bluuebunny/crossref_metadata_2025_split huggingface dataset:
The draft genome of the Temminck's tragopan (Tragopan temminckii) with evolutionary implications
Authors: Li Xuejuan , Wang Xiaoyang , Yu Xiaoping , Yang Chao , Lin Liliang , Huang Yuan 
Published: September 2023

Abstract
Background
High-quality genome data of birds play a significant role in systematic studying their origin and adaptive evolution. The Temminck's tragopan (Tragopan temminckii) (Galliformes, Phasianidae), a larger pheasant, is one of the most abundant and widely distributed species of the genus Tragopan, and was defined as class II of the list of national key protected wild animals in China. The limited genomic data restricted evolutionary trait studies of this taxa.
Results
The whole genome of the Temminck's tragopan was sequenced using Illumina and PacBio platform, and then de novo assembled and annotated. The genome size was 1.06 Gb, with a contig N50 of 4.17 Mb. A total of 117.22 Mb (11.00%) repeat sequences were identified. 16,414 genes were predicted using three
methods
, with 16,099 (98.08%) annotated as functional genes based on five databases. In addition, comparative genome analyses were conducted across 12 Galliformes species. The
results
indicated that T. temminckii formed a basal position of the clade including Lophura nycthemera, Phasianus colchicus, Chrysolophus pictus, Syrmaticus mikado, Perdix hodgsoniae, and Meleagris gallopavo, with a corresponding divergence time of 31.43 million years ago (MYA). Expanded gene families associated with immune response and energy metabolism were identified. Genes and pathways associated with plumage color and feather development, immune response, and energy metabolism were found in positively selected genes (PSGs).
Conclusions
A genome draft of the Temminck's tragopan was reported, genome feature and comparative genome analysis were described, and genes and pathways related to plumage color and feather development, immune response, and energy metabolism were identified. The genomic data of the Temminck's tragopan considerably contribute to the genome evolution and phylogeny of the genus Tragopan and the whole Galliformes species underlying ecological adaptation strategies.
Effect of ticagrelor versus clopidogrel after implantation of drug-eluting stents guided by either intravascular ultrasound or angiography in patients with acute coronary syndrome——Propensity score matching analysis
Authors: Zhao Yinan , Yang Yuxin , Guo Lei , Shen Dapeng , Dong Zhichao , Lin Yajuan , Liu Hao , Wei Yushan , Zhang Bo 
Published: September 2023

Abstract
Background
The effect of different dual antiplatelet therapies on thrombotic events on the background of intravascular ultrasound (IVUS) guidance is unclear. We investigated whether ticagrelor can provide any additional benefit to clopidogrel in reducing thrombotic events in acute coronary syndrome (ACS) treated with drug- eluting stent (DES), when guided by IVUS or not.
Methods
A total of 5,666 ACS patients who underwent DES implantation and who were discharged on dual antiplatelet therapy were enrolled and grouped according to the use of IVUS or not. Each group was subdivided into two subgroups according to the type of P2Y12 inhibitor used after discharge. Propensity score matching (PSM) was used between the IVUS and no-IVUS groups. Covariate adjustment of Cox proportional hazards model was used between the ticagrelor and clopidogrel groups. Thrombotic event at 12 months was compared in groups separately.
Results
After PSM, 12-month follow-up data were available for 1,174 patients. Major adverse cardiac events (MACE) were less frequent in the IVUS-guided group (2.2% vs. 4.3%, P = 0.081) with a trend toward statistical significance. Comparison of antiplatelet regimens revealed significantly fewer major adverse cardiac and cerebrovascular events (MACCE) with ticagrelor in the entire PSM cohort and angiography-guided subgroup (2.9% vs. 5.7%, P = 0.035; 3.1% vs. 6.4%, P = 0.020, respectively). Among patients in the IVUS-guided group the outcome was comparable (2.5% vs. 4.4%, P = 0.312). Ticagrelor was associated with increasing bleeding incidence in the entire PSM cohort (1.3% vs. 3.3%, P = 0.030), mainly due to Bleeding Academic Research Consortium type 2 bleeding (0.7% vs. 2.6%, P = 0.010). The results were consistent after covariate adjustment of Cox proportional hazards model.
Conclusion T
he benefit of ticagrelor was attenuated in patients receiving IVUS guidance during stent implantation, probably due to the precise implantation of IVUS. Multicenter, randomized studies should be performed to validate this conclusion.
Data-Mining Analysis of Media Frame Effects on Social Perception of Schizophrenia Renaming in Korea
Authors: Kim Il Bin , Choi Joonho , Park Seon-Cheol , Koike Shinsuke , Kwon Jun Soo , Sun Choi Hyo , Yeon Lee Ju , Lee Yu Sang , Kim Eunkyung 
Published: September 2023

Abstract
Background
In 2011, Korean Neuropsychiatric Association renamed schizophrenia from ‘mind split disorder’ (‘Jungshinbunyeolbyung’ in Korean) to ‘attunement disorder’ (‘Johyeonbyung’ in Korean), in a strategic way to reduce social stigma toward people with schizophrenia. However, there remains an elusive consensus that how the renaming effort has contributed to changes in the social perception of schizophrenia in Korea.
Methods
With this regard, we explored whether media frames alter the social perception, in ways of respecting or disrespecting schizophrenia patients before and after the renaming. This study extensively investigated media keywords related to schizophrenia across the time by applying both language and epidemiologic analyses.
Results
In results, the media keywords have been negatively described for schizophrenia patients both before and after the renaming. Further, from an analysis using the regression model, a significant correlation was observed between the frequency of negative keywords and the hospitalization frequency of schizophrenia patients. In addition, the negative keywords deciphering schizophrenia were also significantly more shown under Korean media frames after a specific murder case committed by a schizophrenia patient.
Conclusions
These findings suggest that the social perception of schizophrenia has been scarcely changed, but rather remained negatively biased against schizophrenia patients, in spite of the renaming effort. Notably, the biased media frames have been demonstrated to negatively impact on the social perception, and even on the medical use patterns of general schizophrenia patients. In conclusion, we suggest that the unbiased media frames along with the renaming effort may collectively help reduce the negative social perception of schizophrenia.
Trial registration
This study was approved from the Institute of Review Board (IRB) of the Yoing-In Mental Hospital (IRB No. YIMH-IRB-2019-02).
The causality between C-reactive protein and asthma: A Two-Sample Mendelian Randomization Analysis
Authors: Mou Yong , Cao Wenhao , Wang Rujuan , Liu Xiaofan , Yang Xiuwen , Zhu Jing 
Published: September 2023

Abstract

Background: C-reactive protein (CRP) plays a critical role in asthma development and is usually elevated in asthmatic patients. However, the causal association between CRP and asthma remains unknown.
Results: We utilized single nucleotide polymorphisms (SNPs) associated with both CRP and outcomes of asthma, allergic asthma and obesity related asthma as genetic variables via genome-wide summary association study (GWAS). In our study, 42 SNPs were identified as instrumental variables (Ivs) for mendelian randomization (MR) analyses. According to the primary inference results by inverse variance weighted (IVW)methods, the circulating CRP was demonstrated to be significantly associated with risk of asthma (OR=1.046, 95%CI 1.004-1.090, P=0.030) and obesity related asthma (OR=1.072, 95%CI 1.009-1.138, P=0.025), whereas no distinct causality with allergic asthma (OR=1.051, 95%CI 0.994-1.112, P=0.081). Sensitivity analyses indicated that there’s no horizontal pleiotropy among IVs, and the MR results were proved to be robust by leave-one-out sensitivity analysis, despite of the presence of heterogeneity.
Conclusions:The present study suggested that genetically determined circulating CRP showed an increased risk of developing asthma and obesity related asthma, without causality with allergic asthma.
Deep embedded clustering generalisability and adaptation for mixed datatypes: two critical care cohorts
Authors: de Kok Jip , Rosmalen Frank van , Koeze Jacqueline , Keus Frederik , Kuijk Sander van , Forte José Castela , Schnabel Ronny , Driessen Rob , Herpt Thijs van , Sels Jan-Willem , Bergmans Dennis , Lexis Chris , Doorn William van , Meex Steven , Xu Minnan , Borrat Xavier , Cavill Rachel , Horst Iwan van der , Bussel Bas van 
Published: September 2023

Abstract
We propose X-DEC, a novel deep clustering technique that can integrate mixed datatypes (in this study numerical and categorical variables). Deep Embedded Clustering (DEC) is a promising technique capable of managing extensive sets of variables and non-linear relationships. Nevertheless, DEC cannot adequately handle mixed datatypes. Therefore, we created X-DEC by replacing the autoencoder with an X-shaped variational autoencoder (XVAE) and optimising hyperparameters for cluster stability. We compared DEC and X-DEC by reproducing a previous study that used DEC to identify clusters in a population of intensive care patients. We assessed internal validity based on cluster stability on the development dataset. Since generalisability of clustering models has insufficiently been validated on external populations, we assessed external validity by investigating cluster generalisability onto an external validation dataset. We concluded that both DEC and X-DEC resulted in clinically recognisable and generalisable clusters, but X-DEC produced much more stable clusters.
The role of DNA methylation in chondrogenesis of human iPSCs as a stable marker of cartilage quality
Authors: Hajmousa Ghazaleh , de Almeida Rodrigo Coutinho , Bloks Niek , Ruiz Alejandro Rodríguez , Bouma Marga , Slieker Roderick , Kuipers Thomas B , Nelissen Rob GHH , Ito Keita , Freund Christian , Ramos Yolande F.M. , Meulenbelt Ingrid 
Published: September 2023

Abstract
Background
Lack of insight into factors that determine purity and quality of human iPSC (hiPSC)-derived neo-cartilage precludes applications of this powerful technology towards regenerative solutions in the clinical setting. Here we set out to generate methylome-wide landscapes of hiPSC derived neo-cartilages from different tissues-of-origin and integrated transcriptome-wide data to identify aberrant set-points of transcription.
Methods
We applied in vitro chondrogenesis using hiPSCs generated from two different tissue sources; skin fibroblasts and articular cartilage. Upon differentiation towards chondrocytes these are referred to as hFiCs and hCiC, respectively. Genome-wide DNA methylation and RNA sequencing datasets were generated of the hiPSC-derived neo-cartilages, and the epigenetically-regulated transcriptome was compared to that of neo-cartilage deposited by human primary articular cartilage (hPAC).
Results
Methylome-wide landscapes of neo-cartilages of hiPSCs reprogrammed from two different somatic tissues were 85% similar to that of hPACs. By integration of transcriptome-wide data, changes in transcriptionally active CpGs between hCiC relative to hPAC were prioritized. Among CpG-gene pairs lower expressed in hCiCs relative to hPACs, we identified genes such as MGP, GDF5, and CHAD enriched in closely related pathways and involved in cartilage development that likely mark phenotypic differences in chondrocyte states. Vice versa, among CpG-gene pairs higher expressed, we identified genes such as KIF1A or NKX2-2 enriched in neurogenic pathways and likely reflected off target differentiation.
Conclusions
We did not find significant variation between the different tissue sources of the hiPSCs, suggesting that application of a robust differentiation protocol such as we applied here is more important as compared to the epigenetic memory of the cells of origin. Results of our study could be further exploited to improve quality, purity, and maturity of hiPSC derived neo-cartilage matrix, ultimately to realize introduction of sustainable, hiPSC derived neo-cartilage implantation into clinical practice.
The implications of lipids mobility, drug-enhancers (surfactants)-skin interaction and TRPV1 on licorice flavonoids permeability
Authors: Wang Zhuxian , Hu Yi , Xue Yaqi , Wu Yufan , Zeng Quanfu , Chen Hongkai , Guo Yinglin , Liang Peiyi , Shen Chunyan , Jiang Cuiping , Liu Li , Shen Qun , Zhu Hongxia , Liu Qiang 
Published: September 2023

Abstract
Licorice flavonoids (LFs) attained a considerable interest in cosmetic and skin ailments treatments, however, their lipophilic nature restricts their application. In this paper, we systematically investigated the enhancement efficacy and mechanisms of different penetration enhancers (surfactants) on ten LFs compounds. Herein, the aim was to unveil how seven different enhancers modified the stratum corneum (SC) surface and influence the drug-enhancers-skin interaction, and to relate these effects to permeation enhancing effects of ten LFs compounds in the liquids. The enhancing efficacy was evaluated by ERpermeation, ERretention and ERcom, which was conducted on the porcine skin. It was summarized that heat capsaicin (CaP) and lipophilic Plurol® Oleique CC 497 (POCC) caused the most significance of SC lipids fluidity, SC water loss and surface structures alterations, thereby resulting in a higher permeation enhancing effects than other surfactants. Moreover, CaP could completely occupied drug-skin interaction sites, while POCC only occupied most drug-skin interactions. The enhancing efficacy of both POCC and capsaicin was dependent on the log P values of LFs. For impervious LFs with low drug solubility, enhancing their drug solubility helped them permeate into the SC interface. For high-permeation LFs, their permeation was hardly enhanced or inhibited ascribed to the strong drug-enhancer-skin strength in the SC. More importantly, drug-surfactant-skin energy possessed a good negative correlation with the LFs permeation amount for most LFs molecules. Additionally, transient receptor potential vanilloid 1 (TRPV1) rather than transient receptor potential melastatin 8 (TRPM8) mediated LFs permeation enhancement by capsaicin. The study provided novel insights for drug permeation enhancement from the viewpoint of molecular pharmaceutics, as well as the scientific utilization of LFs compounds and surfactants in topical or transdermal formulations.
Characteristics and survival of multifocal/multicentric breast cancer: a retrospective study of 415 cases
Authors: Tong Ying , Zhang Chuanpeng , Yang Susu , Liu Yitao , Sun Feixiang , Yu Ziyi , Fu Ziyi , Zhao Yi 
Published: September 2023

Abstract
Objectives: This study was to compare the clinicopathological and prognostic characteristics of multifocal/multicentric (MF/MC) with unifocal (UF) breast cancer to study the determinants of cancer multiplicity in survival.
Methods: A retrospective analysis of 83 MF/MC and 332 UF breast cancer patients was conducted. Clinicopathological characteristics and prognostic indicators were compared.
Results: MF/MC breast cancer were more likely to have lymph node metastasis and lymph vascular/perineural invasion. There was a statistically significant difference in the LRFS rate. Cancer multiplicity was not an independent prognostic factor.
Conclusion: MF/MC breast cancer are more aggressive. However, cancer multiplicity did not affect prognosis.
Unit of attentional refreshing in multiple identity tracking: Object and Boolean map
Authors: Lin Juntian , Jia Jianrong , Yu Huadong , Wu Shujie , Zhang Yu , Li Jie 
Published: September 2023

Abstract
Tracking multiple distinct moving objects requires periodically refreshing the objects’ identity-location bindings. Classic theories assume that individual object is the unit of refreshing. Considering that features and locations can be represented as Boolean maps, in the present study we investigated whether Boolean map can also serve as the unit of refreshing in multiple identity tracking (MIT). We used an adapted MIT paradigm, in which every two targets shared the same identity and thus could be represented in one Boolean map. A cue was used to guide the refreshing when tracking was about to end. We examined whether only the cued target was refreshed (i.e., object-based refreshing) or the other target sharing the same identity was also refreshed (i.e., Boolean-map-based refreshing). In Experiment 1, all objects moved randomly. The results showed that while the cued target showed significantly better performance than uncued targets, no significant advantage was observed for the other same-identity target relative to other targets, revealing no Boolean-map-based refreshing. In Experiment 2, same-identity targets moved along parallel trajectories, so that the spatial relationship within each Boolean map remain unchanged during motion. The results showed that the same-identity target, as well as the cued target, was tracked better than other targets, revealing a same-Boolean-map advantage. Taken together, the results indicate that Boolean map can be used as the unit for attentional refreshing in MIT, but only in the circumstance where spatial relationship within each Boolean map remain unchanged as objects move, otherwise the refreshing is based on individual object.
Improved electrochemical performance of bio-derived plasticized starch/ reduced graphene oxide/ molybdenum disulfide ternary nanocomposite for flexible energy storage applications
Authors: Mahmud Eashika , Islam Muhammad Rakibul 
Published: September 2023

Abstract
A ternary nanocomposite of plasticized starch (PS), reduced graphene oxide (rGO), and molybdenum disulfide (MoS2) was prepared via an aqueous casting process, with MoS2 concentrations ranging from 0.25 wt.% to 1.00 wt.%. The structural, surface morphological, optical, and electrochemical properties of the nanocomposites were studied. FTIR analysis reveals the formation of new chemical bonds between PS, rGO, and MoS2, indicating strong interactions among them. The XRD analysis showed a reduction in the crystallinity of the nanocomposite due to the incorporation of nanofiller. FESEM micrograph showed an increment of the surface roughness due to the incorporation of rGO-MoS2 layers. UV-vis spectroscopy demonstrated a reduction of optical bandgap from 4.71 eV to 2.90 eV, resulting from enhanced charge transfer between the layers and defect states due to the addition of nanofillers. The incorporation of MoS2 was found to increase the specific capacitance of the PS from 2.78 Fg− 1 to 124.98 Fg− 1 at a current density of 0.10 mAg− 1. The EIS analysis revealed that the nanofiller results in a significant reduction in charge transfer resistance from 4574 Ω to 0 Ω, facilitating the ion transportation between the layers. The PS/rGO/MoS2 nanocomposite also exhibited excellent stability, retaining about 85% of its capacitance up to 10,000 charging-discharging cycles. These biocompatible polymer-based nanocomposites with improved electrochemical performance synthesized from an easy and economical route may offer a promising direction to fabricate a nature-friendly electrode materials for energy storage applications.
Establishment and characterization of a patient-derived solitary fibrous tumor/hemangiopericytoma cell line model
Authors: Lee Jing Yi , Guan Peiyong , Lim Abner Ming Sun Herbert , Guo Zexi , Li Zhimei , Kok Jessica Sook Ting , Lee Elizabeth Chun Yong , Lim Boon Yee , Kannan Bavani , Loh Jui Wan , Ng Cedric Chuan-Young , Lim Kah Suan , Teh Bin Tean , Ko Tun Kiat , Chan Jason Yongsheng 
Published: September 2023

Abstract
Solitary fibrous tumor/Hemangiopericytoma (SFT/HPC) is a rare subtype of soft tissue sarcoma harboring NAB2-STAT6 gene fusions. Mechanistic studies and therapeutic development on SFT/HPC are impeded by scarcity and lack of system models. In this study, we established and characterized a novel SFT/HPC patient-derived cell line (PDC), SFT-S1, and screened for potential drug candidates that could be repurposed for the treatment of SFT/HPC. Immunohistochemistry profiles of the PDC was consistent with the patient’s tumor sample (CD99+/CD34+/desmin-). RNA sequencing followed by Sanger sequencing confirmed the pathognomonic NAB2exon3-STAT6exon18 fusion in both the PDC and the original tumor. Transcriptomic data showed strong enrichment for oncogenic pathways (epithelial-mesenchymal transition, FGF, EGR1 and TGFβ signalling pathways) in the tumor. Whole genome sequencing identified potentially pathogenic somatic variants such as MAGEA10 and ABCA2. Amongst a panel of 14 targeted agents screened, dasatinib was identified to be the most potent small molecule inhibitor against the PDC (IC50, 473 nM), followed by osimertinib (IC50, 730 nM) and sunitinib (IC50, 1765 nM). Methylation profiling of the tumor suggests that this specific variant of SFT/HPC could lead to genome-wide hypomethylation. In conclusion, we established a novel PDC model of SFT/HPC with comprehensive characterization of its genomic, epigenomic and transcriptomic landscape, which can facilitate future preclinical studies of SFT/HPC, such as in vitro drug screening and in vivo drug testing.
Knowledge and Perceptions on Sexual Reproductive Health and Rights Among University of Rwanda Students: A Mixed-Method Study
Authors: Muhayimana Alice , Ntalindwa Theoneste , Uwase Aline , Gerard Kaberuka , Niringiyumukiza Jean Damascene , Ingabire Allen JC , Nzabonimana Emmanuel , Kearns Irene Josephine , Laetitia Ishimwe Bazakare , Fulgence Maniriho , Dieu Habimana Jean , Mathias Nduwingoma 
Published: September 2023

Abstract
Background: Poor knowledge of sexual reproductive health and rights (SRHR) among university students has been constantly reported in low and middle-income countries. A study conducted on female students at the University of Rwanda (UR) about knowledge of emergency contraceptive method use revealed inadequate knowledge in family planning though they are sexually active. However, no study has assessed knowledge of SRHR in general among UR students. This study aims to explore the UR students’ knowledge and perspectives on SRHR.
Methodology: This was a mixed-method study. An online survey was conducted among a convenient sample of 441 UR students. After reviewing the survey results, 12 structured interviews were conducted among a sample of UR students from each of the six colleges.
In data collection, we used a validated questionnaire with 50 items on SRHR knowledge through Moodle online platform and physical in-depth interviews. SPSS version 25 was used for descriptive and logistic regression analysis, whereas N-vivo 12 was used for qualitative thematic analysis. A p-value <0.05 was considered significant.
Results: The majority had insufficient knowledge (57%).Prior exposure to the SRHR course through YouTube (aOR 3.66; [1.01-13.17]) and SRHR prior exposure through Radio (aOR: 5.58; [1.50-20.75]) were associated with SRHR knowledge. In qualitative analysis, five themes emerged: 1) Prevention of unplanned pregnancies, 2) Knowledge of SRHR Services, 3) Knowledge of contraceptive methods, 4) Perceptions of sexual intercourse among youths before marriage, 5) Perceptions of safe abortion. Participants reported that they use condoms, pills and abstinence, feel ashamed to ask for SRHR information or share their experiences in public, fear the use of long-acting contraceptive methods, and have limited condom access.
Conclusion and Recommendations: UR students do not have sufficient knowledge of SRHR. Every UR student should benefit from SRHR training from reliable sources to enable them to make effective choices regarding their reproductive health.