bluuebunny/crossref_metadata_2025 huggingface dataset:
Improved read/write cost tradeoff in DNA-based data storage using LDPC codes
Authors: Chandak Shubham , Tatwawadi Kedar , Lau Billy , Mardia Jay , Kubit Matthew , Neu Joachim , Griffin Peter , Wootters Mary , Weissman Tsachy , Ji Hanlee
Published: September 2019

With the amount of data being stored increasing rapidly, there is significant interest in exploring alternative storage technologies. In this context, DNA-based storage systems can offer significantly higher storage densities (petabytes/gram) and durability (thousands of years) than current technologies. Specifically, DNA has been found to be stable over extended periods of time which has been demonstrated in the analysis of organisms long since extinct. Recent advances in DNA sequencing and synthesis pipelines have made DNA-based storage a promising candidate for the storage technology of the future.

Recently, there have been multiple efforts in this direction, focusing on aspects such as error correction for synthesis/sequencing errors and erasure correction for handling missing sequences. The typical approach is to use separate codes for handling errors and erasures, but there is limited understanding of the efficiency of this framework. Furthermore, the existing techniques use short block-length codes and heavily rely on read consensus, both of which are known to be suboptimal in coding theory.

In this work, we study the tradeoff between the writing and reading costs involved in DNA-based storage and propose a practical scheme to achieve an improved tradeoff between these quantities. Our scheme breaks with the traditional separation framework and instead uses a single large block-length LDPC code for both erasure and error correction. We also introduce novel techniques to handle insertion and deletion errors introduced by the synthesis process. For a range of writing costs, the proposed scheme achieves 30-40% lower reading costs than state-of-the-art techniques on experimental data obtained using array synthesis and Illumina sequencing.

The code, data, and Supplementary Material is available athttps://github.com/shubhamchandak94/LDPC_DNA_storage.
Multi-omics data analysis implicating epigenetic inheritance in evolution and disease
Authors: Sharma Abhay
Published: September 2019

Recent evidence surprisingly suggests existence of germline mediated epigenetic inheritance in diverse species including mammals. The evolutionary and health implications as well as the mechanistic plausibility of epigenetic inheritance are subjects of immense current interest and controversy, with integrative analysis expected to provide valuable insights. Here, an unbiased gene set enrichment analysis of existing multi-omics data is presented that readily supports a role of sperm DNA methylome in evolution and disease, as also in developmental mechanisms. In mice, differentially methylated sperm genes in cold induced inheritance specifically overrepresent genes associated with cold adaptation. Similarly, in humans, differentially methylated sperm genes associate with disease and adaptation in general, with specific disease association supported by prior evidence. Further, the sperm genes, like disease and adaptation genes, overrepresent genes known to exhibit higher mutability, loss-of-function intolerance, and haploinsufficiency. Finally, both mouse and human sperm genes show enrichment for genes that retain sperm methylation during development and are developmentally expressed. Together, the present analysis provides one-stop evidence to suggest that sperm DNA methylome acts as a melting pot of gene-environment interaction, inheritance, evolution, and health and disease.
Understanding the evolution of interspecies interactions in microbial communities
Authors: Gorter Florien A. , Manhart Michael , Ackermann Martin
Published: September 2019

Microbial communities are complex multi-species assemblages that are characterized by a multitude of interspecies interactions, which can range from mutualism to competition. The overall sign and strength of interspecies interactions have important consequences for emergent community-level properties such as productivity and stability. It is not well understood whether and how interspecies interactions change over evolutionary timescales. Here, we review the empirical evidence that evolution is an important driver of microbial community properties and dynamics on timescales that have traditionally been regarded as purely ecological. Next, we briefly discuss different modelling approaches to study evolution of communities, emphasizing the similarities and differences between evolutionary and ecological perspectives. We then propose a simple conceptual model for the evolution of communities. Specifically, we propose that the evolution of interspecies interactions depends crucially on the spatial structure of the environment. We predict that in well-mixed environments, traits will be selected exclusively for their direct fitness effects, while in spatially structured environments, traits may also be selected for their indirect fitness effects. Selection of indirectly beneficial traits should result in an increase in interaction strength over time, while selection of directly beneficial traits should not have such a systematic effect. We tested our intuitions using a simple quantitative model and found support for our hypotheses. The next step will be to test these hypotheses experimentally and provide input for a more refined version of the model in turn, thus closing the scientific cycle of models and experiments.
The effects of resource subsidy duration on detritus-based stream ecosystem: a stream mesocosm experiment
Authors: Sato Takuya , Ueda Rui , Takimoto Gaku
Published: September 2019

Most of the resource subsidies are temporally variable, and studies have revealed that ecological processes can be mediated by the temporal attributes of subsidies, such as timing and frequency. Less studies have, however, examined the effects of the subsidy duration, an another major temporal attribute, on consumer populations, communities and ecosystem functions. Using an outdoor mesocosm experiment, we demonstrated that, even with the same total amounts, the prolonged subsidy let large-stage fish effectively monopolize the subsidy over small-stage fish, while the pulsed subsidy allowed small-stage fish to increase the ingestion rate of the subsidy. This effect resulted in causing weaker indirect positive effects on in-situ benthic prey and a leaf breakdown rate with the prolonged subsidy than with the pulsed-subsidy although it depended on dominant benthic prey species having different edibility. Increasing evidences have shown that global warming would not only advance, but also prolong the growing seasons, which may, in turn, make subsidies more prolonged. The ecological significance of the subsidy duration might be common in nature, and should be incorporated to better understand ecological processes in spatially and temporally coupled ecosystems.
Performance of Turquoise killifish, model organism in aging, on commercial pelleted diet: a step towards husbandry standardization
Authors: Žák Jakub , Dyková Iva , Reichard Marin
Published: September 2019

Dietary alteration is one of the most universally effective aging interventions, making its standardization a fundamental need for model organisms in aging. Here we address the current lack of standardized formulated diet for Turquoise KillifishNothobranchius furzeri– a promising model organism. We first demonstrated thatN. furzerican be fully weaned onto a standardized commercially available pelleted diet as the sole nutrition when kept in social tanks. We then compared nine somatic and six reproductive parameters between fish fed a typical laboratory diet - frozen chironomid larvae (bloodworms) and fish fed solely on BioMar pellets. Killifish readily consumed the pellets. Although fish consumed 7.5 times less food mass in the form of pellets than bloodworms, they had comparable somatic and reproductive performance. There was no difference between diet groups in body size, specific growth rate, condition or extent of hepatocellular vacuolation. Fish fed a pelleted diet had higher juvenile body mass and more visceral fat. Pellet-fed males had lower liver mass and possessed a lipid type of hepatocellular vacuolation instead of the prevailing glycogen-like vacuolation in the bloodworm-fed group. No significant effect was found on reproductive parameters. The negligible differences between dietary groups and good acceptance of pellets indicates their suitability as a useful starting point for diet standardization (and potential manipulation) inNothobranchius furzeri.
Practical Speedup of Bayesian Inference of Species Phylogenies by Restricting the Space of Gene Trees
Authors: Wang Yaxuan , Ogilvie Huw A. , Nakhleh Luay
Published: September 2019

Abstract

Species tree inference from multi-locus data has emerged as a powerful paradigm in the post-genomic era, both in terms of the accuracy of the species tree it produces as well as in terms of elucidating the processes that shaped the evolutionary history. Bayesian methods for species tree inference are desirable in this area as they have been shown to yield accurate estimates, but also to naturally provide measures of confidence in those estimates. However, the heavy computational requirements of Bayesian inference have limited the applicability of such methods to very small data sets.

In this paper, we show that the computational efficiency of Bayesian inference under the multispecies coalescent can be improved in practice by restricting the space of the gene trees explored during the random walk, without sacrificing accuracy as measured by various metrics. The idea is to first infer constraints on the trees of the individual loci in the form of unresolved gene trees, and then to restrict the sampler to consider only resolutions of the constrained trees. We demonstrate the improvements gained by such an approach on both simulated and biological data.
A deeper understanding of intestinal organoid metabolism revealed by combining fluorescence lifetime imaging microscopy (FLIM) and extracellular flux analyses
Authors: Okkelman Irina A. , Neto Nuno , Papkovsky Dmitri B. , Monaghan Michael , Dmitriev Ruslan I.
Published: September 2019

Stem cells and the niche in which they reside feature a complex microenvironment with tightly regulated homeostasis, cell-cell interactions and dynamic regulation of metabolism. A significant number of organoid models has been described over the last decade, yet few methodologies can enable single cell level resolution analysis of the stem cell niche metabolic demands, in real-time and without perturbing integrity. Here, we studied the redox metabolism of Lgr5-GFP intestinal organoids by two emerging microscopy approaches based on luminescence lifetime measurement – fluorescence-based FLIM for NAD(P)H, and phosphorescence-based PLIM for real-time oxygenation. We found that exposure of stem (Lgr5-GFP) and differentiated (no GFP) cells to high and low glucose concentrations resulted in measurable shifts in oxygenation and redox status. NAD(P)H-FLIM and O2-PLIM both indicated that at high ‘basal’ glucose conditions, Lgr5-GFP cells had lower activity of oxidative phosphorylation when compared with cells lacking Lgr5. However, when exposed to low (0.5 mM) glucose, stem cells utilized oxidative metabolism more dynamically than non-stem cells. The high heterogeneity of complex 3D architecture and energy production pathways of Lgr5-GFP organoids were also confirmed by the extracellular flux (XF) analysis. Our data reveals that combined analysis of NAD(P)H-FLIM and organoid oxygenation by PLIM represents promising approach for studying stem cell niche metabolism in a live readout.
Predicting suitability of regions for Zika outbreaks with zero-inflated models trained using climate data
Authors: Roth Samantha , Teboh-Ewungkem Miranda , Li Ming
Published: September 2019

In recent years, Zika spread through the Americas. This virus has been linked to Guillain-Barré syndrome, which can lead to paralysis, and microcephaly, a severe birth defect. Zika is primarily transmitted by Aedes (Ae.) aegypti, a mosquito whose geographic range has expanded and is anticipated to continue shifting as the climate changes.

We used statistical models to predict regional suitability for autochthonous Zika transmission using climatic variables. By suitability for Zika, we mean the potential for an outbreak to occur based on the climate’s habitability for Ae. aegypti. We trained zero-inflated Poisson (ZIP) and zero-inflated negative binomial (ZINB) regression models to predict Zika outbreak suitability using 20 subsets of climate variables for 102 regions. Variable subsets were selected for the final models based on importance to Ae. aegypti survival and their performance in aiding prediction of Zika-suitable regions. We determined the two best models to both be ZINB models. The best model’s regressors were winter mean temperature, yearly minimum temperature, and population, and the second-best model’s regressors were winter mean temperature and population.

These two models were then run on bias-corrected climate projections to predict future climate suitability for Zika, and they generated reasonable predictions. The predictions find that most of the sampled regions are expected to become more suitable for Zika outbreaks. The regions with the greatest risk have increasingly mild winters and high human populations. These predictions are based on the most extreme scenario for climate change, which we are currently on track for.

Author Summary:

In recent years, Zika spread through the Americas. This virus has been linked to Guillain-Barré syndrome, which can lead to paralysis, and microcephaly, a severe birth defect. Zika is primarily transmitted by Aedes (Ae.) aegypti, a mosquito whose geographic range has expanded and is anticipated to continue shifting as the climate changes. We used statistical models to predict regional suitability for locally-acquired Zika cases using climatic variables. By suitability for Zika, we mean the potential for an outbreak to occur based on the climate’s habitability for Ae. aegypti. We trained statistical models to predict Zika outbreak suitability using 20 subsets of climate variables for 102 regions. Variable subsets were selected for the final two models based on importance to Ae. aegypti survival and their performance in aiding prediction of Zika-suitable regions. These two models were then run on climate projections to predict future climate suitability for Zika, and they generated reasonable predictions. The predictions find that most of the sampled regions are expected to become more suitable for Zika outbreaks. The regions with the greatest risk have high human populations and increasingly mild winters.
%svy_freqs: A generic SAS macro for cross-tabulation between a factor and a by-group variable given a third variable and creating publication-quality tables using data from complex surveys
Authors: Muthusi Jacques , Mwalili Samuel , Young Peter
Published: September 2019

Introduction

In epidemiological studies, cross-tabulations are a simple but important tool for understanding the distribution of socio-demographic characteristics among study participants. They become more useful when comparisons are presented using a by-group variable such as key demographic characteristic or an outcome status; for instance, sex or the presence or absence of a disease status. Most available statistical analysis software can easily perform cross-tabulations, however, output from these must be processed further to make it readily available for review and use in a publication. In addition, performing three-way cross-tabulations of complex survey data such as those required to show the distribution of disease prevalence across multiple factors and a by-group variable is not easily implemented directly using available standard procedures of commonly used statistical software.

Methods

We developed a generic SAS macro, %svy_freqs, to create quality publication-ready tables from cross-tabulations between a factor and a by-group variable given a third variable using survey or non-survey data. The SAS macro also performs classical two-way cross-tabulations and refines output into publication-quality tables. It provides extra features not available in existing procedures such as ability to incorporate parameters for survey design and replication-based variance estimation methods, performing validation checks for input parameters, transparently formatting character variable values into numeric ones and allowing for generalizability.

Results

We demonstrate the application of the SAS macro in the analysis of data from the 2013-2014 National Health and Nutrition Examination Survey (NHANES), a complex survey designed to assess the health and nutritional status of adults and children in the United States (U.S.).

Conclusion

The SAS code use to develop the macro is simple yet comprehensive, easy to follow, straightforward for the end user and simple for a SAS programmer to extend. The SAS macro has shown to shorten turn-around time for statistical analysis, eliminate errors when preparing output, and support reproducible research.
Distribution of Human T-Lymphotropic Virus (HTLV) and Hepatitis C Co-infection in Bahia, Brazil
Authors: Pereira Felicidade Mota , Almeida Maria da Conceição Chagas de , Santos Fred Luciano Neves , Carreiro Roberto Perez , Galvão-Castro Bernardo , Grassi Maria Fernanda Rios
Published: September 2019

Both Human T-lymphotropic virus type 1 (HTLV-1) and hepatitis C virus (HCV) are endemic in Brazil. In Salvador, the capital of the state of Bahia, 2% and 1.5% of the general population is infected with HTLV-1 or HCV. This study aimed to estimate the prevalence and the distribution of HTLV/HCV coinfection in Bahia. This cross-sectional study was conducted at the Central Laboratory of Public Health for the state of Bahia (LACEN-BA). All samples in the LACEN database submitted to serological testing for anti-HCV (chemiluminescence) and anti-HTLV-1/2 (chemiluminescence/ELISA and Western blot) from 2004 to 2013 were included. Infection rate was expressed as the number of infected individuals per 100,000 inhabitants in a given municipality; municipalities were grouped by microregion for further analysis. A total of 120,192 samples originating from 358 of the 417 municipalities in Bahia (85.8%) were evaluated. The overall HCV coinfection rate in HTLV-positive was 14.31% [2.8 (ranging from 0.4 to 8.0) per 100,000 inhabitants.] Twenty-one (5%) of the municipalities reported at least one case of HTLV/HCV coinfection. Most cases (87%) were concentrated in three microregions (Salvador: 79%, Ilhéus/Itabuna: 5%, Porto Seguro: 3%). Coinfection occurred more frequently in males (51%) with a mean age of 59 [(IQR): 46 – 59] years. HTLV/HCV coinfection in the state of Bahia was more frequently found among males living in the microregions of Salvador, Ilhéus/Itabuna and Porto Seguro, all of which are known to be endemic for HTLV infection. Keywords: HTLV; HCV; Coinfection; Bahia; Prevalence
Nuclear gene proximity and protein interactions shape transcript covariances in mammalian single cells
Authors: Tarbier Marcel , Mackowiak Sebastian D. , Frade João , Catuara-Solarz Silvina , Biryukova Inna , Gelali Eleni , Menéndez Diego Bárcena , Zapata Luis , Ossowski Stephan , Bienko Magda , Gallant Caroline J. , Friedländer Marc R.
Published: September 2019

Single-cell RNA sequencing studies into gene co-expression patterns could yield important new regulatory and functional insights, but have so far been limited by the confounding effects of cell differentiation and the cell cycle. We apply a tailored experimental design that eliminates these confounders, and report >80,000 intrinsically covarying gene pairs in mouse embryonic stem cells. These covariances form a network with biological properties, outlining known and novel gene interactions. We provide the first evidence that miRNAs naturally induce transcriptome-wide covariances, and compare the relative importance of nuclear organization, transcriptional and post-transcriptional regulation in defining covariances. We find that nuclear organization has the greatest impact, and that genes encoding for physically interacting proteins specifically tend to covary, suggesting importance for protein complex stoichiometry. Our results lend support to the concept of post-transcriptional ‘RNA operons’, but we further present evidence that nuclear proximity of genes on the same or even distinct chromosomes also provides substantial functional regulation in mammalian single cells.
Small terrestrial mammal distributions in Simien Mountains National Park, Ethiopia: A reassessment after 88 years
Authors: Craig Evan W. , Stanley William T. , Kerbis Peterhans Julian C. , Bryja Josef , Meheretu Yonas
Published: September 2019

Little is known about the distribution and ecology of small mammals inhabiting Simien Mountains National Park despite the presence of mostly endemic species. Prior to this study, the most comprehensive dataset was collected in 1927. This provides a unique opportunity to assess the possible role of climate change over the last 88 years on the elevational distribution of mammals in the Ethiopian highlands. Between September and November 2015, three of us (EWC, WTS, YM) collected non-volant small mammals at four sites (2900, 3250, 3600, and 4000 m a.s.l.) along the western slope of the Simien Mountains using standardized sampling. Over a four-week period we recorded 13 species, comprising 11 rodents and two shrews, all endemic to the Ethiopian Plateau. We found greatest species richness at mid-elevations (3250 m), consistent with a general pattern found on many other mountains worldwide but less so in Africa. We discovered one potentially new species of shrew. No previously unrecorded rodent species were observed. Finally, we compared our species distribution results to the 1927 dataset and found upward elevational shifts in species ranges, suggesting the role and influence of climate change on the small mammal community. Simien Mountains National Park represents an exceptionally valuable core area of endemism and the best protected natural habitat in northern Ethiopia.
A novel antibody targeting ICOS increases intratumoural cytotoxic to regulatory T cell ratio and induces tumour regression
Authors: Sainson Richard C.A. , Thotakura Anil K. , Kosmac Miha , Borhis Gwenoline , Parveen Nahida , Kimber Rachael , Carvalho Joana , Henderson Simon , Pryke Kerstin , Okell Tracey , O’Leary Siobhan , Ball Stuart , Gamand Lauriane , Taggart Emma , Pring Eleanor , Ali Hanif , Craig Hannah , Wong Vivian W. Y. , Liang Qi , Rowlands Robert J. , Lecointre Morgane , Campbell Jamie , Kirby Ian , Melvin David , Germaschewski Volker , Oelmann Elisabeth , Quaratino Sonia , McCourt Matthew
Published: September 2019

The immunosuppressive tumour microenvironment constitutes a significant hurdle to the response to immune checkpoint inhibitors. Both soluble factors and specialised immune cells such as regulatory T cells (TReg) are key components of active intratumoural immunosuppression. Previous studies have shown that Inducible Co-Stimulatory receptor (ICOS) is highly expressed in the tumour microenvironment, especially on TReg, suggesting that it represents a relevant target for preferential depletion of these cells. Here, we used immune profiling of samples from tumour bearing mice and cancer patients to characterise the expression of ICOS in different tissues and solid tumours. By immunizing anIcosknockout transgenic mouse line expressing antibodies with human variable domains, we selected a fully human IgG1 antibody called KY1044 that binds ICOS from different species. Using KY1044, we demonstrated that we can exploit the differential expression of ICOS on T cell subtypes to modify the tumour microenvironment and thereby improve the anti-tumour immune response. We showed that KY1044 induces sustained depletion of ICOShighTRegcells in mouse tumours and depletion of ICOShighT cells in the blood of non-human primates, but was also associated with secretion of pro-inflammatory cytokines from ICOSlowTEFFcells. Altogether, KY1044 improved the intratumoural TEFF:TRegratio and increased activation of TEFFcells, resulting in monotherapy efficacy or in synergistic combinatorial efficacy when administered with the immune checkpoint blocker anti-PD-L1. In summary, our data demonstrate that targeting ICOS with KY1044 can favourably alter the intratumoural immune contexture, promoting an anti-tumour response.
Integrating genome-wide association and transcriptome predicted model identify novel target genes with osteoporosis
Authors: Yin Peng , Zhu Muchun , Hu Fan , Jiang Jiaxin , Yin Li , Wang Shuqiang , Li Yingxiang
Published: September 2019

Osteoporosis (OP) is a highly polygenetic disease which is usually characterized by low bone mineral density. Genome-wide association studies (GWAS) have identified hundreds of genetic loci associated with bone mineral density. However, the biological mechanisms of these loci remain elusive. To identify potential causal genes of the associated loci, we detected trait-gene expression associations by transcriptome-wide association study (TWAS) method. It directly imputes gene expression effects from GWAS data, using a statistical prediction model trained on GTEx reference transcriptome data, with blood and skeletal tissues data. Then we performed a colocalization analysis to evaluate the posterior probability of biological patterns: association characterized by a single shared causal variant or two distinct causal variants. The ultimate analysis identified 276 candidate genes, including 3 novel loci, 204 novel candidate genes and 69 replicated from GWAS. The 3 novel loci located at chr6: 72417543, chr15: 69601206, chr21: 30530692, mapping to gene RIMS1, SPESP1, MAP3K7CL. The results of colocalization analysis indicated that 142 of them showing strong evidence of a single shared causal variant and 134 of them showing evidence of joint causal variants. Their biological function was directly or indirectly associated with the occurrence of OP validated by VarElect tool. Several important OP-associated pathways were detected by protein-protein interaction and pathway enrichment analysis. Target genes were further enriched for differential expression genes in osteoblasts expression profiles, e.g. IBSP, affecting calcium and hydroxyapatite binding, and CD44, regulating alternative splicing of gene transcription. Transcriptome fine-mapping identifies more disease-related genes and provide additional insight into the development of novel targeted therapeutics to treat OP.
centroFlye: Assembling Centromeres with Long Error-Prone Reads
Authors: Bzikadze Andrey V. , Pevzner Pavel A.
Published: September 2019

Although variations in centromeres have been linked to cancer and infertility, centromeres still represent the “dark matter of the human genome” and remain an enigma for both biomedical and evolutionary studies. Since centromeres have withstood all previous attempts to develop an automated tool for their assembly and since their assembly using short reads is viewed as intractable, recent efforts attempted to manually assemble centromeres using long error-prone reads. We describe the centroFlye algorithm for centromere assembly using long error-prone reads, apply it for assembling the human X centromere, and use the constructed assembly to gain insights into centromere evolution. Our analysis reveals putative breakpoints in the previous manual reconstruction of the human X centromere and opens a possibility to automatically close the remaining multi-megabase gaps in the reference human genome.
JunB controls intestinal effector programs in regulatory T cells
Authors: Wheaton Joshua D. , Ciofani Maria
Published: September 2019

Foxp3-expressing regulatory T (Treg) cells are critical mediators of immunological tolerance to both self and microbial antigens. Tregs activate context-dependent transcriptional programs to adapt effector function to specific tissues; however, the factors controlling tissue-specific gene expression in Tregs remain unclear. Here, we find that the AP-1 transcription factor JunB regulates the intestinal adaptation of Tregs by controlling select gene expression programs in multiple Treg subsets. Treg-specific ablation of JunB results in immune dysregulation characterized by enhanced colonic T helper cell accumulation and cytokine production. However, in contrast to its classical binding-partner BATF, JunB is dispensable for maintenance of effector Tregs as well as most specialized Treg subsets. In the Peyer’s patches, JunB activates a transcriptional program facilitating the maintenance of CD25- Tregs, leading to the complete loss of T follicular regulatory cells in the absence of JunB. This defect is compounded by loss of a separate effector program found in both major colonic Treg subsets that includes the cytolytic effector molecule granzyme B. Therefore, JunB is an essential regulator of intestinal Treg effector function through pleiotropic effects on gene expression.
The MYB Activator WHITE PETAL1 Associates with MtTT8 and MtWD40-1 to Regulate Carotenoid-Derived Flower Pigmentation in Medicago truncatula
Authors: Meng Yingying , Wang Zuoyi , Wang Yiqin , Wang Chongnan , Zhu Butuo , Liu Huan , Ji Wenkai , Wen Jiangqi , Chu Chengcai , Tadege Million , Niu Lifang , Lin Hao
Published: September 2019

Carotenoids are a group of natural tetraterpenoid pigments with indispensable roles in the plant life cycle and the human diet. Although the carotenoid biosynthetic pathway has been well characterized, the regulatory mechanisms that control carotenoid metabolism, especially in floral organs, remain poorly understood. In this study, we identified an anthocyanin-related R2R3-MYB protein, WHITE PETAL1 (WP1), that plays a critical role in regulating floral carotenoid pigmentation in Medicago truncatula. Carotenoid analyses showed that the yellow petals of the wild-type M. truncatula contained high concentrations of carotenoids that largely consisted of esterified lutein and that disruption of WP1 function via Tnt1 insertion led to substantially reduced lutein accumulation. WP1 mainly functions as a transcriptional activator and directly regulates the expression of carotenoid biosynthetic genes including MtLYCe and MtLYCb through its C-terminal acidic activation motif. Further molecular and genetic analyses revealed that WP1 physically interacts with MtTT8 and MtWD40-1 proteins and that this interaction facilitates WP1’s function in the transcriptional activation of both carotenoid and anthocyanin biosynthetic genes. Our findings demonstrate the molecular mechanism of WP1-mediated regulation of floral carotenoid pigmentation and suggest that the conserved MYB-basic-helix-loop-helix-WD40 regulatory module functions in carotenoid biosynthesis in M. truncatula, with specificity imposed by the MYB partner.
DeepRes: a new deep-learning- and aspect-based local resolution method for electron-microscopy maps
Authors: Ramírez-Aportela Erney , Mota Javier , Conesa Pablo , Carazo Jose Maria , Sorzano Carlos Oscar S.
Published: September 2019

In this article, a method is presented to estimate a new local quality measure for 3D cryoEM maps that adopts the form of a `local resolution' type of information. The algorithm (DeepRes) is based on deep-learning 3D feature detection. DeepRes is fully automatic and parameter-free, and avoids the issues of most current methods, such as their insensitivity to enhancements owing to B-factor sharpening (unless the 3D mask is changed), among others, which is an issue that has been virtually neglected in the cryoEM field until now. In this way, DeepRes can be applied to any map, detecting subtle changes in local quality after applying enhancement processes such as isotropic filters or substantially more complex procedures, such as model-based local sharpening, non-model-based methods or denoising, that may be very difficult to follow using current methods. It performs as a human observer expects. The comparison with traditional local resolution indicators is also addressed.
Improving accountability for farm animal welfare: the performative role of a benchmark device
Authors: McLaren Josie , Appleyard Tony
Published: September 2019

Purpose

The purpose of this paper is to investigate accountability for farm animal welfare (FAW) in food companies. FAW is an important social issue, yet it is difficult to define and measure, meaning that it is difficult for companies to demonstrate accountability. The authors investigate a proposed solution, the Business Benchmark on Farm Animal Welfare (BBFAW), and how it has disrupted the informal rules or culture of the market. The research questions centre on the process of response to BBFAW and the necessary characteristics for BBFAW to play a performative role in the market.

Design/methodology/approach

This paper employs an analysis of published BBFAW reports (2012–2017) and case study interviews in five BBFAW firms, in order to address the research questions.

Findings

The authors present evidence of a dynamic, repetitive process, starting with recognition of the importance of FAW and BBFAW, followed by internal discussions and the commitment of resources, and changes in communication to external stakeholders. Three necessary characteristics for performativity are proposed: common language, building networks and expanding markets.

Originality/value

This paper reflects a socially important issue that is under-represented in the accounting literature. The results provide an insight into the use of external accounts to drive collaboratively the social change agenda. The performativity process and identified characteristics contribute to expanding this literature in the accounting domain.
Close encounters and the illusion of accountability in the sharing economy
Authors: McDaid Emma , Boedker Christina , Free Clinton
Published: September 2019

Purpose

Online ratings and reviews have recently emerged as mechanisms to facilitate accountability and transparency in the provision of goods and services. The purpose of this paper is to examine the nature and outcome of the accountability that online ratings and reviews create in the sharing economy.

Design/methodology/approach

The study draws on 30 face-to-face and Skype interviews with Airbnb guests and hosts as well as on secondary materials, including content from Airbnb data analytic reports.

Findings

The authors demonstrate that face-saving practices widely condition user ratings and comments. Face saving occurs when individuals attempt to preserve their own identity and the identity of others during a social interaction. At Airbnb, the authors find that reviewers adopt three distinct face-saving strategies: the use of private reviewing channels, the creation of tactful reviews and refraining from reviewing entirely. The authors also find that users are sceptical of rating metrics and public comments and draw upon a wide range of alternative sources, such as private messaging and other publicly available resources, in their decision making.

Originality/value

This paper highlights the overwhelmingly positive character of Airbnb ratings and reviews. It proposes the concept of crowdbased accountability as a limited, partial form of assurance for sharing economy users. Guests and hosts alike prioritise face-saving practices over reviewer responsibilities to provide authentic, reliable accounts to the public. Consequently, reviewers effectively remove the risk of sanctions for those in the network who underperform.
Stakeholder engagement and dialogic accounting
Authors: Bellucci Marco , Simoni Lorenzo , Acuti Diletta , Manetti Giacomo
Published: September 2019

Purpose

The purpose of this paper is to explain how sustainability reporting and stakeholder engagement processes serve as vehicles of dialogic accounting (DA), a form of critical accounting that creates opportunities for stakeholders to express their opinions, and the influence of dialogic interactions on the content of sustainability reports.

Design/methodology/approach

Content analysis is used to investigate reports published by 299 companies that have adopted Global Reporting Initiative guidelines. This paper studies how organizations engage stakeholders, the categories of stakeholders that are being addressed, the methods used to support stakeholder engagement, and other features of the stakeholder engagement process. Companies that disclose stakeholder perceptions, the difficulties met in engaging stakeholders, and actions aimed at creating opportunities for different groups of stakeholders to interact were subjects of discussion in a series of semi-structured interviews that focus on DA.

Findings

Companies often commit themselves to two-way dialogue with their stakeholders, but fully developed frameworks for DA are rare. However, signs of DA emerged in the analysis, thus confirming that sustainability reporting can become a platform for DA systems if stakeholder engagement is effective.

Originality/value

The findings contribute to the accounting literature by discussing if and how sustainability reporting and stakeholder engagement can serve as vehicles of DA. This is accomplished via a research design that is based on in-depth interviews and content analysis of various sustainability reports.
Farmers’ characteristics’ and the propensity to reduce debt
Authors: Greig Bruce , Nuthall Peter , Old Kevin
Published: September 2019

Purpose

The purpose of this paper is to investigate a farm manager’s personal characteristics (personality, age, education, objectives, experience, etc.) as drivers of debt payback success and rates. Traditionally bankers have used historic business statistics, and equity levels, to assess loans and credit worthiness. It is hypothesised that a managers’ personal characteristics are likely to be a better predictor of future debt payback performance.

Design/methodology/approach

The literature was searched to isolate the managers’ personal variables likely to determine debt payback. The information led to defining a quantitative model based on the theory of planned behaviour (TPB) which was hypothesised as determining payback rates where a choice was available. A postal random stratified survey of NZ owner operator farm managers provided the data to test the model and define its parameters using regressions, structural equation modelling and statistical comparisons.

Findings

The modelling results make it clear a manager’s personal characteristics are highly correlated with debt payback and, logically, are very likely to be the drivers. Four random effects equations and a comparison of high- and low-debt payback managers led to this conclusion.

Practical implications

Bankers should use the managers’ personal characteristics, as defined in the regressions, alongside traditional measures when assessing farm business loan requests. This approach is opposite to the traditional methods using mainly historic data.

Originality/value

The use of the TPB in assessing debt payback is a new and novel approach showing how enduring personal characteristics can be used in assessing proposals, and particularly, entrepreneurs’ adventurist investments in situations where historic data are not available.
Building an integrated conceptual model of competitive learning capability
Authors: Muneeb Dilnaz , Khong Kok Wei , Ennew Christine , Avvari Mohan
Published: September 2019

Purpose

The purpose of this paper is to provide insights into the overarching role of learning capabilities by presenting a framework to describe how learning capability development is captured by combining the three main elements of internal marketing orientation, exploratory capabilities and resource recombination.

Design/methodology/approach

This is a conceptual paper building upon the theoretical integration approach of Mayer and Sparrowe (2013) to establish competitive empowerment through learning capability development, effective internal response and resources recombination.

Findings

The competitive learning capability model provides a firm’s foundation for theorizing organizational competitive models from an internal perspective, by mastering learning capability development at the centre of the model.

Research limitations/implications

The paper emphasizes the competitive connotation of learning capabilities as a construct in strategic management. It shows the underlying role of learning across organizational processes; hence, its theoretical significance through the learning capabilities model.

Practical implications

This paper argues that learning is at the centre of organizational competitiveness. Firms can achieve more fruitful results by continuously implementing resource integration strategies built on their learned experiences.

Originality/value

The principal significance of this paper lies in the achievement of conceptualizing learning from a strategic management perspective. Insight in this area helps bridge organizational efforts in pursuit of competitive advantage by exploiting key core learning competencies embedded in a firm’s resources and capabilities.
Re-patronization at hospital healthy cafeterias: what does it take for the occurrence?
Authors: A.R. Abdul Rais , M.S.M. Zahari , C.T. Chik , M.H. Hanafiah
Published: September 2019

Purpose

The purpose of this paper is to confirm the inter-relationship between healthy cafeteria attributes, perceived value, eating behaviour, satisfaction and post-purchase behaviour in the hospital setting.

Design/methodology/approach

A conceptual model proposed comprises of five latent variables representing healthy cafeteria attributes, perceived value, eating behaviour, satisfaction and post-purchase behaviour. A total of 570 completed questionnaires were collected, and the hypotheses were tested using structural equation modelling.

Findings

This study found that eating behaviour and satisfaction significantly mediates the relationship between healthy cafeteria attributes and customers’ post-purchase behaviour. Meanwhile, customers’ perceived value weakly moderates the relationship between healthy cafeteria and eating behaviour.

Originality/value

This paper is among the first few which attempt to holistically measure the attributes that influence people to visit healthy cafeterias and the subsequent effect they have towards their post-purchase behaviour. The novelty of this study is portrayed through the inclusion of eating behaviour and the perceived value dimension in healthy foodservice study, which is still minimal compared to commercial foodservice.
Improving the new product development using big data: a case study of a food company
Authors: Jagtap Sandeep , Duong Linh Nguyen Khanh
Published: September 2019

Purpose

Recently, the concept of big data (BD) has evolved and started to play an essential role in the advancement of new product development (NPD) in various sectors contributing to value creation, idea generation and competitive advantage. However, limited research has been done on how the food industry can exploit BD to improve the processes involved in NPD. The purpose of this paper is to understand the use of BD in new food product development. It helps to find relevant information and integrate sustainability to the early stages of the NPD process in the food industry.

Design/methodology/approach

This research illustrates a case study of a beverage company wherein they used BD analytics to support their NPD team to launch a two-litre lemonade drink in the market for their retailer with less than 5 g sugar per 100 ml in the shortest possible time.

Findings

The use of BD helps to reduce NPD costs and time without affecting the taste and on par with competitor’s products.

Originality/value

The research can support NPD professionals through the application of BD analytics to bring products at lower costs to the market as quickly as possible.
Typology of university students regarding attitudes towards food waste
Authors: Knezevic Blazenka , Kurnoga Natasa , Anic Ivan-Damir
Published: September 2019

Purpose

The purpose of this paper is to examine the knowledge, awareness and concern of young consumers towards avoidable and “edible” food waste, and identify groups of individuals based on their attitudes. In addition, this study describes demographic and behavioural characteristics of each group.

Design/methodology/approach

The data were collected by a questionnaire conducted among university students in Croatia. Factor and cluster analyses were applied to identify the groups of individuals with similar attitudes towards food waste.

Findings

Results show that there are five factors that represent the knowledge, awareness and concern about food waste of young people – awareness of food waste problem; concern about economic aspects of food waste; health concern; concern about environmental impact of food waste; and awareness and concern about expiration date. Based on those factors, four groups of consumers were identified: consumers concerned about economic effects of food waste; unaware consumers neglecting food waste; well-informed consumers; and fully aware consumers, but not ready to take health risk.

Practical implications

The results of the study can be used by marketers and policy makers when planning food waste reduction activities to focus their campaigns towards consumer niches, based on the typology of young consumers.

Originality/value

This study provides a typology of university students based on their knowledge, awareness and concern about food waste in Croatia, as an example of a transition and new EU member state, where the issues about food waste are relatively new and underexplored topic.
Plant-based foods in Canada: information, trust and closing the commercialization gap
Authors: Clark Lisa Frances , Bogdan Ana-Maria
Published: September 2019

Purpose

Despite the growing awareness of links between meat consumption and human, animal and environmental health, consumption rates of protein rich plant-based foods (PBFs) in Canada remain relatively low. The purpose of this paper is to better understand how information sources and trust relate to PBFs in Canadians’ diets, and how these variables may factor into closing the commercialization gap for PBFs in Canada.

Design/methodology/approach

A geographically representative sample of Canadians (n=410) participated in a 20-minute, online survey. The survey consists of 24 questions covering demographic characteristics, motivations behind current and future food choices, frequency of current PBF consumption, sources of information about PBFs and trust levels of these sources.

Findings

Most Canadians get information about PBFs from labels, the internet and family and friends, but only half trust these sources to provide accurate information. Sources of information (e.g. licensed health care professionals) that rank high in trust are only consulted by a minority of respondents. Several information sources (e.g. family and friends) are associated with consumers’ willingness to try new PBFs, whereas other sources (e.g. labels) are associated with Canadians being unlikely to try new PBFs.

Originality/value

Understanding the patterns of where Canadians access information about PBFs and what sources of information are trusted can help to strategically place information about PBF qualities among select information sources and to remove some of the information barriers contributing to the PBF commercialization gap.