bluuebunny/crossref_metadata_2025_split huggingface dataset:
Integrative conformational ensembles of Sic1 using different initial pools and optimization methods
Authors: Gomes Gregory-Neal W. , Namini Ashley , Gradinaru Claudiu C. 
Published: April 2022

ABSTRACTIntrinsically disordered proteins play key roles in regulatory protein interactions, but their detailed structural characterization remains challenging. Here we calculate and compare conformational ensembles for the disordered protein Sic1 from yeast, starting from initial ensembles that were generated either by statistical sampling of the conformational landscape, or by molecular dynamics simulations. Two popular, yet contrasting optimization methods were used, ENSEMBLE and Bayesian Maximum Entropy, to achieve agreement with experimental data from nuclear magnetic resonance, small-angle X-ray scattering and single-molecule Förster resonance energy transfer. The comparative analysis of the optimized ensembles, including secondary structure propensity, inter-residue contact maps, and the distributions of hydrogen bond and pi interactions, revealed the importance of the physics-based generation of initial ensembles. The analysis also provides insights into designing new experiments that can maximally discriminate among the optimized ensembles. Overall, differences between ensembles optimized from different priors were greater than when using the same prior with different optimization methods. Generating increasingly accurate, reliable and experimentally validated ensembles for disordered proteins is an important step towards a mechanistic understanding of their biological function and involvement in various diseases.
Approximations to the expectations and variances of ratios of tree properties under the coalescent
Authors: Lappo Egor , Rosenberg Noah A 
Published: April 2022

AbstractProperties of gene genealogies such as tree height (H), total branch length (L), total lengths of external (E) and internal (I) branches, mean length of basal branches (B), and the underlying coalescence times (T) can be used to study population-genetic processes and to develop statistical tests of population-genetic models. Uses of tree features in statistical tests often rely on predictions that depend on pairwise relationships among such features. For genealogies under the coalescent, we provide exact expressions for Taylor approximations to expected values and variances of ratiosXn/Yn, for all 15 pairs among the variables {Hn,Ln,En,In,Bn,Tk}, consideringnleaves and 2 ≤k≤n. For expected values of the ratios, the approximations match closely with empirical simulation-based values. The approximations to the variances are not as accurate, but they generally match simulations in their trends asnincreases. AlthoughEnhas expectation 2 andHnhas expectation 2 in the limit asn→ ∞, the approximation to the limiting expectation forEn/Hnis not 1, instead equalingπ2/3 – 2 ≈ 1.28987. The new approximations augment fundamental results in coalescent theory on the shapes of genealogical trees.
The fluorescence-activating and absorption-shifting tag (FAST) enables live-cell fluorescence imaging of Methanococcus maripaludis
Authors: Hernandez Eric , Costa Kyle C 
Published: April 2022

AbstractLive-cell fluorescence imaging in methanogenic archaea has been limited due to the strictly anoxic conditions required for growth and issues with autofluorescence associated with electron carriers in central metabolism. Here, we show that the fluorescence-activating and absorption-shifting tag (FAST) when complexed with the fluorogenic ligand 4-hydroxy-3-methylbenzylidene-rhodanine (HMBR) overcomes these issues and displays robust fluorescence in Methanococcus maripaludis. We also describe a mechanism to visualize cells under anoxic conditions using a fluorescence microscope. Derivatives of FAST were successfully applied for protein abundance analysis, subcellular localization, and determination of protein-protein interactions. FAST fusions to both formate dehydrogenase (Fdh) and F420-reducing hydrogenase (Fru) displayed increased fluorescence in cells grown on formate containing medium, consistent with previous studies suggesting increased abundance of these proteins in the absence of H2. Additionally, FAST fusions to both Fru and the ATPase associated with the archaellum (FlaI) showed membrane localization in single cells observed using anoxic fluorescence microscopy. Finally, a split reporter translationally fused to the alpha and beta subunits of Fdh reconstituted a functionally fluorescent molecule in vivo via bimolecular fluorescence complementation. Together, these observations demonstrate the utility of FAST as a tool for studying members of the methanogenic archaea.ImportanceMethanogenic archaea are important members of anaerobic microbial communities where they catalyze essential reactions in the degradation of organic matter. Developing additional tools for studying the cell biology of these organisms is essential to understanding them at a mechanistic level. Here, we show that FAST, in combination with the fluorogenic ligand HMBR, can be used to monitor protein dynamics in live cells of M. maripaludis. Application of FAST holds promise for future studies focused on the metabolism and physiology of methanogenic archaea.
Novel Requirement for Staphylococcal Cell Wall-Anchored Protein SasD in Pulmonary Infection
Authors: Grousd Jennifer A , Riesmeyer Abigail M. , Cooper Vaughn S. , Bomberger Jennifer M. , Richardson Anthony R. , Alcorn John F. 
Published: April 2022

AbstractStaphylococcus aureus can complicate preceding viral infections, including influenza virus. A bacterial infection combined with a preceeding viral infection, known as super-infection, leads to worse outcomes compared to single infection. Most of the super-infection literature focuses on the changes in immune responses to bacteria between homeostatic and virally infected lungs. However, it is unclear how much of an influence bacterial virulence factors have in super-infection. Staphylococcal species express a broad range of cell wall-anchored proteins (CWAs) that have roles in host adhesion, nutrient acquisition, and immune evasion. We screened the importance of these CWAs using mutants lacking individual CWAs in vivo in both bacterial pneumonia and influenza super-infection. In bacterial pneumonia, lacking individual CWAs led to varying decreases in bacterial burden, lung damage, and immune infiltration into the lung. However, the presence of a preceding influenza infection partially abrogated the requirement for CWAs. In the screen, we found that the uncharacterized CWA S. aureus surface protein D (SasD) induced changes in both inflammatory and homeostatic lung markers. We further characterized a SasD mutant (sasD A50.1) in the context of pneumonia. Mice infected with sasD A50.1 had decreased bacterial burden, inflammatory responses, and mortalty compared to wildtype S. aureus. Mice also had reduced levels of IL-1β compared with wildtype, likely derived from macrophages. Reductions in IL-1β transcript levels as well as increased macrophage viability implicate altered macrophage cell death pathways. These data identify a novel virulence factor for S. aureus that influences inflammatory signaling within the lung.ImportanceStaphylococcus aureus is a common commensal bacteria that can cause severe infections, such as pneumonia. In the lung, viral infections increase the risk of staphylococcal pneumonia, leading to combined infections known as super-infections. The most common virus associated with S. aureus pneumonia is influenza, and super-infections lead to worse patient outcomes compared to either infection alone. While there is much known about how the immune system differs between healthy and virally infected lungs, the role of bacterial virulence factors in super-infection is less understood. The significance of our research is identifying new bacterial virulence factors that play a role in the initiation of infection and lung injury, which could lead to future therapies to prevent pulmonary single or super-infection with S. aureus.
Dual pathway architecture underlying vocal learning in songbirds
Authors: Sankar Remya , Leblois Arthur , Rougier Nicolas P. 
Published: April 2022

AbstractSong acquisition and production in songbirds is governed by a dedicated neural circuitry that involves two parallel pathways: a motor pathway for the production and a basal ganglia (BG) pathway for the acquisition. Juveniles learn by imitating adult vocalizations and proceed by trial and error, errors being conveyed by a dopaminergic signal. The complex nature of the relationship between neural control and syrinx musculature makes song learning a complicated problem to solve. Reinforcement learning (RL) has been widely hypothesized to underlie such sensorimotor learning even though this can lead to sub-optimal solutions under uneven contours in continuous action spaces. In this article, we propose to re-interpret the role of a dual pathway architecture, underlying avian vocal learning, that helps overcome these limitations. We posit that the BG pathway conducts exploration by inducing large daily shifts in the vocal production while the motor pathway gradually consolidates this exploration. This process can be understood as a modified form of a simulated annealing process. Simulations on Gaussian performance landscapes and a syrinx-based performance landscape are demonstrated and compared with standard approaches. Taking behavioral constraints into account (60 days of learning, 1000 trials per day), the model allows to reach the global optimum in complex landscapes and thus provides a sound insight into the role of the dual pathway architecture underlying vocal learning.
Business process redesign towards IoT-enabled context-awareness: the case of a Chinese bulk port
Authors: Song Rongjia , Cui Weiping , Vanthienen Jan , Huang Lei , Wang Ying 
Published: April 2022

PurposeThe purpose of this paper is to contribute to the extant literature about the co-evolvement of Business Process Management (BPM) and the Internet of Things (IoT) by proposing the IoT-enabled Context-aware BPM (IoT-CaBPM) framework to bridge from the IoT infrastructure to context-aware business processes.Design/methodology/approachMotivated by the “Three Waves” of BPM research, IoT-enabled context-awareness is, therefore, expected to be achieved for enhancing the business process design, which pilots a new wave of BPR (Business Process Redesign/Reengineering) to enable the business process coevolve with IoT and analytics. This paper reports an illustrative case study of BPR in a Chinese bulk port, one of the hub seaports that widely adopted IoT technologies over the last few years.FindingsThe IoT implementation and data analytics has increased the efficiency and improve the monitoring effectively. The proposed IoT-CaBPM framework availably helps to identify and match nodes of IoT devices, business decisions and analytic models in order to redesign a business process towards context-aware variability. As IoT is rapidly becoming the new dominant IT paradigm is moving towards mature implementation in various industries, the corresponding BPR must be planned and executed strategically for achieving better benefits.Originality/valueDespite some research extend BPM standard by integrating IoT devices as a sort of resources or report generically that the ports operations are affected by IoT, there is still a lack of layers from the IoT infrastructure to context-aware business processes. An industrial BPR case with business models in detail is also a lack for presenting the specific implications and effectiveness of the adoption of such technologies. This paper fills in this gap.
Does e-commerce narrow the urban–rural income gap? Evidence from Chinese provinces
Authors: Yin Zi Hui , Choi Chang Hwan 
Published: April 2022

PurposeA wide urban–rural income gap exists in China despite the implementation of pro-rural policies. Additionally, with the proliferation of the internet and information technology, the promotion effect of e-commerce on the economy has become apparent. Accordingly, China has been actively encouraging rural households to participate in e-commerce activities. This study aims to examine the effect of e-commerce on the urban–rural income gap.Design/methodology/approachIn the study, linear and panel threshold models were applied to provincial-level panel data from 2002 to 2018.FindingsThe results of the linear model show that e-commerce contributes to narrowing the urban–rural income gap. Moreover, the panel threshold model results show that the narrowing effect exists in regions where the e-commerce intensity is at a medium-to-high level and urbanization is at a relatively low level; otherwise, e-commerce has no effect. In addition, in regions with a relatively high level of public expenditure and education, the income-gap-narrowing effect of e-commerce is more than double.Practical implicationsThe urban–rural income gap can be reduced by promoting e-commerce and reducing the urban–rural divide in e-commerce use.Originality/valueTo determine how varying levels of e-commerce development affect the urban–rural income gap across regions, the study proposes four key causes of the digital divide in e-commerce: e-commerce intensity, public expenditure level, urbanization level and education level and applies the variables as threshold variables to examine the non-linear effect of e-commerce on the income gap.
Digital influencers, social power and consumer engagement in social commerce
Authors: Wang Panpan , Huang Qian 
Published: April 2022

PurposeSocial commerce platforms are prevalent in the explosion of social media and e-commerce, and they enable conversations across a broad range of topics. However, their success depends on consumers' willingness to invest their time, attention and money. Digital influencers have shown prominent effects on consumers in those social commerce platforms. This study, thus, aims to attempt to unravel the role of digital influencers in affecting consumer engagement and purchase behaviour in online social commerce communities.Design/methodology/approachA mixed approach with a field interview, an online survey and secondary archive data are presented to confirm all the hypotheses.FindingsSeveral forms of social power from digital influencers (including expert power, informational power, referent power and legitimate reciprocity power) could influence consumer engagement behaviours (including content participation and content creation). Moreover, the two types of consumer engagement behaviours could further influence consumer purchase likelihood in the social commerce community.Research limitations/implicationsSeveral forms of social power from digital influencers (including expert power, informational power, referent power and legitimate reciprocity power) could affect consumer engagement behaviours (including content participation and content creation). Moreover, the two types of consumer engagement behaviours could further affect consumer's purchase expenditure in the social commerce community.Originality/valueThis study draws on the theories of social power and social influence and integrates the literature on consumer engagement to explain how digital influencers affect consumer engagement and their purchase behaviour in an online social commerce community. Firstly, this work extends existing studies on the antecedents of consumer engagement in the social commerce communities by considering the role of digital influencers. Secondly, this research advances the theoretical understanding of the influence of digital influencers through a new lens of social power. The findings also contribute to community managers, users who pursue popularity and companies who target business goals.
Worlds apart: a socio-material exploration of mHealth in rural areas of developing countries
Authors: Eze Emmanuel , Gleasure Rob , Heavin Ciara 
Published: April 2022

PurposeThe implementation of mobile health (mHealth) in developing countries seems to be stuck in a pattern of successive pilot studies that struggle for mainstream implementation. This study addresses the research question: what existing health-related structures, properties and practices are presented by rural areas of developing countries that might inhibit the implementation of mHealth initiatives?Design/methodology/approachThis study was conducted using a socio-material approach, based on an exploratory case study in West Africa. Interviews and participant observation were used to gather data. A thematic analysis identified important social and material agencies, practices and imbrications which may limit the effectiveness of mHealth apps in the region.FindingsFindings show that, while urban healthcare is highly structured, best practice-led, rural healthcare relies on peer-based knowledge sharing, and community support. This has implications for the enacted materiality of mobile technologies. While urban actors see mHealth as a tool for automation and the enforcement of responsible healthcare best practice, rural actors see mHealth as a tool for greater interconnectivity and independent, decentralised care.Research limitations/implicationsThis study has two significant limitations. First, the study focussed on a region where technology-enabled guideline-driven treatment is the main mHealth concern. Second, consistent with the exploratory nature of this study, the qualitative methodology and the single-case design, the study makes no claim to statistical generalisability.Originality/valueTo the authors' knowledge, this is the first study to adopt a socio-material view that considers existing structures and practices that may influence the widespread adoption and assimilation of a new mHealth app. This helps identify contextual challenges that are limiting the potential of mHealth to improve outcomes in rural areas of developing countries.
Testing the market efficiency in Indian stock market: evidence from Bombay Stock Exchange broad market indices
Authors: Elangovan Rajesh , Irudayasamy Francis Gnanasekar , Parayitam Satyanarayana 
Published: April 2022

PurposeDespite volumes of research on the efficient market hypothesis (EMH) over the last six decades, the results are inconclusive as some studies supported the hypothesis, and some studies rejected it. The study aims to examine the market efficiency of the Indian stock market.Design/methodology/approachFor analysis, nine Bombay Stock Exchange (BSE) broad market indices were selected covering the study period from 01 January 2011 to 31 December 2020. The data collected for this study are daily open, high, low and closing prices of selected indices. The tools used in this study are: (1) unit root test to check the stationarity of time series, (2) descriptive statistics, (3) autocorrelation and (4) runs test.FindingsThe empirical findings of the study reveal that BSE broad market indices do not follow a random walk and Indian stock market is as weak-form inefficient.Research limitations/implicationsThe findings from this study provide several avenues for future research. One of the research implications is that anomalies in the statistical results by different academicians in the finance area need to be explained by future researchers.Practical implicationsInvestment companies need to understand that extraordinary skills are required to beat the market to make abnormal returns. In an inefficient market where securities do not reflect the complete available information, it is challenging for the investment brokers to convince the customers about the portfolios they recommend to the public that the rate of return would be more than expected.Social implicationsAs economic growth is related to the growth in the financial sector, developing countries like India depend on the accuracy of the information. In the presence of asymmetric information, the fluctuations in the stock market would have serious harmful consequences on the economy.Originality/valueAmid several controversies surrounding the EMH testing, this study is a modest attempt to provide evidence that the Indian stock market is in weak-form inefficient. However, it is essential to link investors' behaviour and trends observed in the financial sector to fully understand the implications of EMH.
Exploring the planning practices of nurse managers in the unit: a study of nurse managers in the greater Accra region
Authors: Ansah Ofei Adelaide Maria , Parima Yennuten , Achempim-Ansong Gloria , Barnes Theresa 
Published: April 2022

PurposeNurse managers’ planning practices are essential to the practice of management in the unit, and the overall efficiency of the healthcare service delivery. This study aims to explore the planning practices of nurse managers in the Greater Accra Region, Ghana.Design/methodology/approachA descriptive phenomenological design was employed to explore nurse managers' planning practices. In total, 15 nurse managers and 47 nurses from 19 primary and secondary hospitals of the Ghana Health Service and two specialized hospitals in the Greater Accra Region, Ghana, were involved in the study. Data were collected using semi-structured interview guides and probes.FindingsThe findings suggested that plans were widely common to all the units of the hospitals and were considered satisfactory by nurse managers. However, most of these plans were not effectively utilized. Nurse managers had only fair knowledge about the planning process and were moderately involved and communicated ideas to colleagues in the process. Furthermore, nurse managers do not frequently share the vision neither do they even communicate expectations to achieve unit goals and objectives with subordinates.Originality/valueThe research emphasizes the relevance of planning in healthcare management. It highlights the management practice of planning in the context of nurse managers and accentuates the values the healthcare system derives with effective planning practices.