bluuebunny/crossref_metadata_2025_split huggingface dataset:
MiR-181a targets STING to drive PARP inhibitor resistance in BRCA- mutated triple-negative breast cancer and ovarian cancer
Authors: Bustos Matias A. , Yokoe Takamichi , Shoji Yoshiaki , Kobayashi Yuta , Mizuno Shodai , Murakami Tomohiro , Zhang Xiaoqing , Sekhar Sreeja C. , Kim SooMin , Ryu Suyeon , Knarr Matthew , Vasilev Steven A. , DiFeo Analisa , Drapkin Ronny , Hoon Dave S. B. 
Published: November 2023

Abstract
Background
Poly (ADP-ribose) polymerase inhibitors (PARPi) are approved for the treatment of BRCA-mutated breast cancer (BC), including triple-negative BC (TNBC) and ovarian cancer (OvCa). A key challenge is to identify the factors associated with PARPi resistance; although, previous studies suggest that platinum-based agents and PARPi share similar resistance mechanisms.

Methods
Olaparib-resistant (OlaR) cell lines were analyzed using HTG EdgeSeq miRNA Whole Transcriptomic Analysis (WTA). Functional assays were performed in three BRCA-mutated TNBC cell lines. In-silico analysis were performed using multiple databases including The Cancer Genome Atlas, the Genotype-Tissue Expression, The Cancer Cell Line Encyclopedia, Genomics of Drug Sensitivity in Cancer, and Gene Omnibus Expression.

Results
High miR-181a levels were identified in OlaR TNBC cell lines (p = 0.001) as well as in tumor tissues from TNBC patients (p = 0.001). We hypothesized that miR-181a downregulates the stimulator of interferon genes (STING) and the downstream proinflammatory cytokines to mediate PARPi resistance. BRCA1 mutated TNBC cell lines with miR-181a-overexpression were more resistant to olaparib and showed downregulation in STING and the downstream genes controlled by STING. Extracellular vesicles derived from PARPi-resistant TNBC cell lines horizontally transferred miR-181a to parental cells which conferred PARPi-resistance and targeted STING. In clinical settings, STING levels were positively correlated with interferon gamma (IFNG) response scores (p = 0.01). In addition, low IFNG response scores were associated with worse response to neoadjuvant treatment including PARPi for high-risk HER2 negative BC patients (p = 0.001). OlaR TNBC cell lines showed resistance to platinum-based drugs. OvCa cell lines resistant to platinum showed resistance to olaparib. Knockout of miR-181a significantly improved olaparib sensitivity in OvCa cell lines (p = 0.001).

Conclusion
miR-181a is a key factor controlling the STING pathway and driving PARPi and platinum-based drug resistance in TNBC and OvCa. The miR-181a-STING axis can be used as a potential marker for predicting PARPi responses in TNBC and OvCa tumors.
Functional responses to deforestation in fish communities inhabiting neotropical streams and rivers
Authors: Cantera Isabel , Jézéquel Céline , Dejean Tony , Murienne Jérôme , Vigouroux Régis , Valentini Alice , Brosse Sébastien 
Published: November 2023

Abstract
Background
Deforestation is a widespread disturbance for neotropical freshwater ecosystems. While biodiversity declines have been associated with deforestation, its functional consequences for stream and river fish faunas remain poorly understood. In this study, we explored how deforestation affects the different facets of the functional structure of fish communities inventoried using environmental DNA metabarcoding in 64 river and 35 stream sites of French Guiana. Specifically, we investigated how functional richness, divergence, evenness and identity of fish faunas are affected by deforestation.

Results
We showed that anthropogenic disturbances in French Guiana are modifying the functional diversity of freshwater fish communities. These disturbances not only affected the amount of functional traits held by the communities but also the identity of the traits and the internal structure of the functional space. Consequently, different facets of the functional diversity supported by fish assemblages were altered. In streams, deforestation did not affect the overall diversity of traits but reduced functional redundancy, underlined by a shift in functional identity towards assemblages dominated by pelagic detritivores. In contrast, river fish faunas experienced a decline in functional richness, paired with shifts in functional identity and a loss of fish species with extreme functions.

Conclusions
The response to deforestation differed between streams and rivers, but it supports the hypothesis that deforestation is linked to functional changes in fish assemblages. By diminishing the range of the functions in rivers or by jeopardizing the redundancy of functions in streams, deforestation could severely hamper the functioning and stability of neotropical freshwater ecosystems.
Both extracellular vesicles from helicobacter pylori-infected cells and helicobacter pylori outer membrane vesicles are involved in gastric/extragastric diseases
Authors: Wang Chengyao , Li Wenkun , Shao Linlin , Zhou Anni , Zhao Mengran , Li Peng , Zhang Zheng , Wu Jing 
Published: November 2023

AbstractBacterial-derived extracellular vesicles (EVs) have emerged as crucial mediators in the cross-talk between hosts and pathogens, playing a significant role in infectious diseases and cancers. Among these pathogens, Helicobacter pylori (H. pylori) is a particularly important bacterium implicated in various gastrointestinal disorders, gastric cancers, and systemic illnesses. H. pylori achieves these effects by stimulating host cells to secrete EVs and generating internal outer membrane vesicles (OMVs). The EVs derived from H. pylori-infected host cells modulate inflammatory signaling pathways, thereby affecting cell proliferation, apoptosis, cytokine release, immune cell modification, and endothelial dysfunction, as well as disrupting cellular junctional structures and inducing cytoskeletal reorganization. In addition, OMVs isolated from H. pylori play a pivotal role in shaping subsequent immunopathological responses. These vesicles incite both inflammatory and immunosuppressive reactions within the host environment, facilitating pathogen evasion of host defenses and invasion of host cells. Despite this growing understanding, research involving H. pylori-derived EVs remains in its early stages across different domains. In this comprehensive review, we present recent advancements elucidating the contributions of EV components, such as non-coding RNAs (ncRNAs) and proteins, to the pathogenesis of gastric and extragastric diseases. Furthermore, we highlight their potential utility as biomarkers, therapeutic targets, and vehicles for targeted delivery.
decOM: similarity-based microbial source tracking of ancient oral samples using k-mer-based methods
Authors: Duitama González Camila , Vicedomini Riccardo , Lemane Téo , Rascovan Nicolas , Richard Hugues , Chikhi Rayan 
Published: November 2023

Abstract
Background
The analysis of ancient oral metagenomes from archaeological human and animal samples is largely confounded by contaminant DNA sequences from modern and environmental sources. Existing methods for Microbial Source Tracking (MST) estimate the proportions of environmental sources, but do not perform well on ancient metagenomes. We developed a novel method called decOM for Microbial Source Tracking and classification of ancient and modern metagenomic samples using k-mer matrices.

Results
We analysed a collection of 360 ancient oral, modern oral, sediment/soil and skin metagenomes, using stratified five-fold cross-validation. decOM estimates the contributions of these source environments in ancient oral metagenomic samples with high accuracy, outperforming two state-of-the-art methods for source tracking, FEAST and mSourceTracker.

Conclusions
decOM is a high-accuracy microbial source tracking method, suitable for ancient oral metagenomic data sets. The decOM method is generic and could also be adapted for MST of other ancient and modern types of metagenomes. We anticipate that decOM will be a valuable tool for MST of ancient metagenomic studies.
Bacterial quorum sensing orchestrates longitudinal interactions to shape microbiota assembly
Authors: Su Ying , Xu Ming-ying , Cui Ying , Chen Run-zhi , Xie Li-xiang , Zhang Jing-xiang , Chen Yong-qiu , Ding Tao 
Published: November 2023

Abstract
Background
The mechanism of microbiota assembly is one of the main problems in microbiome research, which is also the primary theoretical basis for precise manipulation of microbial communities. Bacterial quorum sensing (QS), as the most common means for bacteria to exchange information and interactions, is characterized by universality, specificity, and regulatory power, which therefore may influence the assembly processes of human microbiota. However, the regulating role of QS in microbiota assembly is rarely reported. In this study, we developed an optimized in vitro oral biofilm microbiota assembling (OBMA) model to simulate the time-series assembly of oral biofilm microbiota (OBM), by which to excavate the QS network and its regulating power in the process.

Results
By using the optimized OBMA model, we were able to restore the assembly process of OBM and generate time-series OBM metagenomes of each day. We discovered a total of 2291 QS protein homologues related to 21 QS pathways. Most of these pathways were newly reported and sequentially enriched during OBM assembling. These QS pathways formed a comprehensive longitudinal QS network that included successively enriched QS hubs, such as Streptococcus, Veillonella-Megasphaera group, and Prevotella-Fusobacteria group, for information delivery. Bidirectional cross-talk among the QS hubs was found to play critical role in the directional turnover of microbiota structure, which in turn, influenced the assembly process. Subsequent QS-interfering experiments accurately predicted and experimentally verified the directional shaping power of the longitudinal QS network in the assembly process. As a result, the QS-interfered OBM exhibited delayed and fragile maturity with prolonged membership of Streptococcus and impeded membership of Prevotella and Fusobacterium.

Conclusion
Our results revealed an unprecedented longitudinal QS network during OBM assembly and experimentally verified its power in predicting and manipulating the assembling process. Our work provides a new perspective to uncover underlying mechanism in natural complex microbiota assembling and a theoretical basis for ultimately precisely manipulating human microbiota through intervention in the QS network.
The influence of sociodemographic factors on students' attitudes toward AI-generated video content creation
Authors: Pellas Nikolaos 
Published: November 2023

AbstractArtificial Intelligence (AI) and Machine Learning (ML) technologies offer the potential to support digital content creation and media production, providing opportunities for individuals from diverse sociodemographic backgrounds to engage in creative activities and enhance their multimedia video content. However, less attention has been paid to recent research exploring any possible relationships between AI-generated video creation and the sociodemographic variables of undergraduate students. This study aims to investigate the multifaceted relationship between AI-generated video content and sociodemographics by examining its implications for inclusivity, equity, and representation in the digital media landscape. An empirical study about the use of AI in video content creation was conducted with a diverse cohort of three hundred ninety-eighth undergraduate (n = 398) students. Participants voluntarily took part and were tasked with conceiving and crafting their AI-generated video content. All instruments used were combined into a single web-based self-report questionnaire that was delivered to all participants via email. Key research findings demonstrate that students have a favorable disposition when it comes to incorporating AI-supported learning tasks. The factors fostering this favorable attitude among students include their age, the number of devices they use, the time they dedicate to utilizing technological resources, and their level of experience. Nevertheless, it is the student’s participation in AI training courses that exerts a direct impact on students’ ML attitudes, along with their level of contentment with the reliability of these technologies. This study contributes to a more comprehensive understanding of the transformative power of AI in video content creation and underscores the importance of considering instructional contexts and policies to ensure a fair and equitable digital media platform for students from diverse sociodemographic backgrounds.
Baseline and interim [18F]FDG-PET/MRI to assess treatment response and survival in patients with M0 esophageal squamous cell carcinoma treated by curative-intent therapy
Authors: Chao Yin-Kai , Chang Chun-Bi , Chang Yu-Chuan , Chan Sheng-Chieh , Chiu Chien-Hung , Ng Shu-Hang , Hsieh Jason Chia-Hsun , Wang Jen-Hung 
Published: November 2023

Abstract
Background
To investigate the value of [18F]FDG-PET/MRI in predicting treatment response and survival in patients with primary M0 esophageal squamous cell carcinoma.

Methods
Patients with esophageal squamous cell carcinoma received [18F]FDG-PET/MRI at baseline and during neoadjuvant or definitive chemoradiotherapy. The treatment response was classified according to the Response Evaluation Criteria for Solid Tumors 1.1. We used Kaplan-Meier and Cox regression analyses to assess the association between PET/MRI parameters and overall survival (OS) or progression-free survival (PFS).

Results
We included 40 M0 patients in the final analysis. The volume transfer constant (Ktrans) from baseline PET/MRI (area under the curve (AUC) = 0.688, P = 0.034) and total lesion glycolysis (TLG) from baseline PET/MRI (AUC = 0.723, P = 0.006) or interim PET/MRI (AUC = 0.853, P < 0.001) showed acceptable AUC for predicting treatment response. The TLG from interim PET/MRI (interim TLG, P < 0.001) and extracellular volume fraction (Ve) on interim PET/MRI (interim Ve, P = 0.001) were identified as independent prognostic factors for OS. Baseline Ve (P = 0.044) and interim TLG (P = 0.004) were significant predictors of PFS. The c-indices of the prognostic models combining interim TLG with Ve for predicting OS, and baseline Ve and interim TLG for predicting PFS were 0.784 and 0.699, respectively. These values were significantly higher than the corresponding c-indices of the TNM staging system (P = 0.002 and P = 0.047, respectively).

Conclusions
Combining the baseline and interim [18F]FDG-PET/MRI qualitative imaging parameters aids in predicting the prognosis of patients with M0 esophageal squamous cell carcinoma.

Trial registration
The study was registered at Clinicaltrials.gov (identifier: NCT 05855291 and NCT 05855278).
Experimental study of the behavior of square footing on reinforced sand with treated geotextile
Authors: Zamani Siavash , Lajevardi Seyed Hamid , Yarivand Akbar , Zeighami Ehsanolah 
Published: November 2023

AbstractBearing capacity of reinforced footing clearly depends on the characteristics of interface between geosynthetic and soil. A suitable solution for increasing the bearing capacity is to treat the geotextile surface by various additives. This study reported the results of plate load test on square model footing resting on reinforced sand with and without treated geotextiles to survey the effects of the treatment of geotextile on settlement and bearing capacity. The treated geotextiles were made using additives onto the surface, with a layer of sand located on the top. Geotextile sides were treated in the same way. Different additives including the lime, cement, emulsion, and the effect of the number of layers were considered. The bearing capacity ratio values (BCR), improvement ratio values (IR) and variation of load-settlement ratio obtained from the treated models were presented. The results showed that the treatment of geotextile has a great effect on the behavior of reinforced sand and thus bearing capacity. Also, the test results indicated that lime-treated geotextiles provided better improvement than other additives. The maximum improvement in the bearing capacity of square footing supported on treated geotextiles was found to be 75% compared with the pristine geotextiles.
Effect of lime-rice husk ash on geotechnical properties of loess soil in Golestan province, Iran
Authors: Zivari Amin , Siavoshnia Mehdi , Rezaei Hamed 
Published: November 2023

AbstractLoess soils have always been among the most problematic soils, according to engineers. Due to the sensitivity and vulnerability of this soil type, researchers are constantly looking for different solutions to improve and stabilize this soil using different methods. In the present study, a mixture of lime and rice husk ash (LRHA) was used to modify the loess soil of the Golestan province, Iran. Lime and RHA were mixed in a ratio of 2:4 and with different contents of 2.5, 5, 7.5, 10 and 12.5% of the dry weight of the soil. To study the effect of curing on the strength properties, the samples were cured and tested for 7, 18 and 28 days. Atterberg limits, modified Proctor, unconfined compressive strength (UCS) and scanning electron microscope tests (SEM) were performed. It was found that increasing LRHA content increased the value of UCS at different curing times, such that UCS increased about five times by the addition of 5% LRHA to the loess at the end of 28 days. As the curing time increased, the optimum amount of the additive also decreased. The results showed that combining the soil with LRHA is an effective method for improving and stabilizing loess soil. According to the results of the study, the optimum value of 5% additive is economically and technically recommended.
Fabrication of a three-dimensional bone marrow niche-like acute myeloid Leukemia disease model by an automated and controlled process using a robotic multicellular bioprinting system
Authors: Alhattab Dana M. , Isaioglou Ioannis , Alshehri Salwa , Khan Zainab N. , Susapto Hepi H. , Li Yanyan , Marghani Yara , Alghuneim Arwa A. , Díaz-Rúa Rubén , Abdelrahman Sherin , AL-Bihani Shuroug , Ahmed Farid , Felimban Raed I. , Alkhatabi Heba , Alserihi Raed , Abedalthagafi Malak , AlFadel AlShaibani , Awidi Abdalla , Chaudhary Adeel Gulzar , Merzaban Jasmeen , Hauser Charlotte A. E. 
Published: November 2023

Abstract

Background
Acute myeloid leukemia (AML) is a hematological malignancy that remains a therapeutic challenge due to the high incidence of disease relapse. To better understand resistance mechanisms and identify novel therapies, robust preclinical models mimicking the bone marrow (BM) microenvironment are needed. This study aimed to achieve an automated fabrication process of a three-dimensional (3D) AML disease model that recapitulates the 3D spatial structure of the BM microenvironment and applies to drug screening and investigational studies.

Methods
To build this model, we investigated a unique class of tetramer peptides with an innate ability to self-assemble into stable hydrogel. An automated robotic bioprinting process was established to fabricate a 3D BM (niche-like) multicellular AML disease model comprised of leukemia cells and the BM’s stromal and endothelial cellular fractions. In addition, monoculture and dual-culture models were also fabricated. Leukemia cell compatibility, functionalities (in vitro and in vivo), and drug assessment studies using our model were performed. In addition, RNAseq and gene expression analysis using TaqMan arrays were also performed on 3D cultured stromal cells and primary leukemia cells.

Results
The selected peptide hydrogel formed a highly porous network of nanofibers with mechanical properties similar to the BM extracellular matrix. The robotic bioprinter and the novel quadruple coaxial nozzle enabled the automated fabrication of a 3D BM niche-like AML disease model with controlled deposition of multiple cell types into the model. This model supported the viability and growth of primary leukemic, endothelial, and stromal cells and recapitulated cell-cell and cell-ECM interactions. In addition, AML cells in our model possessed quiescent characteristics with improved chemoresistance attributes, resembling more the native conditions as indicated by our in vivo results. Moreover, the whole transcriptome data demonstrated the effect of 3D culture on enhancing BM niche cell characteristics. We identified molecular pathways upregulated in AML cells in our 3D model that might contribute to AML drug resistance and disease relapse.

Conclusions
Our results demonstrate the importance of developing 3D biomimicry models that closely recapitulate the in vivo conditions to gain deeper insights into drug resistance mechanisms and novel therapy development. These models can also improve personalized medicine by testing patient-specific treatments.

Graphical Abstract
Correlates of non-institutional delivery to delayed initiation of breastfeeding in Nigeria: logit-decomposition and subnational analysis of population-based survey
Authors: Oyedele Oyewole K. 
Published: November 2023

Abstract
Background
Studies have connected newborn delivery settings and modality to optimal breastfeeding, but how it influences untimely initiation, mostly prevalent in sub-Saharan Africa is unknown. Hence, the role of home delivery on delay initiation of breastfeeding (DIBF) in Nigeria was investigated to inform evidence-based strategy for improved breastfeeding practice.

Methodology
This is a secondary analysis of births (11,469 home and 7632 facility delivery) by 19,101 reproductive age women in the 2018 NDHS. DIBF is the outcome, home birth is the exposure, and explanatory variables were classified as: socio-demographics, obstetrics and economic factors. Descriptive statistics (frequencies and percentages) were reported, and bivariate (chi-square) analysis was carried out at 20% (p < 0.20) cutoff point. Multivariable logistic regression assessed the probability and significance of the outcome per place of birth. Multivariate decomposition further evaluated the endowment and coefficient effect contribution by independent factors to the outcome. Analysis was carried out at p < 0.05 (95% confidence level) on Stata.

Results
56.6% of mothers DIBF, with 37.1% and 19.5% from home and facility delivery, respectively. Home delivery (AOR = 1.34, 95% CI 1.17–1.52) increase the chance of DIBF by 34%, while DIBF probability reduces by 26% in facility delivery (AOR = 0.74, 95% CI 0.65–0.85). DIBF is 5 times more likely in caesarian section delivery (AOR = 5.10, 95% CI 4.08–6.38) compared to virginal birth in facility delivery. Skilled antenatal provider, parity and wealth are negatively associated with DIBF in home birth, while undesired pregnancy, rural residency, partial/no skin-to-skin contact and large child size positively influence DIBF in both home and facility delivery. Skilled antenatal provider (C =  − 66.3%, p < 0.01) and skin-to-skin contact (C =  − 60.6%, p < 0.001) contributed most to reducing the negative DIBF effect with 69% and 31% overall characteristics and coefficient effect component, respectively. DIBF is more likely in Bauchi and Sokoto but less likely in Bayelsa.

Conclusions
High DIBF prevalent in Nigeria was largely due to elevated rate of home birth, positively associated with DIBF. Caesarian section delivery though heightens the chance of DIBF in facility delivery. Strengthening utilization of skilled provider and skin-to-skin contact can eliminate two-third of the adverse DIBF effect and improve early initiation rate. Adopting this strategy will bridge home-facility delivery gap to achieve optimal breastfeeding practice.