bluuebunny/crossref_metadata_2025_split huggingface dataset:
Linking the Resistome and Plasmidome to the Microbiome
Authors: Stalder Thibault , Press Max , Sullivan Shawn , Liachko Ivan , Top Eva M. 
Published: December 2018

AbstractThe rapid spread of antibiotic resistance is a serious human health threat. A range of environments have been identified as reservoirs of the antibiotic resistance genes (ARGs) found in pathogens. However, we lack understanding of the origins of these ARGs and their spread from environment to clinic. This is partly due to our inability to identify the bacterial hosts of ARGs and the mobile genetic elements that mediate this spread, such as plasmids and integrons. Here we demonstrated that the in vivo proximity ligation method Hi-C can determine the in situ host range of ARGs, plasmids, and integrons in a wastewater sample by physically linking them to their host chromosomes. Hi-C detected both previously known and novel associations between ARGs, mobile elements and host genomes, mostly validating this method. A better identification of the natural carriers of ARGs will aid the development of strategies to limit resistance spread to pathogens.
Human cortical organoids expose a differential function of GSK3 on direct and indirect neurogenesis
Authors: López-Tobón Alejandro , Villa Carlo Emanuele , Cheroni Cristina , Trattaro Sebastiano , Caporale Nicolò , Conforti Paola , Iennaco Raffaele , Lachgar Maria , Rigoli Marco Tullio , de la Cruz Berta Marcó , Riso Pietro Lo , Tenderini Erika , Troglio Flavia , de Simone Marco , Liste-Noya Isabel , Piccolo Stefano , Macino Giuseppe , Pagani Massimiliano , Cattaneo Elena , Testa Giuseppe 
Published: December 2018

SummaryThe regulation of proliferation and polarity of neural progenitors is crucial for the development of the brain cortex, with modes and timings of cell division intimately related to the stereotypical acquisition of layer-specific neuronal identities. Animal studies have implicated glycogen synthase kinase 3 (GSK3) as a pivotal regulator of both proliferation and polarity, yet the functional relevance of its signaling for the unique features of human corticogenesis remain to be elucidated. Here we harness human cortical brain organoids to probe the longitudinal impact of GSK3 inhibition through multiple developmental stages. Our results indicate that chronic GSK3 inhibition increases the proliferation of neural progenitors and causes massive derangement of cortical tissue architecture. Surprisingly, single cell transcriptome profiling revealed only a discrete impact on early neurogenesis and uncovered a pivotal role of GSK3 in the regulation of NEUROD1/2 lineages and outer radial glia (oRG) output, without compromising direct neurogenic trajectories. Through this first single cell-level dissection of the GSK3 regulatory network in human corticogenesis, our work underscores the robustness of transcriptional programs in determining neuronal identity independent of tissue architecture.
A field guide for the compositional analysis of any-omics data
Authors: Quinn Thomas P. , Erb Ionas , Gloor Greg , Notredame Cedric , Richardson Mark F. , Crowley Tamsyn M. 
Published: December 2018

AbstractNext-generation sequencing (NGS) has made it possible to determine the sequence and relative abundance of all nucleotides in a biological or environmental sample. Today, NGS is routinely used to understand many important topics in biology from human disease to microorganism diversity. A cornerstone of NGS is the quantification of RNA or DNA presence as counts. However, these counts are not counts per se: the magnitude of the counts are determined arbitrarily by the sequencing depth, not by the input material. Consequently, counts must undergo normalization prior to use. Conventional normalization methods require a set of assumptions: they assume that the majority of features are unchanged, and that all environments under study have the same carrying capacity for nucleotide synthesis. These assumptions are often untestable and may not hold when comparing heterogeneous samples (e.g., samples collected across distinct cancers or tissues). Instead, methods developed within the field of compositional data analysis offer a general solution that is assumption-free and valid for all data. In this manuscript, we synthesize the extant literature to provide a concise guide on how to apply compositional data analysis to NGS count data. In doing so, we review zero replacement, differential abundance analysis, and within-group and between-group coordination analysis. We then discuss how this pipeline can accommodate complex study design, facilitate the analysis of vertically and horizontally integrated data, including multiomics data, and further extend to single-cell sequencing data. In highlighting the limitations of total library size, effective library size, and spike-in normalizations, we propose the log-ratio transformation as a general solution to answer the question, “Relative to some important activity of the cell, what is changing?”. Taken together, this manuscript establishes the first fully comprehensive analysis protocol that is suitable for any and all -omics data.
Role of Physicochemical Properties of Protein in Modulating the Nanoparticle-Bio interface
Authors: Dhar Sunandan , Sood Vishesh , Lohiya Garima , Devenderan Harini , Katti Dhirendra S. 
Published: December 2018

AbstractNanoparticles, on exposure to the biological milieu, tend to interact with macromolecules to form a biomolecular corona. The biomolecular corona confers a unique biological identity to nanoparticles, and its protein composition plays a deterministic role in the biological fate of nanoparticles. The physiological behavior of proteins stems from their physicochemical aspects including surface charge, hydrophobicity, and structural stability. However, there is insufficient understanding about the role of physicochemical properties of proteins in biomolecular corona formation. We hypothesized that the physicochemical properties of proteins would influence their interaction with nanoparticles and have a deterministic effect on nanoparticle-cell interactions. To test our hypothesis, we used model proteins from different structural classes to understand the effect of secondary structure elements of proteins on the nanoparticle-protein interface. Further, we modified the surface of proteins to study the role of protein surface characteristics in governing the nanoparticle-protein interface. For this study, we used mesoporous silica nanoparticles as a model nanoparticle system. We observed that the surface charge of proteins governs the nature of the primary interaction as well as the extent of subsequent secondary interactions causing structural rearrangements of the protein. We also observed that the secondary structural contents of proteins significantly affected both the extent of secondary interactions at the nanoparticle-protein interface and the dispersion state of the nanoparticle-protein complex. Further, we also studied the interactions of different protein-coated nanoparticles with different types of cell (fibroblast, carcinoma, and macrophage). We observed that different cells internalized nanoparticle-protein complex as a function of secondary structural components of the protein. The type of model protein had a significant effect on their internalization by macrophages. Overall, we observed that the physicochemical characteristics of proteins had a significant role in modulating the nanoparticle-bio-interface at the level of both biomolecular corona formation and nanoparticle internalization by cells.
SARM1 deficiency, which prevents Wallerian degeneration, upregulates XAF1 and accelerates prion disease
Authors: Zhu Caihong , Li Bei , Frontzek Karl , Liu Yingjun , Aguzzi Adriano 
Published: December 2018

AbstractSARM1 (sterile α and HEAT/armadillo motifs containing protein) is a member of the MyD88 (myeloid differentiation primary response gene 88) family which mediates innate immune responses. Because inactivation of SARM1 prevents various forms of axonal degeneration, we tested whether it might protect against prion-induced neurotoxicity. Instead, we found that SARM1 deficiency exacerbates the progression of prion pathogenesis. This deleterious effect was not due to SARM1-dependent modulation of prion-induced neuroinflammation, since microglial activation, astrogliosis and brain cytokine profiles were not altered by SARM1 deficiency. Whole-transcriptome analyses indicated that SARM1 deficiency led to strong, selective overexpression of the pro-apoptotic gene XAF1 (X-linked inhibitor of apoptosis-associated factor 1). Consequently, the activity of proapoptotic caspases and neuronal death were enhanced in prion-infected SARM1−/− mice. These results point to an unexpected function of SARM1 as a regulator of prion-induced neurodegeneration, and suggest that XAF1 might constitute a therapeutic target in prion disease.
Temporal identity establishes columnar neuron morphology, connectivity, and function in a Drosophila navigation circuit
Authors: Sullivan Luis F. , Warren Timothy L. , Doe Chris Q. 
Published: December 2018

AbstractThe insect central complex (CX) is a conserved brain region containing 60+ neuronal subtypes, several of which contribute to navigation. It is not known how CX neuronal diversity is generated or how developmental origin of subtypes relates to function. We mapped the developmental origin of four key CX subtypes and found that neurons with similar origin have matching axon/dendrite targeting. Moreover, we found that the temporal transcription factor (TTF) Eyeless/Pax6 regulates the development of two recurrently-connected CX subtypes: Eyeless loss simultaneously produces ectopic P-EN neurons with normal axon/dendrite projections, and reduces the number of E-PG neurons. Furthermore, the transient loss of Eyeless during development impairs adult flies’ capacity to perform celestial navigation. We conclude that neurons with similar developmental origin have similar connectivity, that Eyeless maintains equal E-PG and P-EN neuron number, and that Eyeless is required for the development of circuits that control adult navigation.
Building employees’ organizational citizenship behavior for the environment
Authors: Luu Tuan Trong 
Published: December 2018

PurposeMechanisms behind employees’ pro-environmental behaviors have increasingly been attracting scholarly attention. The purpose of this study is to examine how environmentally specific servant leadership contributes to employees’ organizational citizenship behavior for the environment (employee OCBE).Design/methodology/approachIn this research, employees from resort hotels in Central Vietnam were selected as participants. The data analysis was conducted through structural equation modeling and bootstrapping test.FindingsEnvironmentally specific servant leadership exhibited the positive association with employee OCBE through employee environmental engagement as a mediator. Two moderation mechanisms – organizational support for green behaviors and person-group fit – were also found to serve as enhancers for the effect of environmentally specific servant leadership on employee OCBE.Practical implicationsThe research results provide hospitality organizations with a premise for the focus of servant leadership and organizational support around pro-environmental values. It is also vital for practitioners to build the fit between employees and the organization’s pro-environmental values so as to further promote their positive reaction to environmentally specific servant leadership and engagement in pro-environmental behaviors.Originality/valueThe present study marks the confluence between environmentally specific servant leadership and employee OCBE research streams and provides a moderated mediation mechanism to shed light on such a relationship.
Utilizing the Push-Pull-Mooring-Habit framework to explore users’ intention to switch from offline to online real-person English learning platform
Authors: Chen Yu-Hsin , Keng Ching-Jui 
Published: December 2018

Purpose
The purpose of this paper is to develop an extended Push-Pull-Mooring-Habit (PPMH) framework in order to better understand users’ intention of switching from offline to an online real-person English learning platform service.

Design/methodology/approach
Based on 301 valid responses collected from an online survey questionnaire, structural equation modeling was employed to examine the research model.

Findings
The causal model was validated using SmartPLS 3.0, and all study hypotheses were supported. The results show that push effects (learning convenience, service quality and perceived price), pull effects (e-learning motivation, perceived usefulness), mooring effects (learning engagement, switching cost and social presences) and habit effects (relationship inertia) all significantly influence users’ switching intentions from offline to an online real-person English learning platform.

Practical implications
The findings should help online English learning service providers and marketers to understand the intention of offline English learning users to switch to an online real-person English learning platform, and develop related theories, services and regulations.

Originality/value
The present study extends the prior research of an online real-person English learning platform by providing PPMH as the general framework and demonstrating its efficacy in explaining user switching intentions.
The informational value of feedback choices for performance and revision in a digital assessment game
Authors: Cutumisu Maria 
Published: December 2018

Purpose
This study aims to examine the impact of the informational value of feedback choices (confirmatory versus critical feedback) on students’ performance, their choice to revise and the time they spend designing posters and reading feedback in a computer-based assessment game, Posterlet.

Design/methodology/approach
An empirical correlational study was conducted to collect the choices to seek confirmatory or critical feedback and to revise posters in a poster design task from 106 grade 8 students from a middle school in California via Posterlet.

Findings
The results of the study show that critical uninformative feedback is associated with students’ performance, and critical informative feedback is associated with their learning strategies (i.e. feedback dwell time and willingness to revise), while confirmatory informative feedback is negatively associated with both performance and learning strategies.

Research limitations/implications
The study controlled the choice students were given regarding the valence of their feedback but not regarding the informational value of their feedback. Additionally, the study was conducted with middle-school students, and more research is needed to ascertain whether the results generalize to other populations.

Practical implications
The findings can be used to balance the design of the informational content of feedback messages to support student performance in an open-ended, creative design task. This study may also inform the design and implementation of agents (e.g. virtual characters) able to provide user-adaptive feedback for online interactive learning environments.

Originality/value
This study constitutes the first research to examine the informational value of feedback that is chosen rather than received, the latter being the prevalent model of delivering feedback in education.
Incorporating risk into technical efficiency for Vietnam’s and ASEAN banks
Authors: Ngo Tra Thanh , Le Minh Quang , Ngo Thanh Phu 
Published: December 2018

Purpose
The purpose of this paper is to incorporate risk in technical efficiency of ASEAN banks in a panel data framework for the period 2000 to 2015.

Design/methodology/approach
The directional distance function and semi-parametric framework are employed to estimate efficiency scores for two scenarios, one with only good outputs and the other with a combination of good and bad outputs.

Findings
The findings show there is no evidence of technological progress for banks in ASEAN and concerns about the outperformance of Vietnam’s banks. In addition, performance of Vietnam’s banks tends to be distorted by low level of loan loss reserves.

Practical implications
To reflect the true performance and shorten the period of removing bad assets, the State Bank of Vietnam can request banks in Vietnam to book more loan loss reserves.

Originality/value
By examining such a new approach, this study makes an early attempt to incorporate credit risk into the banking efficiency in ASEAN region.
Information self-disclosure on mobile instant messaging applications
Authors: Mouakket Samar 
Published: December 2018

PurposeThe purpose of this paper is to develop a conceptual framework, which identifies intrinsic, social and extrinsic gratification factors as essential individual factors influencing users’ disclosure of personal information via mobile instant messaging (MIM) applications (apps). In addition, the author has examined whether gender affects those different factors of gratification.Design/methodology/approachData are collected via paper-based survey from university students who use MIM in the United Arab Emirates. Structural equation modeling is used to test the hypotheses that are presented in the model.FindingsThe findings show that intrinsic gratifications (entertainment and escapism) and social gratifications (social interaction) have positive effects on the depth and breadth of self-disclosure via MIM apps. Additionally, women’s self-disclosure of personal information is positively affected by social influence, while men are not influenced by this type of gratification.Originality/valueThe study aims to enhance the current understanding of the limited research on the uses and gratifications approach within the context of MIM apps to identify the gratifications that motivate MIM apps users to disclose personal information.
Reducing emergency department visits among older adults
Authors: Chen Daniel , Torstrick Alex M. , Crupi Robert , Schwartz Joseph E. , Frankel Ira , Brondolo Elizabeth 
Published: December 2018

Purpose
There is mixed evidence regarding the efficacy of low-intensity integrated care interventions in reducing the use of emergency services and costs of care. The purpose of this paper is to examine the effects of a low-intensity intervention formulated for older adults and delivered in an urban medical center serving low-income individuals.

Design/methodology/approach
The intervention included an initial evaluation of stress, psychiatric symptomatology and health habits; potential referrals for lifestyle management and psychiatric treatment; and training for physicians about the impact of lifestyle change in older adults. Participants included older adults (at or above 50 years of age) seen as outpatients in an urban medical center serving a low-income community (n=945). Participants were entered into the intervention at any point during this two-year period. Mixed models analyses examined all visits for all enrolled individuals over a two-year period, comparing visits before the individual received the initial intervention evaluation to those received after this evaluation. Outcomes included total health care costs incurred, average cost per visit, and emergency department (ED) usage within the facility.

Findings
The intervention was associated with reduced likelihood of emergency department use and reduced costs per visit following the intervention. These effects were seen across all participants.

Research limitations/implications
Limitations of the study include the lack of control group.

Practical implications
This program is easy to disseminate and could improve the quality of care and costs.

Originality/value
This study is among the few available to document a decrease in medical costs, as well as decreased ED utilization following a low-intensity integrated care intervention.
HealthPathways implementation on type 2 diabetes
Authors: Chow Josephine S.F. , Gonzalez-Arce Veronica Eugenia , Tam Chun Wah Michael , Neville Ben , McDougall Alan 
Published: December 2018

Purpose
The purpose of this paper is to appraise the development, implementation and acceptance of HealthPathways (HP), specifically in Type 2 Diabetes Mellitus (T2DM), at different levels of the health system in a large metropolitan Local Health District in Australia.

Design/methodology/approach
This study used a programmatic approach and mixed methods including literature reviews, site visits, semi-structured interviews of stakeholders and General Practitioners (GPs), and surveys (GPs and patients) to better understand the development, implementation and acceptance of T2DM pathways.

Findings
Results from this study indicate that 63 percent (n=37) of all survey respondents use HP and nearly half (47 percent) use HP in caring for a patient with diabetes. More than 80 percent of the health professionals found HP a useful tool, which has improved the quality of care, keeps them informed and supports diagnostics process. The use of website has led to an improvement in referral quality (69 percent), has assisted in the provision of more healthcare in the community (87 percent) and made their job easier. Thematic analysis from stakeholder interviews (n=12) emphasizes the importance of established collaborations and the need for standardized tools with common priorities and transparency in processes.

Practical implications
This study has provided insight into the details of delivery of integrated healthcare using HP. It provides a preliminary analysis of the lessons learnt for the implementation of HP.

Originality/value
The results of this study will be ideally placed to inform future policy amendments in the area of integrated healthcare as well as serving as a guide on implementing HP in the future.
From summative to developmental
Authors: Steele Gray Carolyn , Shaw James 
Published: December 2018

Purpose
Models of integrated care are prime examples of complex interventions, incorporating multiple interacting components that work through varying mechanisms to impact numerous outcomes. The purpose of this paper is to explore summative, process and developmental approaches to evaluating complex interventions to determine how to best test this mess.

Design/methodology/approach
This viewpoint draws on the evaluation and complex intervention literatures to describe the advantages and disadvantages of different methods. The evaluation of the electronic patient reported outcomes (ePRO) mobile application and portal system is presented as an example of how to evaluate complex interventions with critical lessons learned from this ongoing study.

Findings
Although favored in the literature, summative and process evaluations rest on two problematic assumptions: it is possible to clearly identify stable mechanisms of action; and intervention fidelity can be maximized in order to control for contextual influences. Complex interventions continually adapt to local contexts, making stability and fidelity unlikely. Developmental evaluation, which is more conceptually aligned with service-design thinking, moves beyond these assumptions, emphasizing supportive adaptation to ensure meaningful adoption.

Research limitations/implications
Blended approaches that incorporate service-design thinking and rely more heavily on developmental strategies are essential for complex interventions. To maximize the benefit of this approach, three guiding principles are suggested: stress pragmatism over stringency; adopt an implementation lens; and use multi-disciplinary teams to run studies.

Originality/value
This viewpoint offers novel thinking on the debate around appropriate evaluation methodologies to be applied to complex interventions like models of integrated care.