bluuebunny/crossref_metadata_2025_split huggingface dataset:
A general and efficient representation of ancestral recombination graphs
Authors: Wong Yan , Ignatieva Anastasia , Koskela Jere , Gorjanc Gregor , Wohns Anthony W. , Kelleher Jerome 
Published: November 2023

AbstractAs a result of recombination, adjacent nucleotides can have different paths of genetic inheritance and therefore the genealogical trees for a sample of DNA sequences vary along the genome. The structure capturing the details of these intricately interwoven paths of inheritance is referred to as an ancestral recombination graph (ARG). Classical formalisms have focused on mapping coalescence and recombination events to the nodes in an ARG. This approach is out of step with modern developments, which do not represent genetic inheritance in terms of these events or explicitly infer them. We present a simple formalism that defines an ARG in terms of specific genomes and their intervals of genetic inheritance, and show how it generalises these classical treatments and encompasses the outputs of recent methods. We discuss nuances arising from this more general structure, and argue that it forms an appropriate basis for a software standard in this rapidly growing field.
Viruses contribute to microbial diversification in the rumen ecosystem and are associated with certain animal production traits
Authors: Yan Ming , Yu Zhongtang 
Published: November 2023

AbstractBackgroundThe rumen microbiome enables ruminants to digest otherwise indigestible feedstuffs, thereby facilitating the production of high-quality protein, albeit with suboptimal efficiency and producing methane. Despite extensive research delineating associations between the rumen microbiome and ruminant production traits, the functional roles of the pervasive and diverse rumen virome remain to be determined.ResultsLeveraging a recent comprehensive rumen virome database, this study analyzes virus-microbe linkages, at both species and strain levels, across 551 rumen metagenomes, elucidating patterns of microbial and viral diversity, co-occurrence, and virus-microbe interactions. Additionally, this study assesses the potential role of rumen viruses in microbial diversification by analyzing prophages found in rumen metagenome-assembled genomes. Employing CRISPR-Cas spacer-based matching and virus-microbe co-occurrence network analysis, this study suggests that rumen viruses may regulate rumen microbes at both strain and community levels via both antagonistic and mutualistic interactions. Moreover, this study establishes that the rumen virome demonstrates responsiveness to dietary shifts and associations with key animal production traits, including feed efficiency, lactation performance, weight gain, and methane emissions.ConclusionsThese findings furnish a substantive framework for subsequent investigations to decode the functional roles of the rumen virome in shaping the rumen microbiome and influencing overall animal production performance.
Structural basis for plasmid restriction by SMC JET nuclease
Authors: Roisné-Hamelin Florian , Liu Hon Wing , Taschner Michael , Li Yan , Gruber Stephan 
Published: November 2023

SummaryDNA loop-extruding SMC complexes play crucial roles in chromosome folding and DNA immunity. Prokaryotic SMC Wadjet (JET) complexes limit the spread of circular plasmids through DNA cleavage; yet the mechanisms for target recognition are unresolved. We show that artificial DNA circularization renders linear DNA susceptible to JET cleavage. Unlike free DNA, JET cleaves immobilized plasmid DNA at a specific site, the plasmid-anchoring point, showing that the anchor hinders DNA extrusion but not DNA cleavage implying that residual unextruded DNA is cleaved. Structures of plasmid-bound JetABC reveal two presumably stalled SMC motor units that are drastically rearranged from the resting state, together entrapping a U-shaped DNA segment, which is further converted to kinked V-shaped cleavage substrate by JetD nuclease binding. Our findings uncover mechanical bending of residual unextruded DNA as principle for non-self DNA recognition and molecular signature for plasmid cleavage. We elucidate key elements of SMC loop extrusion including motor directionality and the structure of a DNA-holding state.
Translation initiation factor eIF1.2 promotesToxoplasmastage conversion by regulating levels of key differentiation factors
Authors: Wang Fengrong , Holmes Michael J. , Hong Hea Jin , Thaprawat Pariyamon , Kannan Geetha , Huynh My-Hang , Schultz Tracey L. , Licon M. Haley , Lourido Sebastian , Dong Wenzhao , Querido Jailson Brito , Sullivan William J. , O’Leary Seán E. , Carruthers Vern B. 
Published: November 2023

AbstractsThe parasiteToxoplasma gondiipersists in its hosts by converting from replicating tachyzoites to latent bradyzoites housed in tissue cysts. The molecular mechanisms that mediateT. gondiidifferentiation remain poorly understood. Through a mutagenesis screen, we identified translation initiation factor eIF1.2 as a critical factor forT. gondiidifferentiation. A F97L mutation in eIF1.2 or the genetic ablation ofeIF1.2(Δeif1.2) markedly impeded bradyzoite cyst formationin vitroandin vivo. We demonstrated, at single-molecule level, that the eIF1.2 F97L mutation impacts the scanning process of the ribosome preinitiation complex on a model mRNA. RNA sequencing and ribosome profiling experiments unveiled that Δeif1.2parasites are defective in upregulating bradyzoite induction factors BFD1 and BFD2 during stress-induced differentiation. Forced expression of BFD1 or BFD2 significantly restored differentiation in Δeif1.2parasites. Together, our findings suggest that eIF1.2 functions by regulating the translation of key differentiation factors necessary to establish chronic toxoplasmosis.
UPF1 ATPase autoinhibition and activation modulate RNA binding kinetics and NMD efficiency
Authors: Chapman Joseph H. , Youle Alice M. , Grimme Acadia L. , Neuman Keir C. , Hogg J. Robert 
Published: November 2023

AbstractThe RNA helicase UPF1 interacts with mRNAs, mRNA decay machinery, and the terminating ribosome to promote nonsense-mediated mRNA decay (NMD). Structural and biochemical data have revealed that UPF1 exists in an enzymatically autoinhibited “closed” state. Upon binding the NMD protein UPF2, UPF1 undergoes an extensive conformational change into a more enzymatically active “open” state, which exhibits enhanced ATPase and helicase activity. However, mechanically deficient UPF1 mutants can support efficient NMD, bringing into question the roles of UPF1 enzymatic autoinhibition and activation in NMD. Here, we identify two additional important features of the activated open state: slower nucleic acid binding kinetics and enhanced ATP-stimulated nucleic acid dissociation kinetics. Computational modeling based on empirical measurements of UPF1, UPF2, and RNA interaction kinetics predicts that the majority of UPF1-RNA binding and dissociation events in cells occur independently of UPF2 binding. We find that UPF1 mutants with either reduced or accelerated dissociation from RNA have NMD defects, whereas UPF1 mutants that are more dependent on UPF2 for catalytic activity remain active on well-established NMD targets. These findings support a model in which the kinetics of UPF1-mRNA interactions are important determinants of cellular NMD efficiency.
Effects of the Russian–Ukrainian war on the value of imports and the food trade balance in Saudi Arabia
Authors: Ghanem Adel Mohammed , Alrwis Khaled Nahar , Alaagib Sharafeldin Bakri , Aldawdahi Nageeb , Al-Nashwan Ibrahim , Ghanem Hossam 
Published: November 2023

PurposeThis study aimed to measure the effects of the Russian–Ukrainian war on the value of imports and the food trade balance in Saudi Arabia.Design/methodology/approachEstimating the suggested model using econometric analysis for the years 1990–2021.FindingsThe amount of deficit increased in the food trade balance from 11.58 billion riyals in 1990 to 72.98 billion riyals in 2021. As for the increase in the index of food production by 10%, it leads to a decrease in the value of food imports for Saudi Arabia by 1.88%. Also, the value of the deficit in Saudi Arabia's food trade balance decreases by 5.24% as a result of a 10% rise in food exports to the country.Originality/valueIn light of the increase in the food price index to 145.8, the value of food imports and the deficit in the food trade balance exceed their counterparts in the current situation for the year 2021, at a rate of 37.1% and 44.5% for each respectively. In view of achieving huge financial surpluses as a result of the rise in oil prices, the Saudi Arabia is able to bear the high import bill and the amount of food trade balance deficit. Finally, the Russian–Ukrainian war leads to an increase in the cost of obtaining food commodities and their unavailability in the markets and thus affects the food security environment. Therefore, this study recommends the necessity of conducting more studies on the impact of the war on the food security of the Kingdom of Saudi Arabia.
Revisiting the puzzle of capital structure determinants: an empirical study based on UK firms
Authors: Rahman Md. Atiqur , Hossain Tanjila , Sen Kanon Kumar 
Published: November 2023

PurposeThis study aims to measure impact of several firm-specific factors on alternative measures of leverage. The authors also aim to study impact of the subprime crisis on such associations.Design/methodology/approachThe authors utilized an unbalanced panel data of 973 firm-year observations on 47 UK listed non-financial firms for the years 1990–2019. Book-based and market-based long-term and total leverage measures have been used as explained variables. The explanatory variables are profitability, size, two measures of growth, asset tangibility, non-debt tax shields, firm age and product uniqueness. Fixed effect and random effect models with clustered robust standard errors have been utilized for data analysis. To find the effect of subprime crisis, original dataset was split to create pre-crisis and post-crisis datasets.FindingsThe authors find that profitability significantly reduces leverage while firms having more tangible assets use significantly more debt in capital structure. Firm size and non-debt tax shield have statistically insignificant positive impact on leverage. Having more unique products reduces use of external debt, albeit insignificantly. Growth, when measured as market-to-book ratio, has inconsistent impact, whereas capital expenditure insignificantly reduces leverage. Age is found to be an insignificant predictor of leverage. After the subprime crisis, firms started relying more on internal fund instead of external debt, more particularly short-term debt. Having more collateral is gradually becoming more important for availing external debt.Research limitations/implicationsData limitations restrict generalization of the findings.Originality/valueThis is one of the pioneering attempts to show how subprime crisis altered the theoretical domain of capital structure research in the UK.
The importance of warehouses in logistics outsourcing: benchmarking the perspectives of 3PL providers and shippers
Authors: Baglio Martina , Colicchia Claudia , Creazza Alessandro , Dallari Fabrizio 
Published: November 2023

PurposeAn ever-increasing number of companies outsource logistics activities to third-party logistics (3PL) providers to beat the competition. From the buyer's (shippers') perspective, selecting the right 3PL provider is crucial, and from the 3PL provider's perspective, it is imperative to be attractive and to retain clients. To this aim, a potential lever can be physical assets, such as warehouses, which the literature has traditionally neglected. The objective is to benchmark the importance of warehouses for 3PL providers to attract/retain clients and for shippers to select the right 3PL provider.Design/methodology/approachThe authors performed an empirical investigation through interviews on dyads (3PL providers/shippers) and utilized the Best-Worst Method (BWM) to rank the criteria used in the 3PL buying process and allow the warehouse's role to emerge.FindingsResults show that the 3PL buying process consists of four phases and three evaluation steps. The selection criteria are classified into three groups: order qualifiers, order winners and retention factors. The warehouse has different levels of importance throughout the process. It appears that it can indirectly enhance the attractiveness and retention capability of 3PL providers through other selection criteria.Originality/valueBy combining the resource-based view and the customer value theory, this research extends the theory on logistics outsourcing by studying the phases of the 3PL buying process and scrutinizing the criteria used in different evaluation steps. The research adds a double perspective of analysis (3PL providers and shippers), which is missing in the literature, and focuses on the importance of warehouses.
Advertising fee as a new supply chain coordination approach between hotels and online travel agencies
Authors: Chen Chi-Jen 
Published: November 2023

PurposeChannel coordination has become an essential part of researching hotel supply chain management practices. This paper develops an improved channel coordination approach to coordinate the profit distribution between hotels and online travel agencies (OTAs) achieved through an introduction of advertising fees. This direction further improves the decentralization of cooperation and achieves Pareto improvement to achieve mutual profitability.Design/methodology/approachThe methodology used in this study involves Stackelberg game theory employed for the decision-making and analysis of both the hotel and OTA. The OTA, acting as the leader, offers a hotel a contract specifying the commission rate that the hotel will pay to the respective OTA. The hotel, acting as a follower, sets a self-interested room rate as a given response. A deterministic, price-sensitive linear demand function is utilized to derive possible analytical solutions once centralized, noncooperative decentralization and cooperative decentralized channel occurs.FindingsResults show that a new channel coordination approach is possible, namely via advertising fees. Prior to channel coordination, the OTA tends to set a higher commission rate, and the hotel sets a higher room rate in response under noncooperative decentralization. As such, this results in a lower channel-wide profit for all. One way to reduce channel-wide profit loss is to use a method of cooperative decentralization, which can, and will result in optimal profit as centralization takes place. However, the lack of incentives makes cooperative decentralization unfeasible. Further improvement is possible by using advertising fees based on a cooperative decentralization agreement, which can reach Pareto improvement.Practical implicationsThis paper helps the OTA industry and hotel owners cooperate by way of smoother coordination. This study provides practitioners with two important practical implications. The first one is that the coordination between the hotel industry and OTA through cooperative decentralization allows for the achievement of higher profitability than that of noncooperative decentralization. The second one is that this paper solves the outstanding problem of insufficient incentives characteristic of cooperative decentralization by means of an advertising fee as a new supply chain coordination approach.Originality/valueThis paper offers both the problem and solution regarding the lack of incentives that hamper cooperative decentralization without the use of advertising fees. This paper is unique in that it derives analytical solutions regarding commissions levied in a typical hotel supply chain under noncooperative decentralization.
Identifying and ranking critical success factors for digital court
Authors: Farzaneh Kondori Narges , Rouhani Saeed 
Published: November 2023

PurposeIn the digital age, courts need to be able to provide their services faster, more efficiently and less costly. Disruptive technologies like artificial intelligence can transform courtroom services in completely new ways. This study aims to investigate and rank the critical success factors of digital courts.Design/methodology/approachThe literature of digital court and the factors influencing its success have been reviewed and a framework consisting of 26 factors in seven categories was designed. These factors have been ranked using the fuzzy TOPSIS method.FindingsThe results show that the factor of Accessibility to the system had the absolute best precedence, followed by the factors of User satisfaction and Information security. The factor of Political convergence of the government and the judicial system had the lowest priority.Originality/valueThis research guides current movements towards employing transformational technologies, tackling modern challenges and providing new opportunities to enhance the digital journey of the court ecosystem actors.
Leverage and regulatory capital ratios in Japan
Authors: Abbas Faisal , Ali Shoaib 
Published: November 2023

PurposeThis study aims to understand how quickly Japanese banks readjust their capital ratios (leverage, regulatory capital, tier-I capital and common equity) following an economic shock.Design/methodology/approachThis study uses a two-step system GMM framework to test the study's hypotheses using the annual data of Japanese commercial and cooperative banks ranging from 2005 to 2020.FindingsThe findings show that banks adjust their leverage ratio faster than regulatory capital, tier-I capital and common equity ratios. In addition to that, the results reveal that the speed of capital adjustment is higher for commercial banks than for cooperative banks, suggesting higher economic costs and implications for commercial banks. Furthermore, it is worth noting that well-capitalised (under-capitalised) banks tend to prioritise the adjustments to common equity (leverage) before considering the adjustments to leverage (common equity). According to the results, high-liquid (low-liquid) banks alter their regulatory capital and tier-I capital ratios (leverage) more quickly (more slowly) than low-liquid (high-liquid) banks.Practical implicationsThe findings suggest that when formulating and implementing new banking regulations, particularly in assessing and adjusting specific capital requirements under Pillar II of Basel III, management (including bankers, regulators and policymakers) should consider the heterogeneity observed in the rate of capital adjustment across various bank characteristics. Additionally, bank managers should also consider the speed of adjustment when determining optimal half-life and target capital structures.Originality/valueTo the author's knowledge, this study represents a pioneering investigation into the rate of adjustment of capital ratios (leverage, regulatory, tier-I and common equity) within Japan's banking sector. The study employs a comprehensive dataset encompassing both commercial and cooperative banks to facilitate this analysis. A notable contribution to the existing body of literature, this study offers a detailed analysis and emphasises the varying degrees of adjustment in capital ratios. The study also highlights the heterogeneous nature of the adjustment rate in these ratios by categorising the data into well-capitalised, under-capitalised, highly liquid and low-liquid banks.
Development of the internal family systems model: Honoring contributions from family systems therapies
Authors: Brenner Elizabeth G. , Schwartz Richard C. , Becker Carol 
Published: November 2023

AbstractWe describe Richard Schwartz's development of the Internal Family Systems model (IFS) from his position as a Structural/Strategic family therapist. Four decades ago, Schwartz struggled to help clients who exhibited serious risk of harm to self and others. Through a process of inquiry, he began to work with the positive intentions behind his most challenging clients' harmful thoughts and behaviors. He applied foundational ideas from family systems thinking to patterns of internal experiences. As he experimented with ways of applying these ideas, he created an approach to healing. We summarize the IFS model delineating ways a range of family systems theory and practice inform its development and contribute to its best practice. Our purposes are to inform IFS practitioners who are not trained in foundational family systems models as well as to acknowledge the significant contributions family therapy theories made in the development and best practice of the IFS model.
The economic hierarchy, linkage, and directions between the three northeastern provinces of China and Russian Far East
Authors: Xu Shuang , Chu Nanchen , Wu Xiangli 
Published: November 2023

AbstractThe economic hierarchy index, economic linkage model, and economic membership model are used to study the economic hierarchy, linkage, and direction of Northeast China and Russian Far East from 2005 to 2020, using the three northeastern provinces of China and 11 Far East federal subjects of Russia as the research objects. The findings are as follows: (1) There is a major polarization effect between developed affluent economic regions and stagnant isolated backward regions in the economic rankings in the 11 Russian Far East federal subjects from 2005 to 2020. (2) The three northeastern provinces of China have more economic linkages with their near Russian neighbors— the east‐oriented Primorsky Territory, the north‐oriented Amur Region, and the north‐oriented Khabarovsk Territory, than with their farther neighbors— the Chukotka Autonomous Area, Magadan Region, and Kamchatka Territory. (3) From 2005 to 2020, the Primorsky Territory has been serving as the focal point of economic linkages between Russian Far East and Northeast China, showing the expanding outward pattern resembling the concentric circles.
Impact of post‐progression survival in second‐line treatment with molecular target agents for unresectable hepatocellular carcinoma
Authors: Tajiri Kazuto , Muraishi Nozomu , Murayama Aiko , Hayashi Yuka , Yasuda Ichiro 
Published: November 2023

AbstractAimSequential therapies are essential to extend overall survival (OS) in patients with unresectable hepatocellular carcinoma (HCC). Several second‐line treatments with molecular target agents have shown survival benefits. However, the significance of post‐progression survival (PPS) in extending OS in patients with HCC given such treatments remains uncertain.MethodsThrough a systematic review of the literature in the PubMed database, this study investigated the correlation between PPS and OS and that between progression‐free survival (PFS) and OS in patients with HCC given second‐line treatments.ResultsIn total, 3935 patients who had received second‐line treatment with regorafenib, ramucirumab, or cabozantinib, which are approved molecular target agents, were identified. In the patients treated with regorafenib, PPS showed a strong correlation with OS (R2 = 0.729, R = 0.854, p < 0.001) whereas PFS showed a weak correlation (R2 = 0.218, R = 0.467, p = 0.021). In the patients treated with ramucirumab, PPS showed a strong correlation with OS (R2 = 0.800, R = 0.894, p = 0.016) whereas PFS showed a negligible correlation (R2 = 0.020, R = 0.140, p = 0.791). In the patients treated with cabozantinib, PPS showed a strong correlation with OS (R2 = 0.856, R = 0.925, p = 0.003) as did PFS (R2 = 0.946, R = 0.973, p < 0.001).ConclusionsPPS plays a more significant role than PFS in extending OS in patients given second‐line treatment for unresectable HCC. Sequential therapies after disease progression in second‐line treatment are essential to acquire good OS. Maintenance of hepatic reserve function and the patient's general condition is essential during systemic treatments for unresectable HCC.