bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genetic association of lipid-lowering drugs with aortic aneurysms: a Mendelian randomization study
Authors: Gao Xiong , Luo Wei , Qu Liyuan , Yang Miaomiao , Chen Siyu , Lei Li , Yan Shaohua , Liang Hongbin , Zhang Xinlu , Xiao Min , Liao Yulin , Lee Alex Pui-Wai , Zhou Zhongjiang , Chen Jiejian , Zhang Qiuxia , Wang Yuegang , Xiu Jiancheng 
Published: February 2024

Abstract

Aims
The lack of effective pharmacotherapies for aortic aneurysms (AA) is a persistent clinical challenge. Lipid metabolism plays an essential role in AA. However, the impact of lipid-lowering drugs on AA remains controversial. The study aimed to investigate the genetic association between lipid-lowering drugs and AA.

Methods and results
Our research used publicly available data on genome-wide association studies (GWASs) and expression quantitative trait loci (eQTL) studies. Genetic instruments, specifically eQTLs related to drug-target genes and SNPs (single nucleotide polymorphisms) located near or within the drug-target loci associated with low-density lipoprotein cholesterol (LDL-C), have been served as proxies for lipid-lowering medications. Drug-Target Mendelian Randomization (MR) study is used to determine the causal association between lipid-lowering drugs and different types of AA. The MR analysis revealed that higher expression of HMGCR (3-hydroxy-3-methylglutaryl coenzyme A reductase) was associated with increased risk of AA (OR = 1.58, 95% CI = 1.20–2.09, P = 1.20 × 10−03) and larger lumen size (aortic maximum area: OR = 1.28, 95% CI = 1.13–1.46, P = 1.48 × 10−04; aortic minimum area: OR = 1.26, 95% CI = 1.21–1.42, P = 1.78 × 10−04). PCSK9 (proprotein convertase subtilisin/kexin type 9) and CETP (cholesteryl ester transfer protein) show a suggestive relationship with AA (PCSK9: OR = 1.34, 95% CI = 1.10–1.63, P = 3.07 × 10−03; CETP: OR = 1.38, 95% CI = 1.06–1.80, P = 1.47 × 10−02). No evidence to support genetically mediated NPC1L1 (Niemann–Pick C1-Like 1) and LDLR (low-density lipoprotein cholesterol receptor) are associated with AA.

Conclusion
This study provides causal evidence for the genetic association between lipid-lowering drugs and AA. Higher gene expression of HMGCR, PCSK9, and CETP increases AA risk. Furthermore, HMGCR inhibitors may link with smaller aortic lumen size.
The Impact of Patterns in Linkage Disequilibrium and Sequencing Quality on the Imprint of Balancing Selection
Authors: Hayeck Tristan J , Li Yang , Mosbruger Timothy L , Bradfield Jonathan P , Gleason Adam G , Damianos George , Shaw Grace Tzun-Wen , Duke Jamie L , Conlin Laura K , Turner Tychele N , Fernández-Viña Marcelo A , Sarmady Mahdi , Monos Dimitri S 
Published: February 2024

Abstract
Regions under balancing selection are characterized by dense polymorphisms and multiple persistent haplotypes, along with other sequence complexities. Successful identification of these patterns depends on both the statistical approach and the quality of sequencing. To address this challenge, at first, a new statistical method called LD-ABF was developed, employing efficient Bayesian techniques to effectively test for balancing selection. LD-ABF demonstrated the most robust detection of selection in a variety of simulation scenarios, compared against a range of existing tests/tools (Tajima's D, HKA, Dng, BetaScan, and BalLerMix). Furthermore, the impact of the quality of sequencing on detection of balancing selection was explored, as well, using: (i) SNP genotyping and exome data, (ii) targeted high-resolution HLA genotyping (IHIW), and (iii) whole-genome long-read sequencing data (Pangenome). In the analysis of SNP genotyping and exome data, we identified known targets and 38 new selection signatures in genes not previously linked to balancing selection. To further investigate the impact of sequencing quality on detection of balancing selection, a detailed investigation of the MHC was performed with high-resolution HLA typing data. Higher quality sequencing revealed the HLA-DQ genes consistently demonstrated strong selection signatures otherwise not observed from the sparser SNP array and exome data. The HLA-DQ selection signature was also replicated in the Pangenome samples using considerably less samples but, with high-quality long-read sequence data. The improved statistical method, coupled with higher quality sequencing, leads to more consistent identification of selection and enhanced localization of variants under selection, particularly in complex regions.
The Addis Ababa Lions: Whole-Genome Sequencing of a Rare and Precious Population
Authors: Barazandeh Marjan , Kriti Divya , Fickel Jörns , Nislow Corey 
Published: February 2024

Abstract
Lions are widely known as charismatic predators that once roamed across the globe, but their populations have been greatly affected by environmental factors and human activities over the last 150 yr. Of particular interest is the Addis Ababa lion population, which has been maintained in captivity at around 20 individuals for over 75 yr, while many wild African lion populations have become extinct. In order to understand the molecular features of this unique population, we conducted a whole-genome sequencing study on 15 Addis Ababa lions and detected 4.5 million distinct genomic variants compared with the reference African lion genome. Using functional annotation, we identified several genes with mutations that potentially impact various traits such as mane color, body size, reproduction, gastrointestinal functions, cardiovascular processes, and sensory perception. These findings offer valuable insights into the genetics of this threatened lion population.
CpG Island Definition and Methylation Mapping of the T2T-YAO Genome
Authors: Xiao Ming , Wei Rui , Yu Jun , Gao Chujie , Yang Fengyi , Zhang Le 
Published: February 2024

Abstract
Precisely defining and mapping all cytosine (C) positions and their clusters, known as CpG islands (CGIs), as well as their methylation status, are pivotal for genome-wide epigenetic studies, especially when population-centric reference genomes are ready for timely application. Here, we first align the two high-quality reference genomes, T2T-YAO and T2T-CHM13, from different ethnic backgrounds in a base-by-base fashion and compute their genome-wide density-defined and position-defined CGIs. Second, by mapping some representative genome-wide methylation data from selected organs onto the two genomes, we find that there are about 4.7%–5.8% sequence divergency of variable categories depending on quality cutoffs. Genes among the divergent sequences are mostly associated with neurological functions. Moreover, CGIs associated with the divergent sequences are significantly different with respect to CpG density and observed CpG/expected CpG (O/E) ratio between the two genomes. Finally, we find that the T2T-YAO genome not only has a greater CpG coverage than that of the T2T-CHM13 genome when whole-genome bisulfite sequencing (WGBS) data from the European and American populations are mapped to each reference, but also shows more hyper-methylated CpG sites as compared to the T2T-CHM13 genome. Our study suggests that future genome-wide epigenetic studies of the Chinese populations rely on both acquisition of high-quality methylation data and subsequent precision CGI mapping based on the Chinese T2T reference.
Quantifying gender disparities and bias online: editors’ introduction to “Gender Gaps in Digital Spaces” special issue
Authors: Horvát Emőke-Ágnes , González-Bailón Sandra 
Published: February 2024

Abstract
This special issue collects studies about how gender divides manifest in digital environments, spanning online repositories, social media, and AI-powered technologies. Computational research helps in assessing the nature and prevalence of gender divides: Identifying differences and bias requires defining benchmarks, systematic departures, and overall incidence. This collection showcases evidence uncovered quantitatively and illustrates how such evidence can advance theoretical understanding of gender dynamics as socially constructed phenomena. Social interactions and discursive practices are shaped by the technologies we use to communicate, work, and organize. These technologies shape, in turn, how we perceive and reinforce gender stereotypes. In this editors‘ note, we discuss how the seven articles included in the special issue unpack communicative processes in the context of various online environments, disentangling gendered dynamics from the use of digital technologies. Ultimately, our goal is to energize a research agenda that requires continued work as technologies morph and evolve in unprecedented directions.
NewickTreeModifier: A simple web tool to prune and modify Newick trees
Authors: Ogoniak Lynn , Steffen Raphael , Grundmann Norbert , Stöver Ben , Müller Kai , Schmitz Jürgen 
Published: February 2024

Abstract
Large-scale selection analyses of protein-coding sequences and phylogenetic tree reconstructions require suitable trees in Newick format. We developed the NewickTreeModifier (NTM), a simple web-based tool to trim and modify Newick trees for such analyses. The users can choose provided master trees or upload a tree to prune it to selected species available in FASTA, NEXUS, or PHYLIP sequence format with an internal converter, a simple species list, or directly determined from a checklist interface of the master trees. Plant, insect, and vertebrate master trees comprise the maximum number of species in an up-to-date phylogenetic order directly transferable to the pruned Newick outfile. NTM is available at https://retrogenomics.uni-muenster.de/tools/ntm.
Exploring the Role of Religious Actors in Generating Respect for the Laws of War: A Common Article 1 Perspective
Authors: Massingham Eve , McRuvie Kirsty 
Published: February 2024

Abstract
In addition to religious personnel, who are directly involved in armed conflict, religious actors, as key actors in our community, have a significant role in respecting and ensuring respect for the laws of war. They are, both in and outside conflict, powerful agents for promoting international humanitarian law awareness and compliance, and ultimately, they can contribute to conditions that ensure greater respect for international humanitarian law. By virtue of their positions, they may have a direct opportunity to influence the positive or negative behaviour of members of the armed forces in their compliance of IHL; communicate directly with those affected by conflict; or be present within the diaspora of a community who are directly affected by the conflict. Other religious actors, spatially and temporally removed from the conflict, will have a role in the broader community conversation around ensuring respect for the law in armed conflict, without having specific linkages to any particular conflict. Through these different roles, religious actors have great leverage to use their influence for humanitarian ends. This role must be both encouraged by, and facilitated by, the State. In this way religious personnel, and religious actors more broadly, can contribute to reducing the humanitarian impacts of the global crisis of armed conflict.
Active vibration control of functionally graded material plates integrated with piezoelectric layers using new Q9ɤ approach
Authors: Malha Nougal , Tiberkak Rachid , Ezzraimi Madjid , Lazar Mohamed Essedik , Attaf Brahim 
Published: February 2024

Abstract
A new efficient approach has been developed to simulate the free vibration, static, dynamic response and active control of functionally graded material (FGM) plates with integrated piezoelectric layers. This approach reinforces the standard first-order shear deformation theory by introducing a novel shear strain fields, alleviating the problem of shear locking, especially in the analysis of thin structures. These new fields accurately predict the shear strain fields, satisfying both compatibility and equilibrium equations while requiring less mesh refinement. Furthermore, this current approach provides higher performance and precision in analysing FGM structures. Additionally, a feedback control system has been implemented using either total piezoelectric layers or partial covering (patch) as actuators and sensors in both static bending control and dynamic vibration control analysis. The present work strengthens the basic techniques for further research in finite element analysis across a broader spectrum of materials and applications.
Linguistic annotation of cuneiform texts using treebanks and deep learning
Authors: Ong Matthew , Gordin Shai 
Published: February 2024

Abstract
We describe an efficient pipeline for morpho-syntactically annotating an ancient language corpus which takes advantage of bootstrapping techniques. This pipeline is designed for ancient language scholars looking to jump-start their own treebank projects, which can in turn serve further pedagogical research projects in the target language. We situate our work in the field of similar ancient language treebank projects, arguing that our approach shows that individual humanities scholars can leverage current machine-learning tools to produce their own richly annotated corpora. We illustrate this pipeline by producing a new Akkadian-language treebank based on two volumes from the online editions of the State Archives of Assyria project hosted on Oracc, as well as a spaCy language model named AkkParser trained on that treebank. Both of these are made publicly available for annotating other Akkadian corpora. In addition, we discuss linguistic issues particular to the Neo-Assyrian letter corpus and data-encoding complications of cuneiform texts in Oracc. The strategies, language models, and processing scripts we developed to handle both linguistic and data-encoding issues in this project will be of special interest to scholars seeking to develop their own cuneiform treebanks.
Does Everyone See the Same Thing?
Authors: Goldstein Naomi E. S. , Serico Jennifer M. , Haney-Caron Emily , Giallella Christy L. , Kalbeitzer Rachel , Zelechoski Amanda D. , Riggs Romaine Christina L. , Kemp Kathleen 
Published: February 2024

Abstract
This chapter covers Session 4 of the Juvenile Justice Anger Management (JJAM) Treatment for Girls. In this session participants learn that situations can be viewed from different perspectives, and the way that each girl sees the situation may influence the way she thinks and feels about it. The session activities include reviewing the previous session, a perspective-taking activity, and a “motive in a hat” game. A cognitive restructuring activity introduces the concept of reframing thoughts to change feelings and behavior while also reinforcing the idea that different interpretations of situations can lead to different emotional and behavioral reactions. The chapter provides the instructions and materials needed to facilitate the session.
Introduction to Problem-Solving
Authors: Goldstein Naomi E. S. , Serico Jennifer M. , Haney-Caron Emily , Giallella Christy L. , Kalbeitzer Rachel , Zelechoski Amanda D. , Riggs Romaine Christina L. , Kemp Kathleen 
Published: February 2024

Abstract
This chapter covers Session 11 of the Juvenile Justice Anger Management (JJAM) Treatment for Girls. In this session the group participants learn about the steps involved in solving a problem. The girls put together all the anger management skills they have learned so far and practice using them in a calm situation or situations where they feel anger or arousal. The facilitators review the steps of social problem-solving, beginning with identifying that a problem exists and ending with a consideration of possible consequences. The facilitators guide the girls in applying these problem-solving steps to their lives and recent events. The chapter includes the materials and script needed for the session activities.
Can I Be a Star?
Authors: Goldstein Naomi E. S. , Serico Jennifer M. , Haney-Caron Emily , Giallella Christy L. , Kalbeitzer Rachel , Zelechoski Amanda D. , Riggs Romaine Christina L. , Kemp Kathleen 
Published: February 2024

Abstract
This chapter covers Session 15 of the Juvenile Justice Anger Management (JJAM) Treatment for Girls. In this session the participants create an anger management play. The play’s purpose is to provide the girls with a creative outlet to practice using the coping skills they have learned and to make these skills more memorable and accessible in the future. The facilitators encourage the girls to come up with ideas of problems and anger-provoking situations that they can incorporate into the plot of the play. The facilitators also help the girls to develop the script and support the participation and creativity of the participants. The chapter highlights the importance of the girls organizing the ideas for the play themselves.
Dress Rehearsal and Play
Authors: Goldstein Naomi E. S. , Serico Jennifer M. , Haney-Caron Emily , Giallella Christy L. , Kalbeitzer Rachel , Zelechoski Amanda D. , Riggs Romaine Christina L. , Kemp Kathleen 
Published: February 2024

Abstract
This chapter covers the final session of the Juvenile Justice Anger Management (JJAM) Treatment for Girls. In this session the participants rehearse and then perform their play in front of a live audience. The purpose of the play is to provide the girls with a creative outlet to practice using the coping skills they have learned and to make these skills more memorable and accessible for future use. Performing the play also gives the girls an opportunity to share what they learned during the entire JJAM program. The play will be performed for a group of staff and participants (depending on the facility’s rules, the availability of staff and residents, and the facilitator’s judgment). The program concludes by presenting the girls with certificates of completion.
Is Anger Normal?
Authors: Goldstein Naomi E. S. , Serico Jennifer M. , Haney-Caron Emily , Giallella Christy L. , Kalbeitzer Rachel , Zelechoski Amanda D. , Riggs Romaine Christina L. , Kemp Kathleen 
Published: February 2024

Abstract
This chapter contains the facilitator materials for Session 1 of the Juvenile Justice Anger Management (JJAM) Treatment for Girls. This session focuses on the introduction, getting to know each other, and developing trust among the participants. The catch phrase for the session is “Building trust is a must.” Goal sheets will be distributed to the girls to encourage them to practice the skills they learned in the session and to use them in real-life situations. However, the use of goal sheets will start with the second session. The chapter also lists the session’s activities, which include people bingo ice breakers, role-play, and setting the ground rules.
Recognition of Anger
Authors: Goldstein Naomi E. S. , Serico Jennifer M. , Haney-Caron Emily , Giallella Christy L. , Kalbeitzer Rachel , Zelechoski Amanda D. , Riggs Romaine Christina L. , Kemp Kathleen 
Published: February 2024

Abstract
This chapter provides the facilitator materials for Session 5 of the Juvenile Justice Anger Management (JJAM) Treatment for Girls. This session is about recognizing anger. The session primarily aims to teach the girls about the different physical reactions people have when they get angry. The girls are encouraged to think about how their bodies react to anger by identifying body parts where they can feel themselves getting angry, referred to as hot spots. The session’s catch phrase is “Getting angry is a clue that there’s something you need to do.” The goal sheet addresses the girls’ need to pay attention to how their bodies react to anger by identifying body parts where they can feel themselves getting angry.
How Do I Keep Myself Calm?
Authors: Goldstein Naomi E. S. , Serico Jennifer M. , Haney-Caron Emily , Giallella Christy L. , Kalbeitzer Rachel , Zelechoski Amanda D. , Riggs Romaine Christina L. , Kemp Kathleen 
Published: February 2024

Abstract
This chapter provides the facilitator materials for Session 8 of the Juvenile Justice Anger Management (JJAM) Treatment for Girls. This session focuses on using self-talk as a method to keep oneself calm. The participants are expected to think of different things they can say to themselves when they think they might lose their temper so that they can stay out of trouble. The Session 8 catch phrase is “Use self-talk at the start so I won’t fall apart.” The goal sheets aim to teach the girls how to use self-talk when they are angry. The chapter also lists the movie clips for the session, which feature self-talk. Also provided are figures for a large master (facilitator) mouth cutout and a catch phrase sign.
How Do I Stop Myself When I’m Angry?
Authors: Goldstein Naomi E. S. , Serico Jennifer M. , Haney-Caron Emily , Giallella Christy L. , Kalbeitzer Rachel , Zelechoski Amanda D. , Riggs Romaine Christina L. , Kemp Kathleen 
Published: February 2024

Abstract
This chapter provides the facilitator materials for Session 9 of the Juvenile Justice Anger Management (JJAM) Treatment for Girls. This session teaches the girls how to delay a reaction to anger. Girls are taught the difference between reacting to an anger-provoking situation right away and taking time to calm down before reacting. The Session 9 catch phrase is “Whatever others do or say, find a way to delay.” The goal sheet encourages participants to take time to calm down before reacting. The girls need to use their tools to try to delay their reactions to situations that make them angry. The chapter provides the materials needed for the session’s activities, such as the catch phrase sign, large master (facilitator) stopwatch cutouts, and movie clips that showcase aggressive responses to use in the discussion of coping skills.
Introduction to Problem-Solving
Authors: Goldstein Naomi E. S. , Serico Jennifer M. , Haney-Caron Emily , Giallella Christy L. , Kalbeitzer Rachel , Zelechoski Amanda D. , Riggs Romaine Christina L. , Kemp Kathleen 
Published: February 2024

Abstract
This chapter provides the facilitator materials for Session 11 of the Juvenile Justice Anger Management (JJAM) Treatment for Girls. This session focuses on methods for problem-solving. The facilitators help the participants put together all of the tools and skills they have learned so far to solve a problem. The girls practice using the tools and skills so they can apply them in real-life situations. The Session 11 catch phrase is “To solve the problem with ease, find the right puzzle piece.”The goal sheet’s aim is to help the participants to think through problems and figure out their best option. The chapter also discusses the session activities, including making posters and creating a catch phrase sign.
Dress Rehearsal and Play
Authors: Goldstein Naomi E. S. , Serico Jennifer M. , Haney-Caron Emily , Giallella Christy L. , Kalbeitzer Rachel , Zelechoski Amanda D. , Riggs Romaine Christina L. , Kemp Kathleen 
Published: February 2024

Abstract
This chapter provides the facilitator materials for Session 16, the final session of the JJAM Treatment. During the first part of this session, the participants will review the previous session’s goal sheets and then will discuss the lessons they learned in each previous session. Then the girls will hold a dress rehearsal of the problem-solving play they have created, followed by a performance in front of a live audience. The performance is followed by a closing ceremony in which each participant is awarded a completion certificate. The catch phrase for this session is “With my tools and our play, practice makes things better than OK.”