bluuebunny/crossref_metadata_2025 huggingface dataset:
From pollution to sustainable environment: unlocking the role of energy intensity and renewable energy in highly pollutant nations
Authors: Zhou Zhi Zhen , Hassan Muhammad Shahid , Saeed Muhammad Ibrahim , Mahmood Haider , Kalim Rukhsana , Houaneb Amira
Published: January 2025

Environmental degradation is among one of the most critical issues of recent times. To address this critical challenge in highly pollutant nations, this research inquires about the role of Energy Intensity (EI) along with Renewable Energy Consumption (REC) and non-REC as controlling indicators in the carbon emissions’ model. The research is significant because it provides potential information to energy policymakers for mitigating the adverse effects of environmental degradation. The Cross-Sectional Dependent (CSD) test is utilized to authenticate the CSD in the variables and the Slope Heterogeneity (SH) test is applied to verify the heterogeneous relationships across the polluted economies. Moreover, CSD-based unit root tests are applied to confirm the stationarity of the series. The CSD-based cointegration test is applied, which cares for both CSD and SH in analysis. Lastly, CSD-based regressions are applied to find the long and short relationships. A period of 1990–2021 is utilized for data analyses as per data availability of all analyzed countries. The results demonstrate significantly increasing effects of EI on emissions leading to mitigated environmental quality. A 1% increase in EI increases emissions by 0.6227%. However, renewable energy significantly mitigates carbon emissions while non-REC is found to significantly escalate carbon emissions. A 1% increase in REC mitigates emissions by 0.2458% and a 1% increase in non-REC raises emissions by 0.65%. This research further confirms the evidence of the Environmental Kuznets Curve (EKC) with an income elasticity of 13.1393 and income square elasticity of -0.6209. The results of EI, REC, and non-REC are similar in all estimations while the validity of the EKC is witnessed in two out of three models. The causal relation suggests feedback between emissions and economic progress, EI, REC, and non-REC, which highlights the interdependence of the energy sector and environmental outcomes. This research suggests that governments of the investigated polluted economies should impose taxes on non-renewable energy consumption. The revenues from these taxes should be utilized to subsidize renewable energy consumption. Both initiatives would help reduce energy intensity in these polluted economies to condense the environmental consequences of the energy sector.
A gearbox fault diagnosis method based on Swin Transformer and Markov transform fields
Authors: Liu Jiangran , Hao Rujiang , Deng Feiyue , Fan Hongli , Lou Haiyang
Published: January 2025

To address the problems of traditional fault diagnosis methods, such as the insensitivity of fault feature extraction, strong dependence on expert experience, insufficient generalization, and low fault recognition rate in gearbox running state detection, a gearbox fault diagnosis method based on the Markov transition field (MTF) and a Swin Transformer is proposed. First, the original one-dimensional vibration signal dataset is preprocessed. then the one-dimensional vibration signal is encoded into a two-dimensional feature map by MTF, which preserves the correlation between data and time. Second, the encoded 2D feature image dataset was input into the Swin Transformer model with a moving window and hierarchical design structure for training to realize the recognition of different faults in the gearbox. Finally, the power transmission fault diagnosis test-bed (DDS) dataset was used for experimental verification, and the fault diagnosis accuracy rate was 99.69%. Experimental results show that the proposed method has higher computational efficiency, better generalization performance, and higher fault identification accuracy than the intelligent diagnosis model based on a time-frequency diagram, CWT diagram, GAF diagram, convolutional neural network (CNN), and Vision Transformer (Vi T), which can provide a reference for fault diagnosis of gearboxes in practical industries.
Method for silver streak detection on embossed surfaces based on inpainting network
Authors: Tanaka Kazumoto
Published: January 2025

Silver streaks in embossed plastic-moulded products are among the most challengigng defects to detect in images. Currently, performing a completely automated inspection is impossible. Compared to embossed textures, silver streaks exhibit slightly higher contrast, and experienced inspectors use this as a key indicator for detection. Therefore, in this study, we developed an artificial intelligence that learns the contrast of the textures of defect-free products to enable automated inspection. Specifically, we used an inpainting network that learns to repair images in which the defect-free texture regions are masked. The proposed method identifies defects by assessing the repair error in defective textures, which the network cannot accurately reconstruct due to a lack of prior learning. The method was tested on real plastic-moulded products and demonstrated extremely high accuracy in detecting silver streaks.
Democracy, Legitimacy, and Authority in International Courts
Authors: Gargarella Roberto
Published: January 2025

Roberto Gargarella reprises his critique of international court adjudication of rights. Using the example of the Inter-American Court of Human Rights, he argues that dominant models concerning the relationship between international tribunals and local authorities are deeply flawed because they fail to give due deference to decisions made through a dialogue among equals in a democratic polity. Rejecting both a deferential approach, which he identifies with the European Court of Human Rights, and a more interventionist approach to international adjudication of rights, which he identifies with the Inter-American Court, Gargarella advances a third way: international courts should base their decisions in part on the quality of democratic decision-making or the “democratic pedigree” of the underlying decision.
International Humanitarian Law in Latin America
Authors: Salmón Elizabeth
Published: January 2025

This chapter focuses on the contributions of truth commissions in Latin America to the classification of situations of violence as noninternational armed conflicts and to the application of international humanitarian law. In particular, the author highlights that, although Latin America has experienced various armed conflicts in the twentieth century, states have been reluctant to recognize the existence of an armed conflict in their territory. In the absence of official recognition, the reports and conclusions of Truth Commissions have qualified certain contexts as noninternational armed conflicts and have analyzed potential violations of international humanitarian law. In this sense, this chapter studies the cases of the truth commissions established in Argentina, Chile, El Salvador, Guatemala, Peru, and Colombia.
Burla y Bulla
Authors: Heffner Hayes Michelle
Published: January 2025

Flamenco encompasses a wide spectrum of emotions, from the haunting gritos/cries of the cante jondo/deep song to lighthearted palos/song forms like tangos, alegrías and bulerías. Derived from the words burla (to mock) and bulla (noise), bulerías is well known as a vehicle for improvisation and comedic play in social gatherings as well as concert performances. Contemporary choreographers, traditional and experimental, explore humor and self-parody in flamenco to display virtuosity, to critique gender and sexual roles, to confront racial stereotypes, and also to expand conventions that constrain creative expression. In this chapter, Michelle Heffner Hayes analyzes the ways in which artists like Belén Maya, Rocío Molina, Juan Carlos Lérida, Fernando López Rodríguez, La Lupi, Miguel Poveda, and others deploy comedy in the name of serious art.
StoryTAILS of a Wounded Sister
Authors: Jones Adanna Kai
Published: January 2025

Through fragmented memories, stories, and allegories, this chapter grapples with the parameters that demarcate the threshold of pain and feminist pleasure, especially with regard to how, when, and why one chooses to “wine”—a rolling-hip dance often performed at Trinidadian-styled Carnivals. The chapter begins with heartbreak and humiliation and ends in an outburst of collective retaliatory laughter as to conceive of the inevitable ways Afro-Caribbean women are still navigating the painful and pleasurable legacies of the nineteenth-century Jamette figure. (The term “Jamette” was originally created by the colonizing class and especially applied to the Afro-Creole, ex-slaves who participated in the Carnivals of post-emancipation Trinidad of the late nineteenth century. Today it is a term that generally refers to a “loose woman.”) In particular, the chapter traverses spaces, places, and national borders to understand the muted ways in which Afro-Caribbean women use their rolling waistlines as strategies for negotiating how, when, and why they participate in the sometimes heartbreaking spaces of Carnival and its associated festivities. Ultimately, the chapter seeks to understand how winin’ mediates heartbreak and healing through a negotiation of pleasure, intimacy, vulnerability, and grotesque eroticism.
Dancing Displa(y)cements
Authors: Schwadron Hannah
Published: January 2025

This chapter introduces the corporeality of humor exchanges in the dance theater and surrounding dynamics of Berlin’s youth theater group Al-Hakawati, of whom more than half the members are recent migrants with political refugee status in Germany. Analyzing the club’s use of political satire, costumed caricature, and embodied joke-work in DestiNations Unknown (2020), the author tracks the funny physicality of migrant artists in residence as they eschew the stigma of refugee status in the making of an “anticolonial museum.” As the cast revises historical plots to mock the rich and powerful, their offstage antics, egged on by male leads, are largely self-deprecatory, returning to regular jokes about the “shitty refugee.” Reading onstage satire alongside self-critical humor in group dynamics, the chapter asks how humor by and about the “refugee” navigates difference of background and experience among the club and their fans while resisting reductionist narratives of integration heralded by the state.
Rethinking Conscientious Objection in Health Care
Authors: Giubilini Alberto , Schuklenk Udo , Minerva Francesca , Savulescu Julian
Published: January 2025

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

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

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

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

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

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

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

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

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

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

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

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

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

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 < .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

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

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

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

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

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.
Single-nucleotide-resolution genomic maps of O6-methylguanine from the glioblastoma drug temozolomide
Authors: Kubitschek Jasmina , Takhaveev Vakil , Mingard Cécile , Rochlitz Martha I , Reinert Patricia B , Keller Giulia , Kloter Tom , Fernández Cereijo Raúl , Huber Sabrina M , McKeague Maureen , Sturla Shana J
Published: January 2025

Temozolomide kills cancer cells by forming O6-methylguanine (O6-MeG), which leads to cell cycle arrest and apoptosis. However, O6-MeG repair by O6-methylguanine-DNA methyltransferase (MGMT) contributes to drug resistance. Characterizing genomic profiles of O6-MeG could elucidate how O6-MeG accumulation is influenced by repair, but there are no methods to map genomic locations of O6-MeG. Here, we developed an immunoprecipitation- and polymerase-stalling-based method, termed O6-MeG-seq, to locate O6-MeG across the whole genome at single-nucleotide resolution. We analyzed O6-MeG formation and repair across sequence contexts and functional genomic regions in relation to MGMT expression in a glioblastoma-derived cell line. O6-MeG signatures were highly similar to mutational signatures from patients previously treated with temozolomide. Furthermore, MGMT did not preferentially repair O6-MeG with respect to sequence context, chromatin state or gene expression level, however, may protect oncogenes from mutations. Finally, we found an MGMT-independent strand bias in O6-MeG accumulation in highly expressed genes. These data provide high resolution insight on how O6-MeG formation and repair are impacted by genome structure and nucleotide sequence. Further, O6-MeG-seq is expected to enable future studies of DNA modification signatures as diagnostic markers for addressing drug resistance and preventing secondary cancers.
‘Splice-at-will’ Cas12a crRNA engineering enabled direct quantification of ultrashort RNAs
Authors: Fei Xinrui , Lei Chao , Ren Wei , Liu Chenghui
Published: January 2025

We present a robust ‘splice-at-will’ CRISPR RNA (crRNA) engineering mechanism that overcomes the limitations of clustered regularly interspaced short palindromic repeats (CRISPR)/Cas system in directly detecting ultrashort RNAs. In this strategy, an intact Cas12a crRNA can be split from almost any site of the spacer region to obtain a truncated crRNA (tcrRNA) that cannot activate Cas12a even after binding an auxiliary DNA activator. While splicing tcrRNAs with a moiety of ultrashort RNA, the formed combination can work together to activate Cas12a efficiently, enabling ‘splice-at-will’ crRNA engineering. Importantly, the ‘splice-at-will’ crRNA exhibits almost the same trans-cleavage activation efficiency as that of a conventional intact crRNA. Therefore, by rationally designing a DNA auxiliary activator with a conserved tcrRNA-complementary sequence and an arbitrary short RNA-of-interest recognition domain, a general sensing system is established that directly utilizes traditional DNA-activated Cas12a to detect ultrashort RNAs. This ‘splice-at-will’ crRNA engineering strategy could faithfully detect ultrashort RNA sequences as short as 6–8 nt, which cannot be achieved by conventional Cas12a and Cas13a systems. Additionally, through flexible splicing site design, our method can precisely distinguish single-base differences in microRNA and other short RNA sequences. This work has significantly expanded the Cas12a-based diagnostic toolbox and opened new avenues for ultrashort RNA detection.
An integrated approach for the accurate detection of HERV-K HML-2 transcription and protein synthesis
Authors: Gleason Charles , Terry Sandra N , Hernandez Matthew M , Jacob Samson , Fenyo David , Johnson Jeffrey R , Deikus Gintaras , Francoeur Nancy , Hahn Aana , Sebra Robert , Zamarin Dmitriy , Molina Henrik , Simon Viviana , Mulder Lubbertus C F
Published: January 2025

Human endogenous retroviruses (HERVs) occupy a large portion of the human genome. Most HERVs are transcriptionally silent, but they can be reactivated during pathological states such as viral infection and certain cancers. The HERV-K HML-2 clade includes elements that recently integrated have in the human germ line and often contain intact open reading frames that possibly support peptide and protein expression. Understanding HERV–K-host interactions and their potential as biomarkers is problematic due to the high similarity among different elements. Previously, we described a long-read single molecule real-time sequencing (PacBio) strategy to analyze HERV-K RNA expression profiles in different cell types. However, identifying HERV-K HML-2 proteins accurately is difficult without robust and reliable methods and reagents. Here we present a new approach to characterize the HML-2 elements that (a) are being translated and (b) produce enough protein to be detected and identified by mass spectrometry. Our data reveal that RNA expression profiling alone cannot accurately predict which HML-2 elements are responsible for protein production, as we observe several differences between the highest expressed RNAs and the elements that are the predominant source of HERV-K HML-2 protein synthesis. These studies represent an important advance toward untangling the complexity of HERV–K-host interactions.
Navigating vagueness: Rule-following and the scope of trust
Authors: Israel Eli Benjamin
Published: January 2025

In this paper, I address a fundamental challenge in the philosophy of trust: how to account for trustee discretion in scenarios that fall outside explicitly defined expectations. I argue that this challenge reveals vagueness as an inherent feature of trusting relationships, often leading to disagreements between trustors and trustees. To resolve this, I propose a novel account of trust grounded in rule-following, shifting the object of trust from particular actions to adherence to rules constitutive of relationships. By focusing on relationships and their constitutive rules, I provide here a framework for understanding and minimizing disagreements through communication and engaged practice. Furthermore, I argue this framework sheds light on the dynamics of trust-related reactive attitudes, in particular, distinguishing between betrayal and mere disappointment.
Cognitive and neural underpinnings of friend-prioritization in a perceptual matching task
Authors: Gao Tianyu , Zhou Yuqing , Pan Xinyue , Li Wenxin , Han Shihui
Published: January 2025

Previous findings of better behavioral responses to self- over other-related stimuli suggest prioritized cognitive processes of self-related information. However, it is unclear whether the processing of information related to important others (e.g.friends) may be prioritized over that related to the self in certain subpopulations and, if yes, whether friend-prioritization and self-prioritization engage distinct cognitive and neural mechanisms. We collected behavioral and electroencephalography (EEG) data from a large sample (N = 1006) during learning associations between shapes and person labels (self or a friend). Analyses of response times and sensitivities revealed two subpopulations who performed better to friend–shape or self–shape associations, respectively (N = 216 for each group). Drift diffusion model (DDM) analyses unraveled faster information acquisition for friend–shape (vs. self–shape) associations in the friend-prioritization group but an opposite pattern in the self-prioritization group. Trial-by-trial regression analyses of EEG data showed that the greater amplitudes of a frontal/central activity at 180–240 ms poststimulus were correlated with faster information acquisition from friend–shape associations in the friend-prioritization group but from self-shape associations in the self-prioritization group. However, the frontal/central neural oscillations at 8–18 Hz during perceptual learning were specifically associated with speed of information acquisition from friend–shape associations in the friend–prioritization-group. Our findings provide evidence for friend-prioritization in perceptual learning in a subpopulation of adults and clarify the underlying cognitive and neural mechanisms.
Pharmacogenetic associations of GATA4 and KCNQ1 with ibrutinib cardiovascular toxicity
Authors: Nugent Kelly I. , Huang Lyucheng , Patel Jai N. , Hertz Daniel L.
Published: January 2025

Ibrutinib treatment is often complicated by cardiovascular side effects (CVSEs). The objective of this retrospective pharmacogenetic study is to replicate a previously reported association of ‘high-risk’ patients, who are homozygous carriers of at least two of GATA4 rs804280 AA, KCNQ1 rs163182 GG, and KCNQ1 rs2237895 AA, with increased risk of hypertension or atrial fibrillation, and explore associations for other pharmacogenes (e.g. CYP3A4, CYP3A5, CYP2D6, and ABCB1) with ibrutinib CVSEs. Univariate associations with P < 0.05 were adjusted for significant pretreatment cardiovascular conditions. In total 57 patients were included in the analysis. In the primary analysis, ‘high-risk’ patients were not more likely to experience hypertension or atrial fibrillation (70 vs. 41%, chi-square P value = 0.06). In secondary analyses, ‘high-risk’ patients were more likely to experience any CVSE during treatment (75 vs. 41%, P = 0.013), develop a cardiac rhythm or function disorder (65 vs. 24%, P = 0.008), and have a treatment modification due to CVSE (45 vs. 8%, P = 0.004). Additionally, high-risk homozygous variant genotypes of KCNQ1 rs163182 GG and rs2237895 AA were each associated with an increased likelihood of treatment modifications due to CVSE (40 vs. 11%, P = 0.021 and 45 vs. 9%, P = 0.004, respectively) and cardiac rhythm or function disorders (60 vs. 27%, P = 0.037 and 60 vs. 27%, P = 0.037). This study found supportive evidence that ‘high-risk’ genotype was associated with increased ibrutinib CVSEs. Validation of these associations is necessary before prospective trials testing whether personalized ibrutinib treatment approaches improve clinical outcomes.
Validation of the ANDON KD-7920 wrist blood pressure monitor in general population according to the ISO 81060-2:2018+AMD1:2020 protocol
Authors: Li Duan , Li Yiming , Li Jiaheng , Gu Yuan , Shang Fujun
Published: January 2025

Objective

This study aimed to evaluate the accuracy of the ANDON KD-7920 oscillometric wrist blood pressure monitor in general population according to the ISO 81060-2:2018+AMD1:2020.

Methods

The same arm sequential method was used for blood pressure measurement among qualified participants according to the ISO 81060-2:2018+AMD1:2020. The validation results were assessed following the criteria of the protocol, and the Bland–Altman scatter plot was used to present the difference between the test device and reference results.

Results

A total of 90 participants were included in the study. According to criterion 1 of the validation protocol, the mean ± SD of the differences between the test device and reference readings was 0.76 ± 6.23 mmHg and −0.13 ± 5.57 mmHg for systolic and diastolic blood pressure, respectively, which met the requirements of less than 5 ± 8 mmHg. According to the criterion 2, the average differences between the test device and reference readings per participant were 0.76 ± 5.56 mmHg and −0.13 ± 5.27 mmHg for systolic and diastolic blood pressure, respectively, which also met the requirements.

Conclusion

The ANDON KD-7920 wrist blood pressure monitor passed all the requirements of the ISO 81060-2:2018+AMD1:2020 and can be recommended for clinical use and self-measurement in general population.
Reimagining apnea monitoring in the neonatal ICU
Authors: Jeanne Emily , Alvaro Ruben , Shalish Wissam
Published: January 2025

Purpose of review

This review outlines the prevalence and complications of apneas and intermittent hypoxemic events in preterm infants, examines current monitoring limitations in neonatal ICUs (NICUs), and explores emerging technologies addressing these challenges.

Recent findings

New evidence from the Prematurity-Related Ventilatory Control (Pre-Vent) study, which analyzed cardiorespiratory data from 717 extremely preterm infants, exposes the varying frequency, duration, and severity of apneas, intermittent hypoxemia, bradycardias, and periodic breathing during hospitalization, and highlights the negative impact of intermittent hypoxemia on pulmonary outcomes at discharge. Although traditional monitoring methods cannot differentiate between apnea types and quantify their burden, recent advancements in sensor technologies and data integration hold promise for improving real-time detection and evaluation of apneas in the NICU. Notably, small wearable mechano-acoustic sensors could improve apnea monitoring through continuous detection of airflow and respiratory efforts. Additionally, integrating bedside physiological data with modalities such as near-infrared spectroscopy, diaphragmatic activity, and electrical impedance tomography could help predict adverse outcomes by monitoring regional oxygen saturation and lung function in relation to apneas.

Enhancing our understanding of neonatal apneas and overcoming the current limitations in apnea monitoring through advanced sensor technologies and data integration could lead to more personalized management and improved outcomes for preterm infants.
Utilizing preterm infant body composition assessments to guide neonatal nutrition
Authors: Buck Catherine O.
Published: January 2025

Purpose of review

The use of body composition to assess the quality of infant growth may add valuable information to pediatric clinical care. Preterm infants have differences in their fat and muscle mass development compared with infants born at term, which may be related to their early nutritional exposures. This review focuses on recent studies examining early nutrition in preterm infants and related body composition outcomes in the newborn period and beyond.

Recent findings

Overall, the evidence shows that early nutrient delivery in parenteral nutrition and through formula supplementation or human milk fortification is associated with increased fat-free mass or lean mass in early life. However, future research is needed to fully understand the link between these body composition changes and longitudinal outcomes in preterm infants.

Inclusion of body composition assessments in preterm infant nutrition research is critical to understand the factors associated with differences in adiposity and lean mass development in preterm infants. Medical fragility in preterm infants limits the routine use of body composition assessment tools which are currently validated, and additional studies are needed to thoroughly assess other methods which may be more feasible to integrate into bedside routine.