bluuebunny/crossref_metadata_2025_split huggingface dataset:
Investigation of the Genomic and Transcriptomic Variations Underlying Tamoxifen Resistance in Breast Cancer
Authors: Solaimani Maryam , Reza Emad , Ranjbar Mojtaba 
Published: March 2024

Abstract

Background: Breast cancer is a global burden responsible for millions of deaths per year. One of the significant challenges in the treatment of it is due to the emergence of resistance towards certain drugs, including well-known medication, Tamoxifen. With recent advances in technology, many genes have been identified to be involved in the progression of breast cancer and the development of resistance. Studying these genes and their potential pathways in cancer is a vital aspect of treatment that can enhance patients' response to therapeutic agents.
Methods: In the present study, we investigated major genes associated with the risk of breast cancer and the creation of tamoxifen drug resistance within them. We analyzed data from GO datasets (GSE231629, GSE241654, and GSE42568). Differentially expressed genes were studied in the limma package in the R language and TAC software. Enrichr carried out gene ontology, gene set enrichment, and genomic pathway analysis. Gephi, Cytoscape, and STRING databases were employed to build the network of protein-protein interactions and miRNA-lncRNA-mRNA network.
Results: analysis of differentially expressed genes demonstrated several hub genes including POSTN, COL1A2, LUM, COL3A1, BRINP3, TBX2-AS1, ARHGAP36, DSCAM-AS1 and SOX2 involved in breast cancer progression and resistance toward tamoxifen drug in MCF7 cell lines. These genes are associated with various biological processes such as intracellular signal transduction, MAPK Cas cade, gene expression, protein phosphorylation, and regulation of cell population proliferation.
Conclusion: Our study demonstrates protein-protein interaction and significant genes involved in the development of breast cancer and tamoxifen resistance in MCF7 cell lines.
Evaluation of radiation therapy on grafted and non-grafted defects - an experimental rat model
Authors: Irie Milena Suemi , Reis Isabella Neme Ribeiro dos , Osuna Luiz Gustavo Gonzáles , de Oliveira Guilherme José Pimentel Lopes , Spin-Neto Rubens , Soares Priscilla Barbosa Ferreira 
Published: March 2024

Abstract
Objectives
To evaluate the effect of radiation therapy in a single dose (15Gy) on grafted and non-grafted defects regarding the bone microarchitecture and collagen maturity.
Materials and Methods
Bone defects were surgically created in rat femurs. The right femur defect was filled by blood clot (“Clot”) and the left femur defect- by deproteinized bovine bone mineral graft (“Xenograft”). The animals were aleatory divided into 2 groups: without radiation therapy (nRTX) and with radiation therapy (RXT). Microtomographic (bone volume fraction - BV/TV, trabecular thickness - Tb.Th, trabecular number - Tb.N, trabecular separation - Tb.Sp), histological, and histomorphometric analyses were performed 14 days after the surgery. Two-way ANOVA with Tukey post-hoc test was used to compare the groups (α = 5%).
Results
Microtomographic analysis revealed that radiotherapy led to smaller BV/TV and Tb.N in both Clot and Xenograft. Regardless of the radiotherapy, defects filled with xenograft showed larger Tb.N. In contrast, Clot groups demonstrated increased values of BV/TV and Tb.Th. Histomorphometric results agreed with those of microtomography. Intermediately and densely packed collagen were predominant among the groups. Histological analysis revealed a disorganized bone formation bridging the cortical borders of the lesion in RTX groups. Primary bone involving the graft particles was commonly observed in all Xenograft groups, and radiotherapy did not affect the percentage of bone-graft contact.
Conclusions
Radiation therapy in a single dose affected the bone repair with smaller amount of newly formed bone in both grafted and non-grafted defects.
Clinical Relevance:
The use of bone substitute grafts might be feasible prior to radiotherapy.
GoiStrat - Gene-of-interest-based sample stratification for the evaluation of functional differences
Authors: Malla Carlos Uziel Pérez , Kalla Jessica , Tiefenbacher Andreas , Wasinger Gabriel , Kluge Kilian , Egger Gerda , Sheibani-Tezerji Raheleh 
Published: March 2024

Abstract

Purpose: Understanding the impact of gene expression in pathological processes, such as carcinogenesis, is crucial for understanding the biology of cancer and advancing personalised medicine. Yet, current methods lack biologically-informed-omics approaches to stratify cancer patients effectively, limiting our ability to dissect the underlying molecular mechanisms.
Results: To address this gap, we present a novel workflow for the stratification and combined analysis of RNA-Seq and DNA methylation samples. Leveraging MSigDB curated gene sets, and utilising graph machine learning and ensemble clustering, we identify specific pathways and functional genes. We applied our workflow to analyse nearly a thousand prostate cancer samples, focusing on the varying expression of the \textit{FOLH1} gene. We identified pathways such as the PI3K-AKT-mTOR gene sets as well as signatures linked to prostate tumour aggressiveness.
Conclusion: Our comprehensive approach provides a novel tool to identify disease-relevant functions of genes of interest (GOI) in large datasets. This integrated approach offers a valuable framework for understanding the role of the expression variation of a GOI in complex diseases and for informing on targeted therapeutic strategies.
Neuromuscular electrical stimulation to combat cognitive aging in people with spinal cord injury: protocol for a single case experimental design study
Authors: Vints Wouter A.J. , Levin Oron , Griensven Martijn van , Vlaeyen Johan W. S. , Masiulis Nerijus , Verbunt Jeanine , Laake-Geelen Charlotte van 
Published: March 2024

Abstract

Introduction
Individuals with spinal cord injury (SCI) can experience accelerated cognitive aging. Myokines (factors released from muscle cells during contractions), such as brain-derived neurotrophic factor (BDNF), are thought to have beneficial effects on cognition. Neuromuscular electrical stimulation (NMES) was shown to elicit a large release of myokines. However, the effects of NMES on cognitive function have not been studied.
Objective
To present the study protocol for a clinical trial evaluating the effects of NMES aimed at improving cognition and BDNF.
Methods
A replicated randomized three-phases single-case experimental design (SCED) with sequential multiple baseline time series and a single-armed prospective trial will be conducted with 15 adults with chronic SCI (> 12 months after injury) above L1 neurological level undergoing 30-minute quadriceps NMES, 3 days per week for 12 weeks.
Main study endpoints
Primary endpoint is cognitive performance (assessed by a smartphone test) conducted three times per week during the baseline phase with random duration of 3 to 8 weeks, the intervention phase of 12 weeks, and the follow-up phase of 3 weeks after a no measurement rest period of 12 weeks. Secondary endpoints are changes in BDNF levels and cognitive performance measured before the baseline period, before and after intervention and after a 12 weeks follow-up.
Conclusion
This will be the first study investigating the effects of 12 weeks NMES on both cognition and BDNF levels in individuals with SCI. The SCED results provide information on individual treatment effect courses which may direct future research.
Keywords
Spinal cord injury, myokine, neuromuscular electrical stimulation, cognition, neuroplasticity, brain-derived neurotrophic factor, single case experimental design, chronic rehabilitation care
Trial registration
ClinicalTrials.gov (NCT05822297, 12/01/2023)
Rainfall erosivity and flooding risk assessment in different climate zones of Iran
Authors: Bagherzadeh Ali , Afshar Ehsan , Taleghani Abolfazl , Chaharjouee Alireza Bagherzadeh 
Published: March 2024

Abstract

Rainfall is a major contributor to soil erosion, which its erosive force is measured by rainfall erosivity. This takes into account the amount and intensity of rainfall and is commonly expressed as the R-factor in RUSLE model. The goal of this study is to evaluate rainfall erosivity in Iran using available data sets. Data have been collected from 2,241,924 precipitation grid points in Iran at 1 km resolution. Thirty years precipitation time series ranged from 1991 to 2020. The mean precipitation values varied between 111.46 (BWh) to 1404.15 (Csa) mm. The mean R-factor ranged from 72.66 (BWk) to 3300.71 (Cfa) MJ mm ha−1 h−1 yr−1. The mean erosivity density varied between 0.33 (Dsa) and 2.35 (Cfa) MJ ha−1 h−1. It was exhibited that the arid BSh, and BSk climate zones focused mainly in the northeast, northwest, west and southwest of the country with total 8.88% of the study area exposed from extreme low to low flooding risk. The arid BWh and BWk climate zones with 86.46% of the surface area in the center of Iran, east, south, and some scattered parts in southwest and west of the country exposed from medium high to extreme high flooding risk.
Quantitative Evaluation of Striatal Uptake Ratios Using an Adaptive Template Registration Method for 123I-Ioflupane Dopamine Transporter SPECT
Authors: Mizumura Sunao , TAMAMURA Naoyuki , EBINA Junya , WATANABE Hikaru , HORI Masaaki 
Published: March 2024

Abstract

123I-FP-CIT (123I-Ioflupane) SPECT shows strong accumulation in the striatum, but morphological standardization is challenging due to low accumulation outside the striatum, particularly in subjects with marked striatal decline. In this study, morphological standardization without MRI was achieved using the adaptive template registration (ATR) method to create a subject-specific optimized template with weighted images of normal-type and egg-shape-type templates. The accuracy of a quantitative method for calculating the ratio with nonspecific accumulation in the occipital lobe was evaluated by placing voxels-of-interest (VOI) on standardized images, particularly targeting the striatum.
Methods: The average images of eight subjects, demonstrating normal-type and egg-shape-type tracer accumulation in 123I-Ioflupane SPECT, were utilized as normal and disease templates, respectively. The study included 300 subjects that underwent both 123I-Ioflupane SPECT and MRI for the diagnosis of suspected Parkinson's disease or for exclusion diagnosis. Morphological standardization of SPECT images using structural MRI (MRI-based method) was considered the standard of truth (SOT). Three morphological standardizations without MRI were conducted. The first involved conventional morphological standardization using a normal template (fixed template method), the second employed the adaptive template registration (ATR) method, with a weighted template, and the third used the split-ATR method, processing the left and right striatum separately to address asymmetrical accumulation. VOIs were set on the striatum, caudate, putamen as regions of specific accumulation, and on the occipital lobe as a reference region for nonspecific accumulation.
Results: Results showed significant and robust linearity in the striatal accumulation ratios for all templates when compared with the occipital lobe accumulation ratio when using the MRI-based method. Comparing intra-class correlations for different linearities, the ATR method and split-ATR method demonstrated higher linearity in the striatum, caudate, and putamen. Notably, in subjects with normal striatal (normal-type) or unclear striatal accumulation (burst striatum-type), no obvious improvement in accuracy was achieved when using the ATR or split-ATR methods. However, in subjects with striatal decline or lateral asymmetry, MRI-based methods accurately reflected striatal accumulation.
Conclusion: The use of optimized templates, such as the ATR and split-ATR methods, improved reproducibility in fully automated processing and demonstrated superior linearity compared to that of MRI-based method, in the ratio to the occipital lobe. The ATR method, which enables morphological standardization when using SPECT images only, proved highly reproducible for clinical quantitative analysis of striatal accumulation, facilitating its clinical use.
Noise pollution from Arctic expedition cruise vessels: understanding causes, consequences and governance options
Authors: Mannherz Fabienne , Knol-Kauffmann Maaike , Rafaly Vonintsoa , Ahonen Heidi , Kruke Bjørn Ivar 
Published: March 2024

Abstract

Significant increase in shipping in the Arctic has caught international and national attention. The rising presence of touristic expedition cruise vessels might describe a special case for noise-emitting activities while they seek exclusive opportunities to experience the Arctic first-hand. This interdisciplinary study explores the sources and potential impacts of shipping noise from cruise expeditions in the Arctic and how this knowledge can assist policymakers and industry in increasing environmental safety. The study provides a comprehensive overview of context-specific noise emissions from Arctic cruise expeditions and potential adverse consequences for Arctic endemic marine mammals. In addition, it discusses governance options for mitigating these consequences. Internationally, legal adaptations in the shipping conventions MARPOL and SOLAS should recognise noise as harmful energy. In turn, this could facilitate the uptake of certification schemes based on noise levels in the Polar Code. These legal actions can be strengthened by extended collective self-governance and through introducing economic incentives at the port level.
A head-to-head comparison of 2-[18F]FDG PET/CT and 2-[18F]FDG PET/MR in patients with nasopharyngeal carcinoma under different disease settings
Authors: Zhang Mengxia , Pang Lifang , Yu Haojun , Shi Hongcheng 
Published: March 2024

Abstract

Objectives
MRI is indispensable for staging of nasopharyngeal carcinoma (NPC) as it offers superior soft-tissue contrast. PET/CT and MRI are complementary in accurate staging of NPC. The combination of MRI and functional imaging from PET in PET/MR is promising in NPC management. We compared the diagnostic performance of PET/CT and PET/MR in 46 patients with NPC under different disease scenarios, including primary nonmetastatic cases, primary metastatic cases, recurrence and/or metastasis after treatment, and post-treatment follow-up cases.
Methods
Forty-six patients (37 males and 9 females) underwent both PET/CT and PET/MR within one day (median age: 54.5 years). Primary tumor extension into risk-stratified anatomic structures, retropharyngeal and cervical lymph node metastasis, distant metastasis and post-treatment follow-up results, as well as maximum of standardized uptake value (SUVmax) were evaluated and compared. Bland-Altman analysis was conducted to assess reproducibility of SUVmax between the two modalities. P < 0.05 was considered statistically significant.
Results
For high-risk structures, PET/MR detected two more sides of tensor/levator veli palatine muscle involvement, one more case of clivus involvement, and ruled out 12 false-positive sides of prevertebral muscle involvement by PET/CT. For medium-risk structures, PET/MR detected four more sides of medial pterygoid muscle involvement. For low-risk structures, abnormal signal on massa lateralis atlantis was detected by PET/MR. PET/MR detected 14 more positive retropharyngeal lymph nodes and more liver micrometastases than PET/CT. Overall, PET/MR changed two patients’ T staging. Furthermore, SUVmax showed high reproducibility between PET/CT and PET/MR (P < 0.001).
Conclusions
PET/MR outperforms PET/CT in delineating muscle, skull-base bone, and nodal involvement, and identifying liver micrometastases, may serve as a single-step staging modality for NPC.
Early characterization and prediction of glioblastoma and brain metastases treatment efficacy using medical imaging-based radiomics and artificial intelligence algorithms
Authors: Moreau Noémie N , Valable Samuel , Jaudet Cyril , Dessoude Loïse , Herault Romain , Modzelewski Romain , Stefan Dinu , Thariat Juliette , Lechervy Alexis , Corroyer-Dulmont Aurélien 
Published: March 2024

Abstract
In brain tumors, glioblastoma (GBM) is the most common and aggressive’s one and brain metastases (BM) are occurring in 20-40% of cancer patients. Even with intensive treatment involving radiotherapy and surgery, which frequently leads to cognitive decline due to doses on healthy brain tissue, the median survival is 15 months for GBM and about six to nine for BM. Despite these treatments, GBM patients respond heterogeneously as do patient with BM. Following standard of care, some patients will respond and have an overall survival of more than 30 months and others will not respond and will die within a few months. Differentiating non-responders from responders as early as possible in order to tailor treatment in a personalized medicine fashion to optimize tumor control and preserve healthy brain tissue is the most pressing unmet therapeutic challenge. Innovative computer solutions recently emerged and could help for this challenge. This review will focus on fifty published research between 2013 to 2024 on (1) the early characterization of treatment efficacy with biomarkers imaging and radiomic-based solutions, (2) predictive solutions with radiomic and artificial intelligence-based solutions, (3) interest of other biomarkers and (4) the importance of the prediction of new treatment modalities efficacy.
Integrated transcriptomic analysis reveals a transcriptional regulation network for the biosynthesis of lignin in Nicotiana tabacum in drought stress response
Authors: Rashidifar Maryam , Askari Hossein , Moghadam Ali 
Published: March 2024

Abstract
Lignin plays a crucial impact on the production of phenolic compounds in tobacco smoke, which have potential health implications associated with tobacco use. The meta-analysis of RNA-seq studies along with high-resolution expression analysis on Nicotiana tabacum clarified a conserved distinctive expression pattern of lignin gene network. According to the results, 67 DEGs associated with lignin biosynthesis network were identified of which 17 genes were introduced by meta-analysis. WGCNA showed 14 clusters for the meta-genes. Various TF families and a number of regulatory factors were identified as the most likely candidate genes associated with the lignin metabolic pathway. Eight major meta-genes were evaluated by using qRT-PCR in two tobacco genotypes with different lignin content under drought stress conditions. Genotype NC100 (high lignin content) and Burly (low lignin content) in response to PEG upregulated CAD2, ATH12 and CAD2, CCR, respectively. Despite the accumulation of lignin, the expression levels of CCoAOMT, F5H, COMT, and ODO1 were reduced in both genotypes. The study's exploration into the complex nature of these pathways and meta-analysis highlights the importance of adopting a more comprehensive approach to gene discovery. It suggests that conducting additional individual investigations is crucial for enhancing the reliability and comprehensiveness of gene identification within intricate metabolite pathways.
A Study of Online Relationships: A Sociocultural Perspective
Authors: Pilek Melane , Laurent Constance de Saint 
Published: March 2024

Abstract

Despite the recognition that technology is ubiquitous and critical in modern interpersonal relationships, little is known about the meaning individuals assign to their close online relationships. Furthermore, there persists a negative bias towards online relationships. This study, using a sociocultural approach, sought to address this gap by qualitatively investing adults’ lived experiences and processes of meaning-making in online relationships. Specifically, we sought to identify common dialogical tensions in participants’ discourses as the moments when meaning is created and negotiated in dialogue with the medium and cultural context. Thirteen semi-structured interviews were carried out in-depth with participants who had diverse experiences of close online relationships, including romantic relationships, dating, familial relationships and friendships. We assumed that the distinctiveness of this research design would highlight the interconnectedness between different types of relationships. Additionally, we expected more pronounced levels of tensions among close relationships enabled by technology. Through the analysis of dialogical discursive tensions, we identified four main tensions in the discourses: opportunities/constraints, authenticity/staginess, safety/risk and proximity/distance. The latter emerged as a fundamental tension, intertwining with other tensions, and prompting reflections on the realness, depth, and validity of online relationships. The analysis unveiled that individuals' experiences with online relationships are shaped by the actual use of the medium, societal representation of technology, and cultural discourses. Often, these cultural discourses and representations contrast with individuals' lived experiences, contributing to the tensions. Navigating these factors poses a significant challenge for participants as they negotiate the complexities of online relationships.
Extraction of uranyl from spent nuclear fuel wastewater via complexation - a local vibrational mode study
Authors: peluzo Barbara , Moura Renaldo , Kraka Elfi 
Published: March 2024

Abstract

The efficient extraction of uranyl from spent nuclear fuel wastewater for subsequent reprocessing and reuse in the nuclear cycle is an essential effort towards minimization of long-lived radioactive waste. N-substituted amides and Schiff base ligands are propitious candidates, where extraction occurs via complexation with the uranyl moiety. In this study, we utilized the local vibra- tional modes theory, paired with QTAIM and NBO analyses, to explore chemical bonding in uranyl nitrate, two uranyl picolinamide, one uranyl Schiff base, and three uranyl diamide complexes. The major focus was on (i) the assessment of the equatorial uranyl-ligand O-U and N-U bonding, includ- ing the question of chelation, and (ii) how the strength of the axial uranium oxygen U=O bonds of the uranyl moiety change upon complexation. Our results reveal that the strength of the equatorial uranium-ligand interactions correlates with their covalent character and with charge donation from the O and N lone pairs into the vacant uranium orbitals. We also found an inverse relationship between the covalent character of the equatorial ligand bonds and the strength of the axial uranium-oxygen bond. In summary, our study provides valuable data for a strategic modulation of N-substituted amide and Schiff base ligands towards maximization of uranyl extraction.
Methods: Quantum chemistry calculations were performed with the PBE0 level of theory, where relativistic effects were accounted for via the NESCau Hamiltonian, implemented in Cologne2020, interfaced with Gaussian16. We use a cc-pwCVTZ-X2C basis set for uranium and Dunning’s cc-pVTZ for the remaining atoms. Uranium-ligand bonding was analyzed with LModeA (local vibrational mode analysis), AIMALL (QTAIM analysis), and NBO 7.0 f(NBO analysis.