bluuebunny/crossref_metadata_2025_split huggingface dataset:
Three-dimensional models of the cervicovaginal epithelia to study host-microbiome interactions and sexually transmitted infections
Authors: Edwards Vonetta L. , McComb Elias , Gleghorn Jason P. , Forney Larry , Bavoil Patrik M. , Ravel Jacques 
Published: November 2021

ABSTRACTTwo-dimensional (2D) cell culture systems have provided controlled, reproducible means to analyze host-pathogen interactions. Although inexpensive, straightforward, and requiring very short time commitment, these models recapitulate neither the functionality of multi-layered cell types nor the microbial diversity of an infected human. Animal models have commonly been used to recreate the complexity of human infections. However, extensive modifications are commonly required to recreate interactions that resemble those in the human reproductive tract microbiologically and physiologically. Three-dimensional (3D) cell culture models have emerged as alternative means of reproducing key elements of human infections at a fraction of the cost of animal models and on a scale that allows for replicative experiments to be readily performed. Here we describe a new 3D model that utilizes transwells with epithelial cells seeded apically and a basolateral extra cellular matrix (ECM)-like layer containing collagen and fibroblasts. In this system, basal feeding creates a liquid/air interface on the apical side. The model produced tissues with close morphologic and physiological resemblance to human cervical and vaginal epithelia, including observable levels of mucus produced by cervical cells. Infection by both Chlamydia trachomatis and Neisseria gonorrhoeae was demonstrated as well as the growth of bacterial species observed in the human vaginal microbiota, enabling controlled mechanistic analyses of the interactions between host cells, vaginal microbiota and STI pathogens. Future experiments may include immune cells to mimic more closely the genital environment. Finally, the modular set up of the model makes it fully applicable to the analysis of non-genital host-microbiome-pathogen interactions.IMPORTANCEInfected sites in humans are a complex mix of host and microbial cell types interacting with each other to perform specific and necessary functions. The ability to understand the mechanism(s) that facilitate these interactions, and interactions with external factors is paramount to being able to develop preventative therapies. Models that attempt to faithfully replicate the complexity of these interactions are time intensive, costly, and not conducive to high throughput analysis. Two-dimensional (2D) models that have been used as a platform to understand these interactions, while cost effective, are generally limiting in experimental flexibility and structural/physiological relevance. Our three-dimensional (3D) models of the cervicovaginal epithelium can facilitate analysis of interactions between the host epithelium, sexually transmitted pathogens and bacteria present in the vaginal microbiota. Due to the modular design, additional cell types and environmental modulators can be introduced to the system to provide added complexity, approaching conditions in the infected human host.
A temporally resolved, multiplex molecular recorder based on sequential genome editing
Authors: Choi Junhong , Chen Wei , Minkina Anna , Chardon Florence M. , Suiter Chase C. , Regalado Samuel G. , Domcke Silvia , Hamazaki Nobuhiko , Lee Choli , Martin Beth , Daza Riza M. , Shendure Jay 
Published: November 2021

AbstractDNA is naturally well-suited to serve as a digital medium for in vivo molecular recording. However, DNA-based memory devices described to date are constrained in terms of the number of distinct signals that can be concurrently recorded and/or by a failure to capture the precise order of recorded events1. Here we describe DNA Ticker Tape, a general system for in vivo molecular recording that largely overcomes these limitations. Blank DNA Ticker Tape consists of a tandem array of partial CRISPR-Cas9 target sites, with all but the first site truncated at their 5’ ends, and therefore inactive. Signals of interest are coupled to the expression of specific prime editing guide RNAs2. Editing events are insertional, and record the identity of the guide RNA mediating the insertion while also shifting the position of the “write head” by one unit along the tandem array, i.e. sequential genome editing. In this proof-of-concept of DNA Ticker Tape, we demonstrate the recording and decoding of complex event histories or short text messages; evaluate the performance of dozens of orthogonal tapes; and construct “long tape” potentially capable of recording the order of as many as 20 serial events. Finally, we demonstrate how DNA Ticker Tape simplifies the decoding of cell lineage histories.
Linking host plants to damage types in the fossil record of insect herbivory
Authors: Schachat Sandra R. , Payne Jonathan L. , Boyce C. Kevin 
Published: November 2021

AbstractStudies of insect herbivory on fossilized leaves tend to focus on a few, relatively simple metrics that are agnostic to the distribution of insect damage types among host plants. More complex metrics that link particular damage types to particular host plants have the potential to address additional ecological questions, but such metrics can be biased by sampling incompleteness due to the difficulty of distinguishing the true absence of a particular interaction from the failure to detect it—a challenge that has been raised in the ecological literature. We evaluate a range of methods for characterizing the relationships between damage types and host plants by performing resampling and subsampling exercises on a variety of datasets. We found that the components of beta diversity provide a more valid, reliable, and interpretable method for comparing component communities than do bipartite network metrics. We found the rarefaction of interactions to be a valid, reliable, and interpretable method for comparing compound communities. Both beta diversity and rarefaction of interactions avoid the potential pitfalls of multiple comparisons. Lastly, we found that the host specificity of individual damage types is challenging to assess. Whereas some previously used methods are sufficiently biased by sampling incompleteness to be inappropriate for fossil herbivory data, alternatives exist that are perfectly suitable for fossil datasets with sufficient sample coverage.
Label-Free Prediction of Cell Painting from Brightfield Images
Authors: Cross-Zamirski Jan , Mouchet Elizabeth , Williams Guy , Schönlieb Carola-Bibiane , Turkki Riku , Wang Yinhai 
Published: November 2021

ABSTRACTCell Painting is a high-content image-based assay which can reveal rich cellular morphology and is applied in drug discovery to predict bioactivity, assess toxicity and understand diverse mechanisms of action of chemical and genetic perturbations. In this study, we investigate label-free Cell Painting by predicting the five fluorescent Cell Painting channels from paired brightfield z-stacks using deep learning models. We train and validate the models with a dataset representing 1000s of pan-assay interference compounds sampled from 17 unique batches. The model predictions are evaluated using a test set from two additional batches, treated with compounds comprised from a publicly available phenotypic set. In addition to pixel-level evaluation, we process the label-free Cell Painting images with a segmentation-based feature-extraction pipeline to understand whether the generated images are useful in downstream analysis. The mean Pearson correlation coefficient (PCC) of the images across all five channels is 0.84. Without actually incorporating these features into the model training we achieved a mean correlation of 0.45 from the features extracted from the images. Additionally we identified 30 features which correlated greater than 0.8 to the ground truth. Toxicity analysis on the label-free Cell Painting resulted a sensitivity of 62.5% and specificity of 99.3% on images from unseen batches. Additionally, we provide a breakdown of the feature profiles by channel and feature type to understand the potential and limitation of the approach in morphological profiling. Our findings demonstrate that label-free Cell Painting has potential above the improved visualization of cellular components, and it can be used for downstream analysis. The findings also suggest that label-free Cell Painting could allow for repurposing the imaging channels for other non-generic fluorescent stains of more targeted biological interest, thus increasing the information content of the assay.
3CAC: improving the classification of phages and plasmids in metagenomic assemblies using assembly graphs
Authors: Pu Lianrong , Shamir Ron 
Published: November 2021

AbstractMotivationBacteriophages and plasmids usually coexist with their host bacteria in microbial communities and play important roles in microbial evolution. Accurately identifying sequence contigs as phages, plasmids, and bacterial chromosomes in mixed metagenomic assemblies is critical for further unravelling their functions. Many classification tools have been developed for identifying either phages or plasmids in metagenomic assemblies. However, only two classifiers, PPR-Meta and viralVerify, were proposed to simultaneously identify phages and plasmids in mixed metagenomic assemblies. Due to the very high fraction of chromosome contigs in the assemblies, both tools achieve high precision in the classification of chromosomes but perform poorly in classifying phages and plasmids. Short contigs in these assemblies are often wrongly classified or classified as uncertain.ResultsHere we present 3CAC, a new three-class classifier that improves the precision of phage and plasmid classification. 3CAC starts with an initial three-class classification generated by existing classifiers and improves the classification of short contigs and contigs with low confidence classification by using proximity in the assembly graph. Evaluation on simulated metagenomes and on real human gut microbiome samples showed that 3CAC outperformed PPR-Meta and viralVerify in both precision and recall, and increased F1-score by 10-60 percentage points.AvailabilityThe 3CAC software is available on https://github.com/Shamir-Lab/3CAC.Contactrshamir@tau.ac.ilSupplementary informationSupplementary data are available at Bioinformatics online.
Numerical investigation of heat transfer effects on combustion in a generic gas turbine burner
Authors: Hepkaya Ender , Yucel Nuri 
Published: November 2021

Purpose
This study aims to methodologically investigate heat transfer effects on reacting flow inside a liquid-fueled, swirl-stabilized burner. Furthermore, particular attention is paid to turbulence modeling and the results of Reynolds-averaged Navier–Stokes and large eddy simulation approaches are compared in terms of velocity field and flame temperature.

Design/methodology/approach
Simulations consist liquid fuel distribution using Eulerian–Lagrangian approach. Flamelet-Generated Manifold combustion model, which is a mixture fraction-progress variable formulation, is used to obtain reacting flow field. Discrete ordinates method is also added for modeling radiation heat transfer effect inside the burner. As a parametric study, different thermal boundary conditions namely: adiabatic wall, constant temperature and heat transfer coefficient are applied. Because of the fact that the burner is designed for operating with different materials, the effects of burner material on heat transfer and combustion processes are investigated. Additionally, material temperatures have been calculated using 1 D method. Finally, soot particles, which are source of luminous radiation in gas turbine combustors, are calculated using Moss-Brookes model.

Findings
The results show that the flow behavior is obviously different in recirculation region for both turbulence modeling approach, and this difference causes change on flame temperature distribution, particularly in the outer recirculation zone and region close to swirler. In thermal assessment of the burner, it is predicted that material of the burner walls and the applied thermal boundary conditions have significant influence on flame temperature, wall temperature and flow field. The radiation heat transfer also makes a strong impact on combustion inside the burner; however, luminous radiation arising from soot particles is negligible for the current case.

Originality/value
These types of burners are widely used in research of gas turbine combustion, and it can be seen that the heat transfer effects are generally neglected or oversimplified in the literature. This parametric study provides a basic understanding and methodology of the heat transfer effects on combustion to the researchers.
Usage of mobile phones to support management of agribusiness activities in Indonesia
Authors: Mariyono Joko , Santoso Siswanto Imam , Waskito Jaka , Utomo Akbar Ario Satrio 
Published: November 2021

PurposeThe purpose of this study is to assess the impact of mobile phone usage on sales and profit as the indicator of business performance, to analyse the facilitating roles of mobile phones and factors affecting farmers' decision to use the mobile phone in agribusiness activities.Design/methodology/approachIntensive farming was selected in this study due to its higher profitability than other crops. Data were compiled from field surveys of 1,040 farmer households in vegetable production regions of Indonesia. This study employed structural equation modelling, identifying mediating variables and quantifying multiple endogenous variables' direct and indirect effects in simultaneous regression equations.FindingsThe results indicate that mobile phone usage enabled farmers to increase sales, obtain market information, acquire improved agronomic technology, access credit and contact customers. The device enhanced profit through mediations of high sales, reasonable prices and access to credit and market information. The personal attributes of farmers determined the adoption of mobile phones to support agribusiness activities.Research limitations/implicationsThis study paid attention to the use of mobile phones, which was considered an integral technology of information and communication. Other components, such as personal computers and other Internet-based devices, need further study.Practical implicationsAs the rate of mobile phone use was still low, farmers should be encouraged to utilise the device. Socialisation and specially designed training workshops on agribusiness information systems using mobile phones are of the best ways.Originality/value Using structural equation modelling enables to analyse of multi-dependent variables in one model. Farm-level data provide a real situation, and policy implications should address the right target. The subject of this investigation is a semi-subsistence farm household that lacked access to information and communication technology.
Inducing organizational resilience through collective mindfulness: A path towards an uninterrupted metamorphosis
Authors: Shela V. , Ramayah T. , Ahmad Noor Hazlina 
Published: November 2021

Purpose
This paper aims to highlight the potential role of collective mindfulness as a key success factor for organizational resilience. It also outlines the processes and essential contexts that support the cultivation of collective mindfulness capability in organizations.

Design/methodology/approach
A review of the relevant articles and current development in the area of organizational resilience and collective mindfulness provided an in-depth understanding and valuable insights into how collective mindfulness can be utilized to engender organizational resilience in the challenging business world.

Findings
This paper provides a brief overview over the crucial role of collective mindfulness capability in augmenting organizational resilience. Additionally, the processes of collective mindfulness and the essential contexts for developing and sustaining this capability is also unveiled.

Originality/value
The paper offers practical solutions for the anxiety faced by many organizations around the globe due to the relentless disruptions by highlighting on the potential role of collective mindfulness. It reveals the way that organizations can undertake to wade through the waves imposed by the current volatile environment by leveraging on collective mindfulness capability.
Indigenous heritage in diplomacy: repositioning Taiwan in the Austronesian network and its cultural implications
Authors: Huang Shu-Mei 
Published: November 2021

PurposeThis paper illustrates how Taiwan has tried to mobilize its prehistory Austronesian linguistic heritage and indigenous cultural memories to reposition itself in the Asia-Pacific. It examines how the attempt has gradually evolved into cross-border exchange and partnership based on the interconnectivity across the Pacific on different levels.Design/methodology/approachThe research is based on policy review of the Taiwan government's growing focus on indigenous culture in strategizing diplomacy and cultural policy from 2000 through 2021 and the researcher's participant observation in expert cultural heritage meetings (2018–2021). It is also complemented by semi-structured interviews with both selected state actors and civil actors.FindingsThe past connection among indigenous communities in Taiwan and the Austronesian peoples contributes to building up new cultural circuits across-borders based upon shared indigenous heritage and demonstrates the extraterritorial role of heritage, which can be the potential base for developing diplomacy.Research limitations/implicationsThe research is limited in not directly engaging with actors in the Pacific given limited time, budget and mobility under the coronavirus disease (COVID) pandemic. The author would like to follow on that in her future research.Originality/valueThe paper sheds light on the uneasy relationship between indigenous heritage making and nation building and its cultural implications. This study demonstrates that the state framework of heritage is not necessarily appropriate to deal with these complicated historical matters, especially when the notion of heritage per se is not decolonised in a settler state.
Heritage making and interpretation in postcolonial Harbin: contemporary urban memory of the Russian-built Harbin Railway Station and beyond
Authors: Zhang Wenzhuo 
Published: November 2021

PurposeThis paper critically analyses the urban memory and heritage interpretation of postcolonial Harbin, a city in China that was founded by the Russians in 1898. It investigates the role and making of Russian colonial heritage in contemporary Harbin with a detailed case study of the Harbin Railway StationDesign/methodology/approachResearch methods include archival analysis, observation and semi-structured interview. In-depth interviews were conducted with local people, architect/urban planners and officials.FindingsLocal people of different generations with different backgrounds have different interpretations of the recently made colonial heritage of the Harbin Railway Station. The urban memory of Harbin has been consistently re-forming with both nostalgia and amnesia. Younger generations tend to regard the colonial heritage as their own heritage and a symbol of Harbin's cultural character without considering much about its related colonial history. In today's Harbin, colonial heritage as the “colonial past presencing” is more about a feel of the Europeanised space rather than the actual historical events of the period, and colonial heritage making becomes a tool for urban development and revitalisation at the institutional level. However, due to the paradigm shift in China's urban development, Harbin is facing new challenges in dealing with its colonial heritage.Originality/valueHarbin is an under-researched case in terms of urban heritage studies. This paper offers a new entry point for understanding the westernisation and colonial heritage making in the contemporary China more deeply and thoroughly and helps to see the trend of China's urban development more clearly.
Asymmetric impact of tourism on the balance of payments in Pakistan: evidence from non-linear ARDL
Authors: Rafiq Asim , Aamir Ameer Muhammad , Nadeem Muhammad 
Published: November 2021

PurposeThe aim of the paper is to determine the asymmetric impact of tourism on the deficit in the balance of payments (BOPs).Design/methodology/approachThe research uses the non-linear autoregressive distributed lag (ARDL) model to investigate the asymmetric impact of tourism on Pakistan's BOPs deficit using quarterly data from 1995 to 2019.FindingsThe finding reveals that due to the positive change in tourism, the BOPs deficit decreases by 27%, although due to the negative change in tourism, the BOPs deficit rises by 2.3%. In addition, the significance of F-statistics (10.609) confirms the existence of co-integration between tourism and the deficit in the BOPs. The Wald test confirms the asymmetric association between tourism and the deficit in the BOPs over the long term.Research limitations/implicationsIn order to improve tourism in Pakistan, policymakers must consider the following implications. First, there is a need for an adequate infrastructure that can help the tourist. Second, the Government must maintain a stable law and order situation as a whole and particularly at tourist destinations. Finally, the Government should develop tourism-friendly policies in order to boost tourism in Pakistan.Originality/valueThe research provides new evidence of the impact of tourism on the BOPs using the novel non-linear ARDL (NARDL) technique. The evidence will help policymakers to develop policies to improve tourism in order to reduce the BOPs deficit.
Testing interaction effects of intellectual capital and burnout on innovative work behaviour of professional nurses
Authors: Narzary Genuine , Palo Sasmita 
Published: November 2021

PurposeThe present study aims to examine the moderating effect of burnout between intellectual capital and innovative work behaviour of professional nurses.Design/methodology/approachMixed-method approach was followed that involves conducting both quantitative surveys and qualitative semi-structured interviews. Quantitative data was collected from 844 staff nurses. Interviews were conducted with a total of 20 participants including director of nursing, chief nursing officer, general manager operation, professor cum principal, doctors, nurse educators, ward in charges and staff nurses working with multi, super speciality private and charitable trust hospitals in Mumbai (India).FindingsIntellectual capital and burnout (intellectual capital*burnout) interaction increased the proportion of innovative work behaviour from 0.09 to 0.15, an increase of 66.67%. The results also reveal a significant and negative (−0.09) moderating effect of burnout between intellectual capital and innovative work behaviour of nurses. Qualitative findings also could confirm and support that human, structural and relational capital help nurses to be innovative. However, whenever nurses feel a loss of energy, enthusiasm, motivation and exhaustion, they tend to become less innovative and continue only with the routine works.Research limitations/implicationsThis study provides a new implication for multi, super speciality private and charitable trust hospitals management to relook at and reduce the level of burnout to mitigate its adverse effect.Originality/valueTo the best of the authors’ knowledge, this is the first study and findings related to professional nurses working in multi, super speciality private and charitable trust hospitals in India.