bluuebunny/crossref_metadata_2025_split huggingface dataset:
Redox proteomics of stomatal immunity reveals role of a lipid transfer protein in plant defense
Authors: Balmant Kelly M , Lawrence Sheldon R , Duong Benjamin V , Zhu Fanzhao , Zhu Ning , Nicklay Joshua , Chen Sixue 
Published: May 2020

ABSTRACTRedox-based post-translational modifications (PTMs) involving protein cysteine residues as redox sensors are important to various physiological processes. However, little is known about redox-sensitive proteins in guard cells and their functions in stomatal immunity. In this study, we applied an integrative protein labeling method cysTMTRAQ and identified guard cell proteins that were altered by thiol redox PTMs in response to a bacterial flagellin peptide flg22. In total, eight, seven and 20 potential redox-responsive proteins were identified in guard cells treated with flg22 for 15, 30 and 60 min, respectively. The proteins fall into several functional groups including photosynthesis, lipid binding, oxidation-reduction, and defense. Among the proteins, a lipid transfer protein (LTP)-II was confirmed to be redox-responsive and involved in plant resistance toPseudomonas syringe pv. tomatoDC3000. This study not only creates an inventory of potential redox-sensitive proteins in flg22 signal transduction in guard cells, but also highlights the relevance of the lipid transfer protein in plant defense against the bacterial pathogens.Sentence summaryThiol-redox proteomics identified potential redox sensors important in stomatal immunity, and a lipid transfer protein was characterized to function as a redox sensor in plant immune response.
First passage time study of DNA strand displacement
Authors: Broadwater D. W. Bo , Cook Alexander W. , Kim Harold D. 
Published: May 2020

AbstractDNA strand displacement, where a single-stranded nucleic acid invades a DNA duplex, is pervasive in genomic processes and DNA engineering applications. The kinetics of strand displacement have been studied in bulk; however, the kinetics of the underlying strand exchange were obfuscated by a slow bimolecular association step. Here, we use a novel single-molecule Fluorescence Resonance Energy Transfer (smFRET) approach termed the “fission” assay to obtain the full distribution of first passage times of unimolecular strand displacement. At a frame time of 4.4 ms, the first passage time distribution for a 14-nt displacement domain exhibited a nearly monotonic decay with little delay. Among the eight different sequences we tested, the mean displacement time was on average 35 ms and varied by up to a factor of 13. The measured displacement kinetics also varied between complementary invaders and between RNA and DNA invaders of the same base sequence except for T→U substitution. However, displacement times were largely insensitive to the monovalent salt concentration in the range of 0.25 M to 1 M. Using a one-dimensional random walk model, we infer that the single-step displacement time is in the range of ∼30 µs to ∼300 µs depending on the base identity. The framework presented here is broadly applicable to the kinetic analysis of multistep processes investigated at the single-molecule level.
Membrane bending by protein phase separation
Authors: Yuan Feng , Alimohamadi Haleh , Bakka Brandon , Trementozzi Andrea N. , Fawzi Nicolas L. , Rangamani Padmini , Stachowiak Jeanne C. 
Published: May 2020

AbstractMembrane bending is a ubiquitous cellular process that is required for membrane traffic, cell motility, organelle biogenesis, and cell division. Proteins that bind to membranes using specific structural features, such as wedge-like amphipathic helices and crescent-shaped scaffolds, are thought to be the primary drivers of membrane bending. However, many membrane-binding proteins have substantial regions of intrinsic disorder, which lack a stable three-dimensional structure. Interestingly, many of these disordered domains have recently been found to form networks stabilized by weak, multi-valent contacts, leading to assembly of protein liquid phases on membrane surfaces. Here we ask how membrane-associated protein liquids impact membrane curvature. We find that protein phase separation on the surfaces of synthetic and cell-derived membrane vesicles creates a substantial compressive stress in the plane of the membrane. This stress drives the membrane to bend inward, creating protein-lined membrane tubules. A simple mechanical model of this process accurately predicts the experimentally measured relationship between the rigidity of the membrane and the diameter of the membrane tubules. Discovery of this mechanism, which may be relevant to a broad range of cellular protrusions, illustrates that membrane remodeling is not exclusive to structured scaffolds, but can also be driven by the rapidly emerging class of liquid-like protein networks that assemble at membranes.Significance StatementCellular membranes take on an elaborate set of highly curved and bent shapes, which are essential to diverse cellular functions from endocytosis to cell division. The prevailing view has been that membrane bending is driven by proteins with curved shapes, which assemble at the membrane surface to form solid scaffolds. In contrast, here we show that proteins which form liquid-like assemblies on membranes are also potent drivers of bending. These “liquid scaffolds” apply compressive stress to the membrane surface, generating a diverse and dynamic family of membrane shapes. These data, which come at a time when liquid-like protein assemblies are being identified throughout the cell, suggest that liquid-like protein assemblies may play an important role in shaping cellular membranes.
Raman spectroscopy-based measurements of single-cell phenotypic diversity in microbial communities
Authors: García-Timermans Cristina , Props Ruben , Zacchetti Boris , Sakarika Myrsini , Delvigne Frank , Boon Nico 
Published: May 2020

AbstractMicrobial cells experience physiological changes due to environmental change, such as pH and temperature, the release of bactericidal agents, or nutrient limitation. This, has been shown to affect community assembly and other processes such as stress tolerance, virulence or cell physiology. Metabolic stress is one such physiological changes and is typically quantified by measuring community phenotypic properties such as biomass growth, reactive oxygen species or cell permeability. However, community measurements do not take into account single-cell phenotypic diversity, important for a better understanding and management of microbial populations. Raman spectroscopy is a non-destructive alternative that provides detailed information on the biochemical make-up of each individual cell.Here, we introduce a method for describing single-cell phenotypic diversity using the Hill diversity framework of Raman spectra. Using the biomolecular profile of individual cells, we obtained a metric to compare cellular states and used it to study stress-induced changes. First, in twoEscherichia colipopulations either treated with ethanol or non-treated. Then, in twoSaccharomyces cerevisiaesubpopulations with either high or low expression of a stress reporter. In both cases, we were able to quantify single-cell phenotypic diversity and to discriminate metabolically stressed cells using a clustering algorithm. We also described how the lipid, protein and nucleic acid composition changed after the exposure to the stressor using information from the Raman spectra. Our results show that Raman spectroscopy delivers the necessary resolution to quantify phenotypic diversity within individual cells and that this information can be used to study stress-driven metabolic diversity in microbial communities.ImportanceMicrobes that live in the same community respond differently to stress. This phenomemon is known as phenotypic diversity. Describing this plethora of expressions can help to better understand and manage microbial processes. However, most tools to study phenotypic diversity only average the behaviour of the community. In this work, we present a way to quantify the phenotypic diversity of single cells using Raman spectroscopy - a tool that can describe the molecular profile of microbes. We demonstrate how this tool can be used to quantify the phenotypic diversity that arises after the exposure of microbes to stress. We also show its potential as an ‘alarm’ system to detect when communities are changing into a ‘stressed’ type.
PlasmidHawk: Alignment-based Lab-of-Origin Prediction of Synthetic Plasmids
Authors: Wang Qi , Liu Tian Rui , Leo Elworth R. A. , Treangen Todd J 
Published: May 2020

ABSTRACTWith advances in synthetic biology and genome engineering comes a heightened awareness of potential misuse related to biosafety concerns. A recent study employed machine learning to identify the lab-of-origin of DNA sequences to help mitigate some of these concerns. Despite their promising results, this deep learning based approach had limited accuracy, is computationally expensive to train, and wasn’t able to provide the precise features that were used in its predictions. To address these shortcomings, we have developedPlasmidHawkfor lab-of-origin prediction. Compared to a machine learning approach,PlasmidHawkhas higher prediction accuracy;PlasmidHawkcan successfully predict unknown sequences’ depositing labs 63% of the time and 80% of the time the correct lab is in the top 10 candidates. In addition,PlasmidHawkcan precisely single out the signature sub-sequences that are responsible for the lab-of-origin detection. In summary,PlasmidHawkrepresents a novel, explainable, accurate tool for lab-of-origin prediction of synthetic plasmid sequences.PlasmidHawkis available athttps://gitlab.com/treangenlab/plasmidhawk.git
Investigating the entropy generation around an airfoil in turbulent flow
Authors: Saffarian Mohammad Reza , Jamaati Farzad , Mohammadi Amin , Gholami Malekabad Fatemeh , Ayoubi Ayoubloo Kasra 
Published: May 2020

Purpose
This study aims to evaluate the amount of entropy generation around the NACA 0012 airfoil. This study takes place in four angles of attack of 0°, 5°, 10° and 16° and turbulent regime. Also, the variation in the amount of generated entropy by the changes in temperature and Mach number is investigated.

Design/methodology/approach
The governing equations are solved using computational fluid dynamics techniques. The continuity, momentum and energy equations and the equations of the SST k-ω turbulence model are solved. The entropy generation at different angles of attack is calculated and compared. The effect of various parameters in the generation of entropy is presented.

Findings
Results show that the major part of the entropy generation is at the tip of the airfoil. Also, increasing the angle of attack will increase the entropy generation. Also, results show that with increasing the temperature of air colliding with the airfoil, the production of entropy decreases.

Originality/value
Entropy generation is investigated in the NACA 0012 airfoil at various angles of attack and turbulent flow using the SST turbulence model. Also, the effects of temperature and Mach number on the entropy generation are investigated.
Analyzing reputation of Swiss universities on Twitter–The role of stakeholders, content and sources
Authors: Vogler Daniel 
Published: May 2020

PurposeThis study investigated the reputation of Swiss universities on Twitter. It gives detailed insights on how the reputation of universities was constituted in a digitized media environment.Design/methodology/approachThe reputation of universities was conceptualized as a multidimensional construct with an overarching scientific and corporate dimension. It was measured for academic and societal stakeholders as well as for the media. Tweets about Swiss universities were collected through the Twitter application programming interface (API) and analyzed with a manual content analysis.FindingsAcademic stakeholders had a stronger focus on the scientific dimension of reputation and evaluated universities more positively than societal stakeholders or the news media. The news media were the main source of negative evaluations of universities on Twitter.Research limitations/implicationsThe study showed a dichotomy between the scientific dimension on the one hand, and the corporate dimensions of reputation on the other hand, and thus implies a decoupling of scientific and corporate reputation. However, the findings should be explored beyond Twitter to be more generalizable.Practical implicationsThe news media play an important role in the constitution of the scientific and corporate reputation of universities on Twitter. An orientation toward the news media, therefore, remains a promising strategy to manage reputation.Social implicationsThe news media are an important source of information for academic and societal stakeholders. Thus, they can contribute to integrating academic and societal stakeholder groups by producing a common base of knowledge of higher education and its organizations.Originality/valueThis is the first study to comprehensively measure the reputation of universities on Twitter.
Custom management development program architecture: in pursuit of critical mass for impact
Authors: Haskins Mark E. , Shaffer George R. 
Published: May 2020

Purpose
This article highlights two potentially overlooked and undervalued features of custom management development program architecture that can facilitate and further the positive impact of program participants upon their return to work.

Design/methodology/approach
The insights presented are based on having worked with a number of large, custom management development program clients and seeking to foster greater, better, and a longer lasting impact accruing to the program sponsor when the program participants returned to work.

Findings
Two program design features are highlighted and discussed: (1) tiered critical mass participant throughput and (2) program transportability. A real-world based example is provided to depict these two program design aspects.

Practical implications
The two program design ideas presented are easily understood and immediately actionable for anyone engaged in responding to a custom management development program opportunity with an eye towards enhancing the impact for a sponsoring client.

Originality/value
Organizational sponsors of custom management development programs are interested in their program providers enhancing returning program participants’ ability to impact their work teams, departments, and business units with their program learnings. This article is unique in identifying and describing two potentially overlooked program design considerations that can aid in that pursuit.
Visual mapping of identity: negotiating ethnic identity
Authors: Dekel-Dachs Ofer , Moorlock Emily 
Published: May 2020

Purpose
This paper aims to offer a novel participatory visual research method, the mapping of identity (MOI) protocol that embraces the complex nature of contemporary consumers’ lived reality.

Design/methodology/approach
The MOI protocol is a two-phase methodology. The first phase includes collage creation, based on a taxonomy of attachments, followed by an elicitation interview structured around the participant’s collage. In phase two, the categories elicited in phase one are synthesised into key themes in collaboration between the researcher and the participant.

Findings
MOI methodology provides an effective platform for participants to bring together disjointed memories, fragments and thoughts. Two individual cases are presented that seem similar on the surface; however, when deconstructing these narratives, their lived experiences and the effect that these narratives have on the construction of the self are very different. Treating participants as co-researchers and letting the choices they make in their collage creation lead the interview empowers the participant and enables the researcher to better understand their complex identity articulations.

Research limitations/implications
This study contributes a visual methodology capable of exploring and celebrating the complexities of self-identity.

Practical implications
MOI is a useful tool for facilitating self-exploration in liquid markets. Marketing experts should provide materials that are not too confining and facilitate consumers in expressing multiple voices.

Social implications
The participatory nature of MOI methodology allows for the emergence of stories from those that might otherwise go unheard, helping to understand unfamiliar and sometimes unrecognised identities.

Originality/value
Marketing literature recognises the complex nature of contemporary lived reality; however, some of the intricate aspects of this reality have not been dealt with in all their complexity. A reason for this gap is the paucity of suitable research methods. The MOI protocol presented in this paper addresses this, providing an effective visual tool to explore the complex web of contemporary consumer life.
Digital transformation at logistics service providers: barriers, success factors and leading practices
Authors: Cichosz Marzenna , Wallenburg Carl Marcus , Knemeyer A. Michael 
Published: May 2020

PurposeThe rapid advancement of digital technologies has fundamentally changed the competitive dynamics of the logistics service industry and forced incumbent logistics service providers (LSPs) to digitalize. As many LSPs still struggle in advancing their digital transformation (DT), the purpose of this study is to discover barriers and identify organizational elements and associated leading practices for DT success at LSPs.Design/methodology/approachThis study utilizes a two-stage approach. Stage 1 is devoted to a literature review. Stage 2, based on multiple case studies, analyzes information collected across nine international and global LSPs.FindingsThis research derives a practice-based definition of DT in the logistics service industry, and it has identified five barriers, eight success factors and associated leading practices for DT. The main obstacles LSPs struggle with, are the complexity of the logistics network and lack of resources, while the main success factor is a leader having and executing a DT vision, and creating a supportive organizational culture.Practical implicationsThe results contribute to the emerging field of DT within the logistics and supply chain management literature and provide insights for practitioners regarding how to effectively implement it in a complex industry.Originality/valueThe authors analyze DT from the perspective of LSPs, traditionally not viewed as innovative companies. This study compares their DT with that of other companies.
Mothers' negotiation of welfare support: the emergence of privatized entitlement
Authors: Benjamin Orly 
Published: May 2020

PurposePrevious accounts of exclusion, primarily those proposed in the context of access to welfare, marginalize the role of negotiation and its potential for highlighting distinct barriers and possibilities within specific institutional configurations. Furthermore, when negotiation is examined in the context of access to social services, it is rarely considered as reflecting changes in exclusion or the need to distinguish among exclusionary outcomes in mothers' lives. The author proposes a conceptualization of the distinction between civic exclusion and isolated exclusion, introducing the latter as a specific condition in which mothers are forced to respond to their children's needs by resorting to privatized entitlement.Design/methodology/approachStructured interviews were conducted between 2016 and 2017 with 90 mothers “providing in poverty” from seven marginalized categories in Israel. The interviews were analyzed using a grounded theory perspective.FindingsThree negotiation positions are revealed: positive citizenship, privatized entitlement and inconsistent gains. These positions reflect specific conditions of civic exclusion, which manifests in the form of multiple disadvantage in the lives of mothers, regardless of available forms of welfare support; and isolated exclusion, which manifests as the inability to protect one's children from harsh material scarcity, regardless of attempts to establish eligibility.Research limitations/implicationsLongitudinal data could better reflect the ramifications of isolated exclusion, particularly when translated into privatized entitlement.Practical implicationsThe consequences of isolated exclusion should be studied, in order to prevent negotiation failure leading to this phenomenon.Originality/valueUp until recently, the notion of exclusion was used without relevant distinctions obscuring the meaning of failing to negotiate access to welfare, in mothers' lives. Conceptualizing negative outcomes of negotiation as leading to isolated exclusion and privatized entitlement clarifies the meaning of poverty as dependency. Further, without relevant distinctions, scholars' and activists' effort to introduce higher commitment to mothers' negotiation among street-level bureaucrats cannot be accounted for.
On ontological approaches to academic research in architecture
Authors: Hurol Yonca 
Published: May 2020

Purpose
This study aims to define the main characteristics and possibilities of ontological approaches to research in architecture by considering content, methodologies and subject position in this type of research and questions if there is a future for this type of research or not.

Design/methodology/approach
The primary data collection method of this research is based on the ethos of the author who has taught research courses for many years. This research has also been questioned through the discussions made within a related PhD course.

Findings
Results of this research reveal that the spontaneous ideology of architecture might have influenced the neglection of the ontological approaches in academic research in architecture.

Social implications
Architecture has an interesting position towards reductionism because architectural thinking has ontological characteristics. The ontological approaches to academic research seems to be more applicable to architecture. However, research in architecture does not necessarily have this ontological character.

Originality/value
The “ontological approach to academic research” covers a larger set of research than the method of ontology, which is used to discuss the categories, limitations in research. Thinking on ontological approaches to research is needed because there is a considerable increase in the use of mixed research methods, which combine qualitative and quantitative research. The second reason for this is the criticisms about the unethical reductionism directed towards contemporary science by philosophers. However, there is no sufficient literature on the ontological approaches to research. This is true also for the academic research in architecture.