bluuebunny/crossref_metadata_2025_split huggingface dataset:
Improved assembly of the Pungitius pungitius reference genome
Authors: Wang Dandan , Rastas Pasi , Yi Xueling , Löytynoja Ari , Kivikoski Mikko , Feng Xueyun , Reid Kerry , Merilä Juha 
Published: June 2024

Abstract
The nine-spined stickleback (Pungitius pungitius) has been increasingly used as a model system in studies of local adaptation and sex chromosome evolution but its current reference genome assembly is far from perfect, lacking distinct sex chromosomes. We generated an improved assembly of the nine-spined stickleback reference genome (98.3% BUSCO completeness) with the aid of linked-read mapping. While the new assembly (v8) was of similar size as the earlier version (v7), we were able to assign 4.4 times more contigs to the linkage groups and improve the contiguity of the genome. Moreover, the new assembly contains a ∼22.8 Mb Y-linked scaffold (LG22) consisting mainly of previously assigned X-contigs, putative Y-contigs, putative centromere contigs, and highly repetitive elements. The male individual showed an even mapping depth on LG12 (pseudo X chromosome) and LG22 (Y-linked scaffold) in the segregating sites, suggesting near-pure X and Y representation in the v8 assembly. A total of 26,803 genes were annotated, and about 33% of the assembly was found to consist of repetitive elements. The high proportion of repetitive elements in LG22 (53.10%) suggests it can be difficult to assemble the complete sequence of the species’ Y chromosome. Nevertheless, the new assembly is a significant improvement over the previous version and should provide a valuable resource for genomic studies of stickleback fishes.
Post-release survival of Whiteleg skate (Amblyraja taaf) caught as bycatch on demersal longlines in deep waters of the Southern Ocean (Crozet Archipelago)
Authors: Faure Johanna , Authier Matthieu , Massiot-Granier Félix , Plard Floriane , Péron Clara 
Published: June 2024

Abstract
Whiteleg skate (Amblyraja taaf) is a bycatch species commonly discarded in demersal longline fisheries targeting Patagonian toothfish around the Crozet archipelago (Southern Ocean). While there are global conservation issues on elasmobranchs, the post-release survival of this deep-sea species remains unknown. This study is the first tagging programme conducted on Whiteleg skates to investigate their fate after being released at sea. Almost 3000 skates were captured, double-tagged with conventional tags and released between 2020 and 2022 to assess survival using capture–mark–recapture (CMR) models. Our primary result was an estimated annual apparent survival rate higher than 92% for skates released in good condition (with 185 skates recaptured after up to 944 days at liberty). Low detection rate highlighted methodological challenges for CMR models. However, skate size and depth of capture had an effect on apparent survival probability with smaller individuals having lower values (&lt;65 cm; 0.84 ± 0.04) as well as skates caught at shallower depths (&lt;1200 m; 0.83 ± 0.04). Overall, this study suggests that the mandated release of skates in good condition is effective to limit fishing impact on skates in this fishery. To further limit this impact, we recommended changes in fishing practices (hauling speed and soak time).
Correlation of Genogroup I, Genotype 1 (GI.1) Norovirus Neutralizing Antibody Levels With GI.1 Histo-Blood Group Antigen–Blocking Antibody Levels
Authors: Atmar Robert L , Ettayebi Khalil , Neill Frederick H , Braun Ralph P , Sherwood James , Ramani Sasirekha , Estes Mary K 
Published: June 2024

Abstract

Background
The in vitro cultivation of human noroviruses allows a comparison of antibody levels measured in neutralization and histo-blood group antigen (HBGA)–blocking assays.

Methods
Serum samples collected during the evaluation of an investigational norovirus vaccine (HIL-214 [formerly TAK-214]) were assayed for neutralizing antibody levels against the vaccine's prototype Norwalk virus/genogroup I, genotype 1 (GI.1) (P1) virus strain. Results were compared with those previously determined using HBGA-blocking assays.

Results
Neutralizing antibody seroresponses were observed in 83% of 24 vaccinated adults, and antibody levels were highly correlated (r = 0.81; P &lt; .001) with those measured by HBGA blocking.

Conclusions
Genogroup I, genotype 1 (GI.1)–specific HBGA-blocking antibodies are a surrogate for neutralization of GI.1 norovirus.
Clinical Trials Registration. Clinicaltrials.gov NCT02475278
Wolbachia populations across organs of individual Culex pipiens: highly conserved intra-individual core pangenome with inter-individual polymorphisms
Authors: Trouche Blandine , Schrieke Hans , Duron Olivier , Eren A Murat , Reveillaud Julie 
Published: June 2024

Abstract
Wolbachia is a maternally inherited intracellular bacterium that infects a wide range of arthropods including mosquitoes. The endosymbiont is widely used in biocontrol strategies due to its capacity to modulate arthropod reproduction and limit pathogen transmission. Wolbachia infections in Culex spp. are generally assumed to be monoclonal but the potential presence of genetically distinct Wolbachia subpopulations within and between individual organs has not been investigated using whole genome sequencing. Here we reconstructed Wolbachia genomes from ovary and midgut metagenomes of single naturally infected Culex pipiens mosquitoes from Southern France to investigate patterns of intra- and inter-individual differences across mosquito organs. Our analyses revealed a remarkable degree of intra-individual conservancy among Wolbachia genomes from distinct organs of the same mosquito both at the level of gene presence–absence signal and single-nucleotide polymorphisms (SNPs). Yet, we identified several synonymous and non-synonymous substitutions between individuals, demonstrating the presence of some level of genomic heterogeneity among Wolbachia that infect the same C. pipiens field population. Overall, the absence of genetic heterogeneity within Wolbachia populations in a single individual confirms the presence of a dominant Wolbachia that is maintained under strong purifying forces of evolution.
‘Tis new to thee’: response to Gruenewald, Knijp, Schoenmaker, and van Tilburg
Authors: Demekas Dimitri , Grippa Pierpaolo 
Published: June 2024

ABSTRACT
In ‘Embracing the Brave New World: A Response to Demekas and Grippa’, a response to our article ‘Walking a Tightrope: Financial Regulation, Climate Change, and the Transition to a Low-Carbon Economy’, both published in the Journal of Financial Regulation, Gruenewald, Knijp, Schoenmaker, and van Tilburg claim that climate risk is a clear and present danger to financial stability that justifies imposing higher capital requirements on supervised firms. Until the current prudential risk framework is revised to fully capture climate risk, they advocate ad hoc measures, such as adjustments to risk weights, which, they believe, would have the desired effect. In this article, we argue that these claims are misguided. Given the nature of climate risk, risk assessment models cannot provide a reliable basis for calibrating capital requirements. On the basis of the evidence, prudential tools would have only a negligible impact on the transition. And the idea of adjusting risk weights for climate exposures has been abandoned—for good reasons. Ultimately, there is nothing financial regulation can do about the energy transition that an appropriately designed carbon tax cannot do better. Central banks and financial regulators should resist the pressure to take on additional responsibilities that are essentially political and that they cannot properly discharge.
On alert for Ebola: public health risk assessment of travellers from Uganda to the USA during the 2022 outbreak
Authors: Fowler Jennifer J , Preston Leigh Ellyn , Gearhart Shannon L , Figueroa Argelia , L  Christensen Deborah , Mitchell Colby , Hernandez Estephania , Grills Ardath W , Morrison Stephanie M , Wilkinson Melanie , Talib Tahab , Marie Lavilla Kayla , Watson Tureka , Mitcham Dionne , Nash Ronnae , Veguilla Maria A Colón , Hansen Sabrina , Cohen Nicole J , Nu Clarke Seseni A , Smithson Ar'reil , Shearer Emma , Pella Danielle Gilliard , Morris Joseph D , Meehan Sarah , Aboukheir Mahmoud , Adams Kara , Sunavala Zenia , Conley Jake , Abouattier Maeva , Palo Matthew , Pimentel Linda Capewell , Berro Andre , Mainzer Hugh , Byrkit Ramona , Kim Daniel , Katebi Volha , Alvarado-Ramy Francisco , Roohi Shahrokh , Wojno Abbey E ,   Viral Special Pathogens Group, Brown Clive M , Gertz Alida M 
Published: June 2024

Abstract

Background
On 20 September 2022, the Ugandan Ministry of Health declared an outbreak of Ebola disease caused by Sudan ebolavirus.

Methods
From 6 October 2022 to 10 January 2023, Centers for Disease Control and Prevention (CDC) staff conducted public health assessments at five US ports of entry for travellers identified as having been in Uganda in the past 21 days. CDC also recommended that state, local and territorial health departments (‘health departments’) conduct post-arrival monitoring of these travellers. CDC provided traveller contact information, daily to 58 health departments, and collected health department data regarding monitoring outcomes.

Results
Among 11 583 travellers screened, 132 (1%) required additional assessment due to potential exposures or symptoms of concern. Fifty-three (91%) health departments reported receiving traveller data from CDC for 10 114 (87%) travellers, of whom 8499 (84%) were contacted for monitoring, 1547 (15%) could not be contacted and 68 (1%) had no reported outcomes. No travellers with high-risk exposures or Ebola disease were identified.

Conclusion
Entry risk assessment and post-arrival monitoring of travellers are resource-intensive activities that had low demonstrated yield during this and previous outbreaks. The efficiency of future responses could be improved by incorporating an assessment of risk of importation of disease, accounting for individual travellers’ potential for exposure, and expanded use of methods that reduce burden to federal agencies, health departments, and travellers.
The WTO Agreement on Sanitary and Phytosanitary Measures
Authors: Gruszczynski Lukasz , Scott Joanne 
Published: June 2024

Abstract
The 1995 World Trade Organization (WTO) Agreement on Sanitary and Phytosanitary Measures (SPS) is concerned with trade and food safety regulation and with the regulation of pests and diseases in agriculture. It establishes legal standards while affirming the right of each Member to choose its own level of SPS protection. However, the question of whether the balance has been properly struck remains a matter of ongoing debate. The commentary has been updated to reflect 15 years of change in the SPS case law and practice since publication of the first edition in 2007. It critically examines current issues, such as use of experts in the dispute settlement process, applicable standards of review, or legal treatment of private standards in the area of food safety, and assesses the suitability of the current regime to address the existing needs of developing countries. The commentary also examines how science-based criteria and the traditional General Agreement on Tariffs and Trade (GATT) standards (i.e. non-discrimination and least trade-restrictive means) are used to discipline national SPS measures. It explores the transparency obligations and procedural rules that govern control, inspection, and approval processes in importing countries. A separate section is dedicated to the operation of the SPS Committee as a site for transnational governance in the SPS field. The book also investigates the agreement’s attempt to establish a framework to draw together the diverse institutions and regulatory regimes already populating the food safety arena. The updated commentary has been extended by two new chapters, one that reviews Article 5.7 SPS in greater detail and one that deals with the SPS rules in the selected regional trade agreements.
Additional Obligations
Authors: Gruszczynski Lukasz 
Published: June 2024

Abstract
This chapter covers the additional obligations laid down in the Agreement on the Application of Sanitary and Phytosanitary Measures (the SPS Agreement). These particularly include: non-discrimination and consistency (Articles 2.3 and 5.5), least trade-restrictive means (Articles 5.4 and 5.6), equivalence (Article 4) and regionalization (Article 6). For consistency, equivalence and regionalization, the agreement has been supplemented by more detailed guidelines adopted by the SPS Committee, which are analyzed here as well. The chapter explains how these additional obligations aim to inculcate regulatory reflexivity by requiring Members to explain their choices by reference to specified benchmarks. It also looks into the correlation between the public perceptions of risk and relative levels of public fearfulness that may justify different levels of protection.
International Standards
Authors: Gruszczynski Lukasz 
Published: June 2024

Abstract
This chapter explores the nature and role of international standards in the Sanitary and Phytosanitary (SPS) system. Although the SPS Agreement does not confer binding force on international standards, it does constitute them as benchmarks against which Members justify their SPS measures. The chapter looks at the activities of the SPS ‘sister organizations’ identified in Annex A(3), including the Codex Alimentarius Commission, the World Organization for Animal Health (OIE), and International Plant Protection Convention (IPPC). Following an overview of the activities of these bodies, the chapter examines the relationship between them and the SPS Agreement. It looks both at the stance of the AB in articulating this relationship, and at the monitoring activities of the SPS Committee.
The International Law Commission's Draft Conclusions on Peremptory Norms
Authors: Tladi Dire 
Published: June 2024

Abstract
In 2022, the ILC adopted the Draft Conclusions on Peremptory Norms of General International Law. The text of the Draft Conclusions consists of twenty-three Draft Conclusions and addresses two aspects, namely the identification of peremptory norms and their legal consequences. Attached to the Draft Conclusions is an Annex with a non-exhaustive list of jus cogens norms previously identified by the Commission. The International Law Commission’s Draft Conclusions on Peremptory Norms examines the ILC’s Draft Conclusions. It serves, in part, as a commentary on the ILC’s work and provides a broader understanding of the Draft Conclusions from the perspective of an insider. The book goes beyond a commentary as it provides an analysis and evaluation of the legal issues raised by the Draft Conclusions. Relying inter alia on the debates within the Commission and the doctrinal debate surrounding the concepts covered, the book will not only offer commentary on what is addressed in the Draft Conclusions but also an assessment of the choices made by the Commission and the consequences of those choices.
Definitional Issues
Authors: Tladi Dire 
Published: June 2024

Abstract
This chapter covers two Draft Conclusions, namely Draft Conclusion 2 and Draft Conclusion 3. It begins with Draft Conclusion 3 which contains the definition of jus cogens, which in turn is taken from Article 53 of the Vienna Convention. It then provides a comment on Draft Conclusion 2, which describes the general nature of jus cogens. The chapter also provides an analysis of the relationship between Draft Conclusion 2 and Draft Conclusion 3. Through this relationship a tension is revealed in the work of the Commission, namely the tension between the positivist inclination of Article 53 of the Vienna Convention, reflected in Draft Conclusion 3, and the natural law foundations of jus cogens, as reflected in Draft Conclusion 2.
The First CriterionA Norm of General International Law
Authors: Tladi Dire 
Published: June 2024

Abstract
This chapter is concerned with Draft Conclusion 5, which addresses the first criterion, namely that the norm in question must be a norm of general international law. The Draft Conclusion identifies three possible bases of jus cogens, namely customary international law, treaty law, and general principles of law. According to the Draft Conclusion, customary international law is the most common basis of jus cogens, while treaty law and general principles of law may also serve as bases of jus cogens. The chapter provides a commentary and analysis on the Commission’s decision to adopt this bifurcated approach. In particular, the chapter assesses the Commission’s decision to treat treaty law and general principles of law as less likely bases of jus cogens.
Consequences of Jus Cogens for Treaties
Authors: Tladi Dire 
Published: June 2024

Abstract
Chapter 8 concerns the consequences of jus cogens for treaties. The consequence most synonymous with peremptory norms is invalidity of a treaty conflicting with jus cogens as provided for in the Vienna Convention. These consequences are addressed in four separate Draft Conclusions, namely Draft Conclusion 10 on invalidity, Draft Conclusion 11 on separability, Draft Conclusion 12 on termination, and Draft Conclusion 13 on reservations. These Draft Conclusions are, in the main, sourced from the Vienna Convention. As such the chapter is more descriptive, while also assessing the choices the Commission made between sticking to the Vienna Convention and moving beyond the text.
Consequences of Jus Cogens for Other Sources of Obligations
Authors: Tladi Dire 
Published: June 2024

Abstract
Chapter 9 addresses consequences of jus cogens for other sources of obligation. These are addressed in Draft Conclusion 14 (customary international law), Draft Conclusion 15 (unilateral acts), and Draft Conclusion 16 (decisions of international organisations). These Draft Conclusions essentially apply the Vienna formula, discussed in Chapter 8, to other sources of obligations. Particular issues addressed in the chapter concern the possibility of modification of jus cogens if customary international law conflicting with jus cogens does not arise. With respect to decisions of international organisations, the chapter provides an analysis of the Commission’s treatment of decisions of the Security Council. It might be noticed that there is no provision for general principles of law as a source of obligations. The chapter provides some insight as to why the Commission might have left general principles of law unaddressed.
Non-Exhaustive List of Jus Cogens Norms
Authors: Tladi Dire 
Published: June 2024

Abstract
Chapter 14 concerns Draft Conclusion 23 which refers to a list of jus cogens in an Annex. It is the only Draft Conclusion in the whole set that dedicates itself to primary rules of international law. The list was a source of criticism from the very beginning of the Commission’s work. The chapter traces the debates and assesses the Commission’s decision to persist with the list notwithstanding the criticism. It does so by evaluating the main arguments against the list as against the arguments for the list. In the process, the chapter also describes the methodology for arriving at the list, which is meant to respond to the criticism directed at the list.
Prospects and Concluding Thoughts
Authors: Tladi Dire 
Published: June 2024

Abstract
Chapter 15 is the concluding chapter. It provides an account of how the Draft Conclusions were received in the Sixth Committee of the General Assembly subsequent to the adoption and discusses the prospects for the Draft Conclusions to influence the development of international law in the long term. While the Draft Conclusions received significant support from the majority of States, a handful of States opposed them and blocked consensus on the adoption of the customary General Assembly resolution to take note of the Draft Conclusions and the Annex containing the list of jus cogens norms. The future prospects of the Draft Conclusions are considered in the context of this reception.
Intrathecal methotrexate, central nervous system toxicity, and response to N-methyl-D-aspartate antagonism: An adult case series
Authors: Donaghy Ryan , Singer Lauren , Dixit Karan 
Published: June 2024

Abstract

Background
Methotrexate (MTX) is administered for the treatment of central nervous system (CNS) hematologic cancers, prophylaxis of CNS dissemination of certain hematological cancers, and in solid tumor leptomeningeal disease. MTX treatment can be limited by CNS toxicity. Dextromethorphan is used to treat MTX neurotoxicity, with most data derived from pediatric case series. In this report, we profile 4 adult patients who developed intrathecal (IT) MTX neurotoxicity to better characterize their response to dextromethorphan treatment.

Methods
A case series of 4 patients who developed neurologic symptoms attributed to IT MTX neurotoxicity subsequently treated with dextromethorphan was devised. Demographic data, clinical characteristics, electroencephalography results, magnetic resonance imaging, cerebrospinal fluid (CSF) characteristics, and dextromethorphan treatment outcomes were described.

Results
Of the 4 patients developing MTX neurotoxicity, neurologic symptoms developed over a timeframe of 2 to 14 days from the precedent MTX exposure. Radiologic phenotypes included subcortical white matter diffusion-restricting lesions, bi-hemispheric subcortical white matter T2-FLAIR hyperintensities, as well as other findings described in the report. Time elapsed from initiation of dextromethorphan to neurologic symptom resolution ranged from 1 to 2 days.

Conclusions
The profiles of 4 adult patients developing suspected IT MTX neurotoxicity syndromes with subsequent response to Dextromethorphan add further data to guide the management of such patients.
Evaluation of Chemical-Inducible Gene Expression Systems for Beet Cyst Nematode Infection Assays in Arabidopsis thaliana
Authors: Liu Xunliang , Mitchum Melissa G. 
Published: June 2024

Cyst nematodes co-opt plant developmental programs for the establishment of a permanent feeding site called a syncytium in plant roots. In recent years, the role of plant developmental genes in syncytium formation has gained much attention. One main obstacle in studying the function of development-related genes in syncytium formation is that mutation or ectopic expression of such genes can cause pleiotropic phenotypes, making it difficult to interpret nematode-related phenotypes or, in some cases, impossible to carry out infection assays due to aberrant root development. Here, we tested three commonly used inducible gene expression systems for their application in beet cyst nematode infection assays of the model plant Arabidopsis thaliana. We found that even a low amount of ethanol diminished nematode development, deeming the ethanol-based system unsuitable for use in cyst nematode infection assays, whereas treatment with estradiol or dexamethasone did not negatively affect cyst nematode viability. Dose and time course responses showed that in both systems, a relatively low dose of inducer (1 μM) is sufficient to induce high transgene expression within 24 h of treatment. Transgene expression peaked at 3 to 5 days post-induction and began to decline thereafter, providing a perfect window for inducible transgenes to interfere with syncytium establishment while minimizing any adverse effects on root development. These results indicate that both estradiol- and dexamethasone-based inducible gene expression systems are suitable for cyst nematode infection assays. The employment of such systems provides a powerful tool to investigate the function of essential plant developmental genes in syncytium formation. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .