bluuebunny/crossref_metadata_2025_split huggingface dataset:
Contribution Evenness: A functional redundancy metric sensitive to trait stability in microbial communities
Authors: Royalty Taylor M. , Steen Andrew D. 
Published: April 2020

AbstractThe concept of functional redundancy has received considerable attention in both the macroecology and microbial ecology literature. As a result, multiple metrics of functional redundancy have been proposed. These vary in how they weight trait levels, species abundance, functional richness, and species richness. Here we present a new functional redundancy metric tailored for community-aggregated traits, which are traits that are quantified at the community level and can be quantitatively partitioned among species. We call this metric Contribution Evenness (CE) because it measures how evenly species contribute to a community-aggregated trait. As CE is an evenness measurement, it ranges from 0 and 1, where 0 corresponds to a single species contributing to a community-aggregated trait and 1 corresponds to all species contributing equally. Usingin silicosimulations of species extinctions, we demonstrate that CE reflects the stability of an ecosystem function to species extinction, a hypothesized ecological consequence of functional redundancy. As a positive control and to illustrate how CE can be used with sequence data, we analyzed the functional redundancy of eight nitrogen-transforming pathways using 2,631 metagenome-assembled genomes from 47 marine sites. CE for marine nitrogen cycle marker genes was consistent with our qualitative understanding of which nitrogen pathways are most functionally redundant in the ocean. We found that, on average, the NH4+assimilation pathway was the most functionally redundant (0.44 ± 0.08) while dissimilatory nitrate reduction was the least redundant (0.005 ± 0.005). As demonstrated here, CE provides a promising framework for measuring trait stability in microbiomes.
Chronic consumption of alcohol increase alveolar bone loss
Authors: de Almeida Juliano Milanezi , Pazmino Victor Fabrizio Cabrera , Novaes Vivian Cristina Noronha , Bomfim Suely Regina Mogami , Nagata Maria José Hitomi , Oliveira Fred Lucas Pinto , Ervolino Edilson 
Published: April 2020

AbstractBackgroundThis study evaluated the effects of the chronic consumption of different concentrations of alcohol on the experimental periodontitis (EP).Methods160 rats were divided into 4 groups: (EP-NT) rats with EP and no alcohol exposure; (EP-A14) rats with EP exposed to 14% alcohol; (EP-A25) rats with EP exposed to 25% alcohol; (EP-A36) rats with EP exposed to 36% alcohol. The animals from the EP-A14, EP-A25 and EP-A36 groups were subjected to different concentrations of alcohol 30 days before EP induction. The histological characteristics, percentage of bone in the furcation (PBF) and bone metabolism in the furcation region were evaluated. The PBF and tartrate-resistant acid phosphatase (TRAP) data were subjected to statistical analysis.ResultsThe EP-A14, EP-A25 and EP-A36 groups had lower PBFs compared with the EP-NT group. A more severe inflammatory process and a greater number of TRAP+ cells were also observed. In the EP-A14, EP-A25 and EP-A36 groups, the inflammatory process became more severe as the ingested alcoholic concentration increased. An increase in RANKL immunostaining and a significantly higher number of TRAP+ cells were also observed.ConclusionWe conclude that chronic alcohol consumption increases the severity of experimental periodontitis in a dose-dependent manner by increasing the magnitude of local inflammatory responses and stimulating alveolar bone resorption.
Molecular basis for the distinct cellular functions of the Lsm1-7 and Lsm2-8 complexes
Authors: Montemayor Eric J. , Virta Johanna M. , Hayes Samuel M. , Nomura Yuichiro , Brow David A. , Butcher Samuel E. 
Published: April 2020

AbstractEukaryotes possess eight highly conserved Lsm (like Sm) proteins that assemble into circular, heteroheptameric complexes, bind RNA, and direct a diverse range of biological processes. Among the many essential functions of Lsm proteins, the cytoplasmic Lsm1-7 complex initiates mRNA decay, while the nuclear Lsm2-8 complex acts as a chaperone for U6 spliceosomal RNA. It has been unclear how these complexes perform their distinct functions while differing by only one out of seven subunits. Here, we elucidate the molecular basis for Lsm-RNA recognition and present four high-resolution structures of Lsm complexes bound to RNAs. The structures of Lsm2-8 bound to RNA identify the unique 2′,3′ cyclic phosphate end of U6 as a prime determinant of specificity. In contrast, the Lsm1-7 complex strongly discriminates against cyclic phosphates and tightly binds to oligouridylate tracts with terminal purines. Lsm5 uniquely recognizes purine bases, explaining its divergent sequence relative to other Lsm subunits. Lsm1-7 loads onto RNA from the 3′ end and removal of the Lsm1 C-terminal region allows Lsm1-7 to scan along RNA, suggesting a gated mechanism for accessing internal binding sites. These data reveal the molecular basis for RNA binding by Lsm proteins, a fundamental step in the formation of molecular assemblies that are central to eukaryotic mRNA metabolism.
Dyrk1b is a key Regulatory Kinase Integrating Fgf, Shh and mTORC1 signaling in Skeletal Muscle Development and Homeostasis
Authors: Bhat Neha , Narayanan Anand , Fathzadeh Mohsen , Srivastava Anup , Mani Arya 
Published: April 2020

ABSTRACTThe advent of human genetics has provided unprecedented opportunities for discovery of novel disease pathways. Mutations inDYRK1Bhave been associated with metabolic syndrome and sarcopenic obesity in humans, underscoring the critical role of the encoded protein in skeletal muscle development and homeostasis. By the novel creation of Dyrk1b knockout zebrafish models we demonstrate that Dyrk1b kinase activity is critical for specification of the paraxialmyoD. Mechanistically, Dyrk1b mediates and amplifies Fgf signaling in the paraxial domain by the transcriptional suppression of its negative feedback inhibitorsprouty1. In the adaxialmyoDdomain, Dyrk1b amplifies Shh signaling and partially rescues defects caused by its disruption. The investigations of C2C12 terminal differentiation revealed that Dyrk1b also plays a critical role in myofiber fusion. Combined biochemical and proteomic analysis of C2C12 myoblasts undergoing differentiation showed that Dyrk1b kinase activation is induced by shh inhibition, and triggers differentiation by inhibiting mTOR, subsequent upregulation of 4e-bp1 and induction of autophagy. In conclusion, we demonstrate that Dyrk1b plays a critical role in sustaining myocyte specification and differentiation by integrating Fgf, Shh and mTORC1 signaling pathways.
Modulation of cell adhesion and migration by poly-dispersed-acid-functionalized-single-walled carbon nanotubes in lung epithelial cells
Authors: Behera Sushreesangita P. , Saxena Rajiv K. 
Published: April 2020

AbstractEpithelial cell lining of the lung alveoli is under constant onslaught of airborne pathogens and pollutants that may cause injury and disruption of the epithelial lining. Repair mechanisms involve proliferation and migration of nearby healthy epithelial cells to the site of injury. Using murine LA4 and human A549 lung epithelial cell lines, andin vitromodels of cell migration we have examined the modulation of cellular adhesion and migration by poly-dispersed acid-functionalized single-walled carbon nanotubes (AF-SWCNTs). Flow cytometric and confocal microscopy studies indicated that AF-SWCNTs were efficiently internalized by both cell lines and were localized essentially in the cytoplasmic area. In the scratch wound repair model, exposure to AF-SWCNTs blocked the filling of the scratched area of the cellular monolayers in both cells. Behaviour of the cells around the scratch area was examined in by live-cell imaging time-lapse micrography. The results indicated active cell proliferation around the scratch area that was totally blocked by AF-SWCNTs in LA4 cells and significantly inhibited in A549 cells. Cell migration across a porous membrane in transwell assay system also indicated a marked inhibition of migration of both cells across the membrane. Effect of AF-SWCNTs on the expression levels of important cell proteins involved in cell migration and adhesion were examined by western blotting and immunofluorescence staining. Expressions of proteins like β-Catenin, NM-Myosin and Vimentin that play crucial role in cell migration were suppressed in AF-SWCNTs-exposed cells whereas the expression levels of E-cadherin and Claudin-1, involved in cell-cell adhesion remained unaltered. Our results provide an insight into the mechanism of repair of lung epithelial cell layers.
A temperature-sensitiveMycobacterium smegmatis glgEmutation leads to a loss of GlgE enzyme activity and thermostability and the accumulation of α-maltose-1-phosphate
Authors: Syson Karl , Batey Sibyl F. D. , Schindler Steffen , Kalscheuer Rainer , Bornemann Stephen 
Published: April 2020

AbstractBackgroundThe bacterial GlgE pathway is the third known route to glycogen and is the only one present in mycobacteria. It contributes to the virulence ofMycobacterium tuberculosis. The involvement of GlgE in glycogen biosynthesis was discovered twenty years ago when the phenotype of a temperature-sensitiveMycobacterium smegmatismutation was rescued by theglgEgene. The evidence at the time suggestedglgEcoded for a glucanase responsible for the hydrolysis of glycogen, in stark contrast with recent evidence showing GlgE to be a polymerase responsible for its biosynthesis.MethodsWe reconstructed and examined the temperature-sensitive mutant and characterised the mutated GlgE enzyme.ResultsThe mutant strain accumulated the substrate for GlgE, α-maltose-1-phosphate, at the non-permissive temperature. The glycogen assay used in the original study was shown to give a false positive result with α-maltose-1-phosphate. The accumulation of α-maltose-1-phosphate was due to the lowering of thekcatof GlgE as well as a loss of stability 42 ºC. The reported rescue of the phenotype by GarA could potentially involve an interaction with GlgE, but none was detected.ConclusionsWe have been able to reconcile apparently contradictory observations and shed light on the basis for the phenotype of the temperature-sensitive mutation.General SignificanceThis study highlights how the lowering of flux through the GlgE pathway can slow the growth mycobacteria.
Kallikrein-related peptidase 14 activates zymogens of membrane type matrix metalloproteinases (MT-MMPs) - a CleavEx library-based analysis
Authors: Falkowski Katherine , Bielecka Ewa , Thøgersen Ida B. , Bocheńska Oliwia , Płaza Karolina , Kalińska Magdalena , Sąsiadek Laura , Magoch Małgorzata , Pęcak Aleksandra , Wiśniewska Magdalena , Gruba Natalia , Wysocka Magdalena , Wojtysiak Anna , Brzezińska-Bodal Magdalena , Sychowska Kamila , Pejkovska Anastasija , Rehders Maren , Butler Georgina , Overall Christopher M , Brix Klaudia , Dubin Grzegorz , Lesner Adam , Kozik Andrzej , Enghild Jan J. , Potempa Jan , Kantyka Tomasz 
Published: April 2020

ABSTRACTKallikrein-related peptidases (KLKs) and matrix metalloproteinases (MMPs) are secretory proteinases known to proteolytically process components of the extracellular matrix (ECM), thus modulating the pericellular environment in physiology and excessively in pathologies like cancer. However, the interconnection between these groups of proteases remains elusive. To test this hypothesis, we have developed a peptide library-based exposition system (Cleavage ofexposed amino acid sequences, CleavEx) aiming at investigating the potential of KLK14 to recognize and hydrolyze proMMP sequences specifically. Initial assessment of the library identified a total of ten MMP activation domain sequences which were validated by Edman degradation. The CleavEx analysis revealed that membrane-type (MT) MMPs are likely targeted by KLK14 for activation. Correspondingly, commercially available proMT-MMPs, namely proMMP14-17 were investigatedin vitroand found to be effectively processed by KLK14. Again, the expected neo-N-termini of the activated MT MMPs were yielded and confirmed by Edman degradation. In addition, the productivity of proMMP activation was analyzed by gelatin zymography, which indicated the release of fully active, mature MT-MMPs upon KLK14 treatment. Lastly, MMP14 was shown to be processed on the cell surface by KLK14 using murine fibroblasts stably overexpressing human MMP14.Herein, we propose KLK14-mediated selective activation of cell-membrane located MT-MMPs as an additional layer of their regulation within the ECM. As both, KLKs and MT-MMPs are implicated in cancer, the activation described herein may constitute an important factor in tumor progression and metastasis.
A subcellular atlas ofToxoplasmareveals the functional context of the proteome
Authors: Barylyuk Konstantin , Koreny Ludek , Ke Huiling , Butterworth Simon , Crook Oliver M. , Lassadi Imen , Gupta Vipul , Tromer Eelco , Mourier Tobias , Stevens Tim J. , Breckels Lisa M. , Pain Arnab , Lilley Kathryn S. , Waller Ross F. 
Published: April 2020

ABSTRACTApicomplexan parasites cause major human disease and food insecurity. They owe their considerable success to novel, highly specialized cell compartments and structures. These adaptations drive their recognition and non-destructive penetration of host’s cells and the elaborate reengineering of these cells to promote growth, dissemination, and the countering of host defenses. The evolution of unique apicomplexan cellular compartments is concomitant with vast proteomic novelty that defines these new cell organizations and their functions. Consequently, half of apicomplexan proteins are unique and uncharacterized, and these cells are, therefore, very poorly understood. Here, we determine the steady-state subcellular location of thousands of proteins simultaneously within the globally prevalent apicomplexan parasiteToxoplasma gondii. This provides unprecedented comprehensive molecular definition to these cells and their novel compartments, and these data reveal the spatial organizations of protein expression and function, adaptation to hosts, and the underlying evolutionary trajectories of these pathogens.
Foreign versus local firms: implications for environmental sustainability
Authors: Balasubramanian Sreejith , Shukla Vinaya 
Published: April 2020

PurposeManaging environmental consequences while sustaining economic development necessitate strong commitment and participation of all firms across sectors. However, the environment-related role of foreign and local firms is unclear from previous research. With increasing trade liberalization and entry of foreign firms, this question has become particularly relevant. The purpose of this paper is to contrast the roles and contributions of foreign and local firms from an environmental sustainability perspective.Design/methodology/approachUsing data collected through a structured survey (395 responses) and semi-structured interviews (19 numbers) from the United Arab Emirates (UAE) construction sector (research setting), the study analyses and understands the hypothesized differences between foreign and local firms on three key environmental sustainability aspects: the extent of environmental practices implementation, the strengths/influences of drivers and barriers affecting the implementation, and the environmental, cost-related, and organizational performance benefits derived.FindingsForeign firms were found to implement environmental practices to a greater extent, have a greater internal drive to implement these practices, and face lower barriers to implementation than local ones. Local firms though were found to be not far behind foreign ones with regards to the environmental, cost-related, and organizational performance benefits derived.Practical implicationsFindings from the study are expected to help policymakers and practitioners develop policies/interventions that ensure all firms irrespective of their nature of ownership contribute equitably to environmental sustainability.Originality/valueThis study is arguably the first comprehensive attempt to understand how various environmental sustainability aspects are perceived and performed by local and foreign firms.
Corporate cash savings and discretionary accruals
Authors: Jia Jianjun , Shao Lili , Sun Zhenzhen , Zhao Fang 
Published: April 2020

PurposeThis paper assesses how discretionary accruals (DAs) affect corporate cash savings policies and the motivation behind this cash saving behavior and, also whether the linkage between DAs and cash saving affect the market-perceived cash value.Design/methodology/approachWe construct the measure of DAs using the previous five-year average information to investigate the association of DAs with the change in cash. Moreover, the Faulkender and Wang (2006) methodology is utilized to examine the market-perceived cash value in DAs.FindingsThe key finding is that firms with high DAs save significantly more cash. A one standard deviation increase in DAs saves cash by 12.59%. Furthermore, the value of cash is low for these firms. The effect is stronger in firms with poor governance but not present in financially constrained firms.Research limitations/implicationsThe empirical evidence highlights DAs have negative effect on market-perceived cash value, which underscores the insight that managers manage earnings opportunistically using DAs.Originality/valueTaken together, we provide more evidence on the literature of accruals in earnings manipulation.
Development of disaster risk reduction policy in Thailand
Authors: Kitagawa Kaori 
Published: April 2020

PurposeThis exploratory study discusses the policy learning process of the development of disaster risk reduction (DRR) policy.Design/methodology/approachThe paper discusses how DRR has and has not developed in Thailand through the two major disasters: the 2004 Indian Ocean Tsunami and the 2011 Great Flood. The information was collected by documentary analysis to gain a historical and critical understanding of the development of the system and policy of DRR in Thailand. Additionally, key stakeholders' interviews were undertaken to supplement the analysis.FindingsThe paper demonstrates that Thailand's DRR development has been “reactive” rather than “proactive”, being largely directed by global DRR actors.Research limitations/implicationsBeing a small-scale study, the sample size was small. The analysis and argument would be consolidated with an increase in the number of interviews.Practical implicationsThe model can help deconstruct which dimension of the learning process a government has/has not achieved well.Originality/valueThe application of the “restrictive-expansive policy learning” model, which identifies different dimensions of policy learning, reveals that the Thai government's policy learning was of a mixed nature.
Building information modelling for building services engineering: benefits, barriers and conducive measures
Authors: Chiu Wai Yee Betty , Lai Joseph H.K. 
Published: April 2020

PurposeMandating the use of building information modelling (BIM) in building projects has sprawled, but the uptake of BIM in building services engineering (BSE) remains sluggish. The purpose of this paper is to explore how to achieve wider adoption of BIM in BSE.Design/methodology/approachThrough an extensive literature review, the benefits of, barriers to and measures conducive to, using BIM for BSE were identified and classified. Built upon the review and a focus group meeting, a questionnaire was devised for an industry-wide survey in Hong Kong and the survey data were processed by statistical analyses.FindingsOn the ranking of the benefits, strong agreements existed between the BSE and non-BSE respondent groups; yet no significant agreement was found between the two groups on the rankings of the barriers or the conducive measures. The top conducive measure, according to the BSE group, is “Allow enough time in project programme for BIM model development”.Research limitations/implicationsThe data collection and analysis methods of this study may be used for similar BIM studies in other places.Practical implicationsThe priority of the conducive measures, which aid policy or decision makers in formulating how to get BIM effectively implemented in BSE, are useful information in the pursuit of a more productive and sustainable built environment.Originality/valueThis BIM study is specifically on BSE rather than the other disciplines (e.g. architecture, structural engineering) that have been widely studied.
Multiplex boundary work in innovation projects: the role of collaborative spaces for cross-functional and open innovation
Authors: Ungureanu Paula , Cochis Carlotta , Bertolotti Fabiola , Mattarelli Elisa , Scapolan Anna Chiara 
Published: April 2020

PurposeThis study investigates the role of collaborative spaces as organizational support for internal innovation through cross-functional teams and for open innovation with external stakeholders. In particular, the study focuses on collaborative spaces as tools for multiplex (i.e., simultaneous internal and external boundary management in innovation projects).Design/methodology/approachThe authors conducted a qualitative study in a multi-divisional organization that set up in its headquarters a collaborative space for collaborative product development. Data were collected through semi-structured interviews and participant observations.FindingsFindings highlight that the relation between expectations and experiences about the collaborative space impact on employees' ability to perform boundary work inside and outside the organization. In addition to the collaborative space's affording role for expectations about hands-on collaborative innovation (space as laboratory), the study also highlights a set of collaboration constraints. These latter are generated by perceived boundary configurations (i.e. degree of boundary permeability and infrastructure in internal and external collaborations) and by discrepancies between expectations (space as laboratory) and actual collaboration experiences in the space (i.e. space as maze, cloister, showcase and silo). We show that space-generated constraints slow down internal and external boundary work for innovation and generate a trade-off between them.Originality/valueUsing the process-based perspective of boundary work, the paper connects studies on cross-functional teaming and open innovation through the concept of “multiplex boundary work.” It also contributes to the literature on boundary work by showing the challenges of using collaborative spaces as organizational support tools for multiplex boundary spanning.