bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evolutionary conservation of A/T-ending codons reflects co-regulation of expression and complex formation
Authors: Benisty Hannah , Hernandez-Alias Xavier , Weber Marc , Anglada-Girotto Miquel , Mantica Federica , Radusky Leandro , Senger Gökçe , Weghorn Donate , Irimia Manuel , Schaefer Martin H. , Serrano Luis 
Published: January 2022

AbstractBackgroundIn a wide variety of organisms, synonymous codons are used with different frequencies, a phenomenon known as codon bias that plays an important role in determining expression levels. However, the importance of codon bias to facilitate the simultaneous turnover of thousands of protein-coding transcripts to bring about phenotypic changes in cellular programs such as development, has not yet been investigated in detail.ResultsHere, we discover that genes with A/T-ending codon preferences are expressed coordinately and display a high codon conservation in mammals. This feature is not observed in genes enriched in G/C-ending codons. A paradigmatic case of this phenomenon is KRAS, from the RAS family, an A/T-rich gene with a high codon conservation (95%) in comparison to HRAS (76%). Also, we find that genes with similar codon composition are more likely to be part of the same protein complex, and that genes with A/T-ending codons are more prone to form protein complexes than those rich in G/C. The codon preferences of genes with A/T-ending codons are conserved among vertebrates. We propose that codon conservation, a feature of expression-coordinated transcripts, is linked to the high expression variation and coordination of tRNA isoacceptors reading A/T-ending codons.ConclusionsOur data indicate that cells exploit A/T-ending codons to generate coordinated, fine-tuned changes of protein-coding transcripts. We suggest that this orchestration contributes to tissue-specific and ontogenetic-specific expression, which can facilitate, for instance, timely protein complex formation.
A deep learning pipeline for segmentation of Proteus mirabilis colony patterns
Authors: Doshi Anjali , Shaw Marian , Tonea Ruxandra , Minyety Rosalía , Moon Soonhee , Laine Andrew , Guo Jia , Danino Tal 
Published: January 2022

ABSTRACTThe motility mechanisms of microorganisms are critical virulence factors, enabling their spread and survival during infection. Motility is frequently characterized by qualitative analysis of macroscopic colonies, yet the standard quantification method has mainly been limited to manual measurement. Recent studies have applied deep learning for classification and segmentation of specific microbial species in microscopic images, but less work has focused on macroscopic colony analysis. Here, we advance computational tools for analyzing colonies of Proteus mirabilis, a bacterium that produces a macroscopic bullseye-like pattern via periodic swarming, a process implicated in its virulence. We present a dual-task pipeline for segmenting (1) the macroscopic colony including faint outer swarm rings, and (2) internal ring boundaries, unique features of oscillatory swarming. Our convolutional neural network for patch-based colony segmentation and U-Net with a VGG-11 encoder for ring boundary segmentation achieved test Dice scores of 93.28% and 83.24%, respectively. The predicted masks at times improved on the ground truths from our automated annotation algorithms. We demonstrate how application of our pipeline to a typical swarming assay enables ease of colony analysis and precise measurements of more complex pattern features than those which have been historically quantified.
YAP restricts renal inflammation and mitigates kidney damage in nephronothisis related kidney disease
Authors: Ferri Giulia , Goffette Valentine , Porée Esther , Braeg Simone , Carvalho Shana , Quatredeniers Marceau , Kuehn E. Wolfgang , Saunier Sophie , Viau Amandine 
Published: January 2022

ABSTRACTNephronophthisis (NPH) is an orphan recessive kidney disease mostly caused by mutations in NPHP1 and 20 other genes encoding proteins that localize to primary cilia. To date the pathways linking altered primary cilia function to progressive kidney scarring in NPH remain poorly defined and therapeutic options allowing NPH patients to escape end-stage kidney disease are lacking.Distinct proteins mutated in NPH interact with components of the Hippo pathway, an important regulator of cell fate. YAP (Yes-associated protein) overactivation has been shown to induce renal scarring while YAP inhibition showed protective effect in kidney diseases unrelated to NPH. Yet, the therapeutic potential of YAP inhibition in NPH has not been formerly assessed.Here we studied the impact of both genetic and pharmacologic YAP inhibition on the NPH-like phenotype caused by a bi-allelic mutation of Lkb1, a ciliary kinase interacting with NPHP1. Contrary to non NPH renal disease, our results reveal an unexpected protective role of YAP in Lkb1 mutant kidneys. Indeed, YAP genetic disruption drastically increase kidney disease burden in Lkb1 deficient mice, while pharmacologic inhibition of YAP failed to improve their phenotype.Collectively these results suggest that YAP inhibition is not a valid therapeutic strategy in NPH and suggest that LKB1 and YAP are parallel negative regulators of a yet uncharacterized pathway detrimental for kidney health.
Out of the blue: the independent activity of sulfur-oxidizers and diatoms mediate the sudden color shift of a tropical river
Authors: Arce-Rodríguez Alejandro , Libby Eduardo , Castellón Erick , Avendaño Roberto , Cambronero Juan Carlos , Vargas Maribel , Pieper Dietmar H. , Bertilsson Stefan , Chavarría Max , Puente-Sánchez Fernando 
Published: January 2022

AbstractRío Celeste (“Sky-Blue River”) is a river located in the Tenorio National Park (Costa Rica) that has become an important hotspot for eco-tourism due to its striking sky-blue color. A previous study suggested that this color is not caused by dissolved chemical species, but by precipitation of lightscattering aluminosilicate particles at the mixing point of two colorless streams, the acidic Quebrada Agria and the neutral Río Buenavista. We now present microbiological information on Río Celeste and its two tributaries, as well as a more detailed characterization of the particles that occur at the mixing point. Our results overturn the previous belief that the light scattering particles are formed by the aggregation of smaller particles coming from Río Buenavista, and rather point to chemical formation of hydroxyaluminosilicate colloids with Quebrada Agria as the main contributor to the phenomenon, with Río Buenavista acting as a secondary source of silica to the reaction. We also show how the sky-blue color of Río Celeste arises from the tight interaction between chemical and biological processes. Sulfur-oxidizing bacteria generate an acidic environment in Quebrada Agria, which in turn cause dissolution and mobilization of aluminum and other metals, while in Río Buenavista the growth of diatoms transforms dissolved silicon into colloidal biogenic forms. The local interaction between these two well-known biological activities gives rise to the unique Río Celeste phenomenon, in what constitutes a textbook example of emergent behavior in environmental microbiology.
Meta-analysis of the black soldier fly (Hermetia illucens) microbiota based on 16S rRNA gene amplicon sequencing
Authors: IJdema Freek , De Smet Jeroen , Crauwels Sam , Lievens Bart , Van Campenhout Leen 
Published: January 2022

AbstractBlack soldier fly larvae (BSFL) belong to the most widely reared insect species as an alternative protein source at industrial scale. Bacteria in the larval gut can provide benefits for the animal, though some bacteria can also be pathogenic for the insect. Accurate characterization of the BSFL microbiota is important for the production of BSFL in terms of yield and microbiological safety. In this study, 16S ribosomal RNA gene sequence data sets from 11 studies were re-analysed to gain better insights in the BSFL gut microbiota, potential factors that influence their composition, and differences between the gut and the whole larvae microbiota. A core gut microbiota was found consisting of members ofEnterococcus, Klebsiella, Morganella, Providencia, andScrofimicrobium.Further, the factors “Study”, “Age” and “Feed” significantly affected the microbiota gut composition. When compared to whole larvae, a significantly lower number of observed zero-radius Operational Taxonomic Units and a lower diversity was found for gut samples, suggesting that the larvae harboured additional microbes on their cuticle or in the insect body. Universal choices in insect sample type, primer selection and bio-informatics can strengthen future meta-analyses and improve our understanding of the BSFL gut microbiota towards the optimization of insect production.
In vivo inactivation of RAD51-mediated homologous recombination leads to premature aging, but not to tumorigenesis
Authors: Matos-Rodrigues Gabriel , Barroca Vilma , Muhammad Ali-Akbar , Allouch Awatef , Koundrioukoff Stephane , Lewandowski Daniel , Despras Emmanuelle , Guirouilh-Barbat Josée , Frappart Lucien , Kannouche Patricia , Dupaigne Pauline , Cam Eric Le , Perfettini Jean-Luc , Romeo Paul-Henri , Debatisse Michelle , Jasin Maria , Livera Gabriel , Martini Emmanuelle , Lopez Bernard S. 
Published: January 2022

AbstractGenetic instability is a hallmark of both cancer and aging. Homologous recombination (HR) is a prominent DNA repair pathway maintaining genomic integrity. Mutations in many HR genes lead to cancer predisposition. Paradoxically, the consequences of mutations in the pivotal HR player, RAD51, on cancer development remain puzzling. Moreover, in contrast with other HR genes, RAD51 mouse models are not available to experimentally address the role of RAD51 on aging and carcinogenesis, in vivo. Here, we engineered a mouse model with an inducible dominant negative form of RAD51 (SMRad51) that suppresses RAD51-mediated HR without stimulating alternative non-conservative repair pathways. We found that, in vivo expression of SMRad51 did not trigger tumorigenesis, but instead induced premature aging. We propose that these in vivo phenotypes result from the exhaustion of proliferating progenitors submitted to chronic endogenous replication stress resulting from RAD51-mediated HR suppression. Our data underline the importance of the RAD51 activity for progenitors homeostasis, preventing aging, and more generally for the balance between cancer and aging.
The oncogene FOXQ1 is a selective activator of Wnt/β-catenin signalling
Authors: Pizzolato Giulia , Moparthi Lavanya , Söderholm Simon , Cantù Claudio , Koch Stefan 
Published: January 2022

AbstractThe forkhead box transcription factor FOXQ1 is aberrantly induced in various cancers, and contributes to tumour growth and metastasis. It has been suggested that FOXQ1 exacerbates cancer by activating the oncogenic Wnt/β-catenin signalling pathway. However, the mode of action of FOXQ1 in the Wnt pathway remains to be resolved. Here, we report that FOXQ1 is a bimodal transcriptional activator of Wnt target gene expression in normal and cancer cells. Using co-immunoprecipitation, proximity proteomics, and reporter assays, we show that FOXQ1 engages the Wnt transcriptional complex to promote gene expression via TCF/LEF transcription factors. In parallel, FOXQ1 differentially regulates the expression of Wnt target genes independently of β-catenin and TCF/LEFs, which is facilitated by spatially separated activator and repressor domains. Our results suggest that FOXQ1 is a novel component of the Wnt transcriptional complex that reinforces and specifies Wnt signalling in a context-dependent manner.
Palatal morphology predicts the paleobiology of early salamanders
Authors: Jia Jia , Li Guangzhao , Gao Ke-Qin 
Published: January 2022

AbstractEcological preferences and life history strategies have enormous impacts on the evolution and phenotypic diversity of salamanders, but the yet established reliable ecological indicators hinder investigations on the paleobiology of early salamanders. Here we statistically demonstrate using geometric morphometric analysis that both the shape of the palate and many non-shape variables particularly associated with vomerine teeth are ecologically informative in early stem- and basal crown-group salamanders. The morphology of the palate is heavily impacted by convergence constrained by feeding mechanisms and also exhibits clear stepwise evolutionary patterns with alternative phenotypic designs to cope with similar functional demand. Paleoecological disparities in early salamanders had took place before the Middle Jurassic and have achieved all ecological preferences in the Early Cretaceous. Metamorphosis is significant in the expansion of ecomorphospace of the palate in early salamanders. The common ancestor of salamanders is metamorphosed and terrestrial, and share unified lifestyles with other modern amphibians.
Dual specificity phosphatase 7 drives the formation of cardiac mesoderm in mouse embryonic stem cells
Authors: Sladeček Stanislava , Radaszkiewicz Katarzyna Anna , Bőhmová Martina , Gybeľ Tomáš , Radaszkiewicz Tomasz Witold , Pacherník Jiří 
Published: January 2022

AbstractDual specificity phosphatase 7 (DUSP7) is a protein belonging to a broad group of phosphatases that 14 can dephosphorylate phosphoserine/phosphothreonine as well as phosphotyrosine residues within the 15 same substrate. DUSP7 has been linked to the negative regulation of mitogen activated protein kinases 16 (MAPK), and in particular to the regulation of extracellular signal-regulated kinases 1 and 2 (ERK1/2). 17 MAPKs play an important role in embryonic development, where their duration, magnitude, and 18 spatiotemporal activity must be strictly controlled by other proteins, among others by DUSPs. In this 19 study, we focused on the effect of DUSP7 depletion on the in vitro differentiation of mouse embryonic 20 stem (ES) cells. We showed that even though DUSP7 knock-out ES cells do retain some of their basic 21 characteristics, when it comes to differentiation, they preferentially differentiate towards neural cells, 22 while the formation of early cardiac mesoderm is repressed. Therefore, our data indicate that DUSP7 23 is necessary for the correct formation of neuroectoderm and cardiac mesoderm during the in vitro 24 differentiation of ES cells.
Differential UBE2H-CTLH E2-E3 ubiquitylation modules regulate erythroid maturation
Authors: Sherpa Dawafuti , Müller Judith , Karayel Özge , Chrustowicz Jakub , Xu Peng , Gottemukkala Karthik V. , Baumann Christine , Gross Annette , Czarnezki Oliver , Zhang Wei , Gu Jun , Nilvebrant Johan , Weiss Mitchell J. , Sidhu Sachdev S. , Murray Peter J. , Mann Matthias , Schulman Brenda A. , Alpi Arno F. 
Published: January 2022

AbstractThe development of haematopoietic stem cells into mature erythrocytes – erythropoiesis – is a controlled process characterized by cellular reorganisation and drastic reshaping of the proteome landscape. Failure of ordered erythropoiesis is associated with anaemias and haematological malignancies. Although the ubiquitin (UB) system is a known crucial post-translational regulator in erythropoiesis, how the erythrocyte is reshaped by the UB system is poorly understood. By measuring the proteomic landscape ofin vitrohuman erythropoiesis models, we found dynamic differential expression of subunits of the CTLH E3 ubiquitin ligase complex that formed distinct maturation stage-dependent assemblies of structurally homologous RANBP9-and RANBP10-CTLH complexes. Moreover, protein abundance of CTLH’s cognate E2-conjugating enzyme UBE2H increased during terminal differentiation, which depended on catalytically active CTLH E3 complexes. CRISPR-Cas9 mediated inactivation of all CTLH E3 assemblies by targeting the catalytic subunitMAEA,orUBE2H, triggered spontaneous and accelerated maturation of erythroid progenitor cells including increased heme and haemoglobin synthesis. Thus, the orderly progression of human erythropoiesis is controlled by the assembly of distinct UBE2H-CTLH modules functioning at different developmental stages.
The effect of employee's mindfulness on voluntary pro-environment behaviour at the workplace: the mediating role of connectedness to nature
Authors: Kumar Sachin , Panda Tapan Kumar , Pandey Krishan Kumar 
Published: January 2022

PurposeLimited research efforts have been undertaken despite the pivotal role of employees' voluntary behaviours in the success of organizations' environmental sustainability programs. In this context, the present study examined the association between employee's mindfulness (EM) and voluntary pro-environmental behaviour (VPEB) at the workplace, and also the mediating effect of connectedness to nature (CNS) on this relationship.Design/methodology/approachGrounded in the re-perceiving theory, a model was developed with EM as an independent variable, CNS as the mediator and employees VPEB at the workplace as the dependent variable. Based on the online responses from 421 employees working in manufacturing as well as services sectors in India, analysis was undertaken by utilizing confirmatory factor analysis, Pearson correlation and the PROCESS macro of Hayes (2017).FindingsEM was noted to be positively influencing employee's VPEB at the workplace, and the mediation analysis indicated that CNS partially intervenes in this relationship.Practical implicationsCorporate leaders striving to achieve the organization's environmental sustainability goals could strive to build a pro-environment culture at the workplace by developing employees' mindfulness and sense of CNS. As the findings have depicted, this would positively influence employee's VPEB at the workplace which in turn will help organizations in achieving their environmental sustainability goals.Originality/valueThis study is the first to examine how EM through CNS motivates employees to engage in VPEB, especially in the organizations' context. Moreover, the re-perceiving theory of mindfulness was also extended in the organizations' environmental sustainability context.
Succeeding in competitive arenas with arena-relevant marketing capabilities
Authors: Ehrensperger Elena , Greenberg Daria , Krohmer Harley , Nagel Felix , Hoyer Wayne , Zhang Z. John 
Published: January 2022

PurposeThe purpose of the study is to introduce the idea of arena-relevant marketing capabilities and examine their impact on firm performance. Arena-relevant marketing capabilities are capabilities particularly relevant for success in a specific competitive arena in which rivals from different industries try to satisfy customer needs with alternative products and services. The authors focus on the luxury arena and pose the following research questions: Which are the arena-relevant marketing capabilities in the luxury competitive arena (i.e. luxury-arena-relevant capabilities)? (2) What is the relative importance of luxury-arena-relevant vs general marketing capabilities for firm performance in the luxury competitive arena?Design/methodology/approachTo identify luxury-arena-relevant marketing capabilities, the authors conduct a qualitative study among 21 top managers of luxury brands. A subsequent large-scale managerial survey empirically tests the effects of luxury-arena-relevant vs general marketing capabilities on firm performance.FindingsThe study identifies four luxury-arena-relevant marketing capabilities: perfection in product creation, exclusive pricing, luxury-congruent storytelling and luxury brand inspiration. It confirms empirically that they have a higher impact on firm performance within the luxury competitive arena than general marketing capabilities.Originality/valueThe study takes an innovative perspective on marketing capabilities by linking them with the concept of a competitive arena and underlines the academic relevance of the concept of arena-relevant marketing capabilities for explaining firm performance.
Public health insurance for elderly: did researchers recognise health as human right for elderly?
Authors: Agrawal Gaurav , Mishra Aditi 
Published: January 2022

Purpose
This study aims to shed some light on the subject matter of the exploration of public medical coverage and elderly done as such far across the world. To achieve this objective, a comprehensive bibliometric examination was used to investigate papers published between the years 1960 and 2020. An aggregate of 366 papers was selected and analysed for the same. The investigation endeavours to recognise the journals with outstanding performance in this field, distribution of papers concerning the year of their publication, most referred to papers. Then various maps depicting bibliometric networks are provided, namely, the joint-authorship network map, inter-country joint-authorship network map and keyword co-occurrence network map.

Design/methodology/approach
To achieve the objective of this study, the Scopus database was used for comprehending the vast magnitude of information about numerous papers included in this paper. VOSviewer has been used to create a joint-authorship network map, inter-country joint-authorship network map and keywords concurrences network map.

Findings
The result of this investigation demonstrates that the highest number of publications came out in the year 2019, the most notable journal is Journal of Aging and Social Policy, and the most referred to research paper is about long-term care insurance (LTCI) in Japan. The USA is the most productive nation with the most elevated number of papers published under its name. Tamiya N. has teamed up with the highest number of authors, which is 29. Again the USA is the nation that participated with the highest number of authors of different countries in the research paper.

Originality/value
This paper accord with the current writing on public health insurance and elderly. A much far-reaching and solid image of this sector is given using the bibliometric analysis technique. The authors keen on directing future exploration on this topic can take guidance from the results of this study.
Market liberalization's impact on management accounting: a case study focused on a regional trade unit of the Polish gas company
Authors: Łada Monika , Kozarkiewicz Alina , Bartnik Bartlomiej , Haslam Jim 
Published: January 2022

PurposeThe impact of market liberalization on management accounting in a post-socialist context is explored by focusing upon a key regional trade unit of the Polish Gas Company, a former state monopoly undergoing transformation.Design/methodology/approachInsights are provided through a contingency theory framework, as modified through a configuration-sequential lens that considers management accounting as an expression of adaptation to a specific configuration of external and internal contingencies.FindingsIn the transitional context, the authors found that the direction, pace and manner of management accounting change were characteristic of a late adopter defending against market liberalization. There was a need here to overcome more barriers than in the case of a more established market economy, including through achieving a sufficient level of technological and institutional maturity.Originality/valueThe study focuses on an early phase of liberalization illuminating impacts through a case study of a regional trade unit in the key gas sector company in Poland. Little research has been done in this area following this approach and scarcely anything to the best of our knowledge on the empirical focus.