bluuebunny/crossref_metadata_2025_split huggingface dataset:
Costal Cartilage Graft Repair Osteochondral Defect in a Mouse Model
Authors: Pang Yidan , Ma Yiyang , Zheng Kaiwen , Zhu Siyuan , Sui Hongyu , Ren Hao , Liu Kang , Li Wei , Huang Yigang , Du Dajiang , Gao Junjie , Zhang Changqing 
Published: October 2023

Objective Osteochondral defects develop into osteoarthritis without intervention. Costal cartilage can be utilized as an alternative source for repairing osteochondral defect. Our previous clinical study has shown the successful osteochondral repair by costal cartilage graft with integration into host bone bed. In this study, we investigate how cartilaginous graft adapt to osteochondral environment and the mechanism of bone-cartilage interface formation. Design Costal cartilage grafting was performed in C57BL/6J mice and full-thickness osteochondral defect was made as control. 3D optical profiles and micro-CT were applied to evaluate the reconstruction of articular cartilage surface and subchondral bone as well as gait analysis to evaluate articular function. Histological staining was performed at 2, 4, and 8 weeks after surgery. Moreover, costal cartilage from transgenic mice with fluorescent markers were transplanted into wild-type mice to observe the in vivo changes of costal chondrocytes. Results At 8 weeks after surgery, 3D optical profiles and micro-CT showed that in the graft group, the articular surface and subchondral bone were well preserved. Gait analysis and International Cartilage Repair Society (ICRS) score evaluation showed a good recovery of joint function and histological repair in the graft group. Safranin O staining showed the gradual integration of graft and host tissue. Costal cartilage from transgenic mice with fluorescent markers showed that donor-derived costal chondrocytes turned into osteocytes in the subchondral area of host femur. Conclusion Costal cartilage grafting shows both functional and histological repair of osteochondral defect in mice. Graft-derived costal chondrocytes differentiate into osteocytes and contribute to endochondral ossification.
Risk factors for delayed sputum conversion: A qualitative case study from the person-in-charge of TB program’s perspectives
Authors: Wardani Dyah Wulan Sumekar Rengganis , Pramesona Bayu Anggileo , Septiana Trisya , Soemarwoto Retno Ariza Soeprihatini 
Published: October 2023

Background: One of the indicators to determine the success of TB treatment is the conversion of sputum from smear positive to negative. However, several factors can lead to this failure of sputum conversion. Objectives: To investigate the risk factors for delayed sputum conversion from the person-in-charge (PIC) of the TB program’s perspective. Design and methods: This qualitative case study was conducted on September 7th, 2022. Thirty-one PICs of the TB program from 31 public health centers ( Puskesmas) in Bandar Lampung, Indonesia, were recruited purposively. All participants were grouped into three FGDs. Developed semi-structured interview questions were used for data collection. Thematic analysis was used to synthesize and cross-reference emerging topics. Results: Three themes emerged in our study: (1) individual factors with the sub-themes of medication adherence, education, initial laboratory examination, comorbid disease, nutrition, and lifestyle; (2) environmental factors with the sub-themes of types of support, sources of support, environmental conditions and stigma; and (3) health service factors with the sub-theme of access to health service facilities. Conclusions: Problems related to TB management are not only the individual's responsibility but need to strengthen support from the environment and health services.
Experiences of Implementing Rooming-in Practice for First-Time Mothers in a Postpartum Care Center
Authors: Wu Hsiao-Ling , Lu Der-Fa , Tsay Pei-Kwei 
Published: October 2023

Introduction Practices promoted by the Baby-Friendly Hospital Initiative have become a part of the current mainstream postpartum infant care. However, adherence to rooming-in practice by health-care facilities is lower than that of other steps under this initiative. Objective The aim of this study was to investigate the experiences in implementing the rooming-in policy among first-time mothers at a postpartum center. Methods The present study is a qualitative research conducted using the descriptive phenomenological method. This study was performed at a postpartum care center in Southern Taiwan between August 2018 and December 2018. Semi-structured interviews were conducted with 20 postpartum mothers during their postpartum care center stay. Results Based on interview data, this study identified three main themes about implementing full-time rooming-in experiences: (a) against the rule of taking plenty of rest during the postpartum period, (b) negative experiences and myths regarding implementing rooming-in experience, and (c) postpartum care centers service content affect first-time mothers’ willingness to implement rooming-in. Conclusions In postpartum care centers, first-time mothers’ willingness to implement full-time rooming-in significantly decreases due to the effects of the “doing-the-month” culture, postpartum physical recovery status, stress of the rooming-in experience, myths regarding rooming-in practice, trusting professional neonate care services more than own care, and attitude toward payment for services.
Fibroblast growth factor 10 reverses cigarette smoke- and elastase-induced emphysema and pulmonary hypertension in mice
Authors: Hadzic Stefan , Wu Cheng-Yu , Gredic Marija , Pak Oleg , Loku Edma , Kraut Simone , Kojonazarov Baktybek , Wilhelm Jochen , Brosien Monika , Bednorz Mariola , Seimetz Michael , Günther Andreas , Kosanovic Djuro , Sommer Natascha , Warburton David , Li Xiaokun , Grimminger Friedrich , Ghofrani Hossein A. , Schermuly Ralph T. , Seeger Werner , El Agha Elie , Bellusci Saverio , Weissmann Norbert 
Published: October 2023

BackgroundCOPD is an incurable disease and a leading cause of death worldwide. In mice, fibroblast growth factor (FGF)10 is essential for lung morphogenesis, and in humans, polymorphisms in the humanFGF10gene correlate with an increased susceptibility to develop COPD.MethodsWe analysed FGF10 signalling in human lung sections and isolated cells from healthy donor, smoker and COPD lungs. The development of emphysema and PH was investigated inFgf10+/−andFgfr2b+/−(FGF receptor 2b) mice upon chronic exposure to cigarette smoke. In addition, we overexpressed FGF10 in mice following elastase- or cigarette smoke-induced emphysema and pulmonary hypertension (PH).ResultsWe found impaired FGF10 expression in human lung alveolar walls and in primary interstitial COPD lung fibroblasts. In contrast, FGF10 expression was increased in large pulmonary vessels in COPD lungs. Consequently, we identified impaired FGF10 signalling in alveolar walls as an integral part of the pathomechanism that leads to emphysema and PH development: mice with impaired FGF10 signalling (Fgf10+/−andFgfr2b+/−) spontaneously developed lung emphysema, PH and other typical pathomechanistic features that generally arise in response to cigarette smoke exposure.ConclusionIn a therapeutic approach, FGF10 overexpression successfully restored lung alveolar and vascular structure in mice with established cigarette smoke- and elastase-induced emphysema and PH. FGF10 treatment triggered an initial increase in the number of alveolar type 2 cells that gradually returned to the basal level when the FGF10-mediated repair process progressed. Therefore, the application of recombinant FGF10 or stimulation of the downstream signalling cascade might represent a novel therapeutic strategy in the future.
Utility of rehabilitation prior to bronchoscopic lung volume reduction:post hocanalysis of the VENT trial
Authors: Brock Judith Maria , Kontogianni Konstantina , Sciurba Frank C. , Criner Gerard J. , Herth Felix 
Published: October 2023

Background and objectiveRehabilitation programmes are a valuable treatment modality for patients with COPD to increase exercise capacity and quality of life. The utility of pulmonary rehabilitation prior to bronchoscopic lung volume reduction (BLVR) is unclear.MethodsWe performed apost hocanalysis of the Valve for Emphysema Palliation Trial (VENT) trial, the first multicentre randomised trial comparing the safety and efficacy of BLVR. Patients completed a pulmonary rehabilitation programme prior to BLVR over 6–10 weeks and maintained by daily practice, consisting of endurance training, strength training and upper/lower limb exercise. Lung function and exercise parameters (6-min walk distance (6MWD)) were assessed before and after rehabilitation and we tried to identify predictors for pulmonary rehabilitation benefit.ResultsLung function and exercise capacity of 403 patients (mean±sdage 63.3±7.4 years, 37.5% female, mean±sdforced expiratory volume in 1 s 30.1±7.6 L) were analysed. Exercise capacity significantly improved from 331.6±98.8 m to 345.6±95.3 m (p<0.001) in 6-min walk testing (6MWT), with 40.3% showing clinically meaningful improvements. Patients also experienced less dyspnoea after 6MWT, while pulmonary function parameters did not change significantly overall. Patients with lower exercise capacity at screening (6MWD <250 m) benefited more from pulmonary rehabilitation. The indication and prerequisites for BLVR were still present in all patients after pulmonary rehabilitation.ConclusionThe national mandatory requirements for rehabilitation prior to BLVR, which apply to all COPD patients, should be reconsidered and specified for COPD patients who really benefit.
The role of red ginseng in men’s reproductive health: a literature review
Authors: Wang Hao , Zhang Jiwei , Ma Dongyue , Zhao Ziwei , Yan Bin , Wang Fu 
Published: October 2023

Abstract
Background
Red ginseng (RG) is a traditional herb commonly used in China, Korea, and other East Asian countries. Recently, it has demonstrated a better clinical value in men’s reproductive health (MRH). The present review aimed to examine the effects of RG treatment on MRH.

Results
Overall, 42 articles related to RG application in MRH were reviewed, of which 31 were animal experiments and 11 were clinical studies. Furthermore, this review analyzed the use of RG in some male reproductive diseases in clinical trials and determined the associated mechanisms of action. The mechanism of action of RG in MRH may be related to oxidative stress, regulation of sex hormones and spermatogenesis-related proteins, and anti-inflammation.

Conclusions
The application of RG for the treatment of male infertility, erectile dysfunction, and prostate diseases has the potential to contribute to MRH.
Deep learning, radiomics and radiogenomics applications in the digital breast tomosynthesis: a systematic review
Authors: Hussain Sadam , Lafarga-Osuna Yareth , Ali Mansoor , Naseem Usman , Ahmed Masroor , Tamez-Peña Jose Gerardo 
Published: October 2023

Abstract
Background
Recent advancements in computing power and state-of-the-art algorithms have helped in more accessible and accurate diagnosis of numerous diseases. In addition, the development of de novo areas in imaging science, such as radiomics and radiogenomics, have been adding more to personalize healthcare to stratify patients better. These techniques associate imaging phenotypes with the related disease genes. Various imaging modalities have been used for years to diagnose breast cancer. Nonetheless, digital breast tomosynthesis (DBT), a state-of-the-art technique, has produced promising results comparatively. DBT, a 3D mammography, is replacing conventional 2D mammography rapidly. This technological advancement is key to AI algorithms for accurately interpreting medical images.

Objective and methods
This paper presents a comprehensive review of deep learning (DL), radiomics and radiogenomics in breast image analysis. This review focuses on DBT, its extracted synthetic mammography (SM), and full-field digital mammography (FFDM). Furthermore, this survey provides systematic knowledge about DL, radiomics, and radiogenomics for beginners and advanced-level researchers.

Results
A total of 500 articles were identified, with 30 studies included as the set criteria. Parallel benchmarking of radiomics, radiogenomics, and DL models applied to the DBT images could allow clinicians and researchers alike to have greater awareness as they consider clinical deployment or development of new models. This review provides a comprehensive guide to understanding the current state of early breast cancer detection using DBT images.

Conclusion
Using this survey, investigators with various backgrounds can easily seek interdisciplinary science and new DL, radiomics, and radiogenomics directions towards DBT.
Telomere and subtelomere high polymorphism might contribute to the specificity of homologous recognition and pairing during meiosis in barley in the context of breeding
Authors: Serrano-León I. M. , Prieto P. , Aguilar M. 
Published: October 2023

AbstractBarley (Hordeum vulgare) is one of the most popular cereal crops globally. Although it is a diploid species, (2n = 2x = 14) the study of its genome organization is necessary in the framework of plant breeding since barley is often used in crosses with other cereals like wheat to provide them with advantageous characters. We already have an extensive knowledge on different stages of the meiosis, the cell division to generate the gametes in species with sexual reproduction, such as the formation of the synaptonemal complex, recombination, and chromosome segregation. But meiosis really starts with the identification of homologous chromosomes and pairing initiation, and it is still unclear how chromosomes exactly choose a partner to appropriately pair for additional recombination and segregation. In this work we present an exhaustive molecular analysis of both telomeres and subtelomeres of barley chromosome arms 2H-L, 3H-L and 5H-L. As expected, the analysis of multiple features, including transposable elements, repeats, GC content, predicted CpG islands, recombination hotspots, G4 quadruplexes, genes and targeted sequence motifs for key DNA-binding proteins, revealed a high degree of variability both in telomeres and subtelomeres. The molecular basis for the specificity of homologous recognition and pairing occurring in the early chromosomal interactions at the start of meiosis in barley may be provided by these polymorphisms. A more relevant role of telomeres and most distal part of subtelomeres is suggested.
Transcriptome analysis reveals a lncRNA-miRNA-mRNA regulatory network in OsRpp30-mediated disease resistance in rice
Authors: Li Minghua , Li Wei , Zhao Meixia , Li Zhiqiang , Wang Guo-Liang , Liu Wende , Liang Chun 
Published: October 2023

Abstract
Background
Long non-coding RNAs (lncRNAs) play critical roles in various biological processes in plants. Extensive studies utilizing high-throughput RNA sequencing have revealed that many lncRNAs are involved in plant disease resistance. Oryza sativa RNase P protein 30 (OsRpp30) has been identified as a positive regulator of rice immunity against fungal and bacterial pathogens. Nevertheless, the specific functions of lncRNAs in relation to OsRpp30-mediated disease resistance in rice remain elusive.

Results
We conducted a comprehensive analysis of lncRNAs, miRNAs, and mRNAs expression patterns in wild type (WT), OsRpp30 overexpression (OsRpp30-OE), and OsRpp30 knockout (OsRpp30-KO) rice plants. In total, we identified 91 differentially expressed lncRNAs (DElncRNAs), 1671 differentially expressed mRNAs (DEmRNAs), and 41 differentially expressed miRNAs (DEmiRNAs) across the different rice lines. To gain further insights, we investigated the interaction between DElncRNAs and DEmRNAs, leading to the discovery of 10 trans- and 27 cis-targeting pairs specific to the OsRpp30-OE and OsRpp30-KO samples. In addition, we constructed a competing endogenous RNA (ceRNA) network comprising differentially expressed lncRNAs, miRNAs, and mRNAs to elucidate their intricate interplay in rice disease resistance. The ceRNA network analysis uncovered a set of gene targets regulated by lncRNAs and miRNAs, which were found to be involved in pathogen recognition, hormone pathways, transcription factor activation, and other biological processes related to plant immunity.

Conclusions
Our study provides a comprehensive expression profiling of lncRNAs, miRNAs, and mRNAs in a collection of defense mutants in rice. To decipher the putative functional significance of lncRNAs, we constructed trans- and cis-targeting networks involving differentially expressed lncRNAs and mRNAs, as well as a ceRNA network incorporating differentially expressed lncRNAs, miRNAs, and mRNAs. Together, the findings from this study provide compelling evidence supporting the pivotal roles of lncRNAs in OsRpp30-mediated disease resistance in rice.
Paralemnalia thyrsoides-associated fungi: phylogenetic diversity, cytotoxic potential, metabolomic profiling and docking analysis
Authors: Taher Mohie el-dien Radwa , Mahmoud Basma Khalaf , Abdelwahab Miada F. , Khedr Amgad I. M. , Kamel Mohamed Salah , Yahia Ramadan , Mohamed Nada M. , Zawily Amr El , Kamel Eman S. , Salem Aliasger K , Abdelmohsen Usama Ramadan , Fouad Mostafa A. 
Published: October 2023

Abstract
Background
Cancer continues to be one of the biggest causes of death that affects human health. Chemical resistance is still a problem in conventional cancer treatments. Fortunately, numerous natural compounds originating from different microbes, including fungi, possess cytotoxic characteristics that are now well known. This study aims to investigate the anticancer prospects of five fungal strains that were cultivated and isolated from the Red Sea soft coral Paralemnalia thyrsoides. The in vitro cytotoxic potential of the ethyl acetate extracts of the different five isolates were evaluated using MTS assay against four cancer cell lines; A549, CT-26, MDA-MB-231, and U87. Metabolomics profiling of the different extracts using LC-HR-ESI-MS, besides molecular docking studies for the dereplicated compounds were performed to unveil the chemical profile and the cytotoxic mechanism of the soft coral associated fungi.

Results
The five isolated fungal strains were identified as Penicillium griseofulvum (RD1), Cladosporium sphaerospermum (RD2), Cladosporium liminiforme (RD3), Penicillium chrysogenum (RD4), and Epicoccum nigrum (RD5). The in vitro study showed that the ethyl acetate extract of RD4 exhibited the strongest cytotoxic potency against three cancer cell lines A549, CT-26 and MDA-MB-231 with IC50 values of 1.45 ± 8.54, 1.58 ± 6.55 and 1.39 ± 2.0 µg/mL, respectively, also, RD3 revealed selective cytotoxic potency against A549 with IC50 value of 6.99 ± 3.47 µg/mL. Docking study of 32 compounds dereplicated from the metabolomics profiling demonstrated a promising binding conformation with EGFR tyrosine kinase that resembled its co-crystallized ligand albeit with better binding energy score.

Conclusion
Our results highlight the importance of soft coral-associated fungi as a promising source for anticancer metabolites for future drug discovery.
Elimination of blaKPC−2-mediated carbapenem resistance in Escherichia coli by CRISPR-Cas9 system
Authors: Tao Shuan , Chen Huimin , Li Na , Fang Yewei , Zhang He , Xu Yao , Chen Luyan , Liang Wei 
Published: October 2023

Abstract
Objective
The purpose of this study is to re-sensitive bacteria to carbapenemases and reduce the transmission of the blaKPC−2 gene by curing the blaKPC−2-harboring plasmid of carbapenem-resistant using the CRISPR-Cas9 system.

Methods
The single guide RNA (sgRNA) specifically targeted to the blaKPC−2 gene was designed and cloned into plasmid pCas9. The recombinant plasmid pCas9-sgRNA(blaKPC−2) was transformed into Escherichia coli (E.coli) carrying pET24-blaKPC−2. The elimination efficiency in strains was evaluated by polymerase chain reaction (PCR) and quantitative real-time PCR (qPCR). Susceptibility testing was performed by broth microdilution assay and by E-test strips (bioMérieux, France) to detect changes in bacterial drug resistance phenotype after drug resistance plasmid clearance.

Results
In the present study, we constructed a specific prokaryotic CRISPR-Cas9 system plasmid targeting cleavage of the blaKPC−2 gene. PCR and qPCR results indicated that prokaryotic CRISPR-Cas9 plasmid transforming drug-resistant bacteria can efficiently clear blaKPC−2-harboring plasmids. In addition, the drug susceptibility test results showed that the bacterial resistance to imipenem was significantly reduced and allowed the resistant model bacteria to restore susceptibility to antibiotics after the blaKPC−2-containing drug-resistant plasmid was specifically cleaved by the CRISPR-Cas system.

Conclusion
In conclusion, our study demonstrated that the one plasmid-mediated CRISPR-Cas9 system can be used as a novel tool to remove resistance plasmids and re-sensitize the recipient bacteria to antibiotics. This strategy provided a great potential to counteract the ever-worsening spread of the blaKPC−2 gene among bacterial pathogens and laid the foundation for subsequent research using the CRISPR-Cas9 system as adjuvant antibiotic therapy.
Bayesian parametric models for survival prediction in medical applications
Authors: Paolucci Iwan , Lin Yuan-Mao , Albuquerque Marques Silva Jessica , Brock Kristy K. , Odisio Bruno C. 
Published: October 2023

AbstractBackgroundEvidence-based treatment decisions in medicine are made founded on population-level evidence obtained during randomized clinical trials. In an era of personalized medicine, these decisions should be based on the predicted benefit of a treatment on a patient-level. Survival prediction models play a central role as they incorporate the time-to-event and censoring. In medical applications uncertainty is critical especially when treatments differ in their side effect profiles or costs. Additionally, models must be adapted to local populations without diminishing performance and often without the original training data available due to privacy concern. Both points are supported by Bayesian models—yet they are rarely used. The aim of this work is to evaluate Bayesian parametric survival models on public datasets including cardiology, infectious diseases, and oncology.Materials and methodsBayesian parametric survival models based on the Exponential and Weibull distribution were implemented as a Python package. A linear combination and a neural network were used for predicting the parameters of the distributions. A superiority design was used to assess whether Bayesian models are better than commonly used models such as Cox Proportional Hazards, Random Survival Forest, and Neural Network-based Cox Proportional Hazards. In a secondary analysis, overfitting was compared between these models. An equivalence design was used to assess whether the prediction performance of Bayesian models after model updating using Bayes rule is equivalent to retraining on the full dataset.ResultsIn this study, we found that Bayesian parametric survival models perform as good as state-of-the art models while requiring less hyperparameters to be tuned and providing a measure of the uncertainty of the predictions. In addition, these models were less prone to overfitting. Furthermore, we show that updating these models using Bayes rule yields equivalent performance compared to models trained on combined original and new datasets.ConclusionsBayesian parametric survival models are non-inferior to conventional survival models while requiring less hyperparameter tuning, being less prone to overfitting, and allowing model updating using Bayes rule. Further, the Bayesian models provide a measure of the uncertainty on the statistical inference, and, in particular, on the prediction.