bluuebunny/crossref_metadata_2025_split huggingface dataset:
MANOCCA: a robust and computationally efficient test of covariance in high-dimension multivariate omics data
Authors: Boetto Christophe , Frouin Arthur , Henches Léo , Auvergne Antoine , Suzuki Yuka , Patin Etienne , Bredon Marius , Chiu Alec , Consortium Milieu Interieur , Sankararaman Sriram , Zaitlen Noah , Kennedy Sean P , Quintana-Murci Lluis , Duffy Darragh , Sokol Harry , Aschard Hugues 
Published: June 2024

Abstract
Multivariate analysis is becoming central in studies investigating high-throughput molecular data, yet, some important features of these data are seldom explored. Here, we present MANOCCA (Multivariate Analysis of Conditional CovAriance), a powerful method to test for the effect of a predictor on the covariance matrix of a multivariate outcome. The proposed test is by construction orthogonal to tests based on the mean and variance and is able to capture effects that are missed by both approaches. We first compare the performances of MANOCCA with existing correlation-based methods and show that MANOCCA is the only test correctly calibrated in simulation mimicking omics data. We then investigate the impact of reducing the dimensionality of the data using principal component analysis when the sample size is smaller than the number of pairwise covariance terms analysed. We show that, in many realistic scenarios, the maximum power can be achieved with a limited number of components. Finally, we apply MANOCCA to 1000 healthy individuals from the Milieu Interieur cohort, to assess the effect of health, lifestyle and genetic factors on the covariance of two sets of phenotypes, blood biomarkers and flow cytometry–based immune phenotypes. Our analyses identify significant associations between multiple factors and the covariance of both omics data.
CACIMAR: cross-species analysis of cell identities, markers, regulations, and interactions using single-cell RNA sequencing data
Authors: Jiang Junyao , Li Jinlian , Huang Sunan , Jiang Fan , Liang Yanran , Xu Xueli , Wang Jie 
Published: June 2024

Abstract
Transcriptomic analysis across species is increasingly used to reveal conserved gene regulations which implicate crucial regulators. Cross-species analysis of single-cell RNA sequencing (scRNA-seq) data provides new opportunities to identify the cellular and molecular conservations, especially for cell types and cell type-specific gene regulations. However, few methods have been developed to analyze cross-species scRNA-seq data to uncover both molecular and cellular conservations. Here, we built a tool called CACIMAR, which can perform cross-species analysis of cell identities, markers, regulations, and interactions using scRNA-seq profiles. Based on the weighted sum models of the conserved features, we developed different conservation scores to measure the conservation of cell types, regulatory networks, and intercellular interactions. Using publicly available scRNA-seq data on retinal regeneration in mice, zebrafish, and chick, we demonstrated four main functions of CACIMAR. First, CACIMAR allows to identify conserved cell types even in evolutionarily distant species. Second, the tool facilitates the identification of evolutionarily conserved or species-specific marker genes. Third, CACIMAR enables the identification of conserved intracellular regulations, including cell type-specific regulatory subnetworks and regulators. Lastly, CACIMAR provides a unique feature for identifying conserved intercellular interactions. Overall, CACIMAR facilitates the identification of evolutionarily conserved cell types, marker genes, intracellular regulations, and intercellular interactions, providing insights into the cellular and molecular mechanisms of species evolution.
Improved prediction of DNA and RNA binding proteins with deep learning models
Authors: Wu Siwen , Guo Jun-tao 
Published: June 2024

Abstract
Nucleic acid-binding proteins (NABPs), including DNA-binding proteins (DBPs) and RNA-binding proteins (RBPs), play important roles in essential biological processes. To facilitate functional annotation and accurate prediction of different types of NABPs, many machine learning-based computational approaches have been developed. However, the datasets used for training and testing as well as the prediction scopes in these studies have limited their applications. In this paper, we developed new strategies to overcome these limitations by generating more accurate and robust datasets and developing deep learning-based methods including both hierarchical and multi-class approaches to predict the types of NABPs for any given protein. The deep learning models employ two layers of convolutional neural network and one layer of long short-term memory. Our approaches outperform existing DBP and RBP predictors with a balanced prediction between DBPs and RBPs, and are more practically useful in identifying novel NABPs. The multi-class approach greatly improves the prediction accuracy of DBPs and RBPs, especially for the DBPs with ~12% improvement. Moreover, we explored the prediction accuracy of single-stranded DNA binding proteins and their effect on the overall prediction accuracy of NABP predictions.
Target and non-target effects of insecticide use during ornamental milkweed production
Authors: Mach Bernadette M , Glynn Sacha E , Daniels Jaret C , Dale Adam G 
Published: June 2024

Abstract
There are widespread public efforts to conserve wildlife in urbanized landscapes via the installation of nursery-grown plants that support Lepidoptera taxa. Insecticides are commonly used during nursery production to suppress key plant pests, and many products have extended periods of toxicity and affect a wide range of herbivore taxa. While there are plentiful toxicological data on bee species, predominantly the Western honey bee (Apis mellifera L.), little is known about how insecticides affect nonpest lepidopterans. Lepidoptera has different modes of exposure (e.g., leaf-feeding) and differences in susceptibility to insecticide target sites compared to bees. Consequently, many products compatible with bee conservation pose an uncertain risk to nonpest lepidopterans and thus may represent an under-recognized conflict with conservation efforts. Using the monarch butterfly (Danaus plexippus, L.), tropical milkweed (Asclepias curassavica, L.), and oleander aphid (Aphis nerii, Fonscolombe, 1841) system, we conducted leaf and whole-plant feeding assays to evaluate effects of acute and chronic monarch exposure to industry standard and alternative reduced-risk insecticides used during nursery production. We also evaluated the efficacy of these insecticides against their target pest, the oleander aphid. Our results indicate that insecticides used to control pests on ornamental milkweed can cause monarch larval mortality up to 4 wk after treatment application. Furthermore, the duration of aphid suppression is often shorter than the duration of adverse effects on monarchs. This study demonstrates a conflict between insect pest management and Lepidoptera conservation during ornamental plant production and has implications for the conservation value of ornamentals after retail sale.
Gonadotropic status in adult women with pituitary stalk interruption syndrome
Authors: Terray Aglaé , Baussart Bertrand , Zins Marie , Goldberg Marcel , Kab Sofiane , Cazabat Laure , Brière Mathilde , Brue Thierry , Barraud Sara , Reznik Yves , Christin-Maitre Sophie , Illouz Frédéric , Raverot Gérald , Young Jacques , Raffin-Sanson Marie-Laure , Hage Mirella 
Published: June 2024

Abstract

Objective
Pituitary stalk interruption syndrome (PSIS) is a rare cause of congenital hypopituitarism. Limited data exist on the gonadotropic status and fertility of adult women with PSIS. Our study aims to describe pubertal development and the evolution of gonadotropic function and fertility in adult women with PSIS.

Design
A retrospective multicentric French study.

Methods
We described gonadotropic function in 56 adult women with PSIS from puberty onward. We compared live birth rates per woman with PSIS with age-matched controls from the large French epidemiological cohort (CONSTANCES). Additionally, we assessed height, body mass index (BMI), blood pressure, other metabolic parameters, and socioeconomic status.

Results and Conclusions
Among 56 women with PSIS, 36 did not experience spontaneous puberty. Of these, 13 underwent ovarian stimulation, resulting in 7 women having a total of 11 children. In the subgroup with spontaneous puberty (n = 20), 4 had a total of 8 pregnancies, while 6 developed secondary gonadotropic deficiency. Women with PSIS had fewer children than controls (0.33 vs 0.63, P = .04). Median height was also lower (160.5 vs 165.0 cm, P &lt; .0001). Although mean blood pressure was lower in women with PSIS compared with controls (111.3/65.9 ± 11.2/8.1 vs 118.7/72.1 ± 10.1/7.7 mmHg, P &lt; .001), there were no significant differences in other metabolic parameters, notably BMI and lipid profile. Employment/academic status was not different in the 2 groups, but fewer women with PSIS were in relationships (42% vs 57.6% in controls, P = .02). The fertility prognosis in patients with PSIS needs optimization. Patients should be informed about the likelihood of declining gonadotropic function over time.
Achieving European Union strategic autonomy: circularity in critical raw materials value chains
Authors: Jakimów Małgorzata , Samokhalov Vsevolod , Baldassarre Brian 
Published: June 2024

Abstract
Why is it important to understand the potential of circular economy for security? With the green transition in full swing and vulnerabilities in value chains as a consequence of the COVID–19 pandemic and Russian aggression towards Ukraine, this question has never been more timely. Titanium metal constitutes a poignant case, as it is a critical raw material essential for the strategic civil aerospace and defence sectors. In addition, circular economy solutions constitute a viable solution to mitigate import dependencies in the case of this particular raw material. The European Union, with one of the largest aviation industries globally, is dependent on titanium imports from Russia and the United States. The latter, in turn, (re)imports titanium scrap from EU aviation manufacturing to increase material efficiency and reduce costs through recycling. Based on extensive stakeholder interviews across several countries and quantitative trade data, this article presents a first-time analysis of how, in the case of the titanium value chain, circular economy solutions can support the EU Open Strategic Autonomy (OSA) objectives, as enshrined in the 2023 Critical Raw Materials Act. We suggest that in order for the EU to achieve both the OSA and decarbonization objectives, it is essential to prioritize the establishment of recycling facilities as part of reshoring of the mid-value titanium industry. With the prospect of Ukraine becoming an EU member state, this strategy could be complemented by investments into the decarbonization of the upstream value chain in Ukraine while meshing it further with the EU industrial base. We argue that such reshoring could be best achieved through careful intergovernmental and industrial negotiations between the US and EU stakeholders within the formerly established channels for aviation dispute resolutions and within the framework of Ukraine's postwar reconstruction and potential EU accession.
Leveraging genome-scale metabolic models to understand aerobic methanotrophs
Authors: Wutkowska Magdalena , Tláskal Vojtěch , Bordel Sergio , Stein Lisa Y , Nweze Justus Amuche , Daebeler Anne 
Published: June 2024

Abstract
Genome-scale metabolic models (GEMs) are valuable tools serving systems biology and metabolic engineering. However, GEMs are still an underestimated tool in informing microbial ecology. Since their first application for aerobic gammaproteobacterial methane oxidizers less than a decade ago, GEMs have substantially increased our understanding of the metabolism of methanotrophs, a microbial guild of high relevance for the natural and biotechnological mitigation of methane efflux to the atmosphere. Particularly, GEMs helped to elucidate critical metabolic and regulatory pathways of several methanotrophic strains, predicted microbial responses to environmental perturbations, and were used to model metabolic interactions in cocultures. Here, we conducted a systematic review of GEMs exploring aerobic methanotrophy, summarizing recent advances, pointing out weaknesses, and drawing out probable future uses of GEMs to improve our understanding of the ecology of methane oxidizers. We also focus on their potential to unravel causes and consequences when studying interactions of methane-oxidizing bacteria with other methanotrophs or members of microbial communities in general. This review aims to bridge the gap between applied sciences and microbial ecology research on methane oxidizers as model organisms and to provide an outlook for future studies.
Persistent Corruption and Supplier Collusion in an Advanced Industrialized Country: The Case of the United States
Authors: Anderson Robert D , Jones Alison , Kovacic William E 
Published: June 2024

Abstract
This chapter focuses on understanding and addressing the continuing challenges of persistent supplier collusion and corruption in the United States (US) public procurement system, notwithstanding the comprehensive system of regulatory controls that is already in place. It begins with a historical perspective, highlighting the recurring scenarios of misconduct that have occurred over the past many decades and recently, that provided impetus for enactment of the current system of regulatory controls. It outlines the current framework of legal controls that seek to detect, punish, and deter misconduct by private suppliers and by public officials responsible for procurement and, finally, highlights contemporary weaknesses in the public procurement regime and suggests possible paths for improvement. To this end, it provides policy recommendations emphasizing the use of existing statutory and regulatory tools more effectively as well as enhancing cooperation between antitrust agencies and public procurement bodies, employing better data analytics, studying past prosecution experiences, and reducing barriers to entry for potential competitors.
Public Interest Assessment and the Federal Communications Commission (FCC)
Authors: Kokkoris Ioannis 
Published: June 2024

Abstract
This chapter looks at the merger review process in the telecommunications sector. It starts with a discussion of the composition of the Federal Communications Commission (FCC) and the relevant regulatory framework before discussing some of the seminal case law that shows the approach the FCC takes in applying its public interest test and how this approach compares with the one antitrust authority takes pursuant to its competition standard. The chapter also discusses some implications that arise from comparing the role and practice of the regulator and that of the competition authority. The analysis features two main aspects in the application of the public interest standard: first, that the regulator does not have a deadline to make a final decision and, secondly, that the merging parties carry the burden of demonstrating that their proposed transaction is in the public interest. The combination of these two factors, the chapter argues, has facilitated the imposition of heavy conditions and the negotiation of voluntary agreements, often unrelated to the substance of the mergers. The chapter reveals that, by contrast, the antitrust agencies under the competition standard have not expressed many or any concerns over the same transactions and have not imposed similar remedies or no remedies at all. The chapter discusses the cases where concurrency in jurisdiction between the Department of Justice (DOJ) and the FCC has led to divergent outcomes and to the recurring supremacy of the public interest standard applied by the FCC over the substantial lessening of competition standard applied by the DOJ.
Concluding Remarks
Authors: Kokkoris Ioannis 
Published: June 2024

Abstract
This concluding chapter reviews the themes explored in the rest of the book, drawing together insights from diverse regulatory regimes. It begins by examining the interrelation between competition and non-competition policy goals. Acknowledging the importance of these broader goals, the chapter underscores the challenges of harmonizing them within the competition law framework and the risk of undue political interference. Concluding remarks on the individual jurisdictions analysed in the rest of the book highlight the nuances of their FDI screening and merger control regimes. Ultimately, this chapter offers a critical perspective on the delicate equilibrium required to reconcile national security concerns and competition principles. It emphasizes the need for dialogue between policymakers, companies, and stakeholders to navigate the evolving landscape of economic governance. As the world grapples with protectionism’s resurgence, the chapter suggests that the test for governments and regulatory bodies lies ahead—one that necessitates an adaptive approach.
Parental Liability in EU Competition Law
Authors: Whelan Peter 
Published: June 2024

Abstract
In enforcing European Union (EU) competition law, the European Commission (the Commission) relies upon a unique doctrine of parental antitrust liability: it imposes fines upon the parent company of an infringing subsidiary where the former exercised decisive influence over the commercial policy of the latter. This contentious aspect of EU competition law enforcement disregards corporate personality and the principle of limited liability and has engendered acute criticism that the doctrine is unfair, ineffective, obscure, disproportionate, contrary to due process, and based upon an extremely flimsy justificatory foundation. Such criticism raises serious, unanswered questions concerning the legitimacy of the Commission’s antitrust enforcement efforts. This monograph critically assesses the extent to which the existing EU-level doctrine of parental antitrust liability is legitimate in design and operation and what can be done to rectify effectively any identified problematic shortcomings. Employing a four-pronged legitimacy framework, it contends that, although the general concept of parental liability can be justified in principle in EU competition law, the current EU-level doctrine of parental antitrust liability suffers from a distinct and problematic lack of legitimacy. Specifically, the doctrine displays significant deficiencies with respect to the criteria of effectiveness, fairness, and legality. A reformulated approach to parental antitrust liability for EU competition law violations is constructed and fully rationalised. Erected around the notion of parental fault, that approach represents a solid normative account of how to impose parental antitrust liability at EU level in a manner that is theoretically robust, effective in practice, fair in substance, and legally sound.
Assessing the Legitimacy of the EU-Level Doctrine of Parental Antitrust Liability
Authors: Whelan Peter 
Published: June 2024

Abstract
This book critically assesses the extent to which the existing EU-level doctrine of parental antitrust liability is legitimate in design and operation and what can be done to rectify effectively any identified problematic shortcomings. To do so, it must first articulate the analytical framework that can be used to assess the legitimacy of the doctrine. This chapter performs this task. Specifically, it articulates a four-pronged legitimacy framework that can be used to determine whether the EU-level doctrine of parental liability is indeed legitimate at present. The criteria in question are: justifiability; effectiveness; fairness; and legality. After providing detailed definitions on pertinent concepts, the chapter explains how the book will employ that legitimacy framework through its remaining chapters in order to achieve its overarching aim.
Deterrence in EU Competition Law and Its Relevance to Parental Liability
Authors: Whelan Peter 
Published: June 2024

Abstract
This chapter identifies deterrence as the enforcement objective that justifies parental antitrust enforcement in EU competition law. To do so, it first provides the relevant context by establishing the crucial place that the objective of deterrence has in EU antitrust enforcement. The chapter then outlines the assumptions articulated in the literature on the specific rationale underpinning the existence of parental antitrust liability in EU competition law. It demonstrates that, although some confusion can be identified regarding the exact purpose of parental antitrust liability, when an enforcement rationale is advanced in the literature concerning such liability, that rationale is almost invariably the deterrence of anticompetitive behaviour. Moving on from that finding, the chapter investigates EU-level decisional practice, jurisprudence, and policy documentation to determine if the assumption generally made about the normative link between parental liability and deterrence actually underpins the support that the European Commission (the Commission) and the EU Courts display towards the EU-level doctrine of parental antitrust liability. Ultimately it argues that, whilst the theoretical justification for allowing parental liability to operate within the EU-level enforcement framework has not been articulated in a detailed, robust, and systematic manner by either the Commission or the EU Courts, the objective of deterrence can be reasonably taken as the primary objective motivating the existence of the doctrine of parental liability within EU competition law.
Parental Liability and the Principle of Ne Bis In Idem
Authors: Whelan Peter 
Published: June 2024

Abstract
This chapter analyses the application of the principle of ne bis in idem (double jeopardy) in the context of parental liability for EU antitrust violations. First, it outlines briefly some essential detail on the principle itself, thereby providing the legal content to be relied upon in the chapter’s substantive analyses. It then critically assesses (and thereby debunks) the claim in the literature that the EU-level doctrine of parental liability—in particular its approach to recidivism—inevitably violates the principle under consideration. The chapter then proceeds to establish a stronger basis for criticism in this context; specifically, it argues that there is at present a distinct lack of clarity on how the principle of ne bis in idem applies to parental liability, to the detriment of the legitimacy of that enforcement doctrine. This lack of clarity results from the ambiguity that, in practice, sometimes creeps into the usage of the term ‘undertaking’ in EU competition law jurisprudence. Finally, the chapter argues that an inherent difficulty exists regarding the rectification of the identified lack of clarity in how the principle of ne bis in idem applies to parental liability. Ultimately, the chapter concludes that, to ensure that the fairness objective of the principle of ne bis in idem is achieved in a principled manner with parental liability, one may need to pursue that objective through reliance upon a different legal principle entirely.
Mergers
Authors: Niels Gunnar , Jenkins Helen , Kavanagh James 
Published: June 2024

Abstract
This chapter deals with the economics of mergers (building on earlier chapters that covered market definition, market power, and oligopoly theory). It explains how counterfactual analysis is used to assess what would happen in the absence of the merger, including in the failing-firm defence. It then turns to unilateral effects, explaining diversion ratios and techniques for simulating price effects. Next the chapter deals with dynamic effects, coordinated effects, non-horizontal mergers, and minority shareholdings and common ownership. Finally, it explains merger efficiencies, and in which situations they benefit consumers sufficiently to offset any anti-competitive effects of the merger.