bluuebunny/crossref_metadata_2025_split huggingface dataset:
Rethinking Conscientious Objection in Health Care
Authors: Giubilini Alberto , Schuklenk Udo , Minerva Francesca , Savulescu Julian 
Published: January 2025

Abstract
The book provides an argument against a right to conscientious objection by health care professionals. In increasingly multicultural societies inspired by pluralism, and given the range of controversial medical procedures that are or will be legal in many countries, claims about health care professionals’ right to abide by their own moral or religious views in the exercise of their profession become more frequent. This book explains why arguments for pluralism, tolerance, and diversity that support a right to freedom of conscience in society at large do not support the same right within the health care profession, or indeed any profession governed by internal norms of professionalism that someone freely decides to enter.
Conscience, Freedom of Conscience, and Conscientious Objection
Authors: Giubilini Alberto , Schuklenk Udo , Minerva Francesca , Savulescu Julian 
Published: January 2025

Abstract
This chapter explains in more detail how the issue of conscientious objection can arise in different contexts. It emphasizes the particular problems when it arises in professional contexts, that is, contexts characterized by professional norms, including health care. It discusses the concepts of conscience, freedom of conscience, and conscientious objection through a philosophical and brief historical overview. The chapter explains how these ethical evaluations and implications differ when the concepts are applied in wider societal contexts versus specific professional contexts that a practitioner freely chooses. In particular, it explains how conscientious objection in health care cannot be defended by an appeal to a human right to freedom of conscience.
Introduction
Authors: Tucker Chris 
Published: January 2025

Abstract
This chapter explains what the issue of weighing reasons is all about, and it introduces the rest of the book. Roughly, the general issue of weighing reasons concerns how what matters systematically interacts to determine whether an act is permissible, required, or supererogatory. Accounts of this systematic interaction need not take the metaphor of weighing reasons on a balance scale seriously, though this book does take that metaphor seriously. Weighing reasons on a balance scale can sound like a simple idea, but it is more complicated than it sounds. Part of this introduction is to prepare the reader for this potentially unexpected complexity.
The Representational Power of Dual Scale
Authors: Tucker Chris 
Published: January 2025

Abstract
This chapter clarifies Dual Scale, especially in two-option cases. It argues that Dual Scale is better suited as a fundamental model than Single Scale and that Single Scale has distorted normative theorizing. It illustrates how Dual Scale represents everything Single Scale can represent as well as what Single Scale can’t represent. Standard decision theory is just a particular version of Single Scale and so needs to be given a dual reading as well. Other alleged alternatives to Dual Scale are discussed in detail. Finally, this chapter gestures at why requirement dilemmas would be conceptually impossible even though prohibition dilemmas aren’t.
Weighing Reasons Against
Authors: Tucker Chris 
Published: January 2025

Abstract
Ethicists often reject the scale as a useful metaphor for weighing reasons. Yet they generally retain the metaphor of a reason’s weight. This combination is incoherent. The metaphor of weight entails a very specific scale-based model of weighing reasons, Dual Scale, at least in two-option cases. Justin Snedegar worries that scale-based models of weighing reasons can’t properly weigh reasons against an option. This chapter shows that there are, in fact, two different reason for/against distinctions, and it provides an account of the relationship between the various kinds of reason for and against. With this account in hand, the chapter reveals that Dual Scale has no problem weighing any kind of reason against. Among other things, it also defends contrastivism about reasons and lays out the book’s assumptions concerning option individuation.
Conclusion
Authors: Tucker Chris 
Published: January 2025

Abstract
This chapter reviews how the book accomplished its five main aims and addresses the worry that it has made weighing reasons too complicated to take seriously. The first aim is to provide a comprehensive account of weighing and weighting reasons that takes those metaphors seriously. The second is to replace Single Scale with Dual Scale. The third is to apply Dual Scale to resolve otherwise puzzling normative phenomena. The fourth is to argue for Weight Pluralism over Weight Monism. The fifth and final aim is to help you understand justifying and requiring weight well enough that you can apply them to resolve puzzling normative phenomena yourself.
Geotransition and the Future of Global Stability
Authors: Steen Bård Nikolas Vik 
Published: January 2025

Abstract
This chapter argues that global instability is likely to increase as China’s rise forces a geographical shift of military resources from the Euro-Atlantic to Pacific Asia. With Europe unlikely to replace the expeditionary capabilities that the United States currently provides, revisionist actors are likely to try to fill the gaps. While the European response to Russia’s invasion of Ukraine suggests that the North Atlantic Treaty Organization (NATO) should be able to adjust to a new reality over time, nonaligned regions that have traditionally relied on the US security umbrella may face greater turbulence in the years to come. The war in Ukraine and increased instability in the Middle East and Africa may be early signs that this dynamic is beginning to play out.
Assessing the Prospects for Armed Conflict in the Taiwan Strait
Authors: Kastner Scott L 
Published: January 2025

Abstract
Taiwan is widely viewed as the single issue that could most realistically lead to armed conflict between China and the United States, and it has become conventional wisdom that the risk of conflict in the Taiwan Strait is growing. This chapter explores that risk. After outlining several stabilizing factors that help to mitigate the likelihood of a cross-strait war, the chapter draws from existing international relations literature—particularly work grounded in the bargaining model of conflict—to show that a cross-strait war nevertheless remains a realistic possibility that could arise through several discrete processes. The chapter emphasizes, however, that a cross-strait war is far from inevitable and offers several concrete policy recommendations to help mitigate the risk of such an outcome.
What a Conflict over Taiwan Would Look Like
Authors: Tertrais Bruno 
Published: January 2025

Abstract
This chapter details the possible unfolding of a conflict over Taiwan, focusing on the canonical scenario of a Chinese invasion of the island. It emphasizes the uncertainties over the outcome of such a war, as well as the real possibilities of escalation to the nuclear level. It outlines the correlation of forces, timeframe, and probability of the conflict. It then assesses the probability of a conflict and describes the variables that would come into play, before describing the military scenario itself as well as possible US reactions. It finally considers the high risk of nuclear escalation to the extremes.
Neuropsychological Profile in Older Adults with End-Stage Kidney Disease during Kidney Transplantation Evaluation
Authors: Pongan Elodie , Rouch Isabelle , Vernaudon Julien , Bachelet Romain , Novais Teddy , Coste Marie-Hélène , Edjolo Arlette , Garnier-Crussard Antoine 
Published: January 2025

Abstract

Background
End-stage chronic kidney disease (CKD) is a significant concern for older adults and is often associated with cognitive impairment (CI). The origin of this CI is multifactorial, involving vascular and metabolic factors. Additionally, renal treatments, including dialysis, may affect cognition. This study aimed to assess the neuropsychological profiles of these patients and understand the effects of dialysis treatment.

Methods
We conducted an observational retrospective study including older adults with end-stage CKD attending for kidney transplantation (KT). Comprehensive neuropsychological assessments were conducted. Composite cognitive scores were computed. Multivariate regression models were used to assess associations between cognition and dialysis status.

Results
We included 223 patients (151 treated with dialysis, 72 with conservative management), mean age of 73.5 ± 3.4. We observed a high prevalence of CI, around 30% for global cognition and affecting all neuropsychological domains. Patients treated with dialysis exhibited lower cognitive performance compared to those not undergoing dialysis, particularly in episodic (p = .031) and working memory (p = .024).

Conclusion
This study confirms the high prevalence of CI in end-stage CKD, with dialysis being associated with worse episodic and working memory compared to non-dialyzed participants. Future investigations are needed to track the long-term cognitive trajectory of patients on the KT waiting list and post-transplantation.

Trial registration
Retrospectively registered, no 22-808 on July 7th, 2022, CNIL register number 22-5808
Steering veridical large language model analyses by correcting and enriching generated database queries: first steps toward ChatGPT bioinformatics
Authors: Cinquin Olivier 
Published: January 2025

Abstract
Large language models (LLMs) leverage factual knowledge from pretraining. Yet this knowledge remains incomplete and sometimes challenging to retrieve—especially in scientific domains not extensively covered in pretraining datasets and where information is still evolving. Here, we focus on genomics and bioinformatics. We confirm and expand upon issues with plain ChatGPT functioning as a bioinformatics assistant. Poor data retrieval and hallucination lead ChatGPT to err, as do incorrect sequence manipulations. To address this, we propose a system basing LLM outputs on up-to-date, authoritative facts and facilitating LLM-guided data analysis. Specifically, we introduce NagGPT, a middleware tool to insert between LLMs and databases, designed to bridge gaps in LLM knowledge and usage of database application programming interfaces. NagGPT proxies LLM-generated database queries, with special handling of incorrect queries. It acts as a gatekeeper between query responses and the LLM prompt, redirecting large responses to files but providing a synthesized snippet and injecting comments to steer the LLM. A companion OpenAI custom GPT, Genomics Fetcher-Analyzer, connects ChatGPT with NagGPT. It steers ChatGPT to generate and run Python code, performing bioinformatics tasks on data dynamically retrieved from a dozen common genomics databases (e.g. NCBI, Ensembl, UniProt, WormBase, and FlyBase). We implement partial mitigations for encountered challenges: detrimental interactions between code generation style and data analysis, confusion between database identifiers, and hallucination of both data and actions taken. Our results identify avenues to augment ChatGPT as a bioinformatics assistant and, more broadly, to improve factual accuracy and instruction following of unmodified LLMs.
Randomization-based Z-estimation for evaluating average and individual treatment effects
Authors: Qu Tianyi , Du Jiangchuan , Li Xinran 
Published: January 2025

Summary
Randomized experiments have been the gold standard for drawing causal inference. The conventional model-based approach has been one of the most popular ways for analysing treatment effects from randomized experiments, which is often carried through inference for certain model parameters. In this paper, we provide a systematic investigation of model-based analyses for treatment effects under the randomization-based inference framework. This framework does not impose any distributional assumptions on the outcomes, covariates and their dependence, and utilizes only randomization as the reasoned basis. We first derive the asymptotic theory for Z-estimation in completely randomized experiments, and propose sandwich-type conservative covariance estimation. We then apply the developed theory to analyse both average and individual treatment effects in randomized experiments. For the average treatment effect, we consider three estimation strategies: model-based, model-imputed, and model-assisted, where the first two can be sensitive to model misspecification or require specific ways for parameter estimation. The model-assisted approach is robust to arbitrary model misspecification and always provides consistent average treatment effect estimation. We propose optimal ways to conduct model-assisted estimation using generally nonlinear least squares for parameter estimation. For the individual treatment effects, we propose to directly model the relationship between individual effects and covariates, and discuss the model’s identifiability, inference and interpretation allowing model misspecification.
Personal and Theoretical Entanglements: Autotheoretical Reflections on Invisible Illness and Trauma in Amy Berkowitz’s Tender Points
Authors: Abdel-Rahman Téllez Shadia 
Published: January 2025

Abstract
Amy Berkowitz’s Tender Points (2015) illustrates the potential of self-narrative to shape and be shaped by theory by approaching the body as the locus of critical thinking. Instead of following a linear narrative, this memoir presents a collage of autobiographical episodes where the personal is not only framed as political, but also as the source of theoretical knowledge. Berkowitz portrays chronic pain and trauma as mirror experiences and echoes of larger structures of oppression rooted in a tradition of the delegitimation of women’s voices reinforced by the culture of patriarchy and institutions of power. Tender Points is a feminist project aiming at contesting the facts and fictions that exist around the female body, pain, and language.
Investigation of the effect of thyroid collar, radiation safety glasses, and lead apron on radiation dose in cone beam CT
Authors: İçöz Derya , Gül Osman Vefa 
Published: January 2025

Abstract

Objectives
Due to the increasing use of cone-beam CT (CBCT) in dentistry and considering the effects of radiation on radiosensitive organs, the aim of this study was to investigate the effect of shielding on absorbed dose of eyes, thyroid, and breasts in scans conducted with different parameters using 2 different fields of view (FOV).

Methods
Dose measurements were calculated on a tissue-equivalent female phantom by repeating each scanning parameter 3 times and placing at least 2 thermoluminescent dosimeters (TLD) on each organ, with the averages then taken. The same CBCT scans were performed in 2 different FOV with shielding including thyroid collar, radiation safety glasses, and lead apron and without shielding. The differences between them were analysed statistically. Descriptive statistics and the Wilcoxon test were used for data analysis.

Results
The difference between measurements with and without shielding was statistically significant for all scans (P &lt; .001). The dose reduction associated with the use of shielding ranged from 26.81% to 52.95%. The dose related to the FOV has shown a significant increase, ranging from 8.30% to 623.54%, due to both the variation in the area affected by the primary beam on the organs and changes in the amount of radiation.

Conclusion
There are significant differences in the absorbed dose depending on shielding and FOV usage. Therefore, the CBCT imaging protocol should be optimized by the operator, and special attention should be paid to the use of thyroid collars and radiation safety glasses, considering their effects on image quality.
Exploring the causes of stiff left atrial syndrome: a case series
Authors: Banthiya Sukriti , Chowdhury Medhat , Govil Dhruva , Thacker Harsh , Saba Souheil 
Published: January 2025

Abstract

Background
Stiff left atrial syndrome (SLAS) is a complication that occurs due to left atrial scarring following procedures such as radiofrequency catheter ablation for atrial fibrillation.

Case summary
We present a series of four patients with pre-existing conditions that ultimately were diagnosed as SLAS. In each case, clinical manifestations of SLAS may overlapped with other conditions and required a high index of clinical suspicion and diligent hemodynamic assessment to differentiate it from other concomitant cardiac conditions.

Discussion
We aim to highlight key differentiating diagnostic features from overlapping cardiac conditions and to summarize current treatment options for patients with SLAS.
Accumulation of trace elements in soil and fauna within a site historically contaminated with coal combustion residues
Authors: Holland Kelly E , Tuberville Tracey D , Beasley James C 
Published: January 2025

Abstract
Legacy contaminants tied to energy production are a worldwide concern. Coal combustion residues (CCRs) contain high concentrations of potentially toxic trace elements such as arsenic (As), mercury (Hg), and selenium (Se), which can persist for decades after initial contamination. Coal combustion residue disposal methods, including aquatic settling basins and landfills, can facilitate environmental exposure through intentional and accidental releases. Wildlife exposed to CCRs can experience numerous deleterious effects, such as on development, reproduction, and survival. In the current study, we quantified and compared concentrations of As, Hg, Se, and strontium (Sr) within soils and target fauna (three vertebrate and three invertebrate taxa) from a CCR-contaminated site and a reference site within the U.S. Department of Energy’s Savannah River Site, South Carolina, United States. Our objectives were to (1) compare current concentrations of tested elements in soil and resident fauna to levels from our reference site, (2) assess natural attenuation of elements in soils by comparing current concentrations to historic levels, and (3) evaluate the biomagnification potential of the elements measured via body burden and trophic position correlations among fauna. Element concentrations were higher in contaminated soils than reference soils; however, concentrations in 2022 were unchanged from concentrations measured in 2003, suggesting no natural attenuation of tested elements. Additionally, target fauna had elevated As, Se, and Sr levels in comparison to reference samples. A positive correlation was observed in southern toads between Sr concentrations and trophic position, as assessed by nitrogen stable isotope ratios, suggesting potential for biomagnification of Sr within our study system. Collectively, our results demonstrate that legacy contaminants are still present and bioaccumulate in a diversity of taxa in a CCR-contaminated site that has not received effluents in more than 50 years, suggesting monitoring programs in CCR-contaminated sites should be maintained long term in the absence of remediation.
Characterization of Tumor Antigens from Multi-omics Data: Computational Approaches and Resources
Authors: Wang Yunzhe , Wengler James , Fang Yuzhu , Zhou Joseph , Ruan Hang , Zhang Zhao , Han Leng 
Published: January 2025

Abstract
Tumor-specific antigens, also known as neoantigens, have potential utility in anti-cancer immunotherapy, including immune checkpoint blockade (ICB), neoantigen-specific T cell receptor-engineered T (TCR-T), chimeric antigen receptor T (CAR-T), and therapeutic cancer vaccines (TCVs). After recognizing presented neoantigens, the immune system becomes activated and triggers the death of tumor cells. Neoantigens may be derived from multiple origins, including somatic mutations (single nucleotide variants, insertion/deletions, and gene fusions), circular RNAs, alternative splicing, RNA editing, and polymorphic microbiome. An increasing amount of bioinformatics tools and algorithms are being developed to predict tumor neoantigens derived from different sources, which may require inputs from different multi-omics data. In addition, calculating the peptide–major histocompatibility complex (MHC) affinity can aid in selecting putative neoantigens, as high binding affinities facilitate antigen presentation. Based on these approaches and previous experiments, many resources were developed to reveal the landscape of tumor neoantigens across multiple cancer types. Herein, we summarized these tools, algorithms, and resources to provide an overview of computational analysis for neoantigen discovery and prioritization, as well as the future development of potential clinical utilities in this field.
Pinworm microbiomes are distinct from their chipmunk host gut microbiota
Authors: San Juan Priscilla A , Palma Lizbeth , Bell Kayce C 
Published: January 2025

Abstract
Mammals house a complex community of gut bacteria, known as the microbiome, as well as endoparasitic helminths. Very little is known about how much of helminth microbiota are derived or distinct from their hosts. Helminths that inhabit the gastrointestinal tract, a microbially rich environment, would likely have many opportunities to derive a microbial community from their host. We characterized and compared the gut microbiome of chipmunk hosts and the internal microbiome of their endoparasitic pinworms, a type of nematode. We sampled fresh feces and used 16S rRNA sequencing to characterize the microbiomes of the Crater Yellow-pine Chipmunk (Tamias amoenus cratericus) and their pinworms (Heteroxynema cucullatum). Microbiomes differed in bacterial species composition between chipmunks and pinworms. Pinworm gut microbiomes also had less diverse bacterial communities than their chipmunk host microbiome. Pinworms and the chipmunks they inhabited shared few bacterial taxa, demonstrating that pinworms have a microbiota distinct from their chipmunk host. Chipmunks collected from different localities showed minor differences in relative abundances of bacterial composition, indicating that locality may have an influence on microbial makeup. Our findings demonstrate that pinworms, although residing and interacting inside the gut of a chipmunk, house their own distinct microbial communities.
First full intracorporeal robotic cystectomy and neobladder in a renal transplant recipient
Authors: Tillou Xavier , Le Bloa Lisa , Courteille Vanja , Bechade Clemence , Waeckel Thibaut 
Published: January 2025

Abstract
The literature regarding robotic-assisted radical cystectomy in kidney transplant recipients is limited. We present the first reported case of robotic-assisted radical cystectomy with a full intracorporeal orthotopic neobladder in a kidney transplant recipient. A 36-year-old man was diagnosed with muscle-invasive urothelial carcinoma 12 years after kidney transplantation. His immunosuppressive regimen consisted of everolimus, mycophenolate mofetil, and prednisolone. After cystectomy and left lymph node dissection, we used a U-shaped neobladder technique slightly modified to adapt to the fixed position of the renal transplant ureter. The surgical time was 305 min, and the blood loss was 200 ml. The patient was discharged 16 days after hospitalization with no surgical complications. Histological analysis revealed no UC (pT0N0) with disseminated carcinoma in situ. Seven months after the surgery, no signs of recurrence or distant/lymph node metastasis were observed. No urinary leakage with complete bladder emptying was reported. Serum creatinine clearance rate was 51 ml/min. Immunosuppressive regimen was not modified after surgery.