bluuebunny/crossref_metadata_2025_split huggingface dataset:
Efficacy of functional connectome fingerprinting using tangent-space brain networks
Authors: Curic Davor , Kalasapura Venugopal Krishna Sudhanva , Davidsen Jörn 
Published: January 2025

ABSTRACTFunctional connectomes (FCs) are estimations of brain region interaction derived from brain activity, often obtained from functional Magnetic Resonance Imaging recordings. Quantifying the distance between FCs is important for understanding the relation between behaviour, disorders, disease, and changes in connectivity. Recently, tangent space projections, which account for the curvature of the mathematical space of FCs, have been proposed for calculating FC distances. We compare the efficacy of this approach relative to the traditional method in the context of subject identification using the Midnight Scan Club dataset, in order to study resting-state and task-based subject discriminability. The tangent space method is found to universally out-perform the traditional method. We also focus on the subject identification efficacy of subnetworks. Certain subnetworks are found to outperform others, a dichotomy which largely follows the ‘control’ and ‘processing’ categorization of resting state networks, and relates subnetwork flexibility with subject discriminability. Identification efficacy is also modulated by tasks, though certain subnetworks appear task independent. The uniquely long recordings of the dataset also allow for explorations of resource requirements for effective subject identification. The tangent space method is found to universally require less data, making it well suited when only short recordings are available.AUTHOR SUMMARYFunctional connectomes, which describe the similarity between the recorded activity of different brain regions, are ubiquitous for researcher trying to understand brain dynamics on short and long time scales in the presence and absence of neurophysiological diseases. This work applies a Tangent Space approach, a novel method to calculate the distance between functional connectomes, to a unique high-quality dataset (the Midnight Scan Club) in order to better understand the variability and uniqueness of connectomes across subjects, and how subject identification (also called fingerprinting) compares across tasks. We also show that not only does the tangent space method offer greater sensitivity to changes, it does so with significantly fewer resources, and in some scenarios reveals qualitatively different interpretations than the traditional method.
Lecanemab binds to transgenic mouse model-derived amyloid-β fibril structures resembling Alzheimer’s disease type-I, type-II and Arctic folds
Authors: Peralta Reyes Fernanda S. , Willbold Dieter , Schröder Gunnar F. , Gremer Lothar 
Published: January 2025

AbstractLecanemab, an Alzheimer’s disease US Food and Drug Administration approved monoclonal antibody was previously reported to have a high affinity against intermediately sized amyloid-β aggregates. Subsequently, it was observed by immunogold labelling that lecanemab can also bind to human type-I amyloid-β fibrils. Therefore, to determine whether lecanemab binds to amyloid-β fibril structures other than type-I, we performed immunogold labelling on extracted amyloid-β fibril preparations from six different Alzheimer’s disease mouse models whose structures were previously solved by cryo-EM. Our results show that lecanemab exhibits high binding affinity to amyloid-β fibril structures that have a flexible N-terminus in common, as it is the case for type-I, type-II and murine type-III amyloid-β fibril polymorphs which resemble or are identical to human structures observed in sporadic and familial cases of Alzheimer’s disease, including a case with the Arctic (E22G) mutation. In contrast, only weak, if any, lecanemab binding was observed for amyloid-β fibril folds with a fixed and ordered N-terminus.Key points-Lecanemab binds to Aβ fibrils from several Alzheimer’s disease tg-mice whose structures resemble the type-I, type-II and Arctic folds found in Alzheimer’s patients, all of which share a flexible, unstructured N-terminus.-Lecanemab is therefore expected to be active against all common familial and sporadic Alzheimer’s cases containing these folds.-Lecanemab binding ability is unaffected by and tolerates the Arctic E22G mutation, at least in type-I or Arctic folds.-Weak, if any, lecanemab binding was observed to Aβ fibrils derived from tg-SwDI mice, whose structures DI1, DI2 and DI3 all share structured and fixed N-termini.-Since the fixed N-termini of tg-SwDI DI1 fibrils and human meningeal Aβ40 fibrils derived from CAA-affected brain are identical, most likely preventing lecanemab binding, treatment with lecanemab may be less or ineffective against CAA, but may explain the reported beneficial low ARIA-E frequency with this antibody.Table of Contents Graphic (TOC)
Competition for light color between marineSynechococcusstrains with fixed and variable pigmentation
Authors: Dufour Louison , Garczarek Laurence , Mattei Francesco , Gouriou Bastian , Clairet Julia , Ratin Morgane , Kehoe David M. , Huisman Jef , Verspagen Jolanda M. H. , Partensky Frédéric 
Published: January 2025

ABSTRACTCompetition between phytoplankton species for light has triggered an extensive diversification of photosynthetic pigments. InSynechococcuscyanobacteria, three major pigment types occur in the ocean: blue light (BL) specialists that have a high ratio of the BL-absorbing chromophore phycourobilin (PUB) to the green light (GL)-absorbing chromophore phycoerythrobilin (PEB), GL specialists that have a low PUB:PEB ratio, and cells that modify their PUB:PEB ratio to match the ambient color, a process called ‘Type IV chromatic acclimation’ (CA4). The abundance of CA4-capable cells in marine ecosystems suggests that CA4 confers a fitness advantage in certain light conditions compared to cells with fixed pigmentation. This hypothesis was tested by performing mono- and co-cultures of a BL specialist, a GL specialist and a CA4-capable strain in chemostats under different light conditions. Monocultures enabled us to parameterize a resource competition model that was used to predict competition between the three pigment types in co-cultures. In line with the model predictions, the BL specialist won in low blue light and the GL specialist won in low and high green light. Interestingly, we found that while the CA4-capable strain was at a disadvantage at low light, it was able to outcompete specialists in high blue light.IMPORTANCESynechococcuscyanobacteria are ubiquitous and abundant in the lit layer of most marine ecosystems. This ubiquity relies in part on the wide pigment diversity of their light-harvesting complexes, with three main pigment types thriving in open ocean waters: green light specialists, blue light specialists and chromatic acclimaters, the latter being capable of matching their pigment content to the ambient spectral field. Here, we simulated the competition for light color that occurs between these pigment types in the field by co-culturing them in various light color and intensity conditions, and compared the resulting data to that of a competition model. This study provides new insights on how this key group of phytoplankton colonized the various spectral niches of the marine environment.
Matching Heterogeneous Cohorts by Projected Principal Components Reveals Two Novel Alzheimer’s Disease-Associated Genes in the Hispanic Population
Authors: Willett Julian Daniel Sunday , Mullin Kristina , Tanzi Rudolph E. , Prokopenko Dmitry 
Published: January 2025

AbstractAlzheimer’s disease (AD) is the most common form of dementia in elderly, affecting 6.9 million individuals in the United States. Some studies have suggested the prevalence of AD is greater in individuals who self-identify as Hispanic. Focused results are relevant for personalized and equitable clinical interventions. Ethnicity as a stratifying tool in genetic studies is often accompanied by genomic inflation due to heterogeneity. In this study, we report GWAS and meta-analyses conducted among NIAGADS subjects who self-identified as Hispanic and All of Us (AoU) sub-cohorts matched to that cohort, using projected genetically-derived principal components, with and without age and sex. In Hispanic NIAGADS subjects, we identified a common variant inPIEZO2that was protective for AD with a p-value just beyond genome-wide significance (p = 5.4 * 10-8). Meta-analyses with genetically-matched AoU participants yielded three (two novel) genome-wide significant AD-associated loci based on rare lead variants: rs374043832 (RGS6/PSEN1), rs192423465 (ASPSCR1), and rs935208076 (GDAP2), which were also nominally significant in AoU sub-cohorts. We also show how genomic inflation can be mitigated in heterogeneous populations while increasing sample size and result generalizability.
PD-1 prelimits both the cytotoxic and exhaustion potential in thymic CD8+ T cells and impacts the maintenance of peripheral tumor immunity
Authors: Mao Zhiming , Hirdler Jacob B. , Gicobi Joanina K. , Maynes Mark , Hsu Michelle A. , Dellacecca Emilia R. , Zhang Wenjing , Teske Jacob J. , Li Ying , Zhao Geoffrey , Lucien-Matteoni Fabrice , Borges da Silva Henrique , Billadeau Daniel D. , Dong Haidong 
Published: January 2025

AbstractDurable T cell immunity against cancer depends on the continual replenishment of effector CD8+ T cells. Thymic output has been correlated with favorable prognosis in cancer patients across a range of ages, suggesting that the thymus is an important source for replenishing T cells capable of controlling cancer progression. However, the effector potential of thymic mature CD8+ T cells and their regulation have not been clearly defined. In this study, we identified the ability of thymic single positive CD8+ T cells to gain effector potential after thymic selection, but they are subject to the regulation of PD-1. We found a previously undisclosed role of PD-1 in limiting both the cytotoxic and exhaustion potential of thymic and peripheral CD8+ T cells. Our results show that although PD-1 inhibition facilitates the expansion of effector CD8+ T cells, effector CD8+ cells gradually lose their antitumor activity within tumor tissues due to advanced exhaustion in the absence of PD-1. Thus, although the preset effector potential in thymic mature CD8+ T cells allows them to rapidly respond to malignant cells in the periphery, PD-1, as a checkpoint, is embedded in the thymic mature CD8+ T cells after positive selection to balance their effector function from exaggeration and exhaustion. Therefore, we propose that a strategy capable of upholding the cytotoxic capacity and avoiding exhaustion of CD8+ T cells during the early stages of PD-1 inhibition therapy is needed to achieve durable antitumor immunity.
Gene expression patterns of the developing human face at single cell resolution reveal cell type contributions to normal facial variation and disease risk
Authors: Khouri-Farah Nagham , Winchester Emma Wentworth , Schilder Brian M. , Robinson Kelsey , Curtis Sarah W. , Skene Nathan G. , Leslie-Clarkson Elizabeth J. , Cotney Justin 
Published: January 2025

AbstractCraniofacial development gives rise to the complex structures of the face and involves the interplay of diverse cell types. Despite its importance, our understanding of human-specific craniofacial developmental mechanisms and their genetic underpinnings remains limited. Here, we present a comprehensive single-nucleus RNA sequencing (snRNA-seq) atlas of human craniofacial development from craniofacial tissues of 24 embryos that span six key time points during the embryonic period (4–8 post-conception weeks). This resource resolves the transcriptional dynamics of seven major cell types and uncovers distinct major cell types, including muscle progenitors and cranial neural crest cells (CNCCs), as well as dozens of subtypes of ectoderm and mesenchyme. Comparative analyses reveal substantial conservation of major cell types, alongside human biased differences in gene expression programs. CNCCs, which play a crucial role in craniofacial morphogenesis, exhibit the lowest marker gene conservation, underscoring their evolutionary plasticity. Spatial transcriptomics further localizes cell populations, providing a detailed view of their developmental roles and anatomical context. We also link these developmental processes to genetic variation, identifying cell type-specific enrichments for common variants associated with facial morphology and rare variants linked to orofacial clefts. Intriguingly, Neanderthal-introgressed sequences are enriched near genes with biased expression in cartilage and specialized ectodermal subtypes, suggesting their contribution to modern human craniofacial features. This atlas offers unprecedented insights into the cellular and genetic mechanisms shaping the human face, highlighting conserved and distinctly human aspects of craniofacial biology. Our findings illuminate the developmental origins of craniofacial disorders, the genetic basis of facial variation, and the evolutionary legacy of ancient hominins. This work provides a foundational resource for exploring craniofacial biology, with implications for developmental genetics, evolutionary biology, and clinical research into congenital anomalies.
Thermal cycling transcription boosts RNA production
Authors: Liu Yuxuan , Shi Lu , Brosius Juergen , Mo Dingding 
Published: January 2025

AbstractEfficient RNA production is essential for therapeutic applications. Currently, mRNA is generated byin vitrotranscription with RNA polymerases at a constant temperature. The success of these transcriptions depends on various factors including sequence composition and size. Sometimes, especially for long RNAs, achieving efficient transcript yields are challenging.We developed a novel approach by incorporating a high-temperature denaturation step. Our protocol includes the following two steps of thermal cycling RNA transcription: the initial enzyme-driven RNA transcription step is done at RNA polymerase active temperature (37 °C); then the nucleic acids melting step is carried out at elevated temperatures (55–70°C); after the reaction is cooled to the temperature of optimal polymerase activity, the first step is repeated.Denaturation enables the generation of optimized, more stable mRNAs, which alleviates the mRNA instability that often occurs during RNA-based therapeutic development. For example, this new thermal cycling RNA transcription approach can employ high GC content, thus increasing RNA stability.For long and difficult templates, the combination of sequence optimization by LinearDesign algorithm in conjunction with transcription via thermal cycling significantly improved mRNA production. Thermal cycling transcription dramatically increased the efficiency of most RNA products while reducing costs, facilitating RNA-based therapeutic development.
Integrative Gene Co-expression Network Analysis Reveals Protein-Coding and lncRNA Genes Associated with Alzheimer’s Disease Pathology
Authors: Zebardast Fatemeh , Sascha Riethmüller Michael Peter , Nowick Katja 
Published: January 2025

AbstractIntroductionAlzheimer’s disease (AD) is a complex neurodegenerative disorder involving widespread molecular disruptions, many of which remain poorly understood. While AD pathology progresses through distinct brain regions, it is unclear whether these regions are similarly affected. Long non-coding RNAs (lncRNAs) have emerged as key regulators in cellular processes, but their roles in AD remain largely unexplored. A comprehensive analysis of the complex molecular interactions underlying AD, particularly the roles of lncRNAs in their interactions with protein-coding genes and the comparison of networks across brain regions, could offer valuable insights into the disease’s progression and underlying mechanisms.MethodTo address this, we applied consensus weighted gene co-expression network analysis using a meta-analytic approach to 396 postmortem brain RNA-seq samples to explore AD pathophysiology mechanisms.ResultsOur study revealed significant network rewiring in AD, with pronounced alterations in the temporal cortex compared to the frontal cortex. While the temporal cortex showed adaptive changes in gene interactions, the frontal cortex exhibited a loss of healthy correlations, potentially reflecting different levels of disease progression. We identified key players in the temporal cortex AD network, including 46 protein-coding genes and 27 lncRNAs. Using the established functions of protein-coding genes as anchors, we provided functional annotations for over 100 lncRNAs across two brain regions, identifying potential lncRNAs involved in AD pathology and highlighting their roles in both healthy and diseased states.ConclusionWe provided novel insights into the molecular interactions underlying AD and introduced new candidate protein-coding and lncRNA genes for further experimental validation and therapeutic exploration.
7-ketocholesterol contributes to microglia-driven increases in astrocyte reactive oxygen species in Alzheimer’s disease
Authors: Radhakrishnan Kayalvizhi , Zhang Yiyu , Mustapha Oluwaseun , Weigel Thaddeus K. , Upchurch Clint M. , Tian Xiaodong , Herbert Franklin , Huang Wenyuan , Leitinger Norbert , Eyo Ukpong B. , Ai Huiwang , Ferris Heather A. 
Published: January 2025

AbstractOxidative stress is a prominent feature of Alzheimer’s disease. Within this context, cholesterol undergoes oxidation, producing the pro-inflammatory product 7-ketocholesterol (7-KC). In this study, we observe elevated levels of 7-KC in the brains of the 3xTg mouse model of AD. To further understand the contribution of 7-KC on the oxidative environment, we developed a method to express a genetically encoded fluorescent hydrogen peroxide (H2O2) sensor in astrocytes, the primary source of cholesterol in the brain. With this sensor, we discovered that 7-KC increases H2O2levels in astrocytes in vivo, but not when directly applied to astrocytes in vitro. Interestingly, when 7-KC was applied to a microglia cell line alone or mixed astrocyte and microglia cultures, it resulted in microglia activation and increased oxidative stress in astrocytes. Depletion of microglia from 3xTg mice resulted in reduced 7-KC in the brains of these mice. Taken together, these findings suggest that 7-KC, acting through microglia, contributes to increased astrocyte oxidative stress in AD. This study sheds light on the complex interplay between cholesterol oxidation, microglia activation, and astrocyte oxidative stress in the pathogenesis of AD.
C-terminal tagging, transmembrane domain hydrophobicity, and an ER retention motif influence the secretory trafficking of the inner nuclear membrane protein emerin
Authors: Mella Jessica , Volk Regan , Zaro Balyn , Buchwalter Abigail 
Published: January 2025

AbstractThe inner nuclear membrane (INM), a subdomain of the endoplasmic reticulum (ER), sequesters hundreds of transmembrane proteins within the nucleus. We previously found that one INM protein, emerin, can evade the INM by secretory transport to the lysosome, where it is degraded. In this work, we used targeted mutagenesis to identify intrinsic sequences that promote or inhibit emerin’s secretory trafficking. By manipulating these sequences across several tag and expression level combinations, we now find that emerin’s localization is sensitive to C-terminal GFP tagging. While emerin’s long, hydrophobic C-terminal transmembrane domain facilitates trafficking to the lysosome, extending its lumenal terminus with a GFP tag biases the protein toward this pathway. In contrast, we identify a conserved ER retention sequence that stabilizes N- and C-terminally tagged emerin by limiting its lysosomal flux. These findings underscore long-standing concerns about tagging artifacts and reveal novel determinants of tail-anchored INM protein targeting.
Through a child’s eyes: eye tracking to study children’s consumer behavior
Authors: Huddleston Patricia , McAlister Anna R. , Alade Fashina 
Published: January 2025

Purpose
This conceptual paper provides an overview of eye-tracking technology (ETT) as a process-tracing method to study children’s consumer behavior. This paper aims to provide a literature review of the child as consumer-focused eye-tracking research, identifying theoretical and research gaps. This paper discusses the benefits, drawbacks and ethical implications of ETT and highlights opportunities and best practices for future research.

Design/methodology/approach
This paper details eye movement and how ETT captures it. This paper delivers a typology of different approaches to eye-tracking research and presents information about ETT equipment and metrics. This paper also summarizes previous studies using eye tracking to study children. This paper concludes with research questions and topics for future research where ETT can be used to study child consumers in contexts such as playing advergames, using social media and shopping (in-person and online).

Findings
ETT is commonly used to assess children’s behavior in a variety of contexts but has scarcely been used to study children’s consumer behavior. ETT has great potential to be used to better understand children as consumers.

Originality/value
To the best of the authors’ knowledge, this is the first paper to review using ETT to study children’s consumer behavior.
Psychological ownership of health promotes self and other-oriented health behaviors
Authors: Rao Mahendra Singh , Leonhardt James M. 
Published: January 2025

Purpose
This research introduces and validates psychological ownership of health as a novel theoretical construct characterized by individuals’ perceived possessiveness, attachment and responsibility toward their health. This study aims to examine the construct’s ability to predict and explain consumers’ health-related decision-making for themselves and others.

Design/methodology/approach
Two online surveys with US participants (N = 680) were conducted. The psychological ownership of health scale was first validated through confirmatory factor analysis. Next, the influence of psychological ownership of health on positive health behaviors and blood donation intentions was assessed using multiple regression analyses and conditional process modeling.

Findings
Psychological ownership of health demonstrated significant positive associations with health-promoting behaviors (dietary choices, physical activity, sleep hygiene) mediated by health self-efficacy. In addition, psychological ownership of health predicted increased blood donation intentions, and this relationship is amplified among individuals high in cultural collectivism.

Practical implications
The findings suggest that interventions fostering psychological ownership of health may simultaneously promote personal health maintenance and prosocial health behaviors. These dual implications offer promising applications for individualized and public health initiatives.

Originality/value
This research advances psychological ownership theory by establishing and validating a health-specific dimension that predicts critical health behaviors at individual and societal levels. By identifying cultural collectivism as a moderator, this research also integrates psychological ownership theory with cultural dimensions theory, revealing cultural variability in health ownership’s influence on prosocial health outcomes.