bluuebunny/crossref_metadata_2025 huggingface dataset:
Efektivitas Penggunaan Aplikasi Open Source dalam Pembelajaran Matematika Komputer
Authors: Setiawan I Made Dedy
Published: January 2025

Mathematics is an important aspect in the higher education curriculum, especially in the field of computer science. The role of mathematics such as calculus, algebra and statistics is urgent for current technological developments. So far, computer mathematics learning in INSTIKI classes has not utilized open source-based applications. For this reason, innovation is needed in mathematics learning, one of which is by utilizing the Geogebra application. The aim of this research is to determine the effectiveness of using open source applications in computer mathematics learning. This research follows a quantitative descriptive research design involving a sample of 50 respondents selected purposively. Data was collected using a questionnaire consisting of 20 statement items and divided into three aspects, namely suitability of the material, convenience and attractiveness. The data was then analyzed descriptively quantitatively. The research results showed that from the suitability aspect of the material, the most dominant answer was obtained, namely strongly agree at 57%, from the convenience aspect, the most dominant answer was obtained, namely agree at 43%, while from the attractiveness aspect, the most dominant answer was obtained, namely strongly agree at 54%. From the research results it can be concluded that the use of open source applications is quite effective in learning computer mathematics.
PENERAPAN PEMBELAJARAN BERBANTUAN TEKNIK ICE BREAKING PADA MATA KULIAH ALJABAR LINEAR TERHADAP HASIL BELAJAR MAHASISWA
Authors: Suryati Kadek , Setiawan I Made Dedy
Published: January 2025

Tujuan dari penelitian ini adalah untuk mengetahui pengaruh penerapan pembelajaran berbantuan teknik ice breaking pada mata kuliah aljabar linear. Jenis penelitian ini adalah penelitian quasi experiment (eksperimen semu). Subjek dari penelitian ini adalah mahasiswa jurusan rekayasa sistem komputer semester dua. Teknik sampel penelitian diambil dengan metode random sampling. Sampel dibagi menjadi satu kelas eksperimen dan satu kelas kontrol. Untuk kelas eksperimen akan diberikan pembelajaran dengan Teknik ice breaking dan untuk kelompok kontrol dengan pembelajaran konvensional. Dengan melaksanakan tiga tahapan yaitu tahapan persiapan, tahap pelaksanaan dan tahap akhir. Metode pengumpulan data yang dilakukan adalah dokumentasi dan metode tes. Jenis data yang dikumpulkan adalah data primer dan sekunder. Untuk metode analisis data akan dilakukan dengan bantuan program SPSS menggunakan uji t. Dari hasil penelitian dan analisis data diperoleh nilai statistik ujinya sebesar 2,8820 dengan nilai signifikasi sebesar 0,0071 dengan taraf signifikan 0,05 maka menunjukkan bahwa adanya pengaruh penerapan pembelajaran berbantuan teknik ice breaking terhadap hasil belajar mahasiswa.
Profil Kemampuan Berpikir Kritis dan Kreatif Siswa SMA Pada Materi Energi Terbarukan
Authors: Aminingsih Amilia , Khoiri Nur , Nuroso Harto , Hayat Muhammad Syaipul
Published: January 2025

Critical and creative thinking skills at SMA Pangudi Luhur (PL) Don Bosko are still classified as moderate critical thinking and less creative thinking, respectively. This illustrates that some students have not been able to interpret information scientifically and develop ideas to solve a problem. This study aims to analyze students' critical and creative thinking skills in understanding renewable energy material at SMA PL Don Bosko. These skills are important to face global challenges related to sustainable energy utilization. The research method used is descriptive with quantitative and qualitative approaches. Data were obtained through tests and questionnaires involving 20 students as respondents. The results of the analysis show that most students have critical thinking skills in the moderate category with an average achievement percentage of 62.94%, with the most dominant aspect of Elementary Clarification. However, students' creative thinking skills are still classified as lacking with an average achievement of 63.8%, with dominant results in the fluency aspect. Factors such as learning approaches, active student involvement, and learning resource support influence the development of these skills. This study suggests integrating a project-based learning model to improve students' critical and creative thinking skills on renewable energy materials.
SEKOLAH PENCETAK WIRAUSAHA DALAM PERSPEKTIF ESD DI SMK BINA UTAMA KENDAL
Authors: Budiati Idha , Febrihastatiwi Dinda , Ajibudiarta Riska , Roshayanti Fenny
Published: January 2025

Tingginya pengangguran lulusan SMK menjadi masalah mendesak yang memerlukan solusi konkret. Direktorat Pembinaan SMK bekerja sama dengan SEAMEO mengembangkan program Sekolah Pencetak Wirausaha (SPW) untuk menumbuhkan jiwa kewirausahaan siswa agar mampu membangun bisnis mandiri dan berkelanjutan. Penelitian ini bertujuan mengeksplorasi implementasi program SPW berbasis ESD di SMK Bina Utama Kendal menggunakan pendekatan deskriptif kualitatif. Data dikumpulkan melalui observasi, kuesioner, dan wawancara terhadap siswa, guru, dan pengelola SPW. Hasil penelitian menunjukkan pada aspek lingkungan, 60% siswa mengurangi sampah plastik melalui daur ulang, meskipun pengelolaan sampah masih perlu diperbaiki. Pada aspek ekonomi, 85% siswa merasa pelatihan SPW meningkatkan keterampilan mengelola usaha berkelanjutan. Pada aspek sosial, 64% siswa merasakan dampak positif program ini, meskipun keterlibatan masyarakat lokal perlu diperkuat. Sehinga program SPW berbasis ESD efektif membantu siswa menjadi wirausahawan mandiri dan berkelanjutan serta dapat menjadi model pendidikan kewirausahaan di sekolah kejuruan lain.
Integrating spirituality into physical therapy: exploring its emerging role as a recognized determinant of health
Authors: Garcia Trepte Alessandra , Goins TR , Eubanks Bridget , E Joseph Valerie , English Adam
Published: January 2025

This masterclass explores the increasing recognition of spirituality as a vital aspect of patient care, alongside other Social Determinants of Health (SDH) such as economic stability and education. The distinction between spirituality and religion is clarified, with spirituality described as a broader, more personal experience that can exist both within and outside of religious contexts. Research demonstrates that spirituality influences health in mostly positive ways, particularly in areas like mental health, resilience, and coping, making it a critical component of holistic, patient-centered care. In physical therapy, incorporating a patient’s spirituality into their plan of care can enhance cultural competence and foster a more holistic care approach. However, many Physical Therapists (PTs) express uncertainty in addressing spiritual concerns, often due to limited training or unclear role expectations. The authors suggest that integrating tools like the Inclusive Spiritual Connection Scale (ISCS), Functional Assessment of Chronic Illness Therapy-Spiritual Well-Being Scale (FACIT-Sp), Spiritual Well-Being Questionnaire (SWBQ), the Spiritual Health and Life-Orientation Measure (SHALOM), or the Spiritual Transcendence Scale (STS), along with enhanced education, could help therapists incorporate spirituality into practice more seamlessly. Integration of spirituality enables PTs to deliver more complete, personalized care that addresses the whole person. Ultimately, the authors advocate for recognizing spirituality as a key determinant of health and an important component of healthcare to ensure more inclusive treatment.
Assessment of the Cardiovascular Risk of High-Fat-High-Fructose Diet in Hereditary Hypertriacylglycerolemic Rats and Venlafaxine Effect
Authors: Sasváriová M , Salvaras L , Sečkárová Micháliková D , Tyukos Kaprinay B , Knezl V , Gáspárová Z , Stankovičová T
Published: January 2025

Metabolic syndrome (MetS) represents a worldwide health problem, affecting cardiovascular and mental health. People with MetS are often suffering from depression. We used hereditary hypertriacylglycerolemic (HTG) rats as an animal model of MetS, and these were fed a high-fat-high-fructose diet (HFFD) to imitate unhealthy eating habits of people having several MetS risk factors and suffering depression. Male HTG rats were fed a standard diet (HTG-SD) or HFFD for eight weeks (HFFD8). Venlafaxine was administered for the last three weeks of the experiment (HFFD8+VE). Heart function was observed on the level of intact organisms (standard ECG in vivo), isolated hearts (perfusion according to Langendorff ex vivo), and molecular level, using the RT-PCR technique. The function of the isolated perfused heart was monitored under baseline and ischemia/reperfusion conditions. Analysis of ECG showed electrical abnormalities in vivo, such as significant QRS complex prolongation and increased heart rate. Ex vivo venlafaxine significantly reduced QT interval after ischemia/reperfusion injury. Baseline values of contractile abilities of the heart tended to be suppressed by HFFD. A significant reduction of LVDP was present in the HFFD8 group. Molecular analysis of specific genes involved in cardiac electrical (Cacna1c, Scn5a), contractile (Myh6, Myh7), metabolic function (Pgc1α) and calcium handling (Serca2a, Ryr2) supported some of the functional findings in vivo and ex vivo. Based on the present effect of venlafaxine on heart function, further research is needed regarding its cardiometabolic safety in the treatment of patients with MetS suffering from depression.
End-to-end 3D instance segmentation of synthetic data and embryo microscopy images with a 3D Mask R-CNN
Authors: David Gabriel , Faure Emmanuel
Published: January 2025

In recent years, the exploitation of three-dimensional (3D) data in deep learning has gained momentum despite its inherent challenges. The necessity of 3D approaches arises from the limitations of two-dimensional (2D) techniques when applied to 3D data due to the lack of global context. A critical task in medical and microscopy 3D image analysis is instance segmentation, which is inherently complex due to the need for accurately identifying and segmenting multiple object instances in an image. Here, we introduce a 3D adaptation of the Mask R-CNN, a powerful end-to-end network designed for instance segmentation. Our implementation adapts a widely used 2D TensorFlow Mask R-CNN by developing custom TensorFlow operations for 3D Non-Max Suppression and 3D Crop And Resize, facilitating efficient training and inference on 3D data. We validate our 3D Mask R-CNN on two experiences. The first experience uses a controlled environment of synthetic data with instances exhibiting a wide range of anisotropy and noise. Our model achieves good results while illustrating the limit of the 3D Mask R-CNN for the noisiest objects. Second, applying it to real-world data involving cell instance segmentation during the morphogenesis of the ascidian embryo Phallusia mammillata, we show that our 3D Mask R-CNN outperforms the state-of-the-art method, achieving high recall and precision scores. The model preserves cell connectivity, which is crucial for applications in quantitative study. Our implementation is open source, ensuring reproducibility and facilitating further research in 3D deep learning.
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

Introduction

Hepatocellular 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.

Methods

The 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.

Results

The 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.

Discussion

This 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.
Xenopus laevis neural stem progenitor cells exhibit a transient metabolic shift toward glycolysis during spinal cord regeneration
Authors: Slater Paula G. , Domínguez-Romero Miguel E. , Campos Guillermo , Aravena Vania , Cavieres-Lepe Javier , Eisner Verónica
Published: January 2025

Spinal cord injury (SCI) results in severe disruption of communication between the brain and body, causing motor, sensory, and autonomic dysfunctions. While SCI in mammals leads to permanent impairment due to limited regenerative capacity, certain non-mammalian species, such as Xenopus laevis larval stages, exhibit remarkable regenerative abilities. During Xenopus laevis spinal cord regeneration, neural stem precursor cells (NSPCs) surrounding the central canal rapidly proliferate in response to SCI, compensating for cellular loss, restoring canal continuity, and generating new neurons to reestablish lost connections. It has been described that mitochondria and cellular metabolism play essential roles in stem cell proliferation, self-renewal, and differentiation. However, the mitochondrial and cellular metabolic response during spinal cord regeneration remains unexplored. This study uses electron and confocal microscopy to investigate the NSPCs mitochondrial response in Xenopus laevis following SCI. We observed that mitochondria exhibit a rapid and transient response after SCI, characterized by a disruption of the mitochondrial localization, a decrease in mitochondrial number per cell section, and an increase in mitochondrial area and circularity. Furthermore, mitochondria adopted a swollen phenotype, which did not impair mitochondrial function or cellular energy balance. This morphological shift was accompanied by a transient decrease in the mitochondrial membrane potential and a metabolic switch favoring glycolysis. Therefore, these findings demonstrate that a transient metabolic shift toward glycolysis occurs during spinal cord regeneration.
Cryptic transmission of a SARS-CoV-2 variant detected by wastewater surveillance in Panama
Authors: Gaitán Melissa , Zaldivar Yamitzel , Hernandez Michelle , Góndola Jessica , Chavarría Oris , Moreno Brechla , Franco Danilo , DeAntonio Rodrigo , Mirazo Santiago , Cancela Florencia , Barnett Maria Eugenia , Martinez Alexander A. , Pascale Juan Miguel , López-Vergès Sandra
Published: January 2025

The COVID-19 pandemic highlighted the critical role of viral genomic surveillance, prompting numerous countries to enhance their monitoring systems for acute respiratory infections (ARIs), especially influenza-like illnesses (ILIs). Given the significance of asymptomatic cases in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission, cases often undetected by the ILI surveillance, a more comprehensive approach was essential to track the circulation of SARS-CoV-2 variants in the population. In response, many countries swiftly adopted wastewater surveillance, which allowed the early detection of SARS-CoV-2 variants before they were identified through molecular characterization from confirmed clinical cases. In this report, we detail the implementation of SARS-CoV-2 wastewater genomic surveillance in Panama during the first half of 2024. Wastewater samples were collected monthly in duplicate at two collection points from three districts of Panama city metropolitan area for testing by SARS-CoV-2 RT-qPCR, and positive samples were analyzed by next-generation sequencing to identify sublineages. A total of 36 wastewater samples and 822 samples obtained through the clinical surveillance were analyzed for molecular detection and sequencing. Sublineages detected by wastewater surveillance were compared to those detected by clinical surveillance for the same period of time. Wastewater surveillance allowed the identification of the Omicron sublineage JN.1.16.1 in the capital city and its surroundings, which was not detected by the clinical surveillance in the country, despite its global circulation. This highlights the critical need to sustain both genomic surveillance programs beyond the pandemic in countries like Panama that serve as pivotal exchange hubs.
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

Introduction

Endometrial 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.

Methods

The 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.

Results

The 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.

Discussion

The 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.
Where the wild things are...stored? The management and return of seized wildlife
Authors: Saito Anna
Published: January 2025

As more and more wildlife is seized across the globe due to the unlawful possession, handling and trading of protected wildlife species, the wildlife which needs to be managed by enforcement agencies keeps expanding. While seizure data alone is deemed insufficient to measure the illegal wildlife trade, given the complexity of the many drivers and pressures associated, the elevated numbers of wildlife seized provide nevertheless evidence of a global illicit trade that is in progress and seemingly prospering. Disentangling what happens to seized wildlife can be difficult. By using multiple methods including documentary analysis, seizure data analysis and key informant interviews, this study examines seizure management in four countries: Kenya and Uganda in East Africa and Germany and Czech Republic in Central Europe. Wildlife continues to be treated in many instances even after seizure on the basis of continued commodification, or enters a transient state of simultaneous commodification and decommodification, which influences seizure management framing and implementation. Dismissed as the unfortunate collateral of the illegal wildlife trade, live animals, dead animals and derivatives pass in the background. While seizure management processes are underdeveloped, patchy, neglected or burdened by resource constraints, responsible authorities, institutions and individuals struggle to find adequate solutions. By laying this much-needed groundwork for understanding seizure management in practice, opportunities to build on this work to investigate more substantive questions around conservation, environmental and restorative justice are created.
Non-enzymatic protein targeting agents as a promising strategy for cancer treatment
Authors: Ambrose Madison , Lee Jeremy , Syed Aleem , Ahmed Zamal , Peng Guang
Published: January 2025

Increased research attention has been brought to non-enzymatic protein targeting agents as a new and effective strategy for advancing cancer treatment. To discover this class of new anticancer drugs, two molecular approaches targeting the non-enzymatic activities of proteins have shown promising experimental, preclinical, and clinical results. In the first approach, selective agents known as PROteolysis-TArgeting Chimeras (PROTACs) employ innate endogenous protein degradation machinery in cells to proteolyze the targeted protein. The combination of the highly selective PROTACs and exploitation of cellular protein degradation pathways provides the opportunity to treat diseases that were previously deemed incurable due to lack of enzymatic activities of the targeted proteins. The second approach targets protein-protein interactions (PPIs) as an alternative non-enzymatic route that alters the functional activities of protein complexes and thus significantly influence cancer cell fitness and survival. To efficiently identify potential chemical leads for these approaches, high-throughput screening (HTS) has been extremely valuable due to its ability to quickly screen large libraries of compounds. In this review paper, we will provide an overview of developing anti-cancer agents targeting non-enzymatic activities of proteins and the potential clinical impact of this new class of inhibitors.
Vibration signal characteristics of debris flow initiation and motion experiments by considering clay content
Authors: Li Zhaodong , Huang Zhiyong , Li Ping , Tian Zhiqi , Jia Enxian , Li Tonglu
Published: January 2025

Micro accelerometers are crucial tools for monitoring and providing early warning of geological disasters. This study focuses on the potential debris flow in Wangjiayuan, Fang County, Hubei Province, aiming to explore the relationship between clay content and debris flow motion characteristics. Physical model experiments were designed with varying clay content to simulate debris flow motion, and micro accelerometers were employed to monitor and record vibration acceleration changes during debris flow initiation and motion. Frequency spectra were generated using Fourier transform to analyze the motion characteristics in the frequency domain. The results showed that the predominant period of debris flow initiation ranged from 15 Hz to 29 Hz, while the period during motion in the middle section of the flow area ranged from 36 Hz to 54 Hz. Higher clay particle content was associated with a decrease in both the frequency range and mean of the predominant period, as well as a reduction in the Fourier amplitude extremum. These findings provide a foundation for monitoring and predicting debris flows, and the vibration signal characteristics of debris flow initiation and motion can be used to infer the clay content, offering insights into early warning systems for such geological hazards.
South African audiologists need business skills to survive: toward a responsive curriculum
Authors: Sebothoma Ben , Khoza-Shangase Katijah , Moroe Nomfundo
Published: January 2025

South African audiologists are struggling to find jobs after completing their compulsory government-mandated year of community service in public healthcare institutions. This is in spite of the documented inequity in audiology service provision, and capacity versus demand challenges around the ear and hearing workforce in the presence of an increasing prevalence of hearing and vestibular disorders. The high prevalence of hearing and vestibular disorders linked to various causes including the quadruple burden of disease that South Africa suffers from indicates that there is a clear need for more audiologists to be employed in various sectors in order to improve access to hearing healthcare and enhance early identification and intervention to reap the economic and quality of life benefits of preventive care. We argue for urgent curriculum reform that is responsive to the context by equipping South African audiology students with the skills to be able to successfully confront the current economic crisis.
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.
Influence of bio-filter configurations on hydraulic aspects while enhancing the sustainable self-purification of agricultural drainage water
Authors: Alrowais Raid , Jatwary Ashraf , Bindzarova Gergelova Marcela , Akrami Mohammad , Alwushayh Bandar , Elkamhawy Elsayed
Published: January 2025

As global climate change exacerbates water scarcity, recycling agricultural drainage water is emerging as a promising solution in water resources-limited regions. This research investigated the hydraulic impact of using gravel bio-filters in contaminated water-courses, focusing on submerged bioreactors as a sustainable engineering solution. This study assessed the hydraulic impacts of installing these bioreactors in polluted waterways using three-dimensional numerical models based on computational fluid dynamics. Results indicated that relative heading-up will increase with the Froude number, demonstrating a direct relationship between flow velocity and heading-up. Altering the shape of bio-filter inlet is predicted to significantly influence heading-up values, with triangular shapes showing the lowest heading-up values compared to basic, rounded, or sloped upstream U.S face shapes. Relative heading-up values will increase by 10.32%, 10.44%, 24.67%, and 31.86% when changing the bio-filter inlet shape from triangular to sloped U.S. face with respect to horizontal and vertical direction, rounded, and basic bio-filter, respectively. Additionally, the number and orientation of shapes in the bio-filter inlet impact relative heading-up, with varying effects predicted based on the inclination angle. These findings provide valuable guidance for mitigating hydraulic impacts and optimizing the design and operation of bioreactors in water resource management, promoting sustainable water purification approaches in contaminated watercourses and conserving surrounding environments.
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

Objectives

This 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.

Methods

Relevant 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.

Results

From 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.

Conclusion

Ferroptosis, 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

Background

Identifying 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.

Methods

We 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.

Results

Extensive 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.

Conclusion

ZINQ-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

Introduction

Idiopathic 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.

Methods

We 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.

Results

A 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.

Discussion

This 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

Introduction

Cerebral 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 methods

Oxygen–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.

Results

Using 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.

Discussion

These 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.
Genome-wide identification and expression analysis of GRAS transcription factors under cold stress in diploid and triploid Eucalyptus
Authors: Liu Jiannan , Chen Hao , Li Chenhe , Du Kang , Yang Jun
Published: January 2025

The GRAS [GRI (Gibberellic Acid Insensitive), RGA (Repressor of GAI-3 mutant), and SCR (Scarecrow)] transcription factors play a pivotal role in the development and stress responses of plants. Eucalyptus is an important fast-growing tree species worldwide, yet its poor cold tolerance limits its cultivation range. This study conducted a bioinformatics analysis of Eucalyptus grandis GRAS family and investigated the expression patterns of GRAS genes in different ploidy Eucalyptus under cold treatment. This study identified 92 EgrGRAS genes, which were divided into eight subfamilies. Interspecies synteny analysis found that E. grandis and Populus trichocarpa have more syntenic GRAS gene pairs. Chromosome localization analysis revealed that 90 EgrGRAS genes were found to be unevenly distributed across 11 chromosomes. Gene structure analysis found similar intron-exon structures in EgrGRAS genes. Protein motif analysis revealed that proteins within the same subfamily have certain structural similarities. The physical and chemical properties of the proteins encoded by EgrGRAS genes vary, but the ranges of amino acid numbers, molecular weights, and isoelectric points (pI) are similar to those of GRAS proteins from other species. Subcellular localization prediction using software found that 56 members of EgrGRAS family are localized in the nucleus, with a few members localized in the cytoplasm, chloroplasts, and mitochondria. Tobacco subcellular localization experiments verified a nuclear-localized GRAS transcription factor. Cis-acting element analysis predicted that EgrGRAS genes are involved in the growth as well as the response to hormones, light induction, and low-temperature stress. Transcriptome data analysis and quantitative real-time PCR (qRT-PCR) experiments in diploid and triploid Eucalyptus urophylla found that some EgrGRAS genes exhibited upregulated expression under different cold treatment durations, with certain genes from the LISCL, PAT1, and DELLA subfamilies significantly upregulated in triploid Eucalyptus. These EgrGRAS transcription factors may play an important role in Eucalyptus response to cold stress. The study lays a molecular foundation for the breeding of cold-resistant Eucalyptus varieties.
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

Background

Glioma, 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.

Methods

To 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.

Results

Downregulation 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.

Conclusion

These 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.
Immunoglobulin M response in largemouth bass (Micropterus salmoides) following ranavirus infection
Authors: Huang Zhenyu , Liu Naicheng , Xue Mingyang , Xu Chen , Fan Yuding , Meng Yan , Jiang Nan , Li Yiqun , Liu Wenzhi , He Yang , Zhou Yong
Published: January 2025

Immunoglobulin M (IgM) and IgM+ B cells are key components of the humoral immune system, providing defense against pathogen invasion. While the role of IgM in the systemic and mucosal immune responses of fish to parasites and bacteria has been partially investigated, its function in viral infections remains underexplored. This study successfully developed a largemouth bass (Micropterus salmoides) model for ranavirus immersion infection. Our findings revealed that viral infection caused significant pathological changes in the gill and head kidney tissues, along with a marked upregulation of adaptive immune gene expression. Interestingly, fish that survived an initial viral infection exhibited minimal mortality and low viral loads in the gill and head kidney tissues when exposed to a higher viral concentration. Notably, in these fish with secondary infections, there was a significant increase in IgM protein levels in both the blood and gill mucus, as well as a pronounced accumulation of IgM+ B cells in the gill and head kidney tissues. Additionally, the serum contained high levels of virus-specific IgM, which demonstrated the ability to neutralize the virus. These findings highlight the crucial role of IgM in the immune response to viral infections in largemouth bass and suggest its potential as a target for enhancing viral resistance in aquaculture.
Carboplatin-resistance-related DNA damage repair prognostic gene signature and its association with immune infiltration in breast cancer
Authors: Dong Shuwen , Li Anqi , Pan Ruixin , Hong Jin , Wang Zheng , Shen Kunwei
Published: January 2025

Introduction

Breast cancer is among the most prevalent malignant tumors globally, with carboplatin serving as a standard treatment option. However, resistance often compromises its efficacy. DNA damage repair (DDR) pathways are crucial in determining responses to treatment and are also associated with immune infiltration. This study aimed to identify the DDR genes involved in carboplatin resistance and to elucidate their effects on prognosis, immune infiltration, and drug sensitivity in breast cancer patients.

Methods

A 3D-culture model resistant to carboplatin was constructed and sequenced. Co-expressed DDR genes were analyzed to develop a predictive model. Immune infiltration analysis tools were employed to assess the immune microenvironment of patients with varying expression levels of these risk genes. Additionally, drug sensitivity predictions were made to evaluate the efficacy of other DNA damage-related drugs across different risk groups. Molecular assays were performed to investigate the role of the key gene TONSL in breast cancer.

Results

By integrating data from public database, we established a prognostic signature comprising thirteen DDR genes. Our analysis indicated that this model is associated with immune infiltration patterns in breast cancer patients, particularly concerning CD8+ T cells and NK cells. Additionally, it demonstrated a significant correlation with sensitivity to other DDR-related drugs, suggesting its potential as a biomarker for treatment efficacy. Compared to the control group, TONSL-knockdown cell lines exhibited a diminished response to DNA-damaging agents, marked by a notable increase in DNA damage levels and enhanced drug sensitivity. Furthermore, single-cell analysis revealed elevated TONSL expression in dendritic and epithelial cells, particularly in triple-negative breast cancers.

Conclusions

Carboplatin resistance-related DDR genes are associated with prognosis, immune infiltration, and drug sensitivity in breast cancer patients. TONSL may serve as a potential therapeutic target for breast cancer, particularly in triple-negative breast cancer, indicating new treatment strategies for these patients.