bluuebunny/crossref_metadata_2025_split huggingface dataset:
The repatriation of wolves to Isle Royale alters the foraging of meso-carnivores
Authors: Lacin Alas Burcu , Rodriguez Curras Mauriel , Smith Matthew M , Potvin Lynette R , Romanski Mark C , Pauli Jonathan N 
Published: October 2024

Abstract
Due to the disproportionate role that large carnivores can have on communities and their global decline over the last century, carnivores are increasingly being repatriated across their historic ranges. The reintroduction of gray wolves (Canis lupus) can precipitate substantive changes to communities and ecosystems. Notably, wolves could have strong effects on smaller and subordinate carnivores, especially in altering their foraging behavior and prey selection. Past studies investigating wolf effects on other carnivores, however, have generally been conducted in relatively complex communities featuring a diverse assemblage of carnivores and prey and have lacked baseline (i.e., pre-repatriation) data. Consequently, researchers have quantified what a community looks like after wolf return, with little information on how the community behaved before. To better understand the effect of large carnivore repatriation on the foraging ecology of a carnivore community, we investigated the impact of reintroduced gray wolves on 2 meso-carnivores: Red Fox (Vulpes vulpes); and American Marten (Martes americana) within an insular and simple vertebrate community at Isle Royale National Park before and after wolf reintroduction. We analyzed &gt;600 scats from 20 individual martens and 63 individual foxes as well as the stable isotopes of 9 and 22 tissue samples from martens and foxes, respectively, at both individual and population levels. We found that the wolf reintroduction had little effect on marten diet but strongly influenced fox diet depending on the analysis conducted. At the population level, our analysis revealed that both foxes and martens were dietary generalists consuming an array of food items including small prey, berries, and human food regardless of wolf presence. However, at the individual level, we found that prior to wolf repatriation foxes primarily consumed berries and small prey but following wolf repatriation the diet of foxes shifted to berries and human foods as well as large carrion. This post-wolf reintroduction shift in diet increased the dietary overlap between foxes and martens. Our work provides new insights into how the return of a large carnivore can alter the foraging ecology of small-bodied carnivores and act both to provision carrion resources as well drive other carnivores to consume more human food and increase dietary overlap.
Neighborhood homicide rate and odds of colorectal adenoma among adult patients seeking colonoscopy
Authors: Hamm Alyshia , Karayeva Evgenia , Oliveira Manoela Lima , Kahouadji Nabil , Grippo Paul , Wolf Patricia G , Mutlu Ece , Tussing-Humphreys Lisa , Kim Sage J 
Published: October 2024

Abstract

Background
Chronic exposure to ambient stressors, including neighborhood crime, may have a detrimental impact on the body’s stress response system with implications for colorectal carcinogenesis.

Methods
We examined associations between the mean neighborhood homicide rates from 2000 and 2018 and diagnosis of colorectal adenoma among patients at the University of Illinois Health and Hospital System in Chicago, Illinois, between 2015 and 2018.

Results
Of the 5225 patients who underwent colonoscopy and were included in the analytic dataset, 60% had colorectal adenoma. Older age, male sex, and higher body mass index (BMI) were associated with greater odds of colorectal adenoma. The neighborhood homicide rate was associated with identifying as Black and Hispanic and higher BMI. A mediation analysis showed that the neighborhood homicide rate effects on colorectal adenoma were mediated through BMI.

Conclusions
The study concluded that older age, male sex, and higher BMI increases the odds of colorectal adenoma, with neighborhood homicide rate indirectly influencing this risk through its association with BMI, particularly among Black and Hispanic individuals.
Kin-State Intervention and the Securitization-Minority Policy Nexus: Hungarians and Russian-Speakers in Central and Eastern Europe
Authors: Csergő Zsuzsa , Kallas Kristina , Kiss Tamás 
Published: October 2024

Abstract
Russia’s full-scale invasion of Ukraine in 2022, launched under the pretext of protecting the rights of Russian kin populations outside of Russia, had a massive impact on security concerns beyond Ukraine. An important consequence was the intensification of insecurities about the presence of large Russian-speaking minorities in Russia’s neighboring states. Scholars have long emphasized that kin-state involvement can lead to the securitization of minority issues, harming the willingness of governments to support collective claims by minorities associated with that kin-state. Yet there is scarce empirical knowledge about whether and under what conditions an assertive kin-state triggers securitization resulting in restrictive minority policy. We assessed this securitization-minority policy nexus comparatively, focusing on the impact of intensifying Hungarian and Russian kin-state activism on policies toward Hungarian and Russophone minorities in five states in Central and Eastern Europe. Our main finding is that intensified kin-state activism does not significantly disrupt previously established paths in minority policy-making, unless a kin-state turns to territorial revisionism. We also found that titular ontological insecurity (faced by actors belonging to a state’s dominant ethnic group) is a helpful heuristic for explaining instances when securitization results in policy restrictions, and we offer conceptual tools for analyzing the salience of both internal and external sources of titular insecurity. Ultimately, our findings highlight the necessity for scholars to distinguish between nonterritorial and territorial types of kin-state intervention in studies about the security dimension of kin-state involvement.
Energy attenuation of seismic metamaterials composed of a periodic array of coated elliptical cylinders
Authors: Huang Wei-Hsiang , Lin Zong-Ying , Chen Tungyang 
Published: October 2024

Abstract
We present a numerical study on energy attenuation of seismic metamaterials consisting of a periodic array of coated elliptical cylinders. The aim is to perceive the effect of aspect ratio for different wave modes so that the metamaterials can interact with the incoming wave causing them to interfere with each other destructively, especially for low-frequency seismic waves with relatively wide bandgap. Previous studies mainly focused on the configuration of coated circular cylinders or spheres, in which the metamaterial is composed of a hard inclusion surrounded by a soft coating layer and dispersed within a hard matrix. Here we utilize numerical simulations based on finite element calculation to analyze the local fields within the unit cell. Effective mass density, mass moment of inertia and shear modulus are analyzed through a homogenization procedure to characterize the macroscopic behavior of the effective medium. The effective behavior will be dependent for different aspect ratios and for different types of wave motions. To verify the effectiveness of energy attenuation, a full-scale model is adopted. Specifically, to identify optimal energy attenuation configurations, we illustrate the attenuation effects of elliptical metamaterials under longitudinal and shear horizontal types of waves. The present study demonstrates that elliptical metamaterials will have more reflexibilities to tune with the aspect ratio of the elliptical geometry as well as the directionality of incidence waves. Based on our simulations, we show the ability of the designed configuration in tuning local resonance frequencies and bandwidths for real implementations and applications of seismic metamaterials.
Education beyond the limits: addressing violence against women and girls
Authors: Skilbeck Adrian 
Published: October 2024

Abstract
This article is a contribution to a suite of articles on violence against women and girls. It sets out the context in which this issue is currently discussed, how it might be understood and how it can be addressed. Education is seen as a key mechanism for the prevention of gender-based violence through the transformation of the attitudes and beliefs that boys and young men hold about women and girls and what it means to be a man. This article considers the challenges of achieving this in the face of online influencers like Andrew Tate with their appeal to masculine entitlement and supremacy, often expressed in terms of misogynistic violence and coercion. Drawing on the work of Jacqueline Rose, Judith Butler, and others, the article argues that this is a task that involves creative and affective pedagogy as well as sustained critical engagement. There is, therefore, an important role for the arts and humanities in providing spaces for exploration, conversation, and reflection about the embodied experience of violence and abuse. Through difficult educational encounters it may be possible to initiate a change in boys and young men from impervious thoughtlessness to a greater recognition and understanding of the impact of harassment and violence, both within the educational setting and beyond.
Beat-to-beat analysis of hemodynamic response to mental and psychological stress in sickle cell anemia
Authors: Abiri Arash , Marmarchinia Sara , Shah Payal , Thuptimdang Wanwara , Coates Thomas D , Khoo Michael C K , Khine Michelle 
Published: October 2024

Abstract

Objectives
Vaso-occlusive crises are a hallmark symptom of SCD. Physical stressors can trigger decreased microvascular blood flow and increase the risk for vaso-occlusive crises. However, the effect of mental and psychological stressors on vascular physiology in SCD is not well-established. We hereby examined fluctuations in continuous blood pressure to evaluate hemodynamic changes in SCD patients during mental and psychological stress.

Methods
Thirteen SCD subjects from the Children’s Hospital Los Angeles and 11 healthy volunteers were recruited. Continuous blood pressure was recorded during 2 mental tasks and 1 psychological stress task. Systolic beat-to-beat blood pressure variability measurements were calculated for each subject. Three very short-term blood pressure variability metrics served as outcome measures: SD, coefficient of variation, and average real variability. Peripheral augmentation index was calculated from arterial waveforms. Linear mixed effects models evaluated associations between patient factors and outcome measures.

Results
SCD patients exhibit increased systolic blood pressure variability in response to psychological stress. All subjects exhibited a decrease in systolic blood pressure variability in response to mental stress tasks. During mental stress, both groups displayed increased augmentation index, reflective of stress-induced vasoconstriction, while psychological stress in SCD patients led to both decreased mean arterial pressure and increased augmentation index, suggestive of uncompensated vasoconstriction.

Conclusion
These findings emphasize the impact of mental and psychological stressors on vascular function in SCD and the potential for monitoring physiological signals to predict vaso-occlusive crisis events.
The LncNAT11–MYB11–F3'H/FLS module mediates flavonol biosynthesis to regulate salt stress tolerance in Ginkgo biloba
Authors: Liu Sian , Zhang Hanyue , Meng Zhaolong , Jia Zhichao , Fu Fangfang , Jin Biao , Cao Fuliang , Wang Li 
Published: October 2024

Abstract
Flavonols are important secondary metabolites that enable plants to resist environmental stresses. Although MYB regulation of flavonol biosynthesis has been well studied, the long non-coding RNA (lncRNA)–MYB networks involved in regulating flavonol biosynthesis remain unknown. Ginkgo biloba is rich in flavonols, which are the most important medicinal components. Based on multi-omics data and phylogenetic trees, we identified GbMYB11 as a potential key transcription factor regulating flavonol biosynthesis. Overexpression and virus-induced gene silencing (VIGS) experiments confirmed that GbMYB11 acts as a pivotal positive regulator in flavonol biosynthesis. In the transcriptome of calli overexpressing GbMYB11, we identified significant up-regulation of GbF3'H and GbFLS in the flavonol biosynthetic pathway. Yeast one-hybrid and dual-luciferase assays demonstrated that GbMYB11 enhances the expression of GbF3'H and GbFLS by binding to their promoters. Interestingly, we identified LncNAT11, an antisense lncRNA complement to GbMYB11, which negatively regulates flavonol biosynthesis by repressing the expression of GbMYB11. Consequently, we established the LncNAT11–GbMYB11–GbF3'H/GbFLS module as a critical regulator of flavonol biosynthesis in G. biloba, and further elucidated that this module can mitigate the accumulation of reactive oxygen species by modulating flavonol biosynthesis during salt stress. These findings unveil a novel mechanism underlying flavonol biosynthesis and an lncRNA–MYB-mediated salt stress tolerance strategy in plants.
ncPlantDB: a plant ncRNA database with potential ncPEP information and cell type-specific interaction
Authors: Liu Liya , Liu Enyan , Hu Yueming , Li Sida , Zhang Shilong , Chao Haoyu , Hu Yanshi , Zhu Yanyan , Chen Yifan , Xie Luyao , Shen Yi , Wu Liangwei , Chen Ming 
Published: October 2024

Abstract
The field of plant non-coding RNAs (ncRNAs) has seen significant advancements in recent years, with many ncRNAs recognized as important regulators of gene expression during plant development and stress responses. Moreover, the coding potential of these ncRNAs, giving rise to ncRNA-encoded peptides (ncPEPs), has emerged as an essential area of study. However, existing plant ncRNA databases lack comprehensive information on ncRNA-encoded peptides (ncPEPs) and cell type-specific interactions. To address this gap, we present ncPlantDB (https://bis.zju.edu.cn/ncPlantDB), a comprehensive database integrating ncRNA and ncPEP data across 43 plant species. ncPlantDB encompasses 353 140 ncRNAs, 3799 ncPEPs and 4 647 071 interactions, sourced from established databases and literature mining. The database offers unique features including translational potential data, cell-specific interaction networks derived from single-cell RNA sequencing and Ribo-seq analyses, and interactive visualization tools. ncPlantDB provides a user-friendly interface for exploring ncRNA expression patterns at the single-cell level, facilitating the discovery of tissue-specific ncRNAs and potential ncPEPs. By integrating diverse data types and offering advanced analytical tools, ncPlantDB serves as a valuable resource for researchers investigating plant ncRNA functions, interactions, and their potential coding capacity. This database significantly enhances our understanding of plant ncRNA biology and opens new avenues for exploring the complex regulatory networks in plant genomics.
ScRAPdb: an integrated pan-omics database for the Saccharomyces cerevisiae reference assembly panel
Authors: Miao Zepu , Ren Yifan , Tarabini Andrea , Yang Ludong , Li Huihui , Ye Chang , Liti Gianni , Fischer Gilles , Li Jing , Yue Jia-Xing 
Published: October 2024

Abstract
As a unicellular eukaryote, the budding yeast Saccharomyces cerevisiae strikes a unique balance between biological complexity and experimental tractability, serving as a long-standing classic model for both basic and applied studies. Recently, S. cerevisiae further emerged as a leading system for studying natural diversity of genome evolution and its associated functional implication at population scales. Having high-quality comparative and functional genomics data are critical for such efforts. Here, we exhaustively expanded the telomere-to-telomere (T2T) S. cerevisiae reference assembly panel (ScRAP) that we previously constructed for 142 strains to cover high-quality genome assemblies and annotations of 264 S. cerevisiae strains from diverse geographical and ecological niches and also 33 outgroup strains from all the other Saccharomyces species complex. We created a dedicated online database, ScRAPdb (https://www.evomicslab.org/db/ScRAPdb/), to host this expanded pangenome collection. Furthermore, ScRAPdb also integrates an array of population-scale pan-omics atlases (pantranscriptome, panproteome and panphenome) and extensive data exploration toolkits for intuitive genomics analyses. All curated data and downstream analysis results can be easily downloaded from ScRAPdb. We expect ScRAPdb to become a highly valuable platform for the yeast community and beyond, leading to a pan-omics understanding of the global genetic and phenotypic diversity.
VFDB 2025: an integrated resource for exploring anti-virulence compounds
Authors: Zhou Siyu , Liu Bo , Zheng Dandan , Chen Lihong , Yang Jian 
Published: October 2024

Abstract
With the escalating crisis of bacterial multidrug resistance, anti-virulence therapeutic strategies have emerged as a highly promising alternative to conventional antibiotic treatments. Anti-virulence compounds are specifically designed to target virulence factors (VFs), disarming pathogens without affecting bacterial growth and thus reduce the selective pressure for resistance development. However, due to the complexity of bacterial pathogenesis, no anti-virulence small molecules have been approved for clinical use thus far, despite the documentation of hundreds of potential candidates. To provide valuable reference resources for drug design, repurposing, and target selection, the virulence factor database (VFDB, http://www.mgc.ac.cn/VFs/) has systematically collected public data on anti-virulence compounds through extensive literature mining, and further integrated this information with its existing knowledge of bacterial VFs. To date, the VFDB has curated a comprehensive dataset of 902 anti-virulence compounds across 17 superclasses reported by 262 studies worldwide. By cross-linking the current knowledge of bacterial VFs with information on relevant compounds (e.g. classification, chemical structure, molecular targets and mechanisms of action), the VFDB aims to bridge the gap between chemists and microbiologists, providing crucial insights for the development of innovative and effective antibacterial therapies to combat bacterial infections and address antibiotic resistance.
Generic Diagramming Platform (GDP): a comprehensive database of high-quality biomedical graphics
Authors: Jiang Shuai , Li Huiqin , Zhang Luowanyue , Mu Weiping , Zhang Ya , Chen Tianjian , Wu Jingxing , Tang Haoyun , Zheng Shuxin , Liu Yifei , Wu Yaxuan , Luo Xiaotong , Xie Yubin , Ren Jian 
Published: October 2024

Abstract
High-quality schematic illustrations are fundamental to the publication of scientific achievements in biomedical research, which are crucial for effectively conveying complex biomedical concepts. However, creating such illustrations remains challenging for many researchers due to the need to devote a significant amount of time and effort to accomplish it. To address this need, we present the Generic Diagramming Platform (GDP, https://BioGDP.com), a comprehensive database of professionally crafted biomedical graphics (bio-graphics). Currently, GDP houses 7 562 high-quality bio-graphics, meticulously categorized into 10 major and 77 minor categories. To increase the design efficiency, GDP provides 204 customizable templates derived from an extensive review of over 2000 literature and 7 textbooks. With the interactive drawing platform and user-friendly web interface implemented in GDP, these resources can facilitate the efficient generation of publication-ready illustrations for the biomedical community. Additionally, GDP incorporates a collaborative submission system, allowing researchers to contribute their artwork, fostering a growing diagramming ecosystem, and ensuring continuous database expansion. Overall, we believe that GDP will serve as an invaluable platform, significantly enhancing the efficiency and quality of scientific illustration for biomedical researchers.
Activatable red/near-infrared aqueous organic phosphorescence probes for improved time-resolved bioimaging
Authors: Li Yang , Wu Zhiqin , Huang Zizhao , Yin Chenjia , Tian He , Ma Xiang 
Published: October 2024

ABSTRACT
Organic red/near-infrared (NIR) room-temperature phosphorescence (RTP) holds significant potential for autofluorescence-free bioimaging and biosensing due to its prolonged persistent luminescence and exceptional penetrability. However, achieving activatable red/NIR organic RTP probes with tunable emission in aqueous solution remains a formidable challenge. Here we report on aqueous organic RTP probes with red/NIR phosphorescence intensity and lifetime amplification. These probes consist of supramolecular assemblies comprising macrocyclic cucurbit[8]uril and amine-containing alkyl-bridged pyridiniums, exhibiting viscosity-activatable phosphorescence with enhanced quantum yield (≤20%) and lifetime. Notably, by utilizing this activatable organic RTP probe, we successfully achieve two-photon imaging of lysosomal viscosity and millisecond-scale time-resolved cell imaging. Moreover, intravital phosphorescence imaging by using an RTP probe enables the monitoring of viscosity variations in inflammatory mice, demonstrating a significantly improved signal-to-background ratio compared with fluorescence imaging. This activatable red/NIR supramolecular platform facilitates versatile high-resolution phosphorescence imaging for in vivo tracking of specific biomarkers and physiological events.
The acceptability and feasibility of a mobile phone delivered brief intervention for hazardous drinking in India
Authors: Nadkarni Abhijit , Fernandes Danielle , Velleman Richard , Onyango Anastasia , Sambari Seema , D’Souza Ethel 
Published: October 2024

Abstract
The effectiveness of Brief Interventions (BIs) for hazardous drinking is well established. However, the implementation of BIs at scale in low- and middle-income countries such as India is rare, primarily due to human resource related barriers. This paper describes the testing of acceptability and feasibility, and the preliminary impact, of a mobile phone delivered BI in an uncontrolled treatment cohort and nested qualitative study. Consenting adult (≥18 years) participants with an Alcohol Use Disorder Identification Test score between 8 to 15 were recruited from educational institutions, workplaces and primary care settings. The TLFB (Time-Line Follow Back) was administered to participants at baseline and 3 months post recruitment. All participants received the BI through text messages or IVR (Interactive Voice Response) over eight weeks; and in-depth interviews were conducted with some participants. The mean pre and post outcomes were compared using paired t-test. Qualitative data was analysed using thematic analyses. 29 participants received the intervention and 16 (55%) completed the outcome assessments. Some key qualitative findings indicated the desire from participants for fewer messages and messages that did not require interaction; and more messages with motivational content and information on practical skills to reduce drinking. The percentage days abstinent was significantly higher at follow up than baseline in all those who had completed the TLFB at baseline and follow up. Feasibility and acceptability testing is an important component of the intervention development process to ensure that the resulting intervention is suitable for the context.