bluuebunny/crossref_metadata_2025_split huggingface dataset:
Analisis dan Karakterisasi Senyawa Silika (Sio2) Berbahan Dasar Batuan Vulkanik di Pulau Ambon
Authors: Nggolaon Delpina , Silahooy Stevi , Jaya Gede Wiratma , Hattu Nikmans 
Published: January 2025

ABSTRAK

Penelitian ini bertujuan untuk melakukan analisis dan karakterisasi senyawa silika (SiO2) berbahan dasar batuan vulkanik di Pulau Ambon yang diekstraksi menggunakan metode kopresipitasi. Hal ini dikarenakan material senyawa silika merupakan salah satu material maju yang saat ini berperan pesat dalam dunia industri karena memiliki banyak keunggulan. Proses analisis dilakukan terhadap hasil pengujian karakterisasi menggunakan beberapa instrumen, antara lain XRF, XRD, dan SEM. Berdasarkan hasil uji XRF, serbuk silika mampu dimurnikan menjadi sebesar 47,40 wt %. Hal ini dikarenakan metode kopresipitasi mampu menghilangkan impuritas pengotor yang terkandung didalam batuan vulkanik. Kemudian untuk mengetahui fasa, struktur morfologi, dan ukuran partikel dari serbuk silika maka dilakukan uji XRD dan SEM. Berdasarkan hasil uji diketahui bahwa serbuk silika memiliki fasa amorf dengan posisi puncak yang paling kuat pada sudut 2θ = 23.68˚. Hasil citra SEM menunjukkan adanya aglomerasi dan menghasilkan distribusi ukuran partikel tertinggi berada pada rentang 11-15 nm dengan ukuran partikel rata-rata sebesar 13,824 nm.

Kata kunci—Batuan Vulkanik, Kopresipitasi, nano-Silika Amorf

ABSTRACT

This research aims to analyze and characterize silica compounds (SiO2) derived from volcanic rocks on the Ambon Island that were extracted using the co-precipitation method. This is because silica compound materials are one of the advanced materials that are currently playing a rapid role in the industrial world because they have many advantages. The analysis process was carried out on the results of characterization tests using several instruments, including XRF, XRD, and SEM. Based on the XRF test results, silica powder was able to be purified to 47.40 wt%. This is because the coprecipitation method is able to remove impurities contained in volcanic rocks. Then, to determine the phase, morphological structure and particle size of the silica powder, XRD and SEM tests were carried out. Based on the test results, it is known that silica powder has an amorphous phase with a strong board peak at at 2θ angles = 23.68˚. The results of the SEM image show that there is agglomerate and produce the highest particle size distribution in the range of 11-15 nm with an average size of 13.824 nm.

Keywords—Volcanic rocks, Co-Precipitation, Amorphous nano-Silica
EFEKTIVITAS DAN KARAKTERISTIK KOMBUCHA SARI BUAH STROBERI (Fragaria x ananassa)TERHADAP BAKTERI Streptococcus mutans DAN Basillus cereus SECARA IN VITRO
Authors: Sitorus Widya Astuti , Rasyidah  , Mayasari Ulfayani 
Published: January 2025

Kombucha merupakan minuman fungsional hasil fermentasi, mengunakan SCOBY. Kombucha dengan penambahan sari buah stroberi merupakan inovasi terbaru yang diharapkan dapat menghambat bertumbuhan bakteri bakteri Streptococcus mutans dan Bacillus cereus yang merupakan bakteri patogen penyebab ganguan pencernaan. Metode yang di gunakan pada penelitian ini ialah pengujian difusi cakram dengan konsentrasi sari buah 20%, 30%, dan 40% dan 50%, dimana setiap perlakuan diulang sebanyak 3 kali. Hasil penelitaian ini menunjukkan rerata zona hambat terhadap bakteri Streptococcus mutans 6,98mm, 8,38mm, 10.6mm, 6.5mm. Sedangkan Bacillus cereus 6,46 mm, 7,5 mm, 9,18 mm dan 5,85 mm. Berdasarkan hasil penelitian dapat disimpulkan Daya hambat kombucha sari buah stroberi terhadap bakteri Streptococus mutans dikategorigakan kuat pada konsentrasi 40% dengan zona hambat 10,61 mm sedangkan dikategorikan sedang pada Bacillus cereus dengan zona hambat tertinggi pada konsentrasi 40% sebesar 9,18mm. Karakteristik kombucha stroberi memiliki pH berkisar 3,21-3,55 dengan aroma khas fermentasi,berwarna merah maroon serta memiliki rasa manis keasaman. Kandungan alkohol pada kombucha sari buah stroberi 0,01 yang berarti minuman ini halal untuk dikonsumsi. Kekentalan pada kombucha sari buah stroberi 0,79 yang berarti bahwa kombucha sari buah stroberi memiliki kadar kekentalan yang rendah
Kata kunci: Kata Kombucha,Stroberi,Bakteri
Single-cell sequencing reveals cell heterogeneity and aberrantly activated pathways associated with microvascular invasion in hepatocellular carcinoma
Authors: Cui Jianwei , Zeng Fanyi , Tang Ming , Yin Shiwu 
Published: January 2025

IntroductionHepatocellular carcinoma (HCC) is the most common primary liver cancer, with microvascular invasion (MVI) identified as a major predictor of early recurrence. However, the intratumor cellular heterogeneity of MVI, the identification of pertinent biomarkers, and the role of intercellular signalling interactions in MVI progression are unclear. This study aims to explore these aspects using single-cell transcriptomic analysis.MethodsThe present study utilized single-cell transcriptomic data from public databases to conduct an in-depth transcriptome analysis of tumour tissues and adjacent nontumor tissues from five patients with hepatocellular carcinoma, with a particular focus on samples from three patients exhibiting microvascular invasion. Bioinformatics tools were employed to analyze gene expression patterns and signalling pathways.ResultsThe findings indicated that MVI-positive malignant cells activate multiple signalling pathways to facilitate invasion and metastasis. Specific malignant cell subtypes strongly associated with MVI were identified, exhibiting distinctive gene expression patterns related to proliferation, invasion, and metabolic reprogramming of tumour cells. Further analysis revealed that the laminin and VEGF signalling pathways are crucial for remodelling the tumour microenvironment and angiogenesis associated with MVI. The MARCKSL1 gene was predominantly expressed in MVI-positive malignant cells and may contribute to MVI progression by interacting with the PTN signalling network. Additionally, MARCKSL1 is linked to tumour resistance to multiple anticancer drugs.DiscussionThis study sheds light on the molecular characteristics and functional heterogeneity of MVI-associated malignant cell subpopulations. The single-cell transcriptome and bioinformatics analyses provided insights into the mechanisms driving MVI, potentially aiding the development of targeted diagnostic and therapeutic strategies. Future research should further validate the role of MARCKSL1 in MVI progression and explore its potential clinical applications.
A comprehensive analysis of the uterine microbiome in endometrial cancer patients - identification of Anaerococcus as a potential biomarker and carcinogenic cofactor
Authors: Kuźmycz Olga , Kowalczyk Aleksandra , Bolanowska Aleksandra , Drozdzowska Anna , Lach Jakub , Wierzbińska Wiktoria , Kluz Tomasz , Stączek Paweł 
Published: January 2025

IntroductionEndometrial cancer (EC) is a significant gynecological malignancy with increasing incidence worldwide. Emerging evidence highlights the role of the uterine microbiome in the pathogenesis of EC. This study aims to characterize the uterine microbiome in EC patients and identify potential microbial biomarkers, with a focus on Anaerococcus as a differentiating taxon.MethodsThe endocervical canal swabs from patients with EC (n=16) and non-cancerous patients (EM, n=13) were collected. The V3-V4 region of the 16S rRNA gene was sequenced using the Illumina platform. Bioinformatic analyses were performed with QIIME2, and statistical comparisons were conducted to assess differences in microbial composition and diversity. In vitro experiments were conducted to assess the functional impact of Anaerococcus on human uterine fibroblasts, including its ability to adhere to the human cells and induce oxidative stress.ResultsThe α-diversity metrics, including Shannon entropy and observed amplicon sequence variants (ASVs), revealed significantly higher microbial diversity in EC samples compared to EM. Anaerococcus was identified as a key taxon differentiating EC from EM groups, showing a higher relative abundance in EC samples. Functional predictions and in vitro assays indicated that Anaerococcus may contribute to carcinogenesis by inducing reactive oxygen species (ROS) production, and has the high ability to adhere to the human endometrial fibroblasts.DiscussionThe study provides evidence of distinct microbial signatures in EC, with Anaerococcus emerging as a potential biomarker. The in vitro findings suggest its role in endometrial carcinogenesis, underscoring its potential as a target for future diagnostic and therapeutic applications.
Study on the effects of land use transformation on habitat quality and its driving mechanisms: a case study of the Qin-Mang River Basin
Authors: Zhao Jiwei , Wang Luyao , Jia Dong , Wang Yaowen 
Published: January 2025

Habitat quality (HQ) is a critical factor for regional ecosystem health and sustainable development, as well as an important basis for formulating ecological protection and land-use planning. The Qin-Mang River Basin, as an integral part of the biodiversity conservation area in the Yellow River Basin, plays a significant role in maintaining the balance and stability of the regional ecosystem. This study is based on land use/land cover changes (LUCC) data from 1992, 2002, 2012, and 2022. It employs a land use transfer matrix to analyze the dynamic trends and patterns of LUCC. HQ changes are evaluated using the InVEST model, and the GeoDetector model is used to identify the key driving factors and their interactions. Additionally, spatial autocorrelation analysis is applied to explore the spatial clustering characteristics of HQ. The results indicate that between 1992 and 2022, the cumulative area of land transfer in the study area exceeded 600 km2, primarily characterized by the conversion of cultivated land to built-up areas. The HQ index decreased from 0.3409 in 1992 to 0.2896 in 2022, with a significant increase in spatial heterogeneity. Altitude, vegetation coverage, temperature, precipitation, and slope are the main driving factors influencing HQ, with natural factors dominating, but human activities gradually playing an increasingly significant role. Furthermore, HQ exhibits significant spatial clustering characteristics, with hotspot and coldspot areas providing scientific evidence for ecological protection and restoration measures. To improve HQ, it is recommended to strictly enforce ecological protection red lines, control the expansion of built-up areas, improve ecological compensation mechanisms, and promote ecological restoration measures such as returning farmland to forest and grassland.
Bibliometric analysis of ferroptosis: a comprehensive evaluation of its contribution to lung cancer
Authors: Yao Feifei , Guo Feng , Sun Chuanzhong , Wang Erdong , Wang Hang , Li Na 
Published: January 2025

ObjectivesThis study employs bibliometric analysis to track evolution and identify trends of key topics in ferroptosis within the context of lung cancer. By identifying emerging research areas, our aim is to provide valuable insights and directions for researchers in this field.MethodsRelevant papers and reviews on ferroptosis in lung cancer were retrieved from the Web of Science Core Collection database on 5 February 2024. Bibliometric analysis was conducted using CiteSpace 6.2.R3, VOSviewer 1.6.20, R 4.3.0, Bibliometric and Microsoft Excel 2019.ResultsFrom 2015 to 2020, publications related to ferroptosis in lung cancer were sparse but showed a steady increase. Post-2020, there has been a significant surge, with a 6.4-fold increase observed by 2023. Overall, authors from 4,033 institutions across 42 countries/regions contributed 606 papers published in 262 academic journals. China emerged as the leading contributor, while the United States maintained dominance. Lifang Ma was the most prolific author, with DIXON SJ, YANG WS, and STOCKWELL BR being the most frequently co-cited. Effective communication and collaboration among scholars are lacking. Key journals include Frontiers in Pharmacology for publication output, and Nature and Cell for citation frequency. Research focuses on molecular mechanisms of ferroptosis, including endoplasmic reticulum stress, tumor microenvironment, and autophagy. Therapeutic targets like GPX4, SLC7A11, P53, FSP1, Nrf2, LSH, STYK1/NOK, and ACSL4 are prominent. Traditional Chinese medicine also shows clinical value in ferroptosis research.ConclusionFerroptosis, as a promising research avenue with significant clinical applications in lung cancer, continues to undergo rapid development. The study of iron death in lung cancer will remain a critical research focus in the future.
ZINQ-L: a zero-inflated quantile approach for differential abundance analysis of longitudinal microbiome data
Authors: Li Shuai , Li Runzhe , Lee John R. , Zhao Ni , Ling Wodan 
Published: January 2025

BackgroundIdentifying bacterial taxa associated with disease phenotypes or clinical treatments over time is critical for understanding the underlying biological mechanism. Association testing for microbiome data is already challenging due to its complex distribution that involves sparsity, over-dispersion, heavy tails, etc. The longitudinal nature of the data adds another layer of complexity - one needs to account for the within-subject correlations to avoid biased results. Existing longitudinal differential abundance approaches usually depend on strong parametric assumptions, such as zero-inflated normal or negative binomial. However, the complex microbiome data frequently violate these distributional assumptions, leading to inflated false discovery rates. In addition, the existing methods are mostly mean-based, unable to identify heterogeneous associations such as tail events or subgroup effects, which could be important biomedical signals.MethodsWe propose a zero-inflated quantile approach for longitudinal (ZINQ-L) microbiome differential abundance test. A mixed-effects quantile rank-score-based test was proposed for hypothesis testing, which consists of a test in mixed-effects logistic model for the presence-absence status of the investigated taxon, and a series of mixed-effects quantile rank-score tests adjusted for zero inflation given its presence. As a regression method with minimal distributional assumptions, it is robust to the complex microbiome data, controlling false discovery rate, and is flexible to adjust for important covariates. Its comprehensive examination of the abundance distribution enables the identification of heterogeneous associations, improving the testing power.ResultsExtensive simulation studies and an application to a real kidney transplant microbiome study demonstrate the improved power of ZINQ-L in detecting true signals while controlling false discovery rates.ConclusionZINQ-L is a zero-inflated quantile-based approach for detecting individual taxa associated with outcomes or exposures in longitudinal microbiome studies, providing a robust and powerful option to improve and complement the existing methods in the field.
Identifying health risk determinants and molecular targets in patients with idiopathic pulmonary fibrosis via combined differential and weighted gene co-expression analysis
Authors: Moin Abu Tayab , Ullah Md. Asad , Nipa Jannatul Ferdous , Rahman Mohammad Sheikh Farider , Emran Afsana , Islam Md. Minhazul , Das Swapnil , Arian Tawsif Al , Elahi Mohammad Mahfuz Enam , Akter Mukta , Rahman Umme Sadea , Halder Arnab , Saikat Shoaib , Hosen Mohammad Jakir 
Published: January 2025

IntroductionIdiopathic pulmonary fibrosis (IPF) is a rare but debilitating lung disease characterized by excessive fibrotic tissue accumulation, primarily affecting individuals over 50 years of age. Early diagnosis is challenging, and without intervention, the prognosis remains poor. Understanding the molecular mechanisms underlying IPF pathogenesis is crucial for identifying diagnostic markers and therapeutic targets.MethodsWe analyzed transcriptomic data from lung tissues of IPF patients using two independent datasets. Differentially expressed genes (DEGs) were identified, and their functional roles were assessed through pathway enrichment and tissue-specific expression analysis. Protein-protein interaction (PPI) networks and co-expression modules were constructed to identify hub genes and their associations with disease severity. Machine learning approaches were applied to identify genes capable of differentiating IPF patients from healthy individuals. Regulatory signatures, including transcription factor and microRNA interactions, were also explored, alongside the identification of potential drug targets.ResultsA total of 275 and 167 DEGs were identified across two datasets, with 67 DEGs common to both. These genes exhibited distinct expression patterns across tissues and were associated with pathways such as extracellular matrix organization, collagen fibril formation, and cell adhesion. Co-expression analysis revealed DEG modules correlated with varying IPF severity phenotypes. Machine learning analysis pinpointed a subset of genes with high discriminatory power between IPF and healthy individuals. PPI network analysis identified hub proteins involved in key biological processes, while functional enrichment reinforced their roles in extracellular matrix regulation. Regulatory analysis highlighted interactions with transcription factors and microRNAs, suggesting potential mechanisms driving IPF pathogenesis. Potential drug targets among the DEGs were also identified.DiscussionThis study provides a comprehensive transcriptomic overview of IPF, uncovering DEGs, hub proteins, and regulatory signatures implicated in disease progression. Validation in independent datasets confirmed the relevance of these findings. The insights gained here lay the groundwork for developing diagnostic tools and novel therapeutic strategies for IPF.
Based on bioinformatics, SESN2 negatively regulates ferroptosis induced by ischemia reperfusion via the System Xc−/GPX4 pathway
Authors: Hu Jiejie , Qin Lijun , Zhu Guoqiang , Ren Jingjing , Wang Hongxia , Jin Jing , Zheng Haixue , Li Dan , Ge Zhaoming 
Published: January 2025

IntroductionCerebral ischemia–reperfusion (IR) causes severe secondary brain injury. Previous studies have demonstrated that ferroptosis is involved in IR-induced brain injury. However, whether IR induces ferroptosis in brain microvascular endothelial cells (BMVECs) is not fully understood.Materials and methodsOxygen–glucose deprivation/reoxygenation (OGDR) was performed in bEND.3 cells to mimic IR injury in vitro, and a focal cerebral IR model was created in C57BL/6 mice. Transcriptomic sequencing of the cells was performed first, followed by bioinformatics analysis. Differentially expressed gene (DEG) enrichment analysis highlighted ferroptosis-related pathways.ResultsUsing Venn analysis, nine ferroptosis-related DEGs were identified, namely, Slc3a2, Slc7a11, Ccn2, Tfrc, Atf3, Chac1, Gch1, Lcn2, and Sesn2. Protein–protein interaction (PPI) analysis combined with molecular complex detection (MCODE) identified six hub genes, namely, Ddit3, Atf3, Sesn2, Trib3, Ppp1r15a, and Gadd45a. Spearman’s correlation analysis revealed a significant correlation between the hub genes and ferroptosis-related DEGs. After reperfusion, the levels of ferroptosis indicators were elevated, and the expression of the ferroptosis-related proteins Xc− and GPX4 decreased. SESN2 is a hub gene and key antioxidant regulator. SESN2 silencing reduced the expression of System Xc− and GPX4, whereas overexpression of SESN2 promoted the expression of System Xc− and GPX4.DiscussionThese results suggest that SESN2 is a negative regulator of ferroptosis. Enhancing the expression of SESN2 can alleviate ferroptosis through the activation of the System Xc−/GPX4 pathway. By integrating bioinformatics analysis with mechanistic exploration, this study revealed that ferroptosis plays a crucial role in IR-induced BMVECs injury, with SESN2 acting as a negative regulator via the System Xc−/GPX4 pathway.
GOLPH3 inhibits glioma cell apoptosis through the JNK signaling pathway
Authors: Xie Shao , Ding Jiahai , Wang Zhaohao , Shi Hengliang , Yu Zheng-Quan 
Published: January 2025

BackgroundGlioma, a primary intracranial tumor, is marked by high rates of mortality and disability, making it a significant health concern. Understanding the molecular mechanisms underlying glioma initiation and progression and identifying potential therapeutic targets for gene therapy are crucial for improving patient outcomes. Golgi phosphoprotein 3 (GOLPH3), predominantly localized at the trans-Golgi network, has been implicated in the pathogenesis of various cancers. However, its precise role in glioma progression remains under active investigation.MethodsTo elucidate the function of GOLPH3, U87 glioma cells were transfected with GOLPH3-specific small interfering RNA (siRNA) to suppress its expression. An in vivo glioma model was generated by implanting GOLPH3-knockdown U87 cells into nude mice. Apoptosis was assessed using flow cytometry, immunofluorescence staining, TUNEL assays, and Western blotting. The activation of the JNK signaling pathway was evaluated by analyzing the phosphorylation levels of JNK and c-Jun through Western blotting.ResultsDownregulation of GOLPH3 in U87 glioma cells significantly enhanced apoptosis, as evidenced by increased levels of cleaved caspase-3 and higher apoptosis rates. Furthermore, GOLPH3 knockdown led to the activation of the JNK signaling pathway, as indicated by elevated phosphorylation of JNK and c-Jun. In vivo, suppression of GOLPH3 expression inhibited tumor growth and increased apoptosis within the tumor microenvironment.ConclusionThese findings suggest that GOLPH3 might play a pivotal role in regulating apoptosis in malignant glioma cells via the JNK signaling pathway. Thus, GOLPH3 may represent a promising therapeutic target for glioma treatment.