bluuebunny/crossref_metadata_2025_split huggingface dataset:
Associations Between Pro/Anti-Tobacco Media and Messaging Exposure and Knowledge and Support of Smoke-Free Policy Among Adults in Armenia and Georgia
Authors: LoParco Cassidy R. , Sargsyan Zhanna , Topuridze Marina , Sturua Lela , Kegler Michelle C. , Petrosyan Varduhi , Torosyan Arevik , Grigoryan Lilit , Bazarchyan Alexander , Berg Carla J. 
Published: September 2023

Context:
Despite high smoking rates, Armenia and Georgia recently adopted smoke-free policies (2022 and 2018).

Objective:
We examined associations between exposure to pro-tobacco media (news opposing smoke-free policies; cigarette, e-cigarette, heated tobacco product [HTP] advertisements) and anti-tobacco media (media, community-based action) and (1) knowledge that the policies applied to alternative tobacco products (ATPs), and (2) support for the policies applying to ATPs and various settings.

Design:
We analyzed 2022 survey data.

Setting:
Data were from 28 communities in Armenia and Georgia.

Participants:
The sample comprised 1468 adults (31.6% past-month smokers).

Methods:
We conducted multivariable regressions, controlling for country and sociodemographics.

Results:
Participants were knowledgeable that the policy applied to ATPs (79.2%) and supportive of them applying to ATPs and various settings (means = 3.43 and 3.00; 1-4 = strongly support). Greater exposure to anti-tobacco media/community-based action correlated with more likely knowing that the policies applied to ATPs and greater support of the policies applying to various settings; HTP advertisement exposure correlated with less support of the policies applying to various settings. Less exposure to news opposing smoke-free policies and greater exposure to media supporting such policies correlated with greater support of the policies applying to ATPs.

Conclusions:
Media and community-based action may promote smoke-free policy knowledge and support. HTP advertisements may uniquely undermine smoke-free policies.
scEGOT: Single-cell trajectory inference framework based on entropic Gaussian mixture optimal transport
Authors: Yachimura Toshiaki , Wang Hanbo , Imoto Yusuke , Yoshida Momoko , Tasaki Sohei , Kojima Yoji , Yabuta Yukihiro , Saitou Mitinori , Hiraoka Yasuaki 
Published: September 2023

AbstractTime-series scRNA-seq data have opened a door to elucidate cell differentiation, and in this context, the optimal transport theory has been attracting much attention. However, there remain critical issues in interpretability and computational cost. We present scEGOT, a comprehensive framework for single-cell trajectory inference, as a generative model with high interpretability and low computational cost. Applied to the human primordial germ cell-like cell (PGCLC) induction system, scEGOT identified the PGCLC progenitor population and bifurcation time of segregation. Our analysis showsTFAP2Ais insufficient for identifying PGCLC progenitors, requiringNKX1-2. Additionally,MESP1andGATA6are also crucial for PGCLC/somatic cell segregation. These findings shed light on the mechanism that segregates PGCLC from somatic lineages. Notably, not limited to scRNA-seq, scEGOT’s versatility can extend to general single-cell data like scATAC-seq, and hence has the potential to revolutionize our understanding of such datasets and, thereby also, developmental biology.
Differential Expression Analysis of miRNAs and mRNAs in Epilepsy Uncovers Potential Biomarkers
Authors: El Abed Fatma , Baraket Ghada , Nyamari Marion N. , Naitore Careen , Awe Olaitan I. 
Published: September 2023

AbstractEpilepsy is a neurological disease defined by episodes of synchronous convulsions. Recently, miRNAs have been proven as promising biomarkers for multiple ailments like tumors and neurodegenerative disorders; their role in epilepsy is still unclear. This study aimed to understand the involvement of miRNAs in the disease and to detect the potential biomarkers for the treatment of epilepsy.RNA transcripts, and miRNA from brain tissue and plasma small extracellular vesicle samples of epileptogenic patients from 6 different studies downloaded from the NCBI sequence read archive (SRA) were analyzed with particular interest in genes that might be involved in epilepsy. Alignment of transcripts to hg38 was done using HISAT2 and the raw counts were generated using HTseq-count. miRNA genes were identified using miRDeep2. EdgeR and GEO2 were used to identify DEGs for both mRNA and miRNA datasets. Finally, TargetScan web tool was used to predict potentially significantly expressed mRNA target genes using the identified miRNA genes.Analysis of these datasets revealed target genes in epilepsy and their associated miRNAs. SIX4 and KCTD7 were under-expressed in epileptogenic zones of the brain compared to the irritative zone. CABP1, SLC20A1 and SLC35G1 were under-expressed in brain tissues. Hsa-miR-27a-3p was identified as a regulator of CABP1 expression, hsa-let-7b-5p regulates SLC20A1 while hsa-miR-15a-5p and hsa-miR-195-5p are regulators for SLC35G1. These observations highlight the importance of miRNAs as novel biomarkers of epilepsy.Understanding and controlling these regulatory interactions may help to define potential therapies for epilepsy. This would also help to better understand miRNA-mediated gene regulation in epilepsy.
A metabolic perspective on polyploid invasion and the emergence of life histories: insights from a mechanistic model
Authors: Milosavljevic Silvija , Kauai Felipe , Mortier Frederik , Van de Peer Yves , Bonte Dries 
Published: September 2023

AbstractWhole genome duplication (WGD, polyploidization), the fusion of unreduced gametes, has been identified as a driver of genetic and phenotypic novelty. Unreduced gamete formation is common in a wide range of species, but surprisingly, few polyploidization events have shown to be ecologically successful. Positive density dependence, by minority cytotype exclusion, and niche shifts are currently considered the most important drivers behind ecological failure or success. Genome doubling also results in increased cell sizes and metabolic expenses which, on their own may be sufficient to drive polyploid establishment in stable environments where their simple ancestors thrive.We developed a mechanistic model, motivated by data from natural plant polyploid species, to test whether realistic changes in size and metabolic efficiency allow polyploids to coexist with, or even invade, their original diploid population. Central to the model is metabolic efficiency, a functional trait that determines how energy gained from size-dependent photosynthetic metabolism is allocated to basal metabolism, somatic growth and reproductive growth.Polyploid invasion was observed across a wide range of metabolic efficiency differences between polyploids and their ancestors. Higher metabolic efficiency facilitates polyploid invasion, but even with minor deficits, establishment was facilitated by recurrent formation in these settings of high competition for nutrients. Interestingly, a long-term coexistence with the diploid ancestor was found to be possible only within a narrow range of this parameter space. Perenniality of the plants did not qualitatively affect these insights. Feedbacks between size-dependent metabolism and allocation of gained energy generated eventually size and age differences, resulting in intra- and intercytotype competition for nutrients as the major force for population dynamics. We thus demonstrate that changes in metabolic efficiency on their own are sufficient to impose establishment, but these advantages do not need to be substantial.
Algebraic Invariants for Inferring 4-leaf Semi-directed Phylogenetic networks
Authors: Martin Samuel , Moulton Vincent , Leggett Richard M. 
Published: September 2023

AbstractA core goal of phylogenomics is to determine the evolutionary history of a set of species from biological sequence data. Phylogenetic networks are able to describe more complex evolutionary phenomena than phylogenetic trees but are more difficult to accurately reconstruct. Recently, there has been growing interest in developing methods to infer semi-directed phylogenetic networks. As computing such networks can be computationally intensive, one approach to building such networks is to puzzle together smaller networks. Thus, it is essential to have robust methods for inferring semi-directed phylogenetic networks on small numbers of taxa. In this paper, we investigate an algebraic method for performing phylogenetic network inference from nucleotide sequence data on 4-leaved semi-directed phylogenetic networks by analysing the distribution of leaf-pattern probabilities. On simulated data, we found that we can correctly identify with high accuracy semi-directed networks as sequences approach 10Mbp in length, and that we are able to use our approach to identify tree-like evolution and determine the underlying tree. We also applied our approach to published transcriptome data from swordtail fish to compare its performance with a pseudolikelihood method for inferring semi-directed networks.
A Unified Framework to Analyze Transposable Element Insertion Polymorphisms using Graph Genomes
Authors: Groza Cristian , Chen Xun , Wheeler Travis J. , Bourque Guillaume , Goubert Clément 
Published: September 2023

AbstractTransposable Elements are ubiquitous mobile DNA sequences evolving among their hosts’ genomes, generating insertion polymorphisms that contribute to genomic diversity. We present GraffiTE, a flexible pipeline to analyze polymorphic mobile elements. By integrating state-of-the-art structural variant detection algorithms and graph genomes, GraffiTE identifies polymorphic mobile elements from genomic assemblies and/or long-read sequencing data, and genotypes these variants using short or long read sets. Benchmarking on simulated and real datasets reports high precision and recall rates. GraffiTE is designed to allow non-expert users to perform comprehensive analyses, including in models with limited transposable element knowledge and is compatible with various sequencing technologies. GraffiTE is freely available athttps://github.com/cgroza/GraffiTE. Here, we demonstrate the versatility of GraffiTE by analyzing human,Drosophila melanogaster,maize, andCannabis sativapangenome data. These analyses reveal the landscapes of polymorphic mobile elements and their frequency variations across individuals, strains, and cultivars.
HiTaxon: A hierarchical ensemble framework for taxonomic classification of short reads
Authors: Verma Bhavish , Parkinson John 
Published: September 2023

ABSTRACTWhole microbiome DNA and RNA sequencing (metagenomics and metatranscriptomics) are pivotal to determining functional roles within microbial communities. A key challenge in analysing these complex datasets, typically composed of tens of millions of short reads, is accurately classifying reads to their taxon of origin. Traditional reference-based short-read classification tools are compromised by reference database biases, leading to interest in classifiers leveraging machine learning (ML) algorithms. While ML classifiers have shown promise, they still lag reference-based tools in species-level classification. To address this performance gap, attention has turned to approaches that incorporate the hierarchical structure of taxonomic classifications, albeit with limited results. Here we introduce HiTaxon, a hierarchical framework for creating ensembles of reference-dependent and ML classifiers. HiTaxon facilitates data collection and processing, reference database construction and model training to streamline ensemble creation. We show that databases created by HiTaxon improve the species-level performance of reference-dependent classifiers, while reducing their computational overhead. Additionally, through exploring hierarchical methods for HiTaxon, we highlight that our custom hierarchical ML approach improves species-level classification relative to traditional strategies. Finally, we demonstrate the improved performance of our hierarchical ensemble over current state-of-the-art classifiers in species classification using datasets comprised of either simulated or experimentally-derived reads.
TGF-β3 increases the severity of radiation-induced oral mucositis and salivary gland fibrosis in a mouse model
Authors: Hanson Ingunn , Juvkam Inga Solgård , Zlygosteva Olga , Søland Tine Merete , Galtung Hilde Kanli , Malinen Eirik , Jeppesen Edin Nina Frederike 
Published: September 2023

AbstractPurposeToxicities from head and neck (H&N) radiotherapy (RT) may affect patient quality of life and can be dose-limiting. Proteins from the transforming growth factor beta (TGF-β) family are key players in the fibrotic response. While TGF-β1 is known to be pro-fibrotic, TGF-β3 has mainly been considered anti-fibrotic. Moreover, TGF-β3 has been shown to act protective against acute toxicities after radio- and chemotherapy. In the present study, we investigated the effect of TGF-β3 treatment during fractionated H&N RT in a mouse model.Materials and methods30 C57BL/6J mice were assigned to three treatment groups. The RT + TGF-β3 group received local fractionated H&N RT with 66 Gy over five days, combined with TGF-β3-injections at 24-hour intervals. Animals in the RT reference group received identical RT without TGF-β3 treatment. The non-irradiated control group was sham-irradiated according to the same RT schedule. In the follow-up period, body weight and symptoms of oral mucositis and lip dermatitis were monitored. Saliva was sampled at five time points. The experiment was terminated 105 days after the first RT fraction. Submandibular and sublingual glands were preserved, sectioned, and stained with Masson’s trichrome to visualize collagen.ResultsA subset of mice in the RT + TGF-β3 group displayed increased severity of oral mucositis and increased weight loss, resulting in a significant increase in mortality. Collagen content was significantly increased in the submandibular and sublingual glands for the surviving RT + TGF-β3 mice, compared with non-irradiated controls. In the RT reference group, collagen content was significantly increased in the submandibular gland only. Both RT groups displayed lower saliva production after treatment compared to controls. TGF-β3 treatment did not impact saliva production.ConclusionsWhen repeatedly administered during fractionated RT at the current dose, TGF-β3 treatment increased acute H&N radiation toxicities and increased mortality. Furthermore, TGF-β3 treatment may increase the severity of radiation-induced salivary gland fibrosis.
Polyimide-Based Flexible Multi-Electrode Arrays: Synthesis, Microfabrication, andin-vivoValidation
Authors: Kumar Kshitij , Deshpande Kaustubh , Kalur Naveen , Chauhan Garima , Chugh Deepti , Ganesh Subramaniam , Ramakrishnan Arjun 
Published: September 2023

AbstractThin film neural microelectrodes are popularly being used in brain-computer interfaces and tools for neurosurgical interventions [8]. Among the various thin films used, polyimide stands out as an excellent material for substrate passivation due to its chemical inertness, biocompatibility, mechanical flexibility, and superior dielectric properties. While polyimide is extensively used as a substrate in thin film neural interfaces, the lack of availability of a clinical-grade polyimide limits their use in human clinical applications. This paper presents a comprehensive solution by developing an ISO-10993-11-approved polyamic acid for fabricating thin-film polyimide microelectrodes. Benchtop tests and in-vivo experiments in anesthetized mice demonstrate the potential of this synthesized polyamic acid and microfabrication processes for commercialization in clinical settings, particularly for brain-computer interfaces and invasive neural microelectrodes.
Tuning gene expression to music: the compensatory effect of music on age-related cognitive disorders
Authors: Gómez-Carballa Alberto , Navarro Laura , Pardo-Seco Jacobo , Bello Xabier , Pischedda Sara , Viz-Lasheras Sandra , Camino-Mera Alba , Currás María José , Ferreirós Isabel , Mallah Narmeen , Rey-Vázquez Sara , Redondo Lorenzo , Dacosta-Urbieta Ana , Caamaño-Viña Fernando , Rivero-Calle Irene , Rodriguez-Tenreiro Carmen , Martinón-Torres Federico , Salas Antonio 
Published: September 2023

AbstractExtensive literature has explored the beneficial effects of music in age-related cognitive disorders (ACD), but limited knowledge exists regarding its impact on gene expression. We analyzed transcriptomes of ACD patients and healthy controls, pre-post a music session (n=60), and main genes/pathways were compared to those dysregulated in mild cognitive impairment (MCI) and Alzheimer’s disease (AD) as revealed by a multi-cohort study (n=1269 MCI/AD and controls). Music was associated with 2.3 times more whole-genome gene expression, particularly on neurodegeneration-related genes, in ACD than controls. Co-expressed gene-modules and pathways analysis demonstrated that music impacted autophagy, vesicle and endosome organization, biological processes commonly dysregulated in MCI/AD. Notably, the data indicated a strong negative correlation between musically-modified genes/pathways in ACD and those dysregulated in MCI/AD. These findings highlight the compensatory effect of music on genes/biological processes affected in MCI/AD, providing insights into the molecular mechanisms underlying the benefits of music on these disorders.
Inducer of CBF Expression 1 (ICE1) Promotes Cold-enhanced Immunity by Directly Activating Salicylic Acid Signaling
Authors: Li Shaoqin , He Li , Yang Yongping , Zhang Yixin , Han Xiao , Hu Yanru , Jiang Yanjuan 
Published: September 2023

ABSTRACTCold stress affects plant immune responses, and this process may involve the salicylic acid (SA) signaling pathway. However, the underlying mechanism by which low temperature signals coordinate with SA signaling to regulate plant immunity remains not fully understood. Here, we found that low temperatures enhanced the disease resistance of Arabidopsis againstPseudomonas syringaepv.tomato(Pst) DC3000. This process required Inducer of CBF expression 1 (ICE1), the core transcription factor in cold-signal cascades. ICE1 physically interacted with Non-expresser ofPRgenes 1 (NPR1), the master regulator of the SA signaling pathway. Enrichment of ICE1 on thePR1promoter and its ability to transcriptionally activatePR1were enhanced by NPR1. Further analyses revealed that cold stress signals cooperate with SA signals to facilitate plant immunity against pathogen attack in an ICE1-dependent manner. Cold treatment promoted interactions of NPR1 and TGA3 with ICE1, and increased the ability of the ICE1–TGA3 complex to transcriptionally activatePR1. Together, our results characterize a previously unrecognized role of ICE1 as an indispensable regulatory node linking low temperature activated- and SA-regulated immunity. Discovery of a crucial role of ICE1 in coordinating multiple signals associated with immunity broadens our understanding of plant–pathogen interactions.
Seasonal migration alters energetic trade-off optimization and shapes life history
Authors: Pierce Allison K. , Yanco Scott W. , Wunder Michael B. 
Published: September 2023

AbstractTrade-offs between current and future reproduction manifest as a set of co-varying life history and metabolic traits, collectively referred to as “pace of life” (POL). Seasonal migration modulates realized environmental dynamics and putatively affects realized POL, however, the mechanisms by which migratory behavior shapes POL remain unclear. We explored how migratory behavior interacts with environmental and metabolic dynamics to shape POL. Using an individual based model of movement and metabolism we compared fitness-optimized trade-offs among migration strategies. We found annual experienced seasonality and migration distance primarily drove POL differentiation through developmental and migration phenology trade-offs. Similarly, our analysis of empirically-estimated metabolic data from 265 bird species suggested seasonal niche conservatism and migration distance interact to drive POL. We show multiple viable life history strategies are conducive to a migratory lifestyle. Overall, our findings suggest metabolism mediates complex interactions between behavior, environment, and life history.Authorship statementAKP and SWY contributed equally to this work. AKP and SWY conceived the project, designed the model, performed analyses, and drafted the manuscript with support from MBW. Simulation and optimization model code written by AKP with input from SWY and MBW. Empirical data analysis and code lead by SWY with input from AKP and MBW. All authors contributed critical input to the manuscript.Data accessibility statementAll R code for models and analyses are available athttps://doi.org/10.5281/zenodo.10145976andhttps://github.com/allipierce/Pierce_et_al_2023_MigrationPOL. The empirically derived data used in this work are all publicly available. DEB data are available from the Add-My-Pet portal athttps://www.bio.vu.nl/thb/deb/deblab/add_my_pet/. Geographic range data are available from BirdLife International athttp://datazone.birdlife.org/species/requestdis. Niche dissimilarity data came fromhttps://doi.org/10.1111/geb.13722and phylogeny data are available from VertLife athttp://vertlife.org/data/.
Mapping the Single-cell Differentiation Landscape of Osteosarcoma
Authors: Truong Danh D. , Weistuch Corey , Murgas Kevin A. , Deasy Joseph O. , Mikos Antonios G. , Tannenbaum Allen , Ludwig Joseph 
Published: September 2023

AbstractThe genetic and intratumoral heterogeneity observed in human osteosarcomas (OS) poses challenges for drug development and the study of cell fate, plasticity, and differentiation, processes linked to tumor grade, cell metastasis, and survival. To pinpoint errors in OS differentiation, we transcriptionally profiled 31,527 cells from a tissue-engineered model that directs MSCs toward adipogenic and osteoblastic fates. Incorporating pre-existing chondrocyte data, we applied trajectory analysis and non-negative matrix factorization (NMF) to generate the first human mesenchymal differentiation atlas. This ‘roadmap’ served as a reference to delineate the cellular composition of morphologically complex OS tumors and quantify each cell’s lineage commitment. Projecting these signatures onto a bulk RNA-seq OS dataset unveiled a correlation between a stem-like transcriptomic phenotype and poorer survival outcomes. Our study takes the critical first step in accurately quantifying OS differentiation and lineage, a prerequisite to better understanding global differentiation bottlenecks that might someday be targeted therapeutically.Statement of SignificanceOS treatment kills proliferating cells without addressing the root cause: dysregulated differentiation. By deconvolving OS tumors by cell type and differentiation archetype, we identified core gene sets linked to cell fate and patient survival. The ability to quantify, and eventually modulate, such archetypes facilitate a novel OS-specific drug-screening strategy.