bluuebunny/crossref_metadata_2025_split huggingface dataset:
Phage cocktail strategies for the suppression of a pathogen in a cross-feeding coculture
Authors: Fazzino Lisa , Anisman Jeremy , Chacón Jeremy M. , Harcombe William R. 
Published: June 2020

SummaryCocktail combinations of bacteria-infecting viruses (bacteriophage), can suppress pathogenic bacterial growth. However, predicting how phage cocktails influence microbial communities with complex ecological interactions, specifically cross-feeding interactions in which bacteria exchange nutrients, remains challenging. Here, we used experiments and mathematical simulations to determine how to best suppress a model pathogen,E. coli, when obligately cross-feeding withS. enterica. We tested whether the duration of pathogen suppression caused by a two-lytic phage cocktail was maximized when both phage targetedE. coli, or when one phage targetedE. coliand the other its cross-feeding partner,S. enterica. Experimentally, we observed that cocktails targeting both cross-feeders suppressedE. coligrowth longer than cocktails targeting onlyE. coli. Two non-mutually-exclusive mechanisms could explain these results: 1) we found that treatment with twoE. coliphage led to the evolution of a mucoid phenotype that provided cross-resistance against both phage, and 2)S. entericaset the growth rate of the co-culture, and therefore targetingS. entericahad a stronger effect on pathogen suppression. Simulations suggested that cross-resistance and the relative growth rates of cross-feeders modulated the duration ofE. colisuppression. More broadly, we describe a novel bacteriophage cocktail strategy for pathogens that cross-feed.Originality-Significance StatementCross-feeding, or exchanging nutrients among bacteria, is a type of ecological interaction found in many important microbial communities. Furthermore, cross-feeding interactions are found to play a role in some infections, and research into treating infections with combinations of bacteriophage in ‘cocktails’ is growing. Here, we used a combination of mathematical modelling and wet-lab experiments to optimize suppression of a model pathogen with a bacteriophage cocktail in a synthetic cross-feeding bacterial coculture. A key finding was that a physiological parameter – growth rate – of the bacteria was important to consider when choosing the most effective cocktail formulation. This work is novel because it highlights an unexpected multispecies-targeting strategy for designing phage cocktails for cross-feeding pathogens and has relevance to many ecological systems ranging from human health to agriculture. We demonstrate how leveraging knowledge of a pathogen’s ecological interaction has the potential to improve precision medicine and management of microbial systems.
Transcription terminator-mediated enhancement in transgene expression in maize: preponderance of the AUGAAU motif overlapping with poly(A) signals
Authors: Wang Po-Hao , Kumar Sandeep , Zeng Jia , McEwan Robert , Wright Terry R. , Gupta Manju 
Published: June 2020

AbstractThe selection of transcription terminators (TTs) for pairing with high expressing constitutive promoters in chimeric constructs is crucial to deliver optimal transgene expression in plants. In this study, the use of the native combinations of four polyubiquitin gene promoters and corresponding TTs resulted in up to >3-fold increase in transgene expression in maize. Of the eight polyubiquitin promoter and TT regulatory elements utilized, seven were novel and identified from the polyubiquitin genes ofBrachypodium distachyon, Setaria italica, andZea mays. Furthermore, gene expression driven by the Cassava mosaic virus promoter was studied by pairing the promoter with distinct TTs derived from the high expressing genes ofArabidopsis. Of the three TTs studied, the polyubiquitin10 gene TT produced the highest transgene expression in maize. Polyadenylation patterns and mRNA abundance from eight distinct TTs were analyzed using 3’-RACE and next-generation sequencing. The results exhibited one to three unique polyadenylation sites in the TTs. The poly(A) site patterns for the StPinII TT were consistent when the same TT was deployed in chimeric constructs irrespective of the reporter gene and promoter used. Distal to the poly(A) sites, putative polyadenylation signals were identified in the near-upstream regions of the TTs based on previously reported mutagenesis and bioinformatics studies in rice andArabidopsis. The putative polyadenylation signals were 9 to 11 nucleotides in length. Six of the eight TTs contained the putative polyadenylation signals that were overlaps of either canonical AAUAAA or AAUAAA-like polyadenylation signals and AUGAAU, a top-ranking-hexamer of rice andArabidopsisgene near-upstream regions. Three of the polyubiquitin gene TTs contained the identical 9-nucleotide overlap, AUGAAUAAG, underscoring the functional significance of such overlaps in mRNA 3’ end processing. In addition to identifying new combinations of regulatory elements for high constitutive trait gene expression in maize, this study demonstrated the importance of TTs for optimizing gene expression in plants. Learning from this study could be applied to other dicotyledonous and monocotyledonous plant species for transgene expression.
Interaction of dengue NS3 with human RNA silencing machinery through HSPA1A
Authors: Kakumani Pavan Kumar , Shanmugam Rajgokul K. , Chinnappan Mahendran , Kaur Inderjeet , Chopra Arun P. , Malhotra Pawan , Mukherjee Sunil K. , Bhatnagar Raj K. 
Published: June 2020

AbstractViruses encode multiple proteins that interact with different host factors to aid in their establishment inside the host. Viral Suppressor of RNA silencing (VSR) are one such class of proteins that have been shown to interact with components of host machinery involved in post transcriptional gene silencing, a known antiviral defence mechanism. In the present study, we showed that dengue NS3, a known VSR not only interacts with HSPA1A, a cellular chaperone, but also modulates its expression levels. Further, we revealed HSPA1A associated with host RNA silencing machinery through its interaction with Argonaute proteins; Ago1, Ago2 and co-localizes with them in the cytoplasm of the cell. Together, these results provide evidence for involvement of other host partners in mediating VSR function of dengue NS3 and aid in deeper understanding of mechanisms underlying viral suppression of RNA silencing.
Stochastic time-dependent enzyme kinetics: closed-form solution and transient bimodality
Authors: Holehouse James , Sukys Augustinas , Grima Ramon 
Published: June 2020

AbstractWe derive an approximate closed-form solution to the chemical master equation describing the Michaelis-Menten reaction mechanism of enzyme action. In particular, assuming that the probability of a complex dissociating into enzyme and substrate is significantly larger than the probability of a product formation event, we obtain expressions for the time-dependent marginal probability distributions of the number of substrate and enzyme molecules. For delta function initial conditions, we show that the substrate distribution is either unimodal at all times or else becomes bimodal at intermediate times. This transient bimodality, which has no deterministic counterpart, manifests when the initial number of substrate molecules is much larger than the total number of enzyme molecules and if the frequency of enzyme-substrate binding events is large enough. Furthermore, we show that our closed-form solution is different from the solution of the chemical master equation reduced by means of the widely used discrete stochastic Michaelis-Menten approximation, where the propensity for substrate decay has a hyperbolic dependence on the number of substrate molecules. The differences arise because the latter does not take into account enzyme number fluctuations while our approach includes them. We confirm by means of stochastic simulation of all the elementary reaction steps in the Michaelis-Menten mechanism that our closed-form solution is accurate over a larger region of parameter space than that obtained using the discrete stochastic Michaelis-Menten approximation.
Tumor Characterization using Unsupervised Learning of Mathematical Relations within Breast Cancer Data
Authors: Axenie Cristian , Kurz Daria 
Published: June 2020

AbstractDespite the variety of imaging, genetic and histopathological data used to assess tumors, there is still an unmet need for patient-specific tumor growth profile extraction and tumor volume prediction, for use in surgery planning. Models of tumor growth predict tumor size and require tumor biology-dependent parametrization, which hardly generalizes to cope with tumor variability among patients. In addition, the datasets are limited in size, owing to the restricted or single-time measurements. In this work, we address the shortcomings that incomplete biological specifications, the inter-patient variability of tumors, and the limited size of the data bring to mechanistic tumor growth models and introduce a machine learning model capable of characterizing a tumor, namely its growth pattern, phenotypical transitions, and volume. The model learns without supervision, from different types of breast cancer data the underlying mathematical relations describing tumor growth curves more accurate than three state-of-the-art models on three publicly available clinical breast cancer datasets, being versatile among breast cancer types. Moreover, the model can also, without modification, learn the mathematical relations among, for instance, histopathological and morphological parameters of the tumor and, combined with the growth curve, capture the (phenotypical) growth transitions of the tumor from a small amount of data. Finally, given the tumor growth curve and its transitions, our model can learn the relation among tumor proliferation-to-apoptosis ratio, tumor radius, and tumor nutrient diffusion length to estimate tumor volume, which can be readily incorporated within current clinical practice, for surgery planning. We demonstrate the broad unsupervised learning and prediction capabilities of our model through a series of experiments on publicly available clinical datasets.
Association between SARS-CoV-2 infection, exposure risk and mental health among a cohort of essential retail workers in the United States
Authors: Lan Fan-Yun , Suharlim Christian , Kales Stefanos N. , Yang Justin 
Published: June 2020

ABSTRACTObjectivesTo investigate SARS-CoV-2 (the virus causing COVID-19) infection and exposure risks among grocery retail workers, and to investigate their mental health state during the pandemic.MethodsThis cross-sectional study was conducted in May 2020 in a single grocery retail store in Massachusetts, USA. We assessed workers’ personal/occupational history and perception of COVID-19 by questionnaire. The health outcomes were measured by nasopharyngeal SARS-CoV-2 reverse transcriptase polymerase chain reaction (RT-PCR) results, GAD-7 (General Anxiety Disorder-7) and PHQ-9 (Patient Health Questionnaire-9).ResultsAmong 104 workers tested, twenty-one (20%) had positive viral assays. Seventy-six percent positive cases were asymptomatic. After multi-variate adjustments, employees with direct customer exposure had an odds of 4.7 (95% CI 1.2 to 32.0) being tested positive for SARS-CoV-2, while smokers had an odds of 0.1 (95% CI 0.01 to 0.8) having positive assay. As to mental health, the prevalence of anxiety and depression (i.e. GAD-7 score > 4 or PHQ-9 score >4) was 24% and 8%, respectively. After adjusting for potential confounders, those able to practice social distancing consistently at work had odds of 0.2 (95% CI 0.1 to 0.7) and 0.1 (95% CI 0.01 to 0.6) screening positive for anxiety and depression, respectively.ConclusionsWe found a considerable asymptomatic SARS-CoV-2 infection rate among grocery workers. Employees with direct costumer exposure were 5 times more likely to test positive for SARS-CoV-2, while cigarette smokers were 90% less likely to have positive assays. Those able to practice social distancing consistently at work had significantly lower risk of anxiety or depression.
Editorial cartoon collections: a review of indexing challenges
Authors: Stead Oliver , Liew Chern Li 
Published: June 2020

PurposeThe difficulty of attributing subject to editorial cartoons for indexing purposes exists both for traditional paper-based cartoon formats and for digitized or born-digital cartoons. This paper presents a selective review of literature on indexing editorial cartoons and the associated challenges.Design/methodology/approachA gap exists in published research on indexing collections of editorial cartoons for online search and retrieval. This paper presents a review of selected works that specifically address the topic of editorial cartoon indexing within a wider context of research that addresses image indexing, subject analysis and indexing challenges more generally. Works that address the interpretation of cartoons by readers and how readers respond to information communicated by editorial cartoons are also considered.FindingsCartoon controversies in transnational and multicultural contexts, experienced through the international news media since 2000, have dramatically increased research attention and publications in this area. Profound changes in media publication since the advent of the Internet have had an impact on editorial cartoonists and cartoon publishing. Subject indexing of editorial cartoons remains a challenge.Research limitations/implicationsThe potential for large indexed cartoon collections to be data-mined for topic modeling for research in the social sciences points to the need for indexers of cartoon collections to improve metadata standards and structures to allow improved access to cartoon metadata for computational analysis.Originality/valueThis paper places discussion of the technical challenges facing indexers of editorial cartoons within a broader context of discussions about the nature and future of editorial cartooning in rapidly changing media and publishing environments.
Lesson Study as a bridge between two learning contexts
Authors: Lundbäck Birgitta , Egerhag Helen 
Published: June 2020

PurposeLesson Study is a model for advancing knowledge about how teachers can enhance teaching through collaboration in schools. This study aims to focus on two learning situations for students in Grades 1–3: elementary school (the first years of school) and school-age educare (activities for students before and after school while their parents are working or studying). The case study aims to describe how teachers use Lesson Study to enhance students' mathematical learning in the two learning situations. The objectives were to describe teachers' perceptions of Lesson Study activities and collaboration and students' knowledge before and after lessons.Design/methodology/approachData were collected as a narrative case study using audio-recorded conversations between researchers and teachers in the different learning contexts. A questionnaire comprising five open-ended questions was used to map students' knowledge of the subject.FindingsTeachers found it advantageous to cooperate with each other across the different learning situations. Mapping students' knowledge before and after a teaching session helped them understand how to create a teaching situation that benefits their students. They saw the value of continued collaboration and called for implementation of the Lesson Study method throughout the school.Research limitations/implicationsAn important limitation of this case study is that it was conducted in a very specific context, and the findings cannot, therefore, be generalized to other situations. However, there is a need for similar case studies to be conducted in different contexts, both in Sweden and in other countries, to pay attention to ways in which elementary schools and school-age educare can develop supplementary teaching situations.Originality/valueThe originality of this case lies in planning and reporting a Lesson Study in two different learning situations in the same school, and the conclusion that educators identify and develop collaborative links in different subjects.
Formulation of historic residential architecture as a background to urban conservation
Authors: Dinler Mesut 
Published: June 2020

PurposeThe paper explores how interpretations of vernacular traditional architecture played a significant role in the development of urban conservation practice in Turkey in the 1960s and 1970s. At the turn of the 20th century, the value of Ottoman historic residential architecture began to develop with the label of the Turkish House. At the turn of the 20th century, historic residential architecture of the Ottoman Empire gained a heritage value and labeled as the Turkish House. Thus, these houses became a part of a national heritage discourse, though their preservation only came to agenda in the early 1970s through preservation programs for Istanbul's waterfront mansions (yali). Turkey simultaneously adapted international heritage developments throughout the 1960s and the 1970s and introduced urban conservation both in practice and in theory to heritage management system of Turkey.Design/methodology/approachThe main research material is derived from the archives of the primary preservation council of Turkey that functioned from 1951 to 1983. The earlier works of the members of the council, journals of the period and urban projects are investigated to outline the complexities of urban conservation.FindingsThis paper explores how modernist efforts of the early 20th century framed traditional Ottoman architecture with the label “Turkish House.” In addition, it reveals how preserving the Turkish House was a major motivation that triggered early urban conservation attempts primarily along Istanbul's Bosporus shores.Originality/valueThe paper outlines dynamics of urban conservation. It outlines that urban conservation did not only emerge as a response to postwar context, but it was also a historic continuation of modernist understandings of “cultural heritage.”
Financialisation and participation in the metropolisation dynamics of European-listed property companies
Authors: Coën Alain , Languillon Raphaël , Simon Arnaud , Zaiter Saadallah 
Published: June 2020

PurposeThis paper aims to explore the relationship between the financialisation dynamics of listed property companies (LPCs) and their participation in the metropolisation dynamics, in ten European countries between 2000 and 2017. The study takes place in a context of globalised real estate markets and modification of traditional urban economics.Design/methodology/approachThe measure of financialisation corresponds to a beta increase, in the sense of the capital asset pricing model, and is corroborated by an informativeness index. LPC-owned properties are classified along two spatial segmentations. Panel models are used to analyse the relation between financial and urban hierarchies (through building arbitrages).FindingsFinancialisation is generally associated with a decrease in the number of assets owned, especially in the Netherlands and the UK, whereas non-financialised companies tend to increase their number of assets, especially in “flight-to-quality” countries such as Germany and Switzerland. In the first case, non-urban spaces and small and medium urban areas are arbitraged in favour of urban cores and metropoles. In the second, investments are reallocated towards hinterlands and the lower segments of the urban hierarchy. Over the study period, the parallelism between the financial hierarchy and the urban hierarchy was reinforced. Spain illustrates the risks of this evolution, whereas Sweden and Belgium present specificities.Originality/valueThis paper illustrates how LPCs function as transmitting channels in the new spatial and urban organisation.
Securitization and earnings management: evidence from the Sarbanes–Oxley act
Authors: Rupp Anin 
Published: June 2020

Purpose
This paper aims to examine whether the opportunistic use of assets securitization for earnings management is systematically widespread. It is hypothesized that with the passage of the Sarbanes–Oxley (SOX) Act of 2002, which imposed more stringent governance over the financial reporting process, there should be a decrease in the opportunistic use of securitization among firms that were not compliant prior to the passage.

Design/methodology/approach
The author use the SOX Act as an exogenous shock to determine whether the act had the intended effect of mitigating opportunistic securitization.

Findings
The empirical results show that there was a significant decrease in securitization among the non-compliant firms relative to the compliant firms and this reduction is related to firms using securitization opportunistically. This evidence suggests that securitization for earnings management was a systematic phenomenon and that SOX was effective in mitigating such behavior.

Originality/value
The contribution of this paper to the literature is twofold. It will identify changes in the use of asset securitization for earnings management purpose by using the exogenous variation in the strength of external governance. Furthermore, it will provide additional evidence of the effectiveness of financial regulations and have potential implications at the policy maker level.
Emotional finance: determinants of phantasy
Authors: Aren Selim , Nayman Hamamcı Hatice 
Published: June 2020

Purpose
In this study, scales are developed for phantasy and its determinants, which is accepted as an important variable in investment preference with an emotional finance perspective. The scales developed in this framework are narrative, divided mind, group feel, informed herding, uninformed herding and phantasy. In addition, the power of these determinants to explain phantasy was investigated.

Design/methodology/approach
For this purpose, the data was obtained between May 01, 2019 and November 30, 2019 via an online survey with convenience sampling. First, a pilot study consisting of 200 subjects was performed. Then, additional data was collected. The total number of subjects was 648. The authors used IBM SPSS Statistics and AMOS for analysis. Exploratory factor analysis and discriminant analysis were performed. In addition, confirmatory factor analysis was performed after an additional data collection process with structural equation modeling.

Findings
As a result of analyses, the validity and reliability of these scales were ensured statistically. It was also found that divided mind directly affects phantasy, but group feel and narrative indirectly affect by informed herding. The “unknown and new investment” preference, which is accepted as a typical feature of the bubble periods, is modeled with the relevant variables. In this framework, it has been found that the variables that refer individuals to the relevant investment preferences are phantasy, group feel, uninformed herding and divided mind.

Originality/value
The study is unique because of its findings and developed scales. The findings are valuable in that the theoretically alleged relations were also obtained empirically.