bluuebunny/crossref_metadata_2025_split huggingface dataset:
Coordinated modulation of multiple processes through phase variation of a c-di-GMP phosphodiesterase in Clostridioides difficile
Authors: Reyes Ruiz Leila M. , King Kathleen A. , Garrett Elizabeth M. , Tamayo Rita 
Published: October 2021

ABSTRACTThe opportunistic nosocomial pathogen Clostridioides difficile exhibits phenotypic heterogeneity through phase variation, a stochastic, reversible process that modulates expression. In C. difficile, multiple sequences in the genome undergo inversion through site-specific recombination. Two such loci lie upstream of pdcB and pdcC, which encode phosphodiesterases (PDEs) that degrade the signaling molecule c-di-GMP. Numerous phenotypes are influenced by c-di-GMP in C. difficile including cell and colony morphology, motility, colonization, and virulence. In this study, we aimed to assess whether PdcB phase varies, identify the mechanism of regulation, and determine the effects on intracellular c-di-GMP levels and regulated phenotypes. We found that expression of pdcB is heterogeneous and the orientation of the invertible sequence, or ‘pdcB switch’, determines expression. The pdcB switch contains a promoter that when properly oriented promotes pdcB expression. Expression is augmented by an additional promoter upstream of the pdcB switch. Mutation of nucleotides at the site of recombination resulted in phase-locked strains with significant differences in pdcB expression. Characterization of these mutants showed that the pdcB locked-ON mutant has reduced intracellular c-di-GMP compared to the locked-OFF mutant, consistent with increased and decreased PdcB activity, respectively. These alterations in c-di-GMP had concomitant effects on multiple known c-di-GMP regulated processes. These results indicate that phase variation of PdcB allows C. difficile to coordinately diversify multiple phenotypes in the population to enhance survival.
Nuclear damage inLMNAmutant iPSC-derived cardiomyocytes is associated with impaired lamin localization to the nuclear envelope
Authors: Wallace Melanie , Zahr Hind , Perati Shriya , Morsink Chloé D. , Johnson Lindsey E. , Gacita Anthony M. , Lai Shuping , Wallrath Lori L. , Benjamin Ivor J. , McNally Elizabeth M. , Kirby Tyler J. , Lammerding Jan 
Published: October 2021

AbstractTheLMNAgene encodes the nuclear envelope proteins Lamins A and C, which comprise a major part of the nuclear lamina, provide mechanical support to the nucleus, and participate in diverse intracellular signaling.LMNAmutations give rise to a collection of diseases called laminopathies, including dilated cardiomyopathy (LMNA-DCM) and muscular dystrophies. Although nuclear deformities are a hallmark ofLMNA-DCM, the role of nuclear abnormalities in the pathogenesis ofLMNA-DCM remains incompletely understood. Using induced pluripotent stem cell-derived cardiomyocytes (iPSC-CMs) fromLMNAmutant patients and healthy controls, we show thatLMNAmutant iPSC-CM nuclei have altered shape or increased size compared to healthy control iPSC-CM nuclei. TheLMNAmutation exhibiting the most severe nuclear deformities, R249Q, additionally caused reduced nuclear stiffness and increased nuclear fragility. Importantly, for all cell lines, the degree of nuclear abnormalities corresponded to the degree of Lamin A/C and Lamin B1 mislocalization from the nuclear envelope. The mislocalization was likely due to altered assembly of Lamin A/C. Collectively, these results point to the importance of correct lamin assembly at the nuclear envelope in providing mechanical stability to the nucleus and suggest that defects in nuclear lamina organization may contribute to the nuclear and cellular dysfunction inLMNA-DCM.
Molecular mechanism of Arp2/3 complex inhibition by Arpin
Authors: Fregoso Fred E. , van Eeuwen Trevor , Simanov Gleb , Rebowski Grzegorz , Boczkowska Malgorzata , Zimmet Austin , Gautreau Alexis M. , Dominguez Roberto 
Published: October 2021

AbstractPositive feedback loops involving signaling and actin assembly factors mediate the formation and remodeling of branched actin networks in processes ranging from cell and organelle motility to mechanosensation. The Arp2/3 complex inhibitor Arpin controls the directional persistence of cell migration by interrupting a feedback loop involving Rac-WAVE-Arp2/3 complex, but Arpin’s mechanism of inhibition is unknown. Here, we describe the cryo-EM structure of Arpin bound to Arp2/3 complex at 3.24-Å resolution. Unexpectedly, Arpin binds Arp2/3 complex similarly to WASP-family nucleation-promoting factors (NPFs) that activate the complex. However, whereas NPFs bind to two sites on Arp2/3 complex, on Arp2-ArpC1 and Arp3, Arpin only binds to the site on Arp3. Like NPFs, Arpin has a C-helix that binds at the barbed end of Arp3. Mutagenesis studies in vitro and in cells reveal how sequence differences within this helix define the molecular basis for inhibition by Arpin vs. activation by NPFs.
SETD2 negatively regulates cell size through its catalytic activity and SRI domain
Authors: Molenaar Thom M. , Kwesi-Maliepaard Eliza Mari , Silva Joana , Malik Muddassir , Faller William J. , van Leeuwen Fred 
Published: October 2021

AbstractCell size varies between cell types but is tightly regulated by cell-intrinsic and extrinsic mechanisms. Cell-size control is important for cell function and changes in cell size are frequently observed in cancer cells. Here we uncover a non-canonical role of SETD2 in regulating cell size. SETD2 is a lysine methyltransferase and a tumor suppressor protein involved in transcription regulation, RNA processing and DNA repair. At the molecular level, SETD2 is best known for associating with RNA polymerase II through its Set2-Rbp1 interacting (SRI) domain and methylating histone H3 on lysine 36 (H3K36) during transcription. Although most of SETD2’s cellular functions have been linked to this activity, several non-histone substrates of SETD2 have recently been identified – some of which have been linked to novel functions of SETD2 beyond chromatin regulation. Using multiple, independent perturbation strategies we identify SETD2 as a negative regulator of global protein synthesis rates and cell size. We provide evidence that this function is dependent on the catalytic activity of SETD2 but independent of H3K36 methylation. Paradoxically, ectopic overexpression of a decoy SRI domain also increased cell size, suggesting that the relevant substrate is engaged by SETD2 via its SRI domain. These data add a central role of SETD2 in regulating cellular physiology and warrant further studies on separating the different functions of SETD2 in cancer development.
ChlamydomonasARMC2/PF27 is an obligate cargo adapter for IFT of radial spokes
Authors: Lechtreck Karl , Liu Yi , Dai Jin , Alkhofash Rama A. , Butler Jack , Alford Lea , Yang Pinfen 
Published: October 2021

AbstractIntraflagellar transport (IFT) carries proteins into flagella but how IFT trains interact with the large number of diverse proteins required to assemble flagella remains largely unknown. Here, we show that IFT of radial spokes inChlamydomonasrequires ARMC2/PF27, a conserved armadillo repeat protein associated with male infertility and reduced lung function.ChlamydomonasARMC2 was highly enriched in growing flagella and tagged ARMC2 and the spoke protein RSP3 comigrated on anterograde trains. In contrast, a cargo and an adapter of inner and outer dynein arms moved independently of ARMC2, indicating that unrelated cargoes distribute stochastically onto the IFT trains. After concomitant unloading at the flagellar tip, RSP3 attached to the axoneme whereas ARMC2 diffused back to the cell body. Inarmc2/pf27mutants, IFT of radial spokes was abolished and the presence of radial spokes was limited to the proximal region of flagella. We conclude that ARMC2 is a cargo adapter required for IFT of radial spokes to ensure their assembly along flagella. ARMC2 belongs to a growing class of cargo-specific adapters that enable flagellar transport of preassembled axonemal substructures by IFT.
Stop hailing, start apping: adoption of app-cab services in an emerging economy
Authors: Chakraborty Debarun , Dash Ganesh , Kiefer Kip , Bhatnagar Shakti Bodh 
Published: October 2021

Purpose
This study aims to extend existing theories and fills research gaps regarding the acceptance and use of new technologies by consumers by exploring the adoption of app-cab services in India. Through the application and comparison of a unified theory of acceptance and use of technology (UTAUT) and UTAUT 2/expanded-UTAUT (E-UTAUT) models, this paper empirically tests the relationships between important constructs related to technology adoption, acceptance and utilization in India’s emerging economy.

Design/methodology/approach
In total, 612 responses to a questionnaire of active and regular users of app-cab services in India are examined. Path analysis and structural equation modeling presents interesting findings indicating that the expanded models have huge implications for the Indian app-cab industry.

Findings
This paper finds that the UTAUT 2/E-UTAUT models are a good fit for consumers and their behavior toward technology-based services. In particular, this study, one of the first of its kind, examines consumer acceptance and use behavior and identifies the factors that influence customer behavior with regard to new technology (app-cab services) in an emerging economy (India). Theoretical and practical implications are discussed.

Originality/value
Very few studies are available on app-cab adoption in emerging economies.
Generating market-creating innovation by working backwards from the future
Authors: Denning Stephen 
Published: October 2021

Purpose
What is required to deliver innovation that meets evolving customer needs is a process of learning from the future.

Design/methodology/approach
The major financial gains in the digital economy usually flow from generating innovations that create entirely new markets by turning non-customers into customers.

Findings
Amazon has developed a highly productive value-creation approach called the PR/FAQ process. It starts by imagining the customer’s needs in the future and then describing in detail the offering that would meet those needs.

Practical/implications
To get more consistent success in generating market-creating innovations, explicit attention to non-users is needed.

Originality/value
Exponential advances in digital technologies, and the interactions between them, are expanding the possibilities for market-creating innovation.
The Virtual Enterprise: enterprise transformation enabled by strategic digital acceleration
Authors: Payraudeau Jean-Stéphane , Marshall Anthony , Dencik Jacob , Ballou Stephen 
Published: October 2021

Purpose
The Virtual Enterprise model expands potential for extreme digitalization, extended value chains and intelligent workflows, along with new partnership and ecosystem approaches.

Design/methodology/approach
Analysis of a new survey of more than 7000 C-suite executives conducted by the IBM Institute for Business Value (IBV) provides new and striking insights into what operational, organizational and cultural environments are most conducive to effective and enduring digital transformation.

Findings
The Virtual Enterprise re-imagines how and where work is done, re-evaluating the necessity for physical assets, infrastructure and talent.

Practical/implications
The single most important characteristic of the Virtual Enterprise is “openness”, which brings value at three levels: inside the enterprise, with partners outside the enterprise and with the wider ecosystem.

Originality/value
The research found that the high technology adopters who focus on “openness” and “ecosystems” enjoy a 40 percent revenue growth performance premium over their advanced competitors.
Integrating multiple dimensions of ecological stability into a vulnerability framework
Authors: Urrutia‐Cordero Pablo , Langenheder Silke , Striebel Maren , Angeler David G. , Bertilsson Stefan , Eklöv Peter , Hansson Lars‐Anders , Kelpsiene Egle , Laudon Hjalmar , Lundgren Maria , Parkefelt Linda , Donohue Ian , Hillebrand Helmut 
Published: October 2021

AbstractEcological stability encompasses multiple dimensions of functional and compositional responses to environmental change. Though no single stability dimension used in isolation can fully reflect the overall response to environmental change, a common vulnerability assessment that integrates simultaneously across multiple stability components is highly desirable for ecological risk assessment.We develop both functional and compositional counterparts of a novel, integrative metric of overall ecological vulnerability (OEV). We test the framework with data from a modularized experiment replicated in five lakes over two seasons, examining functional and compositional responses to both pulse and press disturbances across three trophic groups. OEV is measured as the area under the curve integrated over the entire observation period, with the curve delimiting the difference between the disturbance treatment and undisturbed parallel controls, expressed either as the log response ratio of biomass (functional OEV) or community dissimilarity index (compositional OEV).Both, functional and compositional OEV correlated negatively with functional and compositional ‘resistance’, ‘temporal stability’ and ‘final/extent of recovery’ following both pulse and press disturbances, though less so with ‘resilience’ following a pulse disturbance. We also found a positive correlation between functional and compositional OEV, which reveals the potential to also evaluate the intricate linkage between biodiversity and functional change.Our findings demonstrate that OEV comprises a robust framework to: (a) capture simultaneously multiple functional and compositional stability components, and (b) quantify the functional consequences of biodiversity change. Our results provide the basis for an overarching framework for quantifying the overall vulnerability of ecosystems to environmental change, opening new possibilities for ecological risk assessment and management.Synthesis. Ecological stability comprises multiple dimensions that together encapsulate how ecosystems respond to environmental change. Considering these multiple aspects of stability simultaneously often poses a problem in environmental assessments, which frequently require overarching indicators of risk or vulnerability. While an analysis of multiple dimensions allows for deeper exploration of mechanisms, here we develop and test a new univariate indicator that integrates stability aspects under a broad range of disturbance regimes. Using a modularized experiment in Swedish lakes, we show that this integrative measure captures multiple stability dimensions reflecting compositional and functional vulnerability and their relationships between them.
Large contribution of recent photosynthate to soil respiration in tropical dipterocarp forest revealed by girdling
Authors: Nottingham Andrew T. , Cheesman Alexander W. , Riutta Terhi , Doughty Christopher E. , Telford Elizabeth , Huaraca Huasco Walter , Svátek Martin , Kvasnica Jakub , Majalap Noreen , Malhi Yadvinder , Meir Patrick , Arn Teh Yit 
Published: October 2021

Abstract

Tropical forests are the most productive terrestrial ecosystems, fixing over 40 Pg of carbon from the atmosphere each year. A substantial portion of this carbon is allocated below‐ground to roots and root‐associated micro‐organisms. However, there have been very few empirical studies on the dynamics of this below ground transfer, especially in tropical forests where carbon allocation processes are influenced by high plant species diversity.

We used a whole‐stand girdling experiment to halt the below‐ground transfer of recent photosynthates in a lowland tropical forest in Borneo. By girdling 209 large trees in a 0.48 ha plot, we determined: (a) the contribution of recent photosynthate to root‐rhizosphere respiration and; (b) the relationships among the disruption of this below‐ground carbon supply, tree species composition and mortality.

Mortality of the 209 trees was 62% after 370 days, with large variation among species and particularly high mortality within the Dipterocarpaceae (99%) and Fagaceae (100%) families. We also observed a higher risk of mortality following girdling for species with lower wood density.

Soil CO2 emissions declined markedly (36 ± 5%) over ~50 days following girdling in three of six monitored subplots. In the other three subplots there was either a marginal decline or no response of soil CO2 emissions to girdling. The decrease in soil CO2 efflux was larger in subplots with dominance of Dipterocarpaceae.

Synthesis. Our results indicate high spatial variation in the coupling of below‐ground carbon allocation and root‐rhizosphere respiration in this tropical forest, with a closer coupling in forest dominated by Dipterocarpaceae. Our findings highlight the implications of tree species composition of tropical forests in affecting the dynamics of below‐ground carbon transfer and its release to the atmosphere.
Soil microbes alter competition between native and invasive plants
Authors: Fahey Catherine , Flory Stephen Luke 
Published: October 2021

Abstract

Invasive plants can alter soil microbial communities and generate positive plant–soil feedbacks that facilitate their performance, but the magnitude and direction of feedbacks may change with novel conditions under climate change. We assessed how potential soil legacy effects of plant invasion and simulated drought influenced plant performance and competition in the longleaf pine ecosystem.

We collected soil from a 4‐year factorial invasion (cogongrass Imperata cylindrica) by drought (simulated with rainout shelters) field experiment and used it as live or sterilized soil inoculum in a greenhouse experiment that included two native foundation species, longleaf pine Pinus palustris and wiregrass Aristida stricta, and cogongrass, grown individually or in competition.

There was no evidence of biotic soil legacy effects of invasion or drought for any plant species, but microbes played a significant role in competition. When plants were grown alone, the invader had 12% greater biomass in live soil than sterile soil but both native species had 25% less biomass in live soil. When grown in competition, these effects were reversed for cogongrass (37% smaller in live soil) and pine (17% larger in live soil). In competition, the three species grown in sterile soil produced similar amounts of biomass, whereas live soil created a competitive hierarchy where pine was more competitive than wiregrass and cogongrass.

Synthesis. These results emphasize the importance of soil biota in native plant restoration because, although the invader was highly successful when grown alone, plant–microbe interactions influenced the outcome of competition between native and invasive species by promoting native longleaf pine. There was little evidence that invasive cogongrass inhibited native plants via biotic soil legacies, instead, results suggested that plant–soil interactions can be highly resilient to global change such that the biotic legacy of invasion and drought may not promote or inhibit invasion.
Profiling helicopter emergency medical service winch operations involving physicians in Queensland, Australia
Authors: Thorley Liam , Shepherd Ben , Donohue Andrew , MacKillop Allan 
Published: October 2021

AbstractObjectiveTo analyse the mission profiles of helicopter emergency medical service (HEMS) winch operations involving LifeFlight Retrieval Medicine physicians in Queensland, Australia, specifically focusing on patients' clinical characteristics, extrication methods and scene times.MethodsA retrospective analysis was performed to identify all helicopter winch missions involving physicians during 2019. Demographic, clinical and non‐clinical data were accessed from an electronic database used to log cases and findings presented using descriptive statistics.ResultsOut of 4356 HEMS missions involving physicians, 100 (2.3%) were winch operations. Of these, 31 (31%) occurred overwater and 12 (12%) at night. In total, 106 patients were attended, and eight patient deaths occurred. Most patients were traumatically injured (66%), male (66%) and had a median (interquartile range) age of 43.5 (28–59) years. Thirteen missions (13%) involved drowning victims. This group had a higher burden of injury and comprised half of the patients treated with endotracheal intubation. Median scene time was 30 min (20–40), and the winch stretcher was the predominant patient extrication method. Physician winching occurred in 63 (63%) missions and was associated with increased scene time and increased use of the winch stretcher.ConclusionsWinch operations involving physicians occur infrequently in Queensland HEMS, although almost a third of missions occur overwater. Drowning victims are encountered more frequently than reported elsewhere in Australian HEMS and comprised half of the patients who underwent endotracheal intubation. Patients' severity of illness and injury may contribute to the associations between winching of physicians, increased scene times and increased use of the winch stretcher.
Paving the Way for Evidence‐Driven Transboundary Water Cooperation in Central Asia
Authors: Ziganshina Dinara R. , de Schutter Joop L.G. 
Published: October 2021

AbstractThis paper reviews the achievements and failures in pursuing evidence‐driven and knowledge‐based transboundary water cooperation in Central Asia, with a focus on scientific cooperation under the umbrella of the Interstate Commission for Water Coordination in Central Asia. Despite its limitations, this scientific cooperation has contributed to facilitating evidence‐based dialog between the countries, to collaborative regional exchange of knowledge and expertise and to improved access to available data and information. This paper serves to show that more promising results can be achieved if joint research, fact‐finding, and planning are more widely promoted; water research is invested on a sustainable basis; knowledge between scientists, practitioners, water users, and local populations is co‐produced and shared; local capacity in science is supported and strengthened; traditional and innovative inter‐, trans‐, and multidisciplinary research is better used and developed.
Evaluate River Water Salinity in a Semi‐Arid Agricultural Watershed by Coupling Ensemble Machine Learning Technique with SWAT Model
Authors: Jung Chunggil , Ahn Sora , Sheng Zhuping , Ayana Essayas K. , Srinivasan Raghavan , Yeganantham Dhanesh 
Published: October 2021

AbstractThis study is to establish a new approach to estimate river salinity of semi‐arid agricultural watershed and identify drivers by using hydrologic modeling and machine learning. We augmented the limitations of the Soil and Water Assessment Tool (SWAT) to model salinity by coupling with eXtreme Gradient Boosting (XGBoost), a decision‐tree‐based ensemble machine learning algorithm. Streamflow, precipitation, elevation, main reach length, and dominant soil texture of the top two layers were used along with NO3, NO2, and total phosphorus (TP) output from a calibrated SWAT model are used as predictors to Total Dissolved Solids (TDS) in the XGBoost algorithm. Then, the SWAT model simulations of streamflow, NO3+NO2, and TP from 2000 to 2015 are used as inputs of the XGBoost model to predict monthly water TDS distribution along the river. The predicted river water TDS showed a higher concentration as going downstream from El Paso (inlet) through the Hudspeth canal to Fort Quitman (outlet). Finally, this study carried out cause analysis focusing on soil physical characteristics. The soil salinity level is directly affected by the soil permeability and irrigation water. As a result, the highest TDS is shown in sites with silt loam, whereas the lowest TDS was shown in sites with very cobbly soil. Silt soils can hold more water and are slower to drain than soils of a sand type. These analyses can be used to better understand the mitigation of water salinity.