bluuebunny/crossref_metadata_2025_split huggingface dataset:
Re-evaluation of the phylogenetic diversity and global distribution of the genusCandidatusAccumulibacter
Authors: Petriglieri Francesca , Singleton Caitlin , Kondrotaite Zivile , Dueholm Morten K. D. , McDaniel Elizabeth A. , McMahon Katherine D. , Nielsen Per H. 
Published: December 2021

AbstractCandidatusAccumulibacter was the first microorganism identified as a polyphosphate-accumulating organism (PAO), important for phosphorus removal from wastewater. This genus is diverse, and the current phylogeny and taxonomic framework appears complicated, with the majority of publicly available genomes classified as “CandidatusAccumulibacter phosphatis”, despite notable phylogenetic divergence. Theppk1marker gene allows for a finer scale differentiation into different “types” and “clades”, nevertheless taxonomic assignments remain confusing and inconsistent across studies. Therefore, a comprehensive re-evaluation is needed to establish a common understanding of this genus, both in terms of naming and basic conserved physiological traits. Here, we provide this re-assessment using a comparison of genome,ppk1, and 16S rRNA gene-based approaches from comprehensive datasets. We identified 15 novel species, along with the well-knownCa. A. phosphatis,Ca. A. deltensis andCa. A. aalborgensis. To compare the speciesin situ, we designed new species-specific FISH probes and revealed their morphology and arrangement in activated sludge. Based on the MiDAS global survey,Ca. Accumulibacter species were widespread in WWTPs with phosphorus removal, indicating the process design as a major driver for their abundance. Genome mining for PAO related pathways and FISH-Raman microspectroscopy confirmed the potential for the PAO metabolism in allCa. Accumulibacter species, with detectionin situof the typical PAO storage polymers. Genome annotation further revealed fine-scale differences in the nitrate/nitrite reduction pathways. This provides insights into the niche differentiation of these lineages, potentially explaining their coexistence in the same ecosystem while contributing to overall phosphorus and nitrogen removal.ImportanceCandidatusAccumulibacter is the most studied PAO organism, with a primary role in biological nutrient removal. However, the species-level taxonomy of this lineage is convoluted due to the use of different phylogenetic markers or genome sequencing. Here, we redefined the phylogeny of these organisms, proposing a comprehensive approach which could be used to address the classification of other diverse and uncultivated lineages. Using genome-resolved phylogeny, compared to 16S rRNA gene- and other phylogenetic markers phylogeny, we obtained a higher resolution taxonomy and established a common understanding of this genus. Furthermore, genome mining of gene and pathways of interest, validatedin situby application of a new set of FISH probes and Raman micromicrospectroscopy, provided additional high-resolution metabolic insights into these organisms.
Single-cell Senseless protein analysis reveals metastable states during the transition to a sensory organ fate
Authors: Giri Ritika , Brady Shannon , Papadopoulos Dimitrios K. , Carthew Richard W. 
Published: December 2021

ABSTRACTCell fate decisions can be envisioned as bifurcating dynamical systems, and the decision that Drosophila cells make during sensory organ differentiation has been described as such. We extended these studies by focusing on the Senseless protein, which orchestrates sensory cell fate transitions. Wing cells contain intermediate Senseless numbers prior to their fate transition, after which they express much greater numbers of Senseless molecules as they differentiate. However, the dynamics are inconsistent with it being a simple bistable system. Cells with intermediate Senseless are best modeled as residing in four discrete states, each with a distinct protein number and occupying a specific region of the tissue. Although the states are stable over time, the number of molecules in each state vary with time. The fold-change in molecule number between adjacent states is invariant and robust to absolute protein number variation. Thus, cells transitioning to sensory fates exhibit metastability with relativistic properties.
A Modified TurboID Approach Identifies Tissue-Specific Centriolar Components InC. elegans
Authors: Holzer Elisabeth , Rumpf-Kienzl Cornelia , Falk Sebastian , Dammermann Alexander 
Published: December 2021

ABSTRACTProximity-dependent labeling approaches such as BioID have been a great boon to studies of protein-protein interactions in the context of cytoskeletal structures such as centrosomes which are poorly amenable to traditional biochemical approaches like immunoprecipitation and tandem affinity purification. Yet, these methods have so far not been applied extensively to invertebrate experimental models such asC. elegansgiven the long labeling times required for the original promiscuous biotin ligase variant BirA*. Here, we show that the recently developed variant TurboID successfully probes the interactomes of both stably associated (SPD-5) and dynamically localized (PLK-1) centrosomal components. We further develop an indirect proximity labeling method employing a GFP nanobody-TurboID fusion, which allows the identification of protein interactors in a tissue-specific manner in the context of the whole animal. Critically, this approach utilizes available endogenous GFP fusions, avoiding the need to generate multiple additional strains for each target protein and the potential complications associated with overexpressing the protein from transgenes. Using this method, we identify homologs of two highly conserved centriolar components, Cep97 and Bld10/Cep135, which are present in various somatic tissues of the worm. Surprisingly, neither protein is expressed in early embryos, likely explaining why these proteins have escaped attention until now. Our work expands the experimental repertoire forC. elegansand opens the door for further studies of tissue-specific variation in centrosome architecture.
PlantRNA 2.0: an updated database dedicated to tRNAs of photosynthetic eukaryotes
Authors: Cognat Valérie , Pawlak Gael , Pflieger David , Drouard Laurence 
Published: December 2021

ABSTRACTPlantRNA (http://plantrna.ibmp.cnrs.fr/) is a comprehensive database of transfer RNA (tRNA) gene sequences retrieved from fully annotated nuclear, plastidial and mitochondrial genomes of photosynthetic organisms. In the first release (PlantRNA 1.0), tRNA genes from 11 organisms were annotated. In this second version, the annotation was implemented to 51 photosynthetic species covering the whole phylogenetic tree of photosynthetic organisms, from the most basal group of Archeplastida, the glaucophyte Cyanophora paradoxa, to various land plants. Transfer RNA genes from lower photosynthetic organisms such as streptophyte algae or lycophytes as well as extremophile photosynthetic species such as Eutrema parvulum were incorporated in the database. As a whole, circa 37 000 tRNA genes were accurately annotated. In the frame of the tRNA genes annotation from the genome of the Rhodophyte Chondrus crispus, non-canonical splicing sites in the D- or T- regions of tRNA molecules were identified and experimentally validated. As for PlantRNA 1.0, comprehensive biological information including 5’- and 3’-flanking sequences, A and B box sequences, region of transcription initiation and poly(T) transcription termination stretches, tRNA intron sequences and tRNA mitochondrial import are included.
Extending the boundaries of psychological ownership research: measurement, outcomes, cultural moderators
Authors: Renz Franziska M. , Posthuma Richard , Smith Eric 
Published: December 2021

PurposePsychological ownership (PO) theory and extended self theory explain why someone feels like the owner of his/her job or organization. Yet, there is limited prior research examining whether PO differs as an individual versus collective phenomenon, and in different cultural contexts. The authors extend this literature by examining the dimensionality of PO, multiple outcomes and cultural values as boundary conditions.Design/methodology/approachData from surveys of 331 supervisors from Mexico and the US were collected to examine the relationships between the theorized constructs. The authors apply two-stage least squares (2SLS) regression analysis to alleviate endogeneity concerns and produce robust results.FindingsBoth individual and collective PO (IPO and CPO) are positively associated with organization-based self-esteem (OBSE) and a new outcome, paternalistic leadership behavior. Cultural values are significant moderators with an individualistic orientation enhancing and a power distance orientation attenuating these relationships.Originality/valueThis study extends PO theory and extended self theory by investigating whether IPO and CPO have different outcomes considering contextual differences in cultural values. Additionally, the authors capture the frequency of paternalism instead of its mere occurrence.
The nasty face of the liability of foreignness: MNCs and rent extraction
Authors: Kozan Asli 
Published: December 2021

PurposeThis study aims to clarify the factors that act as a buffer to rent extraction from multi-national corporations (MNCs) in exchange relationships with the host country’s political actors.Design/methodology/approachThis study proposes a conceptual model of the factors that determine rent extraction by host country political actors from MNCs. The model identifies the sources of power the MNC can use to alleviate the power imbalance relative to the political actor to decrease rent extraction. Additionally, it identifies the factors that constrain the power-advantaged political actor, thus moderating the relationship between power imbalance and rent extraction.FindingsThis conceptual paper’s propositions remain for future empirical validation.Originality/valueThis study integrates insights from the international business literature and resource dependence theory (RDT) to identify the determinants of firm-specific rent extraction risk for MNCs. First, the model sheds light on the heterogeneity among MNCs in their susceptibility to rent extraction and their ability to manage their liability of foreignness in the host country. Second, by integrating the horizontal and vertical distribution of power in the political environment to analyze the power-dependence relationship between the MNC and host country political actors, the framework addresses a shortcoming of RDT and accounts for the dynamics of the external environment for MNCs managing their dependencies. This study also provides a basis for discussing the rent extraction MNCs face worldwide and lays the foundation for future empirical works.
Migrant’s library services: a theoretical and empirical study in Spain with guidelines for their creation
Authors: Serrano Pérez Luis , Faba-Pérez Cristina 
Published: December 2021

Purpose
The purpose of this research study was to seek new forms of public libraries helping with the integration of migrants. It comprises a comprehensive and up-to-date bibliographic review and an empirical study involving the librarians and native and migrant users of public libraries in Spain leading to the design of guidelines for library services targeted at migrant users that can help foster the integration of this group of the population.

Design/methodology/approach
The bibliographic review analyses studies of whether migrant users see the public library as a place of meeting and interchange as well as a fundamental institution providing them with services, meeting their information requirements and offering them challenges and projects. The empirical investigation contrasts this theoretical information by administering three questionnaires (one for librarians, one for native users and one for migrant users, with a total of 45 items) focused on the relationship between public libraries and migration. A total of 20 public libraries over the territory of Spain were selected in accordance with diverse criteria, and a total of 233 completed questionnaires were collected.

Findings
The main results of the empirical research indicate that the greatest proportion of migrant users go to Spain’s public libraries on the recommendation of friends and/or relatives. They use them mainly as a place of study, visiting them at least twice a week, even though the representation of collections and specific services for this group is very sparse (only 5% of the collection of the libraries analysed are in a foreign language). On the other hand, the satisfaction expressed towards both the general services of the libraries and the help provided by their librarians is scored highly, getting mean scores of 4.45 and 4.40 out of 5, respectively.

Originality/value
This work not only includes an exhaustive bibliographic review of the relationship between public libraries and migrant users and an empirical investigation carried out in Spain with librarians, native users and migrant users, but also presents a decalogue of guidelines for the design of a range of services focused on the specific needs of the migrant population, thus favouring their integration in the host country.
Contact fatigue life prediction of rolling bearing considering machined surface integrity
Authors: Cui Li , Su Yin 
Published: December 2021

Purpose
Rolling bearings often cause engineering accidents due to early fatigue failure. The study of early fatigue failure mechanism and fatigue life prediction does not consider the integrity of the bearing surface. The purpose of this paper is to find new rolling contact fatigue (RCF) life model of rolling bearing.

Design/methodology/approach
An elastic-plastic finite element (FE) fatigue damage accumulation model based on continuous damage mechanics is established. Surface roughness, surface residual stress and surface hardness of bearing rollers are considered. The fatigue damage and cumulative plastic strain during RCF process are obtained. Mechanism of early fatigue failure of the bearing is studied. RCF life of the bearing under different surface roughness, hardness and residual stress is predicted.

Findings
To obtain a more accurate calculation result of bearing fatigue life, the bearing surface integrity parameters should be considered and the elastic-plastic FE fatigue damage accumulation model should be used. There exist the optimal surface parameters corresponding to the maximum RCF life.

Originality/value
The elastic-plastic FE fatigue damage accumulation model can be used to obtain the optimized surface integrity parameters in the design stage of bearing and is helpful for promote the development of RCF theory of rolling bearing.
Representation and the problem of bibliographic imagination on Wikipedia
Authors: Luyt Brendan 
Published: December 2021

PurposeThe astonishing thing about Wikipedia is that despite the way it is produced, the product is as good as it is and not far worse. But this is no reason for complacency. As others have documented, Wikipedia has representational blind spots, produced by the nature of its editorial community and their discursive conventions. This article wishes to look at the potential effect of sources on certain of these blind spots.Design/methodology/approachThe author used an extended example, the Wikipedia article on the Philippine–American War, to illustrate the unfortunate effects that accompany a lack of attention to the kind of sources used to produce narratives for the online encyclopaedia. The Philippine–American War article was chosen because of its importance to American history. The war brought to the fore a debate over the future of the USA and the legitimacy of a republic acquiring overseas colonies. It remains controversial today, making it essential that its representation on Wikipedia is soundly constructed.FindingsInattention to sources (a lack of bibliographical imagination) produces representational anomalies. Certain sources are privileged when they should not be and others are ignored or considered as sub-standard. Overall, the epistemological boundaries of the article in terms of what the editorial community considers reliable and what the community of scholars producing knowledge about the war think as reliable do not overlap to the extent that they should. The resulting narrative is therefore less rich than it otherwise could be.Originality/valueWhile there exists a growing literature on the representational blind spots of Wikipedia (gender, class, geographical region and so on), the focus has been on the composition of the demographics of the editorial community. But equally important to the problem of representation are the sources used by that community. Much literature has been written that seeks to portray the social world of the marginalized, but it is not used on Wikipedia, despite it easily meeting the criteria for reliability set by the Wikipedia community. This is a tragic oversight that makes Wikipedia's aim to be a repository for the knowledge of the world, a laudable goal to strive for, even if in reality unobtainable, even harder to achieve than ever.
The quality continuum: perceptions of institutional accreditation
Authors: Hoare Alana , Goad Pamela 
Published: December 2021

PurposeAcademics and administrators frequently lament the bureaucracy in higher education, which diverts attention from teaching and research. Heightened monitoring of institutions as a result of dominant neoliberal ideologies shapes perceptions of accreditation as a bureaucratic burden rather than a value-added tool for continuous quality improvement. This paper aims to identify factors that positively and negatively impact a culture of quality in North American accredited postsecondary institutions to address issues of equity and inform policy changes that are relevant to community needs.Design/methodology/approachAcademics’ and administrators’ perceptions of accreditation processes are explored through an interpretivist mixed-methods study that combined focus group and survey results from over 200 participants representative of four-year private and four- and two-year public institutions and tribal colleges in North America.FindingsFindings suggest that a utilitarian and exclusionary mindset perpetuated by neoliberal logics restricts participatory decision-making processes in postsecondary institutions. Furthermore, the research identified a noticeable gap between those who are invited to participate in accreditation processes and those who contribute to decision-making. This lack of inclusive governance inhibits the ability of institutions to respond appropriately to the needs of its community.Originality/valueThe scope of the study and prioritization of qualitative data offers a comprehensive picture of academics’ and administrators’ perceptions and positions them as the experts in their own learning and development. Through participant narratives, strategies for increasing the value of quality assurance processes are illuminated. As a result, the study participants become the change agents who provide the solutions for ameliorating academics’ and administrators’ resistance to quality assurance.
2021 Asia‐Pacific League of Associations for Rheumatology clinical practice guideline for treatment of gout
Authors: Lorenzo Jose Paulo P. , Sollano Ma. Hanna Monica Z. , Salido Evelyn O. , Li‐Yu Julie , Tankeh‐Torres Sandra A. , Wulansari Manuaba Ida Ayu Ratih , Rahman Md Mujibur , Paul Binoy J. , Mok Mo Yin , De Silva Monika , Padhan Prasanta , Lim Ai Lee , Marcial Melvin , Vicera Jennifer Jeanne , Haq Syed Atiqul , Salman Sami , Liyanage Chiranthi K. , Keen Helen I. , Yew Kuang Cheng , Wei James Cheng‐Chung , Hellmi Rakhma Yanti , Chan Charlie E. , Louthrenoo Worawit 
Published: December 2021

AbstractBackgroundGout is the most prevalent inflammatory arthritis in the Asia‐Pacific region and worldwide. This clinical practice guideline (CPG) aims to provide recommendations based on systematically obtained evidence and values and preferences tailored to the unique needs of patients with gout and hyperuricemia in Asia, Australasia, and the Middle East. The target users of these guidelines are general practitioners and specialists, including rheumatologists, in these regions.MethodsRelevant clinical questions were formulated by the Steering Committee. Systematic reviews of evidence were done, and certainty of evidence was assessed using Grading of Recommendations Assessment, Development and Evaluation methodology. A multi‐sectoral consensus panel formulated the final recommendations.ResultsThe Asia‐Pacific League of Associations for Rheumatology Task Force developed this CPG for treatment of gout with 3 overarching principles and 22 recommendation statements that covered the treatment of asymptomatic hyperuricemia (2 statements), treatment of acute gout (4 statements), prophylaxis against gout flare when initiating urate‐lowering therapy (3 statements), urate‐lowering therapy (3 statements), treatment of chronic tophaceous gout (2 statements), treatment of complicated gout and non‐responders (2 statements), treatment of gout with moderate to severe renal impairment (1 statement), and non‐pharmacologic interventions (5 statements).ConclusionRecommendations for clinically relevant scenarios in the management of gout were formulated to guide physicians in administering individualized care.
Dissecting the IL‐6 pathway in cardiometabolic disease: A Mendelian randomization study on both IL6 and IL6R
Authors: Cupido Arjen J. , Asselbergs Folkert W. , Natarajan Pradeep ,   CHARGE Inflammation Working Group, Ridker Paul M. , Hovingh G. Kees , Schmidt A. Floriaan 
Published: December 2021

AimsChronic inflammation is a risk factor for cardiovascular disease (CVD). IL‐6 signalling perturbation through IL‐6 or IL‐6R blockade may have potential benefit on cardiovascular risk. It is unknown whether targeting either IL‐6 or IL‐6 receptor may result in similar effects on CVD and adverse events. We compared the anticipated effects of targeting IL‐6 and IL‐6 receptor on cardiometabolic risk and potential side effects.MethodsWe constructed four instruments: two main instruments with genetic variants in the IL6 and IL6R loci weighted for their association with CRP, and two after firstly filtering variants for their association with IL‐6 or IL‐6R expression. Analyses were performed for coronary artery disease (CAD), ischemic stroke, atrial fibrillation (AF), heart failure, type 2 diabetes (T2D), rheumatoid arthritis (RA), infection endpoints, and quantitative haematological, metabolic and anthropometric parameters.ResultsA 1 mg/L lower CRP by the IL6 instrument was associated with lower CAD (odds ratio [OR] 0.86, 95% confidence interval [CI] 0.77;0.96), AF and T2D risk. A 1 mg/L lower CRP by the IL6R instrument was associated with lower CAD (OR 0.90, 95% CI 0.86;0.95), any stroke and ischemic stroke, AF, RA risk and higher pneumonia risk. The eQTL‐filtered results were in concordance with the main results, but with wider confidence intervals.ConclusionsIL‐6 signalling perturbation by either IL6 or IL6R genetic instruments is associated with a similar risk reduction for multiple cardiometabolic diseases, suggesting that both IL‐6 and IL‐6R are potential therapeutic targets to lower CVD. Moreover, IL‐6 rather than IL‐6R inhibition might have a more favourable pneumonia risk.