bluuebunny/crossref_metadata_2025_split huggingface dataset:
From intent to implementation: Factors affecting public involvement in life science research
Authors: Burns John. A. , Korzec Kora , Dorris Emma R. 
Published: August 2019

AbstractPublic involvement is key to closing the gap between research production and research use, and the only way to achieving ultimate transparency in science. The majority of life science research is not public-facing, but is funded by the public and impacts the community. We undertook a survey of researchers within the life sciences to better understand their views and perceived challenges to involving the public in their research. We had a valid response cohort of n=110 researchers, of whom 90% were primarily laboratory based. Using a mixed methods approach, we demonstrate that a top-down approach is key to motivate progression of life scientists from feeling positive towards public involvement to actually engaging in it. Researchers who viewed public involvement as beneficial to their research were more likely to have direct experience of doing it. We demonstrate that the systemic flaws in the way life sciences research enterprise is organised, including the promotion system, hypercompetition, and time pressures are major barriers to involving the public in the scientific process. Scientists are also apprehensive of being involuntarily involved in the current politicized climate, misinformation and publicity hype surrounding science nowadays makes them hesitant to share their early and in-progress research. The time required to deliberate study design and relevance, plan and build relationships for sustained involvement, provide and undertake training, and improve communication in the current research environment is often considered nonpragmatic, particularly for early career researchers. In conclusion, a top-down approach involving institutional incentives and infrastructure appears most effective at transitioning researchers from feeling positive towards public involvement to actually implementing it.
Dysbiosis personalizes fitness effect of antibiotic resistance in the mammalian gut
Authors: Cardoso Luís Leónidas , Durão Paulo , Amicone Massimo , Gordo Isabel 
Published: August 2019

SUMMARYThe fitness cost of antibiotic resistance in the absence of antibiotics is crucial to the success of suspending antibiotics as a strategy to lower resistance. Here we show that after antibiotic treatment the cost of resistance within the complex ecosystem of the mammalian gut is personalized. Using mice as anin vivomodel, we find that the fitness effect of the same resistant mutation can be deleterious in a host, but neutral or even beneficial in other hosts. Such antagonistic pleiotropy is shaped by the microbiota, as in germ-free mice resistance is consistently costly across all hosts. An eco-evolutionary model of competition for resources identifies a general mechanism underlying between host variation and predicts that the dynamics of compensatory evolution of resistant bacteria should be host specific, a prediction that was supported by experimental evolutionin vivo. The microbiome of each human is close to unique and our results suggest that the short-term costs of resistance and its long-term within-host evolution will also be highly personalized, a finding that may contribute to the observed variable outcome of control therapies.One Sentence SummaryPersonalized Fitness of Resistance Mutations.
Structural elements that modulate the substrate specificity of plant purple acid phosphatases: avenues for improved phosphorus acquisition in crops
Authors: Feder Daniel , McGeary Ross P. , Mitić Natasa , Lonhienne Thierry , Furtado Agnelo , Schulz Benjamin L. , Henry Robert J. , Schmidt Susanne , Guddat Luke W. , Schenk Gerhard 
Published: August 2019

AbstractPhosphate acquisition by plants is an essential process that is directly implicated in the optimization of crop yields. Purple acid phosphatases (PAPs) are ubiquitous metalloenzymes, which catalyze the hydrolysis of a wide range of phosphate esters and anhydrides. While some plant PAPs display a preference for ATP as the substrate, others are efficient in hydrolyzing phytate or 2-phosphoenolpyruvate (PEP). PAP from red kidney bean (rkbPAP) is an efficient ATP- and ADPase, but has no activity towards phytate. The crystal structure of this enzyme in complex with an ATP analogue (to 2.20 Å resolution) provides insight into the amino acid residues that play an essential role in binding this substrate. Homology modelling was used to generate three-dimensional structures for the active sites of PAPs from tobacco (NtPAP) andArabidopsis thaliana(AtPAP12 and AtPAP26) that are efficient in hydrolyzing phytate and PEP as substrates, respectively. In combination with substrate docking simulations and a phylogenetic analysis of 49 plant PAP sequences (including the first PAP sequences reported fromEucalyptus), several active site residues were identified that are important in defining the substrate specificities of plant PAPs. These results may inform bioengineering studies aimed at identifying and incorporating suitable plant PAP genes into crops to improve phosphorus use efficiency. Organic phosphorus sources increasingly supplement or replace inorganic fertilizer, and efficient phosphorus use of crops will lower the environmental footprint of agriculture while enhancing food production.
Segregation of Familial Risk of Obesity in NHANES Cohort Supports a Major Role for Large Genetic Effects in the Current Obesity Epidemic
Authors: Jenkins Arthur B. , Batterham Marijka , Campbell Lesley V. 
Published: August 2019

AbstractThe continuing increase in many countries in adult body mass index (BMI kg/m2) and its dispersion is contributed to by interaction between genetic susceptibilities and an increasingly obesogenic environment (OE). The determinants of OE-susceptibility are unresolved, due to uncertainty around relevant genetic and environmental architecture. We aimed to test the multi-modal distributional predictions of a Mendelian genetic architecture based on collectively common, but individually rare, large-effect variants and their ability to account for current trends in a large population-based sample. We studied publicly available adult BMI data (n = 9102) from 3 cycles of NHANES (1999, 2005, 2013). A first degree family history of diabetes served as a binary marker (FH0/FH1) of genetic obesity susceptibility. We tested for multi-modal BMI distributions non-parametrically using kernel-smoothing and conditional quantile regression (CQR), obtained parametric fits to a Mendelian model in FH1, and estimated FH x OE interactions in CQR models and ANCOVA models incorporating secular time. Non-parametric distributional analyses were consistent with multi-modality and fits to a Mendelian model in FH1reliably identified 3 modes. Mode separation accounted for ~40% of BMI variance in FH1providing a lower bound for the contribution of large effects. CQR identified strong FH x OE interactions and FH1accounted for ~60% of the secular trends in BMI and its SD in ANCOVA models. Multimodality in the FH effect is inconsistent with a predominantly polygenic, small effect architecture and we conclude that large genetic effects interacting with OE provide a better quantitative explanation for current trends in BMI.
Experimental evolution reveals the genetic basis and systems biology of superoxide stress tolerance
Authors: Tan Justin , Olson Connor A. , Park Joon Ho , Sastry Anand V. , Phaneuf Patrick V. , Yang Laurence , Szubin Richard , Hefner Ying , Feist Adam M. , Palsson Bernhard O. 
Published: August 2019

AbstractBacterial response to oxidative stress is of fundamental importance. Oxidative stresses are endogenous, such as reactive oxidative species (ROS) production during respiration, or exogenous in industrial biotechnology, due to culture conditions or product toxicity. The immune system inflicts strong ROS stress on invading pathogens. In this study we make use of Adaptive Laboratory Evolution (ALE) to generate two independent lineages ofEscherichia coliwith increased tolerance to superoxide stress by up to 500% compared to wild type. We found: 1) that the use of ALE reveals the genetic basis for and systems biology of ROS tolerance, 2) that there are only 6 and 7 mutations, respectively, in each lineage, five of which reproducibly occurred in the same genes (iron-sulfur cluster regulatoriscR, putative iron-sulfur repair proteinygfZ, pyruvate dehydrogenase subunit EaceE, succinate dehydrogenasesucA, and glutamine tRNAglnX), and 3) that the transcriptome of the strain lineages exhibits two different routes of tolerance: the direct mitigation and repair of ROS damage and the up-regulation of cell motility and swarming genes mediated through phosphate starvation, which has been linked to biofilm formation and aggregation. These two transcriptomic responses can be interpreted as ‘flight’ and ‘fight’ phenotypes.ImportanceBacteria encounter oxidative stress from multiple sources. During pathogenic infections, our body’s immune system releases ROS as a form of antimicrobial defense whilst bacteria used in industrial biotechnology are frequently exposed to genetic modifications and culture conditions which induce oxidative stress. In order to get around the body’s defences, pathogens have developed various adaptations to tolerate high levels of ROS, and these adaptive mechanisms are not always well understood. At the same time, there is a need to improve oxidative stress tolerance for industrially relevant strains in order to increase robustness and productivity. In this study we generate two strains of superoxide tolerantEscherichia coliand identify several adaptive mechanisms. These findings can be directly applied to improve production strain fitness in an industrial setting. They also provide insight into potential virulence factors in other pathogens, highlighting potential targets for antimicrobial compounds.
Retention and predictors of attrition among patients who started antiretroviral therapy in Zimbabwe’s National Antiretroviral Therapy Programme between 2012 and 2015
Authors: Makurumidze Richard , Mutasa-Apollo Tsitsi , Decroo Tom , Choto Regis C. , Takarinda Kudakwashe C. , Dzangare Janet , Lynen Lutgarde , Van Damme Wim , Hakim James , Magure Tapuwa , Mugurungi Owen , Rusakaniko Simbarashe 
Published: August 2019

AbstractBackgroundThe last evaluation to assess outcomes for patients receiving antiretroviral therapy (ART) through the Zimbabwe public sector was conducted in 2011, covering the 2007-2010 cohorts. The reported retention at 6, 12, 24 and 36 months were 90.7%, 78.1%, 68.8% and 64.4%, respectively. We report findings of a follow up evaluation for the 2012-2015 cohorts to assess the implementation & impact of recommendations from this prior evaluation.MethodsA nationwide retrospective study was conducted in 2016. Multi-stage proportional sampling was used to select health facilities and study participants records. The data extracted from patient manual records included demographic, baseline clinical characteristics and patient outcomes (active on treatment, died, transferred out, stopped ART and lost to follow-up (LFTU)) at 6, 12, 24 and 36 months. The data were analysed using Stata/IC 14.2. Retention was estimated using survival analysis. The predictors associated with attrition were determined using a multivariate Cox regression model.ResultsA total of 3,810 participants were recruited in the study. The median age in years was 35 (IQR: 28-42). Overall, retention increased to 92.4%, 86.5%, 79.2% and 74.4% at 6, 12, 24 and 36 months respectively. LFTU accounted for 98% of attrition. Being an adolescent or a young adult (aHR 1.41; 95%CI:1.14-1.74), receiving care at primary health care facility (aHR 1.23; 95%CI:1.01-1.49), having initiated ART between 2014-2015 (aHR 1.45; 95%CI:1.24-1.69), having WHO Stage 4 (aHR 2.06; 95%CI:1.51-2.81) and impaired functional status (aHR 1.24; 95%CI:1.04-1.49) predicted attrition.ConclusionThe overall retention was higher in comparison to the previous 2007–-2010 evaluation. Further studies to understand why attrition was found to be higher at primary health care facilities are warranted. Implementation of strategies for managing patients with advanced HIV disease, differentiated care for adolescents and young adults and tracking of LFTU should be prioritised to further improve retention.
The effect of APOBEC3B deaminase on double-stranded DNA
Authors: Chapman Joseph , Custance Michael , Shen Birong , Furano Anthony V. 
Published: August 2019

ABSTRACTMutations mediated by the APOBEC3 (A3) family of single-strand specific cytosine deaminases can accumulate in various cancers, as strand-coordinated clusters and isolated lesions. A3-mediated mutations also occur during normal development, accounting for ~20% of heritable mutations. A3B is an archetypical member of this family and is thought to contribute to both cancer initiation and progression. A3B has a strong preference for C in a TC context and catalyzes hydrolysis of the primary amine of un-paired C to generate U. Subsequent repair generates a distinctive pattern of C-substitutions, which along with their context signify their A3B origin. Although single-stranded DNA is the preferred A3B substrate, we report here that in some instances A3B can deaminate the C of TC in a double-stranded DNA context in vitro. These include C paired to O6-methylguanine (O6meG), to an abasic (AP) site, or to a G adjacent to an AP site. AP sites are the most common lesion in DNA, and O6meG levels increase under alkylating conditions caused by environmental nitrosamines and some chemotherapeutic agents. We also show that elevated expression of A3B can enhance double-stranded breaks induced by the alkylating agent MNNG in mammalian cells, but this effect does not require A3B deaminase activity.
Data matters: how earth and environmental scientists determine data relevance and reusability
Authors: Murillo Angela P. 
Published: August 2019

Purpose
The purpose of this study is to examine the information needs of earth and environmental scientists regarding how they determine data reusability and relevance. Additionally, this study provides strategies for the development of data collections and recommendations for data management and curation for information professionals working alongside researchers.

Design/methodology/approach
This study uses a multi-phase mixed-method approach. The test environment is the DataONE data repository. Phase 1 includes a qualitative and quantitative content analysis of deposited data. Phase 2 consists of a quasi-experiment think-aloud study. This paper reports mainly on Phase 2.

Findings
This study identifies earth and environmental scientists’ information needs to determine data reusability. The findings include a need for information regarding research methods, instruments and data descriptions when determining data reusability, as well as a restructuring of data abstracts. Additional findings include reorganizing of the data record layout and data citation information.

Research limitations/implications
While this study was limited to earth and environmental science data, the findings provide feedback for scientists in other disciplines, as earth and environmental science is a highly interdisciplinary scientific domain that pulls from many disciplines, including biology, ecology and geology, and additionally there has been a significant increase in interdisciplinary research in many scientific fields.

Practical implications
The practical implications include concrete feedback to data librarians, data curators and repository managers, as well as other information professionals as to the information needs of scientists reusing data. The suggestions could be implemented to improve consultative practices when working alongside scientists regarding data deposition and data creation. These suggestions could improve policies for data repositories through direct feedback from scientists. These suggestions could be implemented to improve how data repositories are created and what should be considered mandatory information and secondary information to improve the reusability of data.

Social implications
By examining the information needs of earth and environmental scientists reusing data, this study provides feedback that could change current practices in data deposition, which ultimately could improve the potentiality of data reuse.

Originality/value
While there has been research conducted on data sharing and reuse, this study provides more detailed granularity regarding what information is needed to determine reusability. This study sets itself apart by not focusing on social motivators and demotivators, but by focusing on information provided in a data record.
How reading in single- and multiple-column types influence our cognitive load: an EEG study
Authors: Al-Samarraie Hosam , Eldenfria Atef , Zaqout Fahed , Price Melissa Lee 
Published: August 2019

Purpose
The impact of different screen-based typography styles on individuals’ cognitive processing of information has not been given much consideration in the literature, though such differences would imply different learning outcomes. This study aims to enrich the current understanding of the impact of reading in single- and multiple-column types on students’ cognitive processing.

Design/methodology/approach
An electroencephalogram (EEG) was used to record and analyze the brain signals of 27 students while reading from single- and multiple- column layouts.

Findings
The results showed a significant difference in students’ cognitive load when reading text from different types of columns. All students exerted less processing efforts when text was presented in two-column format, thus experiencing less cognitive load.

Originality/value
Using EEG, this study examined the neural consequences of reading in single- and multiple-column types on cognitive load during reading. The findings can be used to enrich the current instructional design practices on how different typographical formats facilitate learners’ cognitive performance.
Weapon equipment management cost prediction based on forgetting factor recursive GM (1,1) model
Authors: Liu Subing , Chunwu Yin , Dazhi Cao 
Published: August 2019

Purpose
The purpose of this paper is to provide a new recursive GM (1,1) model based on forgetting factor and apply it to the modern weapon and equipment system.

Design/methodology/approach
In order to distinguish the contribution of new and old data to the grey prediction model with new information, the authors add forgetting factor to the objective function. The purpose of the above is to realize the dynamic weighting of new and old modeling data, and to gradually forget the old information. Second, the recursive estimation algorithm of grey prediction model parameters is given, and the new information is added in real time to improve the prediction accuracy of the model.

Findings
It is shown that the recursive GM (1,1) model based on forgetting factor can achieve both high effectiveness and high efficiency.

Originality/value
The paper succeeds in proposing a recursive GM (1,1) model based on forgetting factor, which has high accuracy. The model is applied to the field of modern weapon and equipment system and the result the model is better than the GM(1,1) model. The experimental results show the effectiveness and the efficiency of the prosed method.
Application of different numerical models capable to simulate combustion of alternative fuels in internal combustion engine
Authors: Adamczyk Wojciech Piotr , Kruczek Grzegorz , Bialecki Ryszard , Przybyła Grzegorz 
Published: August 2019

Purpose
The internal combustion engine operated on gaseous fuels shows great potential in terms of integration of the renewable and traditional sources for an effective solution for clean energy production challenge. Different fuel mixtures that can be used to power the engine are characterized by various combustion properties, which can affect its overall efficiency. The purpose of this paper is to provide reasonable answer, how the operation condition can change due to different fuel, without enormous cost of prototyping processes using physical models a digital model can be seen as promising technique.

Design/methodology/approach
Presented work discusses the application, and extensive description of two commercial codes Ansys Fluent and Forte for modeling stationary engine fueled by compressed natural gas (CNG) and biogas. To check the model accuracy, all carried out numerical results were compared against experimental data collected at in-house test rig of single cylinder four stroke engine. The impacts of tested gaseous fuel on the engine working conditions and emission levels were investigated.

Findings
Carried out simulations showed good agreement with experimental data for investigated cases. Application on numerical models give possibility to visualize flame front propagation and pollutant formation for tested fuels. The biogas fuel has shown the impaired early flame phase, which led to longer combustion, lower efficiency, power output, repeatability and in some cases higher HC and carbon monoxide (CO) emissions as a result of combustion during the exhaust stroke. Looking at the CO formation it was observed that it instantly accrue with flame front propagation as a result of methane oxidation, while for NOx formation revers effect was seen.

Originality/value
The application of new approach for modeling combustion process in stationary engines fueled by CNG and alternative biogas fuel has been discussed. The cons and pros of the Forte code in terms of its application for engine prototaping process has been discussed.
New business models in supply chains: a bibliometric study
Authors: Delafenestre Régis 
Published: August 2019

Purpose
The purpose of this paper is to find and classify the most relevant works in the literature on the latest technologies applied in global supply chains. To help future researchers find the most relevant the authors according to the authors’ research interest quickly and to provide insights into the most promising areas.

Design/methodology/approach
The authors provide a bibliometric analysis of 292 documents referenced in the Scopus® database clustering by relatedness of works and keywords.

Findings
The authors present insights and deduce new perspectives in the potential search for new business models. The authors show that in specific fields, some works and authors have a much greater influence than others.

Research limitations/implications
Some documents published on the web or in paper form may be missing. The analyses largely depend on the choice of keywords. Another selection might have shown different results.

Practical implications
This paper provides the basis for new research in applications of the latest technologies in supply chains and corresponding new business models.

Originality/value
This work is a first effort to help researchers make sense of the mass of published scientific results on new technologies and their impact on new supply chain business models.