bluuebunny/crossref_metadata_2025_split huggingface dataset:
Early Outcomes of Pulmonary Valve Replacement With the Edwards Inspiris Resilia Pericardial Bioprosthesis
Authors: Sengupta Aditya , Pastuszko Peter , Zaidi Ali N. , Murthy Raghav A. 
Published: September 2023

Background Controversy regarding the optimal pulmonary valve substitute remains, with no approved surgical valve for pulmonary valve replacement (PVR). Furthermore, unfavorable anatomy often precludes transcatheter PVR in patients with congenital heart disease. We therefore sought to evaluate the feasibility of the Edwards Inspiris pericardial aortic bioprosthesis in the pulmonary position in pediatric and adult patients requiring PVR. Methods Data from consecutive patients who underwent PVR from February 2019 to February 2021 at our institution were retrospectively reviewed. Postoperative adverse events included paravalvular or transvalvular leak, endocarditis, explant, thromboembolism, valve thrombosis, valve-related bleeding, hemolysis, and structural valve degeneration. Progression of valve gradients was assessed from discharge to 30 days and one year. Results Of 24 patients with median age of 26 years (interquartile range [IQR]: 17-33; range: 4-60 years), 22 (91.7%) patients had previously undergone tetralogy of Fallot repair and 2 (8.3%) patients had undergone double-outlet right ventricle repair in the neonatal period or infancy. All patients had at least mild right ventricular (RV) dilatation (median RV end-diastolic volume index 161.4, IQR: 152.3-183.5 mL/m2) and at least moderate pulmonary insufficiency (95.8%) or stenosis (8.3%). Median cardiopulmonary bypass and cross-clamp times were 71 (IQR: 63-101) min and 66 (IQR: 60-114) min, respectively. At a median postoperative follow-up of 2.5 years (IQR: 1.4-2.6; range: 1.0-3.0 years), there were no mortalities, valve-related reoperations, or adverse events. Postoperative valve gradients and the severity of pulmonary regurgitation did not change significantly over time. Conclusions At short-term follow-up, the bioprosthesis in this study demonstrated excellent safety and effectiveness for PVR. Further studies with longer follow-up are warranted.
Surface Characterization and Tribology Behavior of PMMA Processed by Excimer Laser
Authors: Qin Dong , Guo Juan , Liang Ming , Chen Ling , He Weimin 
Published: September 2023

AbstractPolyoxymethylene methacrylate (PMMA) is widely used in ophthalmic biomaterials. Misuse of PMMA in extreme environments is likely to damage the ocular surface and intraocular structures. The surface characterization and tribological behavior of PMMA processed using an excimer laser were investigated in this study by contrasting different lubrication conditions and friction cycles. The results show that the roughness of the material surface increases with laser processing, which changes its physical structure. Under lubrication, the laser-treated PMMA exhibits better hydrophilicity, especially during the use of eye drops. No obvious relationship exists between the laser-processing time and friction behavior. However, the laser treatment may contribute to the formation of friction and wear mechanisms of PMMA materials. Laser-treated PMMA in saline solution exhibits better abrasive resistance by showing a lower wear rate than that in eye drops, although it has a higher friction coefficient. In this study, the different friction stages in laser-treated PMMA were clarified under two lubrication conditions. The wear rates of the laser-treated PMMA were found to decrease with the number of cycles, and the friction coefficient has a similar variation tendency. The wear behavior of the laser-treated PMMA is dominated by the main abrasive wear and secondary transferred film formation. This study provides a theoretical basis for the development and application of ophthalmic biomaterials in complex environments by examining the material surface interface behavior and wear mechanism after laser processing using PMMA as the research matrix.
Prediction of plant secondary metabolic pathways using deep transfer learning
Authors: Bao Han , Zhao Jinhui , Zhao Xinjie , Zhao Chunxia , Lu Xin , Xu Guowang 
Published: September 2023

Abstract
Background
Plant secondary metabolites are highly valued for their applications in pharmaceuticals, nutrition, flavors, and aesthetics. It is of great importance to elucidate plant secondary metabolic pathways due to their crucial roles in biological processes during plant growth and development. However, understanding plant biosynthesis and degradation pathways remains a challenge due to the lack of sufficient information in current databases. To address this issue, we proposed a transfer learning approach using a pre-trained hybrid deep learning architecture that combines Graph Transformer and convolutional neural network (GTC) to predict plant metabolic pathways.

Results
GTC provides comprehensive molecular representation by extracting both structural features from the molecular graph and textual information from the SMILES string. GTC is pre-trained on the KEGG datasets to acquire general features, followed by fine-tuning on plant-derived datasets. Four metrics were chosen for model performance evaluation. The results show that GTC outperforms six other models, including three previously reported machine learning models, on the KEGG dataset. GTC yields an accuracy of 96.75%, precision of 85.14%, recall of 83.03%, and F1_score of 84.06%. Furthermore, an ablation study confirms the indispensability of all the components of the hybrid GTC model. Transfer learning is then employed to leverage the shared knowledge acquired from the KEGG metabolic pathways. As a result, the transferred GTC exhibits outstanding accuracy in predicting plant secondary metabolic pathways with an average accuracy of 98.30% in fivefold cross-validation and 97.82% on the final test. In addition, GTC is employed to classify natural products. It achieves a perfect accuracy score of 100.00% for alkaloids, while the lowest accuracy score of 98.42% for shikimates and phenylpropanoids.

Conclusions
The proposed GTC effectively captures molecular features, and achieves high performance in classifying KEGG metabolic pathways and predicting plant secondary metabolic pathways via transfer learning. Furthermore, GTC demonstrates its generalization ability by accurately classifying natural products. A user-friendly executable program has been developed, which only requires the input of the SMILES string of the query compound in a graphical interface.
Integrated omic profiling of the medicinal mushroom Inonotus obliquus under submerged conditions
Authors: Hao Jinghua , Wang Xiaoli , Shi Yanhua , Li Lingjun , Chu Jinxin , Li Junjie , Lin Weiping , Yu Tao , Hou Dianhai 
Published: September 2023

Abstract
Background
The Inonotus obliquus mushroom, a wondrous fungus boasting edible and medicinal qualities, has been widely used as a folk medicine and shown to have many potential pharmacological secondary metabolites. The purpose of this study was to supply a global landscape of genome-based integrated omic analysis of the fungus under lab-growth conditions.

Results
This study presented a genome with high accuracy and completeness using the Pacbio Sequel II third-generation sequencing method. The de novo assembled fungal genome was 36.13 Mb, and contained 8352 predicted protein-coding genes, of which 365 carbohydrate-active enzyme (CAZyme)-coding genes and 19 biosynthetic gene clusters (BCGs) for secondary metabolites were identified. Comparative transcriptomic and proteomic analysis revealed a global view of differential metabolic change between seed and fermentation culture, and demonstrated positive correlations between transcription and expression levels of 157 differentially expressed genes involved in the metabolism of amino acids, fatty acids, secondary metabolites, antioxidant and immune responses. Facilitated by the widely targeted metabolomic approach, a total of 307 secondary substances were identified and quantified, with a significant increase in the production of antioxidant polyphenols.

Conclusion
This study provided the comprehensive analysis of the fungus Inonotus obliquus, and supplied fundamental information for further screening of promising target metabolites and exploring the link between the genome and metabolites.
Identification of copy number variation in Tibetan sheep using whole genome resequencing reveals evidence of genomic selection
Authors: Shi Huibin , Li Taotao , Su Manchun , Wang Huihui , Li Qiao , Lang Xia , Ma Youji 
Published: September 2023

Abstract
Background
Copy number variation (CNV) is an important source of structural variation in the mammalian genome. CNV assays present a new method to explore the genomic diversity of environmental adaptations in animals and plants and genes associated with complex traits. In this study, the genome-wide CNV distribution characteristics of 20 Tibetan sheep from two breeds (10 Oula sheep and 10 Panou sheep) were analysed using whole-genome resequencing to investigate the variation in the genomic structure of Tibetan sheep during breeding.

Results
CNVs were detected using CNVnator, and the overlapping regions of CNVs between individual sheep were combined. Among them, a total of 60,429 CNV events were detected between the indigenous sheep breed (Oula) and the synthetic sheep breed (Panou). After merging the overlapping CNVs, 4927 CNV regions (CNVRs) were finally obtained. Of these, 4559 CNVRs were shared by two breeds, and there were 368 differential CNVRs. Deletion events have a higher percentage of occurrences than duplication events. Functional enrichment analysis showed that the shared CNVRs were significantly enriched in 163 GO terms and 62 KEGG pathways, which were mainly associated with organ development, neural regulation, immune regulation, digestion and metabolism. In addition, 140 QTLs overlapped with some of the CNVRs at more than 1 kb, such as average daily gain QTL, body weight QTL, and total lambs born QTL. Many of the CNV-overlapping genes such as PPP3CA, SSTR1 and FASN, overlap with the average daily weight gain and carcass weight QTL regions. Moreover, VST analysis showed that XIRP2, ABCB1, CA1, ASPA and EEF2 differed significantly between the synthetic breed and local sheep breed. The duplication of the ABCB1 gene may be closely related to adaptation to the plateau environment in Panou sheep, which deserves further study. Additionally, cluster analysis, based on all individuals, showed that the CNV clustering could be divided into two origins, indicating that some Tibetan sheep CNVs are likely to arise independently in different populations and contribute to population differences.

Conclusions
Collectively, we demonstrated the genome-wide distribution characteristics of CNVs in Panou sheep by whole genome resequencing. The results provides a valuable genetic variation resource and help to understand the genetic characteristics of Tibetan sheep. This study also provides useful information for the improvement and breeding of Tibetan sheep in the future.
Profile and potential bioactivity of the miRNome and metabolome expressed in Malva sylvestris L. leaf and flower
Authors: Villani Valentina , Di Marco Gabriele , Iacovelli Federico , Pietrucci Daniele , Canini Antonella , Gismondi Angelo 
Published: September 2023

AbstractMalva sylvestris L. (common mallow) is a plant species widely used in phytotherapy and ethnobotanical practices since time immemorial. Characterizing the components of this herb might promote a better comprehension of its biological effects on the human body but also favour the identification of the molecular processes that occur in the plant tissues. Thus, in the present contribution, the scientific knowledge about the metabolomic profile of the common mallow was expanded. In particular, the phytocomplex of leaves and flowers from this botanical species and the extraction capacity of different concentrations of ethanol (i.e., 95%, 70%, 50%, and 0%; v/v in ddH2O) for it were investigated by spectrophotometric and chromatographic approaches. In detail, 95% ethanol extracts showed the worst capacity in isolating total phenols and flavonoids, while all the hydroalcoholic samples revealed a specific ability in purifying the anthocyanins. HPLC–DAD system detected and quantified 20 phenolic secondary metabolites, whose concentration in the several extracts depended on their own chemical nature and the percentage of ethanol used in the preparation. In addition, the stability of the purified phytochemicals after resuspension in pure ddH2O was also proved, considering a potential employment of them in biological/medical studies which include in vitro and in vivo experiments on mammalian models. Here, for the first time, the expressed miRNome in M. sylvestris was also defined by Next Generation Sequencing, revealing the presence of 33 microRNAs (miRNAs), 10 typical for leaves and 2 for flowers. Then, both plant and human putative mRNA targets for the detected miRNAs were predicted by bioinformatics analyses, with the aim to clarify the possible role of these small nucleic acids in the common mallow plant tissues and to try to understand if they could exert a potential cross-kingdom regulatory activity on the human health. Surprisingly, our investigations revealed that 19 miRNAs out of 33 were putatively able to modulate, in the plant cells, the expression of various chromosome scaffold proteins. In parallel, we found, in the human transcriptome, a total of 383 mRNAs involved in 5 fundamental mammalian cellular processes (i.e., apoptosis, senescence, cell-cycle, oxidative stress, and invasiveness) that theoretically could be bound and regulated by M. sylvestris miRNAs. The evidence collected in this work would suggest that the beneficial properties of the use of M. sylvestris, documented by the folk medicine, are probably linked to their content of miRNAs and not only to the action of phytochemicals (e.g., anthocyanins). This would open new perspectives about the possibility to develop gene therapies based on miRNAs isolated from medicinal plants, including M. sylvestris.
Study on the impact of exogenously applied methyl jasmonate concentrations on Solanum lycopersicum under low temperature stress
Authors: Gul Nadia , Masoodi Khalid Z , Ramazan Salika , Mir Javid I , Aslam Saima 
Published: September 2023

Abstract
Background
To decipher the capability of Methyl Jasmonate (MeJA) in resisting cold stress in Solanum lycopersicum assessment regarding various physiological parameters in response to diverse doses of MeJA was done. Low temperature (LT) were given to the plants with MeJA (J1C, J2C, J3C) or without MeJA (LT) application. MeJA in the form of foliar spray was given before stress, during stress and after stress. Three concentrations of MeJA were used under normal and LT stress conditions that includes of J1 (0.5 µM), J2 (10 µM), and J3 (15 µM).

Results
Oxidative stress, growth characteristics, stress tolerance parameters, antioxidant response and photosynthetic parameters were investigated. In our current study we observed that oxidative stress markers declined by MeJA supplementation under cold stress conditions. MeJA boosted antioxidant enzyme activity along with photosynthetic parameters. The best concentration of MeJA was J2 based on results obtained. This is the first study related to MeJA best dose screening in Solanum lycopersicum under LT stress conditions.

Conclusion
The LT stress in the Solanum lycopersicum plant was reduced by MeJA. The adverse consequences of LT stress can be significantly attenuated by the J2 concentration of MeJA. So, the optimal concentration of MeJA supplied exogenously to LT stressed Solanum lycopersicum can be a smart strategy to mitigate harmful impact of LT stress on detox system and overall growth of plant.
Outcomes and associated factors of traumatic brain injury among adult patients treated in Amhara regional state comprehensive specialized hospitals
Authors: G/Michael Solomon , Terefe Bewuketu , Asfaw Marye Getnet , Liyew Bikis 
Published: September 2023

AbstractBackgroundGlobally, traumatic brain injury is the leading cause of death and disability which affects more than 69 million individuals a year.ObjectiveThis study aimed to assess the outcome and associated factors of traumatic brain injury among adult patients treated in Amhara regional state comprehensive specialized hospitals.MethodInstitutional-based cross-sectional study design was conducted from January 1, 2018, to December 30, 2020. A simple random sampling technique was used and a checklist was used to extract data between March 15 and April 15, 2021. The data were entered into Epi-data version 4.2 and exported to SPSS version 25 for analysis after being checked for consistency. Associated variables with outcomes of traumatic brain injury were determined by a binary logistic regression model. The degree of association was interpreted by using AOR and a 95% confidence interval with ap-value less than or equal to 0.05 at 95% CI was considered statistically significant.ResultIn this study road traffic injury was the most frequent cause of traumatic brain injuries among adult patients, accounting for 181 (37.5%), followed by assault, accounting for 117 (24.2%) which affects adult age groups. One-third of the participant had a moderate Glasgow coma scale of 174(36%). Only 128(26.8%) patients arrived within one hour. One hundred sixty, 160 (33.1%) of patients had a mild traumatic brain injury, whereas, 149(36%) of patients had a severe traumatic brain injury. Regarding computerized tomography scans findings, the hematoma was the most common (n = 163, 33.7%). Ninety-one, 91(18.8%) of participants had cerebrospinal fluid otorrhea, and, 92(19%) were diagnosed with a positive battle sign. The overall prevalence of unfavorable outcomes after traumatic brain injury was found to be 35.2% (95%CI (30.8–39.1). Having additional Injury, hypoxia, time to hospital presentation after 24 h, severe Glasgow Coma Scale, moderate Glasgow Coma Scale, tachypnea, bradypnea, and cerebrospinal fluid Othorrhea, were factors associated with unfavorable outcomes.Conclusion and recommendationIn this study, the overall unfavorable outcome was experienced by about four out of every 10 victims of traumatic brain injury. Time of arrival > 24 h, low Glasgow coma scale, additional injury, Cerebrospinal fluid otorrhea, abnormal respiration, and hypoxia were significant predictors of unfavorable outcomes. To reduce the adverse effects of traumatic brain injury in adults, it is therefore desirable to guarantee safe road traffic flow and improve health care services.
E-scooter-related orthopedic injuries and the treatments applied: are these scooters a new means of transportation or a new source of trauma?
Authors: İğrek Servet , Ulusoy İbrahim 
Published: September 2023

Abstract
Introduction
E-scooters have become increasingly popular in Turkey due to easy accessibility. In parallel with this, the number of e-scooter-related injuries has increased gradually. The aim of this study was to determine the types of e-scooter-related orthopedic injuries, to evaluate hospitalization and surgical treatments, and to investigate the loss of work of patients and the burden incurred by the healthcare system.

Materials and methods
This retrospective multicentre study included all orthopaedic referrals, who were admitted to two major trauma departments in Diyarbakır from January 2022 to July 2022. Patient data were analyzed, including demographic characteristics, injury pattern, types of injury and subsequent treatment.

Results
In a total of 62 patients, 105 orthopaedic injuries were identified, comprising 72.5% males and 27.5% females, with a median age of 34.21 years. Fifty-six (90.3%) patients were riders, and six were pedestrians. All associated e-scooters were rented. There were 44 fractures (41.9% of the total recorded injuries) including 8 (12.9%) open fractures. Surgery was required by 32 patients (51.6%) and 35 (56.4%) required hospital admission leading to hospitalization of 3.7 days on average. The average job loss of working patients after injury was determined as 2.4 months. Helmet use was detected in 6.4% of the e-scooter users, but no other protective equipment was detected in any of the patients. Furthermore, 19,3% of the patients had a blood alcohol level of > 10 mg/dl.

Conclusions
The injuries that may result from an e-scooter accident can have long-term hospitalization and long-term job loss in the community. This imposes a significant financial burden on the national healthcare system and adversely affects public health. There is a need for precautions to be implemented such as infrastructure organisation, increased awareness of motor vehicle riders and e-scooter riders, and increased enforcement of rule compliance including not using e scooters after alcohol consumption and the use of protective equipment.
Serum liver fibrosis markers predict hepatic decompensation in compensated cirrhosis
Authors: Chen Qingling , Mei Ling , Zhong Rui , Han Ping , Wen Jun , Han Xu , Zhai Lu , Zhao Lili , Li Jia 
Published: September 2023

Abstract
Background and aim
The literature is sparse on the association between serum liver fibrosis markers and the development of hepatic decompensation in patients with compensated cirrhosis. We aimed to assessed whether the serum liver fibrosis markers are predictive of the occurrence of hepatic decompensation.

Methods
We ascertained 688 cirrhotic patients with varying etiologies, between December 2015 to December 2019. Serum hyaluronic acid (HA), laminin (LN), collagen IV (CIV), and N-terminal propeptide of type III collagen (PIIINP) levels were measured at enrollment. All subjects were followed for at least 6 months for occurrence of hepatic decompensation. Cox proportional hazard regression models were used to estimate the hazard ratios (HRs) of hepatic decompensation during follow-up.

Results
During a median follow-up of 22.0 (13.0–32.0) months, decompensation occurred in 69 (10.0%) patients. Multivariate analysis indicated that higher LN (HR: 1.008, 95% confidence interval [CI]: 1.002–1.014, P = 0.011) and CIV (HR: 1.004, 95% CI: 1.001–1.007, P = 0.003) levels were independently associated with hepatic decompensation. Furthermore, patients in the tertile 2 and tertile 3 groups for CIV levels had HRs of 4.787 (1.419, 16.152) (P = 0.012) and 5.153 (1.508, 17.604) (P = 0.009), respectively, for occurrence of decompensation event compared with those in the tertile 1 group.

Conclusion
Serum liver fibrosis markers, particularly in CIV, appeared to be reliable biomarkers of disease progression and liver decompensation in patients with compensated cirrhosis with varying etiologies.