Authors: Macura Irena Jovanovic , Djuricic Ivana , Major Tamara , Milanovic Desanka , Sobajic Sladjana , Kanazir Selma , Ivkovic Sanja 
Published: January 2024

IntroductionDuring fetal development, the proper development of neural and visual systems relies on the maternal supplementation of omega-3 fatty acids through placental transfer. Pregnant women are strongly advised to augment their diet with additional sources of omega-3, such as fish oil (FO). This supplementation has been linked to a reduced risk of preterm birth, pre-eclampsia, and perinatal depression. Recently, higher doses of omega-3 supplementation have been recommended for pregnant women. Considering that omega-3 fatty acids, particularly docosahexaenoic acid (DHA), play a crucial role in maintaining the delicate homeostasis required for the proper functioning of the retina and photoreceptors the effects of high-dose fish oil (FO) supplementation during pregnancy and lactation on the retina and retinal pigmented epithelium (RPE) in healthy offspring warrant better understanding.MethodsThe fatty acid content and the changes in the expression of the genes regulating cholesterol homeostasis and DHA transport in the retina and RPE were evaluated following the high-dose FO supplementation.ResultsOur study demonstrated that despite the high-dose FO treatment during pregnancy and lactation, the rigorous DHA homeostasis in the retina and RPE of the two-month-old offspring remained balanced. Another significant finding of this study is the increase in the expression levels of major facilitator superfamily domain-containing protein (Mfsd2a), a primary DHA transporter. Mfsd2a also serves as a major regulator of transcytosis during development, and a reduction in Mfsd2a levels poses a major risk for the development of leaky blood vessels.ConclusionImpairment of the blood-retinal barrier (BRB) is associated with the development of numerous ocular diseases, and a better understanding of how to manipulate transcytosis in the BRB during development can enhance drug delivery through the BRB or contribute to the repair of central nervous system (CNS) barriers.
Breast cancer but not the menopausal status is associated with small changes of the gut microbiota
Authors: Zeber-Lubecka Natalia , Kulecka Maria , Jagiełło-Gruszfeld Agnieszka , Dąbrowska Michalina , Kluska Anna , Piątkowska Magdalena , Bagińska Katarzyna , Głowienka Maria , Surynt Piotr , Tenderenda Michał , Mikula Michał , Ostrowski Jerzy 
Published: January 2024

BackgroundPossible relationships between gut dysbiosis and breast cancer (BC) development and progression have been previously reported. However, the results of these metagenomics studies are inconsistent. Our study involved 88 patients diagnosed with breast cancer and 86 cancer-free control women. Participants were divided into groups based on their menopausal status. Fecal samples were collected from 47 and 41 pre- and postmenopausal newly diagnosed breast cancer patients and 51 and 35 pre- and postmenopausal controls, respectively. In this study, we performed shotgun metagenomic analyses to compare the gut microbial community between pre- and postmenopausal BC patients and the corresponding controls.ResultsFirstly, we identified 12, 64, 158, and 455 bacterial taxa on the taxonomy level of phyla, families, genera, and species, respectively. Insignificant differences of the Shannon index and β-diversity were found at the genus and species levels between pre- and postmenopausal controls; the differences concerned only the Chao index at the species level. No differences in α-diversity indexes were found between pre- and postmenopausal BC patients, although β-diversity differed these subgroups at the genus and species levels. Consistently, only the abundance of single taxa differed between pre- and postmenopausal controls and cases, while the abundances of 14 and 23 taxa differed or tended to differ between premenopausal cases and controls, and between postmenopausal cases and controls, respectively. There were similar differences in the distribution of enterotypes. Of 460 bacterial MetaCyc pathways discovered, no pathways differentiated pre- and postmenopausal controls or BC patients, while two and one pathways differentiated cases from controls in the pre- and postmenopausal subgroups, respectively.ConclusionWhile our findings did not reveal an association of changes in the overall microbiota composition and selected taxa with the menopausal status in cases and controls, they confirmed differences of the gut microbiota between pre- and postmenopausal BC patients and the corresponding controls. However, these differences were less extensive than those described previously.
Identification of colon cancer subtypes based on multi-omics data—construction of methylation markers for immunotherapy
Authors: Xu Benjie , Lian Jie , Pang Xiangyi , Gu Yue , Zhu Jiahao , Zhang Yan , Lu Haibo 
Published: January 2024

BackgroundBeing the most widely used biomarker for immunotherapy, the microsatellite status has limitations in identifying all patients who benefit in clinical practice. It is essential to identify additional biomarkers to guide immunotherapy. Aberrant DNA methylation is consistently associated with changes in the anti-tumor immune response, which can promote tumor progression. This study aims to explore immunotherapy biomarkers for colon cancers from the perspective of DNA methylation.MethodsThe related data (RNA sequencing data and DNA methylation data) were obtained from The Cancer Genome Atlas (TCGA) and UCSC XENA database. Methylation-driven genes (MDGs) were identified through the Pearson correlation analysis. Unsupervised consensus clustering was conducted using these MDGs to identify distinct clusters of colon cancers. Subsequently, we evaluated the immune status and predicted the efficacy of immunotherapy by tumor immune dysfunction and exclusion (Tide) score. Finally, The Quantitative Differentially Methylated Regions (QDMR) software was used to identify the specific DNA methylation markers within particular clusters.ResultsA total of 282 MDGs were identified by integrating the DNA methylation and RNA-seq data. Consensus clustering using the K-means algorithm revealed that the optimal number of clusters was 4. It was revealed that the composition of the tumor immune microenvironment (TIME) in Cluster 1 was significantly different from others, and it exhibited a higher level of tumor mutation burdens (TMB) and stronger anti-tumor immune activity. Furthermore, we identified three specific hypermethylation genes that defined Cluster 1 (PCDH20, APCDD1, COCH). Receiver operating characteristic (ROC) curves demonstrated that these specific markers could effectively distinguish Cluster 1 from other clusters, with an AUC of 0.947 (95% CI 0.903-0.990). Finally, we selected clinical samples for immunohistochemical validation.ConclusionIn conclusion, through the analysis of DNA methylation, consensus clustering of colon cancer could effectively identify the cluster that benefit from immunotherapy along with specific methylation biomarkers.