bluuebunny/crossref_metadata_2025_split huggingface dataset:
PhyteByte: Identification of foods containing compounds with specific pharmacological properties
Authors: Westerman Kenneth , Harrington Sean , Ordovas Jose M , Parnell Laurence D 
Published: January 2020

AbstractBackgroundPhytochemicals and other molecules in foods elicit positive health benefits, often by poorly established or unknown mechanisms. While there is a wealth of data on the biological and biophysical properties of drugs and therapeutic compounds, there is a notable lack of similar data for compounds commonly present in food. Computational methods for high-throughput identification of food compounds with specific biological effects, especially when accompanied by relevant food composition data, could enable more effective and more personalized dietary planning. We have created a machine learning-based tool (PhyteByte) to leverage existing pharmacological data to predict bioactivity across a comprehensive molecular database of foods and food compounds.ResultsPhyteByte uses a cheminformatic approach to structure-based activity prediction and applies it to uncover the putative bioactivity of food compounds. The tool takes an input protein target and develops a random forest classifier to predict the effect of an input molecule based on its molecular fingerprint, using structure and activity data available from the ChEMBL database. It then predicts the relevant bioactivity of a library of food compounds with known molecular structures from the FooDB database. The output is a list of food compounds with high confidence of eliciting relevant biological effects, along with their source foods and associated quantities in those foods, where available. Applying PhyteByte to thePPARGgene, we identified irigenin, sesamin, fargesin, and delta-sanshool as putative agonists of PPARG, along with previously identified agonists of this important metabolic regulator.ConclusionsPhyteByte identifies food-based compounds that are predicted to interact with specific protein targets. The identified relationships can be used to prioritize food compounds for experimental or epidemiological follow-up and can contribute to the rapid development of precision approaches to new nutraceuticals as well as personalized dietary planning.
A novel phylogenetic analysis and machine learning predict pathogenicity of human mtDNA variants
Authors: Akpınar Bala Anı , Carlson Paul O. , Paavilainen Ville O. , Dunn Cory D. 
Published: January 2020

ABSTRACTLinking mitochondrial DNA (mtDNA) variation to clinical outcomes remains a formidable challenge. Diagnosis of mitochondrial disease is hampered by the multicopy nature and potential heteroplasmy of the mitochondrial genome, differential distribution of mutant mtDNAs among various tissues, genetic interactions among alleles, and environmental effects. Here, we describe a new approach to the assessment of which mtDNA variants may be pathogenic. Our method takes advantage of site-specific conservation and variant acceptability metrics that minimize previous classification limitations. Using our novel features, we deploy machine learning to predict the pathogenicity of thousands of human mtDNA variants. Our work demonstrates that a substantial fraction of mtDNA changes not yet characterized as harmful are, in fact, likely to be deleterious. Our findings will be of direct relevance to those at risk of mitochondria-associated metabolic disease.
Fully Automated Peptide Mapping Protocol for Multi-Attribute Method by Liquid Chromatography–Tandem Mass Spectroscopy with a High-Throughput Robotic Liquid Handling System
Authors: Qian Chen , Niu Ben , Jimenez Rod Brian , Wang Jihong , Albarghouthi Methal , Chen Xiaoyu 
Published: January 2020

ABSTRACTThe multi-attribute method (MAM) based on liquid chromatography–tandem mass spectroscopy is emerging as a powerful tool to directly monitor multiple product quality attributes simultaneously. Preparation of samples for MAM, however, is labor intensive, involving protein denaturation, disulfide bond reduction, free cysteine alkylation, and enzymatic digestion steps, which require significant analyst hands-on time while limiting result turnaround. Such complexity can also render nontrivial variations across analysts and laboratories. We describe the development of a fully automated peptide mapping procedure with a high-throughput robotic liquid handling system to improve sample handling capability and outcome reproducibility while saving analyst hands-on time. The automated procedure is completely hands-free, and setup requires the analyst only to prenormalize the sample concentrations and load buffers and reagents at their designated positions on the robotic deck. The robotic liquid handler performs all the subsequent preparation steps and stores the digested samples on a chiller unit to await retrieval. The convenience and flexibility provided by this automated peptide mapping method provides substantial benefits over manual sample preparation protocols. The optimized, automated procedure showed good reproducibility and results that were comparable to those of the manual procedure with respect to sequence coverage, digestion completeness, and quantification of posttranslational modifications. With this increased throughput, coupled with fast MAM analysis, more comprehensive characterization can be achieved.
Comparing Phylogeographies: Incompatible Geographical Histories in Pathogens’ Genomes
Authors: Singer Benjamin , Di Nardo Antonello , Hein Jotun , Ferretti Luca 
Published: January 2020

AbstractModern phylogeography aims at reconstructing the geographic diffusion of organisms based on their genomic sequences and spatial information. Phylogeographic approaches usually ignore the possibility of recombination, which decouples the evolutionary and geographic histories of different parts of the genome. Genomic regions of recombining or reassorting pathogens often originate and evolve at different times and locations, which characterised their unique spatial histories. Measuring the extent of these differences requires new methods to compare geographic information on phylogenetic trees reconstructed from different parts of the genome. Here we develop for the first time a set of measures ofphylogeographic incompatibilityaimed at detecting differences between geographical histories in terms of distances between phylogeographies. We study the effect of varying demography and recombination on phylogeographic incompatibilities using coalescent simulations. We further apply these measures to the evolutionary history of human and livestock pathogens, either reassorting or recombining, such as the Victoria and Yamagata lineages of influenza B and the O/Ind-2001 foot-and-mouth disease virus strain. Our results reveal diverse geographical paths of diffusion that characterise the origins and evolutionary histories of different viral genes and genomic segments. phylogeography, recombination, viral evolution
Imidacloprid Movement into Fungal Conidia is Lethal to Mycophagous Beetles
Authors: Choudhury Robin A. , Sutherland Andrew M. , Hengel Mathew J. , Parrella Michael P. , Gubler W. Douglas 
Published: January 2020

AbstractApplications of systemic pesticides can have unexpected direct and indirect effects on nontarget organisms, producing ecosystem-level impacts.We investigated whether a systemic insecticide (imidacloprid) could be absorbed by a plant pathogenic fungus infecting treated plants and whether the absorbed levels were high enough to have detrimental effects on the survival of a mycophagous beetle. Beetle larvae fed on these fungi were used to assess the survival effects of powdery mildew and imidacloprid in a factorial design. Fungal conidia were collected from treated and untreated plants and were tested for the presence and concentration of imidacloprid.Survival of beetles fed powdery mildew from imidacloprid-treated leaves was significantly lower than that of beetles from all other treatments.Imidacloprid accumulated in fungal conidia and hyphae was detected at levels considered lethal to other insects, including coccinellid beetles.Water-soluble systemic insecticides may disrupt mycophagous insects as well as other nontarget organisms, with significant implications for biodiversity and ecosystem function.
Tyrosine-Derived Polycarbonate Nerve Guidance Tubes Elicit Pro-Regenerative Extracellular Matrix Deposition When Used to Bridge Segmental Nerve Defects in Swine
Authors: Burrell JC , Bhatnagar D , Brown DP , Murthy NS , Dutton J , Browne KD , Laimo FA , Ali Z , Rosen JM , Kaplan HM , Kohn J , Cullen DK 
Published: January 2020

AbstractPromising biomaterials should be tested in appropriate large animal models that recapitulate human inflammatory and regenerative responses. Previous studies have shown tyrosine-derived polycarbonates (TyrPC) are versatile biomaterials with a wide range of applications across multiple disciplines. The library of TyrPC has been well studied and consists of thousands of polymer compositions with tunable mechanical characteristics and degradation and resorption rates that are useful for nerve guidance tubes (NGTs). NGTs made of different TyrPCs have been used in segmental nerve defect models in small animals. The current study is an extension of this work and evaluates NGTs made using two different TyrPC compositions in a 1 cm porcine peripheral nerve repair model. We first evaluated a nondegradable TyrPC formulation, demonstrating proof-of-concept chronic regenerative efficacy up to 6 months with similar nerve/muscle electrophysiology and morphometry to the autograft repair control. Next, we characterized the acute regenerative response using a degradable TyrPC formulation. After 2 weeksin vivo, TyrPC NGT promoted greater deposition of pro-regenerative extracellular matrix (ECM) constituents (in particular collagen I, collagen III, collagen IV, laminin and fibronectin) compared to commercially available collagen-based NGTs. This corresponded with dense Schwann cell infiltration and axon extension across the lumen. These findings confirmed results reported previously in a mouse model and reveal that TyrPC NGTs were well tolerated in swine and facilitated host axon regeneration and Schwann cell infiltration in the acute phase across segmental defects - likely by eliciting a favorable neurotrophic ECM milieu. This regenerative response ultimately can contribute to functional recovery.
Cell competition acts as a purifying selection to eliminate cells with mitochondrial defects during early mouse development
Authors: Lima Ana , Lubatti Gabriele , Burgstaller Jörg , Hu Di , Green Alistair , Gregorio Aida Di , Zawadzki Tamzin , Pernaute Barbara , Mahammadov Elmir , Montero Salvador Perez , Dore Marian , Sanchez Juan Miguel , Bowling Sarah , Sancho Margarida , Karimi Mohammad , Carling David , Jones Nick , Srinivas Shankar , Scialdone Antonio , Rodriguez Tristan A. 
Published: January 2020

AbstractCell competition is emerging as a quality control mechanism that eliminates unfit cells in a wide range of settings from development to the adult. However, the nature of the cells normally eliminated by cell competition and what triggers their elimination remains poorly understood. In mouse, prior to gastrulation 35% of epiblast cells are eliminated. Here we have performed single cell transcriptional profiling of these cells and find that they show the hallmarks of cell competition and have mitochondrial defects. We demonstrate that mitochondrial defects are common to a range of different loser cell types and that manipulating mitochondrial function is sufficient to trigger competition. Importantly, we show that in the embryo cell competition eliminates cells with mitochondrial DNA mutations and that even non-pathological changes in mitochondrial DNA sequence can induce cell competition. Our results therefore suggest that cell competition is a purifying selection that optimises mitochondrial performance prior to gastrulation.
More filtering on SNP calling does not remove evidence of inter-nucleus recombination in dikaryotic arbuscular mycorrhizal fungi
Authors: Chen Eric C.H. , Mathieu Stephanie , Hoffrichter Anne , Ropars Jeanne , Dreissig Steven , Fuchs Jörg , Brachmann Andreas , Corradi Nicolas 
Published: January 2020

AbstractWe respond to a recent reanalysis of single nucleus sequence data from Chen et al. 2018eLife, which indicated that evidence of inter-nuclear recombination in dikaryotic arbuscular mycorrhizal fungi decreases when heterozygous, duplicated sites being supported by less than 5 reads, are removed from the dataset. Here, we show that applying a more stringent methodology for filtering SNP calls that focuses exclusively on single copy and homozygous regions with at least 5 reads supporting a given SNP, still recovers several hundreds putative inter-nucleus recombination events within the same dataset. We also provide evidence for retaining SNPs supported by less than 5 reads for genotyping individual nuclei using the same dataset.
Color Data v2: a user-friendly, open-access database with hereditary cancer and hereditary cardiovascular conditions datasets
Authors: Berger Mark J. , Williams Hannah E. , Barrett Ryan , Zimmer Anjali D. , McKennon Wendy , Hong Huy , Ginsberg Jeremy , Zhou Alicia Y. , Neben Cynthia L. 
Published: January 2020

ABSTRACTPublicly-available genetic databases promote data sharing and fuel scientific discoveries for the prevention, treatment, and management of disease. In 2018, we built Color Data, a user-friendly, open access database containing genotypic and self-reported phenotypic information from 50,000 individuals who were sequenced for 30 genes associated with hereditary cancer. In a continued effort to promote access to these types of data, we launched Color Data v2, an updated version of the Color Data database. This new release includes additional clinical genetic testing results from more than 18,000 individuals who were sequenced for 30 genes associated with hereditary cardiovascular conditions, as well as polygenic risk scores for breast cancer, coronary artery disease, and atrial fibrillation. In addition, we used self-reported phenotypic information to implement the following four clinical risk models: Gail Model for five-year risk of breast cancer, Claus Model for lifetime risk of breast cancer, simple office-based Framingham Coronary Heart Disease Risk Score for ten-year risk of coronary heart disease, and CHARGE-AF simple score for five-year risk of atrial fibrillation. These new features and capabilities are highlighted through two sample queries in the database. We hope that the broad dissemination of this data will help researchers continue to explore genotype-phenotype correlations and identify novel variants for functional analysis, enabling scientific discoveries in the field of population genomics.Database URL:https://data.color.com/
Kamal Youbi: a knack for startups
Authors: Chaker Fadwa , Aaminou Mohamed Wail 
Published: January 2020

Supplementary materials
Teaching Notes are available for educators only.

Learning outcomes
Discover first-hand entrepreneurship facets in Africa through a real-lived story; and identify key success factors for entrepreneurship in emerging countries.

Case overview/synopsis
The case describes the main entrepreneurial milestones of a young Moroccan entrepreneur. By telling his success stories and his failures, the challenges he stumbled over and how he quickly got on his feet after each fall. The case ends with a description of the creation process and evolution of MyAppConverter®, a highly innovative startup, describes the huge potential of the firm and the main difficulties faced by the founders. With limited financial resources, the associates need to quickly detect the misfunctioning part of the business model and get it fixed before the crucial pitch they are making at the end of the month before world leading investors.

Complexity academic level
Bachelor in business administration.

Subject code
CSS 3: Entrepreneurship.
The influence of disorderly environment on consumers’ reference for boundaries
Authors: Du Weiyu , Fang Di , Ye Yang , Qiu Sainan 
Published: January 2020

Purpose
The purpose of this paper is to examine the influence of disorderly environment on consumers’ preferences for boundaries and the mediating effect of personal control in this process.

Design/methodology/approach
The authors examined hypotheses in two studies. In Study 1, the authors measured environmental orderliness, preference for boundaries and other control variables like positive and negative emotions. In Study 2, the authors primed participants’ concept of environmental orderliness and measured personal control as well as the same variables in Study 1.

Findings
Consumers in disorderly environments prefer bounded logos more compared to those in orderly environments. Personal control mediates the effect of chaotic physical environment on the preference for boundaries. Compared with the counterparts in the orderly environment, consumers in the disorderly environment have a lack of personal control, thus giving the preference to logos with boundaries.

Research limitations/implications
This paper discusses the mechanism of the process that the disorderly environment triggers the individual’s preference for bounded design, which enriches the research related to physical environment in the field of consumer behavior. However, it fails to examine the influence of disorderly environment on the preference for real bounded products and did not discuss the invisible boundary.

Originality/value
The impact of the disorderly environment on consumers’ boundary preferences, which the research focuses on, has further deepened the understanding of the boundaries, and to some extent, the authors filled the research gap in this field.
Alleviating knowledge contribution loafing among engineering designers by ethical leadership: the role of knowledge-based psychological ownership and emotion regulation strategies
Authors: Sun Hui , Zhang Lianying , Meng Junna 
Published: January 2020

PurposeThis paper aims to examine how ethical leadership alleviates knowledge contribution loafing among engineering designers through the mediating effect of knowledge-based psychological ownership and the moderating effect of emotion regulation strategies.Design/methodology/approachThis study adopts a questionnaire survey to obtain 344 valid sample from engineering designers and uses partial least squares-structural equation modeling to analyze data.FindingsThe results demonstrate that ethical leadership is a key factor to alleviate knowledge contribution loafing. Knowledge-based psychological ownership is a main factor causing knowledge contribution loafing and mediates the influence of ethical leadership on knowledge contribution loafing. Furthermore, cognitive reappraisal (a response-focused emotion regulation strategy) moderates the relationship between ethical leadership and knowledge contribution loafing, and the effect of ethical leadership on knowledge contribution loafing is stronger when cognitive reappraisal is high.Practical implicationsEngineering design organizations may inspire ethical leadership and pay attention to psychological state of designers. Leaders may help designers overcome knowledge-based psychological ownership by the influence of ethical leadership. During the process of knowledge interaction, designers may adopt cognitive reappraisal strategy consciously.Originality/valueThis study addresses the knowledge gap that ethical leadership affects knowledge contribution loafing with knowledge-based psychological ownership as the intermediary. This study also advances the literature on leadership and emotion regulation and extends the scope of social learning theory in knowledge management domain through examining the moderate role of emotion regulation strategies.
Research watch: what really helps recovery in relation to severe mental health difficulties?
Authors: Holttum Sue 
Published: January 2020

Purpose
The purpose of this paper is to examine three recent papers on mental health services and how they support recovery following a diagnosis of a severe mental health condition.

Design/methodology/approach
A search was carried out for recent papers on mental health and recovery. The author selected three papers that seemed to advance understanding of not only whether, but also how recovery of a meaningful life may be best supported in mental health services.

Findings
One paper suggested how staff were able to support service users’ personal goals and focus on recovery in acute inpatient settings, and what got in the way. The author suggests practical ways to address the barriers. A second paper reported the testing of a new model for supporting staff in primary and secondary care to work together so that service users with a diagnosis of bipolar or schizophrenia were better supported to work towards valued goals. A third paper reviewed 40 studies of how people can experience positive change after a first diagnosis of psychosis, and how change happened.

Originality/value
By studying the issues in detail, all three papers show how improved support for recovery and inclusion can be implemented against the backdrop of many years of service shortcomings.
Future studies, mental health and the question of citizenship
Authors: Morgan Phil , Brannelly Tula , Eales Sarah 
Published: January 2020

Purpose
The purpose of this paper is to examine the value of utilising future studies to explore citizenship for people with mental health challenges.

Design/methodology/approach
This paper critiques the discipline of future studies and considers it in the context of the citizenship and mental health literature. It explores how future studies can be utilised to promote marginalised voices, such as those of people with mental health challenges.

Findings
Technology is leading to rapid change in society including what it means to be a citizen (Isin and Nielsen, 2008; Isin and Ruppert, 2015). Whilst citizenship has been promoted within mental health for a long time, change has been slow (Rowe and Davidson, 2016). In order to create inclusive opportunities for people with mental health challenges, any focus on citizenship in mental health needs to not only address the present time but to anticipate and influence future technological directions.

Originality/value
This paper is original in bringing together mental health and the future impact on society of new technologies. It stands to offer a new perspective to discussions on citizenship.