bluuebunny/crossref_metadata_2025_split huggingface dataset:
Estimation of seismometer clock time offsets using Kalman Filter towards accurate seismic velocity change
Authors: Takano Tomoya , Nishida Kiwamu 
Published: September 2024

SUMMARY
Monitoring seismic velocity changes obtained from ambient noise correlations is widely used to understand changes in rock properties in response to earthquakes, volcanic activities and environmental changes. Since continuous seismic data have been accumulated, this method can estimate long-term changes in seismic velocity, such as crustal recovery after a major earthquake and temporal variations in seismic velocity related to long-term environmental change. Changes in seismic velocity can be estimated with a high temporal resolution by measuring the phase differences of ambient noise correlations based on a seismic interferometry method. Still, these phase differences are influenced not only by seismic wave velocity changes but also by errors in clock timing in seismometers. The clock drift occurs due to out-of-synchronization with the GPS clock and the drift of the internal clock. Therefore, to accurately monitor temporal changes in crustal structure by measuring the phase differences of noise correlations, it is crucial to evaluate the contribution of errors in clock timing to the phase differences. Recently, a method using an extended Kalman filter based on a state-space model was developed for reliable detection of temporal changes in the waveforms of ambient noise correlations, with the state-space model offering the advantage of flexible modelling of time-series data. In this study, we incorporated the time-shifts caused by clock time errors of the seismometer into the state-space model of the temporal changes in ambient noise correlations. We estimated seismic velocity changes, amplitude changes of noise correlations and clock time errors from 2010 April to 2021 September at seismic stations around the Shinmoe-dake volcano in Japan, which experienced eruptions in 2011 and 2018, respectively. Several stations exhibited clear clock time offsets, and the occurrence of clock time-shifts coincided with the dates when the data logger was turned off for seismic station maintenance or replacement of the seismometer. The proposed method provides stable estimations with respect to the signal-to-noise ratio of the waveform, and this stable estimation facilitates accurate timing of seismic recordings, enabling precise analysis of seismic phase arrival times.
Review and Evaluate the Bioinformatics Analysis Strategies of ATAC-seq and CUT&Tag Data
Authors: Cheng Siyuan , Miao Benpeng , Li Tiandao , Zhao Guoyan , Zhang Bo 
Published: September 2024

Abstract
Efficient and reliable profiling methods are essential to study epigenetics. Tn5, one of the first identified prokaryotic transposases with high DNA-binding and tagmentation efficiency, is widely adopted in different genomic and epigenomic protocols for high-throughputly exploring the genome and epigenome. Based on Tn5, the Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) and the Cleavage Under Targets and Tagmentation (CUT&Tag) were developed to measure chromatin accessibility and detect DNA–protein interactions. These methodologies can be applied to large amounts of biological samples with low-input levels, such as rare tissues, embryos, and sorted single cells. However, fast and proper processing of these epigenomic data has become a bottleneck because massive data production continues to increase quickly. Furthermore, inappropriate data analysis can generate biased or misleading conclusions. Therefore, it is essential to evaluate the performance of Tn5-based ATAC-seq and CUT&Tag data processing bioinformatics tools, many of which were developed mostly for analyzing chromatin immunoprecipitation followed by sequencing (ChIP-seq) data. Here, we conducted a comprehensive benchmarking analysis to evaluate the performance of eight popular software for processing ATAC-seq and CUT&Tag data. We compared the sensitivity, specificity, and peak width distribution for both narrow-type and broad-type peak calling. We also tested the influence of the availability of control IgG input in CUT&Tag data analysis. Finally, we evaluated the differential analysis strategies commonly used for analyzing the CUT&Tag data. Our study provided comprehensive guidance for selecting bioinformatics tools and recommended analysis strategies, which were implemented into Docker/Singularity images for streamlined data analysis.
Competition Law
Authors: Whish Richard , Bailey David 
Published: September 2024

Abstract
Competition Law explains competition law and policy in the EU and UK. The intention is to provide the reader with an understanding of competition law and policy, to introduce the reader to key economic concepts, legal principles and tools in competition law, and to provide insights into the numerous different issues that arise when applying competition law to market behaviour. Describing the economic rationale for the law, the chapters consider the application of EU and UK competition law to various business practices, including cartels, cooperation agreements, exchanges of information, distribution agreements, licences of intellectual property rights, unilateral conduct, joint ventures, and mergers. The text has been updated to include changes to EU law on digital markets as a result of the Digital Services Act and the Digital Markets Act. It also discusses the changes to UK law as a consequence of the Digital Markets, Competition and Consumers Act 2024, including the creation of a regulatory scheme for digital platforms having a ‘strategic market status’ and amendments to the Competition Act 1998 and the Enterprise Act 2002. It also discusses the European Commission’s Guidelines on Vertical Restraints of 2022 and Horizontal Cooperation Guidelines of 2023, including its guidance on sustainability agreements. The text incorporates extensive new legislation, case-law, decisional practice, guidelines and periodical literature at EU and UK level.
Article 101(3)
Authors: Whish Richard , Bailey David 
Published: September 2024

Abstract
This chapter examines Article 101(3) of the Treaty of Functioning of the European Union (TFEU). Article 101(3) provides a ‘legal exception’ to the prohibition in Article 101(1) by providing that it may be declared inapplicable in respect of agreements, decisions or concerted practices, or of categories of agreements, decisions or concerted practices, that satisfy four conditions. After making some preliminary comments on the application of Article 101(3), this chapter discusses the four conditions in Article 101(3). It then considers the implications of Regulation 1/2003 for undertakings and their professional advisers, and in particular their need to ‘self-assess’ the application of Article 101(3) to agreements. The final section of this chapter describes the system of so-called block exemptions.
Articles 101 and 102: private enforcement in the courts of Member States
Authors: Whish Richard , Bailey David 
Published: September 2024

Abstract
This chapter describes the private enforcement of competition law, that is to say, the situation where litigants take their disputes to a domestic court or, quite often, to arbitration. Section 2 deals with the private enforcement of Articles 101 and/or 102 as a matter of EU law, with particular emphasis on the Damages Directive. Section 3 deals with private actions in the UK courts. Section 4 considers the use of competition law not as a ‘sword’, where the claimant’s cause of action is based on an infringement of competition law, but rather as a ‘shield’, that is to say as a defence, for example to an action for breach of contract or infringement of an intellectual property right. Section 5 contains a brief discussion competition law and arbitration.
Horizontal agreements (1): cartels
Authors: Whish Richard , Bailey David 
Published: September 2024

Abstract
This chapter is concerned with the prohibition of cartels. It begins with a discussion of the widespread consensus among competition authorities worldwide that cartels should be condemned, and gives examples of recent enforcement that led to the imposition of significant fines and sentences of imprisonment. It also looks at anti-cartel enforcement in the EU. The chapter then considers the application of Article 101 to particular types of cartels: horizontal price fixing, market sharing, production quotas, collusive tendering, agreements on standard terms, exchanges of information, advertising restrictions and other anti-competitive horizontal restraints. The final section of the chapter looks at anti-cartel enforcement action against cartels in the UK.
Abuse of dominance (1): non-pricing practices
Authors: Whish Richard , Bailey David 
Published: September 2024

Abstract
This chapter considers abusive non-pricing practices under Article 102 TFEU and the Chapter II prohibition in the Competition Act 1998. It deals in turn with exclusive dealing agreements; tying; refusals to supply; preferential treatment, unfair trading conditions, abusive non-pricing practices that are harmful to the single market; and miscellaneous other non-pricing practices which might infringe Article 102 or the Chapter II prohibition. Reference is made to the case-law of the Court of Justice and the Commission’s Guidance on the Commission’s Enforcement Priorities in Applying Article [102 TFEU] to Abusive Exclusionary Conduct by Dominant Undertakings, as amended in March 2023.
The relationship between intellectual property rights and competition law
Authors: Whish Richard , Bailey David 
Published: September 2024

Abstract
This chapter considers the relationship between intellectual property rights and competition law. After a brief introduction, it deals in general terms with the application of Article 101 to licences of intellectual property rights. The chapter proceeds to discuss the provisions of Regulation 316/2014, the block exemption for technology transfer agreements. It also considers the application of Article 101 to various other agreements concerning intellectual property rights such as technology pools and settlements of litigation. This is followed by a section on the application of Article 102 to the way in which dominant undertakings exercise their intellectual property rights, including an examination of the controversial subject of refusals to license intellectual property rights which are sometimes found to be abusive. The chapter concludes with a look at the position in UK competition law.
Cost-based performance optimization of a single system under a hierarchical imperfect maintenance policy
Authors: Liang Xiaojun , Cui Lirong , Wang Ruiting , Jiang Weixin 
Published: September 2024

Abstract
Accepted by: M. Zied Babai
Due to the influence of external factors such as repair sites and seasonal climate change, it is difficult to restore the performance of a system to any intermediate level between perfect and minimal maintenance through imperfect maintenance. This article first categorizes the states of the system just before repair into three classes based on its internal degradation level: failure, major defect and minor defect, with three corresponding thresholds. Subsequently, the corresponding repairs are carried out to dwindle the system’s degradation to different levels. In detail, if the internal degradation level of the system just before repair is recognized as minor defect, an imperfect repair, termed as type I imperfect repair, is implemented to scale down the degradation level below the minor defect threshold. If the degradation level is identified as major defect, an upgraded imperfect repair, termed as type II imperfect repair, is executed to only lower the degradation to the level between the minor defect threshold and major defect threshold. Otherwise, if the degradation before repair is beyond the failure threshold, replacement will be carried out instead of these imperfect repairs. Thus, a novel hierarchical imperfect maintenance structure is introduced. Then, a multi-variable repair cost model is constructed when considering the related costs incurred from inspection, type I imperfect repair, type II imperfect repair, replacement and even system downtime. Finally, with the aid of the stationary law of Markov chains and the semi-regenerative process, the cost-based performance optimization with three parameters, including the inspection interval, minor defect threshold and major defect threshold, is explored through a numerical experiment, and the closed-form expression of the optimal cost rate is provided.
A generalized approach for pricing American options under a regime-switching model
Authors: Zheng Yawen , Zhu Song-Ping 
Published: September 2024

Abstract
Accepted by: Giorgio Consigli
Regime-switching models gained their popularity over the past decade because of their distinctive advantage of modelling different financial market statuses in a discrete rather than continuous manner as in stochastic volatility models. When they are used in option pricing, the clear advantage is that they enable a larger parameter space for models to be calibrated for specific market dynamics and thus allow a better quantitative risk management in terms of utilizing financial derivatives. However, when they are used to price American-style financial derivatives, a large number of economic statuses result in a demand for improved computational efficiency. This paper provides a new algorithm of high computational efficiency supplemented with a theorem that pre-analyses the associated matrices and their eigenvalues, without concern about the possibility of duplicated roots being mistakenly identified as simple roots due to rounding errors or the presence of two extremely closely positioned simple roots within the original system.
An Enteric Bacterial Infection Triggers Neuroinflammation and Neurobehavioral Impairment in 3xTg-AD Transgenic Mice
Authors: Park Gwoncheol , Kadyan Saurabh , Hochuli Nathaniel , Salazar Gloria , Laitano Orlando , Chakrabarty Paramita , Efron Philip A , Zafar M Ammar , Wilber Aaron , Nagpal Ravinder 
Published: September 2024

Abstract

Background
Klebsiella pneumoniae is infamous for hospital-acquired infections and sepsis, which have also been linked to Alzheimer disease (AD)-related neuroinflammatory and neurodegenerative impairment. However, its causative and mechanistic role in AD pathology remains unstudied.

Methods
A preclinical model of K. pneumoniae enteric infection and colonization is developed in an AD model (3xTg-AD mice) to investigate whether and how K. pneumoniae pathogenesis exacerbates neuropathogenesis via the gut-blood-brain axis.

Results
K. pneumoniae, particularly under antibiotic-induced dysbiosis, was able to translocate from the gut to the bloodstream by penetrating the gut epithelial barrier. Subsequently, K. pneumoniae infiltrated the brain by breaching the blood-brain barrier. Significant neuroinflammatory phenotype was observed in mice with K. pneumoniae brain infection. K. pneumoniae-infected mice also exhibited impaired neurobehavioral function and elevated total tau levels in the brain. Metagenomic analyses revealed an inverse correlation of K. pneumoniae with gut biome diversity and commensal bacteria, highlighting how antibiotic-induced dysbiosis triggers an enteroseptic “pathobiome” signature implicated in gut-brain perturbations.

Conclusions
The findings demonstrate how infectious agents following hospital-acquired infections and consequent antibiotic regimen may induce gut dysbiosis and pathobiome and increase the risk of sepsis, thereby increasing the predisposition to neuroinflammatory and neurobehavioral impairments via breaching the gut-blood-brain barrier.
Bacterial Membrane Vesicles: The Missing Link Between Bacterial Infection and Alzheimer Disease
Authors: Butler Catherine A , Ciccotosto Giuseppe D , Rygh Nathaniel , Bijlsma Elly , Dashper Stuart G , Brown Angela C 
Published: September 2024

Abstract
Periodontitis is a common chronic inflammatory disease, affecting approximately 19% of the global adult population. A relationship between periodontal disease and Alzheimer disease has long been recognized, and recent evidence has been uncovered to link these 2 diseases mechanistically. Periodontitis is caused by dysbiosis in the subgingival plaque microbiome, with a pronounced shift in the oral microbiota from one consisting primarily of Gram-positive aerobic bacteria to one predominated by Gram-negative anaerobes, such as Porphyromonas gingivalis. A common phenomenon shared by all bacteria is the release of membrane vesicles to facilitate biomolecule delivery across long distances. In particular, the vesicles released by P gingivalis and other oral pathogens have been found to transport bacterial components across the blood-brain barrier, initiating the physiologic changes involved in Alzheimer disease. In this review, we summarize recent data that support the relationship between vesicles secreted by periodontal pathogens to Alzheimer disease pathology.
From Viral Infections to Alzheimer's Disease: Unveiling the Mechanistic Links Through Systems Bioinformatics
Authors: Onisiforou Anna , Zanos Panos 
Published: September 2024

Abstract

Background
Emerging evidence suggests that viral infections may contribute to Alzheimer's disease (AD) onset and/or progression. However, the extent of their involvement and the mechanisms through which specific viruses increase AD susceptibility risk remain elusive.

Methods
We used an integrative systems bioinformatics approach to identify viral-mediated pathogenic mechanisms, by which Herpes Simplex Virus 1 (HSV-1), Human Cytomegalovirus (HCMV), Epstein-Barr virus (EBV), Kaposi Sarcoma-associated Herpesvirus (KSHV), Hepatitis B Virus (HBV), Hepatitis C Virus (HCV), Influenza A Virus (IAV) and Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) could facilitate AD pathogenesis via virus-host protein-protein interactions (PPIs). We also explored potential synergistic pathogenic effects resulting from herpesvirus reactivation (HSV-1, HCMV, and EBV) during acute SARS-CoV-2 infection, potentially increasing AD susceptibility.

Results
Herpesviridae members (HSV-1, EBV, KSHV, HCMV) impact AD-related processes like amyloid-β (Aβ) formation, neuronal death, and autophagy. Hepatitis viruses (HBV, HCV) influence processes crucial for cellular homeostasis and dysfunction, they also affect microglia activation via virus-host PPIs. Reactivation of HCMV during SARS-CoV-2 infection could potentially foster a lethal interplay of neurodegeneration, via synergistic pathogenic effects on AD-related processes like response to unfolded protein, regulation of autophagy, response to oxidative stress, and Aβ formation.

Conclusions
These findings underscore the complex link between viral infections and AD development. Viruses impact AD-related processes through shared and distinct mechanisms, potentially influencing variations in AD susceptibility.
Unveiling the Intricate Link Between Anaerobe Niche and Alzheimer Disease Pathogenesis
Authors: Drakes NyEmma , Kondrikova Galina , Pytel Dariusz , Hamlett Eric D 
Published: September 2024

Abstract
Dysbiosis within microbiomes has been increasingly implicated in many systemic illnesses, such as cardiovascular disease, metabolic syndrome, respiratory infections, and Alzheimer disease (Ad). The correlation between Ad and microbial dysbiosis has been repeatedly shown, yet the etiologic cause of microbial dysbiosis remains elusive. From a neuropathology perspective, abnormal (often age-related) changes in the brain, associated structures, and bodily lumens tend toward an accumulation of oxygen-depleted pathologic structures, which are anaerobically selective niches. These anaerobic environments may promote progressive change in the microbial community proximal to the brain and thus deserve further investigation. In this review, we identify and explore what is known about the anaerobic niche near or associated with the brain and the anaerobes that it is harbors. We identify the anaerobe stakeholders within microbiome communities and the impacts on the neurodegenerative processes associated with Ad. Chronic oral dysbiosis in anaerobic dental pockets and the composition of the gut microbiota from fecal stool are the 2 largest anaerobic niche sources of bacterial transference to the brain. At the blood-brain barrier, cerebral atherosclerotic plaques are predominated by anaerobic species intimately associated with the brain vasculature. Focal cerebritis/brain abscess and corpora amylacea may also establish chronic anaerobic niches in direct proximity to brain parenchyma. In exploring the anaerobic niche proximal to the brain, we identify research opportunities to explore potential sources of microbial dysbiosis associated with Ad.
Heterotrophic nitrification by Alcaligenes faecalis links organic and inorganic nitrogen metabolism
Authors: Qin Ya-Ling , Liang Zong-Lin , Ai Guo-Min , Liu Wei-Feng , Tao Yong , Jiang Cheng-Ying , Liu Shuang-Jiang , Li De-Feng 
Published: September 2024

Abstract
Heterotrophic nitrification remains a mystery for decades. It has been commonly hypothesized that heterotrophic nitrifiers oxidize ammonia to hydroxylamine and then to nitrite in a way similar to autotrophic AOA and AOB. Recently, heterotrophic nitrifiers from Alcaligenes were found to oxidize ammonia to hydroxylamine and then to N2 (“dirammox”, direct ammonia oxidation) by the gene cluster dnfABC with a yet-to-be-reported mechanism. The role of a potential glutamine amidotransferase DnfC clues the heterotrophic ammonia oxidation might involving in glutamine. Here, we found Alcaligenes faecalis JQ135 could oxidize amino acids besides ammonia. We discovered that glutamine is an intermediate of the dirammox pathway and the glutamine synthetase gene glnA is essential for both A. faecalis JQ135 and the Escherichia coli cells harboring dnfABC gene cluster to oxidize amino acids and ammonia. Our study expands understanding of heterotrophic nitrifiers and challenges the classical paradigm of heterotrophic nitrification.
Development of bait station to complement attract-and-kill agents of Zeugodacus tau (Diptera: Tephritidae)
Authors: Lin Jia , Yue Guoqing , Xiao Kang , Chen Jun , Hao Xuxing , Yang Deqing , Yang Jianquan , Zheng Minlin , Ji Qinge 
Published: September 2024

Abstract
Zeugodacus tau (Walker) (Diptera: Tephritidae) is an important agricultural pest currently managed primarily through the application of insecticides due to limited control strategies. Bait station devices are target specific and have emerged as a behaviorally based alternative to traditional insecticide sprays for managing Z. tau. In this study, we designed a bait station by integrating female-biased olfactory, visual, and gustatory elements, and a killing agent in a wax-matrix. Our results showed that the wax-matrix integrated with spinetoram showed the highest toxicity to immature and mature Z. tau females. Furthermore, the color and shape of the spinetoram bait station significantly influenced its attractiveness and toxicity to female Z. tau. Green sausage-shaped exteriors were the most effective color and shape examined. Subsequent experiments showed a length-dependent effect on mortality and visiting frequencies of Z. tau females when the bait stations were 9–13 cm long. The addition of the olfactory stimulus of 5% ammonium acetate to the bait station attracted a higher number of mature Z. tau females than the control. The killing efficacy of the weathered bait station was similar to that of the fresh station within an 8-week period (over 794 mm of rainfall). The bait station developed herein would provide new insight into the attract-and-kill strategy for Z. tau and alleviate the pressure of the actual management program for this pest.