bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pushing the limits of HiFi assemblies reveals centromere diversity between twoArabidopsis thalianagenomes
Authors: Rabanal Fernando A. , Gräff Maike , Lanz Christa , Fritschi Katrin , Llaca Victor , Lang Michelle , Carbonell-Bejerano Pablo , Henderson Ian , Weigel Detlef 
Published: February 2022

ABSTRACTAlthough long-read sequencing can often enable chromosome-level reconstruction of genomes, it is still unclear how one can routinely obtain gapless assemblies. In the model plantArabidopsis thaliana, other than the reference accession Col-0, all other accessionsde novoassembled with long-reads until now have used PacBio continuous long reads (CLR). Although these assemblies sometimes achieved chromosome-arm level contigs, they inevitably broke near the centromeres, excluding megabases of DNA from analysis in pan-genome projects. Since PacBio high-fidelity (HiFi) reads circumvent the high error rate of CLR technologies, albeit at the expense of read length, we compared a CLR assembly of accession Ey15-2 to HiFi assemblies of the same sample performed by five different assemblers starting from subsampled data sets, allowing us to evaluate the impact of coverage and read length. We found that centromeres and rDNA clusters are responsible for 71% of contig breaks in the CLR scaffolds, while relatively short stretches of GA/TC repeats are at the core of >85% of the unfilled gaps in our best HiFi assemblies. Since the HiFi technology consistently enabled us to reconstruct gapless centromeres and 5S rDNA clusters, we demonstrate the value of the approach by comparing these previously inaccessible regions of the genome between twoA. thalianaaccessions.
Replication-associated inversions are the dominant form of bacterial chromosome structural variation
Authors: D’Iorio Matthew , Dewar Ken 
Published: February 2022

AbstractStructural arrangement of a bacterial chromosome varies widely between closely related species and can result in significant phenotypic outcomes. The appearance of large-scale chromosomal inversions that are symmetric relative to the dnaA gene (usually linked to oriC, the origin of replication) has been previously observed; however, the overall prevalence of replication-associated structural rearrangements (RASRs) in bacteria and their causal mechanisms are currently unknown. The decreased cost of full-length genome sequencing has led to a rapidly growing collection of complete genomes spanning multiple different clades, therefore allowing an opportunity to examine chromosomal inversions in the context of species spanning diverse phylogenetic classifications. Here we systematically identify the locations of large, chromosomal inversions in species with multiple complete sequenced genomes using the Refseq and Genbank NCBI databases to investigate potential mediating biological mechanisms. Out of the 239 species available with 10 or more complete genomes, 206 contained sequences with at least one large (≥50Kb) inversion in their set of within-species sequence comparisons. We observed 73.4% of the 127,161 large inversions were centered at a point within 10% proportionate distance to the annotated dnaA gene, which is often nearby the origin of replication. Inversions offset from the annotated dnaA sequence were generally confirmed to be centered on the actual origin of replication. Equidistant breakpoints from the replication origin and prevalence of flanking repeats provide evidence that the breaks that are formed during the replication process are then repaired to opposing positions. We also found a strong relationship between the later stages of replication and the range in variation of distance from symmetry, suggesting that replication fork arrest may be a mechanistic cause for the asymmetry in some inversions.
Canonical Wnt signaling promotes formation of somatic permeability barrier for proper germ cell differentiation
Authors: Chen Ting-An , Lin Kun-Yang , Yang Shun-Min , Tseng Chen-Yuan , Wang Yu-Ting , Lin Chi-Hung , Luo Lichao , Cai Yu , Hsu Hwei-Jan 
Published: February 2022

AbstractMorphogen-mediated signaling is critical for proper organ development and stem cell function, and well-characterized mechanisms spatiotemporally limit the expression of ligands, receptors, and ligand-binding cell-surface glypicans. Here, we show that in the developing Drosophila ovary, canonical Wnt signaling promotes the formation of somatic escort cells (ECs) and their protrusions, which establish a physical permeability barrier to define morphogen territories for proper germ cell differentiation. The protrusions shield germ cells from Dpp and Wingless morphogens produced by the germline stem cell (GSC) niche and normally only received by GSCs. Genetic disruption of EC protrusions allows GSC progeny to also receive Dpp and Wingless, which subsequently disrupt germ cell differentiation. Our results reveal a role for canonical Wnt signaling in specifying the ovarian somatic cells necessary for germ cell differentiation. Additionally, we demonstrate the morphogen-limiting function of this physical permeability barrier, which may be a common mechanism in other organs across species.
Suggestions for takt production subcontract clauses – a conceptual study
Authors: Keskiniva Kimmo , Saari Arto , Junnonen Juha-Matti 
Published: February 2022

Purpose
This study aims to provide a foundation for the development of subcontracts that suit takt production in construction.

Design/methodology/approach
This is a non-empiric conceptual study, which integrates takt production and general construction literature into new proposals for subcontract clauses suitable for takt production in construction. This study uses literature reviews, from which proposals regarding takt production viable subcontract clauses are conducted via logical reasoning.

Findings
A total of 13 proposals for takt production applicable subcontracts are provided in this study. The proposals emphasize detailed and collaborative planning, suitable payment methods and flexibility for takt plan modification.

Originality/value
Previous takt literature has not properly addressed the development of subcontracts for takt production, despite regular attempts to use subcontracting in takt production. This study aims to aid main contractors to create fair and suitable subcontracts, so that adhering to takt schedules could be more viable in practice. This study also acts as a foundation for further empirical studies regarding the subject.
Performance implication of exploration and exploitation in foreign markets: the role of marketing capability and operation flexibility
Authors: Ju Min , Gao Gerald Yong 
Published: February 2022

PurposeThe purpose of this paper is to examine the performance impact of foreign ventures' exploration and exploitation strategies in emerging markets. Exploration and exploitation represent key strategic choices and have been extensively studied in the context of domestic markets. Yet the implication of such innovation strategies for foreign ventures operating in emerging markets has been under-researched. We aim to investigate whether foreign ventures can realize the value of exploration and exploitation strategies in emerging markets and also the moderating role of marketing capability and operation flexibility to enable the implementation process.Design/methodology/approachThis study adopts the hierarchical moderated regression approach using a sample of foreign ventures operating in high-tech manufacturing industries in China.FindingsThe authors find that both exploration and exploitation have positive effects on firms' financial performance. Marketing capability strengthens the performance impact of exploration, but exhibits no such impact of exploitation. Moreover, operation flexibility positively moderates the effects of both exploration and exploitation on performance.Research limitations/implicationsThis study provides important insights into whether foreign ventures can boost performance through exploration and exploitation strategies in emerging markets as well as the implementation-level factors that can facilitate such positive effects.Originality/valueThe study is novel in revealing the moderating role of marketing capability and operation flexibility in facilitating the performance outcome of exploration and exploitation strategies.
Successful reconfiguration and network evolution within the multinational company
Authors: Valdemarin Stefano , Mayrhofer Ulrike 
Published: February 2022

PurposeThis article aims to contribute to a better understanding of how multinational companies can succeed the reconfiguration of their internal structures. The theoretical framework is based on the concept of reconfiguration as a dynamic capability, the Uppsala evolution model and the business network view.Design/methodology/approachThe authors conducted a case study on the reconfiguration of two vertically-related business units within the Solvay group, a world leader in the chemical industry. The empirical study is based on interviews, observations and secondary data.FindingsThe paper shows how a multinational enterprise can succeed in reorganizing its internal structures to overcome internal liability of outsidership and to be more competitive and profitable. The reconfiguration enabled Solvay to become a fully integrated leader in the polyamide plastics industry.Originality/valueThe paper explains how the internal reorganization has improved the competitiveness and profitability of the integrated business units.
Political sentiment and stock crash risk
Authors: Cao Cathy Xuying , Chen Chongyang 
Published: February 2022

PurposeThis paper examines the relation between political sentiment and future stock price crash risk.Design/methodology/approachThis study employs firm-level political sentiment from earnings conference calls. The empirical analysis applies panel regressions on 40,254 US firm-year observations between 2002 and 2020, controlling for various firm-specific determinants of crash risk and firm-, industry- as well as time-fixed effects.FindingsThe study identifies a negative association between both the level and the change of political sentiment and stock crash risk. Further analysis shows that the predictive power of political sentiment is independent of either non-political sentiment or political risk and remains consistently strong during periods of either high or low economic policy uncertainty. Moreover, the predictive effect of political sentiment is more pronounced for firms with high litigation risk.Research limitations/implicationsThe evidence highlights the important role of political sentiment in predicting stock crash risk. The results are consistent with the signaling hypothesis that managers tend to use their tone in conference calls to convey informative messages on firm outlooks.Practical implicationsThe study provides a recommendation on risk management: soft information such as political and non-political sentiment in earnings conference calls is useful in managing stock crash risk. The study findings also call for careful consideration of social costs, such as stock crash risk, associated with political policies. Ill-conceived policies may lead to market crashes, which can potentially outweigh the upsides of well-meaning political reforms.Originality/valueTo the authors best knowledge, this is the first study to identify the effect of time-varying firm-level political sentiment conveyed in conference calls on stock price crash.
The impact of COVID-19 pandemic on earnings management and the value relevance of earnings: US evidence
Authors: Liu Guoping , Sun Jerry 
Published: February 2022

Purpose
The purpose of this study is to examine whether the COVID-19 pandemic has affected earnings management and the value relevance of earnings in the USA.

Design/methodology/approach
Discretionary accruals, the explanatory power and slope coefficient of earnings are compared between 2019 (prepandemic year) and 2020 (pandemic year). Univariate and regression analyses are performed.

Findings
There was a significant decline in discretionary accruals from 2019 to 2020, suggesting that firms engaged in more income-decreasing earnings management to take a big bath in reporting earnings in the pandemic year. Meanwhile, the explanatory power and slope coefficient of earnings both were lower in 2020 than in 2019, consistent with the notion that the pandemic has impaired the value relevance of earnings.

Originality/value
This study explores the consequences of the pandemic from accounting perspective. It also enriches accounting research on economic crises.
Dead-end jobs or steppingstones? Precarious work in Albania
Authors: Drishti Elvisa , Carmichael Fiona 
Published: February 2022

Purpose This study asks whether lower quality forms of employment lead to career transitions into higher quality forms of employment acting as steppingstones, or bridges or, whether instead they lead to dead-ends, or traps, in which workers move between unstable jobs with low prospects for upward mobility and unemployment.Design/methodology/approach This study uses a unique longitudinal dataset recording monthly employment states over 3 years for 373 individuals in the Albanian city of Shkoder. The analysis uses sequence and regression analysis to investigate whether people employed in lower quality, more precarious jobs remain in these kinds of jobs or instead are able to transition into higher quality, permanent and full-time employment.Findings In line with previous evidence for the region, the analysis confirms the precarization of many working lives particularly for women, young people and those with lower educational attainment. This evidence is more supportive of the dead-end hypothesis than the idea that a lower quality job can be a steppingstone into a better job.Originality/value This study contributes to the limited knowledge of labour market functioning in developing post-socialist Western Balkans countries. Recent flexicurity policies have generated an increased prevalence of more precarious employment arrangements in Albania. This investigation addresses previous research limitations regarding point-in-time transitions and unobserved heterogeneity using retrospective longitudinal data and controlling for personality traits.
Salvage radiotherapy following HiFU: An institutional series and literature review
Authors: Mesci Aruz , Gouran‐Savadkoohi Mohammad , Ribeiro Derek , Dayes Ian , Lukka Himanshu , Schnarr Kara , Quan Kimmen , Goldberg Mira , Hallock Abhirami , Tsakiridis Theodoros 
Published: February 2022

AbstractIntroductionAlgorithms for the treatment of prostate cancer (PrCa) rely on risk grouping, and those who fall into low (LR) and favourable intermediate risk (FIR) categories have multiple options for treatment. High‐intensity focused ultrasound (HiFU) is a local treatment modality that uses ultrasound waves to ablate prostate cancer. In case of treatment failure, optimal salvage modality after HiFU remains unclear.MethodsHere, we describe a retrospective review of our regional cancer database for men who underwent salvage radiotherapy after failure of HiFU treatment for prostate cancer. Oncologic and toxicity outcomes of the men identified in our database are discussed.ResultsWe identified 14 men in our regional database who received salvage radiotherapy (70–74 Gy with or without androgen deprivation therapy (ADT) after primary HiFU, in the period of 2009–2017. No cases of any grade 3 or higher toxicity were observed. In our cohort, 50% (7/14) of patients developed secondary biochemical failure at a median follow‐up of 54 months post‐radiotherapy, with a mean time to biochemical failure of 39 months.We compare our data to other available reports to date consisting mostly of small, non‐randomized studies. Our biochemical control rates are noticeably lower compared with those reported by other studies but our length of follow‐up is longer, compared with other studies.ConclusionThe available data to date suggest that salvage radiotherapy after HiFU failure is well‐tolerated albeit with only modest efficacy.
Impairment of a cyanobacterial glycosyltransferase that modifies a pilin results in biofilm development
Authors: Suban Shiran , Sendersky Eleonora , Golden Susan S. , Schwarz Rakefet 
Published: February 2022

SummaryA biofilm inhibiting mechanism operates in the cyanobacterium Synechococcus elongatus. Here, we demonstrate that the glycosyltransferase homologue, Ogt, participates in the inhibitory process – inactivation of ogt results in robust biofilm formation. Furthermore, a mutational approach shows requirement of the glycosyltransferase activity for biofilm inhibition. This enzyme is necessary for glycosylation of the pilus subunit and for adequate pilus formation. In contrast to wild‐type culture in which most cells exhibit several pili, only 25% of the mutant cells are piliated, half of which possess a single pilus. In spite of this poor piliation, natural DNA competence was similar to that of wild‐type; therefore, we propose that the unglycosylated pili facilitate DNA transformation. Additionally, conditioned medium from wild‐type culture, which contains a biofilm inhibiting substance(s), only partially blocks biofilm development by the ogt‐mutant. Thus, we suggest that inactivation of ogt affects multiple processes including production or secretion of the inhibitor as well as the ability to sense or respond to it.
Surviving sepsis campaign: International guidelines for management of sepsis and septic shock in adults 2021 ‐ endorsement by the Scandinavian society of anaesthesiology and intensive care medicine
Authors: Rehn Marius , Chew Michelle S. , Olkkola Klaus T. , Ingi Sigurðsson Martin , Yli‐Hankala Arvi , Hylander Møller Morten 
Published: February 2022

AbstractThe Clinical Practice Committee of the Scandinavian Society of Anaesthesiology and Intensive Care Medicine endorses the clinical practice guideline Surviving sepsis campaign: international guidelines for management of sepsis and septic shock 2021. The guideline serves as a useful bedside decision aid for clinicians managing adults with suspected and confirmed septic shock and sepsis‐associated organ dysfunction.
Caesarean section following antepartum stillbirth in Western Australia 2010–2015: A population‐based study
Authors: Bailey Helen D. , Adane Akilew A. , White Scott W. , Farrant Brad M. , Shepherd Carrington C.J. 
Published: February 2022

BackgroundThere is scant literature about antepartum stillbirth management but guidelines usually recommend reserving caesarean sections for exceptional circumstances. However, little is known about caesarean section rates following antepartum stillbirth in Australia.AimsWe aimed to describe the onset of labour, mode of birth, and use of analgesia and anaesthesia following antepartum stillbirth and to identify factors associated with caesarean section.Material and MethodsIn this retrospective cohort study, we used a population‐based dataset of all singleton antepartum stillbirths ≥20 weeks gestation in Western Australia between 2010‐2015. The overall, primary and repeat caesarean section rates for antepartum stillbirths were calculated and multivariable Poisson regression analyses were performed to identify associated factors, and to calculate relative risks (RRs) and 95% confidence intervals (CIs).ResultsThis study included 634 antepartum stillbirths. Labour was spontaneous for 134 (21.1%), induced for 457 (72.1%), and 43 (6.8%) had a prelabour caesarean section. The overall, primary and repeat caesarean section rates were 8.5%, 4.6% and 23.0% respectively and increased with gestation (P trends all <0.01). Other factors associated with an increased caesarean section risk included: any placenta praevia or placental abruption, birth at a metropolitan private hospital, large‐for‐gestational‐age birthweight, and any maternal chronic condition. During labour, the most frequently used types of analgesia were systemic narcotics (46.0%) and regional blocks (34.7%) while among those who had a caesarean section, 40.7% had a general anaesthetic.ConclusionsIn Western Australia between 2010–2015, the caesarean section rates among women with antepartum stillbirths were low, in line with current guidelines.
Does governance matter for the public debt–inflation relationship in developed countries? Panel quantile regression approach
Authors: Nguyen Van Bon 
Published: February 2022

AbstractSimilar to most countries in the world, developed countries also run the economy in the direction of fiscal deficits. Borrowing is one of the solutions for budget deficits, which causes public debt to increase in these countries. Does high public debt increase inflation, and what is the role of governance in the public debt–inflation relationship? For these research questions, this study uses a panel quantile regression approach, the two‐step GMM (Generalized Method of Moments) Arellano–Bond estimator, and the FE‐IV (Fixed‐Effect Instrumental Variable) estimator to investigate empirically the effects of public debt, governance, and their interaction on inflation for a group of 34 developed countries from 2002 to 2019. The results show that public debt and governance reduce inflation, but their interaction stimulates it. These findings suggest some important policy implications on better governance for governments in developed countries to keep inflation at a low rate.
How Students’ Big Five personality traits manifest in perceived social loafing behavior
Authors: Sherif Dalia M. 
Published: February 2022

BackgroundSocial loafing (SL) has a detrimental impact on cooperative learning. SL dysfunctionalities are causing more faculty to avoid assigning group projects as part of their course work.AimsThis qualitative case study examines how students’ personalities are expressed in social loafers’ behavior during university‐level group assignments at a Texas university. The case study added further depth and breadth to current literature on SL in cooperative learning by exploring the perpetrator’s personality expressions.Sample(s)Ten faculty members were interviewed, 32 students were surveyed, and 10 loafers were identified and self‐assessed.MethodsA qualitative case study was used to provide in‐depth investigation of Big Five personality in SL behavior.ResultsThe faculty interviews and students’ surveys revealed that Openness to Experience and Conscientiousness were not expressed in SL behavior for university‐level group assignments assessed by four IPIP facets. Openness to Experience (values, ideas, actions, and fantasy) was not expressed. Faculty and students indicated that loafers were not curious, barely prepared, with very short attention spans after which they get lost. Social loafers showed no originality, no active imagination, and no deep thinking.Conscientiousness (achievement striving, dutifulness, competence, and order) was not expressed. For Extraversion, Agreeableness, and Neuroticism, some facets were expressed, and others were withheld.ConclusionThe results of this study provide faculty with a multifaceted understanding of students’ personality traits to better guide their group interaction and cooperative learning.